@article {pmid40608175, year = {2025}, author = {Ye, Z and Yu, Y and Cao, Z and Ye, Z and Gu, X and Shen, X and Cai, B and Lin, B and Ji, C and Qiao, N and Wu, Z and Chen, Z and Ma, Z and Chen, L and Liang, B and Liao, Y and He, W and Shen, Q and Han, J and Cao, X and Zhou, X and Shou, X and Shen, M and Wang, Y and Zhang, Z and Ye, H and Zhang, Q and Gao, R and Zhang, Y}, title = {Microbiome and metabolic disorder in prolactinoma: intrinsic gender differences and extrinsic therapy effects.}, journal = {Pituitary}, volume = {28}, number = {4}, pages = {83}, pmid = {40608175}, issn = {1573-7403}, support = {24ZR1408900//Natural Science Foundation of Shanghai Municipality/ ; 320.6750.2023-13-11//Wu Jieping Medical Foundation/ ; 2023ZD0506800//National Major Science and Technology Projects of China/ ; 82202906//National Natural Science Foundation of China/ ; }, abstract = {PURPOSE: Prolactinoma is the most common functional pituitary adenoma. As for gender disparity in the metabolic state, males tended to have higher rates of metabolic disorders, while treatment with dopamine agonists enabled partial improvement in metabolic disorders. Oral medication used to be the first-line treatment option; thus, the efficacy of dopamine receptor agonists is linked to the intestinal microenvironment. The gut microbiome is known to interact with host physiology and metabolic profile. Therefore, it is necessary to uncover the linkages between the alteration of gut microbiota and prolactinoma. METHODS: 28 Patients diagnosed with prolactinoma and 31 healthy controls were included. Fecal samples were collected for 16 S rRNA gene sequencing and metagenomic sequencing to identify featured intestinal microflora between patients and healthy individuals, as well as to examine how gender and dopamine agonists affect the gut microbiome’s structure. RESULTS: Agathobacter, Blautia, Dorea, Fusicatenibacter, and Mediterraneibacter were prominent in the PRLoma group. Bilophila wadsworthia, Clostridium sp. CAG:7, Megasphaera elsdenii, and Mycoplasma sp. CAG:472 were independently associated with metabolic disorders in male patients. This metabolic regulatory effect may result from the levels of Xylose, the glycine to serine ratio, N2-acetyl, N6, N6-dimethyllysine levels, and the cholesterol to oleoyl-linoleoyl-glycerol (18:1 to 18:2) ratio in plasma. Furthermore, administering dopamine agonists reduced harmful species such as Fusobacterium mortiferum, Bacteroides fragilis, and Ruminococcus biciculans, potentially contributing to an improved metabolic status. CONCLUSIONS: Patients with prolactinoma have different intestinal flora than healthy individuals. In addition to the occurrence of prolactinoma and concomitant serum prolactin excess, the gender effect and administration of dopamine agonists are also involved in regulating intestinal microbiota and the metabolic status of the host.}, }
@article {pmid40608216, year = {2025}, author = {Kamruzzaman, M and Goo, T and Park, T}, title = {Hierarchical structural component model for pathway analysis of multinomial phenotypes.}, journal = {Genes & genomics}, volume = {47}, number = {8}, pages = {923-933}, pmid = {40608216}, issn = {2092-9293}, support = {NRF-2022R1A2C1092497//National Research Foundation of Korea/ ; }, abstract = {BACKGROUND: Many statistical methods for pathway analysis have been used to identify novel pathways from biomarkers associated with a certain disease. However, most of these methods are based on single pathway analysis and do not consider multiple pathways simultaneously. To address this issue, a hierarchical structural component model (HisCoM) was developed, which takes into account all pathways at the same time, as well as takes into consideration the correlations among them. HisCoM has been successfully applied to the analysis of continuous, count, and binary phenotypes. OBJECTIVE: In this study, our goal is to propose HisCoM-Categ by extending HisCoM for pathway analysis for both nominal or ordinal multinomial phenotypes, when the phenotypes have more than two possible unordered or ordered discrete categories. METHODS: The foundation of the proposed HisCoM-Categ is the multivariate extension of generalized linear models. Specifically, HisCoM-Categ accounts for the hierarchical structure of biomarkers and pathways, as well as the correlations that exist among pathways. RESULTS: Through the simulation study, HisCoM-Categ was shown to have higher power compared to the other existing methods. In addition, HisCoM-Categ was illustrated with two different omics datasets, including metabolomic, and metagenomic datasets. HisCoM-Categ for ordinal multinomial phenotypes was illustrated by the metabolomic and metagenomic datasets. Those applications demonstrated that HisCoM-Categ successfully identified the well-known pathways that are associated with multinomial phenotypes. CONCLUSIONS: The current study proposes a novel pathway analysis method HisCoM-Categ to identify pathways that have been associated with multinomial phenotypes.}, }
@article {pmid41182402, year = {2025}, author = {Tekgül, ZB and Adıgüzel, A}, title = {Microbial viability assessment with PMA-qPCR: challenges, opportunities, and future directions.}, journal = {Archives of microbiology}, volume = {207}, number = {12}, pages = {343}, pmid = {41182402}, issn = {1432-072X}, abstract = {Since molecular analyzes are insufficient to distinguish living and non-living cells, lead to misleading results, and dead cells also multiply their DNA/RNA, a method that can give more sensitive results was needed. PMA (propidium monoazide), which is used to prevent the DNA of dead cells from negatively affecting the experimental results, is a viability indicator that binds only to the DNA of damaged cells and prevents them from being multiplied by PCR, and was first introduced in 2006. Recently the interest in the use of PMA in many fields such as microbiome and metagenomic studies, environmental microbiology, food microbiology, antibiotic and disinfectant effectiveness tests, clinical microbiology and diagnosis, and cell culture and biotechnology has increased considerably. Therefore, the purposes of use, principles, applications in various fields and limitations of PMA have been investigated. The current review of this vitality marker, which has a history of less than 20 years, will lead to its use of many new scientific studies and will provide convenience to scientists by bringing together studies on the use of this dye.}, }
@article {pmid41661326, year = {2026}, author = {Umemura, A and Sasaki, A and Sasaki, D and Iizuka, A and Chiba, M and Aihara, K and Ubukata, N and Kumagai, H and Tanahashi, Y and Iwasaki, T and Ando, T and Nitta, H}, title = {Impact of laparoscopic sleeve gastrectomy on gut and oral microbiota diversity, weight loss, and the metabolic outcomes.}, journal = {Surgery today}, volume = {}, number = {}, pages = {}, pmid = {41661326}, issn = {1436-2813}, abstract = {PURPOSE: Metabolic and bariatric surgery (MBS) alters the gut microbiota (GM). Changes in oral microbiota (OM) after MBS have not yet been thoroughly investigated. In this study, we evaluated the changes in GM and OM before and after laparoscopic sleeve gastrectomy (LSG) in patients with severe obesity and investigated the relationship between improvements in GM/OM, weight loss, and the metabolic effects. METHODS: Thirty-seven severely obese patients who underwent LSG were enrolled in this study. We retrieved samples from the feces and oral mucosa from baseline to 1-year after LSG. These samples were subjected to a 16 S rRNA metagenomic analysis using a next-generation sequencer. We evaluated the significant changes in GM/OM and compared the results with clinical outcomes. RESULTS: Regarding OM diversity, g_Actinomyces (p = 0.003), o_Rothia (p = 0.020), and g_Streptococcus (p = 0.004) increased. With regard to GM, g_Slackia (p = 0.039), g_Bacillus (p = 0.030), g_Roseburia (p = 0.027), and g_Faecalibacterium (P = 0.003) increased, the proportion of p_ Firmicutes increased, and p_Bacteroidetes decreased in both groups. Changes in g_Akkermansia did not contribute to GM/OM diversity. The weight loss and remission rates of type 2 diabetes were higher in patients with increased normal oral flora and a recovery of g_Faecalibacterium in GM. CONCLUSIONS: We clarified that the LSG reconstructs GM/OM as weight loss and the metabolic effects are enhanced.}, }
@article {pmid41764137, year = {2026}, author = {Zhao, S and Zou, Y and Wang, Z and Ye, L and Chen, Y and Cao, Z and Xu, X and Gao, A and Ying, X and Chen, M and Qin, K and Zhang, Y and Gu, W and Wang, J and Ning, G and Wang, W and Liu, R and Jin, J and Hong, J}, title = {Gut Microbiota and Bile Acid Profiles as Predictors of PCOS Remission: Findings from a Sleeve Gastrectomy Treatment Study.}, journal = {Obesity surgery}, volume = {36}, number = {4}, pages = {1607-1620}, pmid = {41764137}, issn = {1708-0428}, abstract = {OBJECTIVE: To identify predictive biomarkers from the perspectives of gut microbiota and bile acid metabolites for polycystic ovary syndrome (PCOS) remission following metabolic bariatric surgery in patients with PCOS and obesity. METHODS: We conducted a one-year follow-up of patients with obesity and PCOS who underwent sleeve gastrectomy (SG) to assess their PCOS remission status. Metagenomics and bile acid metabolomics were performed and compared between the remission and non-remission groups to identify differential microbial species and bile acid metabolites. The associations between these biomarkers and PCOS remission was then evaluated using Generalized Estimating Equations (GEE) models and Receiver Operating Characteristic (ROC) analysis. RESULTS: SG led to marked improvements in metabolic parameters and hyperandrogenemia. These changes were accompanied by substantial shifts in the gut microbiome, which correlated with alterations in gonadal hormone levels. Based on PCOS outcomes, patients were categorized into remission and non-remission groups. The remission group showed a higher abundance of A. equolifaciens and Clostridium sp CAG 299, along with lower baseline circulating levels of ursodeoxycholic acid (UDCA). These factors were positively associated with PCOS remission. ROC analysis demonstrated that the combination of A. equolifaciens, Clostridium sp CAG 299, UDCA, and average follicle number yielded an AUC of 0.93 for predicting remission. CONCLUSION: A composite biomarker signature incorporating specific gut microbiota profiles, circulating UDCA levels, and ovarian follicle count shows strong potential as an effective predictor of PCOS remission after SG.}, }
@article {pmid41851512, year = {2026}, author = {Zhang, S and Yang, B and Xie, Z and Jiang, F and Liu, K}, title = {Occurrence of Antibiotics at a Typical Livestock Farm in Northwest China: Emergence Characteristics and Ecological Risk Assessment.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {116}, number = {4}, pages = {}, pmid = {41851512}, issn = {1432-0800}, support = {2024TCYCQNBS03//"Tianchi Talents" Young Doctors Recruitment Program/ ; 252102321066//Key Research &amp; Development and Promotion of Special Project (Scientific Problem Tackling) of Henan Province/ ; }, abstract = {This study analyzed veterinary antibiotics (VAs) and resistance genes (ARGs) in manure and soil at a typcial livestock farm in Northwest China using LC-MS and metagenomics. Sulfonamides (SAs) were highest in chicken manure, while quinolones (QNs) dominated cattle manure and adjacent soil (172.784 ng g−1 total QNs). Transfer rates of QNs and tetracyclines from manure to soil exceeded 100%, indicating significant ecological risk via the food chain. Metagenomics revealed the tetracycline resistance gene tetA (58) dominated the soil ARG pool. Significant positive correlations (p < 0.05) existed between QN concentrations (including ciprofloxacin, lomefloxacin) and quinolone resistance genes (flu), and between soil tetracyclines and multidrug resistance genes (mul). Ecological risk modeling confirmed a high mixed contamination risk for QNs (RQ = 2.36 > 1).}, }
@article {pmid41866595, year = {2026}, author = {Taha, MME and Abdelwahab, SI and Binjomah, AZ and Memish, Z and Sahli, KA and Qadri, M and Alarifi, A and Khardali, A and Farasani, A and Madkhali, F and Moshi, JM and Alsaadi, KH and Alshahrani, S}, title = {Mapping the genomic frontier: a comprehensive bibliometric analysis and thematic evolution of whole-genome sequencing for Mycobacterium tuberculosis (1994-2025).}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41866595}, issn = {1573-0972}, abstract = {Whole-genome sequencing of Mycobacterium tuberculosis (WGS-TB) has revolutionized tuberculosis research by providing high-resolution insights into drug resistance, transmission dynamics, and evolutionary pathways. However, the global research landscape, collaboration networks, and thematic evolution of WGS-TB remain underexplored. A comprehensive dataset of WGS-TB publications was retrieved from Scopus. Analyses were conducted using Bibliometrix for productivity trends, Lotka’s and Bradford’s Laws, normalized word cloud, and thematic mapping; VOSviewer for co-authorship, co-occurrence, bibliographic coupling, and unsupervised term clustering; and CiteSpace for reference co-citation analysis (RCCA) and thematic evolution. Between 1994 and 2025, WGS-TB publications exhibited exponential growth, particularly after 2015. The United States, China, and the United Kingdom were leading contributors, supported by globally connected institutions. Collaboration networks revealed strong North–South partnerships, with South Africa acting as a critical bridge. Keyword and thematic analyses identified dominant themes such as drug resistance, genomics, and epidemiology, with emerging areas including metagenomic sequencing and mutation dynamics. Bradford’s Law identified 12 core journals, while RCCA delineated clusters in drug resistance surveillance and molecular epidemiology. This study offers the first integrative mapping of WGS-TB research, illuminating its thematic evolution, global collaboration structure, and emerging directions in genomic surveillance and precision medicine.}, }
@article {pmid41903015, year = {2026}, author = {Ma, N and Zhang, H and Yuan, L and Lian, P and Yang, W and Huang, Y}, title = {Bioremediation of enrofloxacin and modulation of nitrogen cycling in a simulated aquaculture system by the fungus Cladosporium cladosporioides 11.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41903015}, issn = {1573-0972}, support = {NO. 2025A005//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.2023TD12//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.2023TD12//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.2023TD12//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.2023TD12//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.2023TD12//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; }, abstract = {While microbial bioremediation is a promising strategy for antibiotic removal, the potential of fungi in mitigating antibiotic contamination and its associated ecological impacts in aquaculture systems remains largely unexplored. This study evaluated the bioremediation efficacy of the fungus Cladosporium cladosporioides 11 (CC11) in a simulated aquaculture ecosystem. The introduction of CC11 significantly accelerated enrofloxacin (ENR) removal in the aquaculture system and mitigated ENR bioaccumulation in crucian carp. Meanwhile, CC11 application notably lowered the accumulation of total nitrogen and ammonium nitrogen in the water column. Metagenomic analysis revealed that CC11 helped maintain a more active nitrogen-cycling microbial community, sustaining higher abundances of key genes involved in nitrogen fixation (nifB/K/T/Z) and assimilatory nitrate reduction (nasA/C/E/B/D) under ENR stress. Furthermore, CC11 restored specific bacterial taxa correlated with these functional genes, including methylotrophs associated with nif genes and Comamonadaceae members linked to nas genes, thereby reinforcing the functional network for nitrogen transformation. These findings demonstrate that CC11 acts as a multifunctional bioremediation agent, capable of simultaneously enhancing antibiotic removal and regulating nitrogen dynamics, offering a sustainable strategy for managing ENR pollution in aquaculture environments.}, }
@article {pmid41910822, year = {2026}, author = {Kumar, V and Nautiyal, CS}, title = {From hidden allies to precision symbionts: unleashing endophytes for sustainable agroecosystems.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41910822}, issn = {1573-0972}, abstract = {Plants, together with their resident endophytes, constitute a functional holobiont whose integrated traits enable plant growth, stress resilience, disease resistance, and ecosystem remediation. This review discusses advances across ten converging domains that are reshaping research and applications of endophytes, including the following: genomics and metagenomics that identify core genes for colonization, nitrogen fixation, hormone modulation, and stress adaptation; functional genomics and systems biology deciphering host-microbe signaling networks; synthetic biology and CRISPR-based tools for the rational improvement of beneficial traits; microbiome engineering aimed at designing and stabilizing endophytic consortia; multi-omics integration connecting genomic, transcriptomic, proteomic, and metabolomic layers during colonization and under stress; environmental and climatic factors shaping endosphere diversity; bioinformatic platforms predicting biosynthetic gene clusters, secretomes, and metabolic potential; and agricultural and environmental applications in biocontrol and bioremediation. Remaining challenges are the uncultured majority of endophytes, context-dependent transitions between mutualism and pathogenicity, limited field validation, and evolving biosafety frameworks. Thus, the forward framework developed here emphasizes the importance of standard strain benchmarking, causal multi-omics workflows, synthetic community design, and multisite agronomic trials. For their part, endophytes form a scalable, climate-resilient platform for the dual purposes of sustainable agriculture and environmental restoration. In the process, endophytes are emerging as a tractable and scalable foundation for climate-resilient biotechnology, wherein molecular innovation connects with field-level sustainability.}, }
@article {pmid41944841, year = {2026}, author = {Tom, A and Kurian, PS and Philip, S and Mathew, D and Vijayaraghavan, R and Sumbula, V and Varkey, ME}, title = {Exploratory profiling of microbial communities associated with tapping panel dryness in Hevea brasiliensis.}, journal = {Archives of microbiology}, volume = {208}, number = {6}, pages = {}, pmid = {41944841}, issn = {1432-072X}, abstract = {Tapping Panel Dryness (TPD) is a complex physiological disorder in Hevea brasiliensis that leads to the cessation of latex flow, causing significant economic loss, yet its underlying cause remains unclear. Anatomical investigation of bark samples collected from TPD-affected samples exhibited deformed latex vessels, blocked sieve tubes, and DNA-containing bodies within phloem elements. Metagenomic profiling indicated largely similar microbial composition and diversity between healthy and TPD-affected bark samples, except for the presence of low-abundance taxa such as phytoplasma only in affected samples. However, predicted metabolic pathways differed significantly between healthy and TPD samples. The combined anatomical, cytological, and molecular evidences in the current study supports the potential involvement of a biotic factor in the etiology of TPD.}, }
@article {pmid41981555, year = {2026}, author = {Bangera, SR and Subbiah, R and Govindaraj, S and Ibegbu, C and Reznik, D and Read, TD and Hartman, TJ and Paul, S and Torres-Patarroyo, N and Lymon, KJ and Ciers-Davis, NA and Nguyen, ML and Bruner, DW and Flowers, L and Velu, V and Xiao, C}, title = {Characterizing Oral Microbiome and Periodontal Disease in Oral HPV-Positive (COMP-HPV) individuals with HIV: an observational longitudinal study protocol.}, journal = {BMC oral health}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12903-026-08193-x}, pmid = {41981555}, issn = {1472-6831}, support = {P51 OD011132/CD/ODCDC CDC HHS/United States ; R01 DE032243/DE/NIDCR NIH HHS/United States ; P30 AI050409/AI/NIAID NIH HHS/United States ; R01 CA285198/CA/NCI NIH HHS/United States ; }, abstract = {BACKGROUND: Human papillomavirus (HPV) is a major cause of oropharyngeal and other cancers, occurs more frequently among people with HIV (PWH). Despite antiretroviral therapy, HPV-related cancer incidence remains elevated in this group. Oral dysbiosis in PWH may impair mucosal immunity, promoting HPV persistence and inflammation. Periodontal disease, frequently observed in PWH, further contributes to microbial imbalance and immune dysregulation, increasing susceptibility to oral HPV infection. This study investigates the relationship among oral microbiome composition, periodontal disease and oral HPV infection behavior in PWH, considering immunologic and social determinants of health. METHODS: The characterizing oral microbiome and periodontal disease in oral HPV-positive individuals (COMP-HPV), an observational longitudinal study will enroll 500 PWH and follow them up for two years. Oral rinse for HPV testing and periodontal assessment will be collected every six months; saliva for inflammatory markers, oral rinse for microbiome and oral cytobrush for immunological profiling will be collected annually. Immune profiling will include high-dimensional flow cytometry and 10X RNA-sequencing to characterize innate and adaptive immune subsets, with emphasis on HLA-DR–positive populations, enabling evaluation of oral immune modulation during HPV infection. The study has four specific aims such as to examine associations between oral microbiome composition (16S and metagenomics) and oral HPV infection, including prevalence, incidence, persistence, and clearance; to assess the impact of periodontal disease on oral HPV infection and investigate whether the oral microbiome mediates this relationship; to determine how oral microbiome composition influences immunological responses in HPV-positive PWH and to evaluate the role of social determinants on oral microbiome composition and HPV infection. Data from this longitudinal study will be used to understand the natural history of oral HPV infection, the interplay with periodontal disease, microbial alterations, and immunological changes, providing evidence to guide interventions for reducing HPV-associated disease in PWH. TRIAL REGISTRATION NUMBER: Not applicable. DISCUSSION: The COMP-HPV study aims to contribute to the body of research designed to investigate mechanisms underlying oral HPV infection among PWH to improve immune responses to reduce HPV infection and relevant carcinoma.}, }
@article {pmid41986587, year = {2026}, author = {Ishibashi, N and Akase, Y and Ito, A and Kishimoto, K and Watanabe, S and Yokoyama, H and Mekata, T}, title = {Genome characterization and environmental DNA-based detection of a novel adenovirus from red seabream (Pagrus major).}, journal = {Archives of virology}, volume = {171}, number = {5}, pages = {}, pmid = {41986587}, issn = {1432-8798}, support = {25K09243//JSPS KAKENHI/ ; }, abstract = {A novel piscine adenovirus, Pagrus major adenovirus 1 (PmAdV-1), was identified in red seabream (Pagrus major) by metagenomic sequencing. The 29,519 bp genome encodes 22 predicted open reading frames and exhibits a unique organization, with the fiber gene positioned upstream of the conserved adenovirus gene cluster. Phylogenetic analyses indicate that PmAdV-1 forms a sister lineage to red-eared slider adenovirus 1 within a clade of fish and reptilian adenoviruses, but its assignment to the genus Testadenovirus remains uncertain. A virus-specific qPCR assay was developed to monitor PmAdV-1 in environmental DNA from rearing seawater. Viral loads transiently increased in some juvenile tanks without marked mortality. These findings expand current knowledge of fish adenovirus diversity.}, }
@article {pmid41991788, year = {2026}, author = {Imran, H and Nouha, F and Wael, T and Haroun, BA and Wissal, M and Thouraya, BH and Darine, T}, title = {Mesorhizobium inoculation and Water-nitrogen regimes enhance Potato-chickpea intercropping performance and Rhizosphere microbiome diversity.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {5}, pages = {}, pmid = {41991788}, issn = {1573-0972}, abstract = {Increasing water scarcity poses significant threats to crop production and agricultural sustainability. Water deficit and the environmental impacts of synthetic nitrogen fertilization necessitate the development of sustainable cropping systems that enhance resource use efficiency while mitigating climate and economic risks. This study investigates the effects of Mesorhizobium ciceri inoculation (CMG6 strain (SI-DP 40653)), varying water–nitrogen regimes, and a potato-chickpea intercropping system (IC) on plant performance, metabolic responses, rhizospheric microbial diversity. Field trials, located in northeastern Tunisia, showed that IC combined with efficient M. ciceri inoculation significantly outperformed sole cropping (SC) across all physiological parameters. Under standard conditions, this synergy bolstered chickpea biomass and photosynthetic capacity. Notably, under reduced nitrogen input, inoculated intercropping (IC) boosted chickpea shoot biomass by more than twofold compared with sole cropping (SC). Intercropping also improved drought resilience, reducing stress-induced metabolic decline by approximately 40% relative to monocropping systems. Secondary metabolite production was stimulated, with higher accumulation of polyphenols and tannins observed particularly under reduced nitrogen conditions in inoculated systems. Additionally, intercropping improved potato productivity under low-nitrogen conditions while maintaining stable yields under drought stress. Metagenomic analysis showed that water stress accounted for approximately 22% of microbial community variation. However, intercropping and inoculation reshaped rhizosphere communities by enhancing the abundance and diversity of beneficial bacterial groups, particularly Bacilli, and buffering drought-induced shifts. These results emphasized the synergistic benefits of IC and Rhizobium inoculation in improving crop productivity, stress resilience, and soil health while reducing reliance on synthetic inputs.}, }
@article {pmid42020676, year = {2026}, author = {Purohit, HV and Chakraborty, J and Kothari, RK and Bhatt, AR}, title = {Gene Exchange Mechanisms in Natural and Engineered Probiotics Within the Human Gut Implications for Antibiotic Resistance and Metabolic Modulation.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42020676}, issn = {1867-1314}, abstract = {The human gut microbiome is a dynamic and densely populated ecosystem where microbial gene exchange plays a central role in shaping both ecological interactions and host physiology. This review critically examines the mechanisms and implications of horizontal gene transfer (HGT) among natural and engineered probiotics within the human gut, with a specific focus on antibiotic resistance dissemination and metabolic modulation. We provide an in-depth analysis of the molecular pathways of conjugation, transformation, and transduction under anaerobic gut conditions, highlighting their roles in the spread of mobile genetic elements, including antibiotic resistance genes (ARGs) and functional metabolic traits. Special emphasis is placed on the dual nature of gene exchange: while beneficial traits such as vitamin biosynthesis and polysaccharide degradation can be horizontally acquired to enhance probiotic efficacy and host-microbe symbiosis, the uncontrolled dissemination of ARGs or synthetic constructs poses significant clinical and ecological risks. Through a synthesis of recent findings from metagenomics, microbial ecology, and synthetic biology, we explore how natural probiotics may act as reservoirs of ARGs, and how engineered strains—if not properly contained—may contribute to genetic instability in the gut. We also evaluate current containment strategies such as chromosomal integration, kill switches, auxotrophy, and orthogonal circuit design to limit horizontal spread, alongside emerging tools for in situ gene transfer monitoring. Finally, we discuss regulatory challenges and propose a context-dependent risk assessment framework in which the consequences of probiotic gene exchange are determined by cargo properties, host ecological niche, gut inflammatory status, and biocontainment design.}, }
@article {pmid42043563, year = {2026}, author = {Chatterjee, S and Dutta, S and Ghosh, J and Saha, S and Mondal, M and Sarkar, J and Mondal, N and Ghosh, W}, title = {Warming responses, antibiosis potentials, and ecological implications of cryo-adapted copiotrophs from a Trans-Himalayan lake-desert ecosystem.}, journal = {Archives of microbiology}, volume = {208}, number = {7}, pages = {}, pmid = {42043563}, issn = {1432-072X}, support = {Intramural Faculty Grant//Bose Institute/ ; }, abstract = {A Trans-Himalayan lake-desert ecosystem was explored for the low-to-high temperature adaptations of copiotrophic psychrophiles having potentials for substantive carbon remineralization under natural and/or anthropogenically-influenced conditions of high organic matter delivery to the environment. Overall 27 bacterial species were isolated from the brackish-water and sediment-surface of Tso Moriri (a massive lake on the Changthang plateau that remains frozen for approximately one third of the year), and the fine talus covering a lake-side rocky mountain. In Luria broth (LB), all isolates grew at 4 °C and 15 °C; at -10 °C, 13 could grow while others remained only metabolically-active. Catabolizing different complex-organic-compounds, all isolates achieved considerable growth at 4 °C; 20 accomplished low growth at -10 °C. LB-based growth dwindled with rising temperature: 23, 11, and none of the isolates grew at 28 °C, 37 °C, and 42 °C respectively. In agar-overlay assays, most actinobacterial isolates inhibited other mesophilic bacteria. The isolates’ genomes, and their habitats’ metagenomes, encompassed diverse genes for extreme-temperature adaptation, carbohydrate catabolism, antibiosis and antibiotic-resistance. All in-vitro findings collectively engender the following hypothesis, via contextual inferences pending field-study-based validations. Warming-induced cessation of organotrophic growth, within high-altitude cryospheres, would curb the production of simple-fatty-acids, CO2 and N2O. Short-supply of acetate and CO2 would, in turn, cut-back methanogenesis. Such negative-feedback control of greenhouse gas production at the micro-habitat level can add-up in the biome-scale to mitigate broader environmental warming; it, however, endangers the ecosystem from thermally-better-adapted foreign microbes that can usher positive-feedback cycles of warming. In the latter scenario, antibiosis potentials of native actinobacteria become pivotal to microbiome protection.}, }
@article {pmid42046064, year = {2026}, author = {Tang, S and Cai, L and Hao, Y and Jiang, Q and Luan, X and Fang, X and Li, Z and Zhu, J}, title = {SCFAs inhibited NETosis to alleviate lung inflammation in COPD: a potential role for GPR43.}, journal = {Respiratory research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12931-026-03688-1}, pmid = {42046064}, issn = {1465-993X}, support = {82575021//the National Natural Science Foundation of China/ ; 2408085MH230//Anhui Provincial Natural Science Foundation/ ; 2022AH020044//the Science Fund for Distinguished Young Scholars in Universities of Anhui Province/ ; 2024AKLCMF04//the Foundation of Anhui Provincial Key Laboratory of Chinese Medicinal Formula/ ; }, abstract = {BACKGROUND: Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide, and poses a significant socioeconomic burden attributable to its high mortality and morbidity. Short-chain fatty acids (SCFAs), as the key metabolites produced by gut microbiota, have been considered to be involved in the regulation of pulmonary inflammation. However, the underlying bridging mechanisms through the gut-lung axis remain elusive. METHODS: To delineate cellular heterogeneity during COPD progression, we profiled lung tissues from rats at distinct stages (Days 0, 7, 14, and 28) using scRNA-seq, followed by bulk transcriptomic analysis to pinpoint critical dysregulated pathways. Gas chromatography-mass spectrometry (GC-MS) was employed to quantify the differential SCFA levels. The protective effects of SCFAs against pulmonary inflammation in COPD were evaluated via pulmonary function testing, HE staining, and ELISA. Flow cytometry, Western blotting, immunofluorescence and scanning electron microscopy were employed to explore the mechanism of SCFAs regulating neutrophil extracellular trap (NET) formation in vitro and in vivo. Finally, metagenomic sequencing was applied to investigate the impact of SCFAs on gut microbial communities. RESULTS: ScRNA-seq demonstrated the intense immune activation during the progress of COPD, characterized by neutrophil accumulation exceeding 50% of cellular composition on the 14th day in the lung tissue. Transcriptomic analysis further pinpointed neutrophil-driven NETosis as the key pathogenic pathway. The results of GC-MS showed the significant downregulation of SCFAs represented by acetic acid and propionic acid in COPD. Exogenous supplementation with SCFAs (acetic acid and propionic acid) activated the key receptor GPR43, suppressed the expression of NETs marker proteins (NE, MPO, and CitH3) and attenuated inflammatory cytokine levels in COPD rats. Rescue experiments with NETs inducers/inhibitors and GPR43 agonists/antagonists further elucidated the regulatory mechanisms of SCFAs/GPR43 axis in COPD inflammation. Furthermore, metagenomic sequencing revealed that SCFAs reshaped the intestinal flora in COPD by enriching the abundance of beneficial bacteria. CONCLUSION: As one of the key receptors for gut microbiota-derived SCFAs, GPR43 may be involved in the process by which SCFAs alleviate pulmonary inflammation in COPD through regulating NET formation. These findings provide valuable experimental evidence for promoting the clinical translation of therapeutic strategies characterized by gut microbiota and their metabolites.}, }
@article {pmid42057016, year = {2026}, author = {Chen, H and Shi, X and Huang, Z and Li, X and Zhou, Y and Tan, D and Xie, Z and Wu, X and Zhou, M and Hong, D}, title = {Co-occurrence of viral encephalitis and autoimmune encephalitis: overlapping peaks encephalitis or coincidence condition?.}, journal = {BMC neurology}, volume = {26}, number = {1}, pages = {}, pmid = {42057016}, issn = {1471-2377}, support = {No.82101419//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Many studies have shown that autoimmune encephalitis (AE) can occur after viral encephalitis. However, no reports have focused on the interval between viral infection peaks and probable AE peaks. OBJECTIVES: To assess the possibility that viral infection and neuronal autoantibodies are concomitantly present within a 72-hour interval in patients diagnosed with encephalitis. METHODS: We retrospectively analyzed encephalitis patients admitted to our institution between 2018 and 2025. The inclusion criteria were as follows: the interval from the initial onset of symptoms to serum and cerebrospinal fluid (CSF) sampling was less than 72 h, with concomitant detection of viral central nervous system (CNS) infection and neuronal autoantibodies. Viral detection was performed using metagenomic next-generation sequencing (mNGS), whereas neuronal autoantibodies were measured by cytometric bead array (CBA). RESULTS: Among 347 patients with encephalitis, fifteen patients had concomitant detection of viral central nervous system (CNS) infection and neuronal autoantibodies within 72 h after the initial onset of symptoms.These fifteen patients presented with prominent clinical manifestations including headache, seizures, psychosis and memory disorders. Cerebrospinal fluid (CSF) analysis revealed features consistent with aseptic or viral encephalitis. A variety of neuronal autoantibodies were identified, namely NMDA-R-IgG, CASPR2-IgG, LGI1-IgG, LON5-IgG, GFAP-IgG, GAD65-IgG and mGluR5-IgG.Metagenomic next-generation sequencing (mNGS) assays demonstrated that 5 patients were infected with Human Herpesvirus Type 1 (HSV-1) and 10 patients with Epstein-Barr Virus (EBV). CONCLUSIONS: The concomitant detection of viral infection and neuronal autoantibodies in serum or cerebrospinal fluid (CSF) within a short time window (≤ 72 h) after the initial onset of symptoms was defined in this study as Overlapping Peak Encephalitis (OPE) or coincidence condition, which suggests that it represents a distinct clinical entity. This finding underscores the importance of simultaneously performing both metagenomic next-generation sequencing (mNGS) and neuronal autoantibody assays in patients with suspected viral encephalitis. Early identification of such comorbid conditions is of paramount importance; timely diagnosis combined with antiviral therapy and immunomodulatory intervention may significantly improve clinical outcomes.}, }
@article {pmid42283754, year = {2026}, author = {Chen, X and Fang, Z and Li, S and Wu, Q and Liu, W and Xiang, L and Liu, Q and Tan, L and Weng, Q}, title = {Isolation and genomic analysis of a novel Pseudomonas phage from karst cave in China.}, journal = {Archives of virology}, volume = {171}, number = {7}, pages = {}, pmid = {42283754}, issn = {1432-8798}, mesh = {*Genome, Viral ; *Caves/virology/microbiology ; *Pseudomonas Phages/genetics/isolation &amp; purification/classification ; Phylogeny ; China ; *Pseudomonas/virology ; DNA, Viral/genetics ; Sequence Analysis, DNA ; Genomics ; Geologic Sediments/virology ; }, abstract = {Bacteriophages (phages) in extreme environments like karst caves remain largely unexplored. Here, we report vB_Psp_JHDO137a, a novel phage isolated from cave sediment infecting Pseudomonas sp. The 41,530-bp dsDNA genome places it within the genus Ghunavirus (family Autographiviridae). Notably, its genome lacks auxiliary metabolic genes (AMGs), in contrast to AMG-rich profiles reported in cave metagenomic surveys and underscoring the necessity of isolation-based approaches to complement environmental sequencing data.}, }
@article {pmid42283827, year = {2026}, author = {Wiśniewski, P and Maździarz, M and Kwietniewska, K and Krawczyk, K}, title = {Shifts in Rhizosphere Bacterial Community Composition and Predicted Functional Potential Associated with Impatiens parviflora Invasion in Temperate Forest.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02807-1}, pmid = {42283827}, issn = {1432-184X}, support = {No. 12.610.002-110//Uniwersytet Warmi&#x144;sko-Mazurski w Olsztynie/ ; No. 12.610.002-110//Uniwersytet Warmi&#x144;sko-Mazurski w Olsztynie/ ; No. 12.610.002-110//Uniwersytet Warmi&#x144;sko-Mazurski w Olsztynie/ ; }, abstract = {Impatiens parviflora is a widespread invasive plant in temperate European forests, yet its influence on rhizosphere microbial communities remains poorly understood. This study provides initial metagenomic insights into taxonomic shifts and predicted functional potential of bacterial communities associated with this invader. Rhizosphere soils were collected from eight I. parviflora-invaded and eight non-invaded control plots in a mixed coniferous forest in northern Poland and analysed using Oxford Nanopore shotgun sequencing, with functional inference performed using the taxonomy-dependent FAPROTAX database. Bacterial richness was significantly higher in invaded soils, whereas Shannon and Simpson diversity indices did not differ between treatments, indicating an expansion of rare taxa without changes in overall diversity structure. The invaded rhizosphere was characterised by a uniform depletion of dominant bacterial orders, with no significantly enriched taxa detected, contrasting with the selective enrichment of microbial groups often reported for other invasive plant species. FAPROTAX-based predictions indicated consistently lower inferred abundances of 37 metabolic processes in invaded plots, including those related to nitrogen cycling and degradation of complex plant polymers. Because these functional predictions are derived from taxonomic composition, they represent inferred ecological potential rather than measured activity. Overall, these results generate testable hypotheses regarding plant-soil feedbacks and highlight the utility of long-read metagenomics for exploring microbial dynamics potentially contributing to the ecological success of I. parviflora in temperate forests.}, }
@article {pmid42284845, year = {2026}, author = {Wang, W and Sun, X and Hao, R and Li, F}, title = {Algal community composition drives lake greenhouse gas emissions via dissolved organic matter transformation and microbial processing.}, journal = {Journal of environmental management}, volume = {411}, number = {}, pages = {130177}, doi = {10.1016/j.jenvman.2026.130177}, pmid = {42284845}, issn = {1095-8630}, abstract = {Lakes are important sources of greenhouse gases, yet bloom-driven emissions are often assessed from total algal biomass, ignoring algal functional composition. This study examined how cyanobacteria (Microcystis aeruginosa), green algae (Chlorella vulgaris), diatoms (Cyclotella meneghiniana), and dominance-based mixtures regulate DOM transformation and CO2/N2O production under eutrophic conditions. It integrated to pure-culture experiments, water-sediment microcosms, sterilization controls, DOM fluorescence spectroscopy, gas monitoring, and metagenomics to resolve an algae-DOM-microbe-gas cascade. Cyanobacteria produced protein-like DOM and stimulated carbon mineralization, with CO2 exceeding 20 mmol L-1 by day 36; cyanobacteria-dominant mixtures followed a similar high-CO2 trajectory. Green algae generated tyrosine-like DOM and caused the strongest NO2[-] accumulation, reaching 5.21 mg L[-1] by day 21, corresponding to the highest N2O production; this pattern also occurred in green-algae-dominant mixtures. Diatom-only and diatom-dominant treatments favored humic-like DOM, organic carbon retention, and the weakest short-term CO2/N2O accumulation. Sterilization reduced inorganic carbon and greenhouse gas production, supporting microbial control. Background summer metagenomics provided functional context, showing algal-DOM turnover potential through carbon metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, and the TCA cycle, while nirK and other nitrogen genes indicated capacity for substrate-driven incomplete nitrogen reduction. Functional differentiation among Candidatus_Planktophila, Limnohabitans, Rhodoferax, and Cyanobium linked DOM processing with potential gas-production pathways. These results show algal community composition, rather than biomass alone, regulates greenhouse gas production by shaping DOM quality, nutrient intermediates, and microbial C-N pathways. Incorporating algae composition into greenhouse gas assessment, this novel algae-DOM-microbe-gas framework provides mechanistic support for improving eutrophication management and lake-emission mitigation.}, }
@article {pmid42284910, year = {2026}, author = {Fu, J and Li, Z and Hu, C and Yao, L and Cao, M and Dong, Y and Wang, P and Liang, Y and Tong, L and Shi, J}, title = {Metagenomic insights into the distribution and potential influencing factors of antibiotic resistance genes in historically polluted lake sediments.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {298}, number = {}, pages = {107898}, doi = {10.1016/j.aquatox.2026.107898}, pmid = {42284910}, issn = {1879-1514}, abstract = {Lake sediments serve as time-integrated archives of the evolution and persistence of environmental antibiotic resistance genes (ARGs), providing insights into how sustained environmental pressures shape resistome structure in human-impacted lake systems. Industrially polluted lakes, as systems subjected to strong anthropogenic disturbance, are characterized by high-intensity contaminant loading in sediments; however, the accumulation patterns and environmental factors associated with ARG persistence in such environments remain poorly understood. This study investigated the horizontal and vertical distributions and potential influencing factors of ARGs along sediment depth gradients (0-40 cm, 40-80 cm, and 80-120 cm) in a lake historically polluted by industrial activities (Ya'er Lake). Results indicated that bacitracin (27.3-43.6%) and multidrug resistance genes (25.4-33.1%) dominated the resistome, with pronounced enrichment in shallow sediments near discharge outlets, reflecting the influence of legacy pollution inputs. ARGs exhibited significant vertical stratification (p < 0.05): highest abundance in shallow layers, peak diversity in middle layers, and shifts with depth of key subtypes. Host-tracking assigned ARGs to 34 major genera across four phyla, with Pseudomonadota, Actinomycetota, Bacillota, and Thermodesulfobacteriota identified as the major ARG hosts. Microbial communities and mobile genetic elements (MGEs) jointly shaped ARG persistence, with shallow sediments showing broader host-MGE coupling and deeper sediments showing stronger signatures of environmental filtering and selective MGE-mediated maintenance. Overall, ARGs shifted from surface enrichment associated with historical wastewater inputs to a more selective persistence pattern with burial depth, indicating contaminated lake sediments as long-term reservoirs and potential dissemination sources of ARGs.}, }
@article {pmid42284942, year = {2026}, author = {Yang, X and Peng, AD and Huang, YH and Cheng, JH and Zhong, HT and Zhou, HT and Liu, PQ and Ji, XH and Li, C and Zhang, SR and Lai, JL and Luo, XG}, title = {Ecological risk assessment of 1,4-thioxane and its remediation by a synthetic microbiome based on a sulfur transformation system: From multi-omics to water application.}, journal = {Water research}, volume = {303}, number = {}, pages = {126258}, doi = {10.1016/j.watres.2026.126258}, pmid = {42284942}, issn = {1879-2448}, abstract = {Among the chemicals in weapons abandoned by Japan in China during World War II, 1,4-thioxane, a typical degradation product of mustard gas, has environmental persistence and potential ecological risks. However, its toxicity mechanism and efficient remediation strategy remain unclear. This study first employed multi-omics technologies (16S sequencing, metagenomics, and metabolomics) to analyze the toxic effects of 1,4-thioxane (0-100 mg·L[-1], 120 days) on water microecology. Subsequently, an efficient degrader, Pseudomonas sp. M1, was screened, and transcriptome analysis revealed significant upregulation of Fe-S cluster assembly-related genes (sufB, sufU, sufS), which are key components of the SUF sulfur conversion system. These three genes were heterologously expressed in Escherichia coli to construct three engineered strains, each capable of degrading 1,4-thioxane via the SUF system. When mixed in equal proportions to form a synthetic microbiome, they completely degraded 100 mg·L[-1] 1,4-thioxane in culture medium within 16 h and achieved 100% removal in simulated polluted water within 15 days. Integrated multi-omics analysis demonstrated that 1,4-thioxane is highly persistent (residual rate > 98%) but significantly inhibits nitrogen cycling, manifested by NH4[+] accumulation (1.5-3.1-fold increase) and NO3[-] depletion (24.9-87.6% decrease), along with reduced ammonia monooxygenase, nitrite oxidoreductase, and nitrate reductase activities (67.8-91.0%, 53.2-90.1%, and 42.8-80.9% reductions, respectively). Ionome analysis showed K and P accumulation and Mo depletion; 16S sequencing revealed reduced microbial diversity, suppression of nitrogen-cycling genera, and enrichment of Pseudomonas; metagenomics uncovered widespread suppression of nitrogen metabolism pathways, dysregulation of antibiotic resistance genes, and decreased viral abundance; and metabolomics confirmed global inhibition of the alanine-aspartate-glutamate pathway. This is the first study to combine multi-omics toxicity analysis with synthetic microbiome remediation based on the SUF sulfur conversion system. The findings provide a theoretical basis and technical support for ecological risk assessment and bioremediation of sites contaminated by relic Japanese chemical weapons.}, }
@article {pmid42285959, year = {2026}, author = {Lyu, C and Wang, Z and Zhao, R and Zhao, H and Liu, S and Lian, H and Wang, X}, title = {Preoperative gut microbial network alterations and BCAA-Related metabolic disturbance in postoperative delirium after cardiac surgery: a prospective matched multi-omic study.}, journal = {Translational psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41398-026-04161-9}, pmid = {42285959}, issn = {2158-3188}, abstract = {Postoperative delirium (POD) is a frequent neuropsychiatric complication after cardiac surgery, yet the biological basis of individual susceptibility remains unclear. In this prospective cohort study, 317 adults undergoing elective on-pump cardiac surgery were enrolled and followed for POD during the first 7 postoperative days. Thirty patients who developed POD were then matched 1:1 with 30 non-POD controls by age, sex, and primary diagnosis for multi-omic analyses. Preoperative fecal samples were collected from the first bowel movement after admission and before prophylactic antibiotic administration, and postoperative fecal samples were collected from the first postoperative bowel movement. Paired fecal samples underwent shotgun metagenomic sequencing, and perioperative serum samples underwent untargeted metabolomic profiling. Preoperatively, α- and β-diversity were comparable between groups, but patients who subsequently developed POD exhibited a less connected and less integrated microbial network structure. Postoperatively, gut microbial composition differed significantly between groups (PERMANOVA R[2] = 0.053, P < 0.001). Metagenomic profiling identified 35 differentially abundant species and 16 differentially enriched KEGG level 3 pathways, with POD-associated features showing inferred functional shifts toward amino-acid catabolism, including branched-chain amino acid (BCAA)-related pathways. Untargeted metabolomics demonstrated marked perioperative remodeling in both groups, but POD was associated with a 27-metabolite panel characterized predominantly by lower postoperative levels or impaired recovery, with pathway enrichment converging on valine, leucine, and isoleucine metabolism. Integrative analyses further linked POD-associated microbial taxa with amino-acid catabolic pathways and lower levels of BCAA-related serum metabolites. These findings suggest that POD is associated with preoperative alterations in microbial network organization and a postoperative microbiome-metabolome disturbance pattern centered on amino-acid metabolism, particularly the BCAA axis.}, }
@article {pmid42286003, year = {2026}, author = {Hensen, ADO and Harmanus, C and Verbeek-Menken, PH and Koopman, JPR and Lamers, OAC and Roozen, GVT and Janse, JJ and Balke-Buijs, M and van der Stoep, MYEC and Meij, P and van Amerongen-Westra, IM and Schipper, P and Crul, C and Pattacini, L and Rox, K and Farowski, F and Tsakmaklis, A and Vehreschild, MJGT and Kuijper, EJ and Smits, WK and Roestenberg, M}, title = {Experimental human colonisation with non-toxigenic Clostridioides difficile: a placebo-controlled randomised clinical trial.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-74327-y}, pmid = {42286003}, issn = {2041-1723}, support = {101007799//Innovative Medicines Initiative (IMI)/ ; }, abstract = {Clostridioides difficile infections remain a major global healthcare burden, underscoring the need for novel therapies. Human colonisation models provide mechanistic insight into C. difficile colonisation and facilitate identification of novel intervention targets. We conducted a placebo-controlled, randomised clinical trial (NCT05693077) administering non-toxigenic C. difficile (NTCD) capsules to healthy participants to assess safety and colonisation as primary endpoints, and microbiota susceptibility as a secondary endpoint. A total of 69 healthy participants (18-45 years), not previously colonised with C. difficile and without recent antibiotic use, were enrolled following a health assessment. NTCD capsules administered for five consecutive days at low or high dose, was safe with no dose-response relationship in colonisation outcomes. Vancomycin pretreatment induced colonisation success: with 5% colonisation without, 32% after one day, and 84% after five days vancomycin pretreatment. Some participants that cleared vancomycin rapidly acquired non-challenge C. difficile strains prior to NTCD challenge. Microbiota profiling (using shotgun metagenomics) revealed reduced α-diversity and pronounced community restructuring. These findings highlight the impact of antibiotic-mediated microbiota disruption, the widespread environmental presence of C. difficile, and the feasibility of meaningful microbiota assessment in small-scale intervention trials, thereby providing a robust tool to investigate this globally impactful infection.}, }
@article {pmid42286360, year = {2026}, author = {Morelli, S and Romano, S and Cosenza, G and Abate, S and Lombardi, L and Pilli, E}, title = {A damage-aware NGS workflow for conservative species identification from ultra-degraded DNA.}, journal = {Analytical and bioanalytical chemistry}, volume = {}, number = {}, pages = {}, pmid = {42286360}, issn = {1618-2650}, abstract = {Species identification from highly degraded DNA remains a major challenge across ecology, conservation genetics, wildlife forensics, and museum science, where samples are often scarce, contaminated, and embedded in complex matrices. Under these conditions, standard reference-based and metagenomic classifiers are prone to false-positive assignments, particularly when ultra-fragmented DNA and conserved genomic regions are not explicitly accounted for. Here, we present a damage-aware next-generation sequencing (NGS) workflow for conservative species identification from minute quantities of highly degraded DNA, designed to minimize misclassification in low-input and damage-rich datasets. The workflow integrates micro-sampling, half-uracil-DNA-glycosylase (half-UDG) library preparation, PCR duplicate removal, multi-genome mapping against a curated reference panel, and a post-mapping read-ubiquity classifier that distinguishes species-specific reads from those shared across conserved loci. Using collagen-rich substrates as a proof-of-concept, we demonstrated accurate species attribution from samples as small as 1 mm[2], including mixtures and mineral-containing matrices. The workflow reliably identifies dominant biological sources, reduces false-positive assignments driven by conserved genomic regions, and remains robust to common physical and chemical treatments such as swelling, heating, and plaster addition. Overall, this study provides a proof-of-concept framework for conservative species identification in challenging degraded DNA contexts. The workflow may be adaptable to a broader range of degraded DNA contexts-including wildlife monitoring, regulatory enforcement, forensic investigations, and the analysis of processed biological materials-although further validation across diverse matrices will be required.}, }
@article {pmid42286394, year = {2026}, author = {Shen, Q and Chen, J and Chen, Y and Liu, J and Mao, L and Shi, W and Ndjekadom, A and Wang, J and Wang, X and Liu, Y and Yang, S and Ji, L and Wu, P and Tong, F and Yang, H and Zhang, W}, title = {Metagenomic characterization of the virome of Aedes albopictus in Anhui Province, China, with phylogenetic analysis of CRESS-DNA viruses and Parvoviridae.}, journal = {Virus genes}, volume = {}, number = {}, pages = {}, pmid = {42286394}, issn = {1572-994X}, support = {22KJA320001//Jiangsu Province Higher Education Basic Science (Natural Science) Research Project/ ; No. 2023YFD1801300//National Key Research and Development Program of China/ ; No. 82341106//National Natural Science Foundation of China/ ; }, abstract = {Aedes albopictus is a globally important mosquito species capable of transmitting a variety of viruses. In this study, a total of 440 Ae. albopictus individuals were collected from Fanchang, Anhui Province, and 22 tissue libraries were constructed for metagenomic sequencing. A total of 649,930,614 reads were obtained and assembled into 209,335 contigs, of which 18,339 showed similarity to known viral proteins, spanning 13 viral families including both DNA and RNA viruses. Because several DNA virus-related sequences were recovered from the dataset, we further focussed on CRESS-DNA virus-related sequences and members of the family Parvoviridae. Phylogenetic analysis showed that three CRESS-DNA virus-related sequences clustered within Smacoviridae and Genomoviridae, while two Parvoviridae genomes were assigned to Brevihamaparvovirus and Protoparvovirus. These findings provide a metagenomic overview of the Ae. albopictus-associated virome in Anhui Province and provide baseline information on mosquito-associated DNA virus-related sequences in this region.}, }
@article {pmid42286497, year = {2026}, author = {Gao, X and Sanui, A and Rasmika Dewi, DAP and Lucaci, AG and Mason, CE and Suzuki, H}, title = {Shotgun metagenomic dataset of surface microbiomes at a train station in Shinagawa, Tokyo.}, journal = {BMC genomic data}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12863-026-01451-5}, pmid = {42286497}, issn = {2730-6844}, support = {U54AG089334//National Institute for Health and Care Research/ ; JPMJCR20H1//JST CREST/ ; 20K10436//JSPS KAKENHI/ ; JAHMEC.G-02, 2022//Japan Architectural Health, Management and Education Center Research grant/ ; }, abstract = {OBJECTIVES: The urban microbiome is a significantly underexplored ecosystem which contributes to the health and resilience of the human population and less is known about the microbiome of urban transportation systems that commuters interact with daily. Shotgun metagenomic sequencing data from swab samples were collected at a representative medium-scale urban commuter railway station in Tokyo, Japan, with daily passenger volumes on the order of tens of thousands, in October 2021. The dataset was generated as part of the nationwide "Urban Microbiomes in Japan" project and provides a resource for comparative analyses of urban microbial diversity and future public health surveillance studies in urban environments.<br><br>DATA DESCRIPTION: Three surface swab samples were collected in October 2021 from concrete floor areas near ticket gates at a major railway station in Shinagawa, Tokyo. Samples were collected using Isohelix swabs with DNA/RNA Shield stabilization solution. Metagenomic DNA was extracted and subjected to shotgun sequencing, generating 2 &#xd7; 150 bp paired-end reads.}, }
@article {pmid42286668, year = {2026}, author = {Lawther, K and Dimonaco, NJ and Donnelly, P and Guinguina, A and Krizsan, SJ and Huws, SA}, title = {Dietary inclusion of Asparagopsis taxiformis significantly reduces methane emissions in dairy cows by mechanistically altering vitamin B12-dependent and other methanogenesis precursor pathways.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02447-0}, pmid = {42286668}, issn = {2049-2618}, abstract = {BACKGROUND: Ruminant products are widely consumed due to their high protein and micronutrient content, but ruminant production contributes significantly to greenhouse gas emissions, with methane (CH4) accounting for 33% of anthropogenic emissions. CH4 is generated via fermentative processes by the rumen microbiome, primarily through hydrogen utilisation by methanogenic archaea. Feeding beef cattle the red seaweed Asparagopsis taxiformis (ASP) has been shown to reduce CH4 emissions by up to 80%. However, the microbial mechanisms underlying this reduction remain poorly understood. In this study, Nordic Red dairy cows (122 ± 13.7 days in milk) were fed grass silage and concentrate (60:40 dry matter basis) either with or without 0.5% ASP (organic matter basis) in a Latin square design, and rumen fluid was collected 19 days into each of the 3 experimental periods.<br><br>RESULTS: ASP supplementation reduced CH&#x2084; yield by 54% (g CH&#x2084;/kg DM). Metagenomic analysis revealed genes encoding pyruvate and propionate production pathways were more abundant in ASP treated animals, while those associated with acetate and CH&#x2084; were reduced. Additionally, genes encoding vitamin B12 biosynthesis enzymes showed reduced abundances (e.g., adenosylcobinamide-GDP ribazoletransferase, EC 2.7.8.26, -29.92%). Vitamin B12 and its related cofactors are&#xa0;critical for methanogenic methyltransferases and C1 metabolism. Dominant taxa including Prevotella and Methanobrevibacter declined, while less abundant taxa increased their contribution to methane-related pathways, indicating niche displacement and community restructuring. CONCLUSION&#xa0;: ASP supplementation modulates the rumen microbiome through mechanisms extending beyond direct methanogen inhibition. The reduced abundance of genes involved in C1 metabolism and vitamin B12-dependent methanogenic processes suggest methane suppression is linked to broader restructuring of microbial metabolic networks. The redistribution of methane-related functions from dominant taxa to a wider taxonomic community indicates ecological reorganisation and functional resilience of the rumen microbiome. Collectively, these results reveal the multiple modes of action of ASP, establishing its promise as an effective methane mitigation strategy. Video Abstract.}, }
@article {pmid42286752, year = {2026}, author = {Abedini, R and Salekdeh, GH and Hashemi, M}, title = {Beyond metagenomics: culturomics uncovers aerobic and facultative anaerobic bacterial diversity in the camel gut.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42286752}, issn = {2524-4671}, abstract = {While metagenomics has transformed our view of microbial ecosystems, culture-based methods remain indispensable for accessing microbial functionality and biotechnological potential. In this study, we applied a culturomics strategy to explore the diversity, abundance, and distribution of culturable aerobic and facultative anaerobic bacteria along the gastrointestinal tract of dromedary camels (Camelus dromedarius) grazing on pristine desert flora. Using six culture media-including modified YCFA formulations-we isolated 97 bacterial species across 42 genera, 31 families, and four phyla: Firmicutes, Proteobacteria, Actinomycetota, and Bacteroidota. Strikingly, 88.6% of this diversity was recovered using YCFA-based media, and four candidate novel species were identified. The rumen harbored the most diverse and Gram-positive-dominated community, whereas the small intestine was enriched with Gram-negative taxa, many with pathogenic potential. These findings highlight the camel's unique physiological adaptation to extreme arid environments, characterized by efficient fiber degradation under nutrient- and water-limited conditions and the presence of stress-tolerant gut microbes capable of resisting acidic and osmotic challenges. Overall, this study establishes a foundational understanding of the camel gut microbiota and underscores the complementary power of culture-dependent methods to metagenomics. Future integration with anaerobic culturing and multi-omics analyses will further unveil the ecological and biotechnological potential of desert-adapted microbial life.}, }
@article {pmid42286784, year = {2026}, author = {Yu, Y and Wu, H and Ji, H and Hu, Y and Fang, Y and Lin, Y and Zhang, Y and Zhou, Y}, title = {Metagenomic analysis reveals resistome characteristics and high-risk resistance genes in the pig nasal cavities, feces, and farm dust.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00589-y}, pmid = {42286784}, issn = {2524-4671}, support = {2024-2026QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; 32402702//National Natural Science Foundation of China/ ; LMS25C170002//Natural Science Foundation of Zhejiang Province/ ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) poses a threat to global public health. Swine farms are critical AMR reservoirs. Comprehensive resistome profiling and risk assessment across pig-associated niches remain limited. Metagenomic analysis of antibiotic resistance genes (ARGs) in pig nasal cavities, feces, and farm dust was performed.<br><br>RESULTS: Nasal and dust samples exhibited significantly increased ARG diversity and abundance compared with feces. We identified 78 potentially hazardous ARGs and proposed an improved risk classification framework integrating host promiscuity, mobility, and human health risks. These ARGs were classified into four risk levels: 25 Level I (current high risk), 25 Level II (potential future threats), 18 Level III (host-promiscuous but nonmobile), and 10 Level IV (host-specific). High-risk ARGs mainly confer aminoglycoside, macrolide-lincosamide-streptogramin (MLS), and tetracycline resistance. Metagenome-assembled genome (MAG) analysis revealed that bacterial taxa enriched in ARGs were predominant in nasal and dust samples. Moreover, these environments presented higher mobile genetic element (MGE) abundance and similar ARG-MGE co-occurrence patterns. Notably, 74.12% of the mobile ARGs were predicted to be plasmid-borne, and these ARGs tended to be assigned higher health risk levels than chromosomal ARGs.<br><br>CONCLUSIONS: These findings provide a practical framework for ARG risk assessment and highlight the nasal cavity and dust as underappreciated but important AMR reservoirs in pig farms.}, }
@article {pmid42286862, year = {2026}, author = {Othman, EM and Bencurova, E and Ferretti, P and Bork, P and Rodriguez Del Rio, A and Huerta-Cepas, J and Caruana, I and Abdel-Latif, R and Akash, A and Albacete, A and Lafi, F and Dandekar, T and Naseem, M}, title = {Diet and microbiome shape small-molecule cytokinin pools in mammals.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2679497}, doi = {10.1080/19490976.2026.2679497}, pmid = {42286862}, issn = {1949-0984}, mesh = {Animals ; *Cytokinins/blood/metabolism ; Humans ; Mice ; *Diet ; *Gastrointestinal Microbiome ; *Mammals/metabolism ; Metabolomics ; Metagenomics ; Feces/chemistry ; Swine ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; *Microbiota ; }, abstract = {Cytokinins (CKs) are adenine-derived metabolites traditionally characterized as plant hormones, yet their origin, distribution, and functions in mammalian systems remain largely undefined. Using integrated metabolomics, microbiome, and metagenomics approaches, we provide a systematic characterization of CK occurrence and potential sources in mammals. Serum profiling across five animal species revealed consistent detection of multiple CK derivatives, with concentrations markedly lower than in plant tissue. The CK storage form, zeatin-O-glucoside, predominated in mammalian sera, followed by trans-zeatin and kinetin, indicating a CK composition distinct from that in plants. Species-specific differences, such as reduced trans-zeatin in mice and lower kinetin in humans, further suggest divergent regulatory patterns. In mice, CKs were present in vascular tissues of the kidney, heart, and liver, demonstrating systemic distribution. Dietary manipulation showed that starvation significantly reduced CK abundance in serum, colon, feces, and urine, confirming that diet is a major contributor to the mammalian CK pool. Meta-omics analysis of gut microbiomes identified CK-related genes across multiple microbial taxa, with the highest representation in human microbiomes, followed by those of mouse and pig. Germ-free mouse experiments showed substantially lower CK levels than conventionally raised counterparts, establishing a microbiome-dependent contribution. Collectively, our findings identify CKs as diet and microbiome modulated metabolites in mammals, warranting future investigation to elucidate their physiological significance in mammalian biology.}, }
@article {pmid42287197, year = {2026}, author = {De Visscher, J and Tytgat, B and Hodgson, DA and Wilmotte, A and Willems, A and Verleyen, E and Vyverman, W}, title = {Functional Genetic Potential Of Benthic Microbial Mat Communities In Arctic, Antarctic And Sub-Antarctic Lakes.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag060}, pmid = {42287197}, issn = {1574-6941}, abstract = {Benthic microbial mat communities are key drivers of ecosystem functioning in polar lakes and ponds, forming the base of aquatic food webs and contributing substantially to nutrient cycling. Although Arctic, Sub-Antarctic and Antarctic microbial mats differ in community composition, their functional genetic potential remains poorly understood. We applied shotgun metagenomic sequencing to study 17 microbial mat communities from Arctic and (Sub-)Antarctic lakes differing in salinity, catchment vegetation and climatic conditions. Stress response genes, especially cold stress, and phosphorus cycling and metabolism genes were highly abundant in all lakes. A large proportion of functional genes was shared between regions, with core functions dominated by transport mechanisms and energy production. However, clear differences in particular gene abundances were observed. Several East-Antarctic lakes and inland ponds in the Transantarctic Mountains showed a dominance of oxygenic photosynthesis and Calvin cycle genes for carbon fixation, likely reflecting the dominance of Cyanobacteriota. In Arctic and Sub-Antarctic lakes with catchment vegetation and higher arthropod abundances, lignin and chitin degradation genes were more important. Our study shows that, despite distinct biogeographic patterns in community composition, the functional genetic potential of polar lake microbial mats mainly reflects climatic and local environmental conditions, emphasising specific adaptations to extreme polar environments.}, }
@article {pmid42287489, year = {2026}, author = {da Silveira Bastos, IMA and Cardoso, MS and Laux, M and Ribeiro, RR and García, GJY and Bahia, PA and de Sousa, PMV and Alves, BGT and de Rezende, DHC and Rosado, AS and Bezerra, JDP and Landell, MF and Melo, VMM and Tavares, TCL and Góes-Neto, A}, title = {Worldwide diversity and ecology of mangrove fungi: a systematic review of ITS metabarcoding studies and a quantitative, integrative analysis of raw sequence data.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42287489}, issn = {1573-0972}, mesh = {*Fungi/classification/genetics/isolation &amp; purification ; *DNA Barcoding, Taxonomic ; *Biodiversity ; *Wetlands ; *Mycobiome ; Basidiomycota/genetics/classification ; Geologic Sediments/microbiology ; *Rhizophoraceae/microbiology ; Ecosystem ; Ascomycota/genetics/classification/isolation &amp; purification ; Phylogeny ; }, abstract = {Fungi are integral components of the mangrove microbiome, playing critical roles in decomposition, nutrient cycling, and symbiosis. Our study synthesizes the findings from a global systematic review of fungal ITS metabarcoding studies conducted in mangrove ecosystems. This review consolidates data from 23 original research articles (1,154 samples) and provides a comprehensive overview of the diversity, community structure, and ecological functions of fungi in these critical coastal habitats. The analyses revealed a consistent core fungal mycobiome in mangroves worldwide. This community is dominated by Ascomycota, with Basidiomycota as the second most abundant phylum. A consistent set of ten highly abundant genera underpins this core community, and fungal diversity and composition are strongly influenced by the specific substrate. Non-rhizospheric sediment harbors the highest diversity, while live plant organs host a more specialized and less diverse community, slightly dominated by potential plant pathogens. Rhizospheric sediment supports a unique assemblage rich in wood-decomposing fungi. The primary ecological role of fungi in mangroves is decomposition, which is essential for breaking down lignocellulosic litter, cycling nutrients, and storing carbon in sediments. A surprisingly high relative abundance of fungi classified as plant pathogens was identified on mangrove plant tissues, suggesting an underappreciated role of fungal diseases in these ecosystems. Metabarcoding provides a far broader view of fungal diversity than traditional collection and culturing methods. It has uncovered a vast number of uncultured taxa and has been particularly effective in revealing the significant, and likely underestimated, presence of macrofungi in mangrove soils. Our study also highlights that current short-read metabarcoding can severely underestimate certain fungal groups, particularly the endomycorrhizal Glomeromycota, due to technical limitations. Altogether, our synthesis provides a global baseline against which future mangrove mycobiome studies can be benchmarked.}, }
@article {pmid42287798, year = {2026}, author = {Winssy, TD and Anandham, R and Maragatham, S and Uma, D and Karthikeyan, S and Balachandar, D}, title = {Long-term nutrient management shapes soil microbial and metabolic signatures in a century-old semi-arid agroecosystem.}, journal = {Journal of environmental management}, volume = {411}, number = {}, pages = {130209}, doi = {10.1016/j.jenvman.2026.130209}, pmid = {42287798}, issn = {1095-8630}, abstract = {Semi-arid tropical soils inherently contain low soil organic carbon (SOC) and limited nutrient reserves, resulting in poor productivity. Intensive cropping with synthetic fertilizers, further deteriorate soil quality and impair ecosystem functioning. In contrast, organic amendments alone or combined with synthetic fertilizers sustain soil biodiversity through microbially mediated processes. However, how long-term nutrient management shapes soil microbiomes and their functional diversity in semi-arid tropical systems remains largely unknown. To address this gap, we investigated a 116-year-old long-term nutrient management experiment using a multi-omic framework. Shotgun metagenomics characterized the total microbiome (bacteria, archaea, and eukaryota) and associated carbon- and nitrogen-cycling genes under four contrasting nutrient management practices: unfertilized control, inorganic fertilizer alone (IC), organic amendment alone (OM), and integrated nutrient management combining organic and inorganic inputs (INM). OM and INM significantly improved soil nutrient stocks, SOC, microbial biomass, and enzyme activities compared with IC and Control. These treatments also enhanced microbial diversity and shifted communities toward copiotrophic and functionally beneficial taxa, whereas IC and Control were dominated by stress-tolerant oligotrophs. Pathway analysis showed that carbon fixation dominated the C-cycling gene pool, with alternative autotrophic pathways prevailing over the Calvin cycle, particularly under OM and INM. These treatments also supported higher abundances of methanogenic and decomposition-associated genes, indicating enhanced carbon turnover. Nitrogen-cycling functions exhibited pathway-specific responses: OM enriched N-fixation and assimilatory nitrate reduction genes, whereas INM enhanced denitrification and dissimilatory nitrate reduction pathways. IC showed increased nitrification potential but the weakest biologically regulated N pathways. Volatomics profiling showed that OM and INM produced more diverse and metabolically active volatile organic compounds that were strongly associated with SOC and key biological attributes. Collectively, our study underscores the importance of carbon-rich organic inputs in rebuilding soil carbon stocks, reinforcing biological processes, and enhancing nutrient cycling for long-term sustainability of agriculture in semi-arid tropical regions.}, }
@article {pmid42287872, year = {2026}, author = {Wu, J and Wang, B and Li, Y and Zhang, X and Peng, Y and Liu, Q and Zhang, C and Lian, B and Cao, H and Li, K and Wang, H}, title = {Divergent responses of prokaryotic and eukaryotic microbiomes drive assembly, stability, and functional dynamics in the Bohai sea.}, journal = {Marine environmental research}, volume = {220}, number = {}, pages = {108193}, doi = {10.1016/j.marenvres.2026.108193}, pmid = {42287872}, issn = {1879-0291}, abstract = {Coastal oceans, critical for biodiversity and biogeochemistry, are increasingly altered by anthropogenic pressures that interact with natural spatiotemporal variability. However, the relative influence of spatial versus temporal drivers on microbiomes assembly, association, and function remains unclear. To resolve this, we integrated multi-kingdom amplicon and metagenomic sequencing to analyze microbial communities across spatial (Laizhou Bay vs. open Bohai Sea) and temporal (seasonal to interannual) gradients in the Bohai Sea, a semi-enclosed coastal system heavily influenced by recurrent human activities. Our results demonstrate that temporal variation exerts relatively stronger influences than spatial heterogeneity on the structure and dynamics of microbial communities in the Bohai Sea. Microeukaryotes exhibited the greatest responsiveness to spatiotemporal change, followed by archaea, with bacteria showing the highest stability. Archaeal and microeukaryotic communities were primarily governed by stochastic processes, whereas bacterial assembly transitioned from deterministic to stochastic control along spatiotemporal gradients. Microbiome co-occurrence networks were increasingly complex but less stable under spatiotemporal variability, dominated by competitive interactions and demonstrating a clear complexity-stability trade-off. Metagenomic analysis revealed a scale-dependent hierarchy of environmental drivers regulating metabolic pathways, with temperature predominant at the regional scale, DO in summer, and DON within homogeneous sub-regions. Two parallel microbial strategies for coping with anthropogenic pressure were identified, including enhanced catabolic pathways for xenobiotic degradation and a seasonally dynamic, mobile antibiotic resistome. This study provides a multidimensional and systematic perspective by demonstrating that temporal dynamics are the principal regulator of coastal microbiomes structure, stability, and function, with critical implications for predicting the responses of anthropogenically stressed coastal ecosystems under continuous environmental change.}, }
@article {pmid42287875, year = {2026}, author = {Yang, X and Wu, P and Li, C and Zheng, Q and Shi, X and Su, H and Wang, T and Xiong, X and Liu, Y and Xiao, Y and Xu, S and Zou, J and Liu, Y}, title = {Bacterial communities and antibiotic resistance genes in seawater adjacent to inhabited and uninhabited xisha coral reef islands: Insights from 16S rRNA and metagenomic sequencing.}, journal = {Marine environmental research}, volume = {220}, number = {}, pages = {108197}, doi = {10.1016/j.marenvres.2026.108197}, pmid = {42287875}, issn = {1879-0291}, abstract = {The Xisha coral reefs are highly biodiverse ecosystems in the South China Sea, China. Bacterial communities drive energy flow and biogeochemical cycling in coral-reef ecosystems, and serve as indicators of reef health. Yet the composition and dynamics of both bacterial assemblages and ARGs within the Xisha coral reefs remain poorly resolved. This study used 16S rRNA amplicon and metagenomic sequencing to compare bacterial community structure across surface and bottom waters, and surface-water ARGs profiles, in Beijiao Reef (BJ; an uninhabited reef) and Qilianyu Islands (QLY; an inhabited island) of the Xisha Islands. The results revealed bacterial community composition, bacterial co-occurrence network structure, and ARGs profiles differed markedly between the two reef areas. Dominant genera-Prochlorococcus_MIT9313, Salinimonas, Synechococcus_CC9902, Vibrio, and Alteromonas-were significantly more abundant in BJ (p < 0.05), whereas QLY showed higher abundances of Planococcus, Psychrobacter, Jeotgalibacillus, Salinicoccus, and Marinococcus (p < 0.05). The QLY bacterial co-occurrence network exhibited greater complexity (higher clustering coefficients and modularity), whereas the BJ network was simpler but displayed significantly higher closeness-centrality values (p < 0.001). Surface waters of the Xisha Islands were dominated by tetracycline, aminoglycoside, and macrolide resistance genes, whereas sulfonamide and multidrug resistance genes were less abundant. In addition, ARGs concentrations in BJ were slightly higher than those in QLY, suggesting that human habitation may not be a key environmental factor influencing ARGs concentrations in the seawater of the Xisha Islands. Correlation analysis showed that high-abundance ARGs in BJ (msbA, RanA, tetB(P), tet(T)) were linked to phototrophic Prochlorococcus_MIT9313 and Synechococcus_CC9902, whereas QLY dominant ARGs (baeS, patB, MexW) correlated with Gram-negative Vibrio and Pseudomonas. These ARGs are involved in bacterial efflux mechanisms, reflecting adaptive responses to environmental stress. This study provides valuable insights for assessing water quality and evaluating the impacts of human habitation pressure on coral reef ecosystems in the Xisha Islands.}, }
@article {pmid42287910, year = {2026}, author = {Li, H and Li, Y and Zhang, Z and Li, X and Zhao, K and Fan, Z and Liu, K}, title = {The ablation cycle drives glacier microbiome dynamics and downstream dissemination risk of the resistome.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142686}, doi = {10.1016/j.jhazmat.2026.142686}, pmid = {42287910}, issn = {1873-3336}, abstract = {Glacial ecosystems on the Tibetan Plateau undergo pronounced hydrological shifts across the glacial ablation cycle, driven by the onset and retreat of the Indian summer monsoon. To elucidate how transitions between four distinct hydrological ablation stages (pre-ablation, early ablation, late ablation, and frozen) shape microbial community structures and antibiotic resistance gene (ARG) profiles, we analyzed 112 samples collected across four stages from multiple glacier catchments on the southeastern Tibetan Plateau using metagenomic sequencing. Our results indicated that warmer stages favored thermotolerant Proteobacteria and reduced overall community diversity and evenness. ARG abundances exhibited ablation-dependent fluctuations, with Betaproteobacteria identified as predominant potential hosts. Furthermore, ARGs and virulence factors associated with mobile genetic elements were enriched during early and late ablation stages relative to the frozen stage, suggesting elevated potential for horizontal gene transfer coinciding with peak meltwater discharge. Notably, while upstream meltwaters generally exhibited higher ARG abundances, the upstream-downstream disparity tended to diminish from the pre-ablation to the late ablation stage, likely reflecting enhanced microbial mixing driven by glacier melt. Together, these findings reveal that glacier meltwater microbiomes are primarily shaped by ablation dynamics rather than spatial heterogeneity. More importantly, dynamics across the glacial ablation cycle drive shifts in meltwater hydrology that facilitate the downstream environmental mobility of glacial resistomes, posing growing antimicrobial resistance risks within the One Health framework.}, }
@article {pmid42288243, year = {2026}, author = {Huiling, Y and Jinghui, Z and Xinxin, Y and Hang, J and Jianxiang, W and Lina, Z and Ping, XU and Chao, Z and Jianming, MO and Jing, D and Haixia, LI and Jie, LI and Ling, JI and Chang, LU}, title = {Diagnostic Performance and Clinical Impact of Metagenomic Next-Generation Sequencing in 841 Patients with Suspected Lower Respiratory Tract Infections: A Four-Year Retrospective Study from a Tertiary Hospital in Shenzhen, China.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108885}, doi = {10.1016/j.ijid.2026.108885}, pmid = {42288243}, issn = {1878-3511}, abstract = {BACKGROUND: Accurate pathogen identification is critical for managing lower respiratory tract infections (LRTIs), particularly in suspected polymicrobial infection or after empiric treatment failure. Although metagenomic next-generation sequencing (mNGS) has been increasingly used in clinical practice, its long-term diagnostic performance and clinical impact in LRTIs have not been systematically evaluated in a large single-center cohort.<br><br>METHODS: We conducted a retrospective cohort study of 841 hospitalized patients with suspected LRTIs who underwent bronchoalveolar lavage fluid (BALF) testing by both mNGS and conventional culture between December 2021 and December 2025. Positive detection rates, polymicrobial identification, pathogen distributions across age and underlying disease categories, method concordance, and clinical impact were evaluated.<br><br>RESULTS: mNGS yielded significantly higher overall and polymicrobial detection rates than culture. Pathogen profiles differed between mNGS and culture and varied across age and underlying diseases subgroups. Over half of pathogens were identified exclusively by mNGS, and over half of these mNGS-exclusive detections influenced diagnostic and antimicrobial management. Furthermore, Mycobacterium tuberculosis complex, nontuberculous mycobacteria, Cryptococcus neoformans, and Pneumocystis jirovecii retained clinical significance even at low sequencing read counts.<br><br>CONCLUSIONS: In this real-world cohort, mNGS expanded pathogen detection, improved recognition of mixed infections, and provided meaningful clinical value in LRTI.}, }
@article {pmid42288291, year = {2026}, author = {Chen, K and Zhang, X and Li, G and Luo, W and Zhou, H and Shen, Y and Nghiem, LD}, title = {Mechanistic insights into nitrogen loss during food waste composting revealed by metagenomic and qPCR analyses under varying substrate C/N ratios.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135157}, doi = {10.1016/j.biortech.2026.135157}, pmid = {42288291}, issn = {1873-2976}, abstract = {Nitrogen loss during composting can be substantial; however, it can be reduced by applying new insights to better control the substrate C/N ratio and optimise overall composting performance. This study provides mechanistic insights into how substrate C/N governs nitrogen loss during kitchen waste composting. By combining nitrogen speciation analysis, qPCR, and metagenomics analyses, this study explored the potential biochemical mechanisms of nitrogen loss. The results showed that a high substrate C/N ratio significantly reduced nitrogen loss by approximately 37 % (C/N of 25) and 47 % (C/N of 30) compared to the baseline C/N of 20. A higher substrate C/N ratio enhanced nitrogen fixation and assimilation processes while suppressing ammonification and denitrification related potential. The relative abundance of key ammonification-related genera (e.g. Thermobifida and Leuconostoc) and denitrification-related genera (e.g. Pseudomonas and Geobacillus) were decreased at a high substrate C/N ratio, resulting in synergistic mitigation of NH3 and N2O emissions. A small reduction in germination index was observed at substrate C/N ratio of 30 compared with 25. Overall, the results suggest the need to optimize substrate C/N ratio for nitrogen conservation while maintaining overall composting performance.}, }
@article {pmid42288625, year = {2026}, author = {Shin, DW and Oh, S and Hong, YJ and Park, KU}, title = {Direct microbiota profiling of apheresis-associated products for microbiological insights in cell therapy.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-57771-0}, pmid = {42288625}, issn = {2045-2322}, abstract = {Cellular therapies require rigorous prevention of bacterial contamination during cell collection, manufacturing, and infusion. We characterized 16 S rRNA profiles in blood-derived specimens obtained during leukapheresis. Leukapheresis donors provided five specimen types: buffy coats (BCs), whole-blood plasma (WBP), apheresis plasma stored at room temperature for 24 h (AP24) and 72 h (AP72), and saliva. Species-level identification was performed using next-generation sequencing-based 16 S rRNA analysis and a database-weighted method. In total, 40 samples from eight donors were analyzed. Plasma specimens (WBP, AP24, and AP72) exhibited higher alpha diversity than saliva (Shannon index, p < 0.05). Beta diversity analysis identified three distinct clusters corresponding to BC, plasma specimens, and saliva (permutational multivariate analysis of variance, p = 0.001). Streptococcus oralis subsp. tigurinus was predominant across all specimens types, Bifidobacterium kashiwanohense predominated in blood-derived specimens, and Enhydrobacter aerosaccus was observed exclusively in plasma specimens. Skin swab culture performed before and after venipuncture site disinfection exhibited no bacterial growth post-disinfection, suggesting that skin-derived carryover is unlikely to fully explain the detected microbial DNA signals. This study provides microbial DNA profiles of various blood-derived specimens obtained during leukapheresis. These findings provide preliminary reference information that may assist interpretation of molecular microbial signals in cellular therapy manufacturing.}, }
@article {pmid42288650, year = {2026}, author = {Yang, Y and Guo, Y and Xu, T and Wu, Y and Cao, J and Wen, Z and Liu, S}, title = {Enrichment risk and drivers of manure-derived antibiotic resistance genes in black soldier fly larval gut.}, journal = {npj antimicrobials and resistance}, volume = {}, number = {}, pages = {}, doi = {10.1038/s44259-026-00237-0}, pmid = {42288650}, issn = {2731-8745}, support = {ASTIP//the Agricultural Science and Technology Innovation Program/ ; 2022YFD1301800//National Key R&amp;D Program of China/ ; CARS-42-10//China Agriculture Research System of MOF and MARA/ ; 325QN438//Hainan Provincial Natural Science Foundation of Chin/ ; }, abstract = {Black soldier fly larvae (BSFL) are promising for converting animal manure into protein; however, the risk of antibiotic resistance gene (ARG) enrichment in the larval gut during this process remains unclear. Here, we employed metagenomic and metatranscriptomic analyses to investigate this risk during BSFL conversion of duck manure. Our results demonstrated that within the BSFL treatment system, ARG abundance and diversity in manure decreased significantly over time. Concurrently, total abundance and transcriptional activity of ARGs in the larval gut were significantly lower than those in manure. However, comparative sequence analysis suggested the potential for ARG exchange between bacterial communities in manure and larval gut. Klebsiella, Escherichia, Citrobacter, and Pseudomonas were identified as the primary hosts in the gut. The enrichment and dynamics of these manure-derived ARGs were jointly driven by shifts in physicochemical properties (notably organic matter and total nitrogen), mobile genetic elements, and the bacterial community. Validation experiments demonstrated that modulating these key physicochemical drivers can mitigate ARG abundance in the larval gut. Overall, this study highlights the potential enrichment risk of manure-derived ARGs in the BSFL gut, identifies key hosts and drivers, and provides actionable mitigation strategies for safer BSFL application.}, }
@article {pmid42289139, year = {2026}, author = {Kevill, JL and Knight, ME and Jain, Y and Marsden, KA and Williams, RC and Herridge, K and Courtene-Jones, W and Robins, P and Malham, SK and Jones, DL}, title = {Fate and transport of viruses, bacteria and antimicrobial resistance associated with wet wipes and microplastics through wastewater treatment to coastal waters.}, journal = {Water research}, volume = {303}, number = {}, pages = {126281}, doi = {10.1016/j.watres.2026.126281}, pmid = {42289139}, issn = {1879-2448}, abstract = {Microplastics (MPs) in wastewater are increasingly recognised as potential vectors for pathogens and antimicrobial resistance (AMR), yet their role across treatment remains poorly understood. This study tracked viral, bacterial, and AMR associations with MPs from hospital wastewater through to coastal receiving waters, including simulated combined sewer overflow (CSO) events, using quantitative real-time PCR, and shotgun metagenomics. MP concentrations found naturally in the wastewater matrix, declined from 467 to 33 particles L[-1] during WWTP passage, achieving 93% removal. Norovirus (GI and GII) and bacteria colonised beads and wet wipes throughout, with wet wipes retaining higher viral and AMR loads than plastic beads, likely due to structural complexity. Sequential sampling across treatment stages showed a reduction in norovirus and bacterial loads by ∼1 log, yet pathogens remained detectable on beads and wet wipes in final effluent. NoV GI predominated, while NoV GII concentrations and the class I integron-integrase (intI1) gene varied by treatment stage and sample type. Metagenomics showed enrichment of potentially pathogenic genera (Aeromonas, Pseudomonas, Flavobacterium) in bead and wet wipe biofilms, and network analysis identified associations between Aeromonas and clinically relevant beta-lactam resistance genes (OXA, CTX). Shifts at the activated sludge stage indicated bead and wet wipe associated communities in effluent reflect treatment microbiota rather than influent sources. Environmental MP concentrations are below those required to deliver an infectious viral dose, suggesting MP-mediated transmission is unlikely under normal conditions. However, during CSO events, beads and wet wipes retained high viral loads and may act as pathogen transport vectors. These findings highlight CSO management as a priority for reducing MP-associated pathogen risks in receiving waters.}, }
@article {pmid42289215, year = {2026}, author = {Dai, J and Tan, X and Ma, J}, title = {Artificial intelligence in clinical metagenomic pathogen detection: A critical review of pipeline integrations, challenges, and future directions.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {107592}, doi = {10.1016/j.mimet.2026.107592}, pmid = {42289215}, issn = {1872-8359}, abstract = {Metagenomic next-generation sequencing (mNGS) has expanded the scope of clinical diagnostics by enabling culture-independent detection of microorganisms in patient samples. However, mNGS clinical utility remains constrained by substantial computational demands, reference database biases, and the persistent challenge of distinguishing true pathogens from host background, commensal flora and environmental contamination. Traditional alignment and k-mer-based bioinformatics pipelines frequently struggle to balance speed, sensitivity, and the ability to detect highly divergent or novel organisms. This review critically synthesizes the current landscape of Artificial Intelligence (AI) and Machine Learning (ML) applications across the mNGS diagnostic pipeline, examining deep learning architectures-including Convolutional Neural Networks (CNNs), Long Short-Term Memory networks (LSTMs), and Transformers-as integrated into raw read processing, host sequence depletion, primary taxonomic classification, and ancillary detection of antimicrobial resistance (AMR) and virulence factors. While several AI methodologies report high classification accuracy in benchmarking studies, we note that most performance claims derive from simulated datasets or controlled mock communities rather than prospective clinical validation. Significant gaps persist, including limited AI integration in front-end signal optimization, inadequate automated clinical reporting, absence of standardized benchmarking metrics, and unresolved questions regarding data leakage, reproducibility, and generalizability. Successful clinical translation will require addressing the interpretability limitations of current explainable AI approaches, navigating complex and evolving regulatory landscapes for Software as a Medical Device (SaMD), and bridging the gap between computational feasibility and demonstrated patient-outcome benefit. The development of genomic foundation models and multi-modal clinical integration holds promise for advancing mNGS toward real-time, actionable diagnostics, though substantial evidence gaps remain between current proof-of-concept demonstrations and validated clinical deployment.}, }
@article {pmid42289247, year = {2026}, author = {Lin, Y and Nie, B and Liu, X and Zhang, Q}, title = {Mechanistic insights into superior biofilm formation with heterotrophic nitrification-aerobic denitrification bacteria under polypropylene microplastic stress.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135159}, doi = {10.1016/j.biortech.2026.135159}, pmid = {42289247}, issn = {1873-2976}, abstract = {Microplastics may disturb microbial activity and biofilm development in biological wastewater treatment systems, yet the response of three-dimensional rotating biological contactor start-up biofilms to polypropylene microplastic stress remains unclear. This study evaluated a biofilm initiation strategy using heterotrophic nitrification-aerobic denitrification (HN-AD) bacteria (H-3D-RBCs) and compared it with activated sludge-inoculated systems (A-3D-RBCs) under polypropylene microplastic (PP-MP) exposure. H-3D-RBCs showed superior resistance to PP-MP disturbance, with total nitrogen removal decreasing by only 14 %, compared with an approximately 60 % decline in A-3D-RBCs. Respiratory activity inhibition remained below 15 % in H-3D-RBCs but exceeded 90 % in A-3D-RBCs. 16S rRNA gene sequencing showed that PP-MP reduced species richness and diversity in A-3D-RBCs and was associated with a > 90 % loss of core denitrifying genera, including Corynebacterium and Pseudoxanthomonas, whereas H-3D-RBCs maintained community stability and enriched Pseudoxanthomonas to 13.8 %. Metagenomic analysis indicated that PP-MP impaired nitrification and denitrification potential in A-3D-RBCs, as reflected by decreased genes encoding AMO and HAO, a 51.78 % decrease in nosZ abundance, and enhanced dissimilatory nitrate reduction to ammonium (DNRA), which likely intensified competition with denitrification and promoted nitrogen conversion to ammonia. In contrast, H-3D-RBCs suppressed DNRA and maintained high nosZ abundance. Untargeted metabolomics further showed that PP-MP was associated with metabolic disorders in A-3D-RBCs, especially disruptions in alanine, aspartate, and glutamate metabolism and arginine biosynthesis, whereas H-3D-RBCs preserved these key nitrogen metabolic processes. Overall, this study identifies key vulnerabilities of nitrogen-removal biofilms under PP-MP disturbance and provides multi-omics evidence to support the development of microplastic-resistant biofilm wastewater treatment systems.}, }
@article {pmid42289444, year = {2026}, author = {Masuoka, H and Miyatake, T and Park, J and Negishi, H and Kurokawa, R and Tsuchihashi, H and Makino, S and Suda, W}, title = {Fatigue-associated gut bacteria in Japanese healthy adults characterized by metagenomic analysis.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-56821-x}, pmid = {42289444}, issn = {2045-2322}, support = {J24K18210//Japan Society for the Promotion of Science, Japan/ ; J24K01676//Japan Society for the Promotion of Science, Japan/ ; }, abstract = {Emerging evidence suggests that fatigue caused by accumulated stress may serve as a prodromal symptom of psychiatric disorders, and gut microbiome dysbiosis has been reported in many such conditions. However, little is known about microbial and metabolic signatures associated with fatigue in otherwise healthy individuals. This study aimed to investigate associations between fatigue, the gut microbiome, and fecal metabolites in healthy Japanese adults. We identified characteristic microbial and metabolic differences specific to fatigued healthy individuals. Taxonomic analysis revealed a reduction in potentially beneficial bacteria and an enrichment of Escherichia coli in their gut microbiome. Functional profiling demonstrated enrichment of KEGG orthologs related to oxidative stress and depletion of energy-producing pathways. Correspondingly, key energy metabolites such as citrate were decreased. Notably, some fatigue-associated bacterial alterations overlapped with findings from external datasets on psychiatric disorders and myalgic encephalomyelitis/chronic fatigue syndrome, suggesting associative overlap in gut microbial alterations. These findings suggest associations between host fatigue and gut microbiome alterations involving oxidative stress and impaired energy metabolism. The consistent overlap of fatigue-associated microbial changes with those observed in psychiatric disorders highlights the potential relevance of gut microbial signatures in fatigue-related biological states. This study provides a foundation for future studies on gut microbial and metabolic pathways.}, }
@article {pmid42289756, year = {2026}, author = {Jia, P and Dong, L and Ma, T and Bi, Y and Tu, Y and Diao, Q}, title = {Variations in methane emissions from dairy cows: associations with rumen microbial synergy and metabolic pathway divergence.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42289756}, issn = {1674-9782}, support = {2024YFD1300200//the National key Research and Development Program/ ; CAAS-ASTIP//the Agricultural Science and Technology Innovation Program/ ; }, abstract = {BACKGROUND: Methane (CH4) is a metabolic by-product of rumen microbial fermentation, contributing significantly to global warming and dietary energy loss. Elucidating the mechanisms underlying natural variation in rumen methanogenesis is essential for the development of effective CH4 mitigation strategies. Here, we applied rumen metagenomics to identify the microbial mechanisms for differences in enteric CH4 emissions among dairy cows.<br><br>RESULTS: Enteric CH4 emissions from 111 lactating dairy cows under normal feeding conditions were utilized to characterize the natural variation in rumen methanogenesis. Metagenomic analysis revealed that the comprehensive effects of bacteria involved in starch degradation, lactate metabolism, and volatile fatty acid biosynthesis provide distinct amounts of hydrogen for rumen methanogenesis in high-methane-producing (HMP) and low-methane-producing (LMP) cows. Ciliate protozoa were universally abundant in HMP cows (P&#x2009;<&#x2009;0.05), whereas methanogens enrichment exhibited heterogeneity, with the dominant methanogen Methanobrevibacter exhibiting negative correlations with the other 11 methanogens (P&#x2009;<&#x2009;0.05). Six nutrient metabolic pathways modulating methanogenesis were identified, and HMP-associated methanogenesis was further driven by upregulated formate metabolism and acetoclastic pathways (P&#x2009;<&#x2009;0.05). Random forest model analysis screened 34 microbial genera as biomarkers for CH4 production.<br><br>CONCLUSIONS: This study excluded extrinsic confounders exist for rumen microbiome and CH4 emissions in dairy cows. These findings elucidated the causal microbial and metabolic mechanisms underlying rumen methanogenesis, providing actionable targets for microbiome-based strategies to mitigate CH4 emissions from livestock farming.}, }
@article {pmid42290500, year = {2026}, author = {Oriquat, G and Abdelgawwad El-Sehrawy, AAM and K Abdulsahib, W and Waleed Mustafa, W and Jyothi, SR and Priyadarshini Nayak, P and Janney, JB and Singh, G and Sinha, A and Yazdi, F}, title = {Probiotic, synbiotic effects on the gut-liver axis: omics-enabled mechanisms and therapeutic windows.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {1-18}, doi = {10.1080/17460913.2026.2684877}, pmid = {42290500}, issn = {1746-0921}, abstract = {The gut-liver axis is a two-way communication network where gut microbes and their metabolites affect liver function, while the liver regulates the intestinal environment through bile acids, immune factors, and antimicrobial substances. Disruption of this balance contributes to various liver diseases, including nonalcoholic fatty liver disease, alcohol-associated liver disease, cirrhosis, and liver cancer. Probiotics and synbiotics are potential therapies that aim to restore microbial balance, strengthen the intestinal barrier, and regulate inflammation and metabolism. Recent omics technologies, such as metagenomics, metabolomics, transcriptomics, and proteomics, have helped uncover how these interventions influence important pathways involving short-chain fatty acids, bile acids, and microbial metabolites. Studies suggest that probiotics and synbiotics may improve liver health through effects on metabolism, immune regulation, and fibrosis, although results vary depending on the specific microbial strains and patient characteristics. Emerging approaches include next-generation probiotics, targeted synbiotic combinations, and personalized microbiome-based treatments. Combining multi-omics data with digital health tools may help identify patients who are most likely to benefit. Overall, microbiota-targeted therapies show promise as personalized strategies for managing liver diseases, but further research is needed to overcome challenges in translating findings into consistent clinical applications.}, }
@article {pmid42290753, year = {2026}, author = {Yang, C and Li, M and Yang, S and Pan, J and Ding, Y and Yang, J}, title = {Correction: Channel selection of metagenomic next-generation sequencing in infants pathogen detection: a multicenter cross-sectional study.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1835424}, doi = {10.3389/fped.2026.1835424}, pmid = {42290753}, issn = {2296-2360}, abstract = {[This corrects the article DOI: 10.3389/fped.2025.1632123.].}, }
@article {pmid42291119, year = {2026}, author = {Park, J and Jang, KB and Kang, MG and Kyung, J and Yoon, J and Ryu, S and Kim, Y}, title = {Comparative pangenome analysis of methanogenic archaea from diverse ecosystems reveals potential targets for methane mitigation in rumen microbiome.}, journal = {Journal of animal science and technology}, volume = {68}, number = {3}, pages = {935-953}, pmid = {42291119}, issn = {2055-0391}, abstract = {Rumen methanogenesis is a major biological contributor to methane emissions in ruminants, yet the extent to which functional markers align with taxonomic relationships and how genome content varies across habitats, remains poorly resolved. In this study, we integrated broad phylogenetic frameworks with pangenome-resolved analysis to characterize methanogenic archaea from diverse ecosystems, including seawater, freshwater, sewage, rumen, human gut, soil, and cockroach sources. By combining these insights with pangenome reconstruction and KEGG-based pathway mapping of methanogenesis, we reveal key evolutionary and functional patterns. Notably, phylogenies based on 16S rRNA and mcrA genes showed limited concordance: only two clades exhibited overlap between trees, with most clustering patterns lacking environmental specificity. This discrepancy reflects the deep conservation of 16S rRNA compared with the evolutionary plasticity of mcr genes, shaped by lateral gene transfer, gene loss, and pathway modularity. The pangenome comprised of 8,695 orthogroups across 71 genomes, with core and soft-core genes enriched in translation, amino acid metabolism, and coenzyme biosynthesis, while the shell contained many poorly annotated orthogroups, highlighting annotation gaps in archaeal genomes. KEGG analysis revealed habitat-specific signatures: rumen methanogens were notably depleted in genes of the acetyl-CoA pathway, whereas human gut methanogens lacked key cofactor biosynthesis modules, including those for coenzymes M, B, F420, and methanofuran. From rumen-derived shotgun metagenomes, we identified 53 methane-producing, 4 canonical methanogenic, 10 potential competitor, and 1 methanotrophic metagenome-assembled genomes based on functional gene content. Competitor candidates included nitrate-reducing and Wood-Ljungdahl pathway-utilizing acetogens, suggesting hydrogen redirection under high-hydrogen or inhibitor conditions. These findings support a functional marker strategy that integrates 16S rRNA with pathway-specific genes and a pangenome framework to enhance ecological interpretations of methanogens and to prioritize potential targets for methane mitigation in ruminants.}, }
@article {pmid42291259, year = {2026}, author = {Feng, S and Liu, Q and Chen, Y and Kang, D and Zou, S}, title = {Different grazing intensities affect soil nitrogen cycling by altering microbial nitrogen metabolism in alpine wetlands.}, journal = {iScience}, volume = {29}, number = {6}, pages = {116009}, pmid = {42291259}, issn = {2589-0042}, abstract = {Grazing significantly affects soil nitrogen cycling in eastern Qinghai-Tibet Plateau alpine wetlands. Grazing did not alter soil microbial α-diversity, but shifted community composition via metagenomic analysis. Moderate and heavy grazing reduced soil total and active nitrogen contents by 53.8%-92.0% vs. light grazing, significantly decreased abundances of nitrification genes (amoA and hao) and ammonium assimilation gene (glnA), while increased dissimilatory nitrite reduction to ammonium gene (nirB) by 142.1%. A nitrification bottleneck from impaired nitrification drove active nitrogen decline, and structural equation modeling identified nitrogen cycle gene abundance as the key driver. This study reveals microbial nitrogen cycling mechanisms and provides a scientific basis for sustainable grazing management in alpine wetlands.}, }
@article {pmid42291297, year = {2026}, author = {Ma, M and Wang, L and Chen, M and Shi, S and Gui, X and Huang, X}, title = {Metagenomic next-generation sequencing reveals microbial community characteristics during acute exacerbations of interstitial pneumonia and their associations with clinical phenotypes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1809022}, pmid = {42291297}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Lung Diseases, Interstitial/microbiology/diagnosis ; Female ; *Metagenomics/methods ; *Microbiota/genetics ; Retrospective Studies ; Male ; Bacteria/classification/genetics/isolation &amp; purification ; Aged ; Phenotype ; Middle Aged ; Sensitivity and Specificity ; Metagenome ; }, abstract = {OBJECTIVE: Accurate pathogen detection is crucial for clinical management of interstitial lung diseases (ILDs), but conventional culture methods (CMT) have limited sensitivity. This study evaluated the diagnostic performance of metagenomic next-generation sequencing (mNGS) versus CMT in ILD patients and characterized differences in lower respiratory microbiome between stable (Stable) and acute exacerbation (AE) stage, as well as their associations with clinical indicators.<br><br>METHODS: We retrospectively analyzed ILD patients admitted between September 2021 and November 2023. Multidisciplinary discussion (MDT)-based comprehensive diagnosis served as the reference standard. We compared the sensitivity, specificity, and accuracy of mNGS and CMT. Microbiome analyses were performed to assess community composition and diversity in the Stable and AE groups, and to explore correlations with clinical features (e.g., frequency of exacerbations, oxygenation index, inflammatory markers).<br><br>RESULTS: The sensitivity of mNGS (95.60%) was significantly higher than that of CMT (32.20%). In 61.80% of patients, only mNGS yielded positive results, highlighting its diagnostic advantage. A total of 77 microorganisms were detected; bacteria accounted for 66.67% (e.g., Streptococcus pneumoniae, Haemophilus parainfluenzae). Among fungi, Candida albicans and Pneumocystis jirovecii predominated. Microbial diversity was significantly lower in the AE group than in the Stable group (p&#xa0;<&#xa0;0.01). Candida albicans (p&#xa0;=&#xa0;0.032) and Abiotrophia defectiva (p=0.011) were enriched in AE, whereas Haemophilus parainfluenzae (p&#xa0;=&#xa0;0.038) and Prevotella pallens (p&#xa0;=&#xa0;0.022) were more abundant in Stable. Correlation analyses showed that Candida albicans was positively associated with exacerbation frequency (p&#xa0;<&#xa0;0.05), while Streptococcus salivarius correlated positively with the oxygenation index. Abiotrophia defectiva was positively associated with Erythrocyte Sedimentation Rate (ESR) and body temperature, but negatively associated with lymphocyte count.<br><br>CONCLUSION: Patients in the AE group exhibited altered microbial community structures, and increased fungal colonization may be associated with disease progression, suggesting new targets for clinical intervention.}, }
@article {pmid42291302, year = {2026}, author = {Wang, R and Yang, H and Zhang, C and Zi Neng, X}, title = {The complexity of invasive fungal diseases in the intensive care unit: evaluation of metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1820501}, pmid = {42291302}, issn = {2235-2988}, mesh = {Humans ; *Intensive Care Units ; *Invasive Fungal Infections/diagnosis/microbiology/drug therapy ; *High-Throughput Nucleotide Sequencing/methods ; Female ; *Metagenomics/methods ; Retrospective Studies ; Middle Aged ; Immunocompromised Host ; Male ; Aged ; *Fungi/genetics/classification/isolation &amp; purification ; Adult ; Antifungal Agents/therapeutic use ; }, abstract = {BACKGROUND: In the intensive care unit (ICU), a subset of adult individuals who are non-neutropenic and lack conventional host risk factors frequently develop fungal infections, which constitute a major mortality risk in this population. This patient group has received limited attention to date, and research on diagnostic approaches remains insufficient. This research looks into whether metagenomic next-generation sequencing (mNGS) could be used to diagnose this group of people.<br><br>METHODS: We performed a retrospective analysis of 106 individuals with invasive fungal infections between July 2022 and February 2025. These patients were divided into two groups: immunocompetent and immunocompromised. Demographic and clinical characteristics were analyzed and compared between the two groups. The diagnostic value of mNGS was carefully assessed, and its diagnostic performance was contrasted with that of conventional microbiological tests (CMTs). In addition, the impact of mNGS results from different specimen types on clinical management and antifungal treatment decisions was summarized.<br><br>RESULTS: Among the 106 adult patients, 66.26% were immunocompetent, but many of them had underlying comorbidities. A total of 81 pathogens were identified, of which 74 were detected by mNGS and 44 by CMTs. The predominant fungal pathogens included Candida species, Pneumocystis jirovecii, and Aspergillus fumigatus. mNGS showed a distinct superiority in identifying uncommon pathogens and mixed infections, with its total positive rate markedly exceeding that of CMTs. mNGS results led to beneficial modifications in clinical management for 75 patients (70.75%). The clinical impact varied by specimen type, including bronchoalveolar lavage fluid (BALF; 61 cases), blood (14 cases), and other sterile body fluids (31 cases), with blood specimens yielding the least clinical benefit.<br><br>CONCLUSION: In the ICU, a substantial number of invasive fungal infections occur among patients without classical host risk factors. mNGS offers substantial benefits in identifying fungal pathogens and mixed infections, hence enhancing the diagnostic efficacy of invasive fungal diseases (IFDs). The extent of clinical benefit is affected by the kind of specimen provided for testing.}, }
@article {pmid42292195, year = {2026}, author = {Borgio, JF and Sharma, HS and Almandil, NB and AbdulAzeez, S and van der Spek, PJ}, title = {Editorial: Molecular informatics in personalized medicine, volume II.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1861955}, doi = {10.3389/fmed.2026.1861955}, pmid = {42292195}, issn = {2296-858X}, }
@article {pmid42292299, year = {2022}, author = {Oliveira, C and Shakiba, E and North, D and McGraw, M and Ballard, E and Barrett-D'Amico, M and Glazko, G and Rahmatallah, Y}, title = {16S rRNA Gene-Based Metagenomic Analysis of Rhizosphere Soil Bacteria in Arkansas Rice Crop Fields.}, journal = {Agronomy (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {42292299}, issn = {2073-4395}, abstract = {The rhizomicrobiome is composed of microbes that live in association with plant roots. From nutrient cycling to carbon sequestration, soil microorganisms have provided a solid base for natural and agricultural ecosystems to function. The relationship between plant roots and soil microorganisms is especially relevant in food staples such as rice (Oryza sativa L.), as the various properties of these microbes can influence crop yield and plant health, thereby affecting a major portion of the food supply for an ever-growing world population. In this study, we used 16S rRNA gene-based metagenomic analysis to investigate the impact of crop rotation and soil cultivation methods (no-till or tillage) on rhizosphere bacterial diversity and composition in eight crop fields in Arkansas. Illumina MiSeq sequencing revealed 56 Phyla, with four major Phyla: Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes. Soil microbial communities in the samples studied were phylogenetically diverse but with a stable community structure. Crop rotation and tillage did not significantly affect bacterial diversity.}, }
@article {pmid42292361, year = {2026}, author = {Jiang, H and Lu, E and Liu, Q and Li, Z and Zhu, Y}, title = {Etiological study of pulmonary infections following solid organ transplantation using metagenomic next-generation sequencing and development of a risk prediction model: a retrospective cohort study.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1734832}, pmid = {42292361}, issn = {1664-3224}, mesh = {Humans ; Retrospective Studies ; *Metagenomics/methods ; Female ; *High-Throughput Nucleotide Sequencing ; Male ; Middle Aged ; *Organ Transplantation/adverse effects ; Prognosis ; Risk Assessment ; Adult ; *Respiratory Tract Infections/etiology/diagnosis/microbiology ; Risk Factors ; }, abstract = {OBJECTIVE: To analyze the pathogenic etiology of pulmonary infection after solid organ transplantation and construct a prognostic prediction model based on metagenomic next-generation sequencing (mNGS) technology, systematically identifying key predictors to provide evidence for clinical risk stratification and individualized interventions.<br><br>METHODS: Clinical data were retrospectively collected from patients who developed pulmonary infection after liver or kidney transplantation at a single hospital between January 2020 and December 2023. All patients underwent mNGS detection of bronchoalveolar lavage fluid or sputum for pathogen identification. Collected data included demographic characteristics, transplant-related parameters, underlying diseases, laboratory test results, mNGS pathogen detection outcomes, and prognostic indicators. The dataset was randomly divided into a training set (n=262) and a test set (n=66). Within an AutoML framework, model hyperparameters were optimized using the Improved Dharma Optimization Algorithm (IDRA). Feature importance was validated bidimensionally via LASSO regression and SHAP interpretable models, with an interactive MATLAB-based decision support system developed.<br><br>RESULTS: The overall positive detection rate of pathogens by mNGS significantly exceeded that of conventional methods (84.76% vs. 61.89%, P<0.001). No statistically significant differences existed in baseline characteristics or laboratory indicators between the training and test sets (all P>0.05), confirming randomized stratified sampling validity. Both cohorts showed highly consistent proportions of poor prognosis events (training set: 27.48% vs. test set: 28.79%, &#x3c7;[2]=0.045, P&#xa0;=&#xa0;0.832). The prediction model achieved a ROC-AUC of 0.9694 and PR-AUC of 0.9690 in the training set, and ROC-AUC of 0.9206 (95% CI: 0.854-0.987) with PR-AUC of 0.9273 (95% CI: 0.867-0.988) in the test set, outperforming comparative models. Fourteen key variables were ultimately selected: mNGS bacterial detection, mNGS fungal detection, procalcitonin (PCT), C-reactive protein (CRP), mNGS viral detection, white blood cell count, creatinine, post-transplantation time, neutrophil percentage, diabetes, age, total bilirubin, alanine aminotransferase (ALT), and lymphocyte percentage. The feature overlap rate with AutoML-screened variables was 78.6% (11/14). SHAP analysis revealed descending importance ranking: mNGS bacterial detection, mNGS fungal detection, PCT, etc.<br><br>CONCLUSION: Integrating multidimensional clinical data with explainable machine learning techniques, this study confirms the central role of pathogenic etiology characteristics in prognostic prediction for post-transplant pulmonary infection and demonstrates the potential for real-time risk assessment to inform clinical decisions. However, prospective validation across diverse care settings is required to establish its efficacy as an interventional guide. This work offers innovative tools and methodological frameworks to advance precision diagnosis and management, subject to ongoing refinement through multicenter collaboration.}, }
@article {pmid42292462, year = {2026}, author = {Xing, Y and Wang, J and Li, X and Yin, X}, title = {Behind the mask of relapsing bimodal encephalitis: herpesvirus 7 and Epstein-Barr virus associated with Hashimoto's encephalopathy: a case report.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1782631}, pmid = {42292462}, issn = {1664-3224}, mesh = {Humans ; Female ; *Hashimoto Disease/virology/diagnosis/drug therapy ; *Herpesvirus 4, Human ; *Encephalitis/diagnosis/virology/drug therapy ; Recurrence ; *Herpesvirus 7, Human ; *Epstein-Barr Virus Infections/complications/virology/diagnosis ; Autoantibodies/blood ; *Encephalitis, Viral/virology/diagnosis/drug therapy ; *Roseolovirus Infections/diagnosis/virology/complications/drug therapy ; *Brain Diseases/virology/diagnosis/drug therapy ; Magnetic Resonance Imaging ; Adult ; Electroencephalography ; }, abstract = {BACKGROUND AND PURPOSE: Relapsing bimodal encephalitis in adults remains poorly characterized. We describe a case of relapsing viral encephalitis followed by secondary autoimmune-mediated encephalitis and explore its potential underlying mechanisms.<br><br>CASE DESCRIPTION: A previously healthy adult female initially presented with fever and headache; brain magnetic resonance imaging (MRI) showed punctate white matter hyperintensities, and electroencephalogram revealed background slowing with intermittent &#x3b4; waves. Initial cerebrospinal fluid (CSF) analyses were suggestive of viral encephalitis. Although no pathogen was identified by CSF metagenomic next-generation sequencing (mNGS), she responded favorably to empirical antiviral therapy. 22 days after discharge, she was readmitted with decreased responsiveness, hypersomnia, and acute psychosis. Concurrent MRI revealed progressive white matter lesions. CSF analysis demonstrated oligoclonal bands restricted to the CSF, while autoimmune encephalitis antibody panels were negative. Serum autoantibodies (anti-SSA/SSB, anti-thyroglobulin, and thyroid peroxidase) were elevated. Considering probable autoimmune encephalitis, intravenous immunoglobulin and methylprednisolone were administered, leading to clinical and serological remission with radiological improvement. After 22 months, the patient relapsed with similar clinical manifestations, beginning with fever and headache, followed by decreased responsiveness, and subsequently developed an acute mental disorder. Repeat CSF mNGS detected human herpesvirus 7 (HHV-7) and Epstein-Barr virus (EBV), accompanied by new white matter lesions and recurrent thyroid autoantibodies. The patient responded favorably to the same treatment. At one-month follow-up, the patient developed hyperthyroidism.<br><br>CONCLUSION: HHV-7 and EBV with long latency are likely associated with a cascade of autoimmune encephalitis, presenting as relapsing bimodal encephalitis. Thyroid autoantibodies-rather than conventional neuronal antibodies-appear central to the autoimmune phase, consistent with Hashimoto's encephalopathy.}, }
@article {pmid42292537, year = {2026}, author = {Jung, CG and Gautam, S and Song, Y and Poorey, K and Mishra, U}, title = {Spatiotemporal Dynamics of the Relative Abundance of Soil Nutrient-Degrading Enzyme-Encoding Genes Across Continental US Ecoregions.}, journal = {Ecology and evolution}, volume = {16}, number = {6}, pages = {e73869}, pmid = {42292537}, issn = {2045-7758}, abstract = {Understanding the spatiotemporal patterns in the relative abundance of soil extracellular enzyme-encoding genes is critical for predicting microbial responses to environmental change and their potential role in nutrient cycling. Yet, integrating novel metagenomic observations with spatiotemporal environmental gradients to infer regional patterns and future trajectories has remained unclear. To address this gap, we applied a machine learning (ML) approach, integrating soil metagenomic data with environmental variables-soil properties, topography, vegetation, and climate-to predict the relative abundance of enzyme-encoding genes for soil carbon (C), nitrogen (N), and phosphorus (P) across surface soils of the continental United States. We assessed potential responses under future emission scenarios (SSP2-4.5 and SSP5-8.5) by comparing a baseline (1985-2014) to a future period (2071-2100). The ML model explained 57%-63% of baseline variation. Precipitation was identified as the most influential factor for the relative abundance of C- and N-degrading enzyme-encoding genes, while slope length, representing horizontal distance that water can travel downslope, was the primary driver for P-degrading enzyme-encoding genes abundance. Projections revealed spatially heterogeneous shifts across continental US ecoregions: the relative abundance of C- and N-degrading enzyme-encoding genes decreased in wetter ecoregions and increased in drier ecoregions under future climate, while P-degrading enzyme-encoding genes abundance decreased significantly in semiarid and Mediterranean ecoregions. This study demonstrates the utility of metagenomic data for mapping soil genetic potential and predicting its regional response to environmental change, to inform ecosystem management strategies.}, }
@article {pmid42292847, year = {2026}, author = {You, Q and Jin, M and Zhou, B and Huang, C and Lin, Z and Hu, J and Xue, J and Chen, X and Xiao, Y and Li, R and Zong, Y and Wu, M and Zhang, T and Liu, H}, title = {Gut microbiome components predict response to neoadjuvant short-course radiotherapy followed by camrelizumab and chemotherapy in locally advanced rectal cancer (UNION): a prospective study.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1829108}, pmid = {42292847}, issn = {1663-9812}, abstract = {BACKGROUND: Although the gut microbiome shapes responses to anti-tumor immunotherapy and chemotherapy, its predictive value for neoadjuvant short-course radiotherapy (SCRT) followed by camrelizumab (CAM) and CAPOX in patients with locally advanced rectal cancer (LARC) has not been defined. This exploratory study aimed to evaluate whether the gut microbiome is associated with response to neoadjuvant SCRT followed by CAM and CAPOX.<br><br>METHODS: We obtained a total of 77 fecal samples from 36 patients with LARC, including 17 assigned to the long-course chemoradiotherapy (LCRT) group and 19 to the SCRT group. Samples were collected at three time points: baseline, after radiotherapy, and after chemoimmunotherapy. DNA was extracted, followed by metagenomic sequencing to profile microbiota dynamics during neoadjuvant treatment.<br><br>RESULTS: In this pilot analysis, we observed significant differences in the gut microbiota between the SCRT and LCRT treatment cohorts. Specifically, Bifidobacterium and Dorea were significantly enriched following completion of SCRT sequential CAM and CAPOX therapy. Further analysis revealed that the relative abundances of these two genera changed significantly only before and after the SCRT regimen, with no notable changes observed in the LCRT group. Preliminary ROC analysis suggested potential utility of these taxa for predicting treatment response, though validation in larger cohorts is needed.<br><br>CONCLUSION: The gut microbiome offers potential biomarkers that may stratify response to SCRT followed by CAM and CAPOX, representing a promising exploratory finding with potential clinical relevance.<br><br>CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/, identifier NCT04928807.}, }
@article {pmid42293010, year = {2026}, author = {de Oliveira, SAS and Sheat, S and Margaria, P and Lima, AL and Dos Santos, JA and Rocha, HS and da Silveira, HF and Ramos de Jesus, C and Winter, S}, title = {Association of Rhizoctonia theobromae with cassava witches' broom outbreak in Brazil and genetic relatedness to Southeast Asian isolates.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1799146}, pmid = {42293010}, issn = {1664-462X}, abstract = {BACKGROUND: A new cassava disease outbreak was identified in indigenous communities in Oiapoque, Amapá, Brazil, characterized by stunting, proliferation of thin shoots, broom-like leaf formations, and apical dieback. These symptoms are consistent with Cassava Witches' Broom Disease (CWBD), previously reported in other regions of South America and Asia.<br><br>METHODS: Metagenomic profiling, molecular diagnostics, phylogenetic analyses, and multilocus genotyping were used to investigate microbial communities associated with symptomatic cassava plants.<br><br>RESULTS: Rhizoctonia (Ceratobasidium) theobromae was identified as the predominant fungal species associated with symptomatic plants. Genetic analyses indicated a close relationship between Brazilian isolates and Asian reference strains, suggesting a possible transcontinental introduction and supporting an association between R. theobromae and CWBD. This represents the first confirmed report of R. theobromae in Brazil, expanding its known geographic distribution in the Americas.<br><br>CONCLUSION: The detection of this quarantine pathogen represents a potential threat to cassava production, food security, and preservation of indigenous cassava landraces in Brazil. These findings reinforce the need for surveillance, phytosanitary measures, and further studies on emerging fungal pathogens associated with cassava diseases.}, }
@article {pmid42293020, year = {2026}, author = {Yutong, Z and Yaling, L and Wei, Y and Fengling, S}, title = {Spatiotemporal dynamics of rhizosphere microbial communities in alfalfa across saline-alkali agro-ecosystems.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1792882}, pmid = {42293020}, issn = {1664-462X}, abstract = {The rhizosphere represents a highly active plant-soil interface, where microorganisms play critical roles in the growth and development of alfalfa and in regulating local ecosystem processes. However, the mechanisms by which alfalfa rhizosphere microorganisms respond to spatiotemporal variation in saline-alkali environments remain poorly understood. Here, we collected alfalfa plants from one- to eight-year-old stands across three pastoral regions differing in soil type and characterized their rhizosphere soils. Using soil physicochemical analyzes, soil enzymology, and metagenomics, we examined how rhizosphere microbial communities respond to temporal and spatial variation in saline-alkali soils. Our findings indicate that alfalfa rhizosphere microecology may maintain rhizosphere health by modulating soil physicochemical properties, reducing peroxidase activity, enhancing reductase activity, and increasing the abundance of beneficial microorganisms. These results underscore the potential value of introducing exogenous beneficial bacteria to shape indigenous rhizosphere microecology.}, }
@article {pmid42293161, year = {2026}, author = {Nunez, H and Straub, TJ and Imam, N and Goad, D and Mueller, NT and Mars, RAT and Sew Hoy, C and Paullin, T and Sukhum, KV}, title = {Age-specific early-life gut microbiome associations with eczema and food allergies during early immune development.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1804117}, pmid = {42293161}, issn = {2813-4338}, abstract = {INTRODUCTION: Eczema and food allergy commonly emerge during infancy and are linked to changes in the gut microbiome, yet it remains unclear when microbiome differences associated with allergic disease first appear during development.<br><br>METHODS: We analyzed age-stratified shotgun metagenomic data from 97 children aged 4-36 months, including physician-confirmed cases of eczema or food allergy and non-allergic controls, excluding recent antibiotic or probiotic exposure. Microbial taxa, functional pathways, and composite microbiome metrics were evaluated across three developmental stages: early infancy (4-6 months), mid-infancy (6-12 months), and toddlerhood (12-36 months).<br><br>RESULTS: Differences between allergic and non-allergic children were minimal before 6 months of age but became more apparent during mid-infancy and persisted into toddlerhood. Allergic conditions were associated with reduced abundance of fiber-fermenting and butyrate-producing taxa, enrichment of facultative and inflammation-associated microbes, lower microbiome maturation scores, and shifts in metabolic and inflammatory functional capacity.<br><br>DISCUSSION: These findings suggest that gut microbiome divergence associated with allergic disease becomes more apparent during mid-infancy, highlighting a developmentally relevant period for understanding early immune disruption. The results support further longitudinal and interventional studies aimed at clarifying whether earlier microbiome-targeted strategies may help modify progression along the atopic march.}, }
@article {pmid42293411, year = {2025}, author = {Liu, M and Gong, J and Liu, Y and Yu, J and Hu, Z and Liu, Z}, title = {Multi-omics reveals circadian regulation of bone homeostasis by gut microbiota metabolites: mechanisms and chronotherapeutic implications.}, journal = {Frontiers in immunology}, volume = {16}, number = {}, pages = {1719445}, pmid = {42293411}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Animals ; *Homeostasis ; *Circadian Rhythm ; *Bone and Bones/metabolism/physiology ; Bone Remodeling ; Metabolomics ; Fatty Acids, Volatile/metabolism ; Osteogenesis ; }, abstract = {The gut-bone axis plays a pivotal role in skeletal health, yet the integration of multi-omics approaches to elucidate circadian metabolite-bone interactions remains limited. This review synthesizes evidence from metagenomics, metabolomics, and germ-free models to uncover how microbiota-derived metabolites-including short-chain fatty acids (SCFAs), bile acids, tryptophan derivatives, and gaseous molecules-orchestrate bone remodeling in osteoporosis, osteoarthritis, and bone malignancies. Many studies demonstrate that SCFAs inhibit osteoclastogenesis via GPR43/HDAC signaling and promote osteoblast metabolic reprogramming, while bile acids enhance osteogenesis through FXR/Wnt/β-catenin activation. Tryptophan metabolites repair intestinal barrier integrity and modulate osteoimmunity via the AhR pathway. Single-cell omics reveal circadian oscillations of metabolite receptors (e.g., GPR43, FXR) in bone stromal cells, linking microbial diurnal rhythms to epigenetic regulation of bone turnover. We propose a novel "metabolite-immune-bone triad" model, highlighting microbiome-driven immunometabolic reprogramming as a central regulator of skeletal homeostasis. These insights advance precision microbial therapeutics and chrono-nutritional strategies, bridging multi-omics discoveries with clinical applications for bone disorders.}, }
@article {pmid42293516, year = {2026}, author = {Zou, Y and Liu, L and Chen, H and Luo, Z and Zhu, Z and Li, Z and Lin, B and Zhuang, Z and Li, W and Yang, Q and Yang, X and Zhou, H and Luo, M and Dai, D}, title = {Study protocol for a randomized controlled trial of fecal microbiota transplantation via different routes in children with moderate-to-severe autism spectrum disorder.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1829532}, pmid = {42293516}, issn = {1664-302X}, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) shows promise for autism spectrum disorder (ASD) by modulating the gut-brain axis, but the optimal delivery route remains unknown. Our previous single-arm study suggested efficacy of nasojejunal FMT in children with moderate-to-severe ASD, yet could not exclude placebo effects or compare routes. This randomized controlled trial aims to determine the most effective and tolerable FMT administration route.<br><br>METHODS: This single-center, randomized, triple-blind, double-dummy, placebo-controlled, three-arm parallel-group trial will enroll 75 children (aged 3-16 years) with moderate-to-severe ASD [Childhood Autism Rating Scale, Second Edition (CARS-2) &#x2265;36]. Participants are randomized 1:1:1 to: (1) FMT via nasojejunal tube + sham colonoscopy (FMT-NJT); (2) active FMT via colonoscopy with transendoscopic enteral tube placement (first session) + two subsequent infusions via the indwelling tube + sham nasojejunal intubation (FMT-C); (3) placebo via both routes (sham procedures). Three FMT/placebo sessions (5 mL/kg, max 100 mL) are administered over 5 days. Primary outcome is change in CARS-2 score from baseline to Week 24. Secondary outcomes include changes in Social Responsiveness Scale, Autism Behavior Checklist, Gastrointestinal Symptom Rating Scale, Short Sensory Profile, Children's Sleep Habits Questionnaire, gut metagenomic profiles (baseline, Weeks 2,6,12,24,48), and adverse events.<br><br>RESULTS: This is a study protocol; no results are available.<br><br>CONCLUSIONS: This first head-to-head comparison of FMT routes in pediatric ASD will provide high-level evidence to guide treatment standardization, directly addressing the translational gap identified in our preliminary work.}, }
@article {pmid42293521, year = {2026}, author = {Liu, Z and Xiahou, Y and Li, J and Wu, F and Fan, Y and Liu, R and Zhou, M and Ding, Z and Zhang, Y and Chen, C and Huang, L and Ai, H}, title = {Metagenomic analysis of the DNA virome communities in swine lungs.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1798033}, pmid = {42293521}, issn = {1664-302X}, abstract = {Viruses play critical roles in shaping microbial communities and regulating host metabolism. Investigating the lung virome of pigs can inform swine health management and provide a comparative resource for studies of the human lower respiratory virome. However, viral communities in the porcine lower respiratory tract remain poorly characterized. In this study, lung-associated viral communities were investigated using virus-like particle (VLP) enrichment and DNA metagenomic sequencing of 49 lung-derived samples collected from 17 domestic pigs and 20 wild boars. A total of 18,412 viral operational taxonomic units (vOTUs) were identified. Among the 2,559 vOTUs with genome completeness ≥50%, nearly 95% did not cluster with sequences in current viral reference databases at the species-level threshold (ANI ≥ 95% and AF ≥ 85%), suggesting putative viral novelty in the porcine lung while also reflecting incomplete reference database coverage. Meanwhile, 10,819 vOTUs (accounting for 58.8% of the total 18,412 identified vOTUs) were assigned to known viral taxa, spanning 29 viral orders and 65 viral families. The most prevalent viral families were Microviridae, Circoviridae, Smacoviridae, Adintoviridae, and Autographiviridae. Host prediction linked a subset of vOTUs to putative bacterial hosts, mainly from Pseudomonadota, Bacillota, Bacteroidota and Actinomycetota. In addition, we identified 191 vOTUs carrying 40 auxiliary metabolic genes (AMGs) mapped to 31 metabolic pathways. These AMGs were mainly associated with sulfur metabolism, cysteine and methionine metabolism, folate biosynthesis, and one-carbon pool by folate pathways. Comparative analysis under this study design showed that domestic pigs harbored higher viral diversity with a greater number of unique vOTUs (n = 12,611) than wild boars (n = 3,072). Domestic pigs viromes were enriched in Circoviridae and Microviridae, whereas wild boars showed higher relative abundances of Adintoviridae and Genomoviridae. Putative AMGs related to coenzyme synthesis and DNA methylation were more frequently detected in domestic pigs, whereas AMGs associated with nucleotide biosynthesis and cofactor metabolism were enriched in wild boars. These findings characterize the composition and functional potential of lung-associated DNA viral communities in pigs and provide a resource for future respiratory virome studies.}, }
@article {pmid42293528, year = {2026}, author = {Seth, N and Bansal, M and Mazumdar, S and Mazumdar-Leighton, S and Lakhanpaul, S and Vats, S and Arafat, Y and Babu, CR}, title = {Functional diversity in bacterial communities of an integrated constructed wetland used for in situ bioremediation of sewage.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1803785}, pmid = {42293528}, issn = {1664-302X}, abstract = {Constructed wetlands (CWs) offer effective, economical, environment-friendly and energy-efficient solution to growing challenges of increasing sewage and wastewater loads in urban areas. Although microbial communities form an integral component of constructed wetlands for sewage treatment, functional processes and their dynamics during sewage bioremediation in constructed wetlands remain largely uncharacterized. Moreover, the association of specific bacterial taxa with remediation of different sewage and water quality parameters remains largely unclear. This study explored the functional diversity likely associated with microbial communities of a constructed wetland system used for in situ remediation of 1 MLD (Million Liters per Day) sewage without external energy input since 2014. Different bacterial functional groups in the sludge from a stabilization pond and from rhizospheric sediments of the integrated constructed wetland were predicted using a 16S rRNA gene metagenomic sequencing dataset. Correlation analysis, multivariate statistics and a co-occurrence network were used to assess the bacterial groups associated with changes in water quality as it flows through different components of the integrated CW and highlight association patterns predicting major exchanges which might be operating in the microbial communities. While stabilization pond microbiome was dominated by bacterial groups such as Firmicutes, Desulfobacterota and Methylomirabilota known to be involved in carbon fermentation, sulphate reduction and methanogenesis, the rhizospheric sediments showed prevalence of bacteria associated with nitrogen reduction including Nitrospirota and Planctomycetota contributing to improved sewage quality parameters. Such results indicated complex microbial interactions involving bacteria from diverse functional groups sustaining bioremediation in the CW. The identification of primary bacterial taxa along with their putative functions can help in designing strategies to improve sustainable, nature-based wastewater treatment by CW systems.}, }
@article {pmid42293535, year = {2026}, author = {González-Reguero, D and Robas-Mora, M and García Ordiales, E and Fernández-Pastrana, VM and Penalba-Iglesias, D and Probanza Lobo, A and Jiménez Gómez, PA}, title = {Recovery of organic waste from a wastewater treatment plant, improved with plant growth promoting bacteria: model of Quercus suber L.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1754063}, pmid = {42293535}, issn = {1664-302X}, abstract = {Cork oaks (Quercus suber L.) are key tree species in Mediterranean ecosystems, playing a crucial role in fire mitigation due to their thick, fire‑resistant bark, while also contributing to biodiversity conservation and soil stability. Integrating waste valorization strategies with biofertilizers based on plant growth‑promoting bacteria (PGPB) may enhance reforestation efficiency. This study evaluated different irrigation regimes under controlled phytotron conditions, including water, organic fertilizer derived from a wastewater treatment plant (WWTP), and sterilized WWTP fertilizer, combined with Bacillus pretiosus CECT30673[T] and Pseudomonas agronomica CECT30673[T]. Microbial functional diversity (Shannon index), antibiotic resistance profiles, and rhizosphere community structure were assessed using 16S rRNA‑based metagenomic analyses, including taxonomic composition, beta diversity, and genus‑level relative abundances. Plant performance was evaluated through biomass production, stem length, and nutritional parameters, including protein composition, sugar content, and fatty acid profile. The application of PGPBs together with WWTP‑derived fertilizers resulted in a significant increase in plant biomass and stem length compared to traditional water irrigation. Nutritional quality was also significantly improved, with higher protein, sugar, and fatty acid contents. Additionally, the combined treatments reduced minimum inhibitory concentrations (MICs) within the rhizosphere microbial community while maintaining its functional and structural stability. These results demonstrate that combining PGPBs with WWTP‑derived matrices enhances cork oak growth and nutritional quality without disrupting native soil microbiomes, supporting their potential as sustainable tools for Mediterranean reforestation.}, }
@article {pmid42293540, year = {2026}, author = {Velaz Martín, M and Rießland, H and Rabe, KS and Niemeyer, CM}, title = {Primer choice shapes microbial community interpretation across habitats and informs short-term structured enrichment in environmental and applied systems.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1838890}, pmid = {42293540}, issn = {1664-302X}, abstract = {Microbial communities play central roles in ecosystem functioning across natural and engineered environments, yet their accurate characterization remains challenging due to methodological biases in amplicon sequencing. Primer choice can strongly influence taxonomic resolution, diversity estimates, and ecological interpretation. Here, we systematically compared primer performance across multiple ribosomal marker genes (16S, 18S, 28S rRNA, and ITS) and contrasting habitats, including soil, wastewater, and a photobioreactor-derived suspension. Amplicon-based profiles were benchmarked against shotgun metagenomic data. Primer choice significantly affected community composition, diversity metrics, and concordance with metagenomic profiles across all habitats and markers. Although 16S rRNA gene primers targeting the V3 region showed the highest agreement, no primer set fully reconstructed community structure. Applying the best-performing primer to a structured soil enrichment system using MESIF chips revealed rapid divergence from native soil and convergence toward less diverse communities, consistently favoring copiotrophic, surface-associated taxa while characteristic soil taxa declined. Across the 21-day incubation period, MESIF-associated communities diverged strongly from native soil, whereas medium-specific differences were comparatively smaller. This suggests that early enrichment was dominated by colonization of the structured matrix, while longer incubations and functional analyses will be needed to resolve substrate-specific selection. Overall, our findings highlight primer selection as a critical factor in microbial community analysis and show that combining optimized amplicon sequencing with structured cultivation enables reproducible enrichment, improved community monitoring, and targeted recovery of functionally relevant microorganisms. These insights are relevant for environmental monitoring, wastewater treatment, biotechnology, and controlled environment agriculture.}, }
@article {pmid42293542, year = {2026}, author = {Liu, L and Liu, J and He, J and Xing, Y and Zhang, D and Zhang, X and Ma, C and Xu, M and Li, R and Peng, M and Mei, S}, title = {Multi-kingdom gut microbiota analysis identifies bacterial-viral association in multiple myeloma.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1798330}, pmid = {42293542}, issn = {1664-302X}, abstract = {INTRODUCTION: Alterations in the gut microbiome are closely associated with the progression of multiple myeloma (MM). Previous research has predominantly focused on the bacterial components of the microbiota; however, the virome, a significant component of the microbiota, also plays a critical role, with bacteriophages influencing bacterial community composition and evolution.<br><br>METHODS: This study utilized shotgun metagenomic sequencing of fecal samples to explore the interaction between the gut microbiota and MM development. Fecal samples from 28 MM patients and 20 healthy controls were analyzed to evaluate microbial diversity. Taxonomic profiling of both bacterial and viral communities was performed using the Kraken2 classifier.<br><br>RESULTS: Our analysis confirmed microbial dysbiosis in MM patients and revealed concomitant changes in both bacterial and viral communities. At the phylum level, this study identified a significant increase in the relative abundance of Pseudomonadota (from 1.63 to 8.88%, p&#x202f;<&#x202f;0.001) and a decrease in Bacillota in MM patients compared to controls. Furthermore, several viral taxa were notably enriched in the MM cohort, including the phylum Heunggongvirae (linear discriminant analysis [LDA] = 4.74, p&#x202f;= 0.00003), phylum Uroviricota, and genus Punavirus (specifically Punavirus RCS47). Functional analysis demonstrated shifts in microbial metabolic pathways associated with MM, including a reduced capacity for amino acid and secondary bile acid biosynthesis and an enrichment of pathways associated with biofilm formation and cationic antimicrobial peptide (CAMP) resistance.<br><br>DISCUSSION: This multi-kingdom metagenomic analysis reveals distinct bacterial and viral signatures associated with MM, enhancing our understanding of gut microbial dysbiosis in the disease. These findings lay the groundwork for future mechanistic investigations and highlight the importance of validating these results in larger, independent cohorts.}, }
@article {pmid42293553, year = {2026}, author = {Ali, M and Srivastava, A and Arora, PK}, title = {Probiotics: multifunctional microorganisms for human health and biotechnological applications.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1847515}, pmid = {42293553}, issn = {1664-302X}, abstract = {Probiotics are live microorganisms that, when ingested in sufficient amounts, can have a beneficial impact on health. As crucial agents in maintaining gut homeostasis, enhancing immunity, and preventing of numerous diseases, they are fundamentally important. Probiotic function is based on pathogen inhibition, the release of antimicrobial substances, immune modulation, and the enhancement of the intestinal barrier integrity. Technological advances in the area, including molecular identification, microencapsulation methods, and metagenomics, have also been discussed. In addition, research methodologies for several subclasses of probiotics including Lactobacillus and Bifidobacterium continually being investigated. The role of probiotics in health of human, along with existing challenges related to probiotic viability and strain specificity, has also been discussed. This review highlights the growing understanding of probiotics and underscores their potential for optimizing human health and therapeutic applications.}, }
@article {pmid42293554, year = {2026}, author = {Behera, BK and Ren, W and Kumar, A}, title = {Editorial: Biodegradation of agricultural pesticides.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1874629}, pmid = {42293554}, issn = {1664-302X}, }
@article {pmid42293560, year = {2026}, author = {Tenea, GN and Jarrín-V, P and Reyes, P}, title = {Metagenomic insights into postbiotic-mediated modulation of strawberry surface microbiome and metabolic activity.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1841388}, pmid = {42293560}, issn = {1664-302X}, abstract = {INTRODUCTION: The increasing demand for sustainable alternatives to chemical disinfectants in postharvest fruit handling has incentivized exploration into microbiome-based interventions. We evaluated the impact of lactic acid bacteria (LAB)-derived postbiotic formulations (FF1, FF2, FF3) and a commercial disinfectant (CD) on the microbial community structure of the strawberry fruit surface.<br><br>METHODS: Taxonomic and functional changes in the microbial communities were evaluated using shotgun metagenomic sequencing, enabling comprehensive profiling of microbial composition and functional potential through gene family abundance, EggNOG functional categories, KEGG pathways, and MetaCyc metabolic reconstruction. The tested formulations consisted of a precipitated peptide-protein extract (PP) from Weissella cibaria UTNGt21O (FF2), used as the antimicrobial agent, and an exopolysaccharide (EPS) from W. confusa UTNCys2-2 (FF3), serving as a biopolymer carrier, applied in combination (FF1: PPGt21O + EPSCys2-2) or individually.<br><br>RESULTS: Our integrated analysis revealed that the highly suppressive formulation, FF1, outperformed the CD by fundamentally restructuring the microbial landscape. Taxonomically, FF1 notably reduced the abundance of key opportunistic spoilage or hazardous organisms. Rather than acting as an indiscriminate biocide, FF1 functioned as a targeted ecological disruptor. Functional profiling (eggNOG, KEGG, and MetaCyc) suggested potential shifts in functional capacity, including a reduced relative abundance of genes associated with translation machinery, cellular membrane expansion (stearate biosynthesis), and host lipid degradation (fatty acid &#x3b2;-oxidation). In parallel, the FF1-treated microbiome showed a higher relative abundance of genes linked to stress-response functions, including heat shock proteins and cell wall-related processes such as peptidoglycan maturation. In contrast, less restrictive formulations (FF2 and FF3) permitted the proliferation of opportunists such as Pseudomonas spp. and Xanthomonas fragariae, accompanied by active energy-consuming and tissue-degrading metabolic signatures.<br><br>CONCLUSION: These findings suggest possible underlying mechanisms of LAB-derived postbiotics, demonstrating that FF1 forces the surface microbiome into a metabolically restricted, non-degradative survival state, potentially contributing to the preservation of postharvest strawberry quality.}, }
@article {pmid42293865, year = {2026}, author = {Zhang, H and Zhang, W and Yao, D and Li, X and Ali, HSM and Xi, J and Liang, Y and Zhao, F and Yu, S and Yu, K}, title = {Scion varieties and nitrogen levels affect carbon and nitrogen assimilation in apple via modulating rhizosphere microbial structure and function.}, journal = {Horticulture research}, volume = {13}, number = {3}, pages = {uhaf334}, pmid = {42293865}, issn = {2662-6810}, abstract = {The efficiency of carbon and nitrogen uptake in apple trees is co-regulated by plant genotype and rhizosphere microbial communities. However, the mechanisms by which different scion varieties modulate microbial structure and function under varying nitrogen levels remain poorly understood. In this study, Malus sieversii was used as the rootstock, onto which three scion cultivars (M. sieversii, Malus domestica cv. Hanfu, and Malus domestica cv. Red Fuji) were grafted under two nitrogen regimes. A combination of [13]C/[15]N isotope labeling, Illumina MiSeq amplicon sequencing, and metagenomic analysis was employed to elucidate how scion-rootstock interactions and nitrogen availability affect carbon and nitrogen acquisition. Under nitrogen-deficient conditions, Red Fuji exhibited stronger root activity and larger root surface area, indicating enhanced nutrient foraging capacity. Conversely, under nitrogen application, Hanfu showed significantly greater [13]C and [15]N uptake, with 5.7-fold and 1.6-fold higher [13]C accumulation in roots and stems, respectively, and markedly higher [15]N utilization efficiency in roots and leaves compared with M. sieversii. In parallel, Hanfu under nitrogen input showed enrichment of beneficial microbial taxa and more complex microbial co-occurrence networks. Metagenomic analysis and random forest analyses revealed that the relative abundance of specific functional genes related to carbon and nitrogen transformation (rbcL, abfA, napB/C, nasA) was significantly higher under specific scion-nitrogen combinations, contributing to enhanced microbial carbon fixation and nitrogen reduction. Collectively, these results demonstrate that scion genotype modulates rhizosphere microbial structure, physiological root traits, and carbon-nitrogen distribution patterns, thereby improving nutrient uptake efficiency under different nitrogen inputs.}, }
@article {pmid42293986, year = {2026}, author = {Lou, L and Li, X and Zhang, P and Wu, H and Chen, H and Ma, J and Zhang, K}, title = {Eravacycline-Cefiderocol Combination Therapy for Carbapenem-Resistant Acinetobacter baumannii Infective Endocarditis: A Case Report and Brief Review of the Literature.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {615678}, pmid = {42293986}, issn = {1178-6973}, abstract = {BACKGROUND: Infective endocarditis (IE) caused by carbapenem-resistant Acinetobacter baumannii (CRAB) is rare and associated with limited treatment options because of extensive antimicrobial resistance.<br><br>CASE PRESENTATION: We hereby present a case of prosthetic valve endocarditis (PVE) caused by CRAB, presenting with fever, persistent bloodstream infection, cerebellar hemorrhage, and aortic valve vegetation. The application of a novel combination therapy comprising eravacycline and cefiderocol effectively eliminated the bloodstream infection. Concomitantly, the monitoring of adverse reactions and the subsequent adjustment of medication and dosage ensured the favorable safety. Although bloodstream infection and valve vegetation were controlled, progressive perivalvular leakage indicated the need for timely surgical intervention when clinically feasible.<br><br>CONCLUSION: This case indicates that eravacycline combined with cefiderocol may represent a novel and effective treatment option for refractory IE caused by carbapenem-resistant Gram-negative pathogens, including PVE caused by CRAB.}, }
@article {pmid42294186, year = {2026}, author = {Saenko, EV and Kuznetsova, MV and Nesterova, LY and Valtsifer, IV and Levin, LY and Zaitsev, AV and Karipova, MO and Strelnikov, VN and Valtsifer, VA}, title = {Analysis of Microbial Tolerance and Physicochemical Properties of HFA‑E Hydraulic Fluids Used in Mechanized Mine Roof Supports.}, journal = {ACS omega}, volume = {11}, number = {22}, pages = {31925-31939}, pmid = {42294186}, issn = {2470-1343}, abstract = {This study presents a comparative analysis of microbial tolerance and physicochemical properties of HFA-E (fire-resistant hydraulic fluid, aqueous-based, emulsion type) hydraulic fluids based on commercial "Hydrotol-ITCh HFAE" and "Fimitol P87 AF" concentrates used in mining hydraulic roof support systems. Metagenomic analysis revealed distinct microbial community structures in the two fluids. The Hydrotol-ITCh HFAE-based fluid microbiota consisted predominantly of Bacteria (99.77%), especially Proteobacteria, while the Fimitol P87 AF-based fluid exhibited a more complex and taxonomically diverse community, including a significant proportion of Archaea (47.09%) and Bacteria (52.92%) from groups such as methanogens (Methanobacteriaceae) and sulfate-reducing bacteria (Desulfovibrionaceae), respectively. In vitro tests confirmed the inherent antimicrobial activity of the fluids, which significantly reduced planktonic microbial viability and eradicated the majority of bacteria. The physicochemical properties of the fluids remained stable even under high initial bacterial load, confirming their reliability during microbial contamination. However, under industrial conditions, the Hydrotol-ITCh HFAE-based fluid demonstrated lower contamination and higher emulsion stability (pH reduced to 8.5 after one year of operation versus 6.5 for "Fimitol P87 AF"), which reduced the risk of biocorrosion and the need for additional treatments. This study emphasizes the importance of comprehensive monitoring of microbial diversity and physicochemical parameters for predicting the service life of hydraulic systems, developing effective biocides, and minimizing risks to equipment and personnel. The obtained data can be used to optimize hydraulic fluid compositions and their operational strategies.}, }
@article {pmid42294227, year = {2026}, author = {Tan, AJ and Li, TR and Yang, JJ and Li, XL and Li, WQ and Yu, JW}, title = {Liraglutide and Dapagliflozin Synergistically Reshape Gut Microbiota and Metabolic Profiles to Ameliorate Type‑2 Diabetes in Mice.}, journal = {ACS omega}, volume = {11}, number = {22}, pages = {32363-32379}, pmid = {42294227}, issn = {2470-1343}, abstract = {Background: Type-2 diabetes mellitus (T2DM) poses a formidable global health challenge, characterized by persistent hyperglycemia resulting from insulin resistance and progressive β-cell dysfunction. Liraglutide (LIRA), a GLP-1 receptor agonist, and dapagliflozin (DAPA), an SGLT2 inhibitor, are established therapies with complementary mechanisms. However, the potential synergy of their combination, particularly through modulation of the gut microbiota and host metabolism, remains incompletely understood. To elucidate the gut microbiota-metabolite axis underlying the therapeutic effects of combination therapy in T2DM, we explored the interplay between β-cell function, fecal microbiota composition, and microbial metabolites. Methods: A T2DM mouse model was induced by a high-fat diet and streptozotocin. Mice were treated for 4 weeks with LIRA, DAPA, or their combination (COM). We assessed glycemic control, insulin sensitivity, pancreatic islet morphology, serum biochemistry, gut microbiota (shotgun metagenomic sequencing), and plasma metabolome (nontargeted metabolomics). Integrated multiomics analysis was performed to elucidate microbiota-metabolite interactions. Results: Combination treatment demonstrated superior efficacy compared to monotherapies, resulting in significantly greater improvements in body weight, glucose tolerance, insulin sensitivity, lipid profiles, and liver function. Histologically, COM most effectively restored pancreatic islet architecture, increased β-cell mass, and normalized α/β-cell ratio. Metagenomic analysis revealed that COM induced a unique and restorative remodeling of the gut microbiota, distinct from monotherapies. This was characterized by suppression of pathobionts (e.g., Klebsiella and Enterorhabdus) and enrichment of beneficial taxa (e.g., Akkermansia, Lactobacillus, and Faecalibaculum). Metabolomics profiling showed that COM extensively normalized the diabetic plasma metabolome. Key altered pathways included tryptophan metabolism, sphingolipid metabolism, and branched-chain amino acid degradation. Integrated correlation analysis unveiled significant associations between specific microbial genera and host metabolites, suggesting a functional gut microbiota-metabolite axis underpinning the synergistic benefits. Conclusions: The combination of liraglutide and dapagliflozin exerts synergistic antidiabetic effects that extend beyond glycemic control to encompass pancreatic protection and systemic metabolic improvement. This synergy is mechanistically linked to collaborative remodeling of the gut ecosystem and consequent normalization of host metabolic pathways. Our findings provide a novel rationale for this combination therapy and highlight the gut microbiota as a pivotal target for T2DM management.}, }
@article {pmid42294679, year = {2026}, author = {Henkel, JV and Røy, H and Jørgensen, BB and Rotaru, A-E and Jovicic, D and Marshall, IPG and Jiang, C and Nielsen, PH and Singleton, CM and Arz, HW and Plewe, S and Kjeldsen, KU}, title = {Desulfatiglans-related bacteria associated with conductive mineral particles in marine subsurface sediments.}, journal = {mBio}, volume = {}, number = {}, pages = {e0083826}, doi = {10.1128/mbio.00838-26}, pmid = {42294679}, issn = {2150-7511}, abstract = {UNLABELLED: Acetate is a key intermediate in anaerobic mineralization of organic matter in marine sediments. Recent observations suggest that acetate is oxidized syntrophically in the methanic zone of marine sediments, and that electrically conductive mineral particles could provide niches for electroactive microbial communities that perform this process. We combined radiotracer measurements, a novel procedure for ferromagnetic mineral particle extraction, and metagenomic analyses to examine this process in Baltic Sea sediments. Our results confirm that acetate is oxidized syntrophically across and below the sulfate-methane transition zones of the sediments, where the transfer of reducing equivalents from acetate oxidation to CO2 fuels methanogenesis. Ferromagnetic particles consistently occurred throughout the geochemical zones and mainly consisted of the electrically conductive minerals magnetite and pyrite-greigite. The microbial communities associated with ferromagnetic particles were dominated by members phylogenetically affiliated with the bacterial genus Desulfatiglans. Known Desulfatiglans species are dissimilatory sulfate reducers; however, metagenome-assembled genomes indicate that Desulfatiglandales populations associated with ferromagnetic particles lack genetic potential to respire sulfate. Instead, they may grow by acetate oxidation coupled with extracellular electron transfer, consistent with a conductive mineral-associated lifestyle. We hypothesize that Desulfatiglans relatives are acetate-oxidizing partners in a syntrophic process facilitated by interspecies electron transfer via conductive particles. We identified cytochrome-rich ANME-1 archaea as the predominant methane-cycling microorganisms associated with ferromagnetic particles; however, their potential role as methanogenic syntrophic partners remains uncertain. Overall, our study reveals that distinct microbial communities are associated with ferromagnetic particles and shows conductive minerals as a niche for electroactive microorganisms in marine sediments.<br><br>IMPORTANCE: Acetate is a central intermediate in the anaerobic breakdown of organic matter. In Baltic Sea sediments at and below the sulfate-methane transition zone, we observed acetate oxidation to carbon dioxide at rates similar to methane formation from carbon dioxide reduction, a pattern indicative of syntrophic acetate oxidation. Previous enrichment studies suggest that electrically conductive mineral surfaces can facilitate this process. Motivated by this observation, we extracted ferromagnetic conductive particles from sediments and compared particle-attached microbial communities with bulk sediment. Particle-attached communities were distinct and enriched in the bacterial genus Desulfatiglans. Their genomes lacked genes for sulfate respiration, yet encoded traits consistent with acetate oxidation and extracellular electron transfer. Our findings suggest conductive minerals as distinct microbial niches and highlight Desulfatiglans-related bacteria as a potential key organism in particle-associated acetate oxidation.}, }
@article {pmid42294682, year = {2026}, author = {Ai, C and Tang, X and Han, H and He, Y and Zhang, H and Liu, C and Liao, H and Zhou, S}, title = {Active prophages as key drivers of microbial adaptation in global soil ecosystems.}, journal = {mBio}, volume = {}, number = {}, pages = {e0069326}, doi = {10.1128/mbio.00693-26}, pmid = {42294682}, issn = {2150-7511}, abstract = {Soils harbor the most complex microbial diversity on Earth, in which bacteria are ubiquitously infected by temperate phages. While integrated prophages often enhance host fitness, active (inducible) prophages are traditionally perceived as "molecular time bombs" due to their intrinsic lysis threat. This dual nature has raised fundamental questions about the true contribution of temperate phages to microbial adaptation and ecosystem stability. To address this gap, we conducted a global-scale integrative analysis by synthesizing 123,207 high-quality bacterial genomes, 183 soil-specific viromic data sets, and 3,749 metagenomes. We established the Global Soil Active Prophage Database (GSAPD), comprising 21,397 high-confidence active prophages, which we found to represent 34.3% of the total soil viral population within our analytical framework. Our comparative genomic analysis reveals that active prophages possess significantly larger genomes and greater genetic complexity compared with their dormant counterparts. Crucially, by mapping phage-encoded auxiliary metabolic genes (AMGs) across diverse biomes, we found that active prophages are disproportionately enriched in key pathways for carbon, nitrogen, and sulfur cycling, as well as specialized resistance mechanisms against heavy metal toxicity. These findings suggest that active prophages act as dynamic reservoirs of functional diversity. We demonstrate that their lytic potential is not merely a survival risk, but a sophisticated mechanism underpinning host environmental adaptation and niche expansion. Ultimately, this study provides a comprehensive global catalog of soil viral pathways and redefines the role of temperate phages as pivotal drivers of microbial evolution and biogeochemical cycling in terrestrial ecosystems.IMPORTANCESoils contain immense microbial diversity, yet the ecological role of temperate phages-especially their active (inducible) forms-remains poorly understood. This study provides the first global-scale assessment of active prophages in soils, revealing that they are widespread and functionally distinct from dormant forms. By building a comprehensive database and integrating multi-omics data, we show that active prophages are enriched in genes linked to key biogeochemical processes and stress resistance. These findings challenge the traditional view of active prophages as purely harmful agents and instead highlight their role as dynamic contributors to microbial function and adaptation. Our work offers new insights into how viruses shape ecosystem processes and provides a valuable resource for future studies on soil microbial ecology and nutrient cycling.}, }
@article {pmid42294703, year = {2026}, author = {Kady, MR and Britton, RA}, title = {Revised complete genome sequences of Limosilactobacillus reuteri DSM 20016[T] and ATCC PTA-6475 and confirmation of an intragenic macrosatellite in adhesin gene cmbA.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0400525}, doi = {10.1128/spectrum.04005-25}, pmid = {42294703}, issn = {2165-0497}, abstract = {UNLABELLED: Cell and mucus binding protein A (CmbA) is a cell-wall-anchored adhesin common to human isolates of Limosilactobacillus reuteri, which governs mucosal adhesion in vitro. Recent attempts to sequence cmbA in different L. reuteri strains revealed significant genomic inconsistencies with the publicly available closed genome sequences, especially with that of the L. reuteri type strain, DSM 20016[T]. We report here a revised closed genome sequence for DSM 20016[T] and a closed genome sequence for the closely related L. reuteri ATCC PTA-6475 (MM4-1A). Hybrid long- and short-read sequencing demonstrated that two genomic regions totaling 40 kbp, previously thought to be absent in DSM 20016[T], were in fact intact. The cmbA gene, present in one of these regions, is the longest predicted gene in both genomes and was confirmed to contain an intragenic tandem repeat region. In DSM 20016[T], the region consists of 11 identical ~290 bp tandem direct repeats totaling 3.2 kbp, while ATCC PTA-6475 has 8 repeats totaling 2.3 kbp. This macrosatellite posed a challenge to PCR-based approaches to confirm the length of the gene. Polyacrylamide gel electrophoresis of cell wall extracts from ATCC PTA-6475 showed a ~160 kDa band, which was absent from a cmbA-knockout strain, consistent with the expected size based on whole-genome sequencing and confirmed by mass spectrometry to be CmbA. Overall, we present refined publicly available genome sequences for two frequently studied L. reuteri strains and validate the length of a large gene with a conspicuously high number of identical tandem repeats.<br><br>IMPORTANCE: Studies comparing bacterial genomes and routine cloning work often implicitly assume that the closed genome sequences available from public databases are accurate. However, as technologies improve and we gain new data, inconsistencies can arise which prompt the resequencing of strains, sometimes with surprising results. We show here that a significant sequencing assembly artifact led to a large gap in the publicly available closed genome of the Limosilactobacillus reuteri type strain which has remained uncorrected for nearly two decades, despite a vast body of L. reuteri work over that time. Another region contained a large stretch of repetitive intragenic DNA that still posed a challenge to modern PCR techniques. Therefore, in addition to being useful to L. reuteri biologists, this work serves as an important reminder of the intrinsically experimental nature of sequencing data; it usually pays to resequence early and often.}, }
@article {pmid42294704, year = {2026}, author = {He, Y and Wang, X and Li, S and Zhang, C and Xu, M and Zhou, Y and Sanford, RA and Liang, R and Zhu, Y and Yang, D and Dan, L and Mao, X and Zhang, L and Sun, W and Jiang, Y and Hu, Y and Jiang, Z and Li, Y and Song, W and Hu, N and Zhao, L and Dong, Y and Shi, L}, title = {Ecological plasticity of Halanaerobium microorganisms across terrestrial saline to hypersaline subsurface environments.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0138126}, doi = {10.1128/spectrum.01381-26}, pmid = {42294704}, issn = {2165-0497}, abstract = {UNLABELLED: Members of the genus Halanaerobium are widely distributed in hypersaline environments, including oil and gas reservoirs, and saline lake sediment. However, a comprehensive understanding of their physiological traits, metabolic capacities, adaptive strategies, and biogeography remains limited. In this study, a strictly anaerobic and halophilic strain, H. saccharolyticum_B KY39 was isolated from produced water in the Zhongyuan Oilfield, China. Strain KY39 grew at 20-45°C, 2-30% salinity, pH 5.3-9.0, and up to 50 MPa hydrostatic pressure. It could ferment various carbohydrates (e.g., glucose, xylose, sucrose, and maltose) or use mannitol and pyruvate as electron donors under Fe(III)-reducing conditions. Comparative genomic analyses of 31 high-quality Halanaerobium strains revealed an open pangenome. Genes involved in osmotic and pressure stress responses, including those related to osmoprotectant biosynthesis and ion transport, were highly conserved. The thiosulfate sulfurtransferase (TST) gene, responsible for converting thiosulfate to sulfite, was universally present. Notably, compared to the strains from saline lakes, those from oil and gas reservoirs possessed larger genomes and harbored a broader repertoire of genes related to peptidoglycan biosynthesis, nitrogen fixation, sulfur metabolism, biofilm formation, and carbohydrate uptake, suggesting enhanced metabolic flexibility and environmental adaptation. Moreover, a survey of the available metagenomes revealed that Halanaerobium species were globally distributed across diverse environments exhibiting a broader salinity range. In addition to oil and gas reservoirs and saline lakes, they also widely reside in soils, fermented foods, and marine ecosystems. Collectively, these findings advance the systematic understanding of ecological plasticity and metabolic versatility of Halanaerobium, shedding light on their ecological roles and potential industrial impacts.<br><br>IMPORTANCE: Members of the genus Halanaerobium are prominent inhabitants of surface and deep subsurface hypersaline environments, yet their ecological roles and adaptive strategies remain poorly understood. Here, through the isolation of a novel strain from the production fluid of an oil field combined with comparative genomic analyses across the genus, we revealed the metabolic versatility, stress tolerance, and global distribution of Halanaerobium. Our findings underscore the ecological plasticity, functional diversity, and niche differentiation within this genus, providing fundamental insights into its potential industrial and environmental applications.}, }
@article {pmid42294714, year = {2026}, author = {Sajib, MSI and Oravcova, K and Brunker, K and Everest, P and Fuentes, M and Wilson, C and Murphy, ME and Forde, T}, title = {Rapid and modular workflows for same-day sequencing-based detection of bloodstream infections and antimicrobial resistance determinants using culture-enriched samples.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0324025}, doi = {10.1128/spectrum.03240-25}, pmid = {42294714}, issn = {2165-0497}, abstract = {UNLABELLED: Bloodstream infections (BSI) are a major global health concern, and existing diagnostic methods are too slow to guide targeted antibiotic therapy for critically ill patients. Rapid metagenomic next-generation sequencing (mNGS) can facilitate swift microbiological diagnosis, but identification is challenged by significant host versus bacterial DNA in blood and blood culture media. To accelerate reporting time, we developed M-15, a rapid mNGS-based host DNA depletion workflow optimized for culture-enriched samples, validated with suspected BSI blood culture samples and rapid culture-enriched spiked blood. M-15 was benchmarked with five commercial/published protocols, combined with rapid mNGS, and tested on blood culture samples (n = 33) from suspected BSI cases identified on BACT/ALERT-VIRTUO. To determine whether it is possible to utilize M-15 mNGS prior to blood culture flagging positive, a rapid enrichment method was tested starting with 1-10 colony-forming units of the top 15 bacterial species causing BSI spiked into BACT/ALERT medium enriched with 10 mL sheep blood. All six chemical depletion protocols reduced host DNA by 2.5 × 10[0]- to 4.1 × 10[6]-fold, with the in-house M-15 protocol performing best. With BACT/ALERT specimens, M-15 mNGS identified 28/28 mono-bacterial and 2/4 multi-bacterial species. With rapid culture enrichment and M-15 mNGS, <18% DNA was classified as host, and all bacterial species tested (n = 10) were correctly identified. M-15 mNGS accurately predicted phenotypic AMR/susceptibility for 90.3% (232/257) of drug/bacteria combinations from BACT/ALERT-positive samples. This study demonstrates that M-15 mNGS can facilitate species and AMR gene detection within 5-7 hours of BACT/ALERT positivity and possibly 13-15 hours of sample collection. Further clinical validation is required to assess its performance and the potential to improve patient outcomes in BSI.<br><br>IMPORTANCE: Bloodstream infections (BSI) are among the leading global health challenges, and traditional culture-based diagnostic methods are too slow (often taking >48 hours) to guide critical clinical interventions. This study demonstrates the development and utility of M-15 metagenomic next-generation sequencing (mNGS), a modular Oxford Nanopore-based chemical host DNA depletion and metagenomic sequencing workflow applied to enriched blood culture media for the same-day detection of bacterial etiologies and their antimicrobial resistance (AMR) genes. The selective chemical host DNA depletion method (M-15) described in this study can remove approximately 4.1 &#xd7; 10[6]-fold unwanted host DNA from whole blood, providing high-resolution genomic information from the bacteria at a fraction of the sequencing time/cost (approximately &#xa3;120-&#xa3;160/sample). We have tested this workflow on culture-positive clinical and rapid enriched spiked blood samples and demonstrated its ability to identify bacterial species and AMR genes between 5 and 7 hours post blood culture positivity. Based on our in vitro experiments using rapid enrichment, we believe similar results could be achieved within 13-15 hours from blood sample collection. Although further clinical validation is required, especially to fully assess the rapid version of the protocol, M-15 mNGS offers a promising advancement in BSI diagnosis. This workflow is modular and can be expanded in the future to adapt for other infections, which makes it a versatile tool to improve patient outcomes in sepsis.}, }
@article {pmid42294728, year = {2026}, author = {Mao, Z and Jiang, M and Zhao, Z and Xu, S and Wang, H and Chen, K and Duan, J and Chen, Z and He, D and Xing, P and Wu, QL}, title = {Biofilm-forming traits enrich the plasmid diversity and functional potential in particle-attached bacteria in coastal ecosystems.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0046026}, doi = {10.1128/spectrum.00460-26}, pmid = {42294728}, issn = {2165-0497}, abstract = {UNLABELLED: Planktonic microorganisms play a central role in aquatic biogeochemical processes and are commonly divided into particle-attached (PA) and free-living (FL) fractions. Although these two lifestyles differ in ecological strategy, the contribution of plasmids to their niche differentiation remains poorly resolved. Here, we conducted a plasmid-centric metagenomic analysis of two anthropogenically impacted coastal ecosystems in South China, the Pearl River Estuary (PRE), and Daya Bay (DYB), to determine the environmental and biological drivers of plasmid diversity, and their functional potenitial. We found that plasmid diversity was jointly shaped by different fractions and environmental stressors. The PA fraction contained significantly higher plasmid abundance and richness than the FL fraction, and was enriched in multifunctional and conjugative plasmids. These plasmids were associated with genes adapting to the PA lifestyle or microenvironments, suggesting linkage between particle attachment and plasmid maintenance. Structural equation modeling indicated that different fractions shaped plasmid diversity primarily through biofilm-forming genes. Along an anthropogenic gradient from DYB to PRE, increasing pollution levels were accompanied by higher plasmid diversity and greater abundances of antibiotic and metal resistance genes. Plasmid diversity was strongly correlated with resistance gene abundance. The enrichment of transferable plasmids in the PA fraction, where cell densities are high and intercellular distances are close, suggested that particle-associated habitats favor genetic exchange and the persistence of resistance traits. Together, these results demonstrate that particle-associated microbial communities represent key reservoirs of plasmid diversity and resistance potential in coastal ecosystems and highlight the combined influence of lifestyles and anthropogenic stress on plasmid-mediated microbial adaptation.<br><br>IMPORTANCE: Plasmids play an important role in microbial adaptation by mediating horizontal gene transfer, yet the ecological contexts that favor their persistence and diversification in natural environments remain poorly understood. This study showed that particle-attached microbial communities in coastal waters harbored substantially higher plasmid diversity and resistance potential than free-living communities, and that this enrichment is strongly linked to biofilm-associated traits. By demonstrating how particulate habitats and pollution gradients jointly shape plasmid diversity and resistance gene abundance, our findings identify particle-associated microenvironments as critical reservoirs for plasmid-mediated functions in coastal ecosystems. These results advance understanding of how microbial lifestyle and human activities influence microbial evolution and the environmental dissemination of resistance traits.}, }
@article {pmid42294989, year = {2026}, author = {Thomas, PW}, title = {Hidden Fungal DNA Structures May Shape Sequencing Outcomes.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {48}, number = {6}, pages = {e70153}, doi = {10.1002/bies.70153}, pmid = {42294989}, issn = {1521-1878}, mesh = {*DNA, Fungal/chemistry/genetics ; Genome, Fungal ; *Fungi/genetics ; Nucleic Acid Conformation ; *Sequence Analysis, DNA/methods ; }, abstract = {Fungal DNA is systematically under-detected in shotgun metagenomics, likely due in part to physical barriers like melanized cell walls and complex DNA conformations. Additionally, Oxford Nanopore Technologies sequencing with native fungal DNA often results in rapid pore clogging and unusual translocation dynamics, possibly due to intrinsic, yet undescribed, structural complexities. Exploring these signals could reveal novel fungal genome architectures, enhance sequencing accuracy, and drive advances in fungal biology.}, }
@article {pmid42295167, year = {2026}, author = {Jonouchi, D and Shenoy, S and Saintlouis, R and Singh, A and Kashyap, D and Bhargavi, C and Mansoor, R and Mansoor, E and Honnavar, P}, title = {Vaginal microbiome composition in pregnant and non-pregnant women: community structure, population variation, clinical impact, and metagenomics approaches.}, journal = {Infection and immunity}, volume = {}, number = {}, pages = {e0054225}, doi = {10.1128/iai.00542-25}, pmid = {42295167}, issn = {1098-5522}, abstract = {The vaginal microbiome plays a critical role in reproductive health and undergoes characteristic remodeling during pregnancy that influences maternal and neonatal outcomes. Although the non-pregnant vaginal microbiome shows substantial inter-individual variability, pregnancy is associated with reduced microbial diversity and increased dominance by Lactobacillus species, creating a protective environment for fetal development. Disruption of this balance, termed vaginal dysbiosis, has been linked to adverse obstetric and neonatal outcomes. This narrative review synthesizes current evidence on pregnancy-associated vaginal microbiome dynamics, with emphasis on community state types (CSTs), gestational changes, population-specific variation, and clinical implications. We review studies that use 16S rRNA sequencing, next-generation sequencing, and shotgun metagenomics to characterize microbial composition across pregnancy and the postpartum period. Lactobacillus-dominated communities, particularly those dominated by Lactobacillus crispatus, are consistently associated with microbiome stability and favorable pregnancy outcomes, whereas high-diversity anaerobic communities (CST IV) are linked to bacterial vaginosis, preterm birth, miscarriage, gestational diabetes mellitus, and infection-related complications. The vaginal microbiome composition varies significantly across racial, ethnic, and geographic populations. African-descended populations more often show L. iners-dominant or diverse anaerobic profiles, whereas European populations more commonly show L. crispatus dominance. Future longitudinal and mechanistic studies across diverse populations are needed to establish causality and evaluate microbiome-based interventions to improve maternal and neonatal health.}, }
@article {pmid42295179, year = {2026}, author = {Guitart-Matas, J and Ramayo-Caldas, Y and González-Rodríguez, O and Giler-Baquerizo, N and Migura-Garcia, L and Ballester, M}, title = {Implementation of a high-throughput microfluidic platform for antimicrobial resistance surveillance in swine production systems.}, journal = {Microbial genomics}, volume = {12}, number = {6}, pages = {}, doi = {10.1099/mgen.0.001755}, pmid = {42295179}, issn = {2057-5858}, mesh = {Animals ; Swine/microbiology ; Metagenomics/methods ; Feces/microbiology ; *Microfluidics/methods ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/drug effects ; Shotgun Sequencing ; }, abstract = {Antimicrobial resistance poses a serious threat to public health worldwide and demands interventions with a One Health perspective. A key challenge is determining the collection of antimicrobial resistance genes of a specific environment, also known as the resistome. Surveillance and monitoring of the resistome are essential for tracking the emergence and dissemination of resistance mechanisms. In this study, we took advantage of shotgun metagenomics and metatranscriptomics sequencing data of piglets treated with different post-weaning diarrhoea treatments to generate an antimicrobial resistance gene catalogue of the pig gut microbiome during pre-weaning and post-weaning stages. The selected catalogue, comprising a total of 102 genes and representing the majority of antibiotic classes, has been implemented in the microfluidic Biomark[™] X9 System and validated using total DNA and RNA extracted from piglets' faecal samples. Additionally, this platform has been verified by demonstrating a strong and statistically significant correlation with resistome quantification data from both metagenomic and metatranscriptomic sequencing. Overall, the microfluidic qPCR platform implemented here demonstrated enhanced detection of low-abundance targets, successfully identifying genes and transcripts that remained below the stochastic detection threshold of shotgun sequencing. This approach enables high-throughput monitoring and surveillance of antimicrobial resistance, providing a critical tool to support the reduction of antimicrobial use in farms.}, }
@article {pmid42295208, year = {2026}, author = {Chaudhary, A and Lin, X and Vitaterna, MH and Auch, B and Liachko, I and Green, SJ}, title = {Metagenome-assembled genome sequence of an uncultured Roseburia sp. generated from mouse fecal DNA from the International Space Station.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0104725}, doi = {10.1128/mra.01047-25}, pmid = {42295208}, issn = {2576-098X}, abstract = {The effects of spaceflight stressors, such as microgravity, cosmic radiation, and confinement, on the host physiology and gut microbiome remain unclear. Here, we report the metagenome-assembled genome (MAG) sequence of an uncultured Roseburia sp. strain that showed a significant gravity dose response in the gut microbiome of mice during spaceflight.}, }
@article {pmid42295273, year = {2026}, author = {Mawire, P and Gregori, MNJ and Makumbi, JP and Bezuidt, OK and Makhalanyane, TP}, title = {High-quality metagenome-assembled genomes of carbon-degrading, sulfate-reducing, and sulfur-oxidizing Acidobacteriota from Sub-Antarctic Marion Island soils.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0034226}, doi = {10.1128/mra.00342-26}, pmid = {42295273}, issn = {2576-098X}, abstract = {Here, we present high-quality Acidobacteriota metagenome-assembled genomes (n = 20) belonging to understudied lineages (UBA7541 [n = 13] and SbA1 [n = 7]) from sub-Antarctic soils. Nutrient cycling genes were prevalent in these MAGs, which provide a resource for understanding the ecological role of Acidobacteriota in extreme environments.}, }
@article {pmid42295521, year = {2026}, author = {Ferdous, J and Islam, SMR and Chakma, K and Hasan, MM and Tanni, AA and Ahmed, R and Sikder, U and Biswas, S and Siddiki, AZ and Crandall, KA and Rahnavard, A and Hussain, MH and Sharifuzzaman, SM and Chowdhury, MSN and Mannan, A}, title = {Antimicrobial resistance and gut microbiome profiles in wild and cultured shrimp (Penaeus monodon) from the coast of the northern Bay of Bengal, Bangladesh.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {7}, pages = {}, pmid = {42295521}, issn = {1573-2959}, mesh = {Animals ; *Penaeidae/microbiology ; Aquaculture ; Bangladesh ; *Gastrointestinal Microbiome ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Bays ; Bacteria/drug effects/genetics ; Anti-Bacterial Agents/pharmacology ; Environmental Monitoring ; }, abstract = {The coastal waters of Bangladesh support rich aquatic biodiversity, including the commercially important shrimp Penaeus monodon. However, antimicrobial resistance (AMR) poses a growing threat to aquaculture, ecosystem stability, and human health. In this study, we investigated bacterial AMR profiles and characterized the gut microbiomes of wild (Natural) and cultured P. monodon from the northern Bay of Bengal, Bangladesh. Culture-based and biochemical methods were used to identify bacterial pathogens of shrimp shells, and antimicrobial susceptibility was assessed using the disc diffusion method. Shotgun metagenomic sequencing was used to characterize gut microbial diversity and identify antibiotic resistance genes (ARGs). All Klebsiella isolates were resistant to ampicillin (100%) and showed high resistance to azithromycin (83%) and nitrofurantoin (73%). Pseudomonas isolates were 93.10% resistant to ampicillin, whereas Vibrio isolates had notable resistance to azithromycin (71.05%) and colistin (63.16%). Metagenomic analysis revealed comparable alpha diversity between wild and cultured shrimp, with Vibrio being predominant in both groups and V. parahaemolyticus as the most abundant species. Cultured shrimp harbored greater microbial diversity, including additional genera such as Shewanella, Lactococcus, and Enterobacter. A total of 30 ARGs were detected, primarily associated with β-lactams and tetracycline resistance. Cultured shrimp exhibited a broader ARG spectrum, reflecting potential anthropogenic impacts on aquaculture practices. These findings suggest that cultured shrimp environments can serve as reservoirs of resistant bacteria and ARGs. Therefore, improved antimicrobial stewardship and regular monitoring are essential to curb the spread of AMRs in marine ecosystems.}, }
@article {pmid42283066, year = {2026}, author = {Zhang, J and Liang, J and Lv, F and Guo, Z}, title = {Maternal vaginal colonization screening for term singleton pregnancy: comparative evaluation of metagenomic next-generation sequencing (mNGS) versus real-time quantitative PCR (qPCR).}, journal = {Practical laboratory medicine}, volume = {50}, number = {}, pages = {e00542}, pmid = {42283066}, issn = {2352-5517}, abstract = {OBJECTIVE: To investigate the distribution characteristics of potential high-risk pathogens for early-onset neonatal infection in maternal vaginal secretions, and to perform a head-to-head comparative evaluation of detection performance for target pathogens between metagenomic next-generation sequencing (mNGS) and real-time quantitative polymerase chain reaction (qPCR), with conventional bacterial culture as the reference standard.<br><br>METHODS: A total of 294 valid maternal vaginal secretion samples were prospectively collected and tested in parallel using qPCR, mNGS, and conventional bacterial culture. The Chi-square test was used to compare the differences in pathogen detection rates among the three methods. Receiver operating characteristic (ROC) curve was plotted to calculate the area under the curve (AUC) and 95% confidence interval (CI), to systematically evaluate the detection performance of the two methods for target pathogens.<br><br>RESULTS: The spectrum of potential early-onset neonatal pathogens in maternal vaginal secretions, ranked by detection rate, was as follows: Staphylococcus aureus, Streptococcus agalactiae, Ureaplasma urealyticum, Listeria monocytogenes, and Campylobacter fetus. The detection rates of these target pathogens by qPCR, mNGS, and bacterial culture showed high consistency, with no statistically significant difference in detection rates among the three methods (all P&#x202f;>&#x202f;0.05). ROC curve analysis showed that the AUC values of both qPCR and mNGS for the above major pathogens were all above 0.90, which were significantly different from the null hypothesis of AUC&#x202f;=&#x202f;0.5 (all P&#x202f;<&#x202f;0.05), indicating good detection performance; while there was no significant difference in AUC values between qPCR and mNGS (all P&#x202f;>&#x202f;0.05). In addition, Listeria monocytogenes (3 cases) and Campylobacter fetus (1 case) were only detected by qPCR and mNGS, while not isolated by conventional culture.<br><br>CONCLUSION: This head-to-head comparative study confirms that both mNGS and targeted qPCR have high accuracy and consistency for detecting potential early-onset neonatal pathogens in maternal vaginal secretions. We propose a tiered antenatal screening strategy for maternal vaginal pathogenic colonization: qPCR is recommended as the first-line tool for routine antenatal screening due to its high cost-effectiveness and rapid turnaround time, while mNGS is reserved for high-risk pregnant women (e.g., preterm premature rupture of membranes, clinical chorioamnionitis), culture-negative suspected infection cases, or scenarios requiring comprehensive pathogen profiling, to take full advantage of its unbiased, broad-spectrum detection capability. This integrated screening strategy requires further prospective validation with paired neonatal clinical outcome data to confirm its value in the prevention and early intervention of early-onset neonatal infection.}, }
@article {pmid42283067, year = {2026}, author = {Wei, F and Wang, X and Lv, H and Xia, H and Gan, G and Chen, X and Liu, X and Chen, H and Zhao, L}, title = {Identification of a potential novel Staphylococcus species via genomic sequencing: A neonatal infection case report.}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02631}, pmid = {42283067}, issn = {2214-2509}, abstract = {BACKGROUND: Coagulase-negative Staphylococci (CoNS) are common symbiotic Gram-positive bacteria colonizing human skin and mucous membranes with lower virulence than Staphylococcus aureus. As crucial pathogens of neonatal infections, they often harbor multiple drug resistance genes and can induce neonatal pneumonia, sepsis, suppurative meningitis, and other clinical manifestations.<br><br>CASE PRESENTATION: A preterm neonate at 29[+1] weeks' gestation complicated by respiratory distress syndrome and pneumonia received empirical ceftazidime and penicillin for 8 days. The condition initially improved but suddenly deteriorated on postnatal day 17 with septic shock, fever, and anemia. Routine tests suggested Staphylococcus capitis infection, and targeted anti-infective and supportive treatments relieved symptoms. Given the inconsistenty between the infection severity and that of typical Staphylococcus infections, metagenomic next-generation sequencing (mNGS) and whole-genome sequencing (WGS) were further performed, identifying a potential novel Staphylococcus species closely related to Staphylococcus warneri. Nevertheless, the origin of this potential novel species remains unclear, which needs further verification.<br><br>CONCLUSION: For neonates with sudden clinical deterioration, intractable infection or ambiguous conventional microbial results, mNGS and WGS facilitate accurate pathogen identification and treatment adjustment. This potential novel strain discovery highlights the importance of enhanced vigilance against bacterial multidrug resistance and the emergence of potential novel pathogens in neonatal care.}, }
@article {pmid42283460, year = {2026}, author = {Tothero, GK and Keffer, JL and Emerson, D and Fleming, EJ and Chan, CS}, title = {Distinguishing Leptothrix and Sphaerotilus genera by an integrated genomic-phenotypic analysis supported by new Leptothrix genomes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0176825}, doi = {10.1128/msystems.01768-25}, pmid = {42283460}, issn = {2379-5077}, abstract = {The Sphaerotilus-Leptothrix group of bacteria includes one of the first described microorganisms, Leptothrix ochracea, an uncultured type strain, plus isolates of Leptothrix and Sphaerotilus. This group is unified by the ability to form sheaths and oxidize metals, although L. ochracea exhibits obvious ecological, morphological, and functional differences from the rest of Sphaerotilus-Leptothrix. Recently, there have been calls to combine the group into one genus, Sphaerotilus; however, these studies lacked adequate genomic representation of L. ochracea. Here, we present a comprehensive comparative genomic analysis of the Sphaerotilus-Leptothrix group, including expanded representation of L. ochracea, a closely related novel species, Leptothrix toolikensis, and two new isolates (Leptothrix mechoopdaensis). Analysis of 38 genomes resolves three phylogenetic and functional groups: the ochracea-type Leptothrix (Group 1), the mobilis-type Leptothrix (Group 2), and Sphaerotilus (Group 3). Group 1 genomes form a separate genus based on average nucleotide identity and alignment fraction. The genomes clearly diverge from the rest of Sphaerotilus-Leptothrix in phylogeny, size, and metabolic potential. Group 1 genomes are much smaller (2.59-3.04 Mb) than those of Groups 2 (4.55-6.06 Mb) and 3 (3.94-5.07 Mb), while encoding more metal oxidases and fewer carbohydrate-active enzymes. Group 2 clusters with Group 3 phylogenetically and is similar in organic carbon metabolisms but maintains more metal oxidation genes. Group 2 members lack homogeneity in phenotype and genotype, suggesting that additional isolates and genomes are needed for confident classification. However, Group 1 genomes (L. ochracea and L. toolikensis) show clear divergence, precluding their inclusion in Sphaerotilus and supporting the retention of the genus Leptothrix.IMPORTANCEResearchers have long noted differences in metal oxidation, morphology, and ecology among Sphaerotilus-Leptothrix, but longstanding confusion over phylogeny and genus boundaries led to inconsistent taxonomic classification between the two genera. This confusion stems from previous work that used isolates that are unavailable or lost distinguishing traits in culture, and from limited genomic data. Furthermore, the Leptothrix type strain L. ochracea has never been isolated. This study provides molecular evidence that substantiates calls to reassign some Leptothrix members to the genus Sphaerotilus but adds to an emerging body of evidence that Group 1 L. ochracea and now L. toolikensis represent a functionally distinct lineage. While genomic similarity metrics left taxonomic divisions unclear, integrating metabolic potential with phylogeny resolved genus boundaries based on clear functional groupings. This polyphasic approach for delineating genera clarifies longstanding taxonomic confusion and refines our understanding of functional diversity both across and within Sphaerotilus-Leptothrix lineages.}, }
@article {pmid42283524, year = {2026}, author = {Hashimoto, K and Fukushima, K and Nakamura, S and Kida, H}, title = {Reply to Rojas-Ponce, "Operational considerations for implementing culture-free mycobacterial sequencing in routine laboratory settings".}, journal = {Journal of clinical microbiology}, volume = {}, number = {}, pages = {e0056426}, doi = {10.1128/jcm.00564-26}, pmid = {42283524}, issn = {1098-660X}, }
@article {pmid42283633, year = {2026}, author = {Gomez-Gallego, T and Udaondo, Z and Palacios-Ferrer, R and Díaz-Martínez, L and Ramos, JL}, title = {Development of advanced bioinformatic profiles to improve the detection and functional understanding of fungal acid phosphatases.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0210625}, doi = {10.1128/aem.02106-25}, pmid = {42283633}, issn = {1098-5336}, abstract = {We have retrieved approximately 9,000 protein sequences annotated as fungal acid phosphatase or phytase from the UniProtKB database. Following stringent quality filtering, a curated dataset comprising 3,058 high-confidence sequences was assembled. Phylogenetic analysis resolved these enzymes into eight distinct clades, representing distinct groups of fungal acid phosphatases: purple acid phosphatases, phytases, and groups containing both phytases and acid phosphatases annotations. Based on this classification, we have developed three representative protein profiles referred to as Prf-A-Fungal_phos, Prf-B-Fungal_phos, and Prf-C-Fungal_phos, each designed to capture the phylogenetic and functional diversity of these enzyme families. Heat-map analyses confirmed the breadth and high specificity of these profiles. Application of these profiles to public protein and metagenomic databases enabled the identification of hundreds of previously uncharacterized fungal proteins, with a broad taxonomic distribution and notable prevalence in the Ascomycota and Basidiomycota phyla. Functional validation through heterologous expression of selected candidates in Saccharomyces cerevisiae confirmed their phosphatase activity, supporting the accuracy of the in silico predictions. By integrating large-scale bioinformatics with experimental validation, this study provides robust tools for the discovery of novel fungal phosphatases and for investigation of their ecological roles in nutrient-limited environments.IMPORTANCEFungal acid phosphatases are critical enzymes in global phosphorus cycling, yet no dedicated bioinformatic tools exist to comprehensively identify and classify them across fungal diversity. Here, we present the first PROSITE generalized profiles specific to fungal acid phosphatases, derived from a curated data set of over 3,000 high-confidence sequences spanning eight phylogenetic groups. These profiles exhibit high specificity and sensitivity, enabling the detection of hundreds of previously uncharacterized proteins from public protein databases. Experimental expression of representative candidates in Saccharomyces cerevisiae confirmed their phosphatase activity, validating our in silico predictions. By bridging large-scale bioinformatics with functional validation, this study delivers robust resources to uncover novel fungal phosphatases and to explore their ecological roles in nutrient-limited environments. The developed profiles will advance metagenomic annotation, support soil and environmental microbiology research, and foster biotechnological innovation in sustainable phosphorus management.}, }
@article {pmid41748614, year = {2026}, author = {Ma, Z and Xu, X and Peng, W and Zhang, T and Chen, Z and Cao, S and Zhang, F and Wang, Y and Xiao, H and Zhang, Y and Liu, Z and Liu, Z and Xue, H and Long, Q and Hou, T and Wang, W and Liu, Y and Jin, Z and Zhang, M and Peng, Y and Wen, J and Gaut, B and Zhou, Y}, title = {Population genomics reveals association of transposable elements variants with climatic adaptation in wild Amur grape.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41748614}, issn = {2041-1723}, support = {32300191//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32372662//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Vitis/genetics/physiology ; Polymorphism, Single Nucleotide ; Genome, Plant/genetics ; *DNA Transposable Elements/genetics ; Climate Change ; *Adaptation, Physiological/genetics ; Genetic Variation ; Genetics, Population ; Genomics ; Metagenomics ; Plant Breeding ; *Acclimatization/genetics ; }, abstract = {Amur grape (Vitis amurensis Rupr.) is widely recognized for its cold tolerance traits and serves as a valuable genetic resource for breeding climate-resilient grape cultivars. Here, we construct a graph pangenome reference (Vampan_V1.0) and generate a variant map comprising 48,308,434 short variants and 127,094 TE-associated structural variants (TEVs) using deep resequencing data from 330 samples across 31 natural populations covering the species' distribution range. We discover a biased accumulation of SNPs around TEVs and identify 823 candidate adaptive genes associated with environmental variables. Using machine learning-based genetic offset models, we further show that putative adaptive TEVs significantly reduce genetic offsets by 7.3% to 8.2% under future climate scenarios. Our study shows the power of a graph-based pangenome to resolve complex variation and highlights the impact of TEVs on genetic diversity, local adaptation, and resilience to future climate change, providing insights into utilizing crop wild relatives in climate-resilient crop breeding.}, }
@article {pmid42045813, year = {2026}, author = {Lindstrøm, JC and Gjerdrum, HSV and Brynildsrud, OB and Tannæs, TM and Kristoffersen, AB and Ricanek, P and Leegaard, TM and Bjørnholt, JV and Jørgensen, SB and Tunsjø, HS and Olbjørn, C and Detlie, TE and Jahnsen, J and Kristensen, VA and Høivik, ML and Hov, JR and Moen, AE and , }, title = {Exploring alterations in the gut resistome in medically treated inflammatory bowel disease patients.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {42045813}, issn = {1471-2180}, abstract = {INTRODUCTION: The members of the human gut microbiota contain a large diversity of genes, including antimicrobial resistance genes (ARGs) known as the gut resistome. The resistome is susceptible to alterations when compositional changes occur in the fecal and gut microbiome. Medical treatment may affect members of the gut microbiota. This study hypothesizes that medication used by patients with inflammatory bowel disease (IBD) leads to an increased prevalence and diversity of ARGs in the gut and a corresponding change in the taxonomic composition of the fecal microbiome.<br><br>METHODS: Fecal samples from 16 Crohn&#x2019;s Disease (CD) and 16 Ulcerative Colitis (UC) patients, and 13 symptomatic controls (patients experiencing gastrointestinal symptoms, but with no endoscopic or histologic signs of IBD at inclusion, and no evidence of IBD during follow-up, were classified as symptomatic non-IBD controls) were subjected to metagenomic sequencing. The samples were collected before initiation of IBD medication, and after one year of treatment. Patients were treated with 5- Amino Salicylic Acid, Biological treatment, and Corticosteroids, or a combination of the three. Resistance Gene Identifier Comprehensive Antibiotic Resistance Database (RGI CARD) and regression modelling were used to analyze the abundance and diversity changes in the ARGs and the taxonomy.<br><br>RESULTS: We found significant associations with medicine use and abundance changes for eight resistance genes (Antibiotic Resistance Ontology (ARO) terms), four AMR gene families and 14 AMR drug classes. The use of 5-ASA was associated with abundance changes for the efflux pump efpA. This medication was also associated with significant changes in the &#x201c;pyrazinamide resistant rpsA&#x201d; gene family and with six drug classes (cephamycin, diaminopyrimidine, mupirocin, penem, pyrazinamide and rifamycin). Biological treatment was associated with changes in abundance of five drug classes (Zoliflodacin, lincosamide, macrolide, streptogramin and tetracycline). Corticosteroids were associated with changes in the ARO terms sul2, OXA beta-lactamase AMR gene family, and three drug classes (carbapenem, glycylcycline, and triclosan).<br><br>CONCLUSIONS: All IBD medication groups were found to be associated with significant abundance changes within the fecal resistome between inclusion and follow-up time points, where corticosteroid treatment resulted in less resistance in the microbiota compared to in the persons not treated with corticosteroids (either 5-Aminosalicylic Acid or Biological treatments).<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-05101-9.}, }
@article {pmid42273206, year = {2026}, author = {Montgomery, A and Nupp, S and Gray, CR and Jay, ZJ and Edgcomb, V and Hatzenpichler, R}, title = {Tracking active heterotrophic microbial communities in the Guaymas Basin deep biosphere with BONCAT-FACS.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag111}, pmid = {42273206}, issn = {2730-6151}, abstract = {The marine deep biosphere harbors microbial communities that drive organic matter transformations and biogeochemical cycles. Previous work on these communities has focused either on genomic characterization or metabolic activity measurements. However, to understand microbial ecophysiology in the deep biosphere, taxonomic identity and metabolic function must be connected on both single-cell and ecosystem scales. In this work, we optimized a bioorthogonal noncanonical amino acid tagging fluorescence-activated cell sorting (BONCAT-FACS) workflow for low-biomass deep-biosphere sediments obtained during International Ocean Discovery Program Expedition 385 (IODP 385). BONCAT-FACS with 16S rRNA gene amplicon sequencing as well as metagenomics of sediment communities was applied to characterize translationally active communities in hydrothermally altered subsurface sediments of the Guaymas Basin. Our results revealed a heterotrophic microbial population throughout all sediments examined, with taxa translationally active down to our deepest sampling point, 154 m below the seafloor. Based on 16S rRNA gene identities, the translationally active microbial community was dominated by heterotrophic members of the Gammaproteobacteria, Bacilli, Deinococci, and Alphaproteobacteria. These taxa are likely key contributors to cycling the large quantities of hydrothermally altered organic matter in Guaymas Basin sediments. To further elucidate the metabolic capacity of active taxa, we mapped 16S rRNA gene amplicons to metagenome assembled genomes (MAGs) previously obtained from IODP 385. These MAGs contained genes associated with C1 metabolism, carbohydrate degradation, and fermentation, indicating that active taxa leverage these metabolisms for energy conservation. Our results demonstrate that BONCAT-FACS provides high-throughput and single-cell insights into the metabolic activity of microbes in the low-biomass marine subsurface.}, }
@article {pmid42274245, year = {2026}, author = {Christian, WC and Jay, ZJ and Tolic, N and Nicora, CD and Livingstone, R and Trimmer, S and McDermott, TR and Hatzenpichler, R}, title = {Proteomic stress response by a novel methanogen enriched from the Great Salt Lake.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0041226}, doi = {10.1128/spectrum.00412-26}, pmid = {42274245}, issn = {2165-0497}, abstract = {Methanogenic archaea affect the climate through their production of the greenhouse gas, methane. However, it is unclear how a changing climate and other anthropogenic influences impact methanogen physiology and consequent methane flux. The Great Salt Lake (GSL) is an environment that has been heavily impacted by human activity, more than doubling its salt concentration since the last methanogen was cultured from it in 1985. In this study, we enriched a novel methanogen, for which we propose the name Candidatus Methanohalophilus hillemani, from the GSL at a time when its salinity reached a historical high. Interestingly, Ca. M. hillemani does not increase the expression of energy-conservation or osmotolerance proteins when challenged with salinity or oxygen. In contrast, Ca. M. hillemani prioritizes trace metal uptake and immune functions in response to the presence of the sulfate-reducing bacterium Desulfovermiculus. 16S rRNA gene amplicon data from GSL shore soils with extremely high and variable methane flux indicated the presence of Ca. M. hillemani. Our results show that Ca. M. hillemani is active when challenged with environmental stressors and contributes to the methane flux emanating from the GSL.IMPORTANCEMethanogens are microbes that affect the climate through their production of the greenhouse gas, methane. Changes in climate and land-use patterns are drying up saline lakes, damaging their unique economic and ecological value. As lake levels across the globe fall, it is unclear how methanogens and the amount of methane they produce will concurrently shift. In this study, we measured high methane output from the Great Salt Lake (GSL) across seasons and identified a novel methanogen as part of a larger methanogenic community that is responsible for these emissions. We cultured this novel methanogen from GSL sediments and determined that its methane production was largely unaffected by stress conditions. Our findings indicate that methanogens in saline environments, including a novel cultivated species, may be important and continued sources of methane as salinity increases.}, }
@article {pmid42274374, year = {2026}, author = {Madi, N and Sayeed, A and Cato, ET and Creasy-Marrazzo, A and Islam, K and Khabir, IU and Islam, T and Khan, ZH and Bhuiyan, TR and Begum, Y and Freeman, E and Vustepalli, A and Brinkley, L and Kamat, M and Bailey, LS and Basso, KB and Qadri, F and Khan, AI and Shapiro, BJ and Nelson, EJ}, title = {Ranked placement of phage predation as a determinant of dehydration severity among cholera patients in Bangladesh.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiag286}, pmid = {42274374}, issn = {1537-6613}, abstract = {Virulent bacteriophages (phages) can kill bacterial prey, potentially reducing burden of infection. In cholera, a high phage to Vibrio cholerae ratio is associated with mild dehydration, yet the relative importance of this ratio in disease severity remains unclear. We used machine learning to rank select host, microbial, and environmental factors as determinants of dehydration severity in over 600 cholera patients from across Bangladesh. We found the phage:pathogen ratio ranked among the top classifiers for mild dehydration, behind age and location. We advocate that phage predation be included as a key factor in cholera characterization for scientific, clinical and epidemiological applications.}, }
@article {pmid42275101, year = {2026}, author = {Zhu, XY and Hopkins, FE and Airs, R and Widdicombe, CE and Wilkinson, B and Tarran, GA and Woodward, EMS and Carrión, O and Curson, ARJ and Ma, Q and Hanwell, L and Yang, GP and Christie-Oleza, JA and Lea-Smith, DJ and Zhang, XH and Todd, JD}, title = {Predicted shifts in bacterial and algal contributions to DMSP and DMS dynamics during a coastal spring-summer bloom.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag141}, pmid = {42275101}, issn = {1751-7370}, abstract = {Ubiquitous marine microalgae and bacteria produce the abundant organosulfur compound dimethylsulfoniopropionate (DMSP) and/or catabolise it to climate-active gases, such as dimethylsulfide (DMS), with major consequences for global biogeochemistry and climate. However, their relative and dynamic roles in DMSP synthesis and catabolism remain poorly resolved, particularly during natural bloom events. Here, we combined metagenomics and metatranscriptomics, with measurements of intracellular/particulate DMSP (DMSPp), DMS concentrations and DMSPp production rates, as well as microscopy and flow cytometry, to predict the key microbes and enzymes driving DMSP/DMS dynamics during a spring-summer bloom in the Western English Channel. Microalgae and bacteria expressing the DMSP synthesis genes DSYB/DSYE and dsyB were likely major and significant DMSP producers, respectively, except during the largest observed DMSP spike. This spike coincided with elevated Synechococcus and autotrophic flagellate biomass but minimal DMSP synthesis gene expression. Axenic Synechococcus strains contained no detectable DMSP, implying flagellates with novel DMSP synthesis genes were likely responsible. Microbial DMSP import potential far exceeded catabolism, suggesting strong selection for DMSP uptake. Bacteria were the major predicted DMSP degraders, with DMSP demethylation potential dwarfing cleavage. However, the highest DMS concentrations were linked to Haptophyta expressing the DMSP lyase gene Alma, implying the significance of algal DMSP cleavage. Methanethiol-dependent DMS production was also likely important, with bacterial mddH transcripts coinciding with another major DMS spike. Overall, these results imply dynamic and contrasting roles of microalgae and bacteria, and their pathways, in coastal DMSP/DMS and sulfur cycling.}, }
@article {pmid42275884, year = {2026}, author = {Zhao, J and Zuo, M and Cao, L and Li, Q and Zhang, R and Wu, H and Yuan, J and Lv, C and Yu, Y and Lu, J}, title = {The neutral and acidic polysaccharides from Ginseng are metabolized by specific gut microbial taxa and confer immunomodulatory effects.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {158}, number = {}, pages = {158400}, doi = {10.1016/j.phymed.2026.158400}, pmid = {42275884}, issn = {1618-095X}, abstract = {BACKGROUND: Ginseng (Panax ginseng C. A. Mey.) exerts immunomodulatory effects partly mediated by its polysaccharides and interactions with gut microbiota. However, due to the structural complexity of ginseng polysaccharides, knowledge of their oral fate and direct microbiota interactions remains limited.<br><br>PURPOSE: This study aims to elucidate the oral fate of neutral and acidic polysaccharides in ginseng, analyze core gut microbiota genera and their immunomodulatory effects mechanisms.<br><br>METHODS: Structural analysis was conducted on neutral and acidic polysaccharides from ginseng. Thereafter, in vitro digestion and fermentation were performed, with metagenomic and metatranscriptomic profiling. The results were validated in conventional and pseudo&#x2011;germ-free immunosuppressed mouse models, and the immunomodulatory mechanisms of the core gut microbiota were investigated.<br><br>RESULTS: The in vivo and in vitro findings indicated that neutral and acidic polysaccharides exhibit different digestive properties and gut microbiota degradation patterns, differ in short-chain fatty acid production tendencies, bind to GPR-41/43 receptors, upregulate MAPK-p38 phosphorylation, and promote proliferation of intestinal immune cells.<br><br>CONCLUSION: This work systematically elucidated the digestive characteristics of ginseng polysaccharides and laid the groundwork for future studies on the specificity and structure-function relationships of plant-derived polysaccharides.}, }
@article {pmid42275949, year = {2026}, author = {Zheng, Y and Su, F and Li, H and Wu, H and Cui, P and Song, F}, title = {Wetland succession reshapes microbial degradation of plant- and microbial-derived carbon.}, journal = {Journal of environmental management}, volume = {411}, number = {}, pages = {130154}, doi = {10.1016/j.jenvman.2026.130154}, pmid = {42275949}, issn = {1095-8630}, abstract = {Plant- and microbial-derived organic carbon require distinct microbial enzymes, but how wetland succession regulates these substrate-specific degradation pathways in estuarine soils remains unclear. We collected 0-10 cm soils from four wetland types in the Liaohe River Estuary, China-tidal flat, restored wetland, Suaeda salsa wetland, and reed wetland-with three independent replicate sites per type. Shotgun metagenomic sequencing, CAZy annotation, taxonomic annotation, co-occurrence networks, and Mantel tests were used to examine CAZyme genes targeting plant-, fungal-, and bacterial-derived carbon. We identified 16,346,752 CAZyme-encoding sequences assigned to 749 families. Carbon-cycling gene composition differed significantly among wetland types (ANOSIM R = 0.37, p = 0.034). Gene diversity was higher in early to mid-successional stages, whereas the abundances of plant-, fungal-, and bacterial-derived carbon degradation genes increased along succession. Lignocellulose-degrading genes were most enriched in reed wetland, including AA3, CBM9, and CE1. Microbial hosts shifted markedly, with Bacteroidota increasing from 8.53% to 38.28% among plant-derived carbon degraders. Plant-derived carbon degrader networks were densest in tidal flat soils, suggesting a transition from stress-associated microbial associations to resource-specialized assemblages. Environmental controls were substrate-specific: plant-derived genes correlated only with nitrate, fungal-derived genes with moisture, nitrogen, salinity, and electrical conductivity, and bacterial-derived genes with none of the measured variables. These findings reveal substrate-specific microbial mechanisms linking wetland succession to carbon turnover and identify Bacteroidota, AA3, and nitrate availability as candidate indicators for restoration assessment and carbon-sequestration management.}, }
@article {pmid42276429, year = {2026}, author = {Kang, X and He, P and Zhang, H and Lü, F}, title = {Multi-omic insights into thermal regulation of the resistome through composting-simulating microcosm system.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135119}, doi = {10.1016/j.biortech.2026.135119}, pmid = {42276429}, issn = {1873-2976}, abstract = {Composting is a crucial biosecurity practice that stabilizes organic waste and reduces biological hazards prior to land application, with temperature as a major driver of resistome succession. However, compost temperature is a dependent, composite factor jointly determined by microbial metabolism and management practices. The regulatory pathways of temperature on resistome remain unclear. In this study, temperature gradients from 50°C to 65°C were applied to biowaste in a composting-simulating microcosm system to investigate the genomic and functional regulatory pathways of antimicrobial resistance genes (ARGs) using high-temporal-resolution metagenomic and metatranscriptomic analyses. The succession dynamics of ARGs under temperature-controlled incubation were demonstrated from the ecological niche perspective. Our results revealed that the genomic potential and transcriptional activity of ARGs responded asynchronously to temperatures. ARG sensitivity to temperature was category-specific, with 60°C representing a critical threshold for genomic-level removal of ARGs. The context-anchored members drove the resistome's response trends during temperature-controlled incubation, while abundance-based dynamics did not show significant kinetic shift under elevated temperatures. Temperature shaping the resistome through intra-lineage ARG reduction within context-anchored members rather than community succession. Unassociated fragment members showed transient abundance fluctuations at 55°C. Both context-anchored and unassociated fragment ARG carriers maintained transcriptional homeostasis during temperature-controlled incubation. Viruses had a limited impact on the community resistome. Our study demonstrated temperature-driven regulation of the resistome, providing a basis for optimizing ARG management in composting.}, }
@article {pmid42276430, year = {2026}, author = {Cai, Q and He, J and Qiu, W and Wang, Y and Fang, K and Zou, X and Aili, A and Zhong, Y and Pan, X}, title = {Industrial red mud establishes redox-active interfaces to steer metabolic pathways toward chain elongation in sludge anaerobic fermentation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135151}, doi = {10.1016/j.biortech.2026.135151}, pmid = {42276430}, issn = {1873-2976}, abstract = {Medium-chain fatty acids (MCFAs) production from waste activated sludge (WAS) provides a promising route for sludge valorization, but is often limited by inefficient hydrolysis and restricted interspecies electron transfer. This study evaluated industrial red mud (RM) as a conductive and alkaline regulator to enhance anaerobic chain elongation (CE). With 5 g/L RM addition, MCFAs yield reached 12.6 g COD/L, representing a 164% increase over the control. Spectroscopic analysis showed that the strong alkalinity of RM altered protein secondary structures, facilitating substrate hydrolysis while maintaining stable pH favorable for CE. Increased release of humic-like substances was observed, and electrochemical evidence suggested that the adsorption of these redox mediators onto the RM surface potentially facilitated the formation of redox-active interfaces, which contributed to the enhanced electron transfer capacity. Microbial network analysis demonstrated that RM acted as a topological hub, restructuring the community into a synchronized syntrophic consortium (hydrolysis-acidogenesis-CE) and highly enriching key CE bacteria. Metagenomic analysis revealed an increase in the abundance of genes encoding conductive membrane proteins (cytochromes and Mtr-associated), suggesting a potential enhancement in direct interspecies electron transfer. Meanwhile, RM increased the gene abundance of the CE key pathway (reverse β-oxidation pathway), thereby favoring the genetic potential for MCFAs accumulation. These findings establish a sustainable 'waste-treating-waste' framework, utilizing RM-driven electron reservoirs to facilitate the high-value conversion of WAS in anaerobic systems.}, }
@article {pmid42276515, year = {2026}, author = {Hassanien, A and Saadaoui, I and Sayadi, S}, title = {Archaea as a Resource for Sustainable Biotechnology: From Extremophiles to Valuable Products.}, journal = {Biochimie}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.biochi.2026.06.006}, pmid = {42276515}, issn = {1638-6183}, abstract = {Archaea, a remarkable domain of microorganisms, possess extraordinary survival capabilities that enable them to thrive in the most extreme environments on Earth, including high temperatures, extreme pH, oxygen-deprived habitats, and high salinity. Modern ecological studies have revealed their broad distribution and ecological roles, but traditional culture techniques do not accurately capture the structure of archaeal communities in such settings. This review provides an integrated and up-to-date synthesis of tools used to assess archaeal biodiversity, with particular emphasis on high-throughput culture-independent strategies, including metagenomics, functional metagenomics, and multi-omics. We also provide a quantitative, up-to-date mapping of archaeal biodiversity and bioproduct research (2010-2024), highlighting methodological trends and underexplored niches that are not emphasized in previous reviews. These advancements in archaeal studies have allowed scientists to investigate numerous archaeal strains for potential biotechnological applications and products, and to explore novel genes that lead to the discovery of new metabolites and bioactive molecules. Building on this framework, we critically analyze the current and emerging biotechnological applications of archaea. focusing on metabolites, enzymes, biopolymers, and biofuels, as well as identifying the major scientific and technical bottlenecks that hinder their translation into industrial scale. Finally, we outline key research priorities for utilizing archaeal resources in development of more sustainable and environmentally friendly biotechnologies.}, }
@article {pmid42276765, year = {2026}, author = {Diao, Y and Li, J and Wang, L and Zhang, Q and Xu, C and Peng, A and Lu, C and Lai, B and Chen, R and Chen, J and Pei, X}, title = {Microbiological characteristics of granulomatous lobular mastitis revealed by metagenomic sequencing.}, journal = {Journal of clinical pathology}, volume = {}, number = {}, pages = {}, doi = {10.1136/jcp-2026-210744}, pmid = {42276765}, issn = {1472-4146}, abstract = {AIMS: Granulomatous lobular mastitis (GLM) is a rare, chronic, benign inflammatory disease of the breast with an unclear aetiology. This study aimed to characterise the microbial features of GLM using metagenomic next-generation sequencing (mNGS) and to provide potentially relevant microbial clues for clinical evaluation.<br><br>METHODS: Twenty fresh lesion tissue samples were collected from 15 female patients with GLM, including one representative sample per patient and five additional deep tissue samples. Clinical data collection, mNGS, bioinformatics analysis and data interpretation were performed to characterise the microbial profiles of GLM lesions.<br><br>RESULTS: In this study, all patients presented with palpable breast masses, breast pain and abscess formation. More than half showed increased white blood cell counts, neutrophil percentages, C reactive protein levels and erythrocyte sedimentation rates together with decreased lymphocyte percentages. Based on genus-level filtering, mNGS identified 16 bacterial genera, 14 fungal genera and 3 viral genera, revealing a complex but bacteria-dominated microbial profile. The most frequently detected bacterial genera were Corynebacterium, Cutibacterium, Acinetobacter, Staphylococcus and Hathewaya, with marked interpatient variation in relative abundance, while fungal profiles were relatively more concentrated. In five patients with both superficial and deep tissue samples, microbial profiles differed across sampling depths, particularly for bacterial composition.<br><br>CONCLUSIONS: mNGS revealed a complex, bacteria-dominated microbial profile in GLM lesions and indicated that sampling depth may influence the detected microbial profiles. These findings may provide useful clues for clinical evaluation, but the pathogenic significance of these micro-organisms remains to be elucidated.}, }
@article {pmid42277004, year = {2026}, author = {Clark, JR and Chirman, D and Prakash, H and Terwilliger, A and McNeese, M and Ross, M and Tisza, M and Javornik Cregeen, SJ and Hopkins, L and Deegan, J and Troisi, CL and Boerwinkle, E and Mena, K and Wu, F and Kimata, JT and Johnson, M and Gregory, D and Fletcher, FE and Giordano, TP and Maresso, AW}, title = {Statewide multi-year wastewater sequencing reveals dual origins of HIV-1 signal.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-74140-7}, pmid = {42277004}, issn = {2041-1723}, support = {U19AI14429//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; P30AI161943//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01DA059394//U.S. Department of Health &amp; Human Services | NIH | National Institute on Drug Abuse (NIDA)/ ; }, abstract = {Human immunodeficiency virus 1 (HIV-1) is a retrovirus which has infected 90 million people and resulted in over 40 million deaths. Despite advances in diagnostics, treatment, and prophylaxis, HIV-1 continues to spread due to undiagnosed and untreated infections. Traditional monitoring methods are ineffective when access to testing is limited or people do not seek care, particularly given the long period between infection and symptom onset, allowing undetected transmission to continue. Here, we use a hybrid-capture sequencing approach to track HIV-1 signal in municipal wastewater in 15 different cities over nearly 3 years. We obtain near-complete genomic coverage of HIV-1, enabling detailed genomic analysis. Surprisingly, there are a substantial number of research-associated retroviral vector sequences recovered. Using computational competitive mapping, we identify specific genomic regions that differentiate authentic HIV-1 from vector-derived inputs. In an exploratory analysis of sites with available clinical data, wastewater-derived circulating HIV-1 reads show a positive correlation with community-level HIV diagnosed prevalence that was robust to exclusion of individual high-prevalence sites. This study identifies lentiviral vector contamination as a confounding factor in wastewater HIV-1 detection, recovers authentic circulating HIV-1 signal through an original classification framework, and provides initial evidence that the resulting signal tracks community HIV burden.}, }
@article {pmid42277027, year = {2026}, author = {Wacker, EM and Rühlemann, MC and Franke, A and Ellinghaus, D}, title = {TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42277027}, issn = {2041-1723}, support = {EL 831/5-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2167/2 - 390884018//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Metagenomic shotgun sequencing data from over 600,000 metagenomes are publicly available in repositories such as NCBI's Sequence Read Archive (SRA). Technically advanced and easy-to-use best-practice metagenome software workflows for raw data pre-processing, assembly of metagenome-assembled genomes, and taxonomic and functional annotation of metagenome-assembled genomes are needed for reproducible analysis and harmonization of large-scale metagenomic datasets. We introduce TOFU-MAaPO (Taxonomic Or FUnctional Metagenomic Assembly and PrOfiling), a portable, automated single-command Nextflow pipeline for large-scale analysis of metagenomic short-read sequencing data. It analyzes metagenome files locally or directly from the SRA using accession or study IDs. In a benchmark against three established metagenome software pipelines, the TOFU-MAaPO workflow yielded 12%, 42% to 77% more high-quality metagenome-assembled genomes, likely reflecting the integration of multiple complementary binning tools with a unified refinement strategy. Using its assembly-free taxonomic abundance profiling module, we also automatically downloaded 16,462 uniquely identifiable and accessible human gut metagenome samples from the SRA and taxonomically annotated them against the Genome Taxonomy Database on a high-performance cluster in less than 55 hours, including download time. TOFU-MAaPO makes large metagenome projects more accessible to individual research groups and is freely available at https://github.com/ikmb/TOFU-MAaPO .}, }
@article {pmid42277260, year = {2026}, author = {Jie, Z and Liang, W and Ding, Q and Liu, X and Zhang, Y and Chen, N and Li, S and Tong, X and Gao, H and Lu, R and Huang, X and Guo, R and Chen, J and Zhu, J and Zhang, Z and Liu, N and Xie, Z and Wang, X and Qi, L and Li, Y and Xiao, L and Zhang, S and Jin, X and Xu, X and Yang, H and Wang, J and Zhao, F and Jia, H and Kristiansen, K and Zhang, T and Hao, L and Zhu, L and Chen, C}, title = {Genomic landscape of the human vaginal microbiome is linked to host genetics and population of origin.}, journal = {Nature genetics}, volume = {}, number = {}, pages = {}, pmid = {42277260}, issn = {1546-1718}, abstract = {The vaginal microbiome is essential for women's health, yet its genomic diversity and interaction with the host remain incompletely characterized. Here we present the Global Vaginal Metagenome-assembled Genomes catalog, an extensive repository of vaginal microbial genomes generated by integrating 10,665 in-house Chinese metagenomes, with 2,967 publicly available metagenomes and 1,433 bacterial isolates. The catalog comprises 65,055 genomes from 890 prokaryotes, 11 eukaryotes and 6,590 viral taxonomic units, many not represented in public reference databases. We investigate virus-bacteria interactions, revealing conserved phages-host associations. We then identify substantial intraspecies genomic and functional variations displaying population-specific patterns. A metagenome-genome-wide association study identifies seven host genetic loci associated with vaginal species at study-wide significance and replicated in at least one independent cohort, notably connecting the gene OPRK1 with the potential pathogen Ureaplasma urealyticum. In summary, our research provides a comprehensive reference for future studies on genotype-phenotype interplay within the human vaginal microbiome.}, }
@article {pmid42277454, year = {2026}, author = {Amoia, SS and Giampetruzzi, A and Antònio, LF and Tomàs Pais da Cunha, A and Minafra, A}, title = {A new putative carlavirus identified by metagenomic analysis in a wild weed in Angola.}, journal = {Archives of virology}, volume = {171}, number = {7}, pages = {}, pmid = {42277454}, issn = {1432-8798}, abstract = {A metagenomic analysis was performed by high-throughput sequencing (HTS) to identify viruses infecting a wild weed collected in Seles (Angola), which exhibited clear yellowing symptoms. The analysis led to the discovery of a putatively novel carlavirus, tentatively named 'Seles weed carlavirus'. The complete genome sequence, consisting of 8,597 nucleotides, poly-A tail excluded, exhibited the typical organization of members of the genus Carlavirus, including the replicase polyprotein (ORF1); the triple gene block (ORFs 2-4); the coat protein (ORF5) and an RNA-binding protein (ORF6). The replicase polyprotein and coat protein gene regions of the newly described virus shared the highest amino acid sequence identity with the corresponding sequences of cowpea mild mottle virus (51.40%) and Hainan betaflexivirus (63.08%), respectively. The infection was further confirmed by RT-PCR with multiple specific targeted primer pairs, whose related amplicons were cloned and sequenced.}, }
@article {pmid42277703, year = {2026}, author = {Cumley, N and Quick, J and Brier, T and Wilkinson, S and Kent, C and Hassan-Smith, Z and Loman, N and Hassan-Smith, G}, title = {Pathogen detection in central nervous system infections: moving metagenomic sequencing closer to clinical practice.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13276-9}, pmid = {42277703}, issn = {1471-2334}, abstract = {BACKGROUND: Central nervous system infections (CNSI) contribute significantly to global disability and mortality, but the causative agent is often undetected. Metagenomic sequencing offers the potential to enhance diagnostic sensitivity, particularly in cases of unusual or partially treated infections. However, caution is required in interpretation of metagenomics data due to technical artefacts from contamination or non-specific read mapping which can reveal a broad spectrum of biologically plausible but diagnostically unlikely organisms.<br><br>METHODS: This study compares the performance of metagenomic sequencing with standard clinical microbiology methods using cerebrospinal fluid (CSF) from patients with CNSI and non-infected control samples. To evaluate sensitivity of different laboratory approaches, we sequenced DNA and RNA metagenomic libraries extracted from CSF, using both cell-free and cellular fractions. We then devised a set of simple, easily interpreted yet rigorous filters tailored for clinical metagenomics to generate a framework for result interpretation that can be readily applied by clinical scientists.<br><br>RESULTS: We demonstrate that composite filtering strategies are essential to reduce misleading signals and support standardised workflows. Additionally, our results suggest that a cell-free sample preparation approach can improve confidence in identifying clinically relevant pathogens, highlighting the impact of sample preparation on results quality.<br><br>CONCLUSION: In this study we describe a reproducible method that can be incorporated into a practical framework for clinical application of metagenomic sequencing in CNSI diagnostics.}, }
@article {pmid42277905, year = {2026}, author = {Serrano-Gómez, G and Zaida, S and Pons-Tarín, M and Mayorga, L and Maria, TC and Natalia, B and Francisco, G and Manichanh, C}, title = {Microbial, functional, and virulence biomarkers associated with familial risk of Crohn's disease and ulcerative colitis.}, journal = {Biomarker research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40364-026-00950-y}, pmid = {42277905}, issn = {2050-7771}, support = {PI20/00130//Instituto de Salud Carlos III/ ; PID23-147387OB-100//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; SGR 00459//Ag&#xe8;ncia de Gesti&#xf3; d'Ajuts Universitaris i de Recerca/ ; }, abstract = {BACKGROUND: First-degree relatives of patients with inflammatory bowel disease (IBD) carry elevated disease risk and offer a unique window into preclinical gut microbiome alterations. We investigated whether familial IBD risk is associated with intermediate, disease-specific, or shared gut microbiome configurations in both Crohn's disease (CD) and ulcerative colitis (UC), the two main form of IBD.<br><br>METHODS: Using shotgun metagenomics, we analysed fecal samples from CD (n&#x2009;=&#x2009;68) and UC (n&#x2009;=&#x2009;77) patients, their healthy first-degree relatives (CD-HFDRs, n&#x2009;=&#x2009;37; UC-HFDRs, n&#x2009;=&#x2009;30), and unrelated healthy controls (HCs, n&#x2009;=&#x2009;497), integrated species-level taxonomy, MetaCyc functional pathways, and virulence factor gene (VFG) profiling, with differential abundance analyses adjusted for relevant covariates.<br><br>RESULTS: HFDRs exhibited preserved alpha diversity but intermediate dysbiosis relative to patients and HCs. CD-HFDRs shared CD-associated taxonomic alterations, including depletion of Faecalibacterium prausnitzii, and enrichment of adherence- and invasion-associated VFGs, with 16 of 18 HFDR-enriched VFGs also elevated in CD patients. CD-HFDR functional pathway profiles nonetheless closely resembled those of HCs, revealing a dissociation between taxonomic and functional dysbiosis. Random forest classifiers distinguished HFDRs from HCs with strong performance: species- and VFG-based models achieved an AUCs of 0.966 in CD, and 0.946 in UC. Top predictive features were depletion of F. prausnitzii and enrichment of the E. coli adhesin gene fdeC. UC-HFDRs showed subtler alterations but comparable classifier performance.<br><br>CONCLUSIONS: IBD first-degree relatives harbour a transitional gut microbiome between health and disease, more pronounced in CD, with F. prausnitzii depletion and pathobiont virulence genes emerging as robust microbiome-based risk indicators.}, }
@article {pmid42278013, year = {2026}, author = {Mei, Z and Zhou, H and Du, H and Liu, K and Gao, C and Sheng, Z and Gong, Y}, title = {Heat Stress Induces Metabolic and Physiological Imbalance in Laying Hens, Accompanied by Hepatic Transcriptomic, Cecal Microbial, and Metabolomic Alterations.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/ani16111578}, pmid = {42278013}, issn = {2076-2615}, support = {2023ZD0405203//the Biological Breeding-National Science and Technology Major Project/ ; 2023ZD0407106//the Biological Breeding-National Science and Technology Major Project/ ; HBZY2023B007//the Hubei Fund for Seed Industry High-Quality Development Project/ ; 2025HBSTX4-04//the Earmarked Fund for Hubei Agriculture Research System/ ; 2018YFE128100//the National Key Research and Development Program of China/ ; 2023BBA029//he Major Program of Hubei Province/ ; }, abstract = {Heat stress is a major constraint to productivity and physiological homeostasis in laying hens. This study investigated integrated responses to acute heat stress using a multi-omics approach, including performance traits, serum biochemical parameters, histology, hepatic transcriptomics, cecal metagenomics, and metabolomics. Acute heat stress impaired productive performance, as reflected by changes in egg production and reduced eggshell strength, and induced systemic physiological disturbances, including increased stress- and injury-related blood indicators and disrupted metabolic and electrolyte balance. Histological analysis confirmed liver and intestinal tissue damage. Hepatic transcriptomics revealed inflammatory activation and suppression of metabolic pathways, particularly those involved in lipid metabolism, energy production, and redox homeostasis. Cecal metagenomic and metabolomic analyses showed altered microbial composition and functional potential, along with disruptions in amino acid, lipid, and energy metabolism. Collectively, these findings suggest that acute heat stress is associated with coordinated inflammatory responses and metabolic reprogramming, together with liver and intestinal injury and gut microbiota-metabolite alterations. The study provides a framework for understanding early heat stress responses and highlights potential targets for nutritional and microbiota-based interventions in poultry production. Importantly, serum biochemical indicators such as D-lactic acid and aspartate aminotransferase may serve as potential early biomarkers for monitoring heat-stress-induced physiological disturbances.}, }
@article {pmid42278142, year = {2026}, author = {Yuan, Z and Xie, F and Ding, Y and Li, X and Ghonaim, AH and Jiang, C and Ren, M and Li, S}, title = {Dietary Fiber Levels Modulate Intestinal Mucosal Architecture and the Microbiome-Metabolome Axis to Support Immune Homeostasis in Brooding Wanxi White Geese.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/ani16111709}, pmid = {42278142}, issn = {2076-2615}, abstract = {Dietary fiber is a critical determinant of intestinal health, yet its optimal inclusion level for WWG during the critical brooding period remains undefined. This study aimed to evaluate the effects of varying dietary CF levels (approximately 3%, 5%, and 9%) on the intestinal morphology, immune function, and microbiome-metabolome axis of brooding WWG. A total of 120 one-day-old goslings were randomly assigned to the three dietary treatments for a 28-day trial. Histological analysis revealed that the 9% CF diet significantly improved gut morphology, yielding superior villus-to-crypt ratios in the jejunum and ileum. Molecular assays indicated that higher fiber levels (5-9%) upregulated the expression of nutrient transporters (SGLT1 and GLUT2). Concurrently, the 9% CF diet effectively suppressed the potent pro-inflammatory cytokine TNF-α in the jejunum while appropriately upregulating IL-6 and NF-κB, indicating enhanced mucosal immune vigilance and structural maturation. Multi-omics integration (shotgun metagenomics and LC-MS metabolomics) demonstrated that specific fiber levels significantly shifted microbial abundances, specifically enriching Bacteroidetes and Actinobacteria. These microbial shifts were strongly correlated with enriched metabolic pathways, notably lysine biosynthesis and purine metabolism, which synergistically support mucosal homeostasis. Collectively, these findings demonstrate that a 9% dietary CF inclusion is an effective nutritional strategy to optimize intestinal architecture and microbial-metabolic profiles in brooding WWG.}, }
@article {pmid42278211, year = {2026}, author = {Shematorova, EK and Shpakovski, GV}, title = {Molecular Evolution of the Archaeal DNA-Dependent RNA Polymerase: Cooperative Changes in Subunit Composition and Specific Domains of Small Subunits.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114679}, pmid = {42278211}, issn = {1422-0067}, support = {thematic plan 1&#x444;.4.1//National Research Center "Kurchatov Institute"/ ; }, abstract = {The subunit composition and tertiary structure of DNA-dependent RNA polymerases in archaea, bacteria, and eukaryotes are currently well understood. The single RNA polymerase of archaea resembles the nuclear RNA polymerase II of eukaryotes in its composition and consists of 10-12 subunits. Perhaps the only exception that seems to confirm this rule is the Rpo8 subunit (homologue of the eukaryotic Rpb8), which only some classes of archaea have. The development of metagenomic sequencing has led to a significant revision of the classification system of prokaryotes, in particular to the identification of a number of new Archaea evolutionary lineages. This makes it possible to analyze the subunit composition and structure of RNA polymerase of all currently isolated archaeal phyla. Our analysis shows that the Rpo8 subunit is present only in the RNA polymerase of Archaea species from the Thermoproteota of the Thermoproteati superphylum and from the whole superphylum Promethearchaeati, formerly known as the Asgard. After analyzing the changes in the small Rpo6 subunit (homologue of eukaryotic Rpb6), functionally interacting with Rpo8, we noticed that the largest number of changes in the primary and domain structures of this small subunit occurred in archaeal phyla that lack Rpo8. Shortened forms of Rpo6 without N- or C-terminal regions were observed only in representatives of archaea with an RNA polymerase that does not contain the Rpo8 subunit. Our analysis shows that the changes in Rpo6 are an adaptation of a multisubunit transcription complex to the disappearance of Rpo8. Most likely, the Rpo8 subunit was present in the RNA polymerase of the Last Common Ancestor of Archaea (LCAA) and, in the course of evolution, disappeared in the superphyla Euryarchaeota and Nanobdellati and two divisions of the Thermoproteati superphylum: Bathyarchaeota and Thaumarchaeota.}, }
@article {pmid42278252, year = {2026}, author = {Mechri, S and Najjari, A and Croze, S and Ouzari, HI and Le Roes-Hill, M and Tounsi, S and Lachuer, J and Jaouadi, B}, title = {Unraveling the Taxonomic Diversity and Functional Potential of the Tunisian Salterns, Abbassia and Thyna, via Integrated 16S-18S Amplicons and Shotgun Metagenomics.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114714}, pmid = {42278252}, issn = {1422-0067}, support = {101079425//Centre of Biotechnologie of Sfax/ ; }, mesh = {*Metagenomics/methods ; Tunisia ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Archaea/genetics/classification ; Shotgun Sequencing ; Phylogeny ; *Bacteria/genetics/classification ; Metagenome ; }, abstract = {Hypersaline environments are unique ecosystems harboring specialized microbial communities with significant biotechnological potential. This study provides a comprehensive characterization of the taxonomic diversity and functional potential of two Tunisian salterns, Abbassia (Kerkennah) and Thyna (Sfax), using an integrated approach that combines 16S/18S rRNA gene amplicons (Illumina and full-length Nanopore) with shotgun metagenomics. Taxonomic profiling revealed a high species richness (S ≈ 1250 taxa); however, the Abbassia site was characterized by extreme taxonomic polarization, with over 95% of the community dominated by specialized halophilic Bacillota (Salinicoccus and Jeotgalicoccus). In contrast, Thyna exhibited a more even distribution dominated by Pseudomonadota and methanogenic Archaea. Beyond taxonomy, functional annotation via the HUMAnN 3.0 pipeline identified site-specific metabolic specializations. Abbassia was enriched in biosynthetic pathways and robust stress-response mechanisms, including ectoine biosynthesis and ppGpp-mediated stringent response, reflecting adaptation to stable hypersaline conditions. Conversely, Thyna's microbiome prioritized energy extraction and nutrient recycling, with a high abundance of fermentation and glyoxylate cycle pathways. These findings demonstrate that environmental filtering shapes not only the microbial structure but also the metabolic landscape, highlighting the ecological plasticity of microbial life in extreme Tunisian salterns.}, }
@article {pmid42278256, year = {2026}, author = {Al-Ansari, MM and Mahmood, SM and Al-Alwan, M}, title = {The Human Breast Microbiome: From Homeostasis to Malignancy, Mechanistic Insights and Therapeutic Perspectives.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114723}, pmid = {42278256}, issn = {1422-0067}, support = {RAC# 2240005//King Faisal Specialist Hospital &amp; Research Centre/ ; }, abstract = {Although human mammary glands were traditionally considered sterile, accumulating evidence has established the presence of distinct microbial communities that may have colonized breast tissue primarily via retrograde nipple flow or via hematogenous or lymphatic translocation from other body sites. Comparative studies reveal differences in the microbiota of healthy and diseased breast tissues, with variations in microbial signatures across breast cancer subtypes and in comparison with adjacent normal tissues. This review synthesizes current evidence on the composition of the breast microbiome, the factors shaping its development, and alterations it undergoes in inflammatory and malignant breast diseases. Furthermore, the article discusses mechanistic insights, methodological challenges, and future therapeutic perspectives based on published studies employing culture-independent approaches, such as 16S rRNA gene sequencing and metagenomic analyses. Key host-related factors influencing breast-associated microbial communities, including hormonal regulation, environmental exposure, diet, and therapeutic interventions, are explored. The existing literature is assessed to identify key associations between the breast microbiome and host signaling pathways, as well as the significant challenges that remain unresolved, including low biomass contamination, inter-study variability, limited longitudinal data, and an incomplete understanding of causality. Addressing these limitations is critical for advancing microbiome-based diagnostic and therapeutic strategies for breast disease.}, }
@article {pmid42278324, year = {2026}, author = {Ilinskaya, O and Vagin, K and Kurdy, W and Yakovleva, G and Karamova, N and Zelenikhin, P and Kolpakov, A and Zuev, Y}, title = {Biomineral Complex with Probiotic and Detoxifying Properties for Recovery After Radiotherapy.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114794}, pmid = {42278324}, issn = {1422-0067}, support = {24-14-00059//Russian Science Foundation/ ; }, abstract = {Radiotherapy is a highly effective, safe cancer treatment, and about half of all cancer treatments involve lifesaving radiotherapy. Despite huge advances in technology that have made it safer and more effective, it is still not without side effects. They differ from patient to patient and can include fatigue, nausea, skin reactions, and hair loss, but dysbiosis is the most common complication associated with radiotherapy. Probiotics aimed at restoring the microbiome have found widespread use, but the problem of their rapid inactivation in the gastrointestinal tract has not yet been solved. Our study aims to confirm the effectiveness of a novel biomineral complex, based on a powdered clinoptilolite containing a rock loaded with lactobacilli for restoring the intestinal microbiome of mice exposed to radiation. Based on the 16S rRNA gene analysis, alpha-diversity and dynamics of changes in the fecal metagenome, as well as the functional potential of mice exposed to radiation, were studied, and the prospects of administering the biomineral complex to achieve positive effects were assessed. NMR analysis of the mineral carrier was carried out, and its safety was confirmed. Moreover, per os administration of the complex following irradiation led to a reduction in the level of chromosomal aberrations induced by irradiation. Thus, the biomineral complex has a microbiome-restoring effect and reduces radiation-induced clastogenesis.}, }
@article {pmid42278475, year = {2026}, author = {Ermakov, VS and Falah, K and Nigam, SK}, title = {A Kidney-Microbiome Short- and Medium-Chain Fatty Acid Loop Mediated by OAT1: Implications for the Remote Sensing and Signaling Theory.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114942}, pmid = {42278475}, issn = {1422-0067}, support = {R01 DK109392/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Organic Anion Transport Protein 1/metabolism/genetics ; Signal Transduction ; Mice ; *Kidney/metabolism/microbiology ; *Fatty Acids, Volatile/metabolism ; Mice, Knockout ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {Short-chain fatty acids (SCFAs) and medium-chain fatty acids (MCFAs) include small organic anions derived from the gut microbiome that interact with organic anion transporters of the SLC22 family, many of which are expressed in the kidney proximal tubule. According to the Remote Sensing and Signaling Theory (RSST), crosstalk between organs (e.g., gut-liver-kidney axis, gut-brain axis) and the gut microbiome is mediated by metabolites and signaling molecules transported by multi-specific "drug" transporters. The renal drug transporter OAT1 (SLC22A6) is also a major transporter of gut-microbiome products and uremic toxins (e.g., indoxyl sulfate); it has been shown to act as part of a regulatory feedback loop involving the gut microbiome. SCFAs, especially propionate and butyrate, have been shown to play a central role in the transcriptional regulation of OAT1 through HDAC inhibition. By fecal metagenomics analyses of Oat1 knockout mice, we now find that propionate synthesis is among the most altered pathways in the gut microbiome. In contrast, these pathways were only minimally altered in the Oat3 (Slc22a8) knockout. Metabolomics analyses indicate that serum propionate derivatives (e.g., propionyl glycine) and 3-hydroxybutyrate are dependent on OAT1 in the knockout mice and in humans treated with probenecid, an OAT1 inhibitor. The gut microbiome of the Oat1 knockout mice also exhibited greater fatty acid synthesis, which generates odd-chain-length fatty acids (e.g. heptanoate) when propionate is available. Overall, the data, especially when considered in light of in vitro experiments of others, indicates the in vivo existence of a feedback loop connecting gut-microbiome-derived SCFAs and MCFAs to kidney proximal tubule uptake via OAT1. This bidirectional feedback loop in turn regulates OAT1 expression through HDAC inhibition. The feedback loop is clearly consistent with the Remote Sensing and Signaling Theory-in particular, the centrality of multi-specific "drug" transporters in organ crosstalk and host-microbiome interactions via small molecules with "high information content." The key role of OAT1 function in maintaining tubular secretion in CKD supports the importance of this RSST loop in renal pathophysiology. Modulating this RSST loop could have therapeutic value in chronic kidney disease and other contexts.}, }
@article {pmid42278495, year = {2026}, author = {Zielińska, E and Kycia, K and Mikołajczuk-Szczyrba, A and Piłka, N and Juszczuk-Kubiak, E}, title = {GABA-Producing Bacteria as Potential Psychobiotics in Gut-Brain Axis Regulation.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27114969}, pmid = {42278495}, issn = {1422-0067}, support = {NdS-II/SN/0238/2023/01"//Ministry of Science and Higher Education/ ; }, mesh = {Humans ; *gamma-Aminobutyric Acid/metabolism/biosynthesis ; *Brain/metabolism/physiology ; Animals ; *Probiotics ; *Gastrointestinal Microbiome/physiology ; *Bacteria/metabolism ; *Brain-Gut Axis ; }, abstract = {γ-Aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the central nervous system (CNS) and plays a vital role in maintaining neural balance, regulating mood, and reducing stress responses. Recent metagenomic studies of the gut microbiome have shown that various bacterial species, especially those in the genera Lactobacillus, Bifidobacterium, and Bacteroides, isolated from the human gut and environmental sources such as fermented foods, contain glutamate decarboxylase (GAD) systems that enable GABA production. Microbially produced GABA can influence the microbiota-gut-brain (MGB) axis by activating neural, endocrine, and immune signalling pathways that are crucial for maintaining gut and brain homeostasis. Emerging evidence suggests that supplementation with GABA-producing bacteria, known as psychobiotics, may improve neurotransmitter balance, modulate cytokine production, strengthen the integrity of the intestinal barrier, and alleviate anxiety- and depression-related behaviours. This review summarises current knowledge of GABA-producing bacterial strains derived from the human gut and food environments and explores their potential as emerging psychobiotics in modulating gut-brain communication and mental health.}, }
@article {pmid42278559, year = {2026}, author = {Li, CC and Sun, DS and Lien, TS and Lin, GL and Cheng, CF and Tsai, KW and Wu, WS and Hu, CT and Lin, MD and Lin, WY and Yang, CH and Liou, JW and Chang, HH}, title = {TiO2 Nanoparticles Trigger Gut-to-Gill Bacterial Translocation and Dysbiosis in Zebrafish.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27115036}, pmid = {42278559}, issn = {1422-0067}, support = {111-2320-B320-006-MY3, 112-2320-B-320-007, 114-2320-B-320-004//National Science and Technology Council/ ; TCMMP114-01, TCAS111-02, TCAS112-02, TCAS113-04, TCRD112-033, TCRD113-041, TCRD114-029, TCRD115-030//Tzu Chi Foundation/ ; }, mesh = {Animals ; *Titanium/toxicity/chemistry ; *Zebrafish/microbiology ; *Dysbiosis/microbiology/chemically induced ; *Gills/microbiology/drug effects ; *Bacterial Translocation/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Nanoparticles/toxicity ; RNA, Ribosomal, 16S/genetics ; *Metal Nanoparticles/toxicity/chemistry ; }, abstract = {Titanium dioxide nanoparticles (TiO2-NPs) are widely produced and persist in aquatic ecosystems, yet their indirect effects on host-microbe interactions remain poorly defined. By using zebrafish (Danio rerio) as a sentinel species, this study investigated the effects of subchronic 5 mg/L TiO2-NP exposure. Dynamic light scattering was utilized to characterize the bimodal aggregates (peaks at 917 and 46,841 nm; surface charge: +22.08 mV) that define the environmental state of TiO2-NPs. Parallel 16S rRNA metagenomic profiling on Day 6, prior to mortality, revealed profound gut dysbiosis. A marked increase in Chao1 richness (p < 0.01), alongside a catastrophic 333-fold reduction in beneficial Cetobacterium and an 856-fold enrichment of pathogenic Mycobacterium, was observed. Beta-diversity and hierarchical clustering analyses revealed a striking convergence between gut and gill microbial signatures, supporting a gut-to-gill translocation model. These results suggest that TiO2-NPs exposure induces intestinal dysbiosis, facilitating opportunistic bacterial migration via internal (gut-blood-gill) or external (fecal-water-gill) pathways. This study identifies dysbiosis-driven secondary infection as a novel, overlooked mechanism of nanoparticle toxicity, necessitating a shift in ecological risk assessments toward host-microbe interactions.}, }
@article {pmid42278576, year = {2026}, author = {Kozhakhmetov, S and Kushugulova, A and Vinogradova, E and Rakhmankulova, A and Terzic, M and Bapayeva, G and Aimagambetova, G and Kamzayeva, N and Kim, Y and Primbetov, B and Imankulova, B and Kongrtay, K and Kadroldinova, N and Galym, M and Makhambetova, S and Nurgaliyeva, K and Abdiyeva, Z and Zhumakanova, Z and Baktybayeva, D and Smagulova, B and Ukybassova, T}, title = {Cervicovaginal Mycobiome Restructuring by HPV and Bacterial Community State Types in a Kazakhstani Shotgun Metagenomic Cohort: Lactobacillus iners as a Candida-Permissive Niche Associated with α-9 HPV in Cytologically Normal Women.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27115052}, pmid = {42278576}, issn = {1422-0067}, mesh = {Humans ; Female ; *Lactobacillus/genetics/physiology ; *Vagina/microbiology/virology ; *Candida/genetics/physiology ; *Cervix Uteri/microbiology/virology ; *Papillomavirus Infections/virology/microbiology ; *Mycobiome/genetics ; Metagenomics/methods ; Adult ; Microbiota ; Shotgun Sequencing ; Middle Aged ; *Human Papillomavirus Viruses/genetics ; }, abstract = {Cervicovaginal dysbiosis is an established co-factor of high-risk human papillomavirus (HPV) persistence and cervical neoplastic development, yet most studies address the bacterial compartment in isolation, leaving fungal communities and bacterial-fungal cross-kingdom interactions underexplored, particularly in Central Asian populations. We performed shotgun metagenomic sequencing (mNGS) of cervicovaginal samples from 311 Kazakhstani women undergoing routine cervical screening. HPV status was determined using combined PCR and mNGS methods, and cervical screening was completed using liquid-based cytology (NILM, ASC-US, LSIL, ASC-H). Bacterial, viral, and fungal taxa were profiled from a single shotgun dataset with Kraken2 pipeline. Bacterial community state types (CSTs) were determined based on dominant bacterial species, functional gene content was annotated against KEGG using eggNOG, and covariate-adjusted associations were estimated using MaAsLin3. Mycobiome β-diversity differed significantly by HPV status (p = 0.003). In particular, Candida positivity was significantly associated with HPV presence and with high-risk α-9 HPV in cytologically normal (NILM) samples (OR = 3.6, [1.6-9.6], p ≤ 0.001). Covariate-adjusted analysis was consistent with this positive association (q < 0.05). Concurrently, among CSTs, Lactobacillus iners-dominated CST III and dysbiotic Gardnerella vaginalis-dominated CST IV showed a 3-fold higher Candida albicans prevalence (p < 0.01). Further analysis demonstrated that, functionally, both of these CSTs had depleted capacity for lactate metabolism (ko00620, p < 0.0001) and, in particular, for the genetic capacity for pyruvate-dependent H2O2 generation (half that of the L. crispatus-dominated CST I). These findings support L. iners as a metabolically permissive rather than protective Lactobacillus and suggest cross-kingdom functional signatures as candidate biomarkers for HPV acquisition and persistence in Central Asia, a region previously absent from the cervicovaginal microbiome literature.}, }
@article {pmid42278616, year = {2026}, author = {Gajic, I and Jovicevic, M and Kekic, D and Kabic, J and Vicic, I and Lukovic, B and Tomic, A and Sovljanski, O and Skoric, M and Sikanic, I and Jankovic, M and Smitran, A and Bozic, L and Golic, B and Basic, J and Karabasil, N and Opavski, N}, title = {Evolving Approaches to Bacterial Identification: A Review of Classical and Modern Techniques.}, journal = {International journal of molecular sciences}, volume = {27}, number = {11}, pages = {}, doi = {10.3390/ijms27115092}, pmid = {42278616}, issn = {1422-0067}, support = {7042//Scientific Fund of the Republic of Serbia/ ; }, abstract = {Infectious diseases remain a major global health concern, with a growing burden of antimicrobial resistance and consequent higher mortality in the human population. Accurate bacterial identification is fundamental across clinical, veterinary, agricultural, and research settings, supporting effective diagnosis, antimicrobial stewardship, infection control, food safety, and environmental monitoring; however, conventional approaches are limited by time constraints, reduced sensitivity, and challenges in detecting fastidious or uncultivable organisms. This review provides a comprehensive overview of classical and advanced methods, including microscopy, culture, biochemical testing, immunological and serological assays, proteomic and spectroscopy-based techniques, and molecular approaches, such as polymerase chain reaction (PCR), digital PCR, DNA hybridization, 16S rRNA gene sequencing, whole-genome sequencing, and metagenomics. The integration of artificial intelligence has further enhanced analytical performance. Nevertheless, harmonization of bioinformatics frameworks remains essential, as variability in algorithm-defined cut-off values limits standardized implementation of whole-genome sequencing in routine laboratories. Emerging technologies, including CRISPR-based diagnostics and phage- and nanomaterial-based detection systems, offer promising alternatives. Overall, the integration of these approaches is expected to improve the accuracy, speed, and applicability of bacterial identification across diverse settings; however, these advances should be implemented cautiously, with standardization remaining a key priority alongside technological modernization.}, }
@article {pmid42279294, year = {2026}, author = {Newell, LF and Twohey, E and Sweetnam, J and Skendzel, S and Stingle, J and Vartanian, KA and Davis, BA and Layman, CE and Carbone, L and Ray, K and Fei, SS and Karstens, L and He, FC and El Jurdi, N and Blaes, AH and Meyers, G and Cook, RJ and Baraki, A and Dengel, DR and Holtan, SG}, title = {Attenuation of Immune Senescence Markers After Intensive Cancer Therapy Through Resistance Training: A Pilot Study.}, journal = {Cancers}, volume = {18}, number = {11}, pages = {}, doi = {10.3390/cancers18111710}, pmid = {42279294}, issn = {2072-6694}, abstract = {Background: Chemotherapy and radiation accelerate aging of multiple systems, including the immune and musculoskeletal systems. Resistance training may mitigate some of the late physiologic effects of cancer therapy. Methods: We developed a community-based pilot study of resistance training for long-term cancer survivors meeting criteria for pre-frailty or frailty (N = 8; 6 allogeneic hematopoietic cell transplant, 1 autologous hematopoietic transplant, 1 breast cancer survivor) and their caregivers (N = 8 healthy controls) consisting of a baseline assessment, 10 weeks of personalized resistance training at least once weekly as a group and as many additional times on an individual basis as their schedule allowed, and an end-of-study assessment to measure change in strength and body composition. Blood samples were collected at the start of the study and after the 10-week training program to assess changes in peripheral blood mononuclear cell DNA methylation patterns, gene expression measured by RNA sequencing, and stool microbiome analysis using metagenomics. The median number of resistance training sessions was 25 sessions. Results: Cancer survivors and controls both more than doubled their squat and press volume after 10 weeks. At baseline, cancer survivors exhibited a pro-inflammatory transcriptomic and epigenetic profile with elevated interferon signaling and reduced naïve T cell signatures compared to healthy controls, consistent with immune senescence. After 10 weeks of resistance training, these differences normalized, suggesting that exercise exerted anti-inflammatory and immune-restorative effects in cancer survivors at both gene expression and methylation levels. Ten fecal microbial pathways that were lower in relative abundance in patients compared with controls at baseline were no longer significantly different post-exercise. Conclusions: Our data suggest that in addition to beneficial changes in body composition, resistance training may exert an immune restorative effect in cancer survivors.}, }
@article {pmid42279452, year = {2026}, author = {Yang, L and Meng, W and Yang, T and Zhu, Y and Wang, Z}, title = {Microbiomics: Novel Biomarkers of Colorectal Cancer Diagnosis and Prognosis.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/diagnostics16111582}, pmid = {42279452}, issn = {2075-4418}, abstract = {With colorectal cancer (CRC) accounting for over 1.9 million new cases and 930,000 deaths globally in 2020, there is a critical need for innovative indicators to forecast disease advancement and therapeutic outcomes. The gut microbiome has emerged as a fertile area for discovering such diagnostic and prognostic signals. This narrative review collected current evidence on intestinal microorganisms and their metabolic products as candidate markers for CRC control. Intestinal communities influence malignancy through diverse mechanisms, including metabolic shifts, immune modulation, inflammation, proliferation/apoptosis regulation, genotoxicity, and mucosal barrier disruption. Pathogenic species, such as Fusobacterium nucleatum and enterotoxigenic Bacteroides fragilis, facilitate tumorigenesis via FadA-mediated signaling and Th17/IL-17 responses. In contrast, beneficial taxa like Faecalibacterium prausnitzii and Akkermansia muciniphila provide protective effects through short chain fatty acid production. Macrophage phenotype physiological equilibrium is altered and inflammatory status fluctuates under the former. Metabolically, hydrogen sulfide damages mitochondrial DNA and secondary bile acids stimulate cellular proliferation. While 16S rRNA sequencing and shotgun metagenomics are established detection strategies, innovative platforms like organoids and gene arrays remain in the exploratory stage. Clinical data indicates that F. nucleatum aligns with advanced tumor stage, and its combined detection with colibactin-producing E. coli achieves high sensitivity for early-stage screening. Additionally, A. muciniphila levels can anticipate the efficacy of PD-1 blockade immunotherapy. Microbiota-derived tools represent a transformative direction in oncology. Future research must focus on standardizing protocols and validating multi-marker panels to enhance clinical translation.}, }
@article {pmid42279756, year = {2026}, author = {Abaalkhail, MA and Mohamed, SHS and Aljurbua, MS and Alkhuraisi, RA and Aladhadh, M}, title = {Microbial Diversity of Spontaneously Fermented Camel Milk.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/foods15111969}, pmid = {42279756}, issn = {2304-8158}, abstract = {Camel milk is widely consumed in the world's arid and semi-arid regions because of its favorable nutritional profile and associated human health benefits. The indigenous microbiota of raw camel milk is diverse and composed of different bacterial and fungal groups. This community drives spontaneous milk fermentation, resulting in a variety of traditional products, including Gariss, Shubat, Chal, Dhanaan, Lfrik, and Suusac (or Suusa), depending on geographic region and cultural practice. This fermented milk has improved sensory, nutritional, and health profiles, as well as an extended shelf life, compared to raw milk. Fermentation alters the microbial community structure, with lactic acid bacteria (LAB) consistently becoming dominant, while yeasts and molds are also detected in some products. These patterns have been identified using both culture-dependent and culture-independent approaches, including 16S rRNA gene sequencing and whole-genome shotgun metagenomics. However, the milk's microbial composition is highly variable and is influenced by the original composition, geographical location, fermentation and hygiene practices. The detection of opportunistic pathogens such as E. coli, Salmonella and Listeria in some traditional products raises important food safety concerns. This review presents current knowledge on fermented camel milk microbiology using a cross-regional approach, identifying key gaps in microbial safety and process standardization to support wider acceptance and potential commercialization.}, }
@article {pmid42280335, year = {2026}, author = {Barba-de la Rosa, AP and Treviño, S and Ovando-Vázquez, C and De León-Rodríguez, A and Calva-Cruz, OJ and Barrera-Pacheco, A and Espitia-Rangel, E}, title = {Dietary Supplementation with Amaranth Protein Isolate Modulates the Gut Microbiota in Children with Overweight and Obesity: A Nonrandomized Trial.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, doi = {10.3390/nu18111690}, pmid = {42280335}, issn = {2072-6643}, support = {A3-S-37825//Consejo nacional de ciencia y tecnologia mexico/ ; }, mesh = {Humans ; Child ; Male ; Female ; *Gastrointestinal Microbiome/drug effects ; *Dietary Supplements ; *Amaranthus/chemistry ; Body Mass Index ; Blood Glucose/metabolism ; *Pediatric Obesity/microbiology/blood ; *Plant Proteins/administration &amp; dosage/isolation &amp; purification/pharmacology ; *Overweight/microbiology ; Cholesterol/blood ; Insulin/blood ; Triglycerides/blood ; Feces/microbiology ; }, abstract = {BACKGROUND: Overweight and obesity are chronic diseases that result from complex interactions including genetics, environment, eating behaviors, and limited access to a healthy diet. Amaranth protein (AmProt) has several health benefits, but no studies have examined its effects on the modulation of children's gut microbiota. The work aimed to analyze serum levels and changes in gut microbiota in children aged 8-10 years with different body mass index (BMI) values after supplementation with AmProt.<br><br>METHODS: Participating children were allocated into three groups according to their BMI: normal weight (NW), overweight (OW), and with obesity (OB). Children received AmProt for 90 days. Levels of fasting blood glucose, cholesterol, triglycerides, and insulin were analyzed before and after diet supplementation. HOMA-IR and adinopectin/leptin ratio were evaluated. Feces were collected and metagenome analysis was carried out.<br><br>RESULTS: No changes in glucose levels were observed across groups and treatments; however, cholesterol and triglycerides levels tended to decrease. The HOMA-IR value increased in relation to BMI and no changes were observed after treatment. Firmicutes were highly abundant in all groups. The lower abundance of Ruminococcus was observed in the OW and OB groups. In the OW group, Blautia, Butyricicoccus, and Roseburia were also observed in increased abundance. In all groups, AmProt consumption tended to increase the abundance of Coproccus, Prevotella, and Collinsella. Conclusions: Supplementation of the children's diet with AmProt showed an improvement in serum cholesterol and triglyceride levels, which could be related to changes in the microbiota related to lipid metabolism.}, }
@article {pmid42280338, year = {2026}, author = {Zhang, S and Liu, K and Shi, L and Yan, C and Wang, A and Liu, A and Guo, H and Xie, A and Kong, XJ}, title = {Development of a Metagenomics-Guided Personalized Synbiotic Protocol for Children with Autism Spectrum Disorder: An Exploratory Case Series.}, journal = {Nutrients}, volume = {18}, number = {11}, pages = {}, doi = {10.3390/nu18111694}, pmid = {42280338}, issn = {2072-6643}, support = {92436//Boston Children's Hospital/ ; 233263//Massachusetts General Hospital/ ; }, mesh = {Humans ; *Synbiotics/administration &amp; dosage ; *Metagenomics/methods ; Child, Preschool ; *Autism Spectrum Disorder/microbiology/therapy ; Male ; Child ; Female ; Pilot Projects ; Feces/microbiology ; *Gastrointestinal Microbiome ; Treatment Outcome ; *Precision Medicine/methods ; }, abstract = {BACKGROUND/OBJECTIVES: Gut microbiota dysregulation has been increasingly implicated in the pathophysiology of autism spectrum disorder (ASD), yet clinical responses to standardized probiotic interventions remain inconsistent, likely reflecting substantial inter-individual variability in baseline microbiome composition, host-microbe interactions, immune tone, and metabolic function. Here, we present a pilot implementation of a metagenomics-guided, personalized synbiotic intervention in children with ASD using the Systematic Microbiome Assessment and Reconstruction Therapy (SMART) framework.<br><br>METHODS: Seven children (aged 5-12 years) underwent longitudinal fecal shotgun metagenomic profiling, and dietary habits, food sensitivities, and regional dietary background were recorded as contextual factors potentially influencing microbiome composition and response to intervention. Individualized synbiotic formulations were constructed based on microbial taxonomic composition and inferred functional capacity and iteratively refined over time. Gastrointestinal outcomes were assessed through caregiver-reported clinical observations, whereas behavioral changes were evaluated using standardized instruments.<br><br>RESULTS: Several participants demonstrated improvements in gastrointestinal symptoms and selected behavioral domains. Notably, in a subset of participants, improvements in gastrointestinal function preceded measurable behavioral changes.<br><br>CONCLUSIONS: Although limited by a small sample size and lack of a control group, these findings provide preliminary evidence supporting the feasibility of implementing a metagenomics-guided personalized synbiotic framework in ASD and generate hypotheses for future investigation. This work presents a preliminary conceptual framework for integrating microbial composition and inferred functional profiling into individualized intervention design and highlights the potential value of microbiome-informed stratification in future studies of treatment response. Larger controlled studies with objective outcome measures are warranted to further evaluate feasibility, reproducibility, and potential clinical utility.}, }
@article {pmid42280669, year = {2026}, author = {Zhang, L and Dong, J and Zhao, J and Jiang, H and Zhang, W}, title = {Rhizosphere Functional Plasticity and the Keystone Taxon Sphingomonas Facilitate Sweet Cherry Adaptation to Semi-Arid Stress.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/plants15111632}, pmid = {42280669}, issn = {2223-7747}, support = {2023LHMS03007//Department of Science and Technology of Inner Mongolia Autonomous Region/ ; }, abstract = {Translocation of elite cultivars across distinct climatic regions often induces transplantation shock. Although the rhizosphere microbiome can facilitate host acclimation, the underlying functional mechanisms remain unclear. Here, we investigated microbiome-mediated adaptation in "Hongdeng" sweet cherry (Prunus avium L.) moved from a humid coastal region (Dalian, DL) to a semi-arid inland habitat (Hohhot, HS). We integrated plant physiological assays, metagenomic sequencing, and structural equation modeling (SEM) to compare the source population (DL), the introduced population (HS), and a locally acclimated reference cultivar ("Summit", HSY). The introduced trees adjusted physiologically to the semi-arid environment by elevating proline levels and antioxidant enzyme activities. Although environmental stress reduced microbial alpha diversity, the core taxonomic framework persisted. Community assembly analysis indicated that the semi-arid climate intensified environmental filtering. Network analysis identified Sphingomonas as a keystone taxon; notably, it maintained a highly connected topological role despite a stable relative abundance. Furthermore, structural equation modeling showed that the environmental stress index positively correlated with the upregulation of microbial DNA repair pathways (R = 0.81, p < 0.001). Ultimately, the SEM demonstrated that environmental stress primarily shapes microbial functional profiles rather than driving species turnover, thereby contributing to host adaptation. The successful establishment of introduced sweet cherry in semi-arid regions is tied more closely to rhizosphere functional plasticity than to taxonomic restructuring. These findings highlight the role of the keystone taxon Sphingomonas in maintaining rhizosphere homeostasis, offering a theoretical framework for targeted microbiome engineering to mitigate transplant shock and enhance crop resilience.}, }
@article {pmid42280715, year = {2026}, author = {Beckett, T and Hesse, U}, title = {Transcriptome Profiling of Leaves and Roots from Rooibos (Aspalathus linearis) Using Oxford Nanopore Sequencing.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/plants15111679}, pmid = {42280715}, issn = {2223-7747}, support = {PMDS22062326365//National Research Foundation/ ; N/A//Rooibos Council of South Africa/ ; }, abstract = {Rooibos (Aspalathus linearis) is one of the few endemic South African plants that has achieved economic importance and international acclaim, mostly as a herbal tea. Plant production, limited to a small mountainous region in South Africa, is at risk as commercial rooibos longevity is in decline, mostly due to low stress tolerance. Transcriptome data can serve to identify molecular markers for improved stress response, which would speed up selection and facilitate the establishment of breeding programmes. Previously, rooibos leaf transcriptomes have been sequenced using Illumina, which yields short reads, hampering correct reassembly of full-length transcripts. Here, we established Oxford Nanopore-based, long-read transcriptome analysis for leaf and root samples from rooibos. We report on potential pitfalls in data pre-processing (PolyA tail trimming and rRNA removal), and compare two assemblers (RATTLE and RNA-Bloom2) and two clustering algorithms (VSEARCH and CD-HIT). The best assembly comprising 169,122 transcripts was generated using RNA-Bloom2 with short-read polishing, followed by CD-HIT clustering. Of the 95,054 predicted proteins, only 67% were also present in the Illumina dataset. The remainder comprised substantially shorter, mostly full-length sequences from a wide range of primary and secondary biosynthesis pathways. Functional annotation indicated that this transcriptome represents a high-quality, comprehensive resource for data mining. In the leaf fraction, comparative transcriptomics identified overexpressed rooibos transcripts potentially involved in photosynthesis, photorespiration and carbon fixation. In the roots, overexpressed transcripts encoded enzymes potentially involved in regulation of root growth and secondary metabolite biosynthesis. These transcripts may represent first targets for molecular marker development.}, }
@article {pmid42281243, year = {2026}, author = {Stanford, J and Hoedt, EC and Gómez-Martín, M and Clarke, ED and Duncanson, K and Burrows, T and Collins, CE}, title = {Contrasting dietary patterns remodel gut microbial function and generate multi-omic signatures associated with cardiometabolic markers.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2685381}, doi = {10.1080/19490976.2026.2685381}, pmid = {42281243}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Feces/microbiology ; Biomarkers/urine/blood ; Female ; Adult ; Male ; *Diet ; Australia ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Cross-Over Studies ; Middle Aged ; Metabolome ; Metabolomics ; Blood Pressure ; }, abstract = {Diet is a modifiable determinant of gut microbiome composition, yet the impact of contrasting whole-dietary patterns on microbial metabolic capacity and coordinated host metabolic signatures remains incompletely characterized. In a randomized crossover feeding trial, 34 Australian adults were provided with a Healthy Australian Diet (HAD), aligned with national dietary guidelines, and a Typical Australian Diet (TAD), reflecting average population intake for two weeks each, separated by a two-week washout. Fecal microbiome composition and function were assessed using shotgun metagenomics, plasma and urine metabolites by untargeted metabolomics, with cardiometabolic markers including blood pressure, plasma lipids, and glucose quantified. HAD was associated with reduced taxonomic and functional alpha diversity relative to baseline, with no change following TAD. Species-level responses were modest, 105 functional pathways differed between diets, with 99 increasing following HAD, predominantly related to amino acid and nucleotide biosynthesis and vitamin/cofactor metabolism. Multi-omic integration using DIABLO achieved strong discrimination of dietary responses (held-out accuracy 91.7%; permutation p = 0.005). In total, 77 individual omic feature-cardiometabolic outcome associations survived FDR correction (q < 0.05), spanning microbial gene functions, plasma metabolites, and urinary metabolites linked to cholesterol, blood pressure, and triglyceride responses. These exploratory findings suggest that integrated microbiome-metabolome profiling may capture inter-individual variation in dietary cardiometabolic responses, though replication in larger, independent, robustly designed studies is needed before translational personalized nutrition strategies can be assessed.}, }
@article {pmid42281420, year = {2026}, author = {Góngora, E and Altshuler, I and Ellis, M and Okshevsky, M and Greer, CW and Whyte, LG}, title = {In Situ Mesocosm Experiment Shows the Capability of the Microbial Community of a Canadian High Arctic Shoreline to Degrade the New Generation of Ship Fuels.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c10583}, pmid = {42281420}, issn = {1520-5851}, abstract = {The warming effects of climate change are leading to a reduction in sea ice, which could open new shipping routes across the Arctic, leading to the possibility of hydrocarbon spills washing onto a shoreline. The behavior and biodegradability of new low-sulfur fuels (LSFs), currently being used by vessels worldwide, has not been assessed on Arctic beaches. We deployed mesocosm experiments on a remote Canadian high Arctic beach for 33 days using two LSFs (marine diesel and ultra-low-sulfur fuel oil, ULSFO) and Bunker C fuel oil (currently being phased out). Bunker C was mostly removed from beach sediments by natural attenuation (14.6% biodegradation, 62.8% nonbiological removal), while the LSFs were more easily biodegraded (37.6-72.8% biodegradation, 2.9-10.0% nonbiological removal). Native beach sediment microorganisms, including putatively novel taxa, adapted to the presence of fuel by expressing multiple aliphatic hydrocarbon biodegradation genes, but only few aromatic hydrocarbon degradation genes. Our results suggest that, while not as biodegradable as marine diesel, ULSFO appears to be a more environmentally friendly alternative to Bunker C due to its higher biodegradability under in situ Arctic environmental conditions. However, limited aromatic hydrocarbon biodegradation under cold and nutrient-poor environmental conditions could negatively affect the efficacy of natural attenuation.}, }
@article {pmid42282013, year = {2026}, author = {Dobbler, PT and Ravi, A and Větrovský, T and Pěchoučková, E and Nemec, A and Kyselková, M}, title = {Single-contig bacterial genomes recovered from cattle fecal metagenomes at farms with variable antibiotic use.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9715194/v1}, pmid = {42282013}, issn = {2693-5015}, abstract = {Cattle feces represent a complex microbial reservoir with implications for animal health and the environmental dissemination of microorganisms and antibiotic resistance genes. Metagenomic studies have shown that cattle fecal communities are dominated by Bacillota and Bacteroidota, whereas low-abundance taxa, including potential pathogens, often remain underrepresented due to methodological detection limits. Here, we present 84 single-contig, medium- to high-quality metagenome-assembled genomes (MAGs) recovered from cattle feces after enrichment for bacteria able to grow in acetate-supplemented minimal medium. The MAGs were classified within the phyla Actinomycetota (20 MAGs), Bacillota (5), Bacteroidota (21), Patescibacteriota (5), and Pseudomonadota (33), with 41 MAGs representing putative novel taxa at species to family level. Nineteen MAGs carried antibiotic resistance genes and six MAGs were assigned to opportunistic pathogenic species. This dataset thus provides a genomic resource for studies of bacterial diversity and antimicrobial resistance at the animal-environment interface within a One Health framework.}, }
@article {pmid42282041, year = {2026}, author = {Schutz, C and Queiroz, A and Mota, T and Ward, A and Barr, D and Janssen, S and Shey, M and Wilkinson, R and Wilkinson, K and Burton, R and Lelouvier, B and Andrade, B and Meintjes, G}, title = {Microbial product translocation and mortality in adults hospitalised with HIV-associated tuberculosis: a prospective observational cohort study.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9856875/v1}, pmid = {42282041}, issn = {2693-5015}, abstract = {Background: HIV-associated tuberculosis (HIV-TB) results in unacceptably high mortality rates despite appropriate treatment. Patients hospitalized with HIV-TB often have disseminated tuberculosis and sepsis syndrome which may result in gastro-intestinal barrier dysfunction and facilitate microbial product translocation. Microbial product translocation may contribute to HIV-TB deaths by driving systemic inflammation. Objectives: To assess microbial product translocation and gastrointestinal epithelial damage in patients hospitalized with HIV-TB and the association with 12-week mortality and biomarkers of tuberculosis dissemination. To describe the bacterial blood microbiome (abundance and diversity) in patients with HIV-TB, its association with mortality and tuberculosis dissemination and compare to outpatient controls. Methods: Patients hospitalized with a new diagnosis of HIV-TB were enrolled and prospectively followed for 12 weeks. Markers of microbial product translocation and gastrointestinal damage were measured in a subset (n=373) and bacterial 16s rDNA was quantitated and metagenomic sequencing performed in 235 patients. Microbial product translocation and gastrointestinal epithelial damage marker concentrations were compared between hospitalized patients who died and survivors and inpatients compared to HIVpositive outpatient controls. Logistic regression analysis was performed to determine associations with mortality. Bacterial abundance, diversity and immune perturbation was measured and analysed across patient outcome groups and in patients with tuberculosis dissemination. Results: Patients hospitalized with HIV-TB had significantly higher concentrations of bacterial 16s rDNA, soluble CD14 (sCD14), lipopolysaccharide binding protein (LBP), trefoil factor 3 (TFF3) and lower endotoxin core antibody IgM (EndoCAB), compared to outpatient controls. Soluble CD14 and TFF3 were significantly higher and EndoCAB lower in inpatients who died versus survivors. TFF3 was independently associated with mortality. LPS, sCD14, LBP, EndoCAB and TFF3 showed significant trends in patients with positive biomarkers of tuberculosis dissemination. Metagenomic sequencing showed higher diversity in hospitalised HIV-TB patients compared to controls, but diversity was not different between outcome groups. Mycobacterium genus proportions were increased in hospitalised patients who died compared to survivors. Conclusion: We found evidence of increased gastrointestinal epithelial damage and microbial product translocation in patients hospitalized with HIV-TB and in patients with positive biomarkers for tuberculosis dissemination, however, only TTF3 (a marker of gastrointestinal epithelial damage), was independently associated with mortality.}, }
@article {pmid42282268, year = {2026}, author = {Frame, LA and Warren, A and Al Qalam, A and Corr, PG and Farah, M and Karam, M and Rangoussis, K and Fahim Devin, M and Celikkol, Z and Gordon, L and Villarreal, D and Catto, E and Udam, Y and Thompson, K and Lubinski, O and Samman, A and Badawi, A and Hack, H and Hunter, M and Hines, I and Servetas, S and Jackson, SA and Hasan, NA and Kogan, M}, title = {Brain health and the gut microbiome (bMicrobiome Study): a proof-of-concept, feasibility study integrating shotgun metagenomics, metrology, and multidimensional phenotyping across the cognitive aging spectrum.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2679810}, pmid = {42282268}, issn = {2993-3935}, abstract = {BACKGROUND: Associations between the gut microbiome and cognitive decline remain inconsistent, reflecting methodological variability, small cohorts, and limited integration of behavioral and lifestyle factors. The microbiota-gut-brain axis may influence cognition through metabolic, immune, and neuroendocrine pathways affecting mood, decision-making, and health behaviors.<br><br>METHODS: This prospective, proof-of-concept study integrated multidimensional phenotyping with metagenomic sequencing (shotgun) in adults (50-90&#x2009;y) around Washington, DC. Participants were classified as healthy controls (HC) or mild cognitive impairment (MCI) by clinical history; early Alzheimer's disease (eAD) participants were unable to complete study requirements. Longitudinal assessment used Boston Cognitive Assessment (BoCA), patient-reported outcomes (PROMIS-29), dietary intake and quality (DietID&#x2122;), readiness-for-change (adapted URICA), at-home stool sample collection.<br><br>RESULTS: Seventeen participants completed sufficient assessments (HC n&#x2009;=&#x2009;11; MCI n&#x2009;=&#x2009;6). Substantial overlap in gut microbiome composition was observed between HC and MCI. Poorly characterized or uncommon taxa drove trends; unassigned taxa were common. Assessment revealed high diet quality and variability in dietary patterns and key components (vegetables, whole grains, fat, fish). Participants demonstrated high readiness to engage in nutritional behavior change, with individuals with MCI reporting greater concern about maintaining changes and a stronger desire for external support.<br><br>CONCLUSIONS: Integrating multidimensional phenotyping with metagenomics is feasible in cognitive decline. Findings highlight biological and behavioral heterogeneity, limitations of species-level inference, and diet and behavioral readiness as modifiable contextual factors.}, }
@article {pmid42282663, year = {2026}, author = {Torres-Morales, J and Dewhirst, F and Kauffman, KM and Mark Welch, J and Borisy, G}, title = {Site-specialization of human oral Porphyromonas species.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.02.729646}, pmid = {42282663}, issn = {2692-8205}, abstract = {Site-specificity within the human oral cavity reflects adaptation mechanisms such as genome divergence and metabolic specialization. Members of the genus Porphyromonas are distributed across oral sites in health and disease, yet the specific distribution of taxa and the functional basis of their site-specificity remain poorly understood. We analyzed 1,242 metagenomes from nine oral sites in healthy individuals and 24 subgingival plaque samples from individuals with periodontitis. Competitive mapping to a dereplicated genus-level pangenome of 84 reference genomes, combined with phylogenomic, gene-level detection, and functional profiling, revealed distinct site-specific distribution patterns, ecotype differentiation, and metabolic specialization across Porphyromonas taxa. Porphyromonas pasteri was the most abundant and widespread taxon in healthy subjects, comprising two ecotypes--one mucosal, one plaque-associated. Porphyromonas gingivalis was rare in healthy subjects but present in periodontal disease, although detected in only half of periodontitis samples. P. gingivalis exhibited the broadest metabolic repertoire, suggestive of a survival strategy adaptive to disparate conditions. In contrast, Porphyromonas catoniae, restricted to healthy dental plaque, lacked biosynthetic pathways for cobalamin, biotin, and serine, implying nutritional dependency on other taxa or the host. Porphyromonas endodontalis, detected in subgingival plaque across both health and disease, also lacked several metabolic pathways. A 44 kb conjugative element identified in P. gingivalis was detected across healthy and periodontitis subgingival plaque microbiomes independently of the P. gingivalis chromosome, indicating horizontal transfer. These findings reveal genomic divergence and complex metabolic specialization among Porphyromonas taxa, refining our understanding of their role in the ecological structure of the human oral microbiome.}, }
@article {pmid42282812, year = {2026}, author = {Jiang, AK and Grant, MR and Arp, G and Dufault-Thompson, K and Clarke, AM and Li, Y and Lehman, D and Jarmusch, AK and Hall, B and Jiang, X}, title = {Discovery of BilV reveals a multienzymatic basis for bilirubin reduction across vertebrate gut microbiomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.06.01.729425}, pmid = {42282812}, issn = {2692-8205}, abstract = {Gut bacteria reduce bilirubin to urobilinogen, allowing it to be excreted through feces and urine, but studies have long noted a heterogeneous mixture of partially reduced bilirubin-derived intermediates, suggesting that multiple enzymes are involved. Here we identify bilirubin vinyl reductase (BilV), a novel Old Yellow Enzyme family reductase encoded in the genomic neighborhood of the known bilirubin reductase (bilR). Using heterologous expression and LC-MS/MS, we show that BilR acts on the methine bridges in the bilirubin reduction pathway; co-expression with BilV enables vinyl-group reduction and complete conversion to urobilinogen. In bacterial genomes, bilV co-occurs primarily with the bilR -insertion subtype and is largely absent alongside bilR -short. Analysis of 1,197 gut metagenomes across 14 vertebrate species reveals that this differential co-occurrence shapes pathway availability across hosts: carnivores and omnivores carry balanced bilR and bilV , whereas avian microbiomes, dominated by bilR -short, are depleted for bilV . These findings establish that bilirubin reduction to urobilinogen involves two enzymes with complementary regioselectivity, and that their distribution across vertebrate gut microbiomes varies in concert with host bile pigment chemistry.}, }
@article {pmid40542918, year = {2026}, author = {Zhang, W and Li, XJ and Liu, F and Zhang, J and Tian, J and Gao, Y}, title = {Fungen: clustering and correcting long-read metatranscriptomic data for exploring eukaryotic microorganisms.}, journal = {Science China. Life sciences}, volume = {69}, number = {6}, pages = {1896-1909}, pmid = {40542918}, issn = {1869-1889}, mesh = {*Gene Expression Profiling/methods ; *Transcriptome/genetics ; Fungi/genetics/classification ; *Metagenomics/methods ; Cluster Analysis ; *Eukaryota/genetics ; Clustering Algorithms ; *Software ; High-Throughput Nucleotide Sequencing ; Soil Microbiology ; }, abstract = {Long-read metatranscriptomics is a powerful and cost-effective technology for elucidating the genetic diversity and expression dynamics of active eukaryotic microorganisms by characterizing full-length transcripts. However, its potential has been limited by the lack of high-quality reference genomes and high sequencing error rates. We present Fungen, a reference-free tool that constructs accurate transcripts from long-read metatranscriptomic data through read clustering and error correction. Fungen achieves superior accuracy in transcript determination while significantly reducing memory usage and offering a 22 to 56-fold speed improvement over existing methods. This novel approach overcomes the challenges posed by sequence similarity among closely related species, enabling the analysis of deeply sequenced metatranscriptomes by generating reliable gene clusters and accurate sequences. Two applications showcase Fungen's capabilities to perform high-resolution taxonomic assignments and gene profiling in marine direct RNA datasets, as well as resolving reliable annotation identities in full-length rRNA targeted sequencing datasets. When applied to soil metatranscriptomic data, Fungen offers valuable insights into the in situ fungal composition and gene expression dynamics, revealing specialized life strategies of plant-pathogenic fungi in soil environments. Overall, Fungen provides a fast, scalable, and accurate solution for analyzing complex metatranscriptomic datasets, paving the way for a comprehensive understanding of eukaryotic diversity and function from long-read sequencing data.}, }
@article {pmid41680419, year = {2026}, author = {Pedrazzini, C and Funari, R and Cucini, C and Nardi, F and Grabenweger, G and Widmer, F and Enkerli, J}, title = {Population genomics identifies Italian and North American origins of Popillia japonica in Switzerland.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41680419}, issn = {2045-2322}, support = {No. 861852//European Union's Horizon 2020/ ; }, mesh = {Animals ; Switzerland ; *Coleoptera/genetics/classification ; Phylogeny ; North America ; Introduced Species ; Italy ; Genetics, Population ; *Metagenomics/methods ; Genomics ; }, abstract = {The Japanese beetle (Popillia japonica), native to Japan, is a major invasive species in North America and Europe. Its colonization of Europe began on the Azores (1970s), followed by Italy (2014) and southern Switzerland (2017). In 2023, the presence of the pest was reported in three areas of Switzerland: Kloten (Canton of Zürich, north-eastern Switzerland), Basel (Canton of Basel-Landschaft, northern Switzerland), and in eastern Canton of Valais (South Switzerland) near the Italian border. In 2024, P. japonica individuals were discovered in several other Swiss Cantons. To trace P. japonica spread and origins in Switzerland, we investigated 42 individuals from infested areas, comprising scattered findings across Switzerland. Phylogenetic and population structure analyses using whole-genome resequencing, including data of previously sequenced samples from Japan, North America, the Azores, Italy, and Southern Switzerland, revealed distinct P. japonica migration patterns. Populations in Basel, Valais, and central Switzerland likely originated from Ticino/Northern Italy via road or rail transport. Conversely, the population near Zürich Airport was identified as an independent introduction from North America, likely through unintentional air transport. These findings offer insights into P. japonica spread across Switzerland, highlighting the need for enhanced monitoring and identification of invasion pathways.}, }
@article {pmid42265550, year = {2026}, author = {Lu, R and Dumonceaux, T and Anzar, M and Zovoilis, A and Antonation, K and Barker, D and Corbett, C and Nadon, C and Robertson, J and Eagle, SHC and Lung, O and Rudar, J and Surujballi, O and Wajnberg, G and Laing, C}, title = {MNBC-ME categorizes viral and plasmid sequences within metagenomes and identifies putative species or plasmid host.}, journal = {BMC bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12859-026-06497-x}, pmid = {42265550}, issn = {1471-2105}, support = {CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; CSSP-2022-CP-2538//Canadian Safety and Security Program/ ; }, abstract = {BACKGROUND: Plasmids and viruses are two types of mobile genetic elements (ME), that rely on host cells to reproduce and propagate themselves. Recently, metagenomics has greatly facilitated the discovery and characterization of new plasmids and viruses, which relies on accurate identification of these reads in metagenomes. Some state-of-the-art tools can identify plasmid or viral reads, while others are able to identify the probable host or source species of these reads. Since the Minimizer-based Naïve Bayes Classifier (MNBC) tool accurately classifies chromosomal and viral reads to the species level, we extended it to develop the MNBC-ME tool that can also identify plasmid reads and their putative host species.<br><br>RESULTS: A standard reference- and test-sequence framework using simulated variable-length reads was used to benchmark MNBC-ME with eleven other state-of-the-art tools for ME identification: DeepMicroClass, geNomad, PPR-Meta, viralVerify, Plasmer, PlasClass, PlasX, VIBRANT, DeepVirFinder, HOTSPOT, and MOSTPLAS. MNBC-ME was the most consistent tool at classifying chromosomal, viral and plasmid reads of variable lengths, in contrast to the other tools whose precision or recall dropped below 50% in some circumstances. MNBC-ME also exceeded 65% and 70% performance in predicting host genus and family of plasmid reads, respectively.<br><br>CONCLUSIONS: MNBC-ME is tool for identification of both short and long viral- and plasmid-originated reads across a wide variety of read types. It also identifies potential low-level host taxa for plasmid reads, and source taxa for chromosomal and viral reads. It is freely available at https://github.com/ComputationalPathogens/MNBC-ME and can be found as the 'mnbc-me' package in bioconda.}, }
@article {pmid42265587, year = {2026}, author = {Liang, X and Li, J and Liu, P and Lai, Z and Huang, S and Xie, F and Jin, W and Mao, S}, title = {Rumen ecological distribution of Pichia yeasts and their effects on rumen fermentation and microbial community.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05281-4}, pmid = {42265587}, issn = {1471-2180}, support = {32272896//The National Natural Science Foundation of China/ ; 32361143788//The National Natural Science Foundation of China/ ; QTPY2026017//The Fundamental Research Funds for the Central Universities/ ; }, abstract = {Yeast supplementation has been widely studied to enhance rumen fermentation and feed efficiency, yet developing efficient yeasts adapted to the rumen environment remains a challenge. In this study, two rumen-derived Pichia strains (Pichia membranifaciens M12 and Pichia kudriavzevii Y4) were evaluated using in vitro rumen fermentation experiments, including a control and three supplementation groups (2 × 10[5], 2 × 10[6], and 2 × 10[7] CFU/mL) for each strain. Results indicated that the two strains did not affect pH but significantly reduced concentrations of ammonium nitrogen (NH3-N) and microbial crude protein (MCP). At 24 h, NH3-N decreased by up to 13.3% and MCP by 18.5%, while at 48 h, NH3-N showed a reduction of up to 22.0% and MCP decreased by up to 5.7%. P. membranifaciens significantly increased the concentration of total volatile fatty acids by 15.4% and elevated the proportions of acetate and propionate at 48 h. Microbial community analysis revealed that these shifts in fermentation parameters were associated with an altered bacterial community structure. Specifically, P. membranifaciens enriched cellulolytic bacteria (Ruminococcus), while reducing amylolytic and proteolytic taxa (Prevotella), and promoted the propionate‑producer (Succiniclasticum). These findings suggested that P. membranifaciens has the potential to influence rumen microbiota. Further examination of the in vivo prevalence of Pichia yeasts species via ITS (n = 72; average parity 2.8 ± 1.1) revealed a lower prevalence and relative abundance for P. membranifaciens compared to P. kudriavzevii. Metagenomic analysis (n = 8; average parity 2.7 ± 0.9) detected both species at low abundances. Overall, this study indicated that rumen-derived Pichia yeasts have the capacity to modulate rumen fermentation, with P. membranifaciens warranting further in vivo evaluation.}, }
@article {pmid42265917, year = {2026}, author = {Nakamura, K and Okazaki, A and Motooka, D and Matsumoto, N and Hasegawa, Y and Fukuda, S and Yabe, M and Sugiura, A and Yatsuka, Y and Fushimi, T and Onuki, T and Aida, Y and Ohtake, A and Murayama, K and Okazaki, Y}, title = {Nanopore-based haplotype-resolved X-chromosome inactivation analysis for clinical severity assessment in X-linked disorders: an AIFM1 family study with proof-of-concept application to a mosaic PDHA1 carrier.}, journal = {HGG advances}, volume = {}, number = {}, pages = {100632}, doi = {10.1016/j.xhgg.2026.100632}, pmid = {42265917}, issn = {2666-2477}, abstract = {X-chromosome inactivation (XCI) modifies disease severity in females with X-linked variants, but clinically applicable high-resolution assessment remains limited. We report a family with an AIFM1 variant showing marked intrafamilial phenotypic variability and evaluated whether haplotype-resolved nanopore sequencing can inform clinical interpretation. Targeted long-read sequencing was performed in a severely affected hemizygous male, his asymptomatic heterozygous mother, and a severely affected heterozygous sibling. In the hemizygous male, the sample served as a technical control, with all reads mapping to a single haplotype, consistent with a hemizygous X chromosome. Among heterozygous carriers with the identical variant (c.506C>T; p.Pro169Leu), XCI correlated with severity: the affected sibling showed 84% skew favoring activation of the pathogenic allele, whereas the mother showed preferential inactivation (20%). This family-based study shows that using nanopore sequencing for haplotype-resolved X-inactivation (XCI) analysis may provide a practical framework for selected X-linked disorders with variable expressivity.}, }
@article {pmid42266244, year = {2026}, author = {Lin, X and Du, Y and Mai, H and Zhang, X}, title = {Voriconazole-Induced Agranulocytosis in a Cirrhotic Patient with Influenza-Associated Pulmonary Aspergillosis: A Case Report.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {607868}, pmid = {42266244}, issn = {1178-6973}, abstract = {The diagnosis and treatment of influenza-associated pulmonary aspergillosis (IAPA) present significant challenges, and voriconazole, as the first-line treatment for IAPA, rarely causes the serious adverse event of agranulocytosis. We first report a case of voriconazole-associated agranulocytosis in a patient with IAPA complicated by cirrhosis and systematically describe the complete process of diagnosis, treatment, and adverse event management. A 68-year-old male with a history of liver cirrhosis presented with cough, dyspnea, and fever. Testing confirmed influenza A, and chest computed tomography (CT) showed diffuse bilateral pulmonary inflammation. Bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) and culture detected Aspergillus fumigatus, confirming the diagnosis of IAPA. The patient received voriconazole. On Day 20 of hospitalization, agranulocytosis developed and resolved after voriconazole discontinuation and granulocyte colony-stimulating factor (G-CSF) administration, consistent with voriconazole-associated agranulocytosis. After neutrophil recovery, voriconazole was resumed with leukocyte support and close monitoring of complete blood counts (CBC) and drug levels. At one-month follow-up, no recurrence of infection or agranulocytosis was observed. This case emphasizes the value of mNGS in timely diagnosis of IAPA, underscores the importance of closely monitoring CBC in such patients during triazole antifungal therapy, and proves the feasibility of resuming antifungal treatment-including the cautious re-administration of the initially sensitizing agent under strict monitoring-after the correction of agranulocytosis. These findings contribute to a better understanding of the disease and may help to optimize its clinical management.}, }
@article {pmid42266457, year = {2026}, author = {Stach, TL and Deep, A and Madge Pimentel, I and Buchner, D and Borton, MA and Soares, AR and Starke, J and Bornemann, TLV and Rehsen, PM and Dreger, KL and Boenigk, J and Vos, M and Leese, F and Beisser, D and Probst, AJ}, title = {Complex compositional and metabolic response of river sediment microbiomes to multiple anthropogenic stressors.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycaf079}, pmid = {42266457}, issn = {2730-6151}, abstract = {Rivers face constant anthropogenic stress, resulting in significant changes in microbial community composition. What remains unclear is whether stream microbiomes exhibit distinct resilience patterns in composition and/or activity upon exposure to different stressors. By subjecting 64 river-connected mesocosms to multiple stressors, we show that sediment microbiomes of small lowland rivers are highly sensitive to low flow velocity. This stress results in altered community compositions incapable of mitigating the applied stressor within a two-week timeframe despite functional stability (inferred via metagenomics). Transcriptomics revealed a systematic heat shock response in the community and a highly active, metabolically versatile, uncharacterized anaerobic keystone species. Increases in temperature (+ 3.5°C) or salinity (+ 0.5 mS/cm) elicited minor responses at community and transcriptomic levels (e.g. upregulation of photosystems). Following a two-week recovery, transcriptomic-inferred stress responses vanished completely, underscoring the river microbiome resilience. Given the complex community responses observed at the activity and compositional levels, we conclude that maintaining natural river flow is vital to preventing energy loss and reduced microbiome activity in river sediments.}, }
@article {pmid42266956, year = {2026}, author = {Lu, J and Zhong, J and Qiu, W and Zhang, Q}, title = {Intrathecal combined with intravenous eravacycline for the treatment of multisite carbapenem-resistant Acinetobacter baumannii infections (intracranial, pulmonary, and bloodstream) in a post-trauma adolescent female: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1829527}, pmid = {42266956}, issn = {2296-858X}, abstract = {BACKGROUND: Carbapenem-resistant Acinetobacter baumannii (CRAB) is a leading cause of hospital-acquired infection among critically ill patients, with extremely limited therapeutic options, particularly for central nervous system (CNS) infections. Eravacyline, a novel fully synthetic fluorocycline, demonstrates potent in vitro activity against CRAB but exhibits poor penetration across the blood-brain barrier (BBB).<br><br>CASE PRESENTATION: A 17-years-old female with severe traumatic brain injury developed concurrent intracranial, pulmonary, and bloodstream CRAB infections. Initial systemic antimicrobial therapy, including intravenous colistin and eravacycline, failed to control the intracranial infection. After switching to a regimen incorporating intrathecal eravacycline (initial dose 2 mg, followed by 5 mg daily) combined with high-dose intravenous cefoperazone-sulbactam and nebulized colistin, the patient showed rapid clinical and microbiological improvement. Serial cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) revealed a dramatic reduction in pathogen load, with eventual eradication of CRAB.<br><br>CONCLUSION: This case highlights the potential role of intrathecal eravacycline as a salvage therapy for CRAB meningitis, particularly in cases of multifocal, extensively drug-resistant infection. Further pharmacokinetic and safety studies are warranted to optimize its use in CNS infections.}, }
@article {pmid42267106, year = {2026}, author = {Wu, Y and Gao, Q and Yang, H and Wang, Y and Lang, L and Liu, B and Jiang, X and Li, D and Wang, X and Xun, J and Zhang, Q}, title = {Multi-omics analysis identifies gut microbiota-glutamine axis contributing to the pathogenesis of reflux esophagitis.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1805181}, pmid = {42267106}, issn = {1664-302X}, abstract = {BACKGROUND: Reflux esophagitis (RE), a common gastroesophageal reflux disease characterized by esophageal mucosal inflammation, is closely associated with gut microbiota dysbiosis and metabolic abnormalities. The glutamine-glutamate metabolic pathway regulates inflammation and mucosal barrier function, but its role in RE and association with gut microbiota remain unclear. This study aimed to characterize gut microbiota and serum metabolites in RE patients via integrated multi-omics (focusing on the gut microbiota-glutamine axis), and verify the activation status of this pathway in RE inflammatory models and the anti-inflammatory effect of its targeted inhibition.<br><br>METHODS: RE patients and healthy controls (HCs) were enrolled. Fecal metagenomic sequencing and serum untargeted metabolomics (LC-MS/MS) were performed to identify differential gut microbiota and serum metabolites between the two groups, followed by Pearson correlation analysis to explore their associations. In vitro experiments were conducted on human esophageal epithelial cells (HEECs) divided into four groups: normal, inflammatory, glutamine-supplemented, and inflammatory + glutamine + glutaminase inhibitor (BPTES) groups. qPCR was used to detect the mRNA expression of glutamine-glutamate pathway molecules (GLS, c-Myc, SLC1A5), mucosal barrier markers (ZO-1, Occludin), and pro-inflammatory cytokines (IL-8, IL-6, IL-1&#x3b2;, TNF-&#x3b1;). Intracellular concentrations of glutamine, glutamate, and &#x3b1;-ketoglutarate were measured, and the anti-inflammatory effect of BPTES was verified.<br><br>RESULTS: RE patients showed significant differences in gut microbiota diversity and composition compared with HCs, with Bacteroidota, Pseudomonadota, Escherichia coli, and Klebsiella pneumoniae as dominant taxa. Serum metabolomics revealed elevated glutamine and glutamate in RE patients, which were identified as key differential metabolites related to RE pathogenesis. Pearson analysis revealed that alterations in serum metabolite profiles of RE patients were significantly correlated with changes in gut bacterial abundance. Notably, glutamate-glutamate (Glu-Glu) metabolism exhibited negative correlations with multiple bacterial genera (Acrocarpospora, Limnobacter, Pseudobacter, Shewanella, and Tropicimonas). In vitro, inflammatory HEECs exhibited increased intracellular glutamine, glutamate, and &#x3b1;-ketoglutarate, upregulated glutamine-glutamate pathway molecules and pro-inflammatory cytokines, and downregulated mucosal barrier markers. Exogenous glutamine alone failed to alleviate inflammation, while combined with BPTES significantly reversed pathway activation and mitigated inflammation in inflammatory HEECs.<br><br>CONCLUSION: RE patients exhibit significant gut microbiota dysbiosis (dominated by Bacteroidota, Pseudomonadota, Escherichia coli, and Klebsiella pneumoniae) and abnormal glutamine metabolism (elevated serum glutamine and glutamate). Pearson analysis reveals that the glutamine-glutamate pathway correlates negatively with multiple bacterial genera (Acrocarpospora, Limnobacter, Pseudobacter, Shewanella, and Tropicimonas). The glutamine-glutamate pathway is activated in inflammatory esophageal epithelial cells, and targeted GLS inhibition by BPTES reverses pathway activation and mitigates inflammation. These findings highlight the gut microbiota-glutamine axis as potential diagnostic biomarkers and therapeutic targets for RE, providing new insights into pathogenesis and a basis for novel clinical interventions.}, }
@article {pmid42267107, year = {2026}, author = {Mathyk, BA and Shukla, R and Kumar, V and Mishra, SP and Pandya, S and Patten, N and Gerardi, K and Beatty, HW and Persad, AH and Imudia, AN and Yadav, H and Jain, S}, title = {Parabolic flight induces site specific microbiome changes in women.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1817099}, pmid = {42267107}, issn = {1664-302X}, abstract = {INTRODUCTION: The vaginal microbiome plays a central role in women's health by supporting immune function, maintaining mucosal homeostasis, and preventing infections. Spaceflight and its analogs can induce acute physiological stress, which can alter host microbiome interactions. While other studies have analyzed the microbiome changes at certain body sites, the female-specific microbiome changes have not been explored in depth in space medicine research.<br><br>METHODS: Pre- and post-parabolic flight vaginal and oral microbiome were analyzed via metagenomic shotgun sequencing to assess taxonomic composition and metabolic pathways. Host DNA and bad quality sequences were removed using the KneadData tool. Taxonomic and functional profiles were analyzed with MetaPhlAn and HUMAnN. Microbiome data were integrated with stress response parameters including cortisol, proinflammatory cytokines, and urinary short-chain fatty acids.<br><br>RESULTS: Both alpha- and beta diversity analysis showed minimal impact of parabolic flight on oral microbiome while vaginal microbiome showed significant differences. Taxonomic profiling showed marked restructuring of the vaginal microbiome, characterized by increased Firmicutes dominance and enrichment of Lactobacillus species, particularly Lactobacillus crispatus and Lactobacillus jensenii, whereas oral microbiome stayed relatively stable. Overall, only 2.54% of oral species showed significant postflight changes compared to 57.9% of vaginal species (p&#x202f;<&#x202f;0.0001). Random Forest model identified L. crispatus as a key discriminator of postflight vaginal microbiome composition. Metabolic pathway analysis revealed minimal postflight pathway redistribution in saliva samples but greater number of changes in the vaginal microbiome, with significant postflight enrichment of fatty acid biosynthesis and nucleotide metabolism. Vaginal samples demonstrated a threefold greater proportion of altered metabolic pathways compared to oral samples. In addition, urinary acetate, butyrate, and valeric acid levels were significantly reduced postflight. Salivary cortisol increased postflight and positively correlated with L. jensenii.<br><br>CONCLUSION: Parabolic flight induces body site-specific microbiome changes in reproductive age women, with greater taxonomic and functional metabolic remodeling in the vaginal microbiome than in the oral microbiome. These findings highlight the sensitivity of the vaginal microbial ecosystem to spaceflight stressors and underscore the need for longitudinal and mechanistic studies to determine the persistence, clinical significance, and potential health implications of these changes during longer duration space missions.}, }
@article {pmid42267128, year = {2026}, author = {Daurova, A and Daurov, D and Sapakhova, Z and Kanat, R and Abilda, Z and Toishimanov, M and Isgandarov, I and Mukhametov, A and Volkov, D and Shamekova, M and Zhambakin, K}, title = {Rhizosphere microbiome dynamics and plant adaptation to abiotic stress in major oilseed crops: a review.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1832403}, pmid = {42267128}, issn = {1664-462X}, abstract = {Abiotic stresses, such as drought, salinity, extreme temperatures, nutrient deficiencies, and heavy metal contamination, severely limit oilseed crop productivity under accelerating climate change. This review synthesizes recent advances in understanding the critical role of soil and plant-associated microbiomes in conferring stress tolerance to major oilseed species, including rapeseed (Brassica napus), sunflower (Helianthus annuus), soybean (Glycine max), and sesame (Sesamum indicum). Beneficial microorganisms, particularly plant growth-promoting rhizobacteria (PGPR), arbuscular mycorrhizal fungi (AMF), and endophytes, enhance plant tolerance through an integrated network of biochemical, physiological, and molecular mechanisms. Biochemically, they modulate phytohormone levels (e.g., IAA and ABA), produce osmoprotectants, and regulate antioxidant systems (e.g., SOD, CAT, POD) to mitigate oxidative damage. Physiologically, these processes contribute to improved root architecture, water-use efficiency, nutrient acquisition, and ion homeostasis under stress conditions. At the molecular level, microorganisms influence gene expression and signaling pathways associated with stress responses, including activation of stress-responsive genes and metabolic adjustments. These interconnected mechanisms collectively strengthen plant resilience by coordinating metabolic regulation, cellular protection, and adaptive responses within the plant-microbiome system. Agroecological practices (soil type, crop rotation, tillage, fertilization) strongly shape microbial community assembly and functional potential, while multi-omics approaches (metagenomics, metatranscriptomics, metabolomics) reveal stress-driven restructuring and adaptive metabolic shifts in the rhizosphere. Emerging tools such as synthetic microbial consortia (SynComs) and targeted microbiome engineering offer promising, sustainable alternatives to conventional breeding and chemical interventions, enhancing soil health, nutrient cycling, and agroecosystem resilience with reduced environmental footprint. This review presents a comprehensive synthesis with a specific focus on oilseed crops, integrating current knowledge on microbiome dynamics under multiple abiotic stress conditions-an area that remains comparatively underrepresented in the literature. It examines key microbial groups driving adaptation, evaluates omics-based insights into plant-microbiome interactions, identifies critical research gaps, and outlines future directions for microbial inoculants and climate-resilient oilseed production systems.}, }
@article {pmid42267141, year = {2026}, author = {Hardies, SC and Park, J and Cho, BC and Hwang, CY}, title = {Alishewanella Phage LSH1 from the Sea Surface Microlayer Provides a Novel Minimalistic View of the Siphoviral Hub Structure.}, journal = {Computational and structural biotechnology journal}, volume = {35}, number = {1}, pages = {0131}, pmid = {42267141}, issn = {2001-0370}, abstract = {LSH1 is a novel lytic siphovirus isolated, together with its host in the genus Alishewanella, from the surface microlayer of a brackish tidal reservoir in South Korea and characterized with respect to growth properties, genome sequence, gene annotation, mass spectrometry, and electron microscopy. Sequence analysis shows that LSH1 shares only distant similarity to other cultured phages, although a closer metagenomic neighborhood can be defined. LSH1 represents the first isolate from a large, previously unsampled family-level sector of the viral tree. Transmission electron microscopy revealed a tail end distinct from the best structurally characterized siphoviral prototypes and similar in appearance to Salmonella phage Jersey, the prototype of a large structurally uncharacterized group named Guernseyvirinae. Therefore, Jersey was included in the comparative analysis with LSH1. A combination of hidden Markov model comparisons and AlphaFold reconstruction was used to clarify the structural relationships of these phages. Both have structural homologs of portions of the canonical bacteriophage lambda tail hub but lack the lambda components associated with receptor recognition linked to ejection triggering in that system. The LSH1 and Jersey tail hubs are of different sequence lineages, but each represents a relatively minimalistic version of the siphoviral tail hub, with distinct candidates for the structural location of their antireceptors. This study explores the capability of AlphaFold to rapidly augment the relatively few structurally characterized phages with models for diverse variants, fleshing out how much variation there is and perhaps leading to a better treatment of how this variation is evolving.}, }
@article {pmid42267567, year = {2026}, author = {Liu, BZ and Zhao, XY and Sun, ZW and Wang, J and Zeng, JT and Huang, Y and Cai, KQ and Zhao, JG and Yang, SH and Yuan, JL}, title = {Gut microbiota remodeling in HBB-mutant cynomolgus monkeys reveals blood-gut axis disruption associated with β-thalassemia-related gastrointestinal dysfunction.}, journal = {Zoological research}, volume = {47}, number = {3}, pages = {827-842}, doi = {10.24272/j.issn.2095-8137.2025.141}, pmid = {42267567}, issn = {2095-8137}, abstract = {Gastrointestinal symptoms frequently accompany anemia caused by HBB mutations, such as β-thalassemia; however, the mechanisms linking disordered hemoglobin biology to intestinal dysfunction remain incompletely understood. In this study, HBB-mutant cynomolgus monkeys were generated and analyzed together with wild-type (WT) controls through integrated metabolomic and metagenomic profiling. HBB mutation was associated with a marked shift in gut microbial ecology, characterized by reduced microbial diversity and altered abundances of Lactobacillus and Bacteroides. Metabolic profiling revealed broad perturbation of amino acid, lipid, energy, and immune-related metabolic pathways, with 3-oxooctadecanoic acid (HMDB0254633) emerging as a discriminative metabolite between WT and HBB-mutant animals. Multiomics integration indicated that HBB mutation reshaped microbiota-metabolite interactions and may thereby affect host metabolism and immune responses. To examine the functional relevance of this metabolite, 3-oxooctadecanoic acid was administered to C57BL/6 mice with castor oil-induced diarrhea. High-dose treatment alleviated diarrhea severity, improved stool parameters, limited body weight loss, and partially restored gut microbial composition. These findings provide non-human primate evidence that β-thalassemia-associated HBB mutation disrupts intestinal microbiota homeostasis and metabolic output, identifying 3-oxooctadecanoic acid as a candidate biomarker and potential regulator of gastrointestinal dysfunction. This study provides a valuable framework for understanding how host genetic variation contributes to gut microbiome remodeling and gastrointestinal manifestations in β-thalassemia.}, }
@article {pmid42267811, year = {2026}, author = {Gołębiowska, J and Woodhouse, JN and Tobias-Hünefeldt, SP and Grossart, H-P}, title = {Salinity-driven niche partitioning of aquatic viruses in one of Europe's largest estuaries.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0080726}, doi = {10.1128/aem.00807-26}, pmid = {42267811}, issn = {1098-5336}, abstract = {UNLABELLED: Viruses are a vital part of the aquatic food web and hold a profound role in carbon and energy cycling at different trophic levels. Despite the rising interest in aquatic viruses, very few studies were conducted in estuaries, where freshwater and marine communities meet along the salinity gradient. We present a paired analysis of metagenomic and metatranscriptomic data focusing on the viral fraction derived from seasonal sampling between May 2021 and November 2022 in one of Europe's largest estuaries, the temperate mesotidal Elbe River downstream of Hamburg. Our results reveal a sharp delineation of viral communities along specific salinity niches and provide evidence for their adaptation. This implicates viruses as a structural component of microbial and phytoplankton ecology across the estuary. We provide a detailed overview of the spatiotemporal distribution of viruses, including taxonomy and hosts, which emphasizes the role of giant viruses (Megaviricetes) in waters of lower salinity and RNA viruses in marine environments. We identify, besides salinity, total dissolved phosphate and temperature as the main drivers of estuarine viral communities. We find a broad spectrum of metabolic pathways, potentially altered by viruses via auxiliary metabolic genes. Potential metabolisms impacted included the underlying carbon processes like photosynthesis or methane metabolism, but may also extend to some xenobiotics and antibiotics metabolisms in this anthropogenically altered estuary. This is the first detailed molecular study of viruses in the Elbe Estuary, shedding light on viral communities and their ecological roles in controlling microbial populations at the base of the estuarine food web.<br><br>IMPORTANCE: Estuaries are the interfaces between marine and limnic waters, with their own specific hydrological and biochemical processes due to, e.g., salinity gradients, tides, and terrestrial inflows. In particular, they are sites of intensive carbon cycling. Their often high economic importance causes substantial anthropogenic pressure on the ecosystem. All of these result in extremely complex factors interacting and influencing microbial populations. Our study provides a first comprehensive overview of the viral communities in Europe's largest estuary. We made an attempt to disentangle the numerous environmental parameters, and we highlight salinity as the most important factor, providing evidence of its multidimensional influence on the estuarine virome. Our findings deepen our understanding of viral communities and their interactions with microbes and bring us a step closer to their role in aquatic food webs, particularly in carbon turnover in estuaries.}, }
@article {pmid42267859, year = {2026}, author = {Shittu, OE and Enagbonma, BJ and Babalola, OO}, title = {Functional Metagenomics Insights Into the Allium ampeloprasum Rhizosphere Microbiome Under Different Fertilization Regimes.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70307}, doi = {10.1002/mbo3.70307}, pmid = {42267859}, issn = {2045-8827}, support = {//International Centre for Genetic Engineering and Biotechnology (ICGEB) through Grant CRP/ZAF22-03 awarded to OOB/ ; }, abstract = {Fertilization practices shape the taxonomy, functional composition, and metabolic functions of the microbiome within the rhizosphere. Nonetheless, the impacts of various fertilization approaches on the functional composition of Allium ampeloprasum rhizosphere microbiomes remain underexplored. This study investigated how biofertilizers and chemical fertilizers impact the microbial functional categories of the A. ampeloprasum rhizosphere, hypothesizing that fertilization systems influence the metabolic profile. The genomic DNA was successfully extracted from the collected soil samples and processed via shotgun metagenomics sequencing. The application of biofertilizers enhanced the rhizosphere microbiome, revealing similar microbial orders across all plots, although plot G2 was uniquely enriched with those belonging to phyla Bacteroidota, Proteobacteria, actinobacteria, Myxococcota, and Verrucomicrobiota. Biofertilizers promoted a broader range of microbial functions, primarily at EggNOG level 1. Notably, the α diversity significantly differed (p < 0.05) among the soil samples. The functional diversity was linked to the soil physicochemical attributes, particularly the carbon and moisture contents, as illustrated by the RDA. Biofertilizer increases microbial diversity, underscoring the need to understand the rhizosphere microbiome to advance sustainable agricultural methods.}, }
@article {pmid42268526, year = {2026}, author = {Mohit,  and Verma, S and Yadav, A and Venkatesh, V}, title = {Multi-omics insights into immunometabolic dysregulation in neonatal sepsis for precision medicine.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {42268526}, issn = {1573-4978}, abstract = {Neonatal sepsis remains a major global health challenge, contributing substantially to morbidity and mortality despite many advances. Conventional diagnostics often fail to capture the disease complexity and immune dysregulation, leading to delayed diagnosis and sub-optimal treatment. Recent advances in multiomics, including genomics, transcriptomics, proteomics, metabolomics and metagenomics are transforming molecular understanding by enabling a precise view of host-pathogen interactions. These approaches also provide critical insights into metainflammation, a state of chronic, low-grade immune and metabolic dysregulation, playing a pivotal role in neonatal immune vulnerability. Integrating multi-omics with meta-inflammatory profiling may support future risk stratification, biomarker discovery, and precision-oriented neonatal sepsis care. However, clinical translation requires further validation, platform standardization, and feasibility assessment in NICU settings. Such insights may establish the foundation of P4 medicine by emphasizing prediction, prevention, personalisation, and participation in neonatal care. Multi-omics integration may support endotype identification, and data-driven clinical communication after adequate validation. Overall, this review highlights how multiomics and metainflammation driven frameworks may improve mechanistic understanding of neonatal sepsis and guide future development of clinically feasible precision-medicine approaches.}, }
@article {pmid42268876, year = {2026}, author = {Fatima, Z and Surette, MD and Marttala, S and Leto, D and Jayaratne, P and Smaill, F and Smieja, M and Hasan, MR}, title = {Microbiome analysis of bronchoalveolar lavage (BAL) specimens from immunocompromised patients with pneumonia compared to those from healthy volunteers.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0351562}, doi = {10.1371/journal.pone.0351562}, pmid = {42268876}, issn = {1932-6203}, abstract = {BACKGROUND: Metagenomic sequencing of bronchoalveolar lavage (BAL) specimens is increasingly being applied for the diagnosis of lower respiratory tract infections, offering agnostic pathogen detection and a faster turnaround time. While metagenomic sequencing of BAL specimens can reveal a wide range of organisms, their clinical relevance is often unclear because of the challenge of distinguishing true pathogens from background taxa. This study compared the BAL microbiomes of immunocompromised patients with pneumonia to those of healthy volunteers, with the aim of assisting clinical interpretation of metagenomics-based approaches for diagnosing pneumonia in this patient population.<br><br>METHODS: BAL specimens from healthy control volunteers (n&#x2009;=&#x2009;20) were collected during a COVID-19 vaccine trial, while residual BAL specimens from immunocompromised patients (n&#x2009;=&#x2009;52) were obtained from the Hamilton Regional Laboratory Medicine Program (HRLMP) after standard culture and PCR testing. 16S rRNA gene amplicon sequencing was performed using Nanopore technology. Reads were classified using Minimap2 in EPI2ME, and microbiome analyses were conducted using the vegan and MaAsLin2 packages in RStudio (v2026.1.1.403).<br><br>RESULTS: Immunocompromised patients showed significantly lower bacterial read counts and reduced alpha diversity (p&#x2009;<&#x2009;0.0001; Wilcoxon Rank-Sum test), along with higher inter-sample heterogeneity. In contrast, BAL samples from healthy controls exhibited a more homogeneous microbial profile dominated by anaerobic Gram-negative genera, including Prevotella, Veillonella, Selenomonas, and Fusobacterium. Beta diversity analyses using Bray-Curtis and Jaccard distance metrics demonstrated significant compositional separation between cohorts (PERMANOVA p&#x2009;=&#x2009;0.001), with tight clustering of healthy controls and marked dispersion among immunocompromised samples. Differential abundance analysis identified 96 significantly altered species (q&#x2009;<&#x2009;0.05), with immunocompromised patients showing depletion of anaerobic commensals and enrichment of clinically relevant pathogens, including Stenotrophomonas maltophilia, Enterococcus spp., Mycoplasma spp., and Nocardia spp.<br><br>CONCLUSION: Immunocompromised patients demonstrated a markedly disrupted and heterogeneous BAL microbiome, characterized by a loss of anaerobic commensals and an enrichment of potentially pathogenic taxa. This study provides a characterization of the dysbiotic state in immunocompromised pneumonia, offering a baseline reference for future longitudinal studies and clinical trials aimed at improving the interpretation of metagenomic findings in this patient population.}, }
@article {pmid42269300, year = {2026}, author = {Lo, HY and Hsiao, YT and Wu, YJ and Whang, LM and Chen, WH and Tung, HH}, title = {Persistence and dynamics of antibiotic resistome in a drinking water supply system with booster chlorination.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142622}, doi = {10.1016/j.jhazmat.2026.142622}, pmid = {42269300}, issn = {1873-3336}, abstract = {Due to the extensive use of antibiotics worldwide, the prevalence of antibiotic resistance genes (ARGs) in aquatic environments has become a major public health concern. This study investigated the ARGs in a drinking water supply system, with particular emphasis on booster chlorination in the distribution network. To elucidate the dynamics of the antibiotic resistome, environmental DNA was extracted from water collected from five different sections, and the resistome profiles were subsequently reconstructed with metagenome assembly. Our findings revealed that 35 core ARGs persisted but decreased in concentration during water treatment and early distribution, with genes resistant to bacitracin, multidrug, and rifamycin being the most prominent. However, a notable surge of ARGs was observed at the terminal distribution segment. This increase was linked to changes in the resistome structure, which were primarily associated with shifts in the microbial community and, within the DWDS specifically, also linked to horizontal transfer mediated by mobile genetic elements (MGEs) under chlorine stress from booster chlorination. Microbial communities within the drinking water distribution system (DWDS) shifted distinctly from those in the water treatment plant. Under re-chlorination pressure, the chlorine-tolerant Mycobacteriales and the biofilm-forming Hyphomicrobiales and Rhodobacterales became the predominant taxa. Additionally, metagenome-assembled genomes (MAGs) reconstruction further identified that Hyphomicrobium and Mycobacterium were the main ARG carriers in the DWDS, with the latter as the main putative host for the core ARGs. Overall, this study demonstrated that booster chlorination in the water distribution system while controlling microbial regrowth, may simultaneously facilitate ARG dissemination. These findings highlight the need to optimise re-chlorination practices to balance microbial growth control while minimising ARG proliferation in DWDS.}, }
@article {pmid42269354, year = {2026}, author = {Petersen, J and Ringel, V and Päuker, O and Frühling, A and Rohde, M and Jarek, M and Spröer, C and Bunk, B and Huber-Fischer, K and Pradella, S and Freese, HM and Koblitz, J and Neumann-Schaal, M and Brinkmann, H}, title = {Think pink 2.0 - Description of Roseobacter cerffii sp. nov., isolated from the chromerid alga Vitrella brassicaformis, and reclassification of Sulfitobacter sabulilitoris as Billmartinia sabulilitoris, gen. nov., comb. nov.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {4}, pages = {126731}, doi = {10.1016/j.syapm.2026.126731}, pmid = {42269354}, issn = {1618-0984}, abstract = {A Gram-stain-negative, aerobic, pink-pigmented bacterial strain A03A-229[T] was isolated from a non-axenic culture of the chromerid alga Vitrella brassicaformis CCMP3155, which originates from the Great Barrier Reef in Australia. Complete genome sequencing revealed the presence of seven circular replicons, representing one chromosome, two chromids and four plasmids. The 142-kb DnaA-like I chromid, which contains the photosynthesis gene cluster (PGC), traces of ubiquinone-11 and the ability to reduce nitrate are diagnostic for A03A-229[T]. Genomic, physiological, and chemotaxonomic data provided clear evidence that strain A03A-229[T] (= DSM 112523[T] = CECT 31310[T]) represents a new species of the genus Roseobacter, for which the name Roseobacter cerffii sp. nov. is proposed. R. cerffii A03A-229[T] represents the tenth described species of the genus Roseobacter, but phylogenetic (meta-)genome analyses indicated the presence of at least 27 different species. Reconstruction of the metabolic pathways of the genus Roseobacter revealed a highly conserved metabolism with lineage specific adaptations for the formation of compatible solutes and a surprising abundance of four GAPDH genes. The ability to perform aerobic anoxygenic photosynthesis, which is mediated by the PGC, is responsible for the eponymous pink color of this genus, while it only occurs scattered in the sister genus Sulfitobacter. Our phylogenomic analyses provided clear evidence for a distinct taxonomic status of strain Sulfitobacter sabulilitoris HSMS-29[T] (= KACC 19870[T] = NBRC 113549[T]). Based on its phylogenetic position, low average amino-acid identities (AAI) and a PufC-type PGC, we propose the reclassification of this strain as Billmartinia sabulilitoris gen. nov., comb. nov.}, }
@article {pmid42269462, year = {2026}, author = {Riveros, A and Kwon, H and Impellitteri, CA and Jiang, D}, title = {Nitrate reshapes electron partitioning and Se[0] formation during continuous electro-microbial treatment of mixed selenium oxyanions.}, journal = {Water research}, volume = {303}, number = {}, pages = {126244}, doi = {10.1016/j.watres.2026.126244}, pmid = {42269462}, issn = {1879-2448}, abstract = {Selenium in flue-gas-desulfurization (FGD) wastewater occurs as mixed selenate and selenite oxyanions, and requires both aqueous removal and reduction to elemental selenium to prevent secondary waste generation. Here, we introduce a continuous-flow electro-microbial platform that couples flow-electrode capacitive deionization (FCDI) with bio-electrochemical systems (BES) to achieve voltage-driven removal and bio-mediated reduction within a compact reactor configuration. During 41 days of operation treating mixed selenium oxyanions (10 mg Se L[-1] each) in fortified water samples with FGD-relevant nitrate concentrations (20 mg L[-1]), the system achieved removal efficiencies of 84-95% for selenite and 54-78% for selenate. Nitrate unexpectedly enhanced apparent elemental selenium yield from 70% to 99% under 2 V, but decreased selenium-specific Faradaic efficiency from 20% to 8%, likely due to a combination of electron flux diversion and co-respiration between nitrogen and selenium oxyanions. Metagenomics suggested that genes associated with indirect selenium transformation (cysIJ, trxA/B, gshA/B, and ybbN) were 45-115x more abundant than genes encoding dedicated selenate reductases. Together, these results demonstrate FCDI-BES as a promising platform for treating selenium and potentially other redox-active oxyanions and highlight the importance of studying electron-acceptor competition in similar systems.}, }
@article {pmid42269501, year = {2026}, author = {Ghose, M and Parab, AS and Manohar, CS}, title = {Metagenome-based analysis of xenobiotic degradation potential in urban mangrove sediments under chronic anthropogenic impact.}, journal = {Marine pollution bulletin}, volume = {231}, number = {}, pages = {119970}, doi = {10.1016/j.marpolbul.2026.119970}, pmid = {42269501}, issn = {1879-3363}, abstract = {Urban mangrove sediments receive continuous inputs of industrial and domestic pollutants, yet the microbial basis of pollutant transformation in these chronically impacted systems remains insufficiently resolved. This study investigated xenobiotic degradation potential in sediments from two urban mangrove locations along the Mandovi estuary, Goa, India, through reanalysis of previously generated shotgun metagenomic data. The assembled metagenomes showed enrichment of degradation pathways associated with aromatic and aliphatic pollutants commonly linked to urban contamination. A high representation of oxidoreductases and related aromatic transformation functions indicated that xenobiotic processing is closely linked to redox regulation and central carbon metabolism. Pathway completeness did not consistently correspond with relative abundance, suggesting that lower-abundance pathways may still retain structurally coherent degradation capacity. Hydrocarbon-specific annotation revealed the coexistence of aerobic and anaerobic activation strategies, consistent with adaptation to the redox heterogeneity of mangrove sediments. Xenobiotic- and hydrocarbon-associated functions were linked mainly to Pseudomonadota, Actinomycetota, Shewanella, and a substantial fraction of unresolved bacterial lineages, indicating that undercharacterized taxa may contribute importantly to pollutant-processing potential. Supportive metagenome-assembled genome analysis showed that recovered genomes encoded complementary subsets of degradation functions, although these genomes should be treated as illustrative examples rather than representatives of the whole community. Comparison between locations revealed similar core degradation functions but variation in secondary pathways, likely reflecting differences in local pollutant inputs and sediment conditions. These results show that urban mangrove microbiomes retain a functionally structured and redox-adapted metagenomic repertoire for xenobiotic and hydrocarbon degradation, highlighting their relevance to pollutant transformation, environmental monitoring, and native community-based bioremediation.}, }
@article {pmid42269618, year = {2026}, author = {Eriksson, D and Schiller, J and Schickele, A and Priest, T and Mankowski, A and Faucher, E and Ustick, LJ and Kuhn, M and Miravet-Verde, S and Ruscheweyh, HJ and Clerc, C and Gruber, N and Sunagawa, S and Bork, P and Vogt, M}, title = {Variations in the latitudinal diversity gradients of the ocean microbiome.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.05.016}, pmid = {42269618}, issn = {1934-6069}, abstract = {Latitudinal diversity gradients (LDGs), which typically decline from the equator to the poles, are a pervasive macroecological pattern. However, their generality and drivers in the ocean microbiome remain widely unresolved. We integrated global-scale metagenomic data with habitat modeling to study marine microbial LDGs across seasons and depths. Surface mixed-layer microbiomes exhibit diversity peaks at (sub)tropical latitudes and a poleward decline, whereas mesopelagic communities (200-1,000 m) show no latitudinal diversity structuring. Taxonomic resolution reveals that the mixed-layer LDG is underpinned by Alphaproteobacteria and Cyanobacteriia, while other taxa exhibit distinct or contrasting LDGs. Diversity structuring also varies by seasons and regions and is governed by temperature and nutrient availability. Together, these findings highlight that, within the ocean microbiome, LDGs are not universal but reflect lineage-specific ecological strategies and responses to environmental gradients. Our study provides fundamental insights into the structuring of ocean microbiome diversity and lays the foundation for predicting responses to environmental change.}, }
@article {pmid42269619, year = {2026}, author = {Guo, Y and Wang, Z and Li, D and Wang, L and Lan, H and Guo, F and Zhao, Z and Liu, Z and Meng, L and Shen, X and Wang, M and Zhao, W and Zhang, W and Kong, C and Shi, L and Sun, Y and Seim, I and Jiang, A and Ma, K and Su, Z and Zhang, N and Ji, Q and Chen, J and Chen, K and Qi, C and Li, B and He, B and Liu, Y and Zhou, J and Zheng, Y and Zhang, H and Wang, Y and Han, M and Yang, T and Tong, J and Zhang, Y and Wang, Z and Xu, X and Chen, J and Liu, Y and Chen, H and Zeng, T and Wei, X and Li, C and Yang, H and Wang, B and Liu, X and Shao, C and Zhang, W and Gu, Y and Xiao, X and Xu, X and Wang, J and Mock, T and Fan, G and Li, Y and Liu, S and Dong, Y}, title = {The genetic repertoire of deep-sea microbiome: From sequence to structure and function.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.05.009}, pmid = {42269619}, issn = {1934-6069}, abstract = {The deep sea, as the largest and maybe most hostile environment on Earth, is still underexplored, especially regarding its genetic repertoire. Yet, previous work has revealed significant habitat-specific deep-sea biodiversity. Here, we present an integrated deep-sea microbial genetic dataset comprising 502 million nonredundant genes from 2,138 samples and 2.4 million predicted structures and use it to link specific protein structures with genetic variants associated with life in the deep sea and to assess their biotechnology potential. Combining global sequence analysis with biophysical and biochemical measurements revealed unprecedented sequence diversity and substantial structural conservation of proteins. Especially, proteins involved in replication, recombination, and repair were identified as being under rapid evolution and with specialized properties. Among these, a structurally divergent helicase exhibited advantages in controlling nanopore sequencing speed. Thus, our work positions the deep sea as an evolutionary engine that generates and hosts genetic diversity and bridges genetic knowledge with biotechnology.}, }
@article {pmid42269751, year = {2026}, author = {Sun, X and Li, S and Liang, J and Wang, C and Bai, Y and Mao, J and Qu, J}, title = {From Correlation to Causality: Identifying Potential Environmental Drivers of Pathogenic Antibiotic-Resistant Bacteria in River Water Using Causal Machine Learning.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128570}, doi = {10.1016/j.envpol.2026.128570}, pmid = {42269751}, issn = {1873-6424}, abstract = {Pathogenic antibiotic-resistant bacteria (PARB) pose a serious public health threat within the One Health framework, yet identifying their potential environmental drivers in complex aquatic systems remains a challenge. This study systematically compared correlation analysis, explainable machine learning, and causal machine learning within a unified framework. Both Spearman correlation and explainable machine learning identified numerous potentially important factors, notably non-antibiotic pharmaceuticals such as carbamazepine and bezafibrate. However, causal inference via double machine learning, which controls for confounders and interaction effects, revealed a distinctly different driver profile. Under predefined assumptions, this approach estimated potential causal effects for dissolved oxygen, the nitrate-to-ammonium ratio, specific antibiotics (roxithromycin, azithromycin), and non-antibiotic compounds (acenaphthene, 2-chloroanthracene). Taxon-specific analysis further showed that Aeromonas aligned closely with the overall PARB causal profile, whereas Pseudomonas responded primarily to oxidation-reduction potential. Functional profiles suggested potential stress-adaptation mechanisms related to signal transduction and metabolic regulation pathways. By shifting from associative prediction to causal inference, this causal machine learning-guided framework provides a robust analytical basis for identifying environmental drivers and informing targeted management of PARB risks in aquatic ecosystems.}, }
@article {pmid42270066, year = {2026}, author = {Shi, H and Wang, L and Wu, Y and Cai, B}, title = {Synergistic mechanisms by which arbuscular mycorrhizal fungi regulate hyphosphere bacterial communities and functional genes to suppress potential N2O production under tetracycline stress.}, journal = {Environmental research}, volume = {305}, number = {Pt 2}, pages = {125020}, doi = {10.1016/j.envres.2026.125020}, pmid = {42270066}, issn = {1096-0953}, abstract = {Tetracycline (TC), a widely used veterinary antibiotic, frequently accumulates in agricultural soils and disrupts nitrogen (N) cycling, thereby enhancing nitrous oxide (N2O) emissions. However, biologically based mitigation strategies and their underlying mechanisms remain poorly understood. In this study, a soybean pot experiment was conducted with four treatments: control, arbuscular mycorrhizal fungi (AMF) inoculation, TC addition, and AMF combined with TC. By integrating hyphosphere-specific sampling, potential N2O production rate measurements, 16S rRNA gene sequencing, quantitative PCR, metagenomics, and partial least squares path modeling, we systematically elucidated AMF-mediated regulation of N2O production under TC stress. TC significantly increased potential N2O production rate (+21.2%), primarily by selectively suppressing the terminal denitrification step, as evidenced by reduced nitrous oxide reductase (NOS) activity and decreased abundance of the nosZ gene, resulting in denitrification pathway disruption and N2O accumulation. In contrast, AMF inoculation under TC stress reduced potential N2O production rate by 29.5%, restoring it to control levels. Mechanistically, AMF improved hyphosphere soil properties (e.g., increased SOC and TN and enhanced TC dissipation) and selectively enriched functionally competent and TC-tolerant denitrifiers, particularly nosZ-harboring taxa such as Streptomyces, thereby repairing denitrification pathway completeness. Path modeling further demonstrated that AMF mitigated N2O production both directly by enhancing N-cycling microbial functional capacity and indirectly by optimizing soil physicochemical conditions. Our findings reveal the microbial and molecular mechanisms underlying antibiotic-enhanced N2O emissions and highlight AMF as a low-input, nature-based environmental biotechnology strategy to simultaneously remediate antibiotic-contaminated soils and mitigate agricultural greenhouse gas emissions.}, }
@article {pmid42270094, year = {2026}, author = {Deng, L and Gao, X and Guo, C and Hu, X and Qi, J and Wang, J and Huang, X and Zhang, Y and Hu, Z and Wang, H and Hong, B}, title = {Structural and Functional Alterations of Microbiome in Upper and Lower Respiratory Tract in Patients With NSCLC.}, journal = {Cancer control : journal of the Moffitt Cancer Center}, volume = {33}, number = {}, pages = {10732748261460118}, doi = {10.1177/10732748261460118}, pmid = {42270094}, issn = {1526-2359}, abstract = {IntroductionThe airway microbiome plays a pivotal role in lung cancer development, but the microbiome characteristics in upper and lower respiratory tract of non-small cell lung cancer (NSCLC) patients remains unclear.MethodsThis was a prospective case-control study. The study included 60 samples from NSCLC patients and non-cancer controls: 23 sputum (SP) samples (14 NSCLC, 9 controls) and 37 bronchoalveolar lavage fluid (BALF) samples (21 NSCLC, 16 controls). Metagenomic sequencing was performed to characterize microbial composition and diversity, differential taxa, inter-kingdom networks, and functional profiles for bacteria and fungi.ResultsFor bacterial community, BALF samples from NSCLC tend to show higher alpha diversity than that of non-cancer controls (Shannon p = 0.046, Simpson p = 0.089), whereas SP samples from NSCLC show a trend toward lower alpha diversity (Shannon p = 0.053, Simpson p = 0.033). For fungal community, alpha diversity shows no significant difference between NSCLC and non-cancer groups in either SP (Shannon p = 0.250, Simpson p = 0.480) or BALF (Shannon p = 0.800, Simpson p = 0.700) samples. Beta diversity exhibits differences in bacterial community composition between NSCLC and non-cancer controls in both SP (p = 0.018) and BALF samples (p = 0.015), while fungal communities appear relatively stable (p = 0.611 for SP; p = 0.611 for BALF). LEfSe and Random Forest analyses identify bacterium Porphyromonas SGB2015 and fungus Psilocybe cubensis significantly enriched in BALF samples from NSCLC, whereas no species is enriched in SP samples. Cross-kingdom network indicates increased complexity and connectivity in NSCLC-associated microbial communities. Functional analysis shows the enrichment of biosynthetic pathways in SP samples and metabolic pathways in BALF samples from NSCLC.ConclusionThese findings suggest that NSCLC may be associated with compositional, structural, and functional alterations of the airway microbiome, with potentially distinct patterns between upper and lower respiratory tract.}, }
@article {pmid42270219, year = {2026}, author = {Zhang, Z and Zhang, K and Hou, Q and Yang, C and Guo, Z and Li, Y and Wang, C and Wang, Y}, title = {Microbial ecology and flavor formation mechanisms of high-temperature Daqu in the Huang-Huai River basin and adjacent regions: A comparative study from eastern Henan, Jiaodong peninsula, and southern Anhui.}, journal = {Food research international (Ottawa, Ont.)}, volume = {239}, number = {}, pages = {119489}, doi = {10.1016/j.foodres.2026.119489}, pmid = {42270219}, issn = {1873-7145}, abstract = {High-temperature Daqu (HTD) serves as a critical fermentation starter for sauce-aroma type Baijiu. Although strong-aroma Baijiu dominates production in the Huang-Huai River Basin and surrounding regions, knowledge regarding the microbial ecology and flavor-forming potential of HTD in this area remains limited. In this study, we collected HTD samples from Eastern Henan, Jiaodong Peninsula (Qingdao), and Southern Anhui, and performed physicochemical analyses, enzyme activity assays, electronic sensory evaluation, and metagenomic sequencing. Significant differences in microbial community structure were observed among the three regions. Nevertheless, Kroppenstedtia eburnea, Aspergillus chevalieri, and Aspergillus oryzae were consistently dominant across all sites. Compared with the other two regions, HTD from Qingdao showed markedly higher abundances of Bacillus velezensis, Bacillus licheniformis, and Bacillus amyloliquefaciens. However, the overall relative abundance of Bacillus spp. in the Huang-Huai region was lower than that typically reported in HTD from Hubei and Guizhou provinces. Physicochemical factors, particularly density and acidity, were the primary drivers of microbial community heterogeneity and flavor profile variation across regions. Metagenomic analysis revealed a relatively complete dimethylpyrazine synthesis pathway in Qingdao Daqu, whereas the other two regions appeared to depend more on multi-species cooperation. Limosilactobacillus fermentum, enriched in Qingdao samples, harbored key acetoin synthesis genes and showed strong potential for tetramethylpyrazine (TTMP) precursor accumulation. Additionally, gene-potential profiling identified Pichia kudriavzevii as the main candidate for higher alcohol production. Subsequent validation confirmed that isolated P. kudriavzevii strains produced 2-phenylethanol, a key bitter volatile compound in sauce-flavor Baijiu. These results elucidate the regional microbial mechanisms underlying flavor formation in HTD for sauce-aroma Baijiu production in the Huang-Huai River Basin and adjacent areas, providing a theoretical basis for targeted starter culture improvement.}, }
@article {pmid42270261, year = {2026}, author = {Vandana,  and Gupta, S and Sharma, R and Pandey, A and Bishnoi, M and Rawal, R and Das, S and Singh, DP}, title = {Polyphenols-rich Indian barberry berries extract alleviates inorganic arsenic exposure-induced cognitive impairments and associated gut microflora alterations.}, journal = {Food research international (Ottawa, Ont.)}, volume = {239}, number = {}, pages = {119548}, doi = {10.1016/j.foodres.2026.119548}, pmid = {42270261}, issn = {1873-7145}, abstract = {Arsenic, a globally prevalent environmental toxin that can lead to neuro-behavioural changes. Oxidative stress and activation of inflammatory cascades are prominent mechanisms underlying these effects. The present study investigated the effects of polyphenol-rich extracts from Berberis aristata (Indian barberry) against inorganic arsenic-induced cognitive impairments in a murine model and presented mechanistic insights into its functional food properties. Response Surface Methodology (RSM)-guided hydro-alcoholic extracts were prepared and chemically characterized for their antioxidant activity, total phenolic contents (TPC) and free radical scavenging activities (RSA). UHPLC and LC-MS-based profiling of polyphenols, anthocyanins, and proanthocyanidins was performed. In-vitro toxicity studies in hepatic and colonic cancer cell lines, followed by in-vivo evaluation of these extracts in inorganic arsenic-exposed mice for spatial navigation tasks and passive avoidance-based learning were performed. Further assessments included neurotransmitter levels, histopathological investigations, qRT-PCR-based gene expression analysis, inflammatory cytokines and oxido-nitrosative stress markers in the brain and gastrointestinal tract, Evan's blue dye-based ileum permeability, and short chain fatty acids (SCFAs) estimation, along with Oxford Nanopore-based 16S rRNA metagenomics in cecal contents and PICRUSt2-based functional prediction of metagenomic data. RSM-optimized methods for polyphenol extraction yielded extracts with high TPC and RSA, with flavanols, phenolic acids, and proanthocyanidins identified as major polyphenols, and no in-vitro toxicity was observed. The extracts significantly prevented arsenic exposure-induced cognitive impairment, altered neurotransmitter turnover, neuroinflammation and gastrointestinal tract inflammation, oxidative stress-induced damage, increased ileum permeability, SCFA alteration, and gut microbial dysbiosis. These findings underscore the therapeutic/preventive potential of this polyphenol-rich extract against environmental toxicant-induced neurotoxicity, potentially involving gut microbiota-associated pathways.}, }
@article {pmid42270391, year = {2026}, author = {Nakaya, Y and Hashimoto, K and Fukushima, K and Fatimah, M and Matsumoto, Y and Funauchi, A and Tsukaguchi, A and Yamauchi, K and Miyazaki, A and Iwahashi, Y and Tone, M and Naito, M and Shiroyama, T and Hirata, H and Takeda, Y and Nakamura, S and Kumanogoh, A}, title = {Mycobacterium brisbanense Pulmonary Disease Treated with a Macrolide-Based Multidrug Regimen: A Case Report.}, journal = {Internal medicine (Tokyo, Japan)}, volume = {}, number = {}, pages = {}, doi = {10.2169/internalmedicine.7351-26}, pmid = {42270391}, issn = {1349-7235}, abstract = {A 73-year-old woman with a history of tracheostomy for tracheomalacia and bronchiectasis developed a worsening productive cough with progressive nodular/bronchocentric opacities on computed tomography. She was diagnosed with Mycobacterium brisbanense pulmonary disease based on repeated sputum culture results. Antimicrobial susceptibility testing revealed a low minimum inhibitory concentration for clarithromycin, and whole-genome sequencing confirmed the absence of the erm gene. Owing to repeated smear positivity and clinical progression, macrolide-based multidrug therapy was initiated, resulting in both clinical and radiographic improvements. To our knowledge, this is the first reported case of M. brisbanense pulmonary disease in Japan, thus highlighting its potential pathogenicity.}, }
@article {pmid42270613, year = {2026}, author = {Deng, C and Cai, H and Luo, K and Liu, S and Chen, Q and Sun, W and Ni, J}, title = {Nitrate-reducing bacteria bridge nitrogen cycling and antibiotic resistance in river ecosystems.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-74161-2}, pmid = {42270613}, issn = {2041-1723}, support = {U2240205//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {River ecosystems, crucial components of the global nitrogen cycle, are increasingly affected by antibiotic pollution. However, the mechanistic interplay between nitrogen cycling and antibiotic resistance genes (ARGs) dissemination remains poorly understood, limiting effective ecological risk assessments. Here, we identify nitrate-reducing bacteria (NRBs), key drivers of denitrification and greenhouse gas mitigation, as dual-functional hubs that co-regulate nitrogen turnover and ARG dissemination under antibiotic stress. By integrating 173 metagenomes and 10 metatranscriptomes from the Yangtze River, we reconstruct 4200 metagenome-assembled genomes (MAGs) and find that NRBs harbor ~69% of actively transcribed ARGs in river microbiomes, with antibiotic pressure as the dominant ecological driver. Simulated microcosms exposed to antibiotic gradients reveal a hormetic response, where environmentally relevant concentrations enhanced both NRB-driven denitrification efficiency and ARG dissemination. Multi-omics analyses further reveal antibiotic-driven horizontal gene transfer as the predominant selective force co-shaping ARG and nitrate reduction gene dynamics, accelerating both nitrogen cycling and ARG spread. These findings establish NRBs as central hubs bridging antibiotic resistance and nitrogen metabolism, providing a mechanistic framework for predicting co-selection dynamics and mitigating cascading ecological impacts. Our work highlights the need to integrate microbial co-metabolic functions into pollution control strategies and redefine ecological risk assessments in antibiotic-polluted ecosystems.}, }
@article {pmid42270686, year = {2026}, author = {Lee, S and Lee, H and Kim, JW and Kim, HJ and Lee, KJ}, title = {Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-53382-x}, pmid = {42270686}, issn = {2045-2322}, abstract = {Objective evaluation of sequencing resolution is crucial for comparing technologies and ensuring reproducibility in microbiome analysis. Specifically, a systematic approach is necessary to quantitatively assess the effect of various platforms and experimental conditions on species-level resolution. Therefore, this study quantitatively evaluated multiple strategies, including 16S V3-V4 (16P), full-length 16S rRNA gene (16F), and whole metagenome shotgun sequencing (WMS), using a commercial DNA-based mock community (MC) and a domestically developed whole-cell MC (Korea MC [KMC]). The WMS strategy included 12 combinations of input DNA concentrations and sequencing output levels. A total of 64 WMS libraries were constructed for KMC samples, and 112 sequencing datasets were analysed. Taxonomic resolution was assessed using an adjusted F1-score integrating detection sensitivity and abundance-level reproducibility. Qualitatively examining the detected species against the expected species across platforms, WMS showed a true positive abundance ratio of over 90%, 16F was observed to have an average of 60%, and 16P was observed to have an average of less than 10%. The combination of 10 ng input and 10 gigabases output consistently yielded the highest species-level resolution. However, reduced performance was observed in some MCs under 1 ng or 100 ng DNA input conditions. Detection sensitivity varied by taxon and condition. Specifically, Streptococcus pneumoniae and Cryptococcus neoformans were detected only under high-input or -output conditions, whereas Escherichia coli exhibited optimal accuracy at intermediate inputs. Acinetobacter species demonstrated reduced resolution as input DNA increased. KMC samples showed species- and format-specific variability in DNA extraction efficiency. This study presents a quantitative evaluation of species-level resolution across sequencing conditions using defined mock communities. The results highlight how sequencing configuration and taxon-specific characteristics can influence detection performance and provide insights for interpreting microbiome sequencing results under different experimental conditions.}, }
@article {pmid42271018, year = {2026}, author = {Mohssen, M and Zayed, AA and Kigerl, KA and Du, J and Smith, GJ and Schwab, JM and Sullivan, MB and Popovich, PG}, title = {Disruption of the spinal cord-gut axis alters microbial dynamics and carbohydrate cross-feeding in the gut.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10447-x}, pmid = {42271018}, issn = {2399-3642}, support = {890085//Craig H. Neilsen Foundation (Neilsen Foundation)/ ; ABI#2149505//National Science Foundation (NSF)/ ; DBI#2022070//National Science Foundation (NSF)/ ; }, abstract = {Spinal cord-gut communication regulates gut bacteria, yet the underlying mechanisms remain poorly understood. Previous studies relied primarily on gene markers with limited functional analysis or genome-resolved snapshots from small cohorts. Here, we assessed microbiome dynamics via genome-resolved metagenomics on 333 samples from male and female C57BL/6 mice collected before and up to six months after surgical disruption of the spinal cord-gut axis. This resulted in 6,635 microbial draft genomes as a foundation for a new "Mouse B6 Gut Catalog" that significantly expands species and strain representation for this widely used laboratory mouse strain. Sampling revealed that disrupted spinal cord-gut signaling causes persistent, lesion-severity-, sex-, and time-specific shifts in microbial community composition, with consistent depletion of Lactobacillus johnsonii. Feeding purified L. johnsonii to spinal cord-injured mice prevented metabolic defects and systemic inflammation caused by disruption of the spinal cord-gut axis. Analyses using genome-resolved and community-based metabolic profiling indicated altered carbohydrate sharing and utilization of gut microbes, potentially depleting L. johnsonii, providing a genome-inferred mechanism for future hypothesis testing. This study improves murine microbiome catalogs, illustrates how metagenome-informed microbial interventions can provide a mechanistic understanding to improve host health, and underscores the vital role of a healthy spinal cord in regulating gut ecosystem function.}, }
@article {pmid42271211, year = {2026}, author = {Ying, K and Song, X and Chen, J and Wang, Y and Wu, H and Zhang, Q and Yang, X and Peng, W and Wu, H and Zhang, W and Zhang, Q}, title = {Metagenomic characterization and genetic profiling of hepatic viromes in Marmota himalayana from the Three-River-Source region of Qinghai Province.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05231-0}, pmid = {42271211}, issn = {1471-2180}, support = {2024-SF-124//the Key research and development and transformation plan of Qinghai Province/ ; 2023YFD1801300//the National Key Research and Development Program of China/ ; }, abstract = {The Himalayan marmot (Marmota himalayana) is a keystone species in the Tibetan Plateau ecosystem and serves as a potential reservoir host for multiple zoonotic pathogens. To characterize its hepatic virome, this study conducted a systematic analysis of 70 marmot liver samples collected from the Three-River-Source Region in Qinghai Province using viral metagenomics. We identified more than 60 viral species belonging to 13 families. The species accumulation curve indicated that the sequencing effort captured the majority of the viral diversity present. Community analysis revealed that the family Retroviridae was the dominant viral group across all samples, though significant heterogeneity was observed among geographically distinct populations. Specifically, the relative abundance of Anelloviridae was markedly higher in the Chengduo group, whereas Parvoviridae exhibited exceptionally high library-specific enrichment in specific libraries. Furthermore, the study successfully assembled complete or near-complete genomic sequences of multiple strains belonging to the families Polyomaviridae, Anelloviridae, and Parvoviridae. Phylogenetic analysis demonstrated that these newly identified viral strains were most closely related to known marmot-origin viruses, clustering within distinct, host-specific evolutionary clades. This clustering pattern indicating host-associated of the viruses with their marmot hosts. Previous virome studies in marmots have primarily focused on the gut, peripheral blood, and other extrahepatic tissues, with no systematic viral metagenomic profiling of the liver in this species to date. The findings offer crucial scientific insights for the early warning and control of wildlife-origin diseases on the Tibetan Plateau.}, }
@article {pmid42271238, year = {2026}, author = {Bi, JG and Wang, YH and Li, PK and Liu, Q and Zheng, X}, title = {Metagenomic insights into regional gut microbiota variation of invasive Spodoptera frugiperda across the Gaoligong Mountains.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05259-2}, pmid = {42271238}, issn = {1471-2180}, support = {202102AA310055//the Supported by the Major Science and Technique Programs of Yunnan Province/ ; YNWRQNBJ2020101//the Young Top Talents of the High-level Talents Training Support Program in Yunnan Province/ ; 202305AM340031//the Lower Nu River, Mountain Agroecosystem, Observation and Research Station of Yunnan Province/ ; 2026J1054//the Yunnan Provincial Department of Education Science Research Fund Project/ ; }, abstract = {BACKGROUND: The invasive pest Spodoptera frugiperda poses a potential threat to the ecological security of western Yunnan, using the Gaoligong Mountains as an important cross-border corridor and overwintering site. However, the potential role of gut microbiota in the local adaptation of S. frugiperda during its invasion remains poorly understood.<br><br>METHODS: Adult populations were monitored using sex pheromone traps, and metagenomic sequencing was performed on larval gut microbiota from different regions of the Gaoligong Mountains. The gut microbial composition and functional potential were analyzed, with specific focus on the microbial traits potentially associated with host adaptation and invasion.<br><br>RESULTS: S. frugiperda populations persisted year-round in the Gaoligong Mountains, with adult activity peaking from January to May. Microbial diversity was highest in southern samples. Enterococcus, typically dominant in S. frugiperda, displayed low abundance in the central and northern regions. In contrast, Providencia emerged as the dominant genus specifically at the Pianma site (PM, along the China-Myanmar border), where the gut microbiota exhibited higher abundance of site-specific functional genes compared to other regions. These genes encoded proteins including type 1 subunit membrane proteins and outer membrane-targeting proteins. Additionally, the PM samples showed a higher relative abundance of genes K07345, K07347, and K15125. Functional annotation highlighted a strong potential for vancomycin degradation and an enrichment of diverse antimicrobial resistance-associated genes, with adeL being the most abundant.<br><br>CONCLUSIONS: These findings suggest that the PM area may represent an important gateway or a priority monitoring site for the transboundary invasion of S. frugiperda, underscoring the urgency of strengthening local management of invasive pests.}, }
@article {pmid42271362, year = {2026}, author = {Zhang, Z and Lu, T and Dong, B and Liu, J and Zhang, Y and Li, S and Liu, H and Li, X and Guan, T and Guo, H and Yan, Q and Lei, Z and Yu, X and Wang, L and Kang, J and Li, L and Zhao, D}, title = {Gut fungal signatures in colorectal cancer and their potential for supporting diagnosis: a multi-cohort metagenomic analysis.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08403-8}, pmid = {42271362}, issn = {1479-5876}, support = {82370563//National Natural Science Foundation of China/ ; 2024RJ018//Outstanding Young Scientific and Technological Talents Project of Dalian/ ; 2023-MSLH-032//Joint Funds of the National Natural Science Foundation of Liaoning Province/ ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is influenced by host factors and environmental exposures that shape gut microbial ecosystems. Although bacterial and viral alterations in CRC have been widely investigated, the role of gut fungi remains underexplored, partly because of their low biomass and the limited availability of well-curated fungal reference genomes.<br><br>METHODS: We conducted a large-scale metagenomic analysis across 9 publicly available cohorts comprising 1,433 fecal samples to characterize CRC-associated fungal alterations and fungal-bacterial co-abundance patterns. The predictive value of microbial signatures was assessed using LASSO and random forest models, with external validation performed in 6 independent cohorts comprising 272 samples.<br><br>RESULTS: Multi-cohort analysis revealed CRC-associated alterations in gut fungal community structure and selected diversity measures. Differential abundance analysis identified 15 fungal species with recurrent changes across cohorts. Among them, Saccharomyces cerevisiae c86 and Trichophyton rubrum c61 showed predominant enrichment in healthy controls, whereas Barnettozyma c122 and Pseudopithomyces c302 showed predominant enrichment in CRC. Fungal-only models exhibited limited standalone predictive capacity. However, integrating fungal features with bacterial biomarkers modestly improved CRC prediction performance compared with bacterial-only models. In external validation, the random forest-based fungal-bacterial model increased the mean AUC from 0.722 to 0.762, with improved AUCs in 5 of the 6 validation cohorts.<br><br>CONCLUSIONS: This study suggests that CRC is associated with gut fungal dysbiosis and supports the exploratory value of gut fungal signatures as adjunctive features in microbiome-based CRC prediction models. These findings highlight the importance of incorporating fungal communities into CRC microbiome research while emphasizing the need for prospective and mechanistic validation.}, }
@article {pmid42271421, year = {2026}, author = {Stanford, J and Supple, H and Collins, CE and Clarke, ED}, title = {Associations between diet, metabolome, gut microbiota and blood pressure in Australian adults.}, journal = {Nutrition journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12937-026-01336-4}, pmid = {42271421}, issn = {1475-2891}, abstract = {PURPOSE: Early metabolomic and microbial markers of blood pressure (BP) dysregulation may be detectable before clinical hypertension develops. This exploratory study aimed to examine associations among dietary intake, BP, metabolomic profiles (plasma and urine), and gut microbiota composition. A secondary aim was to assess whether circulating metabolites mediate relationships between significant dietary factors and BP.<br><br>METHOD: This was a cross-sectional analysis of baseline data from a randomised cross-over trial. Usual dietary intake was assessed using the Australian Eating Survey (AES)[&#xae;] - Heart version Food Frequency Questionnaire. In-clinic BP measurements were measured and participants provided plasma, urine, and stool samples. Plasma and urine were analysed via untargeted metabolomics. Stool samples were collected for shotgun metagenomic sequencing, though metagenomic data was not included in this analysis. Associations between BP, individual metabolites, microbial taxa, and alpha diversity were assessed using linear regression with false discovery rate (FDR) correction. Causal mediation analysis was performed using nonparametric bootstrapping.<br><br>RESULT: Thirty-four Australian adults (mean age: 38.4&#x2009;&#xb1;&#x2009;18.1 years; 52.9% female) had complete data at baseline. Nut intake (servings/day and % energy) was the only dietary factor significantly associated with systolic BP (SBP), with higher intake linked to a 1.13 mmHg reduction. Twenty-nine plasma lipid metabolites were significantly associated with SBP after FDR correction. Of these, nine lipid-related metabolites, particularly 1,2-dilinoleoyl-GPC (18:2/18:2) and 1-linoleoyl-GPC (18:2), were observed to partially mediate the nut-SBP relationship. No urinary metabolites or microbial taxa were significantly associated with BP.<br><br>CONCLUSIONS: In this exploratory cross-sectional study, specific lipid metabolites were associated with SBP and partly accounted for the nut-SBP association. These hypothesis-generating findings suggest potential biomarkers of nut intake and BP regulation, warranting confirmation in larger longitudinal, interventional, and mechanistic studies.<br><br>TRIAL REGISTRATION: Australian New Zealand Clinical Trials Registry (Registration number ACTRN12622001321730, Registration date 12/10/2022).}, }
@article {pmid42271469, year = {2026}, author = {Xing, J and Jiang, Z and Jing, X and Li, Y and Guo, F and Liu, P and Liu, Z and Sun, N}, title = {Analysis of gut microbiota and intestinal mucosal neurotransmitter changes and their correlation in adolescent depression mice.}, journal = {Annals of general psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12991-026-00686-x}, pmid = {42271469}, issn = {1744-859X}, abstract = {BACKGROUND: Adolescent depression is a major mental health disorder with increasing prevalence and substantial long-term consequences. Although growing evidence suggests that the gut-brain axis is involved in depression, the relationships among gut microbiota, intestinal mucosal neurotransmitters, and adolescent depression remain insufficiently understood. This knowledge gap limits a better understanding of the pathophysiological mechanisms underlying adolescent depression and the identification of potential microbiota-related targets. Therefore, this study aimed to investigate alterations in gut microbiota and intestinal mucosal neurotransmitters, as well as their correlations, in an adolescent mouse model of depression.<br><br>METHODS: We established an adolescent depression mouse model using chronic unpredictable mild stress (CUMS), and collected data with the Smart video tracking system. We collected intestinal contents and mucosal tissues from mice. We analyzed gut microbial composition using metagenomic sequencing and quantified mucosal neurotransmitters with liquid chromatography-tandem mass spectrometry (LC-MS/MS). We analyzed correlations among gut microbiota, intestinal mucosal neurotransmitters, and behavioral indicators.<br><br>RESULTS: Mice in the CUMS group exhibited a significantly reduced sucrose preference rate in the sucrose preference test (P&#x2009;<&#x2009;0.001); a significantly prolonged immobility time in the forced swim test (P&#x2009;<&#x2009;0.01); and a significantly decreased total movement distance in the open field test (P&#x2009;<&#x2009;0.01). No significant intergroup difference was observed in the tail suspension test. Regarding the gut microbiome, the CUMS group showed significantly lower Simpson index (P&#x2009;=&#x2009;0.018) and Pielou's evenness index (P&#x2009;=&#x2009;0.022). Beta diversity analysis indicated a statistically significant but modest between-group difference in community structure (ANOSIM R&#x2009;=&#x2009;0.145, P&#x2009;=&#x2009;0.03); this finding was supported by PERMANOVA (Bray-Curtis; pseudo-F&#x2009;=&#x2009;1.675, R&#xb2; = 0.0897, P&#x2009;=&#x2009;0.033). LEfSe (Linear discriminant analysis Effect Size) analysis suggested 27 candidate taxa with discriminatory signals between groups (nominal P&#x2009;<&#x2009;0.05; exploratory). Neurotransmitter analysis demonstrated that levels of 5-HIAA (5-hydroxyindoleacetic acid), 5-HT (serotonin), 5-HTP (5-hydroxytryptophan), and Kyn (kynurenine) in the colon were significantly decreased in the CUMS group, whereas levels of PA (phenylethylamine) and NE (norepinephrine) were significantly elevated (P&#x2009;<&#x2009;0.05). Spearman correlation analysis found that Lactobacillus and Lactobacillus acidophilus correlated positively with sucrose preference and negatively with immobility in the forced swim test. Lactobacillus acidophilus also showed a positive correlation with 5-HT pathway metabolites: 5-HIAA, 5-HT, 5-HTP, and Kyn.<br><br>CONCLUSION: Adolescent mice exposed to CUMS showed depression-relevant behavioral alterations, shifts in gut microbiota composition, and changes in 5-HT pathway metabolites. Gut microbiota dysbiosis was significantly associated with alterations in 5-HT pathway metabolites. Because this study is correlational, causal relationships require validation in future interventional studies.}, }
@article {pmid42271556, year = {2026}, author = {Kaushik, S and Borck, J and Flatow, E and Frishman, WH and Aronow, WS}, title = {Blood Culture-Negative Infective Endocarditis: A Review.}, journal = {Cardiology in review}, volume = {}, number = {}, pages = {}, pmid = {42271556}, issn = {1538-4683}, abstract = {Blood culture-negative infective endocarditis (BCNIE) represents a diagnostically challenging subset of infective endocarditis in which routine blood cultures remain negative despite fulfillment of Duke-ISCVID diagnostic criteria. BCNIE arises primarily from prior antibiotic exposure, infection with fastidious or nonculturable organisms, or noninfectious conditions that mimic endocarditis. Common fastidious pathogens include Coxiella burnetii, Bartonella species, Brucella species, Tropheryma whipplei, fungi, and nutritionally variant streptococci. Because delayed pathogen identification may postpone targeted therapy, BCNIE is associated with increased diagnostic complexity and substantial morbidity and mortality. Modern evaluation relies on a multimodal strategy integrating serologic testing, prolonged culture incubation, histopathology, advanced molecular diagnostics, and multimodality imaging. Emerging molecular techniques, including 16S/18S polymerase chain reaction and metagenomic next-generation sequencing, have significantly improved microbiologic yield, particularly from excised valve tissue, and are now incorporated into updated Duke-ISCVID criteria. Echocardiography remains central to diagnosis, while cardiac computer tomography and 18 fluoro-2-deoxy-D-glucose positron emission tomography/computer tomography provide complementary value in prosthetic valve disease and detection of periannular complications. Management requires empiric antimicrobial therapy followed by organism-directed treatment once a pathogen is identified, with surgery frequently necessary for heart failure, uncontrolled infection, fungal disease, or structural complications. Multidisciplinary endocarditis teams are increasingly recognized as essential to optimizing outcomes in this complex disease process.}, }
@article {pmid42271557, year = {2026}, author = {Wassel, MA and Makabe-Kobayashi, Y and Iqbal, MM and Huang, C and Amano, M and Shimizu, A and Mandario, MAE and Takatani, T and Sakakura, Y and Hamasaki, K}, title = {Tetrodotoxin (TTX) reshapes the functional potential of the gut microbiome in juvenile tiger pufferfish (Takifugu rubripes) across salinity gradients.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42271557}, issn = {2524-4671}, support = {22K05822 and 25K09271//JSPS KAKENHI/ ; No. JURCAOSIRG23-08//Interdisciplinary Collaborative Research Program of the Atmosphere and Ocean Research Institute, The University of Tokyo/ ; }, abstract = {BACKGROUND: The gut microbiota of aquatic organisms responds dynamically to environmental stressors such as salinity fluctuations. However, how microbial communities respond to combined environmental and dietary stressors, and how these interactions influence functional potential, remains incompletely understood. Here, we investigated whether dietary administration of tetrodotoxin (TTX), a neurotoxin naturally accumulated by juvenile tiger pufferfish (Takifugu rubripes), alters gut bacterial community composition and functional potential across salinity gradients.<br><br>RESULTS: Juvenile T. rubripes were reared under four salinity conditions (34.0, 17.0, 8.5, and 2.1 ppt) and fed either a control or TTX-containing diet (1.22 MU/g). Integrated 16S rRNA gene amplicon and shotgun metagenomic analyses revealed that salinity was the primary driver of gut microbiota structure, with only 5.1% of amplicon sequence variants (ASVs) shared across salinity levels. In contrast, TTX ingestion induced salinity-dependent shifts in specific bacterial taxa rather than broad community restructuring. Core taxa, including Arcobacteraceae, Mycoplasma, Brevinema, and Vibrio, were consistently detected across treatments but exhibited pronounced changes in relative abundance and functional potential under salinity and toxin stress. Metagenomic profiling indicated that Arcobacteraceae encode genetic modules for amino acid and B vitamin biosynthesis that are absent or incomplete in the host genome, suggesting metabolic complementarity. TTX ingestion reduced the genetic representation of these biosynthetic pathways at specific salinities, particularly those associated with Arcobacteraceae. Conversely, phenylalanine biosynthesis potential enriched in TTX-fed fish, primarily associated with Vibrio spp., indicating a possible microbial functional adaptation to toxin administration. Despite these microbiome and functional shifts, TTX ingestion did not affect host growth.<br><br>CONCLUSIONS: Dietary neurotoxin administration reshaped gut microbiome functional profiles in a salinity-dependent manner, highlighting microbiome plasticity and improving our understanding of host-microbiota-environment interactions relevant to aquaculture health management.}, }
@article {pmid42271572, year = {2026}, author = {Peugnet, G and Pisapia, C and Ménez, B and Watkinson, M and Lecourt, L and Peugnet, N and Bouchez, J and Bruxelles, L and Gérard, E}, title = {Ghost-rocks' microbiota: metagenomic insights into their influence on the biogeochemistry of karstic cave and groundwater.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag047}, pmid = {42271572}, issn = {1574-6941}, abstract = {Microbial communities in the critical zone drive key geochemical processes, but many subsurface habitats remain poorly characterized. Ghost-rock karst systems in particular represent unexplored microbial niches. Here, we provide the first genome-resolved metagenomic comparison of ghost-rock and groundwater microbial communities from the Sterkfontein karst system (South Africa). Ghost-rock and groundwater communities host distinct taxonomic and metabolic assemblages. Groundwater communities are dominated by chemolithotrophs capable of oxidizing sulfur- and nitrogen-bearing compounds, and by heterotrophs degrading refractory, plant-derived organic matter. In contrast, primary producers in ghost-rocks likely rely on atmospheric chemosynthesis via trace gas oxidation, while glycogen metabolism and necromass recycling point to adaptations to oligotrophic and fluctuating hydrological conditions. Groundwater taxa with metal-interacting pathways may initiate bedrock colonization via metal oxidation, whereas ghost-rock communities include potential metal reducers that could drive iron and manganese oxide dissolution and influence trace element mobility. Together, these results underscore ghost-rocks as active microbial and geochemical hot spots within karst systems that may play a non-negligible role on biomineralization/bioweathering processes and on shaping (sub)terrestrial landscapes and global biogeochemical cycles.}, }
@article {pmid42272236, year = {2026}, author = {van der Meulen, LWJ and Bergmans, ME and Assil, S and Klarenbeek, N and de Kam, ML and Tibboel, AJ and Brach, T and Herpers, BL and Frieling, J and de Jong, V and Freyee, B and van Doorn, MBA and Rissmann, R and Niemeyer-van der Kolk, T}, title = {S. aureus colonization and clinical symptoms remain stable upon topical XZ.700 treatment: Results of a double-blind randomized clinical trial in patients with mild to moderate atopic dermatitis.}, journal = {British journal of clinical pharmacology}, volume = {}, number = {}, pages = {}, doi = {10.1002/bcp.70630}, pmid = {42272236}, issn = {1365-2125}, support = {//Micreos Human Health B.V./ ; }, abstract = {AIM: Recovering dysbiosis may improve atopic dermatitis (AD) symptoms. XZ.700 is a recombinant chimeric endolysin that specifically targets Staphylococcus aureus and could be a new treatment option for patients with AD. The aim of this first-in-human study was to evaluate the safety, tolerability and efficacy of topical XZ.700 and explore the pharmacodynamic effects in patients with mild to moderate AD.<br><br>METHOD AND MATERIALS: This study consisted of Part A and Part B. In Part A, subjects were randomized and received XZ.700 10&#xa0;&#x3bc;g/g, XZ.700 30&#x2009;&#x3bc;g/g, XZ.700 100&#x2009;&#x3bc;g/g or vehicle twice daily for 7&#xa0;days on nonlesional skin and on all lesions (1%&#x2009;&#x2264;&#x2009;BSA&#x2009;&#x2264;&#x2009;10%). In Part B, subjects received XZ.700 100&#x2009;&#x3bc;g/g or vehicle on all lesions twice daily for 14&#x2009;days (1%&#x2009;&#x2264;&#x2009;BSA&#x2009;&#x2264;&#x2009;15%). Clinical scores and patient-reported outcomes were recorded. Pharmacodynamic measurements were taken.<br><br>RESULTS: In total, 35 patients completed the study. Tolerability of XZ.700 was acceptable. XZ.700 100&#x2009;&#x3bc;g/g showed no evidence of effect on cultured S. aureus (estimated difference -52.9% CFU/mL; 95% CI -88.4% to 90.8%), oSCORAD (1.03; 95% CI -5.20 to 7.26) or EASI (-0.534; 95% CI -2.48 to 1.41). Furthermore, XZ.700 treatment did not result in a significant reduction in the relative abundance of S. aureus via metagenomics or other pharmacodynamic outcomes.<br><br>CONCLUSION: Tolerability and safety of short-term topical administration of XZ.700 100&#x2009;&#x3bc;g/g for 14&#x2009;days were acceptable in most participants; however, some local application-site events occurred, and one hypersensitivity reaction led to discontinuation. XZ.700 did not demonstrate target engagement or clinical benefit vs. vehicle under the tested conditions.}, }
@article {pmid42272618, year = {2026}, author = {Top, FK and Boussiengui, LG and Sall, NC and Faye, M}, title = {First identification of Molluscum contagiosum poxvirus from human in Senegal.}, journal = {Journal of public health in Africa}, volume = {17}, number = {1}, pages = {1586}, pmid = {42272618}, issn = {2038-9922}, abstract = {Herein, we report on the first identification of a human case of Molluscum contagiosum virus (MOCV) in Senegal. In 2024, a male child living in Diamniadio, Dakar region, with no history of travel, tested positive for MOCV. The aetiology was identified using metagenomic sequencing in the framework of the ongoing preparedness activities for the 2024 mpox public health emergency of international concern (PHEIC). Given the overlapping clinical features of MOCV infection and mpox, further research on MOCV is warranted in the West African region, particularly in the current context of high mpox circulation.}, }
@article {pmid42272701, year = {2026}, author = {Luo, L and Guo, Z and Chen, W and Zheng, Y and Chen, C and Li, Q and Wang, N and Ji, Y and Hua, J}, title = {Mycobacterium abscessus infection in a young man with cystic fibrosis: a case report and literature review.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1737211}, pmid = {42272701}, issn = {2296-2360}, abstract = {BACKGROUND: Cystic fibrosis (CF) is a rare autosomal recessive disorder caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Although relatively common in Caucasian populations, CF is rare in China, where it frequently presents with non-specific respiratory symptoms, leading to delayed diagnosis and frequent coinfections with multidrug-resistant pathogens.<br><br>CASE REPORT: A 21-year-old man presented with a 6-year history of recurrent productive cough and intermittent fever over the past 6 months. Imaging revealed bronchiectasis with evidence of infection. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid identified Staphylococcus aureus and Mycobacterium abscessus. Further investigations revealed pancreatic lipomatosis, congenital absence of seminal vesicles, and fat-soluble vitamin deficiencies. CF diagnosis was confirmed by elevated sweat chloride concentration (88&#x2005;mmol/L) and biallelic CFTR mutations. Clinical stability was achieved through a quadruple antimycobacterial regimen (linezolid, moxifloxacin, azithromycin, and minocycline) combined with systemic supportive care. CFTR modulator therapy was deferred due to limited access and financial constraints.<br><br>CONCLUSION: We report a case of CF in a Chinese patient presenting with nontuberculous mycobacterial infection, a condition rarely documented in East Asian populations. We provide a review of the relevant literature, aiming to emphasize the importance of early recognition of CF, personalized antimicrobial strategies, and improved access to essential medications.}, }
@article {pmid42272754, year = {2026}, author = {Wu, H and Shi, L and Wang, C and Liang, Y and Huang, C}, title = {Integrative metagenomic and metabolomic analysis reveals a gut microbiota-metabolite-immune axis in pediatric allergic rhinitis with functional constipation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1779298}, pmid = {42272754}, issn = {2235-2988}, abstract = {OBJECTIVE: This study aimed to delineate the alterations in the gut microbiome and host amino acid metabolism in children with comorbid allergic rhinitis and functional constipation (ARFC), and to explore their links with clinical allergy markers.<br><br>METHODS: We performed shotgun metagenomic sequencing and amino acid-targeted metabolomics on fecal samples from 19 children with ARFC and 16 age-matched healthy controls (HC). Microbial community structure, differentially abundant taxa, and metabolic profiles were analyzed. Integrative analyzes, including correlation networks and machine learning modeling, were employed to investigate microbiota-metabolite-host interactions.<br><br>RESULTS: Significant beta-diversity distinction was found between ARFC and HC gut microbiota (PCoA R[2]=0.228, P&#xa0;=&#xa0;0.001). ARFC children exhibited enrichment of mucin-degrading Bacteroidota (e.g., Bacteroides, Phocaeicola) and depletion of beneficial Bacillota (e.g., Bifidobacterium, Blautia). Metabolomics identified 50 differentially abundant metabolites, with widespread downregulation of immunomodulatory amino acids including L-glutamine and &#x3b3;-aminobutyric acid (GABA). Enriched pathways involved mTOR and FoxO signaling, and neurotransmitter synapses. Integration revealed significant correlations between specific microbial genera (e.g., Bacteroides, Proteus) and metabolites (e.g., kynurenine), and between gut species (e.g., Bacteroides thetaiotaomicron) and serum IgE levels. A machine learning model integrating key microbial and metabolic features, evaluated under a rigorous leave-one-out cross-validation framework, demonstrated robust discriminative performance in this cohort (AUC&#xa0;=&#xa0;0.946).<br><br>CONCLUSION: This multi-omics study unveils a distinct "gut dysbiosis-metabolite dysregulation-immune dysfunction" axis in ARFC children. The synergistic shift towards a mucolytic, pro-inflammatory microbiota alongside deficient immunomodulatory metabolite production, which correlates with clinical allergy markers, provides a novel mechanistic framework for this comorbidity and highlights potential diagnostic biomarkers for future validation.}, }
@article {pmid42272841, year = {2026}, author = {Qiu, X and Qiang, L and Wang, Y and Li, B and Lei, Z and Wang, J}, title = {Triptolide clears Staphylococcus aureus infection by targeting XIAP to induce host apoptosis while maintaining gut microbiota homeostasis.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1834558}, pmid = {42272841}, issn = {1663-9812}, abstract = {BACKGROUND: Staphylococcus aureus (SA) remains a global health threat due to its increasing drug resistance and intracellular persistence, which compromise the conventional antibiotic efficacy. Host-directed therapy (HDT) has emerged as a promising alternative by modulating host immunity. With multi-targeting and immunomodulatory properties, traditional Chinese medicine (TCM) monomers represent ideal candidates for HDT. However, their ability to promote host immunity-mediated SA clearance remains largely unexplored.<br><br>METHODS: Forty-one TCM monomers potentially regulating host apoptosis, a core mechanism of the host innate immune defense against intracellular pathogens, were screened to identify a compound that promotes the clearance of intracellular SA and methicillin-resistant SA (MRSA). The mechanism was investigated in infected macrophages using transcriptomics, proteomics, molecular dynamics simulations, and biochemical assays. The physiological function of the TCM monomer was examined in infected mice through lung pathology and multi-omics analysis, including transcriptomics, proteomics, metagenomics, and metabolomics.<br><br>RESULTS: Triptolide was identified as a potent facilitator of host immunity-mediated intracellular clearance of SA and MRSA, without exerting direct bactericidal effects. Mechanistically, triptolide directly binds to the X-linked inhibitor of apoptosis protein (XIAP), disrupting its interaction with caspases to relieve their inhibition and thereby induce apoptosis. Furthermore, in murine infection models, triptolide treatment reduced bacterial loads, alleviated inflammation, and induced macrophage apoptosis in lungs, concurrently maintaining microbiota homeostasis and improving metabolic function.<br><br>CONCLUSION: This study establishes a proof of concept for triptolide as a HDT candidate against SA and MRSA infections, which not only enhances host apoptosis-mediated pathogen clearance but also maintains host microbiota and metabolic homeostasis.}, }
@article {pmid42272967, year = {2026}, author = {Frisch, S and Aliyazdi, S and Rehner, J and Schmartz, G and Gevaerd, C and Latta, L and Veldung, B and Becker, SL and Keller, A and Schaefer, UF and Loretz, B and Vogt, T and Lehr, CM}, title = {Staphylococcal proliferation on skin models to investigate novel anti-infective treatments against dysbiosis.}, journal = {Bioengineering &amp; translational medicine}, volume = {11}, number = {3}, pages = {e70124}, pmid = {42272967}, issn = {2380-6761}, abstract = {Inflammatory skin conditions like Acne inversa are characterized by dysbiosis, an imbalance of commensal and pathogenic bacteria, posing challenges for specific treatments. Consequently, we investigated how biofilm formation, low-nutrition skin environments, and air interfaces influence susceptibility to anti-infective treatments in mixed bacterial cultures. To achieve this in a cost-effective and reproducible manner, we developed a simplified substrate made of gelatin, hyaluronic acid, chondroitin sulphate, and alginate (=Gel-Alg). This in vitro model simulates biofilm cultivation on skin surfaces for aerobic bacteria. We selected Staphylococcus aureus and Staphylococcus epidermidis as two clinically relevant strains, which are also abundant in Acne inversa. We tested single and mixed cultures under different conditions: (i) nutrient broth, (ii) Gel-Alg substrate, (iii) EpiDerm™ commercial skin model, and (iv) ex vivo human skin. Proliferation, measured by colony-forming units, was comparable across most conditions, except for human skin. Metabolic activity, assessed via Presto Blue staining, revealed significant differences. Dual-species cultivation and quantification by viability PMA qPCR indicated dominance of S. epidermidis over S. aureus in skin-like environments. Treatments with biofilm-dissolving rhamnolipids, the antibiotic vancomycin, and combinations thereof demonstrated varying efficacy in single and mixed cultures. While the drug combination could almost completely eradicate staphylococcal biofilms in broth, susceptibility varied in skin-like models and moreover strongly depended on temperature (37°C vs. 32°C). In conclusion, this study suggests that reductionistic models, while mimicking key features, could be valuable for early selective antimicrobial drug development for specific applications like Acne inversa therapy.}, }
@article {pmid42273068, year = {2026}, author = {Moradi, Z and Alinizi, HR and Mehrvar, M}, title = {Genomic characterization of broad bean wilt virus 1 (Fabavirus alphaviciae) from Iran including phylogenetic relationships.}, journal = {3 Biotech}, volume = {16}, number = {7}, pages = {256}, pmid = {42273068}, issn = {2190-572X}, abstract = {UNLABELLED: The complete genome of a broad bean wilt virus 1 (BBWV1; Fabavirus alphaviciae) isolate (BBWV1-IR) was recovered from an uncultivated Plantago lanceolata plant in Iran by viral metagenomics and validated by RT-PCR. RNA1 (5,779 nucleotides) contains a single ORF encoding replication-associated proteins (Pro-Co, HEL, VPg, Pro, RdRp), while RNA2 (3,414 nucleotides) harbors two overlapping ORFs encoding the large and small coat proteins (LCP and SCP) and two additional proteins (VP47 and VP37). Comparative analyses revealed that BBWV1-IR shared 81-92% and 79.5-83% nucleotide identity in RNA1 and RNA2, respectively, with global isolates. No intragenic recombination was detected; however, reassortment analysis identified three distinct events, including one involving BBWV1-IR, whose RNA1 segment likely originated from Austrian (major) and UK (minor) parental lineages. ORF1 and ORF2a showed substantial variability and high haplotype diversity, with VP37 displaying the greatest nucleotide diversity. Evolutionary analyses indicated that BBWV1 genes were predominantly shaped by negative selection, with essential replication proteins (HEL and Pro) under strong purifying pressure, while VP47 and VP37 experienced more relaxed constraints. A few codons in ORF1 and ORF2a were under episodic positive selection. Phylogenetic analysis clustered 19 non-recombinant isolates into two major clades (A and B), with BBWV1-IR positioned in subclade I of clade A alongside geographically distant isolates, reflecting human-mediated long-distance dispersal. Incongruent clustering of ORF1 and ORF2a in several isolates supports RNA segment reassortment as a key driver of novel variant emergence. Collectively, these findings highlight the roles of mutation, selection, reassortment, and gene flow in shaping BBWV1 evolution, exemplified by the Iranian isolate.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04905-w.}, }
@article {pmid41759875, year = {2026}, author = {Nuranindita, R and Natanegara, S and Wusono, AD and Amirudin, FA and Hitipeuw, D and Rahayu, AA and Daud, MM and Yuwanita, MR and Qanita, NG and Saputra, EY and Jun, H and Jeon, BY and Lee, MR and Ju, JW and Malik, MDA and Garjito, TA and Han, JH and Muh, F}, title = {Metatranscriptomic analysis of Anopheles species from Menoreh Hills endemic area in Central Java, Indonesia.}, journal = {Acta tropica}, volume = {277}, number = {}, pages = {108033}, doi = {10.1016/j.actatropica.2026.108033}, pmid = {41759875}, issn = {1873-6254}, mesh = {Animals ; *Anopheles/microbiology/virology/genetics/classification ; Indonesia ; *Microbiota ; *Mosquito Vectors/virology/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Gene Expression Profiling ; Transcriptome ; Metagenomics ; *Viruses/classification/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND: The mosquito microbiome plays a crucial role in vector competence and disease transmission dynamics, yet comprehensive metatranscriptomic analyses of Anopheles species microbiomes remain limited, particularly in malaria-endemic regions like the Menoreh Hills of Central Java, Indonesia. This study aimed to characterize the microbial and viral community compositions of five Anopheles species and their potential implications for vectorial capacity.<br><br>METHODS: Metatranscriptomic analysis was performed on five Anopheles species (An. barbirostris, An. flavirostris, An. kochi, An. maculatus, and An. vagus) collected from the Menoreh Hills endemic area using RNA sequencing, taxonomic classification, and functional annotation approaches.<br><br>RESULTS: Proteobacteria emerged as the dominant bacterial phylum across all species, with variations in relative abundance of other taxa. Baculoviridae emerged as the overwhelmingly dominant viral family across all species, with other families including Bunyavirales, Herpesvirales, and Nucleocytoviricota present at much lower abundances. Diversity indices revealed An. vagus with the highest microbial diversity and An. barbirostris with the lowest. Adherence-related virulence factors were predominant, particularly in An. maculatus and An. vagus, while carbohydrate-active enzymes AA1 and GT35 were abundant across all species.<br><br>CONCLUSIONS: This study examines microbiome and virome across five Anopheles species from Menoreh Hills. Betabaculovirus dominated virome, while bacterial and fungal communities showed species-specific patterns. Analyses revealed virulence differences. Study limitations include pooled samples. The results provide data for malaria research.}, }
@article {pmid42259326, year = {2026}, author = {Martins, MF and Govindan, R and Almaghlouth, NK and Kirby, JE and Kentoffio, KJ and Farmakiotis, D and Le-Mahajan, A}, title = {A fatal case of Legionella micdadei prosthetic valve endocarditis diagnosed by plasma microbial cell-free DNA metagenomic sequencing.}, journal = {The Lancet. Infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/S1473-3099(26)00223-9}, pmid = {42259326}, issn = {1474-4457}, abstract = {We report a fatal case of Legionella micdadei prosthetic valve endocarditis in a patient who was immunocompromised, characterised by an indolent outpatient course followed by rapid clinical deterioration into mixed shock secondary to valve dehiscence and sepsis. The diagnosis was made by plasma microbial cell-free DNA metagenomic next-generation sequencing (mcfDNA-mNGS) and confirmed by buffered charcoal yeast extract culture of valve tissue. This case underscores the diagnostic limitations of conventional methods in culture-negative endocarditis, the evolving role of mcfDNA-mNGS in culture-negative endocarditis, and the absence of current culture-negative endocarditis guidelines addressing timely diagnosis for patients who are at risk of rapid deterioration. In this Grand Round, we briefly review the state of diagnostics for culture-negative endocarditis and the particularities of Legionella endocarditis. We also propose a framework for deciding when to consider early metagenomic testing, balancing the potential strengths of this technology with its limitations and cost.}, }
@article {pmid42259450, year = {2026}, author = {Yang, W and Wang, X and Li, H and Liu, W and Chen, Z and Ren, B and Guo, T and Guo, J}, title = {Enhanced co-removal of nitrate and tetracycline from wastewater by iron-nitrogen-doped carbon: synergistic role of pyridinic nitrogen and iron.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135105}, doi = {10.1016/j.biortech.2026.135105}, pmid = {42259450}, issn = {1873-2976}, abstract = {Co-pollution of nitrate and tetracycline (TC) poses a critical barrier to efficient biological treatment due to impaired electron transfer, diminished microbial metabolic activity, and disrupted community structure. To address this challenge, this study synthesized an iron-nitrogen-doped carbon material (Fe-NC) featuring electron-withdrawing pyridinic nitrogen and Fe active sites. Under co-contaminated conditions, the nitrate and TC removal efficiencies of the TC/Fe-NC200 system were 100 % and 96 %, which were 21.27 and 2.18 times higher than those of the TC system. Material characterization indicated that Fe-NC might act as an electron transfer station, promoting the removal of nitrate and TC through Fe[3+]/Fe[2+] cycling. Electrochemical analyses showed that Fe-NC promotes the secretion of cytochrome c and flavin mononucleotide, accelerating extracellular electron transfer. Enzyme activity assays indicated that Fe-NC enhances intracellular electron transfer by activating key redox enzymes and upregulating associated gene expressions. Electron transfer system activity and metagenomic analysis further demonstrated that Fe-NC improves microbial respiration and increases the abundance of dominant taxa such as Bacteroidota (11.96 %) and Chryseobacterium (12.00 %), which support both TC degradation and microbial stress tolerance. These mechanistic insights establish a novel, bio-electroactive function for Fe-NC, in which the synergistic effects of Fe redox cycling and pyridinic nitrogen coordination led to improved electron flow, microbial function, and pollutant breakdown. This work not only reveals a previously unexplored pathway for biological co-removal of nitrate and antibiotics but also provides a scalable strategy for enhancing bioremediation efficiency in complex wastewater systems.}, }
@article {pmid42259455, year = {2026}, author = {Wang, Y and Huang, Y and Yin, D and Gong, B and Fan, G}, title = {A segmented electron donor dosing strategy for enhancing thiosulfate-driven partial denitrifying efficiency: Insights into sulfur oxidation pathway, electron transfer and metagenomic microbial ecology.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135106}, doi = {10.1016/j.biortech.2026.135106}, pmid = {42259455}, issn = {1873-2976}, abstract = {Thiosulfate-driven partial denitrification (TPD) is a highly efficient denitrification process that exhibits good stability when coupled with Anammox. This study aimed to enhance the performance of the TPD system by employing different electron donor dosing strategies. The data show that the NO3[-]-N removal efficiency (NRE) and NO2[-]-N accumulation efficiency (NAE) in the segmented dosing group reached 98 % and 90 %, respectively. The study indicates that segmented electron donor dosing significantly enhances the activity of the electron transport chain. Specifically, Complex I and Complex III are associated with electron utilization by nitrate reductase (Nar) and nitrite reductase (Nir). The increased activity of Complex I and the inhibited activity of Complex III in the segmented dosing group contribute to improved NRE and NAE. Metagenomic analysis revealed that Thiobacillus predominated and served as the key functional species for Nar, Nir, and sulfur oxidation. Combined with qPCR analysis, segmented dosing significantly increased the expression levels of functional genes and elevated the NarG/(NirK + NirS) ratio, which further facilitated the accumulation of NO2[-]-N. Furthermore, the segmented dosing group possessed a complete sulfur oxidation pathway capable of fully oxidizing S2O3[2-] to SO4[2-], suggesting a reduced metabolic potential for S[0] production within the system. Overall, this study offers a potential strategy for ensuring a stable supply of nitrite in future anaerobic ammonium oxidation processes.}, }
@article {pmid42259841, year = {2026}, author = {Deng, F and Fan, Y and Yan, J and Zhang, X and Guo, Y and Li, M and Peng, Y and Zhao, L and Liu, F and Zheng, Y and Deng, B and Deng, J and Chen, S and Jiang, H and Chai, J and Zhao, J and Li, Y}, title = {Genome-resolved and culture-based atlas of the feline gut microbiome enables host-adapted probiotic development.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01038-z}, pmid = {42259841}, issn = {2055-5008}, abstract = {Domestic cats (Felis catus) depend on their gut microbiome for metabolism, immunity, and pathogen defense, yet its genomic characterization remains limited. We combined large-scale metagenomics and culturomics to define the feline gut microbiome and identify indigenous probiotic candidates. Analysis of 412 feline fecal metagenomes produced 2852 strain-resolved metagenome-assembled genomes (MAGs) grouped into 514 species-level genome bins, including 106 putative novel taxa. This catalog revealed 24 core species and two enterotypes: ET-P, deaminated by Prevotella, and ET-CB, enriched for Collinsella, Blautia, Bifidobacterium, Ligilactobacillus, MAG-based screening prioritized 113 candidate probiotic species. Culturomics recovered 2904 isolates representing 110 species-level taxa, including 75 putative novel species and a candidate novel genus. Six feline-derived isolates were selected for downstream testing, and five exhibited favorable probiotic traits in vitro, including acid and bile tolerance, anti-Escherichia coli activity, and favorable cytokine responses. In a pathogenic Escherichia coli-induced dirrhea model in cats, a five-strain indigenous consortium improved fecal scores and reduced IL-2, IL-1β, and IL-6, with TNF-α suppression superior to antibiotics or a commercial probiotic. These results establish FelMGDB as a resource for feline microbiome research and highlights indigenous probiotics as promising interventions for feline gut health.}, }
@article {pmid42260308, year = {2026}, author = {Li, L and DU, L}, title = {[Clinical value of cerebrospinal fluid metagenomic next genera-tion sequencing in diagnosing neonatal intracranial infections].}, journal = {Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. Medical sciences}, volume = {}, number = {}, pages = {1-10}, doi = {10.3724/zdxbyxb-2025-0965}, pmid = {42260308}, issn = {1008-9292}, abstract = {OBJECTIVES: To evaluate the diagnostic performance of cerebrospinal fluid (CSF) metagenomic next generation sequencing (mNGS) for neonatal intracranial infections and its impact on clinical decision making.<br><br>METHODS: A retrospective observational study was conducted. Neonates admitted to the Children's Hospital, Zhejiang University School of Medicine from 2020 to 2025 with suspected intracranial infection who underwent CSF mNGS were enrolled. The sensitivity of mNGS and its concordance with CSF culture and PCR were calculated. Clinical impact was assessed using predefined criteria, and samples were categorized into positive impact and no impact groups to identify independent factors influencing the clinical utility of mNGS.<br><br>RESULTS: Among 61 neonates with suspected intracranial infection, 48 were confirmed. Pathogens were identified in 18 cases, of which 9 were detected exclusively by mNGS, accounting for 50% of etiological diagnoses. The sensitivity of mNGS was 31.3% (95% CI: 18.7%-46.3%), higher than that of culture PCR (18.8%, 95% CI: 8.9%-32.6%), but the difference was not statistically significant (P=0.15). The positive and negative concordance rates between mNGS and culture PCR were 66.7% (95% CI: 29.9%-92.5%) and 76.9% (95% CI: 60.7%-88.9%), respectively. mNGS positively influenced clinical decisions in 37.7% (23/61) of patients: 12 cases with positive results guided etiological diagnosis and treatment adjustment, and 11 cases with negative results led to antibiotic de escalation or discontinuation. Multivariate analysis identified a positive mNGS result as an independent factor associated with positive clinical impact (OR = 22.127, P<0.01).<br><br>CONCLUSIONS: CSF mNGS provides valuable support in etiological diagnosis and clinical decision making for neonatal intracranial infections.}, }
@article {pmid42260359, year = {2026}, author = {Lu, F and Li, Y and Chen, X and Chen, Y and Li, C and Nong, G and Liu, J and Wei, Q}, title = {Community-acquired pseudomonas aeruginosa pneumonia in immunocompetent children: a study of 7 cases.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13768-8}, pmid = {42260359}, issn = {1471-2334}, support = {AD22035219//Guangxi Clinical Research Center for Pediatric disease/ ; 2025GXNSFAA069702//The National Natural Science Foundation of Guangxi/ ; }, abstract = {BACKGROUND: To characterize the clinical features and outcomes of community-acquired Pseudomonas aeruginosa (PA) pneumonia in immunocompetent children.<br><br>METHODS: A retrospective analysis was conducted on seven immunocompetent children with community-acquired PA pneumonia hospitalized between January 2015 and June 2025. Pneumonia was defined by acute respiratory symptoms with new radiographic infiltrates. PA infection was confirmed by culture from sterile sites/lower respiratory tract or metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid.<br><br>RESULTS: All patients were male (n&#x2009;=&#x2009;7). Age distribution was as follows: 1-12 months (n&#x2009;=&#x2009;3), 13-36 months (n&#x2009;=&#x2009;1), 37-60 months (n&#x2009;=&#x2009;1), and &#x2265;&#x2009;61 months (n&#x2009;=&#x2009;2). Median age at onset was 18.0 months (IQR: 8.0-123.0). All patients presented acutely with fever and cough; two developed respiratory failure within 72&#xa0;h. Additional clinical features included dyspnea (n&#x2009;=&#x2009;4), lung rales (n&#x2009;=&#x2009;4), hemoptysis (n&#x2009;=&#x2009;3), chest pain (n&#x2009;=&#x2009;2), and wheezing (n&#x2009;=&#x2009;1). Chest imaging showed lobar consolidation (n&#x2009;=&#x2009;5) or mass-like consolidation (n&#x2009;=&#x2009;2). A total of seven cases were identified, with PA confirmed by culture in four patients and by mNGS of bronchoalveolar lavage fluid in three patients. All isolates were susceptible to anti-pseudomonal &#x3b2;-lactam antibiotics except aztreonam. Complications included definite or suspected empyema (n&#x2009;=&#x2009;5), pyopneumothorax (n&#x2009;=&#x2009;3), and bacteremia (n&#x2009;=&#x2009;2). Three patients required pediatric intensive care, two received invasive mechanical ventilation, two underwent closed thoracic drainage, and one required decortication. There were no deaths, but 4 patients sustained significant residual lung injury secondary to necrotizing pneumonia.<br><br>CONCLUSION: Although rare, community-acquired PA pneumonia in immunocompetent children is associated with severe disease and pulmonary complications. Initial therapy with anti-pseudomonal &#x3b2;-lactam antibiotics appears effective in improving outcomes. Repeated cultures are recommended in the cases who remain symptomatic.}, }
@article {pmid42260652, year = {2026}, author = {Le Moigne, A and Andrei, A&#x15e; and Pernthaler, J}, title = {Linking stochastic assembly to functional potential, redundancy, and trait patterns in bacterial communities.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02442-5}, pmid = {42260652}, issn = {2049-2618}, abstract = {BACKGROUND: Stochastic processes shape the taxonomic composition of microbial assemblages. However, their impact on community functioning remains subject to debate, mainly due to functional redundancy. Little is known on the links between stochasticity and functional redundancy. Here, we assessed how stochastic assembly influences redundancy, functional potential, and trait patterns in twenty parallel lake-water bacterial communities enriched under originally identical conditions. Using gene- and genome-resolved metagenomics, we tested whether incomplete dispersal of genes required for cellobiose uptake and processing-"functional dispersal limitation"-explained variation in cellobiose use.<br><br>RESULTS: Several communities were composed of genomes that held the required genes but these communities did not utilize cellobiose, rejecting the notion of "functional dispersal limitation." We quantified redundancy across major functional categories such as signaling, regulation, and transport. Functional redundancy reflected the stochastic assembly from the total set of genomes. It was lower within than between communities, likely reflecting limiting similarity vs. habitat-driven functional convergence. Category-resolved patterns of functional dissimilarity were conserved across various diversity scales and even across randomly sampled sets of 28,000 bacterial genomes from the Genome Taxonomy Database. Among these categories, functions mediating environmental and microbe-to-microbe interactions and genetic information processing had highest and lowest dissimilarity, respectively. Aquatic bacteria showed the greatest differentiation across most categories.<br><br>CONCLUSIONS: Stochastic assembly of bacterial communities shaped the functional trait distribution. Functional redundancy inferred from the metagenomes largely reflected the trait patterns of the total set of MAGs. Functional redundancy and dissimilarity varied according to functional category. Comparison with a null model constructed from genomes of the GTDB allowed us to identify functional selection with various strengths according to the functions. While stochasticity diversified community composition, functional patterns remained conserved, reflecting shared ecological and evolutionary constraints tempered by habitat. Hence, using null models as a reference is important to interpret functional redundancy and may provide a more accurate understanding of how stochastic assembly and ecological constraints shape community-level functional organization. Video Abstract.}, }
@article {pmid42260783, year = {2026}, author = {Hao, M and Sha, Y and Gao, J and Niu, J and Xu, Y}, title = {Concurrent Spinal Dural Arteriovenous Fistula and Varicella-Zoster Virus Meningoencephalitis Unmasked by Corticosteroid-Associated Deterioration: A Case Report on the Diagnostic Value of Serial mNGS.}, journal = {Current medical imaging}, volume = {}, number = {}, pages = {}, doi = {10.2174/0115734056496224260602072444}, pmid = {42260783}, issn = {1573-4056}, abstract = {BACKGROUND: Concurrent spinal dural arteriovenous fistula (SDAVF) and varicella-zoster virus (VZV) meningoencephalitis are exceptionally rare, and overlapping features can delay diagnosis. This case adds to the literature by illustrating how corticosteroid exposure before exclusion of vascular and infectious mimics may be followed by neurological deterioration, and by emphasizing the diagnostic value of serial metagenomic next-generation sequencing (mNGS).<br><br>CASE PRESENTATION: A 48-year-old man developed insidious bilateral lower-limb weakness that progressed to numbness, sphincter dysfunction, and near-paralysis. Initial spinal magnetic resonance imaging showed diffuse thoracolumbar cord lesions; cerebrospinal fluid studies were mildly inflammatory, and myelitis was suspected. He received methylprednisolone pulse therapy followed by oral corticosteroids without improvement. One month later, he presented with fever, severe headache, vomiting, worsening paralysis, and altered mental status. Cerebrospinal fluid demonstrated marked pleocytosis, hypoglycorrhachia, and elevated protein, and mNGS detected abundant VZV sequences. Brain imaging showed hydrocephalus, meningeal enhancement, multifocal ischemic lesions, and intracranial arterial stenoses, consistent with VZV meningoencephalitis and vasculopathy. After external ventricular drainage, intravenous acyclovir, dexamethasone for cerebral edema, and empirical anti-tuberculosis therapy, serial mNGS showed a reduced VZV burden. Repeat spinal imaging revealed tortuous perimedullary vessels and hemosiderin deposition, and angiography confirmed SDAVF from the left T10 intercostal artery. The fistula was coagulated. At 12-month follow-up, he regained slight right-leg movement and partial sensory recovery above L1.<br><br>CONCLUSION: Progressive myelopathy with atypical inflammatory features should prompt vascular evaluation and pathogen testing. Serial mNGS can identify coexisting infection, guide therapy, and help avoid hazardous empirical corticosteroid use when the diagnosis remains uncertain.}, }
@article {pmid42261054, year = {2026}, author = {Foster, NR and Holman, LE and Armbrecht, L and Courtin, J and Jensen, T and Pedersen, MW and Schreiber, L and Schroeder, H and Seersholm, FV and Zampirolo, G and Bohmann, K and Zimmermann, HH}, title = {A Roadmap for Using Hybridisation Capture-Based Target Enrichment of Ancient Environmental DNA in Palaeoecology.}, journal = {Molecular ecology resources}, volume = {26}, number = {5}, pages = {e70152}, doi = {10.1111/1755-0998.70152}, pmid = {42261054}, issn = {1755-0998}, support = {101105307//European Union's Horizon Europe Marie Sklodowska-Curie Actions/ ; 856488//European Union's Horizon 2020 Research and Innovation Program/ ; //Independent Research Fund Denmark/ ; DP250100886//Australian Research Council (ARC)/ ; DP250103420//Australian Research Council (ARC)/ ; }, abstract = {Recovering ancient DNA from environmental samples is transforming the way we understand historical ecosystems. While high-throughput sequencing of the total DNA in environmental samples (shotgun metagenomic sequencing) reveals the taxonomic contents of these samples, the genetic signals of some taxa (e.g., eukaryotes) can be weak compared to the background levels of DNA from organisms such as bacteria, requiring deep sequencing approaches that are costly. Thus, to increase cost-effectiveness, pre-sequencing enrichment of target DNA can be advantageous. One technique to enrich this target DNA is hybridisation capture, where short RNA or DNA baits are designed to match, bind and isolate specific stretches of DNA. Hybridisation capture has previously been applied to recover DNA from ancient skeletal remains, but it is only beginning to emerge as an approach to characterise organisms from ancient environmental samples. Thus, there is limited information on establishing hybridisation capture workflows for ancient environmental DNA applications, including the limitations and advantages. This mini review focuses on establishing a roadmap for the applications of hybridisation capture to ancient environmental DNA samples.}, }
@article {pmid42262077, year = {2026}, author = {Ran, S and Fu, S and Dai, T and Wei, H and Peng, J and Zhou, Y}, title = {Multi-omics profiling of gut-serum axis dynamics in gestational sows with different reproductive performance.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0113225}, doi = {10.1128/spectrum.01132-25}, pmid = {42262077}, issn = {2165-0497}, abstract = {UNLABELLED: Sustainable swine production hinges on optimizing sow reproductive efficiency, yet mechanisms driving healthy litter size and weak piglet rates remain unclear. This study categorized sows into high (group H) and low (group L) healthy litter size groups based on median performance. Multi-omics analyses (16S rRNA sequencing, metagenomics, and serum metabolomics) revealed distinct fecal microbiota and metabolic profiles between groups. The results showed significant differences in microbiota composition between groups L and H. Group H exhibited a marked increase in Bacteroidetes abundance (particularly Prevotella sp. CAG1092), concurrent with reduced Firmicutes populations. Metabolomic analysis identified 197 differentially abundant metabolites, with 85 metabolites significantly enriched in group H. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis indicated that the differentially abundant metabolites were mainly involved in amino acid synthesis and metabolism, and multiple amino acid metabolic pathways were associated with polyamine synthesis. The correlation results showed a significant correlation (P < 0.05) between these metabolites and litter size as well as litter weight. For instance, Prevotellaceae NK3B31 abundance positively correlated with L-alanine, urea, and securinine, while Prevotella sp. CAG1092 exhibited direct associations with reproductive performance. These findings suggest that gut microbiota dysbiosis may disrupt amino acid homeostasis and polyamine regulation, potentially serving as mechanistic links to reproductive efficiency. Reproductive performance dynamically shapes gut microbiota and systemic metabolism in gestating sows, with litter size influencing fecal metabolite diversity and microbial structure. This integrative analysis establishes a framework for improving both sow productivity and economic viability in pig farming.<br><br>IMPORTANCE: Optimizing sow reproductive efficiency is vital for sustainable swine production. This study identifies gut microbiota dysbiosis and metabolic imbalances as key drivers of litter size variability. Sows with lower productivity displayed marked reductions in Bacteroidetes (notably Prevotella spp.) and disrupted amino acid/polyamine metabolism, directly linking microbial shifts to poorer litter outcomes. Integrated multi-omics approaches revealed strong correlations between specific taxa (Prevotella sp. CAG1092), metabolites (L-alanine and urea), and reproductive metrics, underscoring the gut-reproductive axis. These findings elucidate mechanistic connections between microbial ecosystems and host physiology, providing a foundation for targeted strategies like microbiota modulation or dietary interventions to enhance metabolic homeostasis and farrowing success. By bridging microbial ecology with livestock productivity, this work advances practical solutions to improve both animal health and agricultural profitability within precision farming frameworks.}, }
@article {pmid42262118, year = {2026}, author = {Sommer, AJ and Ferrandis-Vila, M and Mamerow, S and Berens, C and Menge, C and Wei, S and Wang, Q and Aarestrup, FM and Otani, S and Sapountzis, P}, title = {Impact of ceftiofur administration and Escherichia coli inoculation on the calf fecal microbiome.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0050126}, doi = {10.1128/msystems.00501-26}, pmid = {42262118}, issn = {2379-5077}, abstract = {The cattle gastrointestinal tract harbors a diverse community of microorganisms, including pathogenic and commensal strains of Escherichia coli. Antimicrobial use in cattle can disrupt the gut microbiome, leading to shifts in bacterial diversity and abundance. Here, we combined shotgun metagenomics and single-cell sequencing to assess how ceftiofur antibiotic treatment impacted microbial diversity and structure. At the start of the experiment, ceftiofur was administered intramuscularly in parallel with the inoculation of a cocktail of extended-beta-lactamase-producing E. coli strains to simulate environmental exposure and acquisition of resistant strains while animals are under antibiotic treatment. Fecal samples were collected from both the antibiotic-treated (ceftiofur and inoculation) and control (inoculation only) calves over the course of 35 days. Read mapping to genome and gene databases showed substantial differences in microbial richness and beta diversity between treatment groups. Treatment group-enriched taxa included Bacteroidaceae and Fibrobacter, which were more abundant in samples that did not receive ceftiofur, and Akkermansia in ceftiofur-treated calves. In ceftiofur-exposed animals, we observed a gradual loss of virulence factors alongside increased abundances of beta-lactam resistance genes, including cfxA5 and cfxA6, likely encoded by CAG-485 (Muribaculaceae). We further profiled individual cells using single-cell sequencing, which revealed a high number of Clostridium carrying macrolide resistance genes lnu(P) and mph(N) in both ceftiofur-treated and control samples. Overall, our complementary approaches reveal distinct remodeling of the calf microbiome following antibiotic and E. coli administration, tied to key functional genes that can be assigned to specific genera or recurrently detected across diverse taxa.IMPORTANCECattle serve as natural reservoirs of zoonotic strains of Escherichia coli, which can cause severe gastrointestinal infections in humans. Antibiotic usage on cattle farms can drive the emergence of antimicrobial-resistant bacterial strains and alter the underlying cattle gastrointestinal microbiome. Consequently, there is a need to understand how antibiotic administration impacts population dynamics of cattle rumen and intestinal microbes. In this study, we combined both shotgun metagenomics and single-cell genomics on feces from ruminating calves to determine microbiome changes following administration of both ceftiofur and E. coli cocktails. We observed considerable variation in the prevalence and abundance of virulence factors, antimicrobial resistance-related genes, and taxa with key roles in animal nutrition and health between the microbiomes of antibiotic-treated and antibiotic-free calves, with potential implications for their subsequent development and overall well-being.}, }
@article {pmid42262136, year = {2026}, author = {Iacovacci, J and Cannon, N and McCulloch, JA and Rancati, T and Trinchieri, G}, title = {Differential co-occurrence analysis: a method to extract ecological modules from clinical microbiome data.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0028426}, doi = {10.1128/msystems.00284-26}, pmid = {42262136}, issn = {2379-5077}, abstract = {UNLABELLED: The human microbiota plays a pivotal role in health, with widespread alterations implicated in conditions ranging from inflammatory disorders to cancer. While correlation-based network analyses have illuminated ecological interactions within these communities, the host environment uniquely mediates microbial relationships, demanding new methods to capture dynamic, condition-dependent modules of species interactions. Here, we present a statistical framework termed differential co-occurrence analysis, which identifies blocks of taxa whose collective presence is strengthened or weakened under distinct host states. By leveraging recent advances in metagenomics that enable detailed taxonomic profiling and higher-order interaction discovery, our method transcends traditional pairwise correlation constraints. Conceptually akin to associative rule mining, it diverges through the integration of robust statistical modeling, directly extracting interactions that differ significantly between conditions. This approach offers a refined lens to dissect microbiota ecology and could pave the way for new insights into microbiome-associated disease mechanisms.<br><br>IMPORTANCE: The research on the role of the intestinal microbiota in the onset of cancer and as a modulator of anticancer treatments, including chemotherapeutics and immune checkpoint inhibitors, is helping medicine to identify novel strategies for cancer prevention, for the delivery of more effective treatments, and in reducing treatment side effects and complications. Within this context, it is of crucial importance to approach the analysis of clinical microbiome data with an ecology-oriented perspective and to develop bioinformatics tools able to identify functional interactions in bacterial communities of patients from observational cohort studies. Clinical microbiome datasets are typically high dimensional, comprising numerous taxa measured across relatively few samples. This imbalance increases the risk of statistical overfitting and undermines the robustness of analytical findings. However, recent advances in metagenomic bioinformatics pipelines and reference databases have enabled the comprehensive extraction of genetic information from microbiome samples, facilitating the precise characterization of bacterial species presence and absence. In our manuscript, we describe a statistical computational method that we named differential co-occurrence analysis, which focuses on the analysis of the co-presence of microbiota taxa across samples associated with different host conditions. The proposed method can reveal modules of interacting taxa that are strengthened or weakened when the host condition changes (e.g., when passing from a healthy state to a disease state). The method is general and applicable to a broad range of ecological datasets featuring presence/absence data structures. Furthermore, the method accommodates the analysis of higher-order co-occurrence patterns beyond pairwise co-occurrence, thereby enabling the investigation of higher-order interactions, whose detection and identification are a major challenge in ecological network analysis.}, }
@article {pmid42262316, year = {2026}, author = {Gao, B and Chen, L and Xu, W and Liu, G and Wei, M and Shen, W and Tu, P and Shan, J}, title = {Uncovering the Hidden Risks: How PLA and PLGA Microplastics Disrupt Gut Microbiota and Metabolic Health.}, journal = {Chemical research in toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.chemrestox.5c00556}, pmid = {42262316}, issn = {1520-5010}, abstract = {Biodegradable plastics are often promoted as an eco-sustainable alternative to conventional polymers. However, their potential to degrade into microplastics still poses significant health risks. Commonly used materials such as polylactic acid (PLA) and poly(lactic-co-glycolic acid) (PLGA) have been widely adopted across various industries. While the toxicity of PLA microplastics has been studied extensively, the biological effects of PLGA microplastics remain largely unknown. Through metagenomic sequencing and untargeted metabolomic profiling, we evaluated the impacts of both PLA and PLGA microplastics on gut bacteria, fungi, virulence factors, microbial metabolic pathways, and metabolites in feces, serum, and liver tissue in this study. Our results demonstrate that both types of biodegradable microplastics disrupt gut microbiota and host metabolic homeostasis. PLA exposure provoked more pronounced changes in gut bacteria, fungi, virulence factors, and fecal and hepatic metabolites. In contrast, microbial metabolic pathways and serum metabolites were more strongly affected by PLGA. Several altered features were common to both microplastics, including enrichment of hepatic metabolic pathways related to valine, leucine, and isoleucine biosynthesis; one-carbon pool by folate; glycine, serine, and threonine metabolism; pantothenate and CoA biosynthesis; taurine and hypotaurine metabolism; and cysteine and methionine metabolism. Other disturbances were material-specific, such as UMP biosynthesis pathways, which were altered exclusively by PLA, while palmitate biosynthesis and unsaturated fatty acid biosynthesis were affected only by PLGA. These findings advance our understanding of the distinct and shared health risks posed by different biodegradable microplastics, providing a clearer basis for assessing their long-term safety.}, }
@article {pmid42262390, year = {2026}, author = {Weissman, JL and Walling, A and Ducklow, H and Zakem, EJ}, title = {Genomic Traits Associated with Copiotrophy Decouple from Maximum Growth Rate Predictions Along Temperature Gradients.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag147}, pmid = {42262390}, issn = {1751-7370}, abstract = {Maximum growth rate is often used as a primary axis of functional variation in studies of microorganisms, in part because emerging tools make it straightforward to estimate from genomic and metagenomic data. However, temperature, via its influence on reaction kinetics, may act as a confounder in studies that measure genomic signatures of growth optimization across environments. Observations suggest that growth optimization need not always indicate rapid growth. For example, strong temperature gradients are the norm across much of the world's oceans, where deep-ocean microbes show elevated signals of genomic growth optimization relative to the faster-growing communities at the surface. Looking across environments, we find a negative relationship between genomic growth optimization and optimal growth temperature, leading to the potential decoupling of genomic traits associated with copiotrophy from maximum growth rate, particularly when measured along a temperature gradient. Our results suggest that, as a result of temperature's confounding effects, genomic signatures of growth optimization often better predict the ecological roles and functional genomic content of microorganisms than do growth rates themselves. Finally, we suggest reframing copiotrophy as growth beyond a thermodynamic baseline maximum growth rate, rather than in relation to a static rate cutoff.}, }
@article {pmid42263510, year = {2026}, author = {Ergunay, K and Bourke, BP and Kamau, M and Fustec, B and Osborne, CJ and Mutura, J and Lebunge, R and Ochieng, G and Onyango, T and Cruz, A and Campos, M and Pott, MC and Romero, U and Deakins, AG and Paoli, J and Liao, HM and von Fricken, ME and McDermott, EG and Jiang, L and Grieco, JP and Achee, NL and Linton, YM}, title = {Unbiased long read metagenomic screening reveals diverse jingmen tick virus genomes across continents.}, journal = {Virology}, volume = {623}, number = {}, pages = {110999}, doi = {10.1016/j.virol.2026.110999}, pmid = {42263510}, issn = {1096-0341}, abstract = {Jingmen tick virus (JMTV) is an emerging tick-associated virus related to flaviviruses. Substantial information gaps remain on the epidemiology and public health impact of JMTV, despite evidence for symptomatic human infections, detection in potential zoonotic reservoirs and widespread global circulation. Using an unbiased metagenomics approach based on long read sequencing, we screened field-collected ticks (n = 3232) of various life stages from locations of spillover risk across continents, from Eastern Africa (Kenya), Central America (Belize), and North America (Arkansas, United States). Signals of virus detection were observed in 32.9% of the pooled samples comprising adult, nymph and larvae stages. JMTV genome segments were assembled in 16.7% of the pools with initial virus detection. Adult ticks comprising Amblyomma gemma, Hyalomma rufipes, Rhipicephalus. evertsi and Rhipicephalus pulchellus from Kenya yielded complete JMTV genome assemblies. Evidence for tick-associated arbo-jingmenviruses was described for the first time in Belize, identified as complete genome segments encoding for non-structural virus proteins in pooled larvae. Analysis of globally distributed complete JMTV genomes revealed a considerable geographic partitioning of diversity and two significantly supported virus clades and genomic underrepresentation in many regions with documented virus activity. Further investigations and expanded screening are needed to elucidate JMTV and arbo-jingmenvirus global epidemiology.}, }
@article {pmid42263617, year = {2026}, author = {Chen, C and Li, J and Wang, F and Cheng, M and Sheng, T and Ahmed, Z and Hu, J and Zhou, Y}, title = {Auxiliary fermentation with Pediococcus acidilactici C1 reshapes flavor formation in sufu: An integrated metagenomic, flavoromic and non-targeted metabolomic deciphering.}, journal = {Food chemistry}, volume = {521}, number = {}, pages = {149979}, doi = {10.1016/j.foodchem.2026.149979}, pmid = {42263617}, issn = {1873-7072}, abstract = {Sufu, a traditional Chinese fermented soybean product, relies on spontaneous microbial succession for flavor, leading to high variability. Starter-assisted fermentation improves flavor; this study explores sufu flavor differences and mechanisms between spontaneous and Pediococcus acidilactici C1-inoculated processes. The findings demonstrated that inoculation with P. acidilactici C1 markedly enhanced the diversity and concentration of flavor compounds in sufu. Notably, 12 key taste-active free amino acids were detected, with glutamate up by 14% and aspartic acid showing an approximate 20-fold increase. A total of 15 key volatile flavor compounds were characterized, among which 8 were newly uncovered, namely ethyl 2-methylbutanoate, ethyl acetate, ethyl butyrate, ethyl caprylate, ethyl 2-ethylhexanoate, ethyl propionate, isoamyl acetate and 3-octanol. Metagenomics revealed enrichment of genes related to carbohydrate transport, amino acid/lipid metabolism, while non-targeted metabolomics confirmed metabolic remodeling. Multi-omics analyses showed P. acidilactici C1 reprogrammed carbon flux and boosted amino acid/lipid-derived volatile biosynthesis, enabling flavor-enhancing starter development.}, }
@article {pmid42263645, year = {2026}, author = {Xing, Y and Huang, X and Luo, J and Wei, D and Chen, H and Sun, X}, title = {Active carbon-fixing microbes and their role in carbon fixation in mangrove sediments.}, journal = {Marine pollution bulletin}, volume = {231}, number = {}, pages = {119962}, doi = {10.1016/j.marpolbul.2026.119962}, pmid = {42263645}, issn = {1879-3363}, abstract = {Mangroves are vital blue carbon ecosystems, yet the microbial drivers of carbon fixation in their soils remain poorly understood. Here, this study investigated the patterns of drivers carbon-fixing microbes and their functional genes across three representative mangrove bays in the Beibu Gulf of the South China Sea (Lianzhou Bay, Maowei Sea and Zhenzhu Bay) using an integrated geochemical and metagenomic approach. The findings showed that: (1) the distribution of total organic carbon (TOC) in mangrove soils was significantly influenced by tidal zonation and mangrove plants, with TOC content in the mid-tidal zone consistently exceeding that in adjacent mudflats by 1.5- to 2.3-fold (p < 0.01); (2) potential dominant carbon fixation pathways inferred from soil microbial communities may vary significantly across different areas, including chemolithoautotrophic taxa (e.g., Nitrospira, Thiobacillus), phototrophic cyanobacteria (e.g., Synechococcus, Cyanobium), and mixotrophic assemblages. Correspondingly, the relative abundances of key functional genes (e.g., narH, narG, fabB, oadB) exhibited significant differences among these bays; (3) environmental factors including salinity, nutrients, and heavy metals jointly influenced the accumulation of carbon fixation genes and their microbial hosts, collectively explaining 63.9% of community variation at the species level. This study provides a mechanistic understanding of microbial functional diversity that underpins carbon cycling in mangrove soils, offering quantitative insights for the conservation and management of blue carbon ecosystems under anthropogenic pressures.}, }
@article {pmid42263665, year = {2026}, author = {Ueland, K and Elahi, T and Rasmussen, M and Wolfe, AE and Purcell, H and Chakka, SR and Mirimo-Martinez, M and Persinger, H and Johnson, K and Boynton, AM and McMillen, K and Byelykh, M and Biernacki, MA and Yeh, AC and Ali, N and Manjappa, S and Wuliji, N and Fredricks, D and Bleakley, M and Holmberg, LA and Peled, JU and Schenk, J and Raftery, D and Ma, J and Hill, GR and Neuhouser, ML and Lee, SJ and Markey, KA}, title = {Plant-based whole-food diets are feasible during auto-HCT and are associated with dose-dependent microbiome modulation.}, journal = {Blood advances}, volume = {}, number = {}, pages = {}, doi = {10.1182/bloodadvances.2026020270}, pmid = {42263665}, issn = {2473-9537}, abstract = {Plant-based whole foods may represent a tractable approach to mitigating microbiome disruption and improving outcomes in patients undergoing auto-HCT for multiple myeloma, a population in whom intestinal dysbiosis has been linked with inferior survival. We conducted a single-arm clinical trial at our center, in which participants undergoing auto-HCT (n = 22) received fresh, pre-prepared, plant-based meals for 5 weeks spanning conditioning, neutropenia, and early recovery, with the goal of supporting the consumption of nutrient-dense, high-fiber foods. The primary endpoints were feasibility and tolerability, defined by successful enrollment, and patient-reported intake of study meals. Dietary intake was quantified using prospective food diaries and 24‑hour dietary recall surveys. Secondary endpoints included changes in gut microbiome composition and function assessed by shotgun metagenomic sequencing and stool short-chain fatty acid (SCFA) measurements. The intervention was feasible and generally well tolerated, with all participants consuming delivered meals to some degree, with adherence sufficient to support planned dietary and correlative analyses. Greater intake of study meals was associated with more pronounced shifts in gut microbial communities, including enrichment of SCFA-producing taxa and compositional changes consistent with a fiber-responsive microbiome. Stool SCFA concentrations increased from baseline to the end of the intervention, suggesting a functional impact of the dietary strategy on microbial metabolite production during the peri-transplant period. These findings demonstrate that a plant-based meal delivery intervention is implementable during auto-HCT and suggest dose-dependent modulation of the gut microbiome and its metabolic output. The trial is registered at ClinicalTrials.gov (NCT06559709).}, }
@article {pmid42263908, year = {2026}, author = {Figueroa-Ortiz, C and Schoninger, S and Chan, JL and Bermudez, TA and Li, Y and Cander, S and Mcgonagle, B and Bacon, CW and Kalchiem-Dekel, O and Chawla, M and Lin, R and Tamari, R and Shaffer, BC and Perales, MA and Redelman-Sidi, G and Shahid, Z and Loganathan, R and Kamboj, M and Papanicolaou, G and Lee, YJ}, title = {Tuberculosis After Allogeneic Hematopoietic Cell Transplant: A 15-Year Case Series Highlighting Diagnostic Challenges.}, journal = {Transplantation and cellular therapy}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jtct.2026.06.007}, pmid = {42263908}, issn = {2666-6367}, abstract = {BACKGROUND: Tuberculosis (TB) is an uncommon but potentially fatal complication after allogeneic hematopoietic cell transplant (HCT). Diagnosis is often delayed due to nonspecific clinical presentations, limited sensitivity of screening tests for latent TB infection, and slow turnaround of conventional TB diagnostic methods.<br><br>OBJECTIVE: The study aim is to describe the clinical and diagnostic characteristics of allogeneic HCT recipients with TB in the era of molecular and sequence based diagnostic methods.<br><br>STUDY DESIGN: We conducted a retrospective review of microbiologically confirmed TB cases among HCT recipients at a tertiary cancer center from 2010 to 2025. We detail clinical, demographic, and diagnostic characteristics including metagenomic next-generation sequencing (mNGS) testing of bronchoalveolar lavage (BAL) and blood (Eurofins Viracor, Lenexa, KS) for two individuals.<br><br>RESULTS: Ten patients were diagnosed with active TB at a median of 122 days post-HCT (range: 36-2,557). The median age was 53 years, and 6 were males. Except for one patient, all patients were foreign-born. Pre-HCT TB screening was performed in 7 patients; however, only 3 had positive (tuberculin skin test, n=1; interferon-gamma release assay [IGRA], n=2), and 1 had indeterminate IGRA results. All patients had abnormal CT chest findings compatible with latent TB. Nine of 10 patients presented with either fever or cough, while one patient was asymptomatic with incidental radiographic abnormalities. TB was diagnosed by MTB PCR in 8 cases, 4 patients had disseminated TB, and 3 died. mNGS results were available in two patients. In both cases MTB was detected in BAL, and in one, MTB was detected in the blood. Among 9 patients with available susceptibility testing data, moxifloxacin resistance was identified in one case.<br><br>CONCLUSIONS: In our cohort, post-HCT TB occurred mainly in foreign-born patients. Infection was diagnosed early after transplant and was frequently disseminated, with high mortality. These results underscore the limitations of current screening methods, and the diagnostic challenges of post-HCT TB.}, }
@article {pmid42263990, year = {2026}, author = {Meng, Q and Zeng, W and Zhang, J and Liu, H and Li, S and Peng, Y}, title = {Efficient nutrient removal from low C/N municipal wastewater using a phototrophic biofilm system integrating simultaneous nitrification-denitrification and phosphorus removal (SND).}, journal = {Environmental research}, volume = {}, number = {}, pages = {124859}, doi = {10.1016/j.envres.2026.124859}, pmid = {42263990}, issn = {1096-0953}, abstract = {Microalgae-bacteria systems based on phosphorus-accumulating organisms (PAOs) offer low-energy and low-carbon-emission solutions for wastewater treatment, but their performance declines with low carbon-to-nitrogen (C/N) ratios municipal wastewater. In this study, a phototrophic biofilm system capable of coupling simultaneous nitrification-denitrification with phosphorus removal (P-SNDPRB) was developed to enhance low C/N ratios (3.32-4.11) municipal wastewater treatment. Before biofilm integration, total nitrogen (TN) removal was below 75%. After integration, TN removal increased to over 82%, while organic matter and phosphorus removal efficiencies remained at 85% and 90% in the P-SNDPRB system, respectively. Microalgae photosynthesis supplied oxygen to the biofilm, enabling denitrification. Chemometric and metagenomic analyses revealed denitrification and phosphorus accumulating metabolism (PAM) as key pathways for nitrogen and phosphorus removal. Flow cytometry sorting showed that biofilm spatial distribution promoted synergistic interactions among Accumulibacter, Competibacter, Nitrosomonas, Chlorella, and Cyanobacteria, further enhancing nitrogen and phosphorus removal. This study provides a low-energy and sustainable approach for the treatment of municipal wastewater with a low C/N ratio.}, }
@article {pmid42264042, year = {2026}, author = {Zheng, Y and Li, X and Jia, Z and Qi, Y and Yin, H}, title = {Microbial-mediated attenuation of carbonaceous organics within urban sewers: Insights from in-pipe sediments microbial communities and metagenomic analyses.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135134}, doi = {10.1016/j.biortech.2026.135134}, pmid = {42264042}, issn = {1873-2976}, abstract = {Sewer sediments consist of diverse microbial communities that actively engage in the degradation of carbonaceous organics, adversely impacting influent quality of wastewater treatment plants. Yet, the underlying biological mechanisms within actual sewers remains underexplored. This study elucidated the microbial-mediated attenuation mechanisms in actual gravity sewers, with integrated approaches including sediments scanning electron microscopy, flow cytometry, extracellular polymeric substances (EPS) characterization, and metagenomic sequencing. Along the 3.56 km trunk sewer, chemical oxygen demand and five-day biological oxygen demand decreased by 55.1 % and 53.9 %, respectively. A spatial shift from anoxic to anaerobic conditions was observed along the sewer, accompanied by increased sediment microbial cell density (2.17 × 10[6]-2.57 × 10[7] cells/g SS) and EPS accumulation (2.22-17.69 mg/g VSS). The downstream enrichment of tryptophan- and tyrosine-like EPS components was consistent with the formation of larger and denser sediment aggregates (21.45-51.55 μm). Metagenomic analysis revealed a spatial shift in carbonaceous organics transformation potential, with upstream sediments enriched in fermentation-related microbial communities and genes associated with simple organic hydrolysis, while downstream reaches showed higher relative abundances of genera and genes associated with complex fatty acid and amino acid transformation through Embden-Meyerhof-Parnas pathway and tricarboxylic acid cycle. Downstream enrichment of pentose phosphate pathway-related genes further supported increased microbial resilience and biosynthetic potential under low-oxygen conditions. These findings underscore the sewer's role as pre-bioreactors, and strengthening sewer maintenance to minimize sediments accumulation is crucial for preventing excessive in-sewer organic matter loss.}, }
@article {pmid42264047, year = {2026}, author = {Xu, YY and Tan, X and Dang, CC and Zhao, ZC and Fang, R and Fan, L and Ren, NQ and Xie, GJ and Wu, YN}, title = {Metagenomic insights into Thermus-mediated sulfur oxidation, nitrogen cycling, and thermoadaptation in thermophilic autotrophic denitrification bioreactors.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135137}, doi = {10.1016/j.biortech.2026.135137}, pmid = {42264047}, issn = {1873-2976}, abstract = {Thermus species are widely recognized as a key group of heterotrophic denitrifiers mediating carbon, nitrogen, and sulfur cycling in geothermal habitats, and have attracted extensive research attention for their thermostable enzyme resources. However, their autotrophic denitrification potential remains poorly characterized, and the systems-level mechanisms underlying their thermal adaptation remain incompletely understood. This study presents three high-quality metagenome-assembled genomes (MAGs) of Thermus from autotrophic sulfur-based denitrification bioreactors. These MAGs encode the complete genetic potential for the Calvin-Benson-Bassham cycle, reductive tricarboxylic acid cycle, and 3-hydroxypropionate bicycle for inorganic carbon fixation. Thermus strains employ a distinct sulfide oxidation route: HS[-] is first oxidized to polysulfides or glutathione persulfide by fccAB, then condensed with sulfite to form thiosulfate via rhodanese, and finally completely oxidized to sulfate by complete sox cluster. T. scotoductus (MAG1) carries genes for nitrate reduction (narGHI) and dissimilatory nitrate reduction to ammonium (nrfA and nrfH). As conspecific strains, MAG2 and MAG3 harbor abundant denitrification genes (nar, nirK, norBC), indicating strong substrate-driven metabolic plasticity. A protein-protein interaction network further elucidated the systems-level thermoadaptive survival mechanisms of T. scotoductus, identifying chaperone-mediated protein homeostasis and DNA repair-dependent genomic stability as core adaptive strategies, alongside orphan nodes (e.g., aceE, lpd, nuoC) with potential independent functions. Collectively, these findings advance our understanding of Thermus' metabolic plasticity, offer valuable thermostable resources for high-temperature wastewater treatment and industrial applications, and bridge critical knowledge gaps in the autotrophic metabolism and thermoadaptive regulation of thermophilic bacteria-laying a robust genomic foundation for the development and optimization of high-temperature biotechnological processes.}, }
@article {pmid42264152, year = {2026}, author = {Gibbons, JA and Nelson, RM and Dabrowski, CN and Narkhede, A and Szalacha, LA and Kneusel, ML and Maru, JS and Huszar, MR and Hoang, LK and Schiavo, V and Eddins, AC and Georgieff, MK and Neu, J and Donovan, SM and Groer, MW and Ho, TTB}, title = {Enteral Iron Dose Effect on Iron Storage, Intestinal Barrier, and Gut Microbiome in Preterm Infants: A Randomized Clinical Trial.}, journal = {The American journal of clinical nutrition}, volume = {}, number = {}, pages = {101389}, doi = {10.1016/j.ajcnut.2026.101389}, pmid = {42264152}, issn = {1938-3207}, abstract = {BACKGROUND: Preterm infants routinely receive enteral iron supplementation to support growth, replace phlebotomy losses, and prevent iron deficiency. However, concerns regarding potential harms, including those on the gut microbiome, have contributed to recommendations for lower dosing.<br><br>OBJECTIVE: To compare the effects of two enteral iron doses on gut health in very-low-birth-weight preterm infants. We hypothesized that higher iron dose would increase abundances of pathogenic bacteria, intestinal inflammation, and barrier dysfunction.<br><br>METHODS: This randomized, double-blind clinical trial assigned preterm infants born <1500 g to receive either the recommended dose, 2 mg/kg/day, or a higher dose of 6 mg/kg/day of total enteral iron. The primary outcome was the fecal microbiome after 2 weeks on iron, assessed by metagenomic sequencing. Secondary outcomes included biomarkers of intestinal inflammation and barrier function (fecal calprotectin, urinary claudin-3, and urinary intestinal fatty acid-binding protein). Iron status, adverse events, and auditory brainstem response latencies at 36 weeks postmenstrual age were also evaluated.<br><br>RESULTS: Among 151 randomized infants who received study iron (77 low-dose; 74 high-dose), bacterial diversity, individual taxa, virulence potential, bacterial overgrowth, and iron-related functional genes were not significantly different between the treatment groups. In subgroup analysis of singletons, treatment groups demonstrated significant differences in temporal shifts in overall bacterial community structure. Infants receiving 2 mg/kg/day had higher post-treatment urinary claudin-3 concentrations, indicating possible differences in intestinal permeability, and a higher prevalence of iron deficiency than those receiving 6 mg/kg/day. Other biomarkers, clinical outcomes, adverse events, and auditory latencies did not differ between groups.<br><br>CONCLUSIONS: Enteral iron supplementation at 6 mg/kg/day was associated with improved iron status and lower intestinal barrier dysfunction, without evidence of harms on gut microbiome compared with the recommended 2 mg/kg/day dose. These findings do not support concerns regarding gut microbiome disruption as a justification for lower iron dosing in preterm infants.<br><br>TRIAL REGISTRATION: Clinicaltrials.gov NCT04497012.}, }
@article {pmid42264207, year = {2026}, author = {Laovechprasit, W and Avila-Reyes, VA and Stacy, BA and Young, KT and Harris, HS and Tuttle, AD and Sirpenski, G and Kennedy, AE and Innis, CJ and Norton, TM and Zirkelbach, B and Stanton, JB}, title = {Surveillance of gastrointestinal viruses of free-ranging and rehabilitated Sea turtles in the United States.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105966}, doi = {10.1016/j.meegid.2026.105966}, pmid = {42264207}, issn = {1567-7257}, abstract = {Sea turtle populations are imperiled globally, primarily due to anthropogenic threats. However, non-anthropogenic factors, such as infectious diseases, can affect their population stability. Viruses are common causes of gastrointestinal disease in many species, and gastrointestinal signs are regularly observed among sea turtles, but little is known about enteric viruses in sea turtles. Establishing basic knowledge of viral diversity and evolutionary relationships is a necessary step towards understanding potential health impacts. This study investigated the viral genome contents of seventy-seven gastrointestinal specimens from six species of sea turtles with varying health conditions from the Atlantic and Pacific coasts of the United States. Forty-eight, non-plant and non-bacteria infecting viruses were detected (≥5 viral-like reads per sample) through random RNA sequencing. Detected viral sequences were then confirmed and characterized by semi-targeted, strand-switching sequencing, which provided deeper sequencing metrics allowing for phylogenetic characterization (>10× depth) for nineteen viruses across eight viral families, including seven putative novel viral species, one putative novel genus, and eleven likely novel viral sequences from taxa that lack established species demarcation criteria. Sixteen RNA viruses were characterized: four double-stranded RNA viruses (Partitiviridae, Totiviridae, and Picobirnaviridae), eleven positive-sense single-stranded RNA viruses (Caliciviridae, Dicistroviridae, unclassified Hepelivirales, and unclassified Picornavirales), and one negative-sense bisegmented RNA virus (Chuviridae). Three DNA viruses were also identified (Parvoviridae, Circoviridae, and unclassified Cressdnaviricota). Viruses identified in this study were often genetically related to viruses previously known to infect aquatic invertebrates and fish. This study provides baseline knowledge of viral communities in sea turtles and will serve as a foundation for future hypothesis-driven research to understand their relevance to sea turtle health.}, }
@article {pmid42264211, year = {2026}, author = {Bhadelia, N and Gikandi, I and Lassmann, B}, title = {Regional Signals Preceding the 2026 Bundibugyo Virus Disease Outbreak.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108862}, doi = {10.1016/j.ijid.2026.108862}, pmid = {42264211}, issn = {1878-3511}, abstract = {BACKGROUND: The May 2026 Bundibugyo virus disease (BVD) outbreak in the Democratic Republic of the Congo was declared a Public Health Emergency of International Concern after substantial undetected community transmission. We describe regional surveillance signals detected by the Biothreats Emergence, Analysis, and Communications Network (BEACON), our open access event based surveillance program, in the weeks preceding outbreak declaration.<br><br>METHODS: We reviewed BEACON reports of VHF-compatible illness clusters detected in the transboundary DRC-Uganda-Burundi-South Sudan region during March-April 2026, prior to the May 15 laboratory confirmation of BDBV.<br><br>RESULTS: BEACON detected four temporally proximal VHF-compatible illness signals: (1) March 9, North Kivu Province-suspected Ebola case under investigation with unresolved laboratory results; (2) March 10, Kasa&#xef; Province-fatal hemorrhagic illness with secondary cases and negative Ebola PCR; (3) March 30, Burundi-35-case undiagnosed cluster near the DRC border with 5 deaths, negative testing for major filoviruses and >200 pathogens, pending metagenomic sequencing; (4) April 22, South Sudan-three suspected VHF cases with negative initial testing. All four signals shared a similar diagnostic phenotype: VHF-compatible presentation, mobilization of investigation teams, negative initial testing, and no publicly reported confirmed etiology. None were formally reported to have been resolved.<br><br>CONCLUSIONS: Our detection of four unresolved VHF signals preceding the confirmed BDBV outbreak highlights gaps in formal follow-up mechanisms for negative cases and fragmented regional diagnostic coordination. In light of confirmed BDBV circulation and Africa CDC's identification of 10 countries at high risk for spread, these preceding signals warrant urgent retrospective investigation and laboratory.}, }
@article {pmid42264215, year = {2026}, author = {Hou, P and Che, Y and Han, J and Deming, C and Amirkhani, A and Kim, CS and Taylor, ME and Velez, D and Cho, E and Holmes, CJ and Suh, G and Castelo-Soccio, L and ,  and McDermott, DH and Murphy, PM and Segre, JA and Kong, HH}, title = {Permissive skin microbiomes in WHIM syndrome: HPV and pathogen expansion.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2026.05.024}, pmid = {42264215}, issn = {1523-1747}, abstract = {Warts, hypogammaglobulinemia, infections, and myelokathexis (WHIM) syndrome is a rare inborn error of immunity (IEI) caused by hyperfunctional pathogenic variants in CXC chemokine receptor 4 (CXCR4), predisposing individuals to recurrent bacterial skin and airway infections and warts. The targeted CXCR4 antagonist plerixafor has shown efficacy in wart regression and potential reduction in bacterial infection frequency. Here, we investigated skin microbiomes of 11 patients with WHIM syndrome using shotgun metagenomics, compared to healthy controls. WHIM skin microbial communities displayed greater inter-individual variability, with highly diverse human papillomavirus profiles and expansion of airway-associated pathogens on the skin. Among patients receiving plerixafor therapy, we observed shifts in the viral composition and a downward trend in viral abundances. Together, these findings demonstrate the distinctive and permissive skin microbiome in WHIM syndrome and highlight the potential microbiome-modulating effects of targeted CXCR4 antagonism.}, }
@article {pmid42264245, year = {2026}, author = {Zhao, Y and Zhang, Y and Tang, S and Peng, T and Bagadi, AH and Jia, X and Wei, Z and Han, J and Li, L and Liu, X and Kong, W and Song, S and Wei, C and Wang, J}, title = {Structural elucidation and gut barrier-protective effects of a glucomannan polysaccharide fraction from Lanzhou lily bulbs.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {152899}, doi = {10.1016/j.ijbiomac.2026.152899}, pmid = {42264245}, issn = {1879-0003}, abstract = {Food-derived dietary polysaccharides have attracted increasing attention as functional ingredients for ulcerative colitis (UC) management. In this study, a homogeneous polysaccharide, designated LDP, was isolated from the bulbs of Lilium davidii var. willmottiae (Lanzhou lily). Structural analyses showed that LDP had a weight-average molecular weight (MW) of 5.082 × 10[3] g/mol and was mainly composed of alternating →4)-α-D-Manp-(1 → and →4)-β-D-Glcp-(1 → residues with minor branching. Conformational analysis and molecular dynamics (MD) simulations indicated that LDP adopted an extended semi-flexible coil conformation in aqueous solution. In dextran sulfate sodium (DSS)-induced colitis mice, LDP markedly alleviated disease symptoms, as evidenced by improved survival, reduced body weight loss, a lower disease activity index and attenuated histopathological injury. Mechanistically, LDP enhanced intestinal barrier integrity, significantly increased acetic acid levels and partially restored short-chain fatty acid (SCFA)-associated beneficial taxa, including Lactobacillaceae, Bifidobacterium, Allobaculum and members of Erysipelotrichaceae/Erysipelotrichia. Integrated metagenomic, proteomic, Western blot and immunological analyses further indicated that LDP attenuated intestinal inflammation by suppressing the TAB1/MAP2K4-centered MAPK signaling pathway, as evidenced by reduced TAB1 and MAP2K4 expression and decreased p38 phosphorylation, and by restoring the Th17/Treg balance in mesenteric lymph nodes (MLNs). These findings suggested that LDP alleviated DSS-induced colitis through coordinated regulation of gut microbiota, microbial metabolism, MAPK inflammatory signaling and mucosal immunity.}, }
@article {pmid42264341, year = {2026}, author = {Zhu, K and Sun, W and Wang, Z and Zha, Y and Qu, X and Wang, B and Zhang, H}, title = {Environmental ubiquity but limited host taxonomic distribution of co-occurring metal(loid)-resistance genes and persistent organic pollutant-transformation genes in global inland waters.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128552}, doi = {10.1016/j.envpol.2026.128552}, pmid = {42264341}, issn = {1873-6424}, abstract = {Human activities have transformed inland waters into reservoirs of co-contamination by heavy metals and persistent organic pollutants, driving microbial adaptation through metal-resistance genes (MRGs) and POP-transformation genes (POPTGs). However, the global biogeography and ecological drivers of these co-occurring functional genes and their hosts remain unresolved. Here, leveraging 1,593 metagenomes, we investigate the global distribution, microbial hosts, co-occurrence patterns, and drivers of MRGs and POPTGs in inland waters. Key MRG subtypes (e.g., ruvB, pstB, arsB) and POPTGs (e.g., hdt, linJ, bphA) co-occurred in phylogenetically constrained hosts-predominantly Proteobacteria (e.g., Pseudomonas, Acidovorax)-exhibiting dual resistance to Cr/Cu and transformation of aromatic/chlorinated POPs. The positive correlations linked MRG-POPTG to mobile genetic elements, suggesting horizontal gene transfer accelerates multi-pollutant resistance. Our findings highlight known POPTGs and MRGs occur together, which is ubiquitous in the environment but restricted to a limited number of taxa (approximately 3.8% ratio of the total 4129 non-redundant MAGs). Finally, a global map of MRG-POPTG-carrying MAGs (MPCMs) abundance is generated, where climatic and anthropogenic factors explained MPCMs hot spots in South Asia, Southeast Asia, South America.}, }
@article {pmid42264402, year = {2026}, author = {Li, C and Tan, Y and Ma, S and Wang, J and Bai, W and Li, Z and Gao, S and Zhao, Q and Qin, J and Ye, Z}, title = {Concentration-dependent roles of hydrazine in immobilized denitrifying biofilm for industrial wastewater treatment.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135122}, doi = {10.1016/j.biortech.2026.135122}, pmid = {42264402}, issn = {1873-2976}, abstract = {Hydrazine-bearing industrial wastewater is challenging to treat biologically because hydrazine can simultaneously act as a reducing substrate and a microbial inhibitor. In this study, an immobilized denitrifying biofilm system was used to evaluate the concentration-dependent effects of hydrazine on denitrification performance, electron contribution, and microbial response under anoxic conditions. Under sufficient co-substrate conditions, 5-10 mg/L hydrazine was effectively removed, with a maximum removal efficiency of approximately 94%, while stable denitrification was maintained. Nitrogen-15 isotope tracing showed that approximately 31% of the electrons released from hydrazine oxidation were transferred to denitrification-coupled nitrate reduction, indicating that hydrazine can partially contribute reducing equivalents in the denitrifying biofilm. However, elevated hydrazine concentrations impaired hydrazine oxidation and denitrification, induced nitrite and ammonium accumulation, and reduced carbon utilization. Mechanistic analyses showed that this deterioration was associated with oxidative stress, membrane damage, and inhibition of key enzymes, particularly nitrite reductase and hydroxylamine oxidoreductase. Metagenomic analysis further revealed a stress-induced shift in the microbial community from central carbon metabolism toward compensatory pathways. Overall, this study provides mechanistic and process-level insights into the feasibility and operational limitations of using immobilized denitrifying biofilms for treating hydrazine-bearing industrial wastewater.}, }
@article {pmid42264404, year = {2026}, author = {Li, Z and Wang, L and Wang, B and Wang, S and Liu, T and Peng, Y}, title = {Controlled transition from anammox to partial denitrification-anammox system enhanced nitrogen removal: Microbial community succession and organic matter management.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135121}, doi = {10.1016/j.biortech.2026.135121}, pmid = {42264404}, issn = {1873-2976}, abstract = {Integrated partial denitrification-anammox (PDA) offers a sustainable strategy for mainstream wastewater treatment. However, the dynamic transitions and microbial mechanisms during the shift from anammox to coupled PDA remain inadequately characterized. In this study, a PDA system was systematically established by the gradual replacement of nitrite with nitrate and controlled increases in acetate concentrations. Subsequently, acetate was replaced with sludge fermentation liquor (SFL) as the organic carbon source. The process achieved progressive enhancement in nitrogen removal, which stabilized at 93.9%-96.1%. The contribution of anammox in nitrogen removal accounted for > 74% of influent total nitrogen. Concurrently, the mean particle size increased from 85.6 μm to 387.5 μm, and this granulation process significantly improved the stability of the PDA system. 16S rRNA sequencing revealed a marked enrichment of Candidatus Brocadia (0.3% to 4.6%) and Thauera (5.8% to 17.3%). Furthermore, metagenomic analysis confirmed the high abundance of anammox-related genes (hdh, hzs) and higher abundance of the genes encoding nitrate reductase (narG/H/I, napA/B) compared to nitrite reductase genes (nirS/K). This metabolic bias reinforced the PD ecological niche, ensuring stable PDA functionality when SFL was used as the carbon source. Notably, enhanced activity of polysaccharide and protein hydrolase highlighted the critical roles of hydrolysis and acidogenesis in sustaining non-competitive PD performance, particularly under SFL conditions. This study provides a potentially reproducible strategy for the cultivation of PDA communities from anammox inoculum, elucidating microbial dynamics and functional stability during process transitions. These findings provide valuable insights for efficient wastewater treatment by replacing external chemical carbon sources to improve the recovery and utilization of sludge resources.}, }
@article {pmid42264456, year = {2026}, author = {Wildbur, C and Dawson, RA and Roy, S and Ah-Peng, C and Espenberg, M and Hernández, M}, title = {Carbon monoxide oxidizers in soils of different ages from Piton de la Fournaise volcano.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag062}, pmid = {42264456}, issn = {1574-6941}, abstract = {Volcanic soils provide a unique environment for studying microbial colonization and succession due to their extreme conditions and distinct geochemical profiles. This study focused on carbon monoxide (CO)-oxidizing microbial communities in volcanic soils at Piton De La Fournaise, Réunion island. Soil samples from three sites (corresponding to eruptions in 1401, 1559, and 2007) were analyzed to assess microbial community structure using 16S rRNA gene sequencing and metagenomic analysis to identify functional genes involved in CO oxidation. Phylum-level analysis showed higher relative abundance of Acidobacteriota and Chloroflexota, lower abundances of Actinomycetota and Bacteroidota, and relatively stable levels of Pseudomonadota, while class-level patterns included rising Alphaproteobacteria and Acidobacteriia, with Ktenobacteria emerging in the 1401 site. CO dehydrogenase-related genes were found in 17 metagenome-assembled genomes across all sites. The CO consumption rate by microbes in soils was measured. CO-oxidizing microbes were present across soil ages, with detectable activity in the 2007 site and greatest activity in the 1401 site, suggesting that these microbes actively use CO as an energy source even in soils with primary vegetation, contrary to general understanding. The findings suggest intricate dynamics of microbial succession in volcanic soils and may challenge conventional expectations about community complexity over time.}, }
@article {pmid42265111, year = {2026}, author = {Campese, L and Longo, A and Pelletier, E and Delmont, TO and Ambrosino, L and Miralto, M and Mele, BH and Alberti, A and Labadie, K and Oliveira, PH and Perdereau, A and Wincker, P and ,  and Iudicone, D}, title = {Eukaryotic MAGs from the NEREA observatory: expanding the coastal microbiome dataset.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07571-y}, pmid = {42265111}, issn = {2052-4463}, support = {101082021//MARCO-BOLO/ ; ID: 862923//AtlantECO/ ; 101081642//OBAMA-NEXT/ ; }, abstract = {Marine ecosystems are hotspots of biodiversity and biogeochemical activity, yet much of their complexity remains largely inaccessible without genome-resolved data. Here we present a curated dataset of 52 eukaryotic metagenome-assembled genomes (MAGs) reconstructed from samples collected between April 2019 and January 2020 at three NEREA (Naples Ecological REsearch for Augmented observatories) sites in the Gulf of Naples. NEREA is a coastal observatory integrating physical, chemical and biological measurements with state-of-the-art metagenomics. The eukaryotic MAGs have an average completeness of ~55% and genome size of ~20 Mb. Predicted proteins were functionally annotated against UniProtKB, InterPro, and eggNOG databases, and each MAG was taxonomically classified using a curated RNA polymerase A reference dataset. The recovered MAGs encompass diverse eukaryotic lineages, primarily Ochrophyta, Chlorophyta and Haptophyta. Building on the Tara Oceans eukaryotic MAG legacy, this release represents the first reconstruction of eukaryotic MAGs from a coastal time series, enabling temporal and functional analyses of eukaryotic plankton.}, }
@article {pmid42265123, year = {2026}, author = {Murchie, TJ and Cocker, SL and Baleka, S and Vogel, NA and Natola, L and Karpinski, E and Tirlea, D and Barrera, MA and Grant, DM and Morien, E and Long, GS and Rutledge, LY and Zazula, GD and Jensen, BJ and Froese, DG and Poinar, HN}, title = {Ground squirrel coprolites preserve complex archives of ancient environmental DNA over 700,000 years.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42265123}, issn = {2041-1723}, abstract = {Permafrost-preserved ground squirrel (Urocitellus) burrows in Yukon, Canada contain coprolites (palaeofaeces) that span from the Holocene to at least the Middle Pleistocene (~700 kya). Using shotgun metagenomics and targeted enrichment, we recover a rich, multi-taxon spectrum of ancient environmental DNA from these pellets, including: plants, insects, microbes, and megafauna consistent with eastern Beringian ecosystems. These coprolites consistently preserve an abundance of eukaryotic DNA, enabling the assembly of >18 mitochondrial genomes (ground squirrel, snowshoe hare, steppe bison, horse, and mammoth), and revealing previously unrecognized diversity within Arctic Urocitellus, including a ~700 kya lineage that predates divergence among several extant clades. Characteristic damage patterns, positive/negative controls, and in silico taxon validations strongly support aDNA authenticity, and comparisons with regional permafrost datasets indicate minimal post-depositional leaching. These results show that permafrost coprolites can yield high-resolution records of Quaternary ecosystems and multi-organism population histories, providing a powerful complement to sedimentary and skeletal ancient DNA.}, }
@article {pmid42265319, year = {2026}, author = {Gionchetta, G and Lee, J and Hansen, O and Beck, K and Bürgmann, H}, title = {Invasion dynamics of antimicrobial-resistant E. coli in river biofilms: impacts on the resistome, microbiomes, and horizontal gene transfer.}, journal = {npj antimicrobials and resistance}, volume = {}, number = {}, pages = {}, doi = {10.1038/s44259-026-00232-5}, pmid = {42265319}, issn = {2731-8745}, support = {ID 100010434//La Caixa Foundation/ ; 186531/SNSF_/Swiss National Science Foundation/Switzerland ; }, abstract = {River biofilms are frequently exposed to invasion by antibiotic-resistant bacteria (ARB) due to episodic or chronic wastewater inputs, yet the ecological processes governing the fate of invaders and their resistance plasmids remain poorly understood. We experimentally exposed river-grown biofilms from sites differing in microbial diversity and wastewater impact to a genetically tagged ARB Escherichia coli carrying a transferable IncPα plasmid with the nptII resistance gene. Over two weeks, we tracked invader and plasmid dynamics using qPCR and plasmid-to-genome ratios as a proxy for horizontal gene transfer (HGT), complemented by 16S rRNA gene sequencing and metagenomics. Both quantification approaches yielded consistent results: the invader transiently established in all biofilms, peaking within 48 h and declining to near-background levels after 14 days. Decreasing plasmid-to-genome ratios indicated limited HGT and progressive plasmid loss. Biofilms impacted by wastewater showed slower declines, suggesting greater plasmid persistence in disturbed environments and increased abundance of specific indigenous antimicrobial resistance genes of public health concern. While the overall resistome exhibited short-lived shifts, and indigenous resistomes remained largely stable. These findings demonstrate that invader-biofilm interactions are dynamic and shaped by community context, supporting the One Health framework and highlighting how environmental conditions modulate antimicrobial resistance risks in freshwater ecosystems.}, }
@article {pmid42256253, year = {2026}, author = {Huang, W and Wang, S and Zhang, Y and Gao, M and Zhong, N and Hao, C and Janak, LP and Wang, L and Meng, S and Zhao, W and Zeng, S}, title = {Streptococcus mutans exacerbates gut microbiota dysbiosis in SHANK3 [-/-] autism model mice via the oral-gut axis.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2681259}, pmid = {42256253}, issn = {2000-2297}, abstract = {BACKGROUND AND OBJECTIVE: Autism spectrum disorder (ASD) is associated with gut microbiota dysbiosis, yet the impact of oral pathobiont translocation via the oral-gut axis remains unclear. This study investigated how Streptococcus mutans (S. mutans), a primary cariogenic pathogen, influences gut microbial structure and function in an ASD mouse model.<br><br>METHODS: SHANK3 knockout (SHANK3[-/-]) and wild-type (WT) mice were divided into four groups: WT control, WT S. mutans-gavaged (WT-S.m), SHANK3[-/-] control, and SHANK3[-/-] S. mutans-gavaged (SHANK3-S.m). Mice were gavaged with S. mutans UA159 twice weekly for five weeks, followed by fecal metagenomic sequencing (n&#x2009;=&#x2009;6 per group).<br><br>RESULTS: S. mutans translocated to the gut in both gavaged groups but did not achieve enhanced colonization in SHANK3[-/-] mice. S. mutans gavage significantly altered the gut microbiota structure in both WT and SHANK3[-/-] mice. In the ASD model, S. mutans gavage led to a significant enrichment of potential pathobionts (e.g. Duncaniella dubosii, Muribaculum gordoncarteri) and a decrease in beneficial bacteria (e.g. Bacteroides caecimuris, Bacteroides faecium). LEfSe analysis identified Parascardovia denticolens and Bacteroides heparinolyticus as specific biomarkers for the SHANK3-S.m group. Microbial networks showed reduced stability in SHANK3-S.m mice, with Enterocloster bolteae as a key node. Functional analysis revealed suppressed butanoate metabolism and enhanced neuroinflammation-related pathways.<br><br>CONCLUSION: Although S. mutans colonized only transiently, it provoked exacerbated ecological instability and pro-inflammatory metabolic alterations in ASD model mice, underscoring the role of the oral-gut-brain axis in ASD.}, }
@article {pmid42256259, year = {2026}, author = {Dewan, A and Mascellino, MT}, title = {Computational and multi-omics systems biology for precision microbiome therapeutics.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1842701}, pmid = {42256259}, issn = {2813-4338}, abstract = {The human gut microbiome represents a complex and dynamic therapeutic target whose effective interrogation requires system-level analytical approaches beyond single-omics or reductive methods. This mini-review synthesizes recent advances in computational modeling and multi-omics integration relevant to the development of predictive, patient-tailored microbiome therapies. We critically assess the analytical strengths and limitations of genome-scale metabolic models (GEMs); generalized Lotka-Volterra and ODE-based community models; agent-based simulations; and statistical machine-learning frameworks and examine how their integration with metagenomics, metatranscriptomics, metaproteomics, and metabolomics can help bridge microbial functional potential with clinically relevant phenotypes. Representative applications-including MintTea for disease module identification, gNOMO2 for integrative microbiome profiling, and AGORA-based community metabolic modeling-illustrate the translational scope of these frameworks across inflammatory, metabolic, and infectious disease contexts. Hybrid ML-GEM frameworks have not yet been directly applied to FMT outcome prediction; however, the mechanistic principles underlying both approaches - metabolic compatibility modeling and data-driven responder stratification - suggest a compelling direction for future investigation, contingent on prospective validation in adequately powered and independent clinical cohorts. Persistent methodological challenges-such as data heterogeneity, batch effects across sequencing platforms, incomplete multi-omics coverage, and limited interpretability of complex machine-learning models-are being actively addressed through standardized preprocessing pipelines, explainable Artificial intelligence (AI) strategies, and federated analytics. While federated approaches enable privacy-preserving, multi-institutional model training, they introduce additional constraints related to non-identically distributed data, communication overhead, and uneven computational capacity. Overall, the convergence of mechanistic modeling, data-driven learning, and distributed analytical infrastructures may assist in advancing microbiome research from a largely correlational perspective toward mechanistic and ultimately prescriptive frameworks for precision microbiome medicine.}, }
@article {pmid42256958, year = {2026}, author = {Elendu, C and Debua, AT and Okolo, EH and Sadiq, HO}, title = {Immune Checkpoint Inhibitor Pneumonitis Complicated by Invasive Pulmonary Aspergillosis in COPD: Diagnostic and Therapeutic Challenges.}, journal = {Clinical case reports}, volume = {14}, number = {6}, pages = {e72755}, pmid = {42256958}, issn = {2050-0904}, abstract = {Checkpoint inhibitor-associated pneumonitis complicated by invasive pulmonary aspergillosis represents a diagnostic challenge in ICI-treated patients, particularly those with COPD receiving corticosteroid therapy. Persistent or worsening respiratory abnormalities despite immunosuppressive treatment should prompt reassessment for superimposed fungal infection, including bronchoscopy, BALF analysis, and microbiologic testing to facilitate diagnosis and targeted therapy.}, }
@article {pmid42257244, year = {2026}, author = {Moulignier, A and Heran, F and Lallemand, F and Bourdillon, P}, title = {Human Pegivirus Encephalitis With Brain Detection and Response to Sofosbuvir Ledipasvir.}, journal = {Annals of clinical and translational neurology}, volume = {}, number = {}, pages = {}, doi = {10.1002/acn3.70450}, pmid = {42257244}, issn = {2328-9503}, abstract = {Human pegivirus (HPgV-1) has been associated with severe encephalomyelitis in immunocompromised patients. Its neurological spectrum remains poorly defined. We report a slowly progressive encephalitis in a person living with well-controlled HIV, characterized by white matter abnormalities and inflammatory cerebrospinal fluid (CSF). HPgV RNA was detected in CSF and brain tissue by metagenomic sequencing, with no alternative pathogen identified. Following off-label treatment with sofosbuvir/ledipasvir, the patient showed sustained clinical improvement, normalization of CSF findings, and disappearance of detectable HPgV RNA. This observation expands the clinical context of HPgV-1 detection and supports further investigation of its role in central nervous system disease.}, }
@article {pmid42257696, year = {2026}, author = {Nebauer, DJ and Nelson, T and Romanis, C and Neilan, BA and Timms, VJ}, title = {Taxonomy bias in metagenome-assembled genome recovery.}, journal = {Microbial genomics}, volume = {12}, number = {6}, pages = {}, pmid = {42257696}, issn = {2057-5858}, abstract = {The recovery of metagenome-assembled genomes (MAGs) from shotgun metagenomic sequencing is rapidly expanding the availability of representative genomes. However, this practice may skew the representation of specific taxa in real-world datasets. This bias is attributed primarily to the known inefficiencies of sequence-by-synthesis platforms in amplifying GC-rich and AT-rich sequence fragments. Here, we recover 216 medium- and high-quality MAGs from an Australian wetland site. Notably, no MAGs were recovered for some dominant cyanobacterial and proteobacterial species known to be present. A new protocol involving read-based classification and alignment to the MAG dataset demonstrated the highly efficient recovery of low-GC organisms in the Actinobacteria and Bacteroidota phyla. Additionally, the recovery of lost taxonomic information was demonstrated through unmatched sample mapping. The findings suggest a bias towards the recovery of smaller, low-GC organisms in MAG recovery, potentially skewing the global representation of microbial diversity. Our pipeline is made publicly available as a tool to help researchers estimate taxonomic losses following MAG recovery efforts.}, }
@article {pmid42258415, year = {2026}, author = {Pan, S and Chen, H and Sun, J and Xu, X and Gao, C}, title = {Species Identification And Antibiotic Susceptibility Testing Of The Nocardia Genus: Advances And Clinical Challenges.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {231}, pages = {}, doi = {10.3791/69977}, pmid = {42258415}, issn = {1940-087X}, mesh = {*Nocardia/drug effects/classification/genetics/isolation &amp; purification ; Humans ; *Anti-Bacterial Agents/pharmacology ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Microbial Sensitivity Tests/methods ; Nocardia Infections/microbiology/drug therapy/diagnosis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The genus Nocardia comprises bacteria widely distributed in nature that can cause infections in both humans and animals. Due to their diverse clinical manifestations and prolonged culture time, infections are frequently misdiagnosed or overlooked. In recent years, advances in biological techniques have markedly improved molecular diagnostic methods, enabling more precise species identification. However, the increasing issue of antimicrobial resistance poses significant challenges for clinical management, particularly among immunocompromised patients, for whom treatment is more complex. Although multiple therapeutic agents are currently available, rising resistance rates highlight the critical importance of antibiotic susceptibility testing. This review discusses molecular identification methods for Nocardia species, including recent advances in 16S rRNA gene sequencing, multilocus sequence analysis (MLSA), matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), whole-genome sequencing (WGS), and metagenomic next-generation sequencing (mNGS). The advantages and limitations of each technique are explored, with particular emphasis on their applications in detecting antibiotic resistance. The review also examines the clinical implementation of these molecular technologies, highlighting their contributions to rapid Nocardia identification, improved diagnostic accuracy, and reduced misdiagnosis. Finally, current limitations and future research directions are discussed, with particular attention to challenges related to cost, sensitivity, and standardization.}, }
@article {pmid42258525, year = {2026}, author = {Siegers, JY and Auerswald, H and Maquart, PO and Szentiványi, T and Guillebaud, J and Hoem, T and Li, X and Suor, K and Pum, L and Khun, L and Nuon, S and Chea, K and Heang, V and Bienes, KM and Su, YCF and Duong, V and Nouhin, J and Boyer, S and Karlsson, EA}, title = {Discovery of a novel coltivirus in a newly identified Bat Bug Species (Heteroptera: Cimicidae) in Cambodia.}, journal = {PLoS neglected tropical diseases}, volume = {20}, number = {6}, pages = {e0014372}, doi = {10.1371/journal.pntd.0014372}, pmid = {42258525}, issn = {1935-2735}, abstract = {Bats and their ectoparasites are significant reservoirs and potential vectors of emerging zoonotic pathogens, yet the viral diversity within bat-associated arthropods remains poorly characterized. This study reports the identification of a novel coltivirus (order Reovirales), provisionally designated Stricticimex coltivirus (SCCV), in a newly described bat bug species, Stricticimex phnomsampovensis, collected from cave-dwelling wrinkle-lipped free-tailed bats (Mops plicatus) in Cambodia. Metagenomic sequencing and phylogenetic analysis revealed that SCCV clusters within the Coltivirus genus, showing closest similarity to Tai Forest Reovirus (TFRV) previously isolated from African bats. SCCV was detected in 18.4% of examined bat bugs and successfully isolated in VeroE6 cells, with replication confirmed in multiple mammalian cell lines. The discovery of SCCV extends the known diversity and geographic range of coltiviruses and highlights bat ectoparasites as overlooked hosts of potentially zoonotic viruses. These findings underscore the importance of integrated One Health surveillance targeting both bats and their ectoparasites to better assess the risk of pathogen spillover in biodiverse regions with high human-animal contact.}, }
@article {pmid42258549, year = {2026}, author = {Vanhnollat, C and Chonephetsarath, S and Somlor, S and Vungkyly, V and Soulaphy, T and Vongsanga, S and Etobayeva, IV and Bigot, T and Wong, G and Letizia, AG and Brey, PT and Buchy, P and Vongphayloth, K}, title = {Detection and genetic characterization of Tembusu virus and other flaviviruses from mosquitoes in Lao PDR.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0351023}, doi = {10.1371/journal.pone.0351023}, pmid = {42258549}, issn = {1932-6203}, mesh = {Animals ; *Flavivirus/genetics/isolation &amp; purification/classification ; Laos ; Phylogeny ; Female ; *Culicidae/virology ; Genome, Viral ; *Mosquito Vectors/virology ; Flavivirus Infections/virology ; Humans ; Mosquito-Borne Diseases ; }, abstract = {BACKGROUND: Lao People's Democratic Republic (Lao PDR), located in Southeast Asia and known for its rich biodiversity, is part of a region recognized as a hotspot for emerging and re-emerging infectious diseases. Among flaviviruses, dengue virus (DENV) and Japanese encephalitis virus (JEV) are recognized public health threats. However, other reemerging mosquito-borne flaviviruses may also infect humans and cause diseases. Despite that, their distribution and public health impact in Lao PDR are not well understood due to limited past surveillance.<br><br>METHODOLOGY: Mosquitoes were collected using CDC light traps from 2021 to 2024, as part of vector and pathogen surveillance studies conducted across six provinces. A total of 2,548 female mosquitoes, representing 100 species from 11 genera, were collected and morphologically identified. Of these, 1,622 mosquitoes were pooled into 1,008 "mini pools" according to species and collection site. The pools were screened for flaviviruses by nested RT-PCR. Positive samples were further analysed by metagenomic sequencing, and coding-complete genomes were recovered and subjected to phylogenetic analysis.<br><br>PRIMARY RESULTS: We recovered thirteen coding-complete genomes through metagenomic sequencing, which included one Tembusu virus (TMUV) strain (TMUV/Mos_L010) from Culex vishnui mosquitoes and 12&#xa0;other insect-specific flaviviruses (ISFVs). Phylogenetic analysis placed TMUV/Mos_L010 in cluster 3, closely related to a TMUV strain known to be pathogenic to dolphins in Thailand, with more than >99% bootstrap support for amino acid homogeneity. The detected ISFVs were part of the classical insect-specific flavivirus (cISFV) lineage and were further classified into five subgroups according to their associated mosquito genera: Aedes (1), Anopheles (1), Culex (2), and Uranotaenia (1).<br><br>CONCLUSIONS: This study documents the first detection of TMUV in Laotian mosquitoes and extends the known distribution of cluster 3 TMUV strains. The discovery of diverse ISFVs shows the rich and underexplored virome among Laotian mosquito populations. These findings highlight the need for enhanced arbovirus surveillance and ecological research to assess zoonotic risks of spillover infections in Southeast Asia.}, }
@article {pmid42258623, year = {2026}, author = {Mosquera, RA and Magana-Ceballos, IG and De Jesus Rojas, W and Huang, X and Koochak, H and Tellez, ME and Castillo-Moguel, JA and Bishehsari, F and Mahdavinia, M and Ramos-Benitez, MJ and Harris, T and Yadav, A and Owens, K and Lemus-Rangel, R and Romero, M and Zuleta, S and Luz, A and Baltazar-Fernandez, A and McBeth, KE and Hashmi, S and Rosario Ortiz, G and Santoyo-Rios, J and Loyo-Rodriguez, JF and Colasurdo, GN}, title = {Multi-Omics Analysis Defines Endotypes and Systemic Inflammation in Primary Ciliary Dyskinesia: A Comparison with Healthy Controls.}, journal = {Annals of the American Thoracic Society}, volume = {}, number = {}, pages = {}, doi = {10.1093/annalsats/aaoag152}, pmid = {42258623}, issn = {2325-6621}, abstract = {INTRODUCTION: Primary ciliary dyskinesia (PCD) is a rare genetic disorder characterized by chronic airway inflammation and progressive lung injury. The inflammatory profile and systemic involvement remain poorly defined. We applied integrated multi omics (transcriptomics, proteomics, and metagenomics) to characterize inflammatory signatures and explore saliva as a noninvasive marker of systemic inflammation. These findings may support improved disease characterization and inform therapy and monitoring.<br><br>METHODS: This cross sectional, multicenter study included participants with PCD and healthy controls from Houston, Texas; Puerto Rico; and Mexico. Demographic and clinical data were collected in the absence of acute infection. Oral swabs underwent a bulk inflammatory transcriptomic profiling of 590-genes using NanoString nCounter&#xae; and microbiome evaluation via metagenomic sequencing. High sensitivity NULISA&#x2122; proteomic profiling of 250-proteins was performed on both saliva and plasma, with results correlated across omic layers. Pathway and gene set analyses were conducted using nSolver Advanced Analysis.<br><br>RESULTS: Seventy-six participants were enrolled: 51 with PCD and 25 healthy controls. PCD patients, especially those older than 10&#x2009;years and those with microtubular defects, showed markedly elevated inflammatory gene and protein expression in saliva and plasma. Five inflammatory endotypes were identified: Neutrophilic protease dominant, Dipeptidyl Peptidase 1(DPP&#x2011;1) profile (78%); neutrophilic recruiting, high&#x2011;Th17 (71%); eosinophilic dominant, high&#x2011;Th2 (51%); Th2/Th17&#x2011;high (47%), and Th2/Th17&#x2011;low (25%). PCD demonstrated increased neutrophil, and CD45&#x2011;related gene expression and activation of ten inflammatory pathways, including NF&#x2011;&#x3ba;B, oxidative stress, T&#x2011;cell-receptor, TREG, Th17, TNF, Th1, Th2, TGF-B signaling, and TLR (P&#x2009;<&#x2009;.01). Saliva and plasma showed strong molecular concordance. Microbiome analysis revealed significant shifts in diversity and abundance linked to inflammatory pathways.<br><br>DISCUSSION: These findings show that PCD is characterized by baseline inflammatory activity with marked endotypic heterogeneity, most frequently involving neutrophilic-immune pathways driven by DPP1-associated protease activity and Th17-mediated neutrophil recruitment, while a distinct subset of patients demonstrates a Th2-predominant inflammatory endotype. Salivary inflammatory profiling, which closely mirrors plasma, may offer a practical, non-invasive approach to capturing this patient-level heterogeneity and monitoring systemic immune activity and treatment response, especially with the new anti-inflammatory medications for bronchiectasis.}, }
@article {pmid42250890, year = {2026}, author = {Ticho, AL and McRae, AN and Cifuentes, L and Fredrick, T and Anazco, D and Espinosa, MA and Garcia Cordova, JM and Romanos, M and Villamarin, J and Johnson, S and Lennon, R and Hurtado Andrade, MD and Chen, J and Camilleri, M and Acosta, AJ}, title = {A subphenotype of obesity with reduced enteroendocrine GLP-1 synthesis and enhanced tirzepatide response.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2026.05.019}, pmid = {42250890}, issn = {1528-0012}, abstract = {BACKGROUND &amp; AIMS: Obesity is a heterogeneous disease characterized by different pathophysiological and behavioral traits that influence response to GLP-1-based therapies. We previously identified an obesity phenotype characterized by fast gastric emptying and increased postprandial hunger. We aimed to elucidate pathophysiologic mechanisms in this phenotype by evaluating plasma enteroendocrine hormones and mucosal gene expression, and to evaluate treatment response to tirzepatide across subphenotypes.<br><br>METHODS: 483 adults with obesity underwent solid meal gastric emptying (SGE) by scintigraphy, postprandial appetite assessment using visual analog scale (VAS), and plasma enteroendocrine hormone profiling. Gaussian mixed modeling identified phenotypic clusters. Associations with plasma short-chain fatty acids (SCFAs) and fecal metagenomics were explored. A separate cohort (n=31) underwent colonic mucosal biopsies with quantification of GCG (GLP-1) and PYY mRNA. Retrospective evaluation of weight loss in participants treated with tirzepatide among each cluster was performed (n=61).<br><br>RESULTS: Three clusters were identified based on SGE and GLP-1. One cluster demonstrated fast SGE, increased postprandial hunger, and discordantly low postprandial GLP-1 (termed dc-GE/GLP-1; n=130, 26.9%), as well as lower plasma PYY and CCK. dc-GE/GLP-1 showed higher plasma SCFA levels, without significant differences in fecal microbial composition. Compared with concordant clusters (c-GE/GLP-1; n=353, 73.1%), dc-GE/GLP-1 had decreased mucosal mRNA expression of GCG (GLP-1) and PYY. At 6-months of tirzepatide, dc-GE/GLP-1 was associated with greater weight loss compared with c-GE/GLP-1 (21.5% vs 11.7%).<br><br>CONCLUSIONS: We identified a subphenotype of obesity with fast gastric emptying and discordantly low GLP-1 plasma levels, reduced mucosal hormone synthesis, and enhanced weight loss to tirzepatide. Further studies are needed to identify mechanisms contributing to GLP-1 deficiency in this subphenotype of obesity.}, }
@article {pmid42251226, year = {2026}, author = {Kim, E and Jang, ES and Nam, Y and Hwang, HJ and Lee, YJ and Kim, TG and Hong, C and Lee, SR}, title = {The human microbiome as a source of novel bioactive natural products: structures, bioactivities, and biosynthetic insights.}, journal = {Journal of natural medicines}, volume = {}, number = {}, pages = {}, pmid = {42251226}, issn = {1861-0293}, support = {2025-glocal-02-004-511-002//Ministry of Education and Busan Metropolitan City/ ; RS-2025-23525419//National Research Foundation of Korea/ ; RS-2024-00403999//Korea Basic Science Institute/ ; WISET-2025-392//Ministry of Science and ICT, South Korea/ ; }, abstract = {The human microbiome, comprising trillions of microorganisms in distinct anatomical locations such as the gut, oral cavity, skin, and vagina, has emerged as a source of bioactive natural products with diverse scaffolds. Through co-evolution with the host, the human microbiome produces small molecules tailored to physicochemical environments that contribute to immune regulation, epithelial barrier maintenance, pathogen defense, and neurochemical signaling. Recent advances in metagenomics, single-cell genomics, synthetic biology, and integrated omics approaches have enabled rapid discovery and structural elucidation of biosynthetic gene clusters (BGCs) and metabolites. Cultivation-driven and genome mining strategies combined with omics analyses have improved the efficiency of discovering microbiome-derived drug leads. These metabolites mediate competitive and cooperative interactions within microbial ecosystems and hold high promise for therapeutic applications such as immunomodulators, anti-infectives, and neuroactive agents. This review outlines the structural features, biosynthetic pathways, and bioactivities of key metabolites across major microbial niches, together with strategies for their discovery, highlighting their potential in advancing drug development and human health.}, }
@article {pmid42251252, year = {2026}, author = {Lockwood, S and Ranaivoson, HC and Randriambolamanantsoa, TH and Razanajatovo, N and Raharinosy, V and Ahyong, V and Héraud, JM and Dussart, P and Lacoste, V and Brook, CE}, title = {Identifying viral infections through metagenomic Next Generation Sequencing of undiagnosed respiratory fevers in Madagascar (2014-2019).}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13715-7}, pmid = {42251252}, issn = {1471-2334}, support = {P200A210054//U.S. Department of Education/ ; GCE/ID OPP1211841//Bill and Melinda Gates Foundation/ ; }, abstract = {BACKGROUND: Respiratory illness contributes to substantial global morbidity and mortality. In Madagascar, an island nation off the southeastern coast of the African continent, hospital-based public health surveillance for respiratory pathogens screens for common respiratory viruses. However, many cases remain undiagnosed.<br><br>METHODS: We conducted metagenomic Next Generation Sequencing (mNGS) to identify the pathogen profile of 102 undiagnosed febrile patients who presented to public hospitals with respiratory symptoms and screened negative on a 14-virus multiplex RT-qPCR. We analyzed the diversity of the respiratory microbiome of each patient from mNGS data and identified viral infections potentially linked to undiagnosed fever. We assembled whole genome consensus sequences of viruses with sufficient read depth and coverage, characterized each phylogenetically, and identified any discrepancies with the primers used in the multiplex RT-qPCR panel. Finally, we compared all whole genome sequences against publicly available global databases in a phylogenetic analysis.<br><br>RESULTS: We identified evidence of infection by a wide range of known human viruses in approximately two thirds (64.7%) of study participants from nine different families of viruses and generated 30 complete or nearly complete consensus sequences of known respiratory viruses including orthopneumoviruses, metapneumoviruses, rhinoviruses, coronaviruses, parainfluenza virus, and bocaparvovirus. mNGS-attributed evidence of infection was predominantly due to orthopneumovirus (also called respiratory syncytial virus [RSV]; n&#x2009;=&#x2009;24; n&#x2009;=&#x2009;8 previously diagnosed) and rhinovirus (n&#x2009;=&#x2009;18) detections, despite previous negative RT-qPCR results for the majority of these cases. Finally, phylogenetic analysis identified two distinct phylogenetic clusters of RSV subtype A, suggesting local transmission following distinct international introductions for this virus.<br><br>CONCLUSION: mNGS provides a sensitive pan-pathogenic tool for virus detection. We demonstrate the diversity of viruses associated with undiagnosed respiratory fevers in Madagascar, emphasize the importance and relevance of the existing respiratory surveillance in the country, and highlight the interconnectedness of regional respiratory infection dynamics with global networks of respiratory pathogen transmission.}, }
@article {pmid42251689, year = {2026}, author = {Tao, M and Zhang, Z and Dai, L and Zeng, Y and Zhang, X}, title = {Metagenomic insights into potential horizontal transfer of resistance/virulence genes in gut microbiota from patients with Crohn disease.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izag090}, pmid = {42251689}, issn = {1536-4844}, support = {2025JJ50123//Hunan Provincial Natural Science Foundation of China/ ; 32101368//National Natural Science Foundation of China/ ; 1053320242393//Fundamental Research Funds for the Central Universities of Central South University/ ; }, abstract = {BACKGROUND: Unraveling the potential horizontal transfer of resistance genes/virulence genes (RGs/VGs) in gut microbiota from patients with Crohn disease (CD) is an interesting but poorly characterized issue.<br><br>METHODS: Quantitative assessment was performed to estimate the relative abundance and diversity of RGs/VGs/mobile genetic elements (MGEs). Differential analysis was applied to identify the CD-specific enriched genetic subtypes. A species-RGs/VGs/MGEs association network was constructed to explore possible co-occurrence patterns of these genetic elements across potential microbial hosts. Integrated with topological metrics and Zi-Pi computational modeling, co-occurrence network analysis was conducted to characterize potential associations among RGs, VGs, and MGEs.<br><br>RESULTS: Comparative metagenomic analyses indicated that the microbiome in group CD exhibited significantly higher relative abundance of RGs compared to that in healthy controls (HC; P&#x2009;=&#x2009;.040), with 131 specific RG/VG subtypes (eg, acrA/T6SS) exhibiting marked enrichment (P&#x2009;<&#x2009;.05). The co-occurrence network revealed intensified interconnectivity between RGs/VGs and MGEs in group CD, in which MGEs accounted for 71% of network nodes (vs 60.80% in HC), and 99.14% of the edges were positively correlated (vs 93.60% in HC). Network topology and Zi-Pi analysis further suggested reduced modularity (0.709 vs 0.979 in HC) and enhanced intergene connectivity (average degree: 12.288 vs 2.156; average weighted degree: 23.359 vs 3.688 in HC). There were no network hubs (0 vs 5 in HC) but abundant modular hubs (60 vs 25 in HC), peripheral nodes (2317 vs 1549 in HC), and connectors (61 vs 36 in HC), which may reflect conditions favorable for enhanced gene transfer potential. Cross-species transfer events were predicted across clinical-environmental-commensal boundaries, exemplified by tet(M) dissemination between Clostridioides difficile and Bacteroides sp., probably implying progressive erosion of ecological barriers.<br><br>CONCLUSIONS: Collectively, we inferred that the gut microbiome of CD patients might represent a high-risk reservoir for the horizontal transfer of pathogenic determinants, which may pose a potential threat for public health and biosecurity.}, }
@article {pmid42251704, year = {2026}, author = {Farace, PD and Marrero Diaz de Villegas, R and Mon, ML and Soria, MA and Talia, PM}, title = {Structural insights into predicted thermophilic GH5 cellulases for industrial lignocellulose bioconversion.}, journal = {Journal of biomolecular structure &amp; dynamics}, volume = {}, number = {}, pages = {1-22}, doi = {10.1080/07391102.2026.2683872}, pmid = {42251704}, issn = {1538-0254}, abstract = {Lignocellulosic biomass can be converted into biofuels and other valuable bioproducts, but it must first undergo physicochemical and enzymatic degradation. Among the various enzymes involved in lignocellulose degradation, thermophilic glycoside hydrolase family 5 (GH5) cellulases have gained significant attention given their ability to sustain enzymatic activity at temperatures exceeding 60 °C. These high temperatures not only accelerate enzymatic reactions, improving reaction rates and process efficiency, but also enhance substrate solubility and reduce the risk of microbial contamination, making them highly valuable for the paper, food, feed, pharmaceutical, and biofuel industries. In this work, we identified five GH5 cellulases with predicted thermophilic properties from termite gut metagenomes and evaluated their structural features using machine-learning classification, comparative structural modeling, interatomic contact analysis, and temperature-dependent flexibility simulations. The candidates, spanning GH5 subfamilies 2, 25, 37, 39, and 40, displayed high structural confidence (pLDDT > 90) and aliphatic indices comparable to those of thermophilic references. Analysis of amino acid composition analysis revealed enrichment in aromatic and charged residues. Hydrophobic contact densities were consistently higher than in mesophilic controls and aligned with thermophilic benchmarks. Temperature-dependent flexibility simulations showed restrained RMSF profiles, more closely resembling the thermophilic reference enzyme than to the mesophilic control. These findings are consistent with a thermophilic profile, pending experimental confirmation, and provide useful insights for the selection and engineering of GH5 cellulases for high-temperature biotechnological applications.}, }
@article {pmid42251735, year = {2026}, author = {Dennu, L and Devic, M and Rigonato, J and Falciatore, A and Lozano, JC and Vergé, V and Mariac, C and Joli, N and Jaillon, O and Sabot, F and Bouget, FY}, title = {Biological and genomic resources for the cosmopolitan phytoplankton Bathycoccus: insights into genetic diversity and function of outlier chromosomes.}, journal = {The Plant journal : for cell and molecular biology}, volume = {126}, number = {5}, pages = {e70982}, doi = {10.1111/tpj.70982}, pmid = {42251735}, issn = {1365-313X}, support = {ANR-20-CE20-0024//Agence Nationale de la Recherche/ ; }, abstract = {Population-scale genome sequencing has become essential for exploring genetic diversity and adaptation, particularly in land plants. In contrast, eukaryotic phytoplankton resources remain limited to model reference genomes or community-level metagenomics, leaving a gap in understanding intraspecific variation and evolutionary processes. To address this, we developed a comprehensive biological and genomic resource for the cosmopolitan and ecologically important genus Bathycoccus. Extensive metagenomic data from across the world Ocean are available for this genus, and previous studies have identified four Bathycoccus species and reconstructed 34 metagenome-assembled genomes (MAGs). Here we report 28 high-quality strain genome sequences using a combination of Oxford Nanopore Technologies long reads and Illumina short reads and associated biological resources. These include 24 Bathycoccus prasinos strains spanning a latitudinal gradient from 40° to 78° N, a reference genome for Bathycoccus calidus, and three genomes of the recently identified B3 clade, which we propose as the Bathycoccus catiminus species. Comparative analyses of sequenced genomes with MAGs highlight the complementarity between resources: While MAGs capture environmental diversity and uncover uncultured taxa, the cultured strain genomes provide complete, non-chimeric high-quality assemblies that resolve structural variations and haplotype-level diversity not detected in MAGs. These include the big outlier chromosome, a putative sexual chromosome revealing a second mating type, and extensive variability in the small outlier chromosome, associated with viral resistance and genome plasticity. Together, these biological and genomic resources establish B. prasinos as a powerful model for studying diversity, adaptation, and evolution of eukaryotic phytoplankton in the ocean, complementing existing global metagenomic datasets.}, }
@article {pmid42251775, year = {2026}, author = {Sahnan, S and Morandini, V and Ferrer, M and Onrubia, A and Torralvo, C and Kaján, GL and Harrach, B and Varsani, A and Kraberger, S}, title = {Four lineages of adenoviruses identified in raptors sampled in Spain.}, journal = {Virology}, volume = {623}, number = {}, pages = {110990}, doi = {10.1016/j.virol.2026.110990}, pmid = {42251775}, issn = {1096-0341}, abstract = {Adenoviruses infect a wide range of vertebrate species from fish to humans, including an especially large number of avian species. This study utilized viral metagenomic workflow coupled with targeted PCR to identify and characterize adenoviruses from cloacal swabs collected from 50 black kites (Milvus migrans), 11 ospreys (Pandion haliaetus), and 35 common kestrels (Falco tinnunculus) sampled in Spain. A total of eleven adenoviral genomes were determined from black kites (n = 8) and common kestrels (n = 3). Amino acid pairwise comparison of the DNA polymerase protein coupled with phylogenetic analysis shows that these viruses fall into four adenovirus lineages: two in the genus Aviadenovirus (raptor adenovirus 2 and 3) and two in the genus Siadenovirus (raptor adenovirus 1 and 4). The genomes of raptor adenovirus 1 and raptor adenovirus 2 belong to the classified species Siadenovirus raptoris and Aviadenovirus falconis, respectively, whereas raptor adenovirus 3 and 4 represent putative new species. This study expands the known host range of raptor-infecting viruses in the species Siadenovirus raptoris and Aviadenovirus falconis to include black kites and common kestrels, respectively. We also expand on the diversity knowledge of adenoviruses in black kites.}, }
@article {pmid42251975, year = {2026}, author = {Chen, C and Wang, M and Sun, L and Cheng, X and Deng, H and Li, RH}, title = {Phosphorus metabolism regulates the trade-off between phosphorus removal and sludge reduction.}, journal = {Bioresource technology}, volume = {458}, number = {}, pages = {135096}, doi = {10.1016/j.biortech.2026.135096}, pmid = {42251975}, issn = {1873-2976}, abstract = {Sludge reduction decreases the phosphorus export flux through waste sludge discharge, thereby increasing the risk of effluent phosphorus instability. However, the regulatory role of phosphorus in sludge reduction remains unclear. Here, side-stream phosphorus recovery was introduced into an anaerobic side-stream reactor (ASSR) based sludge reduction system to redirect phosphorus export from sludge discharge to physicochemical recovery, enabling investigation of how phosphorus flux redistribution regulates sludge reduction. Two parallel systems, a conventional ASSR system (SBR-ASSR) and an ASSR system coupled with phosphorus recovery (SBR-ASSR-PR), were comparatively evaluated using phosphorus mass balance, endogenous respiration analysis, cryptic growth modeling, and metagenomic profiling. Phosphorus recovery increased total phosphorus removal from 77.8% to 97.3% and total nitrogen removal from 72.5% to 82.1%, while reducing the observed sludge yield by 28%. Phosphorus mass balance showed that 34.7% of influent phosphorus was rerouted through the recovery pathway, reducing phosphorus discharge via waste sludge from 74.9% to 57.5%. The resulting lower system phosphorus levels restructured microbial metabolic allocation, suppressing biosynthesis while enhancing decay and substrate reutilization, with the cryptic growth contribution increasing from 35.9% to 46.9%. Metagenomic profiling corroborated this metabolic shift, revealing significant changes in key genes and pathways related to phosphorus cycling, energy maintenance, and denitrification. These findings show that phosphorus metabolism can regulate microbial growth-decay allocation, and that side-stream phosphorus recovery can coordinate nutrient removal, phosphorus recovery, and sludge minimization by restructuring internal phosphorus fluxes and microbial metabolic allocation.}, }
@article {pmid42252081, year = {2026}, author = {Wang, F and Xie, J and Fu, T and Pu, K and Wu, Q and Li, Q}, title = {Negative CSF mNGS Results and Early Shunt Placement in Post-Infectious Hydrocephalus: A Retrospective Cohort Study.}, journal = {World neurosurgery}, volume = {}, number = {}, pages = {125104}, doi = {10.1016/j.wneu.2026.125104}, pmid = {42252081}, issn = {1878-8769}, abstract = {OBJECTIVE: To evaluate the impact of pre-shunt cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) guidance on the timing of ventriculoperitoneal (VP) shunt surgery and clinical outcomes in patients with post-infectious hydrocephalus (PIH), and to explore the value of mNGS in different clinical scenarios.<br><br>METHODS: In this retrospective cohort study, we included 42 patients with PIH who underwent VP shunt surgery at our institution between January 2019 and December 2025. Patients were divided into two groups according to whether pre-shunt CSF mNGS was performed: the mNGS group (n = 19) and the non-mNGS group (n = 23). Primary outcomes included recovery to shunt time (RTS), first negative to shunt time (NTS), decisional shunt to actual shunt time (DTS), and postoperative antibiotic time (PAT). Secondary outcomes included postoperative hospital stay (POHS), functional outcomes (mRS and GCS), POD 90 mortality, infection recurrence, and reoperation.<br><br>RESULTS: Compared with the non-mNGS group, the mNGS group demonstrated significantly shorter NTS (3 [IQR 1-4] days vs. 9 [IQR 4.5-17] days, P = 0.002), DTS (2 [IQR 1-3.5] days vs. 8 [IQR 6-18] days, P < 0.001), and PAT (0 [IQR 0-2] days vs. 4 [IQR 0-10] days, P = 0.010). No significant differences were observed between the two groups in RTS (P = 0.135), functional outcomes, mortality, infection recurrence, or reoperation.<br><br>CONCLUSIONS: Pre-shunt CSF mNGS testing significantly shortens NTS, DTS, and PAT in patients with PIH without compromising clinical outcomes. The mNGS-guided shunt strategy is safe and feasible, supporting its potential clinical application.}, }
@article {pmid42252233, year = {2026}, author = {Dou, ZX and Liu, C and Zhang, Y and Wang, ZQ and Zhao, L}, title = {[A case of microsporidial keratoconjunctivitis].}, journal = {[Zhonghua yan ke za zhi] Chinese journal of ophthalmology}, volume = {62}, number = {6}, pages = {468-472}, doi = {10.3760/cma.j.cn112142-20251002-00402}, pmid = {42252233}, issn = {0412-4081}, abstract = {A 15-year-old male patient presented with recurrent photophobia, lacrimation, and blurred vision in both eyes for 3 years. He had been repeatedly diagnosed with "bilateral keratitis (unknown etiology)"at other hospitals and failed to respond to multiple topical medications. Initially diagnosed as bilateral Thygeson superficial punctate keratitis, he was treated with 0.5% loteprednol etabonate suspension eye drops and other medications. However, his symptoms worsened after 3 weeks of treatment. Subsequently, corneal epithelial tissue metagenomic testing and scrape cytological examination were performed, confirming the diagnosis of bilateral microsporidial keratoconjunctivitis. The treatment regimen was adjusted to topical application of 1% voriconazole eye drops, 0.3% gatifloxacin ophthalmic gel, and 0.1% tacrolimus eye drops. After 3 weeks of treatment, the patient's visual acuity in both eyes recovered to 1.0, conjunctival hyperemia was alleviated, and corneal epithelial punctate infiltration and fluorescein staining improved. One month after treatment, his symptoms were basically relieved, with the corneal infiltration and palpebral conjunctival papillae resolved. No recurrence was observed during the one-year follow-up.}, }
@article {pmid42252320, year = {2026}, author = {Zhou, J and Qiao, Y and Chen, H and Li, L and Su, W}, title = {Spatial scaling of metagenomic diversity reveals ecological disruption in the gut microbiome of gout patients.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-55351-w}, pmid = {42252320}, issn = {2045-2322}, support = {No: 24JRRJ001//Provincial Science and Technology Plan (Basic Research Plan-Natural Science Foundation) Project of Gansu Province in 2024/ ; }, abstract = {Gout, a painful inflammatory arthritis, is characterized by hyperuricemia and monosodium urate crystal deposition, with growing evidence linking its pathogenesis to gut microbiome dysbiosis. However, traditional diversity metrics fail to capture the complex spatial organization of microbial communities. This study addresses this gap by applying the novel metagenomic Diversity-Area Relationship (m-DAR) model to investigate scaling laws in the gout microbiome-quantifying how metagenomic diversity changes with the number of individuals sampled. Our analysis of gut microbiomes from gout patients and healthy controls revealed fundamental ecological disruptions. We found that gout microbiomes exhibited significantly altered scaling patterns: they showed greater inter-individual dissimilarity (higher z-values) at the level of rare genes (q = 0), but weaker scaling of dominant genes (q = 1-3) compared to healthy controls. Crucially, the maximal accrual diversity (MAD) was substantially lower in gout patients, indicating a severely constrained potential for total microbial gene diversity. Furthermore, profiling of metagenomic functional gene clusters (MFGCs) uncovered widespread functional perturbations, including increased diversity scaling for carbohydrate-active enzymes (CAZy) but decreased scaling in essential metabolic pathways (KEGG, KO). These results demonstrate that the gout gut microbiome is defined by a loss of ecological structure, featuring reduced homogeneity in dominant taxa, expanded rare biosphere variation, and an overall collapsed diversity capacity. This work introduces an ecological framework for characterizing dysbiosis in gout that complements traditional diversity metrics and may inform the development of microbiome-based therapeutic strategies. Further research is needed to translate these ecological patterns into clinical applications.}, }
@article {pmid42252423, year = {2026}, author = {Becerra-Lucio, PA and Pérez-Rueda, E and Dias, GM and Labrín-Sotomayor, NY and Mendoza-Mendoza, A and Partida-Martínez, LP and Zarza, E and Peña-Ramírez, YJ}, title = {Environmental contributors to bacterially dominated fermenting consortia of artisanal Mezcal.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05199-x}, pmid = {42252423}, issn = {1471-2180}, support = {786763//Consejo Nacional de Humanidades, Ciencias y Tecnolog&#xed;as/ ; IN220523//PAPIIT-DGAPA UNAM/ ; 5103711808 2021-2024//El Colegio de la Frontera Sur/ ; Omics Unravel Mezcal, a Drink with a Complex Spirit//Qu&#xed;mica Valaner-MGI Mexico/ ; }, abstract = {The production of spontaneously fermented beverages worldwide relies on native microorganisms acquired incidentally through cross-contamination from environmental reservoirs. We examined the microbiota involved in Mezcal fermentation, exploring their origins, dynamics, and ecology. Using shotgun metagenomics, we analyzed four batches of Mezcal, spanning the entire production process from crop to distillation. Bacterial genera such as Leuconostoc and Lentilactobacillus dominated the fermentation samples, whereas Bacillus was the most abundant in the environmental samples. Fermenting yeasts, such as Saccharomyces, accounted for only ~ 10% of the microbial abundance. No significant differences in microbial community structure were observed between the sampled batches, fermentation times, or depths of the fermentation tanks. Weevil samples clustered with fermentation and plant samples, suggesting they may serve as natural reservoirs for Leuconostoc and Lentilactobacillus. Functional differences were observed in COGs related to secondary metabolism during fermentation and correlated with sensory notes identified by a panel of expert tasters, suggesting that variations in the sensory profiles of the final spirit are directly linked to the metabolic products of genes associated with secondary metabolism. Our work analyzed the spontaneous fermentation microbiota, providing fundamental insights into its natural reservoirs and its contribution to Mezcal terroir.}, }
@article {pmid42252476, year = {2026}, author = {Wei, C and Wang, Y and Chen, Z}, title = {Comprehensive analyses of archaeal viral genomes reveal genomic characteristics, divergence, and host interactions.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02445-2}, pmid = {42252476}, issn = {2049-2618}, abstract = {BACKGROUND: The ecological significance of bacteriophages has been extensively investigated, while the role of archaeal viruses across different environments remains poorly understood.<br><br>RESULTS: Here, we present the Archaeal Viral Genome Database (AVGD), a comprehensive survey of archaeal viruses across eight distinct habitat types, including 3708 archaeal viral genomes, with genome sizes ranging from 3 to 188&#xa0;kb, identified from 64,521,709 putative viral genomes using 40 public metagenomic datasets, an integrated public viral genome database (IGN), and pig gut viral databases. Our analysis revealed that the majority (92.93%) of archaeal viruses in the AVGD belong to the class Caudoviricetes. Phylogenetic analysis showed that many archaeal viruses diverged with their respective habitats. Using CRISPR spacer matching, we characterized the host composition of these archaeal viruses and uncovered competitive interaction networks between archaeal viruses and other archaeal viruses targeting the same host or different hosts. Furthermore, we identified 129,067 coding genes from 3708 archaeal viral genomes, most of which were associated with essential archaeal viral cellular functions, including replication, assembly, and packaging. Archaeal viruses also encoded a variety of auxiliary metabolic genes, anti-CRISPR (Acr) proteins for evading host immunity, and DNA methyltransferases for escaping host restriction-modification systems.<br><br>CONCLUSIONS: Together, this study provides a valuable resource and offers new insights into the ecological roles and host interactions of archaeal viruses across diverse environments. Video Abstract.}, }
@article {pmid42252506, year = {2026}, author = {Galtier, A and Warinner, C and Velsko, IM}, title = {Ancient species diversity and niche adaptation in Tannerella and Porphyromonas revealed through pangenomics.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evag136}, pmid = {42252506}, issn = {1759-6653}, abstract = {De novo assembly of ancient and modern bacterial metagenomes can shed light on evolution and ecology of bacterial species that are challenging to culture. Tannerella and Porphyromonas are bacterial genera linked to periodontal disease, and understanding their evolution may reveal insights into their role in oral disease development. We performed pangenomic and phylogenetic analyses on a global set of isolates and metagenome-assembled genomes of the genera Tannerella (n=238) and Porphyromonas (n=976), including 66 genomes from ancient dental calculus samples (up to 14,800 years old), and modern oral samples from present-day living populations. We identify a novel species of oral Tannerella in modern and ancient humans, which we call Ca. Tannerella abscondita, that is related to and often mistaken for Tannerella forsythia but differs in its virulence repertoire. We reveal distinct niche tropism in Tannerella species and Porphyromonas pasteri, but not Porphyromonas gingivalis. There is limited phylogeographic structuring, and virulence genes are homogeneously distributed across continents and oral niches. Saliva-derived strains of T. forsythia and P. gingivalis from Oceania and T. serpentiformis and P. pasteri from Asia show enrichment of pseudogenes related to ecological niche transitions. A phylogenetic analysis of the P. gingivalis major fimbrial protein gene fimA reveals the genes cluster by genotypes, and that no ancient genes are found in genotypes I and Ib. Using de novo assembly for bacterial pangenomics improves the representation of oral genera found in reference databases and enhances our ability to study the evolutionary history of these taxa.}, }
@article {pmid42252693, year = {2026}, author = {Jourdain, L and Leininger, A and Pacheco, AR and Gu, W}, title = {Environmental selection constrains metabolic network architecture despite taxonomic turnover in anaerobic digestion communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag145}, pmid = {42252693}, issn = {1751-7370}, abstract = {Microbial ecosystems often sustain stable metabolic functions despite pronounced taxonomic turnover, yet the mechanisms underlying such reproducible functional states remain poorly understood. Here, we investigated how physicochemical constraints shape functional convergence in anaerobic digestion communities using replicated serial enrichments seeded from four distinct inocula. Across three pH levels and six substrate regimes, replicate communities from different inocula consistently converged toward reproducible metabolite profiles, with pH emerging as the dominant organizing factor. Community composition became progressively environment-driven over time, and after 30 generations, pH explained the largest fraction of compositional variance (PERMANOVA R2 = 0.21, P = 0.001), followed by substrate. Genome-resolved metagenomics revealed that convergence was accompanied by strong pH-dependent structuring of redox-balancing and terminal electron-sink pathways, whereas upstream carbohydrate-entry pathways were conserved. Taxonomic convergence was incomplete and scale-dependent: the ability to correctly assign communities to their inoculum declined from 75% at the genus level to 53% at the phylum level, indicating increasing similarity across inocula at coarser taxonomic resolution despite persistent fine-scale variability. Despite this taxonomic flexibility, communities assembled under identical conditions consistently recruited similar sets of metabolic pathways organized into comparable network architectures. Functional redundancy analyses showed high redundancy and flexible taxonomic implementation for upstream fermentative processes, contrasted with lower redundancy and stronger convergence for terminal methanogenic functions. Together, these results demonstrate that reproducible metabolic function in AD emerges from environmentally constrained assembly of shared metabolic network architectures, rather than deterministic fixation of species composition, highlighting environmental control of metabolic organization as a central principle governing microbiome function.}, }
@article {pmid42252802, year = {2026}, author = {Stang, A and Illig, T and Hiller, K and Weilert, H and Schmidt, R and Gronauer, R and Seifert, M}, title = {Lowered Abundance of Gut Bacteriophage Species Is Associated With Human Cancer Cachexia.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {17}, number = {3}, pages = {e70324}, doi = {10.1002/jcsm.70324}, pmid = {42252802}, issn = {2190-6009}, support = {3465//Asklepios Proresearch, Asklepios Hospitals Hamburg, Germany/ ; }, abstract = {BACKGROUND: Cancer cachexia exemplifies a high medical need condition without effective treatment. Recent studies implicated bacterial gut microbiome alterations to cancer cachexia. Whether the gut bacteriophage profile, an important microbiome component for health and disease, is also related to cancer cachexia remains unknown. We aimed to profile gut microbiome alterations in human cancer cachexia with attention on bacteriophages.<br><br>METHODS: We performed shotgun metagenomic sequencing in stool samples from 78 cachectic and 42 noncachectic patients (53% male, mean age 67&#x2009;&#xb1;&#x2009;8&#x2009;years) with newly diagnosed, advanced-stage (UICC IV) gastrointestinal cancers. Cachexia was defined according to the main criterion agreed upon international consensus (weight loss [WL] adjusted to body mass index [BMI]). Obtained DNA short-reads were used for k-mers-based, phage-inclusive matching with reference databases, de novo phage assembly and inferring microbiome-encoded functions. We replicated significance-based statistical and prediction-oriented machine-learning analyses in 2022 and 2025 generated metagenome datasets to incorporate the recent change by the International Committee on Taxonomy of Viruses (ICTV) from morphology-based (valid until 2022) to revised genome-based phage taxonomy into microbiome findings of cachexia.<br><br>RESULTS: Cachectic and noncachectic patients differed significantly regarding BMI (mean 20.9 vs. 26.4&#x2009;kg/m2), WL (mean -6.5 vs. -0.2&#x2009;kg), survival (median 5 vs. 13&#x2009;months) and clinical cachexia domains (e.g., C-reactive proteine and appetite loss) (all p&#x2009;<&#x2009;0.001) but not for other clinical covariables (e.g., cancer type) (all p&#x2009;>&#x2009;0.05). Read-based mapping (2022/2025) identified 1.312/1.513 species (74/39 phage species), and de novo assembly resulted in 4.184/4.209 contigs (corresponding to 65/39 phage species). Concordantly, both analyses (2022 and 2025) showed that prevalent cachexia associated significantly with beta-diversity (Bray-Curtis distance, PERMANOVA, p&#x2009;<&#x2009;0.05), but not to alpha-diversity (Shannon-Index, ANOVA, p&#x2009;>&#x2009;0.05), reduced microbiome-encoded detoxification functions (e.g., enriched microbial &#x3b2;-glucuronidase and depleted bacterial efflux pumps) and lowered abundance of bacterial species with false-discovery-rate (FDR)-corrected p&#x2009;<&#x2009;0.05 (2022: Faecalibacterium prausnitzii, Roseburia intestinalis, Streptococcus species and Lachnospiraceae species; 2025: Faecalibacterium species, Ruminococcus gauvreauii and Intestinibacter bartlettii). Further, lowered abundance of bacteriophages associated with cachexia, predominantly affecting double-stranded (2022: Caudovirales, Siphoviridae, FDR-corrected p&#x2009;<&#x2009;0.05; 2025: Myoviridae, Siphoridae, p&#x2009;<&#x2009;0.05) but also single-stranded (2022: Inoviridae, Microviridae, p&#x2009;<&#x2009;0.05; 2025: Inoviridae; p&#x2009;<&#x2009;0.05) DNA phage species. In machine-learning models, bacteriophages were top-ranked cachexia predictors (2022: Caudovirales, Siphoviridae; 2025: Myoviridae, Siphoridae). Accuracy was highest when only phage contigs were taken into account (correctly classified instances: 75.0%-85.8%; AUC: 0.703-0.916).<br><br>CONCLUSIONS: The previously unknown link between gut bacteriophages and human cancer cachexia expands the scope for basic, translational and clinical microbiome-targeted research in an area of significant unmet medical need.<br><br>TRIAL REGISTRATION: Study Box of the German Cancer Society (Registration Number ST-U069, Date: 29 May 2018).}, }
@article {pmid42253890, year = {2026}, author = {Liu, Y and Xie, H and Song, Z and Huang, M and Li, M}, title = {Massive ascites and adnexal masses mimicking malignancy: A case report of Chlamydia trachomatis infection diagnosed by metagenomic next-generation sequencing.}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02616}, pmid = {42253890}, issn = {2214-2509}, abstract = {OBJECTIVE: Chlamydia trachomatis (C. trachomatis) is the most commonly reported bacterial sexually transmitted infection among sexually active women. Although often asymptomatic or associated with non-specific clinical manifestations, it can cause inflammatory exudates and encapsulated fluid collections that are similar to adnexal masses on imaging. In rare cases, it may also present with massive ascites, a constellation of findings that may mimic ovarian malignancy.<br><br>CASE: We report the case of a 32-year-old female with a nearly 3-month history of abdominal pain, adnexal masses and massive ascites. The initial workup did not reveal obvious evidence of infection and cytological examination showed no malignant cells. However, advanced gynecological originated cancer could not be fully excluded. Metagenomic next-generation sequencing (mNGS), which detected C. trachomatis in ascitic fluid, facilitated the diagnosis. The patient showed satisfactory clinical improvement following doxycycline treatment.<br><br>CONCLUSION: For young, sexually active women presenting with unexplained ascites and adnexal masses, after excluding malignancy and common infectious diseases such as tuberculosis, C. trachomatis infection should be considered. Modern etiological detection methods, such as mNGS, can be employed to facilitate the diagnosis.}, }
@article {pmid42254105, year = {2026}, author = {Habib, E and Urooj, I and Barry, HD and Awais, M and Kumari, M and Hajj, F}, title = {AI-programmable therapeutics via metagenomic foundation models for rare phage-mediated autoimmune modulations: early translational risks and benefits.}, journal = {Annals of medicine and surgery (2012)}, volume = {88}, number = {6}, pages = {3905-3906}, pmid = {42254105}, issn = {2049-0801}, }
@article {pmid42254157, year = {2026}, author = {Arif, L and Abbasi, MM and Raza, AA and Samadi, A}, title = {From microbiome profiling to precision medicine: diagnostic and therapeutic potential in gastrointestinal disorders: current evidence, challenges, and future directions.}, journal = {Annals of medicine and surgery (2012)}, volume = {88}, number = {6}, pages = {3348-3359}, pmid = {42254157}, issn = {2049-0801}, abstract = {Gastrointestinal (GI) disorders, affecting millions globally (approximately 1.5 billion people with IBS alone), impose a significant healthcare burden and remain challenging to diagnose and manage. Current approaches are often invasive or symptom based, highlighting an urgent need for more precise and personalized strategies. The gut microbiome may offer novel diagnostic biomarkers and therapeutic targets, potentially transforming patient care. It supports GI and systemic health via metabolism, immune modulation, and neurochemical signaling. The dysbiosis of the gut microbiota contributes significantly to the pathogenesis of various GI disorders, including inflammatory bowel disease (IBD), irritable bowel syndrome (IBS), colorectal cancer (CRC), and small intestinal bacterial overgrowth. This narrative review critically evaluates the diagnostic potential of microbiome profiling and its clinical applications in developing personalized therapeutic strategies. We examine cutting-edge techniques such as 16S rRNA sequencing, metagenomics, and metabolomics, and discuss how dietary modulation, precision probiotics, and fecal microbiota transplantation are being increasingly used to reshape gut microbial composition. However, it is critical to note that while microbiome alterations show consistent associations with GI diseases, current evidence remains largely observational and associative. To date, no microbiome-based test has achieved regulatory approval or clinical validation as a standalone diagnostic tool for IBD, IBS, or CRC, and therapeutic applications remain investigational with modest clinical benefits in select conditions. Additionally, we highlight the translational challenges of integrating microbiome-based diagnostics into mainstream clinical practice and propose future research imperatives. This review provides a balanced perspective on the promise and challenges of integrating microbiome-based approaches into clinical gastroenterology, while proposing actionable research priorities to guide future investigations toward clinically validated, patient-centered diagnostic, and therapeutic solutions.}, }
@article {pmid42254407, year = {2026}, author = {Liang, Y and Hu, J and Wang, Z}, title = {A case of severe psittacosis in a hemodialysis patient-the critical role of detailed medical history and next-generation sequencing.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1825118}, pmid = {42254407}, issn = {2296-858X}, abstract = {An 80-year-old male patient on maintenance hemodialysis was admitted with "high fever and cough." Pulmonary imaging suggested pneumonia, but his condition deteriorated rapidly despite empirical broad-spectrum antimicrobial therapy (covering bacteria, atypical pathogens, and fungi), progressing to respiratory failure and delirium. He was transferred to the intensive care unit for continuous renal replacement therapy. Routine microbiological tests (blood culture, sputum culture, respiratory pathogen PCR) were all negative. Detailed history revealed that the patient had kept a parrot for over a month prior to illness onset. Metagenomic next-generation sequencing of blood and sputum specimens detected abundant Chlamydia psittaci sequences. Following confirmation, treatment was adjusted to oral minocycline combined with intravenous azithromycin. The patient's temperature gradually normalized, neuropsychiatric symptoms resolved, and pulmonary imaging showed marked improvement, ultimately leading to successful discharge. This case highlights the importance of considering zoonotic pathogens in immunocompromised patients with refractory pneumonia. Detailed history-taking and metagenomic next-generation sequencing (mNGS) technology are crucial for early diagnosis. Early use of mNGS should be strongly considered in immunocompromised patients with severe pneumonia unresponsive to empiric therapy and negative routine workup, particularly when epidemiological clues such as bird exposure are present.}, }
@article {pmid42254409, year = {2026}, author = {Kong, H and Pan, J and Liu, J and Liang, M and Liu, L and Niu, H and Li, Y}, title = {Successful management of severe Pneumocystis jirovecii pneumonia with inhaled nitric oxide and individualized ventilatory strategies in an immunosuppressed patient: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1808578}, pmid = {42254409}, issn = {2296-858X}, abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) have improved survival in extensive-stage small-cell lung cancer (SCLC) but may cause checkpoint inhibitor pneumonitis (CIP). Management of CIP often requires prolonged high-dose corticosteroids, leading to profound immunosuppression and increased risk of opportunistic infections. Among these, Pneumocystis jirovecii pneumonia (PJP) is a life-threatening complication in non-HIV patients and carries higher mortality than HIV-associated PJP. Early etiological diagnosis is therefore essential. We report a case of severe PJP diagnosed by metagenomic next-generation sequencing (mNGS) and successfully managed with comprehensive respiratory support.<br><br>CASE PRESENTATION: A 69-year-old HIV-negative man with extensive-stage SCLC received four cycles of etoposide-platinum chemotherapy plus adebrelimab. Subsequently, CIP developed and required prolonged high-dose methylprednisolone therapy. He was transferred to our hospital for progressive dyspnea. Evaluation showed severe hypoxemia (PaO&#x2082;/FiO&#x2082; 185&#x202f;mmHg) and markedly elevated serum 1,3-&#x3b2;-D-glucan (3327.99&#x202f;pg./mL). Bronchoalveolar lavage fluid mNGS identified P. jirovecii as the predominant pathogen, with Klebsiella pneumoniae, Pseudomonas aeruginosa, and Candida albicans indicating mixed pulmonary infection. The patient received trimethoprim-sulfamethoxazole, cefoperazone-sulbactam, and caspofungin. Worsening respiratory failure required endotracheal intubation and mechanical ventilation. Lung recruitment maneuvers, individualized positive end-expiratory pressure titration, and adjunctive inhaled nitric oxide progressively improved oxygenation, allowing successful extubation and eventual discharge.<br><br>CONCLUSION: Severe PJP should be considered in non-HIV patients receiving corticosteroids for CIP. mNGS enabled rapid pathogen identification and targeted therapy. Comprehensive respiratory support, including optimized mechanical ventilation and inhaled nitric oxide, may be valuable in managing life-threatening opportunistic infections in immunosuppressed patients.}, }
@article {pmid42254474, year = {2026}, author = {Sparaciari, FE and Saylors, K and Chan, M and Perez, S and Firth, C and Horwood, PF and Karlsson, EA}, title = {Operationalizing metagenomic data from environmental surveillance for one health decision-making in live animal markets: Findings from a multisectoral workshop in Cambodia.}, journal = {Dialogues in health}, volume = {8}, number = {}, pages = {100312}, pmid = {42254474}, issn = {2772-6533}, abstract = {BACKGROUND: Live animal markets (LAMs) are recognized as hotspots for zoonotic disease emergence. Environmental surveillance (ES), particularly when paired with metagenomic sequencing, offers an advanced and actionable approach to pathogen detection in high-risk settings. However, the complexity of metagenomic data and the lack of user-friendly communication tools hinder its integration into routine public health decision-making.<br><br>METHODS: We conducted an exploratory qualitative participatory workshop study with descriptive analysis. A three-day multisectoral workshop was held in Phnom Penh, Cambodia, in May 2024, bringing together stakeholders from health, agriculture, and environment sectors to explore how metagenomic ES data can be visualized, understood, and applied. Through simulation exercises, surveys, and interviews, the workshop evaluated user preferences for data formats, thresholds for action, and decision-making strategies.<br><br>FINDINGS: In total, 52 participants attended the workshop and ten completed semi-structured interviews. Participants discussed their preferred familiar visualizations (bar, pie, and line charts) and intuitive color-coded thresholds (e.g., traffic-light schemes). While digital dashboards were welcomed, analog, printer-friendly formats remained essential due to infrastructure constraints. Key barriers to ES integration included limited bioinformatics capacity, lack of inter-ministerial coordination, and minimal ES prioritization at the provincial level.<br><br>INTERPRETATION: Metagenomic ES data can inform public health actions when visualization tools are tailored to end-user needs and embedded in multisectoral governance. This exploratory participatory workshop generated preliminary stakeholder-informed insights and an initial draft roadmap for future implementation planning in Cambodia. Further expert-led and funded work is needed to validate visualization tools, pathogen-specific thresholds, escalation pathways, and operational use under real-world surveillance conditions.}, }
@article {pmid42254492, year = {2026}, author = {Chang, Z and Wang, X and Zhao, M and Zhang, X and Li, S and Liu, Y and Zhang, S and Wang, J and Wang, X}, title = {MARM: a framework for malignancy risk prediction from host-derived CNV in bronchoalveolar lavage fluid mNGS data with microbial admixture.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1846545}, pmid = {42254492}, issn = {1664-302X}, abstract = {Early identification and risk assessment of malignancy are essential for improving clinical decision-making and patient outcomes. Bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) data contain both microbial and host-derived signals, and a key challenge in extending such data to tumor-associated applications is the robust extraction of host features with discriminative value for malignancy from this complex, admixed background. To address this problem, we developed MARM, a malignancy risk prediction method centered on host-derived copy number variation (CNV). Using host-derived reads from BALF mNGS data, MARM performs genome-wide window-based coverage quantification, normalization and bias correction, reference baseline construction, and principal component-based denoising to derive window-level CNV features for malignancy risk modeling. In addition, a pseudo-label-based extension strategy was introduced to incorporate weakly labeled samples through high-confidence screening, and the performance of XGBoost, Random Forest, and generalized linear models (GLM) was systematically evaluated using CNV features, microbial features, and combined features. Models built on host-derived CNV features consistently outperformed those based on microbial features and achieved performance comparable to combined-feature models, while joint modeling did not provide a stable additional benefit. These findings indicate that, under the current data setting and feature construction strategy, CNV represents a more stable and informative discriminative signal than microbial features. Among the evaluated classifiers, XGBoost showed the best compatibility with window-level CNV features and outperformed Random Forest and GLM overall. On the independent validation set, the pseudo-label-enhanced MARM achieved the best overall performance, with a sensitivity of 0.686, specificity of 0.975, accuracy of 0.847, and Youden index of 0.671. By contrast, microbial features did not show stable independent discriminative ability, and combined modeling did not yield clear or sustained performance gains. Together, these results indicate that, in microbially admixed BALF mNGS data, host-derived CNV is more suitable than the evaluated microbial features as the core modeling signal for malignancy risk prediction. MARM provides a new methodological framework for malignancy prediction in complex clinical samples and offers a reference for deeper exploitation of host-derived signals in mNGS data and related auxiliary diagnostic applications.}, }
@article {pmid42254517, year = {2026}, author = {Liu, S and Luo, X and Zhou, J and Wang, L and Li, R and Luo, Z and Li, N and Xiao, S and Zhang, P}, title = {A comparative study of the gut microbiome and fecal metabolome in hypertensive patients from middle-temperate and tropical cities of China: Daqing and Haikou.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1801806}, pmid = {42254517}, issn = {1664-302X}, abstract = {BACKGROUND: Geographic variations in climate and lifestyle may be associated with hypertension (HTN) through alterations in the gut microbiota and its metabolites. This study aimed to comparatively analyze the gut microbiome and fecal metabolome of hypertensive patients from two Chinese cities characterized by distinct climatic conditions: Daqing (middle-temperate climate) and Haikou (tropical climate). The objective was to identify gut microbial and metabolic characteristics associated with geographic differences and to provide insights into HTN prevention and management.<br><br>METHODS: A cross-sectional study was conducted between May and December 2024, involving hypertensive patients from Daqing and Haikou. Fecal samples were collected from 28 hypertensive patients in Daqing (DQ group) and 32 in Haikou (HK group), and analyzed using shotgun metagenomic sequencing and untargeted metabolomics.<br><br>RESULTS: Differences in microbial composition and metabolite profiles were observed between the two groups. Using ALDEx2 analysis at the genus level, 34 genera were identified as differentially abundant between the DQ and HK groups. After adjusting for potential confounding variables, including age, body mass index, smoking, and drinking status, 6 genera remained significantly associated with geographic grouping. A logistic regression model based on these genera achieved an area under the curve (AUC) of 0.8069, with Pseudescherichia showing the highest individual discriminatory performance (AUC&#x202f;=&#x202f;0.7925). Functional analysis suggested that pathways such as xylene degradation and biofilm formation were relatively reduced in the DQ group. Metabolomic analysis identified 38 differentially abundant metabolites, including 15-hydroxyeicosatetraenoic acid (15-HETE), 7&#x3b1;,25-dihydroxycholesterol, the putative metabolite (3-hydroxypentadecanoyl) lysine, and ginsenoside Rg3. Dysregulated pathways were mainly involved in glycerophospholipid metabolism, ABC transporters, and choline metabolism. Correlation analysis revealed potential associations between differential microbes and metabolites.<br><br>CONCLUSION: Distinct gut microbiome and metabolome profiles were observed between hypertensive patients from the two geographic regions. These findings suggest potential associations between environmental factors and host-microbiome-metabolite interactions.}, }
@article {pmid42254837, year = {2026}, author = {Schmelz, P and Eckensperger, S and Osvatic, J and Séneca, J and Alzubaidy, H and Petersen, JM}, title = {Host depletion kits improve microbiome analyses in environmental samples: seagrass as a test case.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag082}, pmid = {42254837}, issn = {2730-6151}, abstract = {All plants and animals associate with specific communities of symbiotic microorganisms. Characterizing the diversity and functions of these communities is essential for understanding their roles in host health; however, such efforts are often hindered by the dominance of host-derived material in, e.g. DNA extractions. Although various commercial host DNA depletion kits have been developed to overcome these challenges, they have not yet been systematically tested on environmental samples. We used Zostera marina, globally the most widespread seagrass species, as a test case to assess the effectiveness of three different commercially available host DNA depletion kits: QIAamp DNA Microbiome Kit, HostZero Microbial Enrichment Kit, and NEBNext Microbiome DNA Enrichment Kit, when compared to the widely used DNeasy PowerSoil Pro Kit. All three host depletion kits substantially reduced the relative proportion of host DNA, as assessed by 16S rRNA gene amplicon sequencing, and enriched previously identified seagrass-associated bacteria. Furthermore, in metagenomes, only samples processed with host depletion methods allowed for the assembly of metagenome-assembled genomes with high completeness and low contamination. Metagenomic analysis further enabled the recovery of seagrass root core microbiome members, including previously undetected members of the family Sedimenticolaceae, highlighting the value of these techniques for uncovering novel host-associated microbial diversity in environmental samples such as marine plants.}, }
@article {pmid42255303, year = {2026}, author = {Xue, G and Hu, Y and Xue, H and Wang, X and Bai, H and Du, J and Wang, Y and Huo, H and Li, M and Jiang, W}, title = {Biochar enhances cucumber production by modulating rhizosphere microbiota and soil metabolites under continuous cropping systems.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1726191}, pmid = {42255303}, issn = {1664-462X}, abstract = {Biochar, a soil amendment with diverse regulatory functions, has been widely applied to enhance soil conditions. However, its underlying mechanism for alleviating continuous cropping obstacles, from the perspective of rhizosphere microbe-metabolite-plant coupling, remains to be further elucidated. Using cucumber (Cucumis sativus L.) as the model crop, this study explored the rhizosphere-mediated effects of biochar application under continuous cropping conditions via the analytical methods of metagenomics and metabolomics. Six biochar application rates (0, 5, 10, 20, 30, and 40 t ha[-][1]) were tested. All biochar treatments significantly improved cucumber yield by 20%-50%, with the C30 and C40 treatments producing the most pronounced yield enhancement. C10, C20, C30 and C40 treatments had a positive effect on cucumber quality, soil physicochemical properties and enzymatic activities. Vitamin C and soluble protein peaked in C20, whereas some sugar indicators decreased across all biochar treatments. Urease activity was significantly elevated under C20, C30, and C40 treatments. Notably, the C40 treatment led to marked increases in total nitrogen, available phosphorus, and sucrase activity. Biochar amendments also enriched key bacterial phyla involved in carbon and nitrogen cycling, including Actinobacteria, Bacteroidetes, Chloroflexi, and Bacillota. Medium to high application rates (C20, C30, C40) upregulated various secondary metabolic pathways associated with biotic stress resistance, including the biosynthesis pathways of phenylpropanoids, various alkaloids, and the metabolic pathway of phenylalanine. High biochar application rate (C40) characterized lipid metabolism as the core responsive pathway and significantly downregulated galactose metabolism. This study reveals that biochar application represents a promising strategy to mitigate continuous cropping obstacles of cucumber by enhancing nutrient cycling, enzyme activities, soil metabolite composition, and the rhizosphere microbial community in facility systems of the cold and arid northern regions of China.}, }
@article {pmid42255362, year = {2026}, author = {Sun, Y and Kei, K and Qiu, JW and Martín-Durán, JM and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the feather duster worm, Sabellastarte sp. h YS-2021 (Sabellida: Sabellidae) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {11}, number = {}, pages = {274}, pmid = {42255362}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Sabellastarte sp. h YS-2021 (feather duster worm; Annelida; Polychaeta; Sabellida; Sabellidae). The genome sequence has a total length of 1 786.39 megabases. Most of the assembly (97.94%) is scaffolded into 14 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 15.35 kilobases. From the metagenome data, we recovered 5 bins, of which one was a high-quality MAG.}, }
@article {pmid42255501, year = {2026}, author = {Huo, S and Liu, W and Lv, C and Liu, B and Xue, J and Hong, Y and Hao, Y and Chen, M and Xu, A and Tan, X and Feng, X and Li, S}, title = {The re-emergence of psittacosis in China: a scoping review of epidemiology, diagnostics, and One Health priorities.}, journal = {Science in One Health}, volume = {5}, number = {}, pages = {100158}, pmid = {42255501}, issn = {2949-7043}, abstract = {Psittacosis caused by Chlamydia psittaci has re-emerged in China as sporadic cases and localized outbreaks. However, current knowledge remains fragmented across the clinical, veterinary, epidemiological, and public health fields. This scoping review mapped studies on psittacosis in China, identified major knowledge gaps, and defined priorities for research, clinical management, and prevention and control. Following the Arksey and O'Malley framework and Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR), China National Knowledge Infrastructure (CNKI), Wanfang, PubMed, Web of Science, and Embase were searched for studies published between 1 January 1985 and 31 December 2025 and synthesized eligible studies with descriptive statistics and thematic analysis. A total of 424 studies were included. Research interest showed recent sharp increases and was concentrated in Eastern and Central China. Case reports and series dominated the literature, whereas analytic epidemiology, standardized surveillance, and high-resolution molecular studies remained limited. Reported cases were most often documented in middle-aged and older adults with avian exposure, including pet birds and poultry, and the reported occurrence showed a winter-spring pattern. Pneumonia was the predominant clinical presentation, and severe cases could progress to acute respiratory distress syndrome and multi-organ dysfunction. Metagenomic next-generation sequencing (mNGS) was the most frequently reported diagnostic method in recent studies, while PCR and serology remained important complementary tools. Overall, the literature is growing rapidly, but remains uneven in geographic coverage, study design, and integration across human, animal, and environmental sectors. These findings support broader One Health surveillance, stronger analytic and molecular epidemiology, and more standardized approaches to diagnosis, source investigation, and prevention in China.}, }
@article {pmid42256215, year = {2026}, author = {Li, C and Ye, X and Chen, Y and Shen, M and Zhou, Z and Jiang, H and Hu, L and Pan, H and Shen, D and Lin, Y and Wang, L}, title = {Pathogen spectrum of pulmonary infections in kidney transplant recipients and the diagnostic value of mNGS: a sputum and BALF study based on clinical decision-making.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1742153}, pmid = {42256215}, issn = {2235-2988}, abstract = {BACKGROUND: Pulmonary infection is a common and severe post-transplant complication in kidney transplant recipients (KTRs). Their long-term immunosuppression results in an extremely complex pathogen spectrum. Compared with conventional etiological detection methods, metagenomic next-generation sequencing (mNGS) enables rapid and broad-spectrum pathogen identification. However, compared with bronchoalveolar lavage fluid (BALF), research on the diagnostic value of sputum - used as a non-invasive sample - for pulmonary infections in KTRs remains limited.<br><br>METHODS: A retrospective study included 77 kidney transplant recipients (KTRs) with pulmonary infections admitted from July 2021 to January 2025. BALF (n=37) or sputum (n=40) was collected for mNGS. Ninety-two non-immunosuppressed patients with pulmonary infections, treated during the same period and with BALF for mNGS, were also included. We compared pathogen profiles between the two groups and evaluated the diagnostic performance for KTRs pulmonary infections between BALF and sputum.<br><br>RESULTS: The pathogen spectrum in KTRs was dominated by viruses (43.0%) and opportunistic fungi (20.0%), whereas bacteria (67.97%) predominated in the non-immunosuppressed group. The co-infection rate was significantly higher in KTRs than in the non-immunosuppressed group (67.57% vs. 35.87%, P<0.001). In the KTRs cohort, the sputum group had a much higher prevalence of heart disease than the BALF group (52.5% vs. 2.7%, P<0.001). The positive detection rates of sputum and BALF mNGS showed no statistical difference (97.5% vs. 91.89%, P&#xa0;=&#xa0;0.268), but sputum mNGShad a higher concordance rate with the clinical composite diagnosis (95.0%) compared to BALF mNGS (81.08%). In both specimen types, mNGS achieved a significantly higher pathogen detection rate than conventional tests (P<0.001 for both), with poor agreement between the two approaches (Kappa < 0.2).<br><br>CONCLUSION: The pathogen spectrum of pulmonary infections in KTRs differs significantly from that in non-immunosuppressed patients. It is characterized by a predominance of viruses and opportunistic fungi. mNGS is superior to conventional methods for making an etiological diagnosis. Non-invasive sputum mNGS is a valuable diagnostic alternative in KTRs, particularly for patients unable or unwilling to undergo invasive procedures.}, }
@article {pmid42256221, year = {2026}, author = {Giju, JK and John, S and Sivadas, A and Prabhakar, M and K, K and Sunilkumar, D and Nair, BG and Pal, S and Prakash, V}, title = {From dysbiosis to precision medicine: targeting the microbial-metabolic axis in IBD management.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1826972}, pmid = {42256221}, issn = {2235-2988}, abstract = {Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory condition that has a rapidly changing global epidemiology. IBD has been traditionally viewed as a primary immune system dysfunction, but emerging evidence more accurately describes IBD as a perturbance of the intricate balance between host immunity, the intestinal microbiome, and intestinal metabolism. Although genetic and environmental components have long been recognized as contributors, accumulating evidence increasingly highlights the pivotal role of microbial dysbiosis in the pathogenesis of IBD. In patients with IBD, intestinal dysbiosis, which is often characterized by reduced Firmicutes and increased pro-inflammatory bacteria, triggers a cascade of pathogenic events. These pathogenic events include impaired epithelial barrier function, dysregulated immune activation against luminal antigens, and immune reprogramming. Central to these processes are functional changes in microbial metabolism, particularly in pathways involving short-chain fatty acids (SCFAs), bile acids, and redox homeostasis, which critically contribute to the development of chronic mucosal inflammation. The current therapeutic backbone of IBD-including aminosalicylates, biologics, and immunomodulators-largely targets the inflammatory response. However, the challenges such as primary non-response, secondary loss of response, and systemic side effects are often problematic. Consequently, there is an urgent need to develop novel therapeutic and preventive strategies that target the underlying microbial and metabolic causes of the disease rather than modulating immune responses. This review integrates the pathomechanistic implications of the microbiome-metabolic axis in the maintenance of gut homeostasis and its disruption in IBD, with particular emphasis on the global epidemiology of the disease. We further evaluate emerging therapeutic and preventive strategies aimed at restoring the microbiome-metabolic axis, including fecal microbiota transplantation (FMT), probiotic therapy, bacteriophage therapy, and helminth-based therapies. In addition, we explore the potential of advanced approaches such as microbiome engineering and precision genome editing to enable highly personalized therapeutic paradigms. By bridging microbial ecology with clinical pathology, this review highlights the transformative potential of targeting the host-microbiota interface to achieve improved long-term outcomes in IBD.}, }
@article {pmid41654194, year = {2026}, author = {Wei, P and Zhang, L and Hu, Q and Zhu, A and Zhuang, Z and Zhang, Z and Zhang, S and Chen, J and Xiong, X and Qu, B and Zhang, Y and Chen, L and Xu, Z and Chen, Z and Zhong, Q and Xing, X and Li, X and Gao, J and He, Y and Xie, G and Shang, J and Guo, X and Jiang, J and Shi, Y and Zhao, J and Wang, Y and Zhao, J and Jin, Y}, title = {Integrated multiplex PCR and metatranscriptomics reveal upper-lower airway microbial landscapes in pediatric respiratory infections.}, journal = {Virologica Sinica}, volume = {41}, number = {1}, pages = {58-69}, pmid = {41654194}, issn = {1995-820X}, mesh = {Humans ; *Respiratory Tract Infections/microbiology/virology ; *Multiplex Polymerase Chain Reaction/methods ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Female ; Male ; Child, Preschool ; Infant ; *Microbiota/genetics ; Child ; *Bacteria/genetics/classification/isolation &amp; purification ; Nasopharynx/microbiology/virology ; Gene Expression Profiling ; Viruses/genetics/isolation &amp; purification/classification ; Metagenomics ; }, abstract = {Despite widespread use of multiple PCR, a substantial proportion of pediatric acute respiratory tract infections (ARTIs) lack identifiable pathogens and are classified as unknown etiology. The microbial characteristics and clinical relevance of these cases remain unclear. In this study, we compared the airway microbiomes of PCR-positive and PCR-negative ARTIs and examined their relationships with sampling site and disease severity. A total of 514 hospitalized children with ARTIs were enrolled. Nasopharyngeal swabs (NS) and bronchoalveolar lavage fluid (BALF) samples were tested using a 22-target multiplex PCR panel and subsequently stratified by pathogen status for pooled metatranscriptomic sequencing to profile active microbial communities, viral genotypes, and antibiotic resistance genes. PCR identified common respiratory pathogens in 77.0% of NS and 54.1% of BALF samples. Metatranscriptomic analysis showed that PCR-negative pools displayed markedly lower viral activity and comparatively higher bacterial transcript abundance, with notable enrichment of Pseudomonas. Microbial signatures differed between upper and lower airway samples and across clinical severity, with severe cases demonstrating increased bacterial burden and Pseudomonas enrichment, whereas mild infections exhibited relatively stronger viral signals. Under current thresholds, antibiotic resistance genes were detected in patient pools but not in healthy controls. Overall, PCR-negative pediatric ARTIs exhibited distinct, bacteria-enriched microbial profiles. Integrating metatranscriptomics with PCR enhances pathogen characterization and reveals site- and severity-related microbial patterns that may support diagnostic evaluation and clinical management.}, }
@article {pmid42249511, year = {2026}, author = {Stahl, S and Widmaier, H and Sakk, V and Nalapareddy, K and Kissmann, AK and Rosenau, F and Mulaw, MA and Haslam, DB and Geiger, H}, title = {Aging of the adaptive immune system affects the gut microbiome and systemic levels of vitamin B6.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42249511}, issn = {2049-2618}, support = {GRK 2254 HEIST//Deutsche Forschungsgemeinschaft/ ; }, abstract = {BACKGROUND: Age-associated dysregulation of the gut microbiota is a hallmark of aging and has been linked to multiple age-related diseases, yet upstream host factors driving these changes remain incompletely defined. Extensive bidirectional crosstalk between gut microbiota and mucosal immunity has been described. Aging is accompanied by a progressive decline in immune function, collectively termed aging-associated immune remodeling (AAIR). AAIR encompasses widespread compositional and functional changes that impair an effective response to pathogens, vaccines, and tissue damage. We examined whether AAIR is an upstream host factor influencing the composition of the microbiome upon aging.<br><br>RESULTS: Hallmarks of AAIR were also present in the ileal lamina propria, including reduced na&#xef;ve CD4[+] and CD8[+] T cell populations and expansion of memory and regulatory T cell subsets. To test whether mucosal AAIR reflects intrinsic aging of the hematopoietic system, we used an HSC transplantation model where young RAG1[-/-] recipients develop an adaptive immune system derived exclusively from either young or aged donor HSC in an otherwise young host environment. Recipients of aged HSCs recapitulated key features of mucosal AAIR, particularly loss of na&#xef;ve T cells, demonstrating that AAIR in the ileal LP is driven at least in part by aged HSCs. Shotgun metagenomic sequencing of fecal samples revealed that ileal AAIR is associated with alterations in gut microbiota. In detail, there was a reduced abundance of taxa associated with the vitamin B6 (VB6) biosynthesis and salvage pathways. Accordingly, VB6 levels in serum were reduced in mice with aged immune systems.<br><br>CONCLUSION: Our findings link AAIR to reduced microbial VB6 pathway abundance and lower systemic VB6 availability, suggesting that immune aging shapes the functional output of the microbiome in ways that diminish its VB6 biosynthetic capacity. This postulates an immune-microbiome-VB6 association that warrants further investigations for therapeutic strategies to increase VB6 levels upon aging. Video Abstract.}, }
@article {pmid42249581, year = {2026}, author = {Xi, Y and Liping, Z and Yating, X and Yang, X and Jian, C and Caiyun, C and Shuwen, L and Zian, Z and Xiaojian, Y and Shuwen, H and Wei, W}, title = {Genomic Map of Escherichia coli and Single Nucleotide Polymorphism Markers in Colorectal Cancer.}, journal = {Microbial biotechnology}, volume = {19}, number = {6}, pages = {e70397}, pmid = {42249581}, issn = {1751-7915}, support = {2023GZ86//Public Welfare Technology Application Research Program of Huzhou/ ; 2025KY328//Medical and Health Research Project of Zhejiang Province/ ; }, abstract = {Gut microbial single nucleotide polymorphisms (SNPs) offer stable, specific genetic markers for disease diagnosis. Escherichia coli (E. coli), a dominant gut bacterium, is associated with colorectal cancer (CRC), but limited enteric reference genomes hinder SNP annotation in intestinal strains. Metagenomic sequencing profiled gut microbiota in 200 CRC patients and 200 healthy controls. The E. coli strain WDP was fully sequenced via PacBio single-molecule technology for genome assembly and functional annotation. Wilcoxon tests identified differentially abundant microbes, while Lasso regression models integrated microbial features (bacteria, viruses, virus-host pairs) and E. coli SNPs to predict CRC risk. E. coli abundance did not differ between groups, but genomic analysis revealed 7460 CRC-associated SNPs. The SNP-based model achieved superior accuracy (92.86% training, 93.33% testing, 84.00% validation) and AUC (0.986, 0.983, 0.913), outperforming models based on microbial abundances (e.g., Staphylococcus capitis, Zindervirus) or virus-host interactions. PacBio-generated E. coli genomic maps enable precise SNP annotation, establishing E. coli SNPs as highly accurate biomarkers for CRC risk prediction. This approach leverages microbial genetic stability to advance non-invasive early detection, offering a novel target for precision microbiome-based diagnostics.}, }
@article {pmid42249721, year = {2026}, author = {Liu, H and Xu, J and Guo, Y and Lei, Z and Wang, N and Wei, W and Qu, L and Li, M and Feng, Y and Xie, W}, title = {Stepwise Gradient in Fundamental Individualised Niche Differentiation Across Soil Microbiomes.}, journal = {Molecular ecology}, volume = {35}, number = {11}, pages = {e70422}, doi = {10.1111/mec.70422}, pmid = {42249721}, issn = {1365-294X}, support = {SML2023SP218//Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 92051117//National Natural Science Foundation of China/ ; 41776137//National Natural Science Foundation of China/ ; }, abstract = {Individual microbes often respond differently to the same environment, yet the magnitude of such niche variation inherent to individuals remains unresolved and is anticipated to differ substantially from community-level average responses. We conducted metagenomic binning on monthly time-series soil samples from three sites across seasonal cycles. By considering 440,571 genes as dimensions of the fundamental individualised niche (FIN), we traced FIN trajectories of archaea and bacteria during warming, cooling, and turning periods. We found that neither mean temperature nor temperature difference had a significant effect on FIN breadth or overlap. Instead, we discovered a temporally constant, stepwise gradient of niche differentiation across taxonomic categories. At the interdomain level (Archaea vs. Bacteria), niche overlap is approximately 25%, rising to ~40% at the interphylum level and ~60% at the interorder level. This discontinuous gradient likely marks the limit boundaries of niche variation, is closely linked to functional synergy within FINs, and provides a preliminary comparable ecological carrying capacity for each niche step, particularly regarding the interdomain balance.}, }
@article {pmid42250066, year = {2026}, author = {Fu, Y and Jiang, H and Peng, D and Bai, Z and Wang, S and Liu, H and Zhang, W and Shang, W}, title = {Fecal Microbiome and Serum Metabolome Profiles of the Ovarian Failure Mouse Model.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {42250066}, issn = {1559-0291}, support = {KFKT-2024-KY-019//the Key Project Program of the 2024 Scientific Research Fund, Chinese Association of Rehabilitation Medicine/ ; }, abstract = {Ovarian dysfunction is closely associated with reproductive aging and systemic metabolic disturbances; however, the underlying microbial and metabolic mechanisms remain unclear. In this study, we analyzed fecal microbiome and serum metabolome profiles in young (7-week-old) and aged (12-month-old) female C57BL/6J mice using shotgun metagenomic sequencing and untargeted ultra-high-performance liquid chromatography-tandem mass spectrometry. Microbial and metabolic data were processed using QIIME2, HUMAnN, and MetaboAnalyst 5.0. Differential taxa and metabolites were identified using DESeq2 and linear discriminant analysis effect size (LEfSe), and their associations were evaluated using Spearman's correlation analysis. Our results showed that aged mice exhibited significant alterations in gut microbiota composition, including a decreased abundance of Firmicutes and an increased abundance of Bacteroidetes, along with enrichment of the genera Alistipes and Akkermansia. Serum metabolomic profiling identified 246 differential metabolites, primarily involved in amino acid and energy metabolism pathways. Integrated analysis revealed that tryptophan metabolism represents a key pathway linking microbial dysbiosis with systemic metabolic alterations. Notably, enriched microbial taxa, including Akkermansia muciniphila and species within the genus Alistipes, were strongly correlated with tryptophan-related metabolites. These findings indicate that ovarian failure is associated with coordinated alterations in the gut microbiome and serum metabolome, converging on tryptophan metabolism. This study provides new insights into host-microbiome-metabolite interactions in ovarian failure and highlights potential microbial and metabolic targets for therapeutic intervention.}, }
@article {pmid42250131, year = {2026}, author = {Gao, X and Qin, R and Li, S and Yang, Y and He, J}, title = {Congenital tuberculosis transmitted via the placenta: identification by metagenomic next-generation sequencing.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42250131}, issn = {1435-4373}, support = {grant number: kryc-yq-2127//Kuanren Talents Program of the second affiliated hospital of Chongqing Medical University/ ; }, abstract = {BACKGROUND: Congenital tuberculosis (CTB) is a rare disease with high mortality in neonates. Early diagnosis is crucial but often delayed due to atypical clinical and imaging manifestations.<br><br>CASE PRESENTATION: We report a 36-day-old female infant presenting with recurrent fever. Laboratory data showed leukocytosis and neutrophilia with mildly elevated C-reactive protein. Chest computed tomography revealed extensive ground-glass opacities, multiple subpleural nodules, and necrotic hilar and mediastinal lymphadenopathy. The asymptomatic mother was subsequently found to have diffuse miliary nodules on chest CT. Conventional tuberculosis tests (acid-fast smear, culture, GeneXpert, T-SPOT.TB) were negative in both the infant and mother. Metagenomic next-generation sequencing (mNGS) of the placental tissue detected 10 specific Mycobacterium tuberculosis sequences, and Ziehl-Neelsen staining confirmed acid-fast bacilli. Both mother and infant responded well to anti-tuberculosis therapy.<br><br>CONCLUSIONS: CTB should be considered in neonates with persistent pulmonary infection unresponsive to broad-spectrum antibiotics. Examination of placental tissue using mNGS is a valuable diagnostic tool for confirming transplacental tuberculosis transmission.}, }
@article {pmid42250135, year = {2026}, author = {Das, K and Jaiswal, P and Priya, H and Sangwan, S and Paul, S and Prasanna, R and Grover, M}, title = {Microbial innovations for climate-resilient agriculture: mechanisms, applications, and emerging technologies.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {7}, pages = {}, pmid = {42250135}, issn = {1573-0972}, abstract = {Agriculture is increasingly challenged by climate change-driven stresses, including rising temperatures, erratic rainfall, soil degradation, with increased frequency of pests and disease outbreaks. This disrupts crop productivity and threatens global food security, underscoring the urgent need for sustainable, adaptive strategies, which are environment-friendly. Microorganisms, integral to soil health, nutrient cycling, and plant stress physiology, offer promising nature-based solutions for climate resilient agriculture. Yet their potential remains underutilized due to technical, ecological, and socio-economic barriers that hinder widespread adoption. This review addresses these research gaps and practical challenges, while outlining future perspectives for scaling up microbe-based technologies through integration with omics and AI tools. The major points addressed in this review are (1) Major advances in microbial applications that directly support crop resilience and ecosystem sustainability. It examines recent progress made towards enhancing the effectiveness of biofertilizers (including mycorrhizal fungi), biopesticides and developing novel products, detailing how these innovations enhance nutrient acquisition, regulate phytohormonal balance, improve water-use efficiency, mitigate abiotic stresses such as drought, salinity, heat and pH, and minimize losses incurred due to pathogen and pests; (2) Mechanistic insights into microbial mediation of nutrient cycling, soil aggregation, and stress alleviation in terms of plant-microbe or soil-plant microbiome networking; (3) The role of emerging biotechnological tools, including metagenomics, microbiome engineering, and synthetic biology, that enable the design of more effective and context-specific microbial interventions that can be integrated with artificial intelligence (AI) and machine learning (ML) tools for precise application (4) Emphasis on both the benefits and constraints of microbial inoculants is documented as well as novel strategies for their effective use as sustainable solutions for climate ready agriculture. Ultimately, microbial innovations are positioned as pivotal in building climate-resilient agroecosystems capable of sustaining productivity and reducing environmental footprints.}, }
@article {pmid42250463, year = {2026}, author = {Xia, L and Lu, L and Liu, M and Jiao, J and Liu, L and Meng, L and Liu, Y and Li, W and Lu, C and Ma, B}, title = {Proposal of Edaphobacterium genomatis gen. nov., sp. nov. within the family Casimicrobiaceae from metagenome-assembled genomes in accordance with the SeqCode.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {4}, pages = {126735}, doi = {10.1016/j.syapm.2026.126735}, pmid = {42250463}, issn = {1618-0984}, abstract = {Casimicrobiaceae strains inhabit various environments, but their ecological roles in natural soils remain mostly unclear. By actively targeting specific high-altitude datasets during our Global Mollisols Genomic Atlas (GMGA) mining efforts, we discovered a previously unknown lineage within this family. This novel group is represented by five metagenome-assembled genomes (MAGs) recovered from oligotrophic soils in the Southern Brazilian Highland Grasslands, a unique environment within the broad Pampas black soil region. Phylogenetic and comparative genomic analyses showed these five MAGs form a distinct monophyletic clade within Casimicrobiaceae. Their novel taxonomic status is supported by Average Nucleotide Identity (ANI) thresholds, showing clear divergence from all known reference genomes. Functional annotations suggest a chemoorganotrophic lifestyle with microaerobic respiration capacity, while trace-gas scavenging genes indicate potential lithoheterotrophy for maintenance energy under nutrient limitation. Additionally, an autonomous ACC deaminase system and specialized nutrient scavenging pathways (organophosphonate and taurine utilization) highlight its adaptive capacity for rhizosphere interactions and survival in oligotrophic environments. Screening 22,976 public metagenomes demonstrated a widespread global distribution, primarily inhabiting diverse soil (86.4%) and plant-associated (7.0%) environments. Based on these analyses, we propose the name Edaphobacterium genomatis gen. nov., sp. nov. for this novel taxon following the SeqCode (Code of Nomenclature of Prokaryotes Described from Sequence Data) rules. Our results uncover hidden species diversity and highlight the specific functional roles of uncultured microbes in nutrient-limited highland niches within fertile black soil regions.}, }
@article {pmid42250813, year = {2026}, author = {Kadam, R and Jo, S and Panwar, NL and Kim, T and Park, J}, title = {Metagenomic insights into metabolic limitations and biosafety implications of rendered pig carcass anaerobic digestion.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135081}, doi = {10.1016/j.biortech.2026.135081}, pmid = {42250813}, issn = {1873-2976}, abstract = {Global livestock production has intensified, increasing the biosecurity and environmental risks associated with animal mortality management. This study evaluated the feasibility of anaerobic digestion (AD) as a sustainable valorization route for rendered pig carcasses using long-term performance monitoring and whole-metagenome shotgun sequencing. During operation at an organic loading rate (OLR) of 1.0-2.0 kg-VS/m[3]/d, the reactor achieved peak methane (CH4) yields of 400-430 mL-CH4/g-VS and an organic matter removal efficiency > 70%. The buffering capacity generated through carcass proteolysis contributed to maintaining reactor performance under increasing loading conditions. However, increasing the OLR to 3.0 kg-VS/m[3]/d triggered process instability, decreasing the CH4 yield and increasing the total volatile fatty acids (TVFAs) to > 6,000 mg/L, specifically dominated by propionic and butyric acids. Metagenomic analysis identified a specialized consortium dominated by the syntrophic acetogen Cloacamonas and acetoclastic methanogen Methanosaeta during reactor operation at moderate OLRs. Functional profiling revealed that although the community possessed efficient hydrolytic and syntrophic acetate oxidation pathways, propionic acid accumulation and lower completeness of propionate oxidation pathways suggested potential limitations in syntrophic propionate oxidation at elevated OLRs. Furthermore, biosafety-related assessments suggested that AD may offer potential biocontainment advantages over traditional carcass disposal methods based on reduced prevalence of antimicrobial resistance genes and virulence-associated factors. These findings provide a metabolic framework for optimizing carcass-based AD as a viable substrate for renewable energy recovery.}, }
@article {pmid42250815, year = {2026}, author = {Xie, C and Li, D and Li, J and Li, J and Yin, M and Wu, Y and Zhang, C and Luo, R and Zhu, Y and Zhang, Z and Zheng, Z and Peng, Y}, title = {Molecular mechanism of anammox granular sludge disintegration caused by polyethylene terephthalate micro/nanoplastics: a new perspective based on quorum sensing.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135060}, doi = {10.1016/j.biortech.2026.135060}, pmid = {42250815}, issn = {1873-2976}, abstract = {Quorum sensing (QS) regulates the synthesis and secretion of extracellular polymeric substances (EPS), which are essential for maintaining the structural stability of anaerobic ammonium oxidation (Anammox) granular sludge. However, the molecular mechanism linking polyethylene terephthalate micro/nanoplastics (PET-MNPs)-induced QS disruption to EPS inhibition remains unclear. This study investigated the effects of two PET-MNP sizes (80 μm and 300 nm) on Anammox granular sludge under different exposure concentrations. PET-MNPs significantly reduced nitrogen removal performance and caused surface cracking, structural loosening, and granule disintegration. EPS analysis showed that PET-MNPs decreased EPS content, altered protein secondary structure, and increased hydrophilic functional groups, thereby weakening sludge bioadhesion. Metagenomic and metatranscriptomic analyses indicated that PET-MNPs inhibited the abundance and expression of genes involved in the Anammox process, tricarboxylic acid cycle, glycolysis/gluconeogenesis, and Wood-Ljungdahl pathway, resulting in insufficient ATP, NADH, and metabolic precursors required for EPS synthesis. Meanwhile, methionine and fatty acid metabolism were suppressed, limiting precursor supply for acyl-homoserine lactone (AHL) synthesis. Molecular docking showed that PET oligomers could stably bind to LuxR and potentially hinder AHL-LuxR complex formation. Exogenous AHL supplementation promoted EPS re-secretion, confirming the important role of QS imbalance in PET-MNPs-induced EPS reduction. Overall, PET-MNPs destabilized Anammox granular sludge through the combined effects of particle-induced physical damage and oligomer-mediated molecular interference. This study elucidates the molecular mechanism of MNP-induced Anammox granule disintegration and provides a theoretical basis for assessing the ecological risks of emerging pollutants in biological wastewater treatment.}, }
@article {pmid42250818, year = {2026}, author = {Liu, Y and Qian, Z and Peng, Y and Zhang, T and Li, Z and Shi, S and Gu, H}, title = {Enhancing ethanol-driven chain elongation via iron speciation: impacts on metabolic flux and dual FAB/RBO pathway activation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135088}, doi = {10.1016/j.biortech.2026.135088}, pmid = {42250818}, issn = {1873-2976}, abstract = {Anaerobic chain elongation (CE) has emerged as a promising technology for upgrading low-value organic substrates into high-value medium-chain fatty acids (MCFAs); however, achieving targeted metabolic flux and efficient electron transfer remains challenging. To address this, this study explores the role of iron speciation in enhancing chain elongation (CE) driven by ethanol. Two iron-modified activated carbons, Fe3O4@AC and ZVI@AC, were evaluated to assess their impact on microbial metabolic networks. Results revealed that Fe3O4@AC significantly enhanced caproate production (4600.0 mg/L) and electron transfer efficiency (87.0 %), while ZVI@AC triggered a diversion towards alcohol production (940.61 mg/L n-butanol). The superior performance of Fe3O4@AC was attributed to its semiconductive properties, which facilitated interspecies electron transfer (potentially via DIET-like mechanisms) and balanced electron flow, promoting the activation of both fatty acid biosynthesis (FAB) and reverse β-oxidation (RBO) pathways. Metagenomic analysis revealed a shift in microbial community composition, with Massilibacterium enrichment under Fe3O4@AC, highlighting the importance of tailored material design for targeted MCFA production. These findings provide insights into optimizing microbial metabolism for enhanced CE efficiency.}, }
@article {pmid42248018, year = {2026}, author = {Park, S and Shin, JH and Lee, HH and Lee, JG}, title = {Cover crop incorporation maintains the methane oxidation potential and lowers methane emissions in plastic-film-mulched upland arable soils.}, journal = {Journal of environmental management}, volume = {410}, number = {}, pages = {130115}, doi = {10.1016/j.jenvman.2026.130115}, pmid = {42248018}, issn = {1095-8630}, abstract = {Plastic film mulching can transform upland arable soils from sinks for methane (CH4) into sources by limiting gaseous exchange and creating hypoxic microsites. We explored whether incorporating cover crops can help reduce CH4 emissions by maintaining methanotroph functional potential in the presence of mulching. We conducted a field experiment in an upland maize field to compare NPK fertilization and cover crop incorporation, both with and without mulching. We combined CH4 flux measurements with methane oxidation potential (MOP) assays and shotgun metagenomics to analyze CH4-cycling communities and functional gene profiles. Cover crop incorporation under mulching (M-CC) reduced cumulative CH4 emissions by 55% compared with NPK fertilization under mulching (M-NPK) and maintained 17% higher MOP. By contrast, particulate methane monooxygenase (pMMO) genes did not show a uniform enrichment under M-CC. However, M-CC demonstrated higher abundances of genes associated with hydrogenase activity, single-carbon (C1) metabolism, electron transport, and antioxidant biosynthesis. Specifically, there was a 21% to 67% increase in hydrogenase genes, a 14% to 55% rise in C1 metabolism genes, a 28% to 54% increase in electron transport genes, and a remarkable 280% elevation in the antioxidant biosynthesis gene egtD. Using plastic film mulching with incorporated cover crops maintained MOP and promoted greater microbial biomass and metabolic flexibility. These effects were linked to lower CH4 emissions and reduced yield-scale CH4 emissions, all without compromising maize yield.}, }
@article {pmid42248101, year = {2026}, author = {Xu, Z and Zhang, L and Zhu, D and Zhi, S and Ashbolt, NJ and Li, G and Luo, W and Nghiem, LD}, title = {Optimising composting to reduce plasmid and integrative conjugative element conjugation to minimise antibiotic resistomes in livestock manure for safe organic fertilisation.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142573}, doi = {10.1016/j.jhazmat.2026.142573}, pmid = {42248101}, issn = {1873-3336}, abstract = {Antimicrobial resistance is a critical threat to organic fertilizer production from livestock manure by composting. This study provides new insights to the dynamics of antimicrobial resistance genes (ARGs) during composting to propose strategies for their elimination. Results from genome-resolved metagenomics, meta-analysis, and quantitative assessment showed temperature and moisture content as key factors governing ARG dynamics during composting. Although integrative conjugative elements (ICE) could be transferable by some thermophilic bacteria, composting temperature to above 60 °C reduces mobile ARGs driven by plasmid conjugation for elimination. Further controlling moisture content to low than 60% inhibits the secretion of extracellular polymeric substances to restrain ARG rebound by ICE conjugation, particularly at the maturation stage of composting. These results are significantly useful for China, where swine manure accounted for most of livestock manure-derived ARGs (91.5%). Applying findings from this study to optimise the composting of livestock manure could reduce ARG proliferation by up to 59.3% in China.}, }
@article {pmid42248258, year = {2026}, author = {Guo, Y and Jia, X and Chen, Y and Xu, S and Ming, T and Kong, F and Xu, J}, title = {Inhibiting methanogenesis with medium-chain fatty acids: strategy for rapid start-up and stable operation of food waste chain elongation systems.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135078}, doi = {10.1016/j.biortech.2026.135078}, pmid = {42248258}, issn = {1873-2976}, abstract = {Converting food waste (FW) into medium-chain fatty acids (MCFAs) via chain elongation (CE) is an economical and eco-friendly approach, but methanogenic competition remains a key challenge limiting CE efficiency. Traditional inhibition methods (e.g., pH regulation, hydraulic/solids retention time control, chemical additives) require strict operation or external inputs, causing non-specific microbial inhibition, high costs and environmental risks. Innovatively, MCFAs can inherently suppress methanogens with obvious advantages. However, their inhibition mechanisms and dependence on concentration and carbon chain length remain unclear. This study investigated the effects of butyric acid (C4), caproic acid (C6), and caprylic acid (C8) at different concentrations on methane production, medium- and short-chain fatty acids accumulation, and microbial dynamics in FW anaerobic fermentation. The results indicated that the inhibitory effect was primarily driven by undissociated fatty acids, with the potency increasing with longer carbon chain lengths. Notably, C8 at a low undissociated concentration (0.05 mM) completely inhibited methanogenesis. Higher concentrations of C4, C6, and C8 effectively sustained hydrolysis and acidogenesis while promoting CE and leading to the accumulation of caproic acid and caprylic acid. Metagenomic analysis showed that a decline in methanogenesis-related functional genes was accompanied by an increase in reverse β-oxidation related functional genes. These findings provide a feasible strategy for rapid start-up and stable operation of FW-based CE systems, and present a sustainable route for FW valorization toward high-value biochemicals.}, }
@article {pmid42248259, year = {2026}, author = {Gai, T and Zhang, J and Zhang, S and Zhang, L and Li, X and Wu, Y and Yang, Y and Liu, X and Shi, G and Yang, M}, title = {Performance and mechanisms of a biochar-enhanced partial nitritation/anammox process for the treatment of silane tower wastewater.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135083}, doi = {10.1016/j.biortech.2026.135083}, pmid = {42248259}, issn = {1873-2976}, abstract = {The increasing discharge of silane tower wastewater, characterized by high ammonia (NH4[+]-N) and the presence of silane derivatives, poses significant challenges to biological nitrogen removal processes. In this study, a partial nitritation/anammox (PN/A) sludge system was enhanced through the addition of sludge-derived biochar (SBC). The results demonstrated that SBC effectively improved the nitrogen removal performance of PN/A sludge during the treatment of silane tower wastewater. Under low-proportion silane tower wastewater conditions, SBC rapidly promoted R2 sludge granulation within 19 d during phase I. During phase IV, when 100% silane tower wastewater was used as the influent, the NH4[+]-N and total nitrogen removal efficiencies of R2 were stably maintained at 80%-83%. These improvements were mainly attributed to the ability of SBC to promote sludge granulation, enrich functional microorganisms, and enhance extracellular electron transfer (EET) performance. SBC addition enabled the sludge to maintain higher levels of tightly bound extracellular polymeric substances rich in hydrophobic amino acids (HAAs). This study found that SBC-promoted EET was more strongly associated with anammox bacteria than with ammonia-oxidizing bacteria, resulting in a more pronounced enhancement of specific anammox activity than specific ammonia oxidation rate. Metagenomic and metatranscriptomic analyses further revealed that SBC enhanced the biosynthetic pathways and transcriptional expression of genes associated with HAA synthesis in PN/A sludge. Overall, this study provides a novel enhancement strategy for the application of PN/A processes in the treatment of complex industrial wastewater with high NH4[+]-N concentrations.}, }
@article {pmid42248305, year = {2026}, author = {Janes, VA and Stalenhoef, JE and Van der Putten, B and Koster, L and Jakobs, ME and Van Dissel, JT and De Jong, MD and Schultsz, C and Mende, DR}, title = {Metagenomic sequencing as a diagnostic tool for urine culture negative febrile urinary tract infection.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {106783}, doi = {10.1016/j.jinf.2026.106783}, pmid = {42248305}, issn = {1532-2742}, abstract = {OBJECTIVES: The diagnosis of febrile urinary tract infection (fUTI) by urine culture is hampered by antibiotic pre-treatment. We investigated urine metagenomics to diagnose fUTI in patients with positive blood but negative urine cultures.<br><br>METHODS: We performed shotgun metagenomic sequencing on 41 culture-positive and 19 culture-negative urine samples from fUTI patients, comparing urine metagenomics to blood and urine culture including antimicrobial susceptibility testing (AST). mOTUs3.1 performed metagenomic pathogen detection and ResFinder2.0 antimicrobial drug resistance (AMR) gene detection (standard settings). Whole genome sequencing (WGS) was performed on blood culture isolates from culture-negative urine samples. BWA-MEM and sylph aligned metagenomic pathogen reads to their respective WGS assemblies.<br><br>RESULTS: Metagenomics detected the blood culture isolate in 39/41 culture-positive and 17/19 culture-negative urine samples. 11/19 urine culture-negative patients were pre-treated with antibiotics, versus 8/41 urine culture-positives. The blood culture isolate was the most abundant pathogen in 33/41 culture-positive and 15/19 culture-negative urine samples. A median of 93.2% of pathogen-specific metagenomic reads mapped to their WGS assemblies with a median ANI of 98.7% (n=11). Genotypic AMR detection and phenotypic AST matched in 38-96% of cases.<br><br>CONCLUSIONS: Urine metagenomics successfully detected the causative pathogen in urine culture-negative fUTI patients. Genotypic AMR prediction requires further investigation.}, }
@article {pmid42248407, year = {2026}, author = {Tan, Y and Sun, J and Chen, X and Wang, Y and Zhang, C and Gong, L and Cui, X}, title = {Chronic Papillary Conjunctivitis as a Novel Ocular Manifestation of Rickettsia felis Infection: A Case Report.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108861}, doi = {10.1016/j.ijid.2026.108861}, pmid = {42248407}, issn = {1878-3511}, abstract = {PURPOSE: To report the first case of chronic papillary conjunctivitis caused by Rickettsia felis infection.<br><br>CASE: A 27-year-old man presented with a four-year history of unilateral papillary conjunctivitis refractory to multiple antibiotic courses. Examination revealed tarsal conjunctival injection, papillary hypertrophy, mucopurulent discharge, and eyelid laxity with entropion. The patient had a history of cat ownership for 5-6 years, suggesting possible exposure to the cat flea, and remained systemically asymptomatic without fever, rash, or lymphadenopathy. Metagenomic next-generation sequencing (mNGS), serology, and histopathology confirmed Rickettsia felis infection. Given the chronic intracellular nature of the infection, the patient received an extended 2-month course of oral doxycycline (100 mg twice daily) combined with topical therapy, with marked improvement observed by week 8 and subsequent entropion repair surgery.<br><br>CONCLUSION: This represents the first reported case of chronic, isolated rickettsial conjunctivitis without systemic involvement or Parinaud's oculoglandular syndrome features. This case highlights the importance of considering rickettsial infection in chronic, treatment-refractory conjunctivitis and demonstrates the value of metagenomic sequencing for diagnosis.}, }
@article {pmid42248728, year = {2026}, author = {van Dorst, J and Taylor, N and Pushpakumara, BLDU and Tan, ZT and Buchanan, DD and Haber, PS and Nash, E and Visser, S and Volovets, A and Sivam, S and Ooi, CY}, title = {Genotoxic pks + E. coli is strongly associated with ileocolonic neoplasia in adults with Cystic Fibrosis.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2026.05.016}, pmid = {42248728}, issn = {1873-5010}, abstract = {BACKGROUND: Polyketide synthase island-positive (pks+) Escherichia coli is a genotoxic gut bacterium linked to colorectal cancer (CRC) tumorigenesis via the genotoxin colibactin. In adults with Cystic Fibrosis (CF), there is an increased incidence and earlier development of CRC but the biological mechanisms underlying this increased risk remain incompletely understood. We aimed to determine the prevalence of pks+ E. coli in adults with CF.<br><br>METHODS: Stool samples and DNA were analyzed from the SCREENCF study cohort. Metagenomic libraries were sequenced on the NovaSeq X Plus platform, using Illumina protocols. Detection of the pks island was assessed with polymerase chain reaction (PCR) targeting the clbB gene.<br><br>RESULTS: Of the 49 CF participants; pks+ E. coli was detected in 1/35 (3%) of the no pathology (NORMAL) group, 5/12 (42%) in the adenomatous polyps (AP) group, and 2/2 (100%) in the ileocolonic cancer (ICC) group. Individuals with any ileocolonic neoplasia were 34 times more likely to harbor pks+ E. coli than those with NORMAL colonoscopy findings (OR = 34.0, 95% CI 5.00-691, p = 0.002). The presence of pks+ E. coli correlated with higher overall E. coli burden (p = 0.0009), but not with fecal inflammation, other genotoxic bacterial species or overall bacterial composition.<br><br>CONCLUSION: pks+ E. coli is infrequently detected among adults with CF, but its presence is associated with ileocolonic neoplasia, indicating a potential role in pathogenesis. If validated in larger cohorts, pks+ E. coli could provide a clinically meaningful biomarker for early detection, risk stratification and a potential target for precision intervention.}, }
@article {pmid42248819, year = {2026}, author = {Peng, D and Zhou, J and Xiong, M and Chen, Y and Zhang, Y and Hu, Y and Yang, Y and Xu, J and Zheng, Y and Xu, D}, title = {Gut Microbiota Dysbiosis Drives Lethal Bacterial Enteritis in Sturgeons: Insights From Ex Vivo Cultivation and Metagenomic Investigations.}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {e70218}, doi = {10.1111/jfd.70218}, pmid = {42248819}, issn = {1365-2761}, support = {D-8006-25-0392//Shanghai Aquatic Wildlife Conservation and Research Center/ ; K2025-02-08-00-12-F00043//Shanghai Municipal Commission of Agriculture and Rural Affairs/ ; }, abstract = {The Chinese sturgeon (Acipenser sinensis) and Yangtze sturgeon (A. dabryanus) are critically endangered flagship species. To investigate the intestinal microbial changes associated with bacterial enteritis in captive populations, we integrated bacterial isolation with metagenomic sequencing to characterize both healthy and maladjusted gut microbiomes. Healthy sturgeons exhibited a stable microbiota dominated by the beneficial Cetobacterium. In contrast, enteritis was consistently associated with severe dysbiosis, characterized by the depletion of these commensals and the massive expansion of opportunistic pathogens, notably Aeromonas and Citrobacter. Culture-based analyses identified A. veronii, C. freundii and Plesiomonas shigelloides as the dominant cultivable bacteria from diseased individuals; these isolates harboured diverse virulence traits and were multidrug-resistant. Crucially, both sturgeon species showed highly similar microbial responses and pathogenic profiles during enteritis. These findings indicate that sturgeon enteritis is closely correlated with a dysbiosis-driven syndrome. Establishing the healthy baseline provides a critical theoretical foundation for screening autochthonous probiotics and developing targeted pathogen control strategies. Furthermore, the striking cross-species commonality validates the Yangtze sturgeon as a viable surrogate model for advancing disease management and conservation in the difficult-to-breed Chinese sturgeon.}, }
@article {pmid42248870, year = {2026}, author = {Vasquez, YM and Romero, MF and Bowers, RM and Rohwer, RR and McMahon, KD and Woyke, T and Schulz, F}, title = {Vicennial metagenomic time series unveils evolutionary dynamics of giant viruses in a freshwater ecosystem.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73437-x}, pmid = {42248870}, issn = {2041-1723}, support = {DE-AC02-05CH11231//DOE | Office of Science (SC)/ ; }, abstract = {Giant viruses play crucial ecological roles in aquatic ecosystems, yet their evolutionary dynamics in response to environmental changes, particularly in freshwater environments, are not well understood. We analyzed a 20-year time series (2000-2019) of 471 co-assembled metagenomes from Lake Mendota (USA) to reconstruct 1512 giant virus metagenome-assembled genomes, providing insights into viral genome evolution. Viruses in the order Imitervirales dominate the virome, remaining consistent across seasons and years. Our findings reveal gene duplication (23% of genes) and horizontal gene transfer (29% of genes) as key drivers of genomic innovation. A co-occurrence network analysis indicates increased virus-host interactions following the introduction of an invasive predatory zooplankton in 2009, highlighting potential hosts in Bigyra, Perkinsea, and Euglenozoa. While single nucleotide polymorphism analysis shows predominantly purifying selection in viral genes, there is a significant increase in positively selected genes post-invasion, particularly those related to infection. Comparative evolutionary analyses reveal that giant viruses exhibit genome-wide substitution rates similar to co-occurring bacteria but significantly slower than smaller dsDNA phages, suggesting both stability and adaptability. Our study demonstrates that freshwater giant viruses employ various evolutionary strategies to respond to environmental change. These results underscore their significant yet often underappreciated role in freshwater ecosystem dynamics.}, }
@article {pmid42249277, year = {2026}, author = {Guanglin, W and Xiuwen, K and Rong, H}, title = {Awake VV-ECMO for severe pneumonia caused by Elizabethkingia anophelis: a case report.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13735-3}, pmid = {42249277}, issn = {1471-2334}, abstract = {BACKGROUND: Elizabethkingia anophelis is phenotypically similar to E. meningoseptica and is often misidentified by conventional methods, delaying appropriate therapy. Awake venovenous extracorporeal membrane oxygenation (VV-ECMO) avoids complications of deep sedation and mechanical ventilation, but its role in severe pulmonary infection with rare pathogens remains underexplored.<br><br>CASE PRESENTATION: We report a 62-year-old male with chronic hepatitis B who developed type I respiratory failure and septic shock unresponsive to conventional support. VV-ECMO was initiated on January 23, and awake ECMO management was implemented to preserve spontaneous breathing and cough reflex. Serial metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid revealed influenza A H1N1, Aspergillus fumigatus, and multidrug-resistant bacteria (Detailed mNGS results are provided in Supplementary Table 2). On day 32, sputum culture suggested E. meningoseptica, but subsequent mNGS identified E. anophelis (322,376 reads). The anti-infective regimen was adjusted to minocycline-based combination therapy. Under awake ECMO support, the patient's infection markers gradually improved, and he was successfully weaned from ECMO on day 38 and from mechanical ventilation thereafter. He was discharged after recovery.<br><br>CONCLUSION: This case demonstrates that awake ECMO can serve as an effective respiratory support platform in complex severe pneumonia. When conventional testing reports E. meningoseptica, clinicians should suspect possible E. anophelis infection, and timely mNGS is recommended for accurate species identification. Minocycline-based combination therapy appears promising for E. anophelis infections.<br><br>CLINICAL TRIAL: Not applicable.<br><br>CLINICAL PEARL: In critically ill patients with suspected Elizabethkingia infection, do not rely solely on phenotypic identification; use mNGS to distinguish Elizabethkingia anophelis from Elizabethkingia meningoseptica, and consider early minocycline-based therapy.}, }
@article {pmid42249286, year = {2026}, author = {Qiu, X and Li, W and Zhang, M and Lei, S and Chen, H and Wang, X and Miao, Y and Yu, Z and Wu, Y and Hou, Z}, title = {The impact of hydrogen sulfide on gut microbiota of diabetic mice with lower limb arterial ischemia.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05167-5}, pmid = {42249286}, issn = {1471-2180}, support = {H2020206490//Natural Science Foundation of Hebei Province/ ; 20230095//Medical Science Research Subject Plan of Hebei/ ; PD2023002//Clinical Medicine Postdoctoral Research Support Program of Hebei Medical University/ ; B2024003014//Hebei Province Yanzhao Golden Talent Program/ ; H2024206134//Key Project of Natural Science Foundation of Hebei Province (Class A)/ ; }, abstract = {BACKGROUND: The prevalence of hindlimb ischemia (HLI) associated with diabetes mellitus (DM) is high. However, its prevention and treatment face significant challenges. This study explored the effects of hydrogen sulfide (H2S) intervention in mice with DM and HLI, while concurrently investigating its regulatory effects on gut microbial homeostasis.<br><br>METHODS: The diabetic model in C57BL/6J mice was established through intraperitoneal injection of streptozotocin. The HLI model was created by ligating and severing the femoral artery, with subsequent initiation of a 21-day exogenous H2S intervention. Fecal samples from the mice were collected at four time points: before model establishment, 3 days after successful induction of the diabetes model, 3 days after establishment of the HLI model, and after 21 days of H2S intervention for metagenomic analysis. Body weight, blood glucose levels, and hindlimb blood flow in the mice were monitored. Additionally, functional assessment and histopathological examination of the ischemic skeletal muscle were performed to evaluate contractile and morphological properties.<br><br>RESULTS: H2S administration significantly enhanced hindlimb blood perfusion and restored plasma H2S concentrations in diabetic mice with HLI, concurrently improving both function and morphological integrity of the ischemic skeletal muscle. Bacterial abundance at the phylum level showed changes over the course of the experiment, particularly in Bacteroidetes and Firmicutes. In the DM&#x2009;+&#x2009;HLI group, the Firmicutes-to-Bacteroidetes ratio was significantly elevated; however, H2S treatment downregulated this alteration. H2S intervention modulated the abundance of various bacterial species, increasing Lactobacillus murinus and Faecalibacterium prausnitzii, while simultaneously downregulating inflammation-related bacteria such as Ruminococcus sp. JE7A12. Microbial network analysis revealed that the DM&#x2009;+&#x2009;HLI and H2S groups had lower network complexity than the control group. Furthermore, functional metagenomic profiling identified 28 differentially expressed genes, which were annotated to 8 primary and 30 secondary KEGG pathways, with 6 genes specifically enriched in carbohydrate metabolism pathways.<br><br>CONCLUSION: Exogenous H2S administration improved hindlimb blood perfusion, restored contractile function, and preserved morphological integrity of ischemic skeletal muscle in diabetic mice with HLI. Concurrently, H2S treatment altered the abundance of gut microbiota, improving microbial balance. Targeting the gut microbiota via H&#x2082;S suggests a potential translational avenue that warrants causal investigation for the treatment of diabetic limb ischemia. Further studies are warranted to establish causal relationships and elucidate the underlying mechanisms linking H2S, gut microbiota, and vascular recovery.}, }
@article {pmid42249504, year = {2026}, author = {Liu, Y and Xie, Y and Yang, J and Deng, Y and Liu, D and Chang, J and Tang, J and Zhao, H and Chen, X and Tian, G and Liu, G and Cai, J and Jia, G}, title = {Integrated gut metagenomic and muscle proteomic analysis reveals the role of dietary fermented extruded brewers' spent grain in enhancing pork quality through the gut-muscle axis.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42249504}, issn = {1674-9782}, support = {No. 2021ZDZX0009//Sichuan Science and Technology Program/ ; }, abstract = {BACKGROUND: The fact that feeding pigs with probiotic-fermented agricultural by-products improves pork quality has been repeatedly demonstrated and widely applied, but the underlying mechanisms remain unclear. This study explored the effects of fermented extruded brewers' spent grain (FEBSG) on meat quality in growing-finishing pigs, as well as its regulatory mechanisms.<br><br>METHODS: Sixty Duroc&#x2009;&#xd7;&#x2009;Landrace&#x2009;&#xd7;&#x2009;Yorkshire pigs (52.25&#x2009;&#xb1;&#x2009;2.10&#xa0;kg) were randomly assigned to five dietary treatments, in which FEBSG replaced 0, 5%, 10%, 15%, and 20% of soybean meal (SBM). The experiment spanned 10&#xa0;weeks.<br><br>RESULTS: Compared with the control, 20% FEBSG significantly increased final body weight, average daily feed intake, and average daily gain, while decreasing feed to gain ratio (P&#x2009;<&#x2009;0.05). Both 15% and 20% FEBSG improved carcass characteristics and meat quality, including higher carcass weight, loin eye area, and intramuscular fat content, along with lower drip loss and shear force (P&#x2009;<&#x2009;0.05). These treatments also enhanced flavor-related amino acids and unsaturated fatty acids (P&#x2009;<&#x2009;0.05), and improved umami and sweet taste profiles. Moreover, 20% FEBSG increased muscle fiber density and reduced fiber diameter, upregulated MyHC I, MyHC IIa, PGC-1&#x3b1;, AMPK&#x3b1;1, TFAM, and SDH activity, and downregulated MyHC IIb and LDH activity (P&#x2009;<&#x2009;0.05). Proteomic analysis identified 69 differentially expressed proteins, with enrichment in AMPK and PPAR signaling pathways. Metagenomic analysis revealed increased abundance of short-chain fatty acid-producing bacteria, including Clostridium, Lactobacillus, Prevotella, and Bartonella. Correlation analysis demonstrated associations between gut microbiota diversity and meat quality traits, as well as between dominant microbial genera and differentially expressed proteins, volatile fatty acids, muscle fiber characteristics, and the AMPK/PGC-1&#x3b1;/TFAM signaling pathway.<br><br>CONCLUSIONS: Partial replacement of SBM with FEBSG positively influenced growth performance and pork quality in pigs, with the underlying mechanisms may involve the activation of the AMPK/PGC-1&#x3b1;/TFAM signaling pathway via the gut-muscle axis, thereby enhancing mitochondrial biogenesis, muscle development, and metabolism.}, }
@article {pmid42241815, year = {2026}, author = {Zhang, S and Liu, X and Cheng, R and Huang, C and Zhang, Z and Long, S and Yang, Q}, title = {Elucidating the Feammox nitrogen transformation pathway: Key intermediates and putative multi-species metabolic cooperation in a long-term Feammox-dominant system.}, journal = {Water research}, volume = {303}, number = {}, pages = {126223}, doi = {10.1016/j.watres.2026.126223}, pmid = {42241815}, issn = {1879-2448}, abstract = {The emerging Fe(Ⅲ) reduction coupled to anaerobic ammonia oxidation (Feammox) process offers a promising approach toward carbon neutrality in wastewater treatment. However, its nitrogen transformation pathway and metabolic mechanism remain unclear. This study established a Feammox-dominant sequencing batch reactor (Fe-SBR) and operated it for 515 days, achieving an ammonia removal efficiency of 97.9 ± 4.5% during the stable phase. Feammox was confirmed as the dominant process for NH4[+]-N conversion, accounting for 83.2% of ammonia transformation. NH2OH, NO, and N2O were identified as key intermediates in the Feammox nitrogen transformation pathway. By integrating metagenomic analysis of functional gene dynamics with metagenome-assembled genomes (MAGs), a potential coupled iron-nitrogen (Fe-N) metabolic pathway was proposed. This pathway suggested that the Feammox process might be accomplished through multi-species metabolic cooperation, with MtrC-mediated extracellular electron transfer potentially serving as the key link coupling nitrogen transformation to the iron redox cycle. These findings provide novel insights into the Feammox metabolic pathway and lay a theoretical foundation for the future precise control and optimization of this process.}, }
@article {pmid42241861, year = {2026}, author = {Li, Y and Li, P and Li, H and Zhuang, L and Wang, L}, title = {Case study: Metagenomic analysis of microbial restructuring and nitrogen metabolism under probiotic and Chinese herb applications during post-antibiotic-ban shrimp farming.}, journal = {Journal of environmental management}, volume = {410}, number = {}, pages = {130128}, doi = {10.1016/j.jenvman.2026.130128}, pmid = {42241861}, issn = {1095-8630}, abstract = {China's 2020 aquaculture antibiotic ban has driven widespread use of probiotics and Chinese herbs in shrimp farming, yet their ecological effects on microbial communities remain unclear. This case study investigated three commercial Litopenaeus vannamei ponds in eastern China that exhibited contrasting nitrite accumulation and production outcomes under a post-antibiotic ban regime using probiotics and Chinese herbs. All ponds received daily Bacillus licheniformis probiotics and weekly supplements of Effective Microorganisms and a multi-herb blend, including Coptis, Elsholtzia, Sophora, Ligusticum, and Artemisia argyi. Our analysis revealed that Firmicutes-dominated communities replaced typical Proteobacteria-dominated microbiomes. Pond A, characterized by stable production, maintained low nitrite levels (a peak of 0.5 mg/L) and was dominated by Planococcus. In contrast, Ponds B and C, which exhibited elevated nitrite accumulation (peaks of 1.3 mg/L for Pond B and 1.5 mg/L for Pond C) and reduced production, were dominated by Paenisporosarcina. Metagenomic reconstruction indicated that this difference may result from aberrant nitrogen-transforming pathways. Paenisporosarcina correlated positively with nitrite accumulation, whereas Planococcus exhibited negative correlations. Virulence factor gene analysis revealed low abundance of pathogenic Vibrio spp.-associated genes. Importantly, even high-nitrite ponds exhibited minimal antibiotic resistance genes, including the absence of common aquaculture-associated ones such as those conferring resistance to sulfonamides (sul1, sul2), quinolones (qnr), and tetracyclines (tet), confirming the effectiveness of the antibiotic ban. Our case findings indicate that Paenisporosarcina dominance is linked to nitrite accumulation, highlighting a potential target for microbiome management in antibiotic-free shrimp farming.}, }
@article {pmid42241983, year = {2026}, author = {Bettera, L and Buzzanca, D and Levante, A and Cirlini, M and Saadoun, JH and Martinengo, N and Chiarini, E and Faccia, M and Zeppa, G and Calasso, M and Alessandria, V and Gatti, M}, title = {Cheeseomics of Grana Padano PDO cheese: Microbial diversity and flavour profiles compared to non-PDO cheeses.}, journal = {International journal of food microbiology}, volume = {459}, number = {}, pages = {111881}, doi = {10.1016/j.ijfoodmicro.2026.111881}, pmid = {42241983}, issn = {1879-3460}, abstract = {Protected Designation of Origin (PDO) schemes define technological constraints that may shape cheese microbiota and, consequently, volatilome and sensory quality. Here, a "cheesomics" approach to compare Grana Padano PDO (n = 13) with hard cooked cheeses of the same type and ripening time (9 months) produced outside the PDO framework (non-PDO; n = 15). Shotgun metagenomics was used to characterize bacterial and fungal communities and functional profile, while the volatilome was profiled by HS-SPME/GC-MS and sensory attributes were evaluated by trained ONAF panelist. A subset of samples (4 PDO and 4 non-PDO) was further analysed by flash profiling. Lactic acid bacteria dominated all samples, but distinct community and functional signature differentiated PDO and non-PDO cheeses. Grana Padano PDO showed higher sensory scores for odor/aroma and taste (p-value < 0.05), together with a more consistent microbiological profile. Non-PDO cheeses were more heterogeneous and displayed higher abundance of lipid-derived volatiles, including short- to medium-chain free fatty acids and methyl ketones, whereas PDO samples were associated with compounds such as pentanal and 2,5-dimethylpyrazine. Multivariate integration of taxa, VOCs and sensory data revealed partial separation between groups, supporting group-specific co-variation patterns. Functional profiling showed higher contributions (p-value < 0.05) of fermentation-related functions and cellular/extracellular polysaccharides in PDO cheeses, suggesting that sensory performance is not driven by VOC abundance alone. Fungal DNA was detected at very low level and showed limited relevance from a dairy microbiology perspective. Overall, the PDO production framework was associated with a measurable microbiological and metabolic imprint and with enhanced sensory performance relative to comparable non-PDO cheeses.}, }
@article {pmid42242027, year = {2026}, author = {Li, J and Ji, J and Ma, X and Xu, Z and Zhou, L and Guan, Y and Ling, X and Jia, X and Xi, B and Zhao, M}, title = {Bifidobacterium longum alleviation of metabolic dysfunction-associated steatotic liver disease: A multi-omics landscape of microbiota and metabolome reconfiguration.}, journal = {Microbiological research}, volume = {310}, number = {}, pages = {128569}, doi = {10.1016/j.micres.2026.128569}, pmid = {42242027}, issn = {1618-0623}, abstract = {The gut microbiome-host metabolism axis plays a critical role in the pathogenesis of metabolic dysfunction-associated steatotic liver disease (MASLD). Although the probiotic Bifidobacterium longum (B. longum) shows promise in ameliorating metabolic disorders, its functional impact on the microbiome-metabolome interplay in MASLD remains elusive. Herein, we established a MASLD mouse model using a high-fat, high-fructose (HFHF) diet and conducted integrated multi-omics analyses, including liver transcriptomics, gut metagenomics, and serum metabolomics, following B. longum intervention. B. longum supplementation effectively attenuated systemic metabolic dysfunction, hepatic steatosis, and intestinal barrier impairment in MASLD. This amelioration was driven by a two-pronged functional reorganization: the restoration of intestinal integrity and a profound remodeling of the hepatic transcriptome, featuring the downregulation of crucial mediators within the CD14-TLR4-NF-κB signaling cascade, including Cd14 and Runx1. Such functional reorganization coincided with a reconfigured gut microbiota, characterized by an increased abundance of beneficial taxa (e.g., Parabacteroides distasonis, Muribaculum intestinale) and suppression of opportunistic pathobionts (e.g., Ruminococcus gnavus, Clostridioides difficile). Furthermore, these microbial shifts were intrinsically linked to a reconfigured serum metabolome, highlighted by the enrichment of protective tryptophan-derived metabolites (e.g., indole-3-propionic acid) and the reduction of detrimental ones (e.g., 17α-methyltestosterone, 7-HDoHE). Collectively, our results suggest that B. longum mitigates MASLD through modulation of the gut microbiota and host serum metabolome, supporting its potential as a probiotic candidate for the management of metabolic health.}, }
@article {pmid42242076, year = {2026}, author = {Bai, H and He, LY and Qiao, LK and Gao, FZ and Liu, YS and Ying, GG}, title = {Human-associated microbial inputs and bacterial-fungal ecological coupling shape antibiotic resistance risk in environmental dust.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142602}, doi = {10.1016/j.jhazmat.2026.142602}, pmid = {42242076}, issn = {1873-3336}, abstract = {Environmental dust represents a critical exposure matrix, yet the relationships between multi-kingdom dust microbiomes and antimicrobial resistance (AMR)-associated health risks remain insufficiently characterized. We applied shotgun metagenomics to dust samples from pharmaceutical factories, a dairy farm, railway stations, and schools to comprehensively characterize bacterial, fungal, and viral communities, alongside resistome structure. Microbial community composition exhibited significant differences across all three domains among the sampled environments. Specifically, dust from railway stations displayed the strongest human-associated microbial signal and harbored the highest diversity of antibiotic resistance genes (ARGs), and MetaCompare-derived AMR risk. Functional analyses revealed shared bacterial-fungal metabolic organization, with cross-domain taxonomic and functional associations pointing to structured ecological coupling. Variation partitioning analysis showed that shared explanatory components accounted for most of the variation in MetaCompare-based human-health AMR risk, particularly the overlap among bacterial composition, humanization, and fungal functional structure. Notably, Candida and Aureobasidium emerged as divergent fungal indicators, tracking microbiome humanization and resistome risk in opposite directions. By contrast, viral auxiliary metabolic genes accounted for only 3.92% of the abundance-weighted virome, consistent with a host-linked auxiliary layer rather than a dominant independent pathway. Collectively, these findings demonstrate that AMR-related signatures in environmental dust are shaped by the interplay of human-associated microbial inputs and ecologically coupled bacterial-fungal interactions.}, }
@article {pmid42242079, year = {2026}, author = {Yang, F and Zhang, M and Tan, Y and Yuan, Z and Liu, W and Wu, Y and Li, F}, title = {Alkaline woody peat shifts CO2 emissions to CH4 by modulating microbial cross-feeding in Cd-contaminated paddy soil.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142498}, doi = {10.1016/j.jhazmat.2026.142498}, pmid = {42242079}, issn = {1873-3336}, abstract = {Alkaline organic amendments are widely used to remediate cadmium (Cd)-contaminated paddy soils by alleviating acidification and reducing Cd bioavailability, yet their impacts on greenhouse gas emissions remain unclear. Here, we examined how alkaline woody peat (WP) regulates carbon fluxes and microbial interactions in Cd-contaminated paddy soil. Anaerobic incubation and greenhouse pot experiments, together with in situ methane monitoring and metagenomic analyses, were used to compare alkaline-modified WP with acidic WP, CaO alone, and unamended controls. Alkaline WP (AWP-2) increased soil pH from 5.5 to 7.35 and decreased exchangeable Cd from 32% to 13%, confirming its remediation effectiveness. However, this was accompanied by marked changes in greenhouse gas emissions: methane production increased by up to 3.9-fold, while carbon dioxide emissions declined. Metagenomic analyses showed that alkaline WP strongly enriched methanogenic archaea, particularly Methanosarcina, whose relative abundance reached 26.6% compared with 4.2% in the control, while suppressing microbial populations associated with CO2-generating pathways. Functional gene profiles revealed increased abundance of mcrA and reduced representation of genes involved in complete acetate oxidation (maeA, pdc, sucA, porA, aceE, and icd). Genome-resolved analysis further showed that some microbes positively associated with methanogens lacked key genes involved in acetate oxidation to CO2 (e.g., aceE), suggesting a reduced capacity for CO2 generation from acetate and a greater tendency to retain carbon as acetate, thereby potentially favoring acetoclastic methanogenesis. Overall, these results highlighting a potential trade-off between Cd remediation and greenhouse gas mitigation and the need to incorporate microbially driven carbon fluxes into environmental risk assessments of alkaline amendments in contaminated paddy soils.}, }
@article {pmid42242448, year = {2026}, author = {Ammar, M and Fang, Y and Saqib, M and Xiao, J and Sial, AU and Wu, Q and Mansoor, MK and Wu, X and Moaaz, M and Butt, MU and Hafeez, R and Iqbal, K and Zohaib, A and Shen, S and Deng, F}, title = {Metagenomic and serological evidence of emerging tick-borne viruses in livestock, humans, and rats in Pakistan.}, journal = {Virologica Sinica}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.virs.2026.06.001}, pmid = {42242448}, issn = {1995-820X}, abstract = {Tick-borne viruses (TBVs) pose significant emerging threats to public and veterinary health worldwide. In Pakistan, the potential threats posed by TBVs extend far beyond Crimean-Congo hemorrhagic fever virus (CCHFV), which causes outbreaks and severe hemorrhaging with a high fatality rate among humans each year. However, the full extent of the tick-borne virome remains largely unexplored. This study presents the metagenomic profiling of viruses in livestock-associated ticks from Pakistan. Eighty-seven ticks belonging to the genera Ixodes, Rhipicephalus, Haemaphysalis, and Hyalomma species from livestock in Punjab. These ticks were subsequently grouped into 11 pools for RNA sequencing. Our analysis revealed extensive viral diversity, identifying sequences related to 31 viruses spanning at least 11 families. New strains of Jingmen tick virus (JMTV), brown dog tick phlebovirus 2 (BDTPV-2), and Liman tick virus (LMTV) were characterized, confirming their presence in the region. Serological surveys performed among 319 livestock, 253 humans, and 214 rats detected antibodies against these viruses, indicating host exposure. Notably, the presence of JMTV-neutralizing antibodies was confirmed in two livestock animals, one human, and one rat, providing evidence of productive infection. Our findings significantly expand the known diversity and distribution of TBVs in Pakistan, establish the preliminary baseline of the tick virome in the country, and provide serological evidence of cross-species exposure to emerging TBVs. This study highlights the underestimated risk of tick-borne viral zoonoses in Pakistan and underscores the urgent need for enhanced surveillance and risk assessment.}, }
@article {pmid42242497, year = {2026}, author = {Han, J and Lisco, A and Che, Y and Anderson, MV and Laidlaw, E and Kim, CS and Hou, P and Conlan, S and Proctor, DM and Lee-Lin, S and Amirkhani, A and Holmes, CJ and Suh, GS and Brownell, I and ,  and Segre, JA and Sereti, I and Kong, HH}, title = {Expansion of pathogens and restoration of human skin microbiome in CD4 T-cell lymphopenia.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2026.05.019}, pmid = {42242497}, issn = {1523-1747}, abstract = {The microbiome and host immune system maintain a dynamic homeostatic equilibrium at the skin interface. Prior studies have shown that the skin microbiome is profoundly altered in immunodeficient conditions. Patients with idiopathic CD4 lymphopenia (ICL), a rare clinical syndrome with obscure cause, and people living with HIV (PLWH) are two etiologically distinct groups of individuals with CD4 T-cell lymphopenia. We conducted shotgun metagenomic sequencing, metagenome assembly, and read-based mapping to characterize the multi-kingdom taxonomic diversity of skin microbiomes in patients with ICL and PLWH who were followed longitudinally before and after antiretroviral therapy (ART) initiation. Compared with healthy individuals, the skin microbiomes of patients with ICL and ART-naïve PLWH showed greater inter-individual variation and higher relative abundances of eukaryotic viruses. Both patient groups carried pathogenic microbes, including high-oncogenic-risk human papillomaviruses (HPVs) and dermatophytes such as Trichophyton rubrum, which were rarely seen in healthy individuals. In PLWH, high-oncogenic-risk HPV types persisted after 2 months of ART but were mostly cleared after 14 months. The loss of peripheral blood CD4 T-cells was associated with shifts in the skin microbiome and a relative expansion of pathogenic microbes. Investigating microbiome dynamics during immunodeficiency and subsequent immune reconstitution provides additional insights into host-microbial interactions.}, }
@article {pmid42243106, year = {2026}, author = {Lee, M and Kim, D and Song, JH and Park, SJ and Chang, JY}, title = {Efficacy of Lactococcus lactis WiKim0124 in Fat-, Sucrose-, and Fat/Sucrose-Induced Obesity Models.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00915-3}, pmid = {42243106}, issn = {2396-8370}, support = {KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KEB2602-1-2 and KE2501-1//the Ministry of Science and ICT, Republic of Korea/ ; KS2303//the institute's internal research program/ ; KS2303//the institute's internal research program/ ; KS2303//the institute's internal research program/ ; KS2303//the institute's internal research program/ ; KS2303//the institute's internal research program/ ; }, abstract = {Lactococcus lactis WiKim0124 (WiKim0124), a probiotic strain isolated from kimchi, has previously shown anti-obesity effects in high-fat diet (HFD) models. This study investigated whether WiKim0124 and its formulated version, SW01, exert consistent anti-obesity efficacy across distinct diet-induced obesity models through modulation of host lipid metabolism and gut microbial function. In 3T3-L1 adipocytes and FFA-treated HepG2 cells, both treatments inhibited lipid accumulation and modulated lipid metabolism-related markers, indicating enhanced fatty acid oxidation and reduced lipogenesis. In C57BL/6 J mice fed HFD, high-sucrose (HSuc), or HFD + HSuc diets, daily oral administration of WiKim0124 or SW01 significantly reduced body weight gain, adipose tissue mass, and hepatic lipid accumulation. WiKim0124 and SW01 significantly enhanced fatty acid oxidation pathways, as evidenced by increased expression of the markers PPARα, CPT-1α, and UCP2. Gut microbiota analysis showed increased Bacteroidetes and enrichment of Akkermansia muciniphila in treated groups. Shotgun metagenomic functional profiling revealed enhanced short-chain fatty acid-related pathways and enzymes, with distinct patterns depending on treatment and dietary stressors. Microbial functional responses were most pronounced in the HFD + HSuc model, supporting a diet-dependent mode of probiotic action. Together, these findings demonstrate consistent anti-obesity efficacy of WiKim0124 and support the translational potential of its formulated application through integrated modulation of host metabolism and gut microbial function.}, }
@article {pmid42243452, year = {2026}, author = {Das, R and Medhi, MC and Tamang, B}, title = {Microbial diversity and its links to retinol pathways and aroma compounds in ethnic fermented rice beverages of Assam.}, journal = {AMB Express}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13568-026-02062-0}, pmid = {42243452}, issn = {2191-0855}, abstract = {Traditional fermented rice beverages are produced through complex microbial fermentation processes that influence their physicochemical characteristics and metabolite composition. In this study, metagenomic sequencing and GC-MS/MS-based metabolomics were integrated to characterize four indigenous rice beverages: Black Rohi Modh (BR), Rohi Modh (RH), Jou Bidwi (JOU), and Sai Mod (SM). All beverages were mildly acidic, with pH values ranging from 4.1 to 4.5 and titratable acidity between 0.58 and 0.72% lactic acid. Ethanol content varied among samples, with BR showing the highest concentration (8.13% v/v), followed by JOU and RH (approximately 5.5% v/v), while SM exhibited the lowest level (4.28% v/v). Antioxidant activity differed across beverages, with RH and BR demonstrating higher DPPH radical scavenging activity and SM showing the highest ferric reducing antioxidant power (96.93 µmol/mL). Metagenomic analysis generated 57.69 Mb of assembled sequences, identifying 48 microbial phyla and 1,785 species, with Eukarya accounting for 66.12% of the total community. Ascomycota predominated in BR and JOU, whereas Bacillota was more abundant in RH. The genus Saccharomyces was consistently dominant across samples. Functional annotation indicated enrichment in metabolic pathways related to carbohydrate and amino acid metabolism, as well as genes associated with ethanol biosynthesis and retinol metabolism pathways, reflecting microbial metabolic potential rather than direct vitamin production. Metabolomic profiling identified 113-167 metabolites per beverage, with 93 compounds shared among all samples. Correlation analysis revealed significant associations between Saccharomyces cerevisiae and short-chain fatty acids (ρ = 0.62-0.71, FDR < 0.05), indicating a strong positive relationship between microbial abundance and metabolite production.}, }
@article {pmid42243513, year = {2026}, author = {Yi, J and Zhao, Y and Li, Z and Chen, A and Tang, Z and Zheng, L and Ge, H and Yu, Q and Liu, W and Xiang, J and Tang, J}, title = {M.globosa promotes lung cancer progression and M2 macrophage polarization through oxidative phosphorylation.}, journal = {NPJ precision oncology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41698-026-01528-5}, pmid = {42243513}, issn = {2397-768X}, support = {2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; 2025XQLH002//Postgraduate Innovative Project of Central South University/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2403084//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; kq2208299//the National Natural Science Foundation of Changsha/ ; 2019SK2253//the Key Research and Development Program of Hunan/ ; 2019SK2253//the Key Research and Development Program of Hunan/ ; 2019SK2253//the Key Research and Development Program of Hunan/ ; 2019SK2253//the Key Research and Development Program of Hunan/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 81972198//National Natural Science Foundation of China/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50173//the National Natural Science Foundation of Hunan/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; 2025JJ50490//the Natural Science Foundation of Hunan Province/ ; }, abstract = {The lungs are colonized by a variety of microbes which play a significant role in lung cancer progression. In this study, we conducted an in-depth analysis of metagenomic sequencing data obtained from alveolar lavage fluid (ALF) samples of patients with non-small-cell lung cancer (NSCLC) at different clinical stages. The nested qPCR was used to validate the abundance of key fungi and establish a correlation between fungi abundance and patient prognosis. We found that elevated levels of M.globosa correlated with patients at stage1B-3 and worse prognosis. M.globosa enhanced the proliferation of lung cancer cells and promoted tumor growth in vivo by promoting M2-like macrophage polarization, which was primarily driven by oxidative phosphorylation (OXPHOS) activation. The inhibition of OXPHOS in tumor-bearing mice using metformin significantly retarded the tumor growth induced by M. globosa. Together, our clinical observations and experimental findings suggest that intracellular M. globosa infection may contribute to lung cancer progression through immunometabolic remodeling of macrophages.}, }
@article {pmid42243631, year = {2026}, author = {Bauer, C and Reger, N and Rustem, HAL and Tisza, M and Triosi, CL and Javornik Cregeen, S and Ghobrial, L and Gitter, A and Wu, F and Surathu, A and Deegan, J and Mena, KD and Petrosino, J and Boerwinkle, E and Hanson, BM and Maresso, AW}, title = {SeqBoard: a genomics-based data dashboard for comprehensive wastewater virome monitoring.}, journal = {Journal of the American Medical Informatics Association : JAMIA}, volume = {}, number = {}, pages = {}, doi = {10.1093/jamia/ocag088}, pmid = {42243631}, issn = {1527-974X}, support = {//S.B. 1780, 87th Legislature, 2021 Reg. Sess./ ; U19 AI44297/NH/NIH HHS/United States ; //Anonymous Foundation/ ; //UTHealth Houston Seed/ ; //Baylor College of Medicine/ ; //Alkek Foundation Seed/ ; }, abstract = {OBJECTIVES: To develop the first public-facing dashboard that translates genomic sequencing data from wastewater into accessible and actionable community information concerning human pathogenic viruses, representing a shift to sequencing-based public health wastewater monitoring.<br><br>MATERIALS AND METHODS: We developed SeqBoard, a user-friendly dashboard that displays sequencing information from the total wastewater virome. The dashboard integrates diverse expertise and components, including data processing and analysis, visualization and management, security, and stakeholder engagement and feedback. We implemented a 3-tiered system for user interactions, customized to the general public, public health officials, and genomics experts.<br><br>RESULTS: SeqBoard provides an intuitive interface for presenting genomic information as species-specific trend lines, level indicators, and all-site aggregates. It translates complex sequencing data into public health insights, including reporting on dozens of viruses of concern with modules for detections, variant information, and genomic context.<br><br>DISCUSSION: The prevention of the next pandemic will require comprehensive pan-monitoring of deadly viruses and their evolution. Genomics-based dashboards will be essential for early detection of viral activity before significant clinical manifestation, thereby allowing public health systems to provide warnings, ready actions, and develop vaccines.<br><br>CONCLUSION: SeqBoard shows that sequencing data can be translated into useful public health information, serving as a model for future sequencing-based pathogen dashboards. The dashboard is publicly available at https://tephi-ww.uth.edu/public-dashboard and represents the first publicly available dashboard providing pan viral genomic detection data for wastewater monitoring.}, }
@article {pmid42243719, year = {2026}, author = {Almutrafy, AM and Aloufi, AS and Al-Andal, A and Refai, MY and Tashkandi, M and Alnahari, AA and Bagabas, SS and AlDowsari, FMF and Abuauf, HW and Alshehrei, FM and Alshareef, SA and Abulfaraj, AA and Hassan, RN and Jalal, RS}, title = {Comprehensive in silico analysis of eggNOG-annotated orthologous genes infers functional dynamics and energy metabolism in the microbiome of Abutilon fruticosum.}, journal = {BMC plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12870-026-09123-3}, pmid = {42243719}, issn = {1471-2229}, support = {PNURSP2026R357//Princess Nourah bint Abdulrahman University Researchers Supporting Project/ ; }, abstract = {BACKGROUND: Abutilon fruticosum is an ecologically and pharmacologically important wild Malvaceae species whose rhizospheric microbiome remains poorly resolved at the level of orthologous-group (OG) genes. Shotgun metagenomic sequencing and eggNOG/COG-based annotation were used to compare rhizosphere and bulk-soil microbiomes, quantify OG repertoires, and infer in silico functional modules.<br><br>RESULTS: Principal coordinate and Bray-Curtis analyses of COG categories revealed clear functional segregation between rhizosphere and bulk communities, with the rhizosphere enriched in high-abundance OGs linked to energy metabolism, nutrient transport, stress response, and secondary metabolism. Computational ranking identified a cohort of highly recurrent OGs, predominantly associated with Actinobacteria and Proteobacteria but also with Streptophyta, that dominate the predicted functional landscape and are markedly more abundant in silico in rhizospheric soil. Using eggNOG/COG assignments, ten interacting putative functional modules were delineated in silico, encompassing NADH-quinone oxidoreductase-centered bioenergetics, ABC-type nitrogen and sulfur acquisition, fatty-acid and propionate catabolism, sulfur scavenging and detoxification, cell-envelope and biofilm formation, multidrug efflux, DNA maintenance, environmental sensing and transcriptional regulation, specialized competition/protection, and mobile genetic elements. Conceptual, hypothesis-generating frameworks integrating selected modules posit that rhizosphere dominance could arise from the coordinated coupling of ATP/proton motive force (PMF) generation with high-affinity nutrient uptake, sulfur and carbonyl detoxification, iron-sequestering and antioxidant secondary metabolism, and stress-responsive multidrug efflux, based on our analyses.<br><br>CONCLUSIONS: These predictions suggest that specific OG cohorts act as keystone energetic, metabolic, and defense hubs in the A. fruticosum rhizosphere and provide testable hypotheses for future experimental work linking module-level functions to root colonization, stress tolerance, and plant performance. (249 words).}, }
@article {pmid42243998, year = {2026}, author = {Li, S and Sun, Y and Tong, X and Zhang, Z and Ma, X and Li, D and Min, L}, title = {Near-complete inhibition of rumen methanogenesis via microbial and enzymatic modulation using a low dose of Asparagopsis taxiformis combined with 3-nitrooxypropanol.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42243998}, issn = {1674-9782}, support = {SKXRC2025487//Youth S&amp;T Talent Support Programme of Guangdong Provincial Association for Science and Technology/ ; 2024CXTD13//Guangdong Modern Agro-industry Technology Research System/ ; 202408440440//China Scholarship Council/ ; NYQS202613//Special Funding for the Construction of the High-Level Academy of Agricultural Sciences/ ; 2026A1515010802//Guangdong Basic and Applied Basic Research Foundation/ ; }, abstract = {BACKGROUND: Enteric methane (CH4) from ruminants represents a major contributor to agricultural greenhouse gas emissions. The red seaweed Asparagopsis taxiformis (A. taxiformis) is a highly effective CH4 emission inhibitor, but its large-scale application is restricted by limited biomass availability. This study evaluated whether reducing the inclusion level of A. taxiformis (0.32% dry matter, DM) combined with 3-nitrooxypropanol (3-NOP; 0.05% DM) could maintain a high inhibitory efficacy, and elucidated the underlying microbial mechanisms through in vitro fermentation and metagenomics analysis.<br><br>RESULTS: The combined treatment decreased CH4 production by 98.21% (P&#x2009;<&#x2009;0.01) without impairing DM degradation, and markedly shifted rumen fermentation towards propionate, lowering the acetate-to-propionate ratio (1.59 vs. 2.65; P&#x2009;<&#x2009;0.01). Metagenomic profiling revealed substantial reductions in the abundance of Methanobrevibacter and Ruminococcus, along with increased levels of propionate-associated bacteria such as Prevotella, Treponema, Eubacterium, and Selenomonas (P&#x2009;<&#x2009;0.01). Functionally, the combined treatment downregulated key enzymes in hydrogenotrophic and methylotrophic methanogenesis, including methyl-coenzyme M reductase (EC:2.8.4.1) and tetrahydromethanopterin S-methyltransferase (EC:2.1.1.86), thereby blocking terminal methanogenic steps.<br><br>CONCLUSIONS: Collectively, these results demonstrate that co-supplementation with A. taxiformis and 3-NOP achieves near-complete methanogenesis inhibition at drastically reduced seaweed dosage through coordinated changes in fermentation patterns, microbial community structure, and methanogenic enzymatic pathways. This approach provides a practical strategy to overcome biomass limitations of A. taxiformis and warrants validation in long-term in vivo trials.}, }
@article {pmid42244002, year = {2026}, author = {Ansari, MH and Staubach, F and Alacatli, N and Obbard, DJ}, title = {A diverse gut virome in natural populations of Drosophila melanogaster.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00585-2}, pmid = {42244002}, issn = {2524-4671}, abstract = {BACKGROUND: Drosophila melanogaster is not only one of the most important models of antiviral immunity in invertebrates, but is also a powerful model for research of the gut microbiome. Although recent studies have continued to improve our knowledge of the fly gut microbiota, the viral component of the microbiome has remained unexplored.<br><br>RESULTS: Here we explore the viral component of the Drosophila melanogaster gut microbiome using deep metagenomic DNA sequencing. We recovered 3040 non-redundant viral contigs, most of which were bacteriophage-associated sequences, resulting in 167 viral Metagenome-Assembled Genomes. Many of these sequences showed limited similarity to reference viruses and included bacteriophages related to tailed double-strand DNA phage lineages, with putative links to major gut-associated bacteria of D. melanogaster, including Lactobacillus, Acetobacter, and Gluconobacter. Our functional annotation and discovery of auxiliary metabolic genes suggested that these bacteriophages encode putative functional potential related to microbial metabolism and genetic information processing. We also identified evidence of known fly pathogens Drosophila Kallithea nudivirus, Vesanto bidna-like virus, and Drosophila Linvill Road densovirus, some of which were common in our studied populations.<br><br>CONCLUSIONS: Our findings reveal a complex and diverse phage community in the D. melanogaster gut microbiome, paving the way to study host-phage related research in the natural microbial communities.}, }
@article {pmid42244030, year = {2026}, author = {Wang, Y and Zhang, Y and Feng, L and Han, Q and Yu, Q and Li, H}, title = {Host Ecology Shapes Gut Pathogen Evolution: An Eco-Evolutionary Trade-Off in Plateau Wildlife.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70344}, doi = {10.1111/1462-2920.70344}, pmid = {42244030}, issn = {1462-2920}, support = {32471575//National Natural Science Foundation of China/ ; }, abstract = {The intestinal tracts of plateau wildlife function as crucial reservoirs for diverse pathogens. However, the mechanisms through which host ecology influences pathogen community assembly and their interactions remain unclear. By comparing the subterranean-living plateau zokor (Eospalax baileyi) with the aboveground plateau pika (Ochotona curzoniae) across a two-and-a-half-year study, this work provides evidence that the distribution and transmission dynamics of pathogens, virulence factor genes (VFGs), and pathogen-host interaction (PHI) genes are determined by animals' distinct niches. The results demonstrate a clear eco-evolutionary trade-off: the plateau zokor, inhabiting stable yet pathogen-enriched burrow systems, exhibited higher abundances of pathogens, VFGs, and PHI genes in its gut, and formed complex co-occurrence networks. In contrast, the plateau pika, under diverse environmental exposure, possessed higher pathogen and gene diversity but lower overall abundance, alongside simpler interaction networks indicative of opportunistic colonization. Metagenomic binning indicated a close association among VFGs, PHI genes, and mobile genetic elements (MGEs), pointing to their possible joint transfer. Additionally, animal weight and precipitation were identified as key drivers of pathogen dynamics. These findings indicate that the gut sits at the crossroads of animal and environmental health, highlighting how host-mediated pathogen evolution across distinct niches shapes the broader One Health dynamics of the plateau ecosystem.}, }
@article {pmid42244179, year = {2026}, author = {Wang, Y and Zhu, Z and Zhang, Y and Luo, Q and Niu, T and Liu, Y and Chen, J and Yang, R and Zhu, S and Chen, H}, title = {Dynamic microbiome turnover and glycerol-3-phosphate-linked metabolic adjustments underlie resilience to desiccation in intertidal algae.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71330}, pmid = {42244179}, issn = {1469-8137}, support = {2021Z103//Major Scientific and Technological Project of Ningbo/ ; CARS -50//China Agriculture Research System of MOF and MARA/ ; 32373099//National Natural Science Foundation of China/ ; //Ningbo Yongjiang Talent Program/ ; 2021C02069 -9//Key Scientific and Technological Grant of Zhejiang for Breeding New Agricultural (Aquaculture) Varieties/ ; }, abstract = {Tolerance to extreme dehydration has emerged across the tree of life, yet current understanding relies heavily on terrestrial host traits. Marine lineages facing rapid, tide-driven hydration oscillations remain largely unexplored. We used Pyropia haitanensis as a model to determine if intertidal resilience arises from a coordinated holobiont strategy. We integrated time-resolved microbiome profiling and metagenomics. Mechanisms were validated through multi-omics of desiccation-stressed bacterial isolates, inoculation, and antibiotic-depletion experiments, and host physiological assessment. Rapid drying reshaped the microbiome through selective loss of osmosensitive taxa and occupation by stress-tolerant lineages, whereas rehydration promoted selective recolonization and network recovery. Metagenomic analysis revealed enrichment of functional potential for microbial antioxidant, osmoprotective, and extracellular polysaccharide pathways, alongside enrichment of glycerol-3-phosphate (G3P) ABC transporter modules. Host G3P secretion increased, creating a selective nutrient niche that recruited symbionts possessing specialized G3P transporters. Inoculation and microbiota-depletion experiments established a causal role for the microbiome in host resilience. Keystone isolates Sulfitobacter sp. and Alteromonas sp. utilized host-derived G3P to fuel complementary protective mechanisms, with their combination outperforming either taxon alone. These findings highlight an integrated host-microbiome partnership shaped by tidal filtering, a cross-domain strategy that buffers hydration stress and supports intertidal resilience and mariculture practices.}, }
@article {pmid42244577, year = {2026}, author = {Ettinger, CL and Eisen, JA}, title = {Phoronids and their tubes harbor distinct microbiomes compared to surrounding sediment.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.05.28.596327}, pmid = {42244577}, issn = {2692-8205}, abstract = {Phoronids are a phylum of animals with only ∼12 described species, all of which are marine filter feeders that build external tubes for shelter and produce chemical deterrents against predators. Many tube-building invertebrates host distinct microbial communities and even have obligate symbionts for survival in sulfur-rich marine sediments. However, the microbiome of phoronids has only recently begun to be described. To address this, we surveyed the composition of the microbiome of the phoronid, Phoronopsis harmeri , using 16S rRNA gene amplicon and metagenomic sequencing. We found that the phoronid microbiome was dominated by members of the orders Campylobacterales, Desulfobulbales, and Desulfobacterales. We also found that the microbiomes of tubes and phoronids were less diverse than that of surrounding sediment, and that the microbiomes of phoronids, tubes and surrounding sediment were all distinctly structured. Based on analysis of metagenomic data, and even though we were only able to recover low quality MAGs of abundant taxa, we found preliminary evidence that taxa associated with phoronids and their tubes likely participate in sulfur cycling pathways. Future work should perform more robust metagenomic sequencing and chemical analysis to assess if there is a link between known phoronid chemical defenses and microorganisms. Overall, this study provides foundational insight into the microbial communities associated with phoronids and these initial findings suggest that these communities may play an important role in sulfur cycling in marine sediments.}, }
@article {pmid42244712, year = {2026}, author = {Iranzo, J and Wolf, YI and Koonin, EV}, title = {Eco-evolutionary dynamics of defense systems in mobile genetic elements: Cui bono?.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.25.727639}, pmid = {42244712}, issn = {2692-8205}, abstract = {BACKGROUND: Mobile genetic elements (MGEs), including viruses, plasmids, and transposons, are major drivers of evolution in bacteria and archaea. Host-parasite conflicts drive the emergence of a broad variety of defense and counter-defense systems. Recent advances in metagenomics and functional annotation have shown that many defense systems are located on MGEs. The fact that MGEs are, essentially, genomic parasites raises an intriguing question: why do these parasites carry defense systems at high prevalence, often even higher than the host chromosome?<br><br>RESULTS: We developed a simple mathematical model to investigate the factors that promote evolution of defense systems in MGEs and the ecological implications of MGE-encoded defense. Our analysis points to the strength of inter-MGE interference as a key determinant of the evolution of defense systems in MGEs. We identify two qualitatively distinct regimes, depending on the basic reproductive number in mixed coinfections. Weakly interfering MGEs tend to carry low-cost defense systems that enhance the survival of their hosts upon exposure to more damaging MGEs. Although these systems can be occasionally transferred to the host, they typically remain in MGEs. In contrast, strongly interfering MGEs, such as plasmids from the same incompatibility group, can carry high-cost defense systems that are detrimental to the host and the population as a whole, but help their carriers spread by actively replacing their competitors.<br><br>CONCLUSIONS: Analysis of our model shows that the key determinant of the evolution and spread of defense systems in MGEs is the strength of cross-MGE interference. Weakly interfering MGEs would serve as 'MGE banks', typically carrying low-cost defense systems that can benefit the host by protecting it from more damaging MGEs. In contrast, strongly interfering MGEs would carry costly defense systems that mediate inter-MGE conflicts but are deleterious to the host. These MGEs could serve as proving grounds for emerging defense systems, which might eventually become cost-effective once optimized by selection.}, }
@article {pmid42244725, year = {2026}, author = {Steinberger, AJ and Nickodem, CA and Leite de Campos, J and Kates, AE and Goldberg, TL and Safdar, N and Sethi, AK and Shutske, JM and Ruegg, PL and Suen, G and Hite, JL}, title = {Antimicrobial use contributes to resistance gene enrichment across cattle groups on commercial dairy farms.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.22.726633}, pmid = {42244725}, issn = {2692-8205}, abstract = {Antimicrobial use (AMU) in agricultural systems is frequently linked to antimicrobial resistance (AMR). Yet, the scale at which AMU reshapes host-associated resistomes remains unclear. This gap arises, in part, from the scarcity of farm-level AMU data from commercial production systems. Here, we combine detailed AMU records from commercial dairy farms with metagenomic analyses of bovine fecal resistomes from calves, lactating cows, sick cows, and cull cows. At a broad level, resistome profiles were similar regardless of farm AMU. Resistance associated with historically common antibiotics, such as tetracyclines, was frequent on low- and high-AMU farms, indicating that some resistance classes are ubiquitous in dairy systems regardless of current AMU. In contrast, resistance to other drug classes varied systematically with AMU. Higher AMU was associated with increased resistance to aminoglycosides, β-lactams, and macrolides, drug classes that are critical for treating mastitis and bovine respiratory disease. Resistance gene richness and diversity were highest in calves, underscoring the importance of accounting for host traits alongside AMU when evaluating resistance patterns. Together, these findings underscore the need for detailed, farm-level AMU data to understand how management practices shape AMR and to inform strategies for sustaining the effectiveness of existing antimicrobials in agricultural and public-health contexts.}, }
@article {pmid42244773, year = {2026}, author = {Espinoza, JL and Dupont, CL and Phillips, A}, title = {Leviathan: A fast, memory-efficient, and scalable taxonomic and pathway profiler for (pan)genome-resolved metagenomics and metatranscriptomics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.07.14.664802}, pmid = {42244773}, issn = {2692-8205}, abstract = {Functional profiling of metagenomes and metatranscriptomes is essential for understanding microbial community capabilities, yet current methods require computationally expensive translated-search alignments that scale poorly to the large genome-resolved reference databases now common in the field. We introduce Leviathan, an open-source software package for integrated taxonomic and functional profiling that operates at both genome and pangenome resolution. Leviathan combines Sylph for ultra fast alignment-free taxonomic profiling with Salmon for pseudo-alignment-based read quantification in DNA-space against genome-resolved gene catalogs, bypassing the translated-search step that dominates runtime in existing approaches. For each (pan)genome, Leviathan functional profiling produces dual metrics: pathway abundance from aggregated gene-level quantification and pathway coverage from graph-based assessment of enzymatic step completeness. On CAMI-I and CAMI-II datasets, Leviathan achieved up to 74-fold faster runtimes and 14-fold lower memory usage compared to HUMAnN, while improving genome-level assignment accuracy by up to 12% and pangenome-level accuracy by up to 5%. We demonstrate Leviathan's applicability through two case studies: a marine plastisphere metagenomics dataset where differential coverage analysis revealed metabolic shifts between early and mature biofilm communities and a dental caries metatranscriptomics dataset where pangenome-resolved co-expression network analysis identified organism-specific transcriptional patterns diagnostic of health and disease states. Leviathan is available at https://github.com/jolespin/leviathan.}, }
@article {pmid42245494, year = {2026}, author = {Hu, Z and Chen, C}, title = {Revealing gut microbiota profiles and their influencing factors in commercial boars of three breeds by a large-scale metagenome study.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1825304}, pmid = {42245494}, issn = {1664-302X}, abstract = {Boars play a critical role in pig production. Numerous studies have reported important effects of the gut microbiota on pig production traits. However, whether the gut microbiota is associated with reproduction traits in boars remains largely unknown. Understanding the gut microbial composition and its influencing factors in large-scale boar populations is an essential first step to investigate this association. In this study, shotgun metagenomic sequencing was performed on fecal samples of 1,651 commercial boars from three breeds raised in three pig farms to uncover their gut microbial structures. We observed significant differences in boar gut microbial compositions across three breeds, even when raised in the same farm. Permutational multivariate analysis of variance (PERMANOVA) within-farm breeds and with-age stages found that the effect size of each factor on boar gut microbial composition varied across farms and age stages. Breeds accounted for 2% ~ 9% of the variance of boar gut microbial compositions in different farms. We then identified gut microbial taxa enriched in each boar breed using MaAsLin2. Lactic acid and butyrate-producing taxa, such as Lactobacillus amylovorus and Faecalibacterium prausnitzii, were enriched in Duroc boars; Akkermansia muciniphila and Lactobacillus reuteri showed the enrichment in Landrace boars, accompanied by increased relative abundance of Enterobacteriaceae members. Meanwhile, the species from Bacteroides, Prevotella, and Treponema had higher abundances in the gut of Large White pigs than in the other two pig breeds. We also identified bacterial species enriched in each of the three age stages. These breed and age-associated microbial enrichment patterns might reflect the combined effects of long-term genetic selection of pig breeds, age, and differences in feeding diets. The results of this study provide important insights for further investigating the effects of gut microbiota on boar reproductive traits and for developing strategies to modulate the gut microbiota to improve boar health and production performance.}, }
@article {pmid42245495, year = {2026}, author = {Kuźniar, A and Das, AP and Goraj, W}, title = {Editorial: Unveiling microbiome interactions and functions in soil hotspots.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1820854}, doi = {10.3389/fmicb.2026.1820854}, pmid = {42245495}, issn = {1664-302X}, }
@article {pmid42245502, year = {2026}, author = {Abdulsamad, MA and Bardaa, S and Elleuch, M and Mathlouthi, NEH and Ben Ali, M}, title = {Metagenomic characterization of infected diabetic foot ulcers in North Africa: microbial diversity, virulome, and resistome profiling.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1825173}, pmid = {42245502}, issn = {1664-302X}, abstract = {This study provides the first shotgun metagenomic characterization of infected diabetic foot ulcers (DFUs) from North Africa. We analyzed two independent datasets with distinct roles: 25 non-infected US DFUs (PRJNA506988) served as an ecological reference cohort to characterize depth-stratified microbial community patterns and pre-infection ARG ecology; 15 infected Libyan DFUs constituted the primary characterization cohort. Metagenomic sequencing, taxonomic classification, resistome and virulome profiling, and metagenome-assembled genome (MAG) reconstruction were performed. In the US reference cohort, depth-dependent community shifts were documented: Fusobacteriota predominated in deeper ulcers, while Staphylococcaceae and Pseudomonadaceae were enriched in superficial wounds. Eighty ARGs were detected across depth groups, including mecA and the mexAB-oprM efflux system, in clinically non-infected wounds. In the Libyan cohort, four major opportunistic pathogens were identified: Pseudomonas aeruginosa, Staphylococcus aureus, Acinetobacter baumannii, and Corynebacterium striatum. From sample M13, a high-quality P. aeruginosa MAG (99.68% completeness, 0.89% contamination) was reconstructed, classified as ST664 and carrying 220 virulence factors, 60 antibiotic resistance genes (all confirmed by RGI v6.0.2), and 213 mobile genetic elements. These findings represent the first genomic evidence of ST664 in a North African DFU and underscore the need for metagenomics-guided antimicrobial stewardship in chronic wound management.}, }
@article {pmid42245511, year = {2026}, author = {Otto, SJG and McLeod, L and McCarthy, EL and Funk, T and Lacoste, SR and Chai, Z and Links, MG and Barlow, LD and Gow, SP and Ramsay, D and Zaheer, R and McAllister, TA and Stothard, P and Hill, JE and Waldner, CL}, title = {Laboratory tests for bovine respiratory bacteria and antimicrobial resistance in commercial feedlot cattle: comparing culture, long-read metagenomics, and recombinase polymerase amplification.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1806062}, pmid = {42245511}, issn = {1664-302X}, abstract = {INTRODUCTION: The risk to humans and animals from antimicrobial resistance (AMR) has increased the emphasis on antimicrobial stewardship in food animal agriculture. Current stewardship recommendations include increasing diagnostic laboratory testing to inform antimicrobial use for bovine respiratory disease (BRD) management in beef feedlot production, yet the performance of newer molecular and sequencing-based diagnostic tests in commercial settings remains poorly characterized.<br><br>METHODS: Using nasopharyngeal swabs collected from commercial feedlot calves as part of Canadian surveillance, this study evaluated diagnostic laboratory testing approaches for detecting key bacterial BRD pathogens (Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasmopsis bovis) and associated AMR genes. Bayesian latent class models (BLCMs) were applied to compare traditional culture and antimicrobial susceptibility testing (AST) or qPCR with long-read metagenomic sequencing and recombinase polymerase amplification (RPA). Differences in detection of target bacteria and phenotypic or genotypic AMR were assessed across the early feeding period and between age cohorts.<br><br>RESULTS: This represents the first large-scale field evaluation of a recently developed, long-read metagenomic sequencing protocol implemented by a commercial laboratory for detecting BRD bacteria and AMR in respiratory samples (n = 760) collected by private veterinarians from western Canadian beef feedlots. Detection patterns for BRD bacteria and AMR using culture/AST and metagenomics were often similar between fall-placed calves and yearlings, but with differences from RPA. Detection of BRD bacteria had low sensitivity (< 65% for most organisms/tests), but higher specificity (>90% for all organisms/tests). Detection of macrolide and tetracycline resistance had low but variable sensitivity, with higher estimates for AST compared to metagenomics and RPA, and higher but variable specificity (>90% for most resistance outcomes/tests). Despite not using any targeted enrichment, metagenomic sequencing detected M. bovis although with a sensitivity lower than qPCR or RPA. Estimates of predictive value were most informative across the largest range of prevalence for AST, followed by metagenomics and then RPA.<br><br>DISCUSSION: This work demonstrates the potential for large scale implementation of long-read metagenomic sequencing to support antimicrobial stewardship and AMR surveillance for feedlot cattle. The estimates of clinical diagnostic performance and predictive values provide evidence-based guidance for three different laboratory tests for BRD management.}, }
@article {pmid42245748, year = {2026}, author = {Li, JZ and Guan, SY and Zhang, JF and Zheng, JN}, title = {Acute Q Fever in an Elderly Traveler with Multiple Comorbidities Diagnosed by Blood mNGS and Resolved with Omadacycline.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {610202}, pmid = {42245748}, issn = {1178-6973}, abstract = {This article reports a case of acute Q fever in a 61-year-old man. The patient mainly presented with high fever and cough. Extensive multi-system investigations failed to identify an etiology. On the fourth day of admission, the diagnosis of acute Q fever was confirmed by rapid detection of Coxiella burnetii nucleic acid sequence by blood metagenomic Next-Generation Sequencing (mNGS). With the treatment of intravenous omadacycline, the fever was controlled within 24 hours and the clinical symptoms significantly improved. Subsequent sequential therapy with oral doxycycline was administered, and the patient was discharged successfully. This case highlights the value of mNGS in the rapid diagnosis of rare or zoonotic pathogens in patients with fever of unknown origin, especially in patients with potential exposure to endemic areas. Furthermore, the novel tetracycline antibiotic omadacycline, demonstrating favorable efficacy and safety despite the patient's liver dysfunction, offers a valuable treatment option for rapid control of acute Q fever symptoms, especially in severe cases or those intolerant to doxycycline.}, }
@article {pmid42245929, year = {2026}, author = {Yan, W and Wang, X and Shi, K and Wang, L}, title = {Atypical Legionella pneumophila encephalopathy lacking respiratory symptoms and radiographic lesions: A Case Report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1828042}, pmid = {42245929}, issn = {2296-858X}, abstract = {This report details an unusual case of Legionella pneumophila encephalopathy in a 29-year-old male who presented with acute altered consciousness and extreme agitation, notably lacking any respiratory symptoms or typical meningeal signs. Extensive imaging, including chest CT and cranial MRI, revealed no pulmonary infiltrates or structural brain lesions. Cerebrospinal fluid (CSF) analysis demonstrated an aseptic profile with elevated protein, and CSF metagenomic sequencing returned negative. The diagnostic dilemma was ultimately resolved using whole-blood targeted next-generation sequencing (tNGS), which detected Legionella sequences. The patient achieved a rapid and complete neurological recovery following a combined regimen of levofloxacin and high-dose glucocorticoids. This case underscores that Legionella infection can manifest as an isolated, toxin- and immune-mediated encephalopathy without preceding clinical pneumonia. It highlights the critical rescue value of early molecular screening (such as tNGS) in unexplained encephalopathy and supports the judicious use of early steroid intervention to halt the aseptic neurotoxic cascade.}, }
@article {pmid42246002, year = {2026}, author = {Ren, JM and Zhang, XY and Liu, XP and Pei, LH and Jiang, WP and Zhang, XM and Ding, H and Huang, JS}, title = {Specimen-specific differences in clinical metagenomic sequencing reporting patterns in hospitalized patients: a single-center retrospective observational study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1823283}, pmid = {42246002}, issn = {2235-2988}, abstract = {Clinical metagenomic next-generation sequencing (mNGS) is increasingly used in hospitalized patients, but finalized reporting patterns vary across specimen types in routine practice. We conducted a single-center retrospective observational study using routine clinical mNGS data from January 1, 2024, to December 31, 2025. A specimen-specific first-order design retained only the first eligible mNGS order per patient within each specimen category during the study window. Orders were grouped as bronchoalveolar lavage fluid (BALF), blood, cerebrospinal fluid (CSF), and tissue for primary comparisons; heterogeneous "Other" specimens were described separately. The primary endpoint was report-interpreted any-positive at the order level. We summarized specimen-specific report-interpreted positivity, pathogen-group detection, the most frequently reported organisms ranked by order-level report presence, and mixed detections among positive orders. ICU-associated analyses were included as contextual descriptive stratification only. The cohort included DNA-only orders and a subset of PMseq-RNA-tested orders; RNA virus analyses were restricted to PMseq-RNA-tested orders, and DNA-only orders were treated as not tested for RNA virus fields. Among 1, 981 included specimen-specific first orders, BALF accounted for 973, blood 473, CSF 240, and tissue 122. Report-interpreted any-positive differed by specimen type, with BALF highest (876/973, 90.0%; 95% CI, 88.0-91.8%), followed by tissue (95/122, 77.9%; 95% CI, 69.7-84.3%), blood (343/473, 72.5%; 95% CI, 68.3-76.3%), and CSF (63/240, 26.2%; 95% CI, 21.1-32.2%). Among positive orders, at least 2 distinct standardized pathogens were reported in 672/876 BALF orders (76.7%), 182/343 blood orders (53.1%), 39/95 tissue orders (41.1%), and 8/63 CSF orders (12.7%). Across the four primary specimen groups, the most frequently reported organisms included Epstein-Barr virus (n = 485), Candida albicans (n = 285), and cytomegalovirus (n = 262), together with Klebsiella pneumoniae and Acinetobacter baumannii; these rankings reflect report-level frequency rather than adjudicated pathogenic roles, particularly for latency- or reactivation-prone viruses. Of included orders, 277 (14.0%) underwent PMseq-RNA testing. These findings characterize specimen-specific differences in clinical mNGS reporting patterns and provide a specimen-context-aware reference for interpreting routine inpatient reports.}, }
@article {pmid42246191, year = {2026}, author = {Das, D and Dixit, R and Pandey, M}, title = {The Biliary Multi-Omics Landscape: Integrating Microbiome and Metabolomics in Gallbladder Carcinogenesis.}, journal = {Journal of gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jgh.70462}, pmid = {42246191}, issn = {1440-1746}, abstract = {BACKGROUND: Gallbladder cancer (GBC) is a highly aggressive malignancy with a dismal prognosis, frequently diagnosed at advanced stages. While cholelithiasis is a primary risk factor, the role of the biliary microbiome and its metabolic products in driving carcinogenesis is increasingly recognized. This review synthesizes multi-omics data to elucidate the interplay between microbial dysbiosis and metabolomic shifts in GBC.<br><br>METHODS: A systematic literature search was conducted on PubMed (up to January 2026) focusing on biliary bacteria, the gut-bile axis, and multi-omics markers. A narrative synthesis integrated findings from metagenomic, metaproteomic, and metabolomic studies involving human cohorts and experimental models.<br><br>RESULTS: GBC is characterized by profound biliary dysbiosis, specifically the enrichment of Enterobacteriaceae, Streptococcus, and Helicobacter species. This taxonomic shift triggers a pro-carcinogenic metabolomic flux, where microbial 7&#x3b1;-dehydroxylation converts primary bile acids into secondary bile acids, such as deoxycholic acid (DCA), which induce DNA damage and promote tumor growth. Metaproteomic signatures identify bacterial proteins (e.g., QDR3, ompA) that facilitate biofilm formation and oxidative stress evasion. Furthermore, emerging paradigms like cross-species horizontal gene transfer (HGT) suggest that microbial genetic material can directly modulate host oncogenic pathways.<br><br>CONCLUSION: The GBC multi-omics landscape reveals a complex gut-bile axis where microbial and chemical factors converge. These integrated signatures offer potential as noninvasive biomarkers for early diagnosis and precision therapy.}, }
@article {pmid42247317, year = {2026}, author = {Zeng, Y and Wang, S and Zhang, Q and Miao, H and Xu, J and Li, W}, title = {Successful management of Legionella pneumonia in an immunocompromised infant presenting with generalized pustular rash: A case report.}, journal = {Science progress}, volume = {109}, number = {2}, pages = {368504261458101}, doi = {10.1177/00368504261458101}, pmid = {42247317}, issn = {2047-7163}, abstract = {Legionella infection is rare in children, and extrapulmonary manifestations are even less commonly reported. Cutaneous involvement, particularly in the form of generalized pustular eruptions, may present significant diagnostic and therapeutic challenges, especially in immunocompromised patients. We report a male infant under 6 months with X-linked severe combined immunodeficiency (XL-SCID) who presented with a disseminated pustular rash as the predominant clinical feature. Initial blood and pus cultures were negative, and empirical antimicrobial therapy showed limited clinical response. Metagenomic next-generation sequencing (mNGS) was subsequently performed and identified Legionella as the causative pathogen. Based on this finding, the antimicrobial regimen was adjusted to include a macrolide antibiotic combined with trimethoprim-sulfamethoxazole (TMP-SMX), resulting in significant clinical improvement and eventual recovery. This case highlights the atypical presentation of Legionella infection with predominant cutaneous manifestations in children, particularly in the context of primary immunodeficiency, and underscores the diagnostic value of mNGS in cases with inconclusive conventional testing. Early application of advanced molecular diagnostics and timely optimization of targeted antimicrobial therapy are crucial for improving outcomes in rare and complex pediatric infections.}, }
@article {pmid42247440, year = {2026}, author = {Levade, I and Delisle, B and Fournier, &#xc9; and Therrien, C}, title = {RNA metagenomic profiling of mosquito viromes associated with Vector-Borne diseases in Quebec, Canada.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0350663}, doi = {10.1371/journal.pone.0350663}, pmid = {42247440}, issn = {1932-6203}, abstract = {Mosquitoes harbor diverse viral communities, including both medically important arboviruses and insect-specific viruses, yet the viromes of mosquito populations in northern temperate regions remains poorly characterized. In this study, we used metagenomic sequencing to analyse pools of archived mosquito samples from Québec, Canada representing multiple species previously identified as arbovirus carriers. Our analyses identified 60 viral species, including three arboviruses, several insect-specific viruses, and multiple dual-host non-pathogenic viruses, revealing the rich viral diversity present in these mosquito populations. Phylogenetic analysis of complete viral genomes demonstrated genetic relationships with viruses reported from diverse geographic regions. We describe, a newly proposed bipartite Culex tombus-like virus and report the complete resolution of thirty-five viral genomic sequences. These results highlight the utility of metagenomic approaches for comprehensive characterization of the mosquito virome and underscore their potential to enhance surveillance of emerging arboviruses, including West Nile virus, in Québec and similar northern ecosystems.}, }
@article {pmid42247515, year = {2026}, author = {Piñero, M and Librado, P}, title = {Genomic evidence for limited entomophagy in ancient Europeans.}, journal = {Science advances}, volume = {12}, number = {23}, pages = {eaec6939}, doi = {10.1126/sciadv.aec6939}, pmid = {42247515}, issn = {2375-2548}, abstract = {To meet the rising food demands of our growing population, the Food and Agriculture Organization proposed edible insects as sustainable sources of animal protein. Although hundreds of million people already consume insects around the tropics, western societies remain averse to entomophagy. To trace whether ancient Europeans consumed insects, we here apply two complementary genomic approaches. Metagenomic screening on 745 ancient anatomically modern human dental calculus returned limited insect DNA traces, with read abundances well below those observed in Neanderthals, western chimpanzees, and gorillas. In addition, genes encoding stomach-expressed chitinases show two of the most significant signatures of latitudinal differentiation genome-wide. Clines are consistent with evolutionary benefits of entomophagy in tropical regions and with expression quantitative trait locus data supporting low chitin digestibility in present-day Europeans. Ancient genomes confirm that both clines already existed at the onset of agriculture and persisted despite massive migrations. Together, our findings support occasional and possibly incidental insect consumption in Europe over the past ~9000 years.}, }
@article {pmid42247592, year = {2026}, author = {Boulay, A and Németh, V and Criel, B and Stock, M and De Baets, B and Galiez, C and Rousseau, E and Briers, Y and Vázquez, R}, title = {PhaLP 2.0: extending the community-oriented phage lysin database with a SUBLYME pipeline for metagenomic discovery.}, journal = {Database : the journal of biological databases and curation}, volume = {2026}, number = {}, pages = {}, doi = {10.1093/database/baag033}, pmid = {42247592}, issn = {1758-0463}, support = {#325947//FRQNT/ ; //NSERC/ ; 1S91526N//FWO/ ; 1S38519N//FWO/ ; #307935//FRQS/ ; 01P10022//BOF/ ; }, abstract = {As biology becomes increasingly data-driven, so does the field of phage lysins, enzymes that degrade bacterial cell walls and offer promising alternatives to traditional antibiotics. Five years ago, we introduced PhaLP, a centralized resource for Phage Lytic Protein sequences and associated metadata to support global research efforts. Here, we present PhaLP 2.0, an enhanced database designed to address key challenges in computational lysin research by integrating newly identified lysins from thousands of metagenomes. To expand the known diversity of lysins beyond that of cultured phages, we developed SUBLYME, a protein-embedding-based machine-learning Software designed to Uncover and classify Bacteriophage Lysins from Metagenomic datasets. Using embeddings derived from the well-curated sequences of the original PhaLP database, we trained support vector machines to distinguish lysins from non-lysins in viromes and classify them as endolysins or virion-associated lysins. The models achieved an average F1 score of 98% on held-out clusters. SUBLYME enabled the discovery of 743 000 new lysin sequences from EnVhogDB, a virome-derived protein database, increasing the number of known lysin clusters 40-fold, from 1000 to 40 000. SUBLYME and PhaLP 2.0 are accessible online at https://github.com/Rousseau-Team/sublyme and https://phalp.ugent.be, respectively. Together, these advances establish PhaLP 2.0 as a comprehensive and scalable portal for lysin discovery, classification, and sequence analysis, paving the way for future antibacterial applications and evolutionary insights.}, }
@article {pmid42247807, year = {2026}, author = {Sadia, H and Amin, A and Khalid, N and Ahmed, I}, title = {Antimicrobial resistance and virulence in polymicrobial chronic wound infections: A metagenomic perspective.}, journal = {Journal of infection and public health}, volume = {19}, number = {8}, pages = {103280}, doi = {10.1016/j.jiph.2026.103280}, pmid = {42247807}, issn = {1876-035X}, abstract = {BACKGROUND: Chronic wound infections represent a significant clinical and public health challenge due to their polymicrobial nature and the increasing burden of antimicrobial resistance (AMR). Conventional culture-based diagnostics often fail to capture the full microbial diversity and resistance potential associated with these infections.<br><br>METHODS: Chronic wound samples persisting for more than 15 days were collected from patients at a tertiary-care hospital in Pakistan. Samples are categorized into five groups: lower leg (ll-H1), upper leg (ul-H2), foot (ft-H3), chest (ct-H4) and catheter (ca-H5). Shotgun metagenomic sequencing was employed alongside routine culture-based methods to characterize microbial communities, antimicrobial resistance genes, and virulence determinants. Taxonomic and functional profiling were performed to assess microbial diversity and resistance patterns across wound subgroups.<br><br>RESULTS: Metagenomic analysis revealed a predominance of Proteobacteria, Bacteroidetes, and Actinobacteria. Clinically relevant pathogens, including Achromobacter xylosoxidans, Staphylococcus aureus, and Pseudomonas aeruginosa, were frequently detected, along with less commonly reported taxa such as Achromobacter insolitus and Stenotrophomonas maltophilia. Multiple antimicrobial resistance gene clusters and biofilm-associated virulence factors were identified, indicating substantial multidrug resistance potential. Site-specific analysis showed that Pseudomonas aeruginosa dominated ul-H2 (&#x223c;32%), while Enterobacter hormaechei was most abundant in ft-H3 (&#x223c;40%). Culture-based methods primarily recovered common aerobic pathogens, whereas metagenomics detected additional opportunistic and unculturable taxa, highlighting the limitations of routine diagnostics. Resistome analysis identified ARGs conferring resistance to &#x3b2;-lactams, aminoglycosides, fluoroquinolones, tetracyclines, and macrolides.<br><br>CONCLUSIONS: Chronic wound infections in Pakistan harbor diverse polymicrobial communities with substantial antimicrobial resistance and virulence potential. Shotgun metagenomics provides a more comprehensive characterization than culture-based methods by detecting additional pathogens and resistance determinants across wound sites. These findings support the integration of metagenomic diagnostics to improve clinical decision-making, strengthen antimicrobial stewardship, and guide infection control strategies in resource-limited healthcare settings.}, }
@article {pmid41551460, year = {2026}, author = {Cornman, RS and Hepner, MJ and Otto, CRV}, title = {The Appalbees menu: a multiyear, multilocus metagenetic assessment of pollen foraging by Appalachian Bombus affinis workers.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20284}, pmid = {41551460}, issn = {2167-8359}, mesh = {Animals ; Bees/physiology ; *Pollen/genetics/classification ; Virginia ; West Virginia ; DNA Barcoding, Taxonomic ; Appalachian Region ; *Feeding Behavior ; Metagenomics ; Pollination ; }, abstract = {BACKGROUND: Detailed studies of foraging behavior are needed for scientific management of the endangered rusty-patched bumblebee (Bombus affinis) in the disjunct and ecologically differentiated habitats it presently occupies. Current knowledge gaps hinder recovery planning but are challenging to redress through direct observation of rare interactions in the field.<br><br>METHODS: We used genetic metabarcoding to characterize the taxonomic composition of pollen collected by B. affinis workers in the Appalachian mountains of Virginia and West Virginia from 2021-2023. We developed a custom sequence database of the regional flora and compared results for two independent genetic loci, internal transcribed spacer 1 and internal transcribed spacer 2 (ITS1 and ITS2).<br><br>RESULTS: While ITS2 consistently detected more plant diversity, results from the two loci were broadly concordant with a few notable exceptions. The plant genera Hydrangea, Actaea, Rhododendron, Tilia, and (unexpectedly) Laportea were prominent in midsummer samples, with Rubus a consistent contributor in late spring and early summer. Pea flowers (family Fabaceae) were relatively infrequent but the genera Securigera and Trifolium were detected before the Hydrangea bloom and again in late summer afterwards. The diversity of forage plants was highest in late summer, driven primarily by various genera of Asteraceae. Comparing the current data with previous work indicates regional differentiation in forage plants between Appalachia and the upper Midwest, but also allows 'consensus' forage sources that are supported by multiple lines of evidence and shared between regions to be tabulated. These results should help managers focus survey efforts for this endangered species and plan habitat enhancements.}, }
@article {pmid42012700, year = {2026}, author = {Chen, J and Xi, M and Hu, W and He, R and Zhang, W and Zhang, Y and Chen, X and Chen, J}, title = {Adult Onset of MSMD Caused by IL-12Rβ1 Variants: Report of a Young Woman with NTM Infection Lacking Bacille Calmette-Guérin (BCG)-induced Diseases.}, journal = {Journal of clinical immunology}, volume = {46}, number = {1}, pages = {}, pmid = {42012700}, issn = {1573-2592}, support = {23141901900//the Shanghai Science and Technology Innovation Action Plan&#xff0c;experimental animal research&#xa0;project/ ; 23PJD073//the Shanghai Pujiang Program/ ; ynms202306//Basic Research Project of the Sixth People's Hospital of Shanghai/ ; }, abstract = {UNLABELLED: Mendelian susceptibility to mycobacterial disease (MSMD) is characterized by increased susceptibility to infections caused by weakly virulent mycobacteria (such as nontuberculous mycobacteria (NTM) or the Bacillus Calmette–Guérin (BCG) vaccine) in otherwise healthy individuals. In this study, we described a 29-year-old patient with MSMD due to NTM infection identified using metagenomic next-generation sequencing (mNGS) testing. The patient showed a poor response to standard antimycobacterial treatment. Therefore, we performed whole-exome sequencing (WES) and identified three heterozygous variants in IL-12Rβ1 (Ala131Thr, Arg323* and Arg561*). The two deleterious IL-12RB1 variants, Arg323* and Arg561*,were shown to be in trans (paternal and maternal, respectively). Further investigation revealed that two of these variants (Arg323* and Arg561*) could affect the binding between IL-12Rβ1 and IL-12Rβ2, leading to a weakened response of CD4[+] T cells to stimulation with IL-12 plus tuberculosis antigen (TbAg), with reduced expression levels of IFN-γ and its downstream target p-STAT4. However, these variants did not affect the CD4[+] T-cell response to glucan stimulation, as the three heterozygous variant loci do not interfere with the aggregation of IL-12Rβ1 and IL-23R. This autosomal recessive, partial IL-12Rβ1 deficiency ultimately resulted in the patient developing disseminated NTM infection. In clinical treatment, we combined IFN-γ with standard antimycobacterial therapy. The patient showed only a partial response to therapy. Therefore, as detection techniques continue to advance, it is important for clinicians to increase their understanding of MSMD to enable faster and more accurate diagnosis and treatment.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10875-026-02009-x.}, }
@article {pmid42235107, year = {2026}, author = {Candia-Herrera, D and Guerra, M and Carrasco-Fernández, J and Campos-Quiroz, C and Garcia-Gomez, M and Igual, JM and Carro, L and Castro, JF}, title = {Whole genome-based reclassification of the genus Metabacillus: Proposal for five novel genera, Chryseobacillus gen. nov., Cohnibacillus gen. nov., Salimetabacillus gen. nov., Pantoeobacillus gen. nov., and Lutimetabacillus gen. nov. and the description of one novel bacterial species, Chryseobacillus diguaensis sp. nov. isolated from soil in the Digua reservoir.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {4}, pages = {126734}, doi = {10.1016/j.syapm.2026.126734}, pmid = {42235107}, issn = {1618-0984}, abstract = {Comprehensive phylogenomic and comparative genomic analyses were conducted to clarify the taxonomic boundaries of the genus Metabacillus. Phylogenetic trees reconstructed from a set of single-copy orthologous proteins (SCOPs) revealed that the genus, as currently defined, is polyphyletic. The type species of the genus Metabacillus and its closest relatives formed a consistent clade, herein designated as Metabacillus sensu stricto. The remaining species were grouped into three well-supported clades: Kandeliae, Indicus, and Mangrovi, and two single-taxon lineages: M. arenae and M. lacus. The phylogenomic delineation found in these divergent taxa was corroborated by either inconsistent distribution patterns or the absence of previously defined conserved signature indels (CSIs) specific to Metabacillus. Genomic metrics, including Average Nucleotide Identity (ANI), Average Amino acid Identity (AAI), and digital DNA-DNA hybridization (dDDH) further supported the taxonomic delineation proposed here. The observed genomic divergence was mirrored by phenotypic differences, including variations in GC content ranges. Based on this polyphasic evidence, we propose the reclassification of the genus Metabacillus taxa into five novel genera: Chryseobacillus gen. nov. (encompassing the Kandeliae clade), Cohnibacillus gen. nov. (M. lacus), Salimetabacillus gen. nov. (M. arenae), Pantoeobacillus gen. nov. (Indicus clade), and Lutimetabacillus gen. nov. (Mangrovi clade). The core lineage is retained as Metabacillus sensu stricto, for which an emended description of the genus Metabacillus is also provided. A novel bacterial strain, designated as MAU-250[T], was isolated from a soil sample collected on the shore of an artificial reservoir in the Andean foothills of the Maule Region in central Chile. Public metagenome screening supported a low-abundance taxon with broad ecological adaptability, preferentially associated with soil habitats. A polyphasic analysis based on phenotypic traits and genomic distances (78.0% ANIb and 19.8% dDDH against its closest relative) also supported its designation as a novel species, for which the name Chryseobacillus diguaensis sp. nov. is proposed. The type strain is MAU-250[T] (=RGM 3146[T] = IMI 507634[T]).}, }
@article {pmid42235155, year = {2026}, author = {Zhang, YF and Li, MY and Zhang, Y and Ding, H and Yun, L and Li, ZY}, title = {Genome-resolved analysis reveals successional dynamics and functional transitions in chicken gut archaea across the broiler growth cycle.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107186}, doi = {10.1016/j.psj.2026.107186}, pmid = {42235155}, issn = {1525-3171}, abstract = {Archaea are indispensable members of the gut microbiota, playing important roles in host metabolism and gut homeostasis. Despite their ecological significance, the archaeal community within the chicken gut remains poorly understood, particularly regarding its taxonomic diversity, functional potential, and successional dynamics throughout the broiler growth cycle. In this study, we employed a metagenome-assembled genome (MAG) approach to systematically characterize the composition, phylogeny, and functional shifts of the chicken gut archaea. We constructed a genome catalog comprising 172 non-redundant archaeal MAGs, encompassing 11,796 protein clusters. Community analysis revealed that alpha diversity indices differed significantly across growth stages, suggesting that the archaeal community becomes increasingly robust and functionally complex as the host matures. Functional annotation further demonstrated broad metabolic versatility, with distinct metabolic profiles emerging across multiple functional modules at different ages. This study reveals the dynamics of chicken gut archaeal communities and their potential functional characteristics across different production stages, providing a basis for future research into their ecological roles and possible associations with host gut ecosystem stability.}, }
@article {pmid42235160, year = {2026}, author = {Lu, T and Chen, Y and He, Q and Zheng, B and Deng, D and Xiong, X}, title = {Gut bacterial species, serum metabolites, and serum cytokines associated with broodiness in chickens.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107187}, doi = {10.1016/j.psj.2026.107187}, pmid = {42235160}, issn = {1525-3171}, abstract = {Increasing evidence suggests that the gut microbiota, serving as a "virtual endocrine organ", potentially modulates reproductive behavior in poultry via the gut-brain and gut-ovary axes. Broodiness in hens inhibits egg-laying activity and causes major economic losses in native chicken breeds, but its micro-physiological basis remains unclear. This study used shotgun metagenomic sequencing to delineate the cecal bacterial species associated with brooding status in Chinese Kangle chickens. We identified 34 cecal bacterial species exhibiting significantly varying abundances between the broodiness and control groups, including six species (e.g., Bacteroides sp. An51A and Phocaeicola barnesiae) that were significantly enriched in the broodiness group. Additionally, 28 species significantly enriched in the control group were screened. Among them, Subdoligranulum variabile and Oribacterium asaccharolyticum served as key biomarkers for distinguishing brooding status in Kangle chickens and were associated with functional shifts in the cecal microbiome. Non-targeted metabolomic analysis identified 17 differential metabolites, among which seven (e.g., (13E) -11a-hydroxy-9,15-dioxoprost-13-enoic acid and d-arabitol) were defined as metabolic markers of the broody state and were significantly associated with Subdoligranulum variabile and Oribacterium asaccharolyticum. In addition, our results suggest that serum cytokines, such as IFN-γ and IL-22, are potentially associated with the broody state and the alterations in both serum metabolites and the gut microbiota (e.g., Subdoligranulum variabile and Oribacterium asaccharolyticum). These findings provide a new insight into the mechanisms underlying reproductive behavior in poultry and offer a theoretical basis for alleviating broodiness through microecological interventions, thereby improving the reproductive efficiency of indigenous chicken breeds.}, }
@article {pmid42235395, year = {2026}, author = {Li, Y and Zhu, T and Tao, C and Li, S and Cheng, H and Chen, W}, title = {Threshold-dependent control of ARG removal in global wastewater treatment plants: Molecular mechanisms of low-abundance functional genes deciphered via metagenomics and explainable AI.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142574}, doi = {10.1016/j.jhazmat.2026.142574}, pmid = {42235395}, issn = {1873-3336}, abstract = {Wastewater treatment plants (WWTPs) serve as critical barriers against the dissemination of antibiotic resistance genes (ARGs) from urban water environments to nature, yet the molecular mechanisms governing their biological removal remain poorly understood. By combining experimental metagenomic data from 19 Chinese WWTPs with additional data from 31 global WWTPs (50 WWTPs in total), an explainable machine learning (ML) framework was developed. The RFE-SHAP (Recursive Feature Elimination-SHapley Additive exPlanations) based on feature importance was applied to identify key biological features driving ARG removal. The study revealed that low-abundance microbial functional genes particularly those involved in DNA repair, energy metabolism, and quorum sensing exhibit threshold-dependent control over ARG attenuation. ML models (BFGs-GBDT) incorporating the RFE-SHAP-selected functional genes achieved exceptional predictive accuracy (R[2]test = 0.967), outperforming taxonomy-based models (average R[2]test = 0.805). Strikingly, these functionally critical genes, despite their low abundances (0.04 - 0.15%), exerted disproportionate influence on ARG removal efficiency, challenging the prevailing high-abundance-centric paradigm in WWTPs design. The findings not only elucidated the molecular mechanisms of ARG mitigation but also provided a predictive framework for precision engineering of microbial communities to enhance ARG elimination. This study advances wastewater treatment strategies from empirical ARG removal to mechanism-driven environmental risk control.}, }
@article {pmid42235463, year = {2026}, author = {Lin, Q and Mei, X and Zheng, H and Meng, J and He, F and Yang, B and Ru, X and Su, M and Wang, D and Tan, N and Fang, J and Fu, S and Ouyang, N and Yang, Z and Jiang, S and Zhang, Y}, title = {Optimisation and validation of capture mNGS for predicting antimicrobial resistance.}, journal = {EBioMedicine}, volume = {129}, number = {}, pages = {106319}, doi = {10.1016/j.ebiom.2026.106319}, pmid = {42235463}, issn = {2352-3964}, abstract = {BACKGROUND: Antibiotic resistance critically compromises bacterial infection treatment. While antimicrobial susceptibility testing (AST) remains the standard for resistance assessment, its culture dependence is time-consuming. Clinical metagenomic next-generation sequencing (mNGS) offers rapid pathogen detection and antibiotic resistance gene (ARG) profiling. However, low ARG detection sensitivity and unclear genotype-phenotype correlations limit its clinical utility.<br><br>METHODS: We developed capture mNGS approach with probe-based ARG enrichment and a host-attribution algorithm for precise ARG-bacteria linkage. Its ARG detection sensitivity was comparatively analysed against standard mNGS. Using phenotypic AST as reference, we then evaluated the clinical predictive value of capture mNGS-detected ARGs in a retrospective cohort from Sun Yat-sen Memorial Hospital (SYSMH) and an external cohort from Liuzhou Worker's Hospital (LWH). In addition, a prospective cohort from SYSMH was used to explore the clinical utility of ARG detection by mNGS.<br><br>FINDINGS: Compared to standard mNGS, capture mNGS significantly enhanced ARG detection sensitivity, achieving a 44-fold increase in sequencing depth. In our retrospective cohort, key resistance genes detected by capture mNGS accurately predicted phenotypic resistance: blaCTX-M achieved a sensitivity of 1.00 (95% CI: 0.86, 1.00) and specificity of 1.00 (95% CI: 0.59, 1.00) for ceftriaxone resistance prediction, with an area under the receiver operating characteristic curve (AUC) of 0.93 (95% CI: 0.87, 0.99). BlaKPC demonstrated a sensitivity of 0.94 (95% CI: 0.73, 1.00) and specificity of 1.00 (95% CI: 0.95, 1.00) for carbapenem resistance (AUC = 0.97, 95% CI: 0.92, 1.00). Similarly, blaOXA-23 exhibited a sensitivity of 0.95 (95% CI: 0.82, 0.99) and specificity of 1.00 (95% CI: 0.69, 1.00) for carbapenem resistance (AUC = 0.97, 95% CI: 0.94, 1.00), which was externally validated in the LWH cohort. In addition, mecA showed a sensitivity of 0.94 (95% CI: 0.71, 1.00) and specificity of 0.94 (95% CI: 0.81, 0.99) for oxacillin resistance (AUC = 0.94, 95% CI: 0.87, 1.00). Whereas blaTEM/blaSHV showed higher false-positive rates for cephalosporin resistance and ErmB/ErmC showed lower sensitivity (0.6, 95% CI: 0.32, 0.84) for macrolide-lincosamide-streptogramin (MLS) resistance. Capture mNGS reported results (median turnaround time (TAT): 24.71 h (IQR 22.74-41.00)) were shorter than AST (median TAT: 73.16 h (IQR 54.19-93.42)). In a prospective cohort, the time to guide antibiotic therapy based on reported positive ARGs was significantly shorter than that based on reported resistant phenotypes from AST.<br><br>INTERPRETATION: These results highlight that ARGs can be leveraged to rapidly and accurately predict bacterial resistance phenotypes with high sensitivity and specificity, thereby guiding antibiotic management in clinical practice.<br><br>FUNDING: The National Natural Science Foundation of China, the Guangdong Science and Technology Department, Science and Technology Projects in Guangzhou.}, }
@article {pmid42235671, year = {2026}, author = {Peng, D and Liu, X and Wang, L and Pan, Y and Kang, B and Liu, X and Xu, R and Cheng, Y}, title = {A multi-omics signature of microplastic exposure and its clinical, metabolic, and microbial correlates in colorectal cancer.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128426}, doi = {10.1016/j.envpol.2026.128426}, pmid = {42235671}, issn = {1873-6424}, abstract = {Microplastics (MPs) are emerging environmental contaminants with potential human health implications, yet their distribution and biological effects in colorectal cancer (CRC) remain unclear. Here, we investigate the presence of MPs in blood, tumor, and peri-tumor tissues from CRC patients using a multi-omics approach. We find that MPs, particularly polyvinyl chloride (PVC) and polyethylene (PE), are more abundant in tumor and peri-tumor tissues than in blood. Tissue-specific MPs were associated with clinical traits, serum metabolites, and gut microbes. Functional analysis suggested MP-related alterations in microbial pathways involving carbohydrate metabolism, fatty acid degradation, and bile acid biosynthesis. Our findings provide the first integrative evidence suggesting potential links between MPs exposure to metabolic and microbial dysregulation in CRC patients.}, }
@article {pmid42235696, year = {2026}, author = {Tang, P and Shuai, H and Yang, Z and Cen, Q and Mao, Y and Wang, J and Zhou, Y}, title = {Contributions and mechanisms of bioclogging-induced oxygen-limited microsites to nitrogen removal in porous media.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135059}, doi = {10.1016/j.biortech.2026.135059}, pmid = {42235696}, issn = {1873-2976}, abstract = {Nitrate (NO3[-]-N) in wastewater treatment plant (WWTP) effluents has become a contributing factor to the increasing eutrophication risk in receiving waters, whereas the relatively high dissolved oxygen (DO, approximately 7-8 mg L[-1]) in effluents constrains NO3[-]-N removal. Constructed wetland systems based on porous media are major technologies for advanced treatment of WWTP effluents. Although bioclogging in such systems is usually regarded as a negative phenomenon, it may create favorable anoxic microenvironments for denitrification through transport confinement. In this study, vertical saturated flow-through porous-media columns were established to systematically elucidate how bioclogging reshapes oxygen transport and drives microbial functional reorganization under bulk-oxic conditions. The results showed that hydraulic conductivity (k) decreased from 27.5 and 18.1 cm s[-1] in Groups A and B, respectively, to < 0.03 cm s[-1], while NO3[-]-N removal increased from 61 to 64% during start-up to 88-91% at day 24. The two-dimensional plate experiment directly captured the full evolution of pore-scale oxygen-limited microenvironments from discrete patches to connected structures. DO heatmaps further showed that bioclogging-induced transport confinement generated nested confined oxygen-limited microsites within an otherwise bulk-oxic flow field. Denitrification-related genes were enriched in the clogging-affected upper and intermediate layers, indicating that efficient denitrification was more likely associated with bioclogging-induced confined oxygen-limited microsites than simply with medium depth. Metagenomic analysis further revealed a metabolic division of labor within the microbial community, with Ectobacillus mainly associated with upstream nitrate reduction, Nitrospira and Chitinophagaceae playing complementary roles in downstream steps, and Ignavibacterium exhibiting genomic signatures consistent with enhanced organic-carbon metabolism and potential reducing-equivalent generation. Overall, bioclogging coupled bulk-oxic and locally oxygen-limited functions through transport confinement and community-level metabolic partitioning, providing new mechanistic insights into stable nitrogen removal under high-DO effluent conditions.}, }
@article {pmid42235698, year = {2026}, author = {Zhou, X and Yu, Z and Liao, H and Wang, Y and Zhuang, L and Zhou, S}, title = {Bacteria and viruses associated with antibiotic resistome in hyperthermophilic co-composting of cow manure and mushroom residue.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135075}, doi = {10.1016/j.biortech.2026.135075}, pmid = {42235698}, issn = {1873-2976}, abstract = {Antibiotic resistance in livestock-derived wastes represents a critical environmental and public health concern. Here, we applied genome-resolved metagenomic analysis to characterize antibiotic resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and associated viral communities during co-composting of cow manure and mushroom residue. By day 20, hyperthermophilic composting (HTC) achieved markedly higher ARG removal (93%) than conventional thermophilic composting (TC, 84%). This enhanced performance was associated with the enrichment of thermophilic taxa (e.g., Bacillaceae and Sporolactobacillaceae) and the suppression of mesophilic ARG reservoirs (e.g., Enterobacteriaceae and Pseudomonadaceae). Genome-resolved analysis further revealed that a majority of multidrug-resistant ARB were eliminated during HTC, particularly Klebsiella pneumoniae and Escherichia coli harboring diverse ARGs and virulence factor genes. These high-risk pathogens were predicted to be targeted by a subset of lytic phages, including those affiliated with Autographiviridae and Schitoviridae, suggesting a potential role of lytic phages in suppressing resistance- and virulence-associated ARB. Collectively, these findings provide genome-resolved insights into the coordinated roles of thermophile-driven suppression and phage-mediated predation of ARB in ARG removal, highlighting HTC as a promising strategy for safer manure recycling and resistance risk mitigation.}, }
@article {pmid42235960, year = {2026}, author = {Chongdar, N and Goyal, A and Damare, SR}, title = {Genomic Survey of Carbon Monoxide Dehydrogenases Reveals Their Widespread Distribution in Marine Habitats.}, journal = {Environmental microbiology reports}, volume = {18}, number = {3}, pages = {e70375}, doi = {10.1111/1758-2229.70375}, pmid = {42235960}, issn = {1758-2229}, support = {DST/INSPIRE/04/2021/002518//Department of Science and Technology, Govenrnment of India/ ; }, abstract = {Most carbon monoxide (CO) produced in the ocean is consumed by microorganisms encoding carbon monoxide dehydrogenases (CODHs), thereby significantly reducing the flux of CO from the ocean to the atmosphere. CODHs are of two types based on the metal content of their active sites: the oxygen-sensitive, nickel-containing Ni-CODH and the oxygen-tolerant, molybdenum-copper-containing Mo-CODH. Although CODHs have been reported from specific marine environments, their combined distribution across ocean ecosystems remains unclear. Here, we analyzed the NCBI non-redundant protein database and identified 1969 Ni-CODH and 864 Mo-CODH genes from marine prokaryotes spanning diverse oceanic ecosystems. Using metagenomic analyses across three marine biomes, we showed that oxygen availability selectively constrains Ni-CODH gene abundance, but not Mo-CODHs. Thus, Ni-CODHs are restricted to oxygen-limited niches, while Mo-CODHs occur across both oxygenated and oxygen-limited marine environments. Phylogenetic analyses indicated that all previously described CODH clades are represented in the marine ecosphere, highlighting their evolutionary diversity. Genome context analyses suggest that approximately 50% of the marine Ni-CODH potentially participate in carbon fixation via the Wood-Ljungdahl pathway, whereas most marine Mo-CODH likely contribute to the supplementary energy conservation. Together, these results provide an integrated view of CODH distribution and potential function in marine ecosystems.}, }
@article {pmid42236101, year = {2026}, author = {Borghi, E and Tassi, L and d'Orsi, G and Uzzau, S and Pivari, F and Ricci, E and Longoni, G and Mingarelli, A and Previtali, R and Berardi, R and De Diego, L and Vigano', I and Olivotto, S and Compierchio, E and Veggiotti, P and Canevini, MP and Vignoli, A}, title = {Microbiota-gut-brain axis and treatment resistance in epilepsy: a multicentre prospective study protocol (CARE).}, journal = {BMJ open}, volume = {16}, number = {6}, pages = {e111607}, doi = {10.1136/bmjopen-2025-111607}, pmid = {42236101}, issn = {2044-6055}, abstract = {INTRODUCTION: Approximately one-third of people with epilepsy (PWE) experience resistance to treatment, including pharmacological therapies, epilepsy surgery, vagus nerve stimulation (VNS) and dietary interventions such as the ketogenic diet (KD). Emerging evidence suggests that the gut microbiota may influence seizure susceptibility and treatment response through the microbiota-gut-brain axis, potentially contributing to treatment resistance. The MiCrobiota-gut-brain Axis in Resistant Epilepsy project investigates how gut microbial features and associated host epigenetic signatures affect clinical outcomes in PWE undergoing diverse treatment strategies.<br><br>METHODS AND ANALYSIS: This is a multicentre, prospective, longitudinal study involving four clinical centres in Italy and one self-financing partner. Participants aged 3-50 years will be enrolled and stratified into four intervention cohorts: newly diagnosed drug-na&#xef;ve epilepsy scheduled to start anti-seizure medications, focal drug-resistant epilepsy (DRE) undergoing epilepsy surgery, DRE receiving VNS, and DRE initiating KD. Clinical assessments (including body mass index calculation, self-reported monthly seizure count, dietary evaluation, quality of life scale and gastrointestinal symptoms scale), electroencephalography, MRI and biological sample collection (stool and blood) will be obtained at baseline and longitudinally at two or three timepoints over a 12-month observation period. Gut microbiota changes over time will be assessed via metagenomics (using 16S ribosomal RNA sequencing) and metaproteomics; the associated host DNA methylation profiles will be obtained from blood using Illumina EPIC arrays. Primary endpoints include identification of microbial or host methylation changes predictive of therapeutic response (ie, reduction from baseline in monthly seizure count) to the intervention. Data will be analysed using multivariate models and mixed-effect regression. Further, omics data and corresponding metadata will be integrated using multi-omics approaches to identify molecular signatures biomarkers predictive of treatment response and prognosis in PWE.<br><br>ETHICS AND DISSEMINATION: The study received ethical approval from the Research Ethic Board (Comitato Etico Territoriale Lombardia 3, ID 4896 - parere numero 4896_17.07.2024_N_bis). All participants or their legal guardians will provide written informed consent. Results will be disseminated through peer-reviewed publications, conference presentations or lay summaries targeting patient organisations.<br><br>TRIAL REGISTRATION NUMBER: ClinicalTrials.gov Identifier NCT07010445, registered on 2 May 2025.}, }
@article {pmid42236489, year = {2026}, author = {Kehl, AJ and Taylor-Kearney, L and Jaffe, AL and Pereira, JH and Lee, J and Hammel, M and Waldburger, LM and Yeow, C and Valentin-Alvarado, L and Adams, PD and Banfield, JF and Siegel, JB and Prywes, N and Shih, PM}, title = {Diversity-driven biochemical survey reveals widespread dimerization throughout the rubisco superfamily.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73982-5}, pmid = {42236489}, issn = {2041-1723}, support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; }, abstract = {Rubisco is the entry point of nearly all organic carbon into the biosphere and is present in all domains of life. Despite its global importance, biochemical studies of this enzyme superfamily have been limited to a relatively narrow set of subclades. Recent advances in metagenomics have dramatically reshaped our understanding of both microbial and rubisco diversity; however, biochemical characterization of these sequences has not kept pace with the exponential growth in sequence data. To better survey the functional and structural diversity of rubisco, we systematically sample and synthesize a library of diverse rubisco sequences with an emphasis on clades that are sparsely represented in the biochemical literature. Our updated phylogenetic analysis reveals that many deep‑branching rubiscos assemble as dimers, supporting a dimeric origin for the superfamily - in contrast to the ecologically dominant hexadecameric form I. Additionally, we discover and structurally characterize an unusually large catalytic subunit among characterized rubiscos, originating from a early-branching subclade with secondary structural elements not present in canonical rubisco architectures.}, }
@article {pmid42236734, year = {2026}, author = {Wei, Y and Xiao, J and He, J and Zhang, K and Xu, C and Zhang, N and Cheng, L}, title = {An integrated global resource of wetland microbiomes linking environmental metadata, community profiles, and genome-resolved metabolic traits.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07581-w}, pmid = {42236734}, issn = {2052-4463}, support = {32501490//National Natural Science Foundation of China/ ; 32501489//National Natural Science Foundation of China/ ; 32571850//National Natural Science Foundation of China/ ; 32430070, 32025024 and 92251305//National Natural Science Foundation of China/ ; LQ24C030001//Zhejiang Provincial NSFC/ ; LQ21C030009//Zhejiang Provincial NSFC/ ; LZ24C030001//Zhejiang Provincial NSFC/ ; JYB2025XDXM909//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; }, abstract = {Wetlands are biogeochemical hotspots pivotal to global carbon and nutrient cycling, yet genome-resolved studies across diverse wetland types remain limited. To address this, we constructed a global wetland metagenomic dataset, integrating environmental metadata, community profiles, and genome-resolved metabolic traits. This dataset comprises 1,962 samples-including 129 newly sequenced field-collected samples-from lakes, rivers, paddies, marshes, and coastal wetlands, spanning water, soil, and sediment habitats. We generated comprehensive taxonomic profiles for all 1,962 samples, and used 251 samples to reconstruct 5,704 sample-specific metagenome-assembled genomes (MAGs). These MAGs were subsequently dereplicated to establish a normalized, non-redundant catalog of 4,164 representative genomes. We further mapped gene repertoires to 549 KEGG modules to decode the metabolic potential of all 5,704 MAGs. This dataset depicts an overview of microbial genomic diversity across global wetlands and provides a comprehensive resource for understanding the metabolic capabilities, ecology, and evolution of wetland microbiomes.}, }
@article {pmid42237168, year = {2026}, author = {Hou, X and Fu, Y and Jia, Z and Hou, L and Yin, Y and Xu, K}, title = {Multi-omics elucidates the regulatory mechanisms of tryptophan in gut health of weaned piglets.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00586-1}, pmid = {42237168}, issn = {2524-4671}, support = {CARS-35//China Agriculture Research System of MOF and MARA/ ; 2023JJ20043//Natural Science Foundation of Hunan Province Project/ ; 32372913//National Natural Science Foundation of China/ ; 2023RC3204//Science and Technology Innovation Program of Hunan Province/ ; }, abstract = {Tryptophan (Trp), an essential amino acid (AA) implicated in diverse physiological and pathological processes, remains incompletely characterized in its mechanisms regulating intestinal health in weaned piglets. In this study, 27 weaned Bama miniature pigs with highly homogeneous genetic characteristics (6.200 ± 0.242 kg) were randomly divided into three groups and fed a basal diet, a diet supplemented with 0.5-fold Trp, or a diet supplemented with 1.5-fold Trp for 21 days. We used multi-omics approaches to investigate the mechanisms by which Trp regulates intestinal health through dietary interventions with different concentrations. Both Trp-supplemented groups exhibited significantly reduced diarrhea incidence (P = 0.012) and improved intestinal morphology compared to the control group (P < 0.05). While Trp-targeted metabolomics showed no statistically significant alterations, metagenomic analysis revealed Trp-driven microbial remodeling, characterized by increased α-diversity, elevated abundances of Deferribacteres, Turicibacter, Clostridials_Bacteria, and Turicibacter_Sanguinis, alongside decreased Tenericutes and Chryseobacterium. Transcriptome analysis further identified immune-related pathways as central targets of Trp action. Subsequent cytokine quantification confirmed Trp's immunomodulatory effects: pro-inflammatory cytokines (IL-1β, IL-6, IL-17) decreased, while anti-inflammatory IL-10 increased. Collectively, our findings demonstrate that Trp alleviates weaning-associated intestinal dysfunction by reshaping microbial ecosystems and regulating immune homeostasis.}, }
@article {pmid42237383, year = {2026}, author = {Zhang, J and Shi, X and Peng, S and Zhang, C and Qiao, S and Yu, H}, title = {Icariin shapes post-withdrawal fecal resistome dynamics in layer hens.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42237383}, issn = {1674-9782}, support = {B2024064//Hubei Provincial Department of Education Scientific Research Project/ ; 2025RZ026//Research and Innovation Initiatives of Wuhan Polytechnic University/ ; 202409//Open Fund of Hubei Province Key Laboratory of Animal Nutrition and Feed Science/ ; 32402807//Young Scientists Fund of the National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: While the livestock industry actively seeks alternatives to antibiotics, residual low-dose exposures continue to drive the spread of antibiotic resistance genes (ARGs). Icariin, a plant-derived compound, is recognized for improving poultry growth and immunity. However, it remains unclear how this compound influences the environmental persistence of ARGs, mobile genetic elements (MGEs), and horizontal gene transfer (HGT) during the vulnerable recovery phase after antibiotic withdrawal.<br><br>RESULTS: We designed a two-phase feeding trial with laying hens, using longitudinal metagenomic sequencing to track post-withdrawal resistance dynamics. Following initial exposure to a low-dose antibiotic mixture that established a baseline of elevated resistance, hens received either a basal diet, an icariin-supplemented diet, or a copper sulfate-supplemented diet. The data indicate that icariin supplementation consistently reduced the burdens of both ARGs and MGEs. It also suppressed the potential for HGT and restricted the diversity of microbial hosts harboring these resistance elements. Conversely, copper sulfate-a traditional metal-based additive-exacerbated resistance risks by expanding both the abundance and the host range of ARGs and MGEs. Across all treatments, the population of Escherichia and the prevalent ARG subtype bacA correlated strongly with total resistance loads, tracking the overall resistome burden.<br><br>CONCLUSIONS: Compared to conventional copper sulfate treatments, icariin facilitates a safer ecological recovery in the poultry gut by actively lowering ARG and MGE reservoirs after antibiotic withdrawal. These genomic insights, combined with its known physiological benefits, support icariin as a sustainable feed additive. Furthermore, the Escherichia-bacA correlation provides a reliable, streamlined indicator for monitoring resistance risks in farm environments. However, as these findings rely on short-term fecal metagenomic tracking, further validation through multi-environment studies is warranted.}, }
@article {pmid42237400, year = {2026}, author = {Liu, J and Huang, W and Wu, X and Ma, Y}, title = {Coronavirus disease 2019-associated encephalitis and concomitant subdural hematoma: a case report.}, journal = {Journal of medical case reports}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13256-026-06148-y}, pmid = {42237400}, issn = {1752-1947}, support = {82171350//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Coronavirus disease 2019 (COVID-19), induced by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), presents a global pandemic with evolving viral variants. In addition to respiratory symptoms, a growing trend of reports indicates that the central nervous system could also be affected in COVID-19 patients.<br><br>CASE PRESENTATION: Herein, we reported a case of a 61-year-old Chinese male with fever, psychiatric symptoms, and concomitant subdural hemorrhage. Although naso-oropharyngeal swab tests for SARS-CoV-2 ribonucleic acid detections were negative, the metagenomic next-generation sequencing from cerebrospinal fluid (CSF) samples showed the exclusive positive finding of SARS-CoV-2. The patient was diagnosed with probable COVID-19-associated encephalitis, and was recovered after receiving anti-infection medications, high-dose methylprednisolone pulses (1&#xa0;g/day for 5&#xa0;days), and subsequent intravenous immunoglobulin (0.4&#xa0;g/kg body weight for 5&#xa0;days) therapies.<br><br>CONCLUSION: Our case underscores the importance that for patients with fever and unexplained neuropsychiatric symptoms, it is recommended to conduct CSF testing to screen for possible pathogen infections, and to perform cranial imaging promptly to detect concomitant lesions.}, }
@article {pmid42237409, year = {2026}, author = {Guo, D and Chen, Y and Wu, Y and Cheng, J and Lin, Y and Lai, W and Ma, W and Yang, H and Han, L and Ma, L and Jia, H and Liu, X}, title = {Multi-omics characterization of the skin microbiota reveals the anti-aging roles of Stenotrophomonas maltophilia.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02433-6}, pmid = {42237409}, issn = {2049-2618}, support = {WDZC20220819134430002//Shenzhen Science and Technology Program/ ; QD2021005N//Scientific Research Start-up Funds/ ; }, abstract = {BACKGROUND: Shifts in the skin microbiome have shown a close link to chronological age. However, the contribution of the skin microbiome in skin-aging phenotypes remains unclear.<br><br>RESULTS: To explore this, we performed phenotypic, metabolomic, metagenomic, and functional analyses on a cohort with divergent skin-aging phenotypes. Genome-scale metabolic models (GEMs) integrated with metabolomic analysis revealed that Stenotrophomonas maltophilia, enriched in the younger group (categorized by AI-predicted age and skin elasticity), utilizes the glutathione cycle to maintain redox homeostasis. Cellular experiments showed its metabolites enhanced GSH synthesis and alleviated oxidative-stress-induced phenotypic skin-aging by upregulating key genes in fibroblasts, including GCLM, PGD, SOD2, and NQO1. In addition, GEMs highlighted its potential in maintaining youthful skin phenotypes through the regulation of host metabolic pathways involving betaine, lysolecithin, and porphyrin. In parallel, Acinetobacter guillouiae was found to influence host melanin metabolism by degrading dopamine (DA) and 3-methoxytyramine (3-MT), offering potential therapeutic strategies for mitigating pigmentation.<br><br>CONCLUSIONS: Our findings highlight the dynamic interplay between skin microbiota and the host in phenotypic skin-aging, offering new insights for designing interventions to maintain youthful skin. Video Abstract.}, }
@article {pmid42237424, year = {2026}, author = {Yang, L and Chen, J}, title = {mPower: a real data-based power analysis tool for microbiome study design.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02427-4}, pmid = {42237424}, issn = {2049-2618}, support = {R01 GM144351/GM/NIGMS NIH HHS/United States ; }, abstract = {Power analysis is a critical step in designing a microbiome study. Existing power calculation tools for microbiome studies mainly rely on parametric models of the sequencing counts, which underestimate the complexity of microbiome data and could produce overly optimistic power estimates. In this work, we present a new simulation-based power analysis tool, mPower, for microbiome study design. The tool uses a real data-based semi-parametric simulation framework to generate realistic microbiome data, upon which the power assessment is performed. Coupled with a select differential analysis tool, our power tool supports different study designs, including cross-sectional, case-control, and matched-pair studies, with or without confounders. It allows power analysis for both community-level and taxon-level testing. By using microbiome reference datasets from different environments, the users could perform power calculation based on the environment of interest. The mPower is primarily designed for 16S amplicon sequencing data, and it also incorporates a parametric simulation framework that enables power analysis for shotgun metagenomic data. We showcase the application of mPower with several real-world examples. The web interface of mPower is available at https://microbiomestat.shinyapps.io/mPower/. Video Abstract.}, }
@article {pmid42237575, year = {2026}, author = {Tilves, C and Xiao, S and Tanaka, T and Differding, MK and Spira, AP and Ferrucci, L and Mueller, NT}, title = {Longitudinal associations of the gut microbiome with arterial stiffness in US adults: findings from the Baltimore Longitudinal Study of Aging.}, journal = {American journal of epidemiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/aje/kwag119}, pmid = {42237575}, issn = {1476-6256}, abstract = {The gut microbiome affects arterial stiffness in experimental murine models; however, evidence in human longitudinal studies is lacking. In this study, we investigated longitudinal between-person (average) and within-person (change) associations of microbiome features with arterial stiffness. We assessed the fecal microbiome using whole genome metagenomic sequencing, and arterial stiffness using carotid-femoral pulse wave velocity (cfPWV). Our analytic sample consisted of 349 adults from the Baltimore Longitudinal Study of Aging, who contributed 915 visits between 2013-2019. Using linear mixed models, we found higher microbiome evenness and butyrate-producing bacteria were associated with lower cfPWV on average (between-person), but changes in diversity were not associated with changes in cfPWV (within-person). Several potentially pathogenic bacteria were positively associated with cfPWV, both between- and within-person. Butyrate-production pathways were inversely associated with cfPWV between-person and borderline within-person. Trimethylamine-production genes were positively associated with cfPWV between-person and borderline within-person. In addition, changes in other functional pathways including peptidoglycan biosynthesis and L-arginine biosynthesis were associated with changes in cfPWV. In conclusion, cfPWV was associated with both between-person and within-person differences in gut microbiome features, with strength and consistency depending on the feature. These results can inform which microbiome features to target in interventions to improve arterial stiffness.}, }
@article {pmid42237904, year = {2026}, author = {Lei, H and Du, S and Li, C and Yung, L and Wang, P and Leung, LY and Graham, CA and Yen, HL and Li, Y and Lucaci, AG and Mason, CE and Lee, PKH}, title = {Sustained Chlorination of Hospital Surfaces Restructures the Microbiome and Virome and Diversifies Resistance Genes.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c01505}, pmid = {42237904}, issn = {1520-5851}, abstract = {Routine disinfection can reduce microbial burden on hospital surfaces in the short term, but its long-term impacts on surface microbiomes and antimicrobial resistance dynamics remain unclear. We conducted a year-long metagenomic study of 197 in situ hospital surface samples subjected to sustained chlorination to investigate changes in microbiomes, resistomes, and phage-host interactions. Microbial α-diversity increased during the early months, with a decline in dominant Enterobacteriaceae and enrichment of taxa including Propionibacteriaceae and Micrococcaceae, indicating niche replacement. Over time, both diversity and previously suppressed taxa approached baseline levels, suggesting adaptation to sustained disinfection, with evidence of functional shifts. Viral communities exhibited similar temporal dynamics, with composition and relative abundance distinctly shifting. Concurrently, the resistome underwent substantial, largely irreversible restructuring, with decreased total relative abundance and increased diversity of antibiotic resistance genes (ARGs). Chlorination also reduced ARG mobility and pathogenic potential, indicated by weakened co-occurrence with mobile genetic elements and virulence factor genes and lower predicted resistome risks. Phage and host relative abundances remained strongly correlated, although a shift toward lytic viral lifestyles occurred, potentially limiting phage-mediated ARG dissemination. These findings highlight disinfection as both a microbial control measure and ecological pressure, underscoring the need for ecologically informed strategies to manage clinical antimicrobial resistance.}, }
@article {pmid42237982, year = {2026}, author = {Utreja, S and Andreani, GA and Mahmood, S and Patel, MS and Buck, MJ and Rideout, TC}, title = {Dietary pulse prebiotic fibre intake in a rat obese pregnancy model alters maternal caecal microbiome and protects against steatosis in newly weaned offspring.}, journal = {Journal of nutritional science}, volume = {15}, number = {}, pages = {e37}, pmid = {42237982}, issn = {2048-6790}, abstract = {We assessed if supplementation of an obese-inducing diet with yellow pea fibre throughout pre-pregnancy (PP), gestation, and lactation could influence maternal gut microbiome composition and improve metabolic health and liver steatosis in newly weaned rat male and female offspring. Forty female Sprague-Dawley rats were fed a low (CON) or high (HC) calorie diet for a 6-week PP period. At the end of PP, HC animals were randomly assigned to either remain on the HC diet or the HC diet with yellow pea fibre (HC + FBR) for an additional 4-weeks prior to mating and throughout gestation and lactation. At the end of lactation, caecal microbiome profile was evaluated in mothers with shotgun metagenomic sequencing, and newly weaned male and female pups were assessed for serum biochemistry and hepatic fat outcomes. Maternal obesity reduced the beta-diversity of the maternal microbiome and lowered total caecal short-chain fatty acid (SCFA) concentration. HC + FBR consumption increased caecal SCFA concentration and differentially altered the maternal caecal microbiome profile of several species that have been linked with hepatic steatosis including Bifidobacterium pseudolongum, Porphyromonas gingivalis, and several Provetella species. Newly weaned offspring from HC mothers exhibited hepatic steatosis; however, male and female pups from HC + FBR mothers demonstrated normalised liver lipid concentrations (cholesterol and triglyceride) and an increase in caecal acetate and propionate concentrations. Findings suggest that maternal obesity enhances the risk of liver steatosis in offspring and that maternal dietary fibre supplementation may have a protective influence that is partly mediated through changes in the caecal microbiome profile and activity.}, }
@article {pmid42238272, year = {2026}, author = {Gallina, G and Pizzi, C}, title = {Reference-free k-mer based dissimilarity measures for metagenomes comparison.}, journal = {Frontiers in bioinformatics}, volume = {6}, number = {}, pages = {1788907}, pmid = {42238272}, issn = {2673-7647}, abstract = {MOTIVATION: Metagenomics plays a crucial role in unraveling the relationship between microbial communities and the environment in which they live, allowing the development of food and environmental control techniques. Similarly, the study of microbial environments within the human body plays a crucial role towards precision medicine. In these contexts, the problem of metagenomic samples comparison is among the most challenging from the computational point of view due to the size of the datasets and to the incompleteness of microbial databases. Thus, the ability to define and efficiently compute reference-free dissimilarity measures is key to the development of effective and practical tools for metagenomes comparison.<br><br>RESULTS: In this work, we present a systematic experimental validation of reference-free k -mer-based dissimilarity measures. To this purpose, we investigate the correlation between two popular ecological dissimilarity measures, Bray-Curtis and Jaccard, computed using reference-free and reference-based k -mer approaches, for 12 &#x2264; k &#x2264; 31 . Our experiments cover both simulated and real metagenomics settings (samples from the human body and the oceans), and consider both linear and ranking correlation between the computed values. Our results support the hypothesis that the two definitions are indeed correlated for a wide range of values of k , and promote the development of efficient reference-free computational tools based on k -mer statistics for metagenomes comparison.}, }
@article {pmid42238651, year = {2026}, author = {Zhang, Q and Zhang, X and Cao, M and Ma, J and Yan, R and Wang, H and Jia, S}, title = {Study on the Role and Mechanism of γδ T Cells in Atherosclerosis Under a High-Fat Diet.}, journal = {Reviews in cardiovascular medicine}, volume = {27}, number = {5}, pages = {48002}, pmid = {42238651}, issn = {2153-8174}, abstract = {BACKGROUND: This study aimed to investigate the effects of γδ T cell inhibition under a high-fat diet (HFD) on metabolic function, immune inflammation, gut microbiota, and atherosclerosis (AS) progression in ApoE [-/-] mice.<br><br>METHODS: ApoE [-/-] mice were assigned to three groups: a control group (normal diet), a model group (HFD), and an intervention group (HFD + &#x3b3;&#x3b4; T cell receptor (TCR) monoclonal antibody). After 12 weeks, flow cytometry was used to assess &#x3b3;&#x3b4; T cell levels, and cytokines (interferon-gamma (IFN-&#x3b3;), IL-17A) were measured. Inflammatory markers in blood and adipose tissue were quantified, gut microbiota composition was analyzed via fecal metagenomics, and atherosclerosis was evaluated using Oil Red O, Masson's trichrome, and hematoxylin and eosin (HE) staining methods.<br><br>RESULTS: The HFD activated &#x3b3;&#x3b4; T cells and increased pro-inflammatory cytokines in ApoE [-/-] mice. Treatment with the &#x3b3;&#x3b4; TCR monoclonal antibody suppressed &#x3b3;&#x3b4; T cells, reduced IFN-&#x3b3; and IL-17A expression, improved lipid profiles, and decreased tumor necrosis factor-alpha (TNF-&#x3b1;), IL-1&#x3b2;, and IL-6 levels. Gut microbiota analysis showed an increase in beneficial bacteria, and histological staining (Oil Red O, HE, and Masson's trichrome) confirmed a reduction in atherosclerotic lesion burden.<br><br>CONCLUSION: The &#x3b3;&#x3b4; T cells contribute to AS development under the HFD. Inhibition of &#x3b3;&#x3b4; T cells reduces inflammation, improves gut microbiota composition, and attenuates atherosclerosis progression.}, }
@article {pmid42238901, year = {2026}, author = {Zhao, T and Chen, Y and Sun, H}, title = {A case of severe Legionella pneumonia treated with omadacycline and nemonoxacin.}, journal = {Respiratory medicine case reports}, volume = {62}, number = {}, pages = {102437}, pmid = {42238901}, issn = {2213-0071}, abstract = {Severe Legionella pneumophila pneumonia carries high mortality, and treatment is challenged by emerging resistance to conventional fluoroquinolones/macrolides and diagnostic delays. Novel agents such as omadacycline and nemonoxacin show theoretical promise, yet robust clinical evidence in legionellosis is lacking. We report a 59-year-old man with severe community-acquired pneumonia(sCAP) who initially received empiric ceftazidime-avibactam plus nemonoxacin. Respiratory failure did not improve, and the inflammatory markers did not decline. Subsequent bronchoalveolar lavage fluid metagenomic next-generation sequencing(BALF-mNGS) and urinary Legionella antigen confirmed Legionella pneumonia. We then switched to dual therapy with omadacycline and nemonoxacin. The combination led to rapid improvements in inflammatory markers, hypoxemia, and creatine kinase levels. This case provides a clinical rationale for using omadacycline plus nemonoxacin as salvage therapy in severe Legionella pneumonia when conventional regimens fail.}, }
@article {pmid42239023, year = {2026}, author = {Tang, F and Liu, H and Xi, L and Li, C and Wang, X and Wang, B}, title = {Solid-phase enrichment uncovers a hidden Salmonella transmission chain in a recurrent pediatric household cluster: a case report.}, journal = {Frontiers in public health}, volume = {14}, number = {}, pages = {1820049}, pmid = {42239023}, issn = {2296-2565}, abstract = {OBJECTIVES: To describe a household cluster of recurrent pediatric non-typhoidal Salmonella (NTS) infection and compare the yield of conventional culture, solid-phase enrichment, and shotgun metagenomic sequencing across symptomatic children and household contacts.<br><br>METHODS: Longitudinal fecal specimens from a 4-year-old boy (Mo) with three discrete NTS episodes in 2 months, his monozygotic twin (TB), and three adult co-residents were processed by conventional culture; specimens from Episode 2 onwards and all contact specimens additionally received solid-phase enrichment, and a subset shotgun metagenomics. Isolates were characterized by VITEK 2, XbaI-PFGE, and whole-genome sequencing.<br><br>RESULTS: None of Mo's episodes met sepsis criteria (peak WBC 12.52 &#xd7; 10?/L, CRP 5.46 mg/L, PCT 1.14 ng/mL); TB had one self-limited episode, both parents had brief symptomatic periods, and the grandmother was asymptomatic. Conventional culture was positive only at Mo's first episode, whereas solid-phase enrichment recovered Salmonella from three culture-negative pediatric acute-phase specimens (Mo 4.12, TB 4.16, Mo 5.1). Adult contacts were negative by both culture-based methods, but metagenomic sequencing detected Salmonella reads in all three. Mo_0412 and TB_0416 were S. enterica serovar Enteritidis ST11, with identical cgMLST, 99.9966% ANI, and 97% PFGE similarity, indicating a clonal household source. Mo received antibiotics across four classes during his recurrences, vs. two sequential agents in TB.<br><br>CONCLUSION: Conventional culture, solid-phase enrichment, and metagenomic sequencing functioned as complementary modalities, each recovering Salmonella the others missed, supporting a tiered diagnostic strategy for household NTS investigation. Cumulative antibiotic exposure may have contributed to Mo's differential susceptibility, a hypothesis warranting prospective study.}, }
@article {pmid42239051, year = {2026}, author = {Lalgudi, C and Kotaka, M and Yaffe, E and Lopez, JA and Yu, FB and Ng, K and Sonnenburg, JL and Good, BH and Huang, KC and Shi, H}, title = {Path-dependent recovery of the gut microbiome after antibiotics emerges from coupled ecological and evolutionary dynamics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.22.727306}, pmid = {42239051}, issn = {2692-8205}, abstract = {Recovery of the gut microbiome after antibiotic exposure is often incomplete and variable, and the processes underlying this variation remain unclear. We performed longitudinal shotgun metagenomic sequencing of 2876 daily fecal samples from replicated humanized and conventional mouse cohorts exposed to controlled antibiotic perturbations. Metagenomic profiling recapitulated ecological trajectories previously observed by 16S sequencing, while revealing extensive strain-level dynamics, including reproducible sweeps of standing variants and de novo mutations in antibiotic target sites and regulatory loci. We also identified genetic changes whose effects depended on community composition, competitive release, and perturbation history. Cross-housing experiments revealed bidirectional strain transfer, with antibiotic-induced niche clearance enabling replacement of resident strains. In parallel, phage dynamics were heterogeneous and clustered by cage. Together, these findings show that post-antibiotic microbiome recovery is a path-dependent process shaped by selection, transmission, and phage activity, producing divergent outcomes even among closely matched communities exposed to the same perturbations.}, }
@article {pmid42239166, year = {2026}, author = {Ghadermazi, P and Emerson, JB and Olm, MR}, title = {ZipStrain Enables Rapid and Precise Strain-Resolved Metagenomics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.20.726564}, pmid = {42239166}, issn = {2692-8205}, abstract = {Strain-resolved metagenomics characterizes microbial communities at nucleotide-level resolution, enabling researchers to differentiate identical from closely related organisms and characterize population structure and gene content variation. Here we introduce ZipStrain, a program that performs highly accurate strain-resolved metagenomics over 500× faster than available methods while offering superior RAM management. Applied to a dataset of 2,754 samples spanning human populations, we identify a strain-sharing gradient across social relationships, reveal striking variation in clonal structure across bacteria and bacteriophage, and pinpoint genes whose nucleotide identity deviates from genome-wide expectations. ZipStrain is distributed as an open-source Python package and accompanying Nextflow pipeline at https://github.com/OlmLab/ZipStrain .}, }
@article {pmid42239183, year = {2026}, author = {Cirolia, G and Gustafson, JT and Aswani, A and Wolf, A}, title = {Performance of IBD machine learning classifiers varies across microbiome training data independent of geographic diversity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.21.727052}, pmid = {42239183}, issn = {2692-8205}, abstract = {Microbiome-based machine learning classifiers show increasing promise for disease identification across gastrointestinal, metabolic, and immune-mediated conditions. Inflammatory bowel disease (IBD), a chronic immune-mediated disorder associated with disruption of the gut microbiome, has been a particularly successful application area. However, while many predictive models achieve high performance within individual datasets, their ability to generalize across independent populations and geographic contexts remains unclear. Here, we tested whether model class and training dataset composition influence model generalizability across geographically diverse evaluation studies. We compiled seven publicly available shotgun metagenomic studies spanning five geographic regions, comprising 697 individuals with IBD or healthy controls. We trained 246,986 model configurations across seven model classes and five distinct training dataset combinations and evaluated top-performing models on independent studies from the USA, Ireland, Germany, Israel and China. Extreme gradient boosting and random forest models showed the highest and most consistent performance across training datasets, a ranking that was maintained on independent evaluation studies. However, models trained on geographically diverse datasets did not outperform those trained on USA-only datasets. Instead, model performance was strongly dependent on the evaluation study itself, with consistent differences in achievable accuracy across studies. Despite most models achieving similar AUC scores, there was limited overlap in the key microbial species identified. Furthermore, even for the small set of disease predictive microbes shared between models, the direction of enrichment between IBD or healthy subjects often varied in opposing directions across study populations. These findings suggest that study-specific factors constrain generalization and may help explain the lack of consistent microbiome-based biomarkers for IBD.}, }
@article {pmid42239221, year = {2026}, author = {Keown, RA and Sikkema, AP and Barbone, VA and Ferrell, BD and Donnelly, OB and Iredell, SC and Zatopek, KM and Brumm, PJ and Mead, DA and Lohman, GJS and Wommack, KE and Polson, SW}, title = {Single amino acid substitution in DNA Polymerase I dramatically alters infection dynamics of bacteriophage T7.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.20.726624}, pmid = {42239221}, issn = {2692-8205}, abstract = {UNLABELLED: Viruses constitute a significant proportion of Earth's genetic diversity, yet most remain uncharacterized beyond their sequences in viral metagenomes. Linking viral genotypes to phenotypes-especially enzyme function to phage infection dynamics-is challenging due to the lack of cultured virus-host systems. DNA polymerase I (PolA), essential for genome replication in ∼25% of dsDNA phages, provides an opportunity to explore these connections. In phage T7, residue 526 is critical for nucleotide incorporation, with previous in vitro evidence indicating impacts on enzyme efficiency and fidelity. Previous analyses identified three substitutions at this position (Tyr/Y, Phe/F, Leu/L) linked with deeply rooted viral PolA clades. Mutation impacts at residue 526 were tested in vitro and in vivo . The Y526F protein exhibited a 50% reduction in specific activity, and when introduced via High Complexity Golden Gate Assembly into T7 demonstrated a 53% decrease in burst size and significantly longer latent period compared to wild type. The Y526L protein exhibited a 97% decrease in activity, and the Y526L phage was incapable of completing its lifecycle. These findings confirm historical biochemical data, provide in vivo context for these mutations in the T7- E. coli system, and offer experimental support for genotype-to-phenotype associations in viral PolA, informing viral metagenomics studies.<br><br>GRAPHICAL ABSTRACT: Created in BioRender. Keown, R. (2026) https://BioRender.com/mhrmup3.}, }
@article {pmid42239239, year = {2026}, author = {Cho, Y and Tsuboyama, K and Litberg, TJ and Jung, MD and Obisesan, A and Wang, Q and Phoumyvong, CM and Thibeault, J and Ovchinnikov, S and Rocklin, GJ}, title = {Accurate protein stability prediction for small domains using mega-scale experiments.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.19.726285}, pmid = {42239239}, issn = {2692-8205}, abstract = {Predicting absolute protein folding stability is a long-standing challenge in biophysics, with broad applications in protein design and in understanding genetic variation and evolution. Physics-based simulations have shown limited success at predicting stability and are often computationally intractable, and machine learning methods have been constrained by the lack of sufficiently large experimental datasets. We recently introduced cDNA display proteolysis, a cell-free approach that can measure folding stability for nearly one million protein domains in parallel. Here, we applied this method to measure stability for 1.8 million diverse protein domains 60-80 amino acids in length primarily taken from the MGnify metagenomic database and spanning over 200,000 sequence families. Using this new "MGnify Stability dataset", we developed the predictive models SaProtΔG and ESM3ΔG, which accurately predict absolute folding stability for small domains with root mean squared error of 0.8 kcal/mol over a 6 kcal/mol range (Spearman rank correlation of 0.88). These predictors show high accuracy at predicting effects of substitutions, insertions, and deletions, successfully identify global trends toward higher stability in thermophilic organisms, and improve discrimination of stable and unstable computationally designed proteins. Our results illustrate how megascale biophysical measurements can complement existing evolutionary and structural data to enable accurate absolute stability prediction for small domains.}, }
@article {pmid42239480, year = {2026}, author = {Qian, J and Ghadermazi, P and Maret, S and Kemp, JF and Frank, D and Melanson, EL and Hendricks, AE and Krebs, N and Tang, M and Olm, MR}, title = {IgA Targeting in the Infant Gut Is Modulated by Diet and Increasingly Directed Towards Persistent Species.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.19.726352}, pmid = {42239480}, issn = {2692-8205}, abstract = {BACKGROUND: IgA is the dominant antibody in the human gut and a key regulator of host-microbe interactions. Infants begin to produce IgA at around 6 months old and receive large quantities of IgA via human milk, but technical limitations have prevented species-level characterization of IgA binding in early life. This has left basic knowledge gaps about which species are targeted by IgA in infancy, and how modifiable lifestyle factors like breastfeeding and complementary feeding impact IgA targeting.<br><br>RESULTS: Here we adapt Metagenomic Immunoglobulin Sequencing (MIg-Seq) for low-biomass infant fecal samples and apply this optimized protocol to 32 longitudinal samples from 16 infants enrolled in the MINT trial, a four-arm randomized controlled trial comparing meat-based, dairy-based, plant-based, and reference complementary feeding patterns, with fecal sampling at 6 and 12 months (pre and post intervention). Infant IgA targeting mirrors adults at the phylum level, with both age groups showing significantly higher IgA targeting of Pseudomonadota and lower targeting of Bacteroidota relative to other phyla. During the substantial microbiome compositional shifts noted between 6 and 12 months, IgA targeting is significantly more stable than the microbiome itself. Among persistent colonizers, IgA targeting strengthens significantly from 6 to 12 months, with the most pronounced effect observed for Bifidobacterium , a finding robust across all dietary arms and feeding modes. The feeding arm to which infants were enrolled was not significantly associated with IgA binding, but several nutrient-specific associations were discovered. Animal-derived nutrients, particularly cholesterol, are strongly positively correlated with IgA targeting of Bifidobacterium longum , while plant-derived carotenoids are positively associated with IgA targeting of Flavonifractor plautii and Ruminococcus gnavus .<br><br>CONCLUSIONS: This study introduces an experimental and computational framework for species-level IgA profiling in the infant gut. The progressive strengthening of IgA targeting of Bifidobacterium and other beneficial persistent colonizers suggests a role for IgA in reinforcing beneficial microbes during infancy. The nutrient-specific dietary effects on IgA targeting reveal the immunological consequences of the complementary feeding period, and highlight a contrast between animal-versus plant-based diets. Together, these findings point to early nutritional interventions and IgA-based therapeutics as promising tools for promoting healthy immune-microbiome development.}, }
@article {pmid42239539, year = {2026}, author = {Jiang, X and Chen, B and Wang, Q and Liu, Y and Li, N and Zhang, L}, title = {Structural variation analysis suggests strain-level maternal-infant microbial transmission in early life.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1765801}, pmid = {42239539}, issn = {2235-2988}, abstract = {INTRODUCTION: Structural variations (SVs)-large, functionally consequential genomic alterations-serve as high-resolution markers for strain-level differentiation in the human microbiome, yet their relevance to vertical transmission of the maternal microbiota and early-life colonization remains unclear.<br><br>METHODS: Using metagenomic data from a 98-pair longitudinal mother-infant cohort and a 25-pair multi-niche cohort, we profiled microbial taxa, functions, and SVs, characterized variable SVs (vSVs), deletion SVs (dSVs), and transmitted SVs (tSVs), and evaluated the potential influence of delivery mode, feeding regimen, and maternal ecological niches.<br><br>RESULTS: We identified 5,578 SVs across 51 reference strains, with infants showing increasing SV diversity during the first year of life, and observed significantly greater SV similarity within mother-infant pairs than unrelated pairs. Abundance-based analysis identified 90 microbial species shared between mothers and infants. However, when incorporating SV-based tracking, only 14 strains showed patterns consistent with sustained maternal contribution across time points. Furthermore, exploratory subgroup analyses suggested that both delivery mode and feeding regimen may influence the vertical transmission patterns of maternal microbial strains and transmitted SVs. Functionally, tSVs were enriched in pathways linked to carbohydrate, amino acid, and lipid metabolism, as well as transport and environmental adaptation modules such as T4SS. Multi-niche analysis further suggested that the maternal gut showed the strongest inferred signal of SV-supported strain sharing with both the infant gut and oral microbiota.<br><br>DISCUSSION: Together, these findings suggest that microbial SVs can serve as complementary markers for investigating maternal contribution and vertical transmission-related strain-level patterns in early-life microbiome development, providing new insights into microbial inheritance and early-life health trajectories.}, }
@article {pmid42239987, year = {2026}, author = {Zhao, C and Zhang, L and Wang, Y and Yang, G and Ren, C and Cao, X and Yu, Q and Jin, B and Men, Y and Liu, H and Zhang, J}, title = {Microbial Dehalogenation of 3,5,6-Trichlorooctafluorohexanoic Acid under Different Reducing Conditions.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c17496}, pmid = {42239987}, issn = {1520-5851}, abstract = {Chlorinated polyfluoroalkyl substances (Cl-PFAS) have emerged as promising alternatives to legacy PFAS due to their enhanced microbial reactivity and improved environmental degradability. However, their transformation mechanisms under environmentally relevant reducing conditions remain poorly characterized. This study investigated the microbial dehalogenation of 3,5,6-trichlorooctafluorohexanoic acid (CTFE3), a representative Cl-PFAS, under nitrate-, sulfate-, iron-reducing, and methanogenic conditions. Microbial defluorination was observed across all reducing environments, with higher total defluorination efficiencies (∼60%) under nitrate- and sulfate-reducing conditions compared to iron-reducing and methanogenic conditions (∼30%) under the tested experimental conditions. Proposed biotransformation pathway analysis suggested that CTFE3 underwent more diverse and sequential hydrolytic dechlorination under nitrate- and sulfate-reducing conditions, which was associated with more extensive defluorination. Genes associated with hydrolytic dechlorination were consistently enriched under these conditions, but not in iron-reducing or methanogenic environments. Metagenomic binning further identified key taxa (e.g., Methyloversatilis discipulorum, Herbaspirillum seropedicae, Paracoccaceae, and Rhodobacteraceae-related bacteria) harboring both hydrolytic dechlorination and nitrate/sulfate-reduction genes, suggesting their involvement in CTFE3 hydrolytic dechlorination and subsequent defluorination. This study demonstrates that reducing conditions play an important role in shaping CTFE3 transformation patterns and highlight hydrolytic dechlorination as a viable pathway associated with extensive microbial defluorination, thereby offering insights for sustainable Cl-PFAS remediation.}, }
@article {pmid42240391, year = {2026}, author = {de Sousa, LP and Calderon Fajardo, AA and Brandão, MM and Maia de Oliveira, V and Romero, GQ}, title = {Metagenome-assembled genomes of four novel bacterial species from Atlantic rainforest stream sediments in Brazil.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0033626}, doi = {10.1128/mra.00336-26}, pmid = {42240391}, issn = {2576-098X}, abstract = {Here, we report draft genome sequences of four novel bacterial species from Atlantic rainforest stream sediments in southeastern Brazil. The genomes represent distinct lineages within Nitrospirota and Pseudomonadota (average nucleotide identity <95% to known species) and encode diverse metabolic capabilities, including nitrification, denitrification, and aromatic compound degradation.}, }
@article {pmid42240519, year = {2026}, author = {Gharbi, M and Abbassi, MS}, title = {Bacteria as anticancer agents: bioactive metabolites, engineered platforms, and translational mechanisms.}, journal = {Letters in applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/lambio/ovag050}, pmid = {42240519}, issn = {1472-765X}, abstract = {Bacteria represent a vast and underexplored reservoir of bioactive compounds with significant anticancer potential. Numerous bacterial taxa, particularly actinomycetes, Bacillus, Pseudomonas, and marine-derived species, produce structurally diverse metabolites exhibiting cytotoxic, cytostatic, pro-apoptotic, immunomodulatory, and anti-angiogenic activities against cancer cells. Clinically established agents such as actinomycin D and bleomycin highlight the therapeutic relevance of bacterial natural products, while recent discoveries continue to expand the repertoire of bioactive polyketides, peptides, alkaloids, and proteins. These compounds act through multiple mechanisms, including DNA intercalation, induction of apoptosis, cell cycle arrest, metabolic disruption, and modulation of the tumor microenvironment. Advances in metagenomics, genome mining, and synthetic biology have enabled the identification and activation of previously silent biosynthetic gene clusters, significantly enhancing drug discovery potential. In addition to metabolite-based anticancer agents, advances in synthetic biology have enabled the development of engineered bacterial platforms capable of selectively colonizing tumors, delivering therapeutic molecules, and activating prodrug therapies within the tumor microenvironment. Despite ongoing challenges related to toxicity, limited yield, selectivity, and clinical translation, bacterial-derived compounds remain a promising frontier in oncology. This review summarizes bacterial sources, bioactive metabolites, molecular mechanisms, preclinical and clinical applications, and future prospects for developing effective and safe anticancer strategies.}, }
@article {pmid42240631, year = {2026}, author = {Hernández-Velázquez, R and Hernández-Avilés, JS}, title = {Metagenomic insight into the diversity and biogeochemical functions of microbial communities in the maar tropical Lake Atexcac.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {6}, pages = {}, doi = {10.1099/mic.0.001714}, pmid = {42240631}, issn = {1465-2080}, abstract = {Warm monomictic maar lakes in tropical regions represent dynamic systems where thermal stratification generates strong vertical gradients in oxygen availability and redox conditions, shaping microbial community structure and function. Lake Atexcac (Puebla, Mexico) undergoes seasonal stratification and episodic whiting events that provide a framework to examine microbial responses to changing hydrodynamic conditions. In this study, we applied deep shotgun metagenomic sequencing to characterize the taxonomic composition and functional potential of microbial communities across the epilimnion, metalimnion and hypolimnion during two contrasting stratification phases: early stratification associated with a whiting event and a later, well-established stratification period.Metagenomic profiles revealed a clear vertical organization of microbial communities, with samples clustering primarily according to thermal strata and the metalimnion displaying the highest genetic differentiation. Genome-resolved analyses enabled the recovery of a large number of metagenome-assembled genomes, with marked differences in their vertical distribution between hydrodynamic phases. The recovered genomes encompassed diverse metabolic pathways related to carbon, nitrogen and sulphur transformations, reflecting the heterogeneous redox conditions along the water column. Notably, sulphur-related metabolisms were widespread across strata, and Chlorobiota-affiliated genomes and metagenomic reads were consistently detected in suboxic layers. These organisms were found to harbour diverse thiosulphate disproportionation pathways and are thought to play an important role in the sulphur cycle that has not previously been reported in this type of lacustrine system.Overall, this study provides a genome-resolved perspective on microbial diversity and metabolic potential in a stratified tropical maar lake and establishes a baseline for future comparative and process-oriented studies integrating water column and sediment microbial communities.}, }
@article {pmid42241759, year = {2026}, author = {Tabish, RW and Lin, Y and Rochell, SJ and Pacheco, WJ and Bailey, MA and Dozier, WA and Robinson, K and Hauck, R}, title = {Cecal metagenome and mucosal transcriptome of broilers after an enteric challenge and fed diets with different fiber types and concentrations[1].}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107151}, doi = {10.1016/j.psj.2026.107151}, pmid = {42241759}, issn = {1525-3171}, abstract = {This study evaluated the effects of dietary fiber supplementation on broiler gut health during a subclinical enteric challenge. Birds were assigned to either an unchallenged control or a challenged control, followed by six dietary treatments applied to challenged birds. These treatments included 3% oat hulls (OH), 3% soy hulls (SH), and four combinations of 1.5% OH or SH with 1.5% wheat middlings (WM) or sugar beet pulp (SBP). A randomized complete block design was used with 2,160 day-old YP × Ross 708 male broiler chicks allocated to eight treatments, each with nine replicate floor pens and 30 birds per pen. Birds were inoculated with Eimeria followed by Clostridium perfringens, and cecal samples were collected at 21 days of age for shotgun metagenomic and transcriptomic analyses. The enteric challenge significantly reduced microbial diversity, depleted butyrate-producing bacteria, and enriched pathways associated with bacterial growth and virulence while triggering inflammatory signaling and suppressing proliferative pathways in the host. Supplementation with dietary fiber modulated these responses through distinct yet complementary mechanisms. The group receiving OH with WM enriched butyrate-producing bacteria, including Faecalibacterium prausnitzii, reduced C. perfringens abundance, and downregulated inflammatory pathways. Birds fed OH with SBP showed increased populations of lactic acid producing bacteria and Bifidobacterium animalis while suppressing TNFα, NF-κB and IFNγ signaling. Diets containing SH combinations enhanced metabolic pathways related to pyruvate fermentation and stachyose degradation, primarily driven by Lactobacillus species. Despite having distinct microbial compositions, all fiber treatments restored epithelial proliferation pathways in the host transcriptome, indicating convergent potentially beneficial effects on intestinal health. Integration of bacteriome and transcriptome data revealed coordinated relationships between specific bacterial species, including Stutzerimonas stutzeri, Bacteroides caecae, and Eubacteriaceae bacterium ES3, and host genes involved in immune function and energy metabolism. These findings provide a mechanistic framework for developing targeted nutritional strategies using specific fiber combinations to enhance gut resilience in antibiotic-free broiler production systems.}, }
@article {pmid42227946, year = {2026}, author = {Wang, H and Wang, X and Xiu, Z and Wei, H and Cai, H and Chen, J and Zhang, T and Yang, Y}, title = {Substrate-driven microbial specialization and cooperative dechlorination of chlorinated pollutants in estuarine ecosystems.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0023526}, doi = {10.1128/aem.00235-26}, pmid = {42227946}, issn = {1098-5336}, abstract = {Organohalide-respiring bacteria (OHRB) are globally distributed, yet their ecological roles in marine environments remain poorly understood, with few isolates characterized from these systems. Here, we describe a stable anaerobic consortium from estuarine sediments that performs sustained dechlorination of 1,1,2-trichloroethane (1,1,2-TCA) to vinyl chloride (VC) at a rate of 126.3 ± 0.9 µM d[-1]. This activity was associated with the stable co-enrichment of two key populations, Dehalogenimonas and Desulfitobacterium, which increased to dominate the community at 49.7% and 32.5%, respectively. Metagenome-assembled genomes confirmed both populations represent novel species with distinct genomic adaptations. Dehalogenimonas sp. strain H harbors 24 putative reductive dehalogenase genes and complete ectoine biosynthesis pathways (ectABC) essential for osmotolerance, while Desulfitobacterium sp. strain Y represents the first cultivated marine-associated member of this genus. Proteomic analysis confirmed active expression of multiple reductive dehalogenases from strain H, strongly supporting its role as the primary dechlorinator. Concurrently, physiological and genomic data suggest that strain Y is strongly co-selected under 1,1,2-TCA-amended conditions and likely occupies a crucial supportive niche. Alongside its extensive metabolic versatility that likely buffers the consortium against environmental fluctuations, its complete de novo corrinoid biosynthesis pathway implies a complementary role as a vitamin B12 provider for the extreme corrinoid-auxotrophic strain H. This study provides evidence for a stable co-enrichment consistent with nutritional niche differentiation within native microbial communities and suggests a potential cooperative interaction between novel Dehalogenimonas and Desulfitobacterium species, advancing our understanding of halogen cycling in coastal ecosystems.IMPORTANCEEstuaries serve as critical interfaces between terrestrial and marine ecosystems, yet the microbial processes governing chlorinated pollutant fate in these vulnerable zones remain largely unexplored. Our discovery of a novel partnership between Dehalogenimonas and Desulfitobacterium species challenges the conventional understanding that Desulfitobacterium is restricted to terrestrial habitats. Integrative multi-omic and physiological analyses reveal that Dehalogenimonas strain H serves as the highly specialized primary dechlorinator, while Desulfitobacterium strain Y is stably co-enriched and exhibits genomic potential to sustain the consortium by providing essential corrinoid cofactors. The identification of genomic determinants underlying salt tolerance in Dehalogenimonas, including ectoine and mannosylglycerate biosynthesis pathways, provides mechanistic insights into OHRB adaptation to fluctuating salinity. These findings have direct implications for developing bioremediation strategies for contaminated coastal sites and highlight the importance of characterizing microbial diversity in transitional ecosystems.}, }
@article {pmid42228562, year = {2026}, author = {Werner, L and Nissenbaum-Toren, T and Fibelman, M and Leibovitzh, H and Cohen, NA and Brenner, M and Lobel, L and Maharshak, N}, title = {Antibiotic disruption of the gut microbiome triggers IBD-like proteolytic activity.}, journal = {Cell reports}, volume = {45}, number = {6}, pages = {117478}, doi = {10.1016/j.celrep.2026.117478}, pmid = {42228562}, issn = {2211-1247}, abstract = {Antibiotics (Abx) are essential in medicine but can disrupt gut microbiota, potentially contributing to inflammatory bowel diseases (IBDs). This study employed fecal metagenomics and metaproteomics to evaluate the effects of Abx in patients with pouchitis, ulcerative colitis (UC), and non-IBD controls. Each group displayed distinct microbiome profiles, with metaproteomes more affected by Abx than metagenomes. Proteomic analysis revealed increased pancreatic protease activity and fecal proteolytic activity in all groups, except in patients without IBD before Abx, consistent with impaired epithelial barrier integrity. Abx also decreased bacterial protease inhibitors, which may control proteolysis and help maintain gut balance. These findings emphasize the importance of understanding Abx-induced proteolytic shifts in IBD and highlight metaproteomics as a valuable tool for studying host-microbiome interactions. Future research should explore the molecular mechanisms that regulate bacterial protease inhibitor levels and their effects on intestinal health.}, }
@article {pmid42229136, year = {2026}, author = {Delgado, N and Fernández, KG and Zambrano-Alegría, C and Espinosa, ZYD and Ramos-Cabrera, E}, title = {Physiological and microbial alterations induced by pesticides in agricultural systems: A bioassay- and 16S rRNA-based approach.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142560}, doi = {10.1016/j.jhazmat.2026.142560}, pmid = {42229136}, issn = {1873-3336}, abstract = {The extensive use of pesticides in agricultural production systems has increased interest in understanding their potential impacts on soil environmental dynamics. This study evaluates the effects of pesticide application on Lactuca sativa L. and soil microbiota. An initial field survey identified the main active ingredients commercial pesticides, followed by bioassays assessing germination and early development of Lactuca sativa, as well as soil microbial structure through physiological assessments and metagenomic analyses based on 16S rRNA gene sequencing, during a three-week soil experiment. Thirty active ingredients were identified in 92 agricultural products. Chlorpyrifos was identified as one of the most commercialized insecticides, where insecticides represented 69% of marketed phytosanitary products, mainly organophosphates (18%) and pyrethroids (21%), despite its hazardous classification and ban in several countries. Germination assays showed a hormetic response at low dose (2200 mg/L), reaching 70% germination compared with 51% in the control, while the germination index decreased to 75% at the recommended dose (4400 mg/L). Statistical analyses revealed inhibition of hypocotyl elongation (p = 0.001) and cotyledon development (p = 0.029). Soil microbiome analysis showed that high chlorpyrifos concentrations reduced microbial richness and diversity, while beta diversity analyses explained 99% of the variance among treatments. Proteobacteria, Burkholderiales, and Sphingomonadales increased under pesticide exposure, indicating microbial adaptation and biodegradation potential. Functional prediction using PICRUSt2 revealed enrichment of genes K03381, K00446, K01048, and K01560 associated with potential organophosphate degradation pathways. These findings demonstrate that chlorpyrifos induces ecological and seedling alterations even at agronomically recommended concentrations. highlighting the need to strengthen sustainable pesticide management and environmental monitoring strategies.}, }
@article {pmid42229568, year = {2026}, author = {Dang, R and Xiao, L and Zhou, L and Liu, J and Liang, Z and Wang, Y and Song, W and Wang, X and Chu, X and Zhang, X and Song, Y and Song, W and Han, G}, title = {Asymmetric microbial community reassembly under 7-year experimental precipitation decouples soil carbon storage in a coastal wetland.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124851}, doi = {10.1016/j.envres.2026.124851}, pmid = {42229568}, issn = {1096-0953}, abstract = {Climate-driven extremes in precipitation are fundamentally altering the hydrological regimes of wetland ecosystems. However, the mechanistic understanding of how soil microbial communities and their metabolic functions respond to precipitation change, and how these responses regulate soil organic carbon (SOC) dynamic, remains limited. Here, we leveraged a 7-year precipitation manipulation experiment (± 40%) in a coastal wetland and applied genome-resolved metagenomics to systematically examine microbial community structure, ecological networks, and key biogeochemical functions (carbon fixation and degradation). We found that although microbial community structure showed no pronounced response to increased precipitation, decreased precipitation reorganized the community, as evidenced by higher β-diversity and more complex co-occurrence networks with strengthened positive interactions. Compared with dominant species, rare species played a more important role in maintaining the stability of microbial networks. Functional potential for carbon degradation and fixation remained relatively stable under decreased precipitation. In contrast, increased precipitation concurrently suppressed degradation of polysaccharides and aromatic compounds, and some carbon fixation pathways, such as Acetyl-CoA (rAcCoA) pathway. Collectively, decreased and increased precipitation induced asymmetric responses in microbial communities, with decreased precipitation primarily reshaping community composition but having little effect on functional potential, whereas increased precipitation predominantly altered functional profiles without substantially changing community structure. We further found microbial community reassembly decoupled SOC content. Together, this study highlights that prolonged precipitation extremes shape coastal wetland microbiomes through divergent ecological trajectories; however, these microbial shifts may not necessarily translate directly into changes in soil carbon storage.}, }
@article {pmid42229596, year = {2026}, author = {Lou, D and Duan, J and Zhou, B and Zhou, H and Wang, Y and Yang, J and Cui, J and Ma, X and Tan, J and Duan, H}, title = {Characterization and activity enhancement of a novel thermostable 3-quinuclidinone reductase through modulating the microenvironment of catalytic residues.}, journal = {Bioresource technology}, volume = {457}, number = {}, pages = {135058}, doi = {10.1016/j.biortech.2026.135058}, pmid = {42229596}, issn = {1873-2976}, abstract = {The biocatalytic synthesis of chiral alcohols offers a sustainable alternative to traditional chemical catalysis, yet the lack of robust, high-efficiency enzymes remains an industrial bottleneck. Here, a novel thermostable 3-quinuclidinone reductase (SdQR) was discovered via metagenomic mining of hot spring environments and biochemically characterized. Among the candidates, the H161Q variant, situated proximal to the conserved catalytic triad, emerged as a high-potential lead. Experimental validation revealed that the H161Q mutation yielded a 16-fold increase in catalytic efficiency (kcat/Km) over the wild-type enzyme while preserving its exceptional thermostability. Molecular dynamics (MD) simulations and MM-PBSA calculations elucidated the mechanistic basis for this enhancement: the mutation establishes a "structurally rigid yet physicochemically fluid" microenvironment. This subtle shift optimizes the hydrophobic landscape within the active pocket and modulates cofactor binding thermodynamics, lowering the desolvation energy barrier without compromising the robust structural scaffold. This study provides a highly potent biocatalyst for the asymmetric synthesis of (R)-3-quinuclidinol, and highlights a sophisticated engineering paradigm for the precise physicochemical fine-tuning of catalytic microenvironments in industrial enzymes.}, }
@article {pmid42229597, year = {2026}, author = {Fard, MB and Kwon, S and Vrieze, J and Wu, D}, title = {Long-term inhibition under continuous perfluorooctanoic acid exposure during anaerobic digestion of waste microalgal-bacterial aerobic granular sludge: Metagenomic-metatranscriptomic insights.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135056}, doi = {10.1016/j.biortech.2026.135056}, pmid = {42229597}, issn = {1873-2976}, abstract = {Microalgal-bacterial aerobic granular sludge (MB-AGS) is a promising wastewater treatment technology, but the effect of residual perfluorooctanoic acid (PFOA) on the anaerobic digestion of waste MB-AGS (WMB-AGS) remains poorly understood. This study evaluated PFOA effects (100, 500, and 1000 µg/L) on anaerobic digestion of WMB-AGS by comparing short-term single-exposure batch assays with long-term semi-continuous digestion. Under control conditions, methane production reached 76 ± 2 mL CH4/g volatile solids. Relative to the control, methane yield changed marginally in the presence of PFOA, indicating no measurable inhibition in a single-exposure biochemical methane potential (BMP) assay. In contrast, during continuous exposure in the semi-continuous digester, biogas output decreased after introducing 1000 µg/L PFOA (31 ± 1 to 19 ± 1 mL/day) and coincided with increased residual soluble chemical oxygen demand. During 3-day hydrolysis-acidogenesis tests, total volatile fatty acids increased from 82 ± 9 mg/L (control) to 122 ± 12 mg/L (1000 µg/L), suggesting greater accumulation of fermentation intermediates in the early digestion phase. The PFOA distribution showed substantial partitioning into extracellular polymeric substance fractions and sludge solids, with 28.3% remaining in supernatant, 23.2% in loosely bound extracellular polymeric substances, 16.0% in tightly bound extracellular polymeric substances, and 32.6% in sludge solids with no transformation products. Multi-omics analysis supported that dominant microbial communities remained broadly stable, whereas reduced transcription of glycolysis and pyruvate-to-acetyl-coenzyme A conversion genes was consistent with soluble organic accumulation and reduced biogas production. Overall, single-exposure BMP assays underestimated the long-term operational impact of continuous PFOA exposure during anaerobic digestion of WMB-AGS.}, }
@article {pmid42229598, year = {2026}, author = {Dong, C and Pan, J and Li, Y and Liu, M and Li, Y and Zhao, Z and Zhang, Y}, title = {Direct interspecies electron transfer-based simplified microbial consortia for high-efficiency conversion of lignocellulose to methane: Construction, metabolic pathway and performance optimization.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135043}, doi = {10.1016/j.biortech.2026.135043}, pmid = {42229598}, issn = {1873-2976}, abstract = {Establishing direct interspecies electron transfer (DIET)-based methanogenic pathway is likely to address the technical bottlenecks involved in long periods and low rates of methanogenesis during anaerobic digestion of lignocellulose. However, the efficiency of DIET is limited by low abundance of electroactive bacteria and electron competition with conventional methanogenic pathway. Here, we combined cow manures with paddy soils/marine sediments as initial inocula, and constructed two simplified microbial consortia (DIETsimp) for conversion of lignocellulose to methane via a 'top-down' selection. Both DIETsimp dramatically shortened periods of methanogenesis (ca. 15-16 vs 25-40 d, this study vs present level) and increased methane production rates (ca. 32 vs 10-25 mL/gVS·d). Lowering pH dramatically increased conductivity of both DIETsimp, similar to that was found in electrically conductive pili of Geobacter sulfurreducens. Meanwhile, the intensities of characteristic peaks in electrochemical Fourier transform infrared spectra associated with c-type cytochrome in both DIETsimp dramatically increased. Metagenomic analysis showed that, Methanosarcina mazei, capable of accepting electrons via DIET, and electroactive species, Sphaerochaeta globosa and Clostridium aceticum, were the dominant archaea and bacteria in both DIETsimp, respectively. The potential DIET-based methanogenic pathway during anaerobic digestion of lignocellulose that S. globosa and C. aceticum metabolized intermediates (e.g. xylose, glucose, pyruvate and acetate) and transferred electrons to M. mazei for the reduction of CO2 to methane was proposed. At last, we optimized culture conditions (including inoculum ratio, C/N and period) to maximize the performances of both DIETsimp via combining the single-factor experiments with response surface methodology.}, }
@article {pmid42229914, year = {2026}, author = {Li, H and Yang, L and Chen, B and Zhang, L and Zhu, J and Zhang, H and Lin, L}, title = {Pneumococcal Rib Osteomyelitis With Concurrent Lung and Chest Wall Abscess in an Infant.}, journal = {Pediatrics}, volume = {}, number = {}, pages = {}, doi = {10.1542/peds.2025-073077}, pmid = {42229914}, issn = {1098-4275}, abstract = {We present a rare case of a 7-month-old infant with a complex invasive Streptococcus pneumoniae infection involving rib osteomyelitis, a pulmonary abscess, and a chest wall abscess. The patient presented with persistent fever and no respiratory symptoms. On day 9, chest radiography was performed because of persistent fever and marked leukocytosis, consistent with the American College of Radiology Appropriateness Criteria that recommend imaging in febrile infants with high fever (≥39°C) or elevated white blood cell counts (≥20 000/mm3). On day 14, the emergence of a chest wall mass prompted escalation to ultrasonography, which provided noninvasive assessment of soft tissue involvement. Subsequent contrast-enhanced computed tomography scans were undertaken to delineate the extent of contiguous spread, evaluate rib destruction, and exclude alternative diagnoses. Microbiological cultures of sputum and aspirated pus, along with metagenomic sequencing, confirmed the presence of macrolide-resistant S. pneumoniae. Because of benzylpenicillin and cephalosporin allergy, intravenous linezolid was selected, resulting in rapid clinical improvement. A 6-week course (intravenous infusion followed by oral) led to complete resolution on imaging, with no recurrence over 5 years. This case underscores the importance of appropriate imaging modalities in febrile infants without respiratory symptoms and the need to consider extrapulmonary spread in chest wall masses. It highlights the diagnostic value of metagenomic sequencing and susceptibility testing in guiding individualized antimicrobial therapy, particularly in macrolide-resistant settings.}, }
@article {pmid42230119, year = {2026}, author = {Alexander, JL and Mullish, BH and Thomas, L and Weersma, RK and Sokol, H and Roberts, LA and Edwards, LA and Emmanuel, A and Gerasimidis, K and Hall, LJ and Iqbal, TH and Kinross, JM and McIlroy, J and Monaghan, TM and Sergaki, C and Shawcross, DL and Stewart, CJ and Lamb, CA and Williams, HRT and Hansen, R and Hold, G}, title = {Recent advances in our understanding of the gut microbiome: an analysis from the Gut Microbiota for Health Expert Panel of the British Society of Gastroenterology.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2026-338252}, pmid = {42230119}, issn = {1468-3288}, abstract = {At around 10 years ago, at the time of the first publication by the Gut Microbiota for Health Expert Panel of the British Society of Gastroenterology, recognition of the gut microbiome's importance in health and disease was transitioning from fringe interest towards major global pursuit. A decade on, we appraise the considerable progress made in the field, while acknowledging ongoing challenges. Earlier human work characterising the 16S rRNA gene amplicon signature of particular conditions in small cohorts has been superseded by larger, multicentre studies with extensive metadata. Studies increasingly employ shotgun metagenomics and other 'omic' techniques-coupled with refined bioinformatic tools and disease models-to better characterise perturbation in gut microbiome functionality. The arrival of 'gold standard' pipelines for microbiome analysis and increased mechanistic validation of signals are key developments towards more clinically-translatable outcomes. Novel clinical areas where the gut microbiome has relevance have emerged, including early life and the efficacy of certain treatments (including immune checkpoint inhibitors and vaccination). Enthusiasm for 'microbiome diagnostics and treatments' has grown, but barriers to widespread adoption remain. Faecal microbiota transplant (FMT) is established for treating recurrent Clostridioides difficile infection, with donor-derived 'next generation' FMT products licensed for this condition in certain countries. Beyond FMT, other microbial therapeutic techniques-including nutritional, bacteriophage and probiotic therapies-show promise, but have not fulfilled their high expectations yet. Gut microbiome research is now well-established and shows significant translational potential; the future focus will be translational work to drive its utility in clinical diagnostics, prognostics and therapeutics.}, }
@article {pmid42230654, year = {2026}, author = {Li, J and Liang, X and Liu, P and Zhu, W and Jin, W and Mao, S and Xie, F}, title = {Rumen-derived Pichia membranifaciens modulates the rumen microbiome and metabolome and mitigates methane emissions in dairy cows.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01029-0}, pmid = {42230654}, issn = {2055-5008}, abstract = {Methane emissions from ruminants represent a significant environmental challenge and dietary energy loss. While yeasts are potential rumen modulators, specific methane-mitigating species remain poorly characterized. Here, we screened 73 rumen-derived strains in vitro, identifying Pichia membranifaciens M12 as the most effective candidate, reducing methane output by 17.1%. Subsequently, a randomized block trial with 36 dairy cows compared a control group with P. membranifaciens M12 supplementation at 2.5 and 5 × 10[11] CFU/cow/day. Methane yield per unit of dry matter intake significantly decreased in the high-dose group (18.7%, P = 0.003), without compromising lactation performance and animal health. Multi-omics analyses revealed that M12 suppressed hydrogenotrophic methanogens (e.g., Methanobrevibacter) and hydrogen-producing bacteria (e.g., Ruminococcus and Fibrobacter), while enriching specific eukaryotic taxa like Orpinomyces and Entodinium. Metabolomic profiling indicated a significant dose-dependent accumulation of metabolites. Metagenomic function analysis demonstrated the decreased abundance of key methanogenesis genes (e.g., mcrABCDG) and increased abundance of hydrogenase (hyaABC), lactate-forming (ghrB), and propionate-forming (mcmA1 and lcdB), suggesting a redirection of reducing equivalents from methanogenesis toward propionate synthesis, alongside enhanced butyrate production. These findings demonstrate that P. membranifaciens M12 mitigates methane emissions via coordinated ecological and metabolic modulation, highlighting its potential as a sustainable strategy for low-carbon ruminant production.}, }
@article {pmid42230804, year = {2026}, author = {Linh, LTK and My, TN and Thi Tran, N and Song, LH and Nurjadi, D and Boutin, S and Velavan, TP}, title = {Metagenomic profiling reveals shared resistome signatures between humans and pigs in Vietnamese smallholder farms.}, journal = {npj antimicrobials and resistance}, volume = {}, number = {}, pages = {}, doi = {10.1038/s44259-026-00223-6}, pmid = {42230804}, issn = {2731-8745}, support = {PACE-UP; DAAD Project ID: 57592343//Deutscher Akademischer Austauschdienst/ ; }, abstract = {Antimicrobial resistance (AMR) is a global health concern, yet the extent of resistant genes and microbial exchange between humans and livestock in low- and middle-income countries remains underexplored. Vietnam, an AMR hotspot, was studied using shotgun metagenomic sequencing of paired faecal samples from pigs and caretakers across 50 small-scale farms. Results revealed 10,270 antimicrobial resistance genes (ARGs) representing 550 unique types, including clinically relevant mcr, blaOXA-58, and optrA genes. Pigs showed higher total AMR abundance, while workers harboured richer resistomes. Approximately 52% (288/550) of ARGs were shared between hosts, dominated by aminoglycoside, β-lactam, and tetracycline resistance genes, often co-located with mobile genetic elements, indicating horizontal transfer potential. Closely related Escherichia coli strains were identified in both hosts, consistent with strain sharing or exposure to common sources beyond individual farms. These findings highlight the human-pig interface as an important setting for shared AMR signatures and support the need for integrated One Health surveillance and antimicrobial stewardship.}, }
@article {pmid42231385, year = {2026}, author = {Hu, J and Fan, D and Xiao, C and Kang, C and Shi, J and Li, Y and Liu, J and Shen, L and Lin, N}, title = {Curcumin supplementation during high-altitude exposure modulates body composition and its relationship with gut microbiota: a randomized controlled trial.}, journal = {Nutrition journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12937-026-01343-5}, pmid = {42231385}, issn = {1475-2891}, support = {2022NSFSC1422//Natural Science Foundation of Sichuan Province/ ; KJS2525//Open Research Project of the Provincial Key Laboratory of Prevention and Translational Medicine for Major Chronic Diseases at Soochow University/ ; }, abstract = {BACKGROUND: Body composition is crucial for athletic performance and linked to the gut microbiota. Curcumin shows potential to promote muscle regeneration and modulate fat metabolism, but evidence from high-altitude populations remains scarce. This study aimed to evaluate the effects of curcumin on body composition at high altitudes, and explore potential role of gut microbiota.<br><br>METHODS: A total of 102 male Han participants was randomized to curcumin (812&#xa0;mg/d) or placebo groups for 1-week pre-acclimatization and 6-week high-altitude acclimatization. Body composition was assessed via bioelectrical impedance analysis and gut microbiota was analyzed through metagenomic sequencing.<br><br>RESULTS: After high-altitude acclimatization, curcumin significantly reduced the percent body fat (PBF, P&#x2009;=&#x2009;0.030). Soft lean mass (SLM), skeletal muscle mass (SMM) and fat free mass (FFM) were increased in both groups, but the curcumin group exhibited greater increases although without significant difference. Curcumin supplementation significantly attenuated the upper-limbs FFM and arm muscle circumference reduction (P&#x2009;<&#x2009;0.05). The relative abundance of Eubacterium sp. CAG:180 was significantly negative with SLM and SMM (P&#x2009;<&#x2009;0.05). Curcumin significantly increased the abundance of Bifidobacterium pseudocatenulatum, Eubacterium sp. CAG:274 and Eubacterium eligens (P&#x2009;<&#x2009;0.01). Higher abundance of Eubacterium sp. CAG:274, Roseburia inulinivorans, and Bifidobacterium pseudocatenulatum were observed in high-skeletal muscle index participants. Lachnospira pectinoschiza, Clostridium leptum, and Eubacterium sp. CAG:274 were more abundant in low-PBF participants.<br><br>CONCLUSIONS: Curcumin supplementation might increase muscle mass gain and reduce PBF during high-altitude acclimatization that may correlate with changes in gut microbiota composition, and their causal association remains to be further verified.<br><br>TRIAL REGISTRATION: Chinese Clinical Trail Registry, ChiCTR220005965. Registered on May 5, 2022.}, }
@article {pmid42231497, year = {2026}, author = {Vayena, G and Giangeri, G and Gaspari, M and Ghofrani-Isfahani, P and Tsapekos, P and Kougias, PG and Angelidaki, I}, title = {Ecological and metabolic restructuring of anaerobic microbiomes under sulfate stress via magnetite-enhanced cooperative networks.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02443-4}, pmid = {42231497}, issn = {2049-2618}, abstract = {BACKGROUND: Anaerobic digestion systems with elevated sulfate often suffer reduced methane yields, challenged by the competition between sulfate-reducing bacteria and methanogens, and inhibited by hydrogen sulfide introduction. The present work explores the role of magnetite in improving anaerobic digestion performance under elevated sulfate conditions by chemically influencing the anaerobic system and reshaping microbial interaction patterns.<br><br>RESULTS: Magnetite addition mitigated hydrogen sulfide toxicity via precipitation and increased methane production by 19%. Genome-centric metagenomics revealed a notable proliferation of the methanogenic population in the magnetite-amended reactors, consistent with the elevated methane output in the presence of both magnetite and sulfate, without suppressing sulfate-reducing, homoacetogenic, or syntrophic acetate-oxidizing activity. Magnetite was associated with enhanced methanogenesis and a strengthened cooperative syntrophic network among the four microbial guilds, in line with more efficient carbon and electron flow despite sulfate stress. Community genome-scale metabolic modeling supported these trends, validating the feasibility of the proposed interaction network and indicating that interspecies metabolite transfer between partners is stoichiometrically feasible, supporting the observed community behavior.<br><br>CONCLUSIONS: This study demonstrates the role of magnetite not only as a hydrogen sulfide scavenger but also as a community modulator, promoting resilient direct electron transfer-based networks, ultimately unlocking higher-efficiency biogas production in sulfate-impacted digesters. Our findings support the concept that interactions between sulfate-reducers and hydrogenotrophic methanogens are not purely competitive, and that conductive materials such as magnetite can enhance their metabolic coupling even under sulfate stress. Video Abstract.}, }
@article {pmid42231509, year = {2026}, author = {Sarhan, MS and Samadelli, M and Zink, A and Maixner, F}, title = {The Iceman's microbiome: unveiling millennia of microbial diversity and continuity.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42231509}, issn = {2049-2618}, support = {FESR1078-MummyLabs//European Regional Development Fund/ ; }, abstract = {BACKGROUND: The Iceman mummy, a 5300-year-old natural alpine glacier mummy, provides a unique opportunity to study ancient microbial ecosystems. However, disentangling the mummy's endogenous microbiome from modern environmental contaminants introduced during three decades of conservation remains a significant challenge.<br><br>RESULTS: By integrating culture-dependent and culture-independent approaches, including amplicon sequencing, shotgun metagenomics and de novo metagenomic assembly, as well as isolate-level genomics, we performed a comprehensive characterization of the Iceman's microbial landscape. We identified three distinct microbial drivers: endogenous post-mortem succession, ancient glacier-derived relicts, and modern anthropogenic introduction. Metagenomic analysis of internal tissues revealed anaerobic bacteria, including ancient gut taxa, including such as Romboutsia hominis, Clostridium moniliforme, Eubacterium sp., Ruminococcus bromii, Kineothrix sp., Treponema succinifaciens, Enterousia sp., and Huintestinicola butyrica. These taxa, characterized by ancient DNA (aDNA) damage profiles (C to T deamination frequency), show high similarity to ancestral, non-Westernized human gut communities, providing a rare baseline for Copper Age intestinal ecosystems. Conversely, we identified a shift in the external mycobiome, marked by the recent proliferation of psychrophilic yeasts, including Glaciozyma watsonii, Mrakia robertii, Phenoliferia glacialis, and Goffeauzyma sp. While internal bacterial communities remained stable, these external yeast populations showed increased relative abundance and reduced DNA damage signatures between 2010 and 2019, indicating active, modern colonization. Furthermore, strain-level analysis of Pseudomonas sp. 5C2 confirmed that specific environmental strains have successfully colonized the mummy, persisting across multiple tissue sites with minimal genetic divergence.<br><br>CONCLUSIONS: Our study demonstrates that the Iceman is not a static relic but a dynamic biological interface. The coexistence of ancient, endogenous gut microbes and modern, psychrophilic colonizers highlights the potential for ongoing microbial activity even at sub-zero temperatures. These findings underscore that maintaining strict environmental parameters is essential to prevent these specialized microbial communities from transitioning from latent persistence to active microorganisms. Video Abstract.}, }
@article {pmid42231528, year = {2026}, author = {Wang, W and Fortuna, R and Mayengbam, S and Seerattan, RA and Mu, C and Rios, JL and Abughazaleh, N and Vaghef Mehrabani, E and Noye Tuplin, EW and Hart, DA and Sharkey, KA and Herzog, W and Reimer, RA}, title = {Multiomics insights into the effects of prebiotics on physical function and metabolism in adults with obesity and knee osteoarthritis.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2679516}, doi = {10.1080/19490976.2026.2679516}, pmid = {42231528}, issn = {1949-0984}, abstract = {Knee osteoarthritis (OA) is a prevalent, painful, degenerative disease lacking effective disease-modifying drugs. The rise in obesity has increased the prevalence of metabolic OA, underscoring the need for effective management to delay or prevent knee replacement. Prebiotics confer improvement in physical function and metabolic health in adults with comorbid knee OA and obesity by unknown mechanisms. Here, we integrated metagenomic and metabolomic analyzes to investigate prebiotic fiber-linked mechanisms along the gut-knee axis. By reshaping the composition and function of the gut microbiota, prebiotics increased diet-derived carbohydrate availability, mitigated excessive host-glycan degradation and mucosal barrier disruption, reduced systemic inflammation and metabolic dysregulation, ultimately enhancing metabolic health and improving physical performance. In a diet-induced obese rat model, prebiotics reduced tibial cartilage degeneration and synovial membrane thickening, conferring protection against OA onset and progression through a common inflammatory pathway. Our findings provide mechanistic evidence supporting the therapeutic potential of prebiotic supplementation as a conservative management in humans and as a preventive approach for obesity-related knee OA in a preclinical rat model, mediated through the gut-joint axis.}, }
@article {pmid42232316, year = {2026}, author = {Webster, NS and Bell, SC and Luter, HM and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the sponge, Rhopaloeides odorabile Thompson, Murphy, Bergquist &amp; Evans, 1987 (Dictyoceratida: Spongiidae) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {11}, number = {}, pages = {211}, pmid = {42232316}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Rhopaloeides odorabile (Porifera; Demospongiae; Dictyoceratida; Spongiidae). The genome sequence has a total length of 291.63 megabases. Most of the assembly (98.17%) is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.42 kilobases. From the metagenome data, we recovered 162 bins, of which 96 were high-quality MAGs. R. odorabile displays a characteristic high microbial abundance sponge profile, with MAGs representing diverse phyla (i.e., Acidobacteriota, Pseudomonadota, and Chloroflexota) and candidate phyla (i.e., Ca. Latescibacteria, Ca. Poribacteria, and Ca. Tectomicrobia).}, }
@article {pmid42232360, year = {2026}, author = {Li, Y and Yi, G and Han, Z and Fu, J and Xu, L}, title = {Comparison of mNGS microbial detection profiles between percutaneous lung aspiration biopsy and bronchoalveolar lavage fluid in infective pneumonia.}, journal = {Open medicine (Warsaw, Poland)}, volume = {21}, number = {1}, pages = {20261445}, pmid = {42232360}, issn = {2391-5463}, abstract = {OBJECTIVES: To compare the mNGS-based microbial detection profiles of percutaneous lung aspiration biopsy (PLAB) and bronchoalveolar lavage fluid (BALF) in patients with infective pneumonia under real-world clinical sampling strategies.<br><br>METHODS: The study included 166 patients with infective pneumonia, of whom 54 underwent PLAB to obtain unfixed fresh lung tissue from the lesion site, while 112 underwent fiberoptic bronchoscopy to obtain&#xa0;BALF.<br><br>RESULTS: In the BALF group, 3 pathogens of high concern and 5 suspected pathogens, totaling 8 types of pathogens, were detected. In contrast, in the PLAB group, 1 pathogen of high concern and 1 suspected pathogen, totaling 2 types of pathogens were detected. Cumulatively, 348 pathogens were identified in the BALF group. In the PLAB group, 96 pathogens were identified cumulatively, p<0.001. In the BALF group, the most frequently detected pathogen was Streptococcus pneumoniae, with 19 strains of Mycobacterium tuberculosis among the special pathogens. In the PLAB group, the most frequently detected pathogen was Epstein-Barr virus (EBV) (14.58&#x202f;%).<br><br>CONCLUSIONS: BALF and PLAB showed different mNGS microbial detection patterns under different clinical sampling strategies. Because of the retrospective non-paired design, these findings should be interpreted as descriptive comparative data rather than proof of the superior diagnostic performance of either sampling method.}, }
@article {pmid42232489, year = {2026}, author = {Huang, Y and Yang, M and Liu, J and Zhang, M and Penttinen, P and Zhang, L and Ge, L and Zhang, X and Zhao, N}, title = {Phage succession and putative mechanisms of microbial community regulation in Sichuan radish paocai (traditional Chinese fermented vegetable).}, journal = {Food chemistry: X}, volume = {36}, number = {}, pages = {103997}, pmid = {42232489}, issn = {2590-1575}, abstract = {Spontaneous fermentation of Sichuan paocai is shaped by complex microbial and environmental factors, yet phage communities remain understudied. This study presents integrated viromic and metagenomic analysis of radish paocai combined with metabolite profiling to elucidate phage diversity, dynamics, ecological roles, and sources. Time-series metagenomics revealed Lactiplantibacillus increasing from 11% to 71%, while viromics showed phages comprising 78% of viral contigs, with Uroviricota reaching 88% by day 5. Host prediction indicated that 89% of phages targeted Lactiplantibacillus, mainly L. plantarum. Correlation analysis suggested that core phages were associated with fermentation-related metabolites, including volatile compounds (e.g., decanal), implicating that phages might influence metabolism by modulating host activity. Functional annotation showed phage encoded amino acid and carbohydrate metabolism genes, suggesting auxiliary metabolic roles. Source analysis suggested that most phages in radish paocai may be derived from bacterial prophages. This work advances understanding of phage diversity and ecological function in fermented vegetable ecosystems.}, }
@article {pmid42232626, year = {2026}, author = {Han, X and Zhang, L and Zhang, R and Liu, W}, title = {Case Report: Multiple organ dysfunction syndrome in a preterm infant secondary to respiratory syncytial virus and bacterial co-infection.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1825002}, pmid = {42232626}, issn = {2296-2360}, abstract = {This article reports a case of a 1-month 11-day-old preterm infant, born at 36 + 6 weeks gestation, who presented to an outside hospital emergency department with a persistent cough that had not improved over four days. During this period, the infant progressively developed respiratory distress and lethargy. The infant subsequently developed cardiopulmonary arrest, underwent cardiopulmonary resuscitation, and was transferred to our hospital under endotracheal intubation with positive pressure ventilation. Respiratory pathogen polymerase chain reaction testing of a throat swab was positive for respiratory syncytial virus (RSV), while sputum and bronchoalveolar lavage fluid culture and blood metagenomic next-generation sequencing (mNGS) detected Haemophilus influenzae and S. pneumoniae. After 22 days of hospitalization and treatment including invasive mechanical ventilation, antibiotic adjustment, intravenous immunoglobulin (IVIG), and dexamethasone, the infant was discharged without further complications. Metagenomic next-generation sequencing provides rapid diagnostic evidence for mixed infections, while integrated interventions, including IVIG, short-course corticosteroids, and nutritional support, effectively modulate immune responses.}, }
@article {pmid42232631, year = {2026}, author = {Gao, L and Wen, Y and Jing, X}, title = {Case Report: Cervical lymphadenitis resulting from Pseudomonas aeruginosa diagnosed by metagenomic next-generation sequencing.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1795457}, pmid = {42232631}, issn = {2296-2360}, abstract = {Pediatric cervical lymphadenitis is usually caused by Staphylococcus aureus and Streptococcus pyogenes. Cases resulting from Gram-negative bacteria are rare. Herein, we report the case of an 11-year-old boy who developed cervical lymphadenitis. He was diagnosed with a Pseudomonas aeruginosa infection through metagenomics next-generation sequencing of blood and biopsy. After treatment with meropenem, the patient's condition improved and he was discharged. Lymphadenitis may be caused by Gram-negative opportunistic pathogens. Metagenomic next-generation sequencing can help identify the underlying cause.}, }
@article {pmid42232653, year = {2026}, author = {Fan, F and Wang, B and Jia, R and Lyu, J and Han, F}, title = {Amelioration of tic disorder by Jujuboside A via gut microbiota remodeling and intestinal 5-HT signaling.}, journal = {Frontiers in neuroscience}, volume = {20}, number = {}, pages = {1760647}, pmid = {42232653}, issn = {1662-4548}, abstract = {BACKGROUND: Tic disorder (TD) is a common chronic neuropsychiatric condition manifesting during childhood and adolescence. Jujuboside A (JuA) may alleviate TD symptoms; however, the mechanisms underlying its therapeutic effects remain unclear.<br><br>METHODS: We established a rat model of TD and used histological techniques to evaluate the effects of JuA on pathological changes. We also measured 5-hydroxytryptamine (5-HT) and 5-hydroxyindoleacetic acid (5-HIAA) levels and assessed tryptophan hydroxylase 1 (TPH1) mRNA expression. Finally, we analyzed the gut microbiota composition in fecal samples using 16S rRNA metagenomic sequencing.<br><br>RESULTS: JuA administration alleviated pathological changes in rats with TD, increased 5-HT and 5-HIAA levels, and upregulated TPH1 mRNA expression. Compared with no treatment, JuA treatment increased the proportion of Bacteroidia, Muribaculaceae, Bacteroidales, and Bacteroidota, while reducing that of Bacilli, Lactobacillaceae, Lactobacillus, Lactobacillales, and Firmicutes.<br><br>CONCLUSION: These findings indicate that JuA mitigates TD progression, potentially by remodeling the gut microbiota and regulating 5-HT levels.}, }
@article {pmid42232910, year = {2026}, author = {Oskolkov, N}, title = {Refining filtering criteria of Kraken family of tools for accurate taxonomic profiling of ancient metagenomic data.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1603339}, pmid = {42232910}, issn = {1664-302X}, abstract = {Taxonomic profiling is a key component of ancient metagenomic analysis, however it is also susceptible to false-positive identifications. In particular, taxonomic classification tools from the Kraken family, such as Kraken2 and KrakenUniq, are highly sensitive to the choice of filtering options. To address this issue, various filtering approaches have been proposed. In this study, I conduct a comprehensive benchmarking of different filtering strategies for Kraken family of tools using simulated microbial and environmental ancient metagenomic data. I evaluate these approaches based on the balance between sensitivity and specificity of ground truth reconstruction (F1-score), and propose an optimal thresholding strategy tailored to specific sequencing depths in ancient metagenomic datasets.}, }
@article {pmid42232914, year = {2026}, author = {Chamberlain, EJ and Boulton, W and Connors, E and Calianos, T and Bowman, JS and Creamean, JM and Mock, T and Kim, HH}, title = {From microbial diversity to functional potential using dimensionality reduction.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1786397}, pmid = {42232914}, issn = {1664-302X}, abstract = {The high dimensionality of microbial diversity data from 'omics observations can be reduced using Machine Learning, with many recent studies showcasing ML utility for exploratory ecological feature finding and process prediction. Here, we compare the Self Organizing Map (SOM) dimensionality reduction method to the well-documented sample-based Principal Coordinate Analysis (PCoA) and taxa-based Weighted Gene Correlation Network Analysis (WGCNA) using near daily 16S rRNA gene amplicon sequencing data from the 2019 to 2020 MOSAiC International Arctic Drift Expedition. We then map k-means clustering outputs from each method to available metagenomes, extracting functionally distinct seasonal microbial ecotypes in the surface Arctic Ocean. Our results indicate the SOM method better represented expected seasonal transitions and identified a greater number of metabolically distinct functional groups than the more traditional PCoA ordination. Ultimately, we identified four community ecotypes with distinct taxonomic and functional cut-offs driven by seasonality, water mass, and substrate turnover, highlighting the importance of succession in functional diversity for the central Arctic Ocean. These results reinforce ML dimensionality reduction as a meaningful translator in the mining of historical amplicon datasets to address modern mechanistic questions and potentially provide 'omics informed ecotype diversity to leverage in mechanistic biogeochemical models.}, }
@article {pmid42233252, year = {2026}, author = {Hashmi, L and Rehman, SU and Jabeen, F and Kayani, MUR}, title = {GUTAID: a curated database linking gut microbial antigens to autoimmune mechanisms.}, journal = {Database : the journal of biological databases and curation}, volume = {2026}, number = {}, pages = {}, doi = {10.1093/database/baag029}, pmid = {42233252}, issn = {1758-0463}, support = {//Metagenomics Discovery Lab at the SINES/ ; //NUST/ ; }, abstract = {Gut dysbiosis is widely recognized as a contributor to autoimmune diseases, as it can lead to the expression of microbial antigens that disrupt immune regulation through specific molecular mechanisms. However, existing resources do not systematically link gut microbial antigen sequences to the specific autoimmune mechanisms through which they act. Here, we present GUTAID (Gut Microbes in Autoimmune Disorders), a literature-curated database of gut microbial antigens annotated with experimentally supported autoimmune mechanisms. Peer-reviewed studies published from October 1970 to September 2024 were manually screened, yielding 73 potential antigens that operate through nine molecular mechanisms, including protein citrullination, epitope spreading, molecular mimicry, and immune modulation, amongst others. The corresponding protein sequences were retrieved from UniProtKB, and redundancy was removed with MMseqs2. For the database implementation, data were delivered through a lightweight LAMP (Linux-Apache-MySQL/MariaDB-PHP) stack with server-side HTML/Bootstrap rendering, MySQL indexing, and HTTPS-secured downloads. Users can browse, keyword-search, or bulk-download sequence archives via a five-tab interface (Home, Downloads, Search, Team, and About). GUTAID thus enables mechanism-oriented exploration of gut microbial antigens and supports downstream biomarker and therapeutic discovery in autoimmune research. Database URL: https://gutaid.mgdiscoverylab.com/.}, }
@article {pmid42233644, year = {2026}, author = {Dubin, CA and Zhao, C and Pollard, KS and Oskotsky, T and Golob, JL and Sirota, M}, title = {Expanding vaginal microbiome pangenomes via a custom MIDAS database reveals Lactobacillus crispatus accessory genes associated with cervical dysplasia.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0149825}, doi = {10.1128/msystems.01498-25}, pmid = {42233644}, issn = {2379-5077}, abstract = {The vaginal microbiome plays a central role in reproductive health. Vaginal microbiome dysbiosis is associated with many adverse reproductive health outcomes, but most studies have focused on associations at the species level. The potential contribution of intraspecies microbial variation, especially gene content differences across bacterial strains, remains underexplored in reproductive health contexts. The Metagenomic Intra-Species Diversity Analysis (MIDAS) framework enables such analyses, but depends on comprehensive reference databases. We constructed a MIDAS-compatible pangenome database from over 18,000 genomes in the Vaginal Microbiome Genome Collection (VMGC). Compared to the Genome Taxonomy Database (GTDB)-derived reference, the VMGC-derived database expanded the pangenomes of prevalent vaginal species, better capturing vaginal-specific intraspecies diversity. Applying this database to vaginal samples from a cervical dysplasia cohort, we identified 13 Lactobacillus crispatus accessory genes significantly associated with cervical dysplasia, including a HicAB toxin-antitoxin system, three transcriptional regulators, and three phage-derived genes. These findings highlight the utility of body site-specific reference resources and shotgun metagenomic sequencing for uncovering intraspecies microbial variation relevant to reproductive health.IMPORTANCEThe vaginal microbiome plays a critical role in reproductive health, and different bacteria from the same species can carry different genes that influence how the strains interact with the host and other microbes. These strain-level differences are often overlooked when microbiomes are analyzed only at the species level. Existing genomic reference databases are heavily biased toward gut and environmental bacteria, leaving the genetic diversity of vaginal microbes understudied. We built a specialized reference database from over 18,000 vaginal bacterial genomes that better reflects this diversity. We then applied this resource to quantify gene-level variation in vaginal samples from a cervical dysplasia cohort. Focusing on Lactobacillus crispatus, a prevalent and often beneficial vaginal species, we identified 13 genes that were more common in women with cervical dysplasia than in controls. This work demonstrates that body site-specific genomic resources are essential for uncovering strain-level bacterial differences relevant to reproductive health.}, }
@article {pmid42233648, year = {2026}, author = {Hu, J and Zhang, H and Miao, H and Chang, W and Zheng, J and Hu, F and Zhang, D and Guo, W and Hu, P and Han, R and Wang, J and Li, L and Wang, X}, title = {Benchmarking next- versus third-generation sequencing in metagenomics: performance metrics and diagnostic efficacy.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0399325}, doi = {10.1128/spectrum.03993-25}, pmid = {42233648}, issn = {2165-0497}, abstract = {UNLABELLED: This study aimed to compare the analytical characteristics and diagnostic performance of short-read next-generation sequencing (NGS) and long-read third-generation sequencing (TGS) for metagenomic pathogen detection, using defined mock communities and clinical bronchoalveolar lavage fluid (BALF) samples. Mock evaluations included microbe-host gradient mixtures (D1/D2) and six complex microbial panels (M1-M6). Sequencing was performed on Illumina, MGI, and Oxford Nanopore Technologies (ONT) platforms. Clinical validation was conducted on 62 BALF samples. Diagnostic performance was assessed against culture, clinical microbiological tests (CMT), and a composite reference standard (CRS). Turnaround times for Illumina and MGI were approximately 18-20 h and 14-19 h, respectively, whereas the ONT workflow was completed within 4-6 h. The microbe-to-host DNA ratio significantly influenced sequencing performance. Depletion of host DNA notably enhanced ONT detection, reducing the false-negative rate for low-abundance microorganisms from 43.3% to 6.7%. For all mock samples, both the Illumina and MGI platforms demonstrated 100% sensitivity and showed highly concordant detection profiles. In clinical specimens, when evaluated against the composite reference standard, the positive percent agreement (PPA) values of NGS and TGS were 93.3% and 90.7%, respectively, with corresponding negative percent agreements (NPAs) of 77.6% and 83.3%. Both platforms identified numerous pathogens that were missed by culture, especially in polymicrobial infections. Among 22 CRS-defined polymicrobial samples, culture identified all pathogens in only 2 cases, whereas NGS and TGS achieved full pathogen recovery in 18 and 17 cases, respectively. Within the evaluated workflows, short-read sequencing showed slightly higher sensitivity and overall stability, whereas host-depleted ONT offered a substantial turnaround-time advantage and may serve as a useful complementary approach in complex or time-sensitive clinical scenarios.<br><br>IMPORTANCE: Rapid and accurate identification of the microbes causing pneumonia is essential for choosing effective treatment, yet current diagnostic tests are slow and often miss important pathogens. We systematically compared two major DNA sequencing strategies-established short-read platforms and newer long-read nanopore sequencing-using both carefully designed mock communities and real bronchoalveolar lavage samples from patients. We show when removal of human DNA is essential, how mixed infections are best captured, and what trade-offs exist between speed and sensitivity. Our results provide practical guidance on how hospitals can implement sequencing-based diagnostics, when rapid nanopore testing can complement conventional short-read workflows, and how to interpret sequencing read counts in day-to-day clinical decision-making.}, }
@article {pmid42233650, year = {2026}, author = {Kane, M and Moukaha Doukanda, SF and Sankhé, S and Sow, B and Ndione, MHD and Mhamadi, M and Dieng, M and Diop, SMBS and Seye, S and Mbanne, M and Faye, O and Barry, MA and Sembene, PM and Loucoubar, C and Fall, G and Diallo, A and Diagne, CT and Dia, N and Diagne, MM}, title = {Evaluating myxovirus resistance protein A-based rapid testing combined with pathogen sequencing for arboviral and incidental viral infection surveillance in Senegal.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0339225}, doi = {10.1128/spectrum.03392-25}, pmid = {42233650}, issn = {2165-0497}, abstract = {Accurate differentiation between viral and bacterial infections remains challenging in resource-limited, arbovirus-endemic settings, leading to antibiotic misuse and diagnostic uncertainty. Myxovirus resistance protein A (MxA), an interferon-induced host biomarker, may offer a pathogen-agnostic approach to improve rapid diagnosis and clinical triage. We evaluated the performance of an MxA rapid diagnostic test (RDT) using archived samples from febrile patients collected during dengue virus (DENV) and chikungunya virus (CHIKV) outbreaks in Senegal. We tested 171 blood samples from patients with acute febrile illness using an MxA RDT and RT-qPCR for DENV and CHIKV. Samples with discordant results (MxA-positive and RT-qPCR-negative) underwent metagenomic and hybrid-capture Illumina-based sequencing to detect missed infections. Sequencing data were analyzed using maximum-likelihood phylogenetics to assess viral lineage placement. The MxA RDT demonstrated moderate-to-high sensitivity (70.0%-85.1%, depending on virus) and moderate specificity (70.2%) for detecting primary arboviral infections. Among discordant samples, sequencing revealed previously missed pathogens, including DENV serotype 3 (genotype III), Parvovirus B19 (B19V), and Torque teno virus (TTV). Detection of B19V and TTV highlights the broader clinical utility of host-response biomarkers to uncover unexpected viral pathogens in high-diversity settings. MxA's longer persistence than viral RNA enables detection of recent infections missed by PCR. Combined with sequencing, this broadens the diagnostic window, improves clinical triage, and supports identification of underdiagnosed viruses. Future research should integrate MxA testing into routine clinical care and surveillance protocols to enhance outbreak responses in resource-limited regions.IMPORTANCETimely and equitable viral diagnosis is vital in outbreak-prone regions where advanced laboratories are scarce. This study shows how a simple, rapid test for the host biomarker myxovirus resistance protein A can provide real-time detection of viral infections such as dengue and chikungunya, even in remote or frontline health centers. When paired with pathogen sequencing, the test also uncovers infections that standard PCR may miss. This integrated approach demonstrates how field-deployable diagnostics can operate both during and between epidemics, strengthening outbreak preparedness, improving patient triage, and advancing laboratory equity worldwide.}, }
@article {pmid42233654, year = {2026}, author = {Wang, W and Li, Y and Liang, Y and Wang, J and Zhang, Z and Zhang, Y and Xiao, C and Hao, H}, title = {Age-driven shifts of the camel gut microbiome and resistome in extensively reared dromedary camels.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0318325}, doi = {10.1128/spectrum.03183-25}, pmid = {42233654}, issn = {2165-0497}, abstract = {UNLABELLED: Camels are uniquely adapted to arid environments and are commonly raised in extensive grazing systems. The composition of their gut microbiome and antimicrobial resistance genes (ARGs) is expected to change with host development, but age-related patterns have not been well described. In this study, we analyzed fecal samples from juvenile (approximately 6 months old) and adult (6 years) dromedary camels kept under the same grazing management, with no recorded therapeutic antibiotic treatments during the study period. Shotgun metagenomic sequencing was used to profile bacterial communities, ARGs, and mobile genetic elements (MGEs). Juvenile camels showed lower alpha diversity and greater inter-individual variation than adults, and their gut communities were dominated by facultative anaerobes such as Escherichia and Streptococcus. Adult camels carried more stable, fiber-adapted communities enriched in Bacteroidaceae and Prevotellaceae. In parallel with these microbiome changes, the resistome also differed by age. Juveniles carried a wider range of ARGs, with higher contributions from multidrug efflux pumps and vancomycin resistance genes. Adults had a smaller and more concentrated set of ARGs, mainly β-lactamase and tetracycline resistance genes, together with lower ARG richness and diversity. MGEs also showed distinct age-related patterns: transposase genes were more common in juveniles, whereas insertion sequence-associated genes were more abundant in adults, suggesting age-specific routes of potential ARG mobility. Overall, these data indicate that maturation of the camel gut microbiome is accompanied by a reduction and focusing of the resistome and by a shift in the dominant types of MGEs. This study provides an age-stratified reference for ARG reservoirs and MGE-associated ARG mobility in camels studied under conditions with no recorded therapeutic antibiotic treatments and may be useful for future work on antimicrobial resistance in extensively managed livestock.<br><br>IMPORTANCE: Antimicrobial resistance is often studied in animals heavily exposed to antibiotics, leaving a gap in our understanding of its natural development. Camels, rarely treated with antibiotics, offer a unique model. By comparing juvenile and adult gut microbiomes, we found that early-life communities are diverse, unstable, and rich in mobile resistance genes, while adult communities are more stable and carry fewer mobile elements. These findings establish a natural baseline for how resistance genes emerge and settle without drug pressure, providing critical insights for One Health strategies aimed at limiting the spread of resistance in livestock and wildlife.}, }
@article {pmid42233680, year = {2026}, author = {Grettenberger, CL and Macalady, JL and Hamilton, TL}, title = {Metabolic diversity of Ferrovaceae and potential contributions to iron oxidation.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0070026}, doi = {10.1128/aem.00700-26}, pmid = {42233680}, issn = {1098-5336}, abstract = {Active and abandoned metal and coal mines generate acidic, metal-laden water that pollutes downstream areas, commonly referred to as acid mine drainage (AMD). AMD is host to microbial communities, including acidophilic iron oxidizers. Microbially mediated iron oxidation is a desirable (bio)remediation strategy for AMD. Ferrovaceae are Fe-oxidizing bacteria observed in AMD globally and thus could be an asset for bioremediation strategies. To better understand the potential for Ferrovaceae to contribute to AMD bioremediation, we analyzed 240 genomes and metagenome-assembled genomes from Ferrovaceae, including sequences from AMD sites with high iron oxidation rates. Based on our analyses, the phylogenetic and physiological diversity of this group is greater than previously known. We found that while all taxa are likely capable of iron oxidation using a cyc-2 like protein, some may also be capable of iron oxidation using an Mto-like protein. We also identified Ferrovaceae that are likely capable of anoxygenic phototrophy. Our findings indicate that multiple Ferrovaceae populations co-occur and suggest that differences in physiology may promote niche differentiation along resource axes. Physiologically diverse iron oxidizer communities could support a more resilient microbial community, resulting in higher iron oxidation rates and potentially more efficient bioremediation, and thus our results also indicate that future studies that link taxonomy with iron oxidation activity are warranted.IMPORTANCEAcid mine drainage (AMD) pollutes watersheds worldwide. Microbial communities can be leveraged to improve AMD bioremediation because they drive biogeochemical processes in these ecosystems. In AMD streams, iron-oxidizing microbial populations remove iron from the AMD effluent by precipitating iron oxides, which absorb other metals. These communities vary across sites and differ in how rapidly they oxidize iron. The factors that contribute to iron oxidation rates are not well understood, making it difficult to design effective bioremediation strategies. Ferrovaceae populations are widespread in AMD globally, including in sites with exceptionally high rates of iron oxidation. To examine the potential for Ferrovaceae to be key components of bioremediation strategies, we examined the genomic content and functional potential of Ferrovaceae in publicly available metagenomic data sets. Our analysis uncovered several new species of Ferrovaceae as well as an expanded metabolic potential for this group. Comparative genomics suggests that functional diversity leads to co-occurrence of multiple Ferrovaceae species at the same sites. The presence of multiple iron-oxidizing taxa with distinct physiology could be beneficial for bioremediation strategies.}, }
@article {pmid42233768, year = {2026}, author = {Éles, ZB and Rahmani, L and Gyöngyösi, E and Szarka, K and Rebenku, I and Veress, G and Major, T and Kónya, J and Szalmás, A}, title = {Sublineage-Specific A45S Polymorphism Alters the Biological Function of the Human Papillomavirus 11 E7 Protein.}, journal = {Journal of medical virology}, volume = {98}, number = {6}, pages = {e70997}, doi = {10.1002/jmv.70997}, pmid = {42233768}, issn = {1096-9071}, support = {FK125038//National Research, Development and Innovation Office/ ; //Hungarian Academy of Sciences/ ; //Faculty of Medicine, University of Debrecen/ ; //Richter Gedeon Talentum Foundation/ ; }, abstract = {The E7 oncoprotein of human papillomavirus (HPV) plays a crucial role in viral pathogenesis and replication. Although it is generally highly conserved across HPV genotypes, naturally occurring E7 variants can display functional differences that may affect viral persistence, oncogenic potential, and host cellular responses. The prevalent HPV11 A2 sublineage is characterized by a distinctive amino acid substitution at position 45 (A45S) within the E7 protein. In comparative analyses of transfected primary keratinocytes and HPV-negative cancer cells, we here demonstrate that the A45S substitution enhances the interaction of HPV11 E7 with key cellular targets, including pRb family proteins and PTPN14. A further consequence is an increased ability to target both PTPN14 and pRb family proteins for degradation. Functionally, these differences are exemplified by the S45 variant's enhanced ability to activate E2F-driven gene expression, particularly resulting in elevated mRNA levels of key factors involved in homologous recombination-mediated repair of DNA double-strand breaks, a pathway critical for preserving genomic integrity. Together, these findings indicate that the A45S substitution imparts high-risk-like molecular properties to the low-risk HPV11 E7 oncoprotein. To our knowledge, this is the first report to identify a functionally significant alteration in HPV11 E7 activity resulting from a naturally occurring sequence variation. Understanding the underlying mechanisms could provide new strategies for targeting the therapeutically challenging HPV-associated conditions, such as recurrent respiratory papillomatosis.}, }
@article {pmid42234268, year = {2026}, author = {Hoseini, R and Hoseini, Z and Heydarpour, B and Faraji, M}, title = {A systematic review of molecular signaling in the muscle-brain-gut axis: exercise-induced myokines and microbial metabolites as key mediators.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {42234268}, issn = {1573-4978}, abstract = {Exercise physiology is evolving from an organ-based framework toward a systems-level understanding, where molecular interactions between muscle, brain, and the gut microbiome critically influence performance and health. This review systematically examines the genetic, molecular, and cellular bases of this triad, with a focus on translational insights for disease prevention and human optimization. A systematic search of PubMed, Embase, and Web of Science was conducted up to October 2023 to identify studies exploring molecular pathways linking skeletal muscle, cognitive/affective function, and gut microbiota in exercise contexts. Inclusion criteria were original research articles investigating at least two components of the muscle-brain-gut axis. Exclusion criteria included non-English articles, conference abstracts, and studies without molecular data. The PRISMA 2020 guidelines were followed. The search strategy is detailed in Supplementary Material. Evidence was categorized into Grades 1 through 4 based on methodological rigor, omics integration, reproducibility, and translational relevance to human physiology and disease models. Analysis included 154 studies encompassing 987 molecular associations. Among these, 59 associations (Grades 1-2) provided robust evidence for genetically and functionally validated pathways, including myokine-mediated (e.g., irisin, BDNF) and microbially derived metabolites (e.g., SCFAs, tryptophan derivatives) that modulate neuroplasticity, mitochondrial function, inflammation, and HPA axis activity. Psychobiological factors influenced microbial composition, illustrating bidirectional gut-brain-muscle signaling. Most associations (n = 952) were limited by methodological variability or insufficient mechanistic depth. The integration of multi-omics platforms (metagenomics, metabolomics, proteomics) emerges as a key tool for personalized exercise interventions and biomarker discovery. This review synthesizes molecular evidence for the muscle-gut-brain axis as an integrative determinant of exercise responsiveness and disease resilience. We highlight genetic and metabolic pathways with diagnostic and therapeutic potential, aligning with the development of molecular tools for precision medicine. Future interdisciplinary research should leverage artificial intelligence and longitudinal omics to translate these mechanisms into targeted strategies for performance enhancement and disease prevention.}, }
@article {pmid42234577, year = {2026}, author = {Faure, R and Faure, U and Truong, T and Derzelle, A and Lavenier, D and Flot, JF and Quince, C}, title = {SNooPy: a statistical framework for long-read metagenomic variant calling.}, journal = {Nucleic acids research}, volume = {54}, number = {10}, pages = {}, doi = {10.1093/nar/gkag556}, pmid = {42234577}, issn = {1362-4962}, support = {101088572//ERC/ ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBX011089/1//Earlham Institute Strategic Programme/ ; BBS/E/ER/230002C//Earlham Institute Strategic Programme/ ; BB/CSP1720/1//Core Strategic Programme/ ; BBS/E/T/000PR9818//Core Strategic Programme/ ; BBS/E/T/000PR9817//Core Strategic Programme/ ; BB/CCG2220/1//Core Strategic Programme/ ; }, abstract = {Current long-read single-nucleotide variant callers were designed primarily for genomic data-particularly human genomes. While some have been used on metagenomic data, their underlying assumptions and training procedures fail to account for the inherent complexity of metagenomic samples. To date, no long-read variant caller has been purpose-built for metagenomic applications. To address this gap, we present SNooPy, a single nucleotide polymorphism (SNP)-calling tool that implements a new statistical framework tailored to long-read metagenomic data. Unlike previous genomic methods, our approach makes no assumptions about the number of haplotypes present, their evolutionary relationships, or their sequence divergence. We demonstrate that SNooPy outperforms both traditional statistical and deep learning-based SNP callers. Our results suggest that future integration of this framework with deep learning approaches could further enhance variant-calling performance. SNooPy is freely available on github.com/rolandfaure/snoopy.}, }
@article {pmid42234710, year = {2026}, author = {Liu, F and Lai, T and Xu, W and Li, G}, title = {ViralMultiNet: A structure-aware multimodal framework for viral protein function prediction in wastewater surveillance.}, journal = {PloS one}, volume = {21}, number = {6}, pages = {e0349393}, doi = {10.1371/journal.pone.0349393}, pmid = {42234710}, issn = {1932-6203}, abstract = {Accurate functional annotation of viral proteins is essential for genomic surveillance, yet rapid viral evolution causes "functional drift" that challenges conventional sequence-only models. These models often lack interpretability and struggle with fragmented sequences from complex environmental samples such as wastewater. We developed ViralMultiNet, a structure-aware multimodal framework that integrates multi-scale k-mer encodings (4-7-mers) with functional semantic embeddings derived from UniProt annotations. Using a curated Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) dataset of 66,011 samples from wastewater metagenomics (NCBI SRA: SRX28474964), we implemented gated multimodal fusion and triple knowledge distillation to transfer structural insights from a teacher to a student model. Model performance was evaluated via 5-fold cross-validation and external validation on emerging variants. Training efficiency was optimized using Low-Rank Adaptation and Flash Attention. ViralMultiNet achieved robust classification performance with a macro F1 score of 0.921 ± 0.004, accuracy of 0.928 ± 0.003, and AUC of 0.983 in cross-validation. The distilled student model matched teacher performance within a negligible margin (<0.003 F1 difference) while reducing training time by 40.4% (from 94.3 to 56.2 minutes per epoch). Interpretability analysis revealed that model attention peaks consistently aligned with experimentally validated functional domains of the SARS-CoV-2 Spike protein, including the receptor-binding domain (residues 319-541), S1/S2 cleavage site (681-685), and fusion peptide (816-835). ViralMultiNet offers a scalable, interpretable solution for viral protein function prediction. Its ability to generalize across variants and map attention to critical biological regions supports deployment in wastewater-based early warning systems, enhancing global pandemic preparedness.}, }
@article {pmid42223080, year = {2026}, author = {An, SY and Kim, I and Hong, SH and Kim, EH and Suh, JY}, title = {AcrIIA8 is a putative phage structural protein of the HTJ2 family that does not inhibit Streptococcus pyogenes Cas9.}, journal = {Protein science : a publication of the Protein Society}, volume = {35}, number = {7}, pages = {e70651}, doi = {10.1002/pro.70651}, pmid = {42223080}, issn = {1469-896X}, support = {RS-2025-23525174//National Research Foundation of Korea/ ; RS-2024-00440614//National Research Foundation of Korea/ ; BDB-2025-04-04230007//Korea Institute of Marine Science &amp; Technology Promotion/ ; }, mesh = {*Streptococcus pyogenes/enzymology/genetics/virology ; *CRISPR-Associated Protein 9/antagonists &amp; inhibitors/chemistry/metabolism ; *Viral Structural Proteins/chemistry/metabolism/genetics ; *Bacteriophages/chemistry ; }, abstract = {Anti-CRISPR (Acr) proteins are phage-encoded anti-defense factors that suppress CRISPR-Cas immunity in bacteria. AcrIIA8 was previously identified as an inhibitor of Streptococcus pyogenes Cas9 (SpyCas9) through functional assays of metagenomic libraries. Here, we report that AcrIIA8 does not inhibit SpyCas9 in biochemical assays under a range of buffer conditions and temperatures. The solution structure and dynamics of AcrIIA8 reveal a six-stranded β-barrel fold with flexible β1-β2 and β2-β3 loops, characteristic of phage virion-assembly proteins. In addition, genomic context analysis places AcrIIA8 and its homologs within conserved prophage morphogenetic regions at the position expected for type II head-tail joining (HTJ2) proteins. We further detected no interaction between AcrIIA8 and SpyCas9 in NMR titration experiments, suggesting that they do not specifically associate. Taken together, these findings argue against assigning AcrIIA8 as a SpyCas9 inhibitor and instead support its annotation as a putative phage structural protein of the HTJ2 family.}, }
@article {pmid42223254, year = {2026}, author = {Petricciuolo, M and Carnevali, A and Torboli, A and Postinghel, M and Guasticchi, A and Foladori, P and Cadonna, M and Federici, E}, title = {Wastewater-Based Assessment of Antimicrobial Resistance and Bacterial Communities in Urban and Rural Areas in the Province of Trento (Italy).}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70319}, doi = {10.1002/mbo3.70319}, pmid = {42223254}, issn = {2045-8827}, support = {//CINECA/ ; //Ministero dell'Universit&#xe0; e della Ricerca/ ; }, mesh = {Italy ; *Bacteria/drug effects/genetics/isolation &amp; purification/classification ; *Anti-Bacterial Agents/pharmacology ; *Wastewater/microbiology ; *Drug Resistance, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Rural Population ; Sewage/microbiology ; }, abstract = {Wastewater-based epidemiology (WBE) can supplement clinical surveillance for assessing the spread of antimicrobial resistance (AMR) across the population. We have analyzed sewage samples from seven wastewater treatment plants in the Province of Trento (Italy) using both culture-based and metagenomic DNA methods to investigate the prevalence of antimicrobial-resistant bacteria (ARBs) and resistance genes in urban and rural areas. ESBL-Escherichia coli prevalence was higher in urban areas than in rural ones. As determined by qPCR and dPCR, intI1 and genes associated with widespread resistances, namely, to tetracyclines (tetA), sulfonamides (sul1), and fluoroquinolones (qnrS), were abundant regardless of the area of origin. Among the genes coding for clinically relevant resistances, only that related to macrolides resistance (ermB) was abundant, while the others, namely, those to third-generation cephalosporins (blaCTX-M), carbapenems (blaKPC), vancomycin (vanA), and methicillin (mecA), were detected at much lower concentrations. Further, the abundances of ermB, blaKPC, and vanA were significantly higher in urban areas. 16S rRNA amplicon sequencing showed the occurrence of complex bacterial communities and the abundance of Acinetobacter, Pseudomonas, and Streptococcus, genera that may include ARBs reported in the WHO Bacterial Priority Pathogens List, with the latter showing higher prevalence in urban areas. Taken together, our data highlights the importance of implementing WBE studies across geographical areas with different characteristics in terms of vocation, number of municipalities, and population size, such as urban and rural ones. By providing a comprehensive understanding of AMR at the population level, this approach can inform and support more effective public health interventions.}, }
@article {pmid42223272, year = {2026}, author = {Borton, MA and Oliverio, AM and Narrowe, AB and Villa, JA and Rinke, C and Hoyt, DW and Liu, P and McGivern, BB and Bechtold, EK and Ellenbogen, JB and Daly, RA and Smith, GJ and Angle, JC and Flynn, RM and Freiburger, AP and Louie, KB and Stemple, B and Northen, TR and Henry, C and Miller, CS and Morin, TH and Bohrer, G and Wrighton, KC}, title = {Mapping the soil microbiome functions shaping wetland methane emissions.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0068025}, doi = {10.1128/msystems.00680-25}, pmid = {42223272}, issn = {2379-5077}, abstract = {Accounting for only 8% of Earth's land cover, freshwater wetlands remain the foremost contributors to global methane emissions. Yet the microorganisms and processes underlying methane emissions from wetland soils remain poorly understood. Over a five-year period, we surveyed the microbial membership and in situ methane measurements from over 700 samples in one of the most prolific methane-emitting wetlands in the United States. We constructed a catalog of 2,502 metagenome-assembled genomes (MAGs), with more than half of the 70 bacterial and archaeal phyla sampled containing novel lineages. Integration of these data with 133 soil metatranscriptomes provided a genome-resolved view of the biogeochemical specialization and versatility expressed over wetland soil spatial and temporal gradients. Centimeter-scale depth differences best explained patterns of microbial community structure and transcribed functionalities, even more than land cover or temporal information. Moreover, while extended flooding restructured soil redox, this perturbation failed to reconfigure the transcriptional profiles of methane-cycling microorganisms, contrasting with theoretically expected responses to hydrological perturbations. Co-expression analyses, coupled with depth-resolved methane measurements, revealed the metabolisms and trophic structures most predictive of methane hotspots. Mapping the spatiotemporal transcriptional patterns on this compendium of biogeochemically classified soil-derived genomes begins to untangle the microbial carbon, energy, and nutrient processing contributing to wetland methane production.IMPORTANCESoil microbial ecology is increasingly recognized as essential to climate mitigation, but realizing its full potential requires shifting from static genome inventories to dynamic assessments of microbial activity. This study shows that methane-cycling microbes exhibit stable, depth-stratified expression patterns, even in response to major redox and flooding shifts, undermining assumptions that water-table manipulations common in wetland management can alone reduce methanogenesis. Instead, methane cycling is shaped by spatially organized, transcriptionally active networks involving not only methanogens but also methanotrophs, fermenters, and iron reducers. These findings expose the limitations of genome-only models and highlight the need for soil diagnostics that capture in situ activity. Together, we provide a foundation for developing activity-based microbiome tools, embedding microbial functions into Earth system models, and designing interventions that move beyond "single-lever" strategies and instead work with the structure and dynamics of microbial communities as complex, layered systems.}, }
@article {pmid42223530, year = {2026}, author = {Pokharel, SK and Walsh, S and Shehata, N and Ahearne, A and Belin, D and Larson, B and Tabor, B and Wall, D and Stevens, DC}, title = {Predator avoidance promotes inter-bacterial symbiosis with myxobacteria in polymicrobial communities.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag140}, pmid = {42223530}, issn = {1751-7370}, abstract = {Myxobacteria are predatory soil bacteria with the largest known bacterial genomes, rich in biosynthetic gene clusters for specialized metabolites. Despite their ecological importance as potential keystone taxa in soil food webs, there is a disconnect between laboratory-isolated myxobacteria and abundant Myxococcota detected in environmental metagenomic studies. Here, we report the isolation and characterization of stable myxobacterial swarm consortia from rhizospheric soil, consisting of myxobacteria associated with novel Microvirga species. Using metagenomic sequencing, we assembled metagenome-assembled genomes (MAGs) for four consortia, revealing phylogenetically distinct yet stably associated bacterial partnerships. Comparative genomics identified evidence of horizontal gene transfer, including acyl-homoserine lactone (AHL) synthases and ankyrin repeat (ANKYR) proteins shared between consortium members, and genome-scale metabolic modeling predicted complementary auxotrophies. Time-lapse microscopy revealed that Archangium exhibited reduced predation toward its Microvirga companion (0.7% predation rate) compared to non-symbiotic Myxococcus xanthus (14.9% predation rate) but maintained robust predatory capacity against Escherichia coli prey. These findings indicate that predation avoidance and metabolic complementarity can drive stable inter-bacterial symbiosis in predatory myxobacterial communities, providing foundational insights into previously overlooked myxobacterial partnerships that may be prevalent in natural soil ecosystems.}, }
@article {pmid42224759, year = {2026}, author = {Xu, M and Qi, S and Yu, X and Han, S and Xiao, R and Guo, J and Wang, C and Zhu, N and Lu, H}, title = {Resistome risks of biological wastewater treatment communities: A global dataset of activated sludge, anaerobic digestion, and anammox.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142561}, doi = {10.1016/j.jhazmat.2026.142561}, pmid = {42224759}, issn = {1873-3336}, abstract = {Activated sludge (AS), anaerobic digestion (AD), and anammox (AMX) systems are widely used for wastewater treatment. Their microbial communities harbor resistomes, including but not limited to antibiotic resistance genes (ARGs) and metal resistance genes (MRGs), which may pose potential risks to human and ecological health if they are mobilized or transferred to pathogenic hosts. However, cross-process comparisons of resistome risks are limited at a global scale. This study analyzed 225 metagenomic datasets (210 public: 70 each for AS, AD, AMX; plus 15 in-house AMX) to assess resistome risks and identified key influential factors. Overall, within the constraints of current data availability, North America, Europe and Asia systems exhibited comparable risk levels. AD systems exhibited more than 2-fold higher human health resistome risks (potentials for human pathogens of acute resistance concern to acquire ARGs) than AS and AMX systems. Mesophilic and co-digestion AD systems posed 30-90% higher risks than thermophilic and mono-digestion systems with higher abundance of pathogens, ARGs, and MRGs. AMX systems, otherwise, showed higher ecological resistome risks (overall mobility of ARGs/MRGs and potentials for pathogen acquisition) than AS and AD. The conservative AMX communities contained core taxa that harbor 19.8% more ARGs/MRGs per genome and exhibit 31.4% higher horizontal gene transfer potential than non-core taxa. Key operating factors influencing resistome risks included temperature for AD, and organic loading, influent antibiotics and heavy metals for AMX. These findings provide insights into future wastewater treatment towards improved efficacy and reduced resistome risks.}, }
@article {pmid42224761, year = {2026}, author = {Ma, S and Zhao, B and Jing, G and Han, M and Wang, M and Shan, X and Wang, Z and Lu, S and Liu, X and Wu, F}, title = {Vertical stratification and distribution patterns of the ARG resistome in Fuxian Lake: Insights from a global baseline.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142528}, doi = {10.1016/j.jhazmat.2026.142528}, pmid = {42224761}, issn = {1873-3336}, abstract = {Deep lakes are critical reservoirs for antibiotic resistance genes (ARGs), yet global ARG dynamics and vertical mechanisms remain poorly constrained. By combining metagenomics with a global comparative analysis across 17 plateau lakes and 83 Fuxian Lake samples, this study investigates ARG distribution from macro- to micro-scales. The macro-scale analysis identified Longitude, Latitude, and Temperature (all p-values < 0.05) as dominant constraints on ARG abundance. A distinct, synergistic mechanism drives vertical stratification: ARG enrichment occurs in the deep layer (50-150 m) at the lake center, but enrichment shifts to the shallow layer (0-40 m) in the tourism area. This complex pattern is governed by a biotic-abiotic synergy. Specifically, ARG dynamics in the deep layer are jointly regulated by biotic factors and physicochemical constraints such as pH and ORP. Differences observed at the local scale, including the increase in ARG abundance and rare-to-core conversion, contrast with broader patterns observed across plateau lakes. This study provides the first global distribution spectrum of ARGs in plateau lakes and reveals crucial interactive patterns. The persistent presence of high-risk ARGs and critical priority pathogens necessitates heightened vigilance. We propose controlling anthropogenic inputs and mitigating the risk of deep sediment pollutant release as crucial strategies for these vital freshwater resources.}, }
@article {pmid42224764, year = {2026}, author = {Sun, Y and Yu, Z and Wu, C and Wang, J and Feng, X}, title = {First insights into agricultural practice-driven mobilization and methylation of arsenic and mercury in soil with implications for groundwater risk mitigation.}, journal = {Journal of hazardous materials}, volume = {514}, number = {}, pages = {142530}, doi = {10.1016/j.jhazmat.2026.142530}, pmid = {42224764}, issn = {1873-3336}, abstract = {The migration of heavy metals from soils to groundwater via karst conduits (e.g., dolines) in karst terrains threatens the safety of anthropogenic water supplies. Despite widespread recognition of contamination risks, the underlying mechanisms governing the transformation and mobilization of heavy metals, particularly those mediated by agricultural activities, remain inadequately characterized. Here, we systematically studied the impact of rice straw return (RS) on the biogeochemical transformation processes of both arsenic (As) and mercury (Hg) from a co-polluted soil in karst regions using a combination of geochemical, microbial, and spectroscopic approaches. The results indicated that RS enhanced the desorption of As from Fe(III)oxyhydroxides and methylation of As(III). Metagenomic sequencing analyses revealed that RS increased the abundance of Fe-reducing bacteria (FeRB) and As-methylating microorganisms, which collectively drive As mobilization and transformation. Furthermore, RS promoted the release of Hg from Fe(III)oxyhydroxides and stimulated methylmercury (MeHg) formation, primarily due to the increased abundance of Hg-methylating microbes and hgcAB genes, as well as enhanced Hg availability through the transformation of HgS into organic matter bound Hg and nano-HgS. These findings are essential for predicting As and Hg leaching risks from soils to groundwater under the influence of agricultural practices in karst regions worldwide.}, }
@article {pmid42224874, year = {2026}, author = {Kenzi, M and Benbernou, M and Khelifa, H and Tbahriti, HF}, title = {Machine learning-based prediction of antibiotic resistance gene distribution in agricultural soils under different climate change scenarios.}, journal = {The Science of the total environment}, volume = {1042}, number = {}, pages = {181905}, doi = {10.1016/j.scitotenv.2026.181905}, pmid = {42224874}, issn = {1879-1026}, abstract = {Antibiotic resistance genes (ARGs) in agricultural soils represent a major public health concern, as climate change is believed to augment their dissemination and abundance. Understanding the impact of future climate change scenarios on ARG abundance is essential to implement predictive and proactive One Health strategies. In this study, a total of 2301 soil samples from 67 countries across six continents were compiled from three global metagenome databases, namely NCBI SRA, MG-RAST, and JGI IMG/M. Six machine learning models, namely LightGBM, XGBoost, Random Forest, Support Vector Machines, Deep Neural Networks, and Logistic Regression, were used to predict ARG distribution patterns in agricultural soils, and their performance was evaluated using stratified 10-fold cross-validation with metrics such as AUC-ROC, precision, recall, F1 score, and Matthews Correlation Coefficient. WorldClim 2.1 and CMIP6 models were used to project ARG distribution under three Representative Concentration Pathway scenarios, namely RCP 2.6, RCP 4.5, and RCP 8.5, for the years 2050 and 2070. The LightGBM model achieved the best predictive performance, with an AUC-ROC of 0.957 (95% CI: 0.951-0.963), substantially higher than that of the other models, while the Deep Neural Networks model achieved an AUC-ROC of 0.891. The LightGBM model demonstrated high stability across cross-validation folds, with minimal fold-to-fold variance, defined as the standard deviation of AUC-ROC scores across the 10 folds (SD = 0.008). SHAP feature importance analysis identified soil temperature, pH, and organic carbon content as the top three factors influencing ARG relative abundance, with SHAP values of 0.342, 0.287, and 0.251, respectively. Annual precipitation and soil moisture level were also identified as significant contributors to ARG distribution. SHAP dependency plots revealed critical thresholds for ARG relative abundance, with a sharp increase observed independently when soil temperature exceeds 18 °C and when soil pH drops below 6.5. Furthermore, a non-linear accelerating increase in ARG abundance risk was observed as climate change intensity worsened across scenarios. Projections for future climate change scenarios indicate a potential 34.7% increase in high-risk ARG zones by the year 2070, with the largest changes expected in South Asia, Sub-Saharan Africa, and Mediterranean regions. Paired t-tests revealed significant differences in performance among all models (p < 0.001). These findings demonstrate that gradient-boosting methods such as LightGBM outperform deep learning approaches for ARG prediction from soil microbiome data, offering higher accuracy and interpretability. As climate change is projected to increase ARG risks in a non-linear manner, the development of climate-adaptive agricultural practices and global surveillance systems is urgent. This framework provides actionable risk-mapping tools to support precision farming and region-specific policy interventions within the One Health approach.}, }
@article {pmid42225156, year = {2026}, author = {Feng, S and Bao, Y and Zhu, X and Wu, J and Chen, W and Huang, D and Zhou, T and Meng, L and Lee, CH and Li, D and Huang, M}, title = {Biodegradable versus persistent nanoplastics reshape nitrogen metabolism and biofilm architecture in denitrifying biofilters.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135048}, doi = {10.1016/j.biortech.2026.135048}, pmid = {42225156}, issn = {1873-2976}, abstract = {The presence of nanoplastics (NPs) in biological wastewater treatment systems is an emerging concern. Nevertheless, their differential influence on critical biofilm-mediated processes has yet to be fully elucidated. In this study, denitrifying biofilters were exposed to biodegradable polylactic acid nanoplastics (PLA-NPs) and non-biodegradable polystyrene nanoplastics (PS-NPs) to simulate both typical and cumulative high-exposure scenarios. Results showed that long-term NP stress significantly reduced the denitrification performance, with a maximum inhibition of 35% in total nitrogen (TN) removal. Mechanistically, PLA and PS induced distinct biofilm remodeling strategies. PLA exposure enhanced nitrate assimilation pathways, promoting nitrogen sequestration into microbial biomass. In contrast, PS-NPs elicited concentration-dependent stress responses. Low PS exposure was associated with reduced extracellular polymeric substances (EPS) and enhanced carbohydrate degradation potential, whereas high PS concentrations were linked to altered EPS composition, decreased microbial diversity, and directional succession toward stress-tolerant genera. Metagenomic analysis revealed shifts in central carbon metabolic strategies, including enhanced gluconeogenesis and EPS precursor synthesis under NP exposure. Differences in substrate bioavailability between PLA and PS treatments further contributed to distinct carbon utilization patterns within the biofilms. Overall, this study demonstrates that NP biodegradability governs biofilm functional stability, nitrogen transformation, and denitrification performance, providing mechanistic insight into NP-biofilm interactions in engineered systems.}, }
@article {pmid42225158, year = {2026}, author = {Wang, M and Wang, H and Liang, X and Li, J and Wang, C and Cui, L and Yang, S and Lin, J and Yang, Q and Yang, Z}, title = {Enhanced phenanthrene degradation in microalgae-bacteria systems: Mechanistic roles of exogenous and indigenous degraders.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135034}, doi = {10.1016/j.biortech.2026.135034}, pmid = {42225158}, issn = {1873-2976}, abstract = {This study investigates the synergistic mechanisms of phenanthrene (PHE) biodegradation using Chlorella vulgaris consortia with exogenous (EB) and indigenous (IB) bacteria. Results showed that both cooperative systems significantly enhanced algal growth and PHE removal, with biomass increasing by 17.2% (C.v-EB) and 75.0% (C.v-IB), and biodegradation rates reaching 75.3%-78.4%. Mechanistically, C.v-EB relied on enzymatic antioxidant responses (SOD and CAT) and a protein-rich extracellular polymeric substance (EPS) shield to mitigate oxidative stress. In contrast, C.v-IB exhibited superior resilience through non-enzymatic redox regulation (glutathione/thioredoxin systems) and the formation of a dense, biofilm-like EPS matrix supported by active transport genes (wzm/wzt). Metagenomic analysis revealed that C.v-IB possessed higher metabolic redundancy and energy production efficiency, organized into a coordinated "Degradation-Defense-Communication" genomic architecture via quorum sensing. Furthermore, both consortia expanded the metabolic landscape of PHE, effectively eliminating intermediate toxicity through divergent pathways. These findings provide a systematic framework for developing robust algal-bacterial biotechnologies for the remediation of polycyclic aromatic hydrocarbons in wastewater.}, }
@article {pmid42225249, year = {2026}, author = {Nie, X and Qin, J and Liu, M and Wang, H and Hou, K and Duan, Y}, title = {Process-Level Design of Engineered Microalgal-Bacterial Systems for Carbon-Efficient Nitrogen Removal from Low C/N Wastewater: Carbon/Electron Redistribution Revealed by Metabolic Network Analysis.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124883}, doi = {10.1016/j.envres.2026.124883}, pmid = {42225249}, issn = {1096-0953}, abstract = {Carbon scarcity in low carbon-to-nitrogen (C/N) wastewater limits electron donor availability and constrains biological nitrogen removal. Although microalgal-bacterial symbiosis (MBS) is a promising low-input alternative, the mechanisms that sustain nitrogen removal under carbon-limited conditions remain unclear. Here, process-level characterization and metagenomic analysis were combined to investigate community assembly and carbon/electron redistribution in engineered MBS systems. Under the tested conditions, a balanced algae-to-bacteria ratio (1:1) created the most stable niche and achieved >97% NH4[+]-N removal with minimal nitrate accumulation, indicating effective coupling of nitrification, denitrification, and assimilation. EPS dynamics showed a shift from accumulation to reutilization during prolonged carbon limitation: polysaccharides decreased in the later stage as external COD was depleted, suggesting mobilization of EPS as an internal carbon source. Consistently, TCA-cycle genes (e.g., IDH, OGDH, mdh) were enriched whereas glycolysis-related genes (e.g., GAPDH, PGK) declined, indicating a shift in metabolic potential toward greater generation of reducing equivalents. Overall, the results suggest that EPS functions as a dynamic carbon reservoir and that algae-bacteria interactions promote carbon/electron redistribution under carbon-limited conditions. This study provides a process-level basis for designing carbon-efficient wastewater treatment systems.}, }
@article {pmid42226305, year = {2026}, author = {Grundler, F and Ducarmon, QR and Holley, A and Knufinke, M and Strathmeyer, S and Heelemann, S and Geyer, R and Martínez-Téllez, B and MacArthur, MR and Zeller, G and Wilhelmi de Toledo, F and Mesnage, R}, title = {Health benefits of a five-day at-home modified fasting program: a randomised controlled trial.}, journal = {Genome medicine}, volume = {18}, number = {1}, pages = {}, pmid = {42226305}, issn = {1756-994X}, support = {ALTF 1030-2022//EMBO postdoctoral fellowship/ ; RYC2022-036473-I//MCIN/AEI/10.13039/501100011033/ ; }, abstract = {BACKGROUND: Fasting is one of the most cost-effective methods to improve cardiometabolic health. We tested a 5-day hypocaloric (~ 600 kcal/day) and ketogenic, modified fasting program (MFP) in a two-arm randomised controlled trial, where sixty-four healthy subjects were randomised to MFP or control group.<br><br>METHODS: We randomly assigned 64 participants to a group receiving the MFP or to a group of participants who were told to continue with their usual eating behaviour and lifestyle (control group). The changes in blood pressure and body weight were considered as primary endpoints. Secondary outcomes included ketosis, glucose and lipid metabolism, inflammatory markers, antioxidant capacity and well-being. Biological pathways and metabolic processes were explored with nuclear magnetic resonance blood metabolomics and gut metagenomics analyses. Outcomes were assessed at baseline, end of the MFP, after food reintroduction, and one month later.<br><br>RESULTS: MFP participants (n&#x2009;=&#x2009;32) experienced weight loss compared to controls (-&#x2009;0.52&#x2009;&#xb1;&#x2009;0.03&#xa0;kg vs.&#x2009;-&#x2009;0.03&#x2009;&#xb1;&#x2009;0.02&#xa0;kg, p&#x2009;<&#x2009;0.001). Changes in blood pressure caused by the MFP were non-significant at the end of the fasting period. However, blood pressure was significantly reduced following food reintroduction (systolic: -0.56&#x2009;&#xb1;&#x2009;0.12 mmHg vs.&#x2009;-&#x2009;0.16&#x2009;&#xb1;&#x2009;0.12 mmHg, p&#x2009;<&#x2009;0.05 and diastolic: -0.36&#x2009;&#xb1;&#x2009;0.08 mmHg vs.&#x2009;-&#x2009;0.01&#x2009;&#xb1;&#x2009;0.08 mmHg, p&#x2009;<&#x2009;0.01). Serum biochemistry showed the MFP reduced glucose levels and coagulation factors. The MFP also significantly increased physical well-being. Blood metabolomics revealed a significant decrease in chronic inflammation markers. Shotgun metagenomics of the gut microbiome showed significant changes in relative abundance of 11 bacterial species and in the genomic repertoire of 52 carbohydrate-active enzymes (CAZymes), reflecting an increase in families metabolising host-derived glycan substrates. None of these differences in gut microbiome and blood metabolome were shown to be statistically different from the control group one month after the intervention. Comparing MFP effects with a previous cohort's 5-day prolonged fasting showed similar metabolic changes.<br><br>CONCLUSIONS: This MFP is safe and transiently improves cardiometabolic health and physical well-being in healthy individuals.<br><br>CLINICAL TRIAL REGISTRATION: This trial was prospectively registered at ClinicalTrials.gov (NCT05821660) on 6 April 2023 prior to the start of patient recruitment.}, }
@article {pmid42226423, year = {2026}, author = {Xu, Q and Zhang, X and Tian, H and Yang, X and Zhang, J and Li, H and Ma, Z and Zhang, D and Huang, K and Zhang, Y and Zhao, Y and Li, X and Zhao, L and Cheng, J and Xu, D and Li, F and Weng, X and Wu, W and Wang, W}, title = {Integrating rumen microbiome and host metabolome to investigate feed conversion ratio across different fattening stages in Hu sheep.}, journal = {Animal bioscience}, volume = {}, number = {}, pages = {}, doi = {10.5713/ab.260317}, pmid = {42226423}, issn = {2765-0189}, abstract = {OBJECTIVE: Feed conversion ratio (FCR) is a crucial economic trait in animal breeding and management and is also of great significance for environmental sustainability. This study aimed to investigate the potential regulatory mechanisms of FCR in sheep by integrating rumen microbiota and host metabolome through multi-omics analysis.<br><br>METHODS: FCR data were collected from 127 male Hu sheep. Extreme individuals were selected for rumen metagenomic and serum metabolomic analyses to identify key factors driving FCR across early and late fattening stages.<br><br>RESULTS: Bacteroides, Prevotella, and other genera were identified as dominant taxa in the rumen across both stages, suggesting their involvement in FCR regulation. Notably, Nocardia tengcongensis differed significantly between the highest FCR values (HF) and lowest FCR values (LF) groups at different stages, indicating its potential as a predictive biomarker of feed efficiency. Functional analysis revealed that the pentose phosphate pathway (M00004) and lysine biosynthesis via the succinyl-DAP pathway (M00016) were enriched in the LF group, whereas the methanogenesis pathway (M00357) was significantly enriched in the HF group, indicating increased methane production. Thirteen metabolites consistently differed between HF and LF across fattening stages and may serve as predictive biomarkers. In addition, the abundance of Prevotella and Bacteroides increased over time and showed significant correlations with key metabolites.<br><br>CONCLUSION: These findings suggest strong interactions between rumen microbiota and host metabolites that may collectively influence FCR, providing new insights into microbial and metabolic regulation of feed efficiency and a theoretical basis for optimizing feeding strategies in sheep.}, }
@article {pmid42227278, year = {2026}, author = {Li, W and Wang, Z and Fu, H and Ma, YR and Gu, Y and Zhuang, JL and Zhao, YX and Liu, YD and Yang, Q and Shapleigh, JP and Jin, RC and Guo, J and Kartal, B and Rittmann, BE}, title = {A Novel Freshwater Anammox Species of Candidatus Loosdrechtia Thriving Under Dual Salinity and Sulfate Stresses.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c03295}, pmid = {42227278}, issn = {1520-5851}, abstract = {Anaerobic ammonium oxidation (anammox) bacteria are key players in the global nitrogen cycle and are widely applied in energy-efficient nitrogen removal processes. However, their activity is often inhibited in saline and sulfate-rich environments. Here, we report the discovery and characterization of Candidatus Loostrechtia thiotolerans (HSAMX1), a novel nonmarine anammox species that became dominant under combined high salinity (3% by weight) and high sulfate concentrations (∼86 mM). Through integrated metagenomic and metatranscriptomic analyses, we reveal the physiological and molecular strategies enabling HSAMX1 to thrive under dual-stress conditions. In response to osmotic stress, HSAMX1 activated ion export systems and subsequently synthesized organic osmoprotectant solutes to maintain cellular homeostasis. It also encoded and strongly expressed the sulfide:quinone oxidoreductase (SQR) gene, which accounted for over 90% of the total community SQR transcription. Intriguingly, HSAMX1 did not emerge under either salinity or sulfate stress alone, suggesting a previously unrecognized niche shaped by the interactions of these two stressors. These findings expand our understanding of nonmarine anammox diversity and identify a promising candidate for nitrogen removal in sulfate-laden, saline wastewater.}, }
@article {pmid42227352, year = {2026}, author = {Pérez-Carrasco, V and Uroz-Torres, D and Soriano-Lerma, A and Soriano, M and García-Salcedo, JA and Arias-Moliz, MT}, title = {Association Between the Root Canal Microbiome and Apical Lesion Size: An Observational Shotgun Metagenomic Study.}, journal = {International endodontic journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/iej.70190}, pmid = {42227352}, issn = {1365-2591}, support = {//European Society of Endodontology/ ; }, abstract = {AIM: The aim was to characterize the taxonomic and functional composition of the microbiome involved in primary endodontic infections and to evaluate their association with the periapical lesion size using shotgun metagenomic sequencing.<br><br>METHODOLOGY: Samples from primary root canal infections diagnosed with apical periodontitis were analysed with shotgun sequencing. Samples were classified according to the lesion size as small (<&#x2009;3&#x2009;mm) or large (>&#x2009;7&#x2009;mm). The bacterial DNA copies in each group were quantified by qPCR. Taxonomic and functional annotations were made using Bracken/Kraken2 and HUMAnN3 software. Species richness, Shannon, Simpson and Pielou indices were used to measure alpha diversity. The similarity of the bacterial communities between study groups was evaluated by Principal Coordinate Analysis based on Bray-Curtis distances. The ALDEx2 package was used to infer the differences between species, and the edgeR package for KEGG pathways. For all statistical analyses, p&#x2009;<&#x2009;0.05 was considered as significant.<br><br>RESULTS: A total of 49 samples were analysed, 27 with small lesions and 22 with large lesions. Species richness and Shannon indices showed differences between both groups, whereas no differences were seen according to Simpson and Pielou indices. A different community composition (PERMANOVA, p&#x2009;=&#x2009;0.0019) was observed between the two groups. Three species were significantly enriched in the large lesion samples, Filifactor alocis, Lachnospiraceae bacterium oral taxon 500 and Olsenella uli, while three others were enriched in small lesion samples, Acinetobacter baumannii, Acinetobacter pittii and Cutibacterium acnes. Functionally, benzoate, flavonoid and steroid degradation, the sphingolipid signalling pathway and proteasome function were enriched in samples with large lesions. Monoterpenoid biosynthesis, phospholipase D signalling, the sulphur relay system and staurosporine biosynthesis were enriched in small lesions.<br><br>CONCLUSIONS: Teeth with large periapical lesions harbour greater bacterial loads and exhibit a more diverse microbial community than those with small lesions. Differences in species-level taxonomic composition were observed between both groups. Functionally, large lesions are enriched in pathways associated with immune evasion and pro-inflammatory activity, whereas small lesions are characterized by pathways related to apoptosis, metabolic adaptation and anti-inflammatory processes. These findings suggest that lesion severity is also shaped by the functional potential of the microbiome to modulate host inflammation.}, }
@article {pmid42227741, year = {2026}, author = {Duan, J and Marques, AD and Hogenauer, M and Hwang, Y and Zhang, Y and Timperman, A and Higgins, S and Wilson, NG and Fitts, EA and Lim, HK and Bittinger, K and Moustafa, AM and Collman, RG and Bushman, FD}, title = {Optimizing methods for virome analysis based on studies of a synthetic viral community.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0018826}, doi = {10.1128/msystems.00188-26}, pmid = {42227741}, issn = {2379-5077}, abstract = {Studies of whole viral populations-the "virome"-are yielding exciting new insights into biological systems, but methods are still being optimized. Here, we describe generation and use of a synthetic viral community and its use to evaluate technical challenges arising in virome analysis. We spiked the mock community into different human sample types, then passed the samples through different virus enrichment protocols and analyzed by Illumina sequencing. Compared with direct metagenomic sequencing, VLP enrichment protocols greatly increased viral read yields from stool and saliva. Four methods for DNA amplification were compared, with three showing over-amplification of small circular ssDNA viruses, most notably GenomiPhi. Studies of viral particle stability in the presence of nuclease showed that most viral genomes were stable when protected in viral particles, but phage MS2 RNA was unexpectedly labile under some of the conditions tested. Comparison of Illumina 1,000-cycle sequencing versus 300-cycle sequencing showed that longer reads supported generation of longer viral genome assemblies. We tested bacteriophage T4 DNA modified with glucosyl-hydroxymethylcytosine (ghmC) and hydroxymethylcytosine (hmC) and found that both were readily detected, though the recovery of ghmC-modified DNA was reduced compared with T4 genomes with unmodified cytosine. These studies together with published data help provide guidance for virome researchers optimizing analytical protocols.IMPORTANCEA challenge in characterizing the human virome in health and disease is identifying optimal methods for enriching the viral content of samples. Due to the tremendous abundance and diversity of viruses, capturing as broad of a range of viruses as possible for analysis is difficult and potentially complicated by unrecognized biases. This report presents the use of a synthetic viral community for methods optimization in virome studies and illustrates the feasibility and challenges of current virus enrichment strategies for high-throughput virome analysis of different human sample types.}, }
@article {pmid42227750, year = {2026}, author = {Becker, DJ and Dyer, KE and Olbrys, BL and Hightower, MG and Allira, M and Demory, B and Lock, LR and Taylor, KN and Bhata, NN and Hernandez, SM and Lawson, PA and Youssef, NH and Miller, SL and Elshahed, MS and Verrett, TB and Clark, KL}, title = {Molecular detection of relapsing fever Borrelia puertoricensis in migratory Mexican free-tailed bats.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0008526}, doi = {10.1128/msphere.00085-26}, pmid = {42227750}, issn = {2379-5042}, abstract = {UNLABELLED: Bats have been increasingly recognized to host relapsing fever borreliae as well as borreliae that form novel clades adjacent to the Lyme borreliosis group. However, the genetic diversity and zoonotic potential of bat-borne borreliae remain poorly understood, in part because most work to date has focused on bats in the tropics. Fewer bat-borne Borrelia surveys have been conducted in temperate zones, where many bats undertake seasonal migrations that may facilitate pathogen dispersal. We surveyed blood from nearly 400 Mexican free-tailed bats (Tadarida brasiliensis) during their seasonal occupancy in Oklahoma, USA, during 2022 and 2023, for Borrelia spp. Targeted PCR of the 16S rRNA and flaB genes revealed high nucleotide identity to Borrelia puertoricensis, and shotgun metagenomics further demonstrated high amino acid identity to strains isolated from argasid ticks and human blood. This represents the first detection of Borrelia puertoricensis in bats and only the second detection within wild vertebrate hosts. Infection prevalence was low but comparable to that of other borreliae in bats. Our findings suggest that Mexican free-tailed bats may contribute to the dispersal of this emerging tick-borne bacterial pathogen in North America.<br><br>IMPORTANCE: Bacteria in the genus Borrelia are primarily spread by ticks and cause either Lyme borreliosis or relapsing fever. Substantial work has demonstrated the degree to which rodents and songbirds can contribute to the enzootic cycles and dispersal of these human diseases, but comparatively less attention has been paid to the role of wild bats, particularly in temperate regions. We here report human-relevant findings from a two-year, seasonal survey of migratory Mexican free-tailed bats (Tadarida brasiliensis) in Oklahoma, USA. We tested nearly 400 bats and identified Borrelia puertoricensis, a relapsing fever species that could infect humans. Importantly, this represents the first detection of Borrelia puertoricensis in bats and only the second detection in wild vertebrate hosts, expanding the known host range of this emerging tick-borne pathogen. Given the known migratory routes of Mexican free-tailed bats, our results have implications for the role that bats may play in tick-borne pathogen dispersal in North America.}, }
@article {pmid42217859, year = {2026}, author = {Qin, W and Zhang, H and Wang, H and Zhou, J and Wang, F}, title = {Pharmaceutical-driven disinfection by-products formation and antibiotic resistance gene enrichment under intensified chlorination during pandemic.}, journal = {Journal of environmental sciences (China)}, volume = {165}, number = {}, pages = {1-10}, doi = {10.1016/j.jes.2025.06.056}, pmid = {42217859}, issn = {1001-0742}, mesh = {Halogenation ; *Disinfection/methods ; *Drug Resistance, Microbial/genetics ; Pandemics ; *Disinfectants ; *Waste Disposal, Fluid/methods ; *Water Pollutants, Chemical/analysis ; *Chlorine ; Anti-Bacterial Agents ; Wastewater/chemistry ; }, abstract = {Intensified chlorine disinfection during pandemic is widely implemented in hospital and municipal wastewaters to inactivate pathogens. However, high concentrations of residual chlorine in treated wastewaters might bring secondary environmental risks. This study investigated the impacts of intensified chlorine disinfection on disinfection by-product (DBP) formation from six commonly used pandemic-related drugs and antibiotic resistance gene (ARG) enrichment in sewage. Results showed that high chlorine dosage of 2000 µmol/L led to DBP yields and estimated toxicity that were 1-2 orders of magnitude higher than those under normal chlorine dosage of 40-100 µmol/L. Intensified chlorine disinfection and drug overuse during the pandemic evidently increased the contribution of drugs as precursors to DBPs formation (29.2 %-78.8 %) in sewage. Two antibiotics emerged as major dichloroacetonitrile precursors, two bromine expectorants dominated haloacetic acids and Br-DBP formation, while two ICMs were critical precursors of iodinated acetamides. These DBPs were the main contributors to the estimated toxicity of the chlorinated drugs. Bromine expectorants produced DBPs with yields and estimated toxicity 1-2 orders of magnitude greater than other drugs. Metagenomic sequencing results showed that low chlorine up-regulated ARGs and related mobile genetic elements, driving ARGs enrichment and horizontal transfer. High chlorine in short term inhibited the total ARGs, but enriched the multidrug resistance gene subtypes related to the efflux/mutation pathway and transfer, thereby selected highly chlorine-resistant bacteria with strong antibiotic resistance. These findings reveal the environmental risks of intensified chlorine disinfection and suggest that optimizing chlorine dosage is crucial to mitigate these environmental risks and protect public health.}, }
@article {pmid42217876, year = {2026}, author = {Xiao, Y and Ouyang, Q and Wen, X and Tong, H}, title = {Coupling mechanisms between microbial arsenic metabolism and carbon cycling in arsenic-contaminated groundwater.}, journal = {Journal of environmental sciences (China)}, volume = {165}, number = {}, pages = {269-276}, doi = {10.1016/j.jes.2025.10.032}, pmid = {42217876}, issn = {1001-0742}, mesh = {*Arsenic/metabolism/analysis ; *Groundwater/chemistry/microbiology ; *Water Pollutants, Chemical/metabolism/analysis ; *Carbon Cycle ; China ; Bacteria/metabolism ; *Water Microbiology ; Carbon/metabolism ; }, abstract = {Microorganisms in groundwater play a critical role in global carbon (C) cycling. However, how arsenic (As) contamination influences microbially mediated As cycling and its coupling with C metabolism remains poorly understood. Herein, we investigated the associative coupling of microbial function genes between As and C cycling in groundwater from a typical As-contaminated industrial site in southern China. Metagenomic analyses revealed that As concentrations governed microbial community assembly, leading to distinct community structures and dominant taxa. Key microbial groups, including Pseudomonadota and Euryarchaeota, exhibited dual metabolic capabilities for both As and C transformation. Compared to the Safe group (As < 10 μg/L), the Toxic group (As > 10 μg/L) displayed greater dissimilarities in the distribution of As- and C-related functional genes. A strong correlation between As- and C-cycling genes suggests a potential trade-off mechanism between microbial As resistance and organic C utilization. Furthermore, microbial function gene-based co-occurrence networks demonstrated more complex and stable network structures in the Toxic group. The enhanced coupling between As-C functional genes likely increased microbial community resilience against environmental stressors. While observed As-C coupling mechanisms may extrapolate to chemically analogous groundwater systems, their quantitative contribution to global C budgets requires validation across diverse biogeographic contexts. This study offers novel insights into the complex coupling network between As and C metabolic pathways in groundwater microbial communities and underscores their broader implications for global biogeochemical C cycling.}, }
@article {pmid42217938, year = {2026}, author = {Dwivedi, S and Agnihotri, R and Kumar, V and Mishra, S and Tiwari, RK and Adhikari, D and Sharma, P and Kumar, S and Verma, T and Gupta, A and Sinam, G and Pandey, V}, title = {Scientific evidence validating spiritual beliefs for controlling pathogenic microbes in the Ganga river.}, journal = {Journal of environmental sciences (China)}, volume = {165}, number = {}, pages = {93-106}, doi = {10.1016/j.jes.2026.01.083}, pmid = {42217938}, issn = {1001-0742}, mesh = {*Rivers/microbiology ; Archaea ; Bacteria ; *Water Microbiology ; Microbiota ; Bacteriophages ; Biodiversity ; }, abstract = {During the Kumbh, the Ganga at the Sangam in Prayagraj, where it meets the Yamuna, showed greater microbial diversity than either river before their confluence. Mass bathing altered the density and diversity of archaea, bacteria, phages and viruses, while fungi, protozoans, cyanobacteria, green algae and diatoms remained largely unaffected. Notably, this study was the first to report archaeal phages, cyanophages and mycophages in the river system. Archaea species richness was higher in the Yamuna (127 spp. during Pre Kumbh), whereas bacterial diversity was greater in the Ganga (2764 spp.). The Ganga exhibited a higher relative abundance of skin, oral and gut archaea and bacteria, except for gut bacteria, which were more prevalent in the Yamuna. Skin and gut archaea showed strong positive correlations with the number of devotees (r = 0.818 and r = 0.870, respectively), while oral archaea were less affected. Pathogenic microbes with high fatality rates were more common in the Yamuna. Variations in archaeal, bacterial, phage and viral communities were influenced by physico-chemical parameters, ion levels, nutrient content and devotee's load. The Ganga exhibited higher phage diversity and a greater phage-to-bacteria ratio than the Yamuna. Hence, phages regulate the pathogenic bacteria through predator-prey dynamics, consequently reducing infection risks. Despite mass bathing by over 100 million devotees, which sharply increased nutrient and pollution levels, no endemic or epidemic outbreaks were reported.}, }
@article {pmid42218119, year = {2026}, author = {Fessler, JL and Olm, MR and Engleman, EG and Sonnenburg, JL}, title = {Integration of donor microbiota following FMT correlates with anti-PD-1 response in melanoma.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73465-7}, pmid = {42218119}, issn = {2041-1723}, support = {R21CA290426//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; }, abstract = {Fecal microbiota transplantation (FMT) has shown promise in improving anti-PD-1 therapy in melanoma, but the underlying microbial features remain poorly defined. We performed a strain-resolved metagenomic meta-analysis across three independent FMT plus anti-PD-1 melanoma trials (n = 41). Across cohorts, therapeutic benefit was linked to successful integration of donor microbiota, rather than increased diversity or engraftment of specific species. Responders acquired more donor-derived strains, exhibited greater post-FMT similarity to their donor, and maintained a more stable microbiome. Following FMT, non-responders' microbiomes showed greater taxonomic instability, larger fluctuations in estimated microbial load, and increased abundance of pathogen-associated secretion system genes, whereas responders showed enrichment for microbial functions involved in community-level metabolism and communication. Finally, shifts in tumor-infiltrating immune profiles tracked with clinical outcomes and microbiome changes. Together these findings highlight that distinct patterns of microbiome restructuring, including stable community transitions and altered functional capacity, are associated with anti-PD-1 response following FMT.}, }
@article {pmid42218218, year = {2026}, author = {Zhu, G and Yang, G}, title = {Multikingdom microbiome-based machine learning enables multiple sclerosis diagnosis.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01030-7}, pmid = {42218218}, issn = {2055-5008}, support = {32571054 and 82371350//National Natural Science Foundation of China/ ; C7014-24GF//Research Grant Council of the Government of Hong Kong SAR/ ; Institute Digital Medicine internal grant (9229501-13-YG)//City University of Hong Kong/ ; }, abstract = {Emerging evidence suggests a role for the gut bacteria in the pathogenesis of multiple sclerosis (MS); however, the role of other microorganisms and their diagnostic potential for MS remain poorly explored. Here, we analyzed large-scale metagenomic data derived from fecal samples (discovery cohort n = 1152; total n = 1306 across 3 geographically diverse cohorts). Subsequently, we utilized multikingdom gut microbiome data to develop machine learning models to distinguish MS patients from healthy controls. Our analysis identified distinct microbiome alterations, revealing 90 bacterial, 3 fungal, 2 viral species, 119 KEGG orthology genes, and 17 metabolic pathways significantly associated with MS. Machine learning models integrating multikingdom taxonomic and functional features achieved the area under the receiver operating characteristic curves (AUCs) of 0.977 for males and 0.978 for females. On external validation datasets, the ensemble models yielded AUCs of 0.813 in males and 0.745 in females, while the 30-marker models reached AUCs of 0.849 and 0.763, respectively. Notably, the accuracy of the model was associated with Faecalibacterium spp. and L-methionine biosynthesis pathways, which were less abundant in MS patients. Collectively, our findings highlight the potential application of multikingdom and functional gut microbiome markers as non-invasive biomarkers for MS.}, }
@article {pmid42218514, year = {2026}, author = {Fabre, V and Robinson, ML and Martino, F and Monge, R and Forastiero, A and Corso, A and Pasteran, F and Karyakarte, R and Randive, B and Singh, S and Naik, M and Prasad, HB and Schwab, KJ and Simner, PJ and Berman, Y and Foy, WI and Salinas, AB and Gupta, A and Lu, J and Vasquez, AM and Noble-Wang, J and Moser, KA and Perry-Dow, KA and Patrick, M and Rock, C}, title = {Environmental reservoirs of carbapenem-resistant organisms in the intensive care unit: a multicenter longitudinal study in two middle-income country hospitals.}, journal = {Antimicrobial resistance and infection control}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13756-026-01768-x}, pmid = {42218514}, issn = {2047-2994}, support = {75D30121D12750/CC/CDC HHS/United States ; }, abstract = {BACKGROUND: There is limited data regarding environmental reservoirs of carbapenem-resistant organisms (CRO) during non-outbreak settings in resource-limited hospitals, or the role of these reservoirs in healthcare transmission.<br><br>METHODS: Prospective longitudinal study in which sinks and high-touch surfaces (HTS) were sampled prior to room cleaning in intensive care units (ICUs) in two hospitals (hospital A, Argentina, and hospital B, India), July 2023-February 2024. Selective media was used to recover CROs. Whole genome sequencing (WGS) and single nucleotide polymorphism (SNP) pairwise analysis were performed on environmental and clinical isolates to evaluate bacterial transmission dynamics. Metagenomic sequencing was performed to evaluate bacterial diversity of environmental samples.<br><br>RESULTS: Of 541 environmental samples collected, 47.9% in hospital A and 97.5% in hospital B grew at least one CRO. Most CROs tested for the presence of a carbapenemase were positive (63.9-91.0% for hospital A and B isolates, respectively). Carbapenemase producer (CP)-Acinetobacter baumannii and CP-Pseudomonas spp. predominated in HTS and sinks samples, respectively, in hospital A; while CP-Klebsiella pneumoniae predominated in hospital B samples. WGS of 113 CRO isolates and SNP analysis demonstrated certain lineages established enduring reservoirs in the ICUs environment (e.g., blaVIM-36 P. aeruginosa ST395 isolates with 2-9 SNP difference were detected in sinks over 7&#xa0;months). Several clusters involving environmental and clinical isolates that shared an epidemiological link and displayed&#x2009;&#x2264;&#x2009;10 SNP difference were identified (e.g., blaOXA-23 A. baumannii ST195 isolated from three unique patients who stayed in the same private room on sampling months 4, 5, 6 and 7, and from HTS of that room on sampling month 5 displayed 0-3 SNP difference). Metagenomic analysis identified additional AMR genes of clinical importance.<br><br>CONCLUSIONS: CROs were abundant and persisted in the ICU environment in countries with high prevalence of MDROs. Our data suggests movement of clones between the environment and patients.}, }
@article {pmid42218533, year = {2026}, author = {Kim, W and Kim, JE and Hong, YS and Hwang, DW and Kim, J and Lee, JS and Shin, JH and Kim, TW and Nagarkar, D and Byrd, A and Sung, CO and Kim, SY}, title = {Dynamics of tumor ecosystems and microbiome in response to neoadjuvant ABFOLFOX treatment in patients with unresectable colorectal cancer with liver metastasis.}, journal = {Genome medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13073-026-01680-4}, pmid = {42218533}, issn = {1756-994X}, support = {ASA-1 project//This work was supported by the imCORE Network on behalf of F. Hoffmann-La Roche (ASA-1 project)./ ; }, abstract = {BACKGROUND: This study aims to explore the effects of neoadjuvant atezolizumab, bevacizumab, leucovorin, 5-fluorouracil, and oxaliplatin (ABFOLFOX) in patients with unresectable colorectal liver metastases (CRLM), focusing on the molecular dynamics of tumor ecosystems (TE) of CRLM and their impact on treatment outcomes.<br><br>METHODS: The study comprises two cohorts with CRLM tissue samples analyzed with RNA sequencing and immunohistochemical staining: cross-sectional cohort A (n&#x2009;=&#x2009;60, CRLM treated with or without neoadjuvant chemotherapy) and prospectively registered cohort B (n&#x2009;=&#x2009;20 with serial sampling and treated with ABFOLFOX). Shotgun metagenomic sequencing was performed for stool samples from cohort B.<br><br>RESULTS: Durable disease control (PFS&#x2009;&#x2265;&#x2009;24 months) was observed in 35% (7/20) of patients receiving ABFOLFOX. Analysis revealed a progressive increase in the immunogenic microenvironment within CRLM tissues upon the addition of therapeutic agents, specifically bevacizumab, and the most significant TE changes in CRLM were observed in those treated with ABFOLFOX in cohort B. The monocyte lineage was significantly associated with benefit from ABFOLFOX. Good responders exhibited improved immune response and notable activation of the SP140 transcription factor regulon. Moreover, microbiome analysis revealed that high abundance of Prevotella was positively correlated with good response and enhanced immune environment within the tumor. Causal mediation analysis suggested that the gut microbiome partially links the ABFOLFOX treatment response to the tumor microenvironment.<br><br>CONCLUSIONS: ABFOLFOX enhances the TE immune profile of CRLM, which is further augmented by the gut-liver axis characterized by Prevotella abundance, and can induce durable disease control in a subgroup of patients.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov, NCT03698461. May 08, 2019 (prospectively registered).}, }
@article {pmid42218921, year = {2026}, author = {Guo, F and Fu, W and Topalović, O and Zhang, Q and Li, K and Li, H and Qing, X}, title = {Genomic insights into nematode microbiomes reveal novel endosymbionts Rickettsiella.}, journal = {Molecular phylogenetics and evolution}, volume = {}, number = {}, pages = {108650}, doi = {10.1016/j.ympev.2026.108650}, pmid = {42218921}, issn = {1095-9513}, abstract = {BACKGROUND: Bacterial endosymbionts are key drivers of invertebrate ecology and evolution. While the diversity and functional role of the nematode microbiome remain poorly explored.<br><br>METHODOLOGY: We reconstructed and characterized 108 metagenome-assembled genomes from 10 published and 15 newly sequenced nematode genomes.<br><br>PRINCIPAL FINDINGS: We report the first evidence of Rickettsiella in nematodes and discovered novel endosymbionts Cardinium and Wolbachia in plant-parasitic nematodes. The nematode microbiome is enriched with genes for carbohydrate metabolism and the biosynthesis of essential amino acids and vitamins, indicating a potential primary role in host nutrition. Notably, mobile genetic elements like prophages and insertion sequences (IS) are widespread and carry passenger genes involved in vitamin biosynthesis, suggesting horizontal gene transfer facilitates metabolic adaptation. Genomic reduction in the nematode Rickettsiella lineage, reveals extensive gene loss, particularly in amino acid biosynthesis. Crucially, we find no evidence of purifying selection on its residual nutritional pathways, and thus cannot clearly support a mutualistic role for this association.<br><br>CONCLUSION: Our findings expand the known host range of major endosymbiont groups and reveal a spectrum of symbiotic relationships in nematodes, from putative mutualism driven by nutritional supplementation to associations with neutral or parasitic traits, shaped by pervasive horizontal gene transfer and reductive genome evolution.}, }
@article {pmid42219044, year = {2026}, author = {Shil, S and Dutta, SP and Banerjee, D and Paul, S and Khatua, A and Chowdhury, J and Koner, GS and Das, AK and Mukherjee, A and Karmakar, UK and Haldar, S and Debnath, A}, title = {Hypervariable region-specific detection of an avian gut pathobiont in multi-primer 16S rRNA metagenomics: the V9 region identifies Gallibacterium anatis undetected by conventional V3-V4 approaches.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {107565}, doi = {10.1016/j.mimet.2026.107565}, pmid = {42219044}, issn = {1872-8359}, abstract = {Hypervariable region (V-region) selection critically determines which taxa are resolved in 16S rRNA amplicon surveys, yet most commercial poultry gut microbiome studies rely on the V3-V4 primer pair optimised for Illumina short-read platforms. The Ion GeneStudio S5 Prime with multi-primer 16S chemistry simultaneously amplifies six variable regions (V2, V3, V4, V67, V8, V9) from a single library, providing an unprecedented opportunity to benchmark region-specific taxonomic resolution in the same sample set without inter-library bias. 29 commercial broiler caecal samples (HEALTHY n = 10; DISEASED n = 19) were analysed per-V-region on the Ion GeneStudio S5 Prime using the Ion 16S Metagenomics Kit, yielding 46,542 classified reads distributed across six V-regions. From a total sequencing depth of 342,716-1,358,797 reads per sample. Independent ASV-level validation was performed using QIIME2 v2024.10 DADA2 (738 ASVs, SILVA 138), confirming all primary findings. V3 contributed the highest read volume (14,818 reads, 31.8%) and resolved the most genera (52 unique). V9 contributed the fewest reads (2831, 6.1%) but the highest number of region-exclusive genera (11), including the avian pathobiont Gallibacterium anatis. Critically, 121 of 220 total G. anatis reads (55%) were recovered exclusively via V9 primers; zero G. anatis reads were detected by V3 across all 29 samples.". In a parallel differential abundance analysis, G. anatis was the most significantly enriched taxon in diseased caecal microbiota (DESeq2 padj = 1.45 × 10[-6]), a finding that would have been entirely missed by a conventional V3-V4 workflow. In silico analysis of one of the samples from this set, found G. anatis (GenBank PX986441.1) confirmed absence of the 341F primer binding site. Mean sequence identity was uniformly high across all regions (98.74-99.05%), confirming that V9 underperformance is a coverage rather than quality issue. These findings demonstrate significant primer bias in single-region 16S workflows applied to poultry gut microbiome research, with direct implications for diagnostic assay design and pathobiont surveillance programmes.}, }
@article {pmid42219122, year = {2026}, author = {Wang, X and Huang, Y and Xu, J and Lin, B and Chen, X and Li, ZH}, title = {Exogenous floc-granule replacement stabilizes aerobic granular sludge via quorum sensing/quorum quenching-mediated ecological reorganization.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {135039}, doi = {10.1016/j.biortech.2026.135039}, pmid = {42219122}, issn = {1873-2976}, abstract = {Aerobic granular sludge (AGS) operation remains constrained by excessive granule enlargement, particle-size redistribution, and structural instability. In this study, exogenous floc-granule replacement was evaluated as a chemical-free, in situ particle-size management strategy for AGS. A conventional granulation reactor (R1) and an exogenous floc-granule replacement reactor (R2) were operated in parallel to compare granulation dynamics, reactor performance, extracellular polymeric substances (EPS), extracellular acyl-homoserine lactones (AHLs), respiration, bacterial partitioning, metagenomic functional gene profiles, and microbial co-occurrence patterns. During the first replacement window, R2 maintained smaller and more uniform granules than R1, with mean particle size of 220 μm on Day 83 compared with 378 μm in R1. R2 also maintained comparable chemical oxygen demand and NH4[+]-N removal performance and showed lower nitrite accumulation during rapid granulation. Particle-size regulation was accompanied by lower extracellular AHL accumulation, altered EPS composition, and distinct respiratory allocation, reflecting higher autotrophic-to-heterotrophic respiration ratio in R2 than in R1 on Day 82 (0.10 vs. 0.07). Comparative characterization indicated that exogenous flocs represented a distinct biomass fraction with smaller particle size, lower protein-to-polysaccharide ratio, and lower extracellular AHL accumulation than endogenous flocs and mature granules. Metagenomic and co-occurrence network analyses showed higher abundance of quorum quenching (QQ)-related genes and greater representation of QQ- or combined quorum sensing /QQ-associated taxa in R2. Overall, exogenous floc-granule replacement represents a tunable structure-based strategy for regulating AGS particle-size distribution, but its effectiveness should be further evaluated according to application scenario.}, }
@article {pmid42219517, year = {2026}, author = {Velando, F and Molina, L and Hurtado, I and van Dillewijn, P and Segura, A}, title = {Aeonium decorum as a microbial recruitment platform for atmospheric polycyclic aromatic hydrocarbons mitigation in urban gardens.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00914-7}, pmid = {42219517}, issn = {2524-6372}, abstract = {BACKGROUND: In the context of the Sustainable Architecture, green roofs, green walls, green belts or urban farms are becoming popular infrastructures in cities and have been proposed as promising elements to ameliorate air pollution. Atmospheric contaminants are deposited not only on the foliar surface of plants, but also in soils. Plants may interact with pollutants, but their associated microbiomes (epiphytic, endophytic and rhizospheric) may harbor contaminant-degrading bacteria which could play an important role in pollutant mitigation. Therefore, we explored the effects of atmospheric contaminants, using naphthalene as a model compound, on some of the living elements of urban gardens (plants and microbiomes).<br><br>RESULTS: Exposure to gaseous naphthalene had weak effects on Aeonium decorum and Trifolium repens plants (measured as efficiency of photosystem II), and on soil bacterial diversity. Although the presence of naphthalene is not the major driver of soil bacterial community structure, metagenomic and qPCR analysis revealed an increase in polycyclic aromatic hydrocarbon (PAH)-ring hydroxylating dioxygenases in Aeonium planted soils, suggesting a positive effect of this plant species for the selection of potential contaminant-degrading microbes. We have also observed an increment in Pseudomonas (known for their capacity to degrade contaminants) and Solimonas in response to naphthalene. Validation of tools designed to evaluate the exposure of plants to atmospheric contaminants was performed creating urban gardens planted with A. decorum plants and exposed to environmental conditions.<br><br>CONCLUSIONS: Our results suggest that Pseudomonas and Solimonas could be used as markers for biodegradation. A. decorum is proposed as a good candidate for amelioration of atmospheric contaminants and gardens constructed with these plants carried PAH degrading bacteria on leaf surfaces indicating that they have the capacity to respond to the presence of contaminants.}, }
@article {pmid42219665, year = {2026}, author = {Recio, MI and de la Torre, J and Rocha-Martin, J and de la Mata, I and Ramos, JL}, title = {A Biotechnological Approach to Enzyme-Based Fertilisers: Immobilisation of Acid Phosphatases.}, journal = {Microbial biotechnology}, volume = {19}, number = {6}, pages = {e70385}, doi = {10.1111/1751-7915.70385}, pmid = {42219665}, issn = {1751-7915}, support = {PID2021-123469OB-IOO//Agencia Estatal de Investigaci&#xf3;n/ ; MICIU/AEI/10.13039/501100011033//Agencia Estatal de Investigaci&#xf3;n/ ; PREDOC_01447//Consejer&#xed;a de Conocimiento, Investigaci&#xf3;n y Universidad, Junta de Andaluc&#xed;a/ ; }, mesh = {*Acid Phosphatase/metabolism/chemistry ; *Enzymes, Immobilized/metabolism/chemistry ; Hydrogen-Ion Concentration ; Enzyme Stability ; Clay ; *Fertilizers/analysis ; Aluminum Silicates/chemistry ; *Biotechnology/methods ; Temperature ; Soil/chemistry ; }, abstract = {We explore enzyme-based technologies as sustainable alternatives to conventional chemical fertilisers, addressing the challenges associated with using enzymes in free or immobilised form for agricultural applications. We use the metagenome-derived Class A acid phosphatase M2-32, selected for its high activity, broad pH tolerance and thermophilic properties, and evaluated its immobilisation on clay minerals to enhance stability and applicability in soils. Several clays were tested as immobilisation supports. Bentonite caused complete enzyme inactivation, while kaolin formed aggregates and was unsuitable. In contrast, palygorskite, sepiolite and agrozeolite adsorbed more than 99% of the added enzyme. However, only a fraction of the immobilised enzyme retained catalytic activity, with optimal performance observed at moderate protein loading (40-80 μg protein). Among the tested supports, palygorskite consistently provided the highest specific activity (22,000 ± 2200 U/mg), followed by sepiolite (11,000 ± 730 U/mg), whereas agrozeolite (2250 ± 40 U/mg) showed comparatively low activity. ATR-FTIR spectroscopy confirmed successful enzyme immobilisation without significant alteration of the clay structures. Immobilised M2-32 preserved a broad pH range (between 4 and 8.5) and thermophilic behaviour similar to the free enzyme, remaining active up to 50°C. Immobilisation increased substrate affinity while reducing Vmax relative to the free enzyme. To assess environmental compatibility, the effects of free and palygorskite-immobilised M2-32 on soil microbial communities were evaluated using corn rhizosphere microcosms with different organic matter contents. Metabarcoding high-throughput sequencing revealed that microbial diversity and community structure were primarily shaped by soil type, plant presence and incubation time. Enzyme application, whether free or immobilised, did not significantly alter microbial diversity or composition. Overall, these results support palygorskite-immobilised M2-32 as a promising, environmentally compatible candidate for enzyme-based fertiliser development.}, }
@article {pmid42219690, year = {2026}, author = {Zhu, P and Yuan, X and Wang, X and Shi, Y}, title = {Application of Nano Silica Is Associated With Enhanced Wheat Resistance to Fusarium Crown Rot via Regulation of Metabolic Pathways and Soil Microbial Community.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70343}, doi = {10.1111/1462-2920.70343}, pmid = {42219690}, issn = {1462-2920}, support = {SDAIT0107//Shandong Modern Agricultural Technology &amp; Industry System/ ; SDNYXTTG-2023-30//Agricultural Major Technology Collaborative Promotion Plan Project in Shandong Province/ ; }, mesh = {*Triticum/microbiology ; *Fusarium/physiology ; *Soil Microbiology ; *Silicon Dioxide/pharmacology ; Metabolic Networks and Pathways/drug effects ; *Microbiota/drug effects ; *Plant Diseases/microbiology/prevention &amp; control ; *Disease Resistance/drug effects ; Lignin/metabolism ; *Nanoparticles ; }, abstract = {Nano silica (NS) has promising agricultural applications, yet its effects and mechanisms in enhancing wheat resistance to Fusarium crown rot (FCR) caused by Fusarium pseudograminearum (FP) remain underexplored. Here, we conducted a pot experiment with 200 mg/L NS, integrating soil metagenomics, plant physiology, and metabolomics to investigate this process. Soil metagenomic analysis revealed that NS was associated with reshaped microbial community structure and distinct functional pathway variations (GO/KEGG annotations). In wheat, NS treatment was linked to activated fructose/mannose metabolism and phenylpropanoid biosynthesis, increasing SOD and POD activities by 14.5% and 169.9% and reducing MDA content by 37.0%. It was also associated with upregulated lignin-related enzymes (PAL, C4H, and 4CL) and their encoding genes, thus promoting lignin accumulation, enhancing stem strength, and restoring cellulose content. Our findings suggest a potential dual mechanism: NS-associated soil microbiome changes coincide with improved plant antioxidant capacity and defence gene expression, reinforcing stem integrity to alleviate FCR, providing new insights for eco-friendly FCR management.}, }
@article {pmid42219901, year = {2026}, author = {Yang, J and Shi, T and Du, Z and Wang, Y and Shen, J and Wu, C and Fu, B}, title = {Sub-inhibitory polyether ionophores enhance resistance plasmid transfer and transiently perturb the broiler gut resistome.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {81}, number = {6}, pages = {}, doi = {10.1093/jac/dkag190}, pmid = {42219901}, issn = {1460-2091}, support = {32141002//National Natural Science Foundation of China/ ; 81991535//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Ionophores/pharmacology/administration &amp; dosage ; *Plasmids/genetics ; Chickens/microbiology ; Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/drug effects ; *Drug Resistance, Bacterial/genetics/drug effects ; Polyether Compounds ; Cecum/microbiology ; *Gene Transfer, Horizontal/drug effects ; *Bacteria/drug effects/genetics ; Polyether Polyketides ; Conjugation, Genetic/drug effects ; Pyrans ; }, abstract = {BACKGROUND: Chronic sub-inhibitory antimicrobial exposures may shape antibiotic resistance (AMR) dissemination at the animal, food and environment interface. Polyether ionophore coccidiostats remain widely used in poultry production, yet their influence on AMR dissemination at sub-inhibitory exposure is unclear.<br><br>OBJECTIVES: To determine whether sub-minimum inhibitory concentration (MIC) polyether ionophores enhance resistance plasmid transfer in vitro and to characterize their effects on gut microbiota and resistome dynamics in vivo during and after administration.<br><br>METHODS: We investigated the effects of representative polyether ionophores at sub-MICs on resistance spreading phenotypes in vitro and gut resistome dynamics in VREfm-challenged broilers. In vitro plasmid conjugation and related phenotypes were quantified, and in vivo caecal microbiota and resistome were profiled by 16S rRNA gene sequencing and shotgun metagenomics.<br><br>RESULTS: Sub-MIC polyether ionophores increased plasmid conjugation, copy number and biofilm formation in Enterococcus spp., whereas no comparable effects were observed in Escherichia coli. In vivo, salinomycin temporarily disrupted caecal microbiota development and, at Day 20, suppression of indigenous taxa (e.g. Faecalibacterium) was accompanied by a transient surge in VREfm colonization and vanA abundance; resistome expansion was non-persistent. After salinomycin cessation, recovery of beneficial genera like Akkermansia was associated with reduction of the total resistance gene burden towards pre-treatment baseline by Day 42.<br><br>CONCLUSIONS: Polyether ionophores can promote resistance dissemination phenotypes in vitro, but gut ecological resilience may limit long-term impacts after cessation of exposure under recommended dosing conditions. The transient resistome surge during the treatment suggests increased shedding and potential environmental dissemination via manure, warranting surveillance and risk assessment.}, }
@article {pmid42221085, year = {2026}, author = {Liu, F and Yang, K and Wu, M and Li, P and Luo, L}, title = {Case Report: Basal ganglia brain abscess caused by Nocardia farcinica.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1798434}, pmid = {42221085}, issn = {2296-858X}, abstract = {We report a rare case of Nocardia farcinica brain abscess in the basal ganglia, detailing its diagnosis, management, and rehabilitation. Diagnosing brain abscess based solely on clinical and imaging findings remains extremely challenging. Fortunately, metagenomic next-generation sequencing (mNGS) proved valuable in this case by rapidly identifying the pathogen, thereby facilitating targeted antibiotic therapy. This case highlights the importance of differentiating brain abscess from ischemic stroke and intracranial tumors. After completing a full course of anti-infective therapy and comprehensive rehabilitation, the patient achieved significant recovery in activities of daily living (ADL).}, }
@article {pmid42221483, year = {2026}, author = {Yang, H and Liu, S and Chen, X and Yin, C and Xiao, L and Xu, W and Lv, S and Xie, L and Yin, C}, title = {Gut microbiota-associated immunomodulation contributes to the protective effects of fluvastatin against endometriosis in a mouse model, accompanied by increased Akkermansia muciniphila abundance.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1762444}, pmid = {42221483}, issn = {1664-302X}, abstract = {BACKGROUND: Endometriosis (EMs) is a chronic inflammatory disease characterized by tumor-like growth behavior and limited therapeutic options. Increasing evidence suggests that gut microbiota may contribute to EMs progression by promoting chronic inflammation and immune dysregulation. Fluvastatin, a lipid-lowering agent, exhibits anti-inflammatory, anti-tumor, and immunomodulatory effects and has also been reported to influence microbial homeostasis. However, the relationship among fluvastatin treatment, gut microbiota, and EMs progression remains unclear. This study aimed to investigate this relationship.<br><br>MATERIALS AND METHODS: A mouse model of EMs was established by autologous uterine tissue transplantation, followed by oral fluvastatin administration for 3 weeks. Lesion growth, inflammatory responses, and immune characteristics were evaluated by histology, quantitative PCR, flow cytometry, immunofluorescence, and immunohistochemistry. Gut microbiota involvement was assessed using antibiotic-mediated microbiota depletion and fecal microbiota transplantation (FMT). Microbial composition was analyzed by metagenomic sequencing. The role of Akkermansia muciniphila was evaluated by direct oral supplementation.<br><br>RESULTS: Fluvastatin significantly reduced the volume and mass of ectopic lesions and decreased the mRNA expression of pro-inflammatory cytokines. It was also associated with changes in macrophage polarization-related markers and reduced abnormal activation of splenic immune cells. Antibiotic-induced gut microbiota depletion attenuated the protective effects associated with fluvastatin treatment, whereas FMT from fluvastatin-treated mice partially transferred similar protective changes. Metagenomic analysis revealed that fluvastatin reshaped gut microbiota composition and increased the abundance of Akkermansia muciniphila. Moreover, oral supplementation with Akkermansia muciniphila attenuated EMs progression and was associated with anti-inflammatory and immune-related changes similar to those observed after fluvastatin treatment.<br><br>CONCLUSION: These findings suggest that the protective effects associated with fluvastatin treatment are accompanied by changes in gut microbiota composition, including increased abundance of Akkermansia muciniphila. Gut microbiota may contribute to the beneficial effects of fluvastatin in EMs. These results support the potential value of microbiota-informed therapeutic strategies for EMs.}, }
@article {pmid42221497, year = {2026}, author = {Taussig, R and Peralta, R and Bustamante, JP}, title = {A pilot proof-of-concept study of microbial and botanical diversity in honey samples from Necochea, Argentina.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1833002}, pmid = {42221497}, issn = {1664-302X}, abstract = {INTRODUCTION: Honey is a complex biological matrix containing plant-derived, microbial, and viral components that reflect both environmental and hive-associated processes. Traditional methods for determining botanical origin, such as melissopalynology, have limitations in resolution and scope. In this context, untargeted shotgun metagenomics emerges as a promising integrative approach for comprehensive honey characterization.<br><br>METHODS: This pilot study explored the feasibility of applying an untargeted shotgun metagenomic approach to honey samples from Necochea, Buenos Aires province, Argentina. Two honey samples and a pollen control sample from Rosa chinensis were subjected to DNA extraction, shotgun library preparation, and sequencing on an Illumina NextSeq 500 platform.<br><br>RESULTS: The control sample showed exclusive assignment to Rosa chinensis, supporting the validity of the analytical workflow. In both honey samples, plant-derived sequences were predominantly assigned to Helianthus annuus (common sunflower) and Eucalyptus grandis (rose gum), consistent with the regional flora. Key bacterial taxa included Paenibacillus larvae in one sample, Acinetobacter johnsonii in the other, and Apilactobacillus kunkeei, Bradyrhizobium sp., Sphingobium yanoikuyae, and Stutzerimonas stutzeri in both. Apis mellifera filamentous virus was detected in both samples.<br><br>DISCUSSION: Given the limited sample size, these findings should be interpreted as exploratory and hypothesis-generating. Nevertheless, this proof-of-concept supports the potential of untargeted metagenomics as an integrated tool for the simultaneous characterization of botanical origin, microbial communities, and viral content in honey, offering advantages over targeted amplicon-based approaches. Future studies with larger and systematically designed cohorts will be necessary to validate and extend these observations.}, }
@article {pmid42221499, year = {2026}, author = {Chang, N and Li, N and Li, W and Xue, J and Zheng, Y and Zhao, C and Zhang, S and Zhang, Y and Yin, G and Bao, M and Shen, W}, title = {Control efficacy and groundwater risk of antibiotic resistance genes in semi-arid landfill leachate treatment: seasonal insights and engineering implications.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1807935}, pmid = {42221499}, issn = {1664-302X}, abstract = {Landfill leachate is a critical reservoir of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), posing prominent risks to groundwater, especially in semi-arid regions. This study focused on the performance of landfill leachate treatment system in Hohhot (Inner Mongolia, semi-arid region), investigating the seasonal variation across three seasons (spring, summer, and autumn), migration characteristics, and control effect of ARGs/MGEs through process optimization-oriented monitoring. Metagenomic sequencing was employed to analyze four key matrices (raw leachate, ultrafiltration effluent, treated leachate, and adjacent groundwater) across three seasons. The treatment system achieved efficient removal of conventional pollutants but failed to eliminate ARGs, MGEs, and antibiotic-resistant bacteria. Instead, it enriched high-risk hosts (e.g., Pseudomonas_E) and transposases (e.g., tnpA), exacerbating horizontal gene transfer potential. ARGs abundance showed pronounced peaks in summer and autumn among the sampled seasons. Notably, the resistome profile of treated leachate was highly similar to that of groundwater, indicating incomplete ARG containment and hydrological connectivity between the treatment system and groundwater. A dual-track health-environmental risk framework was applied to the detected ARG subtypes, revealing that overall risk burden was concentrated in a small set of high-priority determinants. The top contributors were dominated by mobility- and co-selection-linked markers (intI1, tnpA, IS6100, IS26, and qacE△1) together with clinically relevant resistance genes (sul1, aacA, and aadA), underscoring the coupling between resistance functions and genetic mobility in the leachate-groundwater continuum. Collectively, these findings indicate that semi-arid landfill systems can act as both sinks and sources of high-risk resistance determinants, and they highlight the need to integrate ARGs/MGEs-targeted treatment upgrades, seasonally adaptive operational strategies, and risk-based dual-track monitoring into leachate management. This study therefore provides actionable engineering insights for optimizing leachate treatment performance and mitigating cross-media contamination in water-scarce environments.}, }
@article {pmid42221583, year = {2026}, author = {David Hanna, LB and Steinig, E and Bond, K and Lim, CK and Ramachandran, PS}, title = {Enrichment techniques for clinical metagenomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1723747}, pmid = {42221583}, issn = {2235-2988}, mesh = {*Metagenomics/methods ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; Polymerase Chain Reaction/methods ; CRISPR-Cas Systems ; }, abstract = {Metagenomic next-generation sequencing (mNGS) offers a powerful, hypothesis-free approach for pathogen detection in clinical samples, allowing the identification of both known and novel microorganisms. However, the predominance of host nucleic acid in most samples poses a significant challenge, often overshadowing low-abundance pathogen sequences and increasing the cost of mNGS due to the high sequencing depth required. Enrichment techniques which selectively amplify pathogen-specific sequences can help to overcome this challenge, improving the sensitivity, specificity, and overall efficiency of mNGS - albeit while compromising the hypothesis-free nature and breadth of shotgun mNGS. As such, they can augment the use of mNGS in clinical scenarios where a more targeted approach is needed. This review provides a comprehensive analysis of the main enrichment techniques currently employed in the field, including PCR-based enrichment, CRISPR-Cas9 enrichment, molecular inversion probes (MIP), nanopore adaptive sequencing (AS), and hybridisation capture-based methods. We evaluate each method on a range of metrics including methodology, cost, sensitivity, specificity, and ease of integration into clinical workflows, as well as describing their application to date for purposes including pathogen detection, antimicrobial resistance profiling, and whole-genome sequencing across diverse clinical sample types. Current limitations and future directions for refinement and implementation of these techniques are also discussed. By summarising the current landscape and latest advancements in mNGS enrichment strategies, this review aims to guide the optimisation of mNGS workflows in clinical diagnostics and highlight key areas for future research.}, }
@article {pmid42221911, year = {2026}, author = {Gazulla, CR and Ferrera, I and Balagué, V and Marín-Vindas, C and González-Vega, A and Escánez-Pérez, J and Fraile-Nuez, E and Arrieta, JM and Gasol, JM and Sánchez, O}, title = {Diversity and community structure of aerobic anoxygenic phototrophic bacteria are shaped by the deep chlorophyll maximum.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag076}, pmid = {42221911}, issn = {2730-6151}, abstract = {The surface ocean exhibits strong vertical gradients in light irradiance, nutrients, and temperature, shaping the phytoplankton distribution, which often defines a deep chlorophyll maximum (DCM). Aerobic anoxygenic phototrophic (AAP) bacteria inhabit the euphotic zone, with their abundances generally following the chlorophyll a variability. While AAP bacterial communities are known to differ across regions with contrasting environmental conditions, their vertical distribution remains poorly understood. We hypothesized that the diversity and community structure of AAP bacteria vary across the vertical gradient, in relation to changes in environmental variables and following the DCM profile. To test this hypothesis, we studied the composition of AAP communities at different depths along the DCM structure in the South and Central Atlantic Ocean, by means of amplicon sequencing of the pufM gene. The results show significant differences in richness, community structure, and taxonomic composition of samples from different layers of the DCM, highlighting the dependence of AAP bacteria on its structure. Remarkably, the use of primers with broad phylogenetic coverage enabled the recovery of several AAP phylogroups previously detected only through metagenomics. We show that they represent a significant fraction of marine AAP communities, provide clues about their ecological preferences, and confirm their association with the family Candidatus Luxescamonaceae.}, }
@article {pmid42222018, year = {2026}, author = {Ye, J and Ye, L and Sun, W and Xie, S and Lai, Z}, title = {A case of infective endocarditis caused by Streptococcus gordonii complicated with bacterial meningitis and cerebral infarction -- Application of metagenomic next-generation sequencing (mNGS).}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02608}, pmid = {42222018}, issn = {2214-2509}, abstract = {This study reports a case of infective endocarditis (IE) caused by Streptococcus gordonii. The patient presented with cerebral infarction as the initial manifestation, complicated by bacterial meningitis and mitral regurgitation. The diagnosis of Streptococcus gordonii-induced infective endocarditis was facilitated by metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF). Streptococcus gordonii was detected by CSF mNGS within 40 h after admission, which was 30 h earlier than the positive result of blood culture. During anti-infective therapy, the patient experienced recurrent thromboembolic events and underwent emergency mechanical thrombectomy due to occlusion of the left vertebral artery. Despite aggressive treatment, the patient eventually died of heart failure. This case indicates that Streptococcus gordonii is a rare pathogen of infective endocarditis, and its clinical presentation complicated by cerebral infarction and bacterial meningitis is distinctive; particularly, complex cases requiring mechanical thrombectomy are extremely rare in clinical practice. As an important complement to conventional bacterial culture, mNGS can shorten diagnostic delay, especially in patients with negative blood or CSF cultures. For patients with concurrent cerebral infarction and meningitis, the possibility of infective endocarditis should be highly suspected, and indications for valve replacement surgery should be evaluated as early as possible in high-risk cases.}, }
@article {pmid42222019, year = {2026}, author = {Wang, F and Xie, C and Zhao, M and Pan, Y and Xie, Y and Wang, X and Zhu, W and Xie, Y}, title = {VV-ECMO-supported management of severe ARDS secondary to melioidosis sepsis: A case report and concise review.}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02612}, pmid = {42222019}, issn = {2214-2509}, abstract = {Melioidosis, caused by Burkholderia pseudomallei (B. pseudomallei), is a life-threatening tropical infection that is frequently underdiagnosed because of its heterogeneous and nonspecific clinical presentation. We report a critically ill patient from an endemic area who developed fulminant pneumonia that progressed to septic shock and severe acute respiratory distress syndrome. Despite empirical broad-spectrum antimicrobial therapy, respiratory failure worsened, prompting early etiologic investigation with metagenomic next-generation sequencing, which identified B. pseudomallei and was subsequently confirmed by culture. The patient required early venovenous extracorporeal membrane oxygenation (ECMO) for refractory hypoxemia. Management included a targeted antimicrobial therapy in accordance with current guidelines and CT-guided drainage of a pulmonary abscess as definitive source control. The patient achieved full recovery without recurrence at follow-up. Early identification of the causative pathogen and timely source control were central to the management of melioidosis-associated severe ARDS. Advanced supportive measures, including ECMO, may be considered in selected patients with refractory hypoxemia as part of management involving multiple specialties.}, }
@article {pmid42222035, year = {2026}, author = {Liu, YH and Fang, SR and Chen, W and Wu, YF and Liu, DK and Li, T}, title = {Comparative Study of Confirmed versus Suspected Cases of Vibrio vulnificus Infection in Chaoshan District, Guangdong, China.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {613123}, pmid = {42222035}, issn = {1178-6973}, abstract = {OBJECTIVE: To compare the epidemiological, clinical, and laboratory data of patients with confirmed and suspected Vibrio vulnificus infection in Chaoshan District, Guangdong.<br><br>METHODS: This retrospective study analyzed 25 confirmed cases and 23 suspected cases of V. vulnificus infection at the First Affiliated Hospital of Shantou University Medical College from January 2014 to December 2025. A confirmed case was defined by the presence of a positive result from culture and/or mNGS and a suspected case by the experience of a clear marine trauma followed by rapidly progressive soft tissue manifestations, but without etiological confirmation of V. vulnificus infection after exclusion of other infectious etiologies. The epidemiological history, early clinical manifestations, routine blood parameters, and in-hospital outcomes of the two groups were compared.<br><br>RESULTS: The confirmed group had a greater severity of soft tissue infection (84.0% vs 26.0%, P<0.01) and more involved sites (88.0% vs 47.8%, P<0.01). The laboratory data indicated the confirmed group had more abnormalities in markers of tissue injury (creatinine kinase, lactate dehydrogenase), coagulation function (platelets, prothrombin time, international normalized ratio), liver function (aspartate transaminase, total bilirubin), renal function (serum creatinine), and lipid and nutritional markers (all P<0.05). The confirmed group also had significantly higher rates of in-hospital mortality (32.0% vs 0%), multi-organ dysfunction syndrome (36.0% vs 0%), and surgical intervention (60.0% vs 30.4%), and a greater economic burden (all P<0.001).<br><br>CONCLUSION: There are significant differences in the early clinical manifestations, routine blood parameters, and in-hospital outcomes for patients with confirmed and suspected V. vulnificus infection.}, }
@article {pmid42222136, year = {2026}, author = {Crippen, TL and Kim, D and Swiger, SL and Anderson, RC}, title = {Protist community sites and structure under two barn management systems at a commercial dairy.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1803341}, pmid = {42222136}, issn = {2813-4338}, abstract = {INTRODUCTION: Investigations into the location and load of protists in the environment arounddairies are scarce but are essential to maintaining the health of livestock.Moreover, the design of dairy barns has fluctuated over the decades to maximizecattle health and milk production without regard to influences on environmentalmicrobiomes. Beyond cost, the major emphasis of barn design is the managementof appropriate temperature and comfort for cattle. However, there havebeen no corresponding investigations into whether these design changes affect protist communities within barns.<br><br>METHODS: In this study, community shotgun metagenomic analysis was used to define the spatial composition and relative abundance of protist communities from 118 samples of manure, lagoons, troughs, and house and stable flies at a commercial dairy implementing two free-stall management systems: flow-through and cross-vent. Sequence reads were mapped to the CosmosID database. Viability was not assessed; therefore, results reflect DNA detection only not viability or disease occurrence.<br><br>RESULTS: The protist composition differed significantly between dairy components. Ecological findings showed that troughs and lagoons harbored high protist diversity, including the possible pathogen Neobalantidium coli and potential carriers Paramecium biaurelia and Acanthamoeba. Manure had the lowest protist diversity. Stable flies carried more protist taxa than house flies. Both fly species uniquely carried the non-pathogenic alveolate parasite Hammondia hammondi. The water mold plant pathogen Pseudoperonospora cubensis was identified in all sample types. Of the total relative abundance of protists, 2.10% were amoebas, 7.63% alveolate parasites, 62.71% water molds, 23.31% ciliates, 1.74% foraminifera, and 2.50% diatoms.<br><br>DISCUSSION: These results describe preliminary spatial overlaps and possible avenues of dissemination, providing a basis for assessing appropriate management systems and identifying protist reservoir sites within dairy operations.}, }
@article {pmid42222213, year = {2026}, author = {Zhou, Y and Lai, Y and Zhou, F and Wang, X and He, X and Jin, J and Zhang, R}, title = {Morphological analysis of bronchoalveolar lavage fluid in diagnosing pulmonary aspergilloma in a patient with rheumatoid arthritis: A case report.}, journal = {Experimental and therapeutic medicine}, volume = {32}, number = {1}, pages = {191}, pmid = {42222213}, issn = {1792-1015}, abstract = {Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disorder that primarily affects the joints and may be associated with systemic complications. Patients with RA have an increased susceptibility to opportunistic infections, attributable to inherent immune dysregulation as well as immunosuppressive therapies, including tocilizumab, particularly among those with comorbidities or high disease activity. Notably, the use of tumor necrosis factor inhibitors, such as adalimumab and etanercept, has been associated with a higher incidence of invasive pulmonary aspergillosis and chronic pulmonary aspergillosis. The present study reports a rare case of pulmonary aspergilloma in a 75-year-old female RA patient with prior tuberculosis and long-term tocilizumab use. The patient was diagnosed via bronchoalveolar lavage fluid morphology, fungal culture, Aspergillus galactomannan assay, metagenomic next-generation sequencing and pathology, and the patient achieved symptom resolution and improved imaging after 6 months of treatment with voriconazole. These findings underscore the need for vigilant monitoring and individualized management strategies in this patient population.}, }
@article {pmid42222492, year = {2026}, author = {Tran, TTT and Nguyen, OTK and Hoang, PH and Nguyen, NP and To, HTM and Nguyen, HQ}, title = {Metagenomic and metabolomic analyses of fecal samples from civet-digested coffee in Vietnam.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e21262}, pmid = {42222492}, issn = {2167-8359}, mesh = {*Feces/microbiology/chemistry ; Vietnam ; *Coffee/metabolism/microbiology ; *Metabolomics ; *Metagenomics ; *Gastrointestinal Microbiome/genetics ; Fermentation ; Humans ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/metabolism ; Animals ; }, abstract = {BACKGROUND: Civet-digested coffee originates from the feces of civets that consume coffee cherries, where microbial fermentation in the gastrointestinal tract imparts distinctive flavor attributes, thereby enhancing its global reputation and market value. Gut microbiota is considered important drivers of coffee-bean fermentation, potentially shaping the unique and region-specific flavor characteristics of civet-digested coffee. To address this context, the present study integrated metagenomic and metabolomic analyses to compare the gut microbiota and secondary metabolites involved in coffee-bean fermentation inside Vietnamese civets.<br><br>METHODS: Fecal samples were collected under two dietary conditions: a standardized one containing 20% protein, 6% fiber, and 0.4-1.5% lysine, and the same diet supplemented with coffee cherries. Metagenomic 16S rRNA sequencing and untargeted ultra-performance liquid chromatography quadrupole time-of-flight (UPLC-QTOF) revealed clear differences between the two groups.<br><br>RESULTS: Integrated metagenomic and metabolomic analyses revealed clear distinctions between the two groups. Civets on the coffee-cherry diet exhibited higher microbial diversity at the family and genus levels. Specifically, among 31 classified bacterial genera showing a trend toward significant differences in abundance, Enterococcus and Escherichia/Shigella decreased, whereas Gluconobacter, and Pseudomonas increased following the diet shift. Metabolomic profiling identified 46 metabolites across both ionization modes, and strong correlations were observed between microbial genera and metabolite profiles. Specifically, 6-hydroxyangolensic acid methyl ester, 4-aminobenzoic acid and caffeine were more abundant in civets on a coffee-cherry diet, meanwhile the other nine metabolites were more prevalent in the normal diet. Overall, the findings demonstrate that civet gut microbiota and metabolic output were highly responsive to dietary inputs, and that coffee cherries promoted a unique fermentation environment. This represents the first integrative metagenomic and metabolomic study of civets consuming coffee in Vietnam, providing valuable insights into microbial contributions to coffee fermentation.}, }
@article {pmid42222536, year = {2026}, author = {Yang, H and Zhao, L}, title = {Clinical characteristics and prognostic analysis of patients with herpesvirus meningitis/encephalitis based on cerebrospinal fluid mNGS positivity.}, journal = {Frontiers in neurology}, volume = {17}, number = {}, pages = {1808867}, pmid = {42222536}, issn = {1664-2295}, abstract = {BACKGROUND: Herpes viruses are a major cause of meningitis/encephalitis in adults. However, their individual clinical phenotypes and outcomes remain incompletely delineated. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) offers a powerful tool for precise pathogen identification, facilitating the comparison of distinct herpes virus infections.<br><br>METHODS: This retrospective cohort study analyzed 66 patients with CSF-mNGS confirmed herpes virus meningitis/encephalitis at a single center between October 2019 and August 2025. The cohort was stratified into five etiological groups: herpes simplex virus type 1 (HSV-1, n&#x202f;=&#x202f;10), herpes simplex virus type 2 (HSV-2, n&#x202f;=&#x202f;5), varicella-zoster virus (VZV, n&#x202f;=&#x202f;27), Epstein-Barr virus (EBV, n&#x202f;=&#x202f;15), and human herpesvirus 7 (HHV-7, n&#x202f;=&#x202f;9). Demographic, clinical, laboratory, and neuroimaging data were collected. Outcomes were assessed using the Glasgow Outcome Scale (GOS) at 3&#x202f;months post-discharge.<br><br>RESULTS: Distinct clinical phenotypes were observed. HSV-1 encephalitis typically presented with psychiatric symptoms, seizures, and temporal lobe involvement on MRI. HSV-2 infection manifested primarily as a febrile headache syndrome with minimal brain parenchymal involvement. VZV infection was associated with the most intense CSF inflammatory response (highest WBC and protein), a higher incidence of hypoglycorrhachia (25.9%) and hypochloridia (40.7%), and unique complications like cranial neuritis and vasculopathy. EBV infections occurred in older patients and showed features overlapping with HSV-1. HHV-7 infected a significantly younger population and was strikingly associated with elevated intracranial pressure (ICP&#x202f;&#x2265;&#x202f;330 mmH2O in 33.3%). Multivariate analysis identified a longer interval from symptom onset to hospitalization (OR: 1.118, p&#x202f;=&#x202f;0.025) and an abnormal EEG (OR: 0.066, p&#x202f;<&#x202f;0.001) as independent predictors of an unfavorable outcome (GOS&#x202f;<&#x202f;5). Antiviral or steroid therapy was not significantly associated with prognosis in this cohort.<br><br>CONCLUSION: CSF-mNGS reveals distinct and clinically significant phenotypic differences among various herpesvirus meningitis/encephalitis. VZV is characterized by a vigorous CSF inflammatory response and vascular complications, while HHV-7 predominantly affects younger adults and is significantly associated with intracranial hypertension. These findings underscore the value of mNGS in enabling pathogen-directed diagnosis and management, moving beyond syndromic approaches.}, }
@article {pmid42222738, year = {2026}, author = {Park, JH and Chung, J and Lee, HJ and Na, HS}, title = {Comparison of 16S rRNA gene amplicon and whole-genome shotgun metagenomic sequencing for subgingival oral microbiome profiling.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2679807}, pmid = {42222738}, issn = {2000-2297}, abstract = {BACKGROUND: Periodontitis is a chronic inflammatory disease driven by a dysbiotic subgingival microbiome. While 16S rRNA gene amplicon sequencing is widely used, whole-genome shotgun (WGS) metagenomics is increasingly applied for higher taxonomic and functional resolution.<br><br>OBJECTIVE: The aim of this study was to directly compare 16S rRNA gene amplicon (V1-V2) sequencing and WGS metagenomic sequencing using matched subgingival plaque samples from patients with periodontitis.<br><br>METHODS: Subgingival plaque samples from 28 patients with periodontitis were analyzed using both 16S rRNA gene amplicon (V1-V2) sequencing and WGS metagenomics. Taxonomic composition, microbial diversity, differential abundance and functional analysis were compared across platforms.<br><br>RESULTS: WGS generated markedly higher read counts than 16S rRNA gene amplicon but showed wide variability in non-human reads, whereas 16S rRNA gene amplicon yielded a consistent proportion of non-chimeric reads. High taxonomic overlap was observed at the phylum level but declined at higher taxonomic ranks. WGS preferentially detected taxa such as Actinomyces, Corynebacterium and Olsenella, while the 16S rRNA gene amplicon more frequently captured Saccharibacteria (TM7) and low-abundance taxa. Core genera, including Rothia, Neisseria and Cardiobacterium showed comparable abundance patterns across platforms. When patients were grouped depending on probing pocket depth (PPD), LEfSe analysis resulted in platform-specific enrichment patterns. Functional analyses revealed shared central pathways, such as pyruvate metabolism, while 16S-based PICRUSt2 emphasized reductive and degradative pathways and WGS-based HUMAnN highlighted oxidative and biosynthetic pathways. Notably, WGS-based functional profiles were strongly influenced by microbial read depth.<br><br>CONCLUSIONS: This comparative analysis demonstrates that 16S rRNA gene amplicon (V1-V2) sequencing and WGS both robustly capture core subgingival microbial signatures. While WGS provides higher species-level and functional resolution, the resolution was strongly constrained by microbial read depth in host-rich subgingival samples. These findings provide practical guidance for selecting appropriate sequencing strategies and optimizing sample preparation when designing WGS-based periodontal microbiome studies.}, }
@article {pmid42222901, year = {2026}, author = {Dong, Y and Hu, D and Yang, R and Xin, T and Guan, Y and Zhu, X and Ding, Y and Cui, S and Wang, R and Wang, X and Niu, Y and Kong, X}, title = {Early-Life Obesity Leaves a Metabolic Memory That Accelerates Aging-Related Decline Through the Gut Microbiota-GABA Axis.}, journal = {Molecular nutrition &amp; food research}, volume = {70}, number = {11}, pages = {e70513}, doi = {10.1002/mnfr.70513}, pmid = {42222901}, issn = {1613-4133}, support = {2024YFF1106004//National Key Research and Development Program/ ; PL2025H095//Natural Science Foundation of Heilongjiang Province/ ; }, mesh = {Animals ; *gamma-Aminobutyric Acid/metabolism/pharmacology ; *Aging/metabolism/physiology ; *Obesity/metabolism/microbiology/etiology ; *Gastrointestinal Microbiome/physiology ; Diet, High-Fat/adverse effects ; Male ; Oxidative Stress ; Rats ; Lipid Metabolism ; }, abstract = {Childhood obesity is a critical public health concern. Whether diet-induced transient obesity during development negatively impacts later-life health remains unclear, and mechanisms are poorly understood. This study investigates whether these effects persist into aging and employs integrated omics to explore underlying mechanisms. Using a high-fat diet (HFD) to induce transient developmental obesity in post-weaning rats and larval Drosophila, we examined the long-term effects on aging metabolic health in both species. Transient developmental obesity in rats was linked to accelerated aging, weight loss, worsened metabolism, colonic inflammation, and oxidative stress. Metabolomics revealed persistent gamma aminobutyric acid (GABA) dysregulation associated with intestinal ammonia levels, and gut metagenomics showed a reduction in Lactobacillales, correlating with adverse health outcomes. In Drosophila, exogenous GABA extended HF-diet lifespan. It reduced trehalose, triglycerides (TG), and oxidative stress; concurrently, it restored intestinal Lactobacillus and activated the phosphotransferase system (PTS), thereby improving metabolic homeostasis and redox status. Transient developmental obesity is associated with reduced gut Lactobacillus abundance, which may contribute to decreased GABA levels and subsequent disruption of glucose (GLU) metabolism, potentially involving the PTS pathway. These interconnected alterations may ultimately lead to systemic dysregulation of GLU and lipid metabolism and redox homeostasis in later life, compromising overall health and longevity.}, }
@article {pmid42214867, year = {2026}, author = {Lu, J and Zhang, S and Guo, Y and Wu, H and Hu, Z and Kong, Q and Zhang, J}, title = {Magnetite-facilitated AHL-mediated quorum sensing enhances nitrate removal and mitigates nitrous oxide emissions in constructed wetlands under polycyclic aromatic hydrocarbons stress.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142523}, doi = {10.1016/j.jhazmat.2026.142523}, pmid = {42214867}, issn = {1873-3336}, abstract = {The performance of constructed wetlands (CWs) in removing nitrate (NO3[-]-N) and mitigating nitrous oxide (N2O) emissions can be impaired by trace organic pollutants like polycyclic aromatic hydrocarbons (PAHs). Magnetite has been widely applied as a substrate to regulate nitrogen transformation in CWs; however, its potential role in mediating quorum sensing (QS) to alleviate PAH-induced inhibition remains unclear. In this study, conventional CWs (CW-A) and magnetite-amended CWs (CW-B) were established to evaluate NO3[-]-N removal and N2O emissions and the associated mechanisms under PAH-stress conditions. Results indicated that CW-B maintained a high NO3[-]-N removal efficiency (90.14%), whereas CW-A exhibited a marked decline from 65.06% to 47.32%. Magnetite amendment reduced N2O emissions by 68.97% compared with CW-A. Furthermore, the enhanced performance of CW‑B was closely linked to the strengthening of QS. CW-B sustained elevated levels of acyl-homoserine lactone (AHL) signaling molecules (e.g., C8-HSL) under PAH stress, while these signals were suppressed in CW-A. Metagenomic analysis revealed enrichment of key functional genera (e.g., Tessaracoccus and Pseudomonas) and genes associated with QS and nitrogen transformation (e.g., luxI, nirS, and nosZ) in CW-B, supporting enhanced NO3[-]-N removal and reduced N2O emissions. The reinforced QS further promoted interspecies electron transfer and enhanced microbial network robustness and resilience. Additionally, PAHs stimulated the DNRA process and enhanced the abundance of DNRA-related genes (i.e., nrfA and nrfH) in both CWs, leading to increased effluent total nitrogen. Overall, this study elucidates a magnetite-mediated QS mechanism that enhances nitrogen transformation and microbial metabolic stability in CWs under PAH stress.}, }
@article {pmid42215097, year = {2026}, author = {Wang, Z and Ding, Y and Cheng, S and Xun, Z and Li, Z and Zhu, M and Zhao, X and Hu, W and Meng, X and Zhang, S and Qiu, L}, title = {Integrating multi-omics to link core and region-specific microbiota to flavor metabolism in medium-temperature Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {238}, number = {}, pages = {119428}, doi = {10.1016/j.foodres.2026.119428}, pmid = {42215097}, issn = {1873-7145}, mesh = {Multiomics ; *Microbiota/physiology ; Fermentation ; *Alcoholic Beverages/microbiology/analysis ; Gas Chromatography-Mass Spectrometry ; Volatile Organic Compounds/analysis/metabolism ; China ; Metabolomics/methods ; *Food Microbiology ; *Taste ; *Flavoring Agents/metabolism ; Metagenomics ; Bacteria/metabolism/classification ; Temperature ; Fungi/metabolism/classification/genetics ; }, abstract = {Medium-temperature Daqu (MTD) is a critical fermentation starter for strong-aroma Baijiu, where its complex microbiota governs flavor development. We combined metagenomics with GC-MS metabolomics to analyze 15 MTD samples from six major producing regions in China, moving from descriptive profiling to mechanistic insight. Although microbial communities exhibited substantial regional variation, a conserved core microbiota emerged, consisting of eight fungal genera, including Aspergillus and Rhizopus, and five bacterial genera such as Bacillus. Beta diversity analysis indicated that producer-specific practices were more influential than geography in structuring these communities. Functional metagenomic profiling showed enriched pathways for carbohydrate, amino acid, and ester metabolism. Volatile metabolite analysis identified 94 compounds, primarily esters, with 12 common to all samples. We constructed multi-omics correlation networks to predict functional linkages, which notably connected genera like Talaromyces and Aspergillus to key flavor esters. Based on these predictions, we isolated Wickerhamomyces anomalus and Bacillus velezensis from Daqu. In vitro validation demonstrated their functional roles: W. anomalus produced ethyl acetate, while co-culturing B. velezensis with Saccharomyces cerevisiae significantly enhanced the yield of ethyl decanoate and ethyl laurate. This work delineates both the core and region-specific metabolic features of MTD and translates multi-omics correlations into confirmed microbial activities. It thereby establishes a targeted framework for identifying flavor-active microorganisms, offering a scientific foundation for quality control and directed bioaugmentation in Daqu production.}, }
@article {pmid42215200, year = {2026}, author = {Jones, RC and Visger, CJ and Lopez, CA}, title = {The microbiota of wild fermented cider from U.S. west coast apples.}, journal = {Food microbiology}, volume = {139}, number = {}, pages = {105120}, doi = {10.1016/j.fm.2026.105120}, pmid = {42215200}, issn = {1095-9998}, mesh = {*Malus/microbiology ; Fermentation ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Alcoholic Beverages/microbiology/analysis ; *Yeasts/isolation &amp; purification/classification/genetics/metabolism ; United States ; Food Microbiology ; Fruit/microbiology ; }, abstract = {Traditional methods to produce apple cider rely on wild fermentations, where the indigenous microbes present on the fruit and environment transform the pressed apple juice, or must, to cider. The identification of the diverse bacteria and yeast responsible for wild fermentations is an important step in designing practices that promote desired microbes while preventing expansion of spoilage microbes. Here, we sought to survey the microbial communities found in wild fermented ciders from the western United States using shotgun metagenomics sequencing in packaged cider. There, we found a substantial diversity of bacteria and yeast genomic sequences; however, despite variation in apple origin and cidery, there was consistent identification of Oenococcus oeni, Lentilactobacillus hilgardii, and Brettanomyces bruxellensis. Additionally, Tatumella ptyseos, a member of the plant-associated Erwiniaceae, was identified in all cider batches, with T. ptyseos representing one of the most abundant observed taxa in some batches. Analysis of the identified T. ptyseos strains suggests the presence of adaptations to a cider environment that include carbohydrate fermentation, methionine salvage, and nutrient iron and zinc scavenging. These results provide preliminary support that the microbial communities established in fermenting cider contain core constituents that may stratify based on key metabolic characteristics or adaptations to a low nutrient, high competition environment.}, }
@article {pmid42215210, year = {2026}, author = {Chen, L and Wang, G and Hu, Z and Teng, M and Cao, Q and Qin, X and Du, H and Yang, F and Tu, H and Wang, L}, title = {From diversity to stability: Acidification, antagonism, and resistance driven by Acetilactobacillus jinshanensis during jiang-flavor baijiu fermentation.}, journal = {Food microbiology}, volume = {139}, number = {}, pages = {105130}, doi = {10.1016/j.fm.2026.105130}, pmid = {42215210}, issn = {1095-9998}, mesh = {Fermentation ; Hydrogen-Ion Concentration ; Metagenomics ; *Wine/microbiology/analysis ; Microbiota ; Microbial Consortia ; Metabolomics ; }, abstract = {As a quintessential pillar of Chinese traditional industry, Baijiu relies on solid-state fermentation, a complex ecological succession process driven by highly diverse microbial consortia. While such systemic complexity often introduces stochasticity and uncertainty, baijiu solid-state fermentation is typically dominated by specific keystone species that exhibit remarkable resilience, maintaining high abundance while exerting top-down control over community structure and function. However, the mechanisms enabling these species to emerge from intensely competitive environments remain poorly understood. In this study, we employed Acetilactobacillus jinshanensis, a predominant species in the Moutai-flavor Baijiu microbiome, as a model to address these ecological questions. By integrating shotgun metagenomics, metatranscriptomics, and a pH-dependent generalized Lotka-Volterra model, we demonstrate that A. jinshanensis not only orchestrates environmental acidification but also reshapes the community landscape through active competitive inhibition. Leveraging comparative genomics and AlphaFold3-based structural predictions, we identified a unique GH25-LysM antibacterial module in A. jinshanensis predicted to target peptidoglycan with high specificity, potentially contributing to the suppression of acid-tolerant competitors. Furthermore, targeted metabolomics revealed a novel acid-resistance mechanism centered on an intra- and extracellular choline cycle, which significantly bolsters the organism's fitness under extreme acidic stress via metabolic modulation. Overall, we pinpoint a coupled mechanism set that explains the diversity-to-stability transition driven by A. jinshanensis in fermentation microbial community, offering process-relevant rules for improving reproducibility.}, }
@article {pmid42215376, year = {2026}, author = {Kiguchi, Y and Suzuki, Y}, title = {Giants within: a new class of microbial mobile elements.}, journal = {Trends in genetics : TIG}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tig.2026.05.004}, pmid = {42215376}, issn = {0168-9525}, abstract = {Prokaryotes harbor a diverse spectrum of extrachromosomal elements (ECEs), which are intracellular replicons maintained independently of the primary chromosome. Historically, the ECE research field has focused on relatively small ECEs, such as plasmids. However, the advent of long-read sequencing has revealed that prokaryotes also harbor various types of giant ECEs, spanning hundreds of kilobases to over 1 Mb, that were not hitherto recognized. In this review, we describe how long-read sequencing has enabled the discovery of giant ECEs and compare the genetic architectures and functional repertoires of several recently characterized examples. The functions of most genes in these ECEs remain uncharacterized, and current computational tools frequently misclassify or overlook them. We further discuss how the discovery of these giant ECEs challenges existing classification frameworks that attempt to distinguish megaplasmids, chromids, and chromosomes. Together, these findings highlight giant ECEs as a largely unexplored layer of microbial genetics, whose characterization will have broad implications for our understanding of microbial adaptation and horizontal gene transfer.}, }
@article {pmid42215825, year = {2026}, author = {Lv, J and Wang, JH and Wang, YY and Huang, J and Chen, FR and Fang, S and Wang, XJ and Li, ZT and Shi, YP and Guo, L}, title = {Gut microbial alterations and functional shifts in patients with hypertriglyceridemia: insights from a northwestern Chinese metagenomic study.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42215825}, issn = {1618-1905}, support = {2025JC-YBMS-916//Shaanxi Natural Science Foundation of China/ ; No. 81702067 and 82560411//National Natural Science Foundation of China/ ; }, abstract = {Although hypertriglyceridemia (HTG) is a significant contributor to lipid-associated pathologies such as atherosclerotic cardiovascular disease, its regulation by host‒microbiome interactions remain insufficiently characterized. While the gut microbiota (GM) is known to influence cholesterol metabolism, its specific role in systemic triglyceride (TG) homeostasis, particularly in non-Western populations, is poorly defined. This study aimed to identify preliminary robust GM signatures associated with HTG and to assess their translational potential using integrated multiomics and explainable machine learning approaches. In a cross-sectional investigation of 50 well-phenotyped adults from Northwest China, we combined 16S rRNA sequencing, shotgun metagenomics, and ensemble machine learning (LightGBM/XGBoost) to elucidate the associations between the GM and TGs. Microbial features were rigorously linked to serum lipid profiles through dual-algorithm validation and SHAP interpretability analysis, while functional potential was assessed via KEGG pathway mapping. Subjects with HTG exhibited a distinct gut microbial configuration, marked by consistent enrichment of Faecalibacterium and Bacteroides coprocola (positively correlated with serum TG levels) and depletion of Bifidobacterium pseudocatenulatum and Lactobacillus salivarius (inversely correlated). Machine learning converged on five exploratory consensus biomarker taxa, three of which were independently confirmed by LEfSe analysis (Faecalibacterium). Functional profiling further revealed the upregulation of microbial starch and sucrose metabolism pathways in the HTG cohort. Our findings establish a preliminary gut microbial signature for HTG patients and suggest context‑dependent associations of butyrate-producing taxa such as Faecalibacterium. By integrating multiomics with explainable artificial intelligence, this work addresses key challenges in reproducibility and mechanistic inference in microbiome research. These results pave the way for novel microbiota-targeted therapeutic strategies, including precision probiotics and dietary interventions, to modulate lipid metabolism, pending further validation in expanded cohorts and functional studies.}, }
@article {pmid42215894, year = {2026}, author = {Russell, T and Formiconi, E and Murphy, A and Hortion, J and McElroy, M and Casey, M and Cuartero, LG and Mee, JF and Jahns, H and Kelly, C and Byrne, J and Feeney, ER and Mallon, PW and Gautier, VW}, title = {One health viral metagenomics for pathogen surveillance: robust mNGS workflows for viral detection and genome recovery from swab and tissue specimens.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05105-5}, pmid = {42215894}, issn = {1471-2180}, support = {101132970, EU4H-2022-DGA-MS-IBA3//European Commission/ ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is an untargeted approach that enables detection of pathogens directly from samples without prior knowledge of their genetic sequences. In the context of pandemic preparedness and One Health surveillance, there is a pressing need for robust viral mNGS workflows that perform reliably across diverse hosts sample types and pre-analytical conditions.<br><br>RESULTS: The study evaluated two shotgun mNGS workflows, one for swabs and one for complex tissue matrices, using a reference repository of clinical and post-mortem samples. The panel comprised swabs and tissue samples positive for 18 DNA and RNA viruses (including 12 species) from nine host species and nine anatomical sites, encompassing a range of transport media, storage temperatures and processing timelines. Quality control metrics were embedded throughout nucleic acid extraction, library preparation and sequencing to monitor performance and support interpretation. Overall, 88.9% of 18 DNA and RNA viruses previously detected by PCR were identified, including from samples with low nucleic acid concentrations (<&#x2009;1 ng/&#xb5;l) and variable integrity and purity. The workflows identified viral co-infections that had not been detected by prior targeted testing, as well as Phocid herpesvirus 7 (PHV7) for which no complete reference genome was initially available.<br><br>CONCLUSIONS: These results demonstrate the feasibility and robustness of the swab and tissue mNGS workflows for virus identification across a range of complex clinical specimens supporting their use in investigations of suspected viral diseases of unknown aetiology and is currently being evaluated for early detection of emerging viral threats at the animal-human interface.}, }
@article {pmid42216070, year = {2026}, author = {Liu, LM and Zhang, YL and Zhou, JT and Yu, QQ and Zhang, WY and Wang, WF and Pang, SD and Miao, H and Zhao, YY}, title = {Ureic clearance granule ameliorates chronic kidney disease by reshaping microbial dysbiosis via modulating bile acid metabolism.}, journal = {Chinese medicine}, volume = {21}, number = {1}, pages = {}, pmid = {42216070}, issn = {1749-8546}, support = {82274192//National Natural Science Foundation of China/ ; 82474062//National Natural Science Foundation of China/ ; LHZSZ25H270001//Natural Science Foundation of Zhejiang Province/ ; 2023-ZDLSF-26//Shaanxi Key Science and Technology Plan Project/ ; }, abstract = {BACKGROUND: Chronic kidney disease (CKD) is a highly prevalent global public health problem that inevitably leads to renal failure. Although renin-angiotensin system blockers, as first-line therapy, can reduce proteinuria, they cannot prevent the progression to end-stage renal disease. Therefore, the development of new treatment strategies is urgently required. The uremic clearance granule (UCG) was widely used in patients with CKD. However, the underlying molecular mechanisms of UCG for CKD treatment remain unclear.<br><br>METHODS: Fecal gut microbiota and serum metabolites were analyzed using metagenomics and metabolomics, respectively. The expression of extracellular matrix components, Takeda G protein-coupled receptor 5 (TGR5), glucagon-like peptide-1 receptor (GLP-1R), and nuclear factor kappa B (NF-&#x3ba;B) p65 was examined by in adenine-induced CKD rats.<br><br>RESULTS: UCG improved renal function and alleviated kidney fibrosis in adenine-induced CKD rats. Mechanistically, significantly altered gut bacteria, including Helicobacter hepaticus, Gemella hemolysans, Bacteroides ovatus, Lactococcus cremoris, Bacteroides fragilis, Alistipes finegoldii, and Eubacterium limosum, showed strong linear correlations with serum creatinine levels in CKD rats. UCG treatment improved aberrant changes in these gut bacteria, indicating that UCG can reshape gut microbiota dysbiosis. Microbial-derived metabolites act as a bridge between gut microbiota and host. Further analysis showed that serum bile acids, including ursodeoxycholic acid (UDCA), taurodeoxycholic acid, and hyodeoxycholic acid (HDCA), were strongly correlated with serum creatinine levels in CKD rats, and these aberrant metabolites were reversed by UCG treatment. Notably, both UDCA and HDCA showed strong linear correlations with Bacteroides ovatus, Lactococcus cremoris, Bacteroides fragilis, and Eubacterium limosum, suggesting that UCG regulates microbial-derived metabolites. Moreover, UCG treatment upregulated protein expression of TGR5, GLP-1R, and downregulated NF-&#x3ba;B p65 protein expression in the kidney tissues of CKD rats, indicating that renoprotective effects of UCG are associated with modulation of microbial dysbiosis, regulation of bile acid metabolism and improvement of TGR5, GLP-1R, and NF-&#x3ba;B signaling.<br><br>CONCLUSIONS: This study is the first to demonstrate that UCG ameliorates CKD and renal fibrosis by reshaping microbial dysbiosis and microbial-derived bile acid metabolism. Altered gut microbiota and metabolites may serve as biomarkers to evaluate efficacy of UCG. UCG may exert its renoprotective effects by enhancing TGR5, GLP-1R, and NF-&#x3ba;B p65 expression through regulating microbial dysbiosis-mediated bile acid metabolism.}, }
@article {pmid42216221, year = {2026}, author = {Zhang, K and Duan, C and Chen, J and He, Q and Jin, Y and Liu, J and Lin, R and Han, C}, title = {Bone marrow mesenchymal stem cells synergize with fusobacterium nucleatum to drive colorectal tumorigenesis via gut microbiome dysbiosis.}, journal = {Gut pathogens}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13099-026-00839-z}, pmid = {42216221}, issn = {1757-4749}, support = {2024M761069//Postdoctoral Research Foundation of China/ ; 82470679//National Natural Science Foundation of China/ ; 2023YFC2307001//National Natural Science Foundation of China/ ; 82170570//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The oncogenic role of F. nucleatum (Fn) in colorectal cancer (CRC) is increasingly recognized, yet its interaction with host stromal components, such as bone marrow mesenchymal stem cells (BMSCs), remains poorly understood. Building on our previous discovery that BMSC-derived Wnt3a promotes Fn-driven tumorigenesis, this study aims to investigate the synergistic interplay between BMSCs and F. nucleatum in CRC pathogenesis via the gut microbiome.<br><br>METHODS: Based on the established Apc[Min/+] mouse model of CRC, animals were randomly assigned to four experimental groups: control, Fn-only, BMSCs-only, and Fn+BMSCs co-treatment group. Gut microbiota composition was continuously analyzed over 8 weeks by metagenomic sequencing. Metagenomic functions were predicted using PICRUSt2.<br><br>RESULTS: The Fn+BMSCs co-treatment group exhibited the highest enrichment of F. nucleatum and the greatest reduction in microbial diversity. Fn+BMSCs co-treatment induced a distinct pro-tumorigenic shift, marked by a decline in symbiont Lactobacillus and an increase in pathobiont Escherichia-Shigella. Metagenomic analysis revealed a unique enhancement of butanoate metabolism in the Fn+BMSC co-treatment group. Furthermore, a profoundly elevated LPS level was discovered in the Fn+BMSCs co-treatment group, indicating hyperactivation of the pro-inflammatory and proliferative TLR4/NF-&#x3ba;B pathway.<br><br>CONCLUSIONS: Our findings demonstrate that BMSCs synergize with F. nucleatum to create a tumorigenicmicroenvironment by driving microbial dysbiosis, reprogramming metabolic pathways, and amplifying pro-inflammatory signaling. Our findings reveal that BMSCs fuel CRC progression via multiple mechanisms: by altering the gut microbiome ecology and, as previously discovered, by providing oncogenic Wnt3a signals. Targeting the synergistic BMSC-Fn axis may thus offer a novel therapeutic strategy for CRC.}, }
@article {pmid42216275, year = {2026}, author = {Wong, ELY and Otte, J and Schmitt, I}, title = {Chloroplast and mitochondrial genomes of the lichen-symbiotic green alga Trebouxia illuminate evolutionary relationships and climate associations, and yield new phylogenetic markers.}, journal = {Genome biology and evolution}, volume = {}, number = {}, pages = {}, doi = {10.1093/gbe/evag129}, pmid = {42216275}, issn = {1759-6653}, abstract = {The green-algal genus Trebouxia (Trebouxiophyceae, Chlorophyta) is the most common photosynthetic symbiont of lichens, displaying high phylogenetic diversity, and worldwide distribution across all climate zones. These single-celled terrestrial algae are valuable systems to study diversification, environmental adaptation and species interactions, yet genomic resources remain limited. We present over 30 new chloroplast and mitochondrial genomes of Trebouxia species, extracted from PacBio metagenomes of diverse Umbilicaria lichens from multiple climate zones. The genomes represent previously identified operational taxonomic units (OTUs) T. jamesii (A03), T. sp. (A04), T. incrustata (A06), T. vagua (A10), T. sp. (S02), T. sp. (S03), T. sp. (S04), T. suecica (S05), T. sp. (S08), T. angustilobata (S09), T. simplex (S10), T. sp. (S20), T. barrenoae (S28), a newly designated OTU A57, and several Single-Occurrence Sequences (SOS) from Clade A, I and S. Up to four Trebouxia OTUs were found within a single thallus. Organelle genomes vary considerably in size and structure. The consensus phylogenies from chloroplast (77 genes) and mitochondrial genes (32 genes) are largely congruent with the nuclear ITS tree, differing mainly in the derived clade S sections. All genes are under purifying selection, with mitochondrial genes exhibiting higher nucleotide diversity and hence phylogenetic resolution than chloroplast genes. Certain gene and protein features correlate with temperature variability, and some (such as GC content, arginine and valine content) mirror findings in mycobiont nuclear genomes from the same samples, and highlighting shared signatures of environmental adaptation. We designed primers for new, variable phylogenetic markers, including chloroplast genes ftsH and rpoC1, and mitochondrial genes ATP1, ATP6 and ND6. Overall, this study advances our understanding of organelle genome evolution in Trebouxia, and provides valuable resources for future ecological and evolutionary research.}, }
@article {pmid42216291, year = {2026}, author = {Zwartjes, MSZ and de Jonge, PA and van de Laar, AW and Bruin, SC and Meijnikman, AS and Groen, AK and Gerdes, VEA and Nieuwdorp, M}, title = {Adipose Tissue Inflammation, Oxidative Stress, and Altered Adipogenesis Are Associated With Dyslipidemia in Obesity: A Multiomics Profiling Study.}, journal = {Journal of the American Heart Association}, volume = {}, number = {}, pages = {e047397}, doi = {10.1161/JAHA.125.047397}, pmid = {42216291}, issn = {2047-9980}, abstract = {BACKGROUND: Obesity is an important risk factor for cardiometabolic disease, including dyslipidemia and atherosclerotic cardiovascular disease. Although the role of the liver in dyslipidemia is established, the contribution of adipose tissue is less clear. This study aims to clarify the role of adipose tissue in lipid metabolism and dyslipidemia.<br><br>METHODS: We conducted a cross-sectional analysis of 125 patients from the BARIA (The Immune System and Microbial Tone in Relation to NAFLD/NASH Before and After Bariatric Surgery in the Morbidly Obese in Amsterdam) longitudinal cohort study undergoing bariatric surgery. Comprehensive phenotyping included fasting untargeted plasma metabolomics, lipid, lipoprotein, adipokine profiling, RNA sequencing, and fecal shotgun metagenomics. Tissue transcriptomic and plasma metabolites were compared between individuals with and without dyslipidemia.<br><br>RESULTS: Dyslipidemia was present in 43 of 125 individuals (34.4%), with higher triglycerides (1.62 versus 1.24&#x2009;mmol/L), apoB (apolipoprotein B; 93.15 versus 81.81&#x2009;mg/dL), and lower high-density lipoprotein (1.02 versus 1.35&#x2009;mmol/L) and apoAI (136.40 versus 161.35&#x2009;mg/dL). Plasma adipokines showed limited differences: leptin concentrations were lower in dyslipidemia in unadjusted analysis but reduced after adjustment for age, sex, and body weight (adjusted P=0.057). RNA sequencing identified altered gene expression of liver, jejunum, visceral and subcutaneous adipose tissue, most pronounced in subcutaneous adipose tissue. Dyslipidemia was associated with adipose tissue pathways related to inflammation, oxidative stress, and adipogenesis. Plasma metabolomics revealed associations with endocannabinoid-like, secondary bile acid, plasmalogen, butyrate, and sphingolipid metabolites. Gut metagenome analysis found modest differences.<br><br>CONCLUSIONS: Dyslipidemia in obesity is associated with transcriptomic alterations in adipose tissue, including subcutaneous adipose tissue, involving inflammation, oxidative stress, and adipogenesis. These findings support a role of adipose tissue in lipid regulation beyond hepatic pathways.}, }
@article {pmid42217053, year = {2026}, author = {Ortiz-Gasca, A and Aguirre-Noyola, JL and Ruiz-Rivas, M and de Los Santos-Villalobos, S and Trejo-Aguilar, D and Gómez-Godínez, LJ}, title = {Molecular markers for the study of arbuscular mycorrhizal fungi.}, journal = {Archives of microbiology}, volume = {208}, number = {8}, pages = {}, pmid = {42217053}, issn = {1432-072X}, mesh = {*Mycorrhizae/genetics/classification/isolation &amp; purification ; Genetic Markers ; DNA, Fungal/genetics ; Metagenomics/methods ; DNA, Ribosomal/genetics ; Soil Microbiology ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) are central components of terrestrial ecosystems and agroecosystems. However, their accurate identification remains methodologically challenging due to their complex biology and the limitations of traditional morphological approaches. Over the past three decades, molecular tools have profoundly reshaped AMF research, shifting from spore-based identification and Sanger sequencing of ribosomal markers toward high-throughput amplicon sequencing and, more recently, metagenomic frameworks that enable community-level and functional analyses. This review critically examines the conceptual and technical evolution of AMF identification strategies, comparing morphological characterization, ribosomal DNA markers (SSU, ITS, LSU), multilocus approaches, metabarcoding, and whole-genome metagenomics. We analyze their taxonomic coverage, resolution, and methodological biases, including primer specificity, intragenomic rDNA variation, database limitations, and bioinformatic pipeline effects. Attention is given to how marker selection influences ecological interpretation, cross-study comparability, and functional inference. Finally, we propose practical guidelines for aligning marker choice with study objectives and outline validation strategies-such as mock communities, curated reference databases, and multi-marker integration-to improve reproducibility and taxonomic robustness. By integrating historical perspective, methodological evaluation, and applied recommendations, this review provides a decision-oriented framework to support more accurate and comparable assessments of Glomeromycota diversity.}, }
@article {pmid42217383, year = {2026}, author = {Kong, T and Du, Z and Zhou, J and Zheng, Z and Zhang, J and Zhang, S and Jiang, F and Sun, X and Huang, W and Zhang, R and Li, F and Lin, W and Lan, X and Cao, Y and Yan, G and Sun, W}, title = {Assimilatory sulfate reduction potential in the plastisphere microbiome is linked to plastic mineralization in sulfur-rich mining-impacted river sediments.}, journal = {Water research}, volume = {303}, number = {}, pages = {126182}, doi = {10.1016/j.watres.2026.126182}, pmid = {42217383}, issn = {1879-2448}, abstract = {Microbial communities colonizing plastic surfaces are shaped by environmental factors, yet the role of sulfur in plastisphere assembly and plastic fate remains poorly understood. Here, we collected plastic debris from sulfur-rich, mining-impacted river sediments to characterize plastisphere microbiomes and evaluate their potential roles in plastic transformation. Paenibacillus spp. were identified as core plastisphere members, and their distribution was strongly associated with total sulfur concentrations. Metagenomic binning suggested that Paenibacillus harbored genomic potential associated with plastic transformation/mineralization and sulfate assimilation. An isolate of Paenibacillus provided further laboratory-based evidence that sulfate amendment may support plastic mineralization, although the precise in situ mechanism remains to be clarified. Because both the metagenome-assembled genome and the isolate genome encoded an almost complete assimilatory sulfate reduction pathway but lacked a complete dissimilatory sulfate reduction pathway, the observed sulfate depletion is more conservatively interpreted as sulfate uptake coupled with assimilatory sulfate reduction and subsequent sulfur assimilation into biomass rather than canonical sulfate respiration. Together, these findings suggest that sulfate availability and assimilatory sulfur metabolism may represent underappreciated controls on plastic turnover in sulfur-rich environments by supporting plastic-associated carbon transformation. This study links plastic-carbon fate to local sulfur cycling and provides new insight into microplastic persistence in sulfur-rich aquatic ecosystems.}, }
@article {pmid42217591, year = {2026}, author = {Zhang, J and Liu, J and Tian, Y and Jia, W and Zhang, G and Lyu, A and Lyu, H}, title = {Metabolic interactions of host-gut microbiota: Shaping the future of precision diagnosis and therapeutic discovery in gastrointestinal cancers.}, journal = {Pharmacological research}, volume = {}, number = {}, pages = {108273}, doi = {10.1016/j.phrs.2026.108273}, pmid = {42217591}, issn = {1096-1186}, abstract = {This collection of reviews and research articles highlights the diagnostic and therapeutic potential of gut microbial metabolites across various gastrointestinal cancers, including but not limited to hepatobiliary and pancreatic cancers, gastric cancer, and cholangiocarcinoma. Numerous gut microbial metabolites have been observed to mechanistically regulate cancer cell proliferation and development, supporting their utility as molecular biomarkers for clinical diagnosis and as targets for precision interventions. However, most functional metabolites derived from both host cancer tissues and the gut microbiota remain structurally unidentified; their functional features are largely unexplored due to limitations in conventional measurement technologies. To address these challenges, we propose a transformative functional metabolomics approach-S[2]M[2]ART (Single-Cell Spatial Metabolomics Metagenomics-Artificial Intelligence Recombinational Toolkit)-which will leverage AI-powered multimodal omics and single-cell, spatially-resolved analyses to decode the molecular functions and mechanisms of these metabolites in gastrointestinal cancer development. Collectively, this innovative technique will substantially enhance the applicability and translational potential of microbial metabolites in gastrointestinal cancers and beyond.}, }
@article {pmid42217781, year = {2026}, author = {Kim, S and Kang, MG and Oh, S and Jang, KB and Kim, Y}, title = {Genome-based characterization of flavor development via metabolic interactions between Lentilactobacillus kefiri and Kluyveromyces marxianus during milk kefir fermentation.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2026-28435}, pmid = {42217781}, issn = {1525-3198}, abstract = {Kefir, a fermented milk product comprising complex consortia of bacteria and yeasts, develops its characteristic flavor through coordinated microbial interactions. In this study, we investigated flavor compound biosynthesis and development by kefir-derived lactic acid bacteria and yeast during kefir fermentation, integrating genome-based predictions with metabolite validation. Metagenomic analysis identified Lactobacillus and Kluyveromyces as predominant genera in both kefir grains and fermented milk kefir. Lentilactobacillus kefiri SLAM023B and Kluyveromyces marxianus SLAM005Y were isolated and subjected to hybrid genome sequencing on Illumina and Nanopore platforms. Functional annotation via KEGG pathway mapping revealed featured pathways including amino acid and fatty acid metabolism, as well as interconversion of alcohol, aldehyde, and acid, contributing to the formation and generation of flavor compounds. Notably, K. marxianus SLAM005Y produced fruity fusel alcohols, whereas L. kefiri SLAM023B contributed fatty acid-derived precursors. The coculture of the 2 strains significantly enhanced ester synthesis, particularly ethyl acetate and isoamyl acetate, imparting fruity and creamy sensory notes to the fermentation profile. In addition, increases in ethyl octanoate and C6/C8 fatty acids introduced fruity and cheese-like characteristics, while levels of grassy aldehydes were reduced. Correlation analysis supported the complementary metabolic roles and potential cross-feeding mechanisms between the strains, which help explain the development of kefir flavor. Taken together, this study provides a genomic and functional framework to examine cooperative metabolism in kefir and identifies molecular targets for improving the sensory properties of fermented dairy products.}, }
@article {pmid42214595, year = {2026}, author = {Pan, W and Zhang, L and Liang, L and Du, L and Guo, X}, title = {Nanoplastics Reshape Nitrogen Cycling in Submerged Macrophyte Systems: A Metagenomic Perspective.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124885}, doi = {10.1016/j.envres.2026.124885}, pmid = {42214595}, issn = {1096-0953}, abstract = {Nanoplastics (NPs) pose a potential risk to aquatic ecosystems. Submerged macrophytes are critical for nitrogen removal, but how nitrogen cycling responds to NP-induced stress remains unclear. This study used Myriophyllum aquaticum to evaluate nitrogen cycling in submerged macrophyte-sediment systems exposed to 100 nm polystyrene (PS) NPs at 10, 100, and 1000 μg/L, integrating stable isotope tracing and metagenomic profiling to explore microbial community and nitrogen-cycling gene responses across rhizosphere and non-rhizosphere compartments. Low PS-NP exposure (10 μg/L) slightly increased the NH4[+]-N removal efficiency to 81.5%, whereas medium and high PS-NP exposures (100 and 1000 μg/L) reduced the NH4[+]-N removal efficiency, with values around 70.9%. Low doses stimulated nitrification (NO3[-]-N accumulation) and high doses inhibited N2O emissions; δ[15]N tracing showed disrupted NH4[+]-N to N2 reduction. Plant-only microcosms had the highest N2O release (1.37 mg, 1.5% of total N). Metagenomics revealed concentration-dependent, spatially distinct microbial community shifts: low PS-NPs increased rhizosphere α-diversity, while high concentrations depleted Proteobacteria, enriched Acidobacteria/Bacteroidetes, and reduced key nitrogen-cycling genera (e.g., Dechloromonas, Accumulibacter). In the rhizosphere, denitrification genes (nirK/S,nosZ) were upregulated by 2.5- and 3-fold, respectively, while DNRA (nrfA) and nitrogen fixation (nifH) genes were downregulated by 1.7- and 2.3-fold. Network and canonical correspondence analyses indicated stronger environmental filtering in bulk sediments (explaining 52.0% of variance) and spatially structured nitrogen metabolic pathway reorganization. These findings show concentration-dependent PS-NP exposure differentially shapes microbial community composition and nitrogen-cycling functions in rhizosphere and bulk sediments.}, }
@article {pmid42214685, year = {2026}, author = {Jiang, T and Prioult, G and Quann, E}, title = {Microbial Biotransformation of Polyphenols and Bioactive Substrates: Implications for Metabolite-Guided Synbiotics.}, journal = {The Journal of nutrition}, volume = {}, number = {}, pages = {101621}, doi = {10.1016/j.tjnut.2026.101621}, pmid = {42214685}, issn = {1541-6100}, abstract = {Dietary bioactive compounds-including polyphenols, alkaloids, lignans, and amino acid-derived substrates-exert well-established effects on human health, but are constrained by poor bioavailability. Only 5-10% of ingested polyphenols are absorbed in the proximal gastrointestinal tract; the remainder undergoes biotransformation by colonic microbiota into a diverse repertoire of bioactive metabolites. Accumulating evidence indicates that these microbially derived metabolites, rather than their parent compounds, are the primary mediators of systemic benefits, owing to superior bioavailability, metabolic stability, anti-inflammatory and antioxidant activity, and greater specificity in modulating host metabolic and signaling pathways. Production of these metabolites varies markedly among individuals due to differences in gut microbiota composition, giving rise to distinct metabolic phenotypes-termed metabotypes-that strongly influence clinical and nutritional responsiveness. This review synthesizes recent advances in the microbial biotransformation of dietary polyphenols, amino acids, glucosinolates, and related substrates, and examines how these pathways influence metabolic, cardiometabolic, neurocognitive, and immune outcomes. We further evaluate emerging evidence supporting synergistic synbiotics-targeted combinations of probiotics with specific polyphenol or bioactive precursors-as a strategy to standardize and enhance the generation of beneficial microbial metabolites. These synbiotic strategies demonstrate capacity to convert non-producers into producers, reduce interindividual variability in metabolite output, and improve clinically relevant outcomes in metabolic dysfunction, inflammation-driven disorders, and aging. Together, these findings position metabolite-guided synbiotics as a promising paradigm for precision nutrition. Integration of metagenomics, metabolomics, and computational modeling will enable individualized prediction of metabolite-production capacity and accelerate translation of microbiota-targeted interventions.}, }
@article {pmid41998666, year = {2026}, author = {Yang, F and Du, Y and Ji, J and Zhang, P}, title = {Eosinophilic granulomatous inflammation and multi-organ involvement probable caused by Paragonimus heterotremus infection in a pediatric patient: a rare case report.}, journal = {BMC pediatrics}, volume = {26}, number = {1}, pages = {}, pmid = {41998666}, issn = {1471-2431}, abstract = {BACKGROUND: Paragonimus heterotremus is a parasitic flatworm endemic to Southeast Asia that causes pulmonary and extrapulmonary infections. While more common in adults, pediatric cases are rare and often present atypically, posing diagnostic challenges. Eosinophilic granulomatous inflammation due to parasitic infection is especially difficult to identify in children.<br><br>CASE PRESENTATION: A 9-year-old female child initially exhibited subcutaneous swelling and notable peripheral blood eosinophilia, resulting in two hospital stays without a conclusive diagnosis. Upon admission to our center, laboratory results showed increased white blood cell count, hemoglobin, platelets, and persistent eosinophilia, along with a significantly increased total IgE levels. Imaging revealed granulomatous inflammation in the skin and lungs with mild pleural effusion. Despite negative parasitic serology, a newly developed umbilical mass during hospitalization was surgically excised. Anatomopathological examination and metagenomic next-generation sequencing (mNGS) supported a probable diagnosis of P. heterotremus infection.<br><br>CONCLUSIONS: This case highlights the diagnostic challenges of pediatric eosinophilic granulomatous inflammation due to rare parasitic infections, particularly in non-endemic areas. It highlights the need for heightened clinical awareness, thorough evaluation, and advanced diagnostic tools for timely and accurate identification of uncommon parasitic diseases in children.}, }
@article {pmid42206150, year = {2026}, author = {Sun, K and Wang, F and Niu, T and Wang, H and Liu, Y and Guo, L and Wang, X and Hou, X}, title = {Metagenomic and metabolomic insights into the rhizosphere of Paeonia suffruticosa 'Luoyang Hong' across a continuous cropping chronosequence.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1754999}, pmid = {42206150}, issn = {1664-462X}, abstract = {The cultivation of Paeonia suffruticosa 'Luoyang Hong', a valuable ornamental crop, faces significant challenges due to replanting issues. However, the dynamics of its rhizosphere micro-ecosystem under continuous cropping remain poorly understood. This study systematically investigates the successional patterns of the rhizosphere micro-ecosystem over a 12- to 42-year chronosequence to identify the underlying drivers of these issues. Using an integrated multi-omics approach combining metagenomics and non-targeted metabolomics, we deciphered the rhizosphere mechanisms associated with replanting issues in Paeonia suffruticosa 'Luoyang Hong'. Based on differential changes in metabolites within the soil and root systems, key substances such as succinic acid, trans-ferulic acid, vanillic acid, and Leu-Val-Arg-Lys were identified. The microbial succession demonstrated a distinct temporal progression. Initially, at the 12-year stage, the rhizosphere was enriched with beneficial bacterial genera. However, around the 20-year stage, the abundance of these beneficial genera significantly declined. Subsequently, at the 34-year stage, the community shifted to a dominance of genera associated with organic matter degradation. Finally, at the 42-year stage, a partial recovery of certain beneficial genera and their functions was observed. Despite this recovery, the overall system continued to exhibit signs of continuous degradation. Integrated multi-omics analysis further revealed significant positive correlations, such as that between N,N-dimethyldodecylamine N-oxide and several differential microbial genera, underscoring the complex interactions between metabolites and microbes. Our findings provide a systematic perspective on the micro-ecological dynamics in the rhizosphere of Paeonia suffruticosa 'Luoyang Hong', offering deeper insights into replanting issues and supporting future mitigation strategies.}, }
@article {pmid42206286, year = {2026}, author = {Oladejo, OA and Ibiwoye, DO and Faniyi, AA and Ayoola, MO and Oguntunji, AO and Ayansina, AD and Dahunsi, SO}, title = {Dynamics of enzyme and metabolic profile of broilers fed black soldier fly (Hermetiailucens) larvae-based diets.}, journal = {Biochemistry and biophysics reports}, volume = {46}, number = {}, pages = {102618}, pmid = {42206286}, issn = {2405-5808}, abstract = {This study investigated the impact of replacing fishmeal with black soldier fly larvae meal (BSFLM) on growth performance, microbial enzyme activity, and metabolic functions in broiler chickens. A total of fifty Arbor Acre Plus chicks were distributed across five dietary groups, including a control (100% fishmeal) and four diets containing increasing levels of BSFLM (25%, 50%, 75%, and 100%) in a completely randomized design. Broilers were reared over eight weeks, and cecal samples were subjected to 16S rRNA metagenomic sequencing to profile gut microbial enzyme activities and metabolic functions. Results revealed a progressive increase in microbial enzyme abundance and functional metabolic pathways with higher BSFLM inclusion, particularly in the 50% (T3) and 100% (T5) groups. Key enzymes, including ABC-2-type ATP-binding proteins, RNA polymerase sigma factors, and carbohydrate-active enzymes, were significantly upregulated, supporting enhanced carbohydrate fermentation, amino acid biosynthesis, and central carbon metabolism. Metabolic pathway analysis indicated a dietary shift from carbohydrate-driven fermentation in the control group to a more protein- and lipid-centered metabolism in BSFL-fed birds, with T3 showing a balanced metabolic profile and T5 exhibiting hyper-metabolic activity. These findings demonstrate that BSFLM can replace fishmeal without compromising gut health and may even enhance microbial functionality, with a 50% replacement emerging as an optimal inclusion level to sustain balanced microbial metabolism.}, }
@article {pmid42206340, year = {2026}, author = {Huerta, AI and Joglekar, P and Totsline, N and D'Amico-Willman, KM and Ritchie, DF}, title = {Plant-associated phages across scales: ecological and evolutionary principles for a neglected virosphere.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {381}, number = {1951}, pages = {}, doi = {10.1098/rstb.2025.0124}, pmid = {42206340}, issn = {1471-2970}, support = {//National Institute of Food and Agriculture/ ; //Foundation for Food and Agriculture Research/ ; }, mesh = {*Bacteriophages/physiology/genetics ; *Plants/virology/microbiology ; *Microbiota ; *Biological Evolution ; }, abstract = {Bacteriophages are abundant and influential members of plant-associated microbiomes, yet their ecological and evolutionary roles are less explored than those of marine, soil or clinical virospheres. This gap limits our capacity to predict phage-bacterium interactions, understand microbial community dynamics and design robust phage-based strategies for managing diseases in plants. Here, we synthesize emerging evidence across spatial, temporal and biological scales to outline key principles that govern phage ecology in plant systems. Drawing on insights from well-characterized environments, including oceans, soils and the human gut, we highlight how spatial structure, host population genetics, environmental heterogeneity and fluctuating selection jointly shape infection outcomes and coevolution in plant microbiomes. Recent genomic and metaviromic findings further reveal that plant-associated phages can exhibit both long-term genomic stability and localized adaptive divergence, underscoring the importance of scale-aware ecological frameworks. We also identify major technical and conceptual bottlenecks that impede discovery, including plant and bacterial host-DNA contamination and the limited number of phage genomes isolated from plant ecosystems. By linking these ecological principles to applied challenges, such as the inconsistent field performance of phage-based biocontrol, this perspective offers a roadmap for advancing phage biology in plant systems and for resolving this neglected virosphere. This article is part of the theme issue 'Wild plant pathosystems'.}, }
@article {pmid42206370, year = {2026}, author = {Chen, L and Lin, L and Wang, Z and Yu, L and Ren, B and Zhou, S and Wang, P and Li, Y and Lu, E and Dong, Z}, title = {Fusobacterium nucleatum-Derived Isoleucine Exacerbates Aneurysm by Inducing Ferroptosis in Vascular Smooth Muscle Cells.}, journal = {Arteriosclerosis, thrombosis, and vascular biology}, volume = {}, number = {}, pages = {}, doi = {10.1161/ATVBAHA.126.324050}, pmid = {42206370}, issn = {1524-4636}, abstract = {BACKGROUND: Bacterial communities and their metabolites are increasingly recognized as key contributors to cardiovascular disease, yet their role and mechanistic involvement in abdominal aortic aneurysm (AAA) pathogenesis remain insufficiently defined.<br><br>METHODS: Dental plaques from patients with AAA and matched healthy controls were subjected to metagenomic sequencing, and corresponding plasma samples underwent untargeted metabolomic profiling. In vivo, mice were topically exposed in the oral cavity to Fusobacterium nucleatum (Fn) followed by AngII (angiotensin II) infusion to evaluate its impact on AAA progression. A homologous recombination-based ilvE deletion strategy was used to confirm the role of Fn in isoleucine biosynthesis. Molecular assays were performed to assess ferroptosis-related signatures and histone acetylation in smooth muscle cells, while chromatin immunoprecipitation-quantitative polymerase chain reaction verified the specific acetylation target. In addition, dietary restriction of isoleucine was introduced in the AAA murine model to explore therapeutic relevance.<br><br>RESULTS: Patients with AAA showed a marked enrichment of Fn in dental plaque, and topical application of Fn aggravated AngII-induced AAA in mice. Elevated plasma isoleucine concentrations were observed in both human AAA and experimental models. Genetic deletion of ilvE in Fn diminished bacterial isoleucine release and mitigated AAA development in mice. Mechanistic analyses revealed that Fn-derived isoleucine promoted ferroptosis in smooth muscle cells through H3K9ac (histone H3 lysine 9 acetylation)-dependent transcriptional activation of ACSL4 (acyl-CoA [coenzyme A] synthetase long-chain family member 4), a core regulator of ferroptosis. Dietary isoleucine restriction in the AngII-induced model reduced H3K9ac, suppressed ferroptosis, and alleviated aneurysmal progression.<br><br>CONCLUSIONS: Fn-derived isoleucine drives ferroptosis in smooth muscle cells via H3K9ac-mediated activation of ACSL4, delineating a microbiota-metabolite-epigenetic axis in AAA pathogenesis and nominating dental plaque Fn abundance and circulating isoleucine as exploratory biomarker candidates requiring larger, independent validation.}, }
@article {pmid42206586, year = {2026}, author = {Yeo, S and Park, H}, title = {Dereplication-assisted culturomics enables strain-level ecological analysis of the human gut microbiome.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2681840}, doi = {10.1080/19490976.2026.2681840}, pmid = {42206586}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Enterococcus faecium/isolation &amp; purification/classification/genetics ; Metagenomics/methods ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; *Bifidobacterium/isolation &amp; purification/classification/genetics ; }, abstract = {Recent advances in culturomics have enabled large-scale recovery of microbial isolates from the human gut, generating extensive culture collections that bridge metagenomic predictions and experimental validation. However, these isolate resources remain largely underutilized, as conventional culturomics prioritizes the discovery of novel species while massive collections of commensal isolates persist as unexplored biological datasets. Dereplication, particularly based on MALDI-TOF MS spectral features, has been largely regarded as a logistical tool for managing redundancy rather than an analytical asset. Here, we reposition dereplication as an analytical framework for interpreting large-scale culturomics datasets and resolving strain-level ecological patterns. We applied the SPeDE pipeline to a comprehensive collection of 2,231 isolates, including Bifidobacterium spp. and Enterococcus faecium, recovered from healthy donor feces. Spectrum-derived operational isolation units (OIUs) revealed host-associated strain-level repertoires and lineage-like clustering within species. Notably, distinct spectral clusters observed in E. faecium corresponded to clade-level patterns identified through shotgun metagenomic analysis. These findings demonstrate that dereplication-assisted culturomics can extend beyond redundancy control to enable high-resolution ecological interpretation of cultured microbiome datasets. By reframing dereplication as a bridge between large-scale isolate generation and strain-level microbiome ecology, this study outlines a conceptual and practical direction for the next phase of human microbiome research in the post-culturomics era.}, }
@article {pmid42206864, year = {2026}, author = {Zhao, R and Biddle, JF}, title = {Community structure and methylation of microbes in an artificially forced sediment core.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0353325}, doi = {10.1128/spectrum.03533-25}, pmid = {42206864}, issn = {2165-0497}, abstract = {Epigenetic modifications, such as DNA methylation, may be used in prokaryotes for the adaptation of microbes to external environmental changes. In this study, we examined the microbial community structure, recovered the genomes of the dominant microbes, and tracked methylation in several dominant microbes in a 23-cm artificial sediment core formed in a settling tank that mimics the sediment formation process. Our results indicated that the prokaryotic communities only showed minor variations with depth and were dominated by bacteria (especially taxa of Deltaproteobacteria, Gammaproteobacteria, and Bacteroidota), while archaea (dominated by Bathyarchaeia) accounted for <5% of the total communities throughout the core. We detected methylation by analyzing metagenome sequencing data of methyl-specific enzyme-digested and undigested DNA. We recovered 72 high- or medium-quality metagenome-assembled genomes for the dominant taxa, for 7 of which we detected distinct downcore methylation patterns. This work highlights the diverse processes of epigenetic modification in response to the sediment burial process, which may have a long-term impact on the overall community fitness in the evolving energy-limited conditions in marine sediments.IMPORTANCEThis work reports changes in the epigenetic profiles of microbes buried in a sediment column formed under a controlled, artificially created environment. This approach removes confounding variables of bioturbation and changes in sediment flux. We also use an approach that is accessible for low amounts of DNA to determine methylation status.}, }
@article {pmid42207030, year = {2026}, author = {Ren, P and Kan, Z and Wei, B and Qin, W and Lu, S}, title = {Yellow tea extract ameliorates dexamethasone-induced hepatic steatosis by modulating the gut-liver axis and reshaping microbial metabolites: a multi-omics insight.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d6fo01620k}, pmid = {42207030}, issn = {2042-650X}, abstract = {Long-term glucocorticoid therapy, exemplified by dexamethasone (DEX), frequently induces hepatic steatosis, posing a significant clinical challenge. Yellow tea (YT), a lightly fermented tea, is rich in polyphenols and polysaccharides, yet its protective effects against DEX-induced liver injury remain underexplored. This study investigated the hepatoprotective mechanisms of a yellow tea water extract (YT) using a DEX-induced mouse model, integrated with transcriptomic, metagenomic, and metabolomic analyses. YT intervention (500 mg[-1] kg[-1] day[-1] for 6 weeks) significantly attenuated DEX-induced hepatocellular injury, as evidenced by reduced serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels, decreased hepatic triglyceride (TG) and total cholesterol (TC) accumulation, and suppressed systemic inflammation (lipopolysaccharide (LPS) and tumor necrosis factor-alpha (TNF-α)). Hepatic transcriptomics and subsequent reverse transcription quantitative PCR (RT-qPCR) validation revealed that YT upregulated the antioxidant genes nuclear factor erythroid 2-related factor 2 (Nrf2) and heme oxygenase-1 (HO-1) while downregulating the lipogenic gene sterol regulatory element-binding protein 1c (SREBP-1c) and upregulating the fatty acid oxidation gene peroxisome proliferator-activated receptor alpha (PPAR-α). Gut microbiota analysis showed that YT reshaped the microbial community, notably enriching beneficial taxa such as Bifidobacterium pseudolongum and members of the Muribaculaceae family. Serum metabolomics indicated that this microbiota remodeling was associated with the restoration of perturbed metabolic pathways, notably tryptophan metabolism. Correlation analysis further linked specific microbial shifts with improved metabolic and inflammatory markers. Collectively, these integrated transcriptomic, metagenomic, and metabolomic findings demonstrate that YT alleviates DEX-induced hepatic steatosis through dual mechanisms involving direct hepatic antioxidant and lipid metabolic regulation and systemic modulation via the gut-liver axis, positioning it as a promising dietary strategy against glucocorticoid-associated metabolic complications.}, }
@article {pmid42207032, year = {2026}, author = {Giani, N and John, J and Campbell, B}, title = {Shotgun metagenomics and metatranscriptomics of soil microbial communities under monoculture and polyculture cover crops.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0030926}, doi = {10.1128/mra.00309-26}, pmid = {42207032}, issn = {2576-098X}, abstract = {Here, we present 30 metagenomes, 21 metatranscriptomes, and 334 metagenome-assembled genomes collected from soils under different cover crop species. This data set will be useful for studying microbial interactions, especially functional redundancy, with relevance to agricultural management and sustainability.}, }
@article {pmid42207051, year = {2026}, author = {Sutanto, TPW and Pratama, A and Ishii, E and Iida, T and Matsuda, S}, title = {TsrA modulates type III secretion system 2 expression as a co-regulator of H-NS in Vibrio parahaemolyticus.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0055625}, doi = {10.1128/jb.00556-25}, pmid = {42207051}, issn = {1098-5530}, abstract = {Vibrio parahaemolyticus, a gram-negative marine bacterium, is a major cause of seafood-borne gastroenteritis worldwide. This pathogen relies on type III secretion system 2 (T3SS2), which is encoded on a pathogenicity island, for its enteropathogenicity. Expression of T3SS2 is activated by a regulatory pathway centered on the transcriptional activator VtrB, which is antagonized by the xenogeneic silencer, histone-like nucleoid-structuring protein (H-NS). However, the complete transcriptional network is not yet fully understood. In this study, we identified TsrA as a negative regulator of T3SS2 gene expression. TsrA is a small protein conserved among Vibrio species that lacks a putative DNA-binding motif but has been implicated in the regulation of virulence genes in Vibrio cholerae. In V. parahaemolyticus, deletion of tsrA increased VtrB production and T3SS2 secretion, thereby enhancing T3SS2-dependent pathogenicity. Transcription of vtrB occurs via a two-step activation process, in which TsrA affects the primary activation step, thereby modulating VtrB production. We further provide experimental evidence that TsrA physically interacts with H-NS via its C-terminal region, which correlates with its regulatory activity on vtrB expression. A systematic mutational analysis of the C-terminal 26 residues revealed several residues critical for TsrA regulatory activity. Moreover, the regulatory effect of TsrA on T3SS2 gene expression was dependent on H-NS, demonstrating that TsrA functions in concert with H-NS. Thus, our findings provide new insights into the regulatory mechanisms of virulence gene expression in V. parahaemolyticus by defining the role of TsrA in this network, while also placing TsrA among H-NS co-regulators.IMPORTANCENucleoid-associated proteins (NAPs) play key roles in virulence gene regulation in bacteria. The best-studied NAP is H-NS, which often functions with co-regulators to fine-tune gene expression. TsrA, a small protein lacking a DNA-binding motif conserved among Vibrio species, has been suggested to be functionally related to H-NS in Vibrio cholerae, although its mechanism remains unknown. Here, we demonstrate that TsrA negatively regulates the expression of type III secretion system 2 (T3SS2), a major virulence determinant of Vibrio parahaemolyticus, an important seafood-borne pathogen. TsrA modulates the transcription of vtrB, which encodes the essential activator for T3SS2 expression, through direct physical interaction with H-NS. Our findings reveal a molecular link between TsrA and H-NS, providing mechanistic insights into NAP- and TsrA-mediated regulation of virulence in Vibrio.}, }
@article {pmid42207344, year = {2026}, author = {Cagirgan, OY and Korkmaz, S and Diker, KS}, title = {Intestinal microbiome in necrotic enteritis infection of broiler and comparison of treatment alternatives.}, journal = {Tropical animal health and production}, volume = {58}, number = {5}, pages = {}, pmid = {42207344}, issn = {1573-7438}, support = {VTF-190002//Bilimsel Ara&#x15f;t&#x131;rma Projeleri Birimi, Ayd&#x131;n Adnan Menderes &#xdc;niversitesi/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Clostridium Infections/veterinary/microbiology/drug therapy ; *Poultry Diseases/microbiology/drug therapy ; *Enteritis/veterinary/microbiology/drug therapy ; Clostridium perfringens/physiology ; Anti-Bacterial Agents/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Bacillus/physiology ; *Probiotics/administration &amp; dosage ; Amoxicillin/therapeutic use/administration &amp; dosage ; Necrosis/veterinary/microbiology ; Male ; }, abstract = {Clostridium perfringens is the primary causative agent of necrotic enteritis (NE), a gastrointestinal disease that leads to substantial economic losses in poultry. This study aims to characterize the intestinal microbiome of chickens and assess the effects of Bacillus velezensis on gut microbiota and recovery from necrotic enteritis, comparing its efficacy to antibiotic treatment. The experiment involved five groups, each consisting of 16 chickens. The first group, the start-of-challenge (DB) group, included day-old chicks. The second group, the post-challenge control (DS) group, was reared until the end of the trial. The third group was infected with C. perfringens (NE group). The fourth group received both C. perfringens and B. velezensis (BV group), while the fifth group was treated with C. perfringens and amoxicillin (AB group). All chickens were euthanized via cervical dislocation following the experimental infection. Fecal samples collected from the cecum underwent 16 S rRNA gene-based metagenomic analysis, and the resulting data were statistically evaluated. Macroscopic examination after euthanasia revealed pathological changes in the intestines of chickens in the NE group, which had received only C. perfringens. Their intestines appeared swollen, with slight mild mucosal hemorrhage. In contrast, no macroscopic lesions were observed in the DB, DS, BV, or AB groups. Microbiome analysis showed a decline in microbial diversity within the NE group. The BV group exhibited a microbial composition most similar to that of healthy animals, followed by the AB group. The study concludes that B. velezensis could serve as an alternative to prophylactic antibiotics in mitigating the adverse effects of necrotic enteritis on the gut microbiome.}, }
@article {pmid42207373, year = {2026}, author = {Shao, C and Li, J and Huang, C and Tang, M and Zeng, J and Zhou, W and Zhang, D and Zeng, G and Wang, J and Hua, T and Zhong, C and Hu, J and Xu, X}, title = {Clinical utility of metagenomic next-generation sequencing in precision diagnosis of infectious diseases: a retrospective study based on bronchoalveolar lavage fluid, blood, and cerebrospinal fluid.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42207373}, issn = {1435-4373}, support = {20170522160421261//Bao'an District Science and Technology Program/ ; 2023B110008//Guangdong Provincial Clinical Research Center for Laboratory Medicine/ ; }, abstract = {RESEARCH BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a culture-independent pathogen identification method, which can directly sequence all nucleic acids present in clinical samples, and has shown transformative potential in the diagnostic field of complex, critical and emerging infectious diseases, but its clinical application value has not been fully evaluated. This study aims to compare the diagnostic efficacy of mNGS and traditional microbiological testing (TMT), and evaluate its impact on clinical decision-making.<br><br>RESEARCH METHODS: This retrospective study analyzed the data of the laboratory information system (LIS) of patients who received both mNGS and TMT testing.<br><br>RESEARCH RESULTS: In samples of bronchoalveolar lavage fluid (BALF), blood and cerebrospinal fluid (CSF), the positive rates of mNGS were 86.70%, 77.17% and 53.57% respectively, which were significantly higher than the corresponding positive rates of TMT (41.38%, 14.13%, 17.86%). Clinical correlation analysis showed that 77.84%, 66.20% and 73.33% of the positive mNGS results of the three types of samples were of clinical significance respectively. 15.34%~29.58% of the cases adjusted their treatment regimens according to the positive mNGS results, and 33.33%~61.54% of the cases adjusted their treatment regimens according to the negative mNGS results. Most patients who had their treatment adjusted showed improvement or relief of symptoms. Overall, various pathogenic microorganisms were detected in more than 60% of the samples.<br><br>RESEARCH CONCLUSION: This study confirms the significant advantages of mNGS in the precise diagnosis of infectious diseases, as well as its value in guiding individualized treatment strategies.}, }
@article {pmid42208188, year = {2026}, author = {Gilevska, T and Rotaru, AE and Anestis, K and Fonseca, A and Kümmel, S and Krauss, M and Inostroza, PA and Bonaglia, S}, title = {Wastewater-impacted Skagerrak Sea microbiomes anaerobically demethylate micropollutants.}, journal = {Water research}, volume = {302}, number = {}, pages = {126138}, doi = {10.1016/j.watres.2026.126138}, pmid = {42208188}, issn = {1879-2448}, abstract = {Methylated micropollutants such as naproxen and caffeine persist in wastewater effluents and accumulate in coastal sediments, including Hakefjorden, Skagerrak Sea, yet their anaerobic fate and role in methane emissions remain unresolved. In particular, it is unclear whether pollutant-derived methyl groups are routed mainly to CO2 or can be transformed into CH4 in sulfate-rich coastal sediments. Our primary objective was to resolve this routing by tracing the fate and microbiome responses to [13]C-labeled naproxen and caffeine in sediment microcosms. We show that naproxen underwent rapid O-demethylation to desmethylnaproxen, with 90% ± 15.5% removed within 25 days, producing primarily [13]CO2 and some [13]CH4. Naproxen enriched methylotrophic and hydrogenotrophic Methanomicrobia, alongside Lokiarchaeia, Bathyarchaeia, and bacterial taxa like Eubacterium (Alkalibaculum A sporogenes) and Syntrophomonadaceae. Metagenomics revealed O-demethylation genes in enriched bacterial MAGs affiliated with uncultured Thermoanaerobaculia, indicating a bacterial demethylation potential. In contrast, caffeine was largely recalcitrant to degradation (∼85% ± 5% remaining), yet its [13]C-labeled N-methyl groups fueled trace [13]CH4 production. These results show that methylated micropollutants can activate both bacterial and archaeal demethylation pathways in coastal sediment microbiomes.}, }
@article {pmid42208292, year = {2026}, author = {Majumdar, A and Bagchi, D and Kotta-Loizou, I and Buck, M}, title = {The One Health resistome: Integrating environmental, microbial, and human antimicrobial resistance surveillance and risk analysis in the digital age.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142431}, doi = {10.1016/j.jhazmat.2026.142431}, pmid = {42208292}, issn = {1873-3336}, abstract = {Antimicrobial resistance (AMR) and antibiotic resistance (ABR) represent one of the most pressing global health threats, driven by the complex interplay between human, animal, and environmental factors. The One Health resistome framework recognises that resistance genes circulate continuously across clinical, agricultural, and environmental compartments through horizontal gene transfer, co-selection mechanisms, and anthropogenic contamination. This comprehensive review synthesises current evidence on integrated AMR surveillance, examining how digital technologies are transforming our capacity to monitor, predict, and respond to resistance emergence. Key advances include whole-genome sequencing enabling high-resolution pathogen tracking, metagenomics revealing environmental resistome diversity, machine learning algorithms predicting resistance phenotypes with > 85% accuracy, and point-of-care diagnostics extending sophisticated testing to resource-limited settings. Geographic information systems facilitate spatial hotspot identification, while wastewater-based surveillance provides early warning capabilities, detecting resistance genes before clinical manifestation. Despite technological progress, substantial challenges persist: fragmented data streams across sectors, lack of standardised environmental monitoring methods, limited laboratory capacity in low- and middle-income countries, and chronic underfunding. Emerging technologies, portable nanopore sequencing, CRISPR-based diagnostics, artificial intelligence, and blockchain-enabled data governance promise to address these gaps. Realising comprehensive One Health resistome surveillance requires sustained investment in interoperable digital infrastructure, international standardisation, capacity building, and political commitment to cross-sectoral coordination, prioritising equitable global implementation.}, }
@article {pmid42208296, year = {2026}, author = {Wang, Q and Ma, Y and Niu, J and Liu, Y and Chao, C and Zhao, Y}, title = {Enhanced anti-toxicity memory of Cr(VI)-4-CP stressed denitrification by bio-promoter: Microbial cooperation and multi-path electron transfer drive toxics transformation-migration.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142497}, doi = {10.1016/j.jhazmat.2026.142497}, pmid = {42208296}, issn = {1873-3336}, abstract = {Coexisting heavy metals and organic pollutants in industrial wastewaters posed synergistic inhibition to denitrification by activating dissimilatory nitrate reduction and disrupting electron supply-consumption balance. Taking Cr(VI) and 4-chlorophenol (4-CP) as representative pollutants, this study proposed a combined bio-promoter composed of growth factors and phosphomolybdic acid (PMo12) to accelerate recovery and establish anti-toxicity memory under compound stress. The promoter restored over 90% nitrogen removal within 9 T and maintained 63.6% nitrogen removal under Cr(VI)-4-CP re-stress. Compared to first-stress, the recovered system reduced 37.44 mg/L more Cr(VI) and kept 4-CP below 5 mg/L, thus rapidly relieving Cr(VI)-4-CP toxicity and increasing the supply of direct electron donor nicotinamide adenine dinucleotide (NADH, 65.5%) and energy source adenosine triphosphate (ATP, 27.8%). Meanwhile, the enhanced extracellular polymeric substance (EPS) ensured 11.15 mg/g mixed liquid suspended solids (MLSS) more chromium immobilization with 97.9% distributed intercellularly, preventing Cr(VI) from invading cells and minimizing intracellular oxidative damage. The biofilm-fixed Mo (4.28 mg/g MLSS) shortened electron transfer distance to NO3[-]-N, which, combined with a 17.3% increase in cytochrome (cyt.c), formed a new mode of multi-path electron transfer. Microbacterium with glucose-4-CP co-metabolism and denitrification functions contributed 13.0% of the recovered community, transforming glucose and 4-CP competitive metabolism into collaborative metabolism, further enhancing the anti-toxicity memory, and ensuring efficient denitrification performance.}, }
@article {pmid42208547, year = {2026}, author = {Goldberg, H and Dyhrman, ST and DeMers, MA and Braakman, R and Hennon, GMM}, title = {Forces Shaping Diversity of Hydrogen Peroxide Detoxification Potential in Ocean Microbial Ecosystems.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70315}, doi = {10.1111/1462-2920.70315}, pmid = {42208547}, issn = {1462-2920}, support = {OCE-1937715//National Science Foundation/ ; OCE-2019589//National Science Foundation/ ; }, mesh = {*Hydrogen Peroxide/metabolism ; *Seawater/microbiology ; *Catalase/genetics/metabolism ; Ecosystem ; Oceans and Seas ; *Bacteria/genetics/metabolism/classification ; Bacterial Proteins/genetics/metabolism ; Metagenome ; *Microbiota ; Genome, Bacterial ; }, abstract = {Microbial communities have evolved interactions to support growth and essential ecosystem functions. For example, marine cyanobacteria like Prochlorococcus lack the catalase genes (katE, katG and manganese catalase) required for detoxifying freely-diffusible hydrogen peroxide, relying on co-occurring catalase-carrying 'helper' microbes for this function. However, the eco-evolutionary forces shaping catalase distribution are not well understood. We examined genomes, metagenome-assembled genomes (MAGs), and metagenomes to assess catalase gene distributions across diverse marine prokaryotes-including within the known 'helper' genus Alteromonas-and across surface ocean ecosystems. Within Alteromonas, most genomes contain two katE copies, while katG copy number varies across species. Across ecosystems, the Altermonadaceae family is the predominant katE carrier. Some taxa (e.g., SAR202) lack all catalases, highlighting their dependence on 'helpers'. Overall, streamlined genomes, including from SAR11, generally have one katG copy and lack katE, while larger genomes with higher GC content characteristic of copiotrophs have more copies of both catalases. Finally, in free-living communities, katG gene frequency increases with decreased particulate organic carbon (POC) concentrations, whereas in particle-associated communities, katE gene frequency increases with elevated POC. Together, these observations suggest that hydrogen peroxide detoxification capabilities are widespread and shaped by the contributions of particle-associated microbes to total community metabolism.}, }
@article {pmid42208809, year = {2026}, author = {Korva, M and Bogovič, P and Knap, N and Kogoj, R and Slunečko, J and Zakotnik, S and Suljič, A and Resman Rus, K and Pozvek, P and Strle, F and Avšič-Županc, T and Petrovec, M}, title = {Emerging human pathogen: Identifying Spiroplasma ixodetis as a frequent cause of unlocalised febrile illness.}, journal = {The Journal of infection}, volume = {93}, number = {1}, pages = {106776}, doi = {10.1016/j.jinf.2026.106776}, pmid = {42208809}, issn = {1532-2742}, abstract = {OBJECTIVES: Febrile illness without clear localisation presents a significant diagnostic challenge due to non-specific symptoms and diverse aetiologies. Spiroplasma ixodetis, an emerging tick-associated pathogen previously linked mainly to congenital cataracts, has not been well characterised in adults. We investigated the prevalence and clinical features of S. ixodetis infection in adults with acute febrile illness without localisation.<br><br>METHODS: Shotgun metagenomic sequencing identified S. ixodetis in the initial 209 patient cohort and the sequences were used to developed a novel real-time PCR assay targeting the 23S rRNA gene. Initial cohort screening was followed by testing 128 patients from an additionally selected targeted cohort. Positive results were confirmed by sequencing of 16S and 23S rRNA genes.<br><br>RESULTS: S. ixodetis DNA was confirmed in 7.2% patients from the initial and in 35.2% patients from the additional cohort (60 in total). All were identified in the period from April to October and 57% reported a recent tick-bite. Clinical presentation was homogenous, characterised by fever, headache, bicytopenia and liver enzyme abnormalities. Outcomes were favourable, with 15% requiring hospitalisation.<br><br>CONCLUSION: This study identifies S. ixodetis as a previously unrecognised cause of adult febrile illness without localisation, bridging the gap between previously published data between tick studies and isolated human case reports.}, }
@article {pmid42208810, year = {2026}, author = {Vasil, E and Papanicolas, LE and Miller, SJ and Shoubridge, AP and Taylor, SL and Rogers, GB}, title = {Exposure to antibiotics with anaerobe coverage in later life is associated with higher enteric pathobiont carriage.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {106774}, doi = {10.1016/j.jinf.2026.106774}, pmid = {42208810}, issn = {1532-2742}, abstract = {OBJECTIVES: Infections involving enteric bacteria commonly cause hospitalisation and death in long-term residential aged care (LTC) populations. The risk of such infections has been linked with antibiotic-associated depletion of gut anaerobic commensals and the resulting increase in asymptomatic carriage of gut pathobionts. We sought to determine how antibiotic characteristics, particularly activity against anaerobes, influence pathobiont prevalence in LTC residents.<br><br>METHODS: Stool samples from 164 LTC residents (median age: 87.9 years, interquartile range: 81.3-93.0 years) underwent metagenomic analysis. Associations between prior antibiotic exposures (categorised according to anaerobe coverage and type) and gut microbiome characteristics were explored using multivariable models.<br><br>RESULTS: Of the 164 participants, 138 (84.1%) carried at least one enteric pathobiont. Compared to those with no prior antibiotic exposure, treatment with anaerobe covering (EAC) antibiotics was associated with higher rates of pathobiont carriage (&#x3b2;=1.36, P=0.010) and higher overall pathobiont relative abundance (&#x3b2;=3.53, P=0.013). In contrast, exposure to antibiotics with limited anaerobe coverage (LAC) showed no such associations. Investigation of commonly prescribed EAC and LAC antibiotics (amoxicillin-clavulanate and cefalexin, respectively) were consistent with these findings, with higher detection (&#x3b2;=1.60, P=0.007) and relative abundance (&#x3b2;=3.32, P=0.039) of pathobiont species in amoxicillin-clavulanate recipients. Pathobionts with greater representation included both species with inherent resistance (i.e. Enterococcus faecium) and sensitivity (i.e. Klebsiella pneumoniae) to amoxicillin-clavulanate.<br><br>CONCLUSIONS: Antibiotics that deplete commensal anaerobes are associated with pathobiont prevalence in the gut, even where pathobiont species are sensitive to the administered antibiotic. Off-target disruption of commensal anaerobes should be considered when selecting antibiotic treatments, particularly for LTC individuals.}, }
@article {pmid42208932, year = {2026}, author = {Lv, H and Jin, S and Li, L and Ma, S and Wang, Y and Zhang, Y and Guo, K}, title = {Diagnostic Accuracy of Metagenomic Next-Generation Sequencing for Invasive Pulmonary Aspergillosis: A Systematic Review and Meta-Analysis.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108827}, doi = {10.1016/j.ijid.2026.108827}, pmid = {42208932}, issn = {1878-3511}, abstract = {OBJECTIVES: To systematically evaluate the diagnostic accuracy of metagenomic next‑generation sequencing (mNGS) for invasive pulmonary aspergillosis (IPA), and to compare its sensitivity and specificity with conventional methods.<br><br>METHODS: Meta&#x2011;analysis was performed to pool sensitivity, specificity, and diagnostic odds ratio (DOR). The comparison test between mNGS and conventional diagnostic methods was conducted through pairwise comparisons, and effect size was expressed using the risk difference (RD) and 95% confidence interval.<br><br>RESULTS: Twelve studies were included, the pooled sensitivity of mNGS was 0.75 (95% CI: 0.65-0.84), specificity 0.93 (95% CI: 0.84-0.97), DOR 35.69 (95% CI: 13.70-92.97). The comparative analysis showed mNGS had higher sensitivity compared with galactomannan (RD&#x202f;=&#x202f;0.22, 95% CI: 0.16-0.29), culture (RD&#x202f;=&#x202f;0.40, 95% CI: 0.26-0.55), and (1&#x2192;3)-&#x3b2;-D-glucan (BDG) (RD&#x202f;=&#x202f;0.23, 95% CI: 0.09-0.37). For BDG assay, mNGS also demonstrated superior specificity (RD&#x202f;=&#x202f;0.12, 95% CI: 0.04-0.20).<br><br>CONCLUSION: mNGS demonstrates promising diagnostic accuracy for IPA, with favorable sensitivity and specificity, and shows higher sensitivity than several conventional methods. BALF is the preferred specimen, and combined testing with multiple sample types improves diagnostic yield.}, }
@article {pmid42208954, year = {2026}, author = {Baker, B and Baz Lomba, JA and Bitilinyu-Bangoh, J and Berglöf, A and Bombaywala, S and Calvert-Joshua, T and Kaboré, B and Kingpriest, P and Lang, T and Levy, JI and Lompo, P and Lyimo, E and Martens, L and Mavoko, HM and Mesuere, B and Moremi, N and Mulder, N and Ndure, SL and Rameto, MA and Rinke de Wit, TF and Sebukoto, H and Smith, E and Tahita, MC and Tevuzula, VM and Tippett Barr, BA and Tiwari, A and Tran, T and Ubomba-Jaswa, E and Van Den Bossche, T and Wolday, D and Krolicka, A and Baraka, V and Pitkänen, T and Lood, R}, title = {Project ODIN: advancing environmental genomic surveillance for public health across sub-Saharan Africa.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101426}, doi = {10.1016/j.lanmic.2026.101426}, pmid = {42208954}, issn = {2666-5247}, abstract = {Persistent SARS-CoV-2 transmission, ongoing mpox outbreaks, and the continued spread of endemic diseases such as typhoid fever and cholera underscore the urgent need for global, multiomics surveillance. In this Personal View, we present Project ODIN, a consortium of European and African partners launched in 2023 that aims to meet this challenge by deploying innovative systems for near real-time pathogen detection and actionable public health insights. The project is a collaboration between high-income and low-income countries in northern Europe and sub-Saharan Africa. Focusing on low-income and middle-income countries, ODIN integrates metagenomics with mobile laboratory systems for comprehensive pathogen monitoring across diverse environments. ODIN emphasises standardised sampling, bioinformatics pipelines, and data-sharing protocols to ensure reliable, interoperable results while addressing infrastructure and resource limitations. By bridging gaps in genomic surveillance, these initiatives seek to strengthen outbreak preparedness, improve pathogen detection, monitor antimicrobial resistance, and provide a holistic approach to One Health challenges. Together, these innovations could advance global surveillance capacity-particularly in under-resourced regions-paving the way for effective disease control and evidence-based policy making.}, }
@article {pmid42209028, year = {2026}, author = {Hoeter, K and Marriott, L and Neuberger, EWI and Dagwadordsch, U and Kumar, RS and Simon, P and Bodenstein, M and Kersaudy-Kerhoas, M}, title = {Plasma metagenomic cfDNA sequencing identifies pathogens in culture-negative sepsis following urinary pouch rupture.}, journal = {BMJ case reports}, volume = {19}, number = {5}, pages = {}, doi = {10.1136/bcr-2025-267878}, pmid = {42209028}, issn = {1757-790X}, mesh = {Humans ; Female ; *Sepsis/microbiology/diagnosis/drug therapy/blood ; Anti-Bacterial Agents/therapeutic use ; *Cell-Free Nucleic Acids/blood ; *Pseudomonas Infections/diagnosis/drug therapy/blood ; Metagenomics/methods ; *Klebsiella Infections/diagnosis/drug therapy/blood ; Rupture, Spontaneous ; Klebsiella/isolation &amp; purification/genetics ; }, abstract = {A patient with a complex urological history presented with abdominal pain and respiratory distress after catheter dysfunction. She underwent emergency surgery for a ruptured urinary pouch. Sepsis was later diagnosed based on clinical deterioration, including tachycardia, fever, an elevated respiratory rate and raised inflammatory markers, but blood cultures remained negative. A metagenomic microbial cell-free DNA (cfDNA) assay (iSEP-SEQ), performed early from plasma as part of a research protocol, identified Klebsiella and Pseudomonas at the genus level. Results were obtained retrospectively and were not available in real time; therefore, they did not alter immediate management. These findings were confirmed by cultures from drainage fluid and urine. Broad-spectrum antibiotic treatment led to clinical improvement. This case highlights the limitations of conventional microbiological methods in culture-negative sepsis and illustrates the role of cfDNA-based metagenomic testing as an adjunctive and complementary diagnostic tool for early, accurate pathogen detection. Early use of such tools may support timely and targeted management in complex infectious disease presentations.}, }
@article {pmid42209192, year = {2026}, author = {Leggio, M and Schramm, S and Dietz, L and Ocón, B and Wirtz, S and Puertolas Balint, F and Yilmaz, B and Petzold, J and Liu, LJ and Dedden, M and Ekici, A and ,  and Meng, X and Bingham, D and Ullrich, KA and Heltmann-Meyer, S and Günther, C and Hildner, K and Atreya, R and Atreya, I and Müller, TM and Gerlach, RG and Schroeder, BO and Macpherson, A and Butcher, EC and Neurath, MF and Zundler, S and , }, title = {The endogenous peptide GPR15L shapes the intestinal microbiota to counteract colitis.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-337619}, pmid = {42209192}, issn = {1468-3288}, abstract = {BACKGROUND: The peptide GPR15L is produced by colonic epithelial cells and has been implicated in T cell recruitment to the large intestine. However, its role in chronic colitis has been unclear so far.<br><br>OBJECTIVE: To explore the role of GPR15L in the pathogenesis of experimental colitis and IBD.<br><br>DESIGN: We studied how genetic deletion or overexpression of Gpr15l as well as rectal application of recombinant GPR15L alters the course of acute dextran sodium sulfate colitis and T cell transfer colitis. The impact of GPR15L on microbiota was explored with co-housing, littermate and faecal microbiota transfer studies, by 16S rRNA sequencing as well as anti-microbial assays and shotgun metagenomics. The expression of GPR15L was evaluated across three independent cohorts of patients with IBD and correlated to microbial diversity and flare-free survival.<br><br>RESULTS: GPR15L clearly mitigated experimental colitis, but this was independent of T cell recruitment and GPR15. Instead, we observed that the effects of GPR15L were mediated by altered microbiomes in the large intestine and, consistently, showed that GPR15L acts as an antimicrobial peptide under anaerobic conditions and shapes microbial communities towards a homeostatic phenotype. Rectal supplementation of GPR15L counteracted experimental colitis. In patients with IBD, GPR15L expression was decreased in active inflammation, correlated with microbial diversity and was associated with flare-free survival.<br><br>CONCLUSIONS: GPR15L is a host-defence peptide that plays a beneficial role in the pathogenesis of intestinal inflammation. It seems promising to further evaluate its potential as a future therapeutic approach in IBD.}, }
@article {pmid42209465, year = {2026}, author = {Ghiotto, G and Zampieri, G and Orellana, E and Chatzis, A and Kougias, PG and Camargo, A and Roux, S and Campanaro, S and Kyrpides, NC and Treu, L}, title = {Single nucleotide variants drive evolutionary phage-host arms race in anaerobic carbon dioxide-converting microbiome.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73084-2}, pmid = {42209465}, issn = {2041-1723}, abstract = {Microbial bioconversions are shaped by environmental perturbations and the adaptation of resident microbiomes. Prokaryotes coexist with bacteriophages, yet their coevolutionary trajectories remain underexplored. Here, we investigate the effects of a cultivation vessel leak on an anaerobic consortium performing carbon dioxide reduction. Using time-series shotgun metagenomic sequencing, we reconstruct microbial and viral genomes to track community shifts. We further apply single-nucleotide variant profiling and CRISPR array analysis to monitor viral microdiversity and host defense mechanisms. After bioaugmentation restores bioconversion efficiency, the consortium undergoes pronounced restructuring, with new dominant taxa emerging from the rare biosphere. We identify patterns consistent with phage predation selectively removing certain species, while others exhibit resilience to infection. This shift aligns with a widespread viral outbreak and a transient increased frequency of single nucleotide variants in bacterial CRISPR-Cas defense genes. Expansion of CRISPR spacers further supports that CRISPR-mediated processes influence microbial resilience. Concurrently, phages infecting resilient hosts exhibited adaptive evolution, marked by high genetic heterogeneity. Selective pressure varies across their genomes, targeting infectivity genes and protospacer-adjacent motifs. These findings highlight a dynamic evolutionary arms race driven by the selection of beneficial genetic variants, providing a mechanistic framework for multi-omics investigations, and informing biotechnological applications, including phage-based microbiome manipulation.}, }
@article {pmid42209510, year = {2026}, author = {Dommann, J and Sprecher, VP and Beisel, C and Ballmer, D and Hürlimann, E and Coulibaly, JT and Keiser, J and Schneeberger, PHH}, title = {Combined high-quality metagenomics reveals off-target effects of albendazole, ivermectin-albendazole and moxidectin-albendazole on the human gut bacteria.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01018-3}, pmid = {42209510}, issn = {2055-5008}, support = {101019223/ERC_/European Research Council/International ; 101019223/ERC_/European Research Council/International ; }, abstract = {Human whipworm infections caused by Trichuris trichiura and Trichuris incognita remain a major public health problem, affecting over 400 million people globally and responding poorly to standard benzimidazole chemotherapy. Ivermectin-albendazole and moxidectin-albendazole have emerged as promising combination therapies, but recent in vitro evidence suggests that ivermectin and moxidectin may also affect gut bacteria. We therefore characterized their off-target effects on the gut microbiome in a randomized controlled trial including 204 Trichuris spp.-infected individuals in Côte d'Ivoire treated with albendazole (400 mg), ivermectin-albendazole (200 µg/kg/400 mg), or moxidectin-albendazole (8 mg/400 mg). By combining Illumina short reads and Nanopore long reads, we recovered over 800 high-quality metagenome-assembled genomes. Albendazole and moxidectin-albendazole induced taxonomic shifts with only mild functional consequences. In contrast, individuals receiving higher absolute ivermectin doses based on their bodyweight (≥ 15 mg) showed pronounced changes in taxonomic composition and microbial function, whereas the resistome remained largely stable. These findings confirm that ivermectin can exert antibacterial off-target effects in the human gut beyond those previously observed in vitro. Given its central role in parasite control, its broader microbiome effects warrant careful evaluation in future treatment strategies.}, }
@article {pmid42209552, year = {2026}, author = {Olszyński, RM and Mann, DG and Zakrzewski, PK and Peszek, &#x141; and Ács, &#xc9; and Shemesh, S and Trobajo, R}, title = {Nitzschia excavata sp. nov. (Bacillariaceae), a new diatom species from a post-mining reservoir revealed by morphology, molecular phylogeny, and metabarcoding-based biogeography.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42209552}, issn = {2045-2322}, support = {RRF 2.3.1 21 2022 00008//Sz&#xe9;chenyi Plan Plus programme/ ; RRF 2.3.1 21 2022 00008//Sz&#xe9;chenyi Plan Plus programme/ ; }, mesh = {*Diatoms/genetics/classification/ultrastructure ; *Phylogeny ; *DNA Barcoding, Taxonomic ; Phylogeography ; Mining ; DNA, Ribosomal/genetics ; Poland ; }, abstract = {The Bogdałów post-mining reservoir (Poland) represents a slightly alkaline, moderately mineralised ecosystem formed by flooding a former lignite pit. Its anthropogenic origin and stable physicochemical conditions have enabled the development of species-rich diatom assemblages, particularly numerous Nitzschia (Bacillariaceae) species. To explore this diversity, an integrative approach combining microscopy and DNA-based analyses was employed. Morphological examinations were performed using light and scanning electron microscopy, as well as confocal laser scanning microscopy. Molecular phylogenetic analyses were based on the sequencing of the nuclear SSU rDNA and the chloroplast rbcL and psbC gene markers. This comprehensive study led to the discovery and formal description of Nitzschia excavata sp. nov., distinguishable by unique morphological features and a phylogenetically distinct lineage. Furthermore, environmental DNA metabarcoding and metagenomic database searches revealed sequences identical or closely related to the N. excavata sp. nov. lineage in freshwater habitats across Europe and China, indicating that this taxon has an unexpectedly broad distribution. These findings underscore the value of integrating classical morphological analysis with multi-marker molecular data in diatom taxonomy and demonstrate that anthropogenic habitats may support taxa with broader distributions than previously recognized. The study highlights the important role of metabarcoding and metagenomics in revealing cryptic diversity and clarifying the biogeographic patterns of newly described species.}, }
@article {pmid42209868, year = {2026}, author = {Ajeh, IJ and Ikukpla'si, OSI}, title = {The non-bacterial oncobiome: the role of the mycobiome and virome in tumor plasticity.}, journal = {Journal of the Egyptian National Cancer Institute}, volume = {38}, number = {1}, pages = {}, pmid = {42209868}, issn = {2589-0409}, mesh = {Humans ; Tumor Microenvironment ; *Neoplasms/pathology/microbiology/virology ; *Mycobiome ; *Virome ; Epithelial-Mesenchymal Transition ; Cell Plasticity ; }, abstract = {Tumor plasticity, the capacity of malignant cells to undergo reversible phenotypic switching, is a fundamental driver of lineage diversion and therapeutic resistance. While the bacterial microbiome is a recognized modulator of the tumor microenvironment (TME), the non-bacterial oncobiome, comprising the mycobiome (fungi) and virome (viruses), represents a critical but under-explored frontier in cellular adaptability. This review synthesizes current evidence regarding the mechanistic contributions of fungal and viral constituents to tumor plasticity and characterizes the molecular cross-talk that facilitates host cell reprogramming. We conducted a structured narrative synthesis of literature indexed in PubMed, Scopus, and Web of Science (2020-2026), focusing on high-throughput studies such as ITS sequencing, metagenomics NGS (mNGS), and single-cell network analyses. We specifically evaluated evidence concerning the activation of host pattern recognition receptors and the subsequent transcriptional rewiring of lineage-defining markers. Emerging data indicate that fungal dysbiosis, particularly involving Candida and Malassezia species, triggers the Dectin-1/STAT3 signaling axis, a known inducer of epithelial-mesenchymal transition (EMT). Concurrently, the virome, ranging from integrated oncoviruses to reactivated endogenous retroviruses (ERVs), is shown to hijack the Wnt/ β-catenin pathway, enforcing a progenitor-like stemness state. This inter-kingdom synergy promotes an immune-excluded niche, effectively shielding plastic sub-populations from cytotoxic stress and targeted therapies. The non-bacterial oncobiome provides genomic momentum and inflammatory cues necessary to lower the threshold for phenotypic switching. This review highlights that stabilizing the TME ecosystem through ecologically targeted therapy may be a prerequisite for overcoming drug resistance and improving clinical outcomes in refractory cancers.}, }
@article {pmid42210135, year = {2026}, author = {Feng, W and Xiao, H and Hu, B and Chen, T and Hu, H and Guo, L and Guo, X and Zhu, L and Liu, G}, title = {Clinical characteristics, diagnosis, and management of central nervous system aspergillosis in children: a single-center experience.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13675-y}, pmid = {42210135}, issn = {1471-2334}, support = {2024-1-2092//Capital's Funds for Health Improvement and Research/ ; 2-1-2-6-15//2022 Beijing Major Epidemic Prevention and Control Specially Construction Project/ ; PX2024042//Beijing Municipal Administration of Hospitals Incubating Program/ ; }, abstract = {BACKGROUND: Central nervous system (CNS) aspergillosis is a severe and frequently misdiagnosed infection in pediatric patients. Systematic pediatric data on its clinical, radiological, diagnostic, and therapeutic features remain limited.<br><br>METHODS: We retrospectively identified children aged 0-18 years with proven or probable CNS aspergillosis admitted to Beijing Children's Hospital between January 2010 and December 2024. Demographic, clinical, laboratory, and imaging data were collected. Treatment regimens and clinical outcomes were systematically evaluated.<br><br>RESULTS: Sixteen patients were included (12 males), with a median age of 5 years. Hematological malignancies were the most common predisposing factor. Notably, 25% (4/16) of patients lacked identifiable predisposing conditions. Clinical presentations were nonspecific, with fever, seizures, and impaired consciousness being the most common features, and an initial misdiagnosis occurred in 56.3% (9/16) of cases. In contrast to the low yield of cerebrospinal fluid (CSF) cultures, CSF metagenomic next-generation sequencing (mNGS) detected Aspergillus nucleic acids in all tested patients (7/7). Magnetic resonance imaging (MRI) most commonly revealed irregular cerebral abscesses (14/16), frequently accompanied by meningeal enhancement (14/16) and obstructive hydrocephalus (10/16). Among evaluable patients receiving initial voriconazole monotherapy, a partial response was observed in 22.2% (2/9). Conversely, higher response rates were observed with regimens containing liposomal amphotericin B (L-AmB), including initial combination therapy (75.0%) and salvage treatment (80.0%). The all-cause mortality rate was 37.5% (6/16), and moderate-to-severe disability was present in 30.0% (3/10) of survivors.<br><br>CONCLUSIONS: Pediatric CNS aspergillosis can occur across a broad risk spectrum, often with nonspecific symptoms, leading to frequent misdiagnosis. Our findings support the early incorporation of CSF mNGS and comprehensive neuroimaging (including whole-neuraxis MRI when clinically indicated) to facilitate timely diagnosis and assess dissemination. The observed high rate of progression with initial voriconazole monotherapy and the relatively favorable responses associated with regimens containing L-AmB highlight the need for prospective pediatric studies to refine initial treatment strategies in severe disease.<br><br>CLINICAL TRIAL REGISTRATION: Not applicable.}, }
@article {pmid42210369, year = {2026}, author = {Pangestu, HS and Yang, I and Natasha, A and Rajoriya, S and Hennisa, H and Park, J and Park, K and Kim, J and Kim, SG and Klein, TA and Kim, HC and Oh, Y and Song, JW and Kim, WK}, title = {Molecular prevalence, genomic characterization, and zoonotic potential of novel paramyxovirus and hepacivirus in Alexandromys fortis, Republic of Korea.}, journal = {Veterinary research}, volume = {57}, number = {1}, pages = {}, pmid = {42210369}, issn = {1297-9716}, support = {ProMIS ID C0039-09-ME//Global Emerging Infections Surveillance Branch (GEIS)/ ; RS-2021-KS211475//Korea Institute of Marine Science and Technology promotion/ ; RS-2023-KH140418//Government-wide R&amp;D to Advance Infectious Disease Prevention and Control, Republic of Korea/ ; 2024-ER2502-00//Korea National Institute of Health Research Project/ ; RS-202300249142//Basic Science Research Program through the NRF by the Ministry of Education/ ; NF22SA0082041//Novo Nordisk Foundation PAD award to CBL/ ; U01 AI151810/AI/NIAID NIH HHS/United States ; 2023R1A2C2006105//Basic Research Program through the NRF grant funded by the Korean government (MSIT)/ ; RS-2024-00400152//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET) through High-Risk Animal Infectious Disease Control Technology Development Program, funded by Ministry of Agriculture, Food and Rural Affairs/ ; }, mesh = {Animals ; Republic of Korea/epidemiology ; *Genome, Viral ; Phylogeny ; *Arvicolinae/virology ; *Paramyxoviridae Infections/veterinary/epidemiology/virology ; *Rodent Diseases/virology/epidemiology ; *Zoonoses/virology/epidemiology ; Prevalence ; *Paramyxoviridae/genetics/isolation &amp; purification ; *Hepatitis C/virology/epidemiology/veterinary ; }, abstract = {Rodents are substantial reservoirs of zoonotic viruses with regular human exposure restricted to a limited number of species. Numerous rodent species have been shown to harbor emerging viruses, including paramyxoviruses and hepaciviruses. Reed voles (Alexandromys fortis), a rodent species that inhabits grasslands and riparian environments throughout East Asia, remain poorly characterized in terms of their viral diversity. In this study, 258 A. fortis specimens collected from rural areas in Gyeonggi Province, Republic of Korea (ROK) were screened for paramyxoviruses and subjected to metagenomic next-generation sequencing. Genome characterization, phylogenetic and cophylogenetic assessments, and prediction of signal peptidase cleavage sites were performed to analyze the molecular features of the identified viruses. Zoonotic potential was evaluated using a genome-based machine-learning model. A nearly complete genome of a novel paramyxovirus, designated as Pyeongtaek Alexandromys paramyxovirus (PyAPV), was identified in six A. fortis specimens, with all sequences clustering within the genus Jeilongvirus. A nearly complete genome of a rodent-associated hepacivirus was also obtained from four specimens and classified as a distinct lineage within the species Hepacivirus J. These findings demonstrate the role of A. fortis as a natural reservoir of emerging viruses and expand current knowledge of rodent-associated viral diversity in the ROK.}, }
@article {pmid42210378, year = {2026}, author = {Han, J and Liu, J and Wang, T and Dong, B and Zhang, F and Li, S and Zou, Q and Li, D}, title = {Temporal variations in the gut microbiota of François' langur (Trachypithecus francoisi): implications for adaptation to seasonal dietary change and conservation.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00580-7}, pmid = {42210378}, issn = {2524-4671}, abstract = {Despite growing research on gut microbiota in wild primates, seasonal functional dynamics of the gut microbiota in this endangered folivorous species remain poorly understood. This study investigates the seasonal variations in the gut microbiota of François' langur (Trachypithecus francoisi) and their implications for dietary adaptation and conservation. Using shotgun metagenomic sequencing, fecal samples were collected across four seasons within the Mayanghe National Nature Reserve in China (n = 24). The study identified significant seasonal shifts in microbial diversity and composition. While alpha diversity metrics reflecting community evenness (Shannon and Simpson equivalents) remained stable (Padj > 0.05), species richness (Hill number, q = 0) was significantly lower in Fall compared to Spring and Winter (Padj = 0.013). Results revealed that dominant phyla included Bacillota and Bacteroidota, with a significant enrichment of Faecalibacterium during Fall. Functional analysis showed a predominance of carbohydrate metabolism, which remained stable at broad metabolic levels; however, fine-scale functional units (KOs and CAZy families) exhibited distinct seasonal signatures. A moderate correlation between taxonomic and functional profiles (Mantel r = 0.43, P = 0.001) suggests a partial decoupling. These findings highlight the ecological plasticity of the gut microbiota and underscore how taxonomic flexibility enables functional homeostasis, aiding the physiological resilience of endangered primates in fluctuating environments.}, }
@article {pmid42210496, year = {2026}, author = {Gourabi, MJR and Kargar, M and Kamali, A and Sharahi, JY}, title = {Fungal-Bacterial Interactions in Polymicrobial Infections: Hidden Threats.}, journal = {MicrobiologyOpen}, volume = {15}, number = {3}, pages = {e70320}, doi = {10.1002/mbo3.70320}, pmid = {42210496}, issn = {2045-8827}, mesh = {Humans ; *Coinfection/microbiology/drug therapy ; Biofilms/growth &amp; development ; *Microbial Interactions ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Candida albicans/physiology ; *Bacteria/drug effects ; *Fungi/physiology/drug effects ; *Mycoses/microbiology ; *Bacterial Infections/microbiology ; }, abstract = {Polymicrobial infections involving fungi and bacteria represent a major and increasingly recognized clinical challenge, in which interkingdom interactions significantly amplify disease severity, antimicrobial resistance, and treatment failure. Rather than passive co-existence, fungal-bacterial communities form highly coordinated systems driven by physical adhesion, quorum sensing, metabolic interdependence, and biofilm-mediated structural reinforcement. These cooperative interactions, exemplified by pairs such as Candida albicans-Staphylococcus aureus and Pseudomonas aeruginosa-Aspergillus fumigatus, promote the development of treatment-recalcitrant biofilms with enhanced immune evasion and multidrug tolerance. The global rise of multidrug-resistant (MDR) and extensively drug-resistant (XDR) pathogens has further intensified this burden, with polymicrobial biofilms now representing a post-antibiotic clinical scenario in which therapeutic failure is driven not by individual resistant organisms but by emergent, cooperative resistance architectures. Conventional diagnostic approaches remain insufficient, as culture-based methods frequently fail to capture the complexity of mixed microbial communities. Emerging technologies such as MALDI-TOF mass spectrometry, metagenomic sequencing, and fluorescence in situ hybridization offer improved resolution but are not yet fully integrated into routine clinical practice. Therapeutically, increasing evidence indicates that monotherapy is inherently inadequate in polymicrobial infections due to the emergent nature of microbial cooperation. Effective management therefore requires combination strategies that simultaneously target multiple pathogens and their shared biofilm infrastructure. These include antibiotic-antifungal combinations, phage therapy, enzymatic and nanoparticle-mediated biofilm disruption, metabolic interference, and host-directed immunomodulation. Importantly, recent advances also highlight the role of biophysical properties such as biofilm viscoelasticity and matrix stiffness as critical and previously underappreciated therapeutic targets. This review uniquely integrates biochemical, biophysical, and therapeutic dimensions of polymicrobial infections into a unified systems-level framework in which microbial cooperation is the central driver of pathogenesis, resistance, and treatment failure. Fungal-bacterial interactions are thereby positioned along a dynamic continuum from commensalism to pathogenesis, shaped by host susceptibility and environmental perturbations. Future progress will depend on interdisciplinary strategies combining multi-omics technologies, precision diagnostics, and microbiome-informed therapeutic design to effectively disrupt these complex microbial networks.}, }
@article {pmid42210528, year = {2026}, author = {Zhou, X and Zhang, M and Zhou, J and Han, J}, title = {Multi-target effects of Limosilactobacillus reuteri RE225 on hyperuricemia through xanthine oxidase inhibition, nucleoside degradation, gut microbiota modulation, and renal TLR4-NF-κB suppression.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.70749}, pmid = {42210528}, issn = {1097-0010}, support = {2024S138//Ningbo Public Welfare Research Program/ ; //K.C. Wong Magna Fund of Ningbo University/ ; }, abstract = {BACKGROUND: Hyperuricemia, a major risk factor for gout and kidney disease, requires safe and effective dietary strategies beyond conventional pharmacotherapy. This study investigated the multi-target effects of the food-grade probiotic Limosilactobacillus reuteri RE225 on hyperuricemia. It was evaluated in vitro for xanthine oxidase (XOD) inhibition and nucleoside degradation, and in vivo in hyperuricemic mice gavaged daily with low or high doses of RE225 (1 × 10[6] or 1 × 10[9] CFU). Serum uric acid (UA), XOD activity, inflammatory cytokines, intestinal permeability markers - fluorescein isothiocyanate-dextran (FITC-dextran), lipopolysaccharide (LPS), and d-lactate - and renal TLR4/NF-κB signaling were quantified. Fecal metagenomics and Kyoto Encyclopedia of Genes and Genomes ortholog (KO) profiling were used to assess microbiota structure and function.<br><br>RESULTS: Limosilactobacillus reuteri RE225 dose-dependently inhibited XOD and degraded more than 50% of nucleosides in vitro. In vivo, RE225 reduced serum urate, restored intestinal barrier function, suppressed inflammation, and downregulated renal TLR4/NF-&#x3ba;B signaling. Metagenomic analysis showed that L. reuteri RE225 reversed UA-induced loss of microbial richness and evenness, enriched Faecalibaculum and Erysipelotrichaceae, and shifted functional profiles from proliferation- and inflammation-related modules (K02315, K02970, and K03496) toward carbohydrate utilization and genetic stability pathways (K01784 and K07491).<br><br>CONCLUSION: Limosilactobacillus reuteri RE225 shows promise as a dietary intervention for the management of hyperuricemia. &#xa9; 2026 Society of Chemical Industry.}, }
@article {pmid42210827, year = {2026}, author = {Syatrawati,  and Kuswinanti, T and Nasruddin, A and Rosmana, A and Hikmahwati, }, title = {Metagenomic Insights into Rhizosphere Fungal Communities Across Different Rice Cultivation Systems.}, journal = {Pakistan journal of biological sciences : PJBS}, volume = {29}, number = {3}, pages = {147-159}, doi = {10.3923/pjbs.2026.147.159}, pmid = {42210827}, issn = {1812-5735}, mesh = {*Oryza/microbiology/growth &amp; development ; *Rhizosphere ; *Metagenomics/methods ; *Fungi/genetics/classification ; Soil Microbiology ; Agriculture/methods ; }, abstract = {Background and Objective: Rhizosphere fungi play a crucial role in nutrient cycling and plant protection, yet most are difficult to cultivate using conventional methods. Consequently, their ecological functions remain largely unknown. Therefore, metagenomic approaches allow for comprehensive and accurate mapping of fungal taxonomic profiles without the need for cultivation and this study investigated the variation of rhizosphere fungi across different rice cultivation systems to elucidate their diverse potentials. Materials and Methods: A metagenomic approach was employed to identify fungi originating from the rhizosphere of rice cultivated in various field conditions, including irrigated, rainfed and organic rice fields. The diversity of fungi from rhizosphere samples was assessed to comprehend the relationships and metrics within the rice cropping systems utilized by farmers. Results: The findings indicated that the rhizosphere fungal index from organic rice fields exhibited the highest Shannon and Simpson index values compared to those from irrigated and rainfed rice fields. Conclusion: Metagenomic analysis revealed that the most dominant fungal diversity at the family level was Trichocomaceae, at the genus level was Talaromyces and at the species level was Talaromyces wortmannii.}, }
@article {pmid42211404, year = {2026}, author = {Su, L and Zhang, Y and Xie, Y and Wu, J and Yang, Y and Li, Y and Huang, Y and Liu, X and Wei, X and Chen, Q}, title = {Integrated metabolomics and gut microbiota analyses reveal the protective effects of matrine in ulcerative colitis.}, journal = {Frontiers in chemistry}, volume = {14}, number = {}, pages = {1826894}, pmid = {42211404}, issn = {2296-2646}, abstract = {BACKGROUND: Ulcerative colitis (UC) is a chronic inflammatory bowel disease driven by gut microbial dysbiosis and metabolic dysfunction. Matrine, a natural alkaloid with anti-inflammatory properties, shows therapeutic potential; however, its mechanisms involving the coordinated modulation of bacteria, fungi, and host intestinal luminal metabolism remain unclear.<br><br>METHODS: We evaluated the therapeutic efficacy of matrine using a dextran sulfate sodium (DSS)-induced murine model of ulcerative colitis. Disease severity was assessed via the disease activity index, colon length, and histopathology. Integrated multi-omics approaches, including metagenomics, ITS fungal sequencing, and untargeted metabolomics of intestinal luminal contents, were employed to systematically characterize the regulatory effects of matrine on gut bacteria, fungi, and metabolic profiles.<br><br>RESULTS: Here, we demonstrated that oral matrine significantly alleviated disease severity in a DSS-induced UC mouse model, as evidenced by improved disease activity index, colon length, histopathology, and restoration of tight junction proteins. Integrated multiomics revealed that matrine restored bacterial homeostasis-suppressing Escherichia while enriching SCFAs-producing taxa (Muribaculum, Paramuribaculum, Clostridium). Metagenomic predictions revealed that matrine treatment reversed the model-induced suppression of carbohydrate metabolism and bile acid biosynthesis while upregulating depleted CAZy enzyme families, thereby correcting dysregulated metabolic functions in colitis. Furthermore, matrine rebalanced the mycobiota by normalizing the Ascomycota/Basidiomycota ratio. Intestinal luminal contents untargeted metabolomics identified 43 matrine-responsive metabolites, implicating correction of bile acid metabolism, attenuation of leukotriene-mediated inflammation, and reversal of acylcarnitine-driven epithelial energy disruption. Critically, pro-inflammatory metabolites correlated positively with Escherichia and negatively with beneficial symbionts.<br><br>CONCLUSION: Our findings established that matrine exerted protective effects in UC through a unified "microbiota-metabolism" axis, highlighting its promise as a multi-target therapeutic agent for UC.}, }
@article {pmid42211783, year = {2026}, author = {Ding, F and Li, Y and He, T and Wang, Y and Li, Y and Huang, Y and Yin, G and Yang, J and Liu, Y and Li, Y and Li, T and Hou, L and Liu, M}, title = {Deciphering the drivers of antibiotic resistance gene transmission in the megacity: Co-occurring contaminants and bacterial community.}, journal = {Eco-Environment &amp; Health}, volume = {5}, number = {2}, pages = {100242}, pmid = {42211783}, issn = {2772-9850}, abstract = {Urban waters are widely contaminated with co-occurring microplastics and antibiotics. Human-land interactions (e.g., wastewater discharge, stormwater runoff, and land use) drive contaminant distribution and antimicrobial resistance. Nevertheless, there is a lack of systematic research evaluating the role of co-occurring contaminants in shaping the spread of antibiotic resistance genes (ARGs). In this study, a metagenomic approach was used to characterize the diversity and distribution of ARGs based on contaminant co-occurring patterns. The random forests and partial least squares path model (PLS-PM) were used to identify and prioritize the factors impacting ARGs, leading to a thorough environmental health ecological risk evaluation. Industrial waters, especially pharmaceutical factories, were significant reservoirs and hotspots for the development of ARGs. Urban estuaries further gathered and amplified the effects of co-occurring contaminants, thereby enhancing the prevalence of ARGs. The potential spread of ARGs was dominated by contaminant co-occurring patterns in urban waters, whereas microbial communities dominated in sediments. Urban zoning comprehensively affected environmental health risks, indicating that environmental management strategies, such as controlling pollution sources and implementing remediation, should prioritize water bodies in agricultural areas and sediments in commercial/residential areas.}, }
@article {pmid42211787, year = {2026}, author = {Zhang, R and Chen, YK and Zhu, QY and Feng, RY and Liu, H and Ma, MM and Wang, XJ}, title = {Metagenomic profiling of ocular surface microbiome alterations in patients with progressive supranuclear palsy-Richardson's syndrome.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100605}, pmid = {42211787}, issn = {2666-5174}, abstract = {This study employed shotgun metagenomic sequencing to characterize the ocular surface microbiome in 20 progressive supranuclear palsy-Richardson's syndrome (PSP-RS) patients, 17 Parkinson's disease (PD) patients, and 30 healthy controls (HC). Comparative analysis revealed that PSP-RS patients exhibited significantly altered microbial β-diversity compared to HC, while PD patients showed no such significant changes. Both patient groups demonstrated decreased abundance of g_Vibrio, with PSP-RS patients additionally showing marked increases in g_Acinetobacter and g_Anaerococcus. Importantly, correlation analyses identified that increased g_Acinetobacter abundance was positively associated with ocular motor impairment severity, while elevated g_Anaerococcus levels correlated with both freezing of gait severity and longer disease duration in PSP-RS patients. This is the first shotgun metagenomic investigation of the ocular surface microbiome in PSP-RS and these findings provide evidence that specific alterations in the ocular surface microbiome may contribute to PSP-RS pathogenesis and disease progression.}, }
@article {pmid42211840, year = {2026}, author = {Pesantes, N and Barberá, A and Pérez-Rocher, B and Artacho, A and Vargas, SL and Moya, A and Ruiz-Ruiz, S}, title = {Correction: Influence of mental health medication on microbiota in the elderly population in the Valencian region.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1861757}, doi = {10.3389/fmicb.2026.1861757}, pmid = {42211840}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2023.1094071.].}, }
@article {pmid42211849, year = {2026}, author = {Du, R and Xu, C and Zhao, D and Zeng, H and Cheng, Y and Tang, K and Cai, P and Zhang, Y}, title = {Contrasting microbial iron metabolism in sediments from oxic and hypoxic estuaries.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1824768}, pmid = {42211849}, issn = {1664-302X}, abstract = {Estuarine sediments are pivotal zones for iron (Fe) cycling, mediated by microbial communities and coupled to carbon, nitrogen, sulfur and phosphorus transformations. However, the microbial iron metabolic processes in estuarine sediments remain poorly characterized, particularly under hypoxia. This study compared metagenomes from the Oujiang River Estuary, an oxic estuary, and the Yangtze River Estuary, a seasonally hypoxic estuary, complemented by sediment core incubations to assess geochemical responses to deoxygenation. The taxonomic affiliations of iron metabolism-related genes in the oxic estuary were homogeneous with depth, dominated by Proteobacteria and Thermodesulfobacteriota. In contrast, the hypoxic estuary exhibited strong stratification, with the surface enriched in Proteobacteria and deeper horizons dominated by Chloroflexota and Candidatus Bathyarchaeota. The surface sediments of the hypoxic estuary at 0-8 centimeters below the seafloor showed a hotspot with co-enrichment of dissimilatory iron reduction (e.g., mtrABC) and iron oxidation genes (e.g., mtoA) relative to both deeper layers in the same estuary and the oxic estuary, consistent with elevated genetic potential for Fe redox turnover. This hotspot also harbored high-affinity Fe acquisition systems (siderophores, inorganic Fe transporters, and heme uptake), suggesting the potential for microbial competition for iron. Co-occurrence networks connecting Fe metabolism with carbon, nitrogen, sulfur and phosphorus cycling were more complex in the hypoxic estuary than in the oxic estuary, revealing strong associations between Fe acquisition/redox cycling and organic matter turnover. A 16-day incubation of sediment cores from the oxic estuary showed that short-term deoxygenation enhanced dissolved Fe, phosphate, and ammonium release. Overall, our results suggest that bottom-water hypoxia is associated with major shifts in microbial iron metabolism potential, with implications for iron-organic matter interactions and nutrient regeneration under coastal deoxygenation.}, }
@article {pmid42211850, year = {2026}, author = {Li, L and Liu, R and Yang, H and Zhao, Y}, title = {Metagenomic sequencing reveals structural and functional differentiation of rhizosphere bacterial communities driven by nitrogen and potassium deficiency associated with root rot of Schisandra chinensis.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1827096}, pmid = {42211850}, issn = {1664-302X}, abstract = {BACKGROUND: Frequent incidence of root rot in Schisandra chinensis impairs its yield and quality, yet the rhizosphere microecological mechanism driving this incidence remains unclear.<br><br>METHODS: To clarify this mechanism, healthy and root rot-infected S. chinensis plants were analyzed in this study. The plant growth, rhizosphere soil physicochemical properties, and the structural and functional differences in rhizosphere bacterial communities under both conditions were analyzed.<br><br>RESULTS: Our results showed that root rot significantly inhibited S. chinensis growth and pathogen colonization-induced rhizosphere acidification, with reduced hydrolyzable nitrogen (HN) and available potassium (AK). Analysis of the intergroup differences in bacterial species revealed that the healthy rhizosphere was enriched with Acidobacteriota, Luteitalea, Pseudomonadota, Pseudolabrys, and Methylomirabilota, whereas infected rhizosphere was dominated by Gaiella (Actinomycetota), Gemmatimonas (Gemmatimonadota), Bradyrhizobium, and Sphingomicrobium (Pseudomonadota). Functional annotation based on COG, KEGG, and CAZy databases revealed that the bacteria of the healthy rhizosphere were enriched in defensive-cooperative functions (synergistic metabolism, secondary metabolite synthesis, complex carbon metabolism), while those of the infected rhizosphere exhibited simplified survival functions (individual metabolism, ABC transport, simple carbohydrate metabolism). Redundancy analysis identified HN and AK as key nutrients driving community differentiation in the rhizosphere.<br><br>CONCLUSION: This study revealed that root rot in S. chinensis is closely associated with an imbalance in the rhizosphere environment-bacterial community-function system, with healthy plants exhibiting specific core bacterial biomarkers and more complex synergistic metabolic networks, while HN and AK are key nutrients influencing rhizosphere bacterial communities. This study clarifies the rhizosphere microecological mechanism associated with S. chinensis root rot, providing a theoretical basis for its control.}, }
@article {pmid42212564, year = {2026}, author = {Kim, Y and Kim, JK and Her, M and Kong, HS and Moon, JS and Yun, CS}, title = {Shotgun Metagenomic Diagnosis of Unidentified Pathogens in Hepatic Necrosis Samples from Samgye Chickens.}, journal = {Avian pathology : journal of the W.V.P.A}, volume = {}, number = {}, pages = {1-235}, doi = {10.1080/03079457.2026.2674233}, pmid = {42212564}, issn = {1465-3338}, abstract = {Chicken infectious anemia virus (CIAV), infectious bursal disease virus (IBDV), and Eimeria spp. are major immunosuppressive pathogens in chickens that predispose host to secondary infections, including Clostridium septicum-associated hepatic necrosis. In this case, shotgun metagenomic sequencing was applied to identify C. septicum that could not be isolated by traditional bacterial culture in Samgye chickens. Six 35-day-old Samgye chicken carcasses were submitted for disease diagnosis, histopathological examination, and bacterial and viral isolation/identification were performed. Pooled liver samples were subjected to shotgun metagenomic sequencing to identify microbial composition, virulence factors, and antimicrobial resistance genes. Samgye chickens exhibited dorsal dermatitis, hepatic necrosis, and splenomegaly. Histopathology revealed hepatic necrosis with bacterial colonies and lymphoid depletion. PCR detected CIAV, antigenic variant IBDV, chicken astrovirus, and Eimeria, whereas bacterial culture yielded no growth. Shotgun metagenomic analysis identified C. septicum as predominant bacterium, and CIAV as dominant viral pathogen. The α-toxin and the antimicrobial resistance tetA(P) genes were detected from liver samples. This is the first report of concurrent CIAV, avIBDV, Eimeria spp., and C. septicum infection from Samgye chickens in South Korea, suggesting that immunosuppressive infections may predispose chickens to C. septicum-associated hepatic necrosis and highlight the diagnostic utility of shotgun metagenomic sequencing.}, }
@article {pmid42212611, year = {2026}, author = {Sauer, P}, title = {[Current trends in sepsis diagnosis - from classic culture to advanced molecular identification].}, journal = {Klinicka mikrobiologie a infekcni lekarstvi}, volume = {32}, number = {1}, pages = {24-29}, pmid = {42212611}, issn = {1211-264X}, mesh = {Humans ; *Sepsis/diagnosis/microbiology ; Blood Culture ; *Molecular Diagnostic Techniques/trends ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {Sepsis is a critical condition characterized by life-threatening organ dysfunction caused by a dysregulated host response to infection, where each hour of delay in initiating adequate therapy increases mortality by 7-10%. This paper summarizes current trends in microbiological diagnostics, moving from the gold standard of blood culture toward advanced molecular identification. The traditional culture-based process is limited by a time lag of 12-48 hours. Modern approaches include accelerating identification from positive blood cultures using MALDI-TOF MS and RAST methods, which reduce the time to targeted treatment. Significant innovation is represented by culture-independent technologies such as T2MR, SepsiTest-UMD, Cube Dx, and InfectID-BSI, enabling pathogen detection directly from whole blood within a few hours. The future of sepsis diagnosis is further enhanced by digital PCR for absolute quantification of bacterial load, metagenomic sequencing (mNGS) for identifying unexpected pathogens, and transcriptomics for assessing the host immune response. Integrating these technologies with artificial intelligence (AI) predictive models paves the way for precision medicine and personalized care for septic patients. Keywords: sepsis, blood culture, molecular diagnostics, PCR, mNGS, MALDI-TOF MS, artificial intelligence.}, }
@article {pmid42212684, year = {2026}, author = {Liu, J and Zhao, P and Jiang, D and Li, S and Jin, C and Xu, D and Wang, X and Chen, Y and Tang, B and Qu, X}, title = {Decoding the microbiome: artificial intelligence-targeted gut microenvironment breakthroughs in personalized cancer therapy.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2672791}, doi = {10.1080/19490976.2026.2672791}, pmid = {42212684}, issn = {1949-0984}, mesh = {Humans ; *Precision Medicine/methods ; *Artificial Intelligence ; *Gastrointestinal Microbiome ; *Tumor Microenvironment ; *Colorectal Neoplasms/microbiology/therapy/diagnosis ; Multiomics ; Animals ; }, abstract = {The gut microbiome functions as a key regulator of tumorigenesis and progression, thereby modulating tumor development and treatment outcomes (including chemoresistance, immunotherapy efficacy, and adverse effects) through its influence on the immune microenvironment and metabolite-mediated signaling pathways. Recent advances in multiomics technologies (metagenomics, metabolomics, and transcriptomics) have generated large-scale, comprehensive, and heterogeneous datasets whose complexity exceeds the capabilities of manual analysis, thus necessitating the implementation of artificial intelligence-based approaches. This review systematically examines the crucial role of the gut microbiome in tumorigenesis, with particular emphasis on colorectal cancer (CRC), specifically addressing its utility as a diagnostic and prognostic biomarker. Furthermore, building upon existing applications of artificial intelligence (AI) in microbiome research and cancer diagnosis and treatment, this review presents an AI-driven precision intervention framework and delineates personalized treatment strategies.}, }
@article {pmid42212786, year = {2026}, author = {Zielińska, K and Pantiukh, K and Łabaj, PP and Kosciolek, T and Org, E}, title = {A large-scale comparative metagenomic analysis of short-read sequencing platforms indicates high taxonomic concordance and functional analysis challenge.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0171425}, doi = {10.1128/msystems.01714-25}, pmid = {42212786}, issn = {2379-5077}, abstract = {UNLABELLED: Driven by the increasing scale of microbiome studies and the rise of large, continuously expanding population cohorts, the volume of sequencing data is growing rapidly. As such, ensuring the comparability of data generated across different sequencing platforms has become a pressing concern in efforts to uncover robust links between the microbiome and human health. In this study, we conducted a comprehensive comparison of taxonomic and functional profiles from 1,351 matched human gut microbiome sample pairs, sequenced using both the MGISEQ-2000 (MGI) and NovaSeq 6000 (Illumina NovaSeq) platforms. Taxonomic profiles showed high concordance within and between platforms: 96.44% ± 5.96% of species were shared between MGI-MGI pairs, and 92.07% ± 5.20% were shared between MGI and NovaSeq pairs. The proportion of platform-specific species was low, at 3.42% for MGI-MGI comparisons and 5.89% for MGI-NovaSeq comparisons. No significant differences in Shannon diversity were observed for either within-platform or between-platform comparisons. However, functional profiles revealed notable discrepancies between platforms, which were attributed to differences in pre-sequencing protocols.<br><br>IMPORTANCE: Our findings demonstrate robust taxonomic comparability between MGI and NovaSeq platforms, while revealing systematic functional differences that should be carefully considered in cross-platform metagenomic studies.}, }
@article {pmid42212790, year = {2026}, author = {Zielińska, K and Pantiukh, K and Org, E and Łabaj, PP and Kosciolek, T}, title = {Moving from a taxonomic to a functional perspective in global microbiome analysis requires optimizing multiplexing ratios.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0014426}, doi = {10.1128/msystems.00144-26}, pmid = {42212790}, issn = {2379-5077}, abstract = {Next-generation sequencing has revolutionized microbiome research, yet the transition from taxonomic to functional profiling remains a major technical challenge. While marker gene sequencing provides a widely accessible ecological view, it often lacks the resolution for actionable insights. This perspective argues that shifting to whole metagenomic sequencing is essential for mapping functional potential, such as antimicrobial resistance, and metabolic pathways. However, we identify a critical bottleneck: excessive multiplexing. High multiplexing ratios reduce the number of unique molecules per sample, leading to high duplication rates and the stochastic dropout of low-abundance genes. We demonstrate that functional profiles are far more sensitive to these library complexity issues than taxonomic ones. We recommend prioritizing total sequencing depth and reducing multiplexing to ensure sufficient unique coverage. Additionally, adopting long-read or hybrid architectures is vital for providing the genomic context necessary for strain-level resolution. These optimizations are prerequisites for robust global microbiome synthesis and translational science.}, }
@article {pmid42212800, year = {2026}, author = {Yabe, S and Zheng, Y and Takahashi, S and Yang, C and Nose, Y and Yamazaki, S and Okuma, N and Rachmania, MK and Ningsih, F and Sjamsuridzal, W and Sato, M and Toyooka, K and Ichihashi, Y}, title = {Chromid-like secondary replicons as predicted key sites of biosynthetic gene clusters in Ktedonobacteria.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0019726}, doi = {10.1128/msystems.00197-26}, pmid = {42212800}, issn = {2379-5077}, abstract = {UNLABELLED: Soils harbor immense biosynthetic gene cluster (BGC) diversity that mediates microbial interactions, yet this potential remains unevenly mapped and poorly characterized across diverse bacterial lineages. Ktedonobacteria (phylum Chloroflexota) are an actinomycete-like lineage widely distributed in terrestrial soils, including oligotrophic volcanic deposits; however, their secondary metabolism and genome architecture remain poorly characterized. Here, we integrate targeted cultivation from volcanic soils at Mount Zao (Japan) with genome-resolved metagenomics and comparative analysis of public genomes to examine biosynthetic potential across 183 ktedonobacterial genomes. We identified 1,546 BGCs and grouped them into 1,162 non-redundant gene-cluster families (GCFs) using antiSMASH and BiG-SLiCE. Nearly one quarter of genomes encoded ≥10 distinct GCFs, and several family-level clades exhibited high GCF richness that approached that of Streptomyces within our data set, highlighting a putatively biosynthetically rich yet underexplored soil bacterial lineage. Most ktedonobacterial BGCs were highly divergent from current reference collections and exhibited unusually low intra-genomic redundancy, suggesting broad putative chemical diversity. Long-read assemblies from 10 cultured strains revealed recurrent 1.6-3.5 Mb ECE-like contigs with chromid-like features, but distinct maintenance features. These replicons were consistently enriched in BGCs and mobility-associated genes, with mobility loci concentrated near BGC boundaries. Collectively, our results expand the phylogenetic landscape of soil biosynthetic diversity and highlight ECE-like contigs as major genomic reservoirs for secondary metabolism in Ktedonobacteria.<br><br>IMPORTANCE: Soil bacteria produce many of the small molecules that become medicines and help microbes interact with each other. Yet most of this chemical diversity remains unexplored because many soil lineages are difficult to cultivate and remain genomically underrepresented. Much of what we know comes from well-studied groups such as actinomycetes, leaving many soil lineages largely unexplored. We analyzed 183 genomes from Ktedonobacteria, an actinomycete-like group within the phylum Chloroflexota that is widespread in terrestrial soils, including nutrient-poor volcanic deposits. We uncovered a large and diverse set of gene clusters predicted to produce secondary metabolites, many of which lack close counterparts in current reference collections. We also show that these clusters are concentrated on large ECE-like contigs with chromid-like features, pointing to a dedicated genomic reservoir that can accumulate and reshuffle biosynthetic traits. Our results expand the known sources of soil biosynthetic diversity and provide a foundation for future cultivation and functional characterization of Ktedonobacteria metabolites.}, }
@article {pmid42213267, year = {2026}, author = {Gulnihol, S and Abdukhamid, N and Rustam, T and Firdavs, U and Gholami, AA}, title = {Methodological concerns in the association between gut microbiota and sarcopenia: from cross‑sectional associations to statistical fragility.}, journal = {Aging clinical and experimental research}, volume = {38}, number = {1}, pages = {}, pmid = {42213267}, issn = {1720-8319}, mesh = {Humans ; *Sarcopenia/microbiology ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Aged ; Iran ; }, abstract = {This commentary critically appraises the cross‑sectional study by Nasrollahizadeh et al. on gut microbiota and sarcopenia in Iranian older adults. Key limitations include; after FDR correction for twelve bacterial genera, no significant differences remained between groups; Akkermansia lost significance in sensitivity analyses; Lactobacillus showed a confidence interval including 1.00; four primer pairs lacked validation with no MIQE‑compliant efficiency data; the cross‑sectional design precludes causal inference; and no sample size justification was reported. The study offers valuable hypothesis‑generating data, but evidence remains preliminary. Future longitudinal studies with metagenomic approaches are essential.}, }
@article {pmid42213269, year = {2026}, author = {Song, X and Cai, D and Yu, X and Zhang, X and Zhu, W}, title = {Effects of different cultivation methods on microbial community structure of lettuce based on metagenomic analysis.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {}, pmid = {42213269}, issn = {1678-4405}, support = {Z2021067//Tianjin Municipal Transportation Commission Science and Technology Development Plan Project/ ; Tasks of the Key Laboratory for Microbiological Food Safety Risk Monitoring in Jiangsu Province (2023-2025)//Tasks of the Key Laboratory for Microbiological Food Safety Risk Monitoring in Jiangsu Province (2023-2025)/ ; }, mesh = {*Lactuca/microbiology/growth &amp; development ; Soil Microbiology ; Metagenomics ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Hydroponics/methods ; *Microbiota ; Metagenome ; Biodiversity ; }, abstract = {BACKGROUND: Lettuce cultivation primarily involves two methods: traditional soil-based cultivation and modern hydroponic systems. However, research on the microbial community structure of lettuce under these distinct cultivation approache is still limited.<br><br>METHOD: This study employed whole-genome shotgun metagenomic sequencing (metagenomic sequencing) to analyze the impact of soil-based and hydroponic cultivation systems on the microbial community structure and functional profiles of lettuce.<br><br>RESULTS: The microbial diversity index of soil samples was significantly higher than that of hydroponic samples, indicating a more diverse and complex microbial community in the soil environment. Key functional phylum, including Acidobacteriota and Actinomycetota, were more abundant in soil samples, supporting nutrient cycling and plant-microbe interactions through pathways involved in carbon metabolism, organic matter decomposition, and antibiotic biosynthesis. In contrast, hydroponic samples were dominated by Cyanobacteriota and Verrucomicrobiota, with enrichment of pathways associated with stress response, including quorum sensing, ABC transporters, and oxidative phosphorylation. Although &#x3b1;-diversity did not differ significantly between cultivation systems, their microbial community composition and functional profiles were markedly distinct: soil-grown lettuce exhibited enrichment in sugar catabolism and synergistic prokaryotic metabolic functions, whereas hydroponic lettuce showed a predominance of energy metabolism and enrichment of viral-related pathways. Furthermore, differential distribution of antibiotic resistance genes underscores the role of environmental selective pressures in shaping microbial functional adaptations.<br><br>CONCLUSION: This study demonstrates that different cultivation methods significantly influence the microbial community structure and function in lettuce. These findings provide a theoretical foundation for optimizing cultivation systems and offer scientific guidance for precisely modulating microbial functions to promote lettuce growth and health.}, }
@article {pmid42213733, year = {2026}, author = {Wheelahan, JW and Vaz, PK and Legione, AR and Hartley, CA and Rourke, NL and Lynch, M and McMeekin, B and Dobson, EC and Devlin, JM}, title = {Virological investigation and comparative genomic analysis of elephant endotheliotropic herpesvirus 1B infection in an Australian captive herd of Asian elephants (Elephas maximus).}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0345964}, doi = {10.1371/journal.pone.0345964}, pmid = {42213733}, issn = {1932-6203}, mesh = {Animals ; *Elephants/virology ; *Herpesviridae Infections/veterinary/virology ; *Genome, Viral ; Australia ; Phylogeny ; Viral Load ; *Herpesviridae/genetics ; Genomics ; }, abstract = {Elephant endotheliotropic herpesviruses (EEHV) pose a significant threat to the conservation of Asian elephants (Elephas maximus) worldwide, with a high mortality rate in young elephants. However, several components of EEHV virology remain underexplored, particularly for EEHV1B. This study describes a fatal case of EEHV1B infection in a nine-year-old Asian elephant from an ex situ conservation herd, examining herd viral dynamics, tissue viral loads and comparative genomics. This elephant succumbed to haemorrhagic disease within three days of developing clinical signs, despite therapeutic intervention. Quantitative PCR (qPCR) was performed on serial trunk washes and whole-blood surveillance samples collected before and after the clinical event, as well as on post-mortem tissues preserved in different storage media (DNA/RNA Shield, RNALater, and viral transport medium). Metagenomic next-generation sequencing of infected tissues was performed to characterise the complete viral genome, analyse variation from other published EEHV genomes and assess for evidence of viral recombination between EEHV subspecies. The affected elephant demonstrated a marked viraemia at onset of clinical disease, with viral load peaking at 5.47 x 106 viral genome equivalents per mL of blood, one day after the onset of clinical signs. Samples stored in viral transport medium yielded the greatest viral and host DNA recovery by qPCR, although tissues stored at -80 °C without media were still suitable for molecular detection. Whole genome sequencing demonstrated 96.0% pairwise nucleotide identity between the assembled genome (EEHV1B_AUP_01_2023, GenBank accession: PX651398) and the previously reported EEHV1B sequence (KC462164), and a maximum of 90.9% identity to published EEHV1A genomes, with evidence of recombination between the viral subspecies at several genomic regions. Viral recombination between EEHV subspecies may have significant implications for the pathogenesis of EEHV disease, the reliability of molecular diagnostics and the efficacy of vaccinations and anti-viral therapy.}, }
@article {pmid42213849, year = {2026}, author = {Meijer, J and Skiadas, P and Rainey, PB and Hogeweg, P and Dutilh, BE}, title = {Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities.}, journal = {Science advances}, volume = {12}, number = {22}, pages = {eaeb8246}, doi = {10.1126/sciadv.aeb8246}, pmid = {42213849}, issn = {2375-2548}, mesh = {*Bacteriophages/genetics/physiology ; *Soil Microbiology ; *Evolution, Molecular ; Ecosystem ; *Composting ; Metagenomics ; Phylogeny ; Genome, Viral ; }, abstract = {Bacteriophages play critical roles in microbial ecosystems, yet their dynamics in complex natural communities remain poorly understood compared to simplified laboratory systems. Here, we tracked viral dynamics in 20 compost-derived microbial communities over 1 year. Communities formed two alternative stable types, each dominated by distinct cellulose degraders and comprising hundreds of genera. In one community type, we observed massive, parallel outbreaks of Theomophage, a previously uncharacterized member of the Schitoviridae, reaching up to 74% of metagenomic reads-the largest bacteriophage outbreak documented to date. Despite extensive replication, Theomophage displayed notable genetic stability during outbreaks and over time. In contrast, the experimental migration of viral communities triggered rapid evolution driven by recombination and the accumulation of newly arising mutations, particularly after colonization of communities of the alternative type in which the phage was initially absent. These results reveal the spatial and temporal scales at which bacteriophage microdiversity evolves in complex ecosystems and show that viral mixing, likely common in nature, can rapidly accelerate phage evolution.}, }
@article {pmid42214271, year = {2026}, author = {Lin, Y and Roy, S and Hagedoorn, PL}, title = {Microbial melanin-like material: A factor beyond influencing the brown color of activated sludge.}, journal = {Water research}, volume = {303}, number = {}, pages = {126195}, doi = {10.1016/j.watres.2026.126195}, pmid = {42214271}, issn = {1879-2448}, abstract = {Melanin is a group of phenolic-quinone pigments. Natural melanin is nearly ubiquitous; found in all types of living organisms, ranging from mammals to bacteria. However, its presence and biosynthesis genomic potential in activated sludge have not been investigated. To explore this potential, melanin-like material was extracted from activated sludge collected from a municipal wastewater treatment plant. The extracted melanin-like material was characterized through biochemical analyses in comparison to synthetic melanin and humic acids that are commercially available. Metagenomic analysis of microbial community members in activated sludge and detection of tyrosine-derived melanin synthesis genes was performed. Additionally, the potential application of the extracted melanin-like material as a natural pigment was evaluated by testing its ability to color wool yarn. It was found that melanin-like material extracted from activated sludge accounted for around 11% of sludge dry mass. The isolated material displayed intrinsic autofluorescence, strong UV absorption, high oxidative stability, and free radical-rich EPR signal. FTIR analysis indicated a mixed polymer dominated by pyomelanin-like structures with eumelanin features, distinguishing it from synthetic melanin and humic acid. Metagenomic screening of the sludge community revealed widespread genomic potential for pyomelanin monomeric precursors biosynthesis across key functional genera (e.g. genera Zoogloea, Nitrotoga, Nitrosomonas, Ca. Accumulibacter, Azonexus, Ca. Competibacter, Propionivibrio, and Rhodoferax). These results suggest that microbial melanin-like material is an overlooked contributor to sludge coloration. Furthermore, the extracted pigment exhibited high affinity and wash fastness on wool fibers, demonstrating its potential for valorization as a sustainable biobased colorant.}, }
@article {pmid42214309, year = {2026}, author = {Guo, N and Chen, J and Lei, Z and Qu, L and Xie, W and Yin, K and Yang, Y}, title = {Evidence for the connectivity of antibiotic resistance genes between seamount and coastal environments.}, journal = {Ecotoxicology and environmental safety}, volume = {319}, number = {}, pages = {120325}, doi = {10.1016/j.ecoenv.2026.120325}, pmid = {42214309}, issn = {1090-2414}, abstract = {Antibiotic resistance genes (ARGs) have drawn global attention and are ubiquitously detected in marine environments. Seamounts, prominent seafloor features with high biodiversity, may be hotspots for ARG proliferation and transfer. However, little is known about the existence, microbial associations, or connectivity with terrestrial sources of ARGs in seamounts. In this study, high-throughput sequencing approaches were employed to investigate the distribution, hosts, mobility, and coastal connectivity of ARGs in sediments from the Zhongnan Seamount, South China Sea. The most abundant ARG types were elfamycin, aminoglycoside, and tetracycline. ARG abundance was significantly higher in abyssopelagic zone sediments, suggesting the seamount acts as a sink and deep-sea regions are a major ARG reservoir. Results indicated high horizontal gene transfer potential, with key genes EF-Tu, rpsJ, parC, and parE as predominant mediators. Metagenome-assembled genomes identified 36 bacterial genera as ARG hosts, dominated by Methylomirabilota and Pseudomonadota. The source tracking and genetic connectivity analysis revealed a clear input of coastal ARGs to the seamount, emphasizing the need to investigate global ARG dissemination and its potential ecological effects. Overall, these findings identify the seamount environment as a deep-sea ARG hotspot, providing valuable insights into the prevalence, hosts, and sources of ARGs in the marine ecosystem.}, }
@article {pmid42214347, year = {2026}, author = {Peredo, EL and Kulp, R and Rodriguez, F and Weintraub, MN and Anand, M and Bixler, S and Koller, J and Lee, C and Mathai, D and Tuytschaevers, S and Kumar, G}, title = {Metagenome-assembled genomes from biological soil crusts in sandy sediments of Kitty Todd Nature Preserve, OH, USA.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0038026}, doi = {10.1128/mra.00380-26}, pmid = {42214347}, issn = {2576-098X}, abstract = {Biological soil crusts (BSCs) are complex structures composed of prokaryotes, green microalgae, fungi, and small mosses that bind soil particles together. To further understand the microbial composition and interactions among members of these consortia, we investigated the microbial diversity of BSCs found in a xeric patch in northwestern Ohio.}, }
@article {pmid42214368, year = {2026}, author = {Karmarkar, B and Dhotre, D}, title = {Harnessing gut microbiome enzymes: Segatella copri and Stenotrophomonas maltophilia prolyl peptidases degrade gliadin peptides and improve epithelial barrier function in a celiac disease model.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0321425}, doi = {10.1128/spectrum.03214-25}, pmid = {42214368}, issn = {2165-0497}, abstract = {UNLABELLED: Celiac disease (CeD) is an autoimmune enteropathy triggered by gluten-derived peptides that resist gastrointestinal digestion, notably the proline-rich 33-mer and 11-mer gliadin epitopes. Here, we describe a rational, metagenome-based strategy to identify gut microbiome-derived prolyl peptidases capable of degrading these immunogenic peptides. Integrating metagenomic mining with structure-based in silico screening, we identified two novel enzymes PSP692 from Segatella copri and PSP464 from Stenotrophomonas maltophilia. Recombinant expression, purification, and characterization confirmed their activity under physiologically relevant conditions: PSP692 efficiently degrades the 33-mer at pH 6, while PSP464 targets the 11-mer at pH 4. Functional assays using CaCo-2 cell line, both in bi- and tri-dimensional assays, demonstrated that degradation of gliadin peptides by PSP692 and PSP464 significantly restored the expression of tight junction proteins (ZO-1 and occludin), reduced IL-6 secretion, and improved barrier integrity. These findings establish a foundational strategy for the discovery of microbiome-derived glutenases and provide both a compelling case and a methodology for data-driven discovery of functional enzymes that degrade immunogenic gliadin peptides, with translational potential as adjunct therapies in CeD and gluten-related disorders.<br><br>IMPORTANCE: Celiac disease affects 1.4% of the global population, and, as of date, a gluten-free diet (GFD) is the only therapy available. Adherence to GFD is difficult, and inadvertent exposure to gluten still occurs. To address this, various approaches are utilized to develop adjuvant therapies. These include recombinant enzymes that, to date, have been discovered by serendipity. We have outlined and validated a method to identify enzymes with potential from metagenomic data, which will also be validated experimentally.}, }
@article {pmid42214386, year = {2026}, author = {Sun, H and Dulencin, A and Kirn, TJ and Vo, J and Liachko, I and Rao, D and Manzano-Santana, J and Patel, E and Looi, C and Horton, DB and Barrett, E and Weidner, M and Bachmann, G and Panettieri, RA and Connor, BA and Rogova, M and Nagy-Szakal, D and Couto-Rodriguez, M and Kotwal, S and Wu, Q and Simon, J and Blaser, MJ and Dominguez Bello, MG}, title = {Autologous fecal microbiota transplantation restores the infant gut microbiome and metabolome after antibiotics: a case report.}, journal = {mBio}, volume = {}, number = {}, pages = {e0071126}, doi = {10.1128/mbio.00711-26}, pmid = {42214386}, issn = {2150-7511}, abstract = {UNLABELLED: Antibiotic exposure during infancy disrupts gut microbiome assembly during a critical developmental window. Strategies to restore these ecosystems remain limited. In the REPAIR trial (NCT06609980), eight infants were followed longitudinally; two received amoxicillin for otitis media, and one subsequently underwent autologous fecal microbiota transplantation (aFMT) using stool collected prior to antibiotic exposure. Shotgun metagenomics, Hi-C-assisted resistome profiling, and untargeted metabolomics were performed on samples collected before and after antibiotics. Amoxicillin treatment was associated with displacement of community structure, enrichment of antibiotic resistance genes (ARGs), and altered fecal metabolites, including short-chain fatty acids, bile acids, acylcarnitines, bilirubin derivatives, tricarboxylic acid (TCA) cycle metabolites, and amino acids. In the non-restored infant, microbiota composition and ARG profiles remained persistently altered during follow-up, accompanied by sustained metabolic divergence. In contrast, the aFMT-treated infant demonstrated convergence toward pre-antibiotic community structure, directional restructuring of ARG carriers -including reduction of β-lactam and tetracycline resistance genes- and metabolite profiles trending toward the pre-antibiotic baseline across analytical platforms. Although limited to a case-based comparison, these findings provide integrated ecological and functional evidence that aFMT may promote recovery following antibiotic perturbation during early-life microbiome development and support the rationale for larger controlled clinical trials.<br><br>IMPORTANCE: Antibiotic exposure in early life disrupts the developing gut microbiome during a critical window of host-microbe interaction. However, the extent to which these disturbances resolve naturally, or can be actively reversed, remains unclear. In this study, we use longitudinal sampling in infants to examine microbiome recovery following antibiotics, with and without autologous fecal microbiota transplantation (aFMT). We show that antibiotic exposure leads to coordinated disruptions in microbial composition, antibiotic resistance genes, and metabolic profiles. While partial recovery spontaneously occurs over time, faster and more extensive restoration toward the pre-antibiotic state is observed following aFMT. These findings provide insight into the ecological dynamics of microbiome reassembly in early life and highlight the potential of using controlled perturbations to understand microbiome resilience.<br><br>CLINICAL TRIALS: This study is registered with ClinicalTrials.gov as NCT06609980.}, }
@article {pmid42214591, year = {2026}, author = {Zhu, Y and Li, D and Ma, B and Zhang, T and Zeng, H and Zhang, J and Li, S and Ding, F}, title = {Effluent-released sludge in granular anammox systems: nitrogen transformation potential and potential biosafety concerns.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124887}, doi = {10.1016/j.envres.2026.124887}, pmid = {42214591}, issn = {1096-0953}, abstract = {Granular anaerobic ammonium oxidation (anammox) sludge enables effective biomass retention and supports the stable operation of anammox reactors. During long-term operation, however, effluent-released sludge (ERS) is continuously washed out with the effluent, exhibiting physicochemical and microbial characteristics that differ markedly from those of retained sludge (RS). The functional role and biosafety implications of ERS remain poorly understood. In this study, RS and ERS from the same granular anammox reactor were systematically compared in terms of nitrogen removal performance, microbial community composition, functional gene profiles, and biosafety-related features. RS maintained high anammox activity, whereas ERS showed reduced anammox performance but was characterized by a pronounced enrichment of comammox Nitrospira, supporting more diverse nitrogen transformation pathways. Metagenomic and 16S rRNA analyses further indicated the co-occurrence of comammox Nitrospira and heterotrophic denitrifiers in ERS, suggesting a potential metabolic linkage involving nitrate production and partial reduction to nitrite that may complement anammox activity. Functional pathway analysis revealed diminished autotrophic carbon fixation in ERS, alongside enhanced heterotrophic metabolism and cobalamin biosynthesis. In parallel, ERS exhibited elevated abundances of antibiotic resistance genes and pathogenic taxa. Collectively, these results demonstrate that ERS represents a functionally distinct biomass fraction with unique microbial and metabolic characteristics, as well as potential biosafety implications, warranting further consideration in the evaluation and management of granular anammox systems.}, }
@article {pmid42214592, year = {2026}, author = {Zhu, Y and Liu, H and Yi, Y and Li, Z and Ye, J}, title = {Agricultural allochthonous dissolved organic matter is associated with microbial functional differentiation in methane- and nitrogen-related gene profiles in rural rivers.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124865}, doi = {10.1016/j.envres.2026.124865}, pmid = {42214592}, issn = {1096-0953}, abstract = {Agricultural non-point source (ANPS) pollution introduces chemically complex dissolved organic matter (DOM) into rural rivers, yet how different agricultural practices structure DOM-microbial differentiation at the molecular scale remains unclear. Here, we compared rivers polluted by three dominant ANPS subtypes-aquaculture (AQ), livestock and poultry farming (LP), and crop farming (CF)-across winter and summer in Shanghai, China, by integrating Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) with 16S rRNA gene sequencing and metagenomics. Distinct DOM-microbial differentiation patterns were identified among ANPS subtypes. AQ was characterized by higher proportions of heteroatom-rich compounds (30.6%) and higher-molecular-weight compounds, LP by more aromatic and lignin-/tannin-associated molecular features (AI_mod = 0.261), and CF by CHOS-enriched (26.8%) but overall lower DOM chemodiversity. These molecular fingerprints co-occurred with differences in microbial diversity, community assembly (βNTI), and co-occurrence network topology, indicating relatively stable DOM-microbial templates shaped by long-term agricultural inputs. Seasonal variability further modified DOM composition and microbial differentiation, but responses differed among ANPS subtypes. Event-driven systems (AQ and LP) exhibited pronounced winter-summer shifts, whereas the background-dominated system (CF) showed weaker temporal variability but more persistent DOM-microbial coupling patterns. Low- to medium-molecular-weight (m/z 100-550) DOM fractions showed the strongest co-variation with nitrogen- and methane-related functional gene potentials, suggesting molecular-weight-dependent associations between DOM composition and microbial functional gene profiles. Overall, these findings suggest that ANPS pollution comprises source- and season-specific DOM-microbial templates that can be distinguished using molecular and functional indicators, providing a basis for source-oriented monitoring and targeted management of agriculturally impacted rural river systems.}, }
@article {pmid42214594, year = {2026}, author = {Zhang, Y and Zhang, L and Zhang, S and Yang, C and Wang, Z and Si, G and Peng, Y}, title = {Synergistic Antibiotic-Laden Wastewater Treatment Doubles Denitrification Rate in a Pilot Mineral-Based Autotrophic Biofilter by Breaking Microbial Spatial-Metabolic Constraints.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124860}, doi = {10.1016/j.envres.2026.124860}, pmid = {42214594}, issn = {1096-0953}, abstract = {The practical application of pyrite-based autotrophic denitrification biofilters (PADB) is limited by their low nitrogen removal rate (NRR). This study demonstrates that in a pilot-scale PADB (750 L) treating NO3[-]-N wastewater, heterotrophic bacterial consortia (HBs) severely impair the denitrification activity of autotrophic denitrifying bacteria (ADB) through network encapsulation and metabolic shunting. However, after switching to treating composite wastewater containing antibiotics, the system achieved an antibiotic removal rate of 95.12%. And it's NRR from 32.37 to 63.15 mg N/(L·d), representing a 0.95-fold enhancement. Integrated co-occurrence network and metagenomic analyses revealed a three-stage cascade reaction underlying this improvement: (i) The antibiotic stress halted carbon-feeding from ADB and hydrolytic-acidifying bacteria to HBs (fermentation gene abundance decreased by 1.89-58.45%), depriving HBs of energetic and substrate support and resulting in their selective elimination (0.63-fold decrease in relative abundance). This relieved ADB's metabolic burden and shortened their physical distance to pyrite; (ii) Elevated electron and energy demand in ADB activated dormant genes for electron shuttle synthesis (menC/E: 0 to 342/402 TPM) and upregulated sulfur metabolism genes (∼3.9-fold), enhancing pyrite dissolution and electron harvesting; (iii) This augmented electron flow stimulated ADB's carbon fixation pathway (Calvin-Benson-Bassham cycle genes upregulated 14.89-fold) and amplified energy metabolism (1.33-1.55-fold enhancement in glycolysis and Tricarboxylic Acid cycle), supplying ample material and energy for ADB proliferation and denitrification. Consequently, ADB enrichment accelerated 509-fold, while the abundance of key denitrification genes (napA/B, nosZ) increased by 2.1-11.04-fold. These molecular and population-level changes doubled the system's NRR compared to its original level.}, }
@article {pmid41998770, year = {2026}, author = {Ng, DZW and Yap, GC and Tay, CJX and Huang, CH and Zhao, S and Low, A and Tham, EH and Loo, EXL and Shek, LP and Goh, A and Chong, KW and Goh, SH and Cheng, ZR and Van Bever, HPS and Teoh, OH and Lee, YS and Yap, F and Tan, KH and Chong, YS and Chan, SY and Eriksson, JG and Godfrey, KM and Lay, C and Knol, J and Schuster, SC and Lai, JS and Chong, MF and Lee, JWJ and Lee, BW and Chan, ECY and Ta, LDH}, title = {Maternal-prenatal gut microbiome-systemic metabolome perturbations and TH2-skewed immunity link to offspring gut microbiome disruption and atopic dermatitis susceptibility.}, journal = {Genome medicine}, volume = {18}, number = {1}, pages = {}, pmid = {41998770}, issn = {1756-994X}, support = {NIHR Senior Investigator (NF-SI-0515-10042) and NIHR Southampton Biomedical Research Centre (NIHR203319)//National Institute for Health and Care Research/ ; MOH-000532//Singapore Ministry of Health's National Medical Research Council Clinician Scientist - Individual Research Grant/ ; MC_UU_12011/4/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: Emerging evidence suggests that maternal-prenatal gut microbiome disturbances shape offspring allergic outcomes through modulation of the in utero immune environment. Yet, no comprehensive clinical studies in human mother–offspring dyads have deconvoluted the maternal-prenatal gut microbiome and systemic immune-metabolome signatures underlying offspring allergic predisposition.<br><br>METHODS: We performed a longitudinal nested case&#x2013;control study involving 128 well-characterized mother&#x2013;offspring dyads from defined cases (offspring with atopic dermatitis (AD); n&#x2009;=&#x2009;64) and controls (offspring without AD; n&#x2009;=&#x2009;64). Maternal stool and blood samples were collected at multiple time points during gestation for multi-omic profiling. Structural and functional gut microbiome composition was characterized via metagenomic sequencing, while systemic metabolome and serum immune milieu were profiled using targeted plasma metabolomics and Olink proximity extension assays, respectively. In offspring early-life, stool samples were collected longitudinally up to 6&#xa0;months of age for gut microbiome and metabolome analyses.<br><br>RESULTS: Mothers of AD infants exhibited longitudinal enrichments of gut Klebsiella pneumoniae, Roseburia intestinalis, Clostridioides difficile and Bilophila sp. 4_1_30, alongside depletions in gut Clostridium sp. CAG:678, Romboutsia timonensis, Akkermansia muciniphila, Blautia hansenii and Alistipes ihumii during pregnancy. These taxonomic shifts were associated with systemic metabolomic alterations, including elevated branched-chain amino acids and immune-related metabolites (e.g., creatine, ornithine), and a concurrent pro-inflammatory TH2-skewed immunological milieu marked by increased interleukin-4 (IL-4) and IL-5 and decreased CXCL11. In early life, AD infants harbored a dysbiotic gut microbiome characterized by persistent enrichments of potentially pathogenic Escherichia coli and K. pneumoniae, along with depletion of short chain fatty acid-producing Bacteroides species and beneficial colonizers. Integrated multi-omic analyses across the prenatal-postnatal axis indicated that the impaired establishment of gut microbiome in AD infants may, in part, be attributed to the (1) potential transmission of maternally originated Klebsiella and (2) immunomodulatory effects of a maternal-prenatal pro-inflammatory, TH2-skewed milieu during gestation.<br><br>CONCLUSIONS: Our study uncovers a distinct maternal-prenatal gut microbiome and systemic metabolome&#x2013;immune signature that predisposes offspring to AD by disrupting early-life gut microbial establishment. These findings highlight the gestational period as a critical window for preventive strategies targeting the maternal microbiome or systemic immune-metabolic axes to mitigate allergic disease susceptibility in offspring.<br><br>TRIAL REGISTRATION: This study is registered at ClinicalTrials.gov (NCT 03531658).<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-026-01655-5.}, }
@article {pmid42201863, year = {2026}, author = {Kaptan, D and Flemming Elvers, AC and Kjær Knudsen, A and Schroeder, H and Hollund, HI}, title = {Histological and metagenomic analysis of microbial communities in archaeological human bones.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0340244}, doi = {10.1371/journal.pone.0340244}, pmid = {42201863}, issn = {1932-6203}, mesh = {Humans ; *Bone and Bones/microbiology/pathology ; *Metagenomics/methods ; *Archaeology ; *Microbiota/genetics ; Bacteria/genetics/classification ; Fungi/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Norway ; Phylogeny ; }, abstract = {Buried archaeological bones tend to be heavily degraded by microorganisms. This type of biodegradation was already identified in the 19th century and remains a subject of continuous investigation. However, the underlying processes are still not fully understood, and the organisms responsible for the decay have not been clearly identified. Technological advances in genetic sequencing now allow detailed study of the bone microbiome. And yet, identifying the species causing the observed bioerosion has proven challenging. Relatively few studies have combined the investigation of bone degradation by microscopy, so-called histotaphonomy, with metagenomic analyses. This study aims to bridge this gap. We utilize a large set of human bone samples from medieval cemeteries in south-western Norway. Detailed microscopic analyses have been carried out, showing diverse levels of preservation. The extent of bioerosion is correlated with the results from metagenomic analyses as well as environmental factors. Microbiome diversity is greater and more evenly distributed in well-preserved bones with limited bioerosion, particularly those recovered from burials beneath church floors, contrasting with outdoor cemeteries. Fungal taxa were detected in only a single sample in the metagenomic data despite histological evidence of fungal structures, and their role in bone bioerosion remains unclear. Our findings show that preservation state is strongly associated with microbiome composition. The most prevalent genus found was Streptomyces, supporting previous research suggesting that bacteria within this group could be involved in bone bioerosion.}, }
@article {pmid42201897, year = {2026}, author = {, }, title = {Editorial Note: Host-Associated Metagenomics: A Guide to Generating Infectious RNA Viromes.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0350242}, doi = {10.1371/journal.pone.0350242}, pmid = {42201897}, issn = {1932-6203}, }
@article {pmid42202516, year = {2026}, author = {Sun, X and Lin, Z and Ni, SQ}, title = {Multidrug-resistant bacteria contribute to core bacterial community and ARGs persistence during full-scale pharmaceutical wastewater treatment.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142513}, doi = {10.1016/j.jhazmat.2026.142513}, pmid = {42202516}, issn = {1873-3336}, abstract = {Pharmaceutical wastewater treatment plants (WWTPs) are confronted with a wide range of contaminants, resulting in the accumulation of antibiotic resistance genes (ARGs) and the evolution of multidrug-resistant (MDR) bacteria. However, the ecological roles of these MDR residents during full-scale wastewater treatment remain unclear. In this study, the core bacterial communities as well as potential MDR bacteria for industrial WWTPs were firstly categorized out. Taxa belonging to MDR bacteria were frequently detected to persist with low relative abundance across different treatment units, even in the effluent. Then, the occurrence and health risk of ARGs were evaluated. Certain abundant and prevalent ARGs, such as fabG, macB, and adeF, were found to exhibit high prevalence. Some pivotal mobile genetic elements, acting as key network hubs, can link MDR bacteria with a broad range of ARGs. Finally, the result showed that several metagenome-assembled genomes recovered from the effluents were not only classified as MDR bacteria harboring ARGs with high risk, but also served as important members of the core bacterial community. These findings provide critical insights into the ecological roles of MDR bacteria during the full-scale pharmaceutical wastewater treatment, and emphasize the urgent need for real-time monitoring of wastewater-borne MDR bacteria for ecological health.}, }
@article {pmid42202519, year = {2026}, author = {Li, X and Wang, Y and Dang, X and Zhang, Y and Zhao, C and Hou, S and Li, B and Ma, F and Hao, L and Zhu, T}, title = {Molecular mechanism by which high temperature and RecBCD synergistically lower strand-separation barriers and promote destabilization of representative efflux-pump ARG fragments (macB/tetA) during hyperthermophilic composting.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142445}, doi = {10.1016/j.jhazmat.2026.142445}, pmid = {42202519}, issn = {1873-3336}, abstract = {Hyperthermophilic composting (HC) effectively mitigates antibiotic residues and antibiotic resistance genes (ARGs), yet the molecular basis of ARG-derived DNA destabilization under extreme heat remains unclear. Here, we established an HC system reaching 87.3 ℃ (∼360 K) and combined metagenomics, AlphaFold prediction, molecular dynamics (MD), and free-energy calculations to investigate representative efflux-pump ARG fragments (macB/tetA). HC removed oxytetracycline, enrofloxacin, and sulfamethoxazole by 98.44%, 92.34%, and 99.63%, respectively, while overall ARG abundance declined markedly. Metagenomics identified 796 ARGs, dominated by efflux mechanisms, and qPCR confirmed multi-order decreases in macB and tetA. Nucleic acid processing/degradation genes, including recD/RecBCD-related homologs, were enriched during the high-temperature phase and negatively associated with ARG abundance. Based on these data, we constructed a candidate RecBCD model from metagenomic recB/recC/recD homologs. MD showed that this model maintained overall structural integrity at 360 K. AlphaFold predicted end-loaded candidate RecBCD-DNA complexes (ipTM/pTM ≈ 0.89-0.90) with local duplex opening. Subsequent MD revealed that RecBCD-bound DNA became more flexible, displayed weakened/reorganized hydrogen-bond networks, and sampled more multistate free-energy basins. Umbrella sampling further showed that strand-separation PMFs at 360 K were ∼25-30 kJ·mol[-1] lower than at 330 K, with tetA exhibiting a lower barrier and greater thermal sensitivity than macB. Together, these results support a working model in which high temperature lowers DNA stability and strand-separation barriers, thereby facilitating candidate RecBCD-mediated loading and local processing of representative efflux-pump ARG-derived DNA fragments during HC.}, }
@article {pmid42202778, year = {2026}, author = {Nogal, A and Wang, K and Thompson, KN and Kim, H and Bhosle, A and Piccinno, G and Maharjan, S and Upreti, C and Nguyen, LH and Segata, N and Rimm, EB and Garrett, WS and Chan, AT and Huttenhower, C and Song, M}, title = {Long-lasting gut microbiome and fecal metabolome alterations after colorectal adenoma removal and their relationship to colorectal cancer.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.05.001}, pmid = {42202778}, issn = {1934-6069}, abstract = {Although the gut microbiome is implicated in colorectal cancer (CRC), microbiome and metabolome alterations along the adenoma-carcinoma sequence remain unclear. Here, we profile stool metagenomes obtained from 354 women 12.1 ± 4.8 years following adenoma resection and from their 1:1-matched controls, as well as stool metabolomes from 184 pairs. Metagenomic profiles are compared with those from 14 independent CRC case-control studies. Microbial composition differs between adenoma cases and controls and agrees with CRC-associated alterations (Pearson's rho = 0.26, p < 0.0001). Thirty-one microbes, including Faecalibacterium prausnitzii and Flavonifractor plautii, are altered in both conditions and correlate with lifestyle factors. Thirty metabolites and 7 sub-pathways, particularly sphingolipids, are associated with adenomas. Adenomas also exhibit disease-specific microbe-metabolite associations, including those between Bilophila wadsworthia and alanine-containing dipeptides. These findings reveal gut microbial and metabolomic alterations detectable years after adenoma resection, supporting the presence of an altered microbiome along the adenoma-CRC continuum.}, }
@article {pmid42202790, year = {2026}, author = {Toubon, G and Boulund, F and Escobedo, CM and Brunius, C and Engstrand, L and Larsson, SC and Nordin, E and Schuppe-Koistinen, I and Wolk, A and Wittenbecher, C and Landberg, R}, title = {Gut microbiome composition and functional potential associate with incident type 2 diabetes in 4,685 adults from a Swedish prospective cohort.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {102835}, doi = {10.1016/j.xcrm.2026.102835}, pmid = {42202790}, issn = {2666-3791}, abstract = {Cross-sectional studies link gut microbiome alterations to type 2 diabetes (T2D), but prospective evidence remains limited. We aim to identify taxonomic and functional features associated with future T2D risk. We analyze shotgun metagenomic data from 4,685 participants (mean age, 73.9 years; 49.0% women) in the Swedish SIMPLER cohort, followed for a median 5.3 years, during which 383 developed T2D. Six species are associated with increased T2D risk: Desulfovibrio piger, Alistipes communis, Alistipes finegoldii, Akkermansia muciniphila, Ruminococcus gnavus, and GGB3614_SGB4886 (Lachnospiraceae), while three are protective: Erysipelotrichaceae bacterium, Coprococcus catus, and Clostridia unclassified SGB6317. We observe context-specific associations, including a dietary fiber-modified effect for A. muciniphila indicative of diet-dependent patterns. Three gut metabolic modules are associated with incident T2D: asparagine degradation (higher risk), mannose degradation, and the non-oxidative pentose phosphate pathway (lower risk). These prospective findings offer insights into T2D etiology and may support microbiome-informed strategies for risk prediction and prevention.}, }
@article {pmid42203111, year = {2026}, author = {Wang, L and Bai, L and Li, H and Zhang, P and He, F}, title = {A Case of Imported Infection in China: Initially Treatment-unresponsive Schistosomiasis Coinfection with Bladder Tuberculosis.}, journal = {Indian journal of medical microbiology}, volume = {}, number = {}, pages = {101157}, doi = {10.1016/j.ijmmb.2026.101157}, pmid = {42203111}, issn = {1998-3646}, abstract = {Schistosoma haematobium, endemic to sub-Saharan Africa, causes urogenital disease, differing from Schistosoma japonicum, which affects the hepatointestinal system and is the only endemic schistosome in China. A Chinese male with persistent hematuria after prolonged occupational exposure in Angola was initially attributed to S. japonicum. Following failed treatment, metagenomic sequencing confirmed S. haematobium infection, and subsequent urethral resection detected Mycobacterium tuberculosis DNA, establishing concurrent bladder tuberculosis. This case highlights the need for molecular diagnostics in patients with hematuria after sub-Saharan exposure and the immunomodulatory risks posed by helminth infections.}, }
@article {pmid42203372, year = {2026}, author = {McCann, P and Megaw, J and Gobert, GN}, title = {Parasite-associated microbiomes: An unseen microenvironment.}, journal = {Advances in parasitology}, volume = {131}, number = {}, pages = {31-70}, doi = {10.1016/bs.apar.2026.03.001}, pmid = {42203372}, issn = {2163-6079}, mesh = {Animals ; Humans ; *Microbiota ; *Host-Parasite Interactions ; *Parasites/microbiology/physiology ; Symbiosis ; }, abstract = {Parasites harbor diverse microbial ecosystems that include not only bacteria but also archaea, fungi, viruses and microbial eukaryotes. These parasite-associated microbiomes, long overlooked, are now recognized as important determinants of parasite development, fitness, virulence and interactions with hosts across medical, veterinary, agricultural and ecological systems. However, current understanding of parasite-associated microbiomes remains fragmented, with most studies focusing on a narrow set of human parasites, relying heavily on bacterial surveys and rarely capturing the full multi-kingdom diversity of microbial partners. Important challenges include expanding research to encompass neglected parasite groups and their non-bacterial associates, establishing causal links between microbiome members and parasite phenotypes, and overcoming the technical barriers posed by low-biomass, host-contaminated and/or experimentally intractable systems. Progress will also depend on developing robust reference genomes and analytical tools that can resolve multi-kingdom communities and integrate parasite and symbiont biology. This chapter synthesizes current knowledge across helminths, protozoa, ectoparasites and plant-infecting parasites. We consider how microbiome manipulation may contribute to parasite control while recognizing the evolutionary and ecological complexities involved in altering host-parasite-microbiome interactions. Embracing an explicitly multi-kingdom, holobiont-focused perspective promises to illuminate fundamental aspects of parasitism. Such knowledge may contribute to new avenues for mitigating the impact of parasitic diseases on human and animal health, food security and ecosystems.}, }
@article {pmid42203690, year = {2026}, author = {Fullam, A and Prasoodanan Pk, V and Kuhn, M and Bork, P and Schmidt, TSB}, title = {microntology: a lightweight, data-driven controlled vocabulary to describe Earth's microbial habitats.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag343}, pmid = {42203690}, issn = {1367-4811}, abstract = {MOTIVATION: Data-enabled studies of microbial ecology and evolution depend on high-quality descriptions of microbial habitats, based on curated and consolidated vocabularies.<br><br>RESULTS: We introduce microntology v1.0, a pragmatic controlled vocabulary of 148 terms to describe microbial habitats and lifestyles, and provide manually curated microntology annotations for >300k metagenomic samples from public repositories.<br><br>AVAILABILITY: microntology controlled vocabulary terms and term hierarchies (doi: 10.5281/zenodo.19730167), and curated annotations for 305,626 metagenomic samples (doi: 10.5281/zenodo.18164252) are available via Zenodo and spire.embl.de/downloads. Underlying code is available via github.com/grp-schmidt/microntology and Zenodo (doi: 10.5281/zenodo.20323497). User feedback, suggestions and bug reports are welcome at github.com/grp-schmidt/microntology/issues.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid42203770, year = {2026}, author = {So, Y and Pichler, MJ and Kappel, SS and Jin, C and Eriksen, C and Chatzigiannidou, I and Andersen, MHB and Tsiamis, V and Lukassen, MV and Skytthe, LE and Teneberg, S and Kristiansen, K and Brix, S and Aunsholt, L and Abou Hachem, M}, title = {Dual human milk oligosaccharide-fibre utilisation is a selection cue for the weaning gut microbiome.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73297-5}, pmid = {42203770}, issn = {2041-1723}, support = {1026-00386B//Natur og Univers, Det Frie Forskningsr&#xe5;d (Natural Sciences, Danish Council for Independent Research)/ ; }, abstract = {Gut microbiome (GM) maturation in early life follows organised taxonomic successions, yet how the weaning diet impacts these trajectories remains underexplored. Here, we collected faecal samples at pre-, early and late weaning from seven mother-infant dyads forming the Milkome cohort, designed to evaluate the contribution of human milk oligosaccharides (HMOs) to GM maturation during weaning (NCT07026526). Surprisingly, all preweaning infant faecal consortia grew on multiple dietary fibres, consistent with the prevalence of fibre-degradation genes in their metagenomes. Utilisation of both HMOs and dietary fibres was discovered as a metabolic hallmark of the weaning GM, as supported by metagenomics and the growth of faecal consortia on HMOs, following their enrichment on fibres. The growth of a defined consortium on weaning-mimic substrates, further showed that distinct Clostridia simultaneously deploy HMO and fibre utilisation pathways, which confers competitive growth against HMO- or fibre-utilising bifidobacteria. Metagenomics, culturomics and HMO-utilisation profiles of 137 maternal isolates were concordant with retention of the HMO-utilisation capacity by the adult GM. Our findings highlight dual HMO-fibre utilisation as an unrecognised selection cue of core adult GM species during weaning, which outlines a plausible mechanism of GM maturation in early life and extends the importance of HMOs to the weaning transition.}, }
@article {pmid42203854, year = {2026}, author = {Bostanci, N and Antony, AT and Silbereisen, A and Esmaili, T and Krog, MC and Sterpu, I and Bashir, Z and Engstrand, L and Wiberg-Itzel, E and Nielsen, HS and Hugerth, LW and Schuppe-Koistinen, I}, title = {Shotgun metagenomic mapping of saliva reveals insights into diversity and function of the oral microbiome in pregnancy.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42203854}, issn = {2045-2322}, mesh = {Humans ; Female ; Pregnancy ; *Saliva/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; Adult ; *Mouth/microbiology ; Shotgun Sequencing ; Cross-Sectional Studies ; Metagenome ; Bacteria/genetics/classification ; }, abstract = {The oral microbiome is a complex and dynamic microecosystem that fluctuates continually throughout the lifespan of a woman. Nevertheless, the function of the oral microbiome in reproductive health is not yet fully understood. Monitoring oral health and providing necessary dental care before and during pregnancy could help maintain a balanced oral microecology and support healthier microbial transfer to newborns. Here, we aimed to compare the salivary microbiome of pregnant and non-pregnant women using shotgun metagenomics to describe their taxonomic and functional composition and assess whether the resulting data is better explained by the reproductive stage. We conducted a comparative cross-sectional study involving pregnant women (n = 71; gestational age 37-42 weeks) and non-pregnant women (n = 143 with regular menstrual cycles; 3 saliva samples per participant across different menstrual phases). Shallow shotgun metagenomic sequencing was used to characterize both taxonomic and functional profiles of the oral microbiome. Socransky's color complex analysis was performed to assess group differences in key microbial complexes. Quantitative PCR was used to validate the abundance of selected oral bacteria. Participant data, including demographic, behavioral, clinical, and oral health variables (such as dentist visits), were collected and incorporated as covariates to adjust for potential confounding effects. Additionally, a sensitivity analysis was performed by excluding participants with identified behavioral or clinical risk factors. Ten phyla including Actinomycetota, Bacteroidota, Chloroflexota Bacillota, Fusobacteriota, Pseudomonadota, Spirochaetota, Synergistota Candidatus Saccharimonadota and Mycoplasmatota, 102 genera, and 410 species were identified. Pregnant women had lower saliva microbiome diversity, driven by reduced richness but unchanged evenness. The microbial composition varied between the groups, even after adjusting for confounding factors. Differential abundance analysis, adjusted for potential confounders, identified 25 species that significantly differed between groups (q < 0.05), with 13 taxa more than three-fold higher in pregnant women. Notably, red complex species were more abundant in pregnant women (p < 0.05). Functional pathway analysis identified 40 modules that differed by pregnancy status. These results further suggest a connection between pregnancy and changes to the oral microbiome in women. As many of these changes are in a pro-inflammatory direction, further research is warranted to assess its potential impact on pregnant women and their newborns.}, }
@article {pmid42204574, year = {2026}, author = {Dinesh, D and Morgan, XC and Jensen, J and Bjornevik, K and Schwarzschild, MA and Ascherio, A and Huttenhower, C and Palacios, N}, title = {Shotgun Metagenomic Profiling of the Gut Virome in Prodromal and Confirmed Parkinson's Disease.}, journal = {Annals of neurology}, volume = {}, number = {}, pages = {}, doi = {10.1002/ana.78243}, pmid = {42204574}, issn = {1531-8249}, support = {RF1AG075922/GF/NIH HHS/United States ; R01AG085320/GF/NIH HHS/United States ; R01NS097723/GF/NIH HHS/United States ; UM1 CA186107/GF/NIH HHS/United States ; }, abstract = {We conducted a nested case-control study within the Nurses' Health Study and the Health Professionals Follow-up Study to examine the role of the gut virome (GV) in Parkinson's disease (PD). We applied a novel metagenomic virome profiling approach, Bioinformatic Application for Quantification and Labeling of Viral taxonomy (BAQLaVa), to prospectively collected metagenomic data from 62 participants with PD, 123 healthy controls, and 90 participants with prodromal PD (pPD). Multivariate linear modeling identified 3 viral genome bins (VGBs) that were elevated in PD: MVG081219 (β = 0.86, q = 0.013), MVG041501 (β = 0.95, q = 0.048), MVG081211 (β = 0.66, q = 0.048) and one VGB, MVG098915 (β = -1.42, q = 0.047) that was depleted in participants with PD compared to controls. These four VGBs were similarly associated with pPD. This work suggests that the GV has potential as a future biomarker for PD. ANN NEUROL 2026.}, }
@article {pmid42204631, year = {2026}, author = {Fu, YT and Deng, YP and Duan, DY and Peng, YY and Liu, YL and Zhang, Y and Xu, ZK and Elsheikha, HM and Liu, GH}, title = {Insights into the microbiota profile of Pediculus humanus capitis using metagenomic next-generation sequencing and molecular detection of unexpected pathogen DNA in Hunan Province, China.}, journal = {Parasites &amp; vectors}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13071-026-07471-5}, pmid = {42204631}, issn = {1756-3305}, support = {2024JJ6548//the Hunan Natural Science Foundation Youth Fund Project/ ; 32473057//the National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The head louse, Pediculus humanus capitis, remains a significant public health concern affecting millions of people worldwide and has been implicated as a potential vector for multiple human pathogens. Characterization of the microbiota of head lice could improve our understanding of their public health significance and potential role in pathogen transmission. Here, we characterize the microbiota of head lice and investigate microbiota differences among different clades of head lice.<br><br>METHODS: Head lice were collected from Hunan Province, China, and classified into clade A and clade B (CACB) using polymerase chain reaction (PCR)-based genotyping. The microbiota of pooled CACB of head lice samples&#xa0;(n&#x2009;=&#x2009;46) was investigated by metagenomic shotgun sequencing&#xa0;and comparatively analysed at the&#xa0;phylum,&#xa0;genus, and&#xa0;species levels. In addition, the prevalence of potential pathogen DNA in head lice samples&#xa0;(n&#x2009;=&#x2009;204) was assessed&#xa0;using real-time PCR with stringent negative controls.<br><br>RESULTS: We obtained non-redundant CACB microbial gene catalog comprising 79,232 genes, of which 4.70% (3,722&#xa0;genes) were taxonomically assigned. The relative abundance of bacteria (2.52%) was higher than that of eukaryotes (2.04%), viruses (0.11%), and archaea (0.02%). Comparative analysis identified 655 and 750 unique genes in CACB, respectively. The dominant phyla in the CACB of head lice were Proteobacteria. At the genus level,&#xa0;DNA sequences corresponding to Anaplasma (25.98%; 53/204), Mycobacterium (24.02%; 49/204), Chlamydia (23.53%; 48/204), Ehrlichia (10.29%; 21/204), and Vibrio (0.49%; 1/204) were detected, suggesting the presence of bacterial&#xa0;DNA&#xa0;from these taxa.<br><br>CONCLUSIONS: Our results provide a preliminary characterization of the annotated fraction of the CACB&#xa0;microbiome in head lice. The high proportion of unannotated genes (>95%)&#xa0;underscores the limited representation of louse-associated microbial genomes in public databases and suggests &#xa0;substantial, yet unexplored, microbial diversity. The detection of pathogen DNA does not confirm organism viability or vector competence,however it may&#xa0;suggest prior&#xa0;exposure, mechanical carriage, or residual DNA from&#xa0;blood meals. These exploratory findings contribute new&#xa0;insights into the microbiota associated with human lice.}, }
@article {pmid42204733, year = {2026}, author = {Fang, Q and Liu, J and Xuan, C and Li, C and Jiang, X and Zhang, S and Li, Q and Liu, X and Liu, Q and Zhang, L and Wang, Y and Cui, J and Qu, Y and Zhang, J and Li, P and Chen, X}, title = {Targeting the gut‒kidney axis for lupus nephritis treatment: multimechanism regulatory strategies and evidence from Traditional Chinese medicine.}, journal = {Chinese medicine}, volume = {21}, number = {1}, pages = {}, pmid = {42204733}, issn = {1749-8546}, support = {2022YFC3602000//the National Key Research and Development Program of China/ ; 82274327//the National Natural Science Foundation of China/ ; 32141005//the National Natural Science Foundation of China/ ; }, abstract = {Lupus nephritis (LN) treatment remains challenging because of the limited efficacy and substantial side effects of conventional immunosuppressive therapies. Traditional Chinese medicine (TCM), with its holistic and multitarget approach, offers unique therapeutic potential. The emerging gut-kidney axis theory provides a new framework for understanding LN pathogenesis by linking gut dysbiosis and intestinal barrier injury to renal inflammation. This review systematically examines the role of gut-kidney axis dysregulation in LN progression and establishes connections between the TCM spleen-kidney correlation theory and this modern concept. Accumulating evidence suggests that TCM compounds and active ingredients alleviate renal injury and improve LN through multiple mechanisms. TCM compounds modulate the gut microbiota composition, enhance intestinal barrier integrity, reduce endotoxin translocation, and suppress systemic inflammation. These findings position the gut-kidney axis as a critical target for TCM intervention. Through multicomponent synergy, TCM restores gut homeostasis and inhibits aberrant immune responses. Future studies should integrate multiomics approaches, including metagenomics and metabolomics, and prospective clinical trials should dynamically track the gut microbiota and metabolite profiles in LN patients. Such investigations will clarify the precise mechanisms by which TCM modulates the gut-kidney axis and facilitate the development of personalized TCM-based therapeutic strategies.}, }
@article {pmid42204882, year = {2026}, author = {Jiang, Y and Zhao, J and Chen, Z and Jiang, N and Lu, C and Zhang, Y and Chen, H}, title = {Long-Term Effects of Straw-Biochar Application and Fertilization Gradients on Black Soil Carbon Sequestration via Prokaryote-Fungus-Protist Interactions and Metagenomic-Metabolite Linkages.}, journal = {Environmental microbiology}, volume = {28}, number = {6}, pages = {e70339}, doi = {10.1111/1462-2920.70339}, pmid = {42204882}, issn = {1462-2920}, support = {2022YFD1500302//National Key Research and Development Program of China/ ; 42277282//National Natural Science Foundation of China/ ; 2022A1515010861//Basic and Applied Basic Research Foundation of Guangdong Province/ ; JCYJ20250604174440054//Shenzhen Natural Science Foundation in Basic Research Fund/ ; JCYJ20220530150201003//Shenzhen Natural Science Foundation in Basic Research Fund/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Fungi/metabolism/genetics/physiology ; Metagenomics ; *Charcoal ; *Carbon Sequestration ; Bacteria/metabolism/genetics/classification ; *Fertilizers/analysis ; China ; Microbiota ; Carbon/metabolism ; Metagenome ; }, abstract = {Here, we conducted a seven-year field experiment in black soils of Northeast China to evaluate the effects of carbon (C) management, that is, control, straw return (SD), straw-biochar (BC), and a combined amendment (SDBC), with three fertilization levels (N0: unfertilized control, N60: 60% of conventional rates, N100: conventional rates) on soil microbiomes, metagenomics, and metabolomics. Results showed that BC significantly elevated soil total C (+15%), total N (+10%), and NH 4 + $$ {\mathrm{NH}}_4^{+} $$ (+63%) relative to controls. Microbial community analyses revealed that SD increased prokaryotic richness but reduced protist diversity, whereas BC and SDBC suppressed fungal diversity. Integrated metagenomic and metabolomic profiling uncovered microbial functional adaptations to rich-C conditions under BC and SDBC, characterized by downregulated C metabolism-related genes and concurrent accumulation of lipid-associated metabolites. Crucially, BC decreased the abundance of bacterial virulence factors, contrasting with SD elevating pathogenic potentials. Among three fertilization levels, the reduced rates of N60 optimized microbial network complexity and minimized pathogen invasion risks more effectively than conventional rates of N100 without compromising soil fertility. Collectively, by deciphering prokaryote-fungus-protist interactions and metagenomic-metabolite linkages, our research highlights that straw-derived biochar application and optimized fertilization offers a sustainable strategy to foster beneficial microbial associations, suppresses pathogenic potential, and enhances carbon storage.}, }
@article {pmid42205184, year = {2026}, author = {Wang, X and Wang, H and Liu, J and Zhang, H and Zhou, XJ}, title = {Gut Virome Characteristics and Network Alterations in IgA Nephropathy.}, journal = {Kidney international reports}, volume = {11}, number = {7}, pages = {106550}, pmid = {42205184}, issn = {2468-0249}, abstract = {INTRODUCTION: Emerging evidence implicates gut microbiota dysbiosis in the pathogenesis of IgA nephropathy (IgAN), yet the contribution of the gut virome remains unexplored. This study aimed to characterize virome signatures and virus-microbiota interactions in IgAN.<br><br>METHODS: We performed a rigorously matched case-control study including 32 patients with biopsy-proven IgAN and 32 healthy controls. Fecal viral-like particles and bacterial communities were profiled using metagenomic sequencing and full-length 16S ribosomal RNA (rRNA) sequencing. Statistical analysis included diversity, differential abundance, network analysis, and correlation with clinical indices.<br><br>RESULTS: IgAN subjects displayed significant reductions in gut virome richness (severe IgAN vs. healthy controls, P = 0.03), with a lower relative abundance of Caudoviricetes in severe IgAN (P = 0.045) and enrichment of Tectiliviricetes in mild disease (P = 0.03). We identified 113 differentially abundant bacteriophage contigs (82 up, 31 down; false discovery rate < 0.05); key predicted hosts shifted toward Bacteroides, Clostridium, and Roseburia in IgAN, whereas Faecalibacterium and Alistipes prevailed in controls. Viral and bacterial alpha diversity correlated in healthy controls but not in IgAN (r = 0.38, P = 0.03 vs. r = 0.04, P = 0.81). IgAN virome encoded more glyco-modifying enzymes (P < 0.05), with strong correlations to estimated glomerular filtration rate (eGFR) (r = 0.65, P = 0.001). Viral and bacterial alpha diversity were significantly correlated with proteinuria and gross hematuria (r = 0.18-0.25, - < 0.05).<br><br>CONCLUSION: This study describes potential alterations in gut virome diversity, bacteriophage composition, bacteriome-virome relationships, and predicted functional profiles in IgAN, suggesting potential relevance of the gut virome to intestinal ecological alterations.}, }
@article {pmid42205574, year = {2026}, author = {Liao, G and Xiao, J and Zhang, B and Wang, S and Wan, X and Zhang, C and Lyu, C and Yan, B and Zhao, Y and Kang, C and Zhang, Y and Yuan, F and Zhao, Z and Chen, Y and Guo, L and Zhang, Y}, title = {Enhancement of genetic potential for soil carbon and nitrogen cycling by organic fertilizer substitution improves the ecological environment for licorice cultivation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1758116}, pmid = {42205574}, issn = {1664-302X}, abstract = {BACKGROUND: Excessive chemical fertilizer application has become a core bottleneck restricting the green and sustainable cultivation of Glycyrrhiza uralensis (licorice). Partial organic fertilizer substitution can improve soil microecology and licorice growth traits, yet its regulatory effects on microbial functional genes mediating soil carbon (C) and nitrogen (N) cycling remain unclear.<br><br>RESULTS: Using metagenomic sequencing, we investigated the effects of six fertilization regimes [100% organic fertilizer (OF100), 100% chemical fertilizer (OF0), and organic-inorganic combinations (OF25, OF50, OF75)] on the genetic potential of soil C and N cycling, as well as soil properties and licorice growth traits in bulk and rhizosphere soils of licorice. Organic substitution significantly altered the abundance of C and N cycling-related functional genes: OF100 significantly increased the abundance of genes associated with methane oxidation (pmoA/amoA), carbon degradation (pel, cbh) and nitrification (pmoB/amoB), while OF0 significantly upregulated the methanogenesis-related gene mttA and downregulated nitrogen degradation genes; optimized fertilization (OF50) significantly reduced the abundance of genes linked to excessive carbon degradation (malZ) and nitrogen loss genetic potential (nirK), and markedly increased the abundance of genes for carbon fixation (pccA) and nitrogen mineralization (GDH). PERMANOVA revealed that soil compartment (bulk vs. rhizosphere) explained 62.87% of the total variation in functional gene profiles, which was 5.67 times higher than the contribution of fertilization regime (11.10%).<br><br>CONCLUSION: Rational organic-inorganic fertilization effectively regulates soil microbial functional genes related to C and N cycling, optimizes soil nutrient cycling potential, reduces nutrient loss risk, and enhances nutrient supply efficiency for licorice growth. These findings provide a scientific basis for fertilizer management optimization and sustainable cultivation of licorice.}, }
@article {pmid42205899, year = {2026}, author = {Patil, BL and Shanmugaraj, C and Madhusudan, M}, title = {Metagenomic profiling of endophytic microbiomes associated with fruit pulp and seed kernels of different mango varieties reveals conservation of bacterial communities in seed kernels.}, journal = {3 Biotech}, volume = {16}, number = {6}, pages = {222}, pmid = {42205899}, issn = {2190-572X}, abstract = {UNLABELLED: Bacterial and fungal communities associated with mango pulp and seed kernels from eight Indian mango varieties were profiled using 16 S rRNA and ITS amplicon sequencing. Bacterial diversity was consistently higher in seed kernels (647 ± 238 OTUs) than in pulp tissues (196 ± 112 OTUs). Seed kernel-associated bacterial communities were dominated by Firmicutes (35.8-44.0%) and Bacteroidota (16.8-35.8%) and showed high compositional consistency across varieties, with core genera including Prevotella, Ruminiclostridium, and Lachnoclostridium. In contrast, pulp-associated bacterial communities were enriched in Proteobacteria (6.5-88.5%) and Actinobacteria (4.4-34.6%) and exhibited pronounced inter-varietal variability, particularly in the relative abundance of Bacteroidota (0.8-53.8%). Fungal communities displayed lower richness (14-72 OTUs) and higher variability, with Candida kruisii (15-67%) and Hanseniaspora uvarum (up to 86%) as dominant taxa. Non-metric multidimensional scaling and hierarchical clustering revealed clear tissue-driven segregation of bacterial communities, whereas fungal assemblages showed weaker tissue-associated structuring. Seed kernels harbored approximately 3.3-fold more unique bacterial OTUs than pulp tissues, with the Amrapali seedkernel exhibiting the highest richness (789 OTUs). Across varieties, 82% of kernel-associated bacterial OTUs were shared, compared with 31% in pulp, indicating a conserved kernel microbiome and a more variable, cultivar-specific pulp microbiome. These results highlight strong tissue-level compartmentalization of mango-associated bacterial communities across cultivars.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04848-2.}, }
@article {pmid42205903, year = {2026}, author = {Hameed, A and Ghate, SD and Shastry, RP}, title = {Fecal functional metagenomics reveals increased gut Bacillota/Pseudomonadota (Firmicutes/Proteobacteria) ratio and altered bacterial CAZyme profile in human colorectal cancer.}, journal = {3 Biotech}, volume = {16}, number = {6}, pages = {230}, pmid = {42205903}, issn = {2190-572X}, abstract = {UNLABELLED: Gut microbial dysbiosis has been implicated in the onset and/or progression of colorectal cancer (CC). We recently identified the emergence of low-abundance bacterial taxa affiliated with the phylum Bacillota in the gut microbiome of CC patients, as revealed by 16S rRNA gene amplicon sequencing. Here, we subjected the fecal samples from CC (n = 4) and healthy control (HC, n = 4) participants to functional metagenomics using the Illumina Novaseq 6000 platform. Metagenome-assembled genomes (MAGs) showed compositional differences among bacterial phylotypes in CC and HC. Species observed, richness (Chao1), and diversity (Shannon's) were high in CC, whereas species abundance peaked in HC. The Bacillota to Pseudomonadota ratio was high (> 3-fold) in CC (2.45) as compared to HC (0.70). MAGs revealed a decline in the distribution frequency of COGs involved in carbohydrate transport and metabolism (G), inorganic ion transport and metabolism (P), and unknown function (S) in CC. However, CC and HC samples exhibited marginal variations in terms of G/P (1.29 and 1.18, respectively) and G/S (0.35 and 0.40, respectively) ratios. Analysis further revealed a significant increment in glycosyltransferases GT1, GT2 and GT4, particularly in CC. In contrast, the glycoside hydrolases GH5 and GH9 declined in CC. GT/GH ratios were found to increase > 2-fold in CC (3.94) compared with HC (1.37). The present pilot-scale dataset-specific work reflects perseverance of Bacillota, significant decline in Pseudomonadota, a stable G/P and G/S ratios and enrichment of glycosyltransfererases in CC. Further transcriptomic-based studies in larger cohorts are warranted to gain insights into the implications of dysbiosis and its pathophysiological relevance.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04882-0.}, }
@article {pmid42206066, year = {2026}, author = {Zhang, Q and Li, S and Wang, X and Sun, Y and Liu, J and Gao, J and Deng, C and Zhao, W and Ma, Y and Quan, J and Yin, Q and Jian, D and Zhang, R and Qi, R}, title = {Multi-metal contamination shapes abundance, co-occurrence, and mobility potential of resistance and virulence genes in mining-impacted soils.}, journal = {Infectious medicine}, volume = {5}, number = {2}, pages = {100260}, pmid = {42206066}, issn = {2772-431X}, abstract = {BACKGROUND: Antimicrobial resistance is a growing global public health concern, posing a serious threat to human health. This study aimed to characterize the composition and distribution of microbial communities, metal resistance genes (MRGs), antibiotic resistance genes (ARGs), and virulence factor genes (VFGs) under multi-metal stress and assess the impacts of metal and soil properties on the diversity, abundance, carrying rate (proportion of gene carriers), co-occurrence rate (proportion of microorganisms co-carrying multiple gene types), and mobility potential (MP, likelihood of horizontal gene transfer) of these genes.<br><br>METHODS: Soil samples were collected from eight sampling sites within a metal mining area (metal-contaminated soil group, MS) and four sites located more than 3 km away from the mining area (control group). Metal concentrations and physicochemical properties of the soils were measured using standard methods. Metagenomic sequencing was performed to characterize the composition and distribution of the microbiome, resistome, and virulome. Statistical modeling was applied to examine the effects of heavy metal content and soil properties on the relative abundance, co-occurrence, and mobilome potential of the three gene types.<br><br>RESULTS: Fe, V, Cr, and Cu primarily promoted the diversity, carrying rate, and co-occurrence rate of microbial communities, MRGs, ARGs, and VFGs. In contrast, Ni and Zn exhibited overall inhibitory effects. For every unit increase in Fe and V, the MP of MRGs and VFGs was associated with an increase of 3.0 &#xd7; 10&#x207b;&#x2075; and 1.2 &#xd7; 10&#x207b;&#x2075;, respectively. A per 1 mg/kg increase in Cr and Cu was correlated with a decrease of 4.3 &#xd7; 10&#x207b;&#x2075; and 1.1 &#xd7; 10&#x207b;&#x2074; in the MP of ARGs and of MRGs, respectively. Positive correlations were found between the MP of plasmid&#x2011;mediated ARGs and Cr, and between transposon&#x2011;mediated ARGs and Cr/V. The MP of transposon&#x2011;mediated MRGs correlated positively with Fe, while Cu correlated negatively with plasmid&#x2011;mediated ARGs but positively with insertion sequence&#x2011;mediated ARGs. Ni concentration was positively associated with the MP of IS&#x2011;mediated VFGs.<br><br>CONCLUSIONS: Metals alter the composition and distribution of microbial communities, MRGs, ARGs, and VFGs. A key mechanism underlying this regulation is the modulation of their mobile potential, which either facilitates or restricts horizontal gene transfer.}, }
@article {pmid42188905, year = {2026}, author = {Yao, Y and Yang, Z and Xie, T and Zhang, Y and Huang, F and Meng, C and Wu, Y}, title = {Multi-Omics Analyses of the Gut Microbiota and Metabolism in Cats with Different Body Conditions and the Effects of Fecal Microbiota Transplantation.}, journal = {Veterinary sciences}, volume = {13}, number = {5}, pages = {}, pmid = {42188905}, issn = {2306-7381}, abstract = {Obesity is increasingly recognized in domestic cats and is associated with metabolic disturbances such as insulin resistance and dyslipidemia. The gut microbiota is considered an important regulator of host metabolism, yet its role in feline obesity remains unclear. In this study, a multi-omics approach was used to investigate gut microbiota composition and metabolic profiles in cats with different body conditions and to evaluate the effects of fecal microbiota transplantation (FMT) on the feline gut microbiota and overall metabolism. In Experiment 1, twenty-four cats were classified as obese, normal, or lean, and their gut microbiota and serum metabolites were analyzed. In Experiment 2, fecal microbiota from obese or lean donors were transplanted into recipient cats. Although overall microbial diversity and community structure did not differ significantly among groups, Coriobacteriaceae and Collinsella were enriched in obese cats, whereas Enterobacteriaceae-related taxa were more abundant in normal-weight cats. Serum metabolomics revealed alterations mainly related to amino acid and antioxidant metabolism, including O-acetylcarnitine, glutathione, and tryptophan metabolism. FMT shifted the recipient gut microbial communities toward their respective donor profiles (obese or lean) but did not significantly affect body weight or routine serum biochemical parameters during the experimental period. These findings suggest that gut microbiota remodeling may influence metabolic processes prior to detectable phenotypic changes in cats.}, }
@article {pmid42189102, year = {2026}, author = {Zheng, H and Xie, X and Zhang, L and Cai, Y and Zhang, Q and Yang, F and Liu, X and Basitere, M and Wei, C and Qiu, G}, title = {Intralineage Diversity and Global Biogeography of Ca. Phosphoribacter.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c18078}, pmid = {42189102}, issn = {1520-5851}, abstract = {In wastewater treatment plants (WWTPs), the newly defined polyphosphate-accumulating organism (PAO) "Candidatus Phosphoribacter" demonstrated important contributions to phosphorus removal. However, their phylogenetic and metabolic diversity, as well as ecological distributions, remain largely uncharacterized. By sequencing 81 activated sludge samples from 34 provinces in China and integrating 747 WWTP metagenomes from six continents, we recovered 166 metagenome-assembled genomes (MAGs) of this genus, expanding the number of Ca. Phosphoribacter MAGs by 17 times and identifying 12 novel species. Biogeographical analysis demonstrated their distinct intercontinental distribution. The coexistence of cosmopolitan species and regionally dominant ones was observed globally as a result of metabolic differentiation. Ancestral gene family reconstruction indicated that this genus underwent a streamlining process dominated by gene loss. Vertically inherited ppk2 and horizontally acquired phoU jointly underpinned the genetic basis of a PhoU-dysregulation-driven polyphosphate phenotype. Comparative genomics revealed broad metabolic potential, including versatile carbon utilization, α-glucan metabolism, and three complementary denitrifying phenotypes. Metatranscriptomic analyses further supported glucose uptake and potential α-glucan cycling as a carbon storage polymer. Overall, this study establishes the most comprehensive genomic framework of Ca. Phosphoribacter, elucidates their functional metabolisms, ecological roles, and global distributions, providing new insights into Ca. Phosphoribacter-mediated enhanced biological phosphorus removal (EBPR) for improved engineering implementation and system sustainability.}, }
@article {pmid42189287, year = {2026}, author = {Candeliere, F and Busi, E and Cerri, S and Sola, L and Lombardi, M and Greco, S and Pedroni, S and Amaretti, A and Raimondi, S and Chiavelli, C and Vitale, MG and Bertolini, F and Depenni, R and Franchini, G and Dominici, M and Rossi, M}, title = {Enterotype-specific microbial biomarkers of immune checkpoint inhibitor response revealed by large-scale integrated metagenomic analysis.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00262-026-04432-w}, pmid = {42189287}, issn = {1432-0851}, support = {PE00000019//NextGenerationEU/ ; }, abstract = {The gut microbiota appears to play a critical role in modulating antitumor immune responses and influencing the efficacy of cancer immunotherapy drugs such as immune checkpoint inhibitors. However, the identification of consistent microbial biomarkers of response remains a significant challenge. This lack of consensus is largely driven by multi-source heterogeneity, including geographic variations in lifestyle, and high inter-individual variability. We hypothesize that these inconsistencies arise because microbiome composition is not uniform but organized into distinct enterotypes. To address this, we performed an integrated metagenomic analysis of 569 fecal samples from oncological patients affected by different tumor types treated with immunotherapy. The samples were clustered into two main enterotypes, E1 and E2, each of them containing two subclusters. A total of 166 species (e.g., Collinsella spp., Blautia spp., Bacteroides spp.) were identified as enterotype-specific biomarkers. A preliminary independent concordance assessment of these biomarkers was conducted in 19 oncologic patients with exceptional response to immunotherapy, providing an initial confirmation of selected enterotype-associated signals. Furthermore, we evaluated the predictive potential of gut microbiota profiles for immunotherapy outcomes through machine learning techniques. The models showed encouraging, albeit moderate, performance in the heterogeneous full dataset, supporting the potential of microbiome-based stratification as an exploratory framework for patient classification, while indicating that further validation is needed before clinical application.}, }
@article {pmid42189388, year = {2026}, author = {Chen, P and Ma, M and Li, Y and Chen, X and Xu, Z and Guo, J and Hu, X and Lv, L and Guo, J and Liu, G}, title = {Food processing-derived carbon dots disrupt male fertility via the gut-testis axis.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {42189388}, issn = {1869-1889}, abstract = {Carbon dots (CDs) are unintentionally formed during thermal processing of food and are emerging environmental pollutants that may pose health risks. We investigated the reproductive toxicity of food-derived CDs via the gut-testicular axis by exposing male mice to environmentally relevant doses (25 and 100 mg kg[-1] d[-1]) for 15 weeks. Multi-omics analysis (including metagenomics, transcriptomics, and metabolomics) revealed that CDs significantly altered the gut microbiota composition, reducing beneficial bacteria (Akkermansia muciniphila, P<0.01) while increasing pathogenic bacteria (Desulfovibrionaceae, P<0.001). Functional analysis revealed upregulation of the lipopolysaccharide (LPS) biosynthesis pathway (P<0.001) and reduced levels of barrier-protective tryptophan metabolites. Time-series studies established a mechanistic sequence: microbiota disruption (days 1-3), intestinal barrier dysfunction (days 3-5), blood-testis barrier damage (days 5-7), testicular inflammation, and reproductive dysfunction. Dose-dependent testicular toxicity included reduced testosterone synthesis (P<0.001), impaired spermatogonial stem cell maintenance due to downregulation of PLZF, and impaired fertility. Testicular transcriptomics analysis revealed activation of the IL-17 signaling pathway and inhibition of steroidogenesis. This study provides comprehensive evidence that CD induces male reproductive toxicity through microbiota-dependent mechanisms, emphasizing the environmental health implications of dietary nanoparticle exposure.}, }
@article {pmid42189604, year = {2026}, author = {Lopes, F and Martinez-Martinez, D and Späth, MR and Hoyer-Allo, KJR and Strubl, S and Cukoski, S and Knieps, L and Brodesser, S and Göbel, H and Schwarz, G and van den Berg, BM and Rabelink, TJ and Schermer, B and Benzing, T and Müller, RU and Beyer, A and Cabreiro, F and Koehler, FC}, title = {The Interplay between Gut Microbiota and Diet-Induced Kidney Protection.}, journal = {Kidney360}, volume = {}, number = {}, pages = {}, doi = {10.34067/KID.0000001219}, pmid = {42189604}, issn = {2641-7650}, abstract = {BACKGROUND: On the one hand, dietary interventions are known for their pivotal role in regulating diversity, composition as well as function of the gut microbiome. On the other hand, specific diets show an immense potential in preventing kidney injury from various damaging stimuli in rodents and recent findings, in turn, highlight a central role of gut microbiota in kidney health and disease.<br><br>METHODS: Three protective dietary regimens - a fasting mimicking diet, a diet depleted in sulfur containing amino acids and caloric restriction - were examined in parallel in a rodent model of ischemia-reperfusion injury. To delineate the diet-induced effect on gut microbiota in response to ischemic kidney damage we used comparative shotgun metagenomics for taxonomic as well as functional profiling. We further examined the renal metabolic response using comparative transcriptomics to unravel the interplay between gut microbiota and kidney protection.<br><br>RESULTS: Beneficial dietary preconditioning strategies changed the composition of gut microbiota in an IRI-dependent manner. Using ternary plots to investigate the role of dietary interventions over time before and after ischemic insult, we detected a central role of Lachnospiraceae that commonly expanded in response to renal IRI in dietary-preconditioned mice. Further functional profiling of gut microbiota in our model revealed an increase in plasma levels of bacterial derived short chained fatty acids in diet-induced kidney protection. Comparative bulk transcriptomics in our model, in turn, pointed towards the metabolic use of these bacterial derived short-chained fatty acids in kidneys of protected mice.<br><br>CONCLUSIONS: As proximal tubules lack sufficient glycolytic capacity, products of microbial metabolism may serve as an additional energy source to fulfill their high demands when withstanding ischemic damage. Our data shed light on a close interplay between gut microbiota and diet-induced kidney protection calling for further research at the crossroads of microbiology, metabolism and molecular nephrology.}, }
@article {pmid42190464, year = {2026}, author = {Yergalyiev, T and Roth, C and Rodehutscord, M and Seifert, J and Camarinha-Silva, A}, title = {Age, strain, and gut section shape the microbiome of commercial laying hens.}, journal = {Poultry science}, volume = {105}, number = {9}, pages = {107152}, doi = {10.1016/j.psj.2026.107152}, pmid = {42190464}, issn = {1525-3171}, abstract = {Gut microbiota, among other factors, may influence the overall performance of laying hens. To investigate how host genetics and age shape microbial communities, we profiled the gut microbiome of two commercial laying hen strains, Lohmann Brown-Classic and Lohmann LSL-Classic, across five anatomical sections (crop, gizzard, duodenum, ileum, caeca) at five ages spanning pullet development through late lay (10, 16, 24, 30, 60 weeks of age). We extracted RNA from the luminal content and performed 16S rRNA gene amplicon sequencing based on complementary DNA. Both strain and age had highly significant effects on community composition. The greatest shifts occurred between early development (10 weeks) and the onset of lay (16-24 weeks). To link taxa to function, we applied shotgun metagenomics to samples taken at 16 and 24 weeks, revealing strain-specific changes in functional profiles associated with the transition into egg production. We identified three groups of bacterial species that increased in abundance during the transition: lactic-acid producers (such as Lactococcus raffinolactis, Ligilactobacillus aviarius, Lactobacillus pontis, etc.), potential probiotic bacteria (Megasphaera stantonii, Megamonas funiformis, Phocaeicola coprophilus, etc.), and opportunistic or egg-associated pathogens (Comamonas testosteroni, Aeromonas caviae, Acinetobacter johnsonii, etc.). Corresponding shifts were also observed in the functional profiles of inositol phosphate metabolism. Moreover, MAG-based analyses reported two bacterial species - Gallibacterium anatis and Megamonas hypermegale, to contain high numbers of myoinositol-related genes. Together, our results demonstrate that genetic background and production phase both drive dynamic, section-specific changes in the gut microbiome of laying hens.}, }
@article {pmid42190784, year = {2026}, author = {Qadeer, A and Nazir, MJ and Muhammad, S and Azim, R and Wang, Q and Hussain, MM}, title = {Decoding heavy metal tolerance in rice: Nucleic acid-based technologies shaping global food security.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {152693}, doi = {10.1016/j.ijbiomac.2026.152693}, pmid = {42190784}, issn = {1879-0003}, abstract = {Global rice production is critically threatened by heavy metal contamination, particularly cadmium (Cd) and arsenic (As), which compromises yield, diminishes grain nutritional quality, and exposes billions of consumers to nephrotoxic and carcinogenic risks. Conventional remediation strategies (soil amendments, water management, phytoremediation) are prohibitively expensive, temporally protracted, and fundamentally reactive, while conventional breeding is constrained by linkage drag, polygenic trait architecture, and absence of natural alleles that restrict toxic metal uptake from essential mineral nutrition. This review critically examines how nucleic acid-based technologies have fundamentally reconfigured the discovery-to-deployment pipeline for heavy metal tolerance in rice. We trace the progression from early QTL mapping and positional cloning of transporters through population-scale GWAS and pan-genomics, which have resolved the full allelic series at these loci, to contemporary CRISPR-mediated genome editing, that generated transgene-free, field-validated low-accumulating lines. Transcriptomic, epigenomic, and metagenomic tools have further illuminated the dynamic stress response, non-coding regulatory networks, and rhizosphere microbiome contributions to metal exclusion. Translational case studies including Japan's marker-assisted deployment of OsHMA3 for Cd mitigation and South Asia's development of OsLsi2-edited low-As lines demonstrate that these technologies are not merely academic instruments but operational solutions. However, specificity-versus-essentiality dilemma, multi-metal antagonism (Cd/As redox conflict), and profound regulatory divergence (SDN-1 exemption in the Americas, Japan, and India versus GMO classification in the EU) remain formidable barriers. We conclude that nucleic acid technologies constitute the cornerstone of a second Green Revolution focused on grain quality and safety, contingent upon sustained investment in synthetic biology, digital integration, and internationally harmonized governance frameworks.}, }
@article {pmid42190825, year = {2026}, author = {Li, Y and Qu, C and Sun, H and Li, C and Rehman, F and Guo, J}, title = {Distinct associations between polycyclic aromatic hydrocarbons with different molecular weights and antibiotic resistance gene distribution in river sediments of the Loess Plateau, China.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124845}, doi = {10.1016/j.envres.2026.124845}, pmid = {42190825}, issn = {1096-0953}, abstract = {Although polycyclic aromatic hydrocarbons (PAHs) are widely recognized to influence the distribution of antibiotic resistance genes (ARGs), the roles of PAHs with different molecular weights in shaping ARG patterns remain underexplored. It is hypothesized that different molecular weight PAHs can influence ARGs dissemination through shifts in microbial diversity. Here, the spatial distribution and concentrations of PAHs in Beiluo River sediments were evaluated, followed by an assessment of their relationships with ARG distribution and microbial community structure across 18 sampling sites. Metagenomic sequencing was used to characterize the distribution patterns of ARGs, mobile genetic elements (MGEs), and microbial communities. The partial least squares path model (PLS-PM) suggested that PAH molecular weight was differentially associated with microbial community structure and ARG distribution. Low- and medium-molecular-weight PAHs (PHE and ANT) were positively associated with the dominating phylum Pseudomonadota, which may act as potential ARG hosts and promote the transmission of dominant ARGs, especially bacitracin- and multidrug resistance genes. In contrast, the α-diversity indices of Acidobacteriota, which exhibited relatively low abundance, were negatively correlated with high-molecular-weight PAHs (BbF). The co-occurrence network analysis further suggested that this phylum may serve as a potential host for MLS- and tetracycline resistance genes. Overall, these results contribute to the understanding of interactions among persistent organic pollutants, microbiota, and ARGs in human-disturbed rivers and support the ecological risk evaluation and management of PAH-contaminated aquatic systems.}, }
@article {pmid42190956, year = {2026}, author = {Xia, R and Cui, B and Li, G and Zhou, H and Luo, W and Xu, Z}, title = {Integrated metagenomics unravels the microbial mechanisms driving greenhouse gas and odor emissions during composting.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134984}, doi = {10.1016/j.biortech.2026.134984}, pmid = {42190956}, issn = {1873-2976}, abstract = {While composting is widely used for the resource recovery of organic waste, it is complicated by greenhouse gas and odor emissions. An integrated analysis of emission characteristics and elemental metabolism mechanisms is essential for targeted control strategies. Using integrated metagenomics and modular network analysis, this study identified the biotic and abiotic factors driving gaseous emissions. Results showed that methane (CH4) and nitrous oxide (N2O) emissions mainly occurred during the mesophilic and cooling stages, whereas ammonia (NH3) and hydrogen sulfide (H2S) peaked at the thermophilic stage. Initially, acidogens (e.g. Klebsiella) and methanogens (e.g. Methanobacterium) promoted CH4 production via aceticlastic (e.g. ackA gene) and hydrogenotrophic (e.g. frhB gene) pathways. Meanwhile, nitrate-reducing bacteria and denitrifiers converted nitrate nitrogen to N2O via assimilatory/dissimilatory reduction and denitrification pathways, respectively. As temperature increased into the thermophilic stage, CH4 and N2O production decreased due to the thermal inhibition of acidogens and nitrate-reducing bacteria. However, intense mineralization of organic nitrogen/sulfur compounds released ammonium and sulfate ions, leading to NH3 volatilization and microbial H2S production by sulfate-reducing bacteria (e.g. Desulfitibacter) via synergistic assimilatory/dissimilatory sulfate reduction pathways. Reduced thermal inhibition at the cooling stage restored activity of acidogens and methanogens, which drove CH4 emission via all four pathways. Denitrifiers (e.g. Pusillimonas) with nirS and norC genes and nitrifiers (e.g. Devosia) with hao genes were also enriched, increasing N2O production. Nevertheless, N2O was ultimately reduced to N2 by denitrifiers carrying nosZ at the mature stage. These findings provide fundamental insights for developing targeted strategies to mitigate gaseous emissions during composting.}, }
@article {pmid42191017, year = {2026}, author = {Cavone, C and De Paola, D and Naclerio, G and Bucci, A and Caracciolo, AB and Rutigliano, A and Cotugno, P and Rolando, L and Savino, I and Grenni, P and Celico, F and Uricchio, VF and Ancona, V}, title = {Lavandula angustifolia and microbial bioaugmentation synergistically reshape rhizosphere microbiome and enhance heavy metals removal in historically contaminated soils.}, journal = {New biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.nbt.2026.05.013}, pmid = {42191017}, issn = {1876-4347}, abstract = {Heavy metal contamination poses a serious threat to soil ecosystems and requires sustainable remediation approaches capable of restoring both chemical quality and microbial functionality. This study evaluates the effectiveness of plant-assisted bioremediation (Lavandula angustifolia) and bioaugmentation with a selected bacterial consortium of four strains (Gordonia amicalis, Rhodococcus erythropolis, Acinetobacter puyangensis, and A. tibetensis) in soils that have been historically contaminated with multiple pollutants - as heavy metals (HMs) and polychlorinated biphenyls (PCBs). Microcosms were created with four treatments, i.e. Historically Contaminated Soil (HCS), Plant-assisted bioremediation (PLANT), microbial bioaugmentation (BIOAUG) and the combination of plant-assisted bioremediation and bioaugmentation (PLANT+BIOAUG) and monitored over a 90-days period through chemical analyses, 16S rDNA sequencing, diversity metrics, differential abundance tests and functional prediction. The PLANT+BIOAUG combination demonstrated the highest removal efficiency of Pb (44.75%) and Sn (66.87%), suggesting a robust synergistic interaction between plant and microbial inoculum. Microbial α-diversity remained stable across treatments, while β-diversity analyses (Bray-Curtis, PERMANOVA p = 0.001) revealed significant community restructuring. Taxonomic analyses highlighted shifts in key genera and an enrichment of bacterial families associated with metal transformation, redox processes, and stress tolerance. The functional prediction identified 7,959 KEGG functions, with the combined treatment showing the highest functional redundancy in metal efflux systems, siderophore production, electron transport pathways, and EPS/biofilm formation. Overall, integrating L. angustifolia with a metal-resistant microbial consortium could improve both contaminant removal and microbial functional potential, supporting a robust and sustainable strategy for the remediation of multi-contaminated soils. These results provide valuable insights into synergistic plant-microbe processes and offer practical guidelines for in situ bioremediation within the framework of the circular economy and nature-based models.}, }
@article {pmid42192344, year = {2026}, author = {Liu, L and Su, P and Gong, F and Wang, A and Wang, X and Yang, L and Mo, W and Jiang, T}, title = {Diagnosis and management of mixed Chlamydia abortus and psittaci pneumonia guided by metagenomic next-generation sequencing: a case report.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13691-y}, pmid = {42192344}, issn = {1471-2334}, support = {2023SK4077//the China Hunan Provincial Clinical Medical Technology Demonstration Base for Cardiac Arrest Diseases/ ; }, abstract = {BACKGROUND: Chlamydia abortus primarily causes abortion and stillbirth in animals and is associated with pregnancy-related complications in humans. However, it is an extremely rare cause of pneumonia in humans. While Chlamydia psittaci is a well-established respiratory pathogen, pneumonia resulting from a co-infection with both species has not been previously reported.<br><br>CASE PRESENTATION: A 57-year-old male presented with fever, cough, and shortness of breath. Imaging revealed extensive pulmonary inflammation and consolidation, which rapidly progressed to respiratory failure. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) confirmed a mixed infection with Chlamydia abortus and Chlamydia psittaci. Following the early initiation of targeted doxycycline therapy, the patient's clinical symptoms and pulmonary imaging showed significant improvement, leading to a full recovery and hospital discharge.<br><br>CONCLUSIONS: To our knowledge, this study reports the first case of atypical pneumonia caused by a mixed Chlamydia abortus and Chlamydia psittaci infection in a male patient, thereby expanding the clinical spectrum of these zoonotic pathogens. The case exhibited a "clinical-imaging dissociation," characterized by severe radiographic changes alongside relatively mild clinical symptoms. When conventional diagnostic methods failed to identify the pathogens, mNGS provided a rapid and precise diagnosis. Guided by this result, early targeted therapy with doxycycline achieved a marked therapeutic effect, preventing progression to severe disease and an adverse outcome.<br><br>TRIAL REGISTRATION: Not applicable.}, }
@article {pmid42192666, year = {2026}, author = {Liu, L and Wang, M and Wang, X and Liu, Y and Li, Z}, title = {Root Exudates Are Linked to Antibiotic Resistance Gene Variation by Modulating Rhizosphere Microbial Community Assembly Under Swine Wastewater Irrigation.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/antibiotics15050444}, pmid = {42192666}, issn = {2079-6382}, support = {242300420230//Natural Science Foundation of Henan Province/ ; }, abstract = {Background: Irrigation with swine wastewater may increase the dissemination risk of antibiotic resistance genes (ARGs) in the rhizosphere and alter root exudate composition. However, the relationship between root exudates and ARG dynamics under swine wastewater irrigation remains poorly understood. This study therefore aimed to clarify how root exudates are connected with ARG dynamics under swine wastewater irrigation. Methods: To address this, untargeted metabolomics and metagenomic sequencing were combined to characterize rhizosphere ARG composition, microbial community structure, and root exudate profiles in different soybean cultivars under swine wastewater irrigation. Results: The results showed that irrigation water source and soybean cultivar were associated with variation in soil ARG composition and changes in plant root metabolic profiles. Under wastewater irrigation, the relative abundances of secondary metabolites in root exudates were generally elevated, particularly those of organic nitrogen compounds and organic oxygenated compounds. Cultivar-related variation remained evident in rhizosphere microbial communities and ARG profiles, and differences in exudate composition among cultivars became smaller. Irrigation water source and soybean cultivar were associated with changes in ARG dynamics. This association was mainly linked to variation in rhizosphere microbial community structure rather than direct effects of root exudates on ARGs. Xanthine and 3-isobutylpentanedioic acid, identified as key root exudates, increased under wastewater irrigation and were related to variation in the potential ARG host genus SCGC-AG-212-J23 and the related ARGs. In contrast, 5-methylheptan-3-one decreased under wastewater irrigation and was correlated with variation in SCGC-AG-212-J23, Gp6-AA40, and the related ARGs. Conclusions: Swine wastewater irrigation and soybean cultivar altered root metabolism, which were linked to variation in rhizosphere microbial communities. These changes may have collectively contributed to shifts in rhizosphere ARGs. This could provide a basis for understanding the ecological relationships among root exudates, microorganisms, and ARGs under swine wastewater irrigation.}, }
@article {pmid42192676, year = {2026}, author = {Hassen, KA and Fafetine, J and Augusto, L and Mandomando, I and Garrine, M and Marcos, R and Sileshi, GW}, title = {Mobile Genetic Elements Associated with Antimicrobial Resistance Across One Health Interfaces in Africa: A Systematic Review and Meta-Analysis.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/antibiotics15050456}, pmid = {42192676}, issn = {2079-6382}, support = {500003545//Centre of Excellence in Agri-Food Systems and Nutrition (CE-AFSN), Eduardo Mondlane Univer-sity/ ; }, abstract = {Background: High infectious disease burden and uncontrolled antibiotic usage across human, animal, and environmental contaminants make antimicrobial resistance (AMR) a growing public health problem in Africa. Mobile genetic elements (MGEs) such plasmids, transposons, integrons, conjugative elements, and phages help spread AMR via horizontal gene transfer (HGT) across human, animal, food, and environmental sources. Despite growing evidence for antibiotic resistance genes (ARGs), Africa lacks a one-health-focused synthesis of mobile genetic element-mediated AMR. Objective: This systematic review and meta-analysis aimed to consolidate information on MGEs and ARGs in AMR dissemination throughout Africa's one health interface. Methods: The literature was searched using PubMed, Scopus, and ScienceDirect. Observational. molecular epidemiology, whole genome sequencing (WGS), and metagenomic investigations of MGE-associated AMR in Africa were eligible. The study selection, data extraction, and quality assessment were performed by two independent reviewer and quality was graded using ROBVIS 2 utilizing Rayyan software. Narrative synthesis, random-effect meta-analysis, subgroup analysis, and meta-regression were utilized. Results: A total of 109 studies were included, with 91 studies contributing to the meta-analysis. MGEs reported were plasmids (71.7%) and integrons (54.8%). ARGs carried by MGEs were blaCTMX-M-15 (78.6%), Sul2 (69.6%), blaTEM (59.1%), and tetA (49.9%). Horizontal gene transfer was seen in 259 instances; however, transmission was unclear. In 442 observations, transmission pathways across human, animal, and environmental interfaces showed AMR prevalence of 75.1% in human, 98.0% in human-animal, and 61.3% in one health interface. Whole-genome sequencing was the most frequently used method for detecting MGEsThe pooled pathogen and AMR prevalence rates were 73.3% (95% CI: 60.5-83.7%) and 94% (95% CI: 85-98%), with significant heterogeneity (I[2] = 97.8% and 97.4%, respectively). The prevalence of Escherichia coli was 93% and Salmonella enterica 85% in subgroup analysis. Fluoroquinolones, aminoglycosides, and beta-lactams were prevalent in humans (89.7%) and human-animal interactions (98.0%) according to AMR Class. Conclusions: Horizontal gene transfer has propagated MGE-mediated antimicrobial resistance across human, animal, and environmental interfaces in Africa. To combat AMR in Africa, coordinated, genomics-informed One Health surveillance and antibiotic stewardship are needed. Due to variability and publication bias, these data should be considered cautiously. Pooled data may only show descriptive patterns, and not necessarily precise continent-wide prevalence estimates.}, }
@article {pmid42192677, year = {2026}, author = {Carneiro, PAM and Santos, LRD and Jardim, R and Silva, CBDGE and Araújo, FR and Dávila, AMR}, title = {Resistome and Mobilome Profiling of Raw Cow and Buffalo Milk from the Brazilian Amazon via Shotgun Metagenomics.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/antibiotics15050454}, pmid = {42192677}, issn = {2079-6382}, support = {408696/2024-9//Beef Cattle National Science and Technology Institute/CNPq/ ; }, abstract = {Background/Objectives: Antimicrobial resistance (AMR) is a global health threat, with raw milk serving as a potential reservoir for antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs). This study characterized the resistome and mobilome of raw milk from cows (Bos taurus) and water buffalo (Bubalus bubalis) in the Brazilian Amazon, a region where unpasteurized dairy consumption is culturally ingrained. Methods: Using shotgun metagenomic sequencing, we analyzed 32 pooled milk samples from extensive and semi-intensive farms in the Manaus Metropolitan Region. Results: Sequencing yielded over 3.1 million contigs. While cow milk showed a higher prevalence of positive samples (80%), buffalo milk exhibited a significantly higher abundance and diversity of ARG-associated contigs (301 contigs vs. 85 in cows). Clinically relevant genes were identified, including AbaQ, ArnT, and KpnF, alongside complex multi-AMR cassettes co-occurring with plasmids and widespread viral sequences (dominated by Caudoviricetes). Integrons were ubiquitous in cattle and highly prevalent in buffalo samples. Conclusions: These findings indicate that raw milk in the Amazon harbors a rich reservoir of resistance determinants and MGEs, likely driven by farm-level antibiotic usage. This underscores a critical food safety risk and highlights the need for One Health-based surveillance in the region.}, }
@article {pmid42192724, year = {2026}, author = {Skotareva, AE and Sokolova, EA and Voronina, EN}, title = {West Siberian Soil Resistome: Mobile Antibiotic Resistance in Agricultural Microbiomes.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/antibiotics15050502}, pmid = {42192724}, issn = {2079-6382}, support = {125012300671-8//Russian state-funded project/ ; }, abstract = {Background/Objectives: Soil microbiomes in agroecosystems are natural reservoirs of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), creating conditions for horizontal gene transfer (HGT) to clinically relevant bacteria. Southern West Siberia-a globally significant grain-producing region-lacks metagenomic characterization of its soil resistome. This study aimed to establish the first baseline profile of resistome and mobilome composition for West Siberian agricultural soils. Methods: Twelve composite soil samples were collected from agroecosystems under seven crop types across diverse soil types in southern West Siberia (September 2022). Shotgun metagenomics was performed on an Illumina NovaSeq 6000 platform. Taxonomic profiling used Kraken2/Bracken; ARG annotation used Prokka/DeepARG (identity ≥ 70%, probability score ≥ 0.8); while MGE characterization used Platon, HMMER v3.3.2, and Prokka-based integrase annotation. Resistome load was normalized to the single-copy housekeeping gene rpoB; ARG-MGE associations were defined as co-localization within 10 kb on the same contig. Results: Microbial communities were dominated by Pseudomonadota and Bacillota, with a stable core of Streptomycetaceae, Nitrobacteraceae, and Sphingomonadaceae. Normalized resistome load (N/rpoB 2.30-5.37) indicated moderate anthropogenic pressure. Dominant ARGs included efflux pumps (emrA, drrA, tetA, bcr, fsr), target modification (lnrL), and lipid A modification (arnA) genes. Class 1 integron integrase (intI1/rpoB 0.64-1.59) was detected in all 12 samples, exceeding unity in 9 of 12. ARG-MGE co-localizations were found in 11 of 12 samples. In sample Mg_155, genes emrA-emrB and bcr (NODE_16) and arnA and lnrL (NODE_6) were each independently associated with distinct prophage IntA integrase copies within Pseudomonas contigs, documenting multiple parallel horizontal transfer events encompassing resistance to five antibiotic classes. Conclusions: This work establishes the first metagenomic baseline of resistome and mobilome for West Siberian agroecosystems. The obtained data indicate moderate anthropogenic pressure on soil microbiomes, consistent with temperate agricultural systems with limited organic fertilizer input. The detected ARG-MGE co-localizations and evidence of prophage-mediated transfer of resistance determinants beyond their natural hosts suggest that mobilization potential in the region warrants consideration in future AMR monitoring programs.}, }
@article {pmid42193165, year = {2026}, author = {Liang, Y and Wang, H and Wang, Z and Zhang, Y and Tu, W and Zhou, J and Diao, Y and Pei, H and Huang, J and Zhou, X and Tan, Y}, title = {High-Fiber Diet Supplemented with N-Carbamylglutamate Modulates Uterine Microbiota, Metabolites, and Transcriptome to Improve Reproductive Efficiency in Sows.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/antiox15050542}, pmid = {42193165}, issn = {2076-3921}, support = {No.2023ZD04046//Biological Breeding-National Science and Technology Major Project/ ; 2025M780240//China Postdoctoral Science Foundation/ ; NO.2025(05)//Livestock and Poultry Breeding and Healthy Farming Technology/ ; }, abstract = {Uterine microbiome homeostasis and antioxidant capacity are critical for sow fertility. While high-fiber diets and N-carbamylglutamate (NCG) individually enhance sow fertility, their synergistic effects on the antioxidant status, microbiota, metabolites, and transcriptome remain unclear. Here, sows were assigned to the low-fiber (3.73%) or high-fiber (7.46% crude fiber) group, each without or with 0.05% NCG, throughout the 114-day gestation. Sex hormones and antioxidants in serum were detected. Multi-omics approaches were employed to investigate the impact of a high-fiber diet supplemented with NCG (H + N) on uterine microbiota, metabolites, and gene expression profiles. The study revealed that H + N significantly increased total antioxidant capacity (T-AOC) level in serum. Metagenomic analysis revealed an increased abundance of Clostridium disporicum in the uterine microbiota. Plasma metabolomics identified hydroxylysine as a key metabolite mediating this effect, and this metabolite was positively correlated with elevated abundance of Clostridium disporicum. Subsequent transcriptomic profiling revealed activation of the PI3K-Akt signaling pathway, closely linked to improved T-AOC level. Overall, these findings demonstrated that H + N could modulate the uterine microbiota (specifically Clostridium disporicum), increase hydroxylysine production, and activate the PI3K-Akt signaling pathway. These effects further enhanced hormonal activity and antioxidant capacity, ultimately improving sow reproductive efficiency.}, }
@article {pmid42193259, year = {2026}, author = {Zhang, MY and Ke, ZZ and Deng, PL and Qin, YY and Mo, SL and Qiu, LT and Xu, JJ and Tong, CX and Song, JL}, title = {Rhamnocitrin Ameliorates the Intestinal Fibrosis in DSS-Induced Colitis Mice by Modulating Host-Metabolites and Remodeling the Gut Microbiome.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/antiox15050639}, pmid = {42193259}, issn = {2076-3921}, support = {82273630//National Natural Science Foundation of China/ ; 81960590//National Natural Science Foundation of China/ ; 81760589//National Natural Science Foundation of China/ ; 81560530//National Natural Science Foundation of China/ ; }, abstract = {Ulcerative colitis (UC) is characterized by barrier disruption, microbiota dysbiosis, fibrosis, and impaired autophagy. We investigated the effects of Rhamnocitrin (Rha) in dextran sulfate sodium (DSS)-induced chronic UC mice using histological analysis, molecular assays, and multiomics profiling. Rha alleviated weight loss and colon shortening; improved mucus secretion and tight junction protein expression; suppressed NLRP3 inflammasome activation; activated autophagy via AMPK activation and consequent Akt/mTOR inhibition; and attenuated colonic fibrosis. Multiomics analysis integrating 16S rRNA sequencing, metagenomics, and metabolomics revealed that Rha remodels the gut microbiota and is associated with elevated levels of beneficial metabolites, including butyrate in the colon, glutamate and γ-aminobutyric acid in the liver, and α-linolenic acid in the serum. Correlation analysis revealed close associations between microbiota and metabolite alterations, and improved barrier integrity, reduced inflammation, and attenuated fibrosis. These findings suggest that Rha ameliorates chronic UC by modulating autophagy, microbiota composition, and host metabolism across the gut-liver axis.}, }
@article {pmid42193752, year = {2026}, author = {Guo, T and Wan, B and Ye, Y and Zhang, Y and Mao, M and Li, R and Fang, Y and Lu, Y and Shao, R and Wu, Y and Wang, Y and Wu, J and Yang, H}, title = {A Prevotella-Rich Gut Microbiota and Microbial CAZymes Are Associated with Half-Diving Length in Ducks.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {10}, pages = {}, doi = {10.3390/ani16101460}, pmid = {42193752}, issn = {2076-2615}, support = {2024YFF1000900//National Key Research and Development Program of China/ ; 32302739//National Natural Science Foundation of China/ ; 32360830//National Natural Science Foundation of China/ ; 20243BCE51147//Ganpo Juncai Support Program/ ; QN2023015//Ganpo Juncai Support Program/ ; 20232ACB215003//Natural Science Foundation of Jiangxi Province/ ; }, abstract = {The gut microbiota is closely associated with host growth by nutritional metabolism and immune homeostasis. Half-diving length, a key indicator of duck development and production efficiency, correlates with economic traits like body weight and slaughter yield, yet its link to gut microbiota remains unclear. This study combined metagenomic and metabolomic analyses to explore the association between gut microbiota and duck half-diving length. We found distinct microbial communities between ducks with high (H) and low (L) half-diving lengths: the H group had more carbohydrate-active enzymes (CAZymes) genes (p < 0.05), especially glycoside hydrolases (GHs), and was enriched in MAG3173 (Prevotella sp000431975), which features complete carbohydrate and amino acid metabolic pathways and key CAZymes. Metabolomics revealed slightly higher short-chain fatty acids (SCFAs) levels in the H group, but glycerophospholipids, particularly phosphatidylinositol (PI), were significantly upregulated (p < 0.05). The Prevotella-rich microbial structure in the H group is potentially linked to enhanced polysaccharide degradation capacity and altered SCFAs abundance. This metabolic shift may be associated with host energy supply and lipid metabolic profiles, thereby influencing duck growth. Collectively, this study found significant correlations between duck half-diving length and gut microbial composition, functional capacity, and intestinal metabolic signatures. The study proposes the hypothesis of a potential Prevotella-CAZymes-glycerophospholipid metabolism axis, which might offer a theoretical reference and candidate microbial targets for understanding the microbe-phenotype association in waterfowl.}, }
@article {pmid42193766, year = {2026}, author = {Qiu, G and Bai, H and Shi, J and Xue, Y and Wang, T and Qin, S and Zhou, X and He, K}, title = {Metagenomic and Metabolomic Analysis of Intestinal Excrement Differences Between Natural Hatching and Artificial Peeling out of the Shell in Nipponia nippon.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {10}, pages = {}, doi = {10.3390/ani16101472}, pmid = {42193766}, issn = {2076-2615}, support = {ZJXRDQ-2025-JC28//the Project for Enhancing the Reproductive Capacity of the Red-crowned Crane/ ; }, abstract = {The Nipponia nippon is a critically endangered species, and its breeding efforts are of vital importance for its conservation. Although artificial shell removal is sometimes employed in current breeding programs to increase survival rates, it may also have unknown impacts on chicks' development. To investigate the influence of artificial shell removal on the gut microbiota composition in Nipponia nippon, metagenomic sequencing and untargeted LC-MS/MS analyses were performed. Samples from the early, mid, and late stages of natural hatching (ZE, ZM, ZL) and artificial shell removal (RE, RM, RL) were compared. Results indicated that the natural hatching groups formed a unique, highly diverse, and stable community by the late stage (ZL). Conversely, artificial peeling caused the microbial community succession to stagnate at an intermediate state. The RL group experienced a sharp decline in alpha diversity and a significant enrichment of opportunistic pathogens, such as Edwardsiella, Clostridium, and Fusobacterium. Functionally, the microbial community in the RL group remained in a stage of expanding basic functions rather than reaching an advanced equilibrium state. Metabolomic analysis confirmed this developmental arrest, revealing abnormal accumulations of organic acids, such as citric acid, and indole derivatives in the RL group. This indicates metabolic dysregulation, stress, and altered microbial-host chemical signaling. Furthermore, the significant biomarker Edwardsiella was strongly correlated with multiple differential metabolites in the RL group. Ultimately, these results indicate that artificial peeling intervention disrupts environmental adaptation and induces metabolic alterations in the intestinal development of the Nipponia nippon chicks.}, }
@article {pmid42193830, year = {2026}, author = {Zhou, K and Shi, H and Kong, X and Ma, W and Kang, J and Che, H and Hua, Y}, title = {Wuwei Jianpi San Improves Growth Performance and Immune Status in Yaks Through Modulation of Rumen Microbiota and Host Metabolism.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {10}, pages = {}, doi = {10.3390/ani16101539}, pmid = {42193830}, issn = {2076-2615}, support = {CARS-37, CARS-07G-13//China Agriculture Research System of MOF and MARA/ ; No. Gaufx-03J01//Fuxi Foundation of Gansu Agricultural University/ ; 24YFNA016//Gansu Provincial Key Research and Development Program - Agriculture Field/ ; KJZC-2025-14//Modern Cold and Drought Characteristic Agricultural Science and Technology Sup-port Project of Gansu Province/ ; }, abstract = {To investigate the effects of Wuwei Jianpi San (WJPS), a Chinese herbal compound feed additive, on rumen microecology, host metabolism, and immune function in healthy yaks (Bos grunniens), and to determine the optimal supplementation level, 32 yaks with similar initial body weight were randomly assigned to four groups: a control group and three groups receiving 0.5%, 1.0%, or 2.0% WJPS for 90 days. Growth performance, hematological indices, serum antioxidant and immune parameters, tryptophan metabolites, ruminal short-chain fatty acids (SCFAs), and rumen microbiota were analyzed. WJPS supplementation improved growth performance, as shown by a reduced feed-to-gain ratio in all treated groups and tended to increase average daily gain in the 2.0% group. It also enhanced hematological, antioxidant, and immune status, evidenced by increased white blood cell (WBC) and lymphocyte (Lym) counts and elevated interleukin-2 (IL-2), immunoglobulin G (IgG), and superoxide dismutase (SOD) levels. Moreover, 2.0% WJPS increased total SCFAs, acetate, and n-butyrate, while WJPS reduced kynurenine pathway metabolites, including kynurenine, 3-hydroxykynurenine, and quinolinic acid. Metagenomic analysis showed that WJPS tended to shape rumen microbial composition by increasing Bacillota and decreasing Bacteroidota, and these microbial changes were associated with host immune indices and tryptophan metabolism. Overall, 2.0% WJPS showed the best comprehensive effect.}, }
@article {pmid42195821, year = {2026}, author = {Wang, X and Liu, X and Han, G and Erdene, K and Bai, C and Cao, Q and Zheng, Y and Hai, L and Ao, C}, title = {Allium mongolicum Regel-Mediated Rumen Microbiota Intervention Modulates Hepatic Metabolome to Reduce 4-Alkyl Branched-Chain Fatty Acids in Lamb Longissimus Thoracis Muscle.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/foods15101617}, pmid = {42195821}, issn = {2304-8158}, support = {32260839//National Natural Science Foundation of China/ ; }, abstract = {Deposition of three key 4-alkyl branched-chain fatty acids (KBCFA), including 4-methyloctanoic acid (MOA), 4-ethyloctanoic acid (EOA), and 4-methylnonanoic acid (MNA), causes the gamey flavor in sheep meat. This study integrated metagenomics and metabolomics to evaluate how Allium mongolicum Regel (AMR) supplementation (15 g/d) and rumen fluid transplantation (RFT) modulate rumen microbiota and hepatic metabolism to reduce KBCFA in lamb longissimus thoracis muscle. The experiment consisted of two phases. In Phase I, twelve 3-month-old male Dorper × Small Tailed Han sheep (25 ± 1 kg) were selected as the rumen donor group. These sheep were supplemented with 15 g/d/head of AMR powder in their basal diet until the end of the experiment. In Phase II, thirty 3-month-old male Dorper × Small Tailed Han sheep (23 ± 2 kg) were randomly assigned to one of three groups (n = 10 per group): the control group (STG), which was fed the basal diet and received a physiological saline transplant; the AMR group, which was fed the basal diet supplemented with 15 g/d/head of AMR powder and received a physiological saline transplant; and the rumen fluid transplant group (RTG), which was fed the basal diet and received a rumen fluid transplant from the donor group. Compared to the STG, results showed that the MOA, EOA, and MNA in the AMG decreased by 64.51%, 54.72%, and 49.34%, respectively. Similarly, the MOA, EOA, and MNA in the RTG were reduced by 63.13%, 56.17%, and 49.60%, respectively (p < 0.001). For the rumen metagenome, AMR enriched the genus Prevotella, while RFT increased Butyrivibrio. Hepatic metabolomics revealed a distinct shift where AMR elevated amino acid derivatives and RFT enhanced carnitine-related metabolites. These alterations indicate a potential metabolic shift associated with amino acid metabolism and mitochondrial β-oxidation, rather than lipid elongation. We postulate that this coordinated regulation across the rumen-liver-muscle axis may alter the availability of lipogenic precursors for KBCFA synthesis, ultimately contributing to improved meat flavor.}, }
@article {pmid42195847, year = {2026}, author = {Song, D and Yang, L and Zhang, C}, title = {Omics-Guided Construction of Microbial Consortia for Reproducible Traditional Fermented Foods and Beverages.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/foods15101643}, pmid = {42195847}, issn = {2304-8158}, support = {32460269//National Natural Science Foundation of China/ ; MTXYTD202501//The Science and Technology Innovation Team of Moutai Institute/ ; Qiankehe Platform Talent-ZDSYS [2023] 007//Guizhou Key Laboratory of Microbial Resources Exploration in Fermentation industry/ ; XYNJ20240104//Moutai Institute &amp; Guangdong Li'er'an Chemical Industry Group Co., Ltd./ ; }, abstract = {Traditional fermented foods and beverages (TFFB) rely on complex microbial communities that generate distinctive flavors, nutritional attributes, and cultural value, but spontaneous or empirically controlled fermentations often limit reproducibility. Defined microbial consortia (DMCs) provide a promising route for improving fermentation controllability and product consistency, although overly simplified starters may fail to reproduce the ecological robustness and sensory complexity of traditional systems. This review focuses on how multi-omics and culturomics can support rational DMC design in TFFB. We summarize how metagenomics, metatranscriptomics, metaproteomics, metabolomics, and culturomics reveal community structure, functional potential, active expression, metabolic output, and cultivable strain resources. Particular attention is given to translating multi-omics evidence into strain prioritization through the identification of keystone microorganisms that drive core fermentation functions and helper microorganisms that support ecological or metabolic stability. We further propose an Assembly-Assessment-Redesign (A-A-R) framework for iterative DMC optimization, linking strain selection, functional validation, performance evaluation, and consortium redesign. Finally, we discuss key challenges, including cross-omics integration, experimental verification of microbial functions, standardized validation criteria, and the transfer of laboratory-designed consortia to industrial fermentation systems.}, }
@article {pmid42195939, year = {2026}, author = {Chen, P and Du, G and Chen, J and Fang, F}, title = {Construction of Synthetic Microbial Community with Core Microorganisms for Soy Sauce Fermentation.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/foods15101736}, pmid = {42195939}, issn = {2304-8158}, support = {32172182//National Natural Science Foundation of China/ ; }, abstract = {Core microbes and succession of the microbial community greatly influence soy sauce fermentation process. This study identified seven functionally important core microbes, including Weissella paramesenteroides, Lactiplantibacillus plantarum, Tetragenococcus halophilus, Pediococcus pentosaceus, Zygosaccharomyces rouxii, Candida orthopsilosis, and Aspergillus oryzae for soy sauce fermentation, based on dominant taxa, co-occurrence relationships, and volatile-associated taxa analysis. Four distinct fermentation phases were identified for soy sauce fermentation based on metagenomics and metabolomics data correlation analyses. Acceptable fermentation performance and comparable soy sauce flavor compounds were achieved using a temporal synthetic microbial community for fermentation. The synthetic microbial community was assembled with inoculation of dominant lactic acid bacteria (LAB) in the immediate early phase, other LAB in early and middle phases, and yeasts in the late phase. Glutamate and 4-ethylguaiacol were identified as soy sauce fermentation indicators for early to middle and late fermentation phases, respectively. These results may provide a possible solution for achieving precise control over the brewing process and improving the flavor and quality of soy sauce.}, }
@article {pmid42196007, year = {2026}, author = {Duo, Q and Zhao, Y and Osman, H and Shao, W and Zhao, Y}, title = {Correlation Between Microbial Communities and Volatile Organic Compounds in Camel Milk at Different Lactation Stages in Xinjiang, China.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/foods15101804}, pmid = {42196007}, issn = {2304-8158}, support = {2023B02034-1//Xinjiang Academy of Agricultural Sciences/ ; XJARS-11-09//Xinjiang Academy of Agricultural Sciences/ ; xjnkywdzc-2026002-10//Xinjiang Academy of Agricultural Sciences/ ; }, abstract = {The aroma of camel milk is a key sensory indicator for evaluating its quality and flavor. Camel milk collected at different lactation stages exhibits unique flavor characteristics. However, no systematic study has yet explored the aroma characteristics and variation patterns of camel milk across these stages. This study employs HS-SPME-GC-MS, multivariate statistical analysis, and metagenomics to systematically reveal differences in aroma formation in camel milk across lactation periods and their interactions with microbial communities. A total of 577 metabolites is detected. Through OPLS-DA screening, 24 key differential flavor compounds are identified. ROAV analysis indicates that 2,4-undecadienal and (E)-2-undecenal are the main contributors to the fatty, creamy, fresh green, and citrus aromas of camel milk. Some compounds are more abundant in colostrum, while others are richer in mature milk. For microbiota, colostrum is dominated by Proteobacteria, Psychrobacter, and Janthinobacterium, whereas mature milk is dominated by Acinetobacter and Moraxella. Mature milk shows significantly higher alpha diversity and species richness. Spearman correlation analysis shows that core bacterial groups such as Enterococcus and Lactococcus are significantly positively correlated with characteristic flavor compounds, including aldehydes and lactones. This finding suggests that HS-SPME-GC-MS, combined with multivariate analysis, effectively distinguishes patterns associated with microbes and flavor metabolites in camel milk at different lactation stages, which provides a theoretical basis for quality control and further processing of camel milk.}, }
@article {pmid42196140, year = {2026}, author = {Dobretsov, S and Rittschof, D and Peng, L and Yang, JL}, title = {Functional Microbiomes at the Interface: Mediators in Marine Biofouling and Larval Settlement.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104155}, pmid = {42196140}, issn = {1422-0067}, support = {CL/SQU-SHOU/AGR/24/01//Sultan Qaboos University/ ; }, mesh = {Animals ; *Biofouling ; *Microbiota ; Larva/microbiology ; Biofilms/growth &amp; development ; Quorum Sensing ; Ecosystem ; *Aquatic Organisms/microbiology ; }, abstract = {Natural and artificial marine surfaces are rapidly colonized by microscopic communities, including propagules of some macrofoulers, in a process called biofouling. These microbiomes play an important role in modulating the evolving microbial community, as well as the attachment and settlement of other invertebrate larvae. Microbiomes act as biochemical and biophysical interfaces in marine communities. This review explores the gene-level processes that underlie microbial functions relevant to biofouling and larval settlement, such as quorum sensing, extracellular polymeric substance (EPS), and innate immune system components, as well as biosynthetic and degradative processes that generate signaling molecules. We critically evaluate current knowledge on how microbial metabolites promote or inhibit larval recruitment in corals, barnacles, polychaetes, and bivalves, and how omics-based approaches are uncovering the functional potential of biofilm communities. We evaluate how these interactions influence ecosystem services, such as habitat structuring, reef resilience, and coastal infrastructure maintenance.}, }
@article {pmid42196196, year = {2026}, author = {Wang, Y and Liu, X and Gao, R and An, Y and Ren, C and An, L}, title = {Characteristics of Gut Microbiota in Patients with Chronic Obstructive Pulmonary Disease Based on Metagenomics and Metabolomics.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104213}, pmid = {42196196}, issn = {1422-0067}, support = {CYFH202318//Beijing Chao-Yang Hospital/ ; 20250484825//Beijing Municipal Science and Technology Commission/ ; CFH2026-2-1043//Beijing Municipal Health Commission/ ; 2025ZD0548900//National Health Commission of the People's Republic of China/ ; }, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/metabolism ; *Metagenomics/methods ; *Metabolomics/methods ; Male ; *Gastrointestinal Microbiome/genetics ; Female ; Aged ; Middle Aged ; Feces/microbiology ; Multiomics ; Metabolome ; Biomarkers ; RNA, Ribosomal, 16S/genetics ; China ; Case-Control Studies ; }, abstract = {The gut-lung axis is important in Chronic Obstructive Pulmonary Disease (COPD) pathogenesis; however, most studies rely on low-resolution 16S rRNA sequencing, and integrated multi-omics investigations in Chinese COPD populations are scarce. A total of 104 participants including 74 stable COPD patients and 30 healthy controls from northern China were recruited, and shotgun metagenomic sequencing and untargeted metabolomics were performed. Results showed that alpha diversity of the gut microbiota did not differ significantly between COPD patients and healthy controls, whereas beta diversity showed clear separation. Marked differences in microbial composition from phylum to species levels (e.g., Oscillospiraceae) and altered microbial functions (signal transduction, antibiotic resistance, etc.) were observed in COPD patients. Metabolomic profiling identified 497 differential fecal metabolites and 1260 differential serum metabolites in COPD patients. Importantly, serum riboflavin levels were significantly reduced and positively correlated with pulmonary function indices as well as the key differential gut microbial functional gene K11752. Serum metabolite eremopetasinorol exhibited high diagnostic accuracy for COPD (AUC = 0.947, 95% CI: 0.8-0.98), surpassing fecal metabolites and microbial features. This study provides integrated metagenomic and metabolomic characterization of gut microbiota alterations in Chinese COPD patients, offering novel insights for biomarker discovery and targeted intervention strategies.}, }
@article {pmid42196214, year = {2026}, author = {Kiouri, DP and Batsis, GC and Messaritakis, I and Souglakos, J and Chasapis, CT}, title = {Mapping of Phenotype Specific Host-Microbiome Protein-Protein Interaction Networks in Colorectal Cancer Using Deep Learning.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104232}, pmid = {42196214}, issn = {1422-0067}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism/genetics ; *Protein Interaction Maps ; *Deep Learning ; Phenotype ; *Gastrointestinal Microbiome ; *Protein Interaction Mapping/methods ; *Host Microbial Interactions ; }, abstract = {Colorectal cancer (CRC) pathogenesis is driven by complex protein-protein interactions (PPIs) between the host and the gut microbiome, yet these molecular dialogs remain largely unmapped. This study utilizes a Deep Learning framework, enhanced by protein structure embeddings, to predict approximately 8.9 billion interspecies PPIs from clinical metagenomic data. The model achieved high accuracy with an AUROC of 0.9960, identifying a high-confidence interactome representing roughly 16% of evaluated protein pairs. Phenotype-specific analysis revealed that while microbial hubs shift-transitioning from metabolic enzymes in healthy states to transport and regulatory proteins in CRC-the primary human targets remain remarkably consistent across both cohorts. These core human interactors are predominantly metalloproteins and regulators of ubiquitination, apoptosis, and zinc transport, suggesting these pathways are primary focal points for microbial manipulation regardless of disease state. Furthermore, co-occurring bacterial genera exhibit over 99% overlap in host target profiles, indicating significant functional redundancy in microbial engagement with the host. These findings suggest that CRC probably arises from network-level perturbations of stable host signaling hubs, offering a blueprint for identifying novel therapeutic targets and biomarkers.}, }
@article {pmid42196222, year = {2026}, author = {Zhang, X and Cai, L and Bai, Y and Peng, F}, title = {Comparative Metagenomic Studies Reveal Different Evolutionary Directions of Synthetic Indoor Microbial Communities Under Different Nutritional Conditions.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104238}, pmid = {42196222}, issn = {1422-0067}, support = {2022YFC2807501//Ministry of Science and Technology of the People's Republic of China/ ; NYWSWZX2025-2027-11//Major Special Project on Agricultural Microbial Industry Development in Hubei Province/ ; NIMR-2025-8//the R&amp;D Infrastructure and Facility Development Program of the Ministry of Science and Technology of the People's Republic of China/ ; }, mesh = {*Metagenomics/methods ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Metagenome ; Nutrients ; }, abstract = {The relationship between microorganisms and human health is inseparable. In today's increasingly urbanized world, the relationship between indoor microbial communities and human health is particularly close. Studies have shown that the composition of indoor microbial communities is influenced by various factors, including temperature, humidity, and nutrient conditions. However, research on how to alter indoor microbial community structures by adjusting nutrient components to improve human health is still limited. In this work, we constructed artificial microbial communities composed of common indoor microorganisms, and analyzed the species composition, metabolic capabilities, antibiotic resistance, and virulence of the microbial communities before and after cultivation using metagenomic sequencing technologies and metatranscriptomic sequencing technologies. We then assessed their community characteristics and evolutionary direction under different nutrient conditions. Overall, when the nutrient conditions were altered and reduced, the evolutionary direction of indoor microbial communities changed significantly. Specifically, this evolutionary direction was manifested in a taxonomic succession of community composition, with marked shifts in the relative abundances of constituent species, as well as in a significant alteration of the community-level metabolic functions. In-depth research in this field can help improve the composition of indoor microbial communities, thereby benefiting human health and public health construction in urbanized environments.}, }
@article {pmid42196433, year = {2026}, author = {Zeng, Y and Lau, EYT and Ye, S and Lu, J and Zhang, R and Hu, R and Liang, JQ}, title = {Fecal Cloacibacillus porcorum Improves Non-Invasive Diagnosis of Colorectal Adenoma in the Hong Kong Population.}, journal = {International journal of molecular sciences}, volume = {27}, number = {10}, pages = {}, doi = {10.3390/ijms27104457}, pmid = {42196433}, issn = {1422-0067}, support = {MRP/058/20//ITF-MRP, Hong Kong/ ; N/A//Hong Kong Ph.D. Fellowship Scheme (HKPFS)/ ; }, mesh = {Humans ; *Colorectal Neoplasms/diagnosis/microbiology ; *Adenoma/diagnosis/microbiology ; *Feces/microbiology ; Female ; Hong Kong/epidemiology ; Male ; Middle Aged ; Aged ; Biomarkers, Tumor/genetics ; Metagenomics ; ROC Curve ; }, abstract = {We previously developed a four-marker panel for the diagnosis of colorectal cancer (CRC) and adenoma. This study aimed to identify novel bacterial markers to improve adenoma detection using metagenomics and qPCR. Candidate markers were identified from metagenomic data (n = 492) using ANCOM-BC2 and Spearman's rank correlation analysis and were subsequently validated in an independent cohort (n = 426). Diagnostic performance was assessed both individually and in combination with our previously identified markers and FIT. Metagenomic analysis identified 21 candidate markers that increased along the normal-adenoma-carcinoma axis. Two top candidates, Cloacibacillus porcorum (Cp) and Intestinimonas butyriciproducens, were validated via qPCR and showed significant correlations with metagenomic abundances (both p < 0.0001). ROC analysis demonstrated that Cp levels significantly distinguished CRC and adenoma from controls, whereas I. butyriciproducens distinguished only CRC. The prevalence of Cp was significantly higher in adenoma and CRC than in controls (all p < 0.05). Multivariate analysis confirmed that Cp was independently associated with CRC and adenoma diagnoses. Adding Cp to the four-marker panel improved diagnostic sensitivity from 44.8% to 58.7% for adenoma and from 85.7% to 88.6% for CRC (specificity = 85%). When further combined with FIT, Cp improved sensitivity from 47.6% to 64.3% for adenoma and from 95.2% to 96.2% for CRC (specificity = 84.6%). C. porcorum is a novel bacterial marker that may aid in the non-invasive diagnosis of colorectal adenoma.}, }
@article {pmid42196657, year = {2026}, author = {Zafar, I and Shafiq, S and Khan, MS}, title = {Wastewater Treatment Challenges and Circular Reuse for One Health Sustainability: A Review.}, journal = {International journal of environmental research and public health}, volume = {23}, number = {5}, pages = {}, doi = {10.3390/ijerph23050563}, pmid = {42196657}, issn = {1660-4601}, mesh = {*Wastewater/analysis ; *One Health ; *Waste Disposal, Fluid/methods ; *Water Purification/methods ; Humans ; *Recycling ; Environmental Monitoring ; }, abstract = {Wastewater is a complex and dynamic issue, particularly at the human-animal-environment interface, bearing biological and chemical hazards that may serve as a resource for transmission pathways for pathogens, antimicrobial resistance (AMR) determinants, heavy metals, pharmaceutical residues, per- and polyfluoroalkyl substances (PFAS), and microplastics. Rising global health issues necessitate effective wastewater treatment and advanced research to support risk-informed circular management within a one health framework, incorporating wastewater-based epidemiology (WBE), multi-omics approaches, nanobiotechnology, and green technologies. Inadequate wastewater treatment and uncontrolled discharge result in the generation of more than 380 billion cubic meters of wastewater annually worldwide, contributing to ecological degradation, the spread of AMR, and long-term toxicological risks. Despite significant advances in wastewater treatment, several challenges remain, including complex contaminant mixtures, limited detection and monitoring technologies, variable treatment efficiency, and weak regulatory and governance frameworks. This review highlights key wastewater treatment issues and presents recent advances in WBE and multi-omics approaches, such as metagenomics, resistome profiling, virome analysis, and chemical fingerprinting for contaminant monitoring and public health risk assessment. This review also examines circular reuse strategies focused on water reclamation, nutrient recovery, bioenergy production, and resource recovery, with particular emphasis on nature-based systems, hybrid biological-physicochemical treatment platforms, and green nanobiotechnology as promising approaches to improve treatment performance while minimizing environmental impacts. In conclusion, this review highlights the importance of integrated and sustainable wastewater management approaches within the One Health framework to address emerging challenges and promote environmental resilience, public health protection, and circular resource recovery.}, }
@article {pmid42197004, year = {2026}, author = {Wang, M and Lyu, Y and Zhang, J and Wang, Y and Yang, Y and Mao, YH}, title = {FMT from Exercise and Konjac Glucomannan Preconditioned Donors Rescues Antibiotic-Induced Dysbiosis with Enhanced Ecological Restoration in Mice.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/nu18101544}, pmid = {42197004}, issn = {2072-6643}, support = {2023ZDZX2035; 2024ZDZX2061//Guangdong Scientific Research Platform and Projects for the Higher-educational Institution (Key Area Project)/ ; SL2024A04J01093//the Guangzhou Fundamental and Applied Research/ ; No.82030098//National Natural Science Foundation of China/ ; S202410585045 and 202410585015//the College Students Innovation and Entrepreneurship Training Program/ ; 2023A1515010004//the Guangdong Basic and Applied Basic Research Foundation/ ; }, mesh = {Animals ; *Dysbiosis/therapy/chemically induced/microbiology ; *Fecal Microbiota Transplantation/methods ; *Mannans/pharmacology ; *Anti-Bacterial Agents/adverse effects ; Mice ; *Gastrointestinal Microbiome/drug effects ; Male ; *Physical Conditioning, Animal ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND: Although antibiotics have a wide range of applications in medical clinical practice and possess significant clinical value, their inevitable contribution to gut microbiome dysbiosis warrants attention. Our previous research has confirmed that the combined intervention of exercise and konjac glucomannan (KGM) has a better regulatory effect on gut dysbiosis in mice compared with individual interventions.<br><br>METHODS: This study aims to further investigate whether this effect can be transmitted through fecal microbiota transplantation (FMT), and to compare the recovery effects of autologous FMT (a-FMT), fecal microbiota transplantation after exercise combined with KGM intervention (EK-FMT), and combinative intervention with exercise and KGM (EXE-KGM) on gut microbiome dysbiosis. Sample sizes ranged from five to six animals.<br><br>RESULTS: The results showed that the a-FMT group recovered &#x3b1; diversity the fastest, including Chao, Shannon, and Simpson indices(p < 0.05), within 2 weeks after transplantation when compared with the CTL group. At the end of the experiment, the Bray-Curtis distance of the a-FMT group was closest to the CTL group, while the EXE-KGM group had delayed recovery, there was no significant difference between the EK-FMT group and the EXE-KGM group. Metagenomic analysis and metabolomics analysis indicated that the arginine synthesis and metabolism pathways (KEGG: map00471, map00473, arginine biosynthesis) played a core role in the restoration of the microbiota.<br><br>CONCLUSIONS: The results of this experiment indicate that EK-FMT group can partially transfer the regulatory effects of combined exercise and KGM intervention, a-FMT accelerates the recovery speed of the gut microbiome and arginine metabolism may play an important role in it. This finding provides a theoretical basis and practical direction for special populations to receive special donor fecal treatment.}, }
@article {pmid42197026, year = {2026}, author = {Alsinani, Y and Rostamkhani, F and Shirvani, H}, title = {Exercise and the Gut Microbiome: From Mechanisms to Clinical Applications.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/nu18101565}, pmid = {42197026}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Exercise/physiology ; Fatty Acids, Volatile/metabolism ; }, abstract = {Background/Objectives: The gut microbiome is a critical regulator of host metabolism, immunity, and the gut-brain axis. Exercise is a promising non-pharmacological modulator of microbial ecology, yet human evidence remains heterogeneous and the translational gap persists. This narrative review synthesizes mechanisms, human and animal evidence, and future directions for the exercise-gut microbiome axis. Methods: PubMed, Scopus, Web of Science, and SID were searched for articles published between January 2000 and February 2025. Keywords included exercise, physical activity, gut microbiome, gut microbiota, short-chain fatty acids, and gut-muscle axis. From 218 initial records, 89 original studies (47 human, 42 animal) met inclusion criteria and were critically appraised. Results: Exercise modulates the gut microbiome via splanchnic hypoperfusion, hyperthermia, altered transit time, and immune-mediated barrier regulation. Moderate-intensity continuous training consistently increases alpha diversity and enriches butyrate-producing taxa (Faecalibacterium prausnitzii, Roseburia hominis) and mucin-degrading Akkermansia muciniphila. High-intensity interval training transiently increases intestinal permeability in untrained individuals but, following adaptation, stimulates butyrate production via lactate cross-feeding metabolism-a recent breakthrough. Effects are transient and reversible upon detraining. Animal models establish causality through fecal microbiota transplantation; human randomized controlled trials demonstrate modest, intensity-dependent, and highly individualistic responses. Emerging evidence supports the gut-muscle axis in sarcopenia and personalized exercise prescription guided by microbiome profiling. Conclusion: Exercise shows promise as a low-cost modulator of the gut microbiome for enriching health-associated taxa and improving metabolic outcomes. Definitive evidence linking exercise-induced microbial shifts to enhanced athletic performance in humans remains lacking. Future research requires diet-controlled randomized controlled trials with ≥12-week interventions, shotgun metagenomics, and mechanistic validation of the gut-muscle axis in humans.}, }
@article {pmid42197087, year = {2026}, author = {Yang, H and Li, J and Ren, S and Chai, X and Lu, J and Yan, H and Lu, Y}, title = {Gut Microbiota Changes Following Aerobic Exercise in Malnourished Octogenarians: An Assessor-Blinded Intervention Study Stratified by Nutritional Status.}, journal = {Nutrients}, volume = {18}, number = {10}, pages = {}, doi = {10.3390/nu18101627}, pmid = {42197087}, issn = {2072-6643}, support = {2020YFC2002902//Beijing Sport University/ ; }, mesh = {Humans ; Aged, 80 and over ; *Nutritional Status ; Female ; Male ; *Malnutrition/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; *Exercise/physiology ; Nursing Home Residents ; Feces/microbiology ; Nutrition Assessment ; Nursing Homes ; }, abstract = {BACKGROUND/OBJECTIVES: Global population aging is associated with a rising prevalence of malnutrition among adults aged ≥80 years. Gut dysbiosis is linked to immune decline and impaired nutrient absorption, and aerobic exercise may enhance microbial diversity. This study investigated gut microbiota changes after a 12-week aerobic exercise intervention in octogenarians stratified by nutritional status.<br><br>METHODS: A total of 129 nursing home residents (&#x2265;80 years) were classified via the Mini Nutritional Assessment Short-Form (MNA-SF) into a healthy group (HG, MNA-SF &#x2265; 11) and a malnourished group (MG, MNA-SF < 11). Both groups underwent a 12-week brisk walking intervention (three sessions/week, 1 h/session, 40-60% heart rate reserve). Fecal samples were collected at baseline and post-intervention and were analyzed via shotgun metagenomic sequencing.<br><br>RESULTS: A total of 36 participants completed the intervention (HG = 17, MG = 19). Within-group baseline-to-post-intervention analysis showed no significant changes in alpha or beta diversity in the MG. However, post-intervention between-group comparison revealed higher microbial richness and diversity in the MG vs. the HG, with enrichment of taxa including Faecalibacterium prausnitzii and Streptococcus salivarius. Functional analysis revealed significant enhancements in metabolic pathways related to amino acid biosynthesis, protein synthesis, and quorum sensing in the MG. In contrast, the HG showed limited shifts in microbial diversity but an increase in species involved in carbohydrate metabolism.<br><br>CONCLUSIONS: After 12 weeks, the malnourished group showed higher post-intervention microbial richness and diversity than the healthy group, with differences in taxonomic and predicted functional profiles. Without a non-intervention control group, the microbiota differences observed during the 12-week aerobic exercise period can only be considered observational associations, not causal. Additionally, the high dropout rate (72.1%) limits the generalizability of the findings.<br><br>CLINICAL TRIAL REGISTRATION: The Chinese Clinical Trial Registry on 19 October 2022 (ChiCTR2200064801).}, }
@article {pmid42197123, year = {2026}, author = {Rojas-Flores, SJ and Liza, R and Nazario-Naveda, R and Díaz, F and Delfin-Narciso, D and Cardenas, MG and Cabanillas-Chirinos, L}, title = {Mapping the Convergence of Frontier Technologies for Major Environmental Challenges: A Chemical and Molecular Perspective on the Use of AI for Climate Action and Antimicrobial Resistance.}, journal = {Molecules (Basel, Switzerland)}, volume = {31}, number = {10}, pages = {}, doi = {10.3390/molecules31101571}, pmid = {42197123}, issn = {1420-3049}, mesh = {*Artificial Intelligence ; *Climate Change ; Metagenomics ; Humans ; *Drug Resistance, Microbial ; }, abstract = {The planet faces the critical interconnected challenges of climate change and antimicrobial resistance (AMR); these two crises mutually reinforce each other, threatening global health and ecosystem stability. This study conducts a systematic documentary analysis to map the convergence and identify the structural gaps between two key technological domains: artificial intelligence (AI) for climate action and molecular methods for AMR. The methodology was based on a corpus of 179 scientific documents indexed in Scopus (2010-2025), analyzed with data science tools to identify trends, collaborations, and impact. Quantitative results revealed clear leadership by the United States, accounting for 37.4% of publications, followed by China (26.8%); this leadership reflects the concentration of high-throughput molecular surveillance infrastructure and data science clusters essential for monitoring the environmental resistome. In terms of scientific impact, Spain showed the highest average, with 32.8 citations per article. The most influential work, a review on food security and sustainability, accumulated 275 citations. Network analysis identified authors such as Zhu, Yongguan, with 240 citations in total, as central nodes in international collaborations. Thematically, metagenomics and machine learning emerged as mature and interconnected research cores. This analysis confirms a solid yet still fragmented relationship between the two fields. The analysis reveals that, while metagenomic tools dominate the current literature, a gap persists in correlating genotypic resistance potential with functional phenotypic expression under changing climatic stressors. The results confirm a solid yet still fragmented foundation, highlighting the need for hybrid platforms that transition from descriptive bibliometrics to functional integration for designing systemic solutions. Future work should prioritize the development of hybrid platforms, such as intelligent biosensors, and collaborative governance frameworks that accelerate effective responses to these dual crises.}, }
@article {pmid42197331, year = {2026}, author = {Manoharan, RK and Shin, HD and Lee, Y and Baek, S and Moon, E and Park, YB and Cho, J and La, IJ and Lee, DH and Han, KI and Srinivasan, S}, title = {Shotgun Metagenomic Analysis of Gut Microbiota and Antibiotic Resistance Genes in a High-Fat Diet Mouse Model Treated with Heat-Killed Lactiplantibacillus plantarum beLP1.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14050944}, pmid = {42197331}, issn = {2076-2607}, abstract = {The gut microbiota is a central regulator of metabolic function, and its disruption by a high-fat diet (HFD) is strongly linked to obesity and metabolic impairment. This study evaluated the potential of heat-killed Lactiplantibacillus plantarum beLP1 (beLP1[®]) in alleviating HFD-induced metabolic and microbial imbalances in mice. Male C57BL/6N mice were fed an HFD for 10 weeks, with or without daily oral supplementation of beLP1 (≥3 × 10[10] cells). Compared with untreated HFD mice, beLP1 supplementation reduced serum triglycerides by 35% and lowered liver enzymes AST and ALT by 17% and 36%, respectively. Blood glucose levels remained similar to the HFD group throughout the study period. Shotgun metagenomic analysis revealed that beLP1 restored gut microbial diversity, increased beneficial taxa such as Akkermansia and Faecalibaculum high. and reduced pro-inflammatory species including Streptococcus sp., Mucispirillum schaedleri and Clostridium cocleatum. These microbial changes were associated with partial normalization of the Firmicutes/Bacteroidota ratio and improvements in antibiotic resistance gene (ARG) profiles. Specifically, in silico analysis of the short-chain fatty acid (SCFA) synthesis pathways indicated that the potential for acetate and propionate production was maximized in the beLP1 group, resulting in the highest relative abundance among all groups. This functional enhancement directly correlated with the enrichment of key SCFA-producing taxa, particularly Akkermansia muciniphila, confirming that increased bacterial abundance suggests an enhanced functional potential for SCFA production. Furthermore, beLP1[®] induced a selective modulation of gut ARGs, significantly reducing specific subtypes such as tetracycline and multidrug efflux genes, despite a slight increase in vancomycin resistance markers. Overall, our findings suggest that beLP1[®] attenuated the rate of body weight gain during the initial weeks of HFD exposure and significantly improved markers of hepatic stress and lipid metabolism.}, }
@article {pmid42197333, year = {2026}, author = {Zhao, Z and Wang, X and Wen, F and Zhao, F and Zhang, M and Menghe, B}, title = {Integrated Metagenomic and Metabolomic Profiling Identifies Predictive Biomarkers for Overweight Status in a Mongolian Population.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14050946}, pmid = {42197333}, issn = {2076-2607}, support = {2018YFE0123500//Special Funds for International Science and Technology Cooperation of China/ ; }, abstract = {Mongolians have high overweight prevalence linked to their nomadic lifestyle and diet, but gut microbiota studies in this population are scarce. This study used fecal metagenomic and serum metabolomic analyses of 96 Mongolian participants (normal-weight n = 55, overweight n = 41) to characterize gut microbiome alterations and identify weight-related biomarkers. The analyses revealed that Parabacteroides distasonis, Barnesiella intestinihominis, and Alistipes onderdonkii were significantly reduced in overweight individuals (p < 0.05). Concurrently, the metabolites such as beta-cryptoxanthin, p-cresol, and ribothymidine were significantly down-regulated in the overweight group (p < 0.05). Random forest models from the three datasets showed a strong diagnostic ability for microbial families (AUC > 0.70). A subsequent integrated multi-kingdom classifier that combined microbiota and metabolite data achieved the highest performance (AUC = 0.818). Key features with high predictive contributions were identified, including Lactobacillus crispatus, Alistipes onderdonkii, and Parabacteroides distasonis, and metabolites, such as beta-cryptoxanthin, p-cresol, and picolinic acid. These results show the random forest model has high predictive value for distinguishing normal weight and overweight individuals. In summary, this study identified specific gut microbiota and serum metabolomic profiles linked to overweight in Mongolians. Multi-omics integration established a diagnostic biomarker model, laying a theoretical basis for microbiome-targeted weight management interventions.}, }
@article {pmid42197335, year = {2026}, author = {Naranjo-Moran, J and Ratti, MF and Vera-Morales, M}, title = {Microorganisms from Antarctica: A Review of Their Potential in the Bioremediation of Hydrocarbon-Contaminated Soils.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14050948}, pmid = {42197335}, issn = {2076-2607}, abstract = {Antarctica's extreme cryospheric conditions impose severe thermodynamic constraints on the natural attenuation of hydrocarbon pollutants. Despite the Antarctic Treaty System's protections, the footprint of human logistics has left persistent reservoirs of petroleum hydrocarbons that threaten endemic biodiversity. This review critically synthesizes the state-of-the-art in Antarctic bioremediation, moving beyond traditional culture-dependent studies to integrate recent multi-omics breakthroughs (2020-2025). We analyze the molecular mechanisms limiting bioavailability in frozen soils and highlight the adaptive strategies of psychrophilic consortia, including the modification of membrane fluidity and the expression of cold-active enzymes (e.g., RHDs, AlkB). Notably, we discuss emerging findings on novel long-chain alkane degradation genes (almA, ladA) identified in 2025, which challenge previous assumptions about recalcitrance. Furthermore, the review evaluates the engineering bottlenecks of in situ versus ex situ strategies, emphasizing the synergistic potential of bacterial-fungal co-cultures and the ecological necessity of "climate-smart" remediation to mitigate methane emissions from thawing permafrost. By bridging the gap between fundamental microbial genetics and applied field engineering, we propose a roadmap for the next generation of biotechnological solutions in the warming polar environment.}, }
@article {pmid42197351, year = {2026}, author = {Huang, W and Liang, J and Chan, P and Liu, Z and Guo, L}, title = {Probiotics Exert Colonization Resistance Against F. nucleatum subsp. polymorphum: Disruption by Antibiotics and Underlying Molecular Mechanisms.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14050965}, pmid = {42197351}, issn = {2076-2607}, support = {81670982//National Natural Science Foundation of China/ ; }, abstract = {Fusobacterium nucleatum (F. nucleatum), a key oral pathogen, promotes colorectal cancer (CRC) progression via gut translocation. Although gut probiotics provide colonization resistance against pathogens, antibiotic-induced dysbiosis may facilitate F. nucleatum integration and increase the risk of CRC. The mechanisms underlying probiotic-F. nucleatum antagonism and antibiotic modulation remain unclear. A 33-strain probiotic consortium and F. nucleatum subsp. Polymorphum (F. polymorphum) ATCC 10953 were co-cultured. The inhibitory effects of probiotics on F. nucleatum and the impacts of antibiotics (ABXs) on the microbial community structure in the co-culture system and on the probiotic-mediated inhibition of F. nucleatum were evaluated using spent medium assays, plate confrontation tests, growth curves, qRT-PCR, metagenomic sequencing, and transcriptomics. Hydrogen peroxide/pH/lysine assays and coaggregation models were performed to probe the associated mechanisms. Probiotics strongly inhibited the growth of F. nucleatum in a dose-dependent manner, primarily via organic acids, while F. nucleatum enriched amino acid/vitamin biosynthesis pathways without major growth suppression. Antibiotics weakened probiotic antagonism, shifted species abundance (↓ L. plantarum, ↑ L. paracasei), induced adaptive stress responses in F. nucleatum (↑ nucleotide metabolism, propanediol degradation, pdxS), and reduced lysine biosynthesis. Lysine supplementation restored probiotic abundance and disrupted F. nucleatum coaggregation. Multi-strain probiotics exert potent colonization resistance effects against F. nucleatum, mainly through organic acids and metabolic interference. Antibiotic-induced dysbiosis impairs this protective effect and may promote the persistence of F. nucleatum, which has been implicated in CRC risk. Targeted probiotic strategies may offer novel preventive approaches.}, }
@article {pmid42197355, year = {2026}, author = {Feletti, R and Mori, A and Zaffagnini, A and Castilletti, C and Pomari, E}, title = {The Human Virome in Infectious Diseases: Insights from Chronic and Acute Infections Across Body Sites-A Narrative Review.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14050969}, pmid = {42197355}, issn = {2076-2607}, support = {PE00000007, INF-ACT//EU funding within the MUR PNRR/ ; 5MIL-VISA L1P17//Italian Ministry of Health/ ; }, abstract = {The human virome, comprising eukaryotic viruses, bacteriophages, and viral genetic material, is a dynamic component of the microbiome with growing relevance in infectious diseases. This narrative review is structured to: (i) summarize the general composition of the human virome and methodological challenges, including the fraction of unclassified viral "dark matter"; (ii) describe virome alterations in chronic infections; and (iii) explore site-specific virome dynamics across respiratory, intestinal, and genito-urinary tracts in both chronic and acute infections. In chronic viral infections such as HIV, HBV, HCV, and HPV, a recurrent feature is the expansion of Anelloviridae-particularly torque teno virus-reflecting impaired immune surveillance rather than direct pathogenicity, suggesting their potential as surrogate biomarkers of immune competence. Evidence on virome changes in chronic bacterial and parasitic infections remains limited, highlighting a critical knowledge gap. Acute infections are associated with compartment-specific shifts in eukaryotic viruses and bacteriophage communities, often paralleling changes in bacterial populations and inflammatory responses, with implications for disease severity. Despite advances in metagenomic approaches, a substantial proportion of viral sequences remains unclassified, limiting functional interpretation. Nevertheless, virome profiling provides an ecosystem-level perspective, offering insights beyond single-pathogen detection and supporting emerging applications in diagnostics, immune monitoring, prognosis, and infectious disease surveillance.}, }
@article {pmid42197366, year = {2026}, author = {Huang, Z and Chen, S and Fan, A and Chen, Y and Cai, Q and Zeng, T and Zheng, W and Yang, Y}, title = {Iron-Containing Flocs Derived from Environmental Emergency Response Influenced Nitrogen Cycling Driven by Microorganisms in River Sediments.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14050980}, pmid = {42197366}, issn = {2076-2607}, support = {PM-zx703-202204-155//the Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; PM-zx097-202506-204//the Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; }, abstract = {In situ coagulation is regarded as the most effective measure in response to the frequent metal spills in China. Excessive coagulant is often used in pursuit of extremely high removal rates of contaminants. Yet the secondary ecological impact of the iron-containing coagulation flocs left on the river sediments after emergency response is still unclear. In the current study, we investigated the impact of flocs derived from three different iron-based coagulants, polymeric ferric sulfate (PFS), polymeric ferric chloride (PFC), and ferric chloride (FeCl3), on microbial communities in sediment based on microcosm experiments. Metagenomics, quantitative PCR, and determination of ammonia oxidation potential were adopted to elucidate community shifts. The results indicate that the community structure and function of microorganisms in sediments have been affected, especially processes and species related to nitrogen cycling, and the effect was coagulant-specific. Flocs retrieved from FeCl3 caused a more pronounced decline in diversity, shifts in community composition, and decreased potential ammonia oxidation. Ammonia-oxidizing archaea (AOA) was more sensitive to iron-containing flocs than ammonia-oxidizing bacteria (AOB), while PFS-flocs tended to reduce multiple genes involved in nitrate reduction. This indicates that the pre-polymerization of inorganic coagulants may be the primary factor leading to different microbial ecological effects. Sulfate, on the other hand, may affect specific biogeochemical processes due to its competition for electron donors. Our results confirmed that even without heavy metals as contaminants, coagulant flocs alone could present an effect on nitrogen cycling in sediments. The results will provide a scientific basis for environmental emergency decision-making: in emergency response to metal pollution incidents, the use of coagulants should be limited to only the necessary level.}, }
@article {pmid42197381, year = {2026}, author = {Li, X and Liang, X and Hao, P and Wu, J and Liu, D}, title = {Compound Yeast Culture Reshapes Gut Microbiota and Functional Pathways to Enhance Antioxidant Capacity and Immune Homeostasis in Suckling Calves.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14050995}, pmid = {42197381}, issn = {2076-2607}, support = {2022YFDZ0051//Inner Mongolia Autonomous Region Science and Technology Project/ ; BR22-11-17//Basic Scientific Research Business Project of Universities directly under the Inner Mongolia Autonomous Region/ ; 2023-JSGG-5//National Center of Technology Innovation for Dairy/ ; YLXKZX-NND-012//First-class Disciplines of Inner Mongolia Scientific Research Special Program/ ; }, abstract = {Diarrhea in suckling calves is associated with impaired growth, oxidative stress, immune dysfunction, and intestinal microbial dysbiosis. This study evaluated the effects of compound yeast culture (CYC) supplementation on growth performance, fecal characteristics, antioxidant capacity, immune function, and gut microbiota in diarrheic Holstein calves. Thirty-six approximately 7-day-old calves were enrolled, including 12 healthy calves (CON) and 24 diarrheic calves randomly assigned to a diarrhea group (DIA) or a CYC-supplemented group (DIA-YC; 50 g/d for 30 days). The experimental period lasted 60 days. Compared with the DIA group, calves in the DIA-YC group showed significantly higher average daily feed intake and average daily gain (ADG) during days 31-60 and across the entire period (p < 0.05), with a trend towards increased body weight. Fecal scores were significantly elevated in diarrheic calves during the early and mid-stages but were markedly reduced by CYC supplementation from days 7 to 30; no significant difference was observed between DIA-YC and CON during days 16-30 (p > 0.05). Diarrheic calves exhibited oxidative stress, characterized by decreased total antioxidant capacity (T-AOC) and increased malondialdehyde (MDA). CYC supplementation significantly increased T-AOC, superoxide dismutase (SOD), and glutathione peroxidase (GSH-Px) activities, while reducing MDA levels (p < 0.05). Immune analysis showed higher serum IgG and IL-10 levels and lower TNF-α levels in the DIA-YC group, along with improved intestinal barrier indicators, including diamine oxidase (DAO) activity and endotoxin levels. Metagenomic analysis revealed that diarrhea reduced microbial richness and diversity and altered community structure, whereas CYC partially restored microbial diversity and increased beneficial genera such as Prevotella, Coprococcus, Ruminococcus, and Parabacteroides. Functional analysis indicated that CYC enhanced pathways related to immune regulation, energy metabolism, and antioxidant function. CYC supplementation alleviates oxidative stress and immune dysfunction by modulating gut microbiota, thereby improving growth performance and reducing diarrheal severity in calves.}, }
@article {pmid42197408, year = {2026}, author = {Qie, T and Lin, D and Fan, Q and Sun, G and Wang, H and Liu, Z and Liu, X}, title = {Responses of Soil Nitrogen-Cycling Microbial Communities and Functional Potential to Grazing Intensities in Alpine Meadows.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051022}, pmid = {42197408}, issn = {2076-2607}, support = {KLGE202209//State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems/ ; 32260354//National Natural Science Foundation of China/ ; KLGE-2024-01//State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems/ ; 2023-QN-46//Lanzhou Science and Technology Bureau/ ; 2500011004//Gansu Agricultural University/ ; }, abstract = {Although grazing is a key driver of nitrogen cycling in alpine meadow soils, a systematic understanding of how different grazing intensities shape the structure and functional potential of soil nitrogen-cycling microbial communities remains lacking. In this study, soil samples were collected under five grazing intensities (no grazing, light grazing, moderate grazing, heavy grazing, and extreme grazing) and metagenomic sequencing was employed to analyze variations in nitrogen-cycling microbial communities and functional genes. The results showed that bacteria were the dominant group in nitrogen-cycling communities (relative abundance: 93.99-98.98%), with significant community differentiation across grazing intensities. Light grazing maintained relatively high microbial diversity, whereas moderate and heavy grazing led to more pronounced differences in community composition. Functional gene analysis identified 41 nitrogen-cycling-related genes, primarily involved in denitrification, nitrate reduction, and ammonia assimilation. Light grazing enhanced nitrate reduction and glutamate synthesis; moderate grazing exhibited the strongest ammonia assimilation potential; heavy grazing significantly increased denitrification activity, indicating an elevated risk of nitrogen loss; and under extreme grazing, both the number and abundance of nitrogen-cycling functional genes declined markedly, with functional composition becoming simplified. Collectively, light grazing is more conducive to maintaining the balance between soil microbial diversity and nitrogen-cycling function in alpine meadows, whereas overgrazing disrupts the equilibrium between microbial communities and nitrogen metabolism. This study provides a microbiological basis for the restoration of degraded alpine meadows and sustainable grazing management.}, }
@article {pmid42197422, year = {2026}, author = {Shaik, SM and Schiro, G and Laubitz, D and Madan, JC and Kelley, CP and Daines, M and Rice, SA and Ghishan, FK and Kiela, PR}, title = {Functional Shifts in Gut Microbiota and Associated Metabolites Suggest Gut-Brain Axis Dysregulation in Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal Infections (PANDAS).}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051036}, pmid = {42197422}, issn = {2076-2607}, support = {NA//Alex Manful Fund/ ; RFGA2022-010-23//Arizona Department of Health Services/ ; }, abstract = {Background: Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal infections (PANDAS) are characterized by neuropsychiatric symptoms linked to immune dysregulation. Emerging evidence highlights the role of host-microbiome interactions in modulating neuro-immune functions via gut-brain axis signaling; however, its contribution to PANDAS pathophysiology remains poorly understood. Methods: We conducted microbiome analysis from samples collected across multiple sites of PANDAS patients including nasal, throat and stool. We performed an integrated multi-omics analysis of stool samples from pediatric PANDAS cases and healthy controls, including discordant twin pairs. Microbial composition and function were assessed using 16S rRNA gene sequencing, shotgun metagenomics, while untargeted metabolomic profiling was performed using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS). Results: PANDAS cases exhibited reduced alpha diversity and significantly altered beta diversity compared to controls, indicating shifts in gut microbial composition. Shotgun metagenomic analysis revealed differential enrichment of functional pathways, including diminished quorum sensing, altered gamma-aminobutyric acid (GABA) biosynthesis, and microbial degradation processes. Multiple gut-brain modules (GBMs) and gut metabolic modules (GMMs) associated with neurotransmission, transport activities and metabolism were significantly perturbed in PANDAS. Metabolomic profiling showed reduced functional diversity and distinct clustering of metabolic profiles, with differential abundance of amino acids, bile acids, and neuroactive compounds. Integrative analysis further identified disrupted microbe-metabolite networks allied to gut-brain signaling. Conclusions: Our findings reveal significant functional shifts in gut microbiota composition, functional capacity and metabolite profile in PANDAS, suggesting dysregulation of the gut-brain axis signaling. This study provides a foundation for development of microbiome-based biomarkers and therapeutic strategies for pediatric neuropsychiatric disorders.}, }
@article {pmid42197470, year = {2026}, author = {Zheng, Y and Wu, R and Feng, H and Wu, X and Yang, Y}, title = {Temperature Elevation Alters the Gut Antibiotic Resistome and Carbohydrate-Active Enzymes in the Desert Lizard Eremias roborowskii.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051084}, pmid = {42197470}, issn = {2076-2607}, support = {32560265//National Natural Science Foundation of China/ ; 32260118//National Natural Science Foundation of China/ ; 2023TSYCQNTJ0034//the second group of Tianshan Talent Training Program: Youth Support Talent Project/ ; XJAUGRI2025030//Xinjiang Agricultural University Graduate Research Innovation Program/ ; }, abstract = {In the context of global warming, the resulting persistent thermal stress has become a critical environmental factor influencing the structural and functional homeostasis of gut microbiota in reptiles. In this study, Eremias roborowskii, a desert lizard endemic to the extreme heat conditions of the Turpan Basin, was selected as an ideal model for evaluating the ecological impacts of global warming. Meanwhile, a 60-day controlled laboratory experiment was conducted, exposing the lizards to normal (30 °C ± 1 °C), elevated (37 °C ± 1 °C), and high (42 °C ± 1 °C) temperatures to reflect future climate scenarios. Using shotgun metagenomic sequencing, the gut microbiota was characterized to investigate the dynamics of the antibiotic resistance genes (ARGs) and carbohydrate-active enzymes (CAZymes) under heat stress. The results reveal that elevated temperature selectively promotes heat-tolerant gut microbiota, such as Tetragenococcus and Faecalicatena, by altering host energy metabolism and modulating heat stress adaptation to maintain intestinal homeostasis. Moreover, the observed increase in resistome diversity and richness under elevated temperature may be attributed to temperature-induced shifts in gut microbial composition, particularly the enrichment of heat-tolerant ARG-carrying bacterial taxa. Metabolic changes in CAZymes were caused by gut microbiota remodeling, which optimized carbon utilization and preferentially allocated cell wall synthesis and repair. Furthermore, the pentose phosphate pathway and amino acid biosynthesis pathways were upregulated, providing NADPH for antioxidant defense and precursors for protein synthesis, respectively, thereby contributing to the maintenance of microbial cellular homeostasis. Our study provides a theoretical basis for understanding functional gene adaptation strategies in wildlife microbiomes due to climate change.}, }
@article {pmid42197480, year = {2026}, author = {Duran Yunga, ER and Rodriguez Coyago, ML}, title = {Structure and Function of the Dental Plaque Microbiome in Eubiosis: A Systematic Review of Ethnic-Racial Influences.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051095}, pmid = {42197480}, issn = {2076-2607}, abstract = {While a conserved core microbiome is shared across healthy individuals, significant interindividual taxonomic variation exists; however, the specific influence of genetic ancestry on supragingival plaque structure in eubiosis remains unclear. This systematic review analyzed evidence regarding taxonomic variations in supragingival plaque associated with ethnicity in systemically healthy populations. A search was conducted in PubMed, Scopus, ScienceDirect, and Scielo following PRISMA 2020 guidelines, covering literature up to October 2025. Cross-sectional studies using genomic sequencing or metagenomics were included, with quality assessed via the GRADE system. Six studies met eligibility criteria. Results identified a universal core microbiome structurally dominated by Corynebacterium spp. and Streptococcus spp. However, distinct ethnic-specific taxonomic signatures emerged, such as the enrichment of Fusobacterium spp. in African Americans and Corynebacterium spp. in Caucasians, alongside the exclusive presence of Sneathia spp. in Burmese individuals. Although a basal microbial architecture necessary for homeostasis exists, ethnicity acts as a biological filter defining distinctive bacterial profiles and differential susceptibilities. These findings suggest that while the core microbiome is conserved, the composition of peripheral species in the dental plaque hedgehog structure varies according to ancestry. This supports a transition from standardized dental care to personalized medicine oriented towards the patient's biological heritage.}, }
@article {pmid42197517, year = {2026}, author = {Albastaki, A and Smith, J}, title = {Choosing Between Short-Read 16S, Full-Length ONT 16S, and Long-Read Shotgun Metagenomics for Soil Microbiome Studies: A Critical Review of the Benchmarking Evidence.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051132}, pmid = {42197517}, issn = {2076-2607}, abstract = {Studying soil microbiomes is challenging because soil contains thousands of microbial species at vastly different abundances. The choice of sequencing method has a strong effect on which of these species are detected and how the community is described. Three approaches now dominate soil microbiome research: short-read 16S rRNA amplicon sequencing on Illumina platforms, full-length 16S sequencing on Oxford Nanopore Technologies (ONT) platforms (particularly the R10.4.1 flow cell), and long-read shotgun metagenomics. Each has distinct biases that shape the recovered community, yet researchers routinely select a method based on cost, understanding, or local expertise rather than on a clear knowledge of what each approach methodically over- or under-represents. Here, we review head-to-head benchmarking studies that have applied two or more of these methods to the same soil or directly comparable samples. We show that while long-read and short-read 16S approaches generally converge on dominant taxa and on between-sample differences, they disagree substantially on alpha diversity estimates, rare taxon detection, and the relative abundances of entire phyla. The R10.4.1 flow cell chemistry has narrowed but not eliminated the accuracy gap with Illumina, and shotgun metagenomics reveals systematic biases in both short and long-read assembly that depend on population diversity within the sample. We synthesise this evidence into an evidence-based decision framework tied to specific research questions and recognise the gaps in soil-specific benchmarking that limit current methods. Rather than asking which platform is "best," we argue that method choice should be framed as an important part of study design, with the biases of the chosen method acknowledged and, where possible, controlled for.}, }
@article {pmid42197550, year = {2026}, author = {Zhang, S and Li, G and Zhu, E and Zhao, Y and Yang, X and Huang, S and Zheng, Z}, title = {Rhizosphere Microbial Community and Metagenomic Annotation Responses in a Vallisneria natans-Sediment Microcosm Exposed to Trifluenfuronate and Fluopyram.}, journal = {Microorganisms}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/microorganisms14051166}, pmid = {42197550}, issn = {2076-2607}, support = {2023YFD1700403//the National Key Research and Development Program of China/ ; 2024R054//Zhejiang Shuren University/ ; }, abstract = {Rhizosphere microorganisms play central roles in nutrient cycling and contaminant transformation in sediment-associated freshwater systems, yet their responses to newer pesticides remain insufficiently characterized. In this study, a 28-day Vallisneria natans-rhizosphere sediment microcosm was used to compare the effects of trifluenfuronate and fluopyram at nominal concentrations of 0.01, 0.1, and 1 mg L[-1]. Bacterial community composition was assessed using 16S rRNA gene sequencing, and shotgun metagenomic data were used to evaluate relative functional annotation patterns. Plant physiological traits and rhizosphere sediment enzyme activities were measured as ecological context for interpreting microorganism-associated responses. Fluopyram, particularly at 1 mg L[-1], produced clearer ordination-level shifts in rhizosphere bacterial community composition than trifluenfuronate, although pairwise treatment separation was not statistically resolved after multiple-testing correction. Annotation-based metagenomic profiles also differed between the two pesticides: stronger exposure was associated with reduced relative signals for several xenobiotic-, transport-, and regulation-related annotations, while high-dose fluopyram showed a methane-metabolism-related annotation signal and high-dose trifluenfuronate showed relative enrichment of secondary-metabolism-related annotations. These microbial and annotation-profile responses coincided with stronger inhibition of V. natans growth and greater suppression of rhizosphere sediment enzyme activities under fluopyram exposure. Overall, fluopyram induced more consistent microorganism-associated response patterns than trifluenfuronate in the tested rooted macrophyte-sediment microcosm. The results highlight the sensitivity of rhizosphere microbial communities and metagenomic annotation profiles to pesticide exposure in sediment-associated freshwater systems.}, }
@article {pmid42197616, year = {2026}, author = {Wang, W and Yang, W and Song, W and Huang, S and Lai, J and Zhou, Z and Wang, P and Wang, B}, title = {Rhizosphere Microbial Effects on Soil Quality of Pinus massoniana and Schima superba Mixed Plantations.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/plants15101482}, pmid = {42197616}, issn = {2223-7747}, support = {2023YFD2200902//National R&amp;D Program of China/ ; CAFYBB2024ZA021//Fujian Sanming Demonstration and Model Construction Project of China/ ; }, abstract = {This study aimed to reveal the rhizosphere microbial community structure, carbon-nitrogen-phosphorus (C-N-P) nutrient cycling processes, and functional gene characteristics of Pinus massoniana and Schima superba in mixed forests. Furthermore, we sought to elucidate the microbial mechanisms by which mixed-species afforestation enhances soil quality improvement, providing a theoretical basis in soil microbiology for the cultivation of these mixed forests. The research subjects included pure P. massoniana plantations (CLPs), pure S. superba plantations (CLSs), and individual P. massoniana (HJP) and S. superba (HJS) trees within mixed plantations (HJLs). We collected rhizosphere and bulk soil samples to analyze their physicochemical properties and enzyme activities. Metagenomic sequencing was employed to profile the rhizosphere microbial communities and functional genes involved in C-N-P cycling. Furthermore, by integrating a functional gene co-occurrence network analysis with structural equation modeling (SEM), we systematically elucidated the coupling relationships among the stand types, soil properties, microbial communities, and nutrient cycling. Mixed planting significantly improved soil quality; compared to the CLP and CLS forests, the nitrate nitrogen (NO3[-]-N) content in the mixed forest soils increased by 121.01% and 120.10% (p < 0.05), and the activity of urease (URE) also significantly increased by 123.99% and 49.56%, respectively. Mixing significantly altered the microbial community structure. In the bacterial community of the mixed forests, the abundance of nitrogen-fixing and potentially phosphorus-solubilizing bacteria from the genera Paraburkholderia and Burkholderia increased. In the fungal community, the arbuscular mycorrhizal fungus Rhizophagus, which possesses a nutrient absorption advantage, exhibited absolute dominance, with its relative abundance ranging from 14.84% to 88.81%. The abundances of genes associated with denitrification and phosphorus starvation regulation were significantly upregulated in the mixed forests; notably, the abundance of phosphorus starvation regulation genes in the HJSs was 18.84% higher than that in the CLSs. A co-occurrence network analysis demonstrated that the proportion of positive correlation edges in the HJP nitrogen cycling network reached as high as 75.0%, and the average degree of the HJS phosphorus cycling network (2.691) surpassed that of the CLSs. The structural equation modeling further revealed that the association strength between the fungi and phosphorus cycling genes in the mixed forests increased to R[2] = 0.915 (p < 0.01) from R[2] = 0.213 in the pure forests. This mixed planting practice transforms nutrient cycling from a resource-competitive mode to a microbially synergized mode, thereby forming an efficient endogenous nutrient cycling system. This synergistic rhizosphere microbial effect is a key internal mechanism for overcoming nutrient bottlenecks and should serve as a diagnostic indicator of soil recovery in the ecological restoration of degraded pine forests.}, }
@article {pmid42198637, year = {2026}, author = {Malleret, B and Kwak, ML and Chavatte, JM}, title = {Accelerating Progress on Ticks and Tick-Borne Diseases in Southeast Asia: Regional Challenges, Evidence Gaps, and Priorities (2023-2025).}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {5}, pages = {}, doi = {10.3390/pathogens15050511}, pmid = {42198637}, issn = {2076-0817}, support = {NUHSRO/2025/017/T1/Seed-Sep24/Adhoc/01//Ministry of Education/ ; }, mesh = {Animals ; Humans ; Asia, Southeastern/epidemiology ; Evidence Gaps ; *Tick-Borne Diseases/epidemiology/prevention &amp; control ; *Ticks/microbiology ; }, abstract = {Southeast Asia (SEA) faces persistent gaps in regional understanding and control of ticks and tick-borne diseases (TBDs) despite recent advances (2023-2025). The second international symposium on ticks and TBDs in SEA (Singapore, August 2025), following the inaugural 2023 meeting in Cambodia, served as a catalyst for regional exchange that informed this perspective. SEA's ecological and host diversity supports complex tick-host-pathogen networks, yet evidence remains fragmented due to uneven sampling that has largely focused on livestock and peri-urban environments. Key constraints include limited taxonomic resolution driven by outdated or incomplete identification keys, under-sampling of soft ticks (Argasidae), and the absence of harmonized, open-access regional reference resources (including DNA barcodes and MALDI-TOF MS spectral databases). While MALDI-TOF MS, proteomics, AI-assisted identification, and next-generation sequencing/metagenomics are increasingly applied, their broader regional uptake is limited by the absence of harmonized, open-access reference resources (including DNA barcodes and MALDI-TOF MS spectral databases). Broad ecological surveys and integrated animal and human surveillance remain limited, and vector competence studies are constrained by the scarcity of SEA-derived tick colonies and cell lines. Regional data and recent findings (2024-2026) confirm circulation of multiple TBPs (including Anaplasma, Babesia, Borrelia, Coxiella, Ehrlichia, Rickettsia, and Theileria) and highlight emerging viral findings, including southward reports of Bandavirus dabieense. Human infestations and non-communicable tick bite outcomes (e.g., tick paralysis and alpha-gal syndrome) are recognized but remain under-reported due to low clinical awareness and limited diagnostics. Importantly, the diagnostic chain is further disrupted by missed/insufficient specimen collection at the point of care, and by constrained capacity to identify (especially immature) ticks to species level-limitations compounded by the absence of harmonized, open-access regional reference resources. The symposium identified six priorities: (1) full completion and regional validation of tick identification keys for adults (in progress) and immatures (to be initiated), plus an open-access DNA barcode library anchored by curated, voucher-based collections from all SEA countries; (2) harmonization of molecular and proteomic diagnostic platforms, including expansion of regional MALDI-TOF MS and NGS protocols and reference databases; (3) development of tick colonies and cell lines from locally prevalent species to support vector competence, vaccine, and acaricide testing; (4) expansion of One Health surveillance with enhanced ecological sampling at wildlife-livestock-human interfaces; (5) establishment of open-access, region-wide data platforms for integrated tick, TBP, and ecological metadata sharing; and (6) sustained investment in human resources, training, and policy advocacy to raise research and public health visibility of ticks and TBDs.}, }
@article {pmid42198700, year = {2026}, author = {Mansour, O and Fadeev, AV and Perederiy, AA and Ksenafontov, AD and Boyarintseva, AY and Danilenko, DM and Lioznov, DA and Komissarov, AB}, title = {Whole-Genome Phylogenetic Characterization of Human Parainfluenza Virus Type 4 Circulating in St. Petersburg, Russia.}, journal = {Viruses}, volume = {18}, number = {5}, pages = {}, doi = {10.3390/v18050497}, pmid = {42198700}, issn = {1999-4915}, support = {TVKQ-2024-0003, registration number 124020500002-4//Ministry of Health of the Russian Federation (Project #TVKQ-2024-0003 "Complex approach to genetic characterization and early identifications of pathogens with epidemic and pandemic potential using metagenomic sequencing")/ ; }, mesh = {Humans ; *Phylogeny ; Russia/epidemiology ; *Genome, Viral ; Genetic Variation ; Whole Genome Sequencing ; *Parainfluenza Virus 4, Human/genetics/classification/isolation &amp; purification ; *Rubulavirus Infections/virology/epidemiology ; }, abstract = {Human parainfluenza virus type 4 (hPIV4) remains poorly characterized compared with other hPIV serotypes and information on its genomic diversity is particularly limited for Russia and Eastern Europe. In this study, we report the first complete genome sequences of hPIV4 isolates from Russia and place them in the context of global hPIV4 genetic diversity. Eight hPIV4 viruses were isolated in cell culture from respiratory samples collected from hospitalized children in Saint Petersburg between 2017/2018 and 2023/2024. Complete viral genomes were recovered using a metagenomic whole-genome amplification approach based on SMART-9N technology. Phylogenetic analysis of 178 complete hPIV4 genomes showed clear separation into hPIV4a (n = 132) and hPIV4b (n = 46) subtypes. Based on genetic distance approach, hPIV4a formed two major clusters, with the dominant cluster B subdivided into four subclusters (B1-B4); and subcluster B4 further resolved into four genetic lineages. All Russian isolates belonged to the subcluster B4 and were distributed among multiple co-circulating lineages. In contrast, hPIV4b genomes segregated into three distinct clusters, reflecting structured genetic diversity within the subtype. Collectively, this study provides, to the best of our knowledge, the first p-distance-based framework for hPIV4 whole-genome classification and contributes new complete genome sequences for an underrepresented region.}, }
@article {pmid42198703, year = {2026}, author = {Wang, Z and Liu, Z and Zeng, J and Li, J and Cheng, J and Qi, X and Li, J and Bai, S}, title = {Annual Dynamics and Functional Traits of Viral Communities in Tropical Intertidal Sands of Sanya Bay.}, journal = {Viruses}, volume = {18}, number = {5}, pages = {}, doi = {10.3390/v18050500}, pmid = {42198703}, issn = {1999-4915}, support = {423RC548//Hainan Provincial Natural Science Foundation of China/ ; KJRC2023C14//Department of Science and Technology of Hainan Province/ ; 41506139//National Natural Science Foundation of China/ ; }, mesh = {Seashore ; *Geologic Sediments/virology ; Seasons ; Metagenomics ; *Bays/virology ; *Viruses/classification/genetics/isolation &amp; purification ; Tropical Climate ; Phylogeny ; *Virome ; }, abstract = {Viruses are key regulators of marine microbial communities, yet their temporal dynamics in tropical intertidal sediments remain poorly characterized. We conducted a year-long metagenomic survey of sandy intertidal sediments in Sanya Bay (60 monthly samples from five sites) to examine viral taxonomy, community structure, lytic proteins, and auxiliary metabolic genes (AMGs). Within the classifiable fraction, the assemblages were consistently dominated by Assiduviridae. However, NMDS analysis revealed a significant overall seasonal shift, with October-December samples separating from the rest of the year. Co-occurrence network analysis identified five co-occurrence modules with distinct temporal patterns, alongside a concurrent decline in module abundance and lytic proteins in October. Functional annotation showed that cysteine and methionine metabolism, primarily driven by DNA methyltransferases, was identified as a highly represented AMG category among the annotated functions, while other pathways displayed seasonal variability. Collectively, these findings suggest that although characterized by a classifiable fraction dominated by Assiduviridae, the highly complex tropical intertidal viral communities undergo substantial seasonal reorganization in structure and functional potential.}, }
@article {pmid42198741, year = {2026}, author = {Jia, L and De, R and Li, Z and Han, Z and Liu, L and Dong, H and Feng, S and Liu, R and Zhao, L}, title = {A Prolonged Norovirus Infection and the Molecular Evolution of Human Norovirus Within-Host in a Child with Burkitt Lymphoma.}, journal = {Viruses}, volume = {18}, number = {5}, pages = {}, doi = {10.3390/v18050538}, pmid = {42198741}, issn = {1999-4915}, support = {Discipline Leader -02-20//Beijing Municipal Health Commission/ ; }, mesh = {Humans ; *Burkitt Lymphoma/virology/complications ; *Evolution, Molecular ; *Norovirus/genetics/classification/isolation &amp; purification ; Phylogeny ; *Caliciviridae Infections/virology/complications ; Genome, Viral ; Child ; Feces/virology ; High-Throughput Nucleotide Sequencing ; Mutation ; }, abstract = {It has been reported that chronic infection of human norovirus (HuNoV) may potentially serve as a reservoir for viral variants with the possibility to evade population immunity or alter the binding sites of HBGA receptors. In this study, a child diagnosed with Burkitt lymphoma and positive for HuNoV determined by real-time PCR (qPCR) firstly in 15 August 2016, was followed up until 20 March 2018, and 26 fecal specimens and one vomitus were collected to trace the evolutionary characteristics of HuNoV by phylogenetic analysis, meta-genomics next-generation sequencing (mNGS), and temporal evolutionary analysis of VP1 among 23 specimens positive for HuNoV. There were 15 specimens with partial RdRp gene sequences forming an independent cluster with sequences of GII.P31, 14 with the region C sequences and 11 with P domain sequences of VP1 gene clustered together with HuNoV GII.4 Sydney_2012. All these sequences showed that mutations accumulated nearly in a time order, and more mutations were shown in the key epitopes A-E or near the binding sites for HBGA in subdomain P2 with higher evolutionary rates. Analysis of NGS data identified intra-host viral quasi-species, and two genome sequences of the same length from mNGS were assembled from N705, with mutations located in the region of subdomain P2 (1171 nt-1202 nt) which led to five amino acid mutations. In conclusion, the accumulated mutations of HuNoV, especially in subdomain P2, were explored in a child with Burkitt lymphoma, and the sequencing of HuNoV from immunocompromised individuals was proven critical for monitoring intra-host quasi-species evolution and potential variant emergence, providing basic data for clinical infection control.}, }
@article {pmid42198763, year = {2026}, author = {Kim, MJ and Kim, YJ and Ha, HJ and Park, JS and Rini, IA and Lee, S and Lee, TK}, title = {Biological Trajectory of Virophage Research and the Emergence of Marine Virophages: A Scoping Review.}, journal = {Viruses}, volume = {18}, number = {5}, pages = {}, doi = {10.3390/v18050560}, pmid = {42198763}, issn = {1999-4915}, support = {RS-2021-KS211475//Korea Institute of Marine Science and Technology Promotion/ ; }, mesh = {*Virophages/genetics/physiology ; Genome, Viral ; Giant Viruses/genetics ; *Aquatic Organisms/virology ; Seawater/virology ; Metagenome ; Virus Replication ; }, abstract = {Virophages are satellite viruses that depend on the replication machinery of giant double-stranded DNA viruses and influence the structure and dynamics of viral communities through multilayered interactions among giant viruses, their hosts, and virophages. Since the discovery of the Sputnik virophage in 2008, virophages have been increasingly recognized for their roles in regulating giant virus replication, contributing to host defense mechanisms, and shaping the evolution of mobile genetic elements. However, quantitative syntheses examining how virophage research has developed over time, particularly in marine environments, remain limited. Here, we conducted a bibliometric analysis of virophage research published between 2008 and 2025 using the Web of Science Core Collection. By comparing an overall virophage research corpus with a marine virophage sub-corpus, we assessed publication and citation trends, collaboration structures, and keyword-based intellectual and thematic evolution. Our results show that virophage research has gradually transitioned from an early phase dominated by landmark discoveries and experimental model systems to a data-intensive stage driven by genome- and metagenome-based analyses and computational approaches. Although marine virophage studies represent a relatively small proportion of the total literature, they exhibit sustained citation impact and form a distinct research axis within the field. In particular, marine-focused studies emphasize metagenomic discovery, genome sequence alignment, and the analysis of mobile genetic elements such as polinton-like viruses, highlighting the role of marine environments in accelerating the intellectual transition of virophage research. Collectively, these findings demonstrate that virophage research has moved beyond a "discovery and definition" phase toward data-driven integrative interpretation, with marine virophage research emerging as a key domain for understanding the structure and evolutionary dynamics of marine viral ecosystems.}, }
@article {pmid42199008, year = {2026}, author = {Lépine, G and Davila, AM and Cueff, G and Pickering, G and Ichou, F and Perreau, C and Lefranc-Millot, C and Gilles, M and Thirion, F and Mariotti, F and Rémond, D and Fouillet, H and Polakof, S}, title = {Increasing plant protein sources in the diet modulates gut microbiota and tryptophan metabolism in men at cardiometabolic risk.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2677951}, doi = {10.1080/19490976.2026.2677951}, pmid = {42199008}, issn = {1949-0984}, mesh = {Humans ; Male ; *Tryptophan/metabolism ; *Gastrointestinal Microbiome ; Feces/microbiology ; Cross-Over Studies ; Middle Aged ; *Plant Proteins/metabolism/administration &amp; dosage ; Adult ; Diet ; Cardiometabolic Risk Factors ; Metabolome ; Indoles/metabolism ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; }, abstract = {This study investigated the effect of partially substituting dietary animal with plant protein (PP) sources on the fecal microbiota composition and metabolome in men with increased cardiometabolic risk. In a randomized, controlled, crossover feeding trial (NCT04236518), 19 men with high plasma triglycerides and waist circumference completed two 4-week isoenergetic diets: a flexitarian diet high in PP sources (FLEX, 64% PP) and a more animal-based control diet (CON, 36% PP). Fecal microbiota (shotgun metagenomics: taxa and metabolic pathways) and metabolome (targeted LC-MS) profiles were assessed before and after each diet and integrated with the host plasma metabolome. Delta values (Δd28-d1) were computed (n = 15 participants with all samples available), inter-individual variation was extracted to account for cross-over design, and OPLS-DA analyses comparing FLEX and CON Δd28-d1 were performed. Variables were selected based on their contribution to the diet discrimination effect (VIP > 1.5) and significant differences between groups (p-value < 0.05 from the paired Wilcoxon signed-rank test). The gut microbiota diversity remained unchanged, but FLEX reduced taxa associated with animal-based diets (e.g., Alistipes putredinis). Compared to CON, FLEX increased fecal xanthurenic acid and decreased the genetic potential for indole production. Combined with previously reported plasma changes (increased indole propionic acid and decreased indoxyl sulfate after FLEX), these findings suggest a shift away from indole production toward kynurenine and indole propionic acid-related tryptophan pathways, possibly driven by higher fiber intake, particularly from legumes. A one-month flexitarian diet thus modulated in men specific microbial taxa and metabolism, particularly tryptophan catabolism. These coordinated changes in microbial composition, functional potential, and metabolites indicate that diets higher in PP sources influence gut microbiota activities relevant to cardiometabolic health.}, }
@article {pmid42199353, year = {2026}, author = {Bergot, M and Lefevre, CT and Grouzdev, DS and Menguy, N and Ortet, P and Denis, Y and Viollier, E and Jézéquel, D and Monteil, CL}, title = {Magnetotactic Bdellovibrionota from a ferruginous spring.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag116}, pmid = {42199353}, issn = {2730-6151}, abstract = {Magnetotactic bacteria form a highly diverse group of microorganisms, yet early exploration of their diversity was largely centered on the Pseudomonadota. More recently, metagenomic studies have revealed that magnetotaxis, a form of chemotaxis guided by Earth's magnetic field, is widespread in other deep-branching phyla for which little to no ecological or biological information is available beyond that inferred from their genomes. For most of them, the morphology, ultrastructure and magnetosome chain characteristics responsible for the magnetic guidance remain unknown. While screening extreme environments for novel magnetotactic species, we observed magnetotactic Bdellovibrionota in the anoxic and ferruginous sediments of the Fontaine Goyon spring (France). We characterized their cell morphology and ultrastructure using magnetic enrichment, a single-cell sorting approach, and high-resolution electron microscopy. Cells display the morphology typical of the few predatory bacteria described in this phylum, and biomineralize, on average, five irregularly faceted, bullet-shaped magnetite magnetosomes along the concave side of the cell. Metagenomic analysis of approximately 100 cells revealed a potentially predatory and heterotrophic lifestyle adapted to low-O2 conditions. It also suggests a flexible respiratory metabolism under varying redox conditions, using iron as an alternative terminal electron acceptor. Exploring the diversity of Bdellovibrionota in public databases, we found 21 metagenome-assembled-genomes containing magnetosome genes. None of them harbor the canonical mamK actin-like gene implicated in aligning magnetosomes in described magnetotactic models. Affiliated to an undescribed class, we propose a classification scheme for the magnetotactic Bdellovibrionota species representing the class Bdellonasia class nov., for which no species had been formally described.}, }
@article {pmid42199424, year = {2026}, author = {Zhao, L and Wang, Q and Chen, J and Wang, J}, title = {Multi-omics analyses reveal significant differences in the gut microbiota and metabolites in children with Kawasaki disease in Northwest China.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1767902}, pmid = {42199424}, issn = {1664-3224}, mesh = {Humans ; *Mucocutaneous Lymph Node Syndrome/microbiology/metabolism ; Female ; Multiomics ; Male ; *Gastrointestinal Microbiome ; Child, Preschool ; Metagenomics/methods ; China/epidemiology ; *Metabolome ; Metabolomics/methods ; Infant ; Feces/microbiology ; Bacteria/classification/genetics ; Child ; }, abstract = {BACKGROUND: Kawasaki disease (KD) is a systemic vasculitis characterized by mucocutaneous lymph node syndrome and aberrant immune activation. Previous studies have indicated substantial disruptions in the gut microbiota during the acute phase of KD. However, the detailed characteristics of the gut microbiota and metabolome in children with KD, as well as their clinical relevance, remain poorly understood.<br><br>METHODS: 31 children with KD (KDs) and age/sex-matched healthy controls (HCs) were enrolled to collect their fecal and blood samples. Shotgun metagenomic sequencing and untargeted metabolomic analyses were conducted on these samples.<br><br>RESULTS: Significant reductions in alpha diversity and microbial richness were observed in the gut microbiota of KDs at both species and genus levels. Pathogenic species including Enterococcus avium, Streptococcus peroris and Clostridioides difficile were significantly abundant in the KDs group, while beneficial species containing Faecalibacterium prausnitzii, Anaerostipes hadrus, Akkermansia muciniphila, Eubacterium hallii, Agathobaculum butyriciproducens, Ruminococcus bicirculans, and Roseburia intestinalis were markedly decreased. A total of 49 metabolic pathways were differentially enriched between the two groups, with 22 pathways including nucleotide, carbohydrate, energy, and amino acid metabolism being abundant in KDs, while the other 27 pathways were enriched in HCs. For metabolites, both fecal and blood metabolomes exhibited significant alterations. Notably, fecal metabolites including indole, L-tryptophan, L-lactic acid, 5-HETE, indol-3-acetamid, tetraethylammonium and dopaquinone were elevated in KDs, whereas butyrate, methylxanthine, phosphocholine, methylhistidine, ADP-ribose, vitamin A acid, and chenodeoxycholic acid were reduced. In plasma, cholesterol, phosphocholine, porphobilinogen, pantothenate, cortisol, bile acids and related compounds were enriched in KDs, while amino acids, indole and tryptamine derivatives, nucleotides, nucleic acids, and sugar metabolites were more abundant in HCs.<br><br>CONCLUSIONS: This study represents the first systematic multi-omics investigation of KD in a pediatric population from Northwest China. It establishes a foundational resource characterizing the gut microbiome and metabolome in KD, offering novel biological insights, suggesting potential therapeutic targets, and supporting further mechanistic and clinical research.}, }
@article {pmid42199698, year = {2026}, author = {Li, Q and Wang, X and Zhang, S and Wang, H and Li, X and Zhao, F}, title = {mNGS-Supported Interpretation of Staphylococcus pettenkoferi Bloodstream Infection After Intracerebral Hemorrhage: A Case Report.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {611927}, pmid = {42199698}, issn = {1178-6973}, abstract = {PURPOSE: Staphylococcus pettenkoferi is an uncommon coagulase-negative staphylococcus whose recovery from blood may be difficult to interpret because of the frequent contamination associated with this bacterial group. We report a case in which peripheral-blood metagenomic next-generation sequencing (mNGS) and repeated blood cultures supported clinically significant bloodstream infection after intracerebral hemorrhage.<br><br>PATIENTS AND METHODS: We described the clinical course, imaging findings, microbiological results, and antimicrobial management of an 85-year-old man admitted to the intensive care unit after intracerebral hemorrhage with intraventricular extension. Peripheral-blood mNGS and two sets of peripheral blood cultures were obtained during early fever evaluation.<br><br>RESULTS: Peripheral-blood mNGS, performed on samples obtained immediately after ICU admission and before neurosurgical intervention or intracranial device placement, detected S. pettenkoferi within 24&#xa0;h. At 72&#xa0;h, both peripheral blood culture sets yielded the same organism. Concordant results from mNGS and repeated peripheral blood cultures, together with the clinical context, supported clinically significant bloodstream infection rather than simple contamination. The respiratory tract was considered a presumed source in the setting of clinically suspected aspiration-related pulmonary infection, although it was not microbiologically confirmed.<br><br>CONCLUSION: This case highlights the need for cautious interpretation of uncommon coagulase-negative staphylococci recovered from blood. Peripheral-blood mNGS may provide early etiologic support, but conventional blood culture remains essential for confirmation and antimicrobial susceptibility testing.}, }
@article {pmid42200417, year = {2026}, author = {Lin, L and Gao, G and Sun, S and Wu, X and Fan, S and Wang, H and Zhou, F and Zhang, X}, title = {Host-independent metagenomics reveal gut bacteria contribution to Delia antiqua growth by vitamin B6 provision.}, journal = {Insect molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1111/imb.70046}, pmid = {42200417}, issn = {1365-2583}, support = {2024KJI002//Young Innovation Team Project of Higher Education in Shandong Province/ ; 2024ZDZX10//QLU Major Innovation Projects of Education-Industry Integration Pilot/ ; SDAIT-31-04//Shandong Province Key Agricultural Project for Application Technology Innovation/ ; 32272530//National Natural Science Foundation of China/ ; }, abstract = {Insect guts host a diverse and abundant array of microorganisms. These microbes improve host fitness by extensively involving in a range of crucial physiological processes, which have mainly been revealed by high-throughput sequencing, particularly metagenomics. However, it is almost impossible to make an accurate and complete distinction between the genetic functions of microbial symbionts and insect hosts without host genome data. By comparing metagenomic data from gut germ-free and nonaxenic larvae, we accurately identified the data belonging to the gut microbiome of the onion maggot Delia antiqua (Diptera: Anthomyiidae). Besides, a correlation between bacteria of the genus Wohlfahrtiimonas (Gammaproteobacteria: Pseudomonadaceae) and vitamin B6 metabolism was detected through collinearity analysis. Furthermore, in vitro tests confirmed that the gut bacterium Wohlfahrtiimonas larvae contributed to the growth of D. antiqua larvae via the independent synthesis of vitamin B6. This study provides a comprehensive view of the gut bacterial diversity in D. antiqua and reveals a functional profile that is strictly specific to the gut microbiota of this species. It has preliminarily revealed the functional differentiation between insect hosts and their symbiotic microorganisms. This study also offers a technical reference for the study of microbial symbiotic functions in other insect-microbe symbioses without host genomic data.}, }
@article {pmid42200512, year = {2026}, author = {Vergara, E and Khaleque, HN and Neira, G and Watkin, ELJ and Valdés, JH and Holmes, DS}, title = {Sulphur metabolism as a key factor in the evolution of environmental adaptation of Acidihalobacter.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, doi = {10.1099/mgen.0.001732}, pmid = {42200512}, issn = {2057-5858}, mesh = {Phylogeny ; *Sulfur/metabolism ; *Adaptation, Physiological/genetics ; *Rhodobacteraceae/genetics/metabolism/classification ; Genome, Bacterial ; Evolution, Molecular ; Hydrothermal Vents/microbiology ; Australia ; Oxidation-Reduction ; Italy ; Metagenome ; Pacific Ocean ; Bacterial Proteins/genetics/metabolism ; }, abstract = {This study compares predicted sulphur metabolism genes across four Acidihalobacter type strains and two metagenome-assembled genomes (MAGs), revealing genomic differences that appear to correspond to ecological specialization. Phylogenomic analysis separates the species into two clades: clade I includes Acidihalobacter ferrooxydans from a geothermal region in Italy and the two MAGs derived from deep-sea hydrothermal vents in the Pacific Ocean, while clade II comprises Acidihalobacter aeolianus and Acidihalobacter prosperus from a geothermal region in Italy and Acidihalobacter yilgarnensis from a saline and acidic drainage in Australia. Variations in sulphide/quinone oxidoreductases (SQRs) across the species, in particular in Ah. ferrooxydans and Ah. yilgarnensis, likely relate to the availability and speciation of sulphur substrates, which are strictly governed by local redox potential (Eh) and metal redox cycling in their respective habitats. Notably, only Ah. ferrooxydans (clade I) lacks the canonical sulphur/thiosulphate oxidation (Sox) system for thiosulphate oxidation found in clade II and instead encodes components of an alternative S4I pathway. We hypothesize that this difference reflects an adaptation to dynamic microniches going from highly reduced (sulphide-rich) to oxidized metastable sulphur intermediates. In contrast, the retention of the Sox system in clade II suggests a distinct strategy permitting greater metabolic versatility under fluctuating Eh-pH conditions.Differences in clade I terminal oxidases (cbb3-type cytochrome, bc1 complex) and regulatory elements appear to support further adaptation to environments with elevated H2S, setting this clade apart from clade II members. These adaptations, mainly evidenced by gene redundancy, gene loss and horizontal gene transfer, seem to reflect a unique ecological microniche and evolutionary trajectory for Ah. ferrooxydans distinct from other members of the genus, particularly from a sulphur-based energy metabolism perspective.}, }
@article {pmid42200521, year = {2026}, author = {Wright, RJ and Fisher, BR and Comeau, AM and Langille, MGI}, title = {From classification to confirmation: verifying taxonomic classifications by mapping metagenomic reads to reference genomes.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, doi = {10.1099/mgen.0.001739}, pmid = {42200521}, issn = {2057-5858}, mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *Bacteria/classification/genetics ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Microbiota/genetics ; }, abstract = {Obtaining high precision while maintaining high recall is an ongoing problem for metagenomic taxonomic classification in microbial ecology research. Parameter adjustments can achieve this in simulated samples, but in real samples - especially from environments like marine and soil - the proportion of classified reads drops sharply with precision increases. We, therefore, suggest verification of metagenomic taxonomic classifications obtained from a tool like Kraken by mapping their assigned reads to reference genomes to assess genomic coverage. In simulations, filtering the identified species to only those with ≥0.5% reference genome coverage removed 99.7% of false-positive taxa. Applying this method to samples from real datasets requires a more nuanced approach that considers sequencing depth, whether the samples are high- or low-microbial biomass, and database completeness with respect to the sampled environment. Nevertheless, we show that clinically relevant Kraken-identified taxa, such as Helicobacter pylori identified in human stool samples, lack any reads mapping to their reference genome and are likely false positives driven by contaminating phage sequences within reference genomes. Similarly, in human blood and lung tumour datasets, only 18 and 11 species, respectively, have ≥1% reference genome coverage and likely represent sample collection or sequencing contaminants. Marine and soil samples pose additional challenges due to lower representation in reference databases, leading to low nucleotide identity between sequenced reads and reference genomes and similarity only at higher taxonomic ranks. We recommend genome coverage checking to researchers in all fields of microbial ecology and provide an open-source pipeline on GitHub (GeCoCheck): https://github.com/R-Wright-1/GeCoCheck.}, }
@article {pmid42200658, year = {2026}, author = {Blanchard, JL}, title = {Learning R with generative AI in a metagenomic data science course.}, journal = {Journal of microbiology &amp; biology education}, volume = {}, number = {}, pages = {e0034325}, doi = {10.1128/jmbe.00343-25}, pmid = {42200658}, issn = {1935-7877}, abstract = {Generative artificial intelligence (AI) tools are increasingly used by students in introductory coding courses; however, evidence-based guidance for integrating these tools into biology education remains limited. We examined student experiences with generative AI in a beginner R programming course focused on metagenomic data analysis. An anonymous survey (n = 43) captured quantitative ratings and qualitative reflections on how AI influenced learning, productivity, and problem-solving practices. Most respondents entered the course with little to no prior coding experience (79%) and reported frequent AI use throughout the semester, indicating that AI quickly became embedded in students' workflows. Students rated AI as highly helpful for suggesting R code, explaining syntax and logic, and brainstorming analyses, with over 70% endorsing each use case. However, AI errors were common: over 90% of students encountered incorrect output at least sometimes, including domain-specific misinterpretations and overcomplicated or syntactically incorrect code. Notably, students identified a need for clearer instructional support in core AI-mediated practices. The most frequent recommendation for course redesign was to introduce foundational R concepts prior to AI use, highlighting a threshold-competency principle for effective AI integration. Together, these findings suggest that generative AI can support novice coders but does not substitute for foundational instruction. Effective AI integration requires deliberate pedagogical scaffolding and reflection rather than code generation alone. These principles are likely to remain critical as AI tools become more capable and more widely adopted in undergraduate biology education.}, }
@article {pmid42200756, year = {2026}, author = {Harrison, LB and Sohani, ZN and Lasry, D and Cheng, MP and Lee, TC and Babiker, A and Kadri, SS and Lawandi, A}, title = {Rapid Microbiological Diagnostics for Sepsis: Narrative Review of Current and Prospective Approaches.}, journal = {Critical care explorations}, volume = {8}, number = {6}, pages = {e1415}, doi = {10.1097/CCE.0000000000001415}, pmid = {42200756}, issn = {2639-8028}, mesh = {Humans ; *Sepsis/diagnosis/microbiology ; Blood Culture/methods ; Molecular Diagnostic Techniques/methods ; *Microbiological Techniques/methods ; Rapid Diagnostic Tests ; }, abstract = {OBJECTIVES: In this review, we aim to provide critical care clinicians with a concise introduction to the current and prospective tools that exist for rapid diagnostics in sepsis employed in the microbiology laboratory. Our objective is to provide a primer for clinicians to engage with their colleagues in the microbiology laboratory for the selection and implementation of new and emerging tools.<br><br>DATA SOURCES: The primary literature, restricted to peer-reviewed sources, was queried using relevant search terms (e.g., sepsis, rapid diagnostics, microbiology, etc) using PubMed and Google Scholar (until February 2025), as well as review of citations of relevant articles.<br><br>STUDY SELECTION: After initial searches, literature was screened by each author responsible for the sections of this review: blood culture-based methods (L.B.H.), nonblood culture-based molecular diagnostics (D.L.), and antigen-based methods (Z.N.S.). Titles and abstracts of individual articles were reviewed by the respective section authors and articles describing microbiological diagnostic techniques that decrease the turnaround time for the identification of microorganisms and/or antimicrobial susceptibility testing with relevance to the diagnosis of sepsis were retained.<br><br>DATA EXTRACTION: Data from individual studies was extracted by each respective section author using Zotero reference management software and synthesized narratively.<br><br>DATA SYNTHESIS: Rapid diagnostics for sepsis can be broadly divided into three categories: those applied to incubated positive blood culture specimens, and culture-independent approaches applied directly to clinical specimens, which can be further divided into those based on the direct detection of the nucleic acids of microorganisms, and those based on the detection of antigens. Blood culture-based approaches rely on biological amplification of microorganisms present but aim to measure this amplified signal directly to speed identification of microorganisms or antimicrobial resistance relative to traditional plate-culture-based workflows. Nucleic acid and antigen detection methods can be performed directly on clinical specimens, and so promise more rapid diagnostics in sepsis, but with method-specific tradeoffs in sensitivity, specificity, and interpretation.<br><br>CONCLUSIONS: Evolutionary refinements of blood culture-based diagnostic approaches have decreased time to actionable information significantly while emerging and established culture-independent approaches can reduce time to actionable information to a few hours. In aggregate these interventions may have important clinical benefits, yet significant heterogeneity exists in the applicability and availability of technologies.}, }
@article {pmid42201023, year = {2026}, author = {Rehman, A and Awais, M and Baloch, HNUA and Leghari, MO and Ahmad, A and Javed, H}, title = {Sputum Liquid Biopsy for Lung Cancer Screening, Diagnosis, Subtyping, Surveillance, Response Prediction, and Prognostication: A Scoping Review.}, journal = {Medical sciences (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/medsci14020231}, pmid = {42201023}, issn = {2076-3271}, mesh = {Humans ; *Lung Neoplasms/diagnosis/pathology/metabolism ; *Sputum/metabolism ; Liquid Biopsy/methods ; Biomarkers, Tumor ; Prognosis ; *Early Detection of Cancer/methods ; }, abstract = {Background/Objectives: Liquid biopsy (LB) is transforming cancer care by enabling minimally invasive tumor profiling. While current research and clinical pathways mostly focus on blood LB, sputum represents a non-invasive, readily available respiratory specimen that may offer unique advantages for lung cancer (LC) care. Despite its potential, the maturity, breadth, and clinical applicability of sputum-based LB remain elusive. Methods: We conducted a scoping review to systematically map the existing literature on sputum LB in LC. Electronic databases were searched for studies evaluating sputum-derived biomarkers-cytologic, genomic, epigenetic, transcriptomic, proteomic, metabolomic, metagenomic, and extracellular vesicle-derived products-across the LC care continuum. Study designs, technologies, clinical contexts, and reported outcomes were extracted and synthesized qualitatively. Results: The literature demonstrated substantial heterogeneity in sputum collection, processing, and analytical platforms. Early work focused on cytometry and genetic alterations, while recent studies increasingly explore DNA methylomics, microRNAs, extracellular vesicle-derived products, and multi-omics approaches. The evidence suggests potential utility of sputum biomarkers for early detection and risk stratification, particularly in high-risk populations, with emerging data supporting roles in molecular subtyping, response monitoring, prognostication, and surveillance. However, few studies report prospective validation, direct comparison with blood-based LB, or impact on actual patient outcomes. Conclusions: Sputum LB is a promising yet underdeveloped modality in LC care. This scoping review highlights technological innovations alongside significant methodological heterogeneity and translational gaps. Future research should focus on standardization, prospective validation, impact on patient outcomes, and integration with blood- and other body fluid-based LB, as well as imaging biomarkers. This will enable incorporation of sputum-based LB into actual clinical pathways of LC care.}, }
@article {pmid42201143, year = {2026}, author = {Zhang, W and Eleftherianos, I and Mohamed, A and Smagghe, G and Chakkalakkal, G and Al-Akeel, R and Toprak, U and Tettamanti, G and Keyhani, N and Renault, D}, title = {Evolution, multifunctionality, and agricultural potential of insect microbiomes and the holobiont concept.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag137}, pmid = {42201143}, issn = {1751-7370}, abstract = {Insect-associated microbiomes, as co-evolved members of the holobiont, play pivotal roles in host physiology, ecological resilience, and evolutionary innovation. This review synthesizes recent advances in understanding microbial symbionts' contributions to metabolic adaptation, insecticide detoxification, and immune modulation. Framed within hologenome theory-which posits host-microbe assemblages as units of natural selection-we explore co-evolutionary dynamics driving mutualistic specialization and adaptive plasticity. Cutting-edge tools like genome editing and metagenomics reveal how gut microbiota mediate cross-kingdom interactions, insecticide resistance, and reproductive fitness. Intriguingly, microbial symbionts can enhance host resistance through detoxification while sensitizing hosts to specific toxins, highlighting context-dependent trade-offs. Targeted manipulation of microbial consortia-via detoxification disruption or symbiont engineering-offers new avenues for sustainable pest control, though ecological risks demand rigorous biosafety protocols. A paradigm shift toward holobiont-centered models promises unified strategies for sustainable agriculture and biodiversity conservation in the Anthropocene.}, }
@article {pmid42201824, year = {2026}, author = {Lin, X and Asif, M and Li, W and Zhang, B and Li, Y and Yu, Y and Jiang, X}, title = {Long-Term Straw Return Reverses Antibiotic Resistance Accumulation in Maize Rhizosphere through Integrated Soil-Microbial Mechanisms.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c11371}, pmid = {42201824}, issn = {1520-5851}, abstract = {The impact of long-term agricultural cultivation on antibiotic resistance has emerged as a critical environmental concern. However, previous studies have primarily examined organic fertilizers, and the effects of sustained chemical fertilizer use combined with straw incorporation over extended periods remain poorly understood. Here, we employed a 25-year field trial combined with metagenomic analysis to investigate the differential effects of chemical fertilization and straw incorporation on soil antibiotic resistance gene (ARG) dynamics in the maize rhizosphere. Results showed that long-term cultivation progressively increased ARG and virulence factor gene (VFG) abundance. Metagenomic analyses suggested that shifts in Pseudomonas populations and microbial metabolic pathways were associated with elevated levels of ARGs in the rhizosphere. Field inoculation with a synthetic Pseudomonas community further increased the ARG abundance, accompanied by reduced genomic GC content and enrichment of specific metabolic pathways. In contrast, straw amendment treatments reduced Pseudomonas abundance and soil acidification while increasing the soil total carbon and lignin degradation functional capacity. Our findings indicate that long-term straw incorporation represents a promising strategy for controlling antibiotic resistance dissemination in agricultural systems, offering valuable insights into sustainable crop management practices.}, }
@article {pmid42184159, year = {2026}, author = {Pavlovska, M and Prekrasna-Kviatkovska, Y and Zotov, A and Dzhulai, A and Dykyi, E and Huettel, B and Fuchs, BM and Amann, RI and Teeling, H and Sidhu, C}, title = {Phytoplankton dynamics shape bacterioplankton community structure and metabolism during the austral summer-autumn transition in the Western Antarctic Peninsula.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag053}, pmid = {42184159}, issn = {1574-6941}, abstract = {Seasonal changes in Antarctic coastal waters trigger pronounced shifts in microbial community composition and function, yet sparse spatial and temporal coverage currently limits our understanding of phytoplankton-bacterioplankton coupling. This study combines metagenomic and metatranscriptomic analyses of marine bacterioplankton with environmental data to address the functional dynamics of planktonic communities off the Western Antarctic Peninsula during the austral summer-autumn transition. Diatoms dominated the phytoplankton community, with generally low biomass and abundance, yet a species-specific succession was observed. The bacterioplankton community structure shifted from dominance of copiotrophic taxa (e.g. Polaribacter) towards oligotrophic lineages (e.g. SAR11) adapted to low-nutrient conditions, accompanied by a decrease in microbial carbohydrate-degradation activity. The capacity to degrade algal-derived polysaccharides varied between community members, with ß-glucan, α-glucan, chitin, and host glycan utilization present in all, and fucose, β-galactan and trehalose degradation restricted to specific taxa. DMSP metabolism also showed taxonomic specificity and was shaped by both physical (ice melt and fluctuations in solar irradiation) and biological factors (phytoplankton succession). Together, these findings reveal a complex, taxon-specific coupling between bacterioplankton and phytoplankton communities in the Western Antarctic Peninsula, linking community structure to likely functional gene expression and highlight how Antarctic bacterioplankton drives carbon and sulfur turnover in a polar marine ecosystem.}, }
@article {pmid42184529, year = {2026}, author = {Wang, R and Chen, H}, title = {Metagenomic insights into vertical migration of soil antibiotic and metal(loid) resistance genes under long-term organic fertilizer application and irrigation.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142479}, doi = {10.1016/j.jhazmat.2026.142479}, pmid = {42184529}, issn = {1873-3336}, abstract = {Agricultural irrigation is associated with antibiotic resistance gene (ARG) transmission and resistome succession through the integration of exogenous and indigenous soil communities. However, the long-term field-scale impacts of organic irrigation on vertical resistome migration and its ecological consequences remain underexplored. This study employed metagenomic analyses and field surveys to bridge these knowledge gaps. The results showed that ARGs and metal(loid) resistance genes (MRGs) were most abundant and diverse at 0-20 cm depth, with distinct characteristics in deeper layers depending on manure type. Cattle manure-irrigated soils exhibited a greater potential for vertical ARG diffusion than chicken manure-irrigated soils, despite lower surface-level enrichment. ARG distribution was more strongly associated with groundwater and soil background factors than with organic fertilizer inputs. Mobile genetic elements (MGEs) and heavy metal concentrations were key factors associated with resistome succession. Compared to the control, contigs associated with both ARGs and MRGs increased 5.8-fold and 3.1-fold in chicken and cattle manure-irrigated soils, respectively, suggesting a potentially important role for prophages. While control contigs were distributed in deeper layers, irrigated soils showed pronounced surface enrichment. Irrigation was linked to increased network density and complexity, with chicken manure-irrigated soils exhibiting higher levels of antibiotic-resistant bacteria (ARB). Notably, opportunistic pathogens carrying ARGs, including Ralstonia pickettii and Stenotrophomonas maltophilia, were enriched in irrigated profiles. Microbiome, MGEs, and abiotic factors were collectively associated with resistome succession, with deterministic processes contributing substantially to community assembly. This study provides new insights into the vertical distribution and inferred succession of the resistome in organically irrigated soils.}, }
@article {pmid42184535, year = {2026}, author = {Ma, B and Li, F and Zhang, C and Deng, Y and Sekar, R and Chen, Z and Wang, M and Zamyadi, A and He, S and Huang, T and Guo, J and Zhang, H}, title = {Multivalent manganese-mediated synergistic aerobic denitrification boost nitrogen removal in oligotrophic aquatic systems: Insight into microbial functional and metabolic complementarity.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142496}, doi = {10.1016/j.jhazmat.2026.142496}, pmid = {42184535}, issn = {1873-3336}, abstract = {Efficient nitrogen removal from oligotrophic lakes and reservoirs necessitates the development of innovative, eco-friendly strategies to mitigate the limitation of organic electron donors. We engineered four multivalent manganese (Mn) composite-functionalized bioreactors for oligotrophic water remediation, which demonstrated a sustained total nitrogen removal efficiency exceeding 97.66% over five operational cycles. Manganese powder-doped activated carbon achieved the highest nitrate removal rate, ranging from 0.29956 to 0.39831 mg/L/d. Immobilization with sodium alginate has mitigated manganese oxidative corrosion, thereby resulting in more sustained long-term reactive performance. Furthermore, denitrifying bacteria synergistically promote the enrichment of phosphorus-accumulating microorganisms and manganese-oxidizing bacteria (Burkholderiaceae, Methylophilaceae, and Azospirillaceae), which play pivotal roles in denitrification and manganese cycling, within Mn addition (MNA) reactors. Correlation analyses revealed stronger co-occurrence patterns between denitrification genes and manganese-oxidizing genes in the MNA reactors compared to the control. The abundance of ATP-binding cassette transporter genes, particularly encoding lipopolysaccharide transport (wzt) and lipoprotein release (lolD), increased by 1.37-1.90-fold and 1.31-1.80-fold, respectively, in the MNA reactors relative to the control reactor. Furthermore, the metabolic complementarity network suggested that MNA not only promoted community metabolic competition and complementarity effects but also enhanced higher energy production and respiratory activity. These findings establish a manganese-driven microbial enhancement strategy for sustainable nitrogen removal from polluted surface waters, offering new opportunities for eco-engineered water treatment.}, }
@article {pmid42184563, year = {2026}, author = {Hull, R}, title = {RNA viruses are an integral part in evolution of all organisms.}, journal = {Virology}, volume = {621}, number = {}, pages = {110950}, doi = {10.1016/j.virol.2026.110950}, pmid = {42184563}, issn = {1096-0341}, abstract = {RNA viruses are intracellular symbiotic obligate parasites, needing host factors and energy for their replication with forms of symbiosis ranging from antagonism (pathogenic, not contributing to host metabolism) to mutualism (contributing benefits to the host as well as making demands on host metabolism). As a group, they have several unusual features: a) metagenomic studies suggest that they are probably are the most common group of viruses infecting all organism species and are the most abundant biological entity on earth; b) they have existed ever since the Last Universal Common Ancestor from which all living organisms have evolved; c) a high proportion of their species have + strand RNA genomes, or are retroviruses, that replicate without proof-reading creating many variants (quasispecies); d) they replicate in organelles within the endoplasmic reticulum and other membranes which connect to other organelles and to membrane and metabolic network systems. This paper brings together these facts presenting the hypothesis that RNA viruses and retroviruses form host/mutualistic virus symbionts as an evolutionary unit with the viral responses to evolutionary stresses being rapid and linking closely with the slower host genomic responses. The hypothesis is presented with a background of evolution of organisms and viruses, drivers of evolution, and the evolutionary natural selection pathway from the sources of stresses to impact and molecular reactions to stresses entering the basic organism body, the cell.}, }
@article {pmid42184767, year = {2026}, author = {Chen, D and Ibrar, M and Yan, F and Sun, G and Xue, R and Jia, A and Zhou, J and Gao, Y and Ma, C and Wang, M and Zhang, J and Ma, Z and Liu, L}, title = {The rising power of females: Dioecious shrub enhances soil organic carbon sequestration via fungal necromass in chronosequence of desertified alpine grassland restoration.}, journal = {Journal of environmental management}, volume = {409}, number = {}, pages = {130022}, doi = {10.1016/j.jenvman.2026.130022}, pmid = {42184767}, issn = {1095-8630}, abstract = {Desertification-induced soil organic carbon (SOC) loss poses a major environmental threat to the alpine grasslands of the Qinghai-Tibet Plateau, jeopardizing ecological security and sustainability. While pioneer shrub introduction has yielded positive ecological outcomes, the mechanisms of SOC recovery remain poorly understood. We investigated the effects of a widely used dioecious shrub on rhizosphere SOC dynamics across a 20-year restoration chronosequence, employing a comprehensive framework that combined root exudation measurements, soil physicochemical analysis, metagenomics, and biomarker profiling to decipher the mechanism. Our results reveal that microbial-derived carbon dominated rhizosphere SOC accrual, contributing 20.1-22.0% to the total SOC pool, over 50 times more than plant-derived carbon (0.1-0.4%). The microbial pool was predominantly fungal necromass (>93%), correlated with declining root exudation and suppressed carbon-degrading gene abundance during restoration. In the 20th year after recovery, a striking divergence in the effects of male and female shrubs on rhizosphere SOC became apparent, with female shrubs sustaining 15% more microbial necromass and 47% more lignin phenols than males. Our findings highlight that SOC restoration in the rhizosphere of pioneer shrubs is predominantly driven by a fungal-mediated microbial carbon pump. Moreover, the preferential use of female shrubs offers a dual benefit: enhancing long-term rhizosphere SOC sequestration and controlling shrubs encroachment. This sex-informed strategy therefore provides a scalable framework for degraded alpine grasslands and serves as a transferable model for other drylands undergoing warming-wetting transitions, where alleviated water limitation increasingly enables vegetation-microbe-mediated carbon stabilization.}, }
@article {pmid42184943, year = {2026}, author = {Cai, Q and He, J and Qiu, W and Wang, Y and Fang, K and Zou, X and Aili, A and Zhong, Y and Zhang, J}, title = {In situ assembly of the humic acid-protein conductive network facilitates chain elongation for medium-chain fatty acids anaerobic production from waste activated sludge.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134964}, doi = {10.1016/j.biortech.2026.134964}, pmid = {42184943}, issn = {1873-2976}, abstract = {Biosynthesis of medium-chain fatty acids (MCFAs) from waste activated sludge (WAS) is primarily limited by intracellular reductive stress (NADH accumulation) and energy shortages. This work demonstrates that humic acid (HA), functioning as a redox mediator, effectively enhances the carbon chain elongation (CE) process. Optimal HA supplementation (1000 mg/L) increased the peak MCFAs yield by 98.3%, driving a fundamental shift in the dominant product spectrum from short-chain fatty acids (SCFAs) to MCFAs. Combined metagenomic and electrochemical analyses reveal that this enhancement originates from HA-mediated spatial and metabolic integration across multiple scales. Macroscopically, HA complexes with proteins to construct a conductive biopolymer network. Functioning as a highly efficient extracellular electron sink, this network significantly accelerates transmembrane electron discharge to consume excess intracellular electrons. This rapid electron extrusion alleviates reductive stress and relieves product feedback inhibition on dehydrogenases, concurrently inducing an elevated cellular energy charge (ATP surge). Subsequently, feedback regulation driven by this high-energy state suppresses the competitive acetogenic branch (Pta-ackA pathway), effectively preventing carbon loss. Dominated by the highly enriched CE taxon Candidatus_Microthrix, the microbial consortium exhibits a robust metabolic potential to channel carbon into synergistic RBO and FAB pathways. This metabolic shift, fueled by abundant precursors and energy, effectively circumvents acidic toxicity by rapidly consuming SCFAs. These findings elucidate the critical role of HA in reshaping microbial redox homeostasis, providing a robust mechanistic foundation for high-value carbon recovery engineering from complex solid wastes.}, }
@article {pmid42185267, year = {2026}, author = {Zhou, YL and Feng, JC and Lu, R and Chen, Z and Mara, P and Tao, X and Liu, J and Huang, Y and Hu, J and Yao, J and Edgcomb, VP and Teske, A and Wang, X and Zhang, S}, title = {Diversification in ANME-1 archaea is associated with the presence of highly variable genomic hotspots.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73573-4}, pmid = {42185267}, issn = {2041-1723}, support = {42494884//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42325603//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Anaerobic methanotrophic (ANME) archaea have been primarily documented by metagenomic analysis of environmental samples. The mechanisms that drive their diversification and speciation are poorly understood. Here we analyse the phylogenomic diversity at the species and strain levels of clade ANME-1 from deep-sea cold seeps, as a model system with a well-studied phylogenetic framework. We reconstruct high-quality circular metagenomic-assembled genomes (cMAGs) and identify highly variable genomic hotspots that distinguish them. Genomic differentiation and diversification in ANME-1 is associated with genes involved in prokaryotic defense systems, transport mechanisms and methane metabolism. In addition, heterologous expression of ANME-1 hicAB operons supports their proposed role as toxin/antitoxin systems, possibly involved in mediating responses to environmental stresses.}, }
@article {pmid42185302, year = {2026}, author = {Nishisaka, CS and Quevedo, HD and Pellegrinetti, TA and de Almeida Godoy, F and Rossmann, M and Mendes, LW and Mendes, R}, title = {Bacterial inoculation drives microbiome-mediated resistance to a soil-borne pathogen in wheat.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01021-8}, pmid = {42185302}, issn = {2055-5008}, support = {2020/06077-9//S&#xe3;o Paulo Research Foundation (Fapesp)/ ; 2025/11610-1//S&#xe3;o Paulo Research Foundation (Fapesp)/ ; 402654/2023-4//National Council for Scientific and Technological Development (CNPq)/ ; }, abstract = {Soil microbiomes are fundamental to plant health, mediating nutrient cycling, stress tolerance, and pathogen defense. However, soil-borne pathogens such as Bipolaris sorokiniana severely constrain wheat productivity. Despite growing interest, the mechanisms by which beneficial bacterial inoculation reshapes rhizosphere microbial communities to enhance disease resistance remain poorly understood. Here, we isolated three bacterial strains, Streptomyces virginiae CMAA1738, Paenibacillus ottowii CMAA1739, and Pseudomonas inefficax CMAA1741, with antagonistic activity against B. sorokiniana, and evaluated their effects on wheat under controlled conditions. Through plant bioassays, bacterial inoculation reduced disease severity by ~60% and promoted root growth. Metataxonomic and metagenomic analyses revealed shifts in the structure and functional potential of the rhizosphere microbiome. Structural equation modeling indicated that inoculation was the primary driver of microbiome restructuring and disease suppression. Notably, inoculation restored the diversity of plant growth-promoting genes and biosynthetic gene clusters reduced by pathogen infection, enriching functions associated with stress tolerance, nutrient metabolism, and secondary metabolite production. In addition, Random Forest analysis revealed that variation in disease severity under pathogen pressure was associated with differences in bacterial community composition. Together, these findings demonstrate that bacterial inoculation can restructure the rhizosphere microbiome and restore key functional traits linked to plant resilience.}, }
@article {pmid42185318, year = {2026}, author = {Nguyen, UT and Salamzade, R and Sandstrom, S and Swaney, MH and Townsend, EC and Wu, SY and Cheong, JZA and Sardina, JA and Ludwikoski, I and Rybolt, M and Wan, H and Carlson, CM and Ferro, J and McArthur, O and Suh, WS and Zarnowski, R and Andes, DR and Currie, CR and Kalan, LR}, title = {Large-scale investigation for antimicrobial activity reveals newly-identified defensive species across the healthy skin microbiome.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73524-z}, pmid = {42185318}, issn = {2041-1723}, support = {U19AI142720//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R35GM137828//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, abstract = {The skin microbiome forms a protective barrier to pathogens, including through the production of antimicrobial metabolites. Here, we present EPIC[HHS], a large and taxonomically diverse skin microbiome culture collection of 968 strains from eight body sites. EPIC[HHS] captures >95% of cumulative species-level abundance across 268 skin metagenomes. It includes isolates present at <0.1% relative abundance and the cultured representatives for eight species not previously isolated, markedly expanding current skin microbiome resources. A contact-independent screen assaying ~14,000 pairwise interactions against 22 pathogens revealed widespread antagonism with striking enrichment for antifungal activity. Finally, functional genomic analysis, including 287 EPIC[HHS] isolate genomes, demonstrated a diverse landscape of skin-associated biosynthetic gene clusters that are mostly uncharacterized. Together EPIC[HHS], its functional and genomic characterization, establishes the skin microbiome as a reservoir for specialized metabolism and provides a platform for microbiome-based antimicrobial discovery.}, }
@article {pmid42185326, year = {2026}, author = {Hoggard, M and Gios, E and Tee, HS and Geoghegan, JL and Handley, KM}, title = {DNA viruses are constrained to ecological niches and share similar environmental adaptations with hosts.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73439-9}, pmid = {42185326}, issn = {2041-1723}, abstract = {Viruses are ubiquitous albeit individually constrained by host-range. Less well understood are environmental limitations on virus proliferation. To investigate estuarine viral diversity, niche constraints, and traits of environmental adaptation, we analyse metagenomic and metatranscriptomic data from an estuarine salinity gradient, including water and sediment. We then expand our analysis to globally-distributed viral genomes. Viral distributions vary by estuary habitat, reflecting prokaryote community patterns, and highlighting that virus-host interactions are strongly influenced by environment. Viral lineages, up until approximately the rank of genus, are largely partitioned by ecological niche based on factors such as salinity and the aquatic-terrestrial divide. Across habitat boundaries, viruses feature osmoadaptive traits similar to their prokaryote hosts. These include slightly elevated ratios of acidic to basic amino acids and decreased protein isoelectric points at higher salinities, particularly in virus major tail and capsid proteins, which are not solely explained by reliance on host machinery. Further studies are needed to determine the primary driver of these modifications in viruses (e.g. environment or host) and whether these traits restrict virus distributions beyond host-range limitation. Overall, our findings indicate that successful proliferations of viruses into distinct biomes (e.g. freshwater, saline, terrestrial) are rare, with viruses constrained to specific ecological niches.}, }
@article {pmid42185942, year = {2026}, author = {Wang, Y and Peng, Y and Wang, B and Di, M and Xi, M and Yao, Z and Shi, C and Feng, Q and Yin, D and Li, J and Xu, X and Zhang, R and Peng, X}, title = {A preliminary metagenomic and metabolomic investigation into the effects of Aspergillus niger cultures on microbial homeostasis and antibiotic resistance gene profiles in the rumen of fattening sheep.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42185942}, issn = {1674-9782}, abstract = {BACKGROUND: Under high-concentrate feeding conditions, ruminants often experience rumen microecological imbalance and dysfunction, which can impair growth performance and increase the risk of antibiotic resistance gene (ARG) dissemination.<br><br>RESULTS: To evaluate the ameliorative effects of Aspergillus niger (A. niger) cultures, fattening sheep were randomly allocated into the following five groups: a control group (CON), a control diet supplemented with 250, 500, or 1,000 mg/kg A. niger cultures (designated as LA, MA, and HA, respectively); and an antibiotic group supplemented with 5,000 mg/kg chlortetracycline premix (AN). Microbial community analysis indicated that several bacterial taxa, including Succinivibrio sp900317105, Prevotella sp002353485, Quinella sp017515635, Quinella sp015206805, and Prevotella sp900320255, were significantly enriched in the A. niger culture-supplemented groups (P&#x2009;<&#x2009;0.05). ARG profiling showed that the abundance of tetracycline resistance genes was significantly lower in all A. niger groups compared with the CON and AN groups (P&#x2009;<&#x2009;0.05), while &#x3b2;-lactam resistance genes were significantly reduced in the HA group (P&#x2009;<&#x2009;0.05). Furthermore, the abundances of Rank I and Rank II ARGs were significantly higher in the AN group than in the other groups, whereas the abundances of Rank II and Rank IV ARGs were significantly lower in the A. niger culture groups than in the CON and AN groups. Metabolomic analysis further demonstrated that supplementation with A. niger cultures significantly decreased the concentration of N-decanoyl-L-homoserine lactone (P&#x2009;<&#x2009;0.05) while increasing the levels of N-3-oxotetradec-7Z-enoyl-L-homoserine lactone, indole-3-methyl acetate, and indole-3-propionic acid (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: These findings suggest that A. niger cultures can reduce the abundance of ARGs and mitigate the risk of ARG dissemination by modulating the rumen microbial community and associated metabolites.}, }
@article {pmid42185948, year = {2026}, author = {Michalik, A and Majewska, E and Andriienko, V and Nowak, KH and Stroiński, A and Łukasik, P}, title = {Stable nutritional endosymbiosis across cryptic diversity of a leafhopper species complex.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-12986-3}, pmid = {42185948}, issn = {1471-2164}, support = {2021/41/B/NZ8/04526//Narodowe Centrum Nauki/ ; 2018/31/B/NZ8/01158//Narodowe Centrum Nauki/ ; }, abstract = {BACKGROUND: Ancient nutritional symbioses underpin the ecological success of many sap-feeding insects. In 'true hoppers' - the hemipteran suborder Auchenorrhyncha, obligate bacterial partners provide essential amino acids lacking in plant phloem diets. However, the stability and persistence of such associations across the diversity of hoppers are poorly understood, and investigations are often complicated by insufficiently resolved host identity.<br><br>RESULTS: Here, we combined multitarget amplicon sequencing, metagenomics, and microscopy to assess the compositional and functional diversity of the microbiota across Polish, Swedish, and Austrian populations of leafhoppers morphologically identified as Verdanus abdominalis. Host COI data revealed pronounced cryptic genetic diversity, indicating several deeply divergent lineages within the characterized collection, but limited microbiota variation among populations. 16S rRNA amplicon data confirmed the consistent presence of the ancient bacterial endosymbionts Candidatus Sulcia muelleri and Candidatus Nasuia deltocephalinicola, and metagenomics showed that their reduced but complementary genomes jointly encode the complete set of essential amino acid biosynthesis pathways required by the host. Other microbes were uncommon in these symbioses. Microscopy corroborated these findings, revealing conserved bacteriome organization and spatial separation of Sulcia and Nasuia within distinct bacteriocytes.<br><br>CONCLUSIONS: Our results demonstrate that the Sulcia-Nasuia dual symbiosis remains evolutionarily stable across cryptic Verdanus diversity, underscoring the robustness of ancient nutritional partnerships despite ongoing host diversification.}, }
@article {pmid42186028, year = {2026}, author = {Larroya, A and Romera-Giner, S and Tolosa-Enguís, V and Rodríguez-Ruano, SM and Andrés-García, S and Soro-Conde, I and Codoñer, P and Sanz, Y}, title = {Gut microbiota and western dietary patterns associated with behavioral problems in children and adolescents: a cross-sectional study.}, journal = {Nutrition journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12937-026-01335-5}, pmid = {42186028}, issn = {1475-2891}, abstract = {BACKGROUND: Childhood and adolescence are crucial periods for brain development, during which multiple environmental factors, including gut microbiota and dietary habits, play important roles. However, the combined impact of those factors on neurodevelopment and mental disease risk remains largely unexplored. Here, we aimed to investigate the relationships between gut microbiota and diet and their role in classifying behavioral problems that may precede mental disorders in children and adolescents.<br><br>METHODS: We performed a cross-sectional study, including data from 335 subjects, including 202 children (5-10&#xa0;years) and 133 adolescents (11-17&#xa0;years). Gut microbiota was analysed in stools by shotgun metagenomics. Dietary habits, lifestyle factors and emotional and behavioral difficulties were screened using validated questionnaires. Penalized Logistic Regression models were trained to classify individuals into Healthy and Behavioral Problem groups based on microbial diversity, differential abundance of bacterial species, dietary patterns, and food and nutrient intakes. Mediation analyses were applied to assess whether gut microbiota mediates the effect of diet on behavioral problems.<br><br>RESULTS: A Western diet characterized by poor adherence to dietary recommendations was consistently associated with behavioral problems in all age groups. Individuals with behavioral problems exhibited distinct gut microbiota profiles characterized by lower levels of short-chain fatty acid-producing bacteria (particularly butyrate-producing species) and higher levels of potential pathogens (e.g., Campylobacter coli and Lautropia mirabilis), linked to poor dietary choices. Furthermore, we evidenced the mediation role of the gut microbiota in the association between dietary patterns and food groups and behavioral problems. In adolescents, L. mirabilis was identified as a mediator of the relationship between a Western diet and behavioral problems, while Anaerostipes rhamnosivorans mediated the relationship between fish consumption and behavioral problems. Gut microbiota data enhanced the classification accuracy of logistic regression models for identifying individuals with behavioral problems over models based solely on dietary data.<br><br>CONCLUSION: Integrating dietary habits and gut microbiota data enables more accurate stratification of children and adolescents at risk for behavioral problems. Our findings may help to refine dietary interventions targeting the gut microbiota to improve mental health outcomes in these vulnerable populations.}, }
@article {pmid42186092, year = {2026}, author = {Wang, L and Li, F and Ma, Z and Ungerfeld, EM and Zhang, T and Zhang, Z and Liu, X and Zhang, Q and Zhang, X}, title = {Yeast culture promotes butyrate produced fibrolytic bacteria as intracellular hydrogen sink in the rumen.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02436-3}, pmid = {42186092}, issn = {2049-2618}, support = {32308686//The National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Yeast culture (YC) supplementation is widely adopted to mitigate rumen pH depression and alleviate the inhibition of fiber degradation under starch-rich diets. Yet, the underlying microbial mechanisms, particularly how yeast culture orchestrates fibrolytic communities and affects metabolic hydrogen flow in the rumen, remain a critical knowledge gap. Accordingly, elucidating the microbial basis by which yeast culture modulates fiber degradation and hydrogen utilization under starch-rich diets is of both theoretical and practical importance.<br><br>METHODS: We conducted a study with growing lambs receiving starch-rich diets that differed only in yeast culture supplementation (CON 0%, YC 1%). We evaluated their growth performance, apparent total-tract digestibilities, rumen fermentation end-products, and the rumen metagenome.<br><br>RESULTS: The YC treatment increased the lambs' final body mass (P&#x2009;=&#x2009;0.02), average daily gain (P&#x2009;=&#x2009;0.03), digestibilities of&#xa0;neutral detergent fiber (P&#x2009;<&#x2009;0.001) and&#xa0;acid detergent fiber (P&#x2009;<&#x2009;0.001), and rumen pH (P&#x2009;<&#x2009;0.05), and tended to increase organic matter digestibility (P&#x2009;=&#x2009;0.09). In addition, total VFA concentrations, particularly butyrate, were higher at 6&#xa0;h post-morning feeding (P&#x2009;=&#x2009;0.01). Fibrolytic and hydrogenotrophic taxa (e.g., Ruminococcus_E and Quinella) and CAZyme families, including GH43, GH31, GH9, and GH35, were enriched by the YC treatment, as were bacteria involved in fiber degradation and butyrate production. Furthermore, none of the top five YC treatment-enriched bacterial genomes contained any hydrogenase genes, which indicates that this butyrogenic fibrolytic consortium is significantly different from the hydrogen-producing fiber-degrading microorganisms we are familiar with.<br><br>CONCLUSION: Yeast culture supplementation promoted the proliferation of a distinct butyrogenic consortium that degrades fiber while apparently disposing intracellularly metabolic hydrogen generated during fermentation, rather than releasing it as H2. These findings provide a microbial basis for understanding how yeast culture improves fermentation efficiency under starch-rich diets and suggest that selecting yeast culture products capable of promoting butyrogenic fibrolytic bacteria may be beneficial for ruminant performance and rumen stability. Video Abstract.}, }
@article {pmid42186552, year = {2026}, author = {Méndez-Sánchez, D and Pomahač, O and Valt, M and Bourland, WA and Čepička, I}, title = {An extensive morphological and molecular characterization of the neglected class Odontostomatea (Ciliophora).}, journal = {Marine life science &amp; technology}, volume = {8}, number = {2}, pages = {289-323}, pmid = {42186552}, issn = {2662-1746}, abstract = {UNLABELLED: Odontostomatid ciliates, known for over a century, were historically classified within various taxonomic groups of Ciliophora Doflein, 1901 until their reclassification into the class Odontostomatea. Despite the recognition of 25 valid species, most descriptions predate the advent of silver impregnation and sequencing methods. Consequently, many species were described based solely on observations of live specimens, leading to incomplete or ambiguous records. To date, redescriptions of only three species include 18S rRNA gene sequences data, and their evolutionary relationships remain unresolved. In this study, we investigated 32 populations representing 15 species-including three newly described-across the genera Discomorphella, Epalxella, Limnomylestoma gen. nov., Mircalla gen. nov., Mylestoma, Pelodinium, Saprodinium, and Tostonella gen. nov. Comprehensive analyses were conducted using in vivo microscopy, silver impregnation, and scanning electron microscopy. We also designed specific primers to amplify the partial 18S rRNA gene of various odontostomateans and retrieved additional 18S rRNA sequences from environmental metatranscriptomic and metagenomic datasets. This study represents the most extensive investigation of Odontostomatea to date, confirming the monophyly of the class by revealing the position of Epalxella, reconstructing its internal phylogeny, identifying two main odontostomatean lineages, and revealing its remarkable diversity.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-026-00352-x.}, }
@article {pmid42186601, year = {2026}, author = {Zhang, Z and Jia, Z and Zhang, X and Zou, W and Chen, J}, title = {Late-onset cytomegalovirus pneumonia after autologous stem cell transplantation for angioimmunoblastic T-cell lymphoma: a case report.}, journal = {Therapeutic advances in infectious disease}, volume = {13}, number = {}, pages = {20499361261450721}, pmid = {42186601}, issn = {2049-9361}, abstract = {This case report illustrates a diagnostic and therapeutic challenge in a highly immunocompromised host: severe pneumonia occurring late after autologous hematopoietic stem cell transplantation (auto-HSCT). A 57-year-old male with angioimmunoblastic T-cell lymphoma (AITL) presented with hypoxemic respiratory failure 1 year post-auto-HSCT, a timeline extending beyond the typical high-risk period for opportunistic infections. A profoundly low CD4+ T-cell count (172/µL) was identified as the key predisposing factor. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) enabled rapid, unbiased pathogen detection, confirming cytomegalovirus (CMV) pneumonia (viral load: 3.0 × 10[4] copies/mL) with Klebsiella pneumoniae coinfection. An integrated management strategy was instituted, comprising early empiric coverage for Pneumocystis jirovecii pneumonia, targeted therapy with ganciclovir and levofloxacin, and adjunctive immunomodulation using intravenous immunoglobulin and corticosteroids. This comprehensive approach resulted in full recovery, highlighting that the severity of immune suppression-rather than time since transplantation alone-determines infection risk. This case challenges the conventional time-based risk paradigm and supports immune-guided surveillance. It underscores the transformative role of mNGS in diagnosing complex infections in immunocompromised patients and advocates for a management paradigm that concurrently addresses pathogen eradication and host immune dysfunction.}, }
@article {pmid42186944, year = {2026}, author = {Patin, NV and Pitz, K and Kimbrough, K and Archer, F}, title = {Beyond Biodiversity: Incorporating Uncertainty Into Metabarcoding Data for Improved Inference of Ecological Relationships.}, journal = {Molecular ecology resources}, volume = {26}, number = {4}, pages = {e70160}, doi = {10.1111/1755-0998.70160}, pmid = {42186944}, issn = {1755-0998}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *DNA, Environmental/genetics ; *Metagenomics/methods ; *Computational Biology/methods ; Bayes Theorem ; }, abstract = {Metabarcoding sequence data from environmental DNA (eDNA) is rapidly expanding as a powerful method for biodiversity surveys. In order to interpret these data, tools are needed that account for the uncertainty associated with eDNA sampling, sequencing and analysis. The data resulting from eDNA marker gene analysis differ from many traditional methods of biodiversity surveys because they are highly complex, sparse and compositional. Methodological biases produce uncertainty at every step of the sampling and sequencing process. Thus, it is critical that users have a way of interpreting eDNA results that accounts for their compositional nature and models the uncertainty resulting from factors like patchy sampling, PCR amplification biases and variable sequencing depth. Here, we introduce MAMBO: Metabarcoding Analysis using Modeled Bayesian Occurrences. MAMBO simulates in silico replication and models the uncertainty surrounding the sequencing and analysis process. Further, it uses these modelled sequence count data to correlate two sets of marker genes with a Bayesian regression, facilitating the linkage of different groups targeted by these assays. Compared with correlational network analyses, MAMBO overcomes many of the limitations to robust statistical analyses of eDNA marker gene data and provides an opportunity for new insight into ecological patterns over space and time.}, }
@article {pmid42187250, year = {2026}, author = {Liu, X and Kwok, L-Y and Zhang, W}, title = {Integrated gut microbiota and metabolome signatures revealed by deep metagenomic sequencing in post-stroke cognitive impairment with type 2 diabetes.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0024426}, doi = {10.1128/spectrum.00244-26}, pmid = {42187250}, issn = {2165-0497}, abstract = {UNLABELLED: Post-stroke cognitive impairment (PSCI) is significantly exacerbated in individuals with type 2 diabetes mellitus (T2DM), yet the underlying gut microbial and metabolic mechanisms remain unclear. In this study, baseline fecal samples from 28 diabetic PSCI (PSCI-DM) patients and 29 matched non-PSCI non-diabetic controls were subjected to deep metagenomic sequencing and untargeted metabolomics. Although alpha diversity was preserved, subtle but meaningful shifts were observed in bacterial and fungal composition. The PSCI-DM group exhibited depletion of beneficial butyrate-producing taxa, including Lachnospira spp. and Butyribacter intestini, and enrichment of Butyricimonas virosa. Five fungal species, including Torulaspora globosa and Pichia kudriavzevii, were significantly reduced. Metabolomic profiling identified 45 differentially abundant metabolites, with decreases in neuroprotective compounds, such as 9-oxononanoic acid, C16-ceramide, and nootkatone, and increases in metformin and bile acid derivatives. Abundances of microbial functional pathways linked to energy metabolism were elevated, while those involved in cofactor and neurotransmitter precursor synthesis were reduced. Significant correlations were found between specific microbes and metabolites, suggesting coordinated dysregulation across kingdoms. However, only a limited subset of microbial features remained independently associated with cognitive performance. Specifically, metabolites Nb-palmitoyltryptamine and pipecolic acid, and fungal species Pichia kudriavzevii showed significant correlations with Montreal cognitive assessment (MoCA) scores for cognitive impairment. These findings reveal a tripartite gut ecosystem signature in PSCI-DM and provide a mechanistic foundation for microbiota-targeted therapeutic strategies.<br><br>IMPORTANCE: In the context of type 2 diabetes, post-stroke cognitive impairment represents a clinically prevalent yet mechanistically underexplored condition with limited therapeutic options. This study combined metagenomic sequencing with non-targeted metabolomics to reveal the coordinated dysregulation of bacteria, fungi, and host-related metabolites in the gut of type 2 diabetes mellitus with post-stroke cognitive impairment (PSCI-DM) patients. The research indicates that cognitive impairment is not solely related to the overall decline in microbial diversity, but also involves the targeted reduction of neuroprotective butyrate-producing bacteria, the absence of specific gut fungi, and the corresponding reduction in neural activity and lipid metabolites. These findings collectively establish the gut microbiota-metabolite characteristics of PSCI-DM patients, providing a theoretical basis for targeted probiotic intervention measures to prevent or alleviate cognitive decline in diabetic patients after stroke.}, }
@article {pmid42187318, year = {2026}, author = {Tang, Y and Lin, Z and Liu, Z and Guo, J and Yang, C and Feng, L and Wang, Y and Zhang, P and Chen, Y}, title = {Impact of Corneal Microbial Latency Detected by Metagenomic next-generation sequencing on Postoperative Recovery Following Keratorefractive lenticule extraction.}, journal = {Journal of cataract and refractive surgery}, volume = {}, number = {}, pages = {}, doi = {10.1097/j.jcrs.0000000000001979}, pmid = {42187318}, issn = {1873-4502}, abstract = {PURPOSE: To investigate the microbial species latent in corneas of healthy individuals and determine whether small incision lenticule extraction (SMILE) serves as a risk factor for pathogen reactivation.<br><br>SETTING: The Ophthalmology Department of Peking University Third Hospital, Beijing, China.<br><br>DESIGN: Prospective Cohort Study.<br><br>METHODS: Metagenomic next-generation sequencing (mNGS) was employed to analyze the microbial composition of corneal lenticules from SMILE. Based on the results, patients were categorized into Viral Group (VG) and Non-Viral Pathogen Group (NVPG). Two Matched Groups (MG1 and MG2) were established by selecting pathogen-negative individuals at a 1:4 ratio relative to two positive groups. Using SPSS to analyze baseline characteristics, preoperative ocular parameters and postoperative ocular parameters among groups.<br><br>RESULTS: Among the detected pathogens, latent Herpesviruses were identified in 9 cases (4.31%), Papillomavirus were 4 cases (1.91%), and non-viral pathogens were 20 cases (9.57%). Both VG and NVPG groups showed no significant differences in baseline characteristics or preoperative ocular parameters compared with MG groups. In postoperative ocular parameters, no significant differences were found between VG and MG1, though intergroup variations in intraocular pressure and corneal thickness were observed (p>0.05). However, NVPG demonstrated significantly poorer results than MG2 in 1 month-spherical equivalent (p=0.033) and corneal epithelial staining (p=0.044).<br><br>CONCLUSION: These findings indicate pathogen latency does not affect ocular status and SMILE surgery is unlikely to reactivate latent viruses or exerts minimal influence. Viral latency has almost no impact on postoperative recovery, while latent non-viral pathogens may interfere with postoperative recovery.}, }
@article {pmid42187703, year = {2026}, author = {Sun, Q and Li, J and Xu, G and Zhou, C and Lei, K and Jiang, W}, title = {Source-Specific Nitrogen Inputs Are Associated with Pathway Partitioning Between Denitrification and DNRA in River Water.}, journal = {Biology}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/biology15100741}, pmid = {42187703}, issn = {2079-7737}, support = {Lishui City Key R&amp;D Program Projects.(2023zdyf03)//Lishui Ecological and Environmental Monitoring Center of Zhejiang Province/ ; }, abstract = {Understanding how external nitrogen sources regulate nitrogen fate in river water is critical for improving nitrogen removal and reducing greenhouse-gas risk. Here, short-term microcosm incubations were conducted using source water as the background matrix and seven representative source inputs. By integrating hydrochemical analyses, bacterial community profiling, metagenomics, RT-qPCR, and process-rate measurements, we evaluated source-dependent shifts in nitrogen-cycling pathways. Manure-related inputs generated the highest organic and nitrogen loading, suppressed nitrification, enhanced nrfA (cytochrome c nitrite reductase) abundance and transcription, and promoted DNRA, indicating a shift toward nitrogen retention via ammonium regeneration. In contrast, sewage-related inputs maintained relatively high NO3[-] availability, elevated nirS (cytochrome cd1 nitrite reductase) and nosZ (nitrous oxide reductase) expression, and enhanced denitrification, but also increased N2O production. Metagenomic, transcriptional, and rate-based evidence consistently identified 12 h as a critical window for source-dependent pathway redistribution, highlighting the importance of short-term monitoring for detecting rapid nitrogen-cycle responses following pollution inputs. These findings support source-oriented nitrogen management that considers both nitrogen loading and hydrochemical controls on nitrate fate.}, }
@article {pmid42187710, year = {2026}, author = {Singh, S and Tiwari, H and Singh, M and Gautam, V and Gautam, A and Gautam, HK}, title = {Expanding the Microbial Genomic Landscape and Biotechnological Applications of CRISPR-Cas Systems.}, journal = {Biology}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/biology15100748}, pmid = {42187710}, issn = {2079-7737}, support = {(File No.: ANRF/IRG/2025/000135/LS)//Anusandhan National Research Foundation (ANRF)/ ; CST/D-1187//Council of Science and Technology, Uttar Pradesh, India (CST-UP)/ ; }, abstract = {The CRISPR-Cas systems, identified initially as adaptive immune mechanisms in bacteria and archaea against viral threats, have rapidly evolved into transformative tools in genetic engineering and biotechnology. These RNA-guided systems are broadly classified into Class 1, comprising multi-subunit complexes, and Class 2, characterized by compact single-effector protein, such as Cas9, Cas12, and Cas13. Their remarkable structural and functional diversity enables microorganisms to adapt to diverse ecological niches, offering a vast repertoire of genome-editing strategies. Beyond their natural role in maintaining genome integrity and defense, CRISPR-Cas systems have been extensively repurposed for precise genome modification, transcriptional regulation, epigenetic editing, and nucleic acid detection. Recent advances in computational mining of microbial genomes and metagenomes have uncovered a broad range of novel CRISPR effectors with unique properties, distinct protospacer adjacent motif (PAM) requirements, RNA-targeting capabilities, miniature architectures, and promiscuous cleavage activities that significantly expand the molecular biology toolkit. The development of CRISPR-based technologies such as base editing, prime editing, gene knock-in/out, and live-cell DNA/RNA imaging exemplifies the versatility of these systems. Despite the challenges associated with delivering complex Class 1 systems, both classes are now being actively harnessed across diverse microbial platforms. Concurrently, the CRISPR-Cas research, particularly for guide RNA (gRNA) design and activity prediction, has revolutionized target specificity and editing efficiency. This review presents a comprehensive overview of CRISPR-Cas system diversity, their genomic landscape in microorganisms, and their cutting-edge biotechnological applications. It also emphasizes the transformative potential of CRISPR in synthetic biology, therapeutics, diagnostics, environmental remediation, and agriculture, while also addressing the ethical and biosafety considerations surrounding its deployment. As CRISPR-Cas systems continue to evolve, they stand at the forefront of innovations that bridge natural microbial immunity with engineered precision tools for next-generation biotechnology.}, }
@article {pmid42187714, year = {2026}, author = {Peng, D and Huang, T and Kang, W}, title = {Evolutionary Strategies for Heavy Metal Resistance: Genomic Plasticity in Pseudomonas Versus Stability in Aeromonas and Bacillus.}, journal = {Biology}, volume = {15}, number = {10}, pages = {}, doi = {10.3390/biology15100751}, pmid = {42187714}, issn = {2079-7737}, support = {2025QT02//Central Public-interest Scientific Institution Basal Research Fund, ECSFR, CAFS/ ; 2024FY100200//Science &amp; Technology Fundamental Resources Investigation Program/ ; }, abstract = {Heavy metal resistance represents a critical microbial trait shaped by lineage-specific evolutionary pressures, yet its genomic foundations and diversification across major bacterial taxa remain poorly resolved. This study presented a comparative pangenomic analysis of Aeromonas (n = 32), Bacillus (n = 123), and Pseudomonas (n = 350)-three phylogenetically and ecologically distinct genera frequently enriched in metal-contaminated environments and exhibiting notable differences in resistance architectures. All three genera exhibited open pangenomes, with fitted expansion indices of 0.003 (Aeromonas), 0.03 (Bacillus), and 0.04 (Pseudomonas), each showing strong model fit (R[2] > 0.98). Pseudomonas harbored a significantly greater number of resistance genes, with copper and zinc resistance genes exceeding 25 per strain in some cases. Most heavy metal resistance genes across the three genera were subject to purifying selection (dN/dS < 1), and no significant expansion or contraction of these gene families was observed (p > 0.05). The presence of these genera and their lineage-specific resistance determinants may serve as bioindicators of heavy metal exposure, offering valuable references for assessing contamination levels through environmental metagenomics.}, }
@article {pmid42187862, year = {2026}, author = {Mills, N and Mills, N and Suwannarach, N and Noirungsee, N and Kumla, J and Inwongwan, S and Yongsawas, R and Saksunwiriya, C and Domethong, V and Shoocongdej, R and Disayathanoowat, T}, title = {Fungal Communities Associated with Wooden Coffins in a Prehistoric Burial Cave.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, doi = {10.3390/jof12050380}, pmid = {42187862}, issn = {2309-608X}, support = {2021//U.S. Ambassador's Fund for Cultural Preservation/ ; }, abstract = {Phi Man Long Long Rak Cave, located in Mae Hong Son Province, northern Thailand, is a prehistoric burial site containing ancient wooden coffins that have undergone biodeterioration, likely due to fungal activity. Both culture-dependent and culture-independent approaches were employed to characterize fungal communities and assess their roles in wood degradation. Culture-dependent analysis identified five Aspergillus isolates from the wooden coffins, most of which produced cellulolytic and hemicellulolytic enzymes; some isolates also produced organic acids, indicating significant degradative potential. Culture-independent analysis revealed a community dominated by Aspergillus, together with additional taxa such as Penicillium and Ceriporia that were not detected by cultivation, highlighting greater community diversity and demonstrating the complementarity of the two methods. Functional prediction indicated a predominance of saprotrophic fungi. The presence of shared dominant taxa between soil and coffin-associated substrates suggests ecological connectivity at the soil-coffin interface, although the direction of dispersal cannot be determined from the present data. All tested fungicides inhibited fungal growth, with the highest efficacy observed in the formulation containing the highest proportion of active components. Taken together, these findings provide insights into fungal biodeterioration processes and inform conservation strategies.}, }
@article {pmid42188011, year = {2026}, author = {Li, X and Deng, W and Zhang, Z and Tong, H and Cao, Y}, title = {Revealing the Formation Mechanism of Key Metabolites During Japonica Rice Storage Driven by Microbial Functional Genes.}, journal = {Metabolites}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/metabo16050302}, pmid = {42188011}, issn = {2218-1989}, support = {2023010714-JH3/107//Liaoning Provincial Science and Technology Plan Project General Project/ ; 254358.//China Postdoctoral Science Foundation Project/ ; }, abstract = {BACKGROUND: To elucidate the evolution of metabolites and fungal communities during storage of fragrant japonica rice (Liaoxiangjing 1396), and to investigate the biosynthetic mechanisms of key compounds and their association with quality deterioration, this study examined rice samples stored under simulated conditions for 16 months.<br><br>METHOD: Samples were collected at 4-month intervals (designated R20, R14, R13, R12, and R11). Metabolites were identified using GC-MS non-targeted metabolomics, while fungal community structure was analyzed through metagenomics. Core mechanisms were further elucidated via PLS-DA, KEGG pathway enrichment, and multiomics association analysis.<br><br>RESULT: Results demonstrated that the fatty acid content of rice increased initially and then stabilized (from 12.24 mg/g in R20 to 17.63 mg/g in R12). A total of 263 metabolites were identified, with oxygenated organic compounds (38 species) and lipids/lepidid molecules (24 species) as the predominant categories. Twelve key differential metabolites were screened from the R20 and R12 groups, involving five major metabolic pathways, including amino acid metabolism and lipid metabolism. In the fungal community, Pseudomonas (60.2%) and Pantoea (38.19%) were dominant taxa, with a specific Pantoea species (Pantoea sp.) identified as a core potential biomarker. Multiomics association analysis revealed that Klebsiella dominated the ndhB energy metabolism pathway, while multiple bacteria cooperatively regulated the mcp chemotaxis pathway, interacting with monosaccharide and amino acid accumulation.<br><br>CONCLUSIONS: This study reveals that the storage quality deterioration of fragrant japonica rice is driven by the "metabolite-microbe-pathway" chain regulation, and the dynamic changes in key metabolites and fungal communities can serve as quality early warning targets.}, }
@article {pmid42188051, year = {2026}, author = {Deng, H and Zhang, R}, title = {TCM-Derived Natural Compounds Targeting the Gut Microbiota in Metabolic Dysfunction-Associated Steatotic Liver Disease: Gut-Liver Axis Mechanisms, Safety Considerations, and Translational Challenges.}, journal = {Metabolites}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/metabo16050342}, pmid = {42188051}, issn = {2218-1989}, abstract = {The occurrence and development of metabolic dysfunction-associated steatotic liver disease (MASLD) are closely related to intestinal flora imbalance, intestinal barrier damage, and gut-liver axis dysfunction. Due to their multi-target regulatory effects and advantages in intestinal microecological intervention, Chinese herbal monomers have shown promising application prospects in the prevention and treatment of MASLD. However, basic research on their toxicity still lags behind, and issues related to safety and clinical translation urgently need attention. This article systematically reviews the research progress on how flavonoids, triterpenoids, alkaloids, and polysaccharides improve hepatic steatosis, inflammatory responses, and metabolic disorders from a toxicological perspective by reshaping the intestinal microbiota, repairing the intestinal mucosal barrier, regulating short-chain fatty acid and bile acid metabolism, and synergistically acting on signaling pathways such as TLR4/NF-kB, FXR, TGR5, SIRT1, and the NLRP3 inflammasome. Furthermore, by combining methods such as 16S rRNA sequencing, metagenomics, metabolomics, and multi-omics integration, the article analyzes their application value and limitations in toxicological mechanism research, and discusses the translational bottlenecks faced by Chinese herbal monomers in pharmacokinetics, bioavailability, quality standardization, targeted delivery, and toxicological safety. Existing evidence indicates that Chinese herbal monomers have a three-in-one intervention advantage of microecological remodeling-metabolic regulation-inflammation inhibition, but their long-term medication safety, toxic target organs, dose-effect/toxicity relationships, and potential drug interactions still need further clarification. This article aims to provide a systematic reference for the safety evaluation and clinical translational research of Chinese herbal monomers in the prevention and treatment of MASLD.}, }
@article {pmid42188128, year = {2026}, author = {Sontigun, N and Thanawan, N and Fungwithaya, P}, title = {Epidemiology and Antimicrobial-Resistant Genes of Family Staphylococcaceae in Musca domestica: Case Studies from Chicken Farm, Pig Farms, and Residential Areas in Southern Thailand.}, journal = {Insects}, volume = {17}, number = {5}, pages = {}, doi = {10.3390/insects17050461}, pmid = {42188128}, issn = {2075-4450}, support = {KREF186729//King Mongkut's Institute of Technology Ladkrabang Research Fund/ ; }, abstract = {The major Staphylococcaceae family is recognized as opportunistic pathogens colonizing human and animal skin, mucous membranes, and environments. Musca domestica, the house fly, plays a role in the transmission of AMR bacteria. This study focused on examining the epidemiology and antimicrobial-resistant genes of the family Staphylococcaceae in M. domestica through metagenomic analysis, using samples collected from three animal farms and two residential areas in southern Thailand. Fifty M. domestica were collected from five places surrounding Walailak University, including one chicken farm (CF1), two pig farms (PF2 and PF3), and two residential areas (H1 and H2). All samples were dispatched for analysis using shotgun metagenomic sequencing and analyzed using FastQC, MultiQC, FASTQ, MEGAHIT, QUAST, ABRicate, AMRFinderPlus, ResFinder, ARG-ANNOT, MEGARES, PlasmidFinder, VFDB, Kraken2, Krona and Python. Our findings describe the taxonomic composition of Staphylococcaceae taxa in M. domestica from different environments; the representation of the family Staphylococcaceae in CF1, PF2, PF3, H1, and H2 was recorded at 2%, 0.7%, 0.2%, 0.2%, and 2% of this phylum, respectively. The average populations discovered were Staphylococcus (37.4%), Mammaliicoccus (17.4%), and Macrococcus (10.3%), respectively. Trimethoprim-resistant genes (dfrG and dfrE) were found only in CF1, PF2, and H1. Interestingly, fosfomycin-resistant genes were found only in M. domestica within residential areas. Our findings pertain to the Staphylococcaceae population in M. domestica within residential areas, which exhibited varying multidrug-resistance genes, particularly those resistant to fosfomycin.}, }
@article {pmid42188162, year = {2026}, author = {Tao, M and Zhang, J and Fan, Y}, title = {Metagenomic Analysis of Gut Microbiome Across Developmental Stage of Asian Corn Borer (Ostrinia furnacalis).}, journal = {Insects}, volume = {17}, number = {5}, pages = {}, doi = {10.3390/insects17050495}, pmid = {42188162}, issn = {2075-4450}, support = {Grant No. 32402469//National Natural Science Foundation of China/ ; }, abstract = {Ostrinia furnacalis is one of the most important agricultural pests in Asia. Previous studies utilizing 16S rRNA sequencing have established a foundational understanding of the taxonomic composition of its gut microbiota; however, the dynamic functional transitions across the host's entire life cycle remain poorly understood. In this study, we used metagenomic sequencing to systematically characterize the gut microbiome across six groups representing different life stages and sexes of O. furnacalis: first-instar, third-instar, and fifth-instar larvae, pupae, and adults (both males and females). Microbial richness and evenness vary significantly across six groups representing different life stages and sexes. Species richness is highest in the first-instar larvae (L1D2), while evenness is relatively high in both first- and third-instar larvae (L1D2 and L3D2). Additionally, no sex-based differences were observed in either indicator during the adult stage. Enterococcus mundtii is the primary species driving community succession and rapidly achieves dominance after the third-instar stage. Co-occurrence network analysis revealed that the first-instar larval network exhibits the highest complexity, with positive correlations accounting for 96.6% of all edges. Conversely, the fifth-instar larvae exhibits the greatest proportion of negative correlation edges at 29.13%, while the pupal stage network is the most dispersive, indicating microbial reorganization during metamorphosis. Functional annotation reveals that carbohydrate and amino acid metabolism pathways are significantly enriched during the larval stage. In contrast, the pupal stage is characterized by enrichment in environmental information processing and a notable increase in polysaccharide lyases (PLs). This shift indicates that the microbiota transitioned from degrading plant polysaccharides to foraging host-derived glycans. The number of resistance genes in the first-instar larvae is significantly higher than that in all other groups representing different life stages and sexes. Collectively, this study systematically reveals the dynamic succession patterns of the gut microbiome throughout the life cycle of O. furnacalis and provides a theoretical foundation for the development of microbiome-based pest management strategies.}, }
@article {pmid42188886, year = {2026}, author = {Yi, C and Nicolas, CS and Sun, Z and Wang, Q and Dong, T and Wu, Y}, title = {Effects of a Novel Prebiotic and Postbiotic Dietary Supplement on Gut Microbiota, Intestinal Barrier Markers, and Inflammation in Healthy Dogs.}, journal = {Veterinary sciences}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/vetsci13050417}, pmid = {42188886}, issn = {2306-7381}, support = {202404810411350//Virbac China/ ; }, abstract = {Although prebiotics and postbiotics support gastrointestinal health, evidence for their combined effects in dogs remains limited. This study evaluated a novel prebiotic and postbiotic supplement in healthy dogs undergoing a dietary transition. Thirty-six healthy adult dogs were randomly assigned to control group (CON, high-protein basal diet with placebo chew) or treatment group (TRT, the same basal diet with chew containing prebiotics [baobab fruit pulp and acacia gum] and postbiotics [inactivated Lactobacillus acidophilus and selected yeast fractions]) for a 28-day formal trial following a 7-day adaptation period. The primary outcomes evaluated included clinical fecal scores, specific biomarkers of intestinal barrier function and inflammation, fecal short-chain fatty acids, and microbiota structure. Following the 7-day adaptation, formal trial baseline, fecal scores were already within the healthy range and remained optimal without differing between groups throughout the study. Compared with CON, the TRT group showed lower fecal calprotectin and serum diamine oxidase levels, and higher fecal butyrate (p < 0.05). Metagenomic analysis revealed increased abundances of Bacteroidota, Oscillospiraceae, Prevotellaceae, and Prevotella in TRT (p < 0.05). Overall, in healthy dogs, this supplementation was associated with favorable microbiota modulation and modulated biomarkers of intestinal barrier and inflammation within normal ranges, without altering clinical fecal endpoints.}, }
@article {pmid42176766, year = {2026}, author = {Avolio, E and Olivito, I and Minervini, D and Soda, T and De Bartolo, A and Rocca, C and Alò, R and Facciolo, RM}, title = {Neuronutrition in ASD: Involvement of gut microbiota, oxidative stress and inflammatory markers.}, journal = {Neuroscience and biobehavioral reviews}, volume = {187}, number = {}, pages = {106775}, doi = {10.1016/j.neubiorev.2026.106775}, pmid = {42176766}, issn = {1873-7528}, abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental disorder displaying altered human behaviors, such as social interaction impairments, stereotypical/repetitive activities and emotional dysregulation. Children with ASD are often affected by gastrointestinal problems and gut microbiota dysbiosis. Inflammation and immune dysfunction are key contributors to ASD, as shown by high proinflammatory cytokines and oxidative stress. Indeed, notable implication of the nuclear factor kappa B in the severity of ASD derives from its ability to amplify neuroinflammation. This narrative review focused attention on neuronutrition and gut microbiota manipulation for mitigation of ASD symptoms, including neuroinflammation and oxidative stress. Studies in both rodents and humans with ASD have revealed that both pure and mixed Lactobacillus and Bifidobacterium were effective in ameliorating behavioral symptoms and GABA/glutamate imbalance. Often, the combined use of probiotics and prebiotics can have greater health benefits in ASD. Additionally, dietary interventions and microbiota transfer therapies along with low-to-moderate-intensity exercise have been proposed to improve gastrointestinal and behavioral symptoms. However, despite some encouraging results, biases in the neuronutrition/microbiota literature still exist. Indeed, many studies rely on small sample sizes, cross-sectional designs, and heterogeneous populations that differ in diet, medications, and comorbidities. In this context, the development of a precision diet tailored to individual gut microbiome profiles will allow for a broader understanding of the microbial ecosystem and relative therapeutical applications. Hence, by integrating metagenomics, metabolomics, epigenomics, with evaluation of environmental and nutritional factors, it will be possible to significantly improve the quality of life for people with ASD and their families.}, }
@article {pmid42176818, year = {2026}, author = {Dorofeev, A and Pelevina, A and Gruzdev, E and Beletsky, A and Berestovskaya, Y and Litti, Y and Mardanov, A and Pimenov, N}, title = {Development of an Azonexus- and Competibacter-enriched phosphate-accumulating community in the anaerobic/anoxic sequencing batch reactor: Cooperative denitrification.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134959}, doi = {10.1016/j.biortech.2026.134959}, pmid = {42176818}, issn = {1873-2976}, abstract = {Denitrifying polyphosphate-accumulating organisms (DPAOs) enable simultaneous N and P removal, however, reliable strategies for enriching stable DPAO communities and their metabolic interactions remain insufficiently understood. In this study, DPAO-enriched cultures were developed in a sequencing batch reactor operated under anaerobic/anoxic conditions with acetate as C source. For three independent experiments, activated sludge, collected at different times, was used as the inoculum. Within 0.5-2 months, all experiments exhibited definitive DPAO phenotype dynamics. After 100-200 days of operation, the microbial community was consistently co-dominated by two genera: Azonexus (19-35 %), representing DPAOs, and Competibacter (23-31 %), representing denitrifying glycogen-accumulating organisms (DGAOs). Metagenomic reconstruction revealed that neither Azonexus nor Competibacter harbored the full complement of denitrification genes. The Azonexus metagenome-assembled genome encoded napAB (nitrate reductase), nirS (nitrite reductase), and nosZ (nitrous oxide reductase), while the Competibacter MAG possessed only norBC (nitric oxide reductase) genes. This genomic complementarity provides evidence that complete denitrification in this system could be achieved through cooperation between DPAOs and DGAOs. Consequently, the observed lower phosphorus removal efficiency, compared to anaerobic/aerobic systems, is attributed to the reduced biomass yield of DPAOs and the high essential abundance of DGAOs. These results clarify the ecological role of Azonexus as a DPAO dependent on partnership with DGAOs. Furthermore, the selective conditions favoring Azonexus development in enhanced nutrient removal systems, are evaluated. This work reveals a possible mechanism of syntrophic cooperation between DPAO and DGAO, which has direct implications for the development of resource-saving biological processes for nutrient removal.}, }
@article {pmid42176923, year = {2026}, author = {Pi, D and Zhou, F and Huang, S and Yan, H and Pan, J and Yang, Q and Pan, M and Zhang, Y}, title = {Atractylodes lancea (Thunb.) DC polysaccharide alleviates MASH by regulating the 1‑carbon cycle through intestinal flora remodelling.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {152668}, doi = {10.1016/j.ijbiomac.2026.152668}, pmid = {42176923}, issn = {1879-0003}, abstract = {Metabolic-associated steatohepatitis (MASH) is a severe stage of Metabolic-associated fatty liver disease (MAFLD). Currently, effective pharmacological therapies for MASH are extremely limited. An Atractylodes lancea (Thunb.) DC polysaccharide (ALP) was isolated from Atractylodes lancea (Thunb.) DC, and its preventive effect on MASH and the potential mechanism were investigated. Mice were fed a high-fat, high-cholesterol, high-fructose diet (HFMCD) to induce MASH. MASH model mice were then treated with ALP at low (50 mg/kg/d) or high (100 mg/kg/d) dosages. Faecal metagenomics, nontargeted metabolomics sequencing, biochemical and pathological analyses, ELISAs, western blotting and other detection techniques were conducted to elucidate the mechanism by which ALP alleviates MASH. The research results indicate that both the low-dose (50 mg/kg/d) and high-dose (100 mg/kg/day) of ALP can effectively alleviate MASH, but the high-dose has a more significant effect. ALP effectively reduced liver lipid accumulation and inflammation in MASH model mice by regulating the 1‑carbon cycle through intestinal flora remodelling. ALP may be a promising natural candidate for the treatment of MASH.}, }
@article {pmid42177038, year = {2026}, author = {Strobel, KM and Leibel, SL and Bhute, S and Aja, E and Jacobs, JP and Calkins, K}, title = {Gut microbial differences and function in infants with gastroschisis: a pilot prospective cohort study.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-14}, doi = {10.1163/18762891-bja00121}, pmid = {42177038}, issn = {1876-2891}, abstract = {Newborns with gastroschisis hospitalised in the neonatal intensive care unit (NICU) are at risk for a disrupted gut microbiome. Infants with gastroschisis are particularly vulnerable to a dysbiotic microbiome; they require prolonged parenteral nutrition (PN) due to intestinal dysmotility, which often leads to growth faltering (GF). This pilot study's goals were to (1) compare the gut microbiome in infants with gastroschisis to infants admitted to the NICU without congenital anomalies, (2) identify differences in the gut microbiome between infants with gastroschisis requiring prolonged PN and those who do not, and (3) compare the microbiome in infants with gastroschisis with GF to those without GF. This was a multi-site prospective cohort study including 17 infants born with gastroschisis and 16 infants with a gestational age greater than 34 weeks admitted to the NICU without congenital anomalies (controls). Prolonged PN was defined as more than 28 days. GF was defined as a decline in weight or length z-score from birth to discharge of ≤-0.8. Stool samples were collected weekly during hospitalisation and analysed by shotgun metagenomics to assess bacterial composition, diversity, and function. Gestational age and birth weight were similar in the gastroschisis group and the control group. Infants with gastroschisis showed increased Staphylococcus aureus and decreased Bifidobacterium longum. Those requiring prolonged PN had a reduced abundance of genes in the glucosidase pathway compared to those who did not. Infants with GF showed a lower abundance of genes involved in the NAD-diphosphatase pathway compared to those without GF. Infants with gastroschisis display a distinct microbial composition and function compared to NICU infants without this condition. Among infants with gastroschisis, differences in bacterial functional capacity were observed in those who required prolonged PN and developed GF.}, }
@article {pmid42177062, year = {2026}, author = {Adamek, M and Yılmaz, TM and Erdogmus, S and Moore, S and Ziemert, N}, title = {The ARTS toolset: Resistance-based genome mining for systematic prioritization of bioactive gene clusters.}, journal = {Methods in enzymology}, volume = {730}, number = {}, pages = {35-60}, doi = {10.1016/bs.mie.2025.08.023}, pmid = {42177062}, issn = {1557-7988}, mesh = {*Multigene Family ; *Software ; Genome, Bacterial ; Genome, Fungal ; Fungi/genetics/metabolism ; *Bacteria/genetics/metabolism ; *Computational Biology/methods ; Biological Products/metabolism ; Data Mining/methods ; Genomics/methods ; Metagenome ; }, abstract = {Natural products, especially those produced by bacteria and fungi, have been a rich source of antibiotics and other medically important compounds. Advances in genome sequencing have revealed that many microorganisms harbor far more biosynthetic potential than previously known, but identifying which gene clusters are most likely to produce bioactive compounds remains a major challenge. One promising strategy is to look for genes that protect the producing organism from its own toxic products-so-called resistance genes-which often appear near the biosynthetic genes. In this chapter, we introduce the ARTS toolset, a collection of computational tools designed to identify such resistance-linked biosynthetic gene clusters in microbial genomes. ARTS 2.0 allows users to analyze bacterial genomes and metagenomes, ARTS-DB provides access to precomputed results from tens of thousands of genomes, and FunARTS adapts the approach for fungal genomes. We describe how each tool works and provide examples to guide their use, with additional online tutorial videos provided by the authors.}, }
@article {pmid42177063, year = {2026}, author = {Sélem-Mojica, N and Magaña-Lemus, M&#xc1; and Rosiles-Loeza, PY and Barona-Gómez, F}, title = {Bringing CORASON to Windows: Exploring fungal natural products through biosynthetic gene clusters.}, journal = {Methods in enzymology}, volume = {730}, number = {}, pages = {61-73}, doi = {10.1016/bs.mie.2026.03.001}, pmid = {42177063}, issn = {1557-7988}, mesh = {*Multigene Family ; *Biological Products/metabolism ; *Fusarium/genetics/metabolism ; Phylogeny ; *Software ; Genome, Fungal ; *Biosynthetic Pathways/genetics ; *Computational Biology/methods ; }, abstract = {Biosynthetic gene clusters (BGC) are genomic regions that encode the production of specialized metabolites, including antibiotics, pigments, and toxins. While BGC are traditionally classified into broad categories such as NRPS, PKS, and terpene clusters, these classes often overlook finer relationships among gene clusters that produce structurally or functionally related compounds. Tools like BiG-SCAPE and BiG-SLiCE have been developed to address this issue by organizing BGC into gene cluster families (GCFs). CORASON complements these tools by enabling phylogenetic reconstruction of BGC, identifying conserved core genes, and visualizing GFCs as a continuum of variation in gene presence/absence and sequence identity. Although CORASON is incorporated in BiG-SCAPE visualization, it is also a standalone tool initially designed for bacterial genomes annotated via RAST and implemented through Docker in Linux environments. Here, we demonstrate CORASON's broader applicability using fungal GenBank files and its installation via Conda on Windows. As a case study, we examine metagenome-assembled genomes (MAGs) from Fusarium domesticum, a lesser-known member of the Fusarium genus, which is often present in food-associated microbiomes. Unlike its pathogenic relatives (F. oxysporum, F. graminearum), F. domesticum remains understudied, making it an interesting target for genomic mining. This work expands the accessibility of CORASON for fungal genome analysis and highlights its potential in uncovering novel biosynthetic potential in overlooked microbial taxa.}, }
@article {pmid42177457, year = {2026}, author = {Zhang, H and Abbas, Z and Li, H and Zhu, Y and Hu, X and Si, D}, title = {Synergistic fungal-enzymatic fermentation of corn straw enhances nutritional value, microbial stability, and bio-feed quality.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05190-6}, pmid = {42177457}, issn = {1471-2180}, support = {2024TSYCTD0016//Xinjiang Uygur Autonomous Region "Tianshan Talents" Cultivation Program/ ; }, abstract = {Valorizing mature, dry corn straw into nutritional animal feed is constrained by its recalcitrant lignocellulosic matrix, while conventional silage methods face stability and logistical limitations. Existing enzymatic and bacterial approaches often lack synergistic efficacy and fail to mitigate pathogen risk in dry biomass systems. We engineered a two-stage fungal-enzymatic fermentation strategy employing a consortium of Aspergillus niger LFB-AN14, Coriolopsis trogii LFB-F1, Bacillus subtilis LFB-BS7, and Pediococcus acidilactici A62, integrated with cellulase, xylanase, and laccase under optimized conditions (1% inoculation, 5:5:1:1 ratio, 37 °C, 21 days). Our results demonstrated that the bacterial-enzyme co-treatment (Group A3) significantly reduced fiber content, with neutral detergent fiber (NDF) and acid detergent fiber (ADF) decreasing by 22.6% and 29.1%, respectively, compared to the control (p < 0.001). Lignin degradation was enhanced, accompanied by a 4.5-fold increase in water-soluble carbohydrates (WSC). The metabolic profile revealed elevated lactic acid production (36.54 g/kg FM) and the suppression of undesirable byproducts such as propionic and butyric acids. Microbial community analysis revealed a dominant shift toward Pediococcus (> 50% abundance) and inhibition of pathogenic Enterobacter spp. Structural analyses (SEM, FTIR) confirmed extensive lignocellulose deconstruction, particularly through carbonyl and hydroxyl functional groups. Metagenomic analysis revealed upregulated Auxiliary Activity (AA) enzymes and cellulosome modules, elucidating the mechanistic basis for enhanced degradation. KEGG enrichment highlighted enhanced aromatic compound metabolism and yeast proliferation, reflecting superior metabolic efficiency. This integrated fungal-enzymatic approach establishes a safe, scalable, and metabolically efficient strategy for transforming agricultural residues into high-quality bio-feed, resolving key challenges in fiber digestibility, pathogen control, and storage stability for sustainable livestock production.}, }
@article {pmid42178356, year = {2026}, author = {Chen, S and Xu, S and Muhammad, ZUA and Wang, X and Guo, K and Tao, J and Li, M and Wang, H and Zhang, C and Hou, S}, title = {Two-hourly resolved microbial and viral dynamics in the subtropical Daya Bay.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07491-x}, pmid = {42178356}, issn = {2052-4463}, support = {JCYJ20220530115401003//Shenzhen Science and Technology Innovation Commission/ ; JCYJ20220530115401003//Shenzhen Science and Technology Innovation Commission/ ; 4241003//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Planktonic microbial and viral communities are fundamental drivers of biogeochemical cycling and energy flow in marine ecosystems. These communities display substantial variability in their composition at daily to sub-daily scales, which cannot be captured by conventional low-frequency monthly or weekly sampling. To reveal these high-resolution dynamics, we performed a time-series sampling of planktonic microbial and viral communities in the subtropical Daya Bay at 2-hour intervals over 3 days. Seawater samples were subjected to metagenomic and metatranscriptomic sequencing for the cellular size fraction (>0.2 μm) and metagenomic sequencing for the viral size fraction (0.02-0.2 μm). This approach enabled us to capture fine-scale temporal variations in the genomic composition and transcriptional activities of microbial and viral communities. The resulting comprehensive dataset, including 700 metagenome-assembled genomes (MAGs) and 118,242 viral operational taxonomic units (vOTUs), provides a valuable resource for investigating the metabolic potentials and dynamic interactions within natural planktonic microbial-viral assemblages in subtropical bay ecosystems, offering insights into their ecological roles that are inaccessible through low-temporal-resolution sampling.}, }
@article {pmid42178395, year = {2026}, author = {Sharaf, H and Bobay, LM}, title = {MetaStrainer: Accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag340}, pmid = {42178395}, issn = {1367-4811}, abstract = {MOTIVATION: Metagenomics provides broad insights from microbial communities, but more biological relevant phenotypes are attributed to subtle changes at the strain-level rather than species. Despite development of several tools using different algorithms, resolving individual strains from short-read pair-end sequencing data remains challenging.<br><br>RESULTS: Here we present MetaStrainer, a tool capable of reconstructing strain genotypes from metagenomic data. Compared with existing approaches, MetaStrainer substantially increases genotype accuracy, correctly identifies the number of strains, and accurately estimates their relative abundances. Accuracy of reconstructed genotypes is robust to choice of mapping reference.<br><br>AVAILABILITY: MetaStrainer is implemented in Python 3. Source code and instructions are available on GitHub at www.github.com/lbobay/MetaStrainer and on Zenodo: 10.5281/zenodo.17872331.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid42178569, year = {2026}, author = {Garritano, AN and J Hill, L and Ribeiro, B and Damasceno, T and Medeiros, L and Duarte, G and L S Vilela, C and Majzoub, ME and Allen, MA and Nappi, J and S Peixoto, R and Thomas, T}, title = {Ammonia oxidation and recalcitrant carbon degradation fuel mixotrophic growth in the symbiont community of a deep-sea sponge.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42178569}, issn = {2049-2618}, support = {BAS/1/1095-01-01//KAUST/ ; ANP 21005-4//ANP, Brazil/ ; }, mesh = {Animals ; *Porifera/microbiology ; *Ammonia/metabolism ; *Symbiosis ; Oxidation-Reduction ; *Archaea/metabolism/genetics/classification/isolation &amp; purification ; *Microbiota ; *Carbon/metabolism ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Metagenomics/methods ; Autotrophic Processes ; Carbon Cycle ; Seawater/microbiology ; }, abstract = {BACKGROUND: Sponges are important members of shallow-water, benthic ecosystems, where they often rely on their microbial symbionts to acquire organic or inorganic carbon. Sponges are also found in the deep sea, however, how they metabolically interact there with their symbionts remains underexplored. Here, we combined metagenomic, metatranscriptomic and stable-isotope labelling approaches to investigate the metabolic activities of the microbial community of the deep-sea sponge Calyx sp.<br><br>RESULTS: Approximately 84% of the total estimated microbial abundance was composed of nine heterotrophic phyla, whilst the remaining 16% consisted of two autotrophic ammonia-oxidising archaea. Metatranscriptomic analysis revealed the high expression of genes involved in the degradation of recalcitrant polysaccharides of algal origin, suggesting that an undegraded fraction of marine snow plays a role in the nutrition of this deep-sea holobiont. Additionally, we detected active ammonia oxidation and carbon fixation pathways in the autotrophic community members and, through ex situ incubations with labelled carbonate show a potential to fix 13.67&#xa0;mg CO2 per g dry weight in a year.<br><br>CONCLUSIONS: This study highlights the mixotrophic lifestyle of a deep-sea sponge microbiome, expanding our knowledge of the sponge-microbe symbiosis in the oligotrophic environment of the deep ocean. Video Abstract.}, }
@article {pmid42178714, year = {2026}, author = {Zeamer, AL and Lai, Y and Loew, E and Sanborn, V and Tracy, M and Jo, C and Ferdinand, D and Ward, DV and Bhattarai, SK and Drake, J and McCormick, BA and Bucci, V and Haran, JP}, title = {Microbiome functional gene pathways are indicative of cognitive performance in older adults at risk for Alzheimer's disease.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2676162}, doi = {10.1080/19490976.2026.2676162}, pmid = {42178714}, issn = {1949-0984}, mesh = {Humans ; *Alzheimer Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Aged ; Female ; Male ; *Cognition ; Middle Aged ; *Cognitive Dysfunction/microbiology ; Aged, 80 and over ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Cohort Studies ; Metagenomics ; Metabolic Networks and Pathways/genetics ; }, abstract = {Disturbances in the gut microbiome are increasingly correlated with neurodegenerative disorders, including Alzheimer's disease. Multiple lines of emerging evidence are consistent with the microbiome's involvement in disease pathology in AD by triggering or potentiating systemic and neuroinflammation, thereby influencing disease pathology through the "microbiota-gut-brain axis." Currently, the copathologies contributing to cognitive decline and symptomatic progression in AD remain unknown and understudied. Changes in the gut microbiome composition may offer clues to potential systemic physiologic and neuropathologic changes that contribute to cognitive decline. Here, we recruited a cohort of 260 older adults (aged 60 y or older) living in the community and followed them over time, tracking objective measures of cognition, clinical information, and gut microbiome samples. Subjects were classified as healthy controls, exhibiting mild cognitive impairment, or having dementia based on clinical assessments. Using metagenomic sequencing and gene pathway analyses, we found that certain microbial-encoded metabolic pathways correlated with worse cognitive performance. Specifically, genes involved in the urea cycle, polyamine synthesis, or the metabolism of methionine and cysteine predicted worse cognitive performance. Our study suggests that the gut microbiome composition may be linked to cognitive impairment along the AD continuum and points to microbial metabolic pathways that may potentiate disease.}, }
@article {pmid42178721, year = {2026}, author = {Schulze, K and Goldschmidt, I and Melk, A and Boehne, M and Woltemate, S and Ballmaier, M and Kleiner, S and Lehmann, E and Kramer, M and Vital, M}, title = {Altered SIgA-targeting of gut microbiota is associated with long-term dysbiosis in pediatric solid organ transplant recipients.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2675078}, doi = {10.1080/19490976.2026.2675078}, pmid = {42178721}, issn = {1949-0984}, mesh = {Humans ; *Dysbiosis/microbiology/immunology/etiology ; *Gastrointestinal Microbiome ; Child ; Male ; Female ; *Immunoglobulin A, Secretory/immunology/genetics ; *Transplant Recipients ; Tacrolimus/adverse effects ; Bacteria/classification/genetics/isolation &amp; purification ; Adolescent ; Immunosuppressive Agents/adverse effects/therapeutic use ; *Organ Transplantation/adverse effects ; Feces/microbiology ; Child, Preschool ; Liver Transplantation/adverse effects ; }, abstract = {The composition of the gut microbiota (GM) is altered in solid organ transplantation (SOT) recipients, where the degree of dysbiosis is associated with long-term survival and is believed to be influenced by immunosuppression therapy. At the interface stands secretory (S)IgA, however, little is known about its role in governing dysbiosis in the context of SOT. We performed quantitative metagenomic analyses of the GM accompanied by SIgA sequencing in 48 pediatric SOT recipients (age = 10.6 ± 4.7 y) receiving either heart (n = 11), kidney (n = 10) or liver transplantation (n = 27), and compared the results to age-matched healthy controls (HC, n = 16). We confirmed compositional and functional dysbiosis in SOT recipients, with the degree of dysbiosis being associated with tacrolimus (TAC) levels. Overall, SOT recipients exhibited higher SIgA levels than HC, along with an increased percentage of bacteria targeted and altered target spectra. Furthermore, altered SIgA responses were associated with the degree of dysbiosis. A mechanistic model connecting immunosuppression, GM composition and SIgA-targeting is proposed, suggesting that GM dysbiosis in SOT recipients is mediated by the immune system through the SIgA response; direct drug-mediated effects on fecal communities were not observed in in vitro experiments. Our study provides new insights into factors that contribute to persisting dysbiosis in SOT recipients.}, }
@article {pmid42180198, year = {2026}, author = {Nnorom, MA and Du, B and Wang, Z and Tian, Z and Hough, R and Avery, L and Saroj, D and Guo, B}, title = {Dynamics of the Microbiome and Antibiotic Resistome in Hyper-Mesophilic Anaerobic Digestion of Cattle Manure Assisted with Granular Activated Carbon.}, journal = {ACS environmental Au}, volume = {6}, number = {3}, pages = {435-448}, pmid = {42180198}, issn = {2694-2518}, abstract = {The use of conductive materials, such as granular activated carbon (GAC), for optimization of the anaerobic digestion (AD) process has garnered attention in recent years; however, its impact on the dynamics of the microbiome and resistome in continuous AD systems remains unclear, especially under temperature variation. This study combined culture-based bacterial enumeration and shotgun metagenomics to investigate the impact of two GAC application strategies, suspended and packed, on the fate of pathogens (viable Escherichia coli) and ARGs during the AD of cattle manure at 40 and 45 °C. The results show that GAC mitigated the process imbalance and shock induced by temperature transition. The microbial community in the AD sludge was highly impacted by temperature but not GAC, while GAC biofilms showed notably higher archaeal abundance. All AD reactors reduced viable E. coli, with the highest reduction occurring in the packed GAC reactors (95.70-96.24%), followed by the suspended GAC (94.53-95.69%), and then the non-GAC (92.77-94.24%). Culturable tetracycline-resistant bacteria were reduced below the quantification limit in all reactors. Reduction of ampicillin-resistant bacteria showed stochastic trends at 40 °C but improved at 45 °C, indicating limited impact by GAC. ARGs and mobile genetic elements (MGEs) were reduced in all reactors at comparable levels, regardless of GAC addition. Temperature transition exerted a mixed effect, with higher reduction of some resistance classes (MLS, tetracycline, and multidrug) and lower reduction of others (bacitracin, aminoglycoside, beta-lactam, and streptothricin). Mantel test and Procrustes analysis revealed a significant correlation between the resistome and the bacterial community, inferring that shifts in the ARG host population were a major determinant of the fate of ARGs. Overall, GAC was beneficial to reactor stability but had a minimal influence on the reduction of E. coli, ARGs, and MGEs. It is highly recommended to monitor antimicrobial resistance using both culture-based and culture-independent methods.}, }
@article {pmid42180259, year = {2026}, author = {He, J and Ning, Y and Liang, H and Qin, J and Wei, Y and Liang, S and He, Z and Yin, S}, title = {Special pathogen infections presenting with neck mass as the initial manifestation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1767591}, pmid = {42180259}, issn = {2235-2988}, mesh = {Humans ; Male ; Female ; Middle Aged ; Adult ; Aged ; *Neck/pathology/microbiology ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology/pathology/drug therapy ; *Mycoses/diagnosis/microbiology/pathology/drug therapy ; *Talaromyces/isolation &amp; purification ; Nontuberculous Mycobacteria/isolation &amp; purification ; China ; Lymphadenopathy/microbiology ; }, abstract = {BACKGROUND: The etiology of neck masses is complex. Infections caused by Talaromyces marneffei (TM) and nontuberculous mycobacteria (NTM) are uncommon but often present with insidious clinical manifestations, leading to frequent misdiagnosis.<br><br>METHODS: We collected and analyzed data from 13 patients with TM/NTM infections presenting with neck masses at The First Affiliated Hospital of Guangxi Medical University and The Second Affiliated Hospital of Guangxi Medical University. Clinical manifestations, laboratory findings, infection sites, pathogen types, treatments, and outcomes were described and analyzed.<br><br>RESULTS: Of the 13 patients, six were male and seven female, with a median age of 57 years (range, 27-73 years). All patients were residents of Guangxi and tested positive for anti-interferon-&#x3b3; autoantibodies (AIGAs), with titers of 1:2500 in 12 patients and 1:500 in one. The median time from symptom onset to diagnosis was 5 months (range, 1-19 months). Common clinical features included lymphadenopathy (13/13), fever (11/13), respiratory symptoms (10/13), and rash or skin ulceration (8/13). Frequent laboratory abnormalities included leukocytosis (11/13), neutrophilia (11/13), elevated erythrocyte sedimentation rate (12/13), and elevated C-reactive protein (13/13). Coinfection with two or more pathogens was observed in 12 patients. The lungs and lymph nodes were involved in all 13 patients, followed by bone (11/13), skin or soft tissue (8/13), bloodstream or bone marrow (3/13), and nasopharynx (3/13). Neck mass specimens yielded NTM in nine cases and TM in four. NTM was most frequently identified by metagenomic next-generation sequencing (mNGS), whereas TM was detected by culture. The median follow-up duration was 28 months (range, 1-86 months). During follow-up, 6 patients (46.2%) experienced disease exacerbations. Among the 13 patients, 12 achieved clinical improvement after pathogen-directed antimicrobial therapy, while one patient died.<br><br>CONCLUSION: Neck masses have diverse etiologies. TM and NTM infections presenting initially as neck masses are rare and easily misdiagnosed as tuberculosis, malignancy, or lymphoma. Culture and mNGS are crucial diagnostic tools for TM and NTM, respectively. Clinicians should maintain a high index of suspicion for these infections, particularly in immunocompromised patients in endemic regions.}, }
@article {pmid42180316, year = {2026}, author = {Chen, X and Zhang, M and Yang, L and Chen, Y and Chi, Y and Zhao, Y and Ma, Z and Li, Y and Wang, X}, title = {CRISPR spacer profiling and prophage mining reveal diverse bacteriophages associated with Streptococcus Mutans.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2674332}, pmid = {42180316}, issn = {2000-2297}, abstract = {BACKGROUND: Streptococcus mutans is a key cariogenic bacterium. Current antimicrobials lack species specificity, while phage-based approaches remain experimental and require more S. mutans phage isolates.<br><br>OBJECTIVE: To profile the diversity of S. mutans-associated phages and strain-level heterogeneity in phage exposure using genome-informed CRISPR spacer and prophage analyses.<br><br>MATERIALS AND METHODS: We compiled 944 publicly available S. mutans genomes and dereplicated them into 735 non-redundant strains. CRISPR-Cas systems, spacers, spacer targets, and putative prophages were identified, quality-assessed, and functionally annotated. Phylogenetic relationships of (pro)phages were evaluated using terminase large subunit proteins, and comparative genomics compared spacer-positive and spacer-negative strains.<br><br>RESULTS: CRISPR systems were detected in 548/735 strains, yielding 14,263 spacers, 1,864 phage-targeting spacers mapped to 110 viral genomes, including 41 cultured isolates, 51 metagenome-assembled phages, and 18 uncultured viral genomes. The most frequently targeted cultured phage was phiKSM96, whereas metagenome-assembled Caudoviricetes ctNo011 showed broader targeting. Prophage mining identified 186 regions in 130 strains, including 37 of &#x2265; medium quality and elements related to ctNo011 and phiKSM96. TerL phylogeny showed that most high-quality endogenous prophages clustered with phiKSM96 and ctNo011.<br><br>CONCLUSION: These findings reveal a vast, uncultivated phage repertoire targeting S. mutans, providing a critical genomic roadmap to guide the future isolation of novel phages for caries prevention.}, }
@article {pmid42180431, year = {2026}, author = {Mallawaarachchi, V and Bouras, G and Wick, RR and Grigson, SR and Papudeshi, B and Edwards, RA}, title = {agtools: a software framework to manipulate assembly graphs.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag126}, pmid = {42180431}, issn = {2635-0041}, abstract = {MOTIVATION: Assembly graphs are a fundamental data structure used by genome and metagenome assemblers to represent sequences and their overlap information, facilitating the assembler in constructing longer genomic fragments. Apart from their core use in assemblers, assembly graphs have become increasingly important in a range of downstream applications such as metagenomic binning, plasmid detection, viral genome resolution, and haplotype phasing. However, there is a need for a comprehensive tool that allows programmatic access to manipulate assembly graphs (e.g. parse, convert, filter, and analyze) across different assembly graph formats.<br><br>RESULTS: Here we present agtools, an open-source Python framework to manipulate assembly graphs produced by commonly used assemblers. agtools provides a command-line interface for tasks such as assembly graph format conversion, segment filtering, and component extraction. It also exposes a Python package interface to load, query, and analyze assembly graphs from popular genome and metagenome assemblers. This enables streamlined assembly-graph-based analyses that can be integrated into other bioinformatics software and workflows.<br><br>The source code of agtools is hosted on GitHub at https://github.com/Vini2/agtools and the documentation is available at https://agtools.readthedocs.io/. agtools can also be installed from Bioconda (https://anaconda.org/bioconda/agtools) and PyPI (https://pypi.org/project/agtools/).}, }
@article {pmid42180728, year = {2026}, author = {Wang, T and Wang, M and Zhao, L and Tang, G and Hou, L}, title = {Case Report: Pulmonary brucellosis presenting as multiple cavitary lung lesions on imaging.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1814731}, pmid = {42180728}, issn = {2296-858X}, abstract = {Pulmonary brucellosis is a rare focal manifestation of human brucellosis with non-specific clinical features. Predominant imaging findings include pneumonia, pleural effusion, pulmonary nodules, abscesses, and interstitial changes. Multiple cavitary lesions are exceptionally rare. Herein, we report a case of bilateral multiple pulmonary cavities in a 76-year-old man with a 2-year history of intermittent cough, sputum production, and progressive dyspnea that acutely worsened 10 days prior to admission with intermittent fever, anorexia, and fatigue. Chest computed tomography (CT) revealed bilateral upper lobe irregular mass-like opacities and multiple nodules with heterogeneous density, punctate calcifications, and cavitation; multiple microcavitations in the right middle and lower lobes and the left lower lobe; and enlarged, calcified hilar and mediastinal lymph nodes. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid identified Brucella species, which was confirmed by positive serology. After 3 days of doxycycline (0.1 g bid po) and rifampicin (0.6 g qd po), followed by 140 days of doxycycline (0.1 g bid po), rifapentine (0.6 g biw po), and levofloxacin (0.5 g qd po), along with silibinin meglumine tablets 0.1 g tid po for hepatoprotective therapy, the patient became afebrile with significant symptomatic improvement. Repeat chest CT demonstrated reduction in the right upper lobe consolidation/cavity and left upper lobe consolidation, resolution of the right lower lobe cavity, and complete resolution of the microcavitations. This case underscores that pulmonary brucellosis should be considered in the differential diagnosis of cavitary lung lesions in patients with livestock exposure and that prolonged combination antibiotic therapy can achieve favorable clinical and radiological outcomes.}, }
@article {pmid42181109, year = {2026}, author = {Wunderer, M and Mullaymeri, A and Wagner, AO and Prem, EM}, title = {Comparative phenotypic and genomic analysis of the methanogen Methanomethylovorans thermophila L2FAW and its phylogenomic placement within the Genome Taxonomy Database.}, journal = {Access microbiology}, volume = {8}, number = {5}, pages = {}, pmid = {42181109}, issn = {2516-8290}, abstract = {The genome of the methylotrophic methanogen Methanomethylovorans thermophila L2FAW is not included in the Genome Taxonomy Database (GTDB) so far, even though the strain was first described in 2005. To evaluate its genomic characteristics and placement in the GTDB, we sequenced the genome of M. thermophila L2FAW via Illumina shotgun and Oxford Nanopore sequencing and subsequently did hybrid assembly. The assembled genome consists of 2.25 Mbp (contigs ≥500 bp) with a G+C content of 40 mol%. The quality of the genome is good, which is already apparent from the low L50 (=1) and L90 (=2) metrics. Our assembled genome was highly similar to the metagenome-assembled genome Methanomethylovorans sp014361205 (GCA_014361205.1_ASM1436120v1_genomic) with an average nucleotide identity of 99.9%. Even though KEGG Mapper Reconstruction results revealed that M. thermophila L2FAW harbours all the enzymes necessary for acetoclastic and hydrogenotrophic methanogenesis and gapseq predicted formate as a potential substrate for M. thermophila L2FAW, no metabolic activity could be observed on acetate, H2-CO2 (80:20 vol/vol, 2,000 mbar) and on a mixture of H2-CO2 and formate in lab tests; thus, the obligate methylotrophic lifestyle of the phenotype was confirmed.}, }
@article {pmid42181159, year = {2026}, author = {Bressuire, C and Thirion, F and Chiaravano, L and Ngom, SI and Marion, R and Gilles, M and Quinquis, B and Mathieu, E and Berland, M and Blottière, HM and Le Bourgot, C and Béra-Maillet, C}, title = {Short-chain fructo-oligosaccharides modulate gut microbiota composition and metabolism: dose-response assessment in an ex vivo gut model.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2674335}, pmid = {42181159}, issn = {2993-3935}, abstract = {Short-chain fructo-oligosaccharides (scFOS) are prebiotic fiber rapidly fermented in the colon and known to stimulate beneficial bacteria, such as Bifidobacterium spp. and Lactobacillaceae. While their overall effects on the gut microbiota are established, the dose-response relationship remained only partially characterized. This study aimed to determine the minimum effective dose of scFOS required to modulate gut microbiota composition and functions. An ex vivo chemostat model was used to simulate colonic fermentation with different doses of scFOS (1 to 10 g/d). Microbiota composition and metabolic activity were assessed by qPCR, short-chain fatty acid (SCFA) quantification, and shotgun metagenomics. An increase in scFOS dose led to higher SCFA levels, particularly acetate and butyrate, along with a modification in microbial composition, with a minimum significant effective dose of 2.5 g/d. Significant increase in Bifidobacterium adolescentis, Anaerostipes hadrus, and Clostridium innocuum was observed at the same dose. Functional analysis revealed an enrichment of GH32 genes in the pangenomes of species positively impacted by scFOS. These findings demonstrate that low doses of scFOS can effectively modulate the gut microbiota and enhance SCFA production, supporting their use in dietary interventions aimed at improving intestinal health.}, }
@article {pmid42182002, year = {2026}, author = {Chen, S and Hu, X and Pan, W and Chen, T and Xie, X and Zhang, Y}, title = {Integrated metagenomic and culture-dependent profiling reveals electric shavers as selective reservoirs for multidrug-resistant opportunistic pathogens.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1839764}, pmid = {42182002}, issn = {1664-302X}, abstract = {INTRODUCTION: Personal care items are commonly viewed as passive vehicles for microbial transfer; however, the physicochemical stresses they impose may actively shape microbial persistence, community composition, and the distribution of resistance-associated determinants. Electric shavers may therefore constitute an underrecognized anthropogenic niche for the enrichment of clinically relevant antimicrobial resistance traits.<br><br>METHODS: We sampled electric shavers from 10 individuals at early (day 2) and mature (day 21) usage stages, generating 8 high-quality metagenomes and recovering 97 viable isolates spanning 16 bacterial species. Deep metagenomic sequencing, combined with whole-genome sequencing of 45 representative isolates, was used to resolve the ecological, functional, and evolutionary features of shaver-associated microbiomes.<br><br>RESULTS: Shaver-associated community assembly was dominated by stringent environmental filtering, which promoted the repeated enrichment of stress-adapted lineages across hosts, notably Acinetobacter ursingii MLST3244 and Klebsiella pneumoniae MLST995 and MLST23. We further identified recurrent mobile genetic element-associated resistance islands and plasmid backbones in different host cohorts, suggesting repeated selection under shared anthropogenic pressures rather than direct evidence of de novo convergent evolution. Importantly, viable Klebsiella pneumoniae isolates co-carried extended-spectrum &#x3b2;-lactamase genes such as bla SHV and major virulence determinants, while metagenomic profiling detected reads assigned to mcr- and tet(X)-like gene variants at the community level, targeted PCR further confirmed the presence of these resistance determinants.<br><br>DISCUSSION: Because routine shaving can generate barrier-disrupting micro-abrasions, electric shavers may function as selective reservoirs for multidrug-resistant bacteria. Our findings reveal a previously overlooked exposure interface through which everyday personal care practices may promote the enrichment and persistence of clinically important resistance and virulence determinants.}, }
@article {pmid42182003, year = {2026}, author = {Li, F and Liu, X and Hou, W and Dong, H and Hu, J and Chen, H and Zhong, Y and Wu, Y and Xu, X and Ding, Y}, title = {Archaeal communities as indicators of hydrothermal influence in the Tianxiu vent field, Northwest Indian Ocean.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1837947}, pmid = {42182003}, issn = {1664-302X}, abstract = {Deep-sea hydrothermal sediments represent critical zones for archaea-driven biogeochemical cycling, yet the ecological differentiation of archaeal communities across hydrothermal gradients remains poorly understood. Here, we used 16S rRNA gene amplicon sequencing of sediment cores from two contrasting sites in the Tianxiu hydrothermal field of the Northwest Indian Ocean, and performed metagenomic analysis on the near-vent BC12 sediments, to investigate archaeal community composition, co-occurrence patterns, and metabolic potential in response to the hydrothermal activity. Comparative analysis revealed marked divergence between near-vent site BC12 and far-vent site JL218P. The site BC12, under stronger hydrothermal influence, was enriched in Hydrothermarchaeia, along with Nanoarchaeia and Thermoplasmata, and exhibited a more complex, highly connected co-occurrence network. Correlation analyses further showed that Hydrothermarchaeia abundance was significantly associated with hydrothermal-related geochemical gradients, supporting this lineage as a potential indicator of hydrothermal influence. Metagenomic analysis of BC12 further revealed Hydrothermarchaeia genomes encoding the Wood-Ljungdahl carbon fixation pathway, while genome-centric functional inference suggested enhanced potential for methanogenesis and hydrogen oxidation. In contrast, JL218P was dominated by Nitrososphaeria, showed limited vertical variation, and formed a simpler network structure, with predicted functional profiles more closely associated with nitrification and aerobic ammonia oxidation. Together, these findings identify hydrothermal-related geochemical heterogeneity as a major driver of archaeal community composition, ecological organization, and metabolic differentiation in deep-sea sediments, and advance our understanding of the ecological drivers structuring deep-sea hydrothermal ecosystems.}, }
@article {pmid42182018, year = {2026}, author = {Abilda, Z and Isgandarov, I and Kanat, R and Daurov, D and Sapakhova, Z and Zhambakin, K and Daurova, A and Begaliyeva, D and Choi, K and Shamekova, M}, title = {Genome-resolved metagenomics reveals co-selection of antibiotic and metal resistance in chronically polluted industrial soils.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1829529}, pmid = {42182018}, issn = {1664-302X}, abstract = {INTRODUCTION: Chronic heavy metal contamination can restructure soil microbiomes and may co-select for antibiotic resistance, yet genome-resolved evidence from industrial soils remains limited.<br><br>METHODS: In this study, we applied Oxford Nanopore long-read metagenomic sequencing to soil samples collected across industrially influenced sites in East Kazakhstan to characterize strain-level community composition, profile antibiotic resistance genes and metal resistance genes, and relate these patterns to soil physicochemical properties.<br><br>RESULTS: Across all samples, we identified 3,053 strains, with Actinobacteria and Proteobacteria together accounting for 94.1% of the total community. Heavy metal concentrations varied markedly among sites. The resistome comprised antibiotic resistance genes from several drug classes and 238 distinct metal resistant genes, with aminoglycoside, glycopeptide, and multidrug resistance dominating the antibiotic resistance gene profile, while czcA, ruvB, arsM, and arsT were among the most abundant Metal resistant genes. Multivariate analyses showed that heavy metals, particularly Zn, significantly shaped microbial community structure as well as antibiotic resistance gene and metal resistance gene composition, and redundancy analysis identified Zn and soil pH as the principal environmental drivers. Network analyses further revealed that Bradyrhizobium icense and Conexibacter woesei acted as key super-hosts linking ARGs and MRGs, supporting heavy metal-driven co-selection within the soil microbiome.<br><br>DISCUSSION: Together, these findings show that long-read genome-resolved metagenomics can uncover how chronic industrial pollution maintains metal-adapted microbial communities while promoting the persistence and potential dissemination of antibiotic resistance in soil ecosystems.}, }
@article {pmid42182023, year = {2026}, author = {Duan, J and Chen, Y and Zhang, X and Li, C and Gao, T and Li, K}, title = {Metagenomic analysis suggests that tomato root-knot nematode infestation disrupts rhizosphere microbial networks, consistent with reduced disease suppression.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1798902}, pmid = {42182023}, issn = {1664-302X}, abstract = {INTRODUCTION: The rhizosphere microbiome serves as a critical line of defense for plant health and soil-borne disease suppression. However, the underlying mechanisms by which root-knot nematodes (RKN), a devastating soil-borne pathogen, undermine putative disease-suppressive function through destabilizing microbial interaction networks remain poorly understood.<br><br>METHODS: This study employed metagenomic sequencing coupled with microbial co-occurrence network analysis to systematically compare the community structure, interaction network topology, and functional gene profiles of the rhizosphere microbiome between healthy and RKN-infected tomato plants.<br><br>RESULTS: Our findings revealed that RKN infection significantly altered the community structure of bacteria, fungi, and viruses. This disturbance was associated with a systematic simplification and loss of modularity within microbial interaction networks. Specifically, intra-domain bacterial networks exhibited reduced scale and connectivity, whereas fungal networks showed strengthened internal cohesion. Cross-kingdom interactions (e.g., bacteria-fungi) were severely weakened, resulting in a topological imbalance characterized by "tight within domains, loose between domains." Functional profiling further indicated a distinct metabolic reprogramming in the infected rhizosphere, with a shift in resource allocation from growth and biosynthesis toward core energy acquisition and stress response.<br><br>DISCUSSION: Collectively, our results suggest that the putative decline in disease-suppressive function following RKN infection may be mechanistically rooted in the destabilization of microbial cooperative networks and the consequent loss of functional redundancy. This study provides a novel network-level ecological framework for understanding plant-microbe-pathogen interactions and lays a theoretical foundation for microbiome-based ecological management strategies against soil-borne diseases.}, }
@article {pmid42182035, year = {2026}, author = {Qian, W and Han, A and Al Hatmi, AMS and Wang, Y and Rafiq, M and Cui, G and Zhou, S and Li, S and Kang, Y}, title = {Concordance between environmental resistomes and pathogenic phenotypes: a case study of multidrug-resistant Klebsiella pneumoniae in a drinking water source in Guizhou, China.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1810806}, pmid = {42182035}, issn = {1664-302X}, abstract = {INTRODUCTION: The persistence of antibiotic resistance in aquatic environments poses a public health concern, particularly when drinking water sources act as reservoirs for multidrug-resistant opportunistic pathogens. However, the linkage between environmental resistomes and the resistance phenotypes of cultivable bacteria remains under-characterized. This case study investigated this relationship in a karst drinking water source in Guizhou, China.<br><br>METHODS: Surface water samples from seven sites were analyzed for antibiotic residues using LC-MS/MS. Metagenomic sequencing was conducted on selected contamination hotspots to characterize microbial communities and antibiotic resistance genes (ARGs). Cultivable bacteria were isolated, identified via 16S rRNA sequencing, and tested for antimicrobial susceptibility. To validate resistance mechanisms, a multidrug-resistant Klebsiella pneumoniae isolate was analyzed for tetA expression using RT-qPCR.<br><br>RESULTS: Antibiotic residues were detected across all sites, with sulfonamides and tetracyclines being the most prevalent. Consistent with this chemical pressure, metagenomic analysis identified corresponding ARGs, including sul1 and tet(Q), which functionally clustered with mobile genetic elements. From the contaminated matrix (sample W2), a multidrug-resistant Klebsiella pneumoniae strain (B8) was recovered. Mechanistic validation revealed a 2.78-fold upregulation of the tetA efflux pump gene in this strain.<br><br>DISCUSSION: These findings demonstrate a concordance among chemical selection pressures, environmental resistomes, and active resistance phenotypes. The results indicate that drinking water sources can harbor and maintain clinically relevant resistant bacteria, supporting the implementation of integrated surveillance strategies to evaluate biological risks.}, }
@article {pmid42182110, year = {2026}, author = {Zhang, Z and Holton, M and Ferrer, DM and Tripp, AD and Richter, A and Dixit, PD and Urtecho, G}, title = {Metagenome-scale Modeling to Assess Microbiome Metabolic Complementarity for Precision Microbiota Transplantation Therapies.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.15.725570}, pmid = {42182110}, issn = {2692-8205}, abstract = {Fecal microbiota transplantation (FMT) holds therapeutic promise beyond recurrent Clostridioides difficile infection, but clinical outcomes remain unpredictable, in part because existing computational models do not fully capture the metabolic compatibility between donor and recipient communities. Here, we present a metagenome-scale metabolic modeling framework that quantifies metabolic niche complementarity between donor and recipient microbiomes to predict transplantation outcomes. Using MICOM-derived community metabolic models, we show that donor taxa whose metabolic flux profiles are more dissimilar from the recipient community engraft at significantly higher rates in both murine and human FMT cohorts. In a human IBS trial, metabolic models accurately predicted post-FMT community composition via leave-one-out cross-validation and recapitulated disease-associated alterations in short-chain fatty acid, sulfur, and gas metabolism. We then performed 2,548 in silico FMT simulations between IBS-D/M patients and donors from the OpenBiome biobank to demonstrate a platform for personalized donor screening. This screen identified super-donors characterized by high taxonomic diversity, broad metabolic niche coverage, and community interaction networks dominated by cross-feeding rather than competition, as quantified by a flux-derived ecological network balance index that strongly predicted engraftment potential. This framework provides a mechanistic, scalable tool for rational donor-recipient matching that could guide personalized microbiome-based therapies.}, }
@article {pmid42182295, year = {2026}, author = {Kumar, A and Keerthipati, P and Lotana, H and White, T and Jones, E and Prescrille, J and Webb, T and Zhu, Y and Somakhin, A and Johnson, D and Tsymbalyuk, O and Simard, M and Qin, X and Ge, Y and Zhang, H and Dilipkumar, S and Gonzalez-Juarbe, N and Drake, WP}, title = {The Vagus Nerve conducts viable translocation of gut flora to the lungs that impacts interstitial lung disease severity in mice.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.15.725489}, pmid = {42182295}, issn = {2692-8205}, abstract = {Communication between gut microbiota and extraintestinal organs is increasingly recognized, yet elucidation of relevant translocation mechanism(s) remains enigmatic. Vagus neuroanatomy and reports of vagal protein transfer to extraintestinal organs suggest that this "superhighway" could translocate bacteria. Here we explore whether the vagus superhighway can translocate bacteria to extraintestinal organs. Gavage of green fluorescent protein-expressing Escherichia coli (GFP- E. coli) into germ-free (GF) or specific-pathogen free (SPF) C57BL/6 mice yielded high bacillary loads in the stomach and lungs, followed by the heart, stool and peripheral muscles, despite negative blood cultures. Notably, confocal microscopy and culture revealed GFP- E. coli within the vagus nerve within five minutes of gavage suggesting rapid translocation. Metagenomic analysis of stool, lung, heart, vagus nerve, and muscle from non-gavaged SPF mice demonstrated significant microbial overlap, supporting that bacterial translocation occurs despite the presence of endogenous microflora. Remarkably, subdiaphragmatic vagotomy performed prior to GFP- E. coli gavage resulted in marked reductions of bacterial transduction in the lungs and other extraintestinal organs, except muscle. Furthermore, vagotomy significantly reduced lung fibrosis in SPF mice following intranasal bleomycin administration. In lung cancer patients undergoing lobectomy, vagotomy inhibited postsurgical reductions in forced vital capacity. These findings identify the vagus nerve as a literal gut-lung axis, facilitating viable bacterial translocation and influencing lung severity.}, }
@article {pmid42182444, year = {2026}, author = {Wright, JT and Yendluri, S and Thomas, NC and Butterfield, CN and Dangerfield, TL and Taylor, DW}, title = {Structural and kinetic insights into a metagenomics-derived Cas12a with high specificity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.13.724879}, pmid = {42182444}, issn = {2692-8205}, abstract = {CRISPR-Cas12a nucleases provide an attractive alternative to Cas9 due to their compact RNA scaffold, T-rich PAM requirement, and improved target specificity. However, the mechanistic features that govern activity and discrimination across Cas12a orthologs remain incompletely understood. Here, we characterize Cas12a-MG29-1, a highly active and specific nuclease identified through metagenomic mining, using cryogenic electron microscopy, mutational analysis, and kinetic modeling. The Cas12a-MG29-1 structure reveals repositioned flexible loops near the distal end of the R-loop, including reduced engagement of one loop region and additional contacts formed by a second distal loop. Structure-guided mutagenesis and loop-swap experiments indicate that distal R-loop architecture modulates target discrimination in a context-dependent manner. Single-turnover cleavage and stopped-flow measurements show that Cas12a-MG29-1 and AsCas12a form reversible R-loops with similar kinetics but differ in strand cleavage following R-loop formation. Global kinetic modeling demonstrates that Cas12a-MG29-1 exhibits accelerated non-target strand cleavage, shifting kinetic partitioning toward product formation. This faster irreversible commitment provides a mechanistic explanation for enhanced activity and specificity without altering initial target interrogation. Together, these findings identify distal R-loop interactions and catalytic commitment as key determinants of Cas12a function and provide a framework for interpreting and engineering next-generation Cas12a orthologs.}, }
@article {pmid42182637, year = {2026}, author = {Cai, X and Pang, S and Tang, C and Li, S}, title = {Relationship between airway stents and airway microorganisms: a literature review.}, journal = {Journal of thoracic disease}, volume = {18}, number = {4}, pages = {418}, pmid = {42182637}, issn = {2072-1439}, abstract = {BACKGROUND AND OBJECTIVE: Airway stent placement is widely used for the management of airway stenosis; however, it can be associated with complications such as granulation, stent migration, and infection, all of which affect patient outcomes. Among these complications, infection is a major concern, yet the relationship between airway stents and microbial colonization remains insufficiently studied. This review aims to summarize the current evidence on the effects of airway stents on the airway microbiome and to discuss their potential clinical implications.<br><br>METHODS: A literature search was conducted in PubMed for relevant studies published from database inception to December 31, 2025. Search terms included "airway stent", "tracheal stent", "bronchial stent", "airway microbiome", "biofilm", and "respiratory infection". Relevant studies were screened according to predefined criteria, and the available evidence was narratively synthesized.<br><br>KEY CONTENT AND FINDINGS: Available evidence suggests that airway stents can alter the airway microenvironment and facilitate microbial colonization, most commonly involving Pseudomonas aeruginosa (P. aeruginosa), Staphylococcus aureus (S. aureus), and Klebsiella pneumoniae (K. pneumoniae). Both metallic and silicone stents lead to similar microbial profiles, dominated by P. aeruginosa and S. aureus. Although microbial colonization frequently occurs after stent implantation, colonization does not necessarily reflect clinically significant infection, and microbiological findings should be interpreted in the clinical context. Most clinical studies report an increased risk of respiratory infection following airway stent placement. In certain specific clinical situations, such as patients with tracheoesophageal fistula, infection rates may decrease after stenting due to restoration of airway integrity. Conventional culture-based methods remain adequate for detecting common respiratory pathogens, while emerging techniques such as metagenomic next-generation sequencing (mNGS) enable broader characterization of airway microbial communities.<br><br>CONCLUSIONS: Airway stents appear to alter the airway's microbial environment by promoting the growth of potentially pathogenic microorganisms. Different stent materials, including silicone stents and self-expanding metallic stents (SEMS), seem to affect the biofilm formation on the stents' surface, which may influence microbial colonization. More studies with larger sample sizes, standardized methodologies, and advanced techniques like metagenomic sequencing are needed to further clarify the microbial changes and improve clinical management.}, }
@article {pmid42182855, year = {2026}, author = {Jia, Y and Zhu, Y and Cai, H}, title = {Polymicrobial Multidrug-Resistant Infection and Fatal Bowel Ischemic Perforation After Urgent Heart Transplantation in a VA-ECMO-Bridged Recipient: A Case Report.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {604688}, pmid = {42182855}, issn = {1178-6973}, abstract = {Post-transplant infection caused by multidrug-resistant organisms (MDROs) is a major challenge in heart transplantation, especially in recipients requiring veno-arterial extracorporeal membrane oxygenation (VA-ECMO) before surgery. We describe a 52-year-old man with non-ST-elevation myocardial infarction and refractory cardiogenic shock who required VA-ECMO, intra-aortic balloon pump support, continuous renal replacement therapy, and mechanical ventilation before urgent heart transplantation. Before transplantation, he had active pneumonia. Donor respiratory culture grew Acinetobacter baumannii, Pseudomonas aeruginosa, and Staphylococcus aureus, whereas donor blood culture and blood metagenomic next-generation sequencing (mNGS) were negative. After transplantation, serial mNGS and conventional cultures revealed rapidly progressive polymicrobial infection involving Stenotrophomonas maltophilia, Burkholderia multivorans, carbapenem-resistant Acinetobacter baumannii, carbapenem-resistant Klebsiella pneumoniae, and vancomycin-resistant Enterococcus faecium. Antimicrobial therapy was repeatedly adjusted, and VA-ECMO was successfully discontinued on postoperative day 13. However, on postoperative day 16, the patient developed bowel ischemia with gastrointestinal perforation, followed by feculent peritonitis, persistent septic shock, progressive multiorgan dysfunction syndrome, and death on postoperative day 24. This case shows that perioperative infection control in VA-ECMO-bridged urgent heart transplant recipients requires more than broad-spectrum antimicrobial escalation. It requires careful assessment of preoperative infection controllability, interpretation of mNGS in conjunction with culture-based susceptibility testing, and early investigation of occult abdominal ischemia when clinical deterioration is unexplained.}, }
@article {pmid42183063, year = {2026}, author = {Zhang, J and Chen, C and Hu, Y and Jia, S and Li, B and Hu, W and Jia, Y and Li, D and Liu, Y}, title = {Interaction between microorganisms and flavour products during cigar fermentation promoted by citrus Reticulata-"Chenpi" derived Enterobacter G5Z-2: based on multi-omics studies and microbial profiles.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {14}, number = {}, pages = {1785975}, pmid = {42183063}, issn = {2296-4185}, abstract = {INTRODUCTION: Cigar fermentation is crucial for developing its characteristic aroma, exogenous microorganisms can be used to enhance fermentation. It is reported that the citrus reticulata 'Chachi' (Chenpi, a traditional fermented ingredient) extract can improve the flavor of cigarette. However, there is no report on the influence of Chenpi-derived microorganisms on the fermentation process and flavor quality of cigar tobacco leaves (CTLs) till now.<br><br>METHODS: A fermentation strain (Enterobacter hoffmannii, G5Z-2) was isolated from Chenpi, and it was applied as a bioaugmentation agent in CTLs fermentation. A multi-omics approach, including metagenomics and metabolomics, was employed to investigate its impact.<br><br>RESULTS: Inoculation with G5Z-2 significantly altered the microbial community structure, suppressing native Pseudomonas and reducing overall alpha diversity while enriching beneficial genera like Aspergillus and Staphylococcus. Metabolomic analysis revealed substantial restructuring of metabolic pathways, particularly the enrichment of amino acid metabolism (such as arginine biosynthesis and phenylalanine metabolism) and nicotinate/nicotinamide metabolism. This led to accelerated degradation of proteins and amino acids, providing precursors for Maillard reaction, and a marked increase (57.5%) in total volatile flavour compounds, including key aroma constituents from carotenoid and cembranoid degradation.<br><br>CONCLUSION: The Chenpi-derived E. hoffmannii G5Z-2 optimises the fermentation process by modulating the microbial consortium and driving metabolic shifts towards favourable flavour development, demonstrating significant potential for improving the quality of Chinese-style cigars.}, }
@article {pmid42184066, year = {2026}, author = {Al Awawdeh, S and Shafie, NH and Ishak, AH and Mohd Esa, N and Loh, SP and Nurdin, A}, title = {Green tea polyphenol-iron oxide chitosan nanoparticles modulate gut microbiota and regulate metabolic pathways.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42184066}, issn = {1573-0972}, support = {GP-IPS/2023/9772000//Universiti Putra Malaysia/ ; FRGS/1/2018/SKK10/UPM/02/5//Ministry of Higher Education, Malaysia/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Polyphenols/pharmacology/chemistry/administration &amp; dosage ; Rats, Sprague-Dawley ; Male ; Rats ; *Chitosan/chemistry ; *Tea/chemistry ; *Metabolic Networks and Pathways/drug effects ; Liver/metabolism/drug effects ; *Nanoparticles/chemistry ; *Ferric Compounds/chemistry ; Proteome ; Proteomics ; Bacteria/classification/genetics/drug effects ; }, abstract = {Green tea polyphenols (GTPP) exhibit antioxidants, anti-inflammatory, and anticancer properties; however, their poor bioavailability limits clinical translation. Nanoparticle-based formulations may enhance absorption and therapeutic potential. This study investigates the therapeutic effects of GTPP encapsulated in iron oxide chitosan nanoparticles (GTPP-IOCHNP) on gut microbiota and hepatic proteome, with particular attention to pathways relevant to inflammation, drug metabolism, and tumorigenesis. Male Sprague Dawley rats were administered a single oral dose of GTPP or GTPP-IOCHNP (200 mg/kg). Cecal microbiota composition was analyzed by metagenomic sequencing, while liver proteome alterations were assessed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Metagenomic analysis revealed that GTPP-IOCHNP promoted Actinobacteriota and Collinsella, both linked to reduced inflammation and improved gut health, while inhibiting Bacteroides and Ruminococcus genera associated with intestinal barrier dysfunction, inflammation, and nephropathy. Blautia was significantly enriched (p < 0.05), supporting short chain fatty acid production, modulation of lipid and carbohydrate metabolism, and transformation of polyphenols into bioactive antioxidant metabolites. Proteomics profiling identified 20 differentially expressed hepatic proteins (p < 0.05). GTPP-IOCHNP significantly downregulated cytochrome P4502D26 (CYP2D6), indicating modulation of CYP2D6 mediated drug metabolism, and suppressed glutamate dehydrogenase 1, implicating inhibition of glutamine-driven energy metabolism linked to cancer and hyperinsulinism. Conversely, significant upregulation of elongation factor 1-alpha-1 (eEF1A1), albumin, and adenosine kinase (ADK) highlighted improved GTPP absorption, systemic transport, and regulation of hepatic energy metabolism. The integrative metagenomic and proteomic analyses reveal that GTPP-IOCHNP improves polyphenol bioavailability by modulating gut microbial ecology and hepatic metabolic pathways, offering a mechanistically driven platform for therapeutic advancement.}, }
@article {pmid42173516, year = {2026}, author = {Ogasawara, K and Uno, K and Tamahara, T and Asano, N and Sudo, K and Kusano, K and Tanabe, M and Kaise, Y and Shindo, T and Shimoyama, Y and Kanno, T and Koike, T and Shimizu, R and Masamune, A}, title = {Antibiotics treatment promotes squamocolumnar junction tumor progression via tumor immune evasion in K19-Wnt1/C2mE mice fed high-fat diet and acidic bile salts.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpgi.00056.2026}, pmid = {42173516}, issn = {1522-1547}, support = {19K08434//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; 23K07368//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; 24K13105//MEXT | JSPS | Japan Society for the Promotion of Science London (JSPS)/ ; }, abstract = {Clinical studies suggested that antibiotics (ABx) administration might increase esophagogastric junction adenocarcinoma risk, but the underlying mechanisms remain unclear. We previously demonstrated that the administration of a high-fat diet (HFD) and acid bile salts (ABS) to K19-Wnt1/C2mE mice might promote the metabolic-driven tumor growth at the squamocolumnar junction (SCJ) cooperatively with gut dysbiosis. To clarify whether ABx-induced dysbiosis promotes the tumorigenesis, we evaluated the effects of HFD+ABS ± ABx treatment on tumor immune evasion in mice. In HFD+ABS+ABx-treated mice, SCJ tumor growth with increased tumor cell proliferation and infiltration of inflammatory cells positive for CD8, programmed cell death protein 1 and programmed cell death-ligand 1 (PD-L1) were observed along with apoptosis suppression. Protein expressions of interferon-gamma (IFN(?)) and phosphorylated signal transducer and activator of transcription (p-STAT) 3 were upregulated in the tumors of the HFD+ABS+ABx group, whose p-STAT1 expression was equivalent to that of the control group. The mice exhibited insulin resistance and metabolic endotoxemia, and metagenomic analysis of their ileal excrement revealed dysbiosis with a decrease in butyrate-producing bacteria and bacterial butanoate metabolism activity. Moreover, IFN(?) stimulation of human-derived NUGC-4 cells increased the protein expression of PD-L1, p-STAT1 and p-STAT3, all of which decreased in response to STAT inhibitors. Transfection with small interfering RNA targeting STAT1 or STAT3 did not attenuate PD-L1 induction, which was inhibited by the combined knockdown. Therefore, oral HFD+ABS+ABx administration to K19-Wnt1/C2mE mice may promote SCJ tumors through tumor immune evasion via IFN(?)-STAT1/STAT3-PD-L1 signaling, along with metabolic endotoxemia.}, }
@article {pmid42173938, year = {2026}, author = {van Beek, N and Bargheet, A and Jian, C and Noordzij, HT and Ponsero, A and Pettersen, VK and Korpela, KE}, title = {Metagenomic survey of pathogen prevalence in the infant gut.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-47440-7}, pmid = {42173938}, issn = {2045-2322}, support = {101039583//ERC Starting Grant/ ; }, abstract = {The human microbiota impacts our health and well-being from infancy throughout our lives. Besides mutualistic and commensal strains, it also contains opportunistic pathogens. Infants may be especially vulnerable to opportunistic pathogen colonisation due to their immature immune systems and low microbial diversity.The study aims to examine associations between opportunistic pathogen prevalence and factors such as breastfeeding, antibiotic use, birth-mode, and the presence of other bacterial taxa. This study analysed 3981 publicly available shotgun metagenomes collected from 1275 infants and 415 mothers across ten countries to identify species that may be considered opportunistic pathogens in the infant gut. The prevalence of C. difficile was decreased in breastfed infants and in those carrying Faecalibacterium and Dorea spp. S. aureus carriage was negatively associated with antibiotic use and positively with skin contact and breastfeeding. K. pneumoniae was acquired later in life and was more prevalent in premature infants, and less commonplace in vaginal deliveries without antibiotics. Our findings indicate that opportunistic pathogen prevalence in the infant gut is influenced by medical and caregiving practices and may be modifiable through targeted interventions. Reducing the spread of these opportunistic pathogens could contribute to global efforts against early life infections.}, }
@article {pmid42174003, year = {2026}, author = {Kumari, R and Ghosh, C and Kumar, R and Shakya, R and Kumar, S and Saini, AK}, title = {Assessment of water quality and microbial contamination in institutional water resources: a necessity to understand health risks.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-53672-4}, pmid = {42174003}, issn = {2045-2322}, support = {project grant MH-32/2024//R&amp;D cell, Miranda House, University of Delhi, India/ ; }, abstract = {Lack of regular monitoring of water sources may lead to undetected contamination, posing serious health risks and necessitating regular water quality assessments. Sampling for physicochemical, microbial analyses, and online surveys across three higher education institutions was done to evaluate water quality. Spatiotemporal variations among physicochemical parameters showed that the pH, EC, and TDS decreased during the wet season, reflecting the dilution effect of rain. However, DO increased from 0.67 to 4.83 ppm, indicating better aeration. PCA showed seasonal variability, whereas the correlation matrix highlighted both positive and negative interrelationships between temperature-pH (- 0.25), DO-ORP (0.11), and TDS-EC (1.00). Potentially toxic metals were either negligible or not detected. Metagenomics revealed the presence of 29 bacterial phyla, 61 classes, 124 orders, 241 families, and 457 genera. Canonical correspondence analysis showed the influence of Mo, EC, salinity, and TDS on Bacteroidota, Chloroflexota, Cyanobacteriota, and Planctomycetota, whereas Verrucomicrobiota, Acidobacteriota, Chlamydiota, Candidatus Melainabacteria, Bdellovibrionota, and Deinococcota were affected by Ni, pH, and COD. Pathogen mapping revealed the presence of Vibrio, Pseudomonas, Enterobacter spp., etc., responsible for diseases such as cholera, diarrhea, and typhoid. Also, occupants' perception about the water quality emphasizes the need for better management of drinking water in HEIs.}, }
@article {pmid42174021, year = {2026}, author = {Min, U and Kim, J and Kim, J and Jin, H and Oh, H and Ahn, S and Shin, H and Lee, W}, title = {Spicy food intake and dietary factors shape the gut microbiome and metabolism of mucin and short-chain fatty acids in healthy adults.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-53556-7}, pmid = {42174021}, issn = {2045-2322}, abstract = {Whether spicy food intake independently modulates mucin metabolism and short-chain fatty acid (SCFA) production or depends on co-ingested factors such as alcohol remains poorly understood. Herein, shotgun metagenomics characterized gut microbial composition, functional pathways, and their relationship with spicy food intake, alcohol consumption, and intestinal fatty acid-binding protein (I-FABP) and liver fatty acid-binding protein (L-FABP) levels in 229 healthy Korean adults. Alcohol intake was positively correlated with urinary I-FABP levels indicating mild epithelial stress, whereas spicy food intake was not associated with either FABP biomarker. Consumption of highly spicy foods resulted in increased abundance of SCFA-producing and mucin-metabolizing taxa, along with mucin degradation and SCFA production. Individuals with high alcohol intake showed stronger enrichment of mucin-degrading taxa with reduced SCFA flux and increased abundance of Proteobacteria and Fusobacteria. The cross-classified dietary groups exhibited distinct mucin and SCFA activity patterns. The Drink-High-Spicy-High (DHSH) group displayed elevated mucin turnover and SCFA production with dysbiosis. These findings suggest that spicy food may modulate mucus layer metabolism in a context-dependent manner, whereas alcohol more consistently perturbs mucin-SCFA networks and epithelial integrity.}, }
@article {pmid42174437, year = {2026}, author = {van Bemmelen, J and Nika, I and Baaijens, JA}, title = {Benchmarking the impact of reference genome selection on taxonomic profiling accuracy.}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-12874-w}, pmid = {42174437}, issn = {1471-2164}, abstract = {BACKGROUND: Over the past decades, genome databases have expanded exponentially, often incorporating highly similar genomes at the same taxonomic level. This redundancy can hinder taxonomic classification, leading to difficulties distinguishing between closely related sequences and increasing computational demands. While some novel taxonomic classification tools address this redundancy by selecting a subset of genomes as references, insights regarding the impact of different reference genome selection methods across taxonomic classification tools are lacking.<br><br>RESULTS: We systematically evaluate genome selection and dereplication methods on bacterial and viral datasets using simulated metagenomic samples and a bacterial mock community. For bacterial species-level profiling, incorporating all available genomes generally yields the highest accuracy, while having a limited impact on computational resource usage. In contrast, for highly similar bacterial strain-level and SARS-CoV-2 lineage-level datasets we find that selection significantly improves abundance estimation accuracy. Incorporating location-based metadata further enhances viral profiling performance by prioritizing locally relevant genomes. Across viral experiments, smaller reference sets significantly reduce memory and runtime requirements during both indexing and profiling, although this comes at an additional pre-processing cost.<br><br>CONCLUSIONS: Reference genome selection influences both accuracy and computational efficiency in taxonomic profiling, but its benefits seem context- and resolution-dependent. Our results demonstrate that reference set design does not have a one-size-fits-all solution, and that selection strategies should be adapted based on the biological and computational setting.}, }
@article {pmid42174665, year = {2026}, author = {Nolan, S and Trego, A and Waters, N and Thorn, C and Fenton, O and Richards, KG and O'Flaherty, V and Ijaz, UZ and Abram, F}, title = {Using feeding regime as a microbial selective pressure to optimise biogas production and digestate sanitisation from slurry-based anaerobic digestion.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00902-x}, pmid = {42174665}, issn = {2524-6372}, support = {14 F847//Irish Department of Agriculture, Food and Marine/ ; }, abstract = {BACKGROUND: The urgent need to adopt sustainable agricultural practices has positioned anaerobic digestion (AD) as a pivotal technology. Indeed, slurry-based AD can mitigate agricultural pollution by capturing greenhouse gas from stored slurry and converting it into biomethane, a valuable source of renewable energy, while generating digestate that can be used as fertiliser. For such a strategy to be effectively and widely deployed however, AD must be optimised. To this end, efforts have typically focused solely on biogas yields, yet improvements in pathogen load reduction may potentially negate the need for a costly pasteurisation step. Hence, optimisation of AD for sanitisation as well as improved biogas output is desirable. To address this, we set up triplicate 10-L CSTR bioreactors, which were fed with a combination of slurry and fats, oils and grease for 216 days. An organic loading rate (OLR) of 2 g VS L[-1] d[-1] was used throughout the trial, with a retention time of 21 days. For the first 98 days, bioreactors were fed each weekday (Monday to Friday), with 3 × feedstock on Fridays to maintain the OLR over the weekend. On Day 99 and for the remainder of the trial, the feeding regime was changed to every three days, still maintaining the 2 g VS L[-1] d[-1] OLR. The change in feeding regime was prompted by a noticeable increase in E. coli removal on Mondays, indicating that feeding regime could potentially function as a controllable ecological selection pressure.<br><br>RESULTS: After an initial period of adaptation to the new operating conditions (from day 99-150), the change in feeding regime resulted in improved E. coli removal, achieving consistently the required reduction in numbers to satisfy EU sanitisation standards (<&#x2009;1000&#xa0;CFU&#xa0;g[-1]). Additionally, methane production increased significantly in all bioreactors with an average of 58% higher methane yield per gram VS fed when compared to the previous 5-day feeding regime. Interestingly, process optimisation led to a more tailored microbial community as revealed by metagenomics. Specifically, we observed selection for improved carbon oxidation, syntrophic acetate oxidation and methanogenesis, as well as overall reduced microbial richness and decreased functional diversity. This could potentially lead to a reduced ecosystem stability however the emergence of Methanosarcina prevalence, known for its robustness, together with the detection of the two main methanogenic pathways-acetoclastic and hydrogenotrophic-after process optimisation might confer some resistance against future perturbations. The impact of microbial shifts on ecosystem stability needs to be further assessed experimentally.<br><br>CONCLUSIONS: Taken together, we demonstrate that feeding regime can function as a microbial selection pressure in anaerobic digestion. The switch from a 5-day to a 3-day feeding regime led to shifts in microbial pathways, underpinning the simultaneous improvement in methane production and E. coli removal. While further research is required to assess the impact of the observed microbial community dynamics on system stability, our findings suggest that full scale on-farm AD operators could explore the effects of feeding intervals on their process performance.}, }
@article {pmid42175291, year = {2026}, author = {Dicko, A and Barro, SG and Somda, NS and Sombie, S and Bandaogo, O and Sanou, G and Esona, MD and Bonkoungou, JIO}, title = {Application of Metagenomics and Artificial Intelligence for Pathogen Characterization in Domestic Animals and Epizootic Prediction: A Systematic Review and Meta-Analysis.}, journal = {Studies in health technology and informatics}, volume = {336}, number = {}, pages = {2095-2096}, doi = {10.3233/SHTI260622}, pmid = {42175291}, issn = {1879-8365}, mesh = {Animals ; *Metagenomics/methods ; *Artificial Intelligence ; *Animals, Domestic/microbiology ; *Disease Outbreaks/veterinary/prevention &amp; control ; *Animal Diseases/diagnosis/microbiology ; }, abstract = {Sub-Saharan Africa suffers devastating animal health losses exceeding $20 billion each year. By combining metagenomics with artificial intelligence (AI), a promising path emerges for faster diagnostics and proactive disease prediction. Our PRISMA-guided review of 1,225 studies reveals that metagenomics achieves 94.2% diagnostic sensitivity (compared to 67.3% with conventional methods), while AI dramatically shortens turnaround from 48-72h to just 4-8h, offering a valuable 14-18 day early warning window for epizootics.}, }
@article {pmid42175403, year = {2026}, author = {Tang, R and Wang, R and Han, Y}, title = {Mycobacterium avium complex pulmonary disease in rheumatoid arthritis-associated interstitial lung disease under non-biologic immunomodulatory therapy: A case report.}, journal = {Medicine}, volume = {105}, number = {21}, pages = {e48801}, doi = {10.1097/MD.0000000000048801}, pmid = {42175403}, issn = {1536-5964}, mesh = {Humans ; Male ; *Lung Diseases, Interstitial/complications/drug therapy/etiology ; Aged ; *Arthritis, Rheumatoid/complications/drug therapy ; *Mycobacterium avium-intracellulare Infection/drug therapy/diagnosis/complications/etiology ; Mycobacterium avium Complex/isolation &amp; purification ; }, abstract = {RATIONALE: Rheumatoid arthritis (RA) is a well-recognized risk factor for nontuberculous mycobacterial infections, especially among patients receiving glucocorticoids or biological disease-modifying antirheumatic drugs. However, cases of Mycobacterium avium complex (MAC) pulmonary disease in RA patients without such immunosuppressive therapies are rarely reported, which challenges the conventional risk stratification.<br><br>PATIENT CONCERNS: A 78-year-old male with a 3-year history of RA and interstitial lung disease (ILD) presented with progressive dyspnea and chest tightness. He had no fever, joint swelling, or typical infection flares. Before admission, he was treated with Tripterygium Glycosides and Iguratimod (non-biologic, non-glucocorticoid agents).<br><br>DIAGNOSIS: The patient had chest tightness and weight loss. Chest high-resolution computed tomography showed asymmetric progression of ILD, along with tree-in-bud signs, centrilobular nodules, and suspicious fibrocavities. Bronchoscopy revealed necrotizing granulomatous inflammation, and quantitative metagenomic sequencing of bronchoalveolar lavage fluid confirmed MAC (no drug-resistant genes detected).<br><br>INTERVENTIONS: The patient was put on a 4-drug anti-MAC regimen (rifampicin, azithromycin, ethambutol, amikacin). However, he was lost to follow-up after being transferred to a tuberculosis specialist hospital. He eventually died of unknown causes, and there were prior reports of his nonadherence to treatment.<br><br>OUTCOMES: For RA patients with ILD who show asymmetric imaging progression or discordant inflammatory markers, it is crucial to actively screen for atypical pathogens like MAC, even in the absence of glucocorticoid or biologic exposure. This case highlights the necessity of expanding nontuberculous mycobacterial infection risk assessment beyond traditional immunosuppressive therapies in RA-ILD patients.<br><br>LESSONS: For patients with autoimmune disease-associated interstitial pneumonia, particularly those with progressive interstitial lung disease (ILD) despite stable autoimmune serology, proactive screening for atypical pathogens such as nontuberculous mycobacteria is critical. When imaging shows asymmetric lesions, tree-in-bud opacities, centrilobular nodules, or fibrocavitary changes, clinicians should prioritize comprehensive etiological evaluation - including bronchoscopy and histopathology - to avoid misdiagnosing these opportunistic infections.}, }
@article {pmid42175735, year = {2026}, author = {Li, J and Liu, Q and He, C and Zhu, Y and Yin, C and Pang, X}, title = {Microbial Life-History Strategies and Functional Gene Regulation Drive Soil Nitrogen and Phosphorus Bioavailability During Succession in an Arid Valley Ecosystem.}, journal = {Molecular ecology}, volume = {35}, number = {10}, pages = {e70408}, doi = {10.1111/mec.70408}, pmid = {42175735}, issn = {1365-294X}, support = {32572029//National Natural Science Foundation of China/ ; 2025ZYD0007//Sichuan Province Science and Technology Support Program/ ; XZ202501JX0012//Science and Technology Projects of Xizang Autonomous Region, China/ ; DJ-ZDXM-2024-28//Power Construction Corporation of China/ ; }, mesh = {*Nitrogen/metabolism ; *Soil Microbiology ; *Phosphorus/metabolism ; *Ecosystem ; *Soil/chemistry ; Microbiota/genetics ; Tibet ; Metagenomics ; Bacteria/genetics ; }, abstract = {Arid valley ecosystems are highly vulnerable to environmental change and face accelerating degradation due to climate warming and anthropogenic disturbance. Although soil microorganisms are known to drive nutrient cycling during succession, their adaptive strategies under persistent nutrient limitation remain poorly understood. This study integrated metagenomics, enzymatic stoichiometry and co-occurrence network analysis to investigate microbial community composition, life-history strategies, and nitrogen (N) and phosphorus (P) cycling functional genes along a successional gradient in an arid valley on the southeastern Tibetan Plateau. We found that microbial communities experienced consistent N limitation throughout succession, which shaped their functional potential and biogeochemical roles. Notably, during the transition from bare soil to biological soil crusts (BSCs), shifts in microbial life-history strategies towards resource acquisition (A-strategy) were accompanied by increased network complexity. Key functional genes, particularly those involved in nitrification (nxrB, amoC), dissimilatory nitrate reduction (nirB, nifH, nirD), inorganic P solubilization (gcd, ppk) and organic P mineralization (phnJ, phoA, phnM, phnI), were significantly upregulated during the BSCs stage. These genetic traits facilitated the transformation of organic and mineral nutrients into bioavailable forms, thereby supporting ecosystem development. This is manifested as a higher bioavailability of DON (+110%) and Bio-P (+97%) in the BSCs stage compared to bare land. Our results demonstrate that microbial communities adapt to resource constraints through trait-based strategies and functional gene regulation, highlighting the BSCs stage acts as a critical biogeochemical trigger in early succession. These insights advance our understanding of microbial-mediated nutrient cycling in arid ecosystems and inform restoration strategies under global change.}, }
@article {pmid42175741, year = {2026}, author = {Yuan, S and Wang, X and Chang, Z and Zhang, B and Wang, M and Yu, J and Chen, Z}, title = {Climate Change Elevates the Risk of Antibiotic Resistance in Global Surface Ocean.}, journal = {Global change biology}, volume = {32}, number = {5}, pages = {e70929}, doi = {10.1111/gcb.70929}, pmid = {42175741}, issn = {1365-2486}, support = {42277386//National Natural Science Foundation of China/ ; 24JCYBJC01900//Tianjin Natural Science Foundation/ ; }, mesh = {*Climate Change ; *Drug Resistance, Microbial/genetics ; Oceans and Seas ; *Microbiota ; Virulence Factors/genetics ; *Seawater/microbiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Understanding how climate change affects antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in marine microbiomes is critical to safeguarding global health, yet a systematic, global-scale analysis of their responses and associated health risks remains lacking. Here, we analyzed 890 surface-ocean metagenomic samples, the largest dataset collected using a standardized sampling pipeline to date. Our analysis revealed distinct biogeographical patterns in the composition of ARGs and VFGs across spatial and temporal gradients. Using machine learning, we mapped global distributions of ARGs and VFGs across the surface ocean by leveraging their strong associations with climate-releated environmental factors, revealing clear differences between polar and low-latitude areas. We then quantified the community-level antibiotic resistance risk and identified global risk zones, finding that high-risk regions are the least extensive and occur primarily at low latitudes. Furthermore, we estimated how this risk would change under future climate scenarios, suggesting that anthropogenic climate change is projected to increase the antibiotic resistance risk index of the surface ocean by altering environmental factors, most notably carbonate concentrations. Under the SSP5-8.5 scenario, which respresents a high greenhouse gas emissions pathway, the risk index is projected to rise across 33.0% (95% CI: 32.2%-33.5%) of the surface ocean by 2100, mainly in low-latitude regions, driven by an increase in genes involved in antibiotic efflux, inactivation, and motility. In contrast, effective greenhouse-gas mitigation would limit this increase to 3.7% (95% CI: 3.4%-4.1%). This study advances our understanding of how climate shapes marine antibiotic resistome and underscores the urgency of climate mitigation.}, }
@article {pmid42176010, year = {2026}, author = {Davolos, D and Chimenti, C and Fassio, G and Russini, V and Lepri, A and Nocella, E}, title = {Understanding Hepatopancreas-Associated Microbiota in the Supralittoral Tylos ponticus (Crustacea, Isopoda, Oniscidea): Insights from Next-Generation Sequencing Approaches.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02785-4}, pmid = {42176010}, issn = {1432-184X}, abstract = {Tylos isopods, which are found exclusively in supralittoral beaches, play an important ecological role in the harsh sea-land interface contributing significantly to lignocellulose degradation. Herein, we investigated the hepatopancreatic microbiota in the oniscidean isopod Tylos ponticus Grebnitzky, 1874 from an Italian supralittoral zone characterized by the accumulation of beached leaves from the seagrass Posidonia oceanica. To characterize this Tylos-microbe system, we combined three Next Generation Sequencing techniques: 16S rRNA gene metabarcoding, whole-genome sequencing of cultured hepatopancreatic bacteria and shotgun metagenomic sequencing of uncultured bacterial communities. Comparative analyses revealed that some bacterial taxa were associated with the hepatopancreas of T. ponticus but were also detected in the supralittoral sandy beach where the detritivores Tylos live. However, distinct components of the microbial community may be adapted within the hepatopancreas. Moreover, the assembled and annotated genomes of hepatopancreatic bacteria allowed us to identify genes encoding lignocellulose-degrading CAZymes for a better understanding of the role of symbionts in aiding lignocellulose degradation. Finally, our shotgun sequencing data confirmed the presence of an uncultured Candidatus Hepatoplasma (Mollicutes) in the hepatopancreas of T. ponticus, with the provisional taxonomic assignment as Candidatus Hepatoplasma cf. vulgare Tp. We compared this data with recently reported metagenome-assembled genomes of uncultured Hepatoplasmataceae members from isopods, including Candidatus Tyloplasma litorale identified from the semiterrestrial isopod Tylos granuliferus, Candidatus Hepatoplasma vulgare from the terrestrial isopod Armadillidium vulgare, and Candidatus Hepatoplasma scabrum from the terrestrial isopod Porcellio scaber. In such a scenario, a deeper understanding of halophilic bacteria in the supralittoral zone also has broad relevance to applied research, particularly to the biotechnological sector related to marine biomass conversion and plastic degradation.}, }
@article {pmid42176043, year = {2026}, author = {Khan, I and Naeem, I and Ali, S and Gulbin, M and Iqbal, A and Shafiq, M}, title = {Metagenomic surveillance identifies a high-risk antibiotic resistance profile in community wastewater: a pilot study from Pakistan.}, journal = {Naunyn-Schmiedeberg's archives of pharmacology}, volume = {}, number = {}, pages = {}, pmid = {42176043}, issn = {1432-1912}, abstract = {Environmental antimicrobial resistance surveillance in low- and middle-income countries (LMICs) faces critical data gaps, particularly in Pakistan, where approximately 90% of municipal wastewater is discharged untreated. In the absence of systematic monitoring in regions like Khyber Pakhtunkhwa, we conducted a pilot shotgun metagenomic sequencing study on two strategically selected community wastewater sites in Mardan. To translate complex metagenomic data into actionable public health intelligence, we developed the Antibiotic Resistance Risk Index (ARRI), a novel framework integrating antibiotic resistance gene (ARG) proportional abundance, pathogen taxonomic expansion, and WHO priority weighting. Our analysis revealed that the urban site (MCW2) exhibited a "critical" resistance profile, characterized by a 54% increase in ARG allelic richness (628 unique variants) despite a 19.9% decline in total relative ARG abundance. Taxonomic compositional changes consistent with an aerobic shift, including a 34-fold decline in Thermodesulfobacteria and a 46% increase in Pseudomonadota, were observed alongside an increased proportion of WHO priority pathogens, including Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli. This site served as a reservoir for last-resort resistance determinants, including blaNDM, blaIMP, blaCTX-M, and mcr, which emerged exclusively in the urban drainage environment. The resistome contained 159 ARG families and 26 MGE types. Network analysis showed that 90.8% of ARG-MGE pairs exhibited coordinated increase in relative abundance, with all carbapenemase-linked pairs showing parallel trends. Consequently, ARRI scores escalated from 8.7 (moderate risk) to 34.2 (critical risk) at the urban site. These findings reveal the environmental circulation of hospital-associated resistance through decentralized sanitation infrastructure, representing a convergence of hospital-associated and community resistance profiles in LMIC settings. This study demonstrates that risk-weighted surveillance enables high-resolution, actionable AMR monitoring, providing a baseline methodology for environmental AMR surveillance in resource-limited settings.}, }
@article {pmid42176229, year = {2026}, author = {Cagle, GA and Baiser, B and Bernardin, JR and Bittleston, LS and Young, EB and Gray, SM and Freedman, ZB}, title = {Carbon regime structures functional trait trajectories during primary succession in microorganisms.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag134}, pmid = {42176229}, issn = {1751-7370}, abstract = {Primary succession is a foundational process in ecology, but how microbial communities shift functionally during succession, and whether these dynamics follow predictable patterns, remains unresolved. We conducted a systematic review of functional primary succession in microorganisms and applied a consistent metagenomic pipeline to evaluate functional richness, rRNA operon copy number (RRN), and average genome size (AGS) over time. We also explored the yield-acquisition-stress (Y-A-S) life-history framework using functional gene annotations. Across autotrophic systems, RRN tended to decrease and AGS tended to increase during succession, whereas heterotrophic systems exhibited more variable trajectories. These consistent shifts in autotrophic systems suggest a transition from early colonization by copiotrophic taxa with small genomes and high RRN toward later-stage communities with larger genomes, lower RRN, and greater functional versatility. In contrast, heterotrophic systems showed heterogeneous trait trajectories, likely reflecting variation in the timing and predictability of organic inputs. Topic modeling further revealed that early successional stages were enriched in stress-tolerance genes, followed by shifts toward other strategies over time. While certain trait patterns such as RRN and AGS appeared broadly conserved, changes in life-history strategies during succession were context dependent and shaped by resource dynamics and system type. These findings suggest that microbial successional trajectories are structured by differences in resource availability, particularly whether systems are driven by autotrophic inputs or constrained by externally supplied carbon sources.}, }
@article {pmid42176246, year = {2026}, author = {Chen, Y and Wang, S and Chen, A and Lin, Z and Wang, H and Li, W and Liu, J and Yao, J and Tian, D and Lei, Y and Liu, M}, title = {Multi-omics Analysis Reveals the Protection of a Quadruple Probiotic Mixture in Experimental Autoimmune Hepatitis.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42176246}, issn = {1867-1314}, support = {2025M782000//China Postdoctoral Science Foundation/ ; 2023AB006//Shangrao Science and Technology Bureau/ ; 202303021221195//Fundamental Research Program of Shanxi Province/ ; 82270558//National Natural Science Foundation of China/ ; }, abstract = {Autoimmune hepatitis (AIH) is a chronic progressive inflammatory liver disease with a rising global incidence. The treatment of AIH remains challenging because first-line drugs show limited efficacy and systemic side effects. Gut microbiota plays a crucial role in the pathogenesis of AIH, leading to growing interest in developing probiotic-based therapies. In this study, we used multi-omics analysis to investigate the therapeutic effects of a quadruple probiotic mixture (Probiotic-quad) consisting of Bifidobacterium infantis, Lactobacillus acidophilus, Enterococcus faecalis, and Bacillus cereus in a well-established chronic AIH murine model. Our results showed that Probiotic-quad treatment significantly alleviated AIH progression, as evidenced by lower serum liver enzyme levels, ameliorated hepatic inflammatory infiltration and histopathological damage. Metagenomic sequencing results showed that gut dysbiosis in AIH mice was partially reversed after Probiotic-quad administration. Additionally, the integrity of the intestinal epithelial barrier was restored, accompanied by a reduction in serum lipopolysaccharide levels. Untargeted metabolomic and transcriptomic analysis revealed that Probiotic-quad treatment was linked to alterations in hepatic metabolism, including the citrate cycle and tryptophan metabolism, and was associated with reduced activation of the NF-κB and NOD-like receptor signaling pathways. These findings suggest that Probiotic-quad treatment ameliorates AIH severity and is potentially associated with changes in hepatic immune responses, metabolism, gut microbiota, and intestinal barrier function, highlighting its potential as an adjuvant therapy for AIH.}, }
@article {pmid42176375, year = {2026}, author = {Zhang, Y and Wang, R and Su, X and Lang, T and Li, D}, title = {Freeze-thaw specifically regulates microbiome patterns and phosphorus acquisition strategies in the lake-groundwater interaction zone.}, journal = {Water research}, volume = {302}, number = {}, pages = {126129}, doi = {10.1016/j.watres.2026.126129}, pmid = {42176375}, issn = {1879-2448}, abstract = {Freeze-thaw regulates phosphorus cycling in lake-groundwater interaction zones (LIZ) of seasonally frozen regions, where microorganisms and their functional traits play indispensable roles. However, the spatiotemporal dynamics of phosphorus pools and their driving mechanisms in the LIZ remain poorly understood, especially with insufficient quantitative evidence. Using absolute quantitative metagenomics, this study investigated the LIZ of Lake Chagan, a typical eutrophic lake in the seasonally frozen region. Results showed that Losses of Fe-P (44.69%) and Res-P (35.47%) dominated sediment phosphorus dynamics. Freeze-thaw induced opposing trends in diversity and similarity of PCGs-microbial communities between sediment and the lake-groundwater. The assembly of PCGs-microbial communities shifted from stochastic to deterministic processes in lake-groundwater, while stochastic processes persisted in sediments. DIP and DOP in lake-groundwater were driven by genes involved in P-uptake and transport (r = 0.65 and 0.40, respectively, P<0.05), while phosphorus release from sediments was co-regulated by inorganic P-solubilization and organic P-mineralization genes (r = 0.89 and -0.36, respectively, P<0.05). Microbial taxa harboring complete phosphorus cycling pathways (42.2%) and organic P-mineralization genes (48.1%) were relatively rare, with Pseudomonadota as the dominant phylum (65.2% and 57.0%, respectively). This study reveals medium-specific adaptive strategies of microorganisms and PCGs-mediated phosphorus cycling mechanisms, providing scientific support for predicting eutrophication risks and managing lake ecosystems in seasonally frozen regions.}, }
@article {pmid42176511, year = {2026}, author = {Li, K and Jin, F and Tan, S and Zeng, X and Yuan, D and Shu, F and Chen, J and Ouyang, JM and Zhang, L and Li, C and Zhu, J}, title = {Cinchonain Ia inhibits uric acid reabsorption by binding to the TRP-459 residue of the GLUT9 protein.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {157}, number = {}, pages = {158292}, doi = {10.1016/j.phymed.2026.158292}, pmid = {42176511}, issn = {1618-095X}, abstract = {BACKGROUND: Hyperuricemia, a chronic metabolic disorder resulting from purine metabolism abnormalities, imposes a substantial burden on patients, their families, and society. Consequently, discovering more efficient prevention strategies and treatment drugs is of crucial importance. Polygonum capitatum (Buch.-Ham. ex D. Don) H. Gross is a plant belonging to the Polygonaceae family and Polygonum genus. Polygonum capitatum can reduce uric acid levels and alleviate gouty arthritis; However, whether its aqueous extract contains other uric acid-lowering active components besides quercetin and gallic acid still requires further research.<br><br>PURPOSE: This study aims to investigate the protective effects and potential mechanisms of Polygonum capitatum aqueous extract on liver and kidney function, while also identifying new potential pharmacologically active components for hyperuricemia within the extract.<br><br>METHODS: This study established a hyperuricemia rat and mice model and a uric acid-induced renal injury cell model. Liquid chromatography-tandem mass spectrometry was employed to analyze the active components of Polygonum capitatum aqueous extract. The target was analyzed by proteomics. Metagenomics and spatial metabolome were used to analyze gut microbes and metabolites associated with liver and kidney injury. Finally, SPR, DARTS, and CETSA were used to assess the binding potential of active components to targets. Additionally, mutant plasmids were constructed to analyze the binding sites between pharmacologically active components and their targets.<br><br>RESULTS: The aqueous extract of Polygonum capitatum significantly reduced serum uric acid levels and alleviated renal injury in the hyperuricemia rat model, with no apparent damage on liver tissue morphology or hepatic function indicators. Metagenomic and spatial metabolomics analyses demonstrated that the extract increased the relative abundance of beneficial gut microbiota and decreased that of harmful bacteria. It also modulated the levels and distribution of renal metabolites such as l-arginine and N-acetylglucosamine, reduced lipid oxidation in the kidney. Proteomics analysis suggests that renal GLUT9 may be one of the action targets of this extract. LC-MS/MS analysis indicated that the chemical composition of the extract underwent significant changes after entering rat blood and undergoing renal metabolism. Specifically, serves as a new active component in Polygonum capitatum aqueous extract, Cinchonain Ia was found to bind to the TRP-459 residue of GLUT9, inhibiting its expression and thereby reducing uric acid reabsorption in vivo and in vitro, and alleviated oxidative stress, inflammation, and tissue damage. However, overexpression of GLUT9 markedly reversed the inhibitory effects of Cinchonain Ia on inflammation and injury.<br><br>CONCLUSIONS: The aqueous extract of Polygonum capitatum prevents liver damage and alleviates kidney injury by regulating gut microbiota and renal metabolites. Furthermore, Cinchonain Ia, as one of its active components, can bind to the TRP-459 residue of the GLUT9 protein and inhibit its expression, thereby suppressing uric acid reabsorption and lowering serum uric acid levels.}, }
@article {pmid42176589, year = {2026}, author = {Kuerban, Z and Shao, Y and Jiang, R and Shi, Y and Ma, Y and Li, H and Mei, X and Xu, Y and Dong, C and Shen, Q}, title = {Trichoderma modulates Pseudomonas metabolism: Co-inoculation enhances phosphorus acquisition of Pyrus betulifolia in calcareous soil.}, journal = {Microbiological research}, volume = {310}, number = {}, pages = {128552}, doi = {10.1016/j.micres.2026.128552}, pmid = {42176589}, issn = {1618-0623}, abstract = {Phosphorus (P) is poorly available in calcareous soils, limiting pear growth. We evaluated whether Trichoderma brevicompactum TB2 improves P availability and the rhizosphere microbiome. This study used Trichoderma brevicompactum TB2 to investigate the regulatory mechanisms influencing rhizosphere phosphorus transformation and microbiome structure in pear seedlings. Four treatments were analyzed: sterilized soil control (SSC), sterilized soil with TB2 (SST), natural soil control (NSC), and natural soil with TB2 (NST). SST and NST treatments significantly increased plant height, biomass, and soil available phosphorus (AP) while reducing soil pH compared to SSC and NSC. Notably, only the NST treatment significantly enhanced plant phosphorus content and accumulation. Compared to NSC, NST led to significant restructuring of the rhizosphere microbial community (via 16S rRNA) and functional differentiation in phosphorus cycling (as shown by metagenomics), including increased abundances of key phosphorus-metabolism genes (phnN, phnL, phnP, gcd) and improved organic phosphoester hydrolysis and transport pathways. Metagenome-assembled genomes (MAGs) identified five high-quality gcd-containing MAGs, including those from Bacteroidota (bin43, bin16) and Pseudomonas (bin53, bin72, bin13), with a bin13-match strain isolated from the NST rhizosphere. Pot trials confirmed that inoculation with TB2 or PSE significantly improved plant biomass and phosphorus nutrition indices compared to CK. Co-inoculation with TB2 and PSE elicited synergistic effects that exceeded those of the individual inoculants. In natural calcareous soil, TB2 enhances pear growth by recruiting P-solubilizing Pseudomonas and activating rhizosphere P cycling. This offers a practical route to improve P-fertilizer efficiency in orchards.}, }
@article {pmid42176630, year = {2026}, author = {Wu, Y and Ma, W and Sun, Y and Tang, J and Xu, X and Zhu, J and Miao, J and Li, M and Zeng, J and Gou, K and Song, Y and Zou, J}, title = {From active defense to cross-kingdom alarm: Rhizosphere microenvironment remodeling in soybean under polylactic acid nanoplastics and cadmium Co-stress.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142470}, doi = {10.1016/j.jhazmat.2026.142470}, pmid = {42176630}, issn = {1873-3336}, abstract = {As foundational components of the food web, plants face significant environmental threats caused by the coexistence of micro/nanoplastics (MNPs) and heavy metals. This study investigates the combined effects of cadmium and biodegradable polylactic acid nanoplastics on soybean. Under co-exposure conditions, toxicity progressively diminishes from the roots to the leaves of soybeans. By integrating root transcriptomics, root exudate metabolomics, rhizosphere soil metagenomics, and soil physicochemical analyses within a Bayesian structural equation modeling framework, we identified the Flavonoid biosynthesis pathway as a central mediating hub in the rhizosphere microenvironment under combined stress. Soybean roots modulated this pathway as a response strategy, which concurrently served as a signal for rhizosphere microbes to downregulate energy-intensive processes such as Methane metabolism, facilitating microbial adaptation. The down-regulation of the Flavonoid biosynthesis pathway in root exudates further altered rhizosphere soil properties, creating a feedback loop that amplified the expression of stress-related genes in soybean roots.}, }
@article {pmid42176697, year = {2026}, author = {Yao, J and Zhu, T and Tian, W and Xu, J and Nie, M and Wan, J}, title = {Artificial reefs alter viral communities and functional traits in coastal waters.}, journal = {Marine environmental research}, volume = {220}, number = {}, pages = {108131}, doi = {10.1016/j.marenvres.2026.108131}, pmid = {42176697}, issn = {1879-0291}, abstract = {Artificial reefs (ARs) are widely deployed as engineered coastal structures to enhance habitat complexity and support marine resource management, yet their impacts on marine viral ecology remain poorly understood. Viruses regulate microbial communities and biogeochemical processes, and their functional traits are sensitive to environmental change. Here, we investigated how artificial reefs influence viral community composition, functional gene profiles, and virus-environment interactions across paired reef and non-reef sites in coastal shelf systems. Using an integrated viromic and metagenomic approach, we compared viral assemblages in both seawater and sediments under artificial reef influence. ARs significantly modified seawater physicochemical conditions, including pH, sulfate concentration, dissolved oxygen, and salinity, whereas sediment properties remained largely unchanged. These environmental differences coincided with distinct virus-environment association patterns across habitats. Notably, artificial reefs were associated with viral functional profiles characterized by a reduced genomic representation of lysis-related genes and an increased representation of genes involved in DNA replication and nucleotide metabolism. Network analyses further showed differences in the balance of positive and negative virus-host correlations between AR and non-AR sites. Together, these results indicate that engineered coastal structures are linked to habitat-specific patterns in viral functional traits and virus-host associations. Our findings highlight viruses as sensitive indicators of anthropogenic habitat modification and underscore the importance of incorporating viral dynamics into assessments of microbial and biogeochemical responses in engineered coastal ecosystems.}, }
@article {pmid42170880, year = {2026}, author = {Ershova-Menze, E and Westgaard, JI and Hjellnes, H and Falkenhaug, T}, title = {Optimising Zooplankton DNA Metabarcoding: Methodological Considerations for Large-Scale Monitoring.}, journal = {Molecular ecology resources}, volume = {26}, number = {4}, pages = {e70149}, doi = {10.1111/1755-0998.70149}, pmid = {42170880}, issn = {1755-0998}, mesh = {*DNA Barcoding, Taxonomic/methods ; *Zooplankton/genetics/classification ; Animals ; Biodiversity ; DNA/genetics/isolation &amp; purification ; *Metagenomics/methods ; Electron Transport Complex IV/genetics ; }, abstract = {DNA metabarcoding is becoming an increasingly common approach in ecological monitoring of marine and freshwater planktonic communities, yet methodological choices along the metabarcoding workflow and data post-processing approaches remain highly inconsistent across studies, limiting the ability to track biodiversity trends, detect range shifts, or integrate datasets across monitoring programs. This study addresses this methodological bottleneck by combining controlled experimental comparisons with a comprehensive literature synthesis to identify how protocol decisions-from sample preservation and DNA extraction to sequencing platforms and taxonomic assignments-affect the results of COI metabarcoding and its interpretation. Overall biodiversity and community patterns were recovered by all combinations of tested methods, supporting the notion that patterns identified through DNA metabarcoding are robust and comparable across studies. We identify TES (Tris-EDTA-SDS) buffer, optionally paired with at-sea homogenisation, as a practical alternative to ethanol preservation for large-scale monitoring surveys. We show that integrating several classification methods and reference databases for taxonomic assignment improves diversity estimates and confidence in the assignments, and advocate for increased use of tools like BOLDigger that facilitate manual curation of ambiguous/erroneous references. Finally, we demonstrate that introducing stricter filtering thresholds reduces the effect of false positives, pseudogenes and lab-specific contamination, and make comparisons of data generated by different laboratories and methodological configurations more robust, although potentially at the expense of excluding rare taxa. While we intentionally refrain from recommending a universal best practices protocol, this study aims to provide a practical roadmap to help enhance the reliability and reproducibility of marine zooplankton monitoring via DNA metabarcoding.}, }
@article {pmid42171141, year = {2026}, author = {Tagliamonte, S and Neill, HR and Murphy, B&#xd3; and Pourshahidi, KL and De Filippis, F and Ercolini, D and Gill, CIR and Natalia, K and Curran, B and Nicole, M and Mary, S and Dobani, S and Fontana, M and Vitaglione, P}, title = {Dietary N-acylethanolamines are bioaccessible in the small intestine and modulate postprandial hormonal responses: a randomized crossover trial in subjects with ileostomy.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5fo03328d}, pmid = {42171141}, issn = {2042-650X}, abstract = {N-Acylethanolamines (NAEs) are bioactive lipid mediators involved in the regulation of appetite, inflammation, and gut-brain signaling. This study investigated the metabolic fate of dietary NAEs following the consumption of two test meals with differing NAE contents in subjects with ileostomy and evaluated their effects on gastrointestinal hormones, glycaemia, and appetite regulation. An acute, double-blind, randomized, crossover postprandial study was conducted in ileostomy patients who consumed either a high-NAE meal (HNM) or a low-NAE meal (LNM) on two separate occasions. Ileal fluid and plasma samples were collected over an 8-hour postprandial period for analysis of NAEs and endocannabinoids (ECs). Baseline ileal microbiota composition was assessed. At the end of the 8-hour period, participants completed a buffet meal test to evaluate ad libitum energy intake. Dietary NAEs were significantly recovered in ileal fluids after HNM intake, with concentrations approximately 3-fold higher than those after LNM, suggesting partial digestion and release from the food matrix. No significant differences in postprandial plasma NAE concentrations were observed between meals. HNM consumption led to higher postprandial levels of plasma insulin, C-peptide, and glucose-dependent insulinotropic polypeptide, despite no differences in glycemic response or subsequent ad libitum energy intake. Metagenomic analysis identified clusters of ileal microbial taxa associated with circulating lipid profiles, suggesting a role of the small intestinal microbiota in the metabolism of NAEs and ECs. Dietary NAEs reach the small intestine at active concentrations and may influence local signaling via GPR119, with microbiota composition influencing their release from food.}, }
@article {pmid42171373, year = {2026}, author = {Schroer, HW and Beghini, F and Raygoza Garay, JA and Christakis, NA and Bosch, DE}, title = {Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0030526}, doi = {10.1128/msystems.00305-26}, pmid = {42171373}, issn = {2379-5077}, abstract = {Bacteria use antagonistic interbacterial weapons, such as polymorphic toxin secretion systems (TSS), to compete for niches in the human gut microbiome. We hypothesized that TSS influence gut microbiome development and disease-related dysbiosis. We developed a bioinformatic marker gene approach (PolyProf) to quantify TSS including ~200 effector and immunity genes and applied it to ~15,000 publicly available human metagenomes. PolyProf alpha and beta diversity readily distinguished 12 different human disease states and enabled the construction of highly accurate linear regression classifier machine learning models. Elastic net machine learning models integrating bacterial taxonomy with PolyProf had strong predictive value for 12 disease states, outperforming models utilizing taxonomy alone. During microbiome development in the first year of life, PolyProf alpha diversity increases, and beta diversity becomes increasingly like the maternal microbiome, influenced by vertical transfer, delivery mode, and breastfeeding. PolyProf is related to strain sharing among adults through social interactions. In summary, TSS genes strongly correlate with microbiome development and interpersonal strain sharing, suggesting roles for interbacterial antagonism. Since PolyProf distinguishes diverse adult disease statuses, these dynamics may contribute to non-genetic inheritance.IMPORTANCEPrevious research has demonstrated that bacteria compete within the gut microbiome using toxin secretion systems (TSS). How TSS contribute to human microbiome development and the microbiome alterations observed in human diseases is not known. This study develops a new bioinformatic tool for profiling TSS-related genes in metagenomic data. Application of this approach to large-scale human fecal metagenomic data demonstrates the dynamic association of TSS during microbiome development, including the exchange of strains among social contacts. TSS gene abundance patterns are highly predictive of 12 disease states. This study advances the field by enabling TSS profiling in metagenomes and by identifying disease and microbiome development biomarkers that provide hypotheses for future mechanistic studies and may be useful for disease diagnosis.}, }
@article {pmid42171625, year = {2026}, author = {Paietta, EN and Johnston, RA and Kraberger, S and Randrianarisoa, SF and Razanamahenina, TT and Ramboninarimalala, A and Velontsara, JB and Raherinirina, TG and Raveloson, L and Finley, NL and Baitchman, E and McAdoo, BG and Yoder, AD and Varsani, A}, title = {Mammal-infecting DNA viruses identified in lemurs and rodents in Madagascar mirror the evolutionary history of their hosts.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, pmid = {42171625}, issn = {2057-5858}, mesh = {Animals ; Madagascar ; *Lemur/virology ; *DNA Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; *Rodentia/virology ; Rats/virology ; Metagenomics ; Genome, Viral ; }, abstract = {Given that some DNA viruses have been found to exhibit virus-host co-evolution and establish lifelong infection, mammals with unique evolutionary histories in island ecosystems likely host exceptionally diverse viruses. Madagascar is inhabited by endemic non-human primate and rodent lineages interacting with expansive populations of introduced non-native rodents across the island. Using a viral metagenomic workflow on 189 oral swabs of lemurs and rodents in southeastern Madagascar, we characterized genomic sequences of DNA viruses in the families Adenoviridae, Circoviridae, Orthoherpesviridae, Papillomaviridae, Parvoviridae and Polyomaviridae and assessed their phylogenetic relationships to known viruses. Endemic lemurs and tufted-tailed rats displayed particularly novel DNA viral diversity mirroring the geographic isolation and subsequently rich evolutionary history of their hosts. Notably, we provide the first coding-complete sequences in lemurs of herpesviruses, polyomaviruses, adeno-associated viruses and circoviruses. In contrast, the DNA viral communities of black rats in Madagascar were similar to those found in globally distributed black and brown rat populations, given their broad geographic spread and relatively recent introduction to the island. Given the scarcity of viral research in natural populations of lemurs and rodents in Madagascar despite the island's exceptional biodiversity and escalating anthropogenic pressures, this study provides a genomic and phylogenetic foundation for DNA viruses infecting Malagasy lemurs and rodents.}, }
@article {pmid42171661, year = {2026}, author = {Goodall, T and Busi, SB and Jones, B and Thorpe, A and Griffiths, RI and Redhead, J and Hulmes, L and Hulmes, S and Ridding, L and Peyton, J and Pereira, G and Gweon, HS and Read, DS and Pywell, R}, title = {Taxonomic filtering accompanies functional expansion during long-term soil restoration.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag131}, pmid = {42171661}, issn = {1751-7370}, abstract = {The restoration of species-rich calcareous grasslands is a critical conservation objective, yet the recovery of the invisible below-ground microbiome remains poorly quantified compared to above-ground vegetation. Using a unique 143-year land-use chronosequence on Salisbury Plain, UK, we investigated the trajectory of ecosystem reassembly across arable, regenerating (23 and 67 years), and ancient grasslands. By integrating vegetation surveys with soil physiochemistry, microbial profiling, and shotgun metagenomics, we identified a decoupling between floral and edaphic recovery. While the diversity of vegetation recovered relatively rapidly, approaching ancient grassland levels within 23-67 years, soil properties exhibited persistent legacy effects and slow convergence. Bacterial richness decreased with restoration age; this taxonomic contraction was conversely matched by an expansion in inferred metagenomic functional potential. This was reflected in increased functional gene richness and shifts in the relative abundance of specific SEED-annotated functions toward metabolic pathways associated with complex carbon cycling and stress tolerance. These shifts were congruent with the emergence of specific, unnamed genera belonging to Pseudomonadota and Actinomycetota, and the Bacillota species Pristimantibacillus. The soil ecosystem remained distinct from the 143-year stage even after 67 years of recovery, characterised by persistent legacy phosphorus and a slow accumulation of soil organic matter. These findings suggest that passive regeneration alone may be insufficient for full soil functional recovery, and that strategies targeting microbial assembly and long-term carbon dynamics warrant further evaluation.}, }
@article {pmid42171933, year = {2026}, author = {Xu, Y and Sun, X and Xu, S and Deng, S and Zhang, Y}, title = {Clinical profile of microsporidial keratoconjunctivitis in healthy individuals of China -new species and neglected risk factors.}, journal = {Journal of ophthalmic inflammation and infection}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12348-026-00596-9}, pmid = {42171933}, issn = {1869-5760}, abstract = {OBJECTIVE: To characterize microsporidial keratoconjunctivitis (MKC) in immunocompetent individuals in Mainland China, including novel etiologies and risk factors.<br><br>METHODS: A prospective analysis of 20 MKC patients in 2025, including clinical features, pathogens (via corneal scrapings and metagenomic sequencing), risk factors and etc. RESULTS: All patients were misdiagnosed for a median of 1 month. Patients (mean age 28.5 years, 13 F) showed Encephalitozoon hellem (65.0%), E. bieneusi (15.0%, first reported in MKC), and Vittaforma corneae (15.0%). Key risks included bird contact (70.0%, mostly psittacines), contact lens use (40.0%), and water exposure (15.0%). The most common symptom was redness (85.0%); limbal fluorescein positivity occurred in 65.0%. Topical 0.02% PHMB cured 90.0% of 20 cases; one recurrence followed treatment stop. Some E. hellem cases linked to parrots showed potential zoonotic transmission.<br><br>CONCLUSION: MKC in China involves E. bieneusi and parrot-associated E. hellem. Limbal staining aids diagnosis; PHMB is effective. Zoonotic risks related to Psittacine birds and contact lens use require clinical attention.}, }
@article {pmid42172047, year = {2026}, author = {Delgado, LF and Sunyer, JO and Laczny, CC and Hickl, O and May, P and Wilmes, P}, title = {PathoFact 2.0: An Integrative Pipeline for the Prediction of Antimicrobial Resistance Genes, Virulence Factors, Toxins and Toxin-associated Proteins, and Biosynthetic Gene Clusters in Metagenomes.}, journal = {GigaScience}, volume = {}, number = {}, pages = {}, doi = {10.1093/gigascience/giag062}, pmid = {42172047}, issn = {2047-217X}, abstract = {BACKGROUND: Antimicrobial resistance genes (ARG) and virulence factors (VFs) are central contributors to the global health crisis surrounding drug-resistant infections.<br><br>FINDINGS: We introduce PathoFact 2.0, an enhanced pipeline for improved ARG, VF, toxin, and biosynthetic gene clusters (BGC) prediction. Key improvements include an updated machine learning (ML) model for VF identification, expanded hidden Markov model profiles for VFs and toxin-associated proteins, a new ML model for toxin and toxin-associated proteins identification, and the integration of antiSMASH 7.0 for predicting biosynthetic gene clusters.<br><br>CONCLUSIONS: Our upgrades make PathoFact 2.0 a more powerful and user-friendly platform for predicting microbiome-based pathogenicity and resistance, providing a crucial tool for better understanding and addressing the challenges posed by antimicrobial resistance and infectious diseases.PathoFact 2.0 is available at https://gitlab.com/uniluxembourg/lcsb/systems-ecology/pathofact2. It is compatible with Linux operating systems.}, }
@article {pmid42172141, year = {2026}, author = {Long, K and Gravel-Pucillo, K and Waldron, L and Davis, S and Oh, S}, title = {Large-scale manual curation and harmonization of metadata from metagenomic and cancer genomic repositories: challenges and solutions.}, journal = {Database : the journal of biological databases and curation}, volume = {2026}, number = {}, pages = {}, doi = {10.1093/database/baag027}, pmid = {42172141}, issn = {1758-0463}, support = {/CA/NCI NIH HHS/United States ; U24CA289073/NH/NIH HHS/United States ; 3U24CA180996-10S1/NH/NIH HHS/United States ; }, mesh = {*Metadata/standards ; Humans ; *Data Curation/methods ; *Neoplasms/genetics ; *Databases, Genetic ; *Metagenomics ; *Genomics ; }, abstract = {Public omics repositories contain vast amounts of valuable data, but their metadata suffers from extreme heterogeneity, unstandardized terminologies, and quality issues that severely limit data reusability and cross-study integration. While prospective metadata standards exist, the majority of published omics data remain in non-standardized formats requiring retrospective harmonization. We performed comprehensive manual curation and harmonization of metadata, such as participant characteristics and study conditions, from 212 027 omics samples across 468 studies in two repositories: curatedMetagenomicData (93 studies, 22 588 samples) and cBioPortal (375 studies, 189 438 samples). Through systematic ontology mapping, we consolidated redundant, dispersed information into far fewer harmonized columns, reduced unique values, and increased the completeness of major attributes. This curation process revealed common metadata quality issues, including typos, inconsistent terminologies, misplaced values, conflicting annotations, and inappropriately merged information across attributes. We document the challenges, decisions, and solutions during this large-scale metadata harmonization. The harmonized metadata, accessible through the OmicsMLRepoR Bioconductor package, enables repository-wide queries and cross-study analyses previously challenging with heterogeneous metadata. Our experience provides practical guidance for similar curation efforts and demonstrates the value of investing in retrospective metadata improvement for existing public omics resources.}, }
@article {pmid42172324, year = {2026}, author = {Freschlin, CR and Yang, KK and Romero, PA}, title = {Scalable and cost-efficient custom gene library assembly from oligopools.}, journal = {Science advances}, volume = {12}, number = {21}, pages = {eady2279}, doi = {10.1126/sciadv.ady2279}, pmid = {42172324}, issn = {2375-2548}, mesh = {*Gene Library ; Software ; *Oligonucleotides/genetics ; Computational Biology/methods ; }, abstract = {Advances in metagenomics, deep learning, and generative protein design have enabled broad in silico exploration of sequence space, but experimental characterization is still constrained by the cost and scalability of DNA synthesis. Here, we present OMEGA (Oligo-based Multiplexed Efficient Gene Assembly), a low-cost, accessible method for assembling hundreds to thousands of full-length genes in parallel using standard laboratory techniques. OMEGA computationally fragments target genes into short, high-fidelity Golden Gate-compatible oligonucleotides that can be ordered as a pooled library and assembled across multiplexed subpools. We systematically optimized the number of fragments per gene and orthogonal ligation sites per reaction and determine that OMEGA can assemble up to 2.6-kilobase constructs using as many as 70 Golden Gate sites. To validate the approach, we assembled and functionally screened a library of 810 natural and synthetic green fluorescent protein variants, recovering 94 to 97% of target sequences with high uniformity. OMEGA enables precision library construction at scale, with per-gene costs as low as $1.50, and offers a broadly applicable solution for bridging computational protein design with high-throughput experimental validation. We have developed OMEGA as an open-source software package and an easy-to-use Colab notebook to facilitate community adaptation.}, }
@article {pmid42172586, year = {2026}, author = {Singh, R and Gupta, P and Singh, R and Basant, N}, title = {Environmental Antibiotic Contamination and AMR: Integrating Pathways, Impacts, and AI-Driven Mitigation.}, journal = {Environmental toxicology and chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1093/etojnl/vgag115}, pmid = {42172586}, issn = {1552-8618}, abstract = {The widespread contamination of the environment with antibiotic residues is a significant factor contributing to the global crisis of antimicrobial resistance. Antibiotics from various sources, such as effluents from municipal and hospital wastewater treatment plants, agricultural runoffs, discharges from pharmaceutical manufacturing and improper disposal of expired or unused medicines, create selective pressures in the spread of antibiotic resistance genes. These environmental reservoirs act as hotspots for horizontal gene transfer, facilitating the emergence of multidrug-resistant pathogens. Conventional detection methods including culture-based assays, chromatographic quantification, and molecular diagnostics, provide essential insights but are limited by low throughput, reduced sensitivity to new Antibiotic Resistance Genes, and challenges in real-time monitoring across complex environments. Recent advances, such as whole-genome sequencing, metagenomics, and biosensor-based detection, help to address these gaps by enabling more comprehensive surveillance of the resistome. Artificial intelligence further enhances these approaches by improving data interpretation and pattern recognition, thus complementing traditional and molecular methods rather than replacing them. This review examines the pathways of environmental antibiotic contamination, ecological and health impacts of Antimicrobial Resistance (AMR), and limitations of conventional detection methods. It aims to clarify how these pathways contribute to the AMR crisis, assess the effectiveness of existing surveillance techniques, and identify gaps in current research.}, }
@article {pmid42172842, year = {2026}, author = {Chen, X and Tan, QG and Pan, K and Xiao, A and Cheng, H and Wang, X}, title = {Vegetation of exotic fast-growing species Sonneratia apetala increases the potential of methylmercury production: Insights from carbon bioavailability, microbial metabolism and mercury methylators.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142469}, doi = {10.1016/j.jhazmat.2026.142469}, pmid = {42172842}, issn = {1873-3336}, abstract = {Mangrove sediments are hotspots for neurotoxic methylmercury (MeHg) production, with litter-derived organic carbon strongly affecting mercury (Hg) methylation. However, the specific role of carbon bioavailability in regulating net MeHg production remains unclear. This study investigated sediments vegetated by exotic fast-growing Sonneratia apetala (SA) and native Kandelia obovata (KO) in southern China. Contrary to the expectation that larger carbon pools enhance methylation, MeHg levels were 2.1-2.6 times higher in SA sediments despite KO containing 1.2-4.2 times more total organic carbon. This disparity was driven by carbon bioavailability: SA sediments exhibited a significantly higher proportion of available carbon (34-50%) compared to KO (28-36%), which stimulated microbial activity and enriched Hg-methylating microbes (1.4-3.3 times higher in hgcAB gene abundance). Metagenomics showed that SA not only promoted key Hg-methylating taxa (e.g., Desulfobacterales, Syntrophobacteria) but also upregulated their metabolic pathways for labile carbon use and methyl transfer to Hg. Our results demonstrate that carbon bioavailability, governed by species-specific litter chemistry, is the key driver of net MeHg production. The findings provide an in-depth understanding of Hg biogeochemistry by linking soil carbon quality to microbial metabolic networks, and offer novel insights for evaluating the ecological risks associated with exotic species in mangrove restoration.}, }
@article {pmid42172844, year = {2026}, author = {Xu, Y and Xie, T and Zhong, W and Yang, G and Zhang, W}, title = {Probable disseminated Mycobacterium avium complex infection in an apparently immunocompetent patient: A case report and literature review.}, journal = {Journal of infection and public health}, volume = {19}, number = {7}, pages = {103245}, doi = {10.1016/j.jiph.2026.103245}, pmid = {42172844}, issn = {1876-035X}, abstract = {Disseminated Mycobacterium avium complex (MAC) infection is rare in immunocompetent hosts. This often leads to diagnostic delays. We report a challenging case of an apparently immunocompetent patient with pulmonary lesions, osteomyelitis, and skin ulcers. While routine cultures were pending, metagenomic next-generation sequencing (mNGS) rapidly identified MAC, enabling timely treatment. Subsequent culture and species identification confirmed the pathogen as Mycobacterium colombiense. Systematic reviews since 2000 have shown that skeletal and pulmonary involvement are common in this population. Diagnosis has gradually incorporated molecular biological techniques, and with timely treatment, patient outcomes are generally favorable. Our findings highlight the limitations of traditional microbiology and demonstrate that mNGS is a vital adjunctive tool for slow-growing pathogens. We conclude that disseminated MAC should be considered in refractory multifocal infections, even without recognized immunodeficiencies. Early molecular diagnosis, individualized multidrug therapy, and rigorous follow-up are essential for clinical remission.}, }
@article {pmid42172850, year = {2026}, author = {Li, Y and Shi, B and Li, D and Li, YA and Yuan, M and Luo, J and Dong, S and Wen, W and Zhao, R}, title = {Microbial community shift and functional reorganization from influent to effluent in wastewater treatment plants on the Qinghai-Tibet Plateau.}, journal = {Journal of environmental management}, volume = {409}, number = {}, pages = {130036}, doi = {10.1016/j.jenvman.2026.130036}, pmid = {42172850}, issn = {1095-8630}, abstract = {Wastewater treatment plants (WWTPs) on the Qinghai-Tibet Plateau play a critical role in safeguarding fragile high-altitude aquatic ecosystems. However, microbial community structure and functional characteristics in the influent and effluent in high-altitude WWTPs remain poorly understood. Here, we integrated 16S rRNA gene amplicon sequencing with metagenomic gene-centric profiling and genome-resolved reconstruction to investigate influent and final effluent microbiomes from 18 municipal WWTPs across five cities in Qinghai Province. The results showed that alpha diversity was comparable between influent and effluent, whereas microbial community composition differed significantly. Co-occurrence networks revealed a simplified and more modular interaction pattern in effluent, accompanied by fewer keystone taxa compared with influent. Metagenomic analyses showed that major metabolic pathways were retained across treatment stages, but their relative abundances declined toward effluent. Genome-resolved analyses further indicated this treatment-associated functional reorganization primarily reflected shifts in the taxa and genomic coverage supporting these pathways, rather than replacement of pathway categories. Pseudomonadota accounted for the largest proportion of metabolic contributions across carbon, nitrogen, and sulfur transformation pathways, while multiple pathways persisted in effluent but were encoded by fewer genomes with lower coverage. Denitrification-associated steps, particularly nitric oxide and nitrous oxide reduction, constituted major genome-level contributions to nitrogen removal potential. Notably, Patescibacteria were significantly enriched in effluent and exhibited highly simplified genomes dominated by energy-conserving traits. These results reveal treatment-associated microbial and functional reorganization in plateau WWTPs and provide a genome-resolved framework for interpreting microbial metabolic potential in high-altitude wastewater systems.}, }
@article {pmid42172982, year = {2026}, author = {Yan, S and Zhang, Y and Fan, Q and Jia, W and Dai, Y and Li, X and Lu, S and Sheng, Y and Sun, S and Lin, R and Tang, Y and Zhao, C}, title = {Evodiamine targets ZO-1 to ameliorate cholestatic liver disease: Intestinal homeostasis as the core mediator of gut-liver axis repair and bile acid metabolism remodeling.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {157}, number = {}, pages = {158288}, doi = {10.1016/j.phymed.2026.158288}, pmid = {42172982}, issn = {1618-095X}, abstract = {BACKGROUND: Cholestatic liver disease (CLD) is a complex and multifactorial chronic disorder that requires a systematic and integrative management. Evodiamine (EVO), a natural alkaloid derived from Evodiae Fructus, has demonstrated significant therapeutic potential in ameliorating digestive diseases. However, the beneficial effects of EVO on CLD and the underlying mechanisms remain poorly understood.<br><br>OBJECTIVE: This study aims to elucidate the mechanisms through which EVO modulates the progression of CLD, with a particular focus on the regulation of gut-liver axis homeostasis.<br><br>METHODS: The therapeutic efficacy of EVO in bile duct ligation (BDL)- and &#x3b1;-naphthyl isothiocyanate (ANIT)-induced CLD rat models was systematically evaluated. An integrative approach combining network pharmacology with multi-omics analyses (transcriptomic, metagenomic sequencing, targeted bile acid metabolomics) was employed to identify significantly altered molecular networks. Fecal microbiota transplantation (FMT) was conducted to validate the functional role of gut microbiota in the hepato-intestinal protective effects. Direct molecular targets as well as the functional validation were confirmed through molecular docking, pull-down assays, surface plasmon resonance and cellular thermal shift assay.<br><br>RESULTS: EVO achieved significant synchronous hepato-intestine protection in both CLD rats: it markedly ameliorated hepatic injury and hepatic fibrosis, downregulated pro-inflammatory cytokine levels, while preserving intestinal barrier integrity and alleviating intestinal inflammation. Mechanistically, EVO exerted these protective effects by directly targeting the tight junction protein ZO-1 and enhancing its expression and stability. Furthermore, EVO restored intestinal microbial homeostasis, corrected dysregulated BA metabolism-specifically normalizing deoxycholic acid (DCA) levels. FMT experiments demonstrated that the synchronous hepato-intestinal beneficial effects of EVO were partially mediated by gut microbiota.<br><br>CONCLUSION: EVO exerts a protective effect against CLD by directly targeting ZO-1 to strengthen intestinal barrier function, thereby restoring gut microbial balance and rebalancing BAs metabolism (especially DCA levels) in the gut-liver axis. This study uncovers a novel ZO-1-dependent mechanism of EVO in CLD, highlighting EVO as a promising candidate for the treatment of CLD and providing new insights into gut-liver axis-targeted therapies.}, }
@article {pmid42173380, year = {2026}, author = {Du, S and Ding, S and Zhao, Y and Wang, Y and Ju, F and Wu, D}, title = {Maintaining oxygen above a critical threshold prevents acetate-driven phytotoxicity in industrial-scale aerobic composting: metagenomic, MAG, and enzyme-activity evidence.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134949}, doi = {10.1016/j.biortech.2026.134949}, pmid = {42173380}, issn = {1873-2976}, abstract = {Aerobic composting is a key route for organic-waste valorization, yet product utilization is often constrained by phytotoxicity and low germination index (GI), particularly under oxygen-limited operation. Here, we developed an actionable oxygen-control window (O2 ≥ 10% v/v) to mitigate acetate-associated GI inhibition by integrating process monitoring with inhibitor profiling of GI extracts, metagenomics/metagenome-assembled genomes (MAGs), and pyruvate dehydrogenase (PDH) activity measurements. Three composting modes were implemented to create contrasting oxygen regimes: mechanical composting (MC; well-aerated), forced aeration composting (FC; intermittently oxygen-limited), and static composting (SC; ventilation-supported static aerobic). Chemical profiling and mixed-effects/regression analyses identified acetate as the dominant GI-inhibiting compound relative to other candidates (e.g., ammonium, formate, chloride). A bench-scale oxygen-gradient validation experiment (0-21% O2) confirmed an oxygen dose-response of acetate accumulation: acetate reached 1163.5 and 865.4 mg/L at 0% and 5% O2, but remained near baseline at ≥ 10% O2 (85.8 and 80.2 mg/L at 10% and 21% O2, respectively; 24 h), defining an oxygen window for suppressing acetate build-up. To probe mechanism, KEGG-based pathway mapping showed that acetate-linked functions were dominated by pyruvate metabolism, and high-acetate states were associated with reduced PDH-related functional gene abundance (PDHA/B) and lower PDH activity. MAG co-occurrence and correlation analyses further linked acetate-associated states to specific MAG-level contributors (including Thermobifida fusca). Together, these results support a PDH-linked metabolic constraint under oxygen limitation that promotes acetate persistence and GI inhibition, and provide operational guidance to maintain in-pile O2 ≥ 10% (v/v) to reduce acetate-driven phytotoxicity in industrial composting of readily acidogenic wastes.}, }
@article {pmid42166146, year = {2026}, author = {Besteman, MS and Alaux, E and Doloman, A and Tahon, G and Ettema, TJG and Sousa, DZ}, title = {Uncovering syntrophic potential from genome-resolved metagenomics of suspended and granular AD sludges.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag052}, pmid = {42166146}, issn = {1574-6941}, abstract = {Syntrophic microbial interactions are fundamental to the degradation of organic matter (e.g. fatty acids), playing a central role in natural anoxic ecosystems and engineered systems such as anaerobic digestion (AD). Despite their ecological and biotechnological importance, only a limited number of (obligate) syntrophic fatty-acid oxidizers have been successfully isolated. In this study, microbial communities from suspended and granular sludge samples were characterized using 16S rRNA gene amplicon sequencing and shotgun metagenomics. Network analysis of the 16S rRNA gene amplicon data revealed strong positive associations between methanogens and known syntrophic fatty-acid oxidizers, particularly in granular sludge samples. 743 High-Completion Metagenome Assembled Genomes (HC-MAGs) were recovered. This comprehensive HC-MAGs dataset provides a valuable resource for identifying novel microorganisms with genomic potential for syntrophic oxidation of butyrate, propionate and acetate. This analysis identified multiple interesting novel targets, including Syntrophomonadia families DTU052 and CALXsZ01 as potential butyrate oxidizers; Syntrophia families UBA6807, PHBD01, FEN-1087, and FEN-1099 as potential propionate oxidizers; and, Thermacetogeniaceae genus DTU068 together with Chloroflexota family 4572-78 as potential acetate oxidizers. These findings highlight granular sludges as a reservoir for previously uncharacterized syntrophic microorganisms. The recovered HC-MAG dataset also provides a framework to further elucidating fatty-acid oxidizing bacterial lineages within complex anaerobic communities.}, }
@article {pmid42166340, year = {2026}, author = {Sato, M and Kanaly, RA and Mori, JF}, title = {Genomic and transcriptomic insights into Achromobacter-Sphingobium co-colonization within polycyclic aromatic hydrocarbon-exposed bacterial communities.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {5}, pages = {}, doi = {10.1099/mic.0.001712}, pmid = {42166340}, issn = {1465-2080}, mesh = {*Polycyclic Aromatic Hydrocarbons/metabolism ; *Sphingomonadaceae/genetics/metabolism/growth &amp; development ; Biodegradation, Environmental ; Genome, Bacterial ; *Transcriptome ; *Achromobacter/genetics/metabolism/growth &amp; development ; Soil Microbiology ; *Achromobacter denitrificans/genetics/metabolism ; Phylogeny ; Genomics ; Soil Pollutants/metabolism ; Gene Expression Profiling ; Microbial Consortia ; }, abstract = {Efficient and complete biodegradation of polycyclic aromatic hydrocarbons (PAHs), which are persistent and genotoxic petroleum hydrocarbon pollutants, is often considered to require the cooperative activities of multiple bacterial groups, and bacterial (meta)genomic investigations of PAH-exposed ecosystems have contributed to elucidating such interactions. In this study, two bacterial isolates representing dominant genera within a PAH-grown soil bacterial consortium, Achromobacter xylosoxidans strain KK8 and Sphingobium barthaii strain KK22, were utilized as model organisms to investigate the relationship between these bacterial genera during PAH biodegradation. Strain KK8 has previously been characterized as incapable of biodegrading PAHs; thus, Achromobacter in the consortium appears to grow under metabolic dependence on PAH biodegradation products (i.e. salicylic acid) provided by the pioneer PAH-degrading Sphingobium. This metabolic relationship was evidenced through complete genome sequencing and functional gene analysis of strain KK8 conducted in the present study. To further elucidate potential interactions between Achromobacter and Sphingobium, cell-free filtrate-exchange experiments were performed using these isolates, revealing that strain KK8 exhibited a significantly shortened growth lag phase in the presence of the filtrate of strain KK22. Subsequent transcriptomic profiling of strain KK8 indicated that exposure to the Sphingobium filtrate up-regulated functional genes likely associated with Achromobacter colonization, including genes involved in biofilm formation (pga genes) or cell division (fts genes). Enhanced biofilm formation of strain KK8 in response to strain KK22 filtrate was additionally evidenced by biofilm assays. Taken together, these results suggest that the high abundance of Achromobacter within the consortium may be stimulated by Sphingobium when they are present together, potentially via extracellular signalling molecule(s). As the co-occurrence of Achromobacter and Sphingobium has been repeatedly documented in PAH-degrading bacterial communities, elucidating the mechanisms underlying their specific interspecies co-colonization during PAH biodegradation shall be valuable for the future biotechnological applications utilizing these bacteria.}, }
@article {pmid42166940, year = {2026}, author = {Ali, S and Chaudhary, AA and Sheikh, WM and Ali, MAM and Chopra, C and Dar, MA and Wani, AK and Bashir, SM}, title = {Genome-resolved metagenomics of the tumour microbiome: From strain diversity to functional cancer ecology.}, journal = {Pathology, research and practice}, volume = {285}, number = {}, pages = {156543}, doi = {10.1016/j.prp.2026.156543}, pmid = {42166940}, issn = {1618-0631}, abstract = {Advances in genome-resolved metagenomics, spatial transcriptomics, and single-cell sequencing have revealed that tumour-associated microbes are not random contaminants but structured, functionally heterogeneous components of the tumour microenvironment. Strain-level genomic reconstruction uncovers substantial intra-species diversity, encompassing accessory genes, mobile elements, and metabolic modules that collectively influence genotoxicity, immune modulation, drug metabolism, redox regulation, and biofilm formation. These microbial traits often assemble into convergent functional guilds that drive DNA damage, immune polarization, therapeutic resistance, and metastatic potential across tumour types. Integrative multi-omics analyses demonstrate that only a subset of detected microbial taxa is transcriptionally and metabolically active within tumours, underscoring the importance of combining metatranscriptomics, proteomics, metabolomics, and spatial profiling to delineate biologically meaningful host-microbe interactions. Spatial and single-cell mapping further reveal that intratumoural microbes occupy defined intracellular and extracellular microniches often aligned with hypoxic regions, myeloid-rich aggregates, T-cell exclusion zones, and metabolically reprogrammed epithelial states, reinforcing their role as active participants in tumour physiology rather than passive passengers. Mechanistic evidence now indicates that tumour-resident microbial ecosystems modulate responses to chemotherapy, immune checkpoint blockade, and radiotherapy, while contributing to premetastatic niche conditioning. Low-abundance but high-impact keystone microbial genomes can exert a disproportionate influence on tumour progression and therapeutic outcomes, providing new opportunities for biomarker discovery and microbiome-targeted interventions. This review integrates genome-resolved, spatial, and functional perspectives to propose an onco-metagenome framework that links tumour microbial ecology to cancer evolution, immune regulation, and translational intervention.}, }
@article {pmid42166998, year = {2026}, author = {Wu, Q and Zheng, Y and Xia, Y and Ge, C and Deng, H and Zhao, Y and Luo, J and Feng, D}, title = {Decoding the seagrass plastisphere: Metagenomic insights into biogeochemical cycling of biogenic elements and ecological consequences.}, journal = {Environment international}, volume = {212}, number = {}, pages = {110311}, doi = {10.1016/j.envint.2026.110311}, pmid = {42166998}, issn = {1873-6750}, abstract = {Seagrass meadow, a crucial blue carbon ecosystem, is increasingly threatened by plastic pollution. Plastic debris in this sensitive ecosystem creates a new microbial habitat known as "plastisphere". However, the functional role of plastisphere, particularly in driving the cycling of key biogenic elements, remains poorly understood. This knowledge gap raises concerns over potential disruptions to elemental fluxes and subsequent ecological consequences. Here, metagenomic analysis was employed to investigate the metabolic profile of in-situ plastisphere in seagrass meadow, with particular focus on carbon (C), nitrogen (N), phosphorus (P), and sulfur (S) biotransformation. The obtained results revealed that plastisphere microbes were taxonomically distinct from those in natural environments of the seagrass meadow, and these inhabitants were capable of driving diverse metabolic pathways. However, >75% functional gene similarity indicated a significant functional overlap between the plastisphere and natural environments. This niche enriched genes related to heterotrophic organic C degradation (27.71% ± 3.28%) and oxidation (17.86% ± 2.04%) pathways, organic N metabolism (62.18% ± 8.57%) mainly through GS-GOGAT pathways and denitrification (8.70% ± 4.06%), polyphosphate degradation (22.89% ± 2.20%) and organic P mineralization (17.50% ± 1.70%), as well as assimilatory/dissimilatory sulfate reduction (30.60% ± 3.49%) and thiosulfate disproportionation (13.57% ± 2.89%) metabolic pathways. Metabolic linkage within seagrass plastisphere was facilitated by highly connected taxa including Silicimonas and Erythrobacter, which linked electron-donating processes (including organic C degradation and S oxidation) to electron-accepting pathways (e.g., sulfate/nitrate reduction, C fixation). These interactions established the plastisphere as a potential biogeochemical hotspot, potentially amplifying the risks of CO2/N2O emission, H2S accumulation, nutrient competition with seagrass and potential eutrophication from imbalanced P mobilization, ultimately threatening the health and stability of seagrass ecosystem.}, }
@article {pmid42167281, year = {2026}, author = {Bambakidis, T and Liu, S and Wettengel, AM and Holmes, RM and Dinga, BJ and Koning, AA and McIntyre, PB and Borton, MA and Mann, PJ and Crump, BC}, title = {Congo River Bacterioplankton Genomic Diversity Reflects Water Travel Time, Wetland Habitats, and Greenhouse Gases.}, journal = {Environmental microbiology}, volume = {28}, number = {5}, pages = {e70327}, doi = {10.1111/1462-2920.70327}, pmid = {42167281}, issn = {1462-2920}, support = {DEB-1840243//National Science Foundation/ ; OCE-0851101//National Science Foundation/ ; OCE-0851015//National Science Foundation/ ; DGE-0718123//National Science Foundation/ ; DEB-1501836//National Science Foundation/ ; 52379057//China Natural Science Foundation/ ; //David and Lucile Packard Foundation/ ; //U.S. Geological Survey/ ; 10.46936/10.25585/60001289//Joint Genome Institute/ ; }, mesh = {*Wetlands ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Greenhouse Gases/analysis/metabolism ; Congo ; RNA, Ribosomal, 16S/genetics ; *Plankton/genetics/classification ; Ecosystem ; Methane/metabolism ; Phylogeny ; Carbon Cycle ; Biodiversity ; Metagenome ; }, abstract = {Tropical rivers are major contributors to global carbon cycling, yet the microbial communities driving these transformations remain largely uncharacterized. We investigated bacterioplankton communities along the northwest Congo watershed using 16S rRNA and metagenomic sequencing, paired with hydrological, biogeochemical, and greenhouse gas data. In large rivers, community composition correlated with temperature and water travel time, while smaller streams were shaped by nutrient chemistry and landscape. Most sites were dominated by Burkholderiales, but composition varied, especially in DOC-rich Cuvette Centrale wetland streams that hosted distinct communities associated with high methane and CO2, and low oxygen. Indicator species analysis identified specific taxa and metagenome-assembled genomes (MAGs) strongly associated with long travel times, wetlands, and methane, including methanotrophs (Methylcoccaceae, Methylophilaceae, Methylomonas) and MAGs encoding diverse carbon-processing metabolisms. For global context, Congo and northern Thailand river bacterioplankton were more similar to each other than to temperate Connecticut River communities, possibly reflecting shared tropical features such as high precipitation, temperature, and travel time. As in temperate systems, bacterioplankton in large tropical rivers are shaped by temperature and hydrology, while smaller tropical streams reflect localized environmental drivers. The striking similarity of tropical river bacterioplankton from Africa and Asia suggests the primacy of environmental controls on river bacterioplankton.}, }
@article {pmid42167521, year = {2026}, author = {Wolacewicz, M and Decewicz, P and Valdes, ME and Iaconi, OS and Todiras, M and Ferdohleb, A and Rodriguez-Mozaz, S and Borrego, CM and Dziewit, L}, title = {The occurrence and removal of antibiotic residues and antibiotic resistance genes in the largest European constructed wetland at Orhei (Moldova).}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128381}, doi = {10.1016/j.envpol.2026.128381}, pmid = {42167521}, issn = {1873-6424}, abstract = {Constructed wetlands (CWs) are increasingly promoted as low-cost, nature-based solutions for wastewater treatment, particularly in low- and middle-income countries (LMICs), yet their performance in removing pharmaceutical compounds, antibiotic resistance genes (ARGs), and bacterial pathogens remains insufficiently characterized under real-field-scale conditions. Here, we investigated the fate of pharmaceutical compounds (including antibiotic residues), wastewater bacterial communities, and the associated ARGs in the largest European passive treatment system, the vertical-flow CW of Orhei (Moldova), serving nearly 26,000 inhabitants. Metagenomic profiling revealed 783 bacterial families, with a reduction from 33 families in raw sewage to 25 in the final effluent and clear enrichment of autochthonous wetland taxa. A total of 150 ARG types conferring resistance to 16 antibiotic classes were detected. The cumulative ARG load decreased by approximately 78% from influent to effluent. ARGs conferring resistance to fosfomycin, nitroimidazoles, rifamycins, streptothricin, oxazolidinones, and pleuromutilins were not detected in the final effluent, suggesting effective removal to below the detection limit of the applied metagenomic method, while sulfonamide resistance genes (sul1, sul2) persisted across all stages. Out of 29 antibiotic residues analyzed, 13 (including two sulfamethoxazole metabolites) were detected, together with 14 non-antibiotic pharmaceuticals (out of 30 residues analyzed). The removal of individual antibiotics ranged between 85 and 100%, and for other pharmaceuticals between 34 and 100%, although some compounds (e.g., carbamazepine, 10,11-epoxycarbamazepine, alprazolam) showed negative removals. Environmental risk assessment (risk quotients, RQ) indicated no significant risk to freshwater biota (RQ < 0.1) for all detected compounds in the treated effluent. Results demonstrated that a large-scale CW in the LMIC context can substantially reduce antibiotic residues and ARGs, supporting its role as an effective, nature-based component of One Health-oriented wastewater management.}, }
@article {pmid42167540, year = {2026}, author = {Wang, W and Liu, H and Jiang, K and Posum, W and Lu, Z and Chen, X}, title = {A rare case of Porphyromonas endodontalis lung abscess mimicking lung cancer on imaging: The diagnostic value of postoperative metagenomic next-generation sequencing.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108821}, doi = {10.1016/j.ijid.2026.108821}, pmid = {42167540}, issn = {1878-3511}, abstract = {This case highlights the diagnostic challenge of a Porphyromonas endodontalis lung abscess mimicking lung cancer. A 67-year-old male presented with a right lower lobe mass suggestive of malignancy. Following wedge resection, pathology confirmed an abscess. Metagenomic next-generation sequencing (mNGS) of the tissue revealed a microbial profile dominated by oral anaerobes of Porphyromonas endodontalis. Postoperative mNGS identified the oral origin of infection and prompted periodontal treatment, leading to full recovery. This report reveals the decisive value of postoperative mNGS in correcting a diagnosis of infection mimicking lung cancer. It emphasizes that oral anaerobic infections can present as "tumor-like" pulmonary lesions. This case suggests that oral infection sources should be considered in the differential diagnosis of challenging pulmonary lesions and highlights the potential value of a multidisciplinary approach that includes dental evaluation.}, }
@article {pmid42167986, year = {2026}, author = {Thomas, J and Ananthanarayanan, V and Padmanabhan, S}, title = {Metagenomic analysis of oral microbiome around zinc oxide nanoparticle-coated mini-implants: A split-mouth trial.}, journal = {Journal of the World federation of orthodontists}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ejwf.2026.03.003}, pmid = {42167986}, issn = {2212-4438}, abstract = {BACKGROUND: This study aimed to evaluate the changes in the oral microbiome surrounding zinc oxide nanoparticle (NP)-coated orthodontic mini-implants using whole-genome metagenomic sequencing and to compare the microbial colonization and clinical stability with uncoated orthodontic mini-implants.<br><br>METHODS: A randomized split-mouth trial was conducted on 12 orthodontic patients requiring bilateral skeletal anchorage in the maxillary arch. Each patient received one zinc oxide NP-coated mini-implant and one uncoated implant. The implants were coated using radiofrequency magnetron sputtering. Peri mini-implant crevicular fluid samples were collected at 1 week (T1), 4 weeks (T2), and 3 months (T3) postinsertion, and the pooled sample at each time point was subjected to whole-genome shotgun metagenomic sequencing. Taxonomic and functional profiles were analyzed using Kraken and MEGAN6, with diversity indices calculated via the VEGAN R package. Stability was assessed using a 4-point semiquantitative mobility scoring.<br><br>RESULTS: Alpha diversity indices (Shannon and Chao1) showed no comparable differences between coated and uncoated mini-implants at any time point. Descriptive analysis of pooled metagenomic samples showed lower relative abundance or absence of peri&#x2011;implant pathogens, including Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, and Parvimonas micra, around coated implants. Functional gene analysis revealed reduced expression of bacterial motility, chemotaxis, and ribosomal pathways in the coated group. All mini-implants remained clinically successful during follow-up. Mobility scores were significantly lower at 1 month (P = 0.04), but not at 3 months (P = 0.102).<br><br>CONCLUSIONS: Within the constraints of pooled metagenomic analysis, zinc oxide NP-coated mini-implants were associated with a lower relative abundance of selected peri&#x2011;implant pathogens and differences in functional pathway profiles compared with uncoated implants. Overall microbial diversity did not differ significantly between groups. Both implant types remained clinically stable, although coated implants showed reduced early mobility at 1 month. These findings should be interpreted as exploratory, and further validation through patient-level metagenomic studies is warranted.}, }
@article {pmid42168196, year = {2026}, author = {Bowie, KR and Luhung, I and Burke, TR and Roberts, SC and Martinello, RA and Gerstein, M and Peccia, J and Healy, HG}, title = {Disinfection of hospital sink drains enriches pseudomonadota and efflux pump-mediated antibiotic resistance in reestablished biofilms.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73533-y}, pmid = {42168196}, issn = {2041-1723}, support = {1S10OD030363-01A1//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, abstract = {Antimicrobial resistant pathogens and associated infections represent major public health threats affecting healthcare facilities, with sink drain biofilms serving as reservoirs for many of these bacteria. Despite attempts at sink drain biofilm disinfection and removal, drain biofilms inevitably regrow, and disinfection may shape the returning microbial communities and their resistance profiles. We applied culture-based and metagenomic approaches to study these drain disinfection effects on microbial community abundance, taxonomy, and antimicrobial resistance in operational hospital sinks. Drain biofilms regrew to baseline densities in approximately four days. Regrown biofilms contained more viable carbapenem-resistant bacteria and were dominated by Pseudomonadota, including Cupriavidus and Pseudomonas. Long-read sequencing revealed an increase in multidrug efflux pump genes after disinfection, which confer broad resistance to antibiotics and disinfectants. This work provides mechanistic insights into how disinfection influences sink drain biofilm ecology and the enrichment of antimicrobial resistance, with implications for infection prevention strategies in healthcare environments.}, }
@article {pmid42168704, year = {2026}, author = {Zhang, X and Mallick, H and Rahnavard, A}, title = {Meta-analytic microbiome target discovery for immune checkpoint inhibitor response in advanced melanoma.}, journal = {Communications medicine}, volume = {6}, number = {1}, pages = {}, pmid = {42168704}, issn = {2730-664X}, support = {2109688//National Science Foundation (NSF)/ ; 2109688//National Science Foundation (NSF)/ ; }, abstract = {BACKGROUND: Immune checkpoint inhibitors have transformed melanoma therapy, yet only a subset of patients achieve durable responses. Gut microbes have been linked to response, but reported biomarkers vary across studies. We aim to identify reproducible microbial features and test their generalizability across cohorts and treatment settings.<br><br>METHODS: We reprocessed stool metagenomic sequencing data from 15 melanoma cohorts (763 samples from 484 individuals), including 12 cohorts treated with immune checkpoint inhibitors alone and 3 trials combining immune checkpoint inhibitors with fecal microbiota transplantation. Using a unified analysis pipeline, we profiled microbial species, metabolic pathways, and biosynthetic gene clusters, and analyzed their associations with treatment response using Tweedie regression, random-effects meta-analysis, and multimodal integration with leave-one-dataset-out validation.<br><br>RESULTS: Here, we show that responders in immune checkpoint inhibitor-only cohorts are enriched for several short-chain fatty acid-producing commensals, whereas non-responders show higher abundance of taxa associated with disrupted gut communities. In fecal microbiota transplantation plus immune checkpoint inhibitor trials, response associates with distinct communities and shifts in amino-acid, nucleotide and cofactor metabolism. Across cohorts, multiview prediction models repeatedly select gene clusters linked to antimicrobial peptides and surface polysaccharides, but cross-study discrimination remains modest.<br><br>CONCLUSIONS: Microbiome signatures of response are treatment-context dependent and are not captured by a single universal species. These harmonized findings prioritize microbial taxa and functions for mechanistic studies and future microbiome-informed interventions.}, }
@article {pmid42168837, year = {2026}, author = {Tong, L and Liu, Y and Han, F and Jiang, Y and Ying, S and Zhang, B and Cheng, Y and Liu, Z and Shi, Y and Xu, M and Tang, C and Sui, S and Chen, T}, title = {Exploring microbial ecology in public swimming pools: a metagenomic investigation of community structure and environmental correlates.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05157-7}, pmid = {42168837}, issn = {1471-2180}, support = {GWVI-4//The Key Projects in the Three-year Plan of Shanghai Municipal Public Health System (2023-2025)/ ; }, abstract = {Epidemiological studies have identified correlations between swimming and outbreaks of various infectious diseases. However, a comprehensive understanding of the pathogens present in public swimming pool water has yet to be systematically established. Swimming pool water samples were collected from 20 indoor public swimming pools in Shanghai, China during the summer of 2023. After quality inspection of the extracted nucleic acid, the qualified samples were subjected to metagenomic sequencing to profile the microbial communities of swimming pool water. A total of 24,035 microbial species were identified with the abundance of bacteria (99.46%), followed by archaea (0.29%), viruses (0.20%), and fungi (0.05%), including 441 pathogenic species, 23 of which were classified as biosafety level 3 (BSL-3) microorganisms. Environmental sources constituted the dominant origin (86.00%) of the pool water microbiome. Additionally, suburban pools demonstrated greater microbial diversity than urban pools (P < 0.05). The abundance of viruses exhibited a positive correlation with the concentration of urea in pool water (r = 0.31, P < 0.05). This study demonstrated that swimming pool water serves as a potent reservoir and mixing vessel for various highly pathogenic microorganisms. Effective water quality management strategies are essential to mitigating the potential public health threats of public swimming pools.}, }
@article {pmid42168845, year = {2026}, author = {Zhao, Q and Zuo, S and Liu, S and Wang, J and Tang, J and Zou, X and Leng, Y and Li, X and Zhou, M and Tian, J and Wang, P}, title = {Integrative multi-omics analysis reveals host-microbiome metabolic alterations and candidate biomarkers in Parkinson's disease.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05168-4}, pmid = {42168845}, issn = {1471-2180}, support = {2023AFD045//Hubei Provincial Natural Science Foundation / Joint Fund Project Cultivation Project/ ; 2023BCB140//Hubei Provincial plan of science and technology key research project/ ; 2023XKQT1//The Advantages Dicipline Group (Medicine) Project in Higher Education of Hubei Province (2021-2025)/ ; }, abstract = {Alterations in the gut microbiome have been increasingly implicated in Parkinson's disease (PD), but the associated metabolic changes remain incompletely understood. Here, we applied an integrative multi-omics approach combining shotgun metagenomic sequencing and untargeted LC-MS-based plasma metabolomics to investigate host-microbiome alterations in PD. Fecal and plasma samples were collected from 30 PD patients and 30 healthy spouse controls. Significant differences in microbial diversity and taxonomic composition were observed between the two groups. Taxonomic profiling revealed marked gut microbial dysbiosis in PD, including altered abundances of Phocea massiliensis, Bacteroides sp900766005, and Alistipes_A indistinctus. Metabolomic analysis identified 86 significantly altered plasma metabolites, including glycerophospholipids, indoleacetic acid, and kynurenic acid. Integrative pathway analysis suggested links between microbial functional alterations and host metabolic changes. Machine-learning analyses identified three biomarker panels that distinguished PD patients from controls in validation datasets, with the highest area under the curve (AUC) reaching 0.92. In silico molecular docking further suggested potential interactions between several metabolite biomarkers and alpha-2-macroglobulin (A2M) or the human B[act] spliceosome. Overall, these findings provide an integrative view of host-microbiome metabolic alterations associated with PD and highlight candidate biomarkers and exploratory host-metabolite associations for further investigation.}, }
@article {pmid42169289, year = {2026}, author = {Li, Y and Liu, X and Li, C and Xu, X and Tang, C and Zhou, G and Liu, Y and Blank, I}, title = {Elucidating microbial succession and aroma-active metabolite formation in hybrid dry-fermented sausage analogues with texturized pea protein: Integrating flavoromics, metabolomics, and metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {237}, number = {}, pages = {119324}, doi = {10.1016/j.foodres.2026.119324}, pmid = {42169289}, issn = {1873-7145}, mesh = {*Metabolomics/methods ; *Meat Products/microbiology/analysis ; *Odorants/analysis ; Fermentation ; *Metagenomics/methods ; Volatile Organic Compounds/analysis ; *Pea Proteins/metabolism ; Animals ; Gas Chromatography-Mass Spectrometry ; Taste ; Food Microbiology ; Humans ; Microbiota ; Swine ; Tandem Mass Spectrometry ; }, abstract = {Hybrid dry-fermented sausage analogues with texturized pea proteins (TPPs) are emerging, yet flavor formation mechanisms remain unclear. We combined quantitative descriptive analysis with complementary HS-SPME-GC-MS/HS-GC-IMS volatilomics, UHPLC-MS/MS untargeted metabolomics, and marker-gene microbiome sequencing across sausages with different fermentation and ripening stages to map key aroma and their potential microbial and metabolic drivers. Sensory data showed rising fruity, cocoa-chocolate and nutty notes. In total, 47 volatiles were identified by GC-MS and 40 by GC-IMS. Screening of odorants based on relative odor activity value (rOAV) consistently highlighted seven odorants, with a shift from hexanal-dominated raw profiles to linalool-dominated processed profiles, indicating suppression of aldehyde-derived off-notes and enrichment of terpene/ester notes. Metabolomics detected 2467 metabolites, dominated by lipids and organic acids, and short-peptide enrichment suggested intensified proteolysis supplying aroma precursors. Bacterial succession exceeded fungal variation, with Latilactobacillus and Staphylococcus as core taxa. The integrated dataset provides practical markers and microbial/process cues to enhance flavor quality of sustainable hybrid fermented meats.}, }
@article {pmid42169351, year = {2026}, author = {Yang, S and Fu, X and Yang, Z and Zhang, T and Lu, C and Yi, L and Zhao, Q and Gu, Y and Wang, S}, title = {Metagenomic sequencing reveals the similarities and differences in microbial community structure and diversity between fermented whey and Rubing cheese, a fresh goat milk cheese.}, journal = {Food research international (Ottawa, Ont.)}, volume = {237}, number = {}, pages = {119400}, doi = {10.1016/j.foodres.2026.119400}, pmid = {42169351}, issn = {1873-7145}, mesh = {*Cheese/microbiology/analysis ; Animals ; Goats ; *Metagenomics/methods ; Fermentation ; *Whey/microbiology ; *Food Microbiology ; Biogenic Amines/analysis ; China ; Milk/microbiology ; *Microbiota ; Bacteria/genetics/classification ; }, abstract = {Rubing cheese is a traditional handmade goat milk cheese in Yunnan, China, and the fermented whey used in its production affects its quality and safety. This study employed metagenomic sequencing to systematically characterize the microbial communities in fermented whey and Rubing cheese and to quantitatively analyze their biogenic amine (BA) contents. Metagenomic analysis revealed that Rubing cheese had higher microbial diversity than fermented whey. Approximately 403 microbial species were identified in Rubing cheese, and 209 were identified in fermented whey. Notably, fermented whey was rich in lactic acid bacteria (LAB), such as Lactobacillus delbrueckii (L. delbrueckii), Lentilactobacillus hilgardii (Le. hilgardii), and Lacticaseibacillus paracasei (La. paracasei). In contrast, Rubing cheese contained a high abundance of Escherichia coli (E. coli). The total BA content was low in both fermented whey (20.25 mg·kg[-1]) and Rubing cheese (4.69 mg·kg[-1]). These findings provide a scientific basis for establishing standardized production processes for developing functional starter cultures in the industrialization of Rubing cheese production.}, }
@article {pmid42169753, year = {2026}, author = {Song, D and Zhong, X and Zhang, G and Chen, J and Xue, Y and Yang, L}, title = {Linking geographic flavor signatures to microbial origin in high-temperature Daqu: An integrated metaproteomics and metabolomics approach.}, journal = {Food chemistry: X}, volume = {36}, number = {}, pages = {103952}, pmid = {42169753}, issn = {2590-1575}, abstract = {Elucidating the molecular architecture of microbial terroir is vital for precision fermentation, yet functional decoupling between taxonomic abundance and in situ expression remains a fundamental challenge. To resolve this "abundance-activity paradox," we integrated metaproteomics, metabolomics, and metagenomics across the Chishui River gradient. We identified distinct chemosensory fingerprints: upstream thermotolerant consortia (Bacillus and Oceanibacillus) specialize in 2,3,5,6-tetramethylpyrazine biosynthesis mediated by bacterial acetolactate decarboxylase, while downstream microbiota (Weissella and Debaryomyces) prioritize alcohol and ester formation. Crucially, metaproteomic profiling unmasked the "rare biosphere" as a primary driver of core metabolic fluxes. While Bacillus was genomically dominant, keystone functional taxa-specifically low-abundance fungi like Hyphopichia and Paecilomyces-were the actual executors of rate-limiting starch hydrolysis. Furthermore, functional resilience was uniquely maintained through robust fungal co-occurrence networks despite geographic constraints. This study challenges abundance-centric paradigms, providing an activity-based framework for the rational design of synthetic microbial consortia to standardize flavor while preserving regional identity.}, }
@article {pmid42169756, year = {2026}, author = {Chen, Y and Yu, K and Sun, Y and Yan, Y and Yin, G and Wang, J and Li, X and Tang, S and Pronyk, P and Xia, Y}, title = {Plastic leachates drive conjugative transfer of antibiotic resistance genes.}, journal = {Environmental science and ecotechnology}, volume = {31}, number = {}, pages = {100705}, pmid = {42169756}, issn = {2666-4984}, abstract = {Plastic pollution pervades aquatic ecosystems worldwide, releasing leachates that interact intimately with microbial communities. Antibiotic resistance genes (ARGs) disseminate rapidly through horizontal gene transfer via plasmid conjugation, posing a severe and accelerating threat to public health and environmental stability. While microplastic particles are known to promote ARG exchange within biofilms, the influence of soluble chemical leachates derived from degrading plastics has remained unclear. Here we show that photodegraded leachate from polyvinyl chloride (PVC)-a widely used material in water infrastructure-substantially enhances conjugative transfer of ARGs in both laboratory model systems and natural aquatic microbiomes. Exposure increased transconjugant abundance up to 26.4-fold and conjugation efficiency up to 44.6-fold, with non-monotonic responses modulated by leachate concentration and microbial community diversity. Characterization of the leachate revealed high proportions of biolabile dissolved organic matter alongside additives; mechanistic assays demonstrated that these effects arise through elevated intracellular reactive oxygen species (21% increase), activation of the SOS response and DNA-repair pathways, increased extracellular protein production facilitating cell-cell contact, and compensatory adjustments in the electron transport chain that maintain ATP homeostasis. These results demonstrate that plastic leachates act as potent but previously overlooked facilitators of ARG dissemination beyond the physical effects of microplastics. Our findings reveal a critical synergy between plastic pollution and the global antimicrobial-resistance crisis, underscoring the urgent need for targeted regulations on plastic additives and degradation products in aquatic systems.}, }
@article {pmid42170025, year = {2026}, author = {Higashi, K and Ishikawa, H and Kurokawa, K and Mori, H}, title = {PZLAST-MAG: full length protein sequence similarity search server of large-scale MAG proteins.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag129}, pmid = {42170025}, issn = {2635-0041}, abstract = {MOTIVATION: Metagenome-assembled genomes (MAGs) provide access to novel protein sequences from uncultured microbes, offering invaluable resources for studying protein diversity, structure prediction, and evolutionary analysis. However, despite the explosive growth of MAG-derived protein data, tools enabling fast and accurate similarity searches against large-scale MAG protein datasets remain limited.<br><br>RESULTS: We present PZLAST-MAG, a web server for ultra-fast sequence similarity searches against 0.4 billion MAG-derived protein sequences (0.1 trillion amino acids) from over 210&#xa0;000 MAGs indexed in Microbiome Datahub. Implemented on PEZY-SC3 MIMD many-core processors, PZLAST-MAG achieves high accuracy and speed, with performance comparable to widely used tools such as DIAMOND and MMseqs2 based on our benchmark analyses. In addition to tabular alignments, PZLAST-MAG provides interactive visualizations of phylogenetic and environmental distributions and co-occurrence patterns of homologous proteins across MAGs. This combination enables rapid homolog mining of functionally important genes across diverse microbial lineages while simultaneously revealing their taxonomic and ecological contexts. Two use case analyses indicate its utility for homolog mining of metabolic enzyme genes and plasmid-derived genes.<br><br>PZLAST-MAG is provided as a web-based service and is freely available at https://pzlast.nig.ac.jp/pzlast/mag without requiring registration.}, }
@article {pmid42157462, year = {2026}, author = {Singh, HW and Gutleben, J and Bogdanov, A and Chase, AB and Demko, A and Podell, S and Haley, B and Jensen, PR}, title = {Multi-Omic Assessment of Microbial Communities and Their Polyketide Biosynthetic Potential Across Abyssal Sediments.}, journal = {Environmental microbiology}, volume = {28}, number = {5}, pages = {e70320}, doi = {10.1111/1462-2920.70320}, pmid = {42157462}, issn = {1462-2920}, support = {R01GM085770/NH/NIH HHS/United States ; }, mesh = {*Geologic Sediments/microbiology ; *Polyketides/metabolism ; Phylogeny ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Polyketide Synthases/genetics/metabolism ; Metagenome ; Seawater/microbiology ; Biodiversity ; Multiomics ; }, abstract = {Microbially-derived polyketides include some of today's most valuable medicines, yet their discovery has focused on a narrow subset of Earth's microbial biodiversity. Although understudied biomes such as marine sediments have been targeted, these efforts have focused on samples collected from shallow waters. In contrast, abyssal marine sediments (4000-6000 m), which comprise > 80% of the ocean floor, remain poorly explored. This leaves foundational gaps in our understanding of deep-sea microbial diversity and its relationship to biosynthetic potential. Here, we used culture-independent approaches to characterise microbial taxonomic and biosynthetic diversity in abyssal sediments collected from three geochemically distinct plains along an 880 km transect. Sediment communities varied in both taxonomic (16S rRNA gene) and biosynthetic (ketosynthase domain) composition across sites and relative to nearshore sediments, suggesting they harbour unique opportunities for natural product discovery. Ketosynthase phylogenies revealed abyssal clades that diverged from experimentally characterised polyketide synthase pathways, further supporting biosynthetic novelty. Metagenome-assembled genomes linked unique ketosynthase domains to the poorly studied phylum Gemmatimonadota. Sediment metabolomes provided evidence of chemical novelty, with < 10% of the features detected matching previously reported spectra. These baseline findings indicate that abyssal sediments represent reservoirs of unexplored polyketide biosynthetic diversity.}, }
@article {pmid42158361, year = {2026}, author = {Louise Jespersen, M and Kjærgaard Munk, K and Fjermedal, S and Pilgaard, B and Meyer, AS and Aarestrup, FM and Otani, S}, title = {A Hadza-enriched Prevotella/Segatella xyloglucanase shows sequence conservation and functional specialization.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2673265}, pmid = {42158361}, issn = {2993-3935}, abstract = {Bacteria can adapt to their environment through changes in their genetic material. A large proportion of gut bacteria are shaped by host-specific diet, including complex carbohydrates. The bacterial abundance, genetic content within the same bacterial species, and sequence-level variation in genes encoding similar carbohydrate-processing enzymes may therefore vary across hosts with different diets. We previously found that the abundance of diet-degrading genes varies between hominid host populations from Tanzania. We therefore hypothesized that, in addition to these abundance differences, selective pressure could act on individual gene sequences. Here, we investigated Tanzanian hominid gut microbiome differences at the taxonomic, genetic, structural, and functional levels. We analyzed 15,146 metagenome-assembled genomes (MAGs) spanning 1563 species and identified one species with striking host-associated separation. In particular, sequence variation in a xyloglucanase-encoding gene correlated strongly with the host population. This gene was highly conserved in the Hadza population, suggesting a role in the processing of diet-associated polysaccharides. Sequence differences and structural modeling revealed amino acid substitutions near the catalytic site, and biochemical assays using xyloglucan showed that representative variants differed in activity under identical assay conditions. Collectively, our findings suggest that host lifestyle and diet contribute to population-associated sequence variation in genes encoding enzymes involved in degrading polysaccharides.}, }
@article {pmid42158572, year = {2026}, author = {Wong, E and England, J and Jagadeesan, V}, title = {Scedosporium apiospermum Infective Endocarditis With Brain Abscesses in a Lung Transplant Recipient: Review of the Literature and Evaluating the Use of Next-Generation Sequencing.}, journal = {Case reports in infectious diseases}, volume = {2026}, number = {}, pages = {8041837}, pmid = {42158572}, issn = {2090-6625}, abstract = {Scedosporium apiospermum is an emerging cause of invasive mold infection in immunocompromised hosts, often with central nervous system involvement and limited susceptibility to amphotericin B. We describe a 36-year-old lung transplant recipient who presented with fever, meningismus, and multiple enhancing brain lesions nine months post-transplant. Cerebrospinal fluid studies, including metagenomic next-generation sequencing (mNGS), were negative. Cardiac imaging revealed a pedunculated right ventricular septal mass, and plasma cell-free DNA (cfDNA) testing (Karius) identified S. apiospermum. Subsequent brain biopsy and thrombectomy confirmed the diagnosis by histopathology and culture. Following surgical removal of the cardiac mass and treatment with voriconazole, the patient improved with near resolution of brain lesions. This case highlights disseminated S. apiospermum endocarditis diagnosed by plasma cfDNA despite negative CSF mNGS, underscoring that site-specific mNGS may be falsely negative in compartmentalized infections. Plasma cfDNA testing can complement conventional and tissue-based diagnostics for early detection of disseminated mold infections in transplant recipients.}, }
@article {pmid42158968, year = {2026}, author = {Shi, Z and Huang, F and Luo, C and Yang, L and Chen, Y and Qiao, C and Wang, R and Wang, Y and Yan, Y and Wang, L and Fan, L and Shen, W}, title = {Gut Microbiota Alterations in Myelodysplastic Neoplasms Are Associated With Immune Dysfunction and the Therapeutic Mechanism of Hypomethylating Agents.}, journal = {Cancer medicine}, volume = {15}, number = {5}, pages = {e71946}, doi = {10.1002/cam4.71946}, pmid = {42158968}, issn = {2045-7634}, support = {82200151//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; *Myelodysplastic Syndromes/drug therapy/immunology/microbiology ; Male ; Female ; Aged ; Middle Aged ; *Dysbiosis/immunology ; Case-Control Studies ; DNA Methylation/drug effects ; Feces/microbiology ; Aged, 80 and over ; High-Throughput Nucleotide Sequencing ; Metabolic Networks and Pathways ; Adult ; }, abstract = {BACKGROUND: Myelodysplastic neoplasms (MDS) represent a group of heterogeneous clonal disorders characterized by immune dysregulation in their pathogenesis. Gut microbiota dysbiosis plays a critical role in immune modulation.<br><br>METHODS: We collected the fecal samples of 23 newly diagnosed MDS, 10 hypomethylating agents (HMA) treated MDS and 13 age and sex matched healthy controls (HC), and analyzed the gut microbiota compositions and functional pathways using metagenomic next-generation sequencing (mNGS).<br><br>RESULTS: Distinct microbial compositions were observed between newly diagnosed MDS and HC. Notably, the Veillonellaceae family was significantly enriched in MDS patients. Specific bacteroid species demonstrated significant correlations with lymphocyte subtypes, functional activation status, and serum inflammatory cytokines. Functional profiling revealed altered metabolic pathways in newly diagnosed patients, particularly in amino acid metabolism and ATP synthesis. Notably, glutamine/glutamate and tryptophan metabolism pathways were hyperactive in untreated MDS but downregulated following HMA treatment.<br><br>CONCLUSIONS: The gut microbiota altered in MDS patients and was associated with immune dysregulation and inflammation, which may contribute to MDS pathogenesis and mediate therapeutic effects of HMA treatment, highlighting the gut microbiota-metabolism axis as a potential therapeutic target for MDS management.}, }
@article {pmid42159114, year = {2026}, author = {Li, Y and Liu, J and Hu, W and Li, C and Zhang, L and Qiu, S and Zhu, S}, title = {The Value of Second-Generation Metagenomic Sequencing in the Diagnosis of Respiratory Infections.}, journal = {Clinical laboratory}, volume = {72}, number = {5}, pages = {}, doi = {10.7754/Clin.Lab.2025.250525}, pmid = {42159114}, issn = {1433-6510}, mesh = {Humans ; *Respiratory Tract Infections/diagnosis/microbiology ; Male ; Female ; Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; Retrospective Studies ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; Adult ; *Bacteria/genetics/isolation &amp; purification ; Young Adult ; Aged, 80 and over ; }, abstract = {BACKGROUND: This study aimed to compare the results of metagenomic next-generation sequencing (mNGS) and conventional culture detection of pathogenic bacteria in bronchoalveolar lavage fluid (BALF) of patients with respiratory tract infections and analyze the influencing factors and clinical significance of mNGS positive detection.<br><br>METHODS: We retrospectively analyzed BALF samples from 90 respiratory infection patients at the First People's Hospital of Yongkang City from June 1, 2024, through January 28, 2025, using mNGS and conventional culture testing to compare the positivity rate, pathogen distribution, and consistency of the two methods. The relationship between mNGS detection positivity and clinical indicators of patients and patient prognosis was analyzed.<br><br>RESULTS: The positive rate of mNGS detection was 77.78%, while the positive rate of conventional culture detection was 44.44%, and the difference was statistically significant (p < 0.05). mNGS can detect a wider variety of pathogens, mainly gram-negative bacilli, fungi, and atypical pathogens. mNGS has moderate consistency with conventional culture detection results in bacteria, fungi, and atypical pathogens, but low consistency in viruses and para-sites. The positive detection of mNGS is related to factors such as patient age, underlying diseases, peripheral blood white blood cells, and C-reactive protein, which are risk factors affecting the positive detection of mNGS.<br><br>CONCLUSIONS: The pathogenic diagnosis of mNGS in BALF of patients with lower respiratory tract infections is su-perior to conventional culture detection; it can detect more and a wider range of pathogens, helping to promote rational drug use and improve patient prognosis in clinical practice.}, }
@article {pmid42159601, year = {2026}, author = {Yang, Y and Lian, S and Li, X and Tang, Y and Su, Y and Zhang, Z and Li, M and Guo, Y and He, Z and Shen, Y}, title = {Unveiling metagenomic and metabolomic signatures in mild and severe pneumonia caused by Mycoplasma pneumoniae in children.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, pmid = {42159601}, issn = {2057-5858}, mesh = {Humans ; *Mycoplasma pneumoniae/genetics/pathogenicity/metabolism ; *Pneumonia, Mycoplasma/microbiology/metabolism/diagnosis ; Female ; Male ; Child, Preschool ; Child ; *Metagenomics/methods ; *Metabolomics/methods ; Prospective Studies ; Bronchoalveolar Lavage Fluid/microbiology ; Infant ; Severity of Illness Index ; Microbiota ; Machine Learning ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Background. Mycoplasma pneumoniae (MP) is a common causative pathogen of community-acquired pneumonia in children, with clinical presentations ranging in severity. Early stratification and timely intervention are essential for improving patient outcomes. However, a major clinical challenge lies in the limited ability to accurately distinguish between mild and severe cases based solely on early clinical indicators.Methods. This prospective real-world study investigated the differences in microbiome and metabolomics between mild and severe MP pneumonia (MPP) in children. Bronchoalveolar lavage fluid samples were collected from 153 children and subjected to metagenomic sequencing and non-targeted metabolomic analysis. Meanwhile, to enhance early diagnostic accuracy, this study developed a machine learning classification model and validated it using a third-party validation set.Results. The results revealed significant alterations in the abundance of specific bacterial communities in the severe group, most notably the coexistence of MP and Alphainfluenzavirus influenzae, which may contribute to disease exacerbation through synergistic pathogenic mechanisms. Furthermore, the macrolide resistant rate of MP in the severe group exceeded 80%, emphasizing the importance of appropriate antibiotic selection. Metabolomic analysis showed a significant enrichment of metabolites related to cellular energy metabolism and immune regulation in severe cases. The model demonstrated exceptional predictive performance, achieving an area under the curve ranging from 0.909 to 0.991, which significantly outperformed conventional clinical stratification methods.Conclusions. These findings elucidate the distinct pathophysiological mechanisms underlying both mild and severe MP infections and provide a promising framework for improving early diagnosis and personalized treatment strategies in paediatric MPP.}, }
@article {pmid42159642, year = {2026}, author = {Ortigoza, PYA and Luiz, FN and Ghellere, GJ and Meyer, RF and Rosa, LH and Passarini, MRZ}, title = {Biogas production using the microbial community present in the soil from Deception Island, maritime Antarctica.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {42159642}, issn = {1614-7499}, support = {118/2024//Institutional Program to Support Research Groups/ ; 440218/2023-3//CNPq PROANTAR/ ; }, abstract = {The current energy crisis is increasing the production of sustainable energy, such as biogas, a fuel generated by the anaerobic digestion of organic waste. The use of oat, an agricultural waste, makes the anaerobic digestion more sustainable. Antarctic microbial communities can utilize a wide range of substrates and adapt to different temperatures. Thus, this study evaluated methane production through an innovative approach, using microbial enrichment, and assessed archaeal diversity through metagenomic techniques in Antarctic soils, Deception Island, Maritime Antarctica. Metagenomic analyses showed low archaeal diversity and abundance. The Euryarchaeota (95.2%) and Methanobrevibacter were the most abundant and frequent phylum and genus, respectively. The average biogas production values were 595 LN kg VS[-][1] and 561 LN kg VS[-][1] in tests with individual oat (IO) and oat with enriched mixed culture (O + MC), respectively. However, O + MC showed a higher methane production, 4% (319 LN kg VS[-][1]) more than the results from the IO test with inoculum. Soils from Deception Island may represent a promising source of methanogenic communities capable of producing methane using agricultural waste as an alternative for energy production. Future studies are needed to understand the methane production using soil samples from cold environments.}, }
@article {pmid42159838, year = {2026}, author = {Dos Santos Miranda, T and Cosentino, MAC and Moreira, FRR and Schiffler, FB and Coimbra, A and Mouta, R and Medeiros, G and Girardi, DL and Wanderkoke, V and Lima, M and de Oliveira, TH and Francisco, TM and Soffiati, FL and Ferreira, SS and Ruiz-Miranda, CR and Soares, MA and D'arc, M and Dos Santos, AFA}, title = {Fecal virome of paraguayan hairy dwarf porcupine (Coendou spinosus, Cuvier, 1823) in Rio de Janeiro, Brazil.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {}, pmid = {42159838}, issn = {1678-4405}, mesh = {Animals ; *Feces/virology ; *Porcupines/virology ; Brazil ; *Virome ; Genome, Viral ; Phylogeny ; High-Throughput Nucleotide Sequencing ; *Viruses/classification/genetics/isolation &amp; purification ; }, abstract = {The Paraguayan hairy dwarf porcupine (Coendou spinosus, Cuvier, 1823) is a rodent species (Rodentia, Erethizontidae) widely distributed in the Brazilian Atlantic forest. However, little is known about their viral diversity. In this study, we aimed to evaluate, using high-throughput sequencing (HTS), the virome of the feces of seven healthy adult free-living porcupines from Silva Jardim, Rio de Janeiro, Brazil. Total viral nucleic acid was extracted and used for the library preparation for HTS using the Illumina MiSeq platform. The bioinformatics pipeline included quality control, with taxonomic assignments by Kraken2 and Diamond. Unclassified RNA viruses were investigated for viral genome characterization. A total of 41 viral families were classified, of which only seven were validated by both taxonomic analysis tools, including bacteriophages, vertebrate viruses, and unclassified RNA viruses. The most abundant bacterial reads identified belonged to the phylum Proteobacteria. In addition, in-depth analyses of RNA viruses revealed the presence of the Tombusviridae family, a group of plant-infecting viruses possibly associated with the host's diet. This study provides new insights into the fecal virome of Paraguayan hairy dwarf porcupines, contributing to the knowledge of microbial diversity in Erethizontidae and supporting non-invasive virome studies in wildlife.}, }
@article {pmid42159959, year = {2026}, author = {Zhang, Z and Jiang, F and Li, Z and Lin, L and Qi, B and Han, D and Ran, C and Mao, S and Wang, J and Zhou, Z and Wang, M and Li, J and Wang, G and Kang, S and Zhang, T}, title = {Animal gut microbes and microbiomes in the 21st century and beyond.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {42159959}, issn = {1869-1889}, abstract = {Animal gut microbiomes-comprising bacteria, archaea, fungi, viruses, and protozoa-are fundamental to host evolution, physiology, and ecosystem resilience. This review synthesizes 21st-century advances in their diversity, spatiotemporal dynamics, and functional roles across the animal kingdom. Although high-throughput metagenomics has transformed the field, major biases remain: most studies still focus on domesticated vertebrates and fecal samples, leaving substantial "microbial dark matter" in wild hosts, invertebrates, and non-bacterial domains unexplored. We highlight how gut microbiomes mediate adaptation to environmental extremes, including hypoxia, temperature stress, and toxins, and how industrialization disrupts these communities, contributing to biodiversity loss and disease risk. We further integrate eco-evolutionary theory, multi-omics, and spatial modeling to clarify cross-kingdom interactions and functional networks. Finally, we discuss translational applications-including probiotics, fecal microbiota transplantation (FMT), phage therapy, and synthetic consortia-and emphasize the need for global collaborative initiatives, artificial intelligence (AI)-driven discovery, and standardized databases to unlock the full potential of animal gut microbiomes for biodiversity conservation, climate resilience, and planetary health in the coming decades.}, }
@article {pmid42160933, year = {2026}, author = {Geng, C and Deng, T and Ren, K and Chen, X and Xue, S and Chen, L and Huang, C and Xu, M}, title = {Divergent structure but convergent metabolic organization of tetrabromobisphenol A degrading microbial consortia from aerobic and anaerobic conditions.}, journal = {Journal of hazardous materials}, volume = {513}, number = {}, pages = {142454}, doi = {10.1016/j.jhazmat.2026.142454}, pmid = {42160933}, issn = {1873-3336}, abstract = {Microbial consortia drive the degradation of persistent pollutants through complex metabolic interactions. However, how these interactions are reconfigured under contrasting redox conditions to maintain functional efficiency remains a fundamental question in microbial ecology. Here, we used a top-down enrichment approach to investigate the collaborative degradation of tetrabromobisphenol A (TBBPA) under both aerobic and anaerobic conditions, integrating sequential transfer cultivation, metagenomics, network analysis, pure culture experiments, and predictive modeling. Sequential transfers significantly (p < 0.05) enhanced TBBPA degradation efficiencies under both regimes, driving distinct structural successions in the microbial communities. Specialist taxa such as Sphingopyxis (aerobic) and Novosphingobium (anaerobic) were phase-specifically enriched, whereas generalists like Pseudomonas and Comamonas emerged as highly interconnected keystone taxa under both conditions. Pure culture experiments and genomic reconstruction indicated functional partitioning among different taxa, where specialists might mediate debromination and β-scission by haloalkane dehalogenase and cytochrome P450, respectively. Furthermore, generalists harbored genetic modules for downstream ring-cleavage pathways, collectively forming a metabolic network that partitions degradation steps across the community. Partial least squares (PLS) regression and random forest analysis supported this functional partitioning and indicated that the overall TBBPA degradation is an emergent community property driven by community‑level interactions. This study suggests a principle of structure-divergent but convergent metabolic organization in collaborative TBBPA-degrading consortia, providing a mechanistic basis for designing synthetic communities to optimize bioremediation of brominated pollutants across diverse environmental settings.}, }
@article {pmid42161086, year = {2026}, author = {Ziliani, A and Bovio-Winkler, P and Pabst, M and Cabezas, A and Etchebehere, C and Garcia, HA and López-Vázquez, CM and Brdjanovic, D and van Loosdrecht, MCM and Rubio-Rincón, FJ}, title = {Glycine-mediated microbial interactions in biological phosphorus removal systems.}, journal = {Water research}, volume = {302}, number = {}, pages = {126057}, doi = {10.1016/j.watres.2026.126057}, pmid = {42161086}, issn = {1879-2448}, abstract = {Amino acids are less studied substrates in enhanced biological phosphorus removal (EBPR) systems. Glycine, a prevalent amino acid in wastewater, was used in this study to evaluate its role in EBPR processes. We operated a sequencing batch reactor (SBR) for over three months with glycine as the sole carbon source to investigate phosphorus removal performance and microbial dynamics using chemical and molecular analyses. The reactor supported EBPR activity, with glycine enabling anaerobic phosphorus release followed by aerobic uptake. The dissolved organic carbon to phosphorus (DOC:P) removal ratio of 100:9.9 closely matched values reported for systems dominated by polyphosphate-accumulating organisms (PAOs), and net phosphorus removal (20 mg PO4-P L[-1]) fell within the range reported for laboratory-scale EBPR systems fed with mixed carbon sources. Community analyses showed enrichment of Saccharimonadales alongside putative PAOs, including Ca. Phosphoribacter and Ca. Propionivibrio. Genome-resolved analyses indicate distinct but complementary metabolic potentials, including glycine transformation and lactate-related pathways, suggesting distributed carbon processing within the community. Together, these findings expand the understanding of amino acid utilization in EBPR systems and identify potential metabolic linkages that influence phosphorus removal under glycine-fed conditions.}, }
@article {pmid42161088, year = {2026}, author = {Liu, Q and Zhang, Y and Gong, H and Zhou, S and Yang, J and Zhu, D and Huang, Z and Zhu, Y and Niu, H and Dai, X}, title = {Microbial-driven molecular transformation of dissolved organic matter in water-jet loom wastewater reclamation: An integrated FT-ICR MS and metagenomic investigation.}, journal = {Water research}, volume = {302}, number = {}, pages = {126124}, doi = {10.1016/j.watres.2026.126124}, pmid = {42161088}, issn = {1879-2448}, abstract = {Water-jet loom wastewater, a major textile effluent in China, contains recalcitrant dissolved organic matter (DOM) derived from synthetic sizing agents and lubricants, whose incomplete removal constrains high-quality water reuse. Although Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomics provide high-resolution molecular and genetic insights, optimizing treatment efficacy remains hindered by a fragmented understanding of the intricate links between molecular transformations and their microbial drivers. This study established a reactomic-genomic paradigm coupling potential mass difference (PMD)-based molecular network analysis with metagenomic enzyme annotation in a full-scale membrane bioreactor (MBR) system (10000 m[3]·d[-1]). Over 8,000 molecular formulae were resolved across the treatment train. The results revealed that the dissolved air flotation unit prior to MBR selectively removed hydrophobic lipids and aliphatic/peptide-like compounds, leading to the relative enrichment of lignins/CRAM-like recalcitrant matter. The bioreactor served as the major zone of molecular turnover, with oxidation and depolymerization identified as the dominant transformation classes. These transformations were consistent with the enrichment of a Sphingomonadaceae-associated functional guild and abundant oxygenase-related genes, highlighting the role of microbial oxidation in aromatic transformation. Furthermore, a source-oriented framework revealed MBR effluent DOM as a spatially assembled mixture of three components. The recalcitrant influent-derived fraction dominated total effluent intensity (74.3%), while the bioreactor-emergent fraction constituted a consistent biogenic baseline (12.0%). In contrast, the membrane-associated emergent fraction contributed to molecular diversity (45.4% of unique formulae) but weakly to total intensity (9.7%). These findings indicate that the key challenge for high-quality reuse lies in controlling persistent and compositionally complex DOM. This framework provides a molecular basis for targeted process optimization and supports the transition of textile wastewater treatment from discharge compliance toward chemistry-informed reuse.}, }
@article {pmid42161089, year = {2026}, author = {Schoenmakers, S and Nieuwenhuijse, DF and Reiss, I and van der Meeren, L and Mulders, CE and Molenkamp, R and Fraaij, PLA and van Boheemen, S}, title = {No detection of relevant virus-specific DNA or RNA sequences in the placenta.}, journal = {Placenta}, volume = {181}, number = {}, pages = {168-174}, doi = {10.1016/j.placenta.2026.05.010}, pmid = {42161089}, issn = {1532-3102}, abstract = {INTRODUCTION: The existence of a placental bacterial microbiome remains a subject of active debate, with recent studies challenging earlier claims of a resident microbial community. While the role of bacterial and viral pathogens in placental infection and adverse pregnancy outcomes is well established, the potential existence of a resident placental (non-pathogenic) virome remains largely unexplored. Given the placenta's vital role in fetal development, our study aimed to investigate whether viral genetic material is present in placental tissue, rather than to identify viral pathogens, in both uncomplicated and complicated pregnancies using viral metagenomic capture sequencing.<br><br>METHODS: Placental biopsies were obtained from three pregnancy groups: (1) delivered by elective caesarean section (n&#x202f;=&#x202f;6), (2) delivered by emergency caesarean section (n&#x202f;=&#x202f;6), and (3) complicated by preeclampsia (n&#x202f;=&#x202f;5). Samples were processed using VirCapSeq VERT, a targeted enrichment strategy for vertebrate viruses, followed by Illumina NovaSeq 6000 sequencing.<br><br>RESULTS: High quality sequencing yielded an average of 46.6 million reads per sample, with >99.6% of reads aligned to the human genome, and <0.4% of non human sequences. Across all samples, only 12 viral contigs were identified, corresponding to bacteriophages, human endogenous retroviruses, and human gammaherpesvirus 4 (not confirmed by PCR), mostly with low read counts.<br><br>CONCLUSIONS: Our study found no evidence supporting the presence of a resident placental virome. Together with existing data on the absence of a bacterial microbiome, these findings support the concept that the placenta does not harbor a detectable microbial or viral community under controlled sampling conditions.}, }
@article {pmid42161263, year = {2026}, author = {Ni, M and Junker, K and Liu, Y and Fan, Y and Li, Y and Qiao, W and Zhang, XS and Ksiezarek, M and Mead, EA and Tourancheau, A and Jiang, W and Blaser, MJ and Valdivia, RH and Davey, LE and Fang, G}, title = {Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.04.019}, pmid = {42161263}, issn = {1934-6069}, abstract = {The human microbiome continuously adapts to variations in diet and host physiology. Epigenetic phase variation (ePV) mediated by bacterial DNA methylation can generate phenotypic heterogeneity within clonal populations. ePVs have been characterized in human pathogens, but their roles in commensals remain unclear. Here, we cataloged ePVs in infant and adult gut microbiomes, revealing genome-wide and site-specific ePV in response to antibiotics and fecal microbiota transplantation. Long-read metagenomics revealed genome-wide ePV mediated by structural variations of DNA methyltransferases. Analysis of public short-read metagenomic datasets further revealed a high prevalence of genome-wide ePVs in the human microbiome. Site-specific ePVs were identified and associated with antibiotics or probiotic engraftment. Focusing on an Akkermansia muciniphila isolate, we find a specific ePV regulating mucC, a gene of unknown function but whose heterologous expression enhances bacterial tolerance to antibiotics via a bet-hedging strategy. Thus, epigenetic modifications are used by gut bacteria to adapt to fluctuating environments.}, }
@article {pmid42161874, year = {2026}, author = {,  and , }, title = {[Expert consensus on laboratory diagnosis of inflammatory bowel disease (2026)].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {60}, number = {}, pages = {1-17}, doi = {10.3760/cma.j.cn112150-20260413-00324}, pmid = {42161874}, issn = {0253-9624}, support = {82472361//Natural Science Foundation of China/ ; }, abstract = {In recent years, the incidence of inflammatory bowel disease (IBD) in China has shown a significant upward trend. The invasive nature of colonoscopy limits its widespread application in population screening and long-term follow-up, while conventional laboratory parameters still suffer from insufficient sensitivity and specificity. A single test is inadequate for comprehensively assessing the complex pathophysiological processes of IBD. To enhance diagnostic efficacy, it is necessary to establish a multi-index combined evaluation system, integrating comprehensive assessments across dimensions such as inflammatory activity, nutritional metabolism, coagulation function, and infection risk. This consensus integrates relevant hematological and fecal laboratory markers, establishes a stratified application pathway covering initial screening, differential diagnosis, activity monitoring, and efficacy evaluation, and standardizes the clinical application scenarios of indicators such as fecal calprotectin (FC), the anti-Saccharomyces cerevisiae antibody (ASCA)/perinuclear anti-neutrophil cytoplasmic antibody (pANCA) panel, CRP (C-reactive protein)/ESR (erythrocyte sedimentation rate), and NLR (neutrophil-to-lymphocyte ratio). Furthermore, this consensus systematically reviews the clinical potential of cutting-edge technologies, including 16S amplicon sequencing, metagenomic sequencing, and microRNA detection, highlighting their significant prospects in analyzing microbial community structure, identifying occult pathogens, and assessing host regulation. This consensus aims to optimize non-invasive testing strategies for IBD, reduce misdiagnosis and improper treatment, and provide a standardized framework for tiered diagnosis and treatment as well as precision prevention and management.}, }
@article {pmid42162115, year = {2026}, author = {Ranasinghe, PD and Barazanji, N and Bednarska, O and Bergman Jungeström, M and Lundberg, P and Keita, &#xc5;V and Walter, S and Simon, R}, title = {High-resolution metagenomic characterization of gut microbiota composition and functional pathways in irritable bowel syndrome.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42162115}, issn = {2045-2322}, mesh = {Humans ; *Irritable Bowel Syndrome/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; *Metagenomics/methods ; Adult ; Middle Aged ; Feces/microbiology ; *Metagenome ; Case-Control Studies ; }, abstract = {Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder characterized by abdominal pain, altered bowel habits, and frequent comorbidity with anxiety and depression. The gut microbiota has been implicated in gut-brain axis (GBA) dysfunction, but consistent microbial signatures remain unclear. We performed whole metagenome shotgun sequencing of stool samples from 63 female patients with moderate to severe IBS and 34 female healthy controls and assessed microbial composition and functional pathways. Microbial richness and diversity were slightly reduced in IBS, though with high variability and no robust separation from controls. Differential abundance analyses revealed enrichment of Streptococcus sp. and the sulfate-reducing bacterium Desulfovibrio piger in IBS, alongside reductions in Bifidobacterium and Methanobrevibacter. Functional profiling identified 39 differentially abundant pathways: amino acid biosynthesis (e.g., L-isoleucine, L-threonine) was more prominent in IBS, while carbohydrate degradation pathways (e.g., galactose, stachyose) were enriched in healthy controls. These findings indicate modest but significant IBS-associated shifts in gut microbial composition and function that may contribute to IBS symptoms. However, high intra-group variability underscores the complexity of IBS and highlights the need for larger, multi-omics studies to define robust microbial markers. These results contribute to a growing body of evidence emphasizing the complexity of gut microbiota-host interactions and the need for high-resolution, systems-level approaches in microbiome-associated disorders.}, }
@article {pmid42162191, year = {2026}, author = {Han, D and Liu, C and Yang, B and Yu, F and Liu, H and Lou, B and Shen, Y and Tang, H and Zhou, H and Zheng, S and Chen, Y}, title = {Author Correction: Metagenomic fingerprints in bronchoalveolar lavage differentiate pulmonary diseases.}, journal = {NPJ digital medicine}, volume = {9}, number = {1}, pages = {}, doi = {10.1038/s41746-026-02769-1}, pmid = {42162191}, issn = {2398-6352}, }
@article {pmid42162287, year = {2026}, author = {Svanella-Dumas, L and Marais, A and Faure, C and Bergey, B and Comte, R and Candresse, T}, title = {Repeated identification of plant-associated polerovirus 3 (PaPV3) and of a novel polerovirus in the virome of French grain cereals.}, journal = {Archives of virology}, volume = {171}, number = {6}, pages = {}, pmid = {42162287}, issn = {1432-8798}, support = {ViroCAP//Minist&#xe8;re de l'Agriculture, de l'Agroalimentaire et de la For&#xea;t/ ; ViroCAP//Minist&#xe8;re de l'Agriculture, de l'Agroalimentaire et de la For&#xea;t/ ; ViroCAP//Minist&#xe8;re de l'Agriculture, de l'Agroalimentaire et de la For&#xea;t/ ; ViroCAP//Minist&#xe8;re de l'Agriculture, de l'Agroalimentaire et de la For&#xea;t/ ; ViroCAP//Minist&#xe8;re de l'Agriculture, de l'Agroalimentaire et de la For&#xea;t/ ; ViroCAP//Minist&#xe8;re de l'Agriculture, de l'Agroalimentaire et de la For&#xea;t/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; ANR-20-PCPA-0004 DEEP IMPACT//Agence Nationale de la Recherche/ ; }, mesh = {*Edible Grain/virology ; Genome, Viral ; Phylogeny ; *Hordeum/virology ; *Luteoviridae/genetics/classification/isolation &amp; purification ; *Plant Diseases/virology ; France ; *Virome/genetics ; Metagenomics ; }, abstract = {Two novel poleroviruses were repeatedly identified by metagenomics in French barley over the 2018-2023 period. One showed ~ 98.5% nucleotide (nt) identity with plant-associated polerovirus 3 (PaPV3) identified by metagenomics in Slovenia, while the second represents a novel species for which the name barley virus H (BVH) is proposed. Both viruses show a typical polerovirus genome organization but do not have ORF6 or ORF7. In French cereals samples, the most prevalent polerovirus was barley virus G (6.4%) followed by BVH (2.3%), cereal yellow dwarf virus RPV (CYDV-RPV, 1.8%) and PaPV3 (0.9%) suggesting the novel poleroviruses to be as prevalent as CYDV.}, }
@article {pmid42162448, year = {2026}, author = {Bharadava, K and Makarani, N and Kaushal, RS}, title = {Co-selection of antimicrobial and heavy metal resistance in aquatic microbial communities at the water interface.}, journal = {Environmental geochemistry and health}, volume = {48}, number = {8}, pages = {}, pmid = {42162448}, issn = {1573-2983}, mesh = {*Metals, Heavy/pharmacology/toxicity ; *Water Microbiology ; *Drug Resistance, Bacterial ; *Water Pollutants, Chemical ; Wastewater/microbiology ; *Drug Resistance, Microbial ; Humans ; *Anti-Bacterial Agents/pharmacology ; Bacteria/drug effects/genetics ; }, abstract = {Antimicrobial resistance (AMR) and heavy metal resistance (HMR) in aquatic ecosystems are increasing global health concerns driven by anthropogenic pollution of water systems. Municipal wastewater, hospital effluents, industrial discharge, agricultural runoff, and aquaculture activities contribute to the persistence and dissemination of resistant microorganisms and resistance genes in aquatic environments. Clinically important waterborne pathogens, including Escherichia coli, Salmonella Typhi, Shigella spp., and Vibrio cholerae, readily acquire resistance under continuous environmental stress conditions. Heavy metals further enhance AMR persistence through co-selection and cross-resistance mediated by mobile genetic elements carrying both antimicrobial and heavy metal resistance genes. This review summarizes the major environmental drivers, molecular mechanisms, and dissemination pathways associated with AMR-HMR interactions in aquatic systems. Recent advances in wastewater-based epidemiology, metagenomic surveillance, and resistance monitoring are highlighted as emerging tools for environmental and public health assessment. Current mitigation approaches, including advanced oxidation processes, membrane bioreactors, nanomaterial-based filtration, and microbial bioremediation, are also evaluated. A multidisciplinary One Health framework is essential for limiting environmental resistance dissemination and protecting human, animal, and ecosystem health.}, }
@article {pmid42162574, year = {2025}, author = {Panneerselvam, R and Karuppannan, M and S C, GP and Durairaj, E}, title = {Impact of Sevoflurane on the Murine Gut Microbiota: Longitudinal Characterization of Diversity Alterations and Dysbiosis Metrics Using Metagenomics.}, journal = {Asian journal of anesthesiology}, volume = {63}, number = {1}, pages = {20-29}, doi = {10.6859/aja.202503_63(1).0003}, pmid = {42162574}, issn = {2468-824X}, mesh = {Animals ; *Sevoflurane/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; Female ; *Anesthetics, Inhalation/pharmacology ; *Dysbiosis/chemically induced/microbiology ; *Metagenomics/methods ; Feces/microbiology ; Longitudinal Studies ; Sex Factors ; }, abstract = {BACKGROUND: General anesthetics can alter the gut microbiota, but the longitudinal and sex-specific effects of sevoflurane remain unclear. This study examined whether a single exposure to sevoflurane anesthesia induces significant compositional changes in the murine gut microbiome over two weeks, with a secondary focus on sex-specific patterns of alteration.<br><br>METHODS: A controlled animal exposure study was conducted at a tertiary-care academic laboratory animal facility in southern India, approved by an institutional animal ethics committee. Twenty albino mice (6-8 weeks old, ~12 g; both females and males) were randomized to sevoflurane or control groups, subdivided by sex. All animals were housed under standard conditions and completed the study protocol. Experimental animals underwent a single 4-hour exposure to sevoflurane in a controlled chamber; controls experienced identical procedures without sevoflurane. Primary endpoints were gut microbiota alpha and beta diversity (Bray-Curtis distance, Shannon, Simpson indices, richness), phylum- and genus-level differential abundance, and derived Firmicutes: Bacteroidetes and Proteobacteria metrics from serial fecal samples across five time points up to Day 14.<br><br>RESULTS: Sevoflurane exposure led to significant beta diversity separation between groups at both phylum (P = 0.004) and genus levels (P = 0.034), with additional sex effects (P = 0.035 for genus level); alpha diversity indices were significantly reduced in males (P = 0.0079), but not in females. Phylum-level differential abundance was significant in females but not in males. Group and sex effects were present throughout, and derived dysbiosis metrics varied temporally and by sex Conclusion: A single prolonged exposure to sevoflurane induces significant, durable, and sexually dimorphic shifts in the murine gut microbiome. These findings highlight the importance of considering sex as a biological variable in studies of anesthetic effects on gut health.}, }
@article {pmid42162897, year = {2026}, author = {Wang, C and Liu, X and Wan, S and Xie, F and Dai, J and Chen, W and Qu, L and Zhang, L and Li, N and Du, X and Zhu, H and Hua, J}, title = {BLOS1 overexpression enhances goat immune response to Brucella LPS through augmented autophagy with associated gut microbiota remodeling.}, journal = {Veterinary journal (London, England : 1997)}, volume = {}, number = {}, pages = {106706}, doi = {10.1016/j.tvjl.2026.106706}, pmid = {42162897}, issn = {1532-2971}, abstract = {Biogenesis of lysosome-related organelles complex 1 subunit 1 (BLOC1S1, also known as BLOS1) is a key gene involved in phagosome-lysosome maturation, transport, and autophagosome fusion, and it plays a crucial role in host resistance to Brucella infection. This study aimed to examine the effects of BLOS1 overexpression (oeBLOS1) on the stress response of goat macrophages and on intestinal microbiota composition. Peripheral blood mononuclear cells (PBMCs) were isolated from oeBLOS1 and wild-type (WT) goats and differentiated into macrophages. These macrophages were then stimulated with Brucella LPS to assess cytokine secretion and autophagy levels. Metagenomic sequencing was also performed to analyze the structural and functional profiles of the rectal fecal microbiota in these goats. After Brucella LPS stimulation, oeBLOS1 goat macrophages rapidly activated the NF-κB and TLR4 signaling pathways, promoting the synthesis and secretion of cytokines such as TNF-α (P < 0.05). Brucella LPS challenge also significantly increased the transcription of autophagy-related genes such as LAMP2 and BECN1, enhancing autophagic activity and bacterial clearance (P < 0.05). Furthermore, oeBLOS1 altered the intestinal microbiota, significantly enriching pathways linked to membrane transport and cell motility, and reducing the abundance of virulence factors and opportunistic pathogens, which may contribute to intestinal immune homeostasis. In summary, oeBLOS1 may help counteract Brucella LPS-induced infection by promoting the immune response, enhancing autophagy. In addition, it is associated with remodeling gut microbial function, suggesting a potential role in disease resistance.}, }
@article {pmid42163161, year = {2026}, author = {Guan, X and Shen, XL and Hao, YN and Dong, ZQ and Chen, JM}, title = {Complex correlations between mitochondrial DNA variants and gut microbiome in major depressive disorder: a genome-wide association analysis.}, journal = {BMC psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12888-026-08132-8}, pmid = {42163161}, issn = {1471-244X}, abstract = {BACKGROUND: Gut microbiota disturbances and impaired mitochondrial function are both linked with the development of major depressive disorder (MDD). However, little is known about how they interact in MDD.<br><br>METHODS: We used shotgun metagenomic sequencing to explore fecal microbiome based on 63 MDD patients and 30 healthy controls (HCs). Then we performed GWAS for the discriminative taxonomic features of gut microbiota to identify genetic associations between gut microbiome and mitochondrial DNA (mtDNA) in MDD.<br><br>RESULTS: Characteristic gut microbiome-based features, including significant differences in gut microbiota composition and 101 differentially enriched gut microbial species, were found in MDD group vs. HC group. 68 mitochondrial single-nucleotide polymorphisms (mtSNPs) shared between the two groups were identified through GWAS at a Bonferroni-corrected significance level of p&#x2009;<&#x2009;0.05. The genetic variants and their associated gut microbes were mapped to mitochondrial genome, most of which were located in coding regions, including MT-ND, MT-ND4L, MT-ND5, MT-ND6; MT-CO, MT-CO3; MT-RNR, MT-RNR, and MT-TE. Manhattan plots showed 9 mtSNPs in MDD group and 10 mtSNPs in HC group were associated with 20 gut microbial species at a significance of -log10(p) >20. Furthermore, Sankey diagram was used to visualize the relationships of gut microbiota and mtDNA. 36 mtSNPs (-log10(p) >5) were shown to be associated with 54 gut microbes in crosslinked patterns.<br><br>CONCLUSIONS: The current findings provide substantial evidence that complex interactions between gut microbiota and mtDNA contribute to MDD, which enables a better understanding of MDD pathogenesis and suggests new leads for future investigations.<br><br>CLINICAL TRIAL NUMBER: ChiCTR2000029703. Registration Date: Feb. 9[th], 2020. Registration Details are available at the website of Chinese Clinical Trial Registry (https://www.chictr.org.cn).}, }
@article {pmid42163620, year = {2026}, author = {Lu, D and Lu, J and Yang, P and Lou, L and Li, W and Zhou, Y}, title = {Microbiome and Lipidomics Reveal the Mechanism of Eight Zhes Decoction on MAFLD.}, journal = {Combinatorial chemistry &amp; high throughput screening}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113862073460107260407065758}, pmid = {42163620}, issn = {1875-5402}, abstract = {INTRODUCTION: The therapeutic potential of Eight Zhes Decoction (EZD) against metabolic dysfunction-associated fatty liver disease (MAFLD) is well-recognized; however, the underlying biological pathways are not well understood. To address this gap, an integrated investigation using both lipidomics and metagenomics was conducted to reveal the mechanistic rationale behind the effects of EZD.<br><br>METHODS: A MAFLD mouse model was established using a Methionine-Choline-Deficient (MCD) diet combined with CCl&#x2081;. The mice were treated with EZD for four weeks. Hepatic injury was assessed via H&amp;E, Oil Red O, and Masson staining. Untargeted hepatic lipidomics and shotgun metagenomics were employed to profile lipid species and the gut microbiota composition, respectively.<br><br>RESULTS: Histopathological analysis confirmed that EZD significantly alleviated hepatic steatosis, ballooning degeneration, and fibrosis. Lipidomics identified 277 differential lipids; EZD treatment notably downregulated 24 TGs and modulated pathways related to arachidonic acid metabolism and bile secretion. Metagenomics revealed that EZD reshaped the gut microbiota, significantly increasing the abundance of Alistipes sp. while reducing the abundance of Faecalibaculum rodentium.<br><br>DISCUSSION: Correlation analysis demonstrated that the restored Alistipes sp. was negatively correlated with multiple hepatic TGs, whereas Faecalibaculum rodentium was positively correlated with lipid accumulation.<br><br>CONCLUSION: EZD mitigates MAFLD in mice by synergistically regulating hepatic lipid metabolism and gut microbiota. Specifically, the therapeutic effect involves restoring Alistipes sp. and modulating the gut-liver axis, providing experimental evidence for the clinical application of EZD.}, }
@article {pmid42164149, year = {2026}, author = {Scutari, R and Fox, V and Mastropaolo, M and Fini, V and Mussa, M and Bigliano, P and Colagrossi, L and Vrenna, G and Perinzano, A and Scabini, S and Perno, CF and Calcagno, A}, title = {Case Report: Beyond conventional diagnostics: mNGS support in a complex immunocompromised patient diagnosis.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1791094}, pmid = {42164149}, issn = {2296-858X}, abstract = {Next-generation metagenomic sequencing (mNGS) enables the direct and unbiased detection of pathogens from clinical samples, overcoming the limitations of standard methods. It is particularly valuable in immunocompromised patients and in cases of complex infections. We report the case of a man in his 40s, born in North Africa, who was admitted with progressive skin and soft-tissue lesions after a minor foot trauma. The initially localized infection rapidly worsened, leading to bilateral pneumonia, acute respiratory failure, disseminated intravascular coagulation, and death. Histopathological examination revealed granulomatous inflammation with alcohol-resistant bacilli and an undiagnosed cutaneous T-cell lymphoma associated with hemophagocytic syndrome. Conventional microbiological tests identified multiple pathogens, including influenza A virus, herpes simplex virus 1 (HSV-1), Candida albicans, Enterococcus faecalis, Proteus mirabilis, and Pseudomonas aeruginosa; however, their heterogeneous distribution and isolation from non-sterile sites hindered etiological interpretation. Cultures and molecular assays for Mycobacterium species were negative despite findings of histological examination suggestive of granulomatous inflammation with alcohol-resistant bacilli. To clarify the diagnosis, mNGS was performed on blood, serum, and lymph node samples using host DNA depletion and Illumina sequencing. Bioinformatic analysis revealed a diverse microbial landscape, with the detection of Fusarium pseudograminearum, Mycobacterium canettii, and Ralstonia sp., alongside low-level viral sequences [Epstein-Barr virus (EBV) and HSV-1]. These results reflected the patient's severe immune deficiency, characterized by a marked depletion of CD8[+] T cells and NK cells. Although the results became available too late to influence treatment, mNGS provided crucial diagnostic insights, demonstrating its ability to uncover hidden or rare pathogens. Early application of mNGS could significantly improve diagnostic precision and therapeutic decisions in critically ill immunocompromised patients.}, }
@article {pmid42164154, year = {2026}, author = {Wang, S and Wang, X and Sun, K and Jin, Z and Ma, J}, title = {Pulmonary sarcoidosis complicated with pulmonary cryptococcosis: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1822801}, pmid = {42164154}, issn = {2296-858X}, abstract = {Pulmonary sarcoidosis is an idiopathic granulomatous disorder primarily affecting the lungs and mediastinal lymph nodes. Pulmonary cryptococcosis, an opportunistic mycosis caused by Cryptococcus species, may occur concurrently with sarcoidosis, presenting substantial diagnostic challenges, particularly in treatment-naïve patients. A 63-years-old previously healthy female presented with insidious-onset dyspnea and low-grade fever. Chest computed tomography (CT) showed mediastinal and hilar lymphadenopathy, accompanied by small nodules in the right lower lobe. She was diagnosed with pulmonary sarcoidosis at a local hospital and started on prednisone, with symptomatic improvement. However, follow-up imaging showed enlargement and cavitation of the right lower lobe nodules. Admission laboratory tests, including inflammatory markers and fungal serology, were all unremarkable. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) identified sequences of Cryptococcus neoformans. Histopathological examination of mediastinal lymph node specimens confirmed the presence of non-necrotizing granulomas, which is consistent with a diagnosis of sarcoidosis. Meanwhile, the right lower lobe lung biopsy revealed positive staining for Cryptococcus. The patient was treated with fluconazole, resulting in radiological resolution. This case highlights the importance of considering pulmonary cryptococcosis as a potential complication in treatment-naïve sarcoidosis patients who present with abnormal chest shadows. Underlying immune dysregulation in sarcoidosis may obscure both clinical and radiological findings, thereby complicating the diagnostic process.}, }
@article {pmid42164315, year = {2026}, author = {O'Connor, BRW and Allen, D and Quinn, M and Kozey, M and Léveillé, RJ and Whyte, LG}, title = {Bipolar investigation of near-surface glacial ice reveals an active microbial ecosystem driven by photosynthesis and chemolithoautotrophy.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag105}, pmid = {42164315}, issn = {2730-6151}, abstract = {Despite extreme conditions including freezing temperatures, low water activity, and few nutrients, active microorganisms are thought to inhabit glacial ice, yet little is known about their identities and methods of survival. We used flow cytometry, cultivation, metagenomics, and metatranscriptomics to characterize viable and active microbial communities from near-surface englacial ice from White Glacier in the Canadian High Arctic and Johnsons Glacier on Livingston Island, Antarctica. The ice, though low in microbial biomass (10[4] cells/ml), harbors communities capable of growth at subzero temperatures (-5°C), high salinity (12% NaCl), and low pH (pH 3). The communities of both poles were different, with metagenome-assembled genomes (MAGs) from White Glacier belonging to Cyanobacteriota and novel phyla and MAGs from Johnsons Glacier belonging to Pseudomonadota and Actinomycetota. Despite this, both glacial communities shared key metabolic functions, including aerobic respiration, aerobic carbon monoxide oxidation, sulfide oxidation, and denitrification. Metatranscriptomics from White Glacier revealed dominant Cyanobacteriota, performing oxygenic photosynthesis and carbon fixation and accompanied by active lithoautotrophs performing metabolisms such as carbon fixation via the 3-hydroxyproprionate cycle, anoxygenic photosynthesis, sulfide oxidation, and nitrate reduction/denitrification. These metabolisms appear to support an active heterotrophic community performing aerobic respiration and aerobic carbon monoxide oxidation. This study highlights the distinct but functionally similar microbial communities in Arctic and Antarctic glaciers, hinting that there may be a core set of metabolisms required for surviving in englacial ice and suggesting that similar communities could persist in glacial ice on Mars or the icy outer moons, Europa and Enceladus.}, }
@article {pmid42164317, year = {2026}, author = {Domínguez-Huerta, G and Cabello, AM and Santos-Bruña, JJ and Mercado, JM and Ferrera, I}, title = {Ecology of prokaryotic DNA viruses in a highly impacted coastal lagoon revealed through comparative and temporal metagenomics.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag110}, pmid = {42164317}, issn = {2730-6151}, abstract = {Coastal lagoons are highly productive ecosystems, yet their prokaryotic viruses remain poorly studied. The Mar Menor, a hypersaline coastal lagoon in south-eastern Spain, is under strong anthropogenic pressure from continuous agricultural runoff, leading to severe eutrophication. To assess the impact of these unique conditions on viral assemblages, we analyzed a 3-year metagenomic time series of picoplankton communities. We reconstructed the lagoon's prokaryotic DNA viral communities and compared them with their counterparts in open Mediterranean Sea waters to reveal how environmental variability shapes their structure. Viral communities in the Mar Menor showed higher viral operational taxonomic unit relative abundances and diversities and were distinct from those offshore. Temporally, community structure was correlated with water transparency and silicate concentration. The putative hosts of the lagoon viruses were copiotrophic rather than oligotrophic compared to the open sea, and their composition shifted in response to episodic environmental disturbances. Temperate virus levels did not consistently support either the piggyback-the-winner or refugium models, spatially or temporally, indicating that viral replication strategies are governed by factors more complex than trophic status or environmental variability alone. Auxiliary viral genes (AVGs) encoding 2-oxoglutarate/Fe(II)-dependent oxygenase and DNA methyltransferase emerged as potentially relevant functions in the lagoon, as they were more frequent than in the Mediterranean Sea. Similar to targeted hosts, AVG-specific temporal relative abundance patterns were strongly shaped by local disturbances. This study provides the first metagenomic insight into viruses of the Mar Menor, revealing viral ecology in a dynamic, eutrophic lagoon, with implications for predictive models of nutrient cycling.}, }
@article {pmid42164318, year = {2026}, author = {Aizpurua, O and Brenner, E and Martin-Bideguren, G and Garin-Barrio, I and Cabido, C and Alberdi, A}, title = {Beyond the core microbiome: endemic bacteria drive functional and microdiversity differences across salamander populations.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag106}, pmid = {42164318}, issn = {2730-6151}, abstract = {Population-specific variation in animal microbiomes is well documented, yet the functional consequences and underlying mechanisms remain poorly understood. To address this, we conducted genome-resolved metagenomic analyses on gut and skin microbiomes from four populations of Pyrenean brook salamanders (Calotriton asper) inhabiting two distinct environments: Pyrenean subalpine brooks and Atlantic montane streams. From paired faecal and skin swab samples, we reconstructed 539 and 43 metagenome-assembled genomes, respectively, and examined taxonomic composition, metabolic capacity, and microdiversity across environments. Although alpha diversity remained similar across environments, both gut and skin microbiomes exhibited significant differences in community composition and functional potential between environments. Partitioning the gut microbiome into core, endemic, and marginal fractions revealed a dominant core community-shared across environments and accounting for over 85% of reads-that did not drive functional divergence. Instead, functional differences were primarily shaped by low-abundance, population-specific endemic bacteria. Atlantic salamanders hosted endemic taxa with significantly greater metabolic potential and higher strain-level microdiversity than those at the Pyrenees. These patterns were not associated with broad-scale dietary differences and may reflect environmental influences such as temperature and nutrient availability. Our findings highlight the relevance of rare, endemic bacteria in driving microbiome function and underscore the power of genome-resolved metagenomics to uncover functional and evolutionary dynamics in wild host-microbe systems.}, }
@article {pmid42164663, year = {2026}, author = {Glapa-Nowak, A and Nowak, JK and Kurek, S and Walkowiak, J}, title = {What a pickle-a metagenomic perspective on the cucumber fermentation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1809866}, pmid = {42164663}, issn = {1664-302X}, abstract = {Food fermentation involves an interplay between multiple strains and species. This delicate composition during fermentation has been investigated so far using both classical and molecular methods; however, the results remain difficult to interpret. In this perspective article, we discuss the spontaneous fermentation of cucumber from organic and commercial cultivation (from 1st day to 90th day) based on our preliminary data from a nanopore sequencing study. The present study is the first to report the occurrence of coagulase-negative cocci in cucumber fermentation [Staphylococcus saprophyticus (0.01%) and Staphylococcus schleiferi (0.03%)]. Furthermore, we conclude that own-cultivation cucumbers may exhibit a lower incidence and diversity of phages, which have practical implications for designing future studies as well as for direct consumers. Our data also show that, even in the absence of phages (own-cultivation cucumbers <1%), lactic acid bacteria dominance occurs, which contrasts with previous conclusions and contributes to the discussion on the role of phages in maintaining the balance between Enterobacteriaceae and lactic acid bacteria in plant fermentation. The powerful metagenomic approach provides a broader understanding of the day-to-day and sample-to-sample diversity within microbiome communities. The maturity of the fermentation product may play a significant role in exerting specific biological actions. This should be accounted for before planning an intervention study.}, }
@article {pmid42164669, year = {2026}, author = {Yuan, B and Li, C and Wang, Q and Yao, Q and Guo, X and Wang, Z}, title = {Maize stover mulching combined with an optimized fertilization strategy reshapes rhizosphere microbial communities and functions in greenhouse potato.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1670904}, pmid = {42164669}, issn = {1664-302X}, abstract = {Protected cultivation systems offer opportunities for improving potato productivity but are often constrained by inefficient maize stover utilization and suboptimal fertilization practices. In this study, a 4 × 4 factorial experiment was conducted using the potato cultivar 'Jishu No. 1' to decode the rhizosphere microbial mechanisms underpinning plant growth and yield enhancement under greenhouse conditions. We hypothesized that integrated management (the synergy between stover mulching and fertilization) would modify the soil microenvironment, thereby reshaping microbial community assembly patterns and functional gene distributions. The results showed that while split fertilization combined with moderate stover mulching (F2S2, 8,500 kg·hm[-2] stover mulching) was most effective in enhancing plant physiological status, full topdressing combined with the same mulching level (F3S2) achieved the highest agronomic productivity, increasing total yield to 42.33 t·hm[-2]. Metagenomic analysis revealed that the F3S2 strategy significantly reshaped the rhizosphere microbiome, characterized by higher α-diversity and the enrichment of pathways related to carbon metabolism and carbohydrate processing. Notably, F3S2 promoted the recruitment of copiotrophic taxa, particularly Actinobacteriota, whose relative abundance was significantly and positively correlated with soil organic phosphorus (r = 0.623, p < 0.05). In contrast, oligotrophic groups like Acidobacteriota were relatively less abundant in nutrient-rich treatments. These findings demonstrate that moderate stover mulching combined with dynamic fertilization provides a high-resource niche that favors functional microbial groups, thereby driving rhizosphere nutrient cycling to support potato performance. This study underscores the importance of optimized stover and fertilizer management strategies in protected cultivation.}, }
@article {pmid42165181, year = {2026}, author = {Zhang, B and Zhang, J and Duan, F and Xuan, Z and Sun, T and Lu, L}, title = {Enzymatic Galactosylation of Erythritol Enhances Antibacterial Activity against Cariogenic Streptococcus mutans.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c14195}, pmid = {42165181}, issn = {1520-5118}, abstract = {Erythritol is a widely used sweetener with beneficial properties and bioactivities, including the inhibition of Streptococcus mutans, a bacterium that induces dental caries. Galactosylation of compounds is an attractive method for improving antimicrobial activity. In this study, a novel metagenomic β-galactosidase gene, bga7, was successfully expressed in Escherichia coli. The recombinant enzyme was used to galactosylate erythritol, generating a high yield (93.6%) of galactoside product at a concentration of 2 U/mL upon incubation with 20 mM o-nitrophenyl-β-d-galactopyranoside and 0.5 M erythritol at 40 °C and pH 9.0 for 4 h. The product was confirmed to be β-galactosyl-erythritol by MS and NMR analysis. This galactoside demonstrated significantly enhanced inhibition of both the planktonic growth of S. mutans and biofilm formation compared to erythritol alone. Further investigation into the mechanism revealed that the galactoside suppressed the transcriptional levels of four important genes (gtfB, ftf, srtA, and spaP) associated with bacterial adhesion and biofilm formation.}, }
@article {pmid42165232, year = {2026}, author = {Nap, B and Thinnes, CC and Thiele, I}, title = {Whole-body metabolic modelling and its prospects in precision nutrition.}, journal = {The Proceedings of the Nutrition Society}, volume = {}, number = {}, pages = {1-19}, doi = {10.1017/S0029665126103061}, pmid = {42165232}, issn = {1475-2719}, abstract = {Nutrition has long been investigated with respect to its influence on human health. With the availability of various omics data, such as metagenomics and metabolomics, novel insights have been obtained into the influence of nutrition, particularly concerning the gut microbiome. The gut microbiome plays an important role in the breakdown of food-derived compounds and in producing essential bioactive metabolites required for human health. However, this wealth of information made the interactions between nutrition and human health increasingly intricate, and unravelling these links is complex. This review covers the concepts of genome-scale metabolic modelling as a tool to understand the links between nutrition, the gut microbiome and human metabolism and its applications. Genome-scale metabolic modelling treats metabolism as a mathematical problem which was used to develop models of human metabolism that incorporate physiology and organ-specific metabolism, known as whole-body metabolic models (WBMs). WBMs can incorporate physiological data, such as sex, weight, and body fat percentage, as well as nutrition in the form of its metabolite constituents. Finally, the gut microbiome can also be incorporated through a mathematical representation of the species present, based on stool metagenomics. WBMs have already been applied to understand gut microbiome-host co-metabolism in various non-communicable diseases. However, challenges remain, as metabolites measured in food items in public databases typically cover only common metabolites, and engagement with end-users such as nutritionists and policymakers is limited. Nevertheless, WBMs represent a promising step towards digital metabolic twins and thus personalised nutrition and medicine.}, }
@article {pmid42165805, year = {2026}, author = {Brown, TL and Ng, DYK and Savva, GM and Elek, CKA and Docherty, JAD and Cook, R and Ansorge, R and Telatin, A and Kutter, E and Adriaenssens, EM}, title = {The effects of bacteriophage cocktail treatment on healthy gut microbiota: an in vitro human colon model study.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, doi = {10.1099/mgen.0.001731}, pmid = {42165805}, issn = {2057-5858}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics/physiology ; *Colon/microbiology/virology ; Escherichia coli/virology/genetics ; Bacteria/genetics/virology/classification ; Phage Therapy ; Feces/microbiology ; }, abstract = {The human gut microbiome is a complex community that plays an important role in health, where perturbations can result in dysbiosis and disease. Bacteriophages (phages) can provide treatment for bacterial gastrointestinal disease, and commercial preparations such as the Intesti bacteriophage cocktail can be taken orally to target bacterial pathogens. However, interactions between these phages and the native gut microbiota are understudied. To investigate the impact of phage treatment, we used simulated gut models seeded with healthy donor microbiota from three individuals, sequenced the DNA and analysed the bacterial and viral portions from samples obtained over time. Each donor had a unique bacterial composition that diverged with time. When comparing phage-treated to control samples, we observed that Escherichia coli abundance accounted for the largest portion of bacterial community variance and was more associated with the controls. The lower abundance in phage-treated samples may have resulted from the lytic action of phages from the cocktail. Additionally, our analyses of the viral portion revealed a phage bloom exclusive to phage-treated samples. A highly abundant phage in this bloom was matched with the Intesti bacteriophage cocktail, showed similarity to Enterobacteria phage phi92 and provided evidence of productive infection within the model. While we did observe fluctuations in relative abundance of additional viral sequences in the presence of the phage cocktail, these changes were often transient. Furthermore, we detected only slight differences from typical members of the virome and low numbers of active prophages. Our experiments suggest that the phage cocktail had minimal interruption to the native gut microbiota within the model.}, }
@article {pmid42165964, year = {2026}, author = {Chen, S and Hua, Y and Chen, D and Jiang, X}, title = {Laboratory diagnosis of brucellosis: evolving synergy between serological testing and next-generation sequencing.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42165964}, issn = {1435-4373}, abstract = {BACKGROUND: Brucellosis is an animal‑to‑human infection that is hard to identify in practice; its signs are vague and the laboratory tools used in routine care have clear limits. Bacterial culture is regarded as the reference test; the procedure is slow and has modest sensitivity, and in many hospitals clinicians rely mainly on serologic assays when they make a diagnosis. Over the past decade clinical microbiology laboratories have increasingly used next‑generation sequencing (NGS) as a tool for pathogen identification, especially metagenomic NGS (mNGS). In patients with suspected bru-cellosis clinicians and laboratory staff often see a mismatch between test results, with serological assays suggesting infection but NGS reports failing to detect Brucella, a gap between serology and sequencing that remains a frequent and unresolved problem in routine diagnosis.<br><br>OBJECTIVE: This review brings together available data on how serological tests and sequencing-based methods in both metagenomic and targeted formats contribute to the laboratory diagnosis of human brucellosis and where they fall short.<br><br>CONCLUSION: It describes biological and technical sources of false-positive serology and false-negative sequencing and sets out a practical integrated way to judge and confirm mismatched findings so that laboratories and clinicians can use conventional and molecular tools together and reach sound decisions when brucellosis is suspected.}, }
@article {pmid41975257, year = {2026}, author = {Tang, Z and Zhuang, D and Duan, X and Gong, Q and Tian, C and Jiang, P and Yu, J and Li, F and Zhao, F and Shi, G and Yang, H and Du, Q and Li, T and Ye, Z and Zhang, Z}, title = {MicroSSNet: an R package for microbial network construction and analysis at the single-sample and aggregated levels.}, journal = {BMC bioinformatics}, volume = {27}, number = {1}, pages = {}, pmid = {41975257}, issn = {1471-2105}, abstract = {BACKGROUND: Network analysis is a fundamental tool for elucidating microbial interactions, which are crucial for understanding the mechanisms that shape ecosystem structure and function. However, aggregated co-abundance/co-occurrence network approaches that infer pairwise relationships among biological entities from large sample collections often overlook sample-specific interaction patterns. To address this limitation, we developed MicroSSNet, an R package designed for analyzing microbial networks, including both aggregated and single-sample networks.<br><br>RESULTS: We designed MicroSSNet primarily to fill the current gap in bioinformatics tools for constructing single-sample networks (SSNs) from microbiome data, and we evaluated both the performance and limitations of ssPCC-based SSNs using simulated and real datasets. Through Monte Carlo simulations, we assessed the statistical behavior of ssPCC and highlighted scenarios in which ssPCC is less powerful. We then applied MicroSSNet to two distinct datasets: a human gut metagenomic dataset and a soil 16S rRNA gene dataset. In the human gut dataset, SSNs revealed unique edges not detected in the aggregated network. In the soil dataset, SSN features showed some predictive value for group classification. However, SSN-derived patterns should be interpreted cautiously, as they may not exclusively reflect true interaction changes. MicroSSNet additionally implements a full aggregated-network workflow, including bipartite networks and extensive topological property analysis.<br><br>CONCLUSIONS: Together, MicroSSNet offers a framework for constructing and analyzing both single-sample and aggregated microbial networks. In this work, we also highlight the potential and limitations of single-sample network approaches, supporting their application as exploratory tools in microbiome research across individual and population levels. The package is freely available on GitHub (https://github.com/TangZecheng622/MicroSSNet).<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-026-06444-w.}, }
@article {pmid42156610, year = {2026}, author = {Liu, Y and Shao, Q and Zhang, C and Zhang, F and Liu, J and Li, Y and Huang, Z}, title = {The dual role of gastric microbiota dysbiosis in gastric cancer progression and therapy.}, journal = {International journal of clinical oncology}, volume = {}, number = {}, pages = {}, pmid = {42156610}, issn = {1437-7772}, support = {82460559//National Natural Science Foundation of China/ ; 25JRRA1264//Gansu Provincial Joint Scientific Research Fund Major Project/ ; GSWSKY2024-06//Gansu Province Health Industry Science and Technology Innovation Major Projects/ ; CY2022-YB-A04//the Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University/ ; CY2024-MS-B18//the Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University/ ; No.CY2023-MS-B17//the Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University/ ; }, abstract = {Gastric cancer (GC) ranks among the most prevalent malignant neoplasms globally and is one of the leading causes of cancer-related mortality. The gastric microbiota, as a crucial component of the human microecosystem, plays a pivotal role in maintaining human health through its ecological balance. In recent years, with the advancement of technologies such as metagenomics, the dysbiosis of gastric microbiota has increasingly become a focal point of research, particularly in understanding its role in the initiation, progression, and treatment of GC. This review elucidates the current understanding of the roles played by gastric microbiota and their metabolic products in the progression of GC. Additionally, it summarizes and prognosticates the translational value and clinical significance of gastric microbiota in the diagnosis, prognosis, and treatment of GC. The gastric microbiota assumes a dual role in the progression and treatment of GC. Further in-depth studies on the interactions and mechanisms between gastric microbiota and the host represent an emerging and valuable area in the field of GC research.}, }
@article {pmid42156647, year = {2026}, author = {Ravikrishnan, A}, title = {Unlocking the Metagenome: Pipeline for Microbiome Data Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {1-23}, pmid = {42156647}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; Software ; Workflow ; Sequence Analysis, DNA/methods ; Humans ; Data Analysis ; }, abstract = {Metagenomic technologies have revolutionized our understanding of microbes in different spheres of life, revealing the massive diversity and complex functionalities of microbial communities across various environments. Shotgun metagenomics, which involves sequencing the DNA of all the organisms in a sample, is emerging as a powerful tool in assessing the microbial content. Unlike the traditional culturing approach, the shotgun metagenomic technology provides a comprehensive view of the entire microbial community, including potential functions that the organisms could be performing. In this chapter, we describe a typical bioinformatics workflow to generate the taxonomic profiles from metagenomic sequencing data and demonstrate a few basic statistical analyses that can be performed from this data to generate insights. In addition, we discuss the experimental and analytical considerations that must be taken into account while generating and making inferences from metagenomic data. Lastly, we provide insights on automating the workflow for consistent and reproducible large-scale analyses.}, }
@article {pmid42156648, year = {2026}, author = {Yugandhar Reddy, BS and Sripradha, S and Kumar, A}, title = {Targeted Metagenomics Using Next-Generation Sequencing Methods.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {25-32}, pmid = {42156648}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Microbiota/genetics ; Metagenome ; Humans ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenomics allows the discovery of the full diversity of all microbes present in a given niche. The technique is very powerful and has allowed very significant advances delineating the role of the microbiome in several disciplines including health, agriculture, ecology, industry, etc. Here, we describe the method required for processing of samples for metagenomic analysis using Next-Gen sequencing.}, }
@article {pmid42156649, year = {2026}, author = {Rangamaran, VR and Sushmitha, TJ and Tamilmani, KK and Murugesan, H and Gopal, D}, title = {Exploring the Ocean's Microbial World: Techniques and Protocols for Microbiome Research.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {33-46}, pmid = {42156649}, issn = {1940-6029}, mesh = {*Microbiota/genetics ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Oceans and Seas ; *Seawater/microbiology ; Computational Biology/methods ; }, abstract = {Marine microbiomes play a crucial role in oceanic ecosystems, influencing biogeochemical cycles, climate regulation, and marine biodiversity. Accurate characterization of these microbial communities requires standardized protocols for sample collection, processing, sequencing and data analysis. This chapter provides a comprehensive guide to essential methodologies for marine microbiome research including field sampling strategies, DNA and RNA extraction techniques, high-throughput sequencing approaches (such as 16S rRNA amplicon sequencing and metagenomics) and bioinformatics pipelines for data interpretation. Additionally, we discuss quality control measures, best practices for reproducibility, and challenges associated with marine microbiome profiling. By adopting standardized methodologies, researchers can generate reliable, comparable datasets that enhance our understanding of marine microbial ecology and its broader environmental implications.}, }
@article {pmid42156650, year = {2026}, author = {Miliotis, G and Tumeo, A}, title = {Shotgun Metagenomic Analysis of Microbial Community Dynamics in Wastewater Treatment Through Constructed Wetlands.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {47-73}, pmid = {42156650}, issn = {1940-6029}, mesh = {*Wetlands ; *Metagenomics/methods ; *Wastewater/microbiology ; *Water Purification/methods ; *Microbiota/genetics ; Metagenome ; Computational Biology/methods ; Water Microbiology ; }, abstract = {Constructed wetlands (CWs) offer a sustainable, nature-based solution to wastewater treatment, supporting diverse and dynamic microbial communities that drive nutrient cycling, pollutant degradation, and pathogen removal. This chapter presents an end-to-end methodology for performing shotgun metagenomic analyses on microbial populations from CW influent and effluent. We detail approaches for site selection, sample collection, filtration, DNA extraction, and the incorporation of positive and negative controls to ensure reproducibility and data quality. Two modular bioinformatic workflows encompassing quality control, assembly, taxonomic/functional annotation, and metagenome-assembled genome recovery are described alongside options for detecting antimicrobial resistance genes, pathogens, toxins, and plasmids. In addition, an example workflow for the calculation of alpha and beta diversity is provided. Guidelines for data standardization, replication, and compliance with community-driven reporting standards (MIMS, MIMAG) are also included. Incorporating this protocol will facilitate standardized, reproducible insights into CW microbial dynamics, thereby informing ecological understanding and guiding practical interventions that enhance wastewater treatment efficacy and improve public health outcomes.}, }
@article {pmid42156652, year = {2026}, author = {Kosmopoulos, JC and Anantharaman, K}, title = {Computational Microbial and Viral Ecology Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {83-141}, pmid = {42156652}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Computational Biology/methods ; Metagenome ; *Microbiota/genetics ; *Viruses/genetics/classification ; Virome ; Bacteriophages/genetics ; Bacteria/genetics ; Archaea/genetics ; }, abstract = {The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics have revealed that interactions between diverse groups of community members such as archaea, bacteria, and viruses (bacteriophages) are common and have significant impacts on entire microbiomes. Thus, to have a well-developed understanding of microbes as they naturally exist in the environment, biological entities of all kinds must be studied together. While numerous protocols for metagenome analysis exist, comprehensive published protocols for the simultaneous analysis of viruses and prokaryotes together are scarce. Further, as bioinformatic methods for microbiology rapidly advance, existing metagenomic tools and pipelines require frequent re-evaluation. This ensures the adherence to best practices for microbiome and metagenomic data analysis. Here, we offer an expansive approach for the joint analysis of bulk sequence data from a mixed microbial community (metagenomes) and viral-sized fraction communities (viromes). This chapter serves as a beginner's-level guide for researchers with limited bioinformatics expertise who wish to engage in multiscale metagenome and virome analyses. We cover steps from initial study design to sequence read processing, metagenome assembly, quality control, virus identification, microbial and viral genome binning, taxonomic characterization, species-level clustering, and host-virus predictions. We also provide the bioinformatic scripts used in our workflow for reuse in one's own computational methods. Lastly, we discuss additional approaches a researcher can take after processing data with this workflow.}, }
@article {pmid42156658, year = {2026}, author = {Roma Pi, J and Heinken, A}, title = {Personalized Constraint-Based Modeling of Microbial Communities from Metagenomic Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3006}, number = {}, pages = {233-260}, pmid = {42156658}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; Humans ; *Gastrointestinal Microbiome/genetics ; Precision Medicine/methods ; Software ; *Microbiota/genetics ; *Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; RNA, Ribosomal, 16S/genetics ; Systems Biology/methods ; }, abstract = {High-throughput metagenomic sequencing techniques such as 16S rRNA and shotgun sequencing have enabled an unprecedented understanding of the structure and function of microbiome communities such as the human gut microbiome. Tailored dietary or therapeutic interventions targeting the microbiome could advance personalized medicine; however, predicting such interventions requires predictive systems biology methods. Constraint-Based Reconstruction and Analysis (COBRA) is a mechanistic systems biology approach that relies on detailed genome-scale reconstructions of a target organism's metabolism. A resource of genome-scale reconstructions of human microbes, AGORA, and its expansion in size and scope, AGORA2, have been developed through a semi-automated refinement pipeline, DEMETER. A user-friendly analysis pipeline, mgPipe, allows building and interrogating personalized models of microbiome communities from AGORA and AGORA2. Through sample-specific simulations, mgPipe can stratify patients and controls by the distinct metabolic capabilities of their microbiomes, starting from the processed metagenomic sequencing data. Building on this functionality, the protocol provides a comprehensive workflow for the contextualization of metagenomics data through personalized, mechanistic modeling. Comprehensive tutorials for the DEMETER and mgPipe workflows are presented, which will enable both systems biologists and microbiome scientists to contextualize metagenomic data and perform mechanistic simulations of diet-microbiome-host interactions.}, }
@article {pmid42156769, year = {2026}, author = {Chen, R and Luo, S and Feng, Y and Maestre, FT and Sáez-Sandino, T and Gross, N and Le Bagousse-Pinguet, Y and Ochoa, V and Gozalo, B and Guirado, E and García-Gómez, M and Valencia, E and Asensio, S and Martínez-Valderrama, J and Mendoza, BJ and Abades, S and Alfaro, F and Barrett, M and Berdugo, M and Pastor, JLB and Blaum, N and Boldgiv, B and Bowker, M and Castro, H and Chu, H and Cutler, NA and Dai, Z and Deák, B and Durán, J and Espinosa, CI and Fajardo, A and Fan, K and Foronda, A and Fraser, LH and Geissler, K and Grebenc, T and Moltanvan, EG and Hart, SC and Kindermann, L and Köbel, M and Laanisto, L and le Roux, PC and Liancourt, P and Linstädter, A and Louw, MA and Macek, P and Maggs-Kölling, G and Makhalanyane, TP and Manzaneda, AJ and Marais, E and Montesinos, D and Mora, JP and Moreno, G and Munson, SM and Muñoz-Rojas, M and Nair, GR and Neuhauser, S and Nunes, A and Plaza, C and Pueyo, Y and Rey, PJ and Rey, A and Ríos, AL and Rodríguez, A and Lozano, BR and Roman, R and Ruppert, JC and Salah, A and Singh, J and Throop, HL and Travers, S and Nahberger, TU and Uuganbayar, M and Valkó, O and Wang, L and Williams, MA and Xiong, C and Xu, J and Zaady, E and Ma, B and Singh, BK and Delgado-Baquerizo, M}, title = {Functional restructuring of the global soil microbiome under multiple stressors.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73231-9}, pmid = {42156769}, issn = {2041-1723}, support = {42577352//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Microbes, as the planet's most abundant and diverse organisms, drive soil functions globally and are vulnerable to environmental stressors triggered by global change. Yet, knowledge regarding the impacts of multiple environmental stressors on their functional profiles as well as the consequences for soil functionality largely remains unknown. Here, we analyze two global-scale datasets including information on soil metagenomics and multiple environmental stressors. We find that across terrestrial ecosystems worldwide, up to 60% of all functional genes significantly shift when soil microbes experience the high-level of concurrent stressors. In this regard, the relative abundances of genes involved in microbial growth are negatively linked to the increasing number of stressors. Conversely, those genes linked to stress resistance and energy production exhibit positive responses. Taken together, our findings highlight a significant restructuring of global soil functional microbiomes in response to multiple environmental stressors. Consequently, such restructuring drives community-level shifts in matter and energy reallocations, thereby impacting the maintenance of soil functionality under the projected global change.}, }
@article {pmid42156772, year = {2026}, author = {Bamberger, T and Muller, E and Algavi, YM and Greenier, A and Adjangba, C and Slikas, E and Brassington, L and Mariner, B and McCoy, B and Harrison, BR and Partida-Aguilar, M and Marye, A and Harris, A and Rout, E and ,  and Avery, A and Promislow, DEL and Snyder-Mackler, N and Borenstein, E}, title = {Mapping the canine gut microbiome: insights from the Dog Aging Project.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73193-y}, pmid = {42156772}, issn = {2041-1723}, support = {U19AG057377//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; }, abstract = {Companion dogs (Canis lupus familiaris) offer a unique model for studying the gut microbiome and its relation to aging due to their cohabitation with humans, sharing similar environments, diets, and healthcare practices. Here, we present the Dog Aging Project (DAP) Precision cohort, a large population-wide study of the canine gut microbiome. This cohort encompasses over 900 dogs of diverse breeds, environments, and demographics living across the United States. Coupling fecal shotgun metagenomic sequencing with phenotypic and environmental surveys and clinical lab tests, we explore the intricate relationships between microbiome composition, aging, and key factors such as health and living conditions. Our analyses identify multiple factors associated with microbiome composition, including dietary preferences such as commercial versus home cooked nutrition, and behaviors such as coprophagy (feces eating). In addition, we find age-associated gradual shifts in microbiome composition, supporting the development of a metagenomics-based population-level model for canine age prediction based on microbial signatures. We further examined which age-associated microbial patterns observed in humans are recapitulated in dogs by comparing our cohort with the Lifelines-DEEP cohort. Overall, these findings offer insights into the role the gut microbiome plays in our four-legged companions, with potential implications for veterinary medicine and translational aging research.}, }
@article {pmid42157110, year = {2026}, author = {Al Achkar, N and Privitera, GF and Arena, D and Nicotra, R and Ciccarello, L and Rizzo, GF and Pulvirenti, A and Spatafora, M and Restuccia, C and Branca, F}, title = {Exogenous microbial consortia modulate rhizosphere microbiome and yield of grafted tomato grown in the mediterranean greenhouse.}, journal = {BMC plant biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12870-026-08962-4}, pmid = {42157110}, issn = {1471-2229}, support = {CN00000022//AGRITECH National Research Center (European Union Next-Generation EU, PIANO NAZIONALE DI RIPRESA E RESILIENZA, PNRR - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4-D.D. 1032 17/06/2022)/ ; }, abstract = {BACKGROUND: The adoption of sustainable agricultural practices for intensive horticultural production could determine less damage to the ecosystem is a fundamental need increasing worldwide. In this trial the effect of two commercial microbial consortia, applied on two hybrid rootstocks of tomato grafted by two scions, were evaluated both on yield components and on the compositions of the rhizosphere microbiome. The rhizosphere was collected from each grafting combination, in both treated and non-treated plots. Microbiome DNA extracted was then sequenced by amplifying two specific regions ITS1-1F for fungus and 16SV34 for bacteria.<br><br>RESULTS: At the morphological level, the effect of microbial consortia application on the total production and yield showed to be highly dependent on the grafting combination, yield increased by 9.1, 10.3 and 12.6% in treated plots of Auto S2, R1/S1 and R1/S2 respectively but registered a reduction of 22.4% in NG.S2 and 9.3% in R2/S2 plots. The metagenomic sequencing revealed that fungal community composition was significantly influenced by both grafting combinations and microbial treatments (especially on the relative abundance of major phyla; Ascomycota and Basidiomycota), whereas bacterial communities exhibited stronger shifts in response to microbial consortia application than to grafting combinations. Correlation analysis between the rhizosphere microbial taxa, yield, and root weight highlighted significant associations supporting the potential of combined use of these practices. Notably, although the inoculated microorganisms were detected at low abundance or were not detectable in treated soils, pronounced shifts in the overall microbiome structure were observed, suggesting indirect yet significant ecological effects of the consortia.<br><br>CONCLUSION: This study demonstrates that microbial consortia and grafting synergistically enhance tomato productivity and modulate rhizosphere microbial communities in the monoculture degraded soil under intensive Mediterranean greenhouse conditions. These findings advance current understanding of plant genotype &#xd7; microbial consortium interactions by demonstrating that microbial inoculant relevant effects are highly modulated by plant genotype and can indirectly restructure rhizosphere microbial assemblages, contributing to the development of more sustainable and resilient horticultural systems.}, }
@article {pmid42157119, year = {2026}, author = {Li, QX and Luo, LZ}, title = {Cutaneous MAC infection in an immunocompetent patient: a case report confirmed by mNGS.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13549-3}, pmid = {42157119}, issn = {1471-2334}, abstract = {BACKGROUND: Cutaneous infections caused by non-tuberculous mycobacteria (NTM) are rare. Atypical clinical manifestations and the need for precise microbiological identification often result in misdiagnosis and underdiagnosis.<br><br>CASE PRESENTATION: A 65-year-old immunocompetent female initially presented with papular urticaria. Her symptoms improved transiently after anti-inflammatory treatment, but the lesions rapidly progressed to generalized erythematous nodules and ulcers accompanied by fever and lymphadenopathy. Routine microbiological culture and histopathological examination yielded negative results, while metagenomic next-generation sequencing (mNGS) identified Mycobacterium avium complex (MAC) as the causative pathogen.Triple antimicrobial therapy (clarithromycin, doxycycline, and levofloxacin) a favorable clinical response. This case indicates that cutaneous non-tuberculous mycobacterial (NTM) infection has atypical clinical manifestations and is frequently misdiagnosed as common cutaneous eruptions. mNGS can serve as a key diagnostic tool for suspected cutaneous NTM infection, effectively reducing misdiagnosis and missed diagnosis and providing a reliable basis for clinical diagnosis and treatment.<br><br>CONCLUSION: Cutaneous MAC infection, though rare, may occur in immunocompetent individuals. Clinicians should suspect NTM infection in treatment-refractory skin lesions. mNGS is valuable for etiological diagnosis when conventional tests are negative.}, }
@article {pmid42157131, year = {2026}, author = {Ji, T and Cheng, R and Lu, M}, title = {mNGS and IL-5: potential early diagnostic clues for clonorchiasis before eosinophil rise - a case report.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13612-z}, pmid = {42157131}, issn = {1471-2334}, support = {2022YFC2303203-01//National Key R&amp;D Program of China/ ; Z-2017-24-2202//Specialized Research Fund for Pathogenic Metagenomics of the Bacterial Infection and Drug Resistance Prevention of the Chinese Medical Association/ ; }, abstract = {Clonorchiasis, caused by Clonorchis sinensis, often evades early diagnosis in non-endemic regions due to its nonspecific presentation and the delayed appearance of eosinophilia. We report an informative case of a 56-year-old male with acute fever, abdominal pain, and hepatitis, where conventional diagnostics and initial antimicrobial therapy failed. In this case, metagenomic next-generation sequencing (mNGS) of blood identified C. sinensis-specific reads, and cytokine profiling revealed a marked elevation in interleukin-5 (IL-5) before the onset of peripheral eosinophilia. Targeted treatment with praziquantel led to rapid clinical resolution. This case suggests the potential of integrating mNGS and IL-5 monitoring as early diagnostic tools for clonorchiasis, which can allow for intervention prior to classical biomarker emergence.}, }
@article {pmid42157143, year = {2026}, author = {Sheng, G and Zhao, C and Jiang, L and Zhang, X and Gao, F}, title = {Talaromyces marneffei infection of central nervous system in an immunocompetent child in a nonendemic area: a case report and literature review.}, journal = {BMC pediatrics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12887-026-06996-z}, pmid = {42157143}, issn = {1471-2431}, abstract = {BACKGROUND TALAROMYCES MARNEFFEI: (T. marneffei, formerly Penicillium marneffei) is a rare fatal fungus endemic in Southeast Asia and southern China. T. marneffei infections mainly occur in HIV-infected adults, and commonly involves the skin, lung, and reticuloendothelial system. T. marneffei infections of isolated central nervous system (CNS) in immunocompetent pediatric patients in nonendemic areas have rarely been reported. CASE PRESENTATION: We report a rare case of T. marneffei-induced disseminated encephalomyelitis in an immunocompetent girl from a nonendemic area of Eastern China. The main clinical manifestations were abdominal pain with distension and abnormal gait. Contrast-enhanced magnetic resonance imaging (MRI) revealed both brain and spinal cord lesions. The infection status of T. marneffei was quickly determined via the metagenomic next-generation sequencing (mNGS) of spinal cord biopsy tissue. T. marneffei induced disseminated encephalomyelitis was diagnosed. Following successful antifungal treatment with amphotericin B liposomes and voriconazole, the child recovered gradually. To date, only 3 cases of T. marneffei infection of the central nervous system in non-HIV-infected pediatric patients have been reported in the literature. Among them, one child had inborn errors of immunity, and the other two children were from endemic areas. Moreover, the clinical manifestations of those 3 reported cases were disseminated with common infection sites in the lungs. our patient represents a unique case of an immunocompetent child from a nonendemic area with isolated CNS infection. CONCLUSIONS: We report this rare case and aim to promote pediatric clinicians' recognition of T. marneffei isolated CNS infection in immunocompetent pediatric patients from nonendemic regions. Furthermore, the early use of mNGS is recommended when non-HIV-infected pediatric patients present with unexplained clinical manifestations and poor response to conventional treatments. Timely diagnosis and appropriate antifungal therapy can improve patient prognosis.}, }
@article {pmid42157342, year = {2026}, author = {Jing, Y and Liu, S and Leng, L and He, J and Wang, T and Guan, Y and Su, Z and Zhang, W and Li, Y and Luan, P and Cheng, B and Wang, N and Li, H}, title = {Microbiota transplantation and multi-omics profiling integration unveil the mechanism of Alistipes communis-driven abdominal fat deposition in chickens.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42157342}, issn = {1674-9782}, support = {No. 2022YFF1000201//National Key Research and Development Program of China/ ; No. NK20221001//National Major Agricultural Science and Technology Project/ ; No. 32272863//National Natural Science Foundation of China/ ; No. CARS-41//The earmarked fund for CARS-41/ ; }, abstract = {BACKGROUND: Emerging evidence highlights strong correlations between the cecal microbiome and abdominal fat deposition (AFD) in chickens. However, the specific microbial species driving this process remain unclear. This study aims to identify the key microbe and elucidate its underlying mechanism in regulating chicken AFD.<br><br>RESULTS: First, cecal microbiota transplantation confirmed a causal relationship between the cecal microbiota and AFD. Subsequently, metagenomic and metatranscriptomic integrations identified Alistipes communis as a key microbe implicated in AFD. Finally, in vivo gavage integrated with multi-omics revealed that A. communis enhances AFD by disrupting host tryptophan and histidine metabolism. This was evidenced by the elevated concentrations of amino acid metabolism-related metabolites, including L-phosphoarginine and spermine in the cecum.<br><br>CONCLUSIONS: This study provides direct evidence that the cecal microbiome serves as a key driver in chicken AFD and identifies A. communis as a critical AFD regulator, offering valuable insights into the gut microbiome's role in host obesity.}, }
@article {pmid42157352, year = {2026}, author = {Pérez-Pérez, L and Galisteo, C and Castillo-Peinado, LLS and Tomé-Rodríguez, S and Priego-Capote, F and Carvajal, A and Arguello, H}, title = {Metabolomic signatures of colonic infection by Brachyspira hyodysenteriae.}, journal = {Veterinary research}, volume = {57}, number = {1}, pages = {}, pmid = {42157352}, issn = {1297-9716}, support = {PRE2020-093762//Spanish Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; LE088P23//Junta de Castilla y Le&#xf3;n/ ; }, mesh = {Animals ; Swine ; *Brachyspira hyodysenteriae/physiology ; *Swine Diseases/microbiology/metabolism ; *Gram-Negative Bacterial Infections/veterinary/microbiology/metabolism ; *Metabolome ; Colon/metabolism/microbiology ; Gastrointestinal Microbiome ; *Dysentery/veterinary/microbiology/metabolism ; Feces/microbiology ; Metabolomics ; }, abstract = {Despite swine dysentery's relevance in the pork industry, there are still gaps in our understanding of its pathogenesis and the impact of the infection in the gut. This study aimed to characterize the in vivo colonic metabolome of pigs experimentally infected with Brachyspira hyodysenteriae at the onset of fecal shedding (Early_inf group, n = 6) and during acute clinical disease characterized by mucohemorrhagic diarrhea (Acute_inf group, n = 8) compared with non-infected controls (n = 16). The metabolic profile of the colonic contents changed progressively with disease severity, showing an intermediate pattern in the Early_inf group between the control and the Acute_inf groups (p < 0.05). In acute disease, the metabolome was defined by increased concentrations of amino acids, carnitine derivatives, arachidic acid, 1,2-butanediol, and lactic acid, along with decreased levels of anti-inflammatory compounds. In the Early_inf group, increases were observed in amino acids, organic acids, amines, myo-inositol, quinoline, and 1,2-butanediol, whereas linolenic acid and oxalic acid decreased. Integrated analysis of the colonic metabolome and metagenome revealed a strong correlation between metabolic and microbial profiles, particularly in the Acute_inf group, where differential metabolites were associated with B. hyodysenteriae, Campylobacter hyointestinalis, and Velocimicrobium ethanolgignens. Metabolites showed high predictive potential for the disease stage, with lactic acid and arachidic acid being key markers of acute infection and dihydroxyacetone and leucine distinguishing early infection. Overall, this study reveals significant alterations in the colonic metabolome and its association with the microbiota during swine dysentery, providing new insights into the pathophysiology of the disease and contributing to the development of improved prevention and treatment strategies.}, }
@article {pmid41804595, year = {2026}, author = {Long, C and Gui, J and Wang, F and Wang, C and Zhang, L}, title = {Evaluation of the clinical application of MALDI-TOF MS for identification of difficult-to-classify nontuberculous mycobacterial strains isolated in the laboratory.}, journal = {Acta clinica Belgica}, volume = {81}, number = {3}, pages = {293-302}, doi = {10.1080/17843286.2026.2643452}, pmid = {41804595}, issn = {2295-3337}, mesh = {*Nontuberculous Mycobacteria/classification/genetics/isolation &amp; purification ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; Reference Standards ; Reagent Kits, Diagnostic/standards ; Molecular Typing/methods/standards ; Sequence Analysis, DNA/standards ; Nanopore Sequencing/methods/standards ; DNA, Bacterial/isolation &amp; purification ; Metagenomics/methods/standards ; High-Throughput Nucleotide Sequencing/methods/standards ; China ; Humans ; }, abstract = {OBJECTIVES: This study aims to evaluate the clinical application value of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) in the verification and identification of difficult-to-classify nontuberculous mycobacterial (NTM) strains.<br><br>METHODS: From December 2024 to June 2025, 106 suspected NTM isolates were collected from 10 districts in Shenzhen, China. Initial identification was performed using HRM and REBA commercial kits, with targeted nanopore sequencing and mNGS as the composite reference standard. MALDI-TOF MS was used to verify strains unresolved by the kits, and its diagnostic performance was evaluated.<br><br>RESULTS: The HRM kit demonstrated concordance with the reference standard in 98 of 106 samples (concordance rate: 89.1%), whereas the REBA kit concorded in 88 samples (concordance rate: 80.0%). The REBA kit exhibited a tendency toward misidentification of NTM species as Mycobacterium tuberculosis. When the reference results were used as a baseline with tNanopore providing parallel validation (achieving&#x2009;&#x2265;95% concordance with reference results), MALDI-TOF MS demonstrated poor performance in identifying difficult-to-classify NTM strains. Specifically, MALDI-TOF MS showed poor concordance in detecting M. abscessus (Kappa&#x2009;=&#x2009;0.244), while Mycobacterium intracellulare, Mycobacterium kansasii, and Mycobacterium gordonae demonstrated kappa values of 0.543, 0.477, and 0.483, respectively, indicating low concordance overall. Furthermore, 13 species exceeded the detection range of MALDI-TOF MS, resulting in false-positive identifications or detection failures, with Mycobacterium abscessus exhibiting the highest rate of misidentification.<br><br>CONCLUSION: The limitations of MALDI-TOF MS in verifying difficult-to-classify NTM strains have been demonstrated. The findings emphasize that PCR-based molecular detection combined with gene sequence analysis remains the most reliable methodological approach for accurately identifying challenging NTM species in clinical practice.}, }
@article {pmid41942854, year = {2026}, author = {Salengros, A and Dechamps, E and Meunier, L and George, IF}, title = {Uncovering the ecophysiological potential of Motilimonas through genomic profiling analysis.}, journal = {BMC genomics}, volume = {27}, number = {1}, pages = {}, pmid = {41942854}, issn = {1471-2164}, abstract = {BACKGROUND: The Motilimonas genus was proposed in 2017 and presently include three recognized species isolated from various environments. This genus is still poorly characterized, and its ability to degrade chitin has recently been reported. A genomic profiling analysis was conducted on the seven Motilimonas genomes (family Psychromonadaceae) available in the NCBI database.<br><br>RESULTS: The phylogenetic study suggests that Motilimonas sp. E26, Motilimonas sp. 1_MG-2023 G1M02 and Motilimonas sp. Spo1_1 could form a new clade distinct from other already existing clades within the Motilimonas genus (i.e. M. cestriensis, M. pumila and M. eburnea). The genomic features of all Motilimonas genomes are consistent with a moderately copiotrophic lifestyle. For instance, they encode proteins involved in chemotaxis, motility, type IV pili biosynthesis, sugar phosphotransferase systems (PTS) and chitin degradation. Additional shared traits include aerobic respiration, a preference for sugars over organic acids as carbon sources, the use of a &#x201c;compatible solute&#x201d; strategy to tolerate osmotic stress in saline environments, and, except for M. cestriensis MKS20[T], the ability to perform nitrate reduction. Furthermore, all Motilimonas genomes encode a diversity of secretion systems. For example, each genome contains one or several complete type I secretion systems (T1SS), one complete T2SS, and four genomes (Motilimonas sp. Spo1_1, M. sp. E26, M. sp. 1_MG-2023 G1M02 and Motilimonas sp. KMU-193) harbor a complete type VI secretion system (T6SS). Notably, only M. pumila PLHSC7-2[T] possesses genes encoding a complete type III secretion system (T3SS).<br><br>CONCLUSIONS: These findings provide new insights into the ecological versatility and adaptive strategies of the Motilimonas genus. The next step will involve genome-resolved analyses of metagenomic datasets with the objective to investigate the functional ecology of Motilimonas in a broader range of environments contributing to the better understanding of their ecological distribution.<br><br>GRAPHICAL ABSTRACT: [Image: see text]<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-026-12781-0.}, }
@article {pmid42059572, year = {2026}, author = {Zhang, J and Wang, X and Wang, D and Zheng, Z and Wang, H and Ma, L}, title = {Advances and future directions in identifying specific taxa from microbial meta-omics data: from pipeline to deep learning.}, journal = {mSystems}, volume = {11}, number = {5}, pages = {e0080025}, doi = {10.1128/msystems.00800-25}, pmid = {42059572}, issn = {2379-5077}, support = {42577239, 42277193//National Natural Science Foundation of China/ ; MEER-2024-10//Open Fund of Key Laboratory of Mine Ecological Effects and Systematic Restoration, Ministry of Natural Resources/ ; }, mesh = {*Deep Learning ; *Microbiota/genetics ; *Metagenomics/methods ; *Computational Biology/methods ; Ecosystem ; }, abstract = {Molecular profiling enabled by meta-omics technologies has significantly expanded our knowledge of microbial catalog across diverse environments. Increasing attention has now been focused on identifying ecologically significant taxa, particularly keystone that stabilize communities, rare taxa that underpin functional redundancy, and indicators that reflect environmental gradients. However, current pipeline methods remain limited in deciphering complex ecological relationships and modeling the evolution of community dynamics. As a transformative computational tool, deep learning (DL) offers novel strategies to address these challenges through autonomous feature extraction, nonlinear interaction modeling, and integration of multi-modal data sets. Nevertheless, there are still obstacles to the widespread adoption of DL for collaborative identification of specific microbial taxa, primarily including the intrinsic heterogeneity and imbalance of data sets, the difficulty of model generalization across diverse ecosystems, and the limited ecological interpretability of model outputs. This review summarizes existing research advances and proposes to build a unified DL framework for multi-modal data, exploring its implementation pathways, challenges, and potential coping strategies. The envisioned framework establishes a multi-task learning architecture for unified identification of keystone, rare, and indicator taxa, incorporating domain knowledge through ecological constraint layers and explainable AI modules, while providing flexible implementation pathways for heterogeneous data integration and model customization across microbial ecosystems. This framework has the potential to form a closed-loop verification in combination with synthetic microbial community experiments, reshape the paradigm of microbial community research, and promote the transition from empirical classification to mechanistic ecological cognition.}, }
@article {pmid42149940, year = {2026}, author = {Sandi, JD and Brock-Fisher, TM and Kallon, TMPS and Paye, MF and Fofanah, IU and Nosamiefan, D and Kamara, MS and Teh, AJ and Turay, A and Wilkason, C and Baudi, I and Tomkins-Tinch, C and I'Anson, C and Stachler, E and Pekar, JE and Ozonoff, A and Park, D and Happi, C and Sabeti, PC and Grant, DS}, title = {Characterization of the first complete genome sequence of yellow fever virus (YFV) in Sierra Leone: Implications for public health.}, journal = {PLoS neglected tropical diseases}, volume = {20}, number = {5}, pages = {e0014354}, doi = {10.1371/journal.pntd.0014354}, pmid = {42149940}, issn = {1935-2735}, abstract = {Yellow fever virus (YFV), a mosquito-borne orthoflavivirus that causes severe hemorrhagic disease, is endemic in parts of South America and Africa, yet genomic data from Sierra Leone is lacking despite ongoing case-based surveillance. Using hybrid-capture metagenomic sequencing, we generated a complete 10,611 nt YFV genome (98% coverage) from an adult male patient who reported to the Kailahun Government Hospital with fever and muscle pain. Phylogenetic analysis assigned the genome to the West African II genotype via the YFV Nextstrain build. The Sierra Leone genome showed 57 substitutions, three of which were non-synonymous (NS2B: N79S, NS3: V515I, and NS5 (RdRp domain): A643V), relative to its most recent common ancestor with other genomes from Senegal and the Netherlands. Bayesian phylogenetics estimated the time to the most recent common ancestor with these genomes as January 14, 2001 (95% HPD: December 17, 1987 - April 28, 2009), potentially indicative of long-standing transmission within West Africa that has not been genomically characterized, rather than specific localization to Sierra Leone. Together, these findings underscore the need for expanded genomic surveillance to monitor YFV spread and evolution.}, }
@article {pmid42150467, year = {2026}, author = {Wang, X and Zhang, Y and Yu, J and Yang, S and Zhang, T and Song, J and Sun, Z}, title = {Metagenomic insights into nitrate- and sulfate-enhanced anoxic biodegradation of PAHs in subsurface soil.}, journal = {Ecotoxicology and environmental safety}, volume = {318}, number = {}, pages = {120281}, doi = {10.1016/j.ecoenv.2026.120281}, pmid = {42150467}, issn = {1090-2414}, abstract = {Anoxic biodegradation is pivotal for remediating PAH-contaminated subsurface soils, yet its mechanisms remain poorly understood. In this study, nitrate and sulfate were used as electron acceptors to stimulate the anoxic biodegradation of PAHs in soil by indigenous bacteria. A 180-day anoxic incubation experiment was conducted, coupled with high-throughput sequencing for bacterial community composition, quantitative PCR for microbial abundance, metagenomic sequencing for functional gene profiling, and gas chromatography-mass spectrometry for PAH quantification, to characterize microbial community properties, key functional genes, and their contributions to PAH degradation. After 180 days of incubation, the addition of electron acceptors significantly increased the abundances of total and potential PAH-degrading bacteria (which increased by 0.11-0.24 and 0.09-0.46 orders of magnitude per gram of soil, respectively) and promoted the removal of 3- and 4-ring PAHs (59-64% and 26-33%, respectively). Notably, the degradation efficiency followed the order of NO3[-] > mixed electron acceptors > SO4[2-], revealing a clear preference for nitrate. Nitrate amendment selectively enriched key PAH-degrading taxa like Bacillus. Metagenomic analysis revealed the underlying microbial mechanisms: the functional pathway ko00624 (PAH degradation) was enriched, and the abundances of 15 key genes (e.g., pcaH, ligB, and pht5) involved in upstream and downstream metabolic steps were positively correlated with degradation efficiency. Comparative analysis showed that differences across treatments stemmed primarily from ‌elevated expression of shared core genes (e.g., pht4, phdG, nidB), with nitrate (SN) treatment showing the greatest enrichment. These findings elucidate electron acceptor-driven anoxic PAH transformation, highlighting nitrate's dual role as a nutrient and favorable electron acceptor, and provide a basis for targeted subsurface bioremediation.}, }
@article {pmid42150504, year = {2026}, author = {Pan, Z and Wang, W and Torabi, E and Zhang, M and Su, Z and Xu, X and Yin, Y and Xu, W and Duan, Y and Chen, J and Maróti, G and Huang, Q}, title = {Multi-metal contamination is associated with microbial network simplification and functional adaptation in paddy soils: Insights from genome-resolved metagenomics.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142406}, doi = {10.1016/j.jhazmat.2026.142406}, pmid = {42150504}, issn = {1873-3336}, abstract = {The spatial heterogeneity of multi-metal contamination and its ecological consequences for soil microbial communities remain poorly characterized on a national scale, particularly within paddy ecosystems. This study investigated microbial ecological and genomic responses to heavy metal stress across 48 paddy soils from major rice-growing regions in China, categorized into low (LMS), moderate (MMS), and high (HMS) contamination levels. Our results indicate that multi-metal contamination triggered a significant restructuring of microbial communities, which was accompanied by increased alpha diversity and the enrichment of metal-tolerant taxa (e.g., Planctomycetes and Cyanobacteria). Conversely, microbial co-occurrence networks exhibited systematic simplification as contamination levels increased, characterized by reduced connectivity and a significant loss of keystone taxa. This suggests a transition from functionally redundant communities to modularized, survival-oriented network configurations. Metagenomic analysis revealed positive correlations between metal contamination and the abundance of nitrogen, phosphorus, and sulfur-cycling genes, while carbon-cycling genes remained relatively stable. Furthermore, genome-resolved metagenomics demonstrated widespread co-localization of metal resistance genes (MRGs) and nutrient cycling genes within metagenome-assembled genomes, particularly among key taxa (e.g., Burkholderiaceae, MBNT15). Collectively, these findings elucidate the mechanistic basis of microbial adaptation to multi-metal stress in paddy soils, providing critical insights for optimizing soil health management, developing targeted bioremediation strategies, and enhancing environmental risk assessment frameworks for contaminated agricultural ecosystems.}, }
@article {pmid42150526, year = {2026}, author = {Thompson, LR}, title = {Microbial ecology: Rise of the planet of the microbes.}, journal = {Current biology : CB}, volume = {36}, number = {10}, pages = {R432-R434}, doi = {10.1016/j.cub.2026.03.072}, pmid = {42150526}, issn = {1879-0445}, mesh = {*Microbiota/genetics ; Metagenomics ; Ecosystem ; *Bacteria/genetics ; *Metagenome ; }, abstract = {A long-standing tenet of microbiology is that Earth's microbiomes are structured by environment, not geography. In a new study, Kim et al. report the largest metagenomic analysis yet performed, revealing that microbial generalists transcend these boundaries, ferrying genes - including antibiotic resistance determinants - across ecologically distant habitats.}, }
@article {pmid42150690, year = {2026}, author = {Kruger, F and den Haan, R}, title = {Adaptive laboratory evolution and rational engineering enabled xylose utilisation and xylan conversion in natural isolates of Saccharomyces cerevisiae.}, journal = {Journal of biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jbiotec.2026.05.007}, pmid = {42150690}, issn = {1873-4863}, abstract = {Second-generation biofuels produced from renewable lignocellulosic biomass (LCB) are attractive alternatives to environmentally damaging, non-renewable fossil fuels. A key challenge in converting LCB to bioethanol is the incomplete utilisation of all available sugars. To address this, the hemicellulose fraction, consisting mainly of xylan, should be converted to the desired product alongside cellulose. This study aimed to develop natural isolate strains of Saccharomyces cerevisiae capable of xylose utilisation and xylan degradation. Strains YI13, YI59 and FIN1 were selected for potential industrial applications due to their high fermentation performance levels under environmental stress and enhanced ethanol production compared to laboratory strains. Xylose utilisation was achieved in these strains by introducing heterologous xylose isomerase (XI) and xylulokinase (XKS) gene cassettes and a xylose transporter (XTR), followed by adaptive laboratory evolution (ALE) in minimal xylose media. The evolved strains were further engineered for cell-associated xylosidase and secreted xylanase activities, yielding variants with strong enzyme activities, optimized xylose metabolism, and high ethanol production from both xylose and xylan. The final engineered version of YI13 showed the best xylose and xylan conversion, with maximum ethanol titres of ~7.1g/L from 20g/L xylose and ~4.7g/L from 40g/L xylan, among the highest ethanol titres from polymeric xylan by direct microbial conversion reported to date. The development of these S. cerevisiae strains provides a useful platform for future development of robust xylan-converting S. cerevisiae strains for large-scale ethanol production, although validation on real-world lignocellulosic feedstocks is still required.}, }
@article {pmid42151282, year = {2026}, author = {Visci, G and Notario, E and Defazio, G and Caratozzolo, MF and Cox, SN and Fosso, B and Marzano, M and Pesole, G}, title = {Benchmarking short- and long-read sequencing technologies for metagenomic profiling of microbiomes.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-49725-3}, pmid = {42151282}, issn = {2045-2322}, support = {PNC0000002 - CUP: B53C22006420001//Ministero dell'Universit&#xe0; e della Ricerca/ ; PNC-EJ-2022-23683266 PNC-HLS-DA//Ministero dell'Universit&#xe0; e della Ricerca/ ; H93C22000560003//Regione Puglia/ ; }, abstract = {Two culture-independent methods, amplicon-based sequencing and shotgun metagenomics, have significantly advanced the study of microbial communities. To date, short-read sequencing technologies have enabled high accuracy and deep coverage, while long-read sequencing approaches are increasingly being applied to improve genome assembly, despite challenges related to sequencing errors and nucleic acid input requirements. In this benchmark study, we compared the shotgun metagenomics approach across three sequencing technologies, Illumina (short reads), PacBio and Nanopore (long reads), using a 20-species commercial mock microbial community with even species representation. Specifically, we evaluated the effectiveness of the data generated by each platform in reconstructing genomes and identifying specific known taxa, as well as in understanding their functional potential, considering annotated genes, the length of predicted proteins and the number and types of inferred functions. Illumina sequencing provided high-throughput and high-quality data, but its limited read length precluded complete genome assembly. This affected the functional analysis, leading to an underestimation of coding and non-coding genes. Nanopore sequencing yielded the longest reads, resulting in more contiguous assemblies, although it was affected by higher error rates and the choice of assembly method. PacBio offered the best balance between read length and base accuracy, but with a lower number of reads. This affected genome coverage for certain taxa, influencing the quality of their assemblies, the completeness of MAGs (Metagenome Assembled Genomes), and the accuracy of functional annotation. Nevertheless, PacBio successfully retrieved MAGs for all mock community species, and the genome annotation was consistent with the reference. Evaluating the strengths and limitations of different NGS technologies and assembly strategies, this benchmark provides a practical framework for selecting the most suitable approach for optimizing data quality in microbiome genome characterization, according to study-specific goals.}, }
@article {pmid42151303, year = {2026}, author = {de Tacca, LMA and Lima, RN and de Oliveira, MA and Pascoal, PV and Bambil, D and Rosinha, GMS and Signor, D and Freire, M and Rech, E}, title = {The soil microbiome of the Caatinga drylands in Brazil.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-50433-1}, pmid = {42151303}, issn = {2045-2322}, support = {20-122//Conrad Prebys Foundation/ ; }, abstract = {Drylands cover a significant portion of the Earth's surface and play a key role in maintaining global ecological balance. The Caatinga, with its unique biodiversity adapted to the extreme conditions of this semi-arid region, offers a valuable opportunity to expand our knowledge about these ecosystems. Here, this work reveals the high microbial diversity in the soil and rhizosphere of the Caatinga, with the roots presenting more specialized communities. Bacteria such as Bacilli, Alphaproteobacteria and Firmicutes excelled in critical functions such as nutrient cycling. The Interplant differences suggested the influence of root exudates. Altogether, the metagenomic study of interactions between microorganisms in the rhizosphere of selected plants revealed microbial biodiversity and contributed to our understanding of nutrient cycling, plant growth and resistance to water stress. In addition, they demonstrate biotechnological potential to address global challenges such as desertification and food security.}, }
@article {pmid42151510, year = {2026}, author = {de Souza Pereira, LF and Tavares, TCS and Martins, DT and Dias Dantas, CW and de Souza, FOR and Prazeres, MCC and Faturi, C and Rogez, HLG and Ramos, RTJ and Cardenas Alegria, OV and Ribeiro Carneiro Nunes, A}, title = {Characterization of defensome genes and mobile genetic Elements in different types of pasture soil agroecosystems from the Brazilian Amazon.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42151510}, issn = {1618-1905}, abstract = {The Amazon rainforest represents nearly 40% of the world's tropical forests and has undergone extensive conversion to pasture, profoundly altering soil microbial communities. Given that bacteriophage-driven selective pressure shapes bacterial defense systems (the defensome) as well as mobile genetic elements (MGEs), we examined the diversity and distribution of these genetic components in native forest soils and in pasture soils under two management regimes (with and without fertilization) in the Brazilian Amazon. Metagenomic sequencing revealed pronounced differences in bacterial community structure between forest and pasture sites (R = 0.942), whereas phages communities exhibited no significant variation. Pasture soils-particularly those under fertilization-showed higher abundances of functional genes and mobile genetic elements, including conjugative plasmid-associated genes and insertion sequences. Defensome analyses indicated an increased prevalence of retrons and Pycsar systems in managed soils, while a greater diversity of defense genes was observed in non-fertilized pastures. A strong positive correlation was observed between defensome diversity and MGE diversity, suggesting coordinated dynamics between viral selective pressure and horizontal gene transfer. These findings indicate that forest-to-pasture conversion reshapes microbial functional potential and amplifies genetic mechanisms linked to phage defense and gene mobility, with potential consequences for ecosystem functioning and the dissemination of antimicrobial resistance.}, }
@article {pmid42151682, year = {2026}, author = {Blackburn, D and Rahman, B and Saroyia, AP and Parish, AJ and Driscoll, M and Szewczyk, NJ and Vanapalli, SA and Samuel, BS}, title = {Defining Microbiome Impact on Host Physiology During Spaceflight Using Caenorhabditis elegans.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3000}, number = {}, pages = {251-275}, pmid = {42151682}, issn = {1940-6029}, mesh = {Animals ; *Caenorhabditis elegans/microbiology/physiology ; *Space Flight ; *Microbiota ; Weightlessness ; *Host Microbial Interactions ; }, abstract = {Microbiome-integrated Caenorhabditis elegans cultivation methods enable investigation of host-microbiome interactions in the context of space-relevant stresses using three key innovations: introduction of live bacterial communities replacing chemically defined media, implementation of auxin-inducible degradation systems to prevent progeny production, and development of complementary hardware platforms. Polyethylene bags provide gas-permeable cultivation environments for large populations with complex microbiomes supporting downstream molecular analyses, while NemaCapsules with micropillar arrays and passive culturing chambers allow real-time phenotypic assessment through on-orbit imaging, transforming our ability to correlate molecular signatures with physiological outcomes in microgravity.}, }
@article {pmid42152463, year = {2026}, author = {Forshee, MD and Nachman, EJ and Shenoy, ER and Danhof, HA and Ermann Lundberg, L and Roos, S and Britton, RA}, title = {Limosilactobacillus reuteri promotes melatonin release from human intestinal organoids via 5'ectonucleotidase activity.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2670854}, doi = {10.1080/19490976.2026.2670854}, pmid = {42152463}, issn = {1949-0984}, mesh = {*Melatonin/metabolism ; *Limosilactobacillus reuteri/metabolism/growth &amp; development/enzymology ; Humans ; *Organoids/metabolism/microbiology ; *Intestines/microbiology ; Probiotics ; Adenosine/metabolism ; }, abstract = {Strains of Limosilactobacillus reuteri have been used to prevent or treat various conditions; however, the mechanisms by which they exert beneficial effects are not completely understood. Infant colic is one example in which L. reuteri DSM 17938 reduces clinical symptoms. While the etiology of colic is unknown, abnormal melatonin levels in infants have been suggested as a possible contributor. L. reuteri DSM 17938 has been shown to produce adenosine from AMP via production of the extracellular enzyme 5'ectonucleotidase (5'NT). Adenosine is a potent signaling molecule that impacts several important aspects of host physiology, including the release of melatonin from the pineal gland in the brain. A second major source of melatonin production is enteroendocrine cells in the intestine. We hypothesized that the adenosine generated via the 5'NT activity of L. reuteri DSM 17938, would stimulate melatonin release from human intestinal organoids. Here, we characterized the growth conditions that impact L. reuteri DSM 17938 5'NT activity, including carbon source utilization and required metal cofactors. We found zinc to be an essential cofactor for 5'NT activity by L. reuteri and observed carbon utilization altered 5'NT activity levels. Stachyose and raffinose increased levels of 5'NT activity while sucrose decreased 5'NT activity. We demonstrated that L. reuteri DSM 17938 stimulates melatonin release from pediatric human intestinal organoids in a 5'NT-dependent manner. Surprisingly, adenosine was necessary, but not sufficient, for the induction of epithelial melatonin release, thereby suggesting that an additional secreted factor was also required. Furthermore, L. reuteri BG-R46[®], an evolved strain of DSM 17938 that is known to express higher 5'NT activity, was shown to induce higher levels of melatonin secretion. Taken together, this work identifies zinc and carbon sources as key factors altering L. reuteri 5'NT activity levels and demonstrates that the L. reuteri strains stimulate intestinal melatonin release via 5'NT.}, }
@article {pmid42152762, year = {2026}, author = {Yang, W and Guo, J}, title = {Unveiling the Hidden Resistome: A Comprehensive Risk Assessment of Latent Antibiotic Resistance Genes in China's Wastewater.}, journal = {Environmental microbiology}, volume = {28}, number = {5}, pages = {e70330}, doi = {10.1111/1462-2920.70330}, pmid = {42152762}, issn = {1462-2920}, support = {2021YFD1600400//National Key Research and Development Program of China/ ; }, mesh = {*Wastewater/microbiology ; China ; Risk Assessment ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/drug effects ; Metagenome ; Genes, Bacterial ; Escherichia coli/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; }, abstract = {Wastewater systems are important reservoirs of antibiotic resistance genes (ARGs), but the ecological and health risks of numerous latent ARGs (LARGs) remain unclear. In this study, we analysed 636 wastewater metagenomic samples from China and constructed a database containing 1587 LARGs. Across all environments, LARGs encoding serine-β-lactamases were the most abundant and prevalent. A comprehensive risk assessment, integrating host pathogenicity, gene mobility and environmental prevalence, was performed on 561 LARGs identified in metagenome-assembled genomes. Most LARGs exhibited low levels across all three dimensions, suggesting limited transmission risk. Nevertheless, 37 high-risk LARGs were identified, indicating non-negligible threats. Functional validation showed that the top three extremely high-risk LARGs significantly enhanced host resistance to ampicillin and ciprofloxacin when expressed in Escherichia coli, while AlphaFold3 revealed typical resistance protein folding, further supporting their functional activity. Horizontal gene transfer analysis indicated that these high-risk genes have disseminated from wastewater to natural water bodies such as rivers via plasmid-mediated mechanisms. Collectively, wastewater acts not only as an 'accumulation pool' for LARGs but also as a potential source releasing 'super-risky' resistance gene into the environment. Therefore, urgent efforts are needed to monitor and control these high-risk LARGs and their mobile genetic elements to block their environmental spread.}, }
@article {pmid42152807, year = {2026}, author = {Jing, M and Chen, X and Jiang, M and Fang, H and Zhu, X and Jin, X and Jiao, Y and Hou, N and Gong, W and Liu, A}, title = {Microbial and Metabolic Correlates of Endometrial Dysfunction in Polycystic Ovary Syndrome: A Translational Study.}, journal = {BJOG : an international journal of obstetrics and gynaecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1471-0528.70266}, pmid = {42152807}, issn = {1471-0528}, support = {//Hangzhou Joint Fund of the Zhejiang Provincial Natural Science Foundation of China/ ; //Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; }, abstract = {OBJECTIVE: Women with polycystic ovary syndrome (PCOS) exhibit a substantially increased risk of miscarriage, yet the underlying mechanisms remain inadequately understood. This study aimed to investigate whether specific gut microbial dysbiosis and metabolic disturbance are associated with and may potentially contribute to endometrial dysfunction and adverse pregnancy outcomes in women with PCOS.<br><br>DESIGN: Prospective cohort study integrated with mechanistic experiments.<br><br>SETTING: Women's Hospital, School of Medicine, Zhejiang University, China (2022-2024).<br><br>POPULATION: A total of 110 women with PCOS and 110 age- and body mass index-matched controls were enrolled.<br><br>METHODS: We performed 16S rRNA and metagenomic sequencing of gut microbiota, with untargeted and targeted serum metabolomics. Functional validation was conducted using primary human endometrial stromal cells and a PCOS rat model intervened with Parabacteroides merdae (P. merdae) supplementation or faecal microbiota transplantation.<br><br>MAIN OUTCOME MEASURES: Gut microbiota composition, serum metabolites, endometrial senescence markers, and pregnancy outcomes.<br><br>RESULTS: Women with PCOS exhibited significantly higher miscarriage rates than controls, accompanied by a marked depletion of P. merdae abundance and elevated serum levels of branched-chain amino acids, particularly isoleucine. Exogenous isoleucine induced cellular senescence in human endometrial stromal cells in a dose-dependent manner. Restoration of P. merdae levels in the PCOS rat model resulted in decreased serum isoleucine levels, amelioration of the senescent endometrial phenotype, and reduction in the fetal resorption rate.<br><br>CONCLUSIONS: These findings suggest that P. merdae depletion and the concurrent accumulation of isoleucine may be associated with endometrial senescence and elevated risk of miscarriage, suggesting the possible involvement of a gut microbiota-metabolite pathway in PCOS-related reproductive dysfunction. These results also provide a mechanistic basis for future translational investigations.}, }
@article {pmid42152996, year = {2026}, author = {Chauhan, G and Bisht, N and Gautam, P and Arya, M and Kumari, A and Verma, D and Sharma, M}, title = {Cloning and Heterologous Expression of a Novel Thermo-Alkalistable GH-10 Xylanase (rXyn-GM) Retrieved from Tapovan Hot-Spring Soil Metagenome and its Characterization for Kinetic Parameters.}, journal = {Indian journal of microbiology}, volume = {66}, number = {2}, pages = {417-430}, pmid = {42152996}, issn = {0046-8991}, abstract = {UNLABELLED: A cellulase-free xylanase gene of 927 bp size (Xyn-GM) was isolated from the metagenomic library of the Tapovan Hot Spring in Uttarakhand, India. This gene encodes a 308-amino acid xylanase enzyme classified under the glycoside hydrolase family 10 (GH-10). The Xyn-GM gene was introduced into the pET28a (+) vector and expressed in host cells of Escherichia coli BL21 (DE3). The recombinant xylanase (rXyn-GM), with a molecular weight ~ 32.5 kDa, was isolated through a one-step purification process using Ni[2][+]-NTA affinity chromatography. The purified enzyme exhibited broad thermostability (50-100 °C) and pH stability (4.0-11.0), with optimal activity at 70 °C and pH 9.0. Its activity increased by 67% in the presence of 1 mM Mn[2][+]. rXyn-GM retained ~ 65% activity after 2 h at 50 °C and 60 °C and ~ 75% activity at pH 9.0 after 3 h. It showed a preference for beechwood xylan, with kinetic parameters Km 20.9 mg/mL and Vmax 156.25 µmol/mg/min. Furthermore, rXyn-GM catalysed the production of xylo-oligosaccharides from beechwood xylan, suggesting its potential utility as prebiotics in the food and pharmaceutical industries.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-025-01480-1.}, }
@article {pmid42153006, year = {2026}, author = {Yadav, S and Shipra, }, title = {Impact of Climate Change on Zoonotic Diseases and Antimicrobial Resistance.}, journal = {Indian journal of microbiology}, volume = {66}, number = {2}, pages = {280-291}, pmid = {42153006}, issn = {0046-8991}, abstract = {UNLABELLED: Climate change along with infectious disease and antimicrobial resistance are imposing threat to public health globally. Climate change mediates frequent rise in antimicrobial resistance leading to the emergence of zoonotic vectors. Both climate change and AMR contribute significantly to global morbidity and mortality and impose burden on the healthcare sector. Overexploitation of antimicrobials in various sectors causes broader dissemination of AMR. Therefore, the application of a holistic "One Health Approach" is required to combat both climate change and antimicrobial resistance. Increasing public awareness about the negative consequences of climate change and antimicrobial resistance is essential. Also, the discovery of new antimicrobials has become the need of the present world. The application of metagenomics has the potential to shed light on microbial community dynamics (taxonomic abundance and predominant biochemical pathways) in response to climate change. The application of modern tools like functional metagenomics has the potential to yield new antimicrobial compounds for combating AMR.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01430-3.}, }
@article {pmid42153318, year = {2026}, author = {Chasapi, MN and Kontis, N and Lehmann, R and Tasneem, R and Patel, NS and Khan, SA and Martínez de Morentin, X and Chasapi, IN and Aplakidou, E and Galaras, A and Aldakheel, L and Su, M and Baltoumas, FA and Venkateswaran, K and Lagani, V and Gómez-Cabrero, D and Tegnér, J and Pavlopoulos, GA and Soares Rosado, A}, title = {Decoding extremophiles: insights from bioinformatics, machine learning, and data-driven approaches.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {3}, pages = {}, doi = {10.1093/bib/bbag236}, pmid = {42153318}, issn = {1477-4054}, support = {BAS/1/1096-01-01//King Abdullah University of Science and Technology/ ; //KAUST Visiting Student Research Program (VSRP)/ ; 28787-VIROMINE//Hellenic Foundation for Research and Innovation (H.F.R.I.)/ ; 23592-EMISSION//Research Projects to Support Faculty Members and Researchers/ ; }, mesh = {*Computational Biology/methods ; Culture Techniques ; Environmental Microbiology ; *Extremophiles/genetics/isolation &amp; purification/metabolism ; Machine Learning ; }, abstract = {Life thrives in Earth's most inhospitable environments, from boiling hydrothermal vents to hypersaline lakes and frozen polar deserts, thanks to the remarkable adaptations of extremophilic microorganisms. The study of these organisms has rapidly evolved from early cultivation-based discoveries to a data-rich discipline powered by advanced omics technologies. This review comprehensively outlines the current landscape and future directions in extremophile research, emphasizing the pivotal role of bioinformatics, machine learning (ML), and data-driven approaches. We begin by charting the evolution of methodologies, from innovative in situ cultivation techniques and robust biomolecule extraction protocols to modern multi-omics workflows (metagenomics, transcriptomics, proteomics, and metabolomics) that decode the genetic and functional basis of extremophiles. We then catalogue essential bioinformatics resources and specialized databases critical for annotating extremophile genomes and uncovering their unique adaptive strategies, including protein stabilization and syntrophic metabolic relationships. Finally, we explore the transformative potential of artificial intelligence (AI) and ML in overcoming fundamental challenges in the field. These include predicting the functions of uncharacterized "hypothetical" proteins, identifying novel extremozymes, modeling complex genotype-phenotype relationships, and guiding the targeted engineering of industrially relevant strains. By synthesizing insights across these domains, this review highlights how integrating computational biology and AI is poised to unlock the full biotechnological potential of extremophiles and redefine the boundaries of life itself.}, }
@article {pmid42153323, year = {2026}, author = {Wang, J and Liu, Y and Liu, F and Hou, T and Chen, S and Liu, S and Liu, Y}, title = {DCVBin: a novel binning method for single-sample metagenomes based on DNA language model and variational autoencoder.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {3}, pages = {}, doi = {10.1093/bib/bbag241}, pmid = {42153323}, issn = {1477-4054}, support = {62303193//National Natural Science Foundation of China/ ; 20230101064JC//Science and Technology Development Plan Project of Jilin Province, China/ ; //Fundamental Research Funds for the Central Universities/ ; }, mesh = {*Metagenomics/methods ; *Metagenome ; Humans ; Algorithms ; *Software ; Computational Biology/methods ; Autoencoder ; }, abstract = {DNA contigs binning is necessary to reconstruct metagenome-assembled genomes. Current metagenomic DNA contigs binning methods often leverage coverage profiles across multiple related metagenomes and have demonstrated strong performance on co-assembled contigs. However, in single-sample scenarios where coverage information is rare, their performance drops significantly, limiting the in-depth development of metagenomics at the individual sample level. To address this issue, we propose DCVBin, a novel single-sample metagenomic contigs binning method that incorporates semantic features extracted from a DNA language model. Specifically, our approach continues pretraining on a DNA language model to capture more domain-specific semantic representations, which are then integrated with 4-mer frequencies using a variational autoencoder. Clustering is subsequently performed using the k-means algorithm, in which the number of clusters is determined by single copy genes. Experimental results on six publicly available datasets demonstrate that DCVBin achieves high-accuracy single-sample metagenomic binning and outperforms other state-of-the-art methods. Furthermore, DCVBin is included into a disease diagnostic framework that is evaluated on a cohort of gut metagenomes from people with colorectal cancer and healthy people. The framework is shown to be accurate in predicting colorectal cancer using gut metagenomes and has identified a list of potential microbial biomarkers.}, }
@article {pmid42153643, year = {2026}, author = {Jeilu, O and Simachew, A and Hartmann, EM and Alexandersson, E and Johansson, E}, title = {CAZyme fold architecture is conserved between disparate environments despite extreme sequence divergence.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0048526}, doi = {10.1128/msystems.00485-26}, pmid = {42153643}, issn = {2379-5077}, abstract = {Microbial carbohydrate-active enzymes (CAZymes) underpin carbon cycling across Earth's ecosystems; however, how contrasting environments shape CAZyme diversity and structural conservation remains poorly understood. Here, we applied shotgun metagenomics to compare the carbohydrate-degradation potential of two functionally prolific but physicochemically opposed ecosystems: the alkaline-saline soda lakes of the East African Rift Valley and the anaerobic ruminant gut. From 34 metagenomes (12 soda lake and 22 rumen), we recovered 371 quality-filtered metagenome-assembled genomes, of which 84% of soda lake and 52% of rumen MAGs represented novel species. Rumen communities, dominated by Bacteroidota, Fibrobacterota, and Bacillota, exhibited significantly higher taxonomic diversity and were enriched in carbohydrate catabolism and fermentation pathways. Soda lake communities, dominated by Pseudomonadota, displayed greater evolutionary divergence (lower RED scores) and were enriched in pH homeostasis, oxidative and osmotic stress, sulfur cycling, and carbon fixation pathways. To assess whether structural conservation persists despite extreme sequence divergence, we predicted three-dimensional structures for 12 representative enzymes from six glycoside hydrolase families (GH1, GH3, GH5_11, GH9, GH10, and GH28) using AlphaFold 3. All 12 structures adopted canonical GH family folds with high confidence (pTM 0.75-0.97). These results demonstrate that environmental selection drives distinct taxonomic and functional strategies for carbon processing while preserving three-dimensional CAZyme architecture, positioning soda lake and rumen metagenomes as complementary reservoirs for bioprospecting industrially relevant enzymes.IMPORTANCECarbohydrate-active enzymes, or CAZymes, are the molecular machines that microorganisms use to break down plant material and other complex sugars, and they underpin both the global carbon cycle and many industrial processes, from biofuel production to food, feed, and textile manufacturing. In this study, we compared the CAZyme repertoires of two microbial worlds that could hardly be more different: the alkaline, salty soda lakes of the East African Rift Valley, and the anaerobic stomachs of cattle, sheep, and goats. We show that although these communities are taxonomically distinct and their enzyme sequences have diverged dramatically, the three-dimensional shapes of their key carbohydrate-degrading enzymes remain remarkably well preserved. Soda lakes, in particular, hold a large pool of previously uncharacterised enzymes, identifying them as a promising, largely untapped source of robust biocatalysts for sustainable biotechnology and industrial applications.}, }
@article {pmid42153646, year = {2026}, author = {Revel-Muroz, AZ and Sonets, IV and Chistyakov, AS and Vasiluev, PA and Surovoy, YA and Ivanova, VA and Kozlovskaya, LI and Khokhlova, OE and Fursov, MV and Fursova, NK and Ulianov, SV and Tyakht, AV}, title = {Gut Hi-C metagenomes of severe COVID-19 patients: bacteria and yeast involved in gut-lung axis.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0013926}, doi = {10.1128/msphere.00139-26}, pmid = {42153646}, issn = {2379-5042}, abstract = {Antimicrobial resistance (AMR) poses a critical threat to global health, particularly in intensive care units, where vulnerable patients are frequently exposed to multidrug-resistant microorganisms. The human gut microbiome serves as a key reservoir for AMR genes, which can disseminate to other body sites, including the lungs, especially during severe illness. We applied Hi-C metagenomics to stool samples from 11 critically ill COVID-19 patients and analyzed microbial isolates from their lungs to investigate intra-host transmission of AMR genes. Plasmid-resolved microbial interaction networks revealed AMR gene sharing across 13 bacterial genera, primarily from Firmicutes and Proteobacteria, with evidence of plasmid-mediated transfer across phylum boundaries and between gut and lung compartments. Notably, we identified genetically identical Klebsiella pneumoniae strains colonizing both the gut and lungs of a single patient, as well as shared plasmids carrying qnrS-1 and blaCTX-M-231 resistance genes between gut Escherichia coli and lung K. pneumoniae. In addition to bacterial pathogens, Candida yeast species isolated from both niches harbored resistance genes to multiple antifungal classes, including azoles. These findings underscore the dynamic, cross-compartmental nature of AMR dissemination within the human body and highlight the importance of integrative surveillance strategies to control resistance in clinical settings.IMPORTANCEWhile COVID-19 itself caused severe illness, many deaths were ultimately due to secondary microbial infections-often worsened by antibiotic resistance. Plasmids, which shuttle resistance genes between bacterial species, are key players in their spread, yet their roles in transmission, especially across body sites such as the gut and lungs, are to be elucidated. The use of Hi-C metagenomics allowed us to map bacterium-plasmid links in the guts of severe COVID-19 patients and reconstruct high-quality genomes of opportunistic fungi. Comparing these with lung-derived isolate genomes, we gained insight into possible intra-host dissemination routes of resistance genes. Preparing for future pandemics will require not only rapid pathogen detection but also tools to monitor microbiome health and resistance dynamics, and understanding how treatments and microbial imbalances shape infection risks.}, }
@article {pmid42153961, year = {2026}, author = {Zhu, B and Chen, S and Diao, Y and Wang, W and Huang, Y and Liang, L and Lu, X and Han, R and Guo, M and Li, Z and Wang, S and Li, H and Liu, C and Zhou, J and Xiong, D and Li, X and Ning, Y and Shi, X and Wu, F and Wu, K}, title = {Dissecting the Ecological Structure of Health and Disease in the Global Gut Microbiome.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e17087}, doi = {10.1002/advs.202517087}, pmid = {42153961}, issn = {2198-3844}, support = {2023YFC2414500//National Key Research and Development Program of China/ ; 2023YFC2414504//National Key Research and Development Program of China/ ; 2025YFC3410000//National Key Research and Development Program of China/ ; 2025YFC3410005//National Key Research and Development Program of China/ ; 82271953//National Natural Science Foundation of China/ ; 82301688//National Natural Science Foundation of China/ ; 2023B0303020001//Key Research and Development Program of Guangdong/ ; 2023B0303010003//Key Research and Development Program of Guangdong/ ; 2024A1515013058//Natural Science Foundation of Guangdong Province/ ; 2025A1515010507//Natural Science Foundation of Guangdong Province/ ; 2023A1515011383//Natural Science Foundation of Guangdong Province/ ; 2019B121203008-KJ-2024-040/KJ-2024-041//Guangdong Key Laboratory of Battery Safety at Guangzhou Institute of Energy Testing/ ; 2025A03J3357//Science and Technology Program of Guangzhou/ ; ZDYN-2024-A-121//Clinical Collaboration Project on Integrated Traditional Chinese and Western Medicine for Major and Difficult Diseases/ ; 2024SRP200//Research Capacity Improvement Project of Guangzhou Medical University/ ; GCAAL2022001//Guangzhou Key Clinical Specialty (Clinical Medical Research Institute), the Announcement and Leading Science and Technical Foundation of Guangzhou Civil Affairs/ ; 2023B04J0106//Guangzhou Planned Project of Science and Technology/ ; 2025B04J0011//Guangzhou Planned Project of Science and Technology/ ; }, abstract = {The gut microbiota plays a crucial role in human health, but its coordinated ecological dynamics remain largely unclear. We present Wiredancer, a novel scalable framework based on similarity-constrained non-negative matrix factorization (NMF), which extracts continuous and overlapping microbial ecological factors (MEFs). By integrating 20,178 metagenomes spanning 36 countries and over 50 disease states, Wiredancer identified three robust and interpretable MEFs delineating the health-disease continuum. MEF1, the dysbiotic factor dominated by Bacteroides uniformis, was elevated in disease populations; MEF2, the protective factor characterized by Prevotella copri, was reduced compared with the healthy group; and MEF3, the intermediate factor represented by Bifidobacterium adolescentis, reflected a mixed ecological configuration between MEF1 and MEF2. MEFs exhibited high reproducibility across individuals and longitudinal cohorts, but showed significantly increased variability in disease, consistent with the Anna Karenina principle and highlighting disrupted ecological stability. These findings were validated in the largest Chinese metagenomic cohort of major psychiatric disorders, where MEFs were associated with clinical symptoms, peripheral biomarkers, and disease subtypes, and remained essentially stable under short-term treatment. Together, Wiredancer provides a generalizable strategy to define microbiome states and decode ecological transitions, offering new opportunities for precision diagnostics and stratified medicine in complex disorders.}, }
@article {pmid42154322, year = {2026}, author = {Greaves, JC and Rodriguez, RA}, title = {Revealing the hidden burden: wastewater-based epidemiology for underreported and emerging infectious diseases in communities.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {6}, pages = {}, pmid = {42154322}, issn = {1573-2959}, mesh = {Humans ; *Wastewater/virology/microbiology ; *Communicable Diseases, Emerging/epidemiology ; *Wastewater-Based Epidemiological Monitoring ; }, abstract = {Wastewater-based epidemiology (WBE) has become a transformative tool for infectious disease surveillance, providing population-level insights that complement and extend traditional case-based reporting. This review examines the expanding role of WBE in identifying and characterizing underreported, novel, and emerging human pathogens. Evidence reveals that wastewater analysis consistently detects enteric, respiratory, and neglected pathogens that are often missed by clinical systems, thereby revealing the hidden burden of infection within communities. Sequencing-based studies have identified numerous novel and divergent human viruses, highlighting the extensive diversity of the human virome. The frequent co-detection of multiple viral taxa also suggests that interactions and co-infections may influence viral evolution, disease manifestation, and transmission. Despite methodological challenges in quantification and biological validation, WBE has proven capable of detecting both known and novel pathogens before they are clinically recognized. Future developments in long-read sequencing, bioinformatics, and global data integration will enhance the precision and scope of wastewater genomics, positioning it as a central element of early-warning and One Health surveillance frameworks. By illuminating the unseen spectrum of infectious agents, WBE bridges environmental and clinical domains, offering a scalable and equitable strategy for global pathogen discovery and public health preparedness.}, }
@article {pmid42154337, year = {2026}, author = {Sain, M and Rani, S and Singh, SP and Pothal, P and Yadav, S and Suttee, A and Kumar, A and Kumar, S and Ranawat, P and Singh, G and Barnwal, RP}, title = {The Influence of Gut Microbiome on Alpha-Synuclein Aggregation: Implications for Parkinson's Disease Pathogenesis.}, journal = {Molecular neurobiology}, volume = {63}, number = {1}, pages = {}, pmid = {42154337}, issn = {1559-1182}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Parkinson Disease/metabolism/pathology/microbiology ; *alpha-Synuclein/metabolism ; Animals ; Dysbiosis ; *Protein Aggregates ; }, abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder traditionally characterized by dopaminergic neuronal loss in the substantia nigra and the accumulation of misfolded α-synuclein (α-syn) aggregates. While genetic susceptibility and environmental exposures are well-recognized contributors to PD, growing evidence indicates that disease initiation and progression may also involve peripheral mechanisms originating in the gastrointestinal (GI) tract. Early non-motor symptoms such as constipation, along with the presence of α-syn pathology in the enteric nervous system, have led to increasing interest in the gut-brain axis as a critical modulator of PD pathogenesis. Recent literatures reveal that gut microbiota dysbiosis can influence neurodegeneration through immune activation, intestinal barrier dysfunction, and altered production of microbial metabolites, including short-chain fatty acids, bile acids, lipopolysaccharides, and tryptophan-derived compounds. However, the precise molecular mechanisms by which these microbial factors modulate α-syn aggregation, propagation, and clearance remain incompletely understood. In this article, we review current clinical and experimental literature linking gut microbiota alterations to α-syn pathology, with particular emphasis on inflammatory signaling, microbial metabolites, and impaired proteostatic pathways that promote α-syn misfolding. We further integrate emerging concepts of "body-first" and "brain-first" PD subtypes and discuss proposed routes of α-syn transmission from the enteric to the central nervous system, including vagal, hematogenous, and immune-mediated pathways. By highlighting underexplored mechanistic connections between gut dysbiosis and α-syn biology, this review underscores the potential of microbiome-targeted strategies for early diagnosis and disease modification. A deeper understanding of gut-brain communication may ultimately enable personalized therapeutic approaches and reshape current paradigms of PD pathogenesis.}, }
@article {pmid42154370, year = {2026}, author = {Benekos, K and Katsanos, A and Laspas, P and Panos, GD and Vagiakis, I and Fousekis, FS and Luca, R and Zhou, B and Kostoulas, C and Georgiou, I and Katsanos, KH and Skondra, D and Konstas, AG}, title = {An Update and Overview of the Ocular and Extraocular Microbiome and Its Impact on Ophthalmic Care.}, journal = {Advances in therapy}, volume = {}, number = {}, pages = {}, pmid = {42154370}, issn = {1865-8652}, abstract = {The microbiome has been described as the last human "organ" and is currently the topic of great research interest worldwide. The application of culture-independent methods, like 16S ribosomal next-generation sequencing, has offered researchers the opportunity to identify bacterial populations that were impossible to detect previously using conventional culture methods. Further standardization of these new approaches to characterizing the microbiome is desirable. The present review discusses the mounting evidence suggesting that alterations in the microbiome and microbial metabolites, such as short-chain fatty acids in the gut, mouth, and ocular surface, may play a key role in the pathogenesis of ocular pathologies such as ocular surface disease, glaucoma, uveitis, age-related macular degeneration, and diabetic retinopathy. Clarifying the probable role of the microbiome in ocular diseases would not only offer valuable insights into pathogenesis but could also enable the development of novel therapeutic approaches. As yet, microbial-based therapeutic applications in ophthalmology are limited. Nevertheless, recently emerging strategies utilizing probiotics and prebiotics, or even fecal transplantation to regulate microbiome composition, offer promising research avenues for developing future innovative therapies for ocular diseases. Further studies employing standardized methodological protocols are needed to ensure the reproducibility of results and to eventually unlock the precise links between the microbiome and the eye.}, }
@article {pmid42154390, year = {2026}, author = {Khan, I and Irfan, M and Bacha, AS and Khan, I and Ali, Y and Li, Z}, title = {Host-Microbiota Metabolic Interactions in Atherosclerosis: Oral, gut, and Blood Perspectives.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {42154390}, issn = {1867-1314}, abstract = {Atherosclerosis is a chronic inflammatory disease influenced by host-microbiota interactions beyond traditional risk factors. Microbial communities in the oral cavity, gut, and blood contribute to vascular dysfunction through metabolic and immune mechanisms, yet an integrated perspective across these compartments remains lacking. This narrative review synthesizes current evidence on the distinct and interconnected roles of oral, gut, and blood microbiotas in atherosclerosis pathogenesis. We critically evaluate key microbial metabolites, trimethylamine N-oxide (TMAO), short-chain fatty acids (SCFAs), and secondary bile acids, and their mechanisms of host metabolic and immune modulation. We also examine cross-compartment interactions, emerging multi-omics approaches, and the translational potential of microbiota-targeted interventions. Oral pathogens promote systemic inflammation and endothelial activation. Gut-derived metabolites such as TMAO exacerbate foam cell formation and impair reverse cholesterol transport, whereas SCFAs exert protective effects via immune modulation and gut barrier maintenance. Emerging evidence suggests that blood microbial components contribute to vascular inflammation, though methodological challenges remain. Multi-omics integration (metagenomics, metabolomics, host genomics) reveals interconnected metabolic networks linking microbial activity to atherosclerosis. Microbiota-targeted strategies, including dietary modulation, TMA lyase inhibitors, and probiotics, show promise for risk stratification and therapeutic intervention. The human microbiota regulates atherosclerosis through immunometabolic metabolites, offering promising biomarkers and therapeutic targets. However, clinical translation requires addressing interindividual variability, establishing causality, and standardizing methodologies. This review provides an integrated framework for leveraging microbiota-host interactions in precision cardiovascular medicine.}, }
@article {pmid42154500, year = {2026}, author = {Pouder, E and Alain, K and Mieszkin, S}, title = {Phylogenomic and metabolic insights into iron reduction metabolism in the genus Deferribacter belonging to the order Deferribacterales.}, journal = {Microbial genomics}, volume = {12}, number = {5}, pages = {}, doi = {10.1099/mgen.0.001712}, pmid = {42154500}, issn = {2057-5858}, mesh = {*Phylogeny ; *Iron/metabolism ; Oxidation-Reduction ; Hydrothermal Vents/microbiology ; Genome, Bacterial ; Metabolic Networks and Pathways/genetics ; }, abstract = {Iron is one of the most important elements of the Earth, yet its bioavailability is limited in oceanic environments. In this context, deep-sea hydrothermal ecosystems represent one of the major sources of iron. While some microorganisms involved in its biogeochemical cycle, particularly in Fe(III)-reduction, have been isolated from these ecosystems, the molecular mechanisms underpinning metabolic pathways remain hypothetical and incomplete. Therefore, this study aims to investigate the global metabolism of bacteria within the Deferribacter genus, isolated from hydrothermal systems and a petroleum reservoir, with a specific focus on the Fe(III)-reduction metabolism to identify genes potentially involved in this pathway. This study revealed a conserved carbon metabolism across the four species, while their energetic metabolism exhibited notable differences. These species appear to be able to use different elements as electron sources, showing their ability to adapt to different ecological (micro)niches, particularly in deep-sea hydrothermal vents. The marker genes known for Fe(III)-reduction were identified, with a contrast between the strains isolated from hydrothermal systems and the one isolated from a petroleum reservoir. To further explore this pattern, the study was extended, including 14 genomes of representative strains and 36 metagenome-assembled genomes affiliated to the Deferribacterales order. Phylogenomic analysis revealed a distribution pattern within this order that correlates with environmental origin. Canonical marker genes of Fe(III)-reduction were also identified, with their distribution primarily aligned with specific ecological niches.}, }
@article {pmid42154842, year = {2026}, author = {Wang, D and Wang, N and Liu, J and Zhao, C and Xing, X}, title = {The diagnostic value of fine-needle aspiration cytology in the early diagnosis of pulmonary cryptococcosis.}, journal = {Revista do Instituto de Medicina Tropical de Sao Paulo}, volume = {68}, number = {}, pages = {e33}, doi = {10.1590/S1678-9946202668033}, pmid = {42154842}, issn = {1678-9946}, mesh = {Humans ; *Cryptococcosis/pathology/diagnosis ; Biopsy, Fine-Needle/methods ; Retrospective Studies ; Male ; Female ; Middle Aged ; *Lung Diseases, Fungal/pathology/diagnosis ; Early Diagnosis ; Adult ; Aged ; Lung/pathology/microbiology ; }, abstract = {Pulmonary cryptococcosis, an invasive fungal infection caused by Cryptococcus spp., is often misdiagnosed as tuberculosis or lung cancer due to overlapping clinical and radiological features, leading to treatment delays. In this descriptive study, we aim to characterize the diagnostic findings and clinical utility of fine-needle aspiration cytology (FNAC) in a series of patients with pulmonary cryptococcosis, within the context of other available diagnostic modalities. We retrospectively analyzed 10 patients with pulmonary cryptococcosis who underwent imaging-guided percutaneous lung aspiration. Wright-Giemsa-stained cytology smears were examined under oil immersion, enabling clear visualization of the characteristic morphological features of Cryptococcus. In this case series, FNAC provided a rapid cytological diagnosis within two hours in all 10 cases, consistent with the results obtained by metagenomic next-generation sequencing (mNGS) and serological testing. In contrast, conventional smear microscopy showed lower detection rates, and histopathology required longer processing times. The use of FNAC facilitated early diagnosis, enabling timely initiation of antifungal therapy and helping to avoid unnecessary surgical interventions. Our findings suggest that cytomorphological evaluation by FNAC is a rapid and valuable diagnostic tool in the early clinical management of pulmonary cryptococcosis, effectively complementing existing diagnostic methods.}, }
@article {pmid42154957, year = {2026}, author = {Lorca, R and Bretagne, MC and Boizeau, L and Cappy, P and Allenbach, Y and Rodriguez, C and Salem, JE}, title = {Immune checkpoint inhibitor myocarditis: a metagenomic investigation of infectious pathogens.}, journal = {European heart journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/eurheartj/ehag371}, pmid = {42154957}, issn = {1522-9645}, }
@article {pmid42155010, year = {2026}, author = {Kim, JS and Loe, A and Ma, SF and Ranjan, P and Lipinski, JH and Mikhail, SG and Gurczynski, SJ and Zhou, X and Huffnagle, GB and Downward, JE and Metcalf, JD and Falkowski, N and Stringer, KA and Dickson, RP and Huang, Y and Moore, BB and Martinez, FJ and Murray, S and Noth, I and O'Dwyer, DN}, title = {Gut microbiota associate with disease severity and survival in idiopathic pulmonary fibrosis.}, journal = {American journal of respiratory and critical care medicine}, volume = {}, number = {}, pages = {}, doi = {10.1093/ajrccm/aamag249}, pmid = {42155010}, issn = {1535-4970}, abstract = {RATIONALE: Gut microbiota modify immunity. Dysregulated immunity plays a key role in the pathogenesis of IPF. However, the role of gut microbiota in IPF pathogenesis is unknown.<br><br>OBJECTIVES: Determine associations between gut microbiota, disease severity and lung transplant-free survival in IPF.<br><br>METHODS: Gut microbiota from patients enrolled in the CleanUP-IPF trial were characterized using fecal swab samples (n&#x2009;=&#x2009;411). CleanUP-IPF investigated the clinical efficacy of long-term anti-microbials in IPF. 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing were performed to comprehensively profile gut microbial communities. Associations between baseline microbiota with disease severity, transplant-free survival, and treatment heterogeneity were analyzed using principal component analysis, multivariate generalized linear models, additive models and Cox regression models.<br><br>MEASUREMENTS AND MAIN RESULTS: Gut microbiota composition varied significantly with sex, age, and proton pump inhibitor use. Gut microbial diversity and community composition were significantly associated with impaired gas exchange (percent predicted (pp) DLCO). Several genera including the Lachnospiraceae unclassified genus were associated with improved transplant-free survival (HR 0.34 95% CI 0.14-0.87, P&#x2009;=&#x2009;.02) in patients not assigned to anti-microbial treatment. Patients with a higher abundance of the Lachnospiraceae unclassified genus exposed to long term co-trimoxazole had worse survival (HR 6.09 95% CI 1.36-27.27, P&#x2009;=&#x2009;.02). Survival in pirfenidone treated patients was significantly associated with a higher abundance of the gut Lachnospiraceae unclassified genus.<br><br>CONCLUSIONS: In exploratory post-hoc analysis, gut microbiota correlated with disease severity, associated with treatment heterogeneity and transplant-free survival in patients with IPF.}, }
@article {pmid42155550, year = {2026}, author = {Pandit, S and Hazra, S and Dinda, SK and Bhattacharjee, B and Basu, A and Pradhan, B and Kumar, K and Manna, D}, title = {Advances in the detection of deadly free-living amoebae (FLA).}, journal = {Diagnostic microbiology and infectious disease}, volume = {116}, number = {2}, pages = {117465}, doi = {10.1016/j.diagmicrobio.2026.117465}, pmid = {42155550}, issn = {1879-0070}, abstract = {Free-living amoebae (FLA), including Naegleria fowleri, Acanthamoeba castellanii, Balamuthia mandrillaris, and Sappinia pedata, are ubiquitous protozoa capable of causing severe infections such as primary amoebic meningoencephalitis (PAM), granulomatous amoebic encephalitis (GAE), and Acanthamoeba keratitis (AK). Early diagnosis remains challenging due to disease rarity, nonspecific clinical presentation, and limited access to specialized laboratory methods. Rapid and accurate detection is critical for patient management and public health response, particularly amid changing environmental exposures. This review summarizes current diagnostic approaches in clinical and environmental contexts, including specimen handling, microscopy, culture, immunohistochemistry, antigen detection, and molecular methods such as conventional PCR, real-time PCR, multiplex qPCR, LAMP, and metagenomic next-generation sequencing. Environmental surveillance, biomarker discovery, quality assurance, and standardized protocols are also discussed. By evaluating strengths and limitations of available tools, this review highlights diagnostic gaps and future priorities to enhance sensitivity, turnaround time, and global accessibility.}, }
@article {pmid42155712, year = {2026}, author = {Geng, R and Huang, B and Duan, Z and Zhao, F and Lü, X and Jiang, Z and Yi, Y}, title = {Antimicrobial Efficacy and Food Application Potential of Bacteriocins LL3 and LL4 from Traditional Dairy-Derived Lactococcus lactis.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2026-28309}, pmid = {42155712}, issn = {1525-3198}, abstract = {To combat foodborne pathogens like Salmonella, this study employed an activity-based screening followed by metagenomic mining of the active isolates to discover and characterize bacteriocins from Inner Mongolian dairy products. From the 15 active isolates, Lactococcus lactis D63 and D64 were identified as harboring a putative biosynthetic gene cluster (BGC) encoding 2 bacteriocins, LL3 and LL4. Both peptides form amphipathic α-helical structures that disrupt bacterial membranes, leading to intracellular leakage and cell death. They exhibited effective antimicrobial activity, particularly against Salmonella Typhimurium. Crucially, when applied in a simulated milk model under standard refrigeration (4°C), synthesized LL4 demonstrated robust preservative efficacy by effectively controlling S. Typhimurium, showing comparable performance to the commercial preservative Nisin. Genetic analysis revealed that this BGC exhibits low basal transcription under standard laboratory growth conditions and shares high homology with plasmid elements, suggesting it is a mobile genetic element acquired via horizontal gene transfer. This study presents LL3 and LL4 as promising natural preservatives and validates metagenomic mining as an efficient strategy for uncovering antimicrobial genes.}, }
@article {pmid42155775, year = {2026}, author = {Yao, X and Zhu, Y and Gao, P and Liu, T and Zhang, X and Liu, W and Li, J and Li, D and Zhang, Y and Zhang, Z}, title = {Limitations of endogenous denitrification in low carbon-to-nitrogen wastewater treatment: Insights into carbon allocation imbalance and metabolic adaptation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134915}, doi = {10.1016/j.biortech.2026.134915}, pmid = {42155775}, issn = {1873-2976}, abstract = {Endogenous denitrification (EnD) has been identified as a promising strategy for enhancing nitrogen removal from wastewater with a low carbon-to-nitrogen (C/N) ratio. However, the mechanisms limiting its effectiveness under carbon-starved conditions remain insufficiently understood. This 160-day study compared denitrification performance, carbon allocation, and metabolic responses in two sets of anaerobic/aerobic/anoxic-sequential batch reactors (A/O/A-SBR) under low (3-5) and high (10-15) C/N ratios. Under low C/N, total nitrogen (TN) removal decreased to 69.90 ± 13.31%, with effluent NO3[-]-N accounting for 87.43 ± 14.40% of TN. Concurrently, microbial activity was inhibited. Compared with high C/N ratio, microorganisms under low C/N preferentially allocated limited carbon to extracellular protein (PN) rather than to intracellular polyhydroxyalkanoates or glycogen. PN constitutes 47.39 ± 2.38% of the total internal carbon sources in unit sludge and functions primarily to maintain cellular structural stability. This carbon allocation pattern imposes limitations on the supply of carbon sources available for the EnD process. In addition, despite the enrichment of EnD functional bacteria (15.22 ± 2.03%), functional genes were primarily directed toward survival-related pathways (xenobiotics biodegradation and metabolism and amino acid synthesis). Constraints on energy metabolism further limited carbon utilization and denitrification. Concurrently, while the dispersion of denitrification-related genes under low C/N maintained system stability across multiple bacterial genera, it concomitantly reduced denitrification efficiency. This metabolic shift further limited EnD. This study provides novel insights into constraints on EnD from the perspectives of carbon source allocation and microbial metabolic adaptation, thereby establishing a theoretical foundation for the treatment of low C/N wastewater.}, }
@article {pmid42155781, year = {2026}, author = {Wang, J and Liu, S and Wang, Z and Guo, Y and Liu, J and Shi, L}, title = {Coupling heterotrophic and hydrogenotrophic partial denitrification via gel-based bio-carriers: microbial mechanisms and metabolic modeling.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134914}, doi = {10.1016/j.biortech.2026.134914}, pmid = {42155781}, issn = {1873-2976}, abstract = {Partial denitrification (PD) has emerged as a pivotal technology for addressing the limited nitrite (NO2[-]) supply that hinders the widespread application of anammox, as it efficiently provides NO2[-]. However, its reliance on organic carbon sources restricts its broad implementation. In this study, a system of heterotrophic coupled with hydrogen-autotrophic PD was established using polyvinyl alcohol gel bio-carriers. Operated under a low COD/NO3[-]-N ratio of 2.00 for 90 days, the system achieved remarkable performances, with a NO2[-] transformation ratio (NTR) of 85.50 ± 3.10% and a nitrate (NO3[-]) removal rate (NRR) of 84.70 ± 5.00%. Metagenomic analysis revealed the effective enrichment ofHydrogenophaga(23.90%) as a key hydrogen-autotrophic denitrifier, which formed a functionally complementary consortium with heterotrophic denitrifiers (e.g.,Dokdonella). The abundance ratio of NO2[-] reduction genes in autotrophic to heterotrophic bacteria was 1.3:1. Furthermore, a putative metabolic model was constructed, which posits a potential cross-feeding interaction characterized by "hydrogen production by heterotrophs and consumption by autotrophs." The hydrogenase (EC:1.12.99.6) was proposed as a potential key gene facilitating this synergy between heterotrophic and autotrophic bacteria. The increased abundance ratio of nitrate reductase to nitrite reductase genes to 2.07 was identified as the key factor promoting the high accumulation of NO2[-]. Material characterization confirmed that the gel carriers possessed a hierarchical porous structure, with a mesopore-dominated pore size distribution conducive to hydrogen diffusion and the aggregation of functional microbial communities, thereby providing a stable micro-environment. This study offers a novel technological pathway for stable NO2[-] supply in the treatment of low-carbon wastewater.}, }
@article {pmid42155841, year = {2026}, author = {Zhang, M and Sun, H and Ren, Y and Chen, K and Yan, G and Li, B and Huang, Y and Tan, Z and Sun, W}, title = {Thiosulfate drives vanadium natural attenuation in oligotrophic mine tailings: Insights from DNA-SIP and metagenomics.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128368}, doi = {10.1016/j.envpol.2026.128368}, pmid = {42155841}, issn = {1873-6424}, abstract = {Vanadium (V) accumulation in mine tailing ponds represents a persistent contamination source, posing severe risks to the surrounding ecosystems. Microbial V(V) reduction represents a key pathway of V detoxification, immobilization and attenuation. While thiosulfate (S2O3[2-]), a prevalent byproduct in tailing ponds, is thermodynamically capable of driving V(V) reduction, the occurrence of the S2O3[2-]-driven V(V) reduction and its underpinning microbial mechanisms remain elusive. Here, we investigated the potential of S2O3[2-] to fuel V(V) natural attenuation in the tailing sediment. Microcosm experiments demonstrated that S2O3[2-] amendment significantly accelerated V(V) reduction rates by 1.8-fold compared to thiosulfate-free controls, confirming a stoichiometric coupling between V(V) reduction and S2O3[2-] oxidation. Pseudomonas, Symbiobacterium and Actinotalea were proposed as the active autotrophic taxa responsible for this coupling process using DNA-stable isotope probing (SIP) combined with metagenomics. Metabolic reconstruction revealed a resilient microbial network based on functional redundancy. These key taxa harbored denitrification-related reductases (NarGHI, NapAB, and NirS/K) and respiratory electron-transfer components (cytochrome c oxidases), together with distinct thiosulfate oxidation genes including thiosulfate dehydrogenase (TsdA/DoxD) and sulfurtransferases (TST/GlpE), indicating potential pathways for the S2O3[2-]-driven V(V) reduction process. These findings expand our understanding of the coupled S-V biogeochemical cycle and highlight the intrinsic natural attenuation capacity of tailing environments. This work provides a mechanistic basis for assessing the environmental fate and mobility of vanadium in oligotrophic habitats.}, }
@article {pmid42156214, year = {2026}, author = {Wang, H and Chen, N and Feng, C and Mei, D and Gao, H and Liu, T}, title = {Carbon availability dictates the stability of nitrate-vanadium co-remediation in stratified biofilters.}, journal = {Water research}, volume = {302}, number = {}, pages = {126137}, doi = {10.1016/j.watres.2026.126137}, pmid = {42156214}, issn = {1879-2448}, abstract = {Thermodynamic hierarchies constrain the bioremediation of groundwater co-contaminated with nitrate (NO3[-]) and pentavalent vanadium (V(V)), denitrification preferentially consumes electron donors that would otherwise support metal reduction. Here, we show that spatial stratification of lignocellulosic residues (wheat straw → corn straw → corncob) can transiently alleviate competition between these competing processes, although system performance remains ultimately governed by carbon availability and kinetics. Over 330 days of operation, the stratified biofilter exhibited a biphasic response: (i) a carbon-sufficient phase (0 - 88 d) that enabled synergistic co-removal, increasing NO3[-] and V(V) loading capacities by up to 6.3-fold and 4.0-fold, respectively, relative to single-substrate controls; and (ii) a carbon-limited phase (88 - 330 d) in which denitrification persisted (>50% removal) while V(V) reduction collapsed (≈0%). Spatially resolved metagenomics (n = 15) revealed the mechanism as a thermodynamic "metabolic triage": under carbon limitation, microbial communities maintained denitrification pathways but selectively down-regulated V-reduction modules (sulfite reductase and multiheme cytochromes) by 59% - 69%. While distinct functional niches emerged-characterized by rapid efflux (top), deep reduction (middle), and sequestration (bottom), spatial organization alone could not override thermodynamic limits. Our findings establish that sustained metal co-remediation requires dynamic carbon management strategies to actuate latent genetic potential, providing a design framework for overcoming competitive inhibition in engineered aquifers.}, }
@article {pmid42156216, year = {2026}, author = {Deng, X and Wang, Y and Zhu, H and Guo, Y and Wang, Q and Han, J and Yu, K and Zhou, B}, title = {Metagenomic profiling of resistome and mobilome dynamics in diverse freshwater aquaculture modes.}, journal = {Water research}, volume = {302}, number = {}, pages = {126133}, doi = {10.1016/j.watres.2026.126133}, pmid = {42156216}, issn = {1879-2448}, abstract = {The widespread presence of antibiotic resistance genes (ARGs) in aquaculture environments poses a growing threat to public health. However, comprehensive understanding of ARG distribution and transmission potential across different freshwater aquaculture modes remains limited. This study employed integrated short- and long-read metagenomic sequencing to characterize the resistome, mobilome, and associated microbial communities across three predominant freshwater aquaculture modes (grass carp, crayfish, and crab ponds), using water, sediment, and intestinal samples analyzed at both contig and metagenome-assembled genome (MAG) levels. The results revealed that aquaculture modes and environmental media jointly shaped microbial and ARG compositions. At the contig level, the crayfish system harbored the highest relative abundance of both ARGs and mobile genetic elements (MGEs), with gut samples consistently emerging as the dominant reservoir across all modes. A significant positive correlation between ARG and MGE alpha diversity indicated that the gut microbiome, particularly in crayfish, provides a selective environment that co-enriches resistance genes and their mobile carriers. High-risk core ARGs (Rank I) were at least 19 times more abundant in the crayfish gut than in any other compartment, underscoring the intestinal microbiome as a hotspot for clinically relevant resistance accumulation. At the MAG level, over half of the recovered MAGs met near-complete or high-quality thresholds, and approximately 38% of ARG-carrying MAGs were classified as multidrug-resistant (MDR). MDR MAG abundance was significantly higher in gut than in sediment and water samples, with the crayfish gut as the most enriched compartment. Critically, several crayfish-associated MDR MAGs affiliated with Klebsiella aerogenes carried virulence factor genes (VFGs) and exhibited ARG-MGE-VFG co-localization within prophage sequences, suggesting phage-mediated co-dissemination of resistance and virulence traits. These findings highlight the intestinal microbiome of aquaculture species as a critical hotspot for resistance dissemination and provide a scientific basis for evaluating freshwater aquaculture-associated ARG risks under the One Health framework.}, }
@article {pmid42156414, year = {2026}, author = {Maziers, N and Le Chatelier, E and Plaza Oñate, F and Fromentin, S and Thirion, F and Pons, N and Borruel, N and Casellas, F and Torrejon, A and Robles-Alonso, V and Manichanh, C and Varela, E and Derrien, M and Veiga, P and Oozeer, R and Sunagawa, S and Lombard, V and Terrapon, N and Henrissat, B and ,  and Guarner, F and Ehrlich, SD}, title = {Fecal microbiome of patients with ulcerative colitis reflects their phenotype and inflammatory level.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-44895-6}, pmid = {42156414}, issn = {2045-2322}, support = {ANR-11-DPBS-0001, MetaGenoPolis (MGP)//Agence Nationale de la Recherche/ ; FP7-HEALTH-F4-2007-201052, MetaHIT//Seventh Framework Programme/ ; }, abstract = {Inflammatory bowel diseases affect ever-increasing numbers of individuals worldwide. Alterations of the intestinal microbiome were reported for Crohn's disease and at relapse in Ulcerative Colitis (UC); they were not clearly detected in UC at remission. Here we report the characterization of the microbiome by quantitative metagenomics in a cohort of 121 individuals, composed of 65 UC adult patients in remission and 56 healthy controls. A cross-sectional comparison revealed substantial microbiome differences, patients in remission having lower microbiome richness and paucity of the Ruminococcus species driven enterotype. The observed microbiome alterations allowed robust classification of patients by intestinal species abundance, yielding an area under the curve (AUC) of 0.87 in a Receiver-Operator Characteristic (ROC) analysis. Loss of richness was linked to an aggressive UC phenotype and to the importance of past relapses; it was associated with a worse IBD quality of life score (IBDQ-36). Unexpectedly, onset of inflammatory bouts, as assessed by white blood cell count and fecal calprotectin levels, was associated with higher richness; in a longitudinal study of patients at high risk of disease flare, we observed a link between increasing gut microbiome richness over time and calprotectin level, in turn related to clinical inflammatory response and relapse.}, }
@article {pmid42143373, year = {2026}, author = {Huntington, CA and Bonavita, CM and Wells, HL and Tiemann, JD and Navarrete-Macias, I and Johnson, RF and Hensley, LE and Anthony, SJ}, title = {Optimization of environmental air sampling for viral metagenomics in a cave-roosting bat assemblage.}, journal = {One health outlook}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42522-026-00218-3}, pmid = {42143373}, issn = {2524-4655}, support = {#2412522//NSF/ ; }, abstract = {BACKGROUND: Environmental air sampling holds significant potential as a tool for viral surveillance. Its use in agricultural and indoor settings has demonstrated its feasibility and effectiveness but despite this, it has rarely been used in wildlife settings.<br><br>METHODS: To enable future applications, we optimized key parameters in air sampling methodology using a cave-roosting bat assemblage as a model system. We systematically investigated the impact of sampling conditions (flow rate, sampling duration, and sampling location/deployment time) and post-sampling treatments (DNA/RNA Shield ratios and secondary filtration) on three viral metrics - total mammalian virus abundance, mammalian RNA virus abundance, and Shannon diversity index - generated from next-generation sequencing data.<br><br>RESULTS: We first showed that air sampling can recover broad viral diversity, including alphacoronaviruses and betacoronaviruses. The sampling conditions for maximizing viral metrics were larger air sample volumes (&#x2265;24,000 liters) and sampling inside the cave while the bats were roosting, as opposed to at the cave entrance during emergence. Post-sampling treatments had limited impact on viral metrics, but their application may vary depending on the objectives of the study.<br><br>CONCLUSION: This work provides a proof-of-concept for applying air sampling for wildlife viral surveillance in a cave-roosting bat assemblage and identifies key sampling parameters.}, }
@article {pmid42143423, year = {2026}, author = {Faghihinezhad, M and Eshghdoostkhatami, Z and Cupples, AM}, title = {Characterization of multiple trichloroethene, cis-dichloroethene and 1,1-dichloroethene degrading propanotrophic communities.}, journal = {Journal of environmental management}, volume = {408}, number = {}, pages = {129957}, doi = {10.1016/j.jenvman.2026.129957}, pmid = {42143423}, issn = {1095-8630}, abstract = {Aerobic cometabolism offers a viable strategy for the remediation of chlorinated solvent plumes at oxic sites where anaerobic approaches are limited. Here, propane-enriched mixed cultures (derived from agricultural soils and an impacted site sediment) which previously degraded 1,4-dioxane, were evaluated for their capacity to also degrade trichloroethene (TCE), cis-1,2-dichloroethene (cDCE), and 1,1-dichloroethene (1,1-DCE) over successive transfers. Sustained biodegradation of TCE and cDCE was observed across multiple enrichments and cultures enriched on one compound generally degraded the other. In contrast, 1,1-DCE biodegradation was restricted to a subset of cultures and removal times increased over transfers. Further, 1,1-DCE removal was absent at elevated concentrations, both trends consistent with inhibitory or toxic effects. Whole genome sequencing analyses revealed pronounced substrate-dependent selection of microbial communities, with cDCE-degrading cultures being dominated by Mycobacterium and Mycolicibacterium, whereas TCE-degrading cultures were dominated by Rhodococcus. Rhodococcus metagenome-assembled genomes (MAGs) in the TCE degrading cultures classified as R. opacus or R. wratislaviensis. 1,1-DCE degrading cultures were dominated by Pseudonocardia, although the associated MAGs contained a truncated propane monooxygenase alpha subunit, suggesting other enzymes were responsible for 1,1-DCE transformation. Functional gene analysis identified both group 5 (prmABCD) and putative group 6 propane monooxygenases (although their expression was not examined). Together, these results demonstrate that substrate-specific pressures govern propanotrophic community structure and function, and highlight distinct roles of key actinobacterial genera in chlorinated ethene cometabolism. These findings support the development of propane-based bioaugmentation strategies for the treatment of mixed chlorinated solvent contamination under aerobic conditions.}, }
@article {pmid42143455, year = {2026}, author = {Jia, W and Li, J and Wang, K and Cheng, L and Jin, N and Yang, Q and Zhang, D and Xia, X and Xu, N and Wang, M and Meng, J and Zhu, Y and Ding, A}, title = {Convergent shifts in microbial communities: Petroleum hydrocarbon contamination suppresses matrix heterogeneity.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142349}, doi = {10.1016/j.jhazmat.2026.142349}, pmid = {42143455}, issn = {1873-3336}, abstract = {Accurate characterization of microbial communities in aquifers is essential for understanding groundwater ecosystem responses to petroleum hydrocarbon contamination. However, existing studies have focused primarily on groundwater, largely overlooking the coupled interactions between groundwater and aquifer sediments, which may bias aquifer-scale evaluations of microbial functional potential. In this study, contaminated groundwater and corresponding aquifer sediment samples were collected from a petroleum hydrocarbon impacted site, together with uncontaminated groundwater and sediment samples outside the contaminant plume as controls. Petroleum hydrocarbon concentrations and principal component analysis (PCA) revealed comparable contamination levels in groundwater and aquifer sediments. Integrating 16S rRNA gene sequencing analysis and metagenomic sequencing analysis, we found that microbial communities in contaminated groundwater exhibited broader niche breadth, higher niche overlap, and increased representation of low-molecular-weight carbon (LMW-C) metabolism, particularly pathways associated with ribose and amino sugar utilization. In contrast, aquifer sediment communities showed higher abundances of multidrug efflux pump genes and functional pathways involved in naphthalene and benzene degradation (PAH-C and MAH-C). Further correlation and community assembly analyses indicated that petroleum hydrocarbon contamination was the primary driver shaping microbial communities in both matrices, overriding intrinsic physicochemical differences. Meanwhile, sediment-specific properties, such as stronger sorption capacity for organic matter and differences in microbial lifestyles contributed to the observed divergence between groundwater and sediment communities. Overall, this study demonstrates that contamination induced selection dominates microbial community assembly in aquifers, and provides a mechanistic basis for improving the evaluation of natural attenuation potential and informing remediation strategies in contaminated aquifer systems.}, }
@article {pmid42143457, year = {2026}, author = {Zhang, Z and Lv, M and Wang, R and Wang, B and Du, R and Lou, Y and Wang, C and Jiang, X and Hou, H and Li, Z and Chen, F}, title = {Micro-nano biochar interfaces promote adsorption-reduction coupling to accelerate bioelectrodechlorination in groundwater.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142393}, doi = {10.1016/j.jhazmat.2026.142393}, pmid = {42143457}, issn = {1873-3336}, abstract = {Chlorinated aliphatic hydrocarbons (CAHs), such as trichloroethylene (TCE), are frequently detected high-toxicity contaminants in groundwater. Bioelectrodechlorination provides a sustainable alternative for CAHs remediation, but its practical application is hindered by limited interfacial reactivity due to low CAHs bioavailability and inefficient electron supply. Herein, we propose the construction of biochar-based functional electrodes featuring micro-nano interfacial architectures with hierarchical porosity, excellent biocompatibility, and enhanced interfacial extracellular electron transfer (EET) relative to carbon felt, which strengthened the coupling among local contaminant enrichment, cathode-associated biofilm development, and interfacial electron transfer, thereby accelerating TCE reductive dechlorination. The biochar-modified electrode increased the TCE dechlorination rate by 3.67-fold and reduced the interfacial charge-transfer resistance by 1.79-fold. Cathodic polarization at -0.5 V (vs. SCE) achieved the optimal balance between performance and energy efficiency, delivering 98.7% removal within 48 h at a low energy consumption of 4.1 Wh kg[-1] TCE, whereas less negative or more negative potentials decreased dechlorination efficiency by 4.3-11.0%. Under optimized conditions, TCE was efficiently removed and predominantly converted to cis-1,2-DCE. Biochar functionalization promoted biofilm development and selectively enriched electroactive and dechlorinating populations. Metagenomic analysis revealed marked upregulation of reductive dehalogenase genes (tceA, rdhA) and EET-related genes (cytc-c, e-pilin, and riboflavin). Environmental-economic benchmarking further demonstrated that biochar-based bioelectrodechlorination outperforms organic carbon-driven bioreduction and conventional electroreduction in removal efficiency, electron utilization, process controllability, and material sustainability.}, }
@article {pmid42143575, year = {2026}, author = {Zhang, P and Zhao, M and Cheng, Z and Ding, Y and Xia, S and Guo, J}, title = {Bile acid metabolism dysregulation following Helicobacter pylori eradication promotes plasmid-mediated antimicrobial resistance in the gut microbiome.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag126}, pmid = {42143575}, issn = {1751-7370}, abstract = {Antimicrobial resistance (AMR) transmission within the gut microbiome poses a major health risk during antibiotic exposure, primarily via horizontal gene transfer (HGT). However, how antibiotic-induced metabolic remodeling of the intestinal environment modulates plasmid-mediated AMR dissemination remains unclear. Herein, integrating metagenomics, metabolomics, in vitro conjugation assays, and in vivo mouse models, we show that Helicobacter pylori eradication therapy reshapes gut metabolism in ways that enhance transfer of antibiotic resistance genes (ARGs). Metagenomic analysis revealed the expansion of Escherichia populations and the enrichment of plasmid-borne ARGs after H. pylori eradication. Fecal filtrates from treated individuals significantly increased conjugation frequencies of the broad-host-range plasmid RP4 in E. coli. Metabolomic profiling identified a pronounced accumulation of primary bile acids, including glycocholic acid, taurocholic acid, glycochenodeoxycholic acid, and taurochenodeoxycholic acids, which could increase bacterial membrane permeability, induce the SOS response, and upregulate conjugation and pilus assembly genes, thereby accelerating ARG transfer. Molecular docking further suggested these bile acids may likely participates in interacting with global plasmid repressors KorA/KorB, derepressing conjugation operons. In mice, H. pylori eradication therapy elevated fecal primary bile acid levels and significantly promoted in vivo plasmid transfer, with the critical role of bile acids further confirmed through interventions using the bile acid sequestrant cholestyramine or glycocholic acid. Together, these findings demonstrate that dysregulation of bile acid metabolism due to H. pylori eradication creates a permissive gut niche for plasmid-mediated ARG dissemination, providing mechanistic insight into how clinical antibiotic regimens can unintentionally promote microbiome-associated AMR risk.}, }
@article {pmid42143599, year = {2026}, author = {Dong, A and Paju, S and Leskelä, J and Manzoor, M and Putaala, J and Ylikotila, P and Könönen, E and Pussinen, P and Zaric, S}, title = {Microbial burden of periodontal diseases and its clinical application: The stage, grade, and furcation matter.}, journal = {Journal of periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jper.70140}, pmid = {42143599}, issn = {1943-3670}, support = {SGL023/1035/AMS_/Academy of Medical Sciences/United Kingdom ; //Medical Research Council Impact Acceleration Account/ ; 202108410182//Engineering and Physical Sciences Research Council/ ; //Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral &amp; Craniofacial Sciences/ ; //Revealing the Etiology/ ; //Sigrid Jus&#xe9;lius Foundation/ ; TYH2014407//Helsinki and Uusimaa Hospital District/ ; TYH2018318//Helsinki and Uusimaa Hospital District/ ; //Finnish Medical Foundation/ ; //Finnish Dental Society Apollonia/ ; //King's-China Scholarship Council/ ; }, abstract = {BACKGROUND: Periodontal diseases are associated with dysbiotic oral microbial communities, but clinically applicable measures that reflect microbial burden across disease severity and progression remain limited. This study aimed to assess the oral microbial burden of periodontal diseases by evaluating salivary and subgingival lipopolysaccharide (LPS) activity and lipoteichoic acid (LTA) levels, to explore their relationships with microbial dysbiosis and clinical periodontal parameters in individuals with periodontal health (n = 52), gingivitis (n = 194), and periodontitis of varying stages, grades, and furcation involvement (n = 78), and to assess their diagnostic potential.<br><br>METHODS: Saliva and subgingival plaque samples from 324 SECRETO cohort participants were analyzed for microbial virulence factors using a recombinant Factor C assay for LPS and enzyme-linked immunosorbent assay (ELISA) for LTA. Microbial dysbiosis was assessed using a sequencing-derived, simplified dysbiosis index, calculated from subgingival 16S rRNA gene sequencing and salivary shotgun metagenomic profiles, based on the relative abundances of health-associated and periodontitis-associated taxa.<br><br>RESULTS: Subgingival LPS activity was significantly higher in periodontitis patients compared to healthy individuals and increased progressively across disease stages and grades. Salivary LPS activity differed only by periodontal diagnosis and correlated with full-mouth bleeding score (FMBS). LTA levels showed no statistical variations across periodontal conditions. Subgingival LPS activity and LPS/LTA ratio were strongly associated with simplified dysbiosis index. Salivary dysbiosis index was significantly higher in patients with furcation involvement. Receiver operating characteristic (ROC) analyses identified subgingival LPS, salivary LPS, and simplified dysbiosis index as diagnostic biomarkers with good clinical utility (area under the curve [AUC] 0.59-0.87).<br><br>CONCLUSIONS: This study highlights the importance of periodontitis diagnoses, stages and grades of periodontitis and furcation involvement as determining factors for increased salivary and subgingival bioburden. In addition, LPS activity could be used as a reliable periodontal biomarker, while the LPS/LTA ratio is an indirect indicator of microbial dysbiosis.<br><br>TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT01934725.<br><br>PLAIN LANGUAGE SUMMARY: Periodontitis is a common inflammatory disease that affects the tissues supporting the teeth and can lead to tooth loss and broader health consequences if not properly managed. This study explored whether measures of oral microbial burden, particularly bacterial components such as lipopolysaccharide (LPS) and lipoteichoic acid (LTA), could help explain differences in periodontal disease severity and progression. Saliva and subgingival plaque samples were analyzed from individuals with periodontal health, gingivitis, and different stages and grades of periodontitis. We found that microbial burden, especially subgingival LPS activity, increased consistently with more severe and rapidly progressing forms of periodontitis and was closely associated with clinical signs of inflammation. In contrast, LTA levels showed limited variation across disease categories. Importantly, LPS-related measures demonstrated good ability to distinguish periodontal health from disease. These findings suggest that assessing microbial burden, particularly LPS activity, may provide clinically useful information beyond traditional periodontal assessments and could support improved disease classification, risk assessment, and the development of more personalized periodontal care strategies.}, }
@article {pmid42143831, year = {2026}, author = {Deng, Y and Yuan, X and Xu, Y and Jiang, H and Xue, J and Jiang, Y and Wang, Y}, title = {Acetoclastic methanogenesis associated with arsenic methylation in a reducing aquifer: Pathway-specific patterns and mechanistic insights.}, journal = {Water research}, volume = {301}, number = {}, pages = {126114}, doi = {10.1016/j.watres.2026.126114}, pmid = {42143831}, issn = {1879-2448}, abstract = {The distribution of methylated arsenic (MeAs) in reducing groundwater systems remains incompletely understood, in part due to uncertainties regarding how specific methanogenic pathways may influence arsenic biomethylation, a critical issue in arsenic biogeochemistry and risk assessment. To explore this question, we integrated hydrogeochemical characterization, carbon isotopic tracing, metagenomic analysis, and pathway-specific enrichment experiments, focusing on MeAs-rich alluvial-lacustrine aquifers in the central Yangtze River Basin. A strong positive correlation between arsM and mcrA abundances (r = 0.84, p < 0.001) points to a co-occurrence of genetic potential for arsenic methylation and methanogenesis in the studied aquifer. Metagenome-assembled genome (MAG) analysis showed a pathway-specific distribution of arsM gene, a higher proportion of acetoclastic methanogen MAGs harbored complete arsM genes (14.29 %), compared to methylotrophic (9.09 %) and hydrogenotrophic (0.00 %) methanogens. In pathway-specific enrichment assays under controlled laboratory conditions, acetoclastic cultures exhibited the highest capacity for stepwise arsenic methylation (MMA and DMA production), with methylation efficiency reaching approximately 10.2 %, whereas methylotrophic cultures produced only transient MMA and hydrogenotrophic cultures showed minimal methylation. These observations provide insights into pathway-dependent differences in methanogen-associated arsenic methylation, highlighting a possible biogeochemical link between methanogenesis and arsenic cycling in the studied aquifer. These findings contribute to understanding potential controls on MeAs occurrence in reducing groundwater and provide a basis for further investigations in comparable hydrogeological settings.}, }
@article {pmid42144568, year = {2026}, author = {Rui, Z and Wang, X and Yu, C}, title = {Trichoderma koningiopsis-assembled synthetic PGPR community manage Fusarium damping-off and promote growth of Pinus massoniana seedlings.}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.70924}, pmid = {42144568}, issn = {1526-4998}, support = {QKEZDZX[2024]010//the Guizhou Provincial Major Scientific and Technological Program/ ; theNationalNaturalScienceFoundationofChina//32160375/ ; }, abstract = {BACKGROUND: Fusarium oxysporum causes damping-off disease in Pinus massoniana seedlings. While Trichoderma koningiopsis can enhance seedling resistance by regulating rhizosphere plant growth-promoting rhizobacteria (PGPR), the specific bacterial compositions and their role in disease resistance remained undefined. To elucidate this mechanism, we used amplicon and metagenomic sequencing to identify T. koningiopsis-assembled PGPR. Synthetic PGPR communities were constructed from isolated strains to validate their effects on disease suppression and growth promotion.<br><br>RESULTS: Microbial community analysis indicated that T. koningiopsis reshaped the bacterial community: Actinospica, Dyella, and Streptomyces decreased in presence, and Bacillus and Arthrobacter increased. A total of 153 PGPR strains were isolated from the T. koningiopsis-inoculated treatment. Of these, eight strains demonstrated significant inhibitory effects against F. oxysporum, ranging from 33.81% to 59.52%. Four synthetic communities (SynComs) (C1, C2, HT, and 2K) were further constructed, exhibiting superior inhibitory effects against F. oxysporum compared to individual strains. Compared to the control, the C2 and HT SynComs increased seedling height by 10.18% and 9.44%, and reduced disease incidence by 50% and 36.67%, respectively. These treatments also enhanced protective enzyme activity and alleviated membrane damage. At the molecular level, the C2 and HT SynComs boost plant resistance by modulating the plant hormone and mitogen-activated protein kinase (MAPK) signaling pathways, thereby activating the expression of crucial resistance genes such as PR1, FLS2, and CAT1.<br><br>CONCLUSION: Trichoderma koningiopsis alters the composition of rhizosphere PGPR community. The synthetic PGPR community assembled under the influence of T. koningiopsis effectively enhances damping-off resistance and promotes the growth of Masson pine seedlings. &#xa9; 2026 Society of Chemical Industry.}, }
@article {pmid42145141, year = {2026}, author = {Sreekumaran, S and V K, P and M N, A and Premnath, M and P S, S and P R, P and Mathew, J and E K, R}, title = {Comparative Human-Poultry Fecal Resistome Profiling from Broiler Farms Reveals Diverse Antimicrobial Resistance Genes.}, journal = {Foodborne pathogens and disease}, volume = {}, number = {}, pages = {15353141261449964}, doi = {10.1177/15353141261449964}, pmid = {42145141}, issn = {1556-7125}, abstract = {Indiscriminate use of over-the-counter antibiotics has led to the rapid emergence of resistant genes in bacteria, with the ultimate crisis to global health. One of the prominent sectors with the antimicrobial resistance (AMR) concern is the farm animals that exist in close contact with humans where the environmental conditions are favorable for the rapid dissemination of pathogenic organisms and resistance genes. Hence, to understand the threat with environmental AMR, a detailed molecular insight is very important. In this study, fecal samples from both poultry and associated humans were studied by metagenomics analysis. From the results, a primary understanding on the microbial diversity difference could be generated from the selected samples. Here, the poultry samples were identified to have more microbial diversity. At the same time, several pathogens were found to be shared commonly between the hosts. Upon detailed examination, several AMR genes were also observed to be common between the poultry and human samples. The results of the study are highly relevant in light of the "One Health" concept where an integrated approach is targeted.}, }
@article {pmid42145647, year = {2026}, author = {Xing, J and Xu, Z and Zhang, Y and Zhang, H and Zheng, L and Zhang, M and Guo, W and Liu, J and Pan, Y and Zhang, J and Jie, Z and Baele, G and Li, C and D'Souza, A and Zhao, J and Li, J and Chen, T and Wu, H}, title = {Longitudinal cross-species transmission of microbiomes and resistomes across farmers, animals and environment.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.06.26352545}, pmid = {42145647}, abstract = {Understanding the acquisition and dissemination of microbiomes and antimicrobial resistance genes (ARGs) that circulate across human-animal-environment interfaces remains a central One Health challenge, largely because of complex ecological interactions and multiple confounding factors. Although occupational exposure is known to influence the microbiomes and resistomes of farmers, how environmental compartments involve in this system is unclear. Here, we conducted a one-year longitudinal study combining strain-resolved metagenomics (500 metagenomes) with isolate-based whole-genome sequencing (28 isolates) in an ecologically managed, antibiotic-free farming ecosystem spanning animals, farmers, environmental compartments and non-exposed individuals. Assembling 6,075 species-level genomes, we show that animal-associated occupancy reshapes the microbiome and resistome of occupationally exposed farmers and their surrounding environments. Animals and their associated habitats formed the dominant interface for both strain sharing and ARG dissemination across connected ecological compartments, whereas village residents and surrounding river samples - used as ecological controls - showed limited integration into this sharing network. Tracking a frequently shared lineage further revealed within-lineage genetic turnover together with selection-consistent changes following cross-species spread, suggestive of ecological selection across hosts and habitats. Finally, we identify Klebsiella pneumoniae as the most widespread ESKAPE pathogen in this ecosystem, with repeated occurrence across animal, human and environmental compartments, consistent with a neglected but clinically critical broad profile of ecological generalist. Together, these findings identify animals as central interfaces for microbiome and resistome sharing and show how agricultural ecosystems can sustain circulation of opportunistic pathogens and resistance determinants across human-animal-environment interfaces even in the absence of routine antibiotic use.}, }
@article {pmid42146067, year = {2026}, author = {Cooper, G and Ayotte, SH and Du, ML and Wood, JD and Opp, B and Bothner, B and Peyton, BM}, title = {Arsenic detoxification within thermo-alkaline biofilms.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1783099}, pmid = {42146067}, issn = {1664-302X}, abstract = {INTRODUCTION: The fundamental principles driving community composition and dynamics of microbial mats in thermoalkaline springs are largely uncharacterized. High in not only temperature but also arsenic (As), the microbial populations of Yellowstone National Parks (YNP), USA thermal springs require unique detoxification mechanisms to survive and carry out basic biological functions.<br><br>METHODS: While many studies have focused on which microorganisms are present, few studies have integrated the use of metagenome sequencing, imaging techniques, and mass spectrometry to gain insight into how structure and function of the mat dwelling organisms might be impacted by the high arsenical species in the ecosystem.<br><br>RESULTS: Here, we demonstrate via metagenome sequencing that community composition, including microbial genera Roseiflexus, Thermus, and Synechococcus, and as detoxification abilities change with mat depth and distance from the springs. Arsenical speciation confirmed the generation of bioarsenicals by mat-dwelling microorganisms. Microscopy revealed stratification of microorganisms in the mat, potentially reflecting their arsenic redox capabilities.<br><br>DISCUSSION: These data demonstrate how microbial mats are modular, stratified systems that shape and are shaped by environmental and geochemical gradients. Together, these findings characterize novel complexity and associations between geochemical cycles of metals and metabolic adaptations necessary for microorganisms to inhabit thermal springs. In conclusion, these findings demonstrate physiochemical heterogeneity of microbial mats in YNP.}, }
@article {pmid42146533, year = {2026}, author = {Steininger, HM and Iglesias-Aguirre, CE and Panzer, AR and Durack, J and McKean, M and Cabana, MD and Diamond, S and Lynch, SV}, title = {Carbohydrate Metabolism Differs in Infants by Asthma-risk Status and is Associated with the Functional Potential of Bacteroides cellulosilyticus.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.28.721144}, pmid = {42146533}, issn = {2692-8205}, abstract = {Childhood atopic disease is linked to delayed gut microbiome development and metabolic dysfunction, however microbial drivers remain unclear. To explore microbial correlates of asthma risk during a time of active gut microbiome development, we analyzed stool from 6-month-old infants at high asthma risk (HR) or healthy controls (HC), using Genome-resolved metagenomics (HR=7; HC=12) and untargeted metabolomics (HR=11; HC=15). We recovered 82 bacterial species-level metagenomic-assembled genomes (MAGs). Global Taxonomic composition did not differ by asthma risk. Anticipating that key differences might associate with specific genomes, a machine-learning approach pinpointed Bacteroides cellulosilyticus, Hungatella effluvii, and Enterocloster aldenensis as linked with asthma risk status. All three species were more abundant in HC infants and the B. cellulosilyticus genome was enriched for carbohydrate metabolism genes relative to other MAGs. Metabolomic profiling revealed variance associated with asthma risk (PERMANOVA, R2=0.069, p=0.016). HR fecal metabolomes were enriched in simple sugars, whereas HC contained more nitrogenous compounds. Integrative genome-metabolic modeling of compounds that significantly differentiate asthma-risk groups revealed risk-dependent interactions with community-encoded metabolic potential (CEP), for arabinose and agmatine, whose fecal concentrations are linked with B. cellulosilyticus and H. effluvii functional traits respectively. These findings suggest that microbial-influenced metabolic differences associate with asthma risk at 6 months, with B. cellulosilyticus and H. effluvii emerging as candidate bacteria influencing this observed metabolic remodeling.}, }
@article {pmid42146661, year = {2026}, author = {Miller, CJ and Pope, CE and Lavitt, MH and Caverly, LJ and LiPuma, JJ and Penewit, K and Lewis, JD and Salipante, SJ and Hoffman, LR}, title = {The Unified Human Virome Database: A toolkit for expanded human virome analysis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.05.01.722327}, pmid = {42146661}, issn = {2692-8205}, abstract = {Current approaches for computationally analyzing viruses within human microbiomes often rely on databases largely composed of fragmented viral genomes from gastrointestinal samples, limiting identification of viruses exclusively found outside the gastrointestinal tract and analyses requiring high-quality genomes. To address these issues, we created the Unified Human Virome Database (UHVDB), comprising 575,497 high-quality, annotated viral genomes from human gastrointestinal, airway, skin, and urogenital sample metagenomes. We developed an associated toolkit that uses UHVDB to characterize viruses and their potential activity from metagenomes, then applied this toolkit to 1,983 airway sample metagenomes from people with cystic fibrosis. Over half of detected viruses lacked evidence of potential activity and were detected transiently. UHVDB is nearly three times larger than prior viral databases and its ability to identify likely active viruses enables rigorous analysis of viruses from diverse human sample types, expanding the capacity to define virus contributions to health and disease.}, }
@article {pmid42146906, year = {2026}, author = {Orletskaia, VA and Olekhnovich, EI}, title = {Ecological and Functional Stratification of the Stool Microbiome Predicts Response to Immune Checkpoint Inhibitors across Cancer Types.}, journal = {Computational and structural biotechnology journal}, volume = {35}, number = {1}, pages = {0065}, pmid = {42146906}, issn = {2001-0370}, abstract = {Despite the recognized role of the gut microbiome in modulating immune checkpoint inhibitor efficacy, the ecological principles governing this relationship remain elusive. Moving beyond cataloging specific bacteria, we investigated whether general ecosystem properties determine clinical outcome. Through genome-resolved metagenomic analysis, we constructed a comprehensive catalog from 951 stool metagenomes and subsequently analyzed a curated subset of 624 samples from 11 multicancer cohorts, with melanoma (72.7%, n = 456) and other cancer types collectively accounting for 27.3% (n = 171), including gastrointestinal, non-small-cell lung, breast, ovarian, and other types. Our catalog comprises 3,816 operational genomic units and reveals the key ecological determinants of immune checkpoint inhibitor response. Clinical benefit was associated with gut ecosystems dominated by prevalent, autochthonous taxa. Indeed, the population frequency of a taxon was a positive predictor of its favorable outcome association. Functionally, responder-associated microbes were enriched in genomic capacity for complex carbohydrate metabolism, including specialized mucin degradation and amino acid biosynthesis. In contrast, nonresponse was characterized by enrichment of low-prevalence, exogenous oral and food-derived bacteria and enriched for replication-associated pathways. Our results support an ecological interpretation of the "Anna Karenina principle" in microbiomes: response is linked to a stable, functionally coherent microbial community, whereas nonresponse represents a destabilized state with high individual variability. This reframes the search for biomarkers from individual taxa to the assessment of ecosystem stability and functional coherence, providing a foundation for microbiome-targeted strategies to improve cancer immunotherapy outcomes.}, }
@article {pmid42147179, year = {2026}, author = {Belger, C and Wirbel, J and Maghini, D and Carstens, N and van Coller, A and Beasley, JC and Melzheimer, J and Berkman, AY and Strauss, WM and Hetem, RS and Hazelhurst, S}, title = {The Gut Microbiome Profile of Lions in EtoshaNational Park, Namibia.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9092464/v1}, pmid = {42147179}, issn = {2693-5015}, abstract = {Background: The gut microbiome plays a crucial role in carnivore ecology, diet, and health, yet remains poorly characterised in African lions (Panthera leo melanochaita). Previous studies of lion microbiomes have primarily focused on small numbers of captive individuals maintained on controlled diets of Asian origin, reporting Fusobacteriota and Firmicutes as dominant phyla. Some recent literature has begun to describe microbiome composition in free-living African lions; however, genome-resolved analyses and detailed functional characterisation of the wild African lion gut microbiome remain lacking. Results: We present the first comprehensive gut microbiome analysis of free-living African lions, including novel MAGs generated from examining 23 fresh faecal samples from 20 individuals in Etosha National Park, Namibia. The African lion gut was dominated by Bacteroides (22.1%) and Phocaeicola (13.3%) - two related genera - contrasting sharply with the captive lions where Fusobacterium (Bhopal, India) and Firmicutes (Rotterdam, Netherlands) predominate. This divergence likely reflects dietary differences, captivity effects and possibly allopatric separation. While recent work has begun to characterise taxonomic composition in wild African lions, our study extends these findings through the reconstruction of 318 bacterial and 102 viral metagenome-assembled genomes (MAGs) from combined short- and long-read sequencing data. Most MAGs shared <95% average nucleotide identity with existing reference genomes, indicating largely novel species. Supplementing the GTDB database with these MAGs reduced unclassified reads from 24.5% to 9.2%, demonstrating the substantial gaps in existing carnivore gut microbiome databases. Functional analysis revealed metabolic pathway enrichment, particularly for purine metabolism-critical for processing the lions' high-purine diet-with nearly complete pathways for degrading adenine and guanine to urea. Conclusions: This study provides the first in depth description of the microbial taxa in the African lion gut microbiome. Genera in the Bacteroidaceae family dominated. There are large differences with the metagenomics of the n = 3, 4 hybrid and Asiatic lions on controlled diets reported in prior studies. The discovery of over 300 novel MAGs significantly expands microbial reference databases and underscores the unique and understudied nature of apex carnivore microbiomes. These findings show critical microbial contributions to carnivore nutrition and establish a foundation for microbiome-based approaches to wildlife health monitoring and conservation management of threatened lion population.}, }
@article {pmid42148043, year = {2026}, author = {Huang, CY and Nuwagira, E and Tisza, M and Kim, M and Tayebwa, M and Vieira, J and Lam, N and Wallach, E and Wiens, M and Tsai, AC and Valeri, L and Vallarino, J and Allen, JG and Lai, PS}, title = {Effect of Household Air Pollution on the Gut Microbiome and Virome of Adult Women Living in Uganda.}, journal = {Environmental health perspectives}, volume = {134}, number = {1}, pages = {75-90}, doi = {10.1021/EHP.6c00064}, pmid = {42148043}, issn = {1552-9924}, mesh = {Humans ; Uganda ; Female ; *Gastrointestinal Microbiome ; *Air Pollution, Indoor/statistics &amp; numerical data/adverse effects ; Adult ; *Virome ; Middle Aged ; }, abstract = {BACKGROUND: Emerging observational studies suggest that air pollution can influence the gut microbiome. However, this association is often highly confounded by factors, such as diet and poverty. The gut virome may influence respiratory health independent of the gut microbiome. We recently demonstrated in a randomized waitlist-controlled trial (ClinicalTrials.gov NCT03351504) that a clean lighting intervention reduced the level of personal exposure to air pollution among adult women in rural Uganda. OBJECTIVES: To determine the effect of a solar lighting intervention on changes to the gut microbiome and virome and secondarily to determine the association between these changes on lung health. METHODS: Between 2018 and 2019, we collected stool samples and assessed respiratory symptoms and spirometry from 80 adult women living in rural Uganda at baseline and 12 and 18 months postrandomization. The intervention group received a solar lighting system after randomization, while the waitlist-controlled group received one at 12 months. Deep metagenomics sequencing of stool was performed and profiled for nonviral and viral taxonomic composition. The primary analysis focused on pre- vs postintervention changes due to power considerations, adjusting for potential confounding by age, diet, antibiotic use, and season. A sensitivity analysis was conducted using intention-to-treat principles. When comparing pre- vs postintervention periods, we used sparse partial least-squares models to identify nonviral and viral signatures of reduced air pollution exposure. Mixed effects models were used to evaluate changes in health outcomes as well as associations between microbial signatures of reduced air pollution exposure and health. RESULTS: The average age was 39.2 years. The solar lighting intervention led to larger changes in viral compared to nonviral microbial community structure and differential abundance of bacteria, eukaryotes, and viruses. Provision of solar lighting systems was associated with a reduction in the presence of respiratory symptoms from 57.1% to 36.1% (p = 0.002), while there was no impact on lung function. Microbiome and virome signatures had AUCs of 0.74 and 0.76, respectively, in predicting pre- vs postintervention stool samples. Microbiome signatures were associated with a lower risk of respiratory symptoms (OR = 0.68 (0.49 - 0.94), p = 0.020). CONCLUSION: Among adult women living in rural Uganda, both nonviral and viral components of the gut microbial community changed after a clean lighting intervention. Microbiome signatures reflective of lower air pollution exposures were associated with improved respiratory symptoms. These observations suggest that air pollution may influence lung health through the gut-lung axis, warranting further exploration in future intervention studies.}, }
@article {pmid42148573, year = {2026}, author = {Raad, R and Mann, A and Pal, A and Parra, A and Strawn, L and Hamilton, A and Critzer, F and den Bakker, HC}, title = {Metagenomic profiling of bacterial (16S) and fungal (ITS) communities on d'Anjou pears during long-term controlled-atmosphere storage.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0411725}, doi = {10.1128/spectrum.04117-25}, pmid = {42148573}, issn = {2165-0497}, abstract = {D'Anjou pears are routinely stored for up to nine months under controlled-atmosphere (CA) conditions to meet market demands. While this practice maintains fruit quality, limited information exists on pears' natural microbiota throughout storage. The objective of this study was to describe fungal and bacterial composition on marketable and unmarketable conventional, whole, intact pears under two storage practices (bulk vs wrapped) at 3, 6, and 9 months in long-term CA cold storage. Storage practices had a significant effect on the composition and succession of both fungal and bacterial communities. No significant differences in Chao1 index were found between the bacterial and fungal communities on marketable or unmarketable pears. Trends in Chao1 indices of fungal and bacterial communities peaked at mid-storage and declined by 9 months, with wrapped pears showing parallel trends, and bulk pears exhibiting a sharper late-stage reduction. No distinct clusters could be found for 3- and 6-month fungal communities, irrespective of marketability, or whether bulk or wrapped. The principal coordinate analysis of the bacterial communities showed tight clustering by time point for the individually wrapped pears, irrespective of their marketability. Bacterial communities included genera common in food-processing and plant environments, such as Pseudomonas (19.2% relative abundance [RA]) and Acinetobacter (3.31% RA). Fungal communities shifted over time, with spoilage-associated genera like Aureobasidium (23.3% RA), Penicillium (9.28% RA), Botrytis (0.33% RA), and Mucor (0.14% RA) present at different storage stages.IMPORTANCEThis study highlights the influence of storage duration and packaging on microbial succession, establishing initial benchmarks of pear surface microbiomes. The observed lack of significant differences in microbial diversity between marketable and unmarketable pears suggests that these baseline community profiles can serve as critical reference points for identifying other influential factors. Variables such as handling practices may exert a more direct effect on microbial dynamics and, consequently, product quality. Establishing these baselines is essential because they provide a foundation for detecting deviations linked to spoilage or safety risks. Moreover, understanding these patterns can guide the development of targeted microbial control strategies in postharvest systems, enabling interventions that maintain fruit quality, reduce losses, and possibly improve food safety throughout the supply chain.}, }
@article {pmid42148581, year = {2026}, author = {Wang, K and Zhang, D and Shen, K and Qiu, Y and Deng, B and Zhou, J and Qiu, S}, title = {Multi-omics characterization of new and aged Daqu reveals region-specific microbial succession and metabolic signatures in Maotai-flavor liquor fermentation.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0377525}, doi = {10.1128/spectrum.03775-25}, pmid = {42148581}, issn = {2165-0497}, abstract = {Daqu is an essential fermentation starter that drives the formation of the characteristic flavor of Maotai-flavor liquor, yet the ecological and metabolic mechanisms underlying its regional differentiation and maturation remain poorly resolved. Here, we performed genome-resolved metagenomic and untargeted metabolomic analyses on 48 new and aged Daqu samples collected from four major Maotai-flavor liquor-producing regions in Guizhou Province, China. We reconstructed 163 high-quality metagenome-assembled genomes (MAGs) spanning 16 bacterial and 3 archaeal phyla and identified 2,642 metabolites across ionization modes. Distinct regional microbial signatures were observed, with Jinsha Daqu showing the greatest genomic diversity and unique MAGs, whereas Maotai Daqu exhibited the highest community similarity with other regions. Aged Daqu significantly increased microbial richness and functional capacity, enriching thermophilic and spore-forming taxa (e.g., Bacillus, Lentibacillus, Kroppenstedtia) and enhancing carbohydrate-active enzymes (GH13, GH43, and GH3), amino acid degradation, lipid metabolism, and secondary metabolic pathways. Metabolomic profiling revealed elevated amino acid derivatives, fatty acids, esters, and phenolic compounds in aged Daqu, indicating intensified biochemical activity. Multi-omics integration linked dominant microorganisms-including Bacillus thuringiensis, Actinomycetaceae bacterium, and Methylocaldum szegediense to pyrazine biosynthesis, amino acid catabolism, and lipid oxidation, forming coordinated microbial-metabolite modules that underlie region-specific flavor precursor formation. These findings establish a mechanistic model in which microbial terroir, aging-driven succession, and metabolic specialization jointly shape the maturation and flavor potential of Maotai-flavor liquor.IMPORTANCEThis study provides the first genome-resolved, multi-omics framework for understanding how geographic origin and storage aging co-regulate the ecological assembly, functional specialization, and metabolic transformation of Maotai-flavor liquor. By linking specific MAGs, functional pathways, and key flavor precursors, our results offer mechanistic insights into microbial terroir and provide a scientific foundation for microbiome-guided optimization of Maotai-flavor liquor quality.}, }
@article {pmid42148582, year = {2026}, author = {Yu, L and Li, H and Yu, H and Zhou, Y and Wang, X and Luo, L}, title = {Inoculation of Bacillus velezensis SD24 enhancing the accumulation of tea catechin secondary metabolites.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0346925}, doi = {10.1128/spectrum.03469-25}, pmid = {42148582}, issn = {2165-0497}, abstract = {Tea (Camellia sinensis) is a globally significant economic crop, and its desirable quality and health benefits are largely credited to catechin derivatives. Plant growth-promoting rhizobacteria (PGPR), such as Bacillus velezensis, are well-known for enhancing the environmental fitness and disease resistance of plants. However, the regulation of their impact on tea catechin biosynthesis remains unclear. While previous studies have focused on PGPR-facilitated growth promotion in crops like tomatoes and rice, the physiological mechanisms by which microbes regulate secondary metabolism in tea-especially under co-inoculation conditions-remain largely underexplored. This study examined the effects of B. velezensis SD24, isolated from tea rhizosphere soil, on catechin derivative accumulation of tea leaves by altering gene expression and the rhizosphere microbiome. Strain SD24 exhibited broad-spectrum antimicrobial activity against various pathogens due to behaving antimicrobial gene clusters. Tea plants inoculated with SD24 showed significantly increased levels of catechin derivatives in their leaves. This was likely achieved by upregulation of leucoanthocyanidin reductase and anthocyanidin reductase within the phenylpropanoid pathway. Additionally, chlorophyll content was increased. Transcriptomic analysis revealed a notable enrichment in biosynthesis of secondary natural products among the tea genes activated by SD24 inoculation. Metagenomic analysis further demonstrated that SD24 inoculation led to a restructuring of the tea rhizosphere microbiome. Notably, co-inoculation with Piriformospora indica, a beneficial endophytic fungus, suppressed SD24-induced gene expression and catechin accumulation, underscoring its antagonism toward SD24. These findings suggest that B. velezensis SD24 enhances tea quality, probably by transcriptionally activating the synthesis of catechin derivatives, a process associated with the restructuring of the rhizosphere microbiome.IMPORTANCEThe mechanisms through which plant growth-promoting rhizobacteria (PGPR) influence secondary metabolism in perennial crops remain poorly understood. This study demonstrates that Bacillus velezensis SD24, a tea rhizosphere isolate, significantly enhances the accumulation of health-beneficial catechin derivatives in tea leaves. This quality improvement is associated with transcriptionally upregulating key biosynthetic genes (LAR and ANR) and concurrently restructuring the rhizosphere microbiome. Furthermore, we reveal a critical antagonistic interaction, where the beneficial fungus Piriformospora indica suppresses these SD24-induced effects. Our findings provide crucial insights into how specific PGPR strains may directly enhance tea quality by affecting host plant metabolism and the root microbiome, highlighting the complex and tailored microbial interactions that could be harnessed for sustainable agriculture.}, }
@article {pmid42148731, year = {2026}, author = {Qiu, H and Zhang, Z and Qian, H}, title = {Evolutionary plasticity of cyanobacteria under persistent anoxia: mechanistic insights from marine blue holes and global ecological implications.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0025126}, doi = {10.1128/aem.00251-26}, pmid = {42148731}, issn = {1098-5336}, abstract = {Cyanobacteria are generally viewed as obligate oxic photoautotrophs. However, this paradigm was challenged by Z. Li, H. Zhang, T. Wei, L. He, and Y. Wang in Applied and Environmental Microbiology (92:e02576-25, 2026, https://doi.org/10.1128/aem.02576-25); this group identified transcriptionally active Synechococcus in the dark, permanently anoxic Yongle Blue Hole using integrated metagenomic and transcriptomic analyses. This finding suggests adaptive streamlining under long-term oxygen limitation, expands the recognized ecological range of phototrophic microorganisms, and highlights the potential relevance of microbial adaptation to future ocean deoxygenation.}, }
@article {pmid42148775, year = {2026}, author = {Shi, W and Liu, L and Wu, L and Wang, X and Peng, Y and Liu, X and Li, C and Xu, J and Wu, Z and Dong, X and Zheng, Q}, title = {Salinity-driven adaptations and evolution of DNA viruses in estuarine-coastal ecosystems.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0035426}, doi = {10.1128/msystems.00354-26}, pmid = {42148775}, issn = {2379-5077}, abstract = {UNLABELLED: Salinity gradients drive microbial diversity and evolution in estuarine-coastal ecosystems, yet viral adaptation remains less well understood. We used metagenomics to study viral adaptation and functions in three representative estuarine-coastal regions in China. Our results reveal salinity-associated adaptations in DNA viruses, with viruses enriched in medium- to high-salinity environments exhibiting higher frequencies of acidic isoelectric points and charged amino acids compared to those enriched in low-salinity environments. Viral genomes encode diverse genes related to ion transporters and organic osmolyte metabolism, suggesting potential roles in osmotic stress responses. Viral microdiversity also varied systematically along the salinity gradient, indicating reduced genetic variation and stronger purifying selection under more saline conditions. Furthermore, we identified diverse AMGs linked to nutrient cycles, with salinity-driven enrichment revealing viral roles in host metabolism. Overall, our findings highlight salinity as a key driver of viral evolution and functional potential in estuarine-coastal ecosystems, providing new insights into how viruses adapt to environmental gradients.<br><br>IMPORTANCE: Salinity is a defining environmental gradient in estuarine-coastal systems, yet its role in shaping viral molecular evolution remains poorly understood. By integrating metagenomes, viromes, and metatranscriptomes across three estuaries, this study demonstrates that salinity exerts a strong and consistent imprint on DNA viruses. Increasing salinity selects for viral genomes encoding ion-transport and osmolyte-related proteins and drives systematic shifts in viral proteome composition toward osmoadaptive physicochemical properties. At the population level, higher salinity is associated with reduced viral microdiversity and stronger purifying selection, indicating constrained evolutionary space under osmotic stress. Viral auxiliary metabolic gene repertoires are structured along salinity gradients, with functional differentiation in carbon, nutrient, and nucleotide metabolism. Together, these findings identify salinity as a key evolutionary filter linking viral physiological adaptation, evolutionary dynamics, and functional potential in estuarine and coastal ecosystems.}, }
@article {pmid42148776, year = {2026}, author = {Guo, J and Xiang, Z-w and Hu, F-f and Zhang, S-x and Han, W-j and Ding, X and Wang, X and Ye, M-l and Chen, J-h and Rao, T and Wu, L-l and Lian, G-h and Zhang, W and Huang, Y and Chen, Y}, title = {Turicibacter sanguinis is a candidate gut microbial pathobiont that promotes metabolic dysfunction-associated steatohepatitis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0029226}, doi = {10.1128/msystems.00292-26}, pmid = {42148776}, issn = {2379-5077}, abstract = {UNLABELLED: Emerging evidence points to the gut microbiota's involvement in metabolic dysfunction-associated steatohepatitis (MASH), yet the specific causative microbes remain largely unidentified. This study aimed to identify and functionally characterize candidate microbial pathobionts to MASH progression. Differentially abundant microbes were identified by 16S rRNA sequencing in a choline-deficient, L-amino acid-defined, high-fat diet MASH model, validated in other animal MASH models and in public clinical metagenomic data sets, then screened for consistently altered gut taxa. A candidate underwent functional validation via directed oral administration in mice. Mechanisms were explored through bile acid profiling by UHPLC-MS/MS and FXR signaling analysis by qPCR and immunohistochemistry. Additionally, fecal samples from MASH patients before and after treatment were analyzed to correlate microbial abundance with treatment response. Turicibacter sanguinis was consistently enriched in all MASH models and public data sets, with abundance correlating positively with liver injury markers. Its increased abundance exacerbated steatosis, inflammation, and fibrosis in healthy and diseased mice. Mechanistically, Turicibacter sanguinis altered bile acid composition, thereby increasing conjugated and decreasing unconjugated species, and inhibited hepatic FXR signaling, accompanied by suppressed SHP and elevated CYP7A1 and SREBP1c expression, which is consistent with enhanced bile acid synthesis and lipid accumulation. Futhermore, after pharmacotherapy, reduced Turicibater sanguinis levels correlated positively with alanine aminotransferase (ALT) and aspartate aminotransferase (AST) improvements. In conclusion, Turicibacter sanguinis is a clinically relevant microbial pathogen that exacerbated MASH by inducing bile acid dysregulation and suppressing FXR signaling, highlighting its potential as a candidate biomarker for disease monitoring and motivating future evaluation of targeted microbiome interventions.<br><br>IMPORTANCE: Metabolic dysfunction-associated steatohepatitis (MASH) is a growing global health problem with limited treatment options. Although the gut microbiome has been implicated in MASH, the specific bacterial strains that directly drive disease progression remain largely unknown. This study identified Turicibacter sanguinis as a candidate gut microbial pathobiont that promotes MASH, demonstrating its significant enrichment in both animal models and patient samples. By disrupting hepatic metabolic signaling, this bacterium promotes bile acid synthesis and exacerbates liver fat accumulation, inflammation, and fibrosis. Following effective treatment, its abundance decreased significantly in patients. These findings indicate that Turicibacter sanguinis holds promise as a potential target for developing novel microbiome-based diagnostic and therapeutic approaches for MASH.}, }
@article {pmid42149293, year = {2026}, author = {Fulke, AB and Ratanpal, S}, title = {Integrated pragmatic approach of bioinformatics and cheminformatics for tracking the fecal pollution in an urban marine environment.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {6}, pages = {}, pmid = {42149293}, issn = {1573-2959}, mesh = {*Environmental Monitoring/methods ; *Feces/microbiology/chemistry ; *Computational Biology ; *Water Pollution/statistics &amp; numerical data/analysis ; *Cheminformatics ; Cities ; *Water Pollutants, Chemical/analysis ; Humans ; }, abstract = {Fecal contamination in urban marine environments poses an alarming global threat to public health, ecosystems, and economies. Traditional fecal indicator bacteria (FIB) methods, while accessible, suffer from delayed results and inability to differentiate pollution sources. To overcome this, microbial source tracking (MST) employs molecular techniques like qPCR to rapidly identify specific origins (human, animal) using genetic markers. Complementary chemical source tracking utilizes distinct chemical signatures (e.g., sterols and pharmaceuticals) for detection, offering low limits and temporal stability. The burgeoning fields of bioinformatics and cheminformatics are crucial for processing the complex, high-volume data generated by these advanced methods. Bioinformatics tools analyze metagenomic data for microbial community profiling and source attribution, while cheminformatics automates the acquisition of chemical-specific data for environmental exposure modeling, enhancing efficiency and transparency. An integrated pragmatic approach leverages these capabilities with Geographic Information Systems (GIS) and remote sensing. GIS serves as a unifying platform, integrating diverse spatial, temporal, sensor, and analytical data to enable comprehensive spatial analysis, real-time monitoring, and predictive modeling of fecal plumes. Hence, this review is aimed toward this holistic framework, which is essential for effective, targeted management strategies to safeguard water quality.}, }
@article {pmid42149451, year = {2026}, author = {Edelkamp, J and Lousada, MB}, title = {In Situ Laser-Capture Microdissection for Detection of Components of the Hair Follicle and Scalp Microbiome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3031}, number = {}, pages = {233-242}, pmid = {42149451}, issn = {1940-6029}, mesh = {*Hair Follicle/microbiology ; *Laser Capture Microdissection/methods ; *Microbiota/genetics ; Humans ; *Scalp/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; }, abstract = {Laser-capture microdissection (LCM) enables the study of the hair follicle (HF) microbiome in relation to hair health and disease with high spatial resolution. It allows the precise excision of specific HF regions, each containing a unique and conserved microbiome, from full-length HFs encompassing all relevant HF compartments. With LCM, cross-contamination with microbiota from neighboring regions is minimized. Coupled with 16S rRNA gene or metagenomic shotgun sequencing, LCM offers great potential to assess region-specific microbiome changes, particularly in HF-associated disorders.}, }
@article {pmid42149452, year = {2026}, author = {Edelkamp, J and Lousada, MB}, title = {Viable vs. Nonviable Microbiota Evaluation of the Hair Follicle and Scalp Microbiome.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3031}, number = {}, pages = {243-259}, pmid = {42149452}, issn = {1940-6029}, mesh = {Humans ; *Hair Follicle/microbiology ; *Microbiota/genetics ; *Scalp/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; In Situ Hybridization, Fluorescence/methods ; Propidium/analogs &amp; derivatives/chemistry ; Azides/chemistry ; Microbial Viability ; Real-Time Polymerase Chain Reaction/methods ; }, abstract = {Various hair follicle (HF)-associated disorders, such as acne vulgaris, hidradenitis suppurativa, and alopecia areata, are linked to dysbiosis, an imbalance between resident and pathogenic microbes. Characterization of the HF and skin microbiome employs techniques such as 16S rRNA gene sequencing and metagenomic shotgun sequencing, with the latter providing comprehensive taxonomic and functional insights. However, relic DNA from dead microbes and free environmental DNA can persist in samples, meaning that metagenomic data does not exclusively reflect living microbiota. For functional studies on HF dysbiosis or to assess potential therapeutic interventions, we describe here how propidium monoazide (PMA) treatment can be performed before (metagenomics) sequencing to distinguish viable microbial communities. Furthermore, we exemplify qPCR and (fluorescent) in situ hybridization (ISH) of two alternative viability screening methods for the HF and scalp microbiome.}, }
@article {pmid42140743, year = {2026}, author = {Lee, JB and Baek, S and Kim, DK and Kwon, BE and Ahn, JS and Nagasaka, M and Davar, D and Park, H and Kim, H and Im, J and Yang, J and Yang, E and Shin, GH and Choi, S and Kwon, JE and Kim, JM and Kang, SY and Kim, Y and Park, SY and Kim, JH and Oh, HS and Chalita, M and Min, A and Cho, BC}, title = {Phase I trial of CJRB-101 plus pembrolizumab in patients with metastatic non-small cell lung cancer, head and neck squamous cell carcinoma and melanoma.}, journal = {Journal for immunotherapy of cancer}, volume = {14}, number = {5}, pages = {}, doi = {10.1136/jitc-2025-014702}, pmid = {42140743}, issn = {2051-1426}, mesh = {Humans ; *Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use ; Female ; Male ; Middle Aged ; *Carcinoma, Non-Small-Cell Lung/drug therapy/pathology ; Aged ; *Squamous Cell Carcinoma of Head and Neck/drug therapy/pathology ; *Melanoma/drug therapy/pathology ; *Lung Neoplasms/drug therapy/pathology ; Mice ; *Head and Neck Neoplasms/drug therapy/pathology ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology ; Animals ; Adult ; }, abstract = {BACKGROUND: Dysbiosis of gut microbiome leads to resistance to immunotherapy in various advanced solid tumors. CJRB-101 is a live biotherapeutic product consisting of a novel strain belonging to the species Leuconostoc mesenteroides. To modulate the tumor microenvironment, CJRB-101 was combined with pembrolizumab.<br><br>METHODS: Preclinical efficacy and mechanistic studies were performed using humanized non-small cell lung cancer (NSCLC) patient-derived xenograft (PDX) models. This is a multicenter, first-in-human, two-part, phase I, open-label study of CJRB-101 (1&#xd7;10[11]&#x2009;or 4&#xd7;10[11]&#x2009;colony forming unit (CFU)/day) plus pembrolizumab (200&#x2009;mg every three weeks (Q3W)) in advanced NSCLC, melanoma, and head and neck squamous cell carcinoma in both immune checkpoint inhibitor (ICI)-naive and ICI-refractory settings. The primary endpoint was to assess the dose-limiting toxicities (DLTs), adverse events, and preliminary activity of the combination treatment. Exploratory endpoints included stool metagenomics analysis and pharmacodynamics parameters.<br><br>RESULTS: In four PDX models, CJRB-101 with pembrolizumab demonstrated enhanced antitumor efficacy, showing a tumor growth inhibition (TGI) of 77.3% in the CJRB-101 monotherapy group and 61.9% in the combination group, which was significantly improved compared with pembrolizumab alone. A distinct M2-to-M1 repolarization was observed and validated in vitro. Notably, increased activation of cytotoxic T cells was observed, suggesting an immune-mediated antitumor mechanism of CJRB-101. A total of 42 patients were enrolled in the low-dose cohort (one capsule once a day; n=6) and high-dose cohort (two capsules two times a day, n=36). Metastatic NSCLC accounted for 86% (n=36) and 67% (n=28) of the patients were refractory to ICIs. None of the patients experienced DLT. In ICI-na&#xef;ve NSCLC (n=12) with programmed death-ligand 1 (PD-L1) >50%, the overall response rate (ORR) and disease control rate (DCR) were 58% and 75%, respectively. The ORR was 5% and DCR was 41% in the ICI-refractory NSCLC (n=22) with an ORR of 5% and DCR of 41%. After a median follow-up of 15.6 months and 8.9 months for ICI-na&#xef;ve and ICI-refractory NSCLC, the median progression-free survival was 9 months (95%&#x2009;CI 5.6 to not reached) and 1.8 months (95%&#x2009;CI 1.6 to 4.3), respectively. CJRB-101 plus pembrolizumab was well-tolerated, and none of the patients experienced grade >3 treatment-related adverse events.<br><br>CONCLUSIONS: Early clinical data show encouraging antitumor response of CJRB-101 plus pembrolizumab in ICI-na&#xef;ve metastatic NSCLC with PD-L1 >50%.<br><br>TRIAL REGISTRATION NUMBER: NCT05877430.}, }
@article {pmid42140896, year = {2026}, author = {Blázquez-Sánchez, P and Gunkel, J and Useini, A and Zlobin, A and Zakary, JD and Schöler, A and Graefe, N and Engelberger, F and Cantanhede, F and Frank, R and Zhao, Z and Zarei, A and Butenschön, E and Matysik, J and Zimmermann, W and Sträter, N and Sonnendecker, C and Künze, G}, title = {Computational engineering of the polyester hydrolase PHL7 for efficient poly(ethylene terephthalate) degradation in biocatalytic recycling processes.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42140896}, issn = {2041-1723}, support = {887913//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; ScaDS.AI//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; }, mesh = {*Polyethylene Terephthalates/metabolism/chemistry ; Biocatalysis ; *Protein Engineering/methods ; *Hydrolases/metabolism/genetics/chemistry ; Recycling ; Enzyme Stability ; Biodegradation, Environmental ; Molecular Dynamics Simulation ; Metagenome ; *Bacterial Proteins/metabolism/genetics/chemistry ; }, abstract = {Polyethylene terephthalate (PET) plastic waste causes serious environmental pollution due to insufficient recycling rates. Enzymatic PET depolymerization offers a sustainable recycling strategy, but limited stability and activity of current PET-degrading enzymes restrict practical implementation. Here, we engineer Polyester Hydrolase Leipzig 7 (PHL7), a PET hydrolase from a compost metagenome, to enhance its stability and catalytic performance under recycling-relevant conditions. Using Rosetta PROSS-based computational design combined with rational mutagenesis, we introduce up to 24 mutations, generating variants with melting temperatures of 88-95 °C and over 110-fold higher activity in 0.1 M phosphate buffer compared to the parent enzyme. Benchmarking shows that the best variants (R4M6, R4M9, and R4M10) match or exceed the performance of established engineered PET hydrolases, including ICCG and LCC-A2, and approach that of TurboPETase across multiple conditions. Under high substrate loadings, the PHL7-R4 variants degrade 75-78% of 10% (w/w) PET within 24 h at 65 °C, outperforming ICCG, while an optimized variant R4M10-H185Y achieves up to 84% degradation of 20% (w/w) PET. X-ray structure determination and molecular dynamics simulations reveal key stabilizing and activity enhancing mechanisms. These engineered PHL7 variants represent robust biocatalysts for scalable enzymatic PET recycling.}, }
@article {pmid42140961, year = {2026}, author = {Li, CW and Liao, HX and Callaway, RM and Su, ZY and Zou, JK and Liu, A and Wu, YR and Fang, YQ and Peng, SL and Chen, BM}, title = {Divergence among species with "good competitor" and "good cultivator" strategies promotes asymmetric facilitation among co-invaders.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-73076-2}, pmid = {42140961}, issn = {2041-1723}, support = {32471739//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023A1515010669//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; }, abstract = {Facilitative interactions among co-invaders may lead to invasional meltdown, accelerating non-native species accumulation and exacerbating ecological impacts over time. However, it remains unclear why certain non-native combinations promote facilitation while others do not, and may even constrain invasions. To address this question, we examine six invasive species in the Asteraceae family along two strategic dimensions: competitiveness and capacity to cultivate invader-promoting microbial communities. We then create experimental combinations to mix "good competitors" and "good cultivators" to varying degrees to form a "strategic divergence" gradient. We hypothesize greater strategic divergences generate more intense facilitations, whereas similar strategies generate inhibitions. Strategic divergence correlates with facilitation, but interactions are asymmetric: strong competitive suppressors of natives benefit from co-invasions with weaker competitors that cultivate favorable microbial environments but the performance of the latter are generally suppressed by the strong competitors. Metagenomic sequencing further indicates that good cultivators may promote facilitation by repelling pathogens (Ascomycota) and deterring microbes that might be exclusively beneficial for natives (Proteobacteria, Firmicutes, and Planctomycetota). Our results provide empirical evidence for the importance of strategic divergence among invasive species and offer a mechanistic basis for predicting which combinations of co-invading species might generate facilitation and which might result in inhibition.}, }
@article {pmid42141123, year = {2026}, author = {Han, S and Wu, Z and Wu, Y and Wang, Z and Qian, P and Chu, J and Li, J and Zhuang, J and Yang, X}, title = {Decoding the human gut bacterial plasmids in colorectal cancer.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10278-w}, pmid = {42141123}, issn = {2399-3642}, abstract = {Gut plasmids show heightened sensitivity to gut microenvironmental changes compared to their bacterial hosts. To explore their significance in colorectal cancer (CRC), we analyzed metagenomic data from 863 participants (312 CRC, 387 high-risk, 164 low-risk). Plasmid and bacterial profiles were characterized, along with trace elements and metabolites. Differential analysis, functional gene assessment (ARG, MGE, MRG, VFGB), random forest modeling, and structural equation modeling (SEM) were applied. In terms of overall abundance, plasmids in both the high-risk and CRC groups exhibited a decreasing trend. Gut plasmids significantly influenced the functional genes (ARG, MGE, MRG, VFGB) of their bacterial hosts. Six key bacterial hosts (Enterobacterales, Bucrkholderiales, Hyphomicrobiales, Lactobacillales, Bacteroidales, Campylobacterales) and 12 plasmid markers were identified. The plasmid-based model effectively predicted CRC risk. SEM revealed that trace elements (e.g., Ni), metabolites (e.g., 5-Hydroxytryptophol), and host bacteria (e.g., Campylobacterales, Enterobacterales) predominantly exerted negative effects on most plasmids, whereas Ni exhibited a positive influence on plasmids NZ_CP013564.1, NZ_CP024312.1, and NZ_CP48284.1. We characterized the composition of gut plasmids and their bacterial hosts, explored the impacts of gut plasmids on bacterial functionality, and mapped multi-omics interaction networks linking plasmids, hosts, and metabolic features.}, }
@article {pmid42141277, year = {2026}, author = {Jiao, S and Pan, H and García-Palacios, P and Tu, H and Zhang, Y and Liu, Y and Gao, H and Chen, B and Peng, Z and Chen, S and Qi, J and Liang, C and Li, X and Wang, Y and Jin, C and Gao, M and Liu, J and Wang, Y and Zhao, J and Jiang, L and Romero, F and Banerjee, S and Yang, Y and Lu, Y and Delgado-Baquerizo, M and van der Heijden, MGA and Wei, G}, title = {Agricultural soil microbiomes are structurally and functionally more resistant to warming than adjacent natural ecosystems.}, journal = {Nature food}, volume = {}, number = {}, pages = {}, pmid = {42141277}, issn = {2662-1355}, abstract = {Agricultural soil microbiomes experience frequent disturbance from intensive management and may therefore be better equipped to withstand climate warming than microbiomes in undisturbed natural soils. Here we test this by combining a continental-scale warming microcosm experiment across 100 paired agricultural-natural sites with a global meta-analysis and three microbiome manipulation experiments (microbial suspensions, cross-inoculation and synthetic communities). Agricultural soils showed a higher resistance of soil multifunctionality to warming than natural soils, consistent across the meta-analysis. Resistance of microbial community composition was the strongest predictor of functional resistance and was confirmed in artificial soils inoculated with agricultural versus natural microbial suspensions. Introducing soil microbiomes from agricultural ecosystems into previously undisturbed natural soils enhanced functional resistance to warming. Metagenomic analysis revealed that microbial life-history strategies play a crucial role in regulating the resistance of soil microbial community to warming, with communities dominated by stress-tolerant strategies conferring significantly stronger resistance. Our work highlights the potential of microbiome engineering to strengthen ecosystem functioning under climate change.}, }
@article {pmid42141292, year = {2026}, author = {Ghori, R and Ramadoss, D and Ramsland, PA and Blanch, EW and Ammanabrolu, BS}, title = {Comparative metagenomic analysis of microbial communities: unravelling microbial communities from the great Rann of Kachchh and coastal saltpans, Gujarat, India.}, journal = {Extremophiles : life under extreme conditions}, volume = {30}, number = {1}, pages = {}, pmid = {42141292}, issn = {1433-4909}, mesh = {*Microbiota ; India ; *Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Salinity ; *Metagenome ; }, abstract = {Hypersaline environments exhibit extreme physiochemical conditions yet support diverse microbial communities. These communities are not only ecologically important but also possess substantial potential for biotechnological exploitation. In this study, we employed a comparative metagenomic approach to assess microbial diversity using two distinct methodologies: (1) direct DNA extraction from raw sediment, and (2) DNA extraction following halophilic enrichment in selective media. Sediment samples were collected from multiple sites and pooled together within the Rann of Kachchh and close-by saltpans and were analysed using 16S rRNA sequencing coupled with bioinformatics pipelines. The results revealed pronounced differences in microbial community composition between the two approaches. Raw sediment samples exhibited significantly higher alpha diversity, with dominant taxa including Halobacterota, Cyanobacteria, and Desulfobacterota, with a substantial proportion of unclassified genera. In contrast, enriched samples were dominated by fast-growing, culturable genera such as Halobacterium, Alkalibacillus, and Candidatus haloredivivus. Principal Coordinate Analysis (PCoA) of beta diversity demonstrated distinct clustering between raw and enriched communities, even within samples from the same sites, underscoring the selective bias introduced by enrichment procedures. These findings emphasise that the methodological choice strongly influences the observed microbial diversity. The aim of this study was to compare microbial community composition in raw hypersaline sediments and enrichment cultures using metagenomic sequencing, to evaluate how enrichment selectively favours specific halophilic taxa. This comparative approach allows identification of the microbial groups that rapidly proliferate under controlled hypersaline conditions, thereby complementing direct environmental sequencing. By integrating both direct and enrichment-based metagenomic approaches, a more comprehensive understanding of microbial community structure in hypersaline environments can be achieved.}, }
@article {pmid42141512, year = {2026}, author = {Li, Y and Sun, J and Dai, Z and Jin, LN and Chen, Z and Lin, D and Zhu, L}, title = {Antibiotic Metabolites Are an Overlooked Driver of Resistance Dissemination in Plant Systems.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c04146}, pmid = {42141512}, issn = {1520-5851}, abstract = {Antibiotic pollution in agroecosystems is widely recognized, yet the risks posed by their metabolites remain insufficiently addressed. Using lettuce as a model, we investigated how tetracycline (TC) and its metabolites, anhydrotetracycline (ATC) and epitetracycline (ETC), contribute to the dissemination of antibiotic resistance genes (ARGs). TC primarily accumulated in roots and declined during translocation, whereas ATC exhibited greater persistence and became the predominant residue through in planta transformation. At environmentally relevant concentrations (≤0.1 mg·L[-1]), ATC more effectively expanded the mobilizable resistome than the parent compound by inducing reactive oxygen species, activating the SOS response, increasing membrane permeability, and promoting RP4 plasmid conjugative transfer. These processes facilitated the acquisition of multidrug resistance and the colonization of plant tissues by human pathogens, including Stenotrophomonas maltophilia and Pseudomonas aeruginosa, thereby increasing ARG burdens in both rhizosphere and phyllosphere compartments. Metagenomic analysis further confirmed the coselection of nontetracycline ARGs, such as aph3'-I and catB, and the enrichment of efflux systems (acr/emr) in pathogenic bacteria. Our findings challenge the parent-compound-centered paradigm of antibiotic risk assessment by identifying ATC as a key high-risk driver of ARG dissemination in food plants and highlighting the need to incorporate transformation products into future management strategies.}, }
@article {pmid42141881, year = {2026}, author = {Nagy, A and Erdélyi, K and Molnár, Z and Lőrincz, RB and Nagy, O and Koroknai, A and Csonka, N and Kerényi, K and Forgách, P and Horváth, E and Soltész, Z and Nagy, G and Takács, M and Barcsay, E and Szomor, K and Tóth, GE and Cadar, D}, title = {Hungary as a source of West Nile virus diversity and spread in Europe: insights from the 2024 transmission season.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {31}, number = {16}, pages = {}, pmid = {42141881}, issn = {1560-7917}, mesh = {Humans ; Hungary/epidemiology ; *West Nile virus/genetics/isolation &amp; purification/classification ; *West Nile Fever/epidemiology/transmission/virology ; Animals ; Phylogeny ; Phylogeography ; *Culex/virology ; Seasons ; Birds/virology ; Europe/epidemiology ; High-Throughput Nucleotide Sequencing ; Genome, Viral ; Bayes Theorem ; Incidence ; Male ; Mosquito Vectors/virology ; Middle Aged ; }, abstract = {BACKGROUNDWest Nile virus (WNV) has become established across Europe, with Hungary serving as a key transmission hub since 2004. Following reduced activity during 2020-22, the 2024 season marked a resurgence with the largest geographical distribution ever recorded in Europe.AIMTo analyse the 2024 WNV transmission season in Hungary using a One Health approach and characterise circulating strains within the European phylogeographic context using comprehensive genomic surveillance.METHODSComplete and near-complete genome sequencing was performed on 55 specimens from 38 humans, 15 birds and two Culex pipiens mosquito pools using amplicon-based next-generation sequencing. Phylogeographic analysis incorporated 637 European WNV genome sequences (2004-24) with time-scaled Bayesian phylogenetic reconstruction and continuous spatial diffusion modelling.RESULTSHungary reported 113 human WNV cases in 2024 (n = 111 autochthonous, 2 imported), a 3.7-fold increase from 2023 (incidence: 1.16 vs 0.31 per 100,000 population). Neuroinvasive disease predominated (92%, n = 104) with a 7.9% case fatality rate. All 55 sequenced strains belonged to WNV lineage 2. Phylogeographic analysis revealed Hungary's central role in European WNV dissemination since 2004, with multiple introductions and local diversification across distinct clades. Continuous spatial modelling identified Hungary as a persistent transmission hub with bidirectional viral flow to neighbouring countries, contributing to northward expansion.CONCLUSIONHungary remains a critical WNV transmission hub in Central Europe with established endemicity of multiple lineage 2 clades. The analysis highlights Hungary's role as both a recipient and major source of European WNV diversity, emphasising the need for coordinated surveillance and climate-adapted preparedness strategies.}, }
@article {pmid42142571, year = {2026}, author = {Malešević, M and Matijašević, D and Kljajević, N and Gardijan, L and Stanovčić, S and Jovčić, B and Novović, K}, title = {Seasonal Shifts in the Belgrade Airborne Resistome and Virulome: A Metagenomic Perspective.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124700}, doi = {10.1016/j.envres.2026.124700}, pmid = {42142571}, issn = {1096-0953}, abstract = {The atmosphere is a dynamic reservoir for microorganisms and antimicrobial resistance genes (ARGs), yet the seasonal interplay of microbial communities, resistance and virulence determinants with environmental conditions remains poorly characterized, particularly in polluted urban areas. This study presents year-round (summer 2024-spring 2025) shotgun metagenomic monitoring of airborne microbiomes across the Belgrade metropolitan area, a European air pollution hotspot. While community composition shifted seasonally, with an enrichment of Bacillota in autumn and stress-tolerant genera in winter, opportunistic pathogens including Pseudomonas and Acinetobacter were detected year-round. The airborne resistome and mobilome exhibited pronounced seasonal restructuring, with winter showing the highest diversity of resistance genes and plasmid-associated sequences. Mobility-associated genes, including unique toxins and plasmid maintenance systems, were also most prominent in winter. Pathogen-host interaction profiling revealed a functional shift from respiratory and colonization-associated Gram-positive taxa such as Streptococcus pneumoniae and Staphylococcus aureus in autumn to enteric pathogens like Escherichia coli and Salmonella enterica in winter. Network analysis showed that winter formed the densest co-occurrence network, suggesting enhanced potential for co-selection of resistance and virulence traits. Specific plasmid-associated ARGs displayed seasonal patterns, with blaCTX-M linked to multiple plasmids in summer, while blaTEM and aph genes were more prominent in winter. Our findings illustrate that seasonal variations in the airborne genetic landscape are linked to environmental factors and fluctuating reservoirs of clinically relevant resistance and virulence determinants. This highlights the need for integrated longitudinal aerobiome surveillance to understand its implications for public health within the One Health framework.}, }
@article {pmid42142769, year = {2026}, author = {Zhang, Z and Hu, Y and Zu, G and Dang, Q and Sun, X and Wu, Y}, title = {Molecular mechanisms of dissolved organic matter transformation and microbial interactions in composting.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134880}, doi = {10.1016/j.biortech.2026.134880}, pmid = {42142769}, issn = {1873-2976}, abstract = {Industrial composting of food waste digestate (FW) and chicken manure (CM) involves distinct dissolved organic matter (DOM) transformation pathways and different microbial interaction mechanisms. This study used Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) and shotgun metagenomics (for microbial community profiling) to compare interactions between DOM and microbial communities in the two composting processes. Results show that FW is dominated by labile organic matter (OM). This dominance increases the degree of DOM oxidation and the relative abundance of CHO. This labile carbon environment selected for a simplified microbial community dominated by key genera, yet facilitated active potential molecular transformations (PMTs) of DOM. These PMTs were characterized by an increase in thermodynamically limited processes (TLPs), indicating a carbon source-oriented pathway. In contrast, PMTs of DOM in CM favor thermodynamically favorable processes (TFPs), exhibiting higher aromaticity and CHOS abundance. The microbial community remains highly diverse, strongly connected, and functionally complementary, forming a synergistic network that supports coupled nitrogen-sulfur transformations. Environmental factors differentially regulate the two systems. This study indicates that the initial chemical properties of the composting feedstock fundamentally shape the PMTs of DOM pathways and the microbial communities they drive, providing an important theoretical basis for optimizing organic solid waste resource recovery processes.}, }
@article {pmid42142806, year = {2026}, author = {Samuelsen, &#xd8; and López-Causapé, C and Aarestrup, FM and Bortolaia, V and Brouwer, MSM and Cantón, R and Egli, A and Grad, YH and Hamprecht, A and Haussler, S and Holt, KE and Hopkins, KL and Howden, BP and Jeannot, K and Kahlmeter, G and Köser, CU and Mathers, AJ and Naas, T and Pournaras, S and Ruppé, E and Schön, T and Stoesser, N and Turnidge, J and Werner, G and Wright, GD and Giske, CG and Oliver, A}, title = {The role of whole genome sequencing in antimicrobial susceptibility prediction of bacteria: 2025 update from the EUCAST Subcommittee.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2026.05.012}, pmid = {42142806}, issn = {1469-0691}, abstract = {SCOPE: The 2017 European Committee on Antimicrobial Susceptibility Testing (EUCAST) subcommittee report on the role of Whole Genome Sequencing (WGS) in Antimicrobial Susceptibility Testing (AST) concluded that WGS antimicrobial susceptibility prediction (WGS-ASP) was not a sufficiently robust alternative to AST to guide clinical decision making at that stage and that more evidence was required [1]. Since then, the use of WGS, bioinformatic tools, machine learning (ML)/artificial intelligence (AI), databases, and prediction approaches has greatly expanded, along with an increased knowledge of resistance mechanisms and their contribution to antimicrobial susceptibility. In response, a new EUCAST ad hoc subcommittee was established in 2024 to review the literature, with the aim of assessing the current potential and limitations of WGS-ASP.<br><br>METHODS: As in the previous report, the subcommittee reviewed the literature on a 'by organism' basis but expanded the list to also include enterococci, Haemophilus influenzae and Bacteroides fragilis in addition to those already included in the first version: Enterobacterales, Pseudomonas aeruginosa, Acinetobacter baumannii, Neisseria gonorrhoeae, Staphylococcus aureus, Streptococcus pneumoniae, Clostridioides difficile, and Mycobacterium tuberculosis. Additional sections were included to cover advances in metagenomics, other omics technologies and ML/AI. The full report was compiled and reviewed by all subcommittee members before public consultation in November 2025.<br><br>Significant progress has been achieved in WGS-ASP, with growing evidence supporting its ability to distinguish wild-type from non-wild-type isolates and, consequently, susceptible from resistant strains, particularly for M. tuberculosis and when clinical breakpoints align with the ECOFF. Despite these advances, important challenges remain before WGS-ASP can be adopted as a clinical decision-making tool. Addressing these gaps will require integrated phenotypic and genotypic surveillance to strengthen the evidence base for complex resistance mechanisms and newer antimicrobial agents, alongside comparative assessments that consider both ECOFF and clinical breakpoints. The analyses will require reference method phenotypic AST and high-quality genomic data. It is critical to ensure that datasets reflect the target populations and encompass the full spectrum of antimicrobial susceptibility, while developing unified interpretation frameworks and harmonized bioinformatics tools to standardize outputs. Robust external quality assessment schemes will be essential for clinical validation, and emerging technologies such as AI and ML offer promising avenues to enhance predictive accuracy. Finally, improvements in cost and turnaround time, coupled with evaluations of setting-specific cost-effectiveness, will be key to enabling practical implementation of WGS-ASP.}, }
@article {pmid42143007, year = {2026}, author = {Zhang, XD and Shen, XN and Liu, CX and Liu, ZH and Ao, X and Che, TY and Ran, TJ and Li, HL and Zhang, Y and Zhou, CH and Zou, DW}, title = {Analysis of gut microbiome dynamics in patients with type 1 autoimmune pancreatitis before and after glucocorticoid treatment.}, journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pan.2026.05.002}, pmid = {42143007}, issn = {1424-3911}, abstract = {BACKGROUND: Type 1 autoimmune pancreatitis (AIP) is a rare inflammatory pancreatic disease. Emerging evidence suggests that gut microbiota dysbiosis may contribute to the pathogenesis of type 1 AIP. However, no study has systematically characterized gut microbiota alterations before and after glucocorticoid treatment in patients with type 1 AIP.<br><br>METHODS: Fecal samples were collected from 45 healthy controls (HC), 61 patients with type 1 AIP before glucocorticoid treatment, and 27 patients after glucocorticoid treatment for metagenomic sequencing. To investigate the potential role of Streptococcus anginosus in the development of type 1 AIP, heat-killed Streptococcus anginosus was administered by oral gavage in an AIP mouse model.<br><br>RESULTS: Significant differences in both &#x3b1;-diversity and &#x3b2;-diversity were observed among HC and the pre- and post-treatment groups. Compared with the HC group, the pre-treatment group showed increased abundances of Streptococcus, Streptococcus anginosus, and Streptococcus salivarius, along with decreased abundances of Blautia and Dorea formicigenerans. Moreover, the abundances of Streptococcus and Streptococcus anginosus were reduced in the post-treatment group. In the AIP mouse model, oral gavage with heat-killed Streptococcus anginosus significantly increased the pancreatic pathological injury score.<br><br>CONCLUSIONS: Compared with the HC group, the pre-treatment group showed increased abundances of Streptococcus and Streptococcus anginosus, which were reduced in the post-treatment group. In addition, heat-killed Streptococcus anginosus exacerbated pancreatic injury in the AIP mouse model.}, }
@article {pmid42143215, year = {2026}, author = {Martínez, S and Cerdeiras, MP and Douterelo, I and Ijaz, UZ}, title = {Biofilm and sediment phases as key components of microbial community dynamics within secondary drinking water distribution systems.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05149-7}, pmid = {42143215}, issn = {1471-2180}, support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; }, abstract = {BACKGROUND: Secondary drinking water distribution systems (SDWDS), particularly rooftop storage tanks, are critical components of water supply infrastructure in many regions, yet the ecological processes governing microbial community development within these systems remain poorly characterized. Here we present a year-long, phase-resolved metagenomic study of an operational full-scale SDWDS in Uruguay to assess how environmental conditions and surface materials are associated with microbiome dynamics across bulk water, biofilm and sediment phases. We integrated amplicon sequencing, whole-genome sequencing (WGS) metagenomics, culture-based microbiology and physicochemical analyses over a one-year period.<br><br>RESULTS: Microbial communities associated with biofilm and sediment phases consistently exhibited higher richness and diversity than bulk water, with marked seasonal variation. Biofilms formed on concrete and polyethylene surfaces followed distinct successional trajectories, indicating material-associated patterns in community development. Seasonal increases in temperature were associated with greater similarity in community composition across phases, while functional richness remained comparatively stable over time. Functional pathways related to energy production, stress response, and antibiotic resistance showed phase- and time-dependent enrichment, particularly in mature biofilms. Across the system, Proteobacteria, Actinobacteriota, and Bacteroidota were persistent taxa. Temperature and pH were the primary variables associated with temporal shifts in water-phase microbial communities, with chlorine residuals contributing to additional variation.<br><br>CONCLUSIONS: Together, these findings provide in situ ecological insight into microbial succession and phase-specific community dynamics in drinking water storage systems, highlighting the importance of long-term observations in real-world engineered environments.}, }
@article {pmid42143222, year = {2026}, author = {Yao, Y and Li, Z and Luo, L and Lu, X and Wang, H}, title = {Central nervous system infection associated with Human herpesvirus 7 presenting with predominant persecutory delusions as initial psychiatric manifestations after allogeneic stem cell transplantation: a rare case report with diagnostic and therapeutic implications.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13040-z}, pmid = {42143222}, issn = {1471-2334}, support = {82300248//National Natural Science Foundation of China/ ; 82100143//National Key Research and Development Program of China grant 2022YFC2304600/ ; }, abstract = {BACKGROUND: Human Herpesvirus 7 (HHV-7)-associated central nervous system (CNS) infection is an extremely rare complication following allogeneic hematopoietic stem cell transplantation (allo-HSCT), with no prior reports of initial presentation dominated by psychiatric symptoms.<br><br>CASE PRESENTATION: We report a unique case of a 14-year-old female with high-risk acute lymphoblastic leukemia (ALL) who developed acute persecutory delusions and auditory hallucinations as the sole initial manifestations 54 days post-allo-HSCT. Brain magnetic resonance imaging (MRI) revealed multifocal lesions in the right frontal lobe and bilateral parieto-occipital regions. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) confirmed the presence of HHV-7, establishing the diagnosis of HHV-7-associated CNS infection. The patient achieved complete clinical and radiological remission following a comprehensive treatment regimen combining antiviral therapy, glucocorticoids, intravenous immunoglobulin (IVIG), and antipsychotic medication.<br><br>CONCLUSIONS: This is the first documented case of HHV-7-associated CNS infection post-allo-HSCT presenting with persecutory delusions as the initial symptom, expanding the clinical spectrum of HHV-7-related CNS complications in immunocompromised hosts. Our findings emphasize the importance of considering atypical viral encephalitis in the differential diagnosis of acute psychiatric symptoms post-allo-HSCT and highlight the value of early neuroimaging and CSF mNGS for timely diagnosis and targeted intervention.}, }
@article {pmid42143235, year = {2026}, author = {Zhong, M and Zhang, H and Yan, H and Li, Y and Zhu, D and Hu, S and Tan, L and Peng, L and Xie, X and Lan, G}, title = {Clinical characteristics, diagnosis and prognosis of Talaromyces marneffei pneumonia in kidney transplant recipients: a retrospective study.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13557-3}, pmid = {42143235}, issn = {1471-2334}, support = {2025JJ70074//Natural Science Foundation of Hunan Province/ ; 2024JJ2088//Natural Science Foundation of Hunan Province/ ; 2023JJ30755//Natural Science Foundation of Hunan Province/ ; 82370760//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Talaromyces marneffei (TM) is an opportunistic dimorphic fungus that increasingly affects immunocompromised individuals, including kidney transplant recipients. However, data on the clinical features, diagnosis, treatment, and prognosis of Talaromyces marneffei pneumonia (TMP) in this population remain limited.<br><br>METHODS: This retrospective study included 8 HIV-negative kidney transplant recipients diagnosed with TMP at the Second Xiangya Hospital of Central South University between January 2015 and January 2025. Clinical data, including demographic characteristics, clinical manifestations, imaging findings, microbiological results, treatment regimens and outcomes, were collected and analyzed.<br><br>RESULTS: The cohort consisted of 7 males and 1 female with a mean age of 45.12&#x2009;&#xb1;&#x2009;9.03 years. The median time from transplantation to TMP onset was 356.5 days (IQR, 302.75-771.75). All patients presented with fever, and chest CT showed diverse pulmonary lesions, including nodules and patchy opacities. Metagenomic next-generation sequencing (mNGS) was the primary diagnostic tool, identifying TM in 7 cases (87.5%), with a mean diagnostic time of 5&#x2009;&#xb1;&#x2009;2.56 days, while conventional culture was positive in only 3 cases. All patients received antifungal therapy, mainly amphotericin B for induction followed by oral azoles for maintenance. Immunosuppressive regimens were adjusted during treatment. All patients achieved clinical cure without severe adverse events, and graft function remained stable.<br><br>CONCLUSIONS: TMP is a rare but serious infection in kidney transplant recipients receiving long-term immunosuppression. Early diagnosis using mNGS combined with conventional culture can improve detection efficiency. Timely antifungal therapy with amphotericin B followed by azole maintenance, along with careful adjustment of immunosuppressants, is associated with favorable prognosis.}, }
@article {pmid42143297, year = {2026}, author = {Feng, J and Wang, Y and Han, J and Li, J and Xu, W and Hu, X}, title = {Gestational psittacosis: a systematic review of clinical manifestations and outcomes.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13575-1}, pmid = {42143297}, issn = {1471-2334}, support = {2025359//Scientific Research Project of Chengdu Municipal Health Commission/ ; 2025GZX002//Primary Health Care Research Project of Ganzi County People's Hospital/ ; 2024-YF09-00021-SN//Key Research and Development Support Program of Chengdu Science and Technology Bureau/ ; SCKFKY20250217//2025 Scientific Research Project of Sichuan Rehabilitation Medical Association/ ; }, abstract = {BACKGROUND: Gestational psittacosis is a rare but severe zoonotic infection caused by Chlamydia psittaci. This systematic review aims to evaluate the clinical characteristics, diagnostic challenges, therapeutic interventions, and maternal-fetal outcomes of this condition.<br><br>METHODS: A systematic search was conducted in PubMed, Embase, Web of Science, CNKI, and Wanfang Data from inception to October 31, 2025. Two investigators independently performed study selection and data extraction encompassing maternal demographics, clinical manifestations, laboratory findings, diagnostic modalities, antimicrobial regimens, and maternal-fetal outcomes.<br><br>RESULTS: A total of 32 cases from 30 publications were included. The median maternal age was 29 years (IQR: 26-32), and the median gestational age at diagnosis was 26.5 weeks (IQR: 21-30). All patients presented with fever (32/32, 100%), and common symptoms included headache (17/32, 53%), cough (15/32, 47%), and dyspnea (15/32, 47%). Severe disease was frequent: 66% (21/32) required intensive care unit (ICU) admission, 34% (11/32) required endotracheal intubation, and maternal mortality was 13% (4/32). Thrombocytopenia (26/32, 81%), hepatic dysfunction (27/32, 84%), renal impairment (18/32, 56%), and disseminated intravascular coagulation (DIC) (15/32, 47%) were the most prominent laboratory abnormalities. Diagnostic approaches evolved from serology to molecular methods. Recent studies have demonstrated the potential value of metagenomic next-generation sequencing (mNGS) in diagnosis, but further research is needed to confirm its clinical utility. The overall fetal and neonatal mortality was 68% (21/31 with available data), primarily due to stillbirth, spontaneous abortion, or therapeutic induction. These estimates reflect outcomes among reported cases and may overestimate true population-level risk.<br><br>CONCLUSION: Gestational psittacosis is a rare but life-threatening infection associated with substantial maternal morbidity and a high risk of fetal loss, although these outcomes may be influenced by publication bias. mNGS has facilitated earlier diagnosis in recent case reports; however, comparative performance data for gestational psittacosis remain limited.<br><br>TRIAL REGISTRATION: PROSPERO, CRD420251275911 (Registered 30 December 2025).<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid42140478, year = {2026}, author = {Mehne, ZS and Honarjou, E and Kahdouee, MK}, title = {Chronic Infections of the Spine: A Systematic Review of Microbial Etiologies, Diagnostic Approaches, and Treatment Outcomes.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108769}, doi = {10.1016/j.ijid.2026.108769}, pmid = {42140478}, issn = {1878-3511}, abstract = {BACKGROUND: Chronic spinal infections are uncommon but potentially devastating conditions, frequently associated with delayed diagnosis, heterogeneous microbiology, and complex management. Existing evidence remains fragmented, and a comprehensive synthesis of microbial etiologies, diagnostic approaches, and treatment outcomes is needed.<br><br>METHODS: A systematic review was conducted in accordance with PRISMA guidelines. PubMed, Scopus, Web of Science, and Embase were searched for studies published between October 2015 and September 2025 involving adult patients with chronic spinal infections. Data were extracted on causative pathogens, diagnostic modalities, medical and surgical interventions, and clinical outcomes. Risk of bias was assessed using standardized methodological criteria.<br><br>RESULTS: Fifty-five studies comprising 3,036 patients were included. Mycobacterium tuberculosis was the most frequently identified pathogen, followed by Brucella species and pyogenic bacteria. Metagenomic next-generation sequencing (mNGS) demonstrated the highest diagnostic yield, with reported sensitivities ranging from 82% to 92%, and showed particular utility in detecting mixed or atypical infections. Biomarker-based and RNA-derived assays demonstrated promising performance in differentiating tuberculous spondylitis from other spinal conditions. Surgical interventions, including minimally invasive and combined approaches, were associated with high fusion and neurological recovery rates.<br><br>CONCLUSIONS: Chronic spinal infections show marked microbiological heterogeneity. Integrating molecular diagnostics with tailored surgical and antimicrobial strategies may improve diagnostic accuracy and clinical outcomes.}, }
@article {pmid42140665, year = {2026}, author = {Vollmers, J and Correa Cassal, M and Kaster, AK}, title = {Cultivation-independent high-quality microbial genome reconstruction from environmental samples with midi-metagenomics.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.280099.124}, pmid = {42140665}, issn = {1549-5469}, abstract = {Since the majority of microbial organisms still evade cultivation attempts, genomic insights into many taxa are limited to cultivation-independent approaches. However, current methods of metagenomics and single-cell genome sequencing have individual drawbacks, which can limit the quality as well as completeness of the reconstructed genomes. Current attempts to combine both approaches still use whole genome amplification techniques which are prone to bias. Here, we propose a novel approach for the purpose of genome reconstructions that utilizes the potential of cell sorting for targeted enrichment and depletion of different cell types to create distinct cell fractions with sufficient DNA amounts, circumventing amplification. By distributing sequencing efforts over these fractions as well as the original sample, coassemblies become highly optimized for coabundance variation based binning approaches. "Midi-metagenomics" enables accurate metagenome-assembled genome (MAG) reconstruction from individual sorted samples with higher quality than coassembly and binning of multiple distinct samples and therefore improves analyses of the so-called "microbial dark matter".}, }
@article {pmid41915167, year = {2026}, author = {Venetsianou, NK and Paragkamian, S and Kalaentzis, K and Loukas, A and Damianou, C and Lagani, V and Jensen, LJ and Pafilis, E}, title = {LLM-Assessed Relatedness of Microbiome Study Descriptions Aligns more Strongly with Functional than with Taxonomic Profile Similarity.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {41915167}, issn = {1432-184X}, abstract = {UNLABELLED: Microbiome studies reveal the taxonomic and functional composition of microbial communities inhabiting many diverse environments. Comprehensive microbiome repositories, such as MGnify, organize data into studies, each consisting of multiple sequencing runs or assemblies and accompanying metadata. This structure enables integrative, large-scale, cross-study analyses, leading to broader insights across ecosystems, hosts, and experimental contexts. Despite extensive microbiome research, methods for defining similarity between studies and validating those similarity metrics, remain insufficiently established, especially for large-scale analyses. To address this, we evaluate whether taxonomic and functional similarities from MGnify can serve as reliable indicators of study relatedness between study pairs, testing multiple metrics against conceptual relatedness (e.g., shared environments, goals, or methods). To scale validation, we introduce a framework that applies a Large Language Model (LLM) to study descriptions, categorizing study pairs by relatedness. Our results show that functional similarity correlates more strongly with LLM-inferred study relatedness than taxonomic similarity, highlighting both the promise and limitations of current metrics. Via the above, we demonstrate the value of combining microbial profiles with LLM-driven semantic reasoning to navigate the expanding landscape of metagenomic research.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00248-026-02730-5.}, }
@article {pmid42134371, year = {2026}, author = {Govender, KN and Street, TL and Sanderson, ND and Leach, L and Morgan, M and Eyre, DW}, title = {Rapid diagnosis of common, undetected, and uncultivable bloodstream infections from positive blood cultures using Oxford Nanopore sequencing: a metagenomic pipeline analysis.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101333}, doi = {10.1016/j.lanmic.2025.101333}, pmid = {42134371}, issn = {2666-5247}, abstract = {BACKGROUND: Metagenomic sequencing can potentially transform clinical microbiology by enabling rapid pathogen identification and antimicrobial resistance (AMR) prediction in critically ill patients with bloodstream infections. However, the clinical use of metagenomic sequencing has been constrained by its speed, accuracy, and technical feasibility. Our aim was to develop and evaluate a direct-from-positive blood culture workflow using Oxford Nanopore sequencing that overcomes these limitations and delivers rapid, accurate results.<br><br>METHODS: In this metagenomic pipeline analysis, 211 positive (130 aerobic and 81 anaerobic) and 62 negative (30 aerobic and 32 anaerobic) randomly selected blood cultures were processed from Oxford University Hospitals for comparing species identification, AMR detection, and time-to-result against standard culture-based diagnostics performed by the hospital's routine microbiology laboratory. Species prediction was performed using Kraken2 with a comprehensive standard database, applying heuristic and random forest classification models. Additionally, we benchmarked AMR classification tools and databases, including ResFinder, CARD, and NCBI AMRFinderPlus.<br><br>FINDINGS: Across all samples, our method achieved 97% sensitivity and 94% specificity for species identification compared with that of routine culture and matrix-assisted laser desorption ionisation time-of-flight-based diagnostics; both sensitivity and specificity increased to 100% after adjudication of plausible additional infections. We detected 19 additional infections (13 polymicrobial, five previously unidentifiable, and one in a culture-negative sample) and delivered species identification results within 3 h 20 min (IQR 3 h 7 min-3 h 27 min), approximately 10 h earlier than routine diagnostic methods. For the ten most common clinically relevant pathogens, our method yielded AMR results 20 h earlier than current antimicrobial susceptibility testing, with an overall sensitivity of 88% and specificity of 93%. Performance varied by species. For Staphylococcus aureus, the AMR prediction sensitivity was 100% and specificity was 99%, and for Escherichia coli, the prediction sensitivity was 91% and specificity was 94%.<br><br>INTERPRETATION: These findings show that metagenomic sequencing has the potential to rapidly and comprehensively detect pathogens and AMR in bloodstream infections. Integration into clinical practice could help to close diagnostic gaps, reduce empirical antibiotic use, and enable rapid targeted treatment. Nonetheless, improvements in AMR prediction for some species and drugs, along with further multisite validation, are required before clinical implementation.<br><br>FUNDING: National Institute for Health Research (NIHR) Oxford Biomedical Research Centre.}, }
@article {pmid42134579, year = {2026}, author = {Zhao, C and Hu, Z and Wang, D and Xu, M and Hao, Z and Fu, C and Zhang, J and Zhuang, L}, title = {Metagenomic insights into the enhancement of doxycycline hydrochloride removal in constructed wetlands under moderate lead stress.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134878}, doi = {10.1016/j.biortech.2026.134878}, pmid = {42134579}, issn = {1873-2976}, abstract = {Constructed wetlands (CWs) serve as an important ecological barrier preventing contaminated water from entering surface waters and are frequently exposed to antibiotic-heavy metal co-contamination under real operating conditions. However, how heavy metal stress regulates antibiotic removal through microbial processes in CWs remains poorly understood. Here, CWs subjected to doxycycline hydrochloride (DOX) and lead (Pb) co-contamination were established to elucidate the effects of different Pb stress levels on DOX removal performance and the underlying microbial mechanisms. The results showed that DOX removal was maximized under moderate Pb stress (1 mg/L), reaching a highest removal efficiency of 95.8%. Consistent toxicity responses were observed, with moderate Pb exposure significantly reducing effluent biotoxicity, alleviating plant stress, and improving overall system stability. Mass balance analysis demonstrated that microbial transformation dominated DOX removal, accounting for over 79% of total removal. Metagenomic analyses further revealed the underlying microbial mechanisms, showing that moderate Pb stress reshaped microbial community structure, promoted the enrichment of key functional microorganisms, and increased the abundance of DOX degradation-related functional genes. Representative functional taxa included Sphingomonas, Propionibacterium, and Candidatus Woesearchaeota archaeon. In contrast, high Pb stress (10 mg/L) imposed strong metal toxicity that suppressed the activity and diversity of core functional microorganisms, resulting in reduced DOX degradation capacity accompanied by toxicity accumulation. Collectively, this study clarifies how heavy metal stress regulates antibiotic removal through microbial pathways in CWs, and provide a reference for understanding CWs performance under co-contamination.}, }
@article {pmid42134580, year = {2026}, author = {He, J and Xiang, B and Xu, W and Pan, Z}, title = {Comparative study on microbial mechanisms of denitrification failure in AAO process and air-lift internal circulation process under ultra-low C/N ratios.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134881}, doi = {10.1016/j.biortech.2026.134881}, pmid = {42134580}, issn = {1873-2976}, abstract = {Denitrification failure under low-carbon conditions limits biological nitrogen removal. This study compared the recovery performance of a conventional anaerobic-anoxic-oxic (AAO) process and an air-lift internal circulation reactor (AICR) after carbon supplementation, following long-term operation at ultra-low C/N (≈1). Batch experiments showed that the AICR initiated denitrification more rapidly than the AAO. At C/N = 7, the AICR removed 62% of nitrate nitrogen (NO3[-]-N) within 4.5 h, while the AAO removed only 43%. After 10 h, removal efficiencies reached 78% in the AICR and 69% in the AAO. The AICR also had higher adenosine triphosphate (ATP) levels and greater denitrification enzyme activities. Quantitative polymerase chain reaction (qPCR) confirmed that nirS and nosZ copy numbers in the AICR were approximately twice those in the AAO. Metagenomic analysis revealed distinct genomic architectures in the two systems. The AAO relied on a limited number of versatile strains carrying complete denitrification gene clusters. In contrast, the AICR harbored a distributed network where denitrification steps were partitioned among phylogenetically diverse and functionally specialized strains. These differences in community architecture were linked to the distinct flow regimes of the two reactors and corresponded to enhanced functional modularity and metabolic redundancy in the AICR, which contributed to its faster recovery under carbon fluctuations.}, }
@article {pmid42134588, year = {2026}, author = {Chauhan, A and Santhiya, D and Sharma, JG}, title = {Microbial consortium driven degradation of mixed microplastics: systematic review on enzymes and omics-based insights.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134885}, doi = {10.1016/j.biortech.2026.134885}, pmid = {42134588}, issn = {1873-2976}, abstract = {Microplastics (MPs) are among the most persistent pollutants in the environment. Mixed polymer waste further complicates the remediation due to their toxic additives and heterogenous composition. Conventional remediation methods show limited efficiency, especially for mixed MPs. As a result, biological approaches, particularly microbial consortium mediated degradation is a promising alternative. It is gaining increasing attention due to their cooperative metabolism and ability to degrade multiple polymers simultaneously. This review summarizes recent advances in consortium-based degradation of mixed MPs. It compares existing studies and identifies key challenges in translating laboratory findings to real-world. This review further discusses enzymes involved in the degradation of major polymer constituting mixed MPs. In addition, the role of multi-omics approaches like metagenomics, meta-transcriptomics, metabolomics, and integrated systems biology is also highlighted to explain microbial-metabolite interaction, functional pathways, and degradation mechanisms. Further, this review proposed future research directions focusing on green and scalable technologies. These include green biosensors for real-time monitoring, agro based aerogels and biochar for microbial immobilization, and nano-bubble assisted systems to enhance degradation under economic real-world conditions.}, }
@article {pmid42134644, year = {2026}, author = {Liang, M and Wang, X and Li, J and Li, R and Peng, J and Gao, B and An, R and Chen, X and Zhang, J and Liu, X}, title = {Antibiotic-mediated gut microbiota depletion partially attenuates methamphetamine-induced reward and linoleic acid metabolic disturbance.}, journal = {Neuropharmacology}, volume = {296}, number = {}, pages = {111022}, doi = {10.1016/j.neuropharm.2026.111022}, pmid = {42134644}, issn = {1873-7064}, abstract = {Methamphetamine (METH) is a highly addictive psychostimulant that possesses potent toxicity to multiple organs. Emerging evidence has suggested associations between gut microbiota dysbiosis and METH-induced rewarding effects. However, the role and underlying mechanisms of gut microbiota in METH addiction remain poorly understood. Using a mouse conditioned place preference (CPP) model combined with multi-omics profiling of gut microbiota and metabolites, we first investigated how METH exposure affects gut microbiota composition. Then, antibiotic (ABX)-mediated gut microbiota depletion was conducted to explore the role of gut microbiota in the METH-induced associative memory of context-reward (METH reward) and metabolic dynamics. Furthermore, associations among gut microbiota, metabolites, and behavioral phenotypes were determined to reveal the potential key microbial taxa and metabolites in METH reward. Finally, the key metabolite was intervened to reveal the role of it in the METH reward. Our results demonstrated that repeated METH administration induced significant alterations in gut microbiota profiles. ABX-mediated microbiota depletion attenuated METH-induced rewarding effects and metabolic perturbations, especially in linoleic acid (LA) metabolism. METH exposure led to an increase in, while gut microbiota depletion rescued the activation of LA metabolism. Correlation analyses consistently demonstrated associations among specific bacterial species, LA metabolites, and CPP scores. Supplementation of LA could facilitate, while inhibition of its oxidative metabolism could attenuate the METH-induced CPP. These findings highlight LA metabolism as a potential mechanistic link between gut microbiota dysbiosis and METH reward. Future gut microbiota-targeted therapeutic interventions, particularly those modulating LA metabolism, may improve the treatment of METH use disorder.}, }
@article {pmid42135082, year = {2026}, author = {Saranya, RG and Ramesh Babu, K and Viswanathan, P}, title = {Corrigendum to "Investigating gut microbiome dysbiosis in adults with chronic kidney disease: Diabetes-induced alterations via metagenomics and qPCR" [Life Sci. 393 (2026) 124336].}, journal = {Life sciences}, volume = {}, number = {}, pages = {124457}, doi = {10.1016/j.lfs.2026.124457}, pmid = {42135082}, issn = {1879-0631}, }
@article {pmid42135536, year = {2026}, author = {Adedire, DE and Onilude, AA and Odeniyi, OA and Nash, O and Semenya, K and Unuofin, JO}, title = {Snapshot reflection of the seasonal resilience and diversity of fungal phylotypes in the tropical Ikogosi spring.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {42135536}, issn = {1614-7499}, abstract = {Freshwater ecosystems like rivers, streams, and springs harbour diverse microbial communities, including fungal and bacterial phylotypes. These communities are an important part of the aquatic ecosystem, playing key roles in biogeochemical cycles. However, research on the seasonal differences concerning the fungal diversity of Ikogosi Warm Spring's sediments and water has been lacking. In this pilot study, we aimed to bridge this gap by employing high-throughput DNA sequencing to examine the fungal microbiome of this spring during the wet and dry seasons. Metagenomic DNA was extracted from water and sediment samples from different locations of the spring, and the fungal ITS1 region was sequenced using Illumina HiSeq technology. Sequences were processed with the DADA2 pipeline in R, enabling comprehensive taxonomic and diversity analyses. In addition, the spring's sediment and water physicochemical characteristics were assessed, and the impact of environmental variables on fungal communities was examined using redundancy analysis. Taxonomic analysis revealed that the spring was dominated by Ascomycota and Basidiomycota, irrespective of seasonal differences. In water samples, Ascomycota represented 62.0% (wet season) and 89.0% (dry season), while Basidiomycota accounted for 37.7% and 10.7%, respectively. Sediments exhibited a similar dominance, with Ascomycota comprising 65.1% in both seasons and Basidiomycota contributing 34.8% (wet season) and 33.5% (dry season). Alpha diversity indices indicated that fungal diversity was higher during the dry season than in the wet season, with no significant difference at p < 0.05. Redundancy analysis showed that some physicochemical factors, such as potassium and sulphate ions in water samples, were associated with seasonal patterns. These factors also influenced fungal communities in the spring, such as Cladosporium, Trichosporon, and Meyerozyma.}, }
@article {pmid42135633, year = {2026}, author = {Basu, U and Ahanger, SA and Song, T and Gai, X and Hu, X}, title = {Ecological and genomic dynamics of the soil microbiome under sustained pressure from Phytophthora nicotianae, the causal agent of tobacco black shank disease.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05137-x}, pmid = {42135633}, issn = {1471-2180}, support = {202405AD350100, 2023530000241003/YNDG202302XJ02//Yunnan Applied Fundamental Research Projects and the Yunnan Provincial Tobacco Monopoly Bureau/ ; }, abstract = {BACKGROUND: Soil-borne pathogens threaten global agriculture, yet soil microbiome adaptation to persistent pathogen pressure is poorly understood. This study characterized the ecological and genomic long-term shifts in a tobacco field soil microbiome under sustained Phytophthora nicotianae pressure. We conducted a six-year longitudinal metagenomic study in a field with a documented history of tobacco black shank disease. Comparative analysis of the rhizosphere microbiome from Year_1 and Year_6 was performed using shotgun sequencing, non-redundant gene catalog construction, and functional annotation against specialized databases.<br><br>RESULTS: Our analysis revealed a profound genetic remodelling, with 45.6% (116,529) of 255,258 genes showing significant differences in abundance (p&#x2009;<&#x2009;0.05, |log2FC| &#x2265; 1). This restructuring was systematic, characterized by significant enrichment of the soil antibiotic resistome, where 45.88% of antibiotic resistance genes were differentially abundant and showed a distinct trend toward increased abundance. The functional potential for carbohydrate metabolism was reorganized, with 53.2% of CAZymes (Carbohydrate-Active enZYmes) genes showing differential abundance and a predominant depletion. Analysis of COG (Clusters of Orthologous Groups) revealed a strategic functional trade-off, with significant enrichment of defense-related categories like secondary metabolite biosynthesis (+&#x2009;52.9%) alongside a reduction in growth-related processes. Such functional changes were ultimately driven by an taxonomically homogenized community, as indicated by a major reduction in species level alpha diversity (Shannon index: 5.52 to 5.31) that coexisted with a 14.8% significant increase in species level abundance, which showed a selective enrichment of a subset of dominant taxa.<br><br>CONCLUSION: Sustained pathogen pressure triggers a coordinated, multi-level adaptive succession, reshaping the genetic, functional, and taxonomic structure of the soil microbiome into a more defended and specialized state.}, }
@article {pmid42136553, year = {2026}, author = {Yang, L and Chen, X and Jia, A and Liu, Q and Chu, J}, title = {Atypical Streptococcus sinensis infective endocarditis complicated by bacterial meningitis: A case report and literature review.}, journal = {The Journal of international medical research}, volume = {54}, number = {5}, pages = {3000605261447124}, doi = {10.1177/03000605261447124}, pmid = {42136553}, issn = {1473-2300}, mesh = {Humans ; Male ; *Meningitis, Bacterial/microbiology/drug therapy/complications/diagnosis ; Middle Aged ; Anti-Bacterial Agents/therapeutic use ; *Streptococcus/isolation &amp; purification/genetics ; *Endocarditis, Bacterial/microbiology/drug therapy/complications/diagnosis ; *Streptococcal Infections/microbiology/drug therapy/complications/diagnosis ; RNA, Ribosomal, 16S/genetics ; Vancomycin/therapeutic use ; *Endocarditis/microbiology/complications/drug therapy ; Mitral Valve/microbiology ; Ceftriaxone/therapeutic use ; Echocardiography ; }, abstract = {Infective endocarditis caused by Streptococcus sinensis complicated by bacterial meningitis is exceedingly rare. We report a case of a middle-aged man who initially presented with ischemic symptoms in both lower limbs. Echocardiography revealed mitral valvular vegetations, and blood cultures confirmed S. sinensis. During antibiotic therapy, the patient developed somnolence, dysarthria, and left-sided weakness. Metagenomic next-generation sequencing of cerebrospinal fluid detected S. sinensis, thereby confirming infective endocarditis complicated by bacterial meningitis. Given the high surgical risk, combination antimicrobial therapy with vancomycin and ceftriaxone was administered. The patient's consciousness recovered, and inflammatory and cerebrospinal fluid parameters gradually normalized. This case demonstrates that S. sinensis-associated infective endocarditis can occur in patients with immunocompetent status and often involves the mitral valve, with potential intracranial complications. Early identification by blood culture, metagenomic next-generation sequencing, and 16S rRNA sequencing enables precise pathogen diagnosis. Standardized antibiotic therapy and individualized surgical assessment are crucial to optimize outcomes. For patients with neurological complications, multidisciplinary management is essential to improve survival and long-term prognosis.}, }
@article {pmid42136736, year = {2026}, author = {Takahashi, Y and Sada, RM and Matsuo, H and Yamamoto, S and Matsuzaki, S and Okada, A and Sunada, A and Takao, M and Yamamoto, G and Chuang, CK and Liu, CH and Kutsuna, S}, title = {Diagnostic challenges in postoperative pelvic infections associated with Metamycoplasma hominis: a two-case analysis using metagenomic sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1823299}, pmid = {42136736}, issn = {2235-2988}, mesh = {Humans ; Female ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing ; *Mycoplasma hominis/genetics/isolation &amp; purification ; Middle Aged ; *Pelvic Infection/diagnosis/microbiology ; *Postoperative Complications/diagnosis/microbiology ; DNA, Bacterial/genetics ; Adult ; *Mycoplasma Infections/diagnosis/microbiology ; }, abstract = {Postoperative gynecological infections may present diagnostic challenges, particularly in the presence of fastidious genital mollicutes and inherently mixed microbial DNA, both of which limit the diagnostic performance of microbiological methods, including Gram staining, conventional culture, 16S rRNA gene PCR followed by Sanger sequencing. This study aimed to illustrate the limitations of conventional microbiological methods in the diagnosis of gynecologic pelvic infections and highlight key considerations for the clinical use of metagenomic next-generation sequencing (mNGS), based on two contrasting cases of postoperative pelvic infections associated with Metamycoplasma hominis (M. hominis). In both cases, neither conventional culture nor 16S rRNA gene PCR/Sanger sequencing identified the causative organism, and shotgun mNGS was subsequently performed. Although the mNGS findings differed markedly between the two cases, M. hominis was considered the most plausible pathogen. These two cases show that the clinical relevance of organisms detected by mNGS should not be judged by read counts alone, particularly in non-sterile specimens or after antibiotic exposure. Even low-abundance reads may represent clinically meaningful pathogens when interpreted within the clinical context. They also highlighted the value of mNGS as a complementary diagnostic tool for gynecological pelvic infections when conventional diagnostic methods are intrinsically limited.}, }
@article {pmid42136790, year = {2026}, author = {Ariyasiri, A and Altaf, A and Mirza, H and Rehman, M}, title = {Genomics for precision surgical source control in anti-microbial resistant infections: A global review with focus on resource-limited settings.}, journal = {Pakistan journal of medical sciences}, volume = {42}, number = {411AASC}, pages = {S151-S156}, pmid = {42136790}, issn = {1682-024X}, abstract = {BACKGROUND &amp; OBJECTIVE: Antimicrobial resistance (AMR) critically threatens surgical safety, impairing perioperative prophylaxis and complicating infection management. Timely surgical source control is essential but relies on accurate microbiological diagnosis. Conventional culture-based methods are slow and insensitive, often leading to empirical broad-spectrum therapy. This review evaluates the role of advanced genomic diagnostics in enhancing surgical source control for AMR infections, with a focus on challenges and opportunities in low- and middle-income countries (LMICs) like Pakistan.<br><br>METHODOLOGY: A narrative review was conducted via a structured search of PubMed, Google Scholar, and ScienceDirect (January 2015-October 2025). Studies involving genomic tools in the management of AMR-related surgical infections were included. Evidence was synthesized thematically, covering genomic platforms, clinical applications, implementation barriers, and LMIC specific perspectives.<br><br>RESULTS: Genomic tools, particularly metagenomic next-generation sequencing (mNGS) and rapid multiplex PCR, demonstrate superior sensitivity (80.6-95.45%) and faster turnaround times (e.g., roughly 27 hours for mNGS) compared to culture. They improve pathogen detection in complex infections (e.g., prosthetic joints, necrotizing soft tissue), guide targeted antibiotic therapy, and can reduce broad-spectrum use. However, major implementation barriers exist, including high costs, need for specialized infrastructure and expertise, bioinformatic challenges, and ethical data concerns, which are especially pronounced in LMICs.<br><br>CONCLUSION: Genomic diagnostics offer a powerful approach to accelerate and refine surgical source control in the era of AMR. Strategic investments in local capacity, affordable platforms, and integration with antimicrobial stewardship are needed to realize their potential for improving surgical outcomes, particularly in resource-limited settings.}, }
@article {pmid42136862, year = {2026}, author = {Feng, Z and Quan, H and Li, M and He, D and Han, Y and Zou, C and Zhang, W and Chang, J and Lu, M}, title = {Distinct microbial and functional alterations across skin sites and disease severity in pediatric atopic dermatitis: a prospective study.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1805596}, pmid = {42136862}, issn = {2296-858X}, abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin condition frequently associated with microbial dysbiosis.<br><br>OBJECTIVE: This study examined the diversity, composition, and functional profiles of the skin microbiome in children with varying degrees of AD in different skin regions.<br><br>METHODS: Skin samples were collected from 12&#x202f;AD patients and 12 healthy controls. Genomic DNA underwent shotgun metagenomic sequencing to analyze alpha and beta diversity, taxonomic composition, and functional profiles, including the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), virulence factors and pathogen-host interactions (PHI).<br><br>RESULTS: Significant differences were observed in Shannon's diversity index and Chao1 diversity index between severity groups (p&#x202f;=&#x202f;0.007 and 0.004). Cluster analysis revealed partial clustering by severity, with significant differences between mild and moderate groups (p&#x202f;=&#x202f;0.042) and between moderate and severe groups (p&#x202f;=&#x202f;0.036). Staphylococcus and Streptococcus dominated the abundance profile in AD samples. Functional analysis revealed alterations in epidermal microbial activity during AD onset and across different severity levels.<br><br>CONCLUSION: Pediatric AD involves site- and severity-specific microbial shifts. This functional dysregulation and enrichment of virulence factors may push barrier dysfunction and inflammation, suggesting that the microbiome is a critical target for future therapies.}, }
@article {pmid42136870, year = {2026}, author = {Zhou, Y and Chen, L and Wang, L and Zhao, Z and Tu, J and Chen, H and Wang, S}, title = {Cavitary nodule caused by Emergomyces orientalis in a diabetic patient: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1829356}, pmid = {42136870}, issn = {2296-858X}, abstract = {Emergomyces orientalis is a rare thermally dimorphic fungus belonging to the family Ajellomycetaceae. It exists in the environment as a mold producing conidia, which are inhaled and transform into yeast-like cells at body temperature to cause disseminated infections. While primarily associated with immunocompromised individuals, especially those with HIV. Diagnosis remains challenging due to its morphological similarity to Blastomyces dermatitidis and the frequent failure of routine cultures. Thus, molecular methods such as metagenomic next-generation sequencing (mNGS) have become crucial for early identification. This case report describes a 51-year-old man with type 2 diabetes mellitus presented (T2DM) with a 10-day history of back pain, pharyngeal discomfort, and scant sputum. Chest CT showed multiple bilateral pulmonary nodules, one of which had cavitated. mNGS of a percutaneous lung biopsy confirmed Emergomyces orientalis. Histopathology also supported the diagnosis. The patient was discharged on oral itraconazole after partial symptomatic improvement, with outpatient follow-up arranged. Two months of antifungal therapy resulted in mild reduction of cavitary lesions on follow-up CT.}, }
@article {pmid42137133, year = {2025}, author = {Kazemifard, N and Norouzi-Beirami, MH and Baradaran Ghavami, S and Ghanbari-Maman, L and Zali, MR and Shahrokh, S and Kavousi, K}, title = {Microbiome-microRNA interactions in inflammatory bowel disease: insights from metagenomic and transcriptomic data analysis.}, journal = {Gastroenterology and hepatology from bed to bench}, volume = {18}, number = {SI}, pages = {85-96}, pmid = {42137133}, issn = {2008-2258}, abstract = {BACKGROUND: Inflammatory Bowel Disease (IBD) is a chronic inflammation of the gastrointestinal tract, the precise origins of which remain not fully elucidated. This study investigates the complex relationship between gut metagenomics and host transcriptomics in IBD patients, focusing on Ulcerative Colitis (UC) and Crohn's Disease (CD).<br><br>METHOD: One proposed theory suggests that microRNAs produced by the host may significantly influence IBD development by impacting the gut microbiota. Conversely, the gut microbiome may regulate the expression of host microRNAs, leading to dysfunction in the intestinal epithelium. An enrichment analysis was conducted to pinpoint associated pathways. To unravel this intricate interplay, the study utilized data from the IBDMDB database, selecting samples from adult individuals.<br><br>RESULT: The dataset comprised 50 paired metagenomic and host transcriptomic samples, including 8 controls, 18 UCs, and 24 CDs. Computational analyses and network constructions were applied to identify relationships between bacterial species, microRNAs, and other transcripts.<br><br>CONCLUSION: This research offers valuable insights into the dynamic relationship between the gut microbiome and human transcriptomics in IBD, providing a deeper understanding of potential disease mechanisms. Furthermore, it sheds light on the complex tripartite network connecting bacterial species, microRNAs, and transcripts, contributing to a comprehension of IBD pathogenesis and the identification of novel therapeutic targets.}, }
@article {pmid42137225, year = {2026}, author = {Meknas, A and Bessonov, K and Eagle, SHC and Peterson, CL and Robertson, J and Ricker, N and Signorelli, T and Nash, J and Reimer, A}, title = {Sequenoscope: a modular tool for nanopore adaptive sequencing analytics and beyond.}, journal = {Access microbiology}, volume = {8}, number = {5}, pages = {}, pmid = {42137225}, issn = {2516-8290}, abstract = {This article presents Sequenoscope: a bioinformatics pipeline for analysing Oxford Nanopore Technologies (ONT) adaptive sampling sequencing data. Sequenoscope features three main modules: filter_ONT for filtering raw reads and creating a FASTQ file with a subset of reads for further analyses, analyze for generating sequencing and read mapping statistics against the provided reference taxon sequences and plot for interactive data summarization, comparison, and visualization between two datasets/test conditions. Here, we demonstrate the ability of the pipeline to analyse ONT adaptive sampling sequence data and provide examples of the outputs users can expect using data we generated. Adaptive sampling was performed on two ZymoBIOMICS Microbial Community DNA Standards, log-distributed (Cat# D6311) and even-distributed (Cat# D6306) formulations, with targeted depletions of Listeria monocytogenes. By comparing the test and control experimental data in FASTQ files from the sequencing runs, Sequenoscope showed that depletion of L. monocytogenes was successful by providing users with parameters to compare such as taxon coverage, read length and types of pore-level decisions made during sequencing. Although Sequenoscope was designed for ONT adaptive sampling data analysis, it supports short-read data from other sequencing platforms such as Illumina, allowing for the direct comparison of any two experimental conditions or cross-platform benchmarking.}, }
@article {pmid42137573, year = {2026}, author = {Sun, J and Gao, W and Tan, H}, title = {The role of targeted next-generation sequencing and ultrasound in diagnosing fetal cytomegalovirus infection: a case report.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1734139}, pmid = {42137573}, issn = {2296-2360}, abstract = {BACKGROUND: Cytomegalovirus (CMV) infection is a leading cause of congenital infection and neonatal morbidity. Conventional diagnostic methods, such as polymerase chain reaction (PCR) and amniocentesis, remain important in the diagnosis of congenital CMV infection, although each method has its own limitations in clinical practice.<br><br>CASE PRESENTATION: A 31-year-old woman, gravida 3 para 1, presented for routine prenatal evaluation. At 18 weeks of gestation, ultrasound revealed echogenic bowel and fetal ascites. Amniocentesis at 19 weeks showed normal chromosomal results, but targeted next-generation sequencing (tNGS) detected CMV DNA with a high viral load, confirming intrauterine infection.<br><br>RESULTS: Despite counseling regarding poor fetal prognosis, the patient chose to continue the pregnancy under close ultrasound surveillance. Progressive hydrops fetalis was observed at 23 weeks, and the pregnancy was terminated at 24 weeks.<br><br>CONCLUSION: This case suggests that combining tNGS with ultrasound may provide complementary diagnostic information in selected cases of suspected fetal infection. In this patient, tNGS supported the identification of CMV in amniotic fluid when conventional genetic testing was unremarkable. However, as this is a single-case report, the broader diagnostic performance and clinical utility of tNGS require further validation in larger studies.}, }
@article {pmid42137610, year = {2026}, author = {Oguzie, JU and Cummings, DB and Groves, JT and Hagan, AG and Rodriguez, J and Hernandez-Vidal, G and Moreno-Degollado, G and Shittu, I and Marushchak, LV and Nguyen-Tien, T and Trujillo-Vargas, CM and Silva, DB and Li, F and Richeson, JT and Schneider, NE and Gray, GC}, title = {Detection and Genomic Characterization of Novel Respiratory Viruses in US and Mexican Cattle Farms.}, journal = {Transboundary and emerging diseases}, volume = {2026}, number = {}, pages = {3247802}, pmid = {42137610}, issn = {1865-1682}, mesh = {Animals ; Cattle ; United States/epidemiology ; *Cattle Diseases/virology/epidemiology ; Mexico/epidemiology ; *Respiratory Tract Infections/veterinary/virology/epidemiology ; Farms ; Humans ; Genome, Viral ; *Viruses/isolation &amp; purification/genetics/classification ; *Virus Diseases/veterinary/epidemiology/virology ; }, abstract = {Respiratory virus infections in cattle cause an estimated more than $1 billion in production losses and can threaten human health. During February 2024 to May 2025, we employed a One Health approach to surveil for respiratory viruses among cattle, farm workers, and environmental samples from 11 US and Mexican beef or dairy cattle farms. We studied nasal and ocular swabs from cattle, nasal swabs from cattle workers, bioaerosol samples, and other environmental farm samples using molecular and virological techniques. Among 26 distinct viruses identified in cattle, we detected bovine nidovirus 1, influenza D virus (D/OK-like and D/660-like), bovine coronavirus, bovine rhinitis A and B viruses, bovine respirovirus 3 and bovine respiratory syncytial virus (BRSV); 11 of the 26 detected viruses were non-bovine-associated. Two bovine rhinitis A virus was markedly divergent (provisionally designated BRAV-4). Environmental metagenomics additionally identified influenza D virus, bovine coronavirus, and bovine rhinitis B virus. One human nasal swab tested positive for SARS-CoV-2 (cladeLF.7.3). Our findings reveal the presence of emerging, co-circulating, and environmentally linked pathogens at the human-animal-environment interface, underscoring the constant need for One Health surveillance to safeguard livestock and mitigate zoonotic risk.}, }
@article {pmid42137790, year = {2026}, author = {Qi, J and Zhang, K and Zhan, C and Lu, X and Chen, X and Li, X and Zhang, C and Wang, H and Tu, C and Tong, W and Dai, L and Zeng, D}, title = {Microbial and metabolic crosstalk in the rhizosphere shapes the divergent drought resilience of contrasting rice genotypes.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1788826}, pmid = {42137790}, issn = {1664-302X}, abstract = {Drought is a major constraint on rice production, yet the coordinated responses of rhizosphere microbial communities and metabolites across rice genotypes with contrasting drought tolerance remain insufficiently understood. In this study, we combined metagenomic and metabolomic analyses to investigate drought-induced changes in the rhizosphere of three rice genotypes with distinct ecological backgrounds: the drought-sensitive cultivar Bhutan, the upland rice genotype TGR78, and Oryza rufipogon K111. Field experiments were conducted under well-watered and drought conditions, and rhizosphere soil samples were collected for multi-omics profiling. Drought stress reduced plant height and panicle number in all three genotypes, but the magnitude of these effects differed among genotypes. Bhutan showed the greatest reduction in plant height (42.1%) and the largest number of differential metabolites (146), indicating a stronger drought response at both phenotypic and metabolic levels. In contrast, TGR78 and K111 displayed relatively greater phenotypic stability under drought stress. Metagenomic analysis revealed pronounced genotype-dependent shifts in rhizosphere bacterial community composition, whereas metabolomic profiling showed distinct changes in metabolite accumulation patterns among genotypes. Correlation analysis further demonstrated that drought substantially reshaped rhizosphere microbe-metabolite associations, shifting the interaction network from broadly positive and highly connected under well-watered conditions to more selective associations under drought stress. Collectively, these results indicate that rice drought adaptation is associated with genotype-dependent reorganization of the rhizosphere microbiome and metabolic profile. This study provides new insight into rhizosphere-mediated drought responses in rice and offers a basis for developing microbiome-informed strategies for drought-resilient crop improvement.}, }
@article {pmid42137793, year = {2026}, author = {Adeleke, RA and Machailoe, TME and Malemagovha, M and Olanrewaju, OS and Alayande, KA and Obi, LU and Makinde, OM}, title = {Diversity and functional potential of bacterial and fungal endophytes in traditional food wrapping leaves reveal implications for artisanal food safety and quality.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1641069}, pmid = {42137793}, issn = {1664-302X}, abstract = {Plant leaves are widely utilised globally for the packaging and serving of traditionally prepared foods. The microbial communities associated with these wrapping leaves, particularly endophytes, are recognised to potentially influence food quality, safety, and preservation. Specifically, certain endophytes can enhance sensory attributes and nutritional value through fermentative processes, while the presence of harmful microorganisms may lead to spoilage and pose a risk of foodborne illness. This study utilised 16S rRNA, ITS metabarcoding and metagenomic functional analysis (PICRUSt2) to comprehensively investigate the composition and infer the putative functional potential of putative endophytic bacterial and fungal communities present in 53 samples of four different food wrapping leaves. The leaves examined included Thaumatococcus daniellii (n = 10), Alstonia macrophylla (n = 18), Theobroma species (n = 14), and Megaphrynium macrostachyum (n = 11). Distinct microbial community profiles were observed across the different leaf types. Highest bacterial species richness and community variability were detected in A. macrophylla samples, reflected by Principal Coordinates Analysis (PCoA) values (PCoA1 = 43.97%; PCoA2 = 10.68%). Conversely, M. macrostachyum exhibited the greatest fungal species richness and variability (PCoA1 = 20.08%; PCoA2 = 8.72%). Taxonomic analysis identified Proteobacteria as the dominant bacterial phylum and Stenotrophomonas as the dominant bacterial genus. Other notable bacterial taxa included the phyla Bacteroidota and Firmicutes, and genera such as Pseudomonas, Faecalibacterium, and Bacteroides. For fungal communities, Ascomycota was the dominant phylum. Additional fungal taxa included the phylum Basidiomycota and genera Cryptococcus, Candida, and Meyerozyma. A core microbiome analysis revealed that 42 bacterial (notably Stenotrophomonas and Chryseobacterium) and 7 fungal taxa (notably Pleosporaceae and Ascomycota) were shared across all examined wrapping leaves. The identified microbial communities (e.g., Lactobacillus and Geotrichum) encompass taxa with potential beneficial roles, such as enhancing food fermentation and potentially contributing to human gut health upon consumption of the packaged food. However, the detection of potentially pathogenic and toxigenic bacterial taxa highlights a possible public health risk associated with the use of these leaves. Further investigation into the specific functionalities of these associated bacteria and fungi is essential to maximise their beneficial applications while simultaneously mitigating potential health risks posed by harmful strains.}, }
@article {pmid42137803, year = {2026}, author = {Liu, Y and Chen, C and Gao, J}, title = {Topological characteristics and longitudinal dynamics of co-abundance networks involving beneficial commensal bacteria in the pig gut microbiome and its association with average daily gain.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1818141}, pmid = {42137803}, issn = {1664-302X}, abstract = {Microorganisms are intricately interrelated with each other in the gut microecosystem, which influences the colonization and functional roles of probiotics. However, how these interactions dynamically change during host development and whether their topological features influence host phenotypes, such as average daily gain (ADG), remain poorly understood. In this study, we performed metagenome analysis for 2,311 fecal samples collected from a specifically designed eight genetically divergent breed intercrossed mosaic F6 and F7 population, at three developmental ages of 25 days (D25), 120 days (D120), and 240 days (D240) of each individual, covering pre-weaning to market. By constructing their microbiota co-abundance networks, we systematically characterized dynamic changes in beneficial commensal bacteria involved co-abundance networks in the pig gut microbiome across three ages. We elucidated conserved and variable co-abundance features involving these bacteria across developmental stages. We observed that the cross-age stable co-abundance correlations of beneficial commensal bacteria were maintained by a large set of weak correlations. A subset of age-shared co-abundance correlations remained variable across different ages in correlation strength and direction. Topological analysis revealed that beneficial commensal bacteria involved co-abundance networks were highly age-specific. Among the three age stages sampled in this study, the D120 stage represented a critical window for the structural and functional reorganization of gut microbiota. Using metagenomic sequencing data at the D120, we identified two guilds that were significantly associated with ADG from D120 to D240. Guild 1 included short chain fatty acid-producing taxa and was positively associated with ADG, whereas Guild 2 tended to self-utilization of energy and was negatively associated with ADG. We also inferred the ecological interaction mechanisms of ADG-associated microbial communities using genome-scale metabolic models. These findings provided a theoretical basis for stage-specific intervention in the pig gut microbiome using probiotics to improve production traits.}, }
@article {pmid42137806, year = {2026}, author = {Doughan, GE and Walthart, BK and Schau, CE and Skoland, KJ and Mou, KTY and Brown, JT and Bonnema, JL and Plummer, PJ and Zhang, D and Li, G and Karriker, LA}, title = {Presence of antimicrobial resistance genes in biofilms from swine drinking water pipes before and after treatment with peracetic acid.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1770950}, pmid = {42137806}, issn = {1664-302X}, abstract = {Biofilms can be problematic to swine drinking water systems as they can harbor pathogens, decrease water quality, and may contribute to antimicrobial treatment failure. Water-administered antimicrobials are used for disease treatment in swine populations, yet, little is known about water line ecology and the impact it can have on antimicrobial resistance and stewardship. Water line cleaning and disinfection may aid in removal of water line biofilms, improve swine health, and antimicrobial stewardship. Water line samples were collected pre-treatment (0), 24 h post-treatment with 0.78% CID 2000 Pro (peracetic acid) (1), and 3, 5, 7, 14, 21, 42, 56, and 77-days post-treatment from six wean-to-finish swine farms in Iowa, USA. Biofilm was aseptically extracted from the interior of the water line pipe (n = 119) and submitted for metagenomic analysis to detect antimicrobial resistance genes (ARGs). This study demonstrates high prevalence of ARGs in swine water line biofilms that could confer resistance to both medically important antimicrobials to humans and animals such as aminoglycosides, beta-lactams, fluoroquinolones, colistin, and fosfomycin. From 115 samples, a frequency of 3,904 ARGs were reported, with 184 unique ARGs defined. Four samples contained no ARGs. One hundred and fifty-one integron genes representing three classes were found in 115 of 119 samples, indicating mechanisms of potential spread of multiple drug resistance. ARGs and integron genes combined were significantly lower on average by 10 unique ARGs/ integron genes 24-h post-treatment (1) when compared to pre-treatment (0) counts (p-value = 0.01). The number of unique ARG and integron genes quickly rebounded and were not statistically significant compared to pre-treatment counts on post-treatment dates 3, 5, and 7 (adjusted p-value ≥ 0.05), and by post-treatment date 14, unique ARG and integron genes were significantly higher than pre-treatment (adjusted p-value = 0.012). This study demonstrates that swine water line biofilms can harbor antimicrobial resistance genes which could have potential clinical impacts on pig health and treatment response.}, }
@article {pmid42137815, year = {2026}, author = {Geng, S and Shi, X and Zhang, Q and Yang, J and Yang, C and Yang, L}, title = {Organic fertilizer enhances microbial functional genes related to nitrogen and phosphorus cycling in rubber tree (Hevea brasiliensis) rhizosphere.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1833968}, pmid = {42137815}, issn = {1664-302X}, abstract = {INTRODUCTION: Nitrogen (N) and phosphorus (P) are the essential nutrient for rubber growth. However, the effect of organic fertilizer application on soil microbial communities and functional genes related to N and P cycling in rubber plantation are unclear.<br><br>METHODS: A field trial was established in a rubber plantation with two treatments: organic fertilizer (OF) and an unfertilized control (CK). In this study, we used metagenomics analysis to examine the structural and functional alterations in the microbial community within the rhizospheric soil of rubber when organic fertilizers were applied.<br><br>RESULTS: Results showed that compared with the CK treatments, the OF treatment significantly increased soil organic matter (SOM), total nitrogen (TN), total phosphorus (TP), alkali-hydrolyzable nitrogen (AN), and available phosphorus (AP) contents. Taxonomic analysis revealed that OF treatment significantly enriched the phyla Pseudomonadota and Myxococcota, and the genera Pseudolabrys and Gaiella. At the functional level, organic fertilization significantly up-regulated key genes associated with N cycling, including organic N metabolism (gltB), N transport (nrtA, nrtB, nrtC), denitrification (norB, nosZ), nitrification (nxrB), and dissimilatory nitrate reduction (napA, napC). Regarding the P cycle, organic fertilization leads to the downregulation of the high-affinity phosphate transporter gene pstS and the concurrent upregulation of genes governing organic P mineralization (phnA, phoN), regulation (phoB), polyphosphate synthesis (ppk1), and polyphosphate degradation (spoT, relA). The variation partitioning analysis (VPA) results indicated that pH, SOM, and nitrogen nutrients (comprising TN and AN) explained 71.52% of the variation in the abundance of nitrogen-cycling functional genes, while pH, SOM, and phosphorus nutrients (comprising TP and AP) explained 64.95% of the variation in the abundance of phosphorus-cycling functional genes.<br><br>CONCLUSION: In summary, the application of organic fertilizer reshapes soil microbial communities and enhances the functional potential for nitrogen (N) and phosphorus (P) cycling. Our study provides a mechanistic basis for developing sustainable nutrient management strategies to optimize N and P bioavailability in tropical rubber agroecosystems.}, }
@article {pmid42137872, year = {2026}, author = {Parrino, J and Sunshine, J and Tripp, K and Shaffer, M and Sughra, U and Procházková, N and Jara, M and Moll, JM and Noble, R and Muir, L and McIntyre, E and Guduk, E and Zachariah, D and Vernochet, C and Frahm, N and Schmidt, AC}, title = {Impact of Bifidobacterium infantis supplementation on growth, health outcomes, and gut microbiome features in underweight infants from Pakistan.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1783141}, pmid = {42137872}, issn = {2296-861X}, abstract = {BACKGROUND: Alterations in the gut microbiome are implicated in infant malnutrition. Bifidobacterium longum subspecies infantis (B. infantis), a commensal common in breastfed infants, has been shown to have reduced abundance in malnourished infants. This trial (NCT05952076) evaluated if B. infantis strain Bi-26 supplementation could improve growth and health outcomes in underweight infants in Pakistan.<br><br>METHODS: In this double-blind, randomized, placebo-controlled trial, 40 infants aged 30-120&#x202f;days (d) with a weight-for-age Z score (WAZ) below -2 received daily oral Bi-26 or placebo for 28d, with follow-up to d90 for safety. The primary endpoint was change in WAZ from baseline to d56. The intended sample size was 396 infants but study was terminated early due to operational delays. Total B. infantis levels microbiome, metabolome, and cytokine profiles were assessed.<br><br>RESULTS: Bi-26 supplementation increased fecal B. infantis levels at d28 (p&#x202f;=&#x202f;0.001) and d56 (p&#x202f;=&#x202f;0.03) but did not result in significant change in WAZ (p&#x202f;=&#x202f;0.69) or weight gain (p&#x202f;=&#x202f;0.56) compared to placebo. Fewer adverse events (AEs) occurred in the Bi-26 group compared to placebo (40% vs. 80% of infants; 17 vs. 49 events). Probiotic engraftment was impacted by presence of baseline endogenous B. infantis, suggesting that Bi-26 complemented rather than outcompeted endogenous strains. Bi-26 altered microbiome composition with transient alterations in function and metabolite abundance that reverted to baseline by d56, without cytokine differences between groups. B. infantis levels and Bifidobacterium-community types were associated with fewer AEs but not changes in WAZ or weight.<br><br>DISCUSSION: Bi-26 supplementation had an acceptable safety profile but did not improve growth. The findings of this trial support further evaluation of B. infantis strains in larger studies of underweight infants across diverse LMIC settings. Future trials should determine whether sustained metabolic and functional remodeling can translate into measurable improvements in growth and health outcomes.<br><br>CLINICAL TRIAL REGISTRATION: https://www.clinicaltrials.gov/study/NCT05952076, NCT05952076.}, }
@article {pmid42137970, year = {2026}, author = {Feser, M and Arend, D and Beier, S and Bolger, M and Lübke, NC and Meister, M and Steilen, L and Usadel, B and Scholz, U}, title = {Evolving bioinformatics services - the journey of KPI metrics with Scorpion.}, journal = {Journal of integrative bioinformatics}, volume = {}, number = {}, pages = {}, pmid = {42137970}, issn = {1613-4516}, abstract = {Key Performance Indicators (KPIs) are essential for evaluating project success and establishing control mechanisms to monitor development, performance, and user acceptance of services in joint projects. However, the absence of standardized frameworks and effective monitoring tools, combined with service providers' reluctance due to fears of comparability, has limited their adoption in scientific contexts. To address this gap, we developed Scorpion, a flexible tool for KPI monitoring in project management. Scorpion enables service providers to retain control over their metrics while supporting centralized reporting. It offers both web-based and programmatic access, with features for KPI submission, visualization, and user and service management. Initially created for bioinformatics and biodiversity projects, Scorpion is applicable across diverse domains. It is particularly valuable for initiatives like the German National Research Data Infrastructure (NFDI), where funding agencies require KPI reporting for evaluation. We present the Scorpion framework, highlighting its design principles, features, and potential to improve project management practices. Use cases illustrate how Scorpion enhances KPI monitoring efficiency and accuracy, contributing to better impact evaluation, quality assurance, and informed decision-making in project and service management.}, }
@article {pmid42138445, year = {2026}, author = {Ndhlovu, K and Salawu-Rotimi, A and Bopape, FL and Mtsweni, PN and Babalola, OO and Hassen, AI}, title = {Elucidating the Functional and Taxonomic Diversity of Soil Microbial Communities From Three Commercial Soybean Farms in South Africa.}, journal = {Environmental microbiology reports}, volume = {18}, number = {3}, pages = {e70360}, doi = {10.1111/1758-2229.70360}, pmid = {42138445}, issn = {1758-2229}, support = {135456//National Research Foundation (NRF), South Africa/ ; }, mesh = {South Africa ; *Glycine max/growth &amp; development/microbiology ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation &amp; purification ; Bradyrhizobium/genetics/isolation &amp; purification/classification ; Metagenomics ; Nitrogen Fixation ; Phylogeny ; *Biodiversity ; Farms ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Prior to the introduction of the exotic inoculant strain of Bradyrhizobium, South African soils lacked the rhizobia that nodulate soybean. Five decades of soybean inoculation practice resulted in the establishment of the Bradyrhizobium population in many soybean growing fields. However, there is no record of the magnitude of this establishment and its impact on the taxonomic and functional abundance of other microbes. Here we use a shotgun metagenomics approach to elucidate the taxonomic and functional profiles of the soil microbes from selected commercial soybean farms in South Africa. Metagenomics of the total sequences revealed that Proteobacteria, Actinobacteria, Firmicutes, Acidobacteria and Bacteroitedes are the prevalent phyla which differed in their relative abundance. Bradyrhizobium was the predominant genus at all three locations. Predicted functions detected genes essential for nitrogen metabolism, including nitrogen fixation, which have been unveiled in this study at a higher rate in all locations investigated. This study uncovers the microbial communities associated with soybean soils in South Africa. The study also generated vital information on the establishment of Bradyrhizobium spp. in the soils of soybean farms, providing a clue on whether inoculation of soya beans is always necessary. The findings, however, warrant further field investigations before any recommendations are rendered.}, }
@article {pmid42138618, year = {2026}, author = {Ran, L and Mao, Y and He, B and Pan, H and Ma, H}, title = {Wildfire-Altered Soil Water-Extractable Organic Matter Drives Divergent Greenhouse Gas Emissions in Anaerobic Subsurface Soils.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c04642}, pmid = {42138618}, issn = {1520-5851}, abstract = {Intensifying global climate change has increased wildfire frequency. Wildfire-altered soil water-extractable organic matter (burned-WEOM) is hydrologically transported to unburned areas, profoundly affecting cross-ecosystem carbon-nitrogen cycling and greenhouse gas (GHG) emissions. Taking soils from unburned subtropical forests as the research object, this study combined anaerobic incubation with high-resolution mass spectrometry and metagenomic sequencing to elucidate the regulatory mechanisms of burned-WEOM on soil GHG emissions under anaerobic conditions. The results showed that burned-WEOM increased CO2 emissions by 17.0%, induced a 164.6% surge in N2O emissions, and simultaneously inhibited CH4 emissions by 52.9%. With unique properties of high unsaturation and strong electron exchange capacity, burned-WEOM not only reshapes soil organic matter composition but also drives differential GHG emissions by enhancing complete carbon fixation pathways and recalcitrant carbon decomposition, increasing the abundance of anaerobic methane oxidation (AMO) genes and methanotrophs, enriching denitrifying microorganisms (especially fungi), and boosting N2O-generating gene activity without altering the reduction pathway. Moreover, WEOM molecular characteristics drive differences in GHG emissions: CH4 is mainly fueled by reduced, unsaturated lipid-like compounds, N2O is associated with nitrogen-rich, complex aromatic compounds, and CO2 has a broader range of source substrates. This study provides insights that may improve mechanistic understanding of postfire GHG dynamics and inform process representations in climate models.}, }
@article {pmid42138754, year = {2026}, author = {Guimarães, LO and Couto, RDS and Reginato, SL and Mucci, LF and Pandey, RP and de Camargo-Neves, VLF and da Costa, AC and Kirchgatter, K and Leal, E}, title = {Wyeomyia confusa Lispivirus (WcLispV-SP): a novel neotropical mosquito virus in the Lispiviridae family.}, journal = {Archives of virology}, volume = {171}, number = {6}, pages = {}, pmid = {42138754}, issn = {1432-8798}, mesh = {Animals ; Phylogeny ; Genome, Viral ; *Culicidae/virology ; Open Reading Frames ; Brazil ; Viral Proteins/genetics ; RNA, Viral/genetics ; *Mononegavirales/genetics/classification/isolation &amp; purification ; RNA-Dependent RNA Polymerase/genetics ; }, abstract = {Metatranscriptomic analysis of Wyeomyia confusa mosquitoes collected in the Atlantic Forest (Pindamonhangaba, São Paulo, Brazil) led to the identification of a previously uncharacterized virus, designated Wyeomyia confusa Lispivirus (WcLispV-SP), classified within the family Lispiviridae, genus Canmovirus. The viral genome consists of a negative-sense single-stranded RNA (ssRNA-) of 12,698 nucleotides, encoding six open reading frames (ORFs): nucleoprotein (N), two hypothetical proteins (HP/1 and HP/2), glycoprotein (G), ORFan protein, and RNA-dependent RNA polymerase (RdRp-L). Phylogenetic analysis supports the classification of WcLispV-SP as a distinct species within the genus Canmovirus. Structural analysis of the RdRp revealed conserved domains and catalytic motifs characteristic of members of the order Mononegavirales, supporting its functional integrity. These findings expand the known diversity of the Lispiviridae family and highlight the utility of metagenomic approaches for the discovery and characterization of RNA viruses associated with Neotropical sylvatic mosquitoes.}, }
@article {pmid42138983, year = {2026}, author = {Touceda-Suárez, M and Ponsero, AJ and Barberán, A}, title = {Urban greenspaces harbour distinct plasmid communities enriched in heavy metal resistance and competitive traits in arid soils.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {5}, pages = {}, doi = {10.1099/mic.0.001705}, pmid = {42138983}, issn = {1465-2080}, mesh = {*Plasmids/genetics ; *Soil Microbiology ; *Metals, Heavy/pharmacology ; Soil/chemistry ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Gene Transfer, Horizontal ; Metagenome ; Microbiota/genetics ; Cities ; Humans ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Plasmids drive horizontal gene transfer, a fundamental mechanism for soil bacterial evolution and antibiotic resistance emergence. In arid regions, the transformation of natural soils into urban greenspaces introduces dramatic environmental changes that influence the adaptive strategies of soil micro-organisms. Additionally, urban greenspaces can act as interfaces of antibiotic resistance spread between environmental and human microbiomes. Here, we inferred plasmids from soil metagenomes of urban greenspaces in Tucson, AZ, USA, and nearby natural arid habitats. We found urban greenspaces to select for plasmids that carried genes that confer competitive advantages, including motility, prokaryotic defence and resistance to heavy metals. Notably, urban greenspace plasmids exhibited reduced diversity (genetic and functional variants), which could in turn constrain their adaptability to rapid environmental changes. These findings underscore the importance of plasmids as agents mediating soil microbial adaptation to human activities.}, }
@article {pmid42139081, year = {2026}, author = {Shen, H and Song, J and Li, J and Hu, Y and Peng, N and Zhao, S}, title = {Dietary Niches Drive Microbial Community Assembly, Network Reorganization, and Symbiont Evolution in Freshwater Fish Gut Microbiomes.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag125}, pmid = {42139081}, issn = {1751-7370}, abstract = {Host diet is a fundamental ecological factor shaping the assembly and evolution of host-associated microbiomes, yet how dietary niches influence the structure of microbial associations and functional adaptation in freshwater fish remains poorly understood. This study selected five dominant farmed freshwater fish species in China with distinct feeding habits (herbivory, omnivory, filter-feeding, and carnivory) and systematically investigated the adaptive mechanisms of their gut microbiomes by integrating metagenomics, targeted cultivation, comparative genomics, and in vitro assays. We show that dietary niches exert a strong deterministic effect on microbial community assembly, leading to pronounced differences in ecological network topology, including connectivity, modularity, and keystone taxa. Cetobacterium was detected in all five fish species but exhibited a higher relative abundance in omnivorous (16.0%) compared to carnivorous fish (5.4%), suggesting that it may be a core genus within the gut microbiota of freshwater fish. Comparative genomics further revealed that Cetobacterium symbionts exhibit streamlined genome architectures and conserved core metabolic functions, indicative of adaptive evolution toward stable host-associated lifestyles. Guided by metagenomic insights, we isolated multiple Cetobacterium strains displaying host-adapted functional traits, linking community-level ecological patterns to cultivable symbiont resources. In summary, our findings demonstrate that freshwater fish guts function as ecological niches that deterministically structure microbial community assembly and drive symbiont evolution, providing a conceptual framework for understanding host-microbiome co-adaptation in aquatic ecosystems.}, }
@article {pmid42139090, year = {2026}, author = {Parienti, JJ and Yang, SS and Grinspoon, S}, title = {Selected Industry Highlights From IDWeek 2025.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {82}, number = {Supplement_4}, pages = {S85-S86}, doi = {10.1093/cid/ciag206}, pmid = {42139090}, issn = {1537-6591}, mesh = {Humans ; *HIV Infections/complications/drug therapy ; High-Throughput Nucleotide Sequencing ; }, abstract = {This supplement presents scientific reports from industry-sponsored IDWeek 2025 symposia, highlighting selected advances in infectious diseases and HIV care through clinical case scenarios. One article explores therapeutic approaches to metabolic complications in people with HIV, emphasizing treatment strategies and the clinical reasoning that supports individualized management of excess adiposity. The second examines the clinical integration of metagenomic next-generation sequencing for diagnosing central nervous system infections, outlining both its opportunities and limitations within current diagnostic pathways.}, }
@article {pmid42139092, year = {2026}, author = {Waldrop, G and Reddy, SP}, title = {Metagenomic Next-generation Sequencing in Central Nervous System Infections: Clinical Strategies, Evidence, and Best Practices.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {82}, number = {Supplement_4}, pages = {S92-S99}, doi = {10.1093/cid/ciag120}, pmid = {42139092}, issn = {1537-6591}, support = {//Delve Bio/ ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Central Nervous System Infections/diagnosis/cerebrospinal fluid/microbiology ; Immunocompromised Host ; Female ; Middle Aged ; }, abstract = {BACKGROUND: Central nervous system (CNS) infections are diagnostically challenging due to their nonspecific clinical presentations and wide array of potential pathogens. The rising population of immunocompromised patients further complicates this landscape, increasing the prevalence of atypical and opportunistic infections that are often missed by conventional testing.<br><br>OBJECTIVE: This article provides guidance on the use and clinical interpretation of cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) in suspected CNS infections.<br><br>DISCUSSION: We highlight the paradigm shift from targeted molecular testing to agnostic mNGS, emphasizing key factors that impact diagnostic utility, including specimen handling, neuroanatomical factors, host inflammatory response, and pathogen kinetics. Using illustrative cases, we demonstrate how these biological and technical variables influence test sensitivity and result adjudication. We further discuss the impact of mNGS on clinical decision-making and current limitations regarding cost and turnaround time.<br><br>CONCLUSIONS: Cerebrospinal fluid mNGS is a transformative diagnostic tool, particularly for unusual presentations and in immunocompromised hosts. However, it does not replace clinical judgment and requires careful multidisciplinary interpretation. When integrated thoughtfully with clinical and laboratory data, mNGS can meaningfully reduce the diagnostic gap in CNS infections.}, }
@article {pmid42139793, year = {2026}, author = {Jibril, AH and Alencar, ALF and Olsen, JE and Hounmanou, YMG}, title = {Effect of age, severity of diarrhoea, number of pathogens present and blooming of E. coli on metagenomic characteristics of stools from Danish dairy calves with diarrhoea.}, journal = {Veterinary microbiology}, volume = {319}, number = {}, pages = {111070}, doi = {10.1016/j.vetmic.2026.111070}, pmid = {42139793}, issn = {1873-2542}, abstract = {BACKGROUND: Calf diarrhoea causes substantial welfare and economic losses, and it is one of the major drivers of antimicrobial use. This study aimed to characterize the faecal microbiome of diarrhoeic calves, with a specific focus on Escherichia coli, and to assess whether microbial profiles vary with age, diarrhoea severity, and high E. coli abundance in the absence of other detectable enteric pathogens.<br><br>METHODS: Stool samples from Danish diary calves (n&#x202f;=&#x202f;32) below 4 weeks of age were collected from 11 herds and were analysed using direct long-read sequencing (mgt) as well as analyses of a subset of samples by swiping microbiota from faecal samples grown on McConkey agar plates (plate-swipe). Metagenomes were analysed to characterise community structure (Shannon &#x3b1;-diversity; Bray-Curtis PCoA with PERMANOVA) and to assess differential abundance at the species level while adjusting for sample type (mgt/plate swipe), herd, age, number of other pathogens detected by qPCR (rotavirus, coronavirus, Cryptosporidium parvum, Salmonella Dublin, Clostridium perfringens A, B, C, Eimeria and Escherichia coli F5) and recorded as presence/absence and summarised into infection classes (None/Mono/Co-2/Co-3&#x202f;+). Binning was performed to build metagenome assembled genomes (MAGs) of E. coli.<br><br>RESULTS: Microbiome structure was dominated by methodological and contextual factors: sample type (direct metagenomic vs plate swipe) and herd explained far more variation than clinical severity and age. Metagenomic species profiles from plate swabs were comparatively homogeneous and E. coli-rich, whereas direct metagenomes captured higher diversity. Differential abundance identified species enriched with increasing diarrhoea severity and with infection classes, while pathogen-specific contrasts (e.g., C. perfringens A-positive vs negative) revealed discrete sets of bacterial co-occurrences. Classical pathotype markers (virulence-genes) were uncommon among E. coli MAGs.<br><br>CONCLUSIONS: Long-read metagenomics revealed insignificant influence of severity of diarrhoea, age below 4 weeks and number of pathogens detected in stool samples on diversity and microbial communities in diarrheic dairy calves. In contrast, large variation was observed between herds. On average, E. coli constituted about half of the microbiota. MAGs generated by binning indicated non-specific blooming of strains without particular virulence genes.}, }
@article {pmid42139982, year = {2026}, author = {Yuan, M and Dong, S and Luo, J and Li, Y and Li, YA and Wen, W and Zhao, R}, title = {Habitat-driven taxonomic and functional differentiation of microbial communities across water and sediments in a large eutrophic shallow lake deciphered by metagenomics.}, journal = {Microbiological research}, volume = {310}, number = {}, pages = {128553}, doi = {10.1016/j.micres.2026.128553}, pmid = {42139982}, issn = {1618-0623}, abstract = {Shallow lakes in arid and semi-arid regions are vulnerable to hydrological fluctuations and nutrient loading. However, the composition and functional traits of microbial communities and their roles in mediating internal nutrient cycling across the water column and sediments remain poorly understood. Here, we applied an integrated metagenomic framework to investigate microbial community structure and metabolic potential in Wuliangsuhai Lake, a typical eutrophic shallow lake in the Yellow River Basin. Read-based taxonomic profiling revealed pronounced habitat-driven community differentiation, with significantly higher microbial diversity and evenness in sediments than in water. Both habitats were dominated by Pseudomonadota, while water was enriched in Cyanobacteriota, Actinomycetota, and Bacteroidota, and sediments in Actinomycetota, Thermodesulfobacteriota, and Bacillota. Contig-based functional profiling based on a non-redundant catalog of 9.45 million genes showed clear habitat-specific divergence. Sediments were significantly enriched in pathways associated with complex carbon degradation, reductive nitrogen transformations, and sulfur redox metabolism. Genome-resolved analysis recovered 974 non-redundant metagenome-assembled genomes spanning 54 phyla, including one putative novel lineage. Metabolic reconstruction indicated community-wide dominance of heterotrophic carbon oxidation and fermentation, while methanogenic potential was largely confined to sediments. Nitrogen cycling was biased toward reductive processes, and sulfur cycling showed strong representation of both sulfite oxidation and sulfate/sulfite reduction. Metabolic weight scores further revealed a clear functional division of labor among major microbial lineages, with Pseudomonadota contributing broadly across multiple biogeochemical processes. These results indicate pronounced sediment-water functional differentiation in eutrophic shallow lakes, with sediments primarily supporting metabolic processes related to internal nutrient turnover.}, }
@article {pmid42140024, year = {2026}, author = {Mu, Y and Zhang, H and Pan, Y and Tian, Z and Huang, Y and Yang, L and Zhang, C and Zhao, C and Li, D and Liu, X and Jiang, L}, title = {Deciphering the mechanisms underlying regional heterogeneity of high-temperature Daqu through integrated electronic sensory, volatilome, and microbiome analysis.}, journal = {International journal of food microbiology}, volume = {457}, number = {}, pages = {111847}, doi = {10.1016/j.ijfoodmicro.2026.111847}, pmid = {42140024}, issn = {1879-3460}, abstract = {High-temperature Daqu (HTD) is crucial for shaping the style of Moutai-flavor Baijiu, but its quality characteristics exhibit geographical and spatial heterogeneity, resulting in diminished typicity of products from non-core production regions. Therefore, this study employed multiphase detection techniques to analyze HTD samples from the typical region (Guizhou) and emerging region (Shandong), along with their surface and inner layers. Guizhou HTD possessed superior biochemical activity (especially on the surface) and higher response values for W1W, W2W, umami, and salty sensors. It also showed higher concentrations of key flavor compounds, such as pyrazines, acids, and alcohols. Targeted amplicon sequencing showed Kroppenstedtia, Thermoascus, and Thermomyces dominated all samples, but Guizhou HTD had greater microbial diversity and richness. Metagenomics indicated a higher proportion of bacteria in Guizhou HTD, represented by Kroppenstedtia eburnea and Oceanobacillus indicireducens, whereas fungi were more prevalent in Shandong HTD, with Paecilomyces varioti, Aspergillus chevalieri, and Rasamsonia emersonii as the dominant species. Functional annotation demonstrated that carbohydrate metabolism and amino acid metabolism were core biological functions of HTD, with gene abundances showing Guizhou > Shandong and inner > surface. Furthermore, species-enzyme contribution and metagenome-assembled genomes analyses confirmed that HTD exhibited functional redundancy at the ecological scale, yet the species responsible for these functions displayed regional specificity, explaining the phenotypic heterogeneity between Guizhou HTD and Shandong HTD. These findings highlight the pivotal role of the production region in HTD quality and offer insights for improving Moutai-flavor Baijiu flavor in non-core regions.}, }
@article {pmid42140051, year = {2026}, author = {Missaoui, Y and Venditti, M and Zhang, L and Vaccaric, F and Abelouah, MR and Abouda, S and Gaaieda, S and Puglisi, E and Lucini, L and Minnucci, S and Banni, M}, title = {Microplastic-induced gut dysbiosis and metabolic alterations in juvenile European seabass (Dicentrarchus labrax): A multi-omics approach.}, journal = {Marine pollution bulletin}, volume = {230}, number = {}, pages = {119879}, doi = {10.1016/j.marpolbul.2026.119879}, pmid = {42140051}, issn = {1879-3363}, abstract = {Environmental microplastics (MPs) are increasingly recognized as emerging contaminants with the potential to disrupt intestinal homeostasis in marine organisms. However, most experimental evidence is based on pristine particles rather than environmentally weathered forms. This study investigated the intestinal effects of environmentally derived microplastics (EMPs) in juvenile European seabass (Dicentrarchus labrax) using an integrated multi-omics approach. Fish were exposed for five days to two concentrations of EMPs (0.5 and 1 mg/kg of feed), followed by analyses combining histological, transcriptomic, metabolomic, and metagenomic endpoints. EMP exposure led to significant particle accumulation in gut tissues, predominantly consisting of small polyethylene fragments. Gene expression and immunofluorescence analyses revealed activation of p53 and Caspase-3 mediated apoptosis together with NF-κB and IL-6 driven inflammatory signalling, indicating concurrent oxidative and immune stress. Untargeted metabolomics identified marked alterations in lipid metabolism, redox regulation, and amino acid turnover, consistent with mitochondrial dysfunction and impaired energy homeostasis. Parallel metagenomic profiling revealed subtle but coherent shifts in gut bacterial communities, with enrichment of pollutant-tolerant taxa such as Acidovorax and Halioglobus and reduction of beneficial commensals such as Ligilactobacillus. Multi-omics data integration demonstrated a coordinated restructuring of microbial and metabolic networks underlying host physiological stress. Collectively, these findings highlight the intestine as a primary target of microplastic toxicity and provide mechanistic insight into early biological responses to environmentally realistic microplastic exposure in marine fish.}, }
@article {pmid42140215, year = {2026}, author = {Hughes, N and Sathiananthamoorthy, S and Sergaki, C}, title = {Antimicrobial resistance surveillance through wastewater: methodological considerations for metagenomic approaches and public health perspectives.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101400}, doi = {10.1016/j.lanmic.2026.101400}, pmid = {42140215}, issn = {2666-5247}, abstract = {Antimicrobial resistance (AMR) is a recognised global threat with substantial predicted impact on lives, agriculture, and the economy. Metagenomic sequencing is being increasingly used for AMR surveillance and detection, given its capacity for community-level AMR profiling with high-level resolution. This technology has seen an explosion of surveillance efforts and data generation; however, the variation between workflows has direct implications on the sequencing results and their interpretation. In this Personal View, we summarise aspects of the sequencing workflow that need to be considered during metagenomic study design, for meaningful and reliable population-based surveillance. We reflect on the vital role of standardisation for capturing the ground truth of AMR and data comparability and reproducibility, and in addition, review the limitations of the various phenotypic and genotypic methods of AMR detection. We further highlight complex mechanisms of resistance to antimicrobials that could hinder our ability to confidently assess the true AMR burden in the environment and those that are often overlooked during surveillance.}, }
@article {pmid42140378, year = {2026}, author = {Tan, MW and Clister, D and Chandra, QM and Wangsa, CE and Simone, CN and Umaya, C and Choi, J and Park, S and Rani, A and Akter, S and Kim, B and Kim, SH and de Azambuja Ribeiro, RIM and Syahputra, RA}, title = {Circulating microbial metabolites and the gut-prostate axis in prostate cancer: Implications for laboratory biomarkers and therapeutic response.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {}, number = {}, pages = {121086}, doi = {10.1016/j.cca.2026.121086}, pmid = {42140378}, issn = {1873-3492}, abstract = {Prostate cancer progression and treatment response are influenced not only by tumor genomics and androgen receptor signaling but also by systemic host-microbiome interactions along the gut-prostate axis. Increasing evidence indicates that gut microbial metabolism produces bioactive compounds that circulate in human body fluids and can influence immune regulation, hormone metabolism, and therapeutic outcomes. This review synthesizes current evidence on microbiome-derived metabolites that may serve as measurable biomarkers relevant to prostate cancer biology and clinical laboratory diagnostics. Microbial metabolism of dietary substrates generates circulating molecules-including short-chain fatty acids, secondary bile acids, indole derivatives, polyamines, and endotoxin-associated signals-that can modulate inflammation, epithelial barrier integrity, and systemic immune responses involved in tumor progression. In addition, intestinal microbes participate in steroid transformation and enterohepatic cycling of hormones, potentially influencing circulating androgen and estrogen levels that contribute to androgen-driven prostate cancer development and adaptation under androgen deprivation therapy. Importantly, many of these microbial metabolites are detectable in serum or plasma using validated analytical platforms such as liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry, supporting their potential integration into laboratory biomarker panels. Emerging multi-omics approaches combining metagenomics, metabolomics, host transcriptomics, and immune profiling are beginning to clarify mechanistic links between microbial activity and therapy response, including variability in outcomes with androgen-targeted agents, chemotherapy, radiotherapy, and immune checkpoint inhibitors. From a clinical chemistry perspective, characterization of circulating microbiome-derived metabolites may enhance the diagnostic and prognostic performance of established biomarkers such as prostate-specific antigen while providing new opportunities for non-invasive monitoring of disease progression and treatment response. Establishing reproducible microbial metabolic signatures across diverse patient populations will be essential to translate microbiome-informed biomarkers into next-generation diagnostic and prognostic tools in prostate cancer management.}, }
@article {pmid41917256, year = {2026}, author = {Shen, Z and Liu, Y and Liu, Y and Zhang, P and Li, Y and Li, Z and Qi, H}, title = {Clinical characteristics and mixed infection patterns of ocular surface infection with Epstein-Barr virus.}, journal = {Journal of ophthalmic inflammation and infection}, volume = {16}, number = {1}, pages = {}, pmid = {41917256}, issn = {1869-5760}, abstract = {PURPOSE: To analyze the clinical features of ocular surface diseases caused by Epstein-Barr virus (EBV) infection.<br><br>METHODS: A retrospective case series study was conducted. Data from 48 patients (54 eyes) with EBV infection who visited Peking University Third Hospital between January 2023 and October 2025 were collected. Patient demographics and baseline information were recorded. Ophthalmic slit-lamp examination, ocular surface (conjunctiva/cornea) scrapings, bacterial culture of ocular secretions, real-time fluorescence quantitative PCR detection, EBV-specific antibody testing, and metagenomic next-generation sequencing (mNGS) were performed.<br><br>RESULTS: Among patients infected with EBV on the ocular surface, the majority were middle-aged individuals in the 31&#x2013;40 age group. The primary risk factors for onset were keeping pets (10/48), followed by colds (6/48); among those keeping pets, parrots were the most common (5/9). The main clinical manifestations were foreign body sensation (37/54) and yellow discharge (34/54). Common signs included mixed conjunctival hyperemia (31/54), follicles on the lower eyelid conjunctiva (17/54), papillae on the upper eyelid conjunctiva (8/54), and punctate epithelial defects on the cornea (17/54). In most ocular surface scrapings, small round lymphocytes were observed alongside a small number of reactive lymphocytes (44/54), which could simultaneously present with a large number of neutrophils (36/54). There was a significant difference between the presence of yellow discharge and the type of conjunctival hyperemia [Formula: see text]. However, no statistically significant correlation was found between the presence of yellow discharge and the presence of neutrophils in the scraping results [Formula: see text]. Significant differences were found in EBV viral loads among different groups of combined symptoms [Formula: see text] and among different follicle groups [Formula: see text]. No statistically significant correlation was found between the lymphocyte count in the scraping and the EBV viral load in the affected eye [Formula: see text].<br><br>CONCLUSION: EBV infection of the ocular surface is prone to concurrent infections; therefore, a detailed medical history inquiry is crucial. Ocular surface tissue scraping examination can rapidly identify viral infection-related inflammatory characteristics and rule out bacterial/fungal infections, providing effective supportive auxiliary diagnostic evidence for viral ocular surface infection, and precise diagnosis of EBV infection needs to be achieved in combination with molecular biological and serological tests.}, }
@article {pmid42014454, year = {2026}, author = {Muller, E and Bamberger, T and Borenstein, E}, title = {Navigating multi-omic integration methods for human microbiome research.}, journal = {Nature microbiology}, volume = {11}, number = {5}, pages = {1153-1167}, pmid = {42014454}, issn = {2058-5276}, support = {U19AG057377//U.S. Department of Health &amp; Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; 2266/25//Israel Science Foundation (ISF)/ ; }, mesh = {Humans ; *Microbiota/genetics ; *Computational Biology/methods ; Host Microbial Interactions ; *Metagenomics/methods ; Multiomics ; }, abstract = {Multi-omic studies in human microbiome research hold great potential for advancing our understanding of host-microbiome interactions. However, despite the growing availability of multi-omic datasets, analysing such data remains a major conceptual, analytical and computational challenge. Introduction of new multi-omic integration methods to address these challenges further complicates researchers' efforts to navigate this expanding field. In this Review, we outline the landscape of multi-omic integration methods in the context of human microbiome research. In contrast to previous reviews, we specifically emphasize the different biological questions addressed by various integration approaches, including questions related to interactions between different molecular layers, molecular shifts that occur in disease, subgrouping of patients based on molecular profiles, and identification of biological mechanisms that underlie such associations. Our aim is to provide a timely, convenient and comprehensive resource for the microbiome research community, allowing researchers to identify the multi-omic integration approach that is best suited to their data and objectives.}, }
@article {pmid42127855, year = {2026}, author = {Mei, Z and Zhou, H and Liu, K and Gao, C and Du, H and Sheng, Z and Gong, Y}, title = {Traditional Chinese medicine improves performance and intestinal health in laying hens under acute and chronic heat stress by modulating ileal metabolic functions.}, journal = {Poultry science}, volume = {105}, number = {8}, pages = {107056}, doi = {10.1016/j.psj.2026.107056}, pmid = {42127855}, issn = {1525-3171}, abstract = {Heat stress (HS) represents a significant challenge in poultry production, impairing thermoregulation, intestinal function, and productive performance. This study utilized acute (6 h) and chronic (14 d) HS models at 36°C in laying hens to characterize stage-dependent responses and evaluate the protective effects of a ten-ingredient traditional Chinese medicine (TCM) formulation. Both acute and chronic HS significantly increased rectal temperature and respiratory rate. Egg production declined by approximately 18% following acute HS and was further compromised under chronic exposure, along with reduced eggshell strength and weight. Dietary TCM supplementation (0.5%) alleviated physiological stress and partially restored laying performance, with more pronounced recovery observed under chronic HS. Serum analysis and histopathology indicated that TCM attenuated HS-induced impairment of ileal barrier function. Metabolomic profiling revealed stage-dependent responses: acute HS primarily disturbed redox balance, whereas chronic HS induced broader remodeling related to energy and nutrient utilization. TCM supplementation modulated metabolic functions to support immediate stress buffering under acute HS while stabilizing long-term energy support and intestinal capacity under chronic HS. Metagenomic analysis indicated that TCM selectively promoted microbial groups related to intestinal metabolism and nutrient utilization, aligning with metabolomic findings. Correlation analyses linked these TCM-associated microbial and metabolic signatures with improved thermoregulatory responses, oxidative status, and intestinal barrier indicators. Collectively, these results demonstrate that TCM supplementation enhances heat resilience in laying hens through stage-dependent modulation of the gut microbiota-metabolome axis, supporting its application as a nutritional strategy to maintain productivity under thermal challenge.}, }
@article {pmid42127905, year = {2026}, author = {Shen, J and Sun, Z and Song, H and Pu, Y and Wang, P and Hailili, G and Huang, Y and Mei, Z and Chen, H and Huang, L and Yuan, C and Wang, X and Zheng, Y}, title = {Healthful plant-based diet, gut enterotype, and cognition in a rural Chinese elderly cohort: A longitudinal multi-omics study.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {102797}, doi = {10.1016/j.xcrm.2026.102797}, pmid = {42127905}, issn = {2666-3791}, abstract = {The gut microbiome may shape how diet influences cognitive aging, but population-based evidence remains limited. In 784 older adults living in rural China (70-98 years old) with fecal metagenomics and structured dietary assessment, a modified healthful plant-based diet index (mHPDI) is associated with distinct gut microbial structure and taxonomic shifts (15 species, 17 genera). Among participants with repeated cognitive measurements, higher mHPDI is associated with better global cognition, with stronger benefits in participants with non-Prevotella-dominant enterotypes (highest versus lowest tertile β = 0.34, 95% confidence interval [CI], 0.16 to 0.52) than in those with a Prevotella-dominant enterotype (0.04, -0.22 to 0.29; p interaction = 0.04). Enterotype-associated differences in microbial metabolic pathways, including preQ0 and L-isoleucine biosynthesis, parallel this heterogeneity. Moreover, 12 circulating microbiota-related metabolites (primarily amino acids and short-chain fatty acids) are linked to mHPDI. A composite score comprising these metabolites mediates 11.0% of the mHPDI-cognition association (p mediation = 0.02), with branched-chain amino acids as major contributors. These findings suggest that gut microbial context may shape diet-cognition associations.}, }
@article {pmid42128151, year = {2026}, author = {Yang, F and Sui, C and Tian, H and Ao, J}, title = {Metagenomic next-generation sequencing reveals the clinicopathological features of mucormycosis.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108553}, doi = {10.1016/j.micpath.2026.108553}, pmid = {42128151}, issn = {1096-1208}, abstract = {BACKGROUND: Mucormycosis is a rare but highly lethal opportunistic infection driven by mucor fungi, which mainly affects individuals with compromised immune systems, such as diabetic patients and organ transplant recipients. This study aims to investigate the clinicopathological features of patients with mucormycosis diagnosed by metagenomic next-generation sequencing (mNGS).<br><br>METHODS: A systematic analysis was conducted in 15 cases of mucormycosis diagnosed and treated at Hunan Provincial People's Hospital between January 2019 and July 2024. Various detection methods were utilized, including hematoxylin-eosin staining, fungal fluorescence staining, fungal culture, and high-throughput mNGS technology to ensure an accurate diagnosis. Furthermore, we conducted a literature review and analyzed 311 cases of mucormycosis published in the public databases between 2021 and 2024 to assess the underlying pathological characteristics.<br><br>RESULTS: Of the 15 cases treated in our institute, ten (66.7%) were males, with a median age of 41 (range 4-78),five (33.3%) were females, with a median age of 58.5 (range 32-85). Compared to other detection methods including PAS/PASM staining, mNGS proved effective in diagnosing typical mucormycosis infections in 15 of the patients in this study. The literature review of 311 cases indicated that the lungs and bronchi were the main sites of infection, followed by the nasal cavity, brain, and skin. Diabetes emerged as the most prevalent underlying condition, present in more than 40% of cases. Other internal and immune system disorders, such as immunodeficiency disease, were also associated with an increased risk of infection.<br><br>CONCLUSIONS: MNGS is an effective diagnostic tool for mucormycosis.}, }
@article {pmid42128673, year = {2026}, author = {,  and ,  and , }, title = {[Expert consensus on laboratory identification of emerging pathogens based on metagenomic next-generation sequencing technology(2025 edition)].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {60}, number = {5}, pages = {669-684}, doi = {10.3760/cma.j.cn112150-20251117-01086}, pmid = {42128673}, issn = {0253-9624}, support = {2024ZD0532804//National Science and Technology Major Special Project for Noncommunicable Chronic Diseases/ ; 2025ZD01903400//National Science and Technology Major Special Project for Prevention and Control of New Emergencies and Major Infectious Diseases/ ; 2025-I2M-KJ-001, 2025-I2M-XHJC-004//CAMS Innovation Fund for Medical Sciences(CIFMS)/ ; }, mesh = {*High-Throughput Nucleotide Sequencing ; *Metagenomics ; Humans ; Consensus ; *Communicable Diseases, Emerging/diagnosis ; Computational Biology ; }, abstract = {Emerging pathogen infections pose a significant challenge to global public health security. Pathogen metagenomic next-generation sequencing (mNGS), characterized by its hypothesis-free, culture-independent, and unbiased nature, provides a powerful tool for the timely detection and precise identification of emerging pathogens. This consensus was jointly developed by multidisciplinary experts from clinical laboratories, infectious diseases, disease prevention and control, and other relevant fields. It aims to standardize the identification process for clinically suspected emerging pathogen infections, as well as specimen submission, technical requirements, bioinformatic analysis, and reporting and interpretation procedures for the laboratory identification of emerging pathogens using clinical mNGS technology. This framework provides systematic guidance for clinical early warning and practice.}, }
@article {pmid42128675, year = {2026}, author = {Zhou, HJ and Ma, JX and Hu, JR and Han, YX and Yang, B and Zhou, ZM and Li, LL and Liu, JY and Du, XL and Cui, ZG and Kan, B}, title = {[Analysis on the epidemiological characteristics of legionnaires' disease in China based on multi-source data].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {60}, number = {5}, pages = {714-720}, doi = {10.3760/cma.j.cn112150-20260306-00178}, pmid = {42128675}, issn = {0253-9624}, support = {GZNL2024A01025//Special Project of Guangzhou National Laboratory/ ; 2022YFC2305300//National Key Research and Development Program of China/ ; }, mesh = {Humans ; China/epidemiology ; *Legionnaires' Disease/epidemiology/microbiology ; Male ; Middle Aged ; Aged ; Female ; Genotype ; High-Throughput Nucleotide Sequencing ; Legionella pneumophila ; Legionella/genetics ; Adult ; Incidence ; }, abstract = {Objective: To analyze the epidemiological characteristics of Legionnaires' disease in China based on multi-source data. Methods: Based on the metagenomic next-generation sequencing (mNGS) data of bronchoalveolar lavage specimens collected from a third-party medical testing institution from March 2024 to September 2025, this study aggregated nucleic acid detection data for multiple pathogens from the National Pathogenic Bacteria Identification Network's respiratory syndrome surveillance and conducted a meta-analysis by combining published literature. Descriptive epidemiological methods were used to analyze the demographic characteristics, spatiotemporal distribution, and Legionella species and genotype of Legionnaires' disease in China. Results: By integrating three types of data sources, a total of 1 866 Legionnaires' disease cases were included in the study. Chinese Legionnaires' disease patients were predominantly middle-aged and elderly males, accounting for 64.31% of cases. The age distribution of cases exhibited a bimodal pattern, with a significant concentration in the middle-aged and elderly population. The 60-65 age group had the highest incidence. However, in addition to the peak in the middle-aged and elderly population, there was also a peak in the 0-5 age group. The number of cases showed a peak occurring from July to August. The cases exhibited significant regional distribution disparities across the country. Legionella pneumophila infection was predominant (accounting for 95.70%), with other species including Legionella macleodii (20 cases) and Legionella longbeachae (18 cases). Among 412 samples, L. pneumophila genotypes were obtained, divided into 7 sequence types, including ST36 (n=148), ST1 (n=60), ST23 (n=58), ST51 (n=51), ST734 (n=51), ST42 (n=32), and ST47 (n=12). The distribution of STs in different geographical regions had commonalities, but there were also certain regional differences. The results of universal core genome multi-locus sequence typing showed that each ST formed relatively independent branch clusters, indicating clear genetic differentiation between different STs. The overall genetic diversity of Legionella in China was high. Conclusion: Legionella-positive cases have been detected throughout the year in China, with a wide distribution and regional differences. L. pneumophila has a high proportion and a large genetic diversity in its genome.}, }
@article {pmid42128850, year = {2026}, author = {Fujii, N and Nakajima, M and Narihiro, T and Kuroda, K and Kindaichi, T}, title = {Current Understanding of Taxonomy and Ecology of the Phylum Minisyncoccota.}, journal = {Microbes and environments}, volume = {41}, number = {2}, pages = {}, doi = {10.1264/jsme2.ME25084}, pmid = {42128850}, issn = {1347-4405}, mesh = {*Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Phylogeny ; Ecosystem ; Genome, Bacterial ; }, abstract = {The phylum Minisyncoccota (formerly known as "Candidatus Patescibacteria"/candidate phyla radiation [CPR] and designated under SeqCode as Patescibacteriota) represents one of the major bacterial phyla; however, its physiological and ecological characteristics remain unclear. This review summarizes relevant studies on currently available isolate and genomic/metagenomic data, outlining the phylogenetic placement, metabolic features, host interactions, and unique genetic code usage of Minisyncoccota. Minisyncoccota play complementary and interdependent roles within microbial communities, while being restricted by incomplete metabolic capabilities that prevent independent survival. Studies on Minisyncoccota offer important insights into the diversity and evolution of uncultivated bacteria, as well as the hidden interaction networks that shape microbial ecosystems.}, }
@article {pmid42129189, year = {2026}, author = {Lacruz-Pleguezuelos, B and Pérez-Cuervo, A and Coleto-Checa, D and Bazán, GX and Romero-Tapiador, S and Freixer, G and Fernández-Cabezas, J and Aguilar-Aguilar, E and Martín-Segura, A and Cárdenas-Roig, N and Carrasco-Guijarro, L and Fernández, LP and Espinosa-Salinas, I and Ramírez de Molina, A and Morales, A and Tolosana, R and Ortega-Garcia, J and Pancaldi, V and Marcos-Zambrano, LJ and Carrillo de Santa Pau, E}, title = {Network topology of the gut microbiome associates with metabolic health in obesity.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42129189}, issn = {2041-1723}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Male ; Female ; *Obesity/microbiology/metabolism ; Middle Aged ; Cross-Sectional Studies ; Adult ; Feces/microbiology ; Metagenomics ; *Obesity, Metabolically Benign/microbiology/metabolism ; Dysbiosis/microbiology ; Phenotype ; }, abstract = {Obesity is a heterogeneous condition comprising a continuum of phenotypes with various metabolic and inflammatory profiles. Metabolically healthy obesity (MHO) identifies individuals with obesity but a relatively preserved metabolic state, although little is known about the gut microbiome features underlying this phenotype. Here, we analyzed gut microbial network structures of 931 individuals living with metabolically healthy non-obesity (MHNO), MHO, metabolically unhealthy non-obesity (MUNO), and metabolically unhealthy obesity (MUO), performing cross-sectional analyses on feces shotgun metagenomics data. Individuals with MHNO and MHO harbor more robust and functionally cohesive microbial networks, while communities from MUO and MUNO phenotypes exhibit a potentially dysbiotic state with reduced connectivity. A nutritional intervention cohort showed an improvement in network connectivity in parallel with metabolic improvements. Our findings show differences in microbial connectivity and association patterns across metabolic and obesity phenotypes, shedding light on how distinct microbial network structures may associate with host metabolic health and disease.}, }
@article {pmid42129350, year = {2026}, author = {Parkin, K and Christophersen, CT and Verhasselt, V and Palmer, DJ and Cooper, MN and Prescott, SL and Silva, D and Martino, D}, title = {Chlorinated drinking water exposure enriches antimicrobial resistance pathways in the infant gut microbiome: a randomized trial.}, journal = {Communications medicine}, volume = {}, number = {}, pages = {}, doi = {10.1038/s43856-026-01626-2}, pmid = {42129350}, issn = {2730-664X}, abstract = {BACKGROUND: Water chlorination is essential for controlling harmful microbes in drinking water; however, the antimicrobial effects of chlorine-based disinfectants present in tap water may influence early-life gut microbial ecology.<br><br>OBJECTIVE: To investigate the functional and compositional impact of chlorinated drinking water on the gut microbiome of infants.<br><br>DESIGN: The waTer qUality and Microbiome Study (TUMS) was an Australian-based double-blinded, randomised controlled trial. Six-month-old infants (n&#x2009;=&#x2009;197) received either de-chlorinated drinking water via benchtop filtration (treatment, n&#x2009;=&#x2009;99), or regular chlorinated water (control, n&#x2009;=&#x2009;98) for twelve months. Tap water and stool samples were collected at baseline and at end of intervention. Metagenomic sequencing was used for faecal microbiome analysis. Primary outcomes were differences in gut microbiota between groups, secondary outcomes included incidence of allergic sensitization and respiratory conditions.<br><br>RESULTS: At baseline, 170 stool samples (83 control, 87 intervention) were collected, with 130 samples obtained at the end of the intervention (65 control, 65 intervention). Overall community structure was similar between groups after the intervention, including beta diversity (0.56% variance explained; p&#x2009;=&#x2009;0.84), richness (-4.25, 95% CI; -14.85 to 6.35, p&#x2009;=&#x2009;0.43) or Shannon Index (-0.14, 95% CI; -0.32 to 0.04, p&#x2009;=&#x2009;0.12). The chlorinated water group showed enrichment of antibiotic resistance MetaCyc groups and pathways (adjusted p&#x2009;<&#x2009;0.05). Stratified analysis suggested this effect was potentiated by clinical antibiotic use.<br><br>CONCLUSION: Chlorinated drinking water may enhance resistance functions in the infant gut microbiome. While remaining vital for public health, future studies should explore whether adjusting the timing or method of drinking water disinfectants into the infant diet can reduce selective pressures.<br><br>TRIAL REGISTRATION: ACTRN12619000458134; https://www.anzctr.org.au.}, }
@article {pmid42129659, year = {2026}, author = {Chen, J and Li, X and Deng, Z and Ying, Y and Lu, M}, title = {Clinical characteristics of sporadic acute Q fever diagnosed by metagenomic next-generation sequencing: a retrospective analysis and literature review in China.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13477-2}, pmid = {42129659}, issn = {1471-2334}, support = {MISP-102684//MSD Investigator Initiated Studies Program Review Committee/ ; 2022YFC2303203-01//National Key Research and Development Program of China/ ; Z-2017-24-2202//Metagenomics of the Bacterial Infection and Drug Resistance Prevention of the Chinese Medical Association/ ; }, abstract = {BACKGROUND: Acute Q fever manifests sporadically in mainland China, where its clinical spectrum and optimal diagnostic strategies remain under-recognized. This study aimed to delineate the clinical phenotype and antimicrobial prescribing patterns of sporadic acute Q fever diagnosed via metagenomic next-generation sequencing (mNGS).<br><br>METHODS: We conducted a retrospective, single-center cohort study of adult patients with sporadic acute Q fever. A comprehensive literature review of all published sporadic cases across China was subsequently performed to delineate the national clinical spectrum of sporadic Q fever.<br><br>RESULTS: The cohort comprised 22 male patients (mean age 36.7&#xb1;13.5 years). All patients presented with high-grade pyrexia (>39&#xb0;C) accompanied by a characteristic symptom constellation of headache, fatigue, myalgia, and hepatic involvement (100%, mean ALT 122.2&#xb1;56.9 U/L). Pneumonia was observed in 2 patients (2/22, 9.1%). A distinct dissociation was observed between markedly elevated C-reactive protein (mean 67.4 &#xb1; 33.6 mg/L) and normal leukocyte counts. A pooled analysis of 94 published cases and 22 consecutive patients from our center yielded 116 confirmed Q fever cases (male-to-female ratio 11.9:1, the proportion of hepatitis and pneumonia:87.9% and 24.1%) The median interval from symptom onset to pathogen confirmation was 7.8 &#xb1; 2.8 days. mNGS yielded a diagnosis in 77.5 % of 116 patients, the remaining 22.5 % were identified by PCR and antibody testing.<br><br>CONCLUSION: Acute Q fever in China predominantly affects young males, presenting as a systemic febrile illness with a distinctive hepatic phenotype (elevated liver enzymes) rather than prominent pneumonia. The clinical triad of high fever, influenza-like symptoms (headache/myalgia), and "WBC-CRP dissociation" (normal white cell count with elevated CRP) serves as a potential clinical indicator. Empiric doxycycline should be initiated promptly in suspected cases. mNGS is a valuable tool for definitive diagnosis, particularly when empiric therapy fails or in severe/complicated cases.}, }
@article {pmid42129710, year = {2026}, author = {Wang, Z and Tang, J and Yang, K and Cui, Z and Li, Z}, title = {Diagnostic challenges and lessons learned of Guillain-Barré syndrome mimicking central nervous system infection - a case report.}, journal = {BMC neurology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12883-026-04942-1}, pmid = {42129710}, issn = {1471-2377}, abstract = {BACKGROUND: Guillain-Barré syndrome (GBS) is an immune-mediated disorder affecting the peripheral nervous system, often triggered by infections, vaccinations, trauma, or surgery. Typically, it presents as progressive, symmetric limb weakness with hyporeflexia. However, some GBS subtypes can present atypically with symptoms like headache, facial palsy, and confusion. These symptoms overlap significantly with central nervous system (CNS) infections, often causing diagnostic delays.<br><br>CASE PRESENTATION: A 57-year-old man was admitted with cough, sputum, and shortness of breath, having received a rabies vaccination a month earlier. He developed headache, dysphagia, progressive muscle weakness, and impaired consciousness, requiring Intensive Care Unit (ICU) transfer, endotracheal intubation, and mechanical ventilation. The initial cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) detected Pseudomonas aeruginosa (sequence count: 6094), combined with fever and a series of clinical symptoms before transfer to the ICU, CNS infection was considered. Treatment with piperacillin-tazobactam, meropenem, and ciprofloxacin yielded no improvement. Albumino-cytological dissociation in the CSF led to a neurology consultation for suspected GBS, and intravenous immunoglobulin (IVIg) therapy began. Negative CSF bacterial cultures and mNGS, along with positive anti-GT1a IgM ganglioside antibodies and electromyogram(EMG) result indicating nerve damage, confirmed the GBS diagnosis. After five days of IVIg, the patient was weaned from mechanical ventilation and showed significant neurological recovery.<br><br>CONCLUSION: The significant clinical overlap between GBS and CNS infections poses a major diagnostic and therapeutic challenge. This case highlights the importance of thorough history-taking, comprehensive neurological assessment, careful interpretation of lab results, and early neurologist involvement to minimize diagnostic delays in GBS and prevent subsequent treatment delays.}, }
@article {pmid42129938, year = {2026}, author = {Zhao, L and Wu, L and Yin, S and Gao, W and Xiang, X and Xie, Y and Guo, Y and Wang, Z}, title = {Multi-omics reveals effects of several rumen bacteria on reproductive performance of sheep.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02426-5}, pmid = {42129938}, issn = {2049-2618}, support = {2025SNJF019//Three Agriculture Nine Party Science and Technology Cooperation Project/ ; 32573211//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Mounting evidence indicates that the rumen microbiota plays a crucial role in the reproductive health of sheep. However, the potential beneficial effects of rumen microbiota on lambing performance in sheep across different stages of the reproductive cycle and the precise mechanisms underlying these effects remain unclear. We aimed to elucidate the rumen microbial regulatory network underlying differences in reproductive performance in sheep by integrating multi-stage metagenomics and metabolomics.<br><br>RESULTS: No significant difference was observed in the ruminal microbial &#x3b1;-diversity between sheep with high and low litter size. However, significant stage-specific segregation was observed in their community structures. We identified a cohort of key species strongly associated with litter size. These included Asaia bogorensis, Methanolobus zinderi, Erwinia gerundensis, Marinobacter sp. BSs20148, and Lactobacillus amylolyticus enriched during pregnancy; Rhizobium gallicum, Aeromonas caviae, Pseudolysobacter antarcticus, Mucilaginibacter rubeus, Thermococcus paralvinellae, and Janthinobacterium svalbardensis enriched during lactation; Pseudomonas mandelii, Gordonia sp. HY186, Arachidicoccus sp. BS20, Mesotoga prima, Acidovorax ebreus, Donacia cinerea, and Salmonella enterica enriched during estrus. Host plasma metabolomics analysis further revealed an enrichment of a set of core metabolites in the blood of high-fertility sheep, including Inositol, 2-Linoleoylglycerol, lysophosphatidylcholines and neuromodulatory substances such as tyramine and sphingosine-1-phosphate. We constructed stage-specific "rumen microbe-rumen metabolite-plasma metabolite" regulatory axes. These results suggest the influence of the rumen microbiome on plasma metabolic profiles and subsequent fertility outcomes in sheep.<br><br>CONCLUSION: We elucidate the dynamic mechanism by which the rumen microbiota in high-fertility sheep is associated with superior reproductive performance through stage-adaptive community succession and functional remodeling, which in turn may modulate the host's neuroendocrine and lipid metabolic profiles. These findings provide a new perspective for understanding the regulation of fertility in ruminants and lay a theoretical foundation for improving reproductive efficiency through nutritional strategies targeting the rumen microbiota. Video Abstract.}, }
@article {pmid42130304, year = {2026}, author = {Preston, S and Jones, J and Huggett, MJ and Adam, AAS and White, NE and Tan, KC and Richards, Z}, title = {Comparing Microbial Communities of Diseased and Healthy Isopora palifera Corals and Adjacent Waters at the Cocos (Keeling) Islands.}, journal = {Environmental microbiology}, volume = {28}, number = {5}, pages = {e70324}, doi = {10.1111/1462-2920.70324}, pmid = {42130304}, issn = {1462-2920}, support = {LP160101508//Australian Research Council/ ; }, mesh = {*Anthozoa/microbiology/growth &amp; development ; Animals ; *Bacteria/genetics/classification/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Seawater/microbiology ; Islands ; Coral Reefs ; }, abstract = {Growth anomalies (GAs) are coral diseases characterised by tumour-like skeletal lesions reported globally, yet their causes remain poorly understood. Microorganisms are integral to coral health, but the role of bacterial communities in GAs remains unclear. We investigated an outbreak of GAs in Isopora palifera at the Cocos (Keeling) Islands using 16S rRNA amplicon sequencing to compare bacterial communities of GA-affected and asymptomatic corals, surrounding water and potential pollution sources. Significant differences in bacterial beta diversity were observed across sites, with an interaction between location and coral health status. Coral and water samples hosted distinct microbial communities, but there was no evidence linking GA-affected corals to local pollution. Moreover, no consistent bacterial taxa were associated with disease, suggesting that resident microbes may not be primary drivers of GAs. However, our study does not account for transient microbes that may have initiated GAs. Our findings challenge assumptions of single-agent causality and microbial compositional homogeneity in coral diseases. This study advances understanding of microbial dynamics in coral disease ecology and underscores the importance of early-stage investigation and functional metagenomics to identify viral, fungal and microbial functional shifts in disease emergence. Studying outbreaks in minimally impacted systems offers valuable baselines for disentangling natural disease processes.}, }
@article {pmid42130363, year = {2026}, author = {DU, WQ and Liu, LJ and Zhang, L and Tang, YF and Liu, LQ and Li, XF and Xiao, YY}, title = {[A case of Bartonella henselae meningitis characterized by bone marrow hemophagocytosis].}, journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics}, volume = {28}, number = {5}, pages = {618-623}, doi = {10.7499/j.issn.1008-8830.2510033}, pmid = {42130363}, issn = {1008-8830}, mesh = {Humans ; Male ; Adolescent ; *Bartonella henselae ; *Cat-Scratch Disease/complications ; *Lymphohistiocytosis, Hemophagocytic/etiology ; *Bone Marrow/pathology ; *Meningitis, Bacterial ; }, abstract = {A 13-year-old boy with Bartonella henselae meningitis is reported. He presented with recurrent fever with no history of cat scratches and no lymphadenopathy. Cerebrospinal fluid analysis showed an elevated white blood cell count, and Bartonella henselae infection was confirmed by metagenomic next-generation sequencing. Bone marrow examination revealed hemophagocytosis predominantly involving nucleated erythrocytes; to our knowledge, this bone marrow morphological abnormality is the first reported worldwide in association with Bartonella henselae infection. Transient bilateral hip pain occurred during the illness and was considered infection-related joint involvement. The patient improved with treatment and had no neurological sequelae. This case expands the spectrum of clinical and bone marrow manifestations of Bartonella henselae infection and warrants vigilance for possible central nervous system and bone marrow involvement in cases of fever of infectious etiology presenting without typical lymphadenopathy.}, }
@article {pmid42130962, year = {2026}, author = {Tomar, SS and Khairnar, K}, title = {Disruption in the Host-Phage Dynamics and Altered Microbial Diversity in the Upper Respiratory Tract of SARS-CoV-2-Infected Individuals.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {7}, number = {1}, pages = {9-20}, pmid = {42130962}, issn = {2641-6549}, abstract = {BACKGROUND: The upper respiratory tract (URT) is an important site for the predisposition and multiplication of the SARS-CoV-2 virus. Therefore, URT is a critical site for investigating the changes in the microbiome caused by the SARS-CoV-2 infection. This study aims to compare phageome diversity and investigate the correlation of the phageome profiles with the sample type (SARS-CoV-2 or control) to determine the nature of phage-host interactions in the human URT microbiome and to assess the effect of SARS-CoV-2 viral load on host and phage abundance.<br><br>MATERIALS AND METHODS: In this study, we have used the whole-genome shotgun metagenomic approach to investigate URT swab samples (n = 96) collected from SARS-CoV-2-positive individuals (n = 48) (nonhospitalized but symptomatic) and healthy controls (n = 48) belonging to five districts of central India.<br><br>RESULTS: The results revealed distinct phageome profiles among the groups; Detrevirus dominated the composition in the control samples, while Maxrubnervirus was dominant in SARS-CoV-2 samples. Microbial diversity analysis showed significantly higher richness in the SARS-CoV-2 group compared to controls for both bacteria (Chao1: 886.00 vs. 351.00, p < 0.0001) and phages (Chao1: 39.00 vs. 16.00, p = 0.0002). Bacterial diversity (Simpson index) was lower in the SARS-CoV-2 group (0.88 vs. 0.93, p = 0.0024), whereas phage diversity was higher in the SARS-CoV-2 group (0.86 vs. 0.79, p = 0.0384). Viral load, as reflected by cycle threshold (Ct) values, significantly influenced both bacteria (H = 6.69, p = 0.035) and phage (H = 8.97, p = 0.011) abundances. Host-phage interaction networks appeared disrupted in SARS-CoV-2 samples, with a weaker logistic model fit (R [2] = 0.7425) than controls (R [2] = 0.9265).<br><br>CONCLUSION: SARS-CoV-2 infection alters URT microbiome composition, increasing microbial diversity but disrupting host-phage dynamics. SARS-CoV-2 Viral load correlates with the shifts in microbial abundance, indicating infection-driven shifts in microbiome stability compared to healthy controls.}, }
@article {pmid42131203, year = {2026}, author = {Zahra, M and Ouf, A and Azzazy, HME and Moustafa, A}, title = {Metagenomic profiling of gut microbiome signatures across liver disease stages and HCV-related hepatocellular carcinoma in Egyptian patients.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1758563}, pmid = {42131203}, issn = {1664-302X}, abstract = {INTRODUCTION: Dysbiosis in the gut microbiome, particularly concerning the synchronous crosstalk between the gut and the liver, has been associated with various diseases. This study examines the gut microbiome's role in liver diseases among Egyptian patients, with a focus on the hepatitis C virus (HCV) and hepatocellular carcinoma (HCC), both of which are highly prevalent in Egypt.<br><br>METHODS: Utilizing shotgun metagenomic sequencing, we analyzed microbial gene catalogs and taxonomic profiles from 46 Egyptian patients categorized into five groups: healthy individuals, liver disease patients of different etiologies, post-HCV, treated HCV, and HCV-HCC patients.<br><br>RESULTS: Healthy and treated HCV patients exhibited distinct microbial profiles characterized by an abundance of beneficial bacteria, Faecalibacterium and Bifidobacterium (p < 0.05), associated with anti-inflammatory short-chain fatty acid production. Conversely, liver disease and HCC patients displayed increased pathogenic bacteria, Escherichia (p < 0.05), and genes linked to inflammation and oncogenesis, including lipopolysaccharide biosynthesis.<br><br>DISCUSSION: These findings suggest a dominance of Faecalibacterium in healthy Egyptians, likely attributable to traditional dietary patterns, and cytochrome P450 genes as potential HCC biomarkers, possibly connected to aflatoxin exposure. Treated HCV patients showed significant microbiome recovery, reflecting effective antiviral therapy. These findings emphasize that Egypt-specific factors, such as persistent resistance genes post-HCV due to antibiotic use and the prominence of bile acid metabolism genes, are influenced by high HCV prevalence and environmental exposures like aflatoxins. Taken together, the results highlight the need for region-specific microbiome research priorities in Egypt and underscore how local dietary, clinical, and environmental factors may shape future objectives in understanding liver disease pathogenesis and prevention.}, }
@article {pmid42131208, year = {2026}, author = {Hembram, DB and Panda, SP and Das, BK and Soren, D and Singh, NR}, title = {Microbial elicitors to metabolic reprogramming: an integrative model of plant-microbe interactions.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1816468}, pmid = {42131208}, issn = {1664-302X}, abstract = {Plant growth, soil health, and crop productivity with nutritional quality can be significantly enhanced by employing microbial consortia that incorporate diverse microorganisms with complementary functions. Plants produce various types of secondary metabolites such as terpenoids, alkaloids, phenolics, essential oils, and other metabolites through various cellular mechanisms, which are often stimulated by microbial interactions. These metabolites exert beneficial effects on plants and perform multiple roles in agriculture, contributing significantly to growth and economy. This review summarizes microbial consortia-mediated enhancement of plant health and their intricate interactions with host plants. Beneficial microbes of a consortium trigger complex signaling cascades leading to a dynamic regulatory strategy through which plants enhance their secondary metabolite synthesis. Secondary messengers and hormonal cross-talk further integrate the signal to transcription factors, which play a central role in activating or repressing the key genes of the metabolic pathways. Thus, the interplay of microbial signal, secondary messengers, hormonal cross-talk, and key metabolite genes forms the basis of plant secondary metabolite biosynthesis. In addition, recent advances in systems microbiology, including metagenomics, metatranscriptomics, and metabolomics, have enabled a holistic understanding of microbial community dynamics and their collective role in regulating secondary metabolism.}, }
@article {pmid42131214, year = {2026}, author = {Sudianto, E and Shlafstein, MD and Durieu, B and Harmel, M and Cornet, L and Saw, JH}, title = {Taxonomic description of cyanobacteria from extreme habitats through genome-based classification.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1824103}, pmid = {42131214}, issn = {1664-302X}, abstract = {INTRODUCTION: Cyanobacteria form a morphologically and phylogenetically diverse group of oxygenic phototrophic bacteria inhabiting a wide range of environments, including extreme habitats such as hot springs and volcanic steam vents. Many lineages, particularly those from these extreme environments, remain uncultured and are known only from metagenome-assembled genomes (MAGs), limiting their integration into formal taxonomy.<br><br>METHODS: Analysis of 46 steam vent associated samples from Hawai'i using 16S rRNA amplicon sequencing revealed that cyanobacteria dominate these communities. Gloeobacter kilaueensis dominated pit-like environments with low-light conditions, while Leptolyngbyaceae and other families are more dominant in structured soil and wall communities. We further reconstructed 38 high-quality cyanobacterial MAGs and incorporated them into a phylogenomic analysis comprising 343 cyanobacterial genomes, followed by genome-based comparisons against 9,026 reference genomes.<br><br>RESULTS: This revealed eight novel species and one novel genus spanning five orders: Chroococcidiopsidales, Leptolyngbyales, Nostocales, Oculatellales, and Oscillatoriales. Following SeqCode guidelines, we provide the first formal taxonomic descriptions of cyanobacterial MAGs and propose guidelines for integrating genome-based and cultivated material.<br><br>CONCLUSION: These findings highlight Hawaiian steam vents as hotspots of previously uncharacterized cyanobacterial diversity and underscore the importance of genome-based nomenclature.}, }
@article {pmid42131265, year = {2026}, author = {Cheng, J and Ni, J and Zhao, Y and Jiang, L and Huang, Y and Zhang, Y and Yan, P and Long, Z and Fu, H and Jiang, X}, title = {The clinical utility of metagenomic next-generation sequencing in the management of fever in patients with hematological disorders.}, journal = {Nagoya journal of medical science}, volume = {88}, number = {1}, pages = {84-98}, pmid = {42131265}, issn = {2186-3326}, mesh = {Humans ; Male ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Adult ; *Metagenomics/methods ; Aged ; *Hematologic Neoplasms/complications/microbiology ; *Fever/microbiology/drug therapy/diagnosis ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {Patients with hematological malignancies frequently present with severe and intricate infections that pose life-threatening risks. Conventional pathogen detection methods offer limited clinical insights and therapeutic guidance. This retrospective study evaluated the clinical application of metagenomic next-generation sequencing (mNGS) in hematologic patients who remained febrile despite prolonged antibiotic therapy, which means unresponsive to antibiotic therapy. This retrospective analysis included 204 patients with hematologic malignancies, undergoing conventional pathogen detection and peripheral blood mNGS. The cohort was stratified into neutropenia and non-neutropenia groups to compare the diagnostic and therapeutic implications of mNGS versus conventional microbiological tests (CMT). Among the 204 patients with mNGS, the overall positive detection rate was significantly higher than that of CMT (68.1% vs 30.9%, P<0.001). In both the neutropenia and non-neutropenia group, mNGS demonstrated a higher positivity rate for bacteria than for CMT (bacteria, 36.4% vs 15.6%, P<0.01). mNGS proved notably advantageous for bloodstream infections with clinically relevant drug-resistant strains, particularly in the neutropenia cohort (26.4% vs 12.5%, P<0.001). Using a composite reference standard, mNGS manifested sensitivity and specificity rates of 78.4% and 61.9%, respectively. Patients in the neutropenia group derived superior clinical benefit from mNGS, including higher diagnostic accuracy and treatment efficacy (diagnosis, 56.4% vs 40.6%, P=0.036; treatment, 49.3% vs 31.3%, P = 0.016). Additionally, the 30-days mortality rate was notably higher among mNGS-positive patients who tested compared to those who tested negative (17.3% vs 1.5%, P<0.001). mNGS demonstrated clinical relevance in patients with hematologic malignancy who received prolonged antibiotic treatment and holds promise in predicting patient survival prognosis.}, }
@article {pmid42131305, year = {2026}, author = {Toto, F and Cardile, S and Scanu, M and Marzano, V and Petito, V and Masi, L and Puca, P and Giorgio, V and Alterio, T and Diamanti, A and De Angelis, P and Lopetuso, LR and Scaldaferri, F and Putignani, L and Del Chierico, F}, title = {Ecological patterns of the gut mycobiome and microbiome in ulcerative colitis across life stages.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1769892}, pmid = {42131305}, issn = {2235-2988}, mesh = {Humans ; *Colitis, Ulcerative/microbiology/immunology ; *Mycobiome ; *Gastrointestinal Microbiome ; Adult ; Child ; Male ; Female ; *Fungi/classification/genetics/isolation &amp; purification ; Bacteria/classification/genetics/isolation &amp; purification ; Middle Aged ; Young Adult ; Adolescent ; Dysbiosis/microbiology ; Metagenome ; Child, Preschool ; Age Factors ; Aged ; Feces/microbiology ; }, abstract = {INTRODUCTION: Age-related variations in the gut microbial communities may influence immune regulation and inflammatory processes in inflammatory bowel diseases (IBD). However, distinguishing age effects from differences in clinical characteristics remains challenging.<br><br>METHODS: We investigated life-stage-associated patterns of the gut microbiome and mycobiome while accounting for clinical heterogeneity between paediatric and adult ulcerative colitis (UC) populations. We analysed 73 targeted metagenomes of bacteria and 69 targeted metagenomes of fungi from 26 paediatric and 47 adult patients with UC. Microbial diversity metrics and multivariate analyses were applied to evaluate community variation, and mucosal immune markers were assessed by ELISA. Clinical variables, including disease activity, duration, and treatment exposure, were considered when interpreting age-related microbial differences.<br><br>RESULTS: Fungal communities exhibited higher richness in adults and formed distinct age-related clusters in beta-diversity analyses, whereas bacterial composition remained largely comparable across age groups. Children were enriched in inflammation-associated fungi (Saccharomycetes, Aureobasidium, Cladosporium) and depleted in taxa commonly linked to gut health (Clavispora, Vishniacozyma, Betamyces). Stratification by life stage identified young adults as displaying the most pronounced dysbiosis, characterised by Basidiomycota/Ascomycota and Firmicutes/Bacteroidota ratios, and reduced Faecalibacterium prausnitzii abundance. Age-associated immune patterns were observed, with lysozyme levels increasing across life stages, correlating with sIgA, and positively associating with F. prausnitzii, although declining with increasing disease severity.<br><br>DISCUSSION: Age-related variation was more evident in fungal than bacterial communities, suggesting that host developmental and immunological factors contribute to mycobiome configuration beyond clinical imbalance alone. Together, these findings indicate that life stage is linked to ecological variation of the gut mycobiome and mucosal immune responses in UC, while bacterial communities appear primarily shaped by disease-related factors. The transition from childhood to adulthood may represent a critical window of host-fungal interaction relevant for age-tailored microbiome-based strategies.}, }
@article {pmid42131468, year = {2026}, author = {Mazibuko, X and Mtimka, S and Ngobese, LM and Mafuna, T and Simelane, MB and Yakobi, SH and Gumede, X and Pooe, OJ}, title = {Metagenomic Profiling of Taxonomic and Functional Diversity in Soil Microbial Communities at Buffelsdraai Landfill, South Africa: Implications for Bioremediation.}, journal = {Bioinformatics and biology insights}, volume = {20}, number = {}, pages = {11779322251413418}, pmid = {42131468}, issn = {1177-9322}, abstract = {Soil microbial communities in landfills play a crucial in waste degradation and pollution mitigation, yet their diversity and functionality in many regions remain underexplored. This study used shotgun metagenomic sequencing to characterise microbial communities in soil samples from the Buffelsdraai landfill waste site (samples: XM-AA, XM-BB, XM-CC, XM-DD). We identified dominant taxa, namely, Actinobacteria, Acidobacteria, and Bacteroidetes, and evaluated their taxonomic diversity and metabolic potential. Diversity indices revealed high richness in XM-AA (Shannon: 4.188), suggesting the potential of a strong waste-processing capacity, while XM-BB showed reduced diversity (Shannon: 1.453), likely due to contaminant stress (eg, nickel, cobalt). XM-CC and XM-DD exhibited moderate diversity (Shannon: 2.671-2.942) with Actinobacteria dominance (99%), suggesting adaptation to landfill conditions. Functional profiling via Kyoto Encyclopaedia of Genes and Genomes pathways highlighted carbohydrate and lipid metabolism, alongside xenobiotic biodegradation, pointing to potential for organic waste and pollutant breakdown. Physicochemical analyses detected elevated sodium (22 640 mg/kg in cell 1) and trace metals (eg, Ni: 0.1469 mg/kg), influencing microbial composition. These results emphasise microbial diversity's role in landfill soil functionality and position Actinobacteria as a bioremediation target for degrading leachate organics and immobilising metals. This study provides a baseline profile of microbial taxonomic and functional responses to landfill-associated environmental stressors in South Africa. The findings highlight the ecological roles of landfill microbial communities and their potential relevance for future bioremediation research.}, }
@article {pmid42131611, year = {2026}, author = {Zhai, X and Pan, H and Zheng, J}, title = {Spinal infection caused by Coxiella burnetii and surgical treatments: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1785109}, pmid = {42131611}, issn = {2296-858X}, abstract = {Q fever is a rare global zoonosis caused by Coxiella burnetii, with bone and joint involvement being an uncommon manifestation that poses significant diagnostic challenges. This article reports a case of persistent focal spinal infection caused by C. burnetii in an elderly female without a clear epidemiological exposure history, who was initially misdiagnosed with vertebral compression fractures. The diagnosis was confirmed by third-generation nanopore-based metagenomic next-generation sequencing (mNGS), which detected 12,170 reads of C. burnetii with a relative abundance of 98.27%. The patient was initially treated with oral doxycycline (0.1 g q12h) and rifampin capsules (0.45 g daily) for 4 weeks, resulting in decreased inflammatory markers and reduced paravertebral abscess size. After clinical stabilization, surgical intervention (posterior approach T12-L1 vertebral lesion resection, intervertebral bone graft fusion, and pedicle screw rod fixation) was performed under general anaesthesia. Postoperative follow-up for 3 months showed a significant improvement in the patient's low back pain [visual analogue scale (VAS) score from 6 preoperatively to 1 at 3 months] and functional status [Oswestry Disability Index (ODI) from 65% preoperatively to 10% at 3 months], with normalized inflammatory markers and a reduced C. burnetii IgG antibody titre (from 1:256 to 1:128). Serological follow-up revealed persistent negative IgM antibodies throughout the treatment course. This case highlights the diagnostic value of third-generation mNGS for rare spinal infections caused by C. burnetii and the efficacy of a multimodal treatment approach combining targeted antimicrobial therapy and surgical intervention. The rationale for antibiotic selection and surgical management is discussed, along with the limitations of the present case and clinical insights for managing similar cases.}, }
@article {pmid42132311, year = {2026}, author = {Tulloch, RL and Rojahn, J and Neaves, LE and Trujillo-González, A and Holleley, CE and Hahn, EE}, title = {Evaluating the Molecular Potential and Interpretability of DNA in Historical Spirit Collection Media.}, journal = {Molecular ecology resources}, volume = {26}, number = {4}, pages = {e70153}, doi = {10.1111/1755-0998.70153}, pmid = {42132311}, issn = {1755-0998}, support = {//Centre for Biodiversity Analysis/ ; }, mesh = {*DNA/isolation &amp; purification/genetics ; *Specimen Handling/methods ; Animals ; Metagenomics/methods ; DNA Barcoding, Taxonomic/methods ; Museums ; *Preservation, Biological/methods ; }, abstract = {Advancements in historical genomics increasingly leverage museum collections to study past ecosystems, species interactions and biodiversity. Formalin-fixed, ethanol-preserved specimens, once thought inaccessible to molecular analyses due to DNA degradation, are emerging as valuable genomic resources. If recoverable and reliably attributable, DNA within preservation media could provide a non-destructive alternative to conventional tissue sampling, with the potential to expand molecular access to valuable or irreplaceable specimens. We tested whether preservation media contains recoverable DNA suitable for taxonomic inference. We coupled passive adsorption and active filtration of specimen media with hot alkaline lysis DNA extraction followed by metabarcoding and shotgun metagenomics. DNA was recoverable across samples, including 41 of 61 (~67%) targets in a composite sample. However, detections were dominated by non-target taxa, indicating that preservation media retain a layered mixture of specimen-derived DNA and broader collection-level background. Detection success tracked with preservation chemistry (near-neutral pH and low residual formaldehyde) rather than specimen age. Method choice influenced detections: active filtration increased target detections but admitted more background; passive capture was sparser but more selective; shotgun sequencing retrieved broader vertebrate signals, including reptiles, but was heavily enriched for non-targets. Because both target and non-target taxa were often abundant, read-abundance cut-offs were unreliable for attribution. Spirit-media DNA is therefore best interpreted as a collection-level signal and a screening tool to identify jars with molecular potential (e.g., taxa of conservation or biosecurity interest), rather than as a definitive non-destructive proxy for specimen identity. Prioritising chemically favourable jars and implementing rigorous contamination controls should improve signal interpretability and help unlock the value of preservation media for historical genomics.}, }
@article {pmid42132424, year = {2026}, author = {Bae, J and Takemura, M}, title = {Refining a giant virus lineage: a novel order unifying Mamonoviridae and "Manesviridae," unveiled by the discovery of furtivovirus.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {e0203125}, doi = {10.1128/jvi.02031-25}, pmid = {42132424}, issn = {1098-5514}, abstract = {UNLABELLED: The evolutionary origins and taxonomic framework of giant viruses related to the family Mamonoviridae and its relative group, including clandestinovirus, remain unclassified due to gaps in genome size and host range between these two groups. This study aimed to address this gap by integrating our newly isolated virus with publicly available metagenome-assembled genomes (MAGs) to construct a more robust phylogenetic framework. Here, we report the isolation and characterization of a new giant virus, furtivovirus, using the unicellular amoeba Vermamoeba vermiformis as a host. Furtivovirus has a genome of approximately 560 kbp and shares key features with its closest relative, clandestinovirus. Ultrastructural analysis revealed a unique host-nucleus-dependent replication strategy characterized by the breakdown of the nuclear membrane and the packaging of nascent virions directly within the nucleoplasm, distinguishing it from canonical cytoplasmic virion factories. Comprehensive phylogenetic and comparative genomic analyses of shared orthologous groups and nucleocytovirus marker proteins revealed that furtivovirus, clandestinovirus, ushikuvirus, and usurpativirus form a distinct monophyletic clade, for which we propose a new family, "Manesviridae." Further analysis using amino acid-based similarity metrics of Nucleocytoviricota viral genomes, including established MAGs, demonstrated that this new family is robustly placed as a sister group to the family Mamonoviridae. This study elucidated the evolutionary relationships between viruses with large and small genomes that possess similar virion sizes within this lineage. Based on this cumulative evidence, we propose the establishment of a new order to unify these two families, thereby expanding their diversity and clarifying the evolutionary history of this branch within Nucleocytoviricota.<br><br>IMPORTANCE: Giant viruses challenge our traditional understanding of viral evolution, raising the question of how a single related group can diverge to infect different hosts while evolving into vastly different genome sizes and replication strategies. The family Mamonoviridae and its relatives epitomize this evolutionary divergence: one group possesses massive genomes, whereas the other has genomes that are less than half their size. The discovery of furtivovirus and its unique nucleoplasm-dependent replication cycle provides a critical biological context for this genomic disparity. Through deep comparative genomic analysis, we demonstrated that these seemingly disparate lineages share a cohesive evolutionary origin that is distinct from other established orders. This finding highlights the complexity of genome evolution, demonstrating that giant viruses can expand their overall genome size to adapt to uncertain environments while reducing their core essential genes, thereby providing new insights into the evolutionary pressures that shape the diversity of the virosphere.}, }
@article {pmid42132850, year = {2026}, author = {Bright, K and Dienes, B and van Dongen, B and Strashnov, I and Han, X and Aeppli, M}, title = {Emerging investigator series: metagenomic insights into microbial controls of carbon cycling in alpine soils.}, journal = {Environmental science. Processes &amp; impacts}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5em01047k}, pmid = {42132850}, issn = {2050-7895}, abstract = {Alpine riparian zones span topographic gradients from wet soils on the plain near streams to drier soils on adjacent slopes. These differences in soil moisture are generally associated with shifts in the soil redox state from anoxic on the plain to oxic on the slope. In anoxic plain soils, soil organic carbon (SOC) may accumulate due to thermodynamic constraints on microbial activity. Here, we used shotgun metagenomics to examine how microbial diversity and functional potential vary across differing redox conditions on plain and slope soils in two catchments in the Swiss Alps. We complemented these analyses with soil physicochemical characteristics and information on the chemical composition of organic matter. Plain soils had higher SOC stocks and higher relative abundance of phenol compounds relative to slope soils, consistent with SOC preservation and preferential mineralisation of easily degradable organic compounds under anoxic conditions. Microbial communities in plain soils further exhibited greater taxonomic and functional diversity, including increased potential for anaerobic respiration pathways. Genes for nitrate, iron, and sulfate reduction were linked to the Chloroflexota, Acidobacteria, and Desulfobacterota phyla, respectively. Based on NMDS correlations, electron accepting capacity, calcium content, and pH shaped microbial community composition. Slope soils, by contrast, supported less diverse microbial communities, determined mainly by electron donating capacity and clay content. Our work demonstrates how soil redox conditions and microbial functional potential shape carbon cycling across landscape positions in alpine riparian zones. This mechanistic understanding is critical to anticipate changes in carbon cycling in alpine ecosystems in a changing climate.}, }
@article {pmid42132937, year = {2026}, author = {Enuh, BM and Myers, KS and Bott, C and Klaus, S and McCullough, K and McIntosh, L and Beach, N and Young, M and Donohue, TJ and Noguera, DR}, title = {Metagenomes and metagenome-assembled genomes from microbial communities in a biological nutrient removal plant operated at Hamptons Road Sanitation District (HRSD) with high and low dissolved oxygen conditions.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0149225}, doi = {10.1128/mra.01492-25}, pmid = {42132937}, issn = {2576-098X}, abstract = {Aeration is a major cost at biological nutrient removal (BNR) plants. We report on microbial communities in a pilot-scale BNR system before and after a dissolved oxygen transition from 2.5 to 0.2 mg/L implemented over 18 months. Four PacBio metagenomes and 316 metagenome-assembled genomes are announced.}, }
@article {pmid42132952, year = {2026}, author = {Özel, &#x15e; and Lauritano, D}, title = {Oral mucosal microbiome alterations in recurrent aphthous stomatitis: a systematic review of 16 S rRNA gene sequencing studies.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {42132952}, issn = {1573-4978}, mesh = {Humans ; *Stomatitis, Aphthous/microbiology/genetics ; *Mouth Mucosa/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Dysbiosis/microbiology ; Case-Control Studies ; Saliva/microbiology ; Bacteria/genetics/classification ; Recurrence ; }, abstract = {Recurrent aphthous stomatitis (RAS) is a prevalent inflammatory disorder of the oral mucosa characterized by recurrent painful ulcerations in otherwise healthy individuals. This systematic review aimed to evaluate alterations in the oral mucosal microbiome of patients with RAS based on studies using 16 S rRNA sequencing. A systematic search of PubMed, Scopus, and Web of Science was conducted on April 14, 2026. Eligible studies included human case-control investigations evaluating oral mucosal swab samples from patients with clinically diagnosed RAS and healthy controls using 16 S rRNA sequencing. Studies based solely on saliva, culture methods, PCR-only analyses, or lacking controls were excluded. Joanna Briggs Institute Critical Appraisal Checklist for Case-Control Studies was used for the evaluation of selected articles. Six studies met the inclusion criteria. Considerable heterogeneity was observed in alpha and beta diversity outcomes. Most studies reported reduced microbial richness in RAS lesions, whereas others found increased or unchanged diversity. Ulcerated sites frequently demonstrated reduced abundance of health-associated taxa such as Streptococcus and Firmicutes, with increased levels of Proteobacteria and inflammation-associated genera including Neisseria, Haemophilus, Prevotella, and Fusobacterium. Microbial alterations were most pronounced at active ulcer sites, while non-ulcerated or healed mucosa more closely resembled healthy controls. Current evidence suggests that RAS is associated with localized, site-specific microbial dysbiosis rather than generalized oral microbiome disruption. However, methodological heterogeneity and small sample sizes limit definitive conclusions. Future standardized longitudinal studies integrating functional metagenomics are warranted to clarify the role of the microbiome in RAS pathogenesis.}, }
@article {pmid42133155, year = {2026}, author = {Zhang, Q and He, G and Guo, Z and He, Y and Xiong, J and He, T and Lee, SL}, title = {Comparative metagenomic and metabolomic characterization of conventionally and nitrogen-only fertilized maize soils and a forest-derived fermentation-enriched microbial community.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42133155}, issn = {1573-0972}, support = {42367039, 42267038//National Natural Science Foundation of China/ ; 2022YFD1901505//National Key Research and Development Program of China/ ; Z2024417//Guizhou Provincial Science and Technology Department/ ; Liu Jin Xiang [2024] No. 44, 202406670023//Overseas Study Program for Young Key Teachers/ ; }, mesh = {*Nitrogen/metabolism ; *Soil Microbiology ; *Zea mays/growth &amp; development/microbiology ; Forests ; Fermentation ; Soil/chemistry ; *Metagenomics/methods ; *Fertilizers ; *Metabolomics/methods ; China ; *Microbiota/genetics ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Agriculture ; Carbon/metabolism ; }, abstract = {Long-term nitrogen-only fertilization can alter soil physicochemical properties and microbial community structure in maize fields. In this study, nitrogen-only fertilized soil (S) and conventionally fertilized soil (B) were collected from a four-year maize field trial in Anshun City, Guizhou Province, China. Meanwhile, a forest-derived microbial enrichment system (T) was prepared through fermentation using forest soil, rice bran, and molasses. Metagenomic sequencing and untargeted metabolomics were used to compare microbial, functional gene, and metabolite differences between S and B soils within the agricultural field system, and to describe the microbial community composition, functional gene profiles, and metabolite features of T as an independent reference system. The results showed that Pseudomonadota accounted for 44.33% of the microbial community in T, compared with 20.63% in S and 22.31% in B. Carbon and nitrogen metabolism-related genes, including ackA, gltB, and ureC, showed higher relative abundances in T than in S. Pathway-level annotation indicated higher representation of genes or modules related to glycolysis and nitrogen metabolism in T. Metabolomic profiling revealed distinct metabolite patterns in T, including differences in amino acids, carbohydrates, and metabolites annotated to phenylpropanoid-related pathways. Candidatus Rokubacteria also showed high relative abundance among nitrogen-metabolism-associated taxa in T. Overall, this study provides descriptive multi-omics evidence of the microbial composition, functional gene profiles, and metabolite features of a forest-derived fermentation-enriched microbial community. Because T was an artificially enriched system and was not introduced into agricultural soil, these results should be interpreted as baseline data for future controlled validation rather than direct evidence of soil remediation or functional compensation.}, }
@article {pmid42133463, year = {2026}, author = {Che, J and Du, J and Piao, Y and Dong, Y and Zhang, L and Su, D and Zhang, C and Zhao, Y and Du, W and Che, N}, title = {Fungal Species Identification in FFPE Tissues: A Comparative Evaluation of Droplet Digital PCR, ITS Sequencing, and Metagenomic Next-Generation Sequencing.}, journal = {Medical mycology}, volume = {}, number = {}, pages = {}, doi = {10.1093/mmy/myag049}, pmid = {42133463}, issn = {1460-2709}, abstract = {Accurate histological diagnosis of fungal infections is challenging due to morphological similarities among fungi, which can affect treatment outcomes. This study evaluated the performance of droplet digital PCR (ddPCR), internal transcribed spacer (ITS) sequencing, and metagenomic next-generation sequencing (mNGS) using 111 formalin-fixed, paraffin-embedded tissue samples with histologically confirmed fungal infections. All three methods showed comparable detection rates for filamentous fungi (84.2%-94.7%; p = 0.2). For yeast-like fungi, however, mNGS demonstrated significantly higher detection (66.7%) than ddPCR (46.3%) and ITS sequencing (35.2%) (p < 0.01). mNGS also achieved superior genus- and species-level identification (81.1% for both) compared to ddPCR (65.8% and 64.9%) and ITS sequencing (61.3% and 50.5%) (p < 0.01). Additionally, mNGS identified two unusual fungi (Scedosporium apiospermum and Schizophyllum commune) previously misdiagnosed as Aspergillus. These findings support the integration of mNGS into clinical diagnostic workflows for the accurate identification of yeast-like and rare fungal pathogens, thereby enabling targeted antifungal therapy.}, }
@article {pmid42133477, year = {2026}, author = {Tian, B and Liu, Y and Su, KJ and Jiang, LD and Lin, X and Qiu, C and Luo, Z and Tian, Q and Shen, J and Shen, H and Zhang, LS and Xiao, HM and Deng, HW}, title = {Gut Species Porphyromonas asaccharolytica and Bacteroides fragilis Are Associated with Whole Body Fat Percentage.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag117}, pmid = {42133477}, issn = {1365-2672}, abstract = {AIMS: Obesity is linked to various adverse health effects, with body fat percentage being a key indicator of these risks. While the gut microbiota (GM) plays important roles in obesity, the specific species involved remain poorly understood. We aimed to identify gut species that may influence obesity in a cohort of US men.<br><br>METHODS AND RESULTS: We conducted a comprehensive integrative analysis using metagenomics and whole-genome sequencing data in the US cohort. MaAsLin2 was used to identify associations between GM and whole body fat percentage (PFAT). Mendelian randomization (MR) was applied to investigate potential directional relationships between GM species and PFAT, as well as possible interactions between microbial species. Porphyromonas asaccharolytica (P.asaccharolytica) was negatively associated (&#x3b2;=-0.181, P=0.005) with PFAT, while Bacteroides fragilis (B.fragilis) was positively associated (&#x3b2;=0.239, P=0.001); these associations were validated in an independent Chinese cohort. MR analysis suggested that P.asaccharolytica may influence PFAT in part through its potential effect on B. fragilis abundance.<br><br>CONCLUSION: Gut species P.asaccharolytica and B.fragilis are associated with host body fat percentage and may influence obesity individually or collaboratively. The observed associations provide evidence consistent with a potential directional relationship between these species and human adiposity.}, }
@article {pmid42133579, year = {2026}, author = {Lai, X and Gao, Q and Wu, L}, title = {A 56-Year-Old Male Farmer From China With Severe Fever With Thrombocytopenia Syndrome and Pulmonary Aspergillosis: A Case Report and Review of Literature.}, journal = {The American journal of case reports}, volume = {27}, number = {}, pages = {e951798}, doi = {10.12659/AJCR.951798}, pmid = {42133579}, issn = {1941-5923}, mesh = {Humans ; Male ; Middle Aged ; *Severe Fever with Thrombocytopenia Syndrome/diagnosis/complications ; China ; *Pulmonary Aspergillosis/diagnosis/complications ; Farmers ; COVID-19 ; Coinfection ; Aspergillus fumigatus/isolation &amp; purification ; Antifungal Agents/therapeutic use ; }, abstract = {BACKGROUND Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne infectious disease caused by the Dabie bandavirus (commonly known as SFTS virus, or SFTSV). SFTSV-induced immunosuppression during infection renders patients highly susceptible to invasive pulmonary aspergillosis. SFTS-associated pulmonary aspergillosis (SAPA) presents major therapeutic challenges and is linked to drastically worsened outcomes, including high mortality. This report aims to highlight the diagnostic and therapeutic challenges of SAPA and emphasize the value of early diagnosis using metagenomic next-generation sequencing (mNGS). CASE REPORT We report a case of a previously healthy 56-year-old male farmer admitted with SFTS. On hospital day 3, when only mild cough had begun, mNGS of both blood and sputum concurrently detected Aspergillus fumigatus alongside SFTSV. This very early, pre-radiographic diagnosis prompted immediate targeted therapy with voriconazole and favipiravir. Despite this, imaging showed progressive pulmonary infiltrates with cavitation. The clinical course was further complicated by severe acute respiratory syndrome coronavirus 2 co-infection, but the patient recovered with intensive care and was discharged on day 24. A review of 13 literature-reported SAPA cases revealed a mortality rate of 30.77% (4/13). CONCLUSIONS SAPA is a severe, rapidly progressive complication of SFTS with high mortality, typically emerging 1-2 weeks after onset. This case highlights the importance of early diagnosis using rapid methods such as mNGS and the need for timely antifungal intervention to improve patient outcomes. Early antifungal therapy in high-risk patients is crucial.}, }
@article {pmid42134120, year = {2026}, author = {Liang, W and Nong, Q and Huang, H and Huang, J and Shao, J and Wang, M and Hong, P and Liu, S and Zhou, C and Zhong, S}, title = {Correlation analysis between microbial diversity in mixed-fermented shrimp juice and the synthesis pathways of characteristic flavor compounds.}, journal = {Food chemistry}, volume = {518}, number = {}, pages = {149574}, doi = {10.1016/j.foodchem.2026.149574}, pmid = {42134120}, issn = {1873-7072}, abstract = {This study elucidated flavor formation in fermented shrimp juice using metagenomics and correlation analyses. The amino acid nitrogen content peaked at 0.54 g/100 mL on the 30th day, surpassing that of traditional fish sauce. Phenolic compounds, including guaiacol and phenylacetaldehyde, were identified as key flavor contributors. The microbial community gradually developed into a stable microbiota dominated by nine genera, including Aspergillus, Lactiplantibacillus, and Meyerozyma. Metagenomic analysis demonstrated that this core microbiome governed critical metabolic pathways for carbohydrate, amino acid, and lipid metabolisms, collectively driving the efficient flavor development in the fermented product.}, }
@article {pmid42134135, year = {2026}, author = {Huang, Z and Wang, J and Yang, C and Lv, Z and Wang, R}, title = {Integrated transcriptomics and metagenomics analyze the dynamic correlations between cecal mucosal tissue and cecal microbiota in Liangshan Yanying chickens during early postnatal development.}, journal = {Poultry science}, volume = {105}, number = {8}, pages = {106904}, doi = {10.1016/j.psj.2026.106904}, pmid = {42134135}, issn = {1525-3171}, abstract = {Liangshan Yanying chicken, a precious indigenous Chinese breed listed in the Catalog of Livestock and Poultry Genetic Resources in China, is an economic pillar in Liangshan Yi ethnic area and critical for poverty alleviation-to-rural revitalization transition. It has excellent phenotypic traits, high nutritional value, unique flavor, and strong adaptability to 380-4500 m altitudes. However, the co-evolutionary mechanism between its cecal mucosal tissue and gut microbiota (key to intestinal homeostasis and productivity) remains unclear. We systematically investigated their dynamic crosstalk in 1-, 14-, and 28-day-old chickens (n = 10/group) using transcriptomics, metagenomics, bioinformatics, and qPCR. Cecal length increased from 3.77 cm (1 d) to 8.98 cm (28 d), with higher growth rate at 14-28 d. We identified 67 DEGs (34 upregulated immune-related, 33 downregulated development-related) and 16 dynamically changed microbial taxa. Host-microbiota crosstalk was mediated by 52 shared KEGG pathways, with 10 core genes and 13 functional taxa maintaining homeostasis via PI3K-Akt pathway. This study first reveals a "gut microbial homeostasis" model for cecal dynamic homeostasis, providing insights for local poultry intestinal health and breeding.}, }
@article {pmid42134217, year = {2026}, author = {Hua, Y and Xue, Y and Li, Z and Zhang, Y and Liu, Q and Liu, L and Tang, J}, title = {Effect of microplastics on arsenic transport in shallow groundwater of coastal transition zones.}, journal = {Water research}, volume = {301}, number = {}, pages = {126097}, doi = {10.1016/j.watres.2026.126097}, pmid = {42134217}, issn = {1879-2448}, abstract = {Coastal transition zones (CTZs) are dynamic zones where seawater intrusion and freshwater discharge interact. Arsenic (As) is a common contaminant in these zones, however its co-transport with increasing abundance microplastics (MPs) remains unclear. In this study, saturated column experiments combined with Hydrus-1D modeling were used to investigate the co-transport of As with polystyrene (PS), polyethylene (PE), and polylactic acid (PLA). Increasing salinity inhibited As transport in the absence of MPs. Under the same salinity, MPs generally increased As breakthrough, following the order PS > PE > PLA. With salinity increased, PS maintained a slight promoting effect on As breakthrough, whereas PE and PLA exhibited reduced breakthrough under high-salinity conditions. Co-transport was most pronounced at an As:MP ratio of 1:2, although PLA showed a non-linear response and lower As mobility at 1:1. Simulated seawater intrusion indicated that ionic-strength fluctuations produced distinct release peaks. MPs further enhanced non-equilibrium As release during flushing. Metagenomic sequencing of samples from the 21-day experiment indicated that MPs altered the microbial communities and increased the relative abundance of several As-related genes (such as AS3MT and arsC), particularly in the PS treatment. These findings clarify the effects of MPs on As transport and support risk assessment for coastal groundwater systems.}, }
@article {pmid42134269, year = {2026}, author = {Jiang, J and Liu, R and Shen, Y and Yin, Z and Li, Y}, title = {Mechanistic insights into antimony immobilization by sulfur-metabolizing microorganisms under alternating oxic-anoxic conditions.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142328}, doi = {10.1016/j.jhazmat.2026.142328}, pmid = {42134269}, issn = {1873-3336}, abstract = {Antimony (Sb), as a toxic heavy metal(loid) element, poses potential risks to the environment and human health. The migration and transformation of Sb in the environment are closely linked to the macronutrient sulfur. However, under alternating oxic-anoxic conditions, the roles of sulfur and sulfur-metabolizing microorganisms in Sb mobility remain unclear. This study systematically investigated the role of exogenous thiosulfate (S2O3[2-]) in Sb(V) immobilization and the underlying mechanisms by integrating microcosm incubations, speciation analyses, and genome-resolved metagenomic analyses. We found that during the oxic-anoxic-oxic transition, Sb(V) was immobilized under anoxic condition and was released under oxic condition. However, thiosulfate amendment significantly inhibited Sb release through facilitating the sulfur-dependent reduction of Sb(V) to Sb(III) and formation of Sb2O3 precipitates. Complete Sb(V) immobilization was achieved within 14 days, concurrently with the oxidation of S2O3[2-] to SO4[2-], indicating thiosulfate is the primary electron donor for microbial reduction of Sb(V). Key microorganisms, including Ramlibacter (Bin.5), Thiomonas (Bin.105), and Unclassified (Bin.112 and Bin.123), which harbor antimonate/arsenate respiratory reductase gene (arrA) and sulfur oxidation pathway (Sox system), drive the sulfur-dependent Sb immobilization, as evidenced by metagenome-assembled genomes (MAGs) results. These findings enhance our understanding of the coupled cycling of Sb and S in alternating oxic-anoxic environments and provide a potential approach for Sb remediation.}, }
@article {pmid41917812, year = {2026}, author = {Shi, K and Zhang, H and Ji, L and Li, W and Zhang, Q and Liu, N and Liu, J and Guo, S and Huang, S and Chen, Y and Zhang, X and Wang, W and Lei, W and Yang, S and Shen, Q and Wang, X and Wu, P and Liu, Y and Ma, X and Yang, H and Zhang, W}, title = {Systemic remodeling of the multi-organ virome following Echinococcus infection in mice.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41917812}, issn = {1471-2180}, support = {No. 2023YFD1801300//the National Key Research and Development Programs of China/ ; No. 82341106//the National Natural Science Foundation of China/ ; No. 202208170046//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents-Leading Talents/ ; }, abstract = {UNLABELLED: The interaction between parasitic infection and the host virome represents a frontier issue in microbial ecology, yet how Echinococcus infection affects the multi-organ virome and whether these alterations hold diagnostic or interventional potential remains poorly understood. In this study, we performed viral metagenomic sequencing on gut, liver, and lung samples from both infected and uninfected mice, integrating community structure clustering, diversity indices, and differential analyses, including STAMP and LEfSe. Our results reveal that Echinococcus infection induced significant tissue-specific virome remodeling. Compared to healthy controls, gut virome diversity increased, characterized by marked expansion of the class Caudoviricetes, particularly the family Siphoviridae (LDA > 4), alongside Picornaviridae enrichment (LDA > 4). In contrast, virome diversity decreased in both the liver and lung, with significant enrichment of Reoviridae (LDA > 4) in the liver and Retroviridae (LDA > 4) in the lung, respectively. Conversely, Picobirnaviridae (LDA > 4) was significantly reduced in the infected liver and lung. Based on phylogenetic analysis, Echinococcus infection significantly altered the murine gut viral community, with eukaryotic viruses (e.g., norovirus, picobirnavirus, and picornavirus) detected exclusively in infected animals, while bacteriophage populations remained stable across groups. Phage host prediction further revealed that phages enriched in infected samples targeted opportunistic pathogens (Clostridium septicum, Trueperella pyogenes), whereas control phages predominantly targeted commensals (Bacteroides thetaiotaomicron). Together, these findings demonstrate that Echinococcus infection drives both eukaryotic virus enrichment and a shift in phage predation toward pathogens, suggesting that infection-induced immune modulation creates a permissive environment for viral replication and associated bacterial dysbiosis.<br><br>GRAPHICAL ABSTRACT: [Image: see text]<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04923-x.}, }
@article {pmid42119682, year = {2026}, author = {Mardirossian, JM and Abdallah, B and Douglas, GM and Barbour, J and Shapiro, BJ and El Chaar, M}, title = {Early-life acquisition of antimicrobial resistance genes and strain-level genomic concordance across maternal-infant compartments.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105956}, doi = {10.1016/j.meegid.2026.105956}, pmid = {42119682}, issn = {1567-7257}, abstract = {BACKGROUND: Early-life microbial colonization and antimicrobial resistance gene (ARG) acquisition may influence long-term health outcomes. High-resolution genomic studies assessing strain-level concordance and resistome overlap across maternal-infant interfaces during the immediate postnatal period remain limited.<br><br>METHODS: We analyzed 32 healthy mother-newborn dyads in Lebanon (91 samples), including maternal colostrum and breast milk and neonatal meconium and stool. Culture-based isolation, antimicrobial susceptibility testing, shotgun metagenomics, and whole-genome sequencing were used to characterize microbial composition, resistome profiles, and strain-level relatedness.<br><br>RESULTS: Viable bacteria were recovered from 80% of meconium samples, with Escherichia coli and Enterococcus faecalis among the most frequent isolates. Whole-genome sequencing identified highly similar strains (&#x2265;99.9% average nucleotide identity) of E. coli, Klebsiella pneumoniae, and K. oxytoca across maternal and neonatal samples in six dyads. Metagenomic profiling demonstrated early acquisition of multidrug resistance genes, including blaCTX-M-15, tet(M), and oqxA/B, alongside mobile genetic elements such as IncF and Col-type plasmids. The colistin resistance gene mcr-10 was detected in one neonatal stool sample.<br><br>CONCLUSION: These findings demonstrate early-life resistome establishment and strain-level genomic concordance across maternal-infant compartments within the first week of life. While low-biomass samples require cautious interpretation, the observed genomic similarities and shared ARGs are consistent with potential maternal or shared environmental contributions to neonatal microbial and resistance gene acquisition, although the direction of transfer cannot be definitively established. This work underscores the importance of integrating genomic surveillance of maternal and neonatal resistomes in perinatal health research.<br><br>IMPORTANCE: This study provides high-resolution genomic insight into early-life microbial colonization and antimicrobial resistance gene acquisition by integrating culture-based microbiology, shotgun metagenomics, and whole-genome sequencing across matched maternal (colostrum, breast milk) and neonatal (meconium, stool) samples. The identification of viable bacteria and clinically relevant resistance determinants within the first week of life, including instances of strain-level genomic concordance between maternal and neonatal samples, contributes to understanding the early establishment of the neonatal resistome. While low-biomass samples require cautious interpretation, the observed genomic similarities and shared mobile genetic elements suggest potential maternal or shared environmental influences on early colonization dynamics. These findings highlight the value of considering maternal reservoirs in studies of neonatal microbial and resistance gene evolution and underscore the need for genomic surveillance of early-life resistome development in perinatal settings.}, }
@article {pmid42119744, year = {2026}, author = {Mao, N and Liao, C and Hao, J and Sun, H and Zheng, Y and Yin, H and Xie, Y}, title = {Late-window oxygen pulsing unlocks lignin-carbohydrate shielding and enhances fiber deconstruction during maize stover fermentation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134854}, doi = {10.1016/j.biortech.2026.134854}, pmid = {42119744}, issn = {1873-2976}, abstract = {Staged aeration offers a controllable lever to relax the strict-anaerobic paradigm in lignocellulosic fermentation. We compared single-dose air injection at early, mid, and late windows with a cellulase benchmark and anaerobic control, integrating fiber fractions, fermentation products, FTIR metrics, metagenomic functional profiles (CAZy and nitrogen cycling), microbial succession, and network topology. Mid and late aeration promoted ADL reduction and fiber deconstruction, lowering acid detergent lignin and acid detergent fiber by 23-34% and 13-15% versus the control, reaching cellulase-comparable levels. Late aeration produced the strongest structural unlocking, with attenuation of carbohydrate- and lignin-aromatic FTIR regions and reduced carbonyl-associated bands, consistent with disrupted lignin shielding and improved substrate accessibility. Late aeration increased glycosyltransferases yet showed the lowest glycoside hydrolases and auxiliary activities while achieving the largest net ADL and fiber losses, indicating that accessibility rather than terminal hydrolytic potential governs deconstruction intensity. Network analysis showed reduced mean degree and K-core but higher modularity under late aeration, consistent with a more compartmentalized interaction structure and reallocated carbon use. Overall, aeration timing is a scalable, low-input lever for process design. Future work should test generality across feedstocks and develop accessibility-based monitoring and control.}, }
@article {pmid42119966, year = {2026}, author = {Athira, AS and Sreejith, VN and Megha, C and Athira, PS and Reshmi, K and Murugadas, V and Joseph, TC}, title = {Metagenomic Characterization of Bacterial Communities on Beach Macroplastics: Insights into Antimicrobial Resistance and Virulence.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128213}, doi = {10.1016/j.envpol.2026.128213}, pmid = {42119966}, issn = {1873-6424}, abstract = {Macroplastic debris in coastal environments provides stable substrates for microbial colonization, yet comparative assessments with natural substrates remain limited. This study investigated bacterial communities associated with beach macroplastics collected from four sites along the Kochi coast, Kerala, India (Fort Kochi, Cherai, Puthenthode, and Puthuvypin) during the pre-monsoon season, and compared them with those colonizing natural inanimate substrates (driftwood, seaweed, and shells). Composite sampling across multiple transects was employed, and shotgun metagenomic sequencing was used to characterize taxonomic composition, functional pathways, antimicrobial resistance genes (ARGs), and virulence factors. Across all samples, Pseudomonadota (average ∼64.8%) dominated, followed by Bacillota, Actinomycetota, and Bacteroidota. Plastic-associated communities showed greater dominance of specific genera, including Vibrio, Alteromonas, and Pseudoalteromonas, whereas natural substrates exhibited more evenly distributed taxa (Streptomyces, Marinobacter, Sulfitobacter etc). Functional annotation revealed the presence of core metabolic pathways across all samples, while xenobiotic degradation and lipid metabolism pathways were more prominently represented in plastic-associated communities, particularly at urban-influenced sites. A total of 42 ARGs belonging to eight antibiotic classes were identified, with β-lactam resistance genes constituting ∼42% of detected ARGs. Plastic-associated samples showed broader ARG profiles, including blaTEM-116, tetM, and sul1. A total of 73 virulence genes were identified, with plastic samples showing higher abundance of β-lactamase (blaTEM-116, tetM) and adhesion-associated genes (pilA, ompA). In addition, 1,264-2,046 virulence-related gene hits per site were detected, with consistently higher counts observed in plastic-associated communities. Overall, the findings demonstrate that macroplastics support distinct microbial assemblages and functional gene distributions compared to natural substrates, highlighting their role as microbial habitats in human-impacted coastal environments.}, }
@article {pmid42120015, year = {2026}, author = {Ito, T and Li, B and Sakaguchi, T and Yagita-Sakamaki, M and Itoi, H and Murakami, M and Wu, R and Fukada, A and Motooka, D and Ogino, T and Nakamura, S and Okuzaki, D and Takeda, K and Kayama, H}, title = {The IL-10/IL-10Rα axis in fibroblasts limits large intestinal pathology by suppressing type I interferon signaling.}, journal = {International immunology}, volume = {}, number = {}, pages = {}, doi = {10.1093/intimm/dxag022}, pmid = {42120015}, issn = {1460-2377}, abstract = {Recent studies identified that the dysregulation of fibroblast activity, in addition to impairment in epithelial integrity and uncontrolled immune response, is implicated in the pathogenesis of inflammatory bowel disease (IBD). The anti-inflammatory cytokine IL-10 and its receptors IL-10Rα and IL-10Rβ have IBD-associated single nucleotide polymorphisms. In the intestine, IL-10 signaling is essential for maintaining an anti-inflammatory state of myeloid cells and inducing regulatory T cells, thereby preventing intestinal inflammation linked to IBD development. However, its impact on the physiology and pathophysiology of intestinal fibroblasts is poorly understood. Here, we show that Il10ra deficiency leads to increased expression of a subset of genes in colonic fibroblasts, most of which are associated with the type I interferon (IFN) and type II IFN signaling pathways. In addition, Pdgfra-cre; Il10raf/f mice aged 16 weeks or older develop chronic spontaneous colitis and subsequent fibrosis accompanied by enhanced infiltration of myeloid cells and effector CD4+ T cells in the lamina propria of the colon. Moreover, Pdgfra-cre; Il10raf/f mice at 12 weeks of age exhibit more severe clinical symptoms than those of Il10raf/f mice during dextran sodium sulfate-induced colitis that can be suppressed by the administration of anti-IFNAR1 antibody but not anti-IFNGR1 antibody. Therefore, inhibition of type I IFN pathway via IL-10Rα signaling in fibroblasts is one of the IL-10-dependent mechanisms underlying the prevention of large intestinal pathology.}, }
@article {pmid42120057, year = {2026}, author = {Owens, LA and Berkman, LK and Pease, BS and Dunn, CD and Nielsen, CK and Groninger, JW and Bosch, K and Hudman, D and Timm, SR and Goldberg, TL}, title = {Viruses and Parasites in Swamp Rabbits (Sylvilagus aquaticus): A Baseline Survey to Aid Conservation Efforts.}, journal = {Journal of wildlife diseases}, volume = {}, number = {}, pages = {}, doi = {10.7589/JWD-D-25-00059}, pmid = {42120057}, issn = {1943-3700}, abstract = {Technical advancements have enabled the discovery of potential pathogens in an ever-broadening range of wildlife taxa. To further the scope of this body of knowledge and to inform conservation efforts, we examined potential disease agents present in swamp rabbits (Sylvilagus aquaticus) of southeastern Missouri, USA, during winter 2023. This region represents the northernmost portion of the species' range and is characterized by an intermixed landscape of preferred bottomland hardwood forest and agricultural landcover. Concerns about infectious disease threats to swamp rabbits have increased since the emergence of rabbit hemorrhagic disease, caused by rabbit hemorrhagic disease virus 2 (RHDV2; Caliciviridae, Lagovirus europaeus), that has spread to domestic, wild, and feral rabbits and hares, predominantly in the western and midwestern USA. We applied metagenomic and metabarcoding methods, designed to characterize communities of viruses and parasites, to noninvasively collected rabbit fecal samples. We identified seven viruses and eight parasite genera that probably infect mammals. Although some relatives of these agents cause disease, none are unexpected in lagomorphs, and none are considered a health concern. Notably, RHDV2 was not detected. These results provide baseline data for future conservation and management efforts, especially if RHDV2 or other pathogens become a concern for swamp rabbits.}, }
@article {pmid42120383, year = {2026}, author = {Tingley, JP and Andersen, TO and Mihalynuk, LG and Xing, X and Low, KE and Whiteside, DP and Altshuler, I and Jujihara, N and Shearer, AY and Klassen, L and Serin, S and Smith, E and Reintjes, G and Patel, TR and Boraston, AB and Hagen, LH and Pope, PB and Abbott, DW}, title = {Distribution of microbial carrageenan foraging pathways reveals a widespread latent trait within the ruminant intestinal microbiome.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42120383}, issn = {2041-1723}, support = {J-002817; J-003135//Gouvernement du Canada | Agriculture and Agri-Food Canada (Agriculture et Agroalimentaire Canada)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics/physiology ; *Carrageenan/metabolism ; *Ruminants/microbiology ; Rumen/microbiology ; Glycoside Hydrolases/metabolism/genetics ; Feces/microbiology ; Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Seaweed/metabolism ; Bacteroides/metabolism/genetics/isolation &amp; purification ; Metagenomics ; Phylogeny ; }, abstract = {Seaweeds represent a promising source of sustainable, alternative feeds for livestock. Despite their increasing popularity in agriculture, the dietary fate of seaweed polysaccharides, such as carrageenan, is unknown. Here, we apply functional microbiome analyses of ruminant gastrointestinal tract microbiomes to discover catabolic enzymes specific for carrageenan digestion from the red seaweed Mazzaella japonica. M. japonica preferentially increased Bacteroides abundance within the feces over the rumen, and bacterial isolates have the capacity to use carrageenans as a sole carbon source. We identify carrageenan-active polysaccharide utilization loci (CarPULs) and characterize recombinant GH16 subfamily 17 carrageenases, informing previously uncharacterized substrate specificities for the subfamily, and providing insights into pathway specialization of divergent CarPULs. Selective enrichment and metagenomic mining reveals that carrageenan catabolism is widespread among geographically and taxonomically distinct ruminants, suggesting it is a latent trait widely distributed in the Order Artiodactyla and carried within their microbiomes as part of the microbial "dark matter". These pathways are structurally distinct from those found in marine bacteria, highlighting a complex and ancient evolutionary history of CarPULs in ruminant microbiomes.}, }
@article {pmid42120665, year = {2026}, author = {Chen, LG and Zhou, L and Wang, BW and Javed, M and Liu, YF and Yang, SZ and Gu, JD and Mu, BZ}, title = {Microbial assembly and metabolic restructuring following CO2 injection in subsurface oil reservoir.}, journal = {AMB Express}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13568-026-02066-w}, pmid = {42120665}, issn = {2191-0855}, support = {Grant No. 42473082//National Natural Science Foundation of China/ ; No. 42173076//National Natural Science Foundation of China/ ; No. 52074129//the National Natural Science Foundation of China/ ; 21ZR1417400//the Natural Science Foundation of Shanghai/ ; JKJ01231714//the Fundamental Research Funds for the Central Universities of China/ ; }, abstract = {Carbon dioxide (CO2) injection into oil reservoirs is a well-established and promising strategy for enhancing oil recovery while simultaneously sequestering carbon, whose effectiveness is increasingly recognized to be influenced by microbial-mediated mechanisms and biogeochemical processes. However, the impact of CO2-injected and storage on functional microbial communities and their metabolic potential remains poorly understood. The study employed high-throughput sequencing to analyze the composition and diversity of microbial communities in produced water from three production wells with a long-term (> 20 years) history of CO2 injection and two adjacent water-flooding ones in Xinli Oilfield, China. The results showed that CO2-injected wells had significantly higher microbial diversity and distinct metabolic potential relative to the adjacent water-flooding wells. A metabolic difference in the archaeal communities towards hydrogenotrophic and heterotrophic metabolisms, alongside an enrichment of bacterial taxa associated with sulfur and nitrogen cycling was observed. Correlation analysis revealed that microbial differentiation was strong associated with geochemical alteration (especially pH and some inorganic ions), with NH4[+] and S[2-] identified as key factors in this process. Metagenomic analysis based on high-quality metagenome-assembled genomes (MAGs) further demonstrated that CO2 injection led to a different profile of microbial metabolic functions relative to the water-flooding condition, characterized by significantly enhancing hydrogenotrophic methanogenesis, dissimilatory sulfate reduction, and denitrification, while diminishing methylotrophic methanogenesis and Wood-Ljungdahl pathway activity. These findings provide new insights into the microbial mechanisms driving carbon transformation in CO2-flooded oil reservoirs.}, }
@article {pmid42120930, year = {2026}, author = {Huang, L and Zhang, X and Wu, Y and Li, H and Li, M and Shao, C and Yang, Q and Jin, G and Hu, X}, title = {The gut microbiota and metabolomics in the pathogenesis of type 2 diabetes mellitus combined with coronary atherosclerotic heart disease.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-51805-3}, pmid = {42120930}, issn = {2045-2322}, support = {Grant No.202204295107020049)//the Clinical Translation Project of Anhui Province/ ; Grant No. 2208085MH216//the Natural Science Foundation of Anhui Province/ ; Grant No. 2020byfy004//the Major Natural Science and Technology Project of Bengbu Medical Uuniversity/ ; Grant No. AHWJ2023BAc10028//The Scientific Research Program of Anhui Provincial Health Commission/ ; }, abstract = {To investigate the characteristics of intestinal bacteria and their metabolites in healthy controls (CONs) compared with individuals with type 2 diabetes mellitus (T2DM) and individuals with type 2 diabetes mellitus combined with coronary atherosclerotic heart disease (T2DM-CAD). Thirty samples were collected from 10 healthy people, 10 T2DM patients, and 10 T2DM-CAD patients. We determined the gut bacterial composition via metagenomic sequencing analysis and analyzed the gut microbes and their metabolomic changes via metabolomics. The potential key gut microbes and metabolites were explored with random forest and receiver operating characteristic (ROC) curve analyses. Finally, Spearman correlation analysis and linear regression were used to identify the correlations between the gut bacteria and metabolites. Eight gut microorganisms with diagnostic significance were screened out, including Prevotella disiens, Bacteroides sp._AM25_34, Paraprevotella clara, Bacteroides sp._CAG_875, Sutterella wadsworthensis, Prevotella sp. 885, Ruminococcus sp. AM42_11 and Anaerobutyricum hallii. Meanwhile, eight characteristic metabolites were identified, including fructose, salicyluric acid, 12-ketoLCA, pyroglutamic acid, glutamic acid, suberic acid, gallic acid and adipic acid. Additionally, the correlations between the above differential gut microbiota and characteristic metabolites were clarified. Our study revealed that gut flora such as g-Bacteroides, Alistipes_putredinis_CAG_67, and Alistipes_putredinis may be key flora, and that fructose, gallic acid, sebacic acid, and 12-ketoLCA may be key metabolites involved in the pathology of T2DM and T2DM-CAD.}, }
@article {pmid42121077, year = {2026}, author = {Song, C and Li, Y and Deng, Y and He, D and Fan, X}, title = {Gut microbiota profiles associated with temporal lobe epilepsy and psychiatric comorbidities: a family-matched case-control 16S rRNA study.}, journal = {BMC neurology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12883-026-04958-7}, pmid = {42121077}, issn = {1471-2377}, abstract = {We investigated alterations in the intestinal microbiota of patients with temporal lobe epilepsy (TLE) and their associations with drug resistance and psychiatric comorbidities. Thirty TLE patients and 30 family-matched healthy controls sharing the same household diet were recruited, and fecal samples were analyzed by high-throughput 16S rDNA sequencing on the Illumina MiSeq [Formula: see text] bp platform. Differential abundance was assessed using Metastats and LEfSe with Benjamini-Hochberg false-discovery-rate correction, and independently validated using ANCOM-BC to account for the compositional nature of microbiome data. Community α- and β-diversity indices showed no significant differences between groups; however, ANCOM-BC identified species-level signatures in drug-resistant epilepsy, including significant depletion of Bacteroides plebeius and Coprococcus comes. Among psychiatric subgroups, Ruminococcus was significantly reduced in patients with comorbid depression, while Bilophila was enriched in those with comorbid anxiety and depression. Bacteroides stercoris distinguished the anxiety-plus-depression subgroup from the depression-only subgroup with robust support from both ANCOM and ANCOM-BC. Given the modest overall sample size ([Formula: see text] per arm) and small psychiatric and drug-resistance subgroups, these findings should be regarded as exploratory and hypothesis-generating associations rather than definitive biomarkers. They identify candidate microbial taxa warranting validation in larger, longitudinal cohorts combined with metagenomic and metabolomic approaches.}, }
@article {pmid42121260, year = {2026}, author = {Zhou, Z and Lamanna, A and Halder, R and Pansart, E and Narayanasamy, S and Boussoufa, B and Kerkour, T and Wilmes, P and Williams, E}, title = {Integrative analysis of the mouse cecal microbiome across diet, age, and weight in the diverse BXD population.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02369-x}, pmid = {42121260}, issn = {2049-2618}, support = {PRIDE21/16749720/NEXTIMMUNE2//Luxembourg National Research Fund/ ; }, abstract = {BACKGROUND: The gut microbiota adapts to and shapes the host's metabolic state through affecting circulating metabolites and consequent gene regulatory networks, resulting in systemic influences in diverse organs via connections such as the gut-liver axis. Numerous variables such as diet, age, and host genetics modulate the composition of the gut microbiome, but their interactions and specific associative and mechanistic links to host molecular phenotypes remain incompletely unannotated. Integrated multi-omics approaches in genetically diverse populations offer an opportunity to dissect these interactions and identify predictive microbial signatures for host phenotypes, such as body weight and molecular associations with gene expression pathways in gut and liver.<br><br>RESULTS: We sequenced, aligned, and integrated the cecal metagenome, metatranscriptome, and host transcriptome from 232 mice across 175 distinct cohorts according to a low-fat chow diet (CD) or a high-fat diet (HF), four adult ages (between roughly 180 to 730&#xa0;days of age), and 43 distinct genotypes (inbred BXD strains). Genetics and diet exerted the strongest influence on microbiota abundance and activity, followed by age. HF feeding significantly reduced diversity across all ages and all genotypes, altering&#x2009;>&#x2009;300 species. Machine learning models based on microbial profiles reliably predicted body weight within dietary group (AUC&#x2009;=&#x2009;0.84 for CD, 0.79 for HF) and chronological age (AUC&#x2009;=&#x2009;0.84), with model performance of age prediction rising to 0.95 when integrating top microbial features with liver proteomics. Network analyses of expression data revealed links between genes, pathways, and specific microbes, including a negative association between cecal Ido1 expression and short-chain fatty acid (SCFA)-producing Lachnospiraceae, suggesting dietary fat may modulate host tryptophan metabolism through microbiota shifts.<br><br>CONCLUSIONS: Whole metagenome and metatranscriptome sequencing approaches have massively expanded the landscape of microbiome analysis compared to earlier short-read 16S analyses. The resulting datasets quantify hundreds of uniquely identifiable microbes, which can be used to create sets of highly predictive microbial biomarkers for aging and obesity. When trained on controlled mouse populations, these results demonstrate that microbiome profiling can achieve high predictive capacity (AUC&#x2009;=&#x2009;0.95 with multi-omics integration) for complex readouts such as age and body weight (AUC&#x2009;=&#x2009;0.84), even considering genetic and dietary variation, establishing a framework for biomarker development. While at present many bacteria are still functionally unannotated at the species level, multi-omics approaches - including gene expression from the host tissues - provide insights into the functional associations of specific taxa in the microbiome. Video Abstract.}, }
@article {pmid42121284, year = {2026}, author = {Burkhart Colorado, AS and Nusbacher, NM and O'Connor, J and Marden, T and Higgins, J and Neff, CP and Fiorillo, S and Campbell, TB and Borok, M and Boyd, K and Sterrett, J and Palmer, BE and Lozupone, C}, title = {The impact of western versus agrarian diet consumption on gut microbiome composition and immune dysfunction in people living with HIV in rural and urban Zimbabwe.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02410-z}, pmid = {42121284}, issn = {2049-2618}, support = {R01 DK108366/DK/NIDDK NIH HHS/United States ; T15LM009451//U.S. National Library of Medicine/ ; }, abstract = {BACKGROUND: People living with HIV (PLWH) suffer from chronic inflammation even with effective antiretroviral therapy (ART). A high-fat, low-fiber western-type diet has been linked with inflammation, in part through gut microbiome changes. In sub-Saharan Africa (SSA), a region with high HIV burden, urbanization has been linked with a shift from traditional agrarian towards westernized diets, and with changes in food security. To explore the relationship between diet, inflammation, and the gut microbiome in PLWH, we enrolled 1) ART Naïve PLWH who provided samples before and after 24 weeks of ART, 2) PLWH on ART at both timepoints and 3) HIV-seronegative controls. Individuals were evenly recruited from rural and urban Zimbabwe. Using a food frequency survey designed to measure intake of agrarian versus western-type food items in Zimbabwe, we determined how diet differs with urbanization, HIV-infection and treatment, and is related to inflammation and the gut microbiome.<br><br>RESULTS: Individuals residing in a rural area of Zimbabwe less frequently consumed high-fat, low-fiber western type food items and had lower consumption of diverse food items overall, except for sadza, a subsistence staple, processed from home-grown grains. Consumption of a more western-type diet correlated with lower CD4&#x2009;+&#x2009;T cell percentage in untreated and treated PLWH and increased T cell exhaustion in PLWH on ART. PLWH on ART at time of enrollment also consumed diverse food items at a lower frequency and more often were underweight. Low food consumption correlated with muted improvements in T cell exhaustion after 24&#xa0;weeks of ART. Individuals residing in the rural area had more Prevotella-rich/Bacteroides-poor microbiomes, but this was not significantly mediated by diet. Carbohydrate substrate degradation capabilities in the microbiome, based on predictions made using metagenomic polysaccharide utilization loci, correlated with dietary intake patterns.<br><br>CONCLUSIONS: Taken together, this work supports that consumption of more high-fat/low-fiber type food items has the potential to exacerbate HIV pathogenesis in a sub-Saharan setting where HIV burden is high and reinforces the importance of nutritional support for promoting immunologic response to ART in PLWH in SSA. Video Abstract.}, }
@article {pmid42121750, year = {2026}, author = {Moharam, I and Brüggemann, J and Schmitt, F and Schade, B and Böhm, B and Kappe, E and Emmrich, F and Najar, FZ and El-Mayet, FS}, title = {Molecular Epidemiology of Enteric Viral Infections in Poultry Flocks in Southern Germany and the First Complete Genome Sequence of Avian Sicinivirus.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {9}, pages = {}, doi = {10.3390/ani16091331}, pmid = {42121750}, issn = {2076-2615}, abstract = {Enteric viral infections represent a major concern for poultry production, causing growth retardation, impaired feed conversion, and increased mortality, particularly in young birds. To investigate the involvement of RNA and DNA enteric viruses in flocks exhibiting growth problems, seven poultry farms in southern Germany, including broiler, pullet, and breeder operations, were examined for the presence of chicken astrovirus (CAstV), avian reovirus (ARV), and fowl adenovirus-1 (FAdV-1) by means of RT-PCR. All farms exhibited growth retardation, diarrhea, and enteritis-associated lesions. Histopathology revealed features of runting-stunting syndrome in most of the broiler farms and depletion of lymphatic tissue in most of the pullet farms. CAstV was detected in all flocks, ARV in six, and FAdV-1 in four farms. To further characterize the viral agents, metagenomic sequencing of cecal tonsils from one severely affected broiler flock confirmed the presence of a CAstV strain identical (100%) to CAV/Belgium/4134_001/2019. In addition, the complete genome of avian Sicinivirus was assembled for the first time in Germany, showing 96.8% nucleotide identity with a Dutch strain (Chicken/NLD/2019/V_M_056_picorna_2). These findings demonstrate the widespread circulation and co-infection of enteric viruses on German poultry farms and underline the transboundary nature of these infections, emphasizing the need for enhanced surveillance and biosecurity measures to mitigate their impact on poultry health and productivity.}, }
@article {pmid42121788, year = {2026}, author = {Gao, F and Zuo, Z and Wu, Q and Xiao, H and Peng, Z and Zou, L and Jiang, G and Tian, X and Feng, Z and Xie, X and Tian, L}, title = {Analysis of Ochetobibus elongatus (Kner) Dietary Habits Based on Digestive System Morphology, Histology, and Intestinal Content Sequencing Technology.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {9}, pages = {}, doi = {10.3390/ani16091369}, pmid = {42121788}, issn = {2076-2615}, support = {HARS-07//Hunan Provincial Modern Agriculture (Aquaculture) Industry Technology System Project/ ; }, abstract = {Ochetobibus elongatus (Kner) is a migratory fish found in the Yangtze River basin and areas south of it, and listed as a critically endangered (CR) fish on the China Red List of Vertebrates. To achieve group recovery and artificial breeding, this study investigated the dietary characteristics of O. elongatus based on high-throughput sequencing of its intestinal contents, and its digestive system morphology, and its histology. Results showed that the digestive system of O. elongatus lacked a stomach and mainly consisted of the oropharynx, pharyngeal teeth, esophagus, intestine, and anus. The gut index was 0.88, with clear segmentation of the foregut, midgut, and hindgut, and the visceral mass index was 7.35%. Histological analysis of the digestive system revealed the presence of keratinized dental plates or pharyngeal teeth in the pharynx, as well as a high density of taste bud cells in the soft palate of the oral cavity. The surface layer of the intestinal villi contained numerous mucous cells, with the average number of mucous cells per villus gradually increasing from the esophagus to the hindgut, and the foregut having the longest and most abundant mucosal folds. The esophagus exhibited well-developed circular and longitudinal muscle layers, while in the hindgut, both the circular and longitudinal muscle layers were slightly thicker than those in the midgut. High-throughput sequencing of the intestinal contents of O. elongatus revealed the following phyla based on 18S V4 meta-barcoding: Chlorophyta, Diatoms, Arthropoda, Basidiomycetes, and Ascomycetes, with the genus Hypophthalmichthys and algae being the main classifications. In contrast, based on COI meta-barcoding, the study newly identified the phyla Cnidaria and Mollusca, with the genera Chlorophyta, Scenedesmus, Pectinodesmus, and zooplankton such as Pseudodiaptomus. Metagenomic sequencing revealed that the gut microbiota at the phylum level was predominantly composed of Pseudomonadota, Ascomycota, Basidiomycota, Chytridiomycota, and Bacillota, with key genera including Cetobacter, Pseudomonas, Acinetobacter, Aeromonas, and Clostridium. This study indicates that O. elongatus is an omnivore with carnivorous tendencies. Basic biological research on O. elongatus is of great significance for the restoration of the population, artificial breeding, and the development of its artificially formulated feed. It also provides important data for the formulation of biodiversity conservation measures.}, }
@article {pmid42122064, year = {2026}, author = {Hussain, A and Abbas, Q and Nadeem, M and Nazar, A and Athar, A and Rahman, HUU}, title = {Meat-Borne Bacterial Pathogen Detection: Conventional, Molecular and Emerging AI-Based Strategies.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {9}, pages = {}, doi = {10.3390/diagnostics16091360}, pmid = {42122064}, issn = {2075-4418}, abstract = {Meat serves as a prime medium for the growth of foodborne pathogens due to its rich protein content and high water activity, contributing significantly to the global burden of foodborne illnesses. This review synthesizes current advances in meat-borne bacterial pathogen detection with particular emphasis on emerging artificial intelligence (AI)-enabled applications. Major pathogens of concern, including Salmonella, Listeria monocytogenes, Escherichia coli, Campylobacter, Clostridium, and Staphylococcus aureus, are examined in relation to their relevance across the meat supply chain. Recent progress in biosensors (clustered regularly interspaced short palindromic repeats), CRISPR-based assays, isothermal amplification, and metagenomics is evaluated alongside the growing role of AI in automating signal interpretation, enhancing image-based diagnostics, and supporting early contamination prediction. AI-based systems have proved 96.4-104% recovery and 100% bacterial capture ability. Embedding AI methods in a wet lab demands technical and logical modeling, as well as learning and calibration decorum. Nonetheless, AI readiness and full-scale application for meat-borne pathogens surveillance are on the way. Furthermore, additional focus is aligned on meat-borne bacterial pathogen genomic databases, i.e., (NCBI Pathogen Detection, EnteroBase, VFDB, ComBase, and GenBank), which serve as critical training resources for AI models for outbreak tracking, virulence profiling, and antimicrobial resistance (AMR) prediction. By integrating molecular methods, genomic surveillance, and AI-driven analytics, this review presents a framework for strengthening meat safety systems. This will improve early detection capabilities and support data-driven public health interventions in the future.}, }
@article {pmid42122249, year = {2026}, author = {Dragomir, RD and Saftescu, S and Sandu, DL and Dulan, A and Croitoru-Cazacu, IM and Croitoru, AE and Croitoru, VM and Vornicu, V and Nagy, DE and Perva, IT and Sirca, D and Popovici, DI}, title = {Artificial Intelligence-Guided Personalized Gut Microbiome Modulation for Persistent Secondary Gastrointestinal Symptoms in Oncology Patients: Clinical Efficacy and Biological Correlates from a Prospective Validation Study.}, journal = {Cancers}, volume = {18}, number = {9}, pages = {}, doi = {10.3390/cancers18091453}, pmid = {42122249}, issn = {2072-6694}, support = {No Grant Number//Victor Babe&#x219; University of Medicine and Pharmacy Timi&#x219;oara/ ; }, abstract = {Background/Objectives: Persistent gastrointestinal (GI) symptoms following oncologic treatment represent a major unmet need in survivorship care, often managed symptomatically without addressing underlying biological mechanisms. This study aimed to evaluate the clinical efficacy and biological correlates of an artificial intelligence (AI)-guided, personalized microbiome modulation strategy in oncology patients with chronic secondary GI dysfunction. Methods: We conducted a prospective, single-arm, open-label validation study including 29 adult female oncology patients with persistent GI symptoms lasting ≥3 months. Participants underwent baseline multidimensional assessment integrating shotgun metagenomic sequencing, inflammatory and nutritional biomarkers, and clinical symptom profiling. An AI-guided platform generated individualized dietary, supplement, and lifestyle recommendations. Outcomes were assessed at baseline and after a 3-month intervention, focusing on intra-individual changes in stool frequency (primary endpoint), self-reported energy, microbiome composition, and metabolic biomarkers. Paired statistical analyses, correlation testing, and multivariable regression were performed. Results: After three months, stool frequency significantly decreased (4.69 ± 2.41 to 2.07 ± 1.19 episodes/day; p < 0.0001), accompanied by a marked increase in energy levels (4.00 ± 1.04 to 7.24 ± 1.12; p < 0.0001). Microbiome analysis revealed consistent enrichment of butyrate-producing and barrier-supportive taxa, including Faecalibacterium prausnitzii, Eubacterium rectale, Roseburia intestinalis, Akkermansia muciniphila, and Bifidobacterium longum. Butyrate-related biomarkers and vitamin-associated parameters (B-complex, vitamin D) showed significant improvement, while lactate levels normalized. Changes in Bifidobacterium longum were independently associated with stool frequency reduction (β = -0.783, p = 0.0082). Conclusions: AI-guided personalized microbiome modulation was associated with significant clinical improvement and biologically coherent microbial and metabolic shifts in oncology patients with persistent GI symptoms. These findings support a precision supportive-care approach targeting microbiome restoration, warranting further validation in randomized controlled trials.}, }
@article {pmid42122826, year = {2026}, author = {Pardo, JM and Suwannarach, N and Malichan, S and Cuellar, WJ and Siriwan, W}, title = {Mixed-Pathogen Infections in Vegetatively Propagated Crops: From Biological Synergism to Integrated Management.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {9}, pages = {}, doi = {10.3390/plants15091332}, pmid = {42122826}, issn = {2223-7747}, support = {000//Ministry of Higher Education, Science, Research and Innovation/ ; 000//Kasetsart University/ ; CROP-2023-157//Australian Centre for International Agricultural Research/ ; 000//National Research Council of Thailand/ ; }, abstract = {Vegetatively propagated crops, including cassava, sweet potato, banana, and potato, are susceptible to mixed-pathogen infections resulting from the continuous use of clonal planting material and infrequent seed replacement. A diverse array of viruses, bacteria, and fungi can accumulate within these materials over successive cultivation cycles, precipitating seed degeneration and complex disease syndromes that complicate diagnosis and management. Mixed infections frequently trigger synergistic interactions that exacerbate disease severity and yield losses. This review synthesizes data on mixed-pathogen complexes in vegetatively propagated crops, with particular focus on vascular and systemically colonizing pathogens and analyzing starch crops to highlight the epidemiological, biological, and ecological drivers of synergism and antagonism. Furthermore, the review examines host defense responses during coinfection, including the modulation of plant immune pathways, and evaluates how interpathogen dynamics influence pathological outcomes. Although advancements in molecular diagnostics-notably next-generation sequencing and metagenomics-have revolutionized the detection of mixed infections, they have also introduced challenges in differentiating causal agents from commensal microorganisms. Finally, we discuss the implications for integrated disease management, emphasizing clean seed systems, resistance breeding, and phenotyping strategies tailored to multipathogen environments. The dynamics of mixed infections is critical for resilient and sustainable management strategies amidst increasingly complex agricultural and climatic shifts.}, }
@article {pmid42122957, year = {2026}, author = {Terry, C and Hall, LA and Halle-Smith, J and Edwards, LA and Sivakumar, S and Chapple, I and Beggs, A and Iqbal, T and Roberts, KJ}, title = {Pancreatic Cancer in the Holobiont and Therapeutic Targets: A Review.}, journal = {Journal of clinical medicine}, volume = {15}, number = {9}, pages = {}, doi = {10.3390/jcm15093225}, pmid = {42122957}, issn = {2077-0383}, abstract = {Increasing evidence suggests pancreatic cancer develops within a host-microbe ecosystem in which microbial communities across anatomical niches interact with tumour biology, immune regulation, metabolism, and therapeutic response. This review examines pancreatic cancer through the lens of humans as holobionts, integrating evidence from the oral, gut, biliary, and intratumoural microbiomes. Epidemiological and sequencing studies demonstrate consistent microbial alterations across these niches in pancreatic cancer, including oral dysbiosis associated with periodontal pathogens, gut microbial shifts toward pro-inflammatory taxa, disease-specific biliary microbial signatures, and the presence of distinct intratumoural microbial communities. Mechanistic studies indicate that intestinal barrier disruption, microbial translocation, immune and metabolite signalling can influence tumour immune architecture, macrophage polarisation, T-cell infiltration, oncogenic signalling pathways, and chemotherapeutic metabolism, particularly inactivation by tumour-associated bacteria. Microbiome-driven shifts in immunometabolism can reprogramme immune-cell metabolic pathways, impairing effective T-cell activation, promoting tumour-supportive macrophage phenotypes. Emerging therapeutic strategies aim to modulate the microbiome-tumour axis, including dietary interventions, probiotics and immunonutrition, faecal microbiota transplantation, engineered microbial therapies, and microbiome-informed antibiotic strategies. While pre-clinical findings are compelling and early-phase clinical studies suggest feasibility, most evidence remains associative and heterogeneous across cohorts and methodologies. Understanding pancreatic cancer as a multi-site ecological system may help explain inter-patient variability in disease progression and treatment response. This could usher in a new era for therapeutic manipulation where future progress will depend on longitudinal, multi-omic, and interventional studies to determine whether microbiome-targeted strategies can produce clinically meaningful improvements in pancreatic cancer outcomes.}, }
@article {pmid42123237, year = {2026}, author = {Liu, JW and Ma, X and Qian, YT and Wang, JW and Zhu, CY and Ma, DL}, title = {Detection of Nontuberculous Mycobacterial Skin Infection by Next-Generation Sequencing: A Pilot Study.}, journal = {Journal of clinical medicine}, volume = {15}, number = {9}, pages = {}, doi = {10.3390/jcm15093504}, pmid = {42123237}, issn = {2077-0383}, support = {2022- PUMCH-161//National High Level Hospital Clinical Research Funding/ ; 3332024006//the Fundamental Research Funds for the Central Universities/ ; }, abstract = {Background: Nontuberculous mycobacteria (NTM) skin infections pose significant diagnostic challenges in clinical practice, due to nonspecific clinical/histopathological features and limitations of conventional pathogenic detection methods. Metagenomic next-generation sequencing (mNGS) offers a promising approach but requires further evaluation. Methods: A prospective pilot study at Peking Union Medical College Hospital enrolled 20 patients with cutaneous NTM infection, confirmed by positive skin culture or mNGS. All patients underwent thorough clinical assessment, skin biopsy for histopathology and culture, and mNGS testing of skin tissue. Treatment was based on identified species and disease extent. Treatment outcomes were tracked. Results: Among 20 patients (median age 45.5 years), fingers were the most common site affected (n = 10), followed by forearms (n = 7), hands (n = 4), and face (n = 4). Mycobacterium marinum was the predominant pathogen (n = 12), associated with fish bone puncture, followed by M. abscessus (n = 4). mNGS demonstrated a substantially higher positivity rate than culture (95% [19/20] vs. 30% [6/20]) and delivered results faster. Histopathology revealed granulomatous inflammation in all cases. Nineteen patients presented with non-disseminated disease; one immunocompromised patient (GATA2 deficiency) had disseminated M. abscessus infection. Treatment success was achieved in 17 patients (85%) with tailored antibiotic regimens. Adverse drug effects occurred in seven patients. Conclusions: In this pilot study of cutaneous NTM infections, mNGS enabled more rapid diagnosis relative to conventional culture. Clinical presentation and exposure history correlate with specific NTM species. Integrating mNGS with clinical assessment significantly improves diagnosis and management.}, }
@article {pmid42123326, year = {2026}, author = {Zaman, S and Ali, N and Ullah, W and Taimur, N and Akbar, NU and Waheed, A and Muhammad, N and Khan, MS}, title = {Metagenomic Profiling Reveals Extensive Bacterial Diversity in Chicken Manure and Associated Contaminated Wastewater.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, doi = {10.3390/ijms27093741}, pmid = {42123326}, issn = {1422-0067}, mesh = {Animals ; Chickens/microbiology ; *Manure/microbiology ; *Wastewater/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation &amp; purification ; Metagenome ; Microbiota/genetics ; Biodiversity ; }, abstract = {Chicken manure and its potential to contaminate water systems through the dispersal of pathogenic bacteria are major concerns in environmental and public health. In this study, a metagenomic analysis was employed to systematically identify and compare bacterial assemblages in chicken manure (CM) and in a contaminated sample of chicken manure wastewater (CMW). Whole DNA was extracted from CM and CMW, followed by whole-genome shotgun sequencing; data analysis was done using online Galaxy software (ver. 26.0.1.dev1). Metagenomic analysis reveals a complex One Health challenge. Data showed that CM and CMW are different in their microbiota, as indicated by a distinct separation of beta diversity values and limited overlapping of species between sample types. In the current study, we found a greatly significant common functional set of adapted bacterial masses, including major pathogenic bacterial groups as well as opportunistic and environmental bacterial species, indicative of a direct contamination from CM and CMW. Notably, in both CM and CMW, a plethora of opportunistic, enteric, and environmental pathogens like Escherichia coli, Salmonella enterica, and Acinetobacter baumannii were found, coupled with an indication of a direct functional flow between both ecosystems as tangled reservoirs. Chicken manure samples showed differences in taxonomic composition and inferred functional profiles at the time of sampling: CM1 was pathogen-enriched, CM2 exhibited strong nitrogen-supportive metabolism, CM3 was dominated by fiber-degrading decomposers, and CM4 showed high methane-producing potential with environmental risk. Such findings underscore the raising of chickens as a potential source of harmful bacteria for the environment. It is important to note that this study represents a preliminary investigation with certain limitations, including the absence of biological replicates, lack of temporal sampling, and limited capacity to infer dynamic ecological interactions. Yet this metagenomic report is more about describing the taxonomy and functional potential of the bacteria, rather than discussing the actual ecological processes of these microorganisms in the environment. Future studies will be required to explore these aspects.}, }
@article {pmid42123473, year = {2026}, author = {Cheng, R and Liu, T and Liao, C and Wu, X and Zhu, L and Zhang, S}, title = {Integrating Protein Language Models with Multimodal Embeddings to Accelerate Function Prediction of Uncharacterized Proteins.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, doi = {10.3390/ijms27093891}, pmid = {42123473}, issn = {1422-0067}, support = {No. 32401056//National Natural Science Foundation of China/ ; 2024RC3144//Hunan Province Science and Technology Innovation Program/ ; }, mesh = {*Proteins/chemistry/metabolism ; *Computational Biology/methods ; Databases, Protein ; Humans ; Molecular Sequence Annotation ; }, abstract = {Accurate prediction of protein function is fundamental to progress in biotechnology and biomedicine, yet progress remains severely hampered by the widening chasm between exponentially growing genomic data and the limited capacity for functional annotation. High-throughput sequencing and metagenomics have driven an explosion in sequence data that far outstrips experimental characterization. UniProt now contains over 203 million protein entries, of which only ~2% have been experimentally validated. This widening "sequence-function gap" exceeds the reach of traditional homology-based tools such as BLAST (v2.17.0) and HMMER (v3.2), which are inherently constrained by sequence identity thresholds. The emergence of Protein Language Models (PLMs), including ESM and ProtTrans, has introduced a transformative paradigm, thereby shifting functional inference from similarity-based retrieval to geometric reasoning within learned semantic spaces. Nevertheless, current approaches remain largely confined to unimodal or narrowly bimodal frameworks, failing to capture the inherently multidimensional determinants of enzymatic function, including active-site geometry, chemical reaction logic, and literature-embedded semantic context. This review systematically adopts a multimodal global-fusion perspective, elucidating how three-dimensional geometric features, chemical reaction semantics, and textual knowledge graphs are synergistically integrated around PLMs as a core backbone. We delineate complementary mechanisms and integration strategies that together enable fine-grained protein function annotation beyond the performance ceiling of single-sequence methods. Furthermore, we survey the translational potential of such frameworks from computational prediction to real biological applications, and critically examine persistent bottlenecks including activity cliffs, transition-state inference, and conformational dynamics. We identify the integration of physics-informed machine learning with dynamics-aware architectures as a pivotal direction toward a causal, mechanism-level understanding of protein function.}, }
@article {pmid42123477, year = {2026}, author = {Baldo, E and Abeni, D and Agostini, G and Armato, U and Bauer, P and Belloni Fortina, A and Calza, A and Cervadoro, E and Chiarini, A and Ciprandi, G and Dal Prà, I and Faga, A and Farina, S and Geat, D and Giovannini, M and Girolomoni, G and Gisondi, P and Jousson, O and Manara, S and Mira, E and Nicoletti, G and Pagliarello, C and Pedron, R and Peroni, A and Rizzo, V and Segata, N and Tettamanti, G and Zanoni, M and Zumiani, G and Cristofolini, M}, title = {Clinical and Mechanistic Evidence for Comano Thermal Water: A Narrative Review.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, doi = {10.3390/ijms27093893}, pmid = {42123477}, issn = {1422-0067}, mesh = {Humans ; *Mineral Waters/therapeutic use ; Balneology/methods ; Animals ; Skin/drug effects ; }, abstract = {Comano thermal water (CTW) is a hypotonic, bicarbonate-calcium-magnesium mineral water traditionally used to manage chronic inflammatory and relapsing skin diseases. This review summarises and discusses the available clinical, experimental, and translational evidence on CTW, with a particular focus on dermatological indications. The physicochemical properties of CTW, along with the presence of a stable, non-pathogenic microbial community, are examined in relation to their potential biological activity. Clinical studies indicate that CTW-based balneotherapy, alone or in combination with narrowband Ultraviolet B (UVB) phototherapy, is associated with improvements in disease severity, symptom burden, and quality of life in patients with psoriasis and atopic dermatitis, and has a favourable safety and tolerability profile. Experimental data further suggest that CTW may exert anti-inflammatory and immunomodulatory effects, modulate keratinocyte function, support skin barrier restoration, and influence the cutaneous microenvironment, including microbiome-related pathways. The review also outlines emerging evidence for CTW in skin regeneration and in upper airway inflammatory conditions treated via inhalation-based approaches. Overall, this review suggests that CTW may serve as a biologically active therapeutic resource, warranting further investigation as a complementary approach within integrative management strategies for inflammatory and barrier-related conditions.}, }
@article {pmid42123517, year = {2026}, author = {Nguyen-DeMary, K and Vascellari, S and Mastinu, M and Melis, M and Bastiaanssen, TFS and Tomassini Barbarossa, I and Tepper, BJ}, title = {Cranberry Polyphenol Extract (CPE) Oral Rinse Improves Salivary Microbiome in 6-n-Propylthiouracil (PROP) Non-Tasters and Palatability of Aronia Juice.}, journal = {International journal of molecular sciences}, volume = {27}, number = {9}, pages = {}, doi = {10.3390/ijms27093935}, pmid = {42123517}, issn = {1422-0067}, support = {10180//United States Department of Agriculture/ ; }, mesh = {Humans ; *Saliva/microbiology/drug effects ; Female ; Male ; *Vaccinium macrocarpon/chemistry ; *Polyphenols/pharmacology/administration &amp; dosage/chemistry ; *Microbiota/drug effects ; Adult ; Propylthiouracil ; *Plant Extracts/pharmacology/chemistry/administration &amp; dosage ; *Photinia/chemistry ; Taste/drug effects ; *Mouthwashes/pharmacology/chemistry ; *Fruit and Vegetable Juices ; Young Adult ; }, abstract = {Sensitivity to the bitterness of 6-n-propylthiouracil (PROP) is controlled by variations in the TAS2R38 gene. This phenotype is often used as a marker for individual differences in taste perception. Previous findings show that PROP taster status is associated with differences in the salivary microbiome. It is well known that diet and environmental factors influence the risk of oral disease, but there is far less evidence showing how genetic differences play a role. Forty-seven young, healthy, PROP taster-classified adults rinsed with a cranberry polyphenol extract (CPE) oral rinse (0.75 g/L CPE powder in spring water) twice daily for 11 days. Saliva was collected pre- and post-intervention for microbiome analysis using shotgun metagenomic sequencing. At the same time points, participants evaluated two astringent juices (cranberry and aronia berry) for key attributes. At baseline, PROP taster groups differed in their salivary microbiome compositions, but post-intervention, the groups had more similar bacterial compositions. Post-intervention, non-tasters showed decreases in the relative abundance of 15 bacterial species, including a significant reduction (p = 0.037) in Eikenella corrodens, which is one bacterium, among several others, involved in oral biofilm formation. Additionally, after the intervention, sourness was reduced, and overall liking increased significantly for aronia juice. Oral dysbiosis, a risk factor for oral disease, may be controlled by bactericidal mouthwashes. Our results suggest that CPE, a natural alternative to traditional bactericidal rinses, may selectively target pathobionts while preserving salivary microbiota diversity. CPE might also provide greater benefits to non-tasters, who are at greater risk for oral disease.}, }
@article {pmid42124595, year = {2026}, author = {Mejía-Pitta, A and Zhang, Z and Hossain, AA and Bartosik, K and Baca, CF and Peralta, C and Molina, H and Teplova, M and Brady, SF and Micura, R and Patel, DJ and Marraffini, LA}, title = {A 5-hydroxymethylcytosine DNA glycosylase provides defense against T-even bacteriophages.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.02.25.707755}, pmid = {42124595}, issn = {2692-8205}, abstract = {The most abundant prokaryotic mechanisms of defense against phage predation involve the recognition and destruction of the infecting DNA. One method of counter-defense is the incorporation of modified nucleobases into the phage genome to avoid interaction with enzymes that target the viral DNA. T-even coliphages replace cytosine with 5-hydroxymethylcytosine (5hmC) that in some cases are further decorated with glucosyl groups. To explore the diversity of immunity genes that recognize 5hmC, we infected a library of metagenomic DNA inserts from uncultured, non-sequenced soil bacteria with a mutant T4 phage that harbored only non-glucosylated 5hmC on its genome. Bacteria that resisted infection carried a DNA glycosylase, Brig3, that specifically excises 5hmC nucleobases to generate abasic sites in the phage genome and prevent viral proliferation. The crystal structure of Brig3 bound to its substrate revealed a catalytic mechanism in which the 5hmC nucleobase is flipped out of the DNA into the active site and replaced by an asparagine residue that inserts into the double helix to contact the complementary guanosine. Brig3 is encoded within an operon that also encodes BapA, a hydrolase that removes glucosyl groups from glucosyl-5hmC present in the genome of otherwise Brig3-resistant T-even phages carrying this hypermodified base. Our results uncover a defense strategy in which the combined action of BapA and Brig3 widens the immune response to restrict the infection of T-even phages with genomes that are either partially or completely glucosylated.}, }
@article {pmid42125129, year = {2026}, author = {Khantsi, M and Babalola, OO}, title = {Influence of Cowpea Plants on Soil Bacterial Community and Soil Quality: Effects of the Rhizosphere.}, journal = {Plant-environment interactions (Hoboken, N.J.)}, volume = {7}, number = {}, pages = {e70157}, pmid = {42125129}, issn = {2575-6265}, abstract = {Cowpea (Vigna Unguiculata), a vital legume for suitable agriculture and food security in sub-Saharan Africa, plays a crucial role in improving soil health through intricate plant-microbe interactions in the rhizosphere. This review synthesizes current knowledge on the microbial interactions in the rhizosphere, focusing on soil health, microbial diversity, and their contributions to nutrient cycling and plant growth. Cowpea roots foster a diverse microbial consortium, including nitrogen-fixing rhizobia, phosphate-solubilizing bacteria and organic matter decomposers, which enhance soil fertility and structure. The microbial community in the cowpea rhizosphere is shaped by complex soil physiochemical properties, such as potential of hydrogen (pH), nutrient availability, and salinity, which significantly influence plant-microbe interactions. However, contradictions persist regarding pH's effect on microbial diversity, with unresolved questions about how specific environmental conditions regulate microbial taxa. Advanced techniques, including metagenomic analyses, have provided deeper insights into the taxonomic and functional composition of rhizosphere microbiomes, uncovering both abundant and rare microbial taxa involved in these processes. Despite these advancements, gaps remain in understanding the dynamic responses of microbial communities to environmental stresses. Bridging these gaps through integrative multi-omics approaches will enable the development of microbiome-informed strategies to improve cowpea productivity and promote sustainable agricultural practices, ensuring resilience in the face of climate variability.}, }
@article {pmid42125266, year = {2026}, author = {Nõlvak, H and Dang, NP and Truu, M and Peeb, A and Devarajan, AK and Petrich, C and O'Sadnick, M and Tiirik, K and Truu, J}, title = {Microbial succession and hydrocarbon-degrading potential in Arctic sea ice exposed to dispersed crude oil and chemical dispersant.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag022}, pmid = {42125266}, issn = {2633-6685}, abstract = {The increasing oil exploration and transport activities in the Arctic amplify the risk of oil spills in ice-containing marine environments. Chemical dispersants, intended to promote oil biodegradation by breaking hydrocarbons into small droplets, are potential tools in cold marine oil spill mitigation; however, their fate and effectiveness within sea ice remain uncertain. This study examined the influence of dispersed crude oil and the chemical dispersant (FinasolOSR 51) on microbial community dynamics and hydrocarbon-degrading potential compared to clean ice during an 89-day sea-ice mesocosm experiment using shotgun metagenomics and metagenome-assembled genomes. Dispersant addition markedly reshaped microbial communities in both dispersed-oil and dispersant containing ice, causing similar shifts toward psychrophilic hydrocarbon degraders such as Oleispira, Bermanella, and Pseudoalteromonas. Although aliphatic hydrocarbon degradation genes were enriched, several dominant taxa exhibited limited hydrocarbon metabolic capacity yet possessed extensive stress-response traits. Oil hydrocarbon loss in ice remained modest despite the presence of degraders, likely due to the very low microbial abundance. These findings demonstrate that dispersants can strongly shape microbial communities in Arctic sea ice, without necessarily enhancing the biodegradation of oil hydrocarbons. This highlights the need for careful evaluation of dispersants as remediation tools in ice-containing Arctic marine environments.}, }
@article {pmid42125370, year = {2014}, author = {, }, title = {Schmallenberg virus: State of Art.}, journal = {EFSA journal. European Food Safety Authority}, volume = {12}, number = {5}, pages = {3681}, pmid = {42125370}, issn = {1831-4732}, abstract = {This scientific report provides an overview of all research carried out on Schmallenberg virus (SBV), reviewing the current knowledge on SBV regarding genotyping findings, susceptible species, pathogenesis, transmission routes, immunity, seroprevalence, geographical and temporal SBV spread, improved within-herd transmission model, SBV impact assessment and within-herd and regional spread models. Metagenomic analysis identified SBV as a novel orthobunyavirus emerged in 2011 and it has been detected in domestic cattle, sheep, goats and 12 wild species. Seroprevalence studies indicate that SBV has probably spread over the whole of Europe, showing high seroprevalence at national scale, while larger variability is observed at regional scales. Clinical disease frequency is low and experimental infection on pregnant ewes and cows suggest that SBV rarely induces malformations. SBV may be detected from semen with a low frequency though there is no scientific evidence of transmission through insemination. Vector competence studies suggest that Culicoides are likely to be able to transmit SBV but found no evidence that mosquitoes are likely to be able to transmit it. SBV vertical transmission has not yet been identified as a major route. SBV has successfully overwintered, despite lengthy period of minimal vector activity and duration of immunity in cattle lasts for at least one year. A farm-to-farm spread model for SBV shows a rapid spread of infection across the study region and latent period, duration of viraemia, probability of transmission from host to vector and virus replication are sufficient to account for the rapid SBV spread. The between-farm SBV transmission model indicates that the application of movement restrictions has little effect on SBV spread. An impact assessment based on limited data suggests a probable effect of SBV infection on abortion, short gestation, non-return and the number of artificial inseminations required per animal. International trade restrictions by third countries represent the main SBV impact.}, }
@article {pmid42125413, year = {2026}, author = {Wang, J and Qiu, J and Zhang, C}, title = {Crusted scabies complicated by septic shock: a fatal case report with incidental detection of Sarcoptes scabiei DNA in peripheral blood.}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02577}, pmid = {42125413}, issn = {2214-2509}, abstract = {Crusted scabies is a severe form of scabies characterized by massive mite burden and profound immune dysregulation. Secondary bacterial infection is common and may progress to sepsis with fatal outcomes. We report a fatal case of crusted scabies complicated by septic shock in a 58-year-old man with diabetes mellitus and chronic dermatitis. The patient presented with diffuse erythroderma, extensive hyperkeratotic crusts, and deep skin fissures, and several household members had similar pruritic skin lesions. Laboratory investigations revealed marked eosinophilia, extremely elevated serum immunoglobulin E levels, and multiorgan dysfunction. Peripheral blood metagenomic next-generation sequencing identified multiple bacterial pathogens and incidentally detected Sarcoptes scabiei DNA. Despite broad-spectrum antimicrobial therapy, antiparasitic treatment, and intensive supportive care, the patient deteriorated and died. This case highlights crusted scabies as a potentially lethal condition when complicated by severe bacterial infection and underscores the need for cautious interpretation of parasitic DNA detected in blood, particularly in non-invasive ectoparasitic diseases.}, }
@article {pmid42125597, year = {2026}, author = {Pasaribu, B and Herawati, T and Purba, NP and Lewaru, MW and Sofyana, NT and Dilens, CVM and Dewanti, LP and Alina, DN and Agung, MUK}, title = {Shotgun metagenomic dataset of microbial communities in the water column of the Flores Sea, Indonesia.}, journal = {Data in brief}, volume = {66}, number = {}, pages = {112791}, pmid = {42125597}, issn = {2352-3409}, abstract = {The Flores Sea is a crucial component of the Indonesian Throughflow (ITF) pathway, which influences the transport of carbon, oxygen, and nutrients that support marine ecosystems. Here, we present the first dataset of microbial communities from the Flores Sea, Indonesia, generated using shotgun metagenomic sequencing of water column samples. Taxonomic analysis revealed that Proteobacteria (86%) was the most abundant phylum. In the dataset, the most abundant taxa identified through metagenomic analysis demonstrated Pseudoalteromonas lipolytica, Chromohalobacter salexigens, Marinobacter nauticus, Halopseudomonas aestusnigri, Pseudomonas mendocina, Flavobacterium beibuense, and Flavobacterium rakeshii, respectively. Functional annotation indicated that metabolism was major functional category in the microbial community. This metagenomic dataset provides valuable baseline information on microbial communities that may support future ocean monitoring and conservation strategies in the Flores Sea.}, }
@article {pmid42125669, year = {2026}, author = {Szaraz, D and Bohm, J and Machacek, C and Salokova, G and Gachova, D and Ruzicka, F and Danek, Z and Gheit, T and Zavadil, J and Borilova Linhartova, P}, title = {Bacteriome-based oral dysbiosis index in patients with oral squamous cell carcinoma.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2668149}, pmid = {42125669}, issn = {2000-2297}, abstract = {BACKGROUND: Oral dysbiosis plays an important role in the pathogenesis of oral squamous cell carcinoma (OSCC). Our study aimed to perform a pairwise comparison of the oral microbiota, especially the bacteriome, from OSCC tumoral surface vs other oral samples and evaluate the association of a novel bacteriome-based Oral Dysbiosis Index (bbODI) with the OSCC surface.<br><br>MATERIALS AND METHODS: This pilot observational study used 84 patient-matched samples from the OSCC tumoral surface (swabs and biopsies), healthy oral mucosa (tongue and buccal swabs), and supragingival dental plaque swabs. Bacteriomes were analyzed by 16S rRNA amplicon sequencing. The presence of microscopic fungi and selected viruses was also evaluated.<br><br>RESULTS: The relative abundance of the genus Fusobacterium, the ratio of the relative abundances of gram-negative to gram-positive bacterial genera, and the bbODI on the tumour surface significantly differed from patient-matched healthy oral mucosa (both buccal and tongue swabs) and supragingival dental plaque samples. Oral candidosis was found in 25% of patients; all patients were negative for cytomegalovirus and Epstein-Barr virus.<br><br>CONCLUSIONS: Certain characteristics of the bacteriome composition of the OSCC surface differ from patient-matched samples of healthy oral mucosa and supragingival dental plaque. The proposed bbODI appears to be a promising non-invasive tool for the identification of bacteriome disruption on the OSCC surface.}, }
@article {pmid42125783, year = {2026}, author = {Hu, X and Han, L and Ochoa-Hueso, R and Song, J and Yang, X and Wang, G}, title = {From Microbes to Molecules: Biodegradable Microplastics Reshape Soil Carbon Metabolism and Composition of Dissolved Organic Matter.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.6c01030}, pmid = {42125783}, issn = {1520-5118}, abstract = {Microplastics (MPs) are ubiquitous in the environment, yet how conventional MPs (CMPs) and biodegradable MPs (BMPs) alter microbial carbon (C) metabolism and dissolved organic matter (DOM) remains unclear. Using metagenomic sequencing and Fourier transform ion cyclotron resonance mass spectrometry, we found that BMPs altered microbial C cycling profiles more profoundly than CMPs. This was driven by a significant enrichment of functional genes involved in aerobic respiration, C fixation, intracellular C decomposition, and fermentation. In addition, BMPs exerted stronger influences on prokaryotic and viral community structures than CMPs. Notably, BMPs specifically enriched unique microbial taxa and virus-host linkages carrying diverse C-cycling genes, coregulating key metabolic pathways, and promoting a "viral shuttle" mechanism that accelerated DOM turnover. These effects were mediated through enhanced accumulation of labile and recalcitrant C components in relation to fertilization regimes. These findings revealed mechanisms by which BMPs reshape soil carbon dynamics through microbial-viral interactions.}, }
@article {pmid42125851, year = {2026}, author = {Fisher, CJ and Khrongsee, P and Subramaniam, K and Pushinsky, AD and Stevenson, V and Crawford, C and Goncalves, R}, title = {Acute Respiratory Distress Syndrome in a Dog With Canine Respiratory Coronavirus Infection.}, journal = {Journal of veterinary emergency and critical care (San Antonio, Tex. : 2001)}, volume = {}, number = {}, pages = {}, doi = {10.1111/vec.70113}, pmid = {42125851}, issn = {1476-4431}, abstract = {OBJECTIVE: To describe the clinical progression of acute respiratory distress syndrome (ARDS) associated with canine respiratory coronavirus and suspected aspiration in a previously healthy young dog.<br><br>CASE SUMMARY: A 1.5-year-old neutered male Rottweiler was presented for acute respiratory distress. The dog had a productive cough 2&#xa0;weeks prior that was reported to have improved. While at a boarding facility, the dog developed decreased appetite and lethargy, regurgitated, and became acutely dyspneic. The dog was taken to the veterinarian on site, where thoracic radiographs revealed severe consolidation of the cranioventral lung lobes. The dog was presented to a university referral hospital approximately 12&#xa0;h after regurgitation with fever, hypotension, hypoglycemia, and leukopenia, and was treated with positive pressure ventilation after failing high-flow oxygen therapy. The dog remained profoundly hypoxemic, developed acute kidney injury, and was euthanized after 24&#xa0;h. Necropsy revealed diffuse alveolar damage consistent with a diagnosis of ARDS. Bacterial cultures were negative. Real-time polymerase chain reaction results from upper respiratory and fresh lung samples, as well as metagenomics analysis from a lung sample, confirmed the presence of canine respiratory coronavirus.<br><br>Canine respiratory coronavirus is primarily associated with mild upper respiratory signs and has not been previously associated with ARDS. Direct pulmonary damage from the virus, decreased mucociliary clearance secondary to viral ciliary damage followed by aspiration, and secondary pulmonary damage from systemic inflammation and coagulation disturbances are all possible in this case. The practical use of metagenomics, an emerging diagnostic screening tool that provides characterization of a virus's entire genome, is also demonstrated here. Metagenomics has not been previously described in small animal clinical medicine and may aid in surveillance of infectious canine respiratory disease and provide better understanding of the role of "milder" pathogens in patients with multifactorial respiratory failure.}, }
@article {pmid42126224, year = {2026}, author = {Abuah, CY and Sipes, K and Buongiorno, J and Steen, AD and Bradley, JA and Giovannelli, D and Abramov, A and Peters, SL and Giannone, RJ and Hettich, RL and Liang, R and Boike, J and Vishnivetskaya, TA and Lloyd, KG}, title = {Capacity of Arctic fjord sediments to degrade carbohydrates from permafrost active layer.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0045626}, doi = {10.1128/spectrum.00456-26}, pmid = {42126224}, issn = {2165-0497}, abstract = {The degradation of organic matter (OM) by microorganisms in thawing permafrost produces greenhouse gases. Terrestrial OM is transported into fjords through hydrological runoff, but it is unclear whether the microbial mechanisms of OM degradation on land persist after soils enter marine environments, which differ greatly in conditions and microbial communities. This question is particularly relevant for low-OM soils, which dominate Arctic landscapes and are more exposed to oxidants. Here, we compared OM-degrading capacity in permafrost-affected active layer soils and adjacent fjord sediments from Kongsfjorden, Svalbard, focusing on carbohydrate-active enzymes (CAZymes), which target some of the most abundant types of organic matter in soils. Using multi-omics approaches-metagenomics, metagenome-assembled genomes (MAGs), metabolomics, metatranscriptomics, and metaproteomics-we examined CAZyme presence, distribution, and activity. Despite environmental differences, both soils and sediments harbored diverse glycoside hydrolases and polysaccharide lyases, most of which showed evidence of activity. Verrucomicrobia expressed the highest number of CAZyme transcripts, indicating that they dominated active carbohydrate degradation in fjord sediments, while Acidobacteria and Actinobacteria were more active in soils. Notably, CAZymes in fjord sediments targeted primarily soil-derived OM, and the proportions of enzymes degrading terrestrial OM, marine OM, and microbial necromass-remnants of dead microbial cells were similar across both environments. These results suggest that microbial communities in both soils and fjord sediments are equipped to degrade carbohydrates, and that burial of terrestrial-derived OM in fjord sediments may not protect it from microbial breakdown under Arctic warming.IMPORTANCEPermafrost thaw may be a critical climate feedback because microbial degradation of organic matter (OM) can release greenhouse gases. While fjords serve as major carbon burial sites, our results show that burial of terrestrial-derived OM in these sediments does not ensure protection from microbial degradation. Microbial communities in both active layer soils and fjord sediments harbor a broad arsenal of carbohydrate-active enzymes, with evidence of activity across diverse taxa. This functional continuity indicates that once terrestrial material is washed into fjords, it remains vulnerable to microbial breakdown despite different environmental conditions. Understanding these cross-system continuities in microbial function is essential for predicting the fate of OM in a rapidly warming Arctic and highlights the importance of including fjord sediments in global carbon cycle models.}, }
@article {pmid42126240, year = {2026}, author = {Prakash, H and Perez, RK and Ross, M and Tisza, M and Javornik Cregeen, SJ and Deegan, J and Petrosino, JF and Boerwinkle, E and Clark, JR and Maresso, AW}, title = {Detection, persistence, and rising prevalence of oncogenic viruses revealed by wastewater metagenomics.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0054726}, doi = {10.1128/aem.00547-26}, pmid = {42126240}, issn = {1098-5336}, abstract = {Oncogenic viruses cause high-risk cancers in humans and are responsible for nearly 20% of all cancer cases worldwide. Currently, very limited data exist in the realm of wastewater-based viral epidemiology (WBE) for cancer-causing viruses, with existing studies using targeted approaches (i.e., PCR-based approaches) that lack genomic resolution. In this study, we used a hybrid-capture approach to detect, filter, and sequence all known oncogenic virus signals from wastewater samples collected over 3 years (May 2022-May 2025) in 16 Texas cities, covering nearly 25% of the state's population. Once sequenced, we used custom computational tools designed for wastewater metagenomics to assign reads into their respective virus of origin, estimate viral abundances over time, and measure genomic read coverage. Our data indicate that we successfully detected oncogenic viruses, including six known oncogenic viruses, and three suspected oncogenic viruses, across all sampling locations within Texas. We observed a gradual increase in the viral abundance of oncogenic viruses over 3 years, with distinct peaks and dips over the summer and winter months. The prevalence of high-risk viruses such as human papillomavirus (HPV) and Epstein-Barr virus (EBV) rose, with sharp increases in viral abundance observed post-2024. We also obtained nearly 100% genome coverage with viral reads captured using this hybrid-capture technique for nearly all oncogenic viruses, with resolution down to the species and type taxonomic levels in some cases, such as that of HPV. Our study showcases the utility of hybrid-capture techniques to detect and track multiple oncogenic viruses simultaneously.IMPORTANCECancer-causing viruses are of major clinical significance, responsible for nearly 20% of all recorded cancer incidences in humans worldwide. There is a need for improved detection, tracking, and control of oncogenic viruses across the globe. To our knowledge, this work is the first comprehensive WBE approach used to detect all known oncogenic viruses concurrently, demonstrating the feasibility of monitoring the presence and levels of cancer-causing viruses and enabling the possibility of public health interventions in the future. Using this method, we obtain broad genomic coverage at strong depth and specificity, coupled with consistent real-time tracking dynamics of multiple oncogenic viruses. Furthermore, we showcase the ability to identify genomic regions on viral reference genomes from which sequenced reads originate. This information can be an invaluable tool toward understanding the viral prevalence dynamics in general populations, their relationship to cancer incidences in humans, and their mechanisms of viral evolution, including mutations.}, }
@article {pmid42126253, year = {2026}, author = {Hambücken, L and Sudianto, E and Verleyen, E and Saw, JH and Baurain, D and Cornet, L}, title = {An early diverging SQR enzyme in Antarctic Gloeobacterales indicates sulfide tolerance in thylakoid-lacking cyanobacteria.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0042326}, doi = {10.1128/spectrum.00423-26}, pmid = {42126253}, issn = {2165-0497}, abstract = {Oxygenic photosynthesis, which converts solar energy into carbohydrates via a linear electron transport chain and two photosystems (PSII and PSI), first appeared in cyanobacteria approximately 3.3 Ga and drove the Great Oxidation Event around 2.4 Ga. During this period, euxinic conditions-characterized by sulfidic, anoxic oceans-posed a metabolic challenge to cyanobacteria, as sulfide inhibits PSII, the reaction center responsible for water splitting. Here, we report the presence of a sulfide-quinone reductase (SQR) enzyme in Antarctic representatives of Gloeobacterales, the earliest-branching cyanobacterial lineage. Phylogenetic analyses consistently position these SQR sequences at the base of the cyanobacterial clade, likely predating the multiple lateral transfers reported for this gene in the phylum. Additional searches in metagenomic data sets indicate that such sequences are restricted to cold environments. Our findings unveil possible adaptive strategies of early cyanobacteria to cope with sulfidic stress and point to Antarctic lakes as preserved natural laboratories for investigating cyanobacterial diversification and the evolution of oxygenic photosynthesis under euxinic conditions.IMPORTANCEThe diversification of cyanobacteria during and after the Great Oxidation Event occurred in early Proterozoic oceans that were partially euxinic (anoxic and sulfidic), a condition generally considered incompatible with oxygenic photosynthesis due to photosystem II inhibition. The presence of a sulfide quinone reductase in an early diverging cyanobacterium lacking thylakoids, isolated from Antarctica, suggests that oxygenic and anoxygenic photosynthesis coexisted early on in cyanobacterial evolution. The occurrence of these organisms in Antarctic lakes under euxinic conditions offers a natural laboratory for studying the physiology and adaptation of the first oxygenic photosynthetic organisms.}, }
@article {pmid42126918, year = {2026}, author = {Smith, DB and Simmonds, P and Siddell, SG}, title = {Virus taxonomy and the ICTV - 21 FAQs for the perplexed virologist.}, journal = {The Journal of general virology}, volume = {107}, number = {5}, pages = {}, doi = {10.1099/jgv.0.002243}, pmid = {42126918}, issn = {1465-2099}, mesh = {*Viruses/classification/genetics ; *Virology ; *Classification/methods ; Terminology as Topic ; }, abstract = {Just over 125 years has passed since the 'filterable' agents of tobacco mosaic disease and foot-and-mouth disease were first described as infectious, replicating entities smaller than bacteria. Today, viruses are formally classified into more than 16,000 species ranked into genera, families and higher taxa. The development of an official virus taxonomy has been overseen by an International Committee, first constituted in 1966 and renamed as the International Committee on Taxonomy of Viruses (ICTV) in 1975. Despite the engagement of the ICTV in virus taxonomy over the last 60 years, many aspects of virus classification and nomenclature may seem odd or sometimes incomprehensible to virologists more familiar with the taxonomy of cellular organisms. Who runs the ICTV? What are virus species demarcation criteria? Why have all virus species names become binomial? How can a sequence in a metagenomic dataset be assigned to a virus species? This article attempts to answer several such questions and outlines how a large, inclusive and global community of virologists has developed new and responsive policies for virus taxonomy in a decade when the pace of virus discovery has dramatically accelerated.}, }
@article {pmid42127418, year = {2026}, author = {Parizadeh, M and Laforest-Lapointe, I and Serrano-Vázquez, A and Morán-Silva, P and Rojas-Velázquez, L and Torres, J and Ximénez-García, C and Arrieta, MC}, title = {Impact of Maternal, Infant, and Household Factors on Early-life Gut Microbiome Development in a Rural Setting.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag124}, pmid = {42127418}, issn = {1751-7370}, abstract = {Early-life gut microbiome development is influenced by host, microbial, environmental, and social factors. Rural infants typically exhibit greater microbial diversity than their urban counterparts, yet microbiome maturation patterns in less industrialized settings remain underexplored. Additionally, though microbial eukaryotes are integral to gut ecology, most studies to date have focused predominantly on bacterial communities. Using shallow shotgun metagenomics and 18S rRNA gene sequencing, we characterized eukaryotic and bacterial gut microbiomes in an intensively sampled longitudinal cohort of ten infants from a rural community in Morelos, Mexico, each followed monthly from the first to the 18th month, providing an unusually detailed view of early-life microbiome development in a low-resource setting. Although both bacterial and eukaryotic alpha diversity increased over time, they showed distinct colonization trajectories. Age, delivery mode, and environmental exposures, such as animal contact and household factors, influenced bacterial and eukaryotic community compositions, as well as bacterial metabolic composition. Inter-kingdom microbial networks varied with age, with a reduction in taxonomic diversity after the first year of life. Age and mode of birth also influenced changes in the overall community structure and connectivity of microbial co-occurrence patterns, but did not impact the associations among specific microbial taxa. Functional profiling revealed that bacterial metabolic potential diversified with age, whereas the mode of birth had a minimal impact on functional variation. These findings highlight the dynamic nature of bacterial and eukaryotic microbiota in early life and underscore the need to explore how rural environmental exposures shape microbial maturation, with potential implications for immune development and long-term health.}, }
@article {pmid42127818, year = {2026}, author = {Mahler, M and Yuping, L}, title = {Predicting phage anti-defenses that shoot the messenger.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {5}, pages = {811-813}, doi = {10.1016/j.chom.2026.04.014}, pmid = {42127818}, issn = {1934-6069}, mesh = {*Bacteriophages/genetics/physiology ; *Bacteria/virology/genetics ; *Viral Proteins/metabolism/genetics ; Metagenomics ; Signal Transduction ; }, abstract = {Locked in a constant arms race, bacteria and their phage predators have evolved various defenses and counter-defenses. Compared to the numerous identified defenses, phage-encoded counter-defenses are understudied. In a recent Science paper, Tal et al. developed a structure-guided approach to identify phage proteins counteracting nucleotide signaling defenses using metagenomic data.}, }
@article {pmid42127820, year = {2026}, author = {Bickel, S and Berg, G}, title = {Microbial diversity creates a global firewall against pathogens in soil.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {5}, pages = {817-819}, doi = {10.1016/j.chom.2026.04.016}, pmid = {42127820}, issn = {1934-6069}, mesh = {*Soil Microbiology ; Humans ; Metagenomics ; *Biodiversity ; *Bacteria/genetics/classification/isolation &amp; purification ; Melioidosis/microbiology ; *Microbiota ; Tuberculosis/microbiology ; Soil ; Animals ; }, abstract = {Soil is a critical ecological contributor to plant and animal health. In this issue of Cell Host &amp; Microbe, Xiong et al. use global metagenomic data to show that human pathogens linked to diseases like tuberculosis, melioidosis, and sepsis are widespread in humid and agricultural soils harboring reduced microbial diversity.}, }
@article {pmid42127824, year = {2026}, author = {Bouzek, DC}, title = {What the nose knows of cystic fibrosis microbes and hypertonic saline.}, journal = {Cell host &amp; microbe}, volume = {34}, number = {5}, pages = {827-829}, doi = {10.1016/j.chom.2026.04.017}, pmid = {42127824}, issn = {1934-6069}, mesh = {*Cystic Fibrosis/microbiology/drug therapy ; Humans ; Saline Solution, Hypertonic/pharmacology ; *Nasopharynx/microbiology ; *Microbiota ; Metagenomics ; Infant ; *Nose/microbiology ; }, abstract = {In this issue of Cell Host &amp; Microbe, Steinberg et al.[1] present a microbial gene atlas of nasopharyngeal swabs in infants with cystic fibrosis and healthy controls using shotgun metagenomic sequencing. The impacts of clinical interventions on respiratory microbial function can be identified and experimentally validated using the atlas.}, }
@article {pmid42114216, year = {2026}, author = {Que, H and Jiang, X and Wu, X and Li, S}, title = {Construction of a "three-stage and four-level" evaluation system for cerebrospinal fluid pathogens based on mNGS: insights from a case of co-detection of Cryptococcus and Epstein-barr virus.}, journal = {Diagnostic microbiology and infectious disease}, volume = {116}, number = {1}, pages = {117457}, doi = {10.1016/j.diagmicrobio.2026.117457}, pmid = {42114216}, issn = {1879-0070}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) has brought about a revolutionary change in the diagnosis of central nervous system (CNS) infections. Nevertheless, the interpretation of results with multiple detected pathogens still poses a substantial clinical challenge.<br><br>AIM: A preliminary exploration of the application value of the developed "Three-Stage, Four-Level" assessment system in interpreting mNGS cerebrospinal fluid test reports.<br><br>METHODS: Based on a systematic review of relevant domestic and international literature, combined with practical experience in the field, a multi-dimensional "Three-Stage, Four-Level" evaluation system centered on a clinical-microbiological evidence chain was constructed. This study explores the application value of the system through a case of mNGS detection for co-preservation of Cryptococcus and Epstein-Barr virus (EBV) in cerebrospinal fluid (CSF).<br><br>RESULTS: The system effectively integrated multi-source information, facilitating a precise and stratified interpretation of CSF mNGS results. It successfully differentiated Cryptococcus as the pathogenic agent and EBV as a latent pathogen. Consequently, early antifungal therapy was initiated, resulting in a gradual improvement of symptoms and a favorable prognosis.<br><br>CONCLUSION: This case initially demonstrates that the "Three-Stage,Four-Level "evaluation system provides a standardized and operational framework for interpreting mNGS cerebrospinal fluid multiplex pathogen detection results, showing preliminary value in precisely distinguishing pathogen types; however, further validation with larger sample sizes is warranted.}, }
@article {pmid42114574, year = {2026}, author = {Li, X and Cheng, S and Wang, X and Gu, X and Xu, X and Duan, X and Xue, G and Oleskowicz-Popiel, P and Xu, J and Liu, B and Liu, Z and Zhou, A and Makinia, J}, title = {Intrinsic waste component synergy: calcium-rich eggshell waste modulates fungal-bacterial microbiome toward selectively medium-chain fatty acid production.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134795}, doi = {10.1016/j.biortech.2026.134795}, pmid = {42114574}, issn = {1873-2976}, abstract = {The valorization of waste streams into medium-chain fatty acids (MCFAs) through fungi-bacteria synergy is often hindered by substrate competition and distinct ecological niches. This study demonstrates that eggshell waste acts as a bioregulator to optimize this interaction for caproate production. At a 20 g/L dosage, eggshells facilitated high caproate production (22.3 ± 1.3 gCOD/L) driven by in-situ ethanol supply (11.3 ± 1.9 gCOD/L). The amendment established stable micro-niches, significantly enriching yeasts (Wickerhamomyces, Candida, and Issatchenkia, 69.2%) and chain-elongating bacteria (CEB, Caproiciproducens, and Clostridium_sensu_stricto_12, 10.2%), while metagenomics confirmed upregulated glycolysis and reverse β-oxidation pathways. Additionally, yeast synergy with CEB via ethanol cross-feeding in a sugar-rich environment can be disrupted under the sugar-depleted phase. The coculture experiments unveiled that 8 g/L Ca[2+] alleviates fungi-bacteria conflict and promotes CEB functionality. This study presents a waste valorization strategy, leveraging intrinsic waste synergies to optimize fungal-bacterial interactions and drive endogenous ethanol-based caproate production.}, }
@article {pmid42114636, year = {2026}, author = {Zou, G and Zou, N and Tang, Y and Wang, Q and Xiao, H and Chen, Q and Liu, Z and Wang, K and Yang, F and Zhao, H and Qin, Y and Du, A and Chen, Y}, title = {Tire wear particles induce a functional trade-off in bioretention systems: Coupled effects on nitrogen removal and greenhouse gas emissions.}, journal = {Environmental research}, volume = {303}, number = {Pt 1}, pages = {124722}, doi = {10.1016/j.envres.2026.124722}, pmid = {42114636}, issn = {1096-0953}, abstract = {Bioretention systems are widely adopted nature-based solutions (NbS) for mitigating urban stormwater pollution, yet their long-term functional stability is increasingly undermined by the accumulation of tire wear particles (TWPs). This study moves beyond descriptive performance assessment to investigate the underlying biogeochemical mechanisms governing the response of bioretention media to dynamic TWP stress (0, 1, 10, and 100 mgL[-1]). Our results reveal a sophisticated functional trade-off induced by TWPs: although nitrogen removal efficiency was significantly compromised-with NH4[+]-N and total nitrogen (TN) removal rates decreasing by up to 14.64% and 11.02%, respectively-the system's net global warming potential was concurrently mitigated, achieving a 7.41-61.26% reduction in CO2-equivalent emissions. Mechanistically, partial least squares path modeling (PLS-PM) identified that TWPs trigger a metabolic bottleneck in the nitrogen cycle. The accumulation of TWPs significantly inhibited hydroxylamine oxidoreductase (HAO) and hydroxylamine reductase (HyR) activities (path coefficient: -0.742, p < 0.01) and suppressed the abundance of nitrifying bacteria (e.g., Nitrospira). Crucially, metagenomic insights demonstrated that TWPs redirected the nitrogen flux by upregulating the nrfA gene, thereby facilitating dissimilatory nitrate reduction to ammonium (DNRA) as an alternative pathway. These findings demonstrate that high TWP levels impair nitrogen removal through multi-interface synergy, highlighting potential ecological risks. This study provides a novel predictive framework for managing emerging microplastic pollutants in green infrastructure, offering actionable insights for optimizing the multifunctional ecosystem services of urban NbS under anthropogenic stress.}, }
@article {pmid42114650, year = {2026}, author = {Yang, J and Zhang, Z and Li, G and Yan, K and Song, Y and Zhang, J and Guo, Q and Zha, S and Sun, P and Zhang, X and Xia, Z and Yao, Z and Feng, X and Liang, J}, title = {Virus-associated immune dysregulation presenting as facial granulomatous dermatitis in DiGeorge syndrome: a case series.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108776}, doi = {10.1016/j.ijid.2026.108776}, pmid = {42114650}, issn = {1878-3511}, abstract = {Chronic granulomatous dermatitis in children with inborn errors of immunity poses diagnostic challenges, particularly when persistent viral detection coexists with impaired T-cell surveillance. We report two children with 22q11.2 deletion syndrome who developed chronic facial granulomatous dermatitis in the setting of T-cell immunodeficiency and EBV detection. Both patients had persistent facial plaques refractory to conventional antimicrobial or anti-inflammatory treatment, elevated EBV DNA in blood and/or mucosal samples, and granulomatous lymphohistiocytic infiltrates on skin biopsy. Tissue mNGS identified EBV in lesional specimens. In patient 1, EBER positivity and a restricted/skewed TRB repertoire provided stronger support for local EBV-associated immune dysregulation. In patient 2, EBV was detected by mNGS, but EBER staining was negative, additional microorganisms were identified, and TRB findings were more consistent with reactive or oligoclonal expansion, making causal attribution less certain. Rubella virus-associated granuloma, a key differential diagnosis in immunodeficient children, was not supported by lesion-directed testing. These cases highlight chronic granulomatous dermatitis as a possible manifestation of virus-associated immune dysregulation in DiGeorge syndrome and emphasize that mNGS results require careful integration with tissue localization, histopathology, clonality assessment, and immune context.}, }
@article {pmid42114714, year = {2026}, author = {Zhang, D and Yan, Z and Liang, J and Zhong, J and Liu, Y and Li, S and Wang, L and Gong, F and Hu, N and Ding, D and Yu, H}, title = {Uranium-induced differentiation in metabolic responses and functional potential of nitrogen-cycling microorganisms across different soil types.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128317}, doi = {10.1016/j.envpol.2026.128317}, pmid = {42114714}, issn = {1873-6424}, abstract = {Uranium (U) contamination poses a severe ecological risk by disrupting key biogenic element cycles, particularly nitrogen (N) transformation. However, the extent to which intrinsic soil heterogeneity shapes the functional adaptation of N cycling microorganisms to U stress remains poorly understood. This study investigated soil microcosms with metagenomic analysis to unravel the structural and functional differentiation of N cycling communities across forest (FT), grassland (GL), and farmland (FL) soils. Our results indicated that U contamination exerted significant selective pressure, leading to distinct functional differentiation in N cycling processes (R[2] = 0.56) which was primarily shaped by land-use legacy (R[2] = 0.62). Driven by this U-induced pressure, the three soils diverged into unique N cycling adaptive strategies. Specifically, U stress shifted the FT towards a strategy of energetic autonomy, enriching robust nitrate reduction coupled with a metabolic repertoire associated with U(VI) resistance and transformation potential. In the GL, U exposure shaped a complex, self-sustaining co-occurrence network associated with potential functional stability, characterized by cross-pathway complementation among N fixation, nitrification, and anammox. Conversely, U contamination drove the FL into a maladaptive simplification, where the reduction of functional redundancy and the dominance of a single nitrification pathway led to heightened vulnerability. Collectively, this study demonstrates that U stress acts as a selective filter that amplifies pre-existing soil driven discrepancies, driving soil microbial communities onto distinct functional potential trajectories. These findings emphasize the necessity of developing differentiated risk management strategies based on the specific N cycling resilience of various soil types.}, }
@article {pmid42114750, year = {2026}, author = {Saedi, N and Zhang, S and Sahana, G and Villumsen, TM and Stephansen, RB and Lund, MS and Cai, Z and Karaman, E}, title = {Comparison of 16S rRNA Sequencing and Shotgun Metagenome Sequencing for Estimating Genotypic and Phenotypic Parameters of Enteric Methane Emission in Dairy Cattle.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-28157}, pmid = {42114750}, issn = {1525-3198}, abstract = {Methane emissions from ruminants significantly contribute to greenhouse gases, making it crucial for sustainable livestock breeding to understand how both genetic and microbial factors influence methane production. We compared the heritability and microbiability for enteric methane in cows using microbial features derived from 16S rRNA amplicon data and shotgun metagenomics data, together with genome-wide marker data. The features derived from 16S rRNA data were 16s genus (16s-G), 16s species (16s-S), 16s Predicted microbial genes (16s-PMG) and 16s Predicted metabolic pathways (16s-PMP). The features derived from metagenomics data were metagenomic species (M-S) and metagenomic genus (M-G) considering 3 different databases (MGnify, GTDB, and NCBI). The heritability of methane ranged from 0.08 to 0.14. The 16s-G explained 28% of phenotypic variation in methane, and contributed the most to the heritability estimate for methane among other features. For the same feature data sets, we estimated the heritability of each microbial feature. Most microbial features had low heritability, while a subset had high values (up to 0.8). The highest heritabilities were observed for M-S MGnify feature RUG592 sp902767285 (0.95) and M-G NCBI genus feature Leadbettera (0.98). We found that the microbiota in the rumen is primarily determined by environmental factors, whereas host genetics has a significant impact on the abundance of certain functionally important microbes. To the best of our knowledge, this study presents the first comparison of methane heritability in dairy cattle incorporating microbial data (1) from multiple techniques such as 16S rRNA amplicon sequencing and shotgun metagenomic sequencing, and (2) from multiple levels of microbial features such as 16s-G, 16s-S, 16s-PMG, 16s-PMP, and M-S and M-G. Our results highlight heritable microbial species/genus as potential targets for microbiome-informed breeding strategies to reduce methane emissions in dairy cattle.}, }
@article {pmid42115187, year = {2026}, author = {Zhang, J and Chen, F and Xu, X and Zhang, L and Zhang, L and Qin, B and Li, K and Liu, Q and Hou, H and Li, Y and Liu, C and Li, Y and Shi, J and Teng, T and Wang, C and Zhou, X}, title = {Gut microbiota dysbiosis drives depression-like behavior in adolescent rats via lysine-regulated mTOR autophagy pathway.}, journal = {Translational psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41398-026-04095-2}, pmid = {42115187}, issn = {2158-3188}, abstract = {The prevalence of major depressive disorder (MDD) is increasing globally, particularly among adolescents. Although gut-brain axis dysfunction has been implicated in adolescent depression, the mechanisms by which gut microbiota dysbiosis drives depressive behaviors and potential antidepressant targets remain unclear. In this study, fecal microbiota transplantation (FMT) was performed from either healthy controls (HCs) or adolescents with MDD into antibiotic-treated adolescent rats. FMT from MDD adolescents induced depressive-like behaviors in recipient rats. Metagenomic sequencing revealed that FMT from MDD adolescents led to alterations in gut microbiota in recipient rats. While qPCR, Western blotting, immunofluorescence, and transmission electron microscopy (TEM) confirmed that these rats exhibited prefrontal cortex (PFC) autophagy hyperactivation, evidenced by a reduction in SQSTM1/p62 levels, an elevation in the LC3-II/LC3-I ratio, upregulated Beclin1, and increased numbers of autolysosomes. Similar autophagy-related transcriptional changes were observed in peripheral blood from MDD adolescents. Furthermore, ELISA showed reduced plasma lysine levels in MDD adolescents and decreased lysine concentrations in the PFC of FMT-MDD rats. The antidepressant effect of lysine and its interaction with autophagy were explored in a chronic unpredictable mild stress (CUMS) rat model with or without rapamycin (the autophagy activator, RAPA). Lysine supplementation alleviated depressive-like behaviors and suppressed PFC autophagy hyperactivation, while these effects were abolished by RAPA co-treatment. These findings reveal lysine deficiency as a metabolic bridge between gut microbiota imbalance and neuronal autophagy dysregulation, suggesting a gut microbiota-lysine-autophagy axis as an innovative mechanism and therapeutic focus for adolescent depression.}, }
@article {pmid42115271, year = {2026}, author = {Li, Z and Zhang, Q and Yang, J and Lei, R and Lu, W}, title = {Altered gut microbiota and metabolites in children with non-organic anorexia: a multi-omics integration study.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-52084-8}, pmid = {42115271}, issn = {2045-2322}, support = {S2024106612441//Provincial-level College Students' Innovation and Entrepreneurship Project of Zunyi Medical University/ ; S2024106612258//Provincial-level College Students' Innovation and Entrepreneurship Project of Zunyi Medical University/ ; Basic of QKh-ZK [2024] General 312//Science and Technology Department of Guizhou Province/ ; gzwkj2025-401//Science and Technology Fund Project of Guizhou Provincial Health Commission/ ; }, abstract = {Gut microbiota alterations have been linked to childhood eating disorders, but the functional and metabolic changes in non-organic anorexia (NOA) remain poorly understood. This study aimed to characterize the gut microbial composition, function, and metabolic profiles in children with NOA using an integrated multi-omics approach. A case-control study was conducted involving 88 children aged 1-5 years (48 NOA, 40 healthy controls). Gut microbiota composition was assessed via 16S rRNA gene sequencing of all fecal samples. Subsequently, the five most representative samples from each group were selected for deep shotgun metagenomic sequencing and liquid chromatography-mass spectrometry (LC-MS) based non-targeted metabolomics. NOA children showed significantly higher microbial richness and diversity (Chao1, Shannon; P < 0.001). The NOA group had elevated Firmicutes, Bacteroidota, Bacteroides, Faecalibacterium, Subdoligranulum, and Roseburia, but reduced Actobacteriota, Bifidobacterium, and Enterococcus. Metagenomics revealed downregulated riboflavin metabolism and upregulated fat digestion/absorption pathways in NOA (P < 0.05). Metabolomics identified 26 differential fecal metabolites, including decreased L-carnitine derivatives and elevated tyramine glucuronide involved in bile secretion. These metabolites were significantly correlated with altered bacterial genera. Our integrated multi-omics analysis demonstrates that NOA in children is associated with a specific gut ecosystem characterized by altered microbiota structure, perturbed microbial metabolic functions (particularly riboflavin metabolism), and corresponding host-microbiota co-metabolic disturbances. These findings provide novel evidence for the disrupted "microbiota-metabolite" axis in NOA, offering new mechanistic insights.}, }
@article {pmid42115921, year = {2026}, author = {Bulfoni, M and De Martino, M and Gualandi, N and Marzinotto, S and Vesca, G and Krpan, B and Marcon, B and Bertoni, M and Tascini, C and Pipan, C and Curcio, F}, title = {Gut microbiota profiling of the population residing in Friuli-Venezia Giulia through next-generation sequencing.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05117-1}, pmid = {42115921}, issn = {1471-2180}, abstract = {The gut microbiota is an ecological community of symbiotic and commensal microorganisms that play crucial roles in nutrient metabolism, maintaining the structural integrity of the intestinal mucosal barrier, immunomodulation, and pathogen protection. The composition of the gut microbiota varies with age, ethnicity, lifestyle, and dietary habits. Given the microbiota's growing role as a modulator of various physiological and pathological conditions, our study aimed to investigate the genetic profile of the microbiome individuals residing in the Friuli-Venezia Giulia region. We analyzed fecal swab samples from 109 individuals belonging to a general population cohort. The hypervariable V3-V4 regions of bacterial 16 S rRNA were analyzed using Next Generation Sequencing (NGS) on the MiSeq system (Illumina). The relative abundance of phyla, classes, orders, families, and species was defined using the BaseSpace 16s metagenomics app (Illumina). Firmicutes was the most represented phylum (51.1%), followed by Bacteroidetes (38.3%) and Actinobacteria (3%). At the class level, Clostridia (45.2%) and Bacteroidia (37.7%) were predominant, while Clostridiales (46.9%), Bacteroidales (26.6%), and Anaeroplasmatales (12.6%) were notable orders. Lachnospiraceae (21.9%) and Ruminococcaceae (16.2%) were the most frequent families, with Faecalibacterium prausnitzii (10.3%), Bacteroides vulgatus (4.6%), and Bacteroides dorei (3.5%) being prominent species. Each participant's taxa were analyzed to identify genera associated with alterations in gut microbial composition. Significant associations emerged between specific taxa of microorganisms and age, gender, anti-inflammatory drugs, tobacco consumption, and allergies. This study provides valuable insights into gut microbiota composition in a population-based cohort. The characterization of the microbiota in the Friuli-Venezia Giulia (FVG) region lays the foundation for future research into regional variations in microbiota composition and its impact on health.}, }
@article {pmid42116123, year = {2026}, author = {Zhou, J and Cheng, H and Zhang, Y and Liu, T and Chen, X and Lea-Smith, DJ and Todd, JD and Liu, J and He, X and Liu, R and Zhang, XH}, title = {Vertical distribution and metabolic diversity of autotrophic microbes in the deep sediment of the challenger deep.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00908-5}, pmid = {42116123}, issn = {2524-6372}, support = {BB/Y008332/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; NE/X014428//Natural Environmental Research Council/ ; NE/P012671//Natural Environmental Research Council/ ; RPG-2020-413//Leverhulme Trust/ ; ZR2024JQ006//Natural Science Foundation of Shandong Province/ ; 32370118//National Natural Science Foundation of China/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 2025YFF0516900&amp;2025YFF0516903//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: Carbon fixation in marine ecosystems is a vital process that contributes to climate regulation, with ocean sediments playing a critical role in carbon sequestration. This process is driven by chemolithoautotrophy in marine sediments, fueled by reduced compounds, such as those containing nitrogen and sulfur. However, the vertical distribution of microbial autotrophs and their energy coupling systems remain poorly understood in many sediments. In this study, we investigated a 750 cm sediment core from the Challenger Deep, the deepest point on Earth, which harbors abundant and diverse microbes under extreme conditions.<br><br>RESULTS: To explore the autotrophic characteristics across redox conditions in this core, we characterized the microbial community, metagenome, and metagenome-assembled genomes (MAGs), and their potential for carbon fixation processes and associated energy metabolism. The Wood-Ljungdahl (WL) pathway, primarily driven by Planctomycetota and Aerophobota, and the reverse oxidative TCA (roTCA) cycle, primarily driven by Bacteroidota and Gemmatimonadota, were the dominant predicted carbon fixation pathways, with hydrogen as the primary energy source, coupled to nitrogen and sulfur metabolism. Notably, the 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle, mediated by Nitrososphaeria, showed the highest abundance in the oxidized environment (15-27&#xa0;cm below the seafloor), where ammonia oxidation likely served as the primary energy source. Gammaproteobacteria were predicted to utilise sulfur oxidation, whereas Alphaproteobacteria and Chloroflexota used hydrogen to drive the Calvin-Benson-Bassham (CBB), reductive glycine pathway (rGly) in Alphaproteobacteria and the dicarboxylate/4-hydroxybutyrate cycle (DC/4HB) in Chloroflexota, respectively. The abundance of carbon fixation, and nitrogen, sulfur and hydrogen cycling functional genes were significantly correlated with environmental factors (NH4[+] and SiO3[2-]) based on Pearson's correlation analysis.<br><br>CONCLUSION: This study reveals the vertical distribution of microbial carbon fixation potential and diversity in sediments driven by redox conditions, highlights the crucial role of hydrogen as an energy source, and provides new insights for optimizing global deep-sea carbon cycle models. Collectively, these findings extend the redox tower theory by revealing a hadal-sediment specific distribution of autotrophic genes, characterized by persistent enrichment of energetically efficient pathways and dominant hydrogen-based energy coupling across deep sediment layers.}, }
@article {pmid42116193, year = {2026}, author = {Tamang, A and Kumar, A and Thakur, A and Kumar, R and Kumar, D and Hallan, V and Pandey, SS}, title = {Unravelling the fungal endomicrobiome of Picrorhiza kurrooa for increasing in-planta picroside biosynthesis using endophytic Trichoderma harzianum PKRF1.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00909-4}, pmid = {42116193}, issn = {2524-6372}, support = {MLP-201, MLP-207 and MLP-171//Council of Scientific and Industrial Research, India/ ; MLP-201, MLP-207 and MLP-171//Council of Scientific and Industrial Research, India/ ; }, abstract = {BACKGROUND: Endophytic fungi form an integral part of plant microbiomes, influencing host physiology, stress resilience, and secondary metabolism. While next-generation sequencing (NGS) has greatly advanced the identification of endophytes, it often falls short of assigning functional roles, necessitating integration with culture-based approaches for downstream applications. Picrorhiza kurrooa, a critically endangered Himalayan medicinal herb valued for its hepatoprotective picrosides, suffers from reduced metabolite content in tissue culture-derived plants, likely due to microbiome loss in the course of aseptic in-vitro practices. Moreover, the diversity and functional role of fungal endomicrobiome in P. kurrooa remain unexplored.<br><br>METHODS: Internal transcribed spacer (ITS)-based amplicon sequencing was performed to assess and compare the endophytic fungal communities of wild-type (Wt) and in-vitro propagated (Tc) P. kurrooa. Fungal taxa unique to Wt-plants were identified and cross-referenced with culturable isolates. A dominant isolate present only in Wt-plants, Trichoderma harzianum PKRF1, was reintroduced into Tc-plants to evaluate its effect on plant growth and picroside biosynthesis. Whole-genome sequencing and comparative genomics of PKRF1 were also conducted to elucidate its functional capabilities and possible candidates for its endophytic nature.<br><br>RESULTS: Metagenomic analysis revealed a significant reduction in fungal diversity in Tc plants, with several taxa, including Trichoderma, Cyphellophora, and Preussia, exclusively associated with Wt-plants. Inoculation of Tc-plants with PKRF1 led to successful root colonization, enhanced photosynthetic efficiency, biomass, and significantly higher levels of picrosides. Transcript profiling confirmed upregulation of key biosynthetic genes. Genomic analysis of PKRF1 revealed genes associated with multiple plant-beneficial traits, including nutrient acquisition, phytohormone production, stress tolerance, plant colonization, and competitive interactions, distinguishing it from non-endophytic Trichoderma isolates.<br><br>CONCLUSIONS: These findings provide the first comprehensive insight into changes in endophytic fungal diversity of P. kurrooa associated with in-vitro cultivation. Furthermore, the application of cultivated endophytes from wild plants demonstrated the potential to restore microbial functions lost during in-vitro propagation and enhance secondary metabolite production in cultivated plants. Overall, this approach offers a promising strategy to integrate metagenomic information into beneficial plant-microbe interactions for practical applications.}, }
@article {pmid42116465, year = {2026}, author = {Ozaki, GEDN and Maciel, ESO and Souza, BP and da Silva-Padilha, MP and Santos, NMMO and Oliveira, JCS and Souza, VB and Tulini, FL}, title = {Development and characterization of seriguela (Spondias purpurea) water kefir: metagenomic insights and functional potential of a spray-dried probiotic powder.}, journal = {Food research international (Ottawa, Ont.)}, volume = {236}, number = {}, pages = {119194}, doi = {10.1016/j.foodres.2026.119194}, pmid = {42116465}, issn = {1873-7145}, mesh = {*Kefir/microbiology/analysis ; *Probiotics/analysis ; Powders ; Fermentation ; *Metagenomics ; *Spray Drying ; Food Microbiology ; Hydrogen-Ion Concentration ; Antioxidants/analysis ; Fruit/chemistry/microbiology ; Bacteria/classification/genetics ; }, abstract = {Water kefir is a fermented probiotic beverage suitable for those with lactose intolerance, dairy allergies, or vegan diets. Adding fruits during fermentation can modulate microbial dynamics, sensory attributes, and biochemical composition, thereby enhancing functional properties. In this context, Spondias purpurea (seriguela), a bioactive-rich fruit native to the Americas, represents a promising yet underexplored substrate for the development of functional beverages. Therefore, this study investigated the composition of seriguela and its application in water kefir production, followed by physicochemical and metagenomic characterization and the evaluation of spray-dried formulations. Seriguela fruits exhibited an acidic pH (3.63), the presence of coumarins, steroids, and tannins, and remarkable antioxidant activity. Seriguela-flavored kefir maintained microbial levels comparable to those of traditional kefir (7.1 and 6.8 log CFU/mL for bacteria and yeasts, respectively), promoting a predominance of Komagataeibacter saccharivorans, Acetobacter aceti, A. lovaniensis, Liquorilactobacillus mali, Clostridium pasteurianum, and yeasts from the Saccharomyces genus. This change in the microbiota of seriguela-flavored kefir indicates a more homogeneous fermentation with pronounced acetic characteristics and probiotic potential. Furthermore, the spray-dried kefir demonstrated good physical properties, remarkable resistance under simulated gastrointestinal conditions, and moderate stability during refrigerated storage throughout 30 days (75.7% and 82.9% of survival for bacteria and yeasts, respectively, enumerated on De Man, Rogosa &amp; Sharpe agar and potato dextrose agar), highlighting its potential as a stable probiotic product. Overall, these results demonstrate the suitability of seriguela as a functional ingredient in water kefir and confirm spray-drying as a viable strategy for producing stable fermented powders with potential health-promoting properties.}, }
@article {pmid42116469, year = {2026}, author = {Liu, D and Li, J and Zhang, J and Zhang, C}, title = {CO2-modified atmosphere improves the flavor quality of low-salt Xuecai by regulating microbial communities and metabolic functions.}, journal = {Food research international (Ottawa, Ont.)}, volume = {236}, number = {}, pages = {119201}, doi = {10.1016/j.foodres.2026.119201}, pmid = {42116469}, issn = {1873-7145}, mesh = {*Carbon Dioxide/chemistry ; *Taste ; *Microbiota ; *Vegetables/microbiology/metabolism/chemistry ; *Food Microbiology ; *Atmosphere ; Biogenic Amines/analysis/metabolism ; Food Handling/methods ; Volatile Organic Compounds/analysis ; }, abstract = {Low-salt pickled vegetables are often limited by their poor flavor and the accumulation of biogenic amines (BAs). In the present study, the effects of CO2-modified atmosphere (CMA) technology on the dynamics of flavor compounds, microbial communities, and metabolic functions in low-salt Xuecai during pickling were investigated. In comparison with low-salt pickling under natural air conditions, a CMA effectively prevented excessive acidification, enriched volatile metabolites (e.g., isothiocyanates, alcohols, and esters), and minimized the accumulation of bitter-tasting amino acids, resulting in pickled vegetables with excellent flavor quality. Moreover, a CMA significantly inhibited the formation of BAs compared to low-salt natural pickling (P < 0.05; 46.71 vs. 114.29 mg/kg after 90 days of pickling), thereby enhancing the safety of low-salt Xuecai. In addition, metagenomic analysis showed that using a CMA for low-salt Xuecai production inhibited halophilic and spoilage microorganisms while enriching Lactobacillus-related populations. Metabolic pathway analysis revealed that the expression levels of the tricarboxylic acid cycle, amino acid metabolism, and genes encoding enzymes (i.e., amino acid decarboxylases, amine deiminases, and amine synthases) related to BA production were lower under a CMA. This, in turn, improved the flavor quality and inhibited the generation of BAs in low-salt Xuecai. Our study offers an alternative method for developing low-salt fermented foods.}, }
@article {pmid42116470, year = {2026}, author = {Wang, L and Zhu, N and Cai, F and Lin, X and Lai, C and Hu, H and Tao, Q and Song, J and Dai, W and Jia, X and Zhang, W}, title = {Fructooligosaccharides alleviate early-life antibiotic-exposed food allergy via the Indole-3-propionic acid-AhR-Nrf2 Axis: A multi-omics prospective cohort study.}, journal = {Food research international (Ottawa, Ont.)}, volume = {236}, number = {}, pages = {119200}, doi = {10.1016/j.foodres.2026.119200}, pmid = {42116470}, issn = {1873-7145}, mesh = {*NF-E2-Related Factor 2/metabolism ; Animals ; *Indoles/metabolism ; *Oligosaccharides/pharmacology ; Gastrointestinal Microbiome/drug effects ; Mice ; *Propionates/metabolism ; *Food Hypersensitivity/prevention &amp; control/etiology/metabolism/drug therapy ; *Receptors, Aryl Hydrocarbon/metabolism ; *Anti-Bacterial Agents/adverse effects ; Humans ; Male ; Female ; Prospective Studies ; Dysbiosis/chemically induced ; Oxidative Stress/drug effects ; Multiomics ; }, abstract = {BACKGROUND: Gut microbiota is critical in food allergy (FA) development. While early-life antibiotics increase FA risk, the mechanism is unclear, and current treatments cannot correct underlying immune defects.<br><br>OBJECTIVE: To investigate how early-life antibiotics exacerbate FA and whether fructo-oligosaccharides (FOS) can restore gut-immune balance.<br><br>METHODS: We linked early-life antibiotic use to gut dysbiosis and metabolites in a birth cohor, modeled mechanisms and FOS intervention in antibiotic-exposed FA mice, and validated FOS efficacy in a pediatric trial.<br><br>RESULTS: Early-life antibiotics caused persistent gut dysbiosis (notably Lactobacillus depletion) and disrupted tryptophan metabolism, ultimately resulting in oxidative stress, barrier damage, and T-cell imbalance. FOS restored Lactobacillus and the tryptophan metabolite indole-3-propionic acid (IPA). IPA alleviates mitochondrial dysfunction and reactive oxygen species accumulation via activation of the aryl hydrocarbon receptor (AhR)-nuclear factor erythroid 2-related factor 2 (Nrf2)-heme oxygenase-1 (HO-1) antioxidant pathway, and enhances intestinal barrier integrity, ultimately rebalancing T-cell homeostasis and attenuating FA. In a pediatric trial, metagenomic sequencing revealed that FOS enriches both Lactobacillus johnsonii and Clostridium sporogenes, synergistically promoting IPA production-which correlates with reduced SCORAD scores and improved weight gain.<br><br>CONCLUSIONS: Early-life antibiotics cause lasting disruptions in gut microbiota and metabolism that worsen FA. FOS mitigates FA by boosting microbiota-derived IPA to activate the protective AhR-Nrf2-HO-1 pathway, highlighting its therapeutic potential for FA, particularly in patients with prior antibiotic exposure.}, }
@article {pmid42116511, year = {2026}, author = {Xu, H and Kong, W and Tang, Q and Fan, K and Liu, M and Mo, K and Xu, Z and Zhang, W}, title = {Analysis of microbiome succession and metabolome dynamics in Jiupei during Chinese strong-flavor Baijiu fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {236}, number = {}, pages = {119274}, doi = {10.1016/j.foodres.2026.119274}, pmid = {42116511}, issn = {1873-7145}, mesh = {*Fermentation ; *Microbiota ; *Metabolome ; Food Microbiology ; Taste ; Volatile Organic Compounds/analysis ; Bacteria/metabolism/classification/genetics ; *Wine/microbiology/analysis ; Fungi/metabolism/classification ; Metabolomics ; Flavoring Agents ; China ; }, abstract = {Microbial successions during Jiupei fermentation are critical for the flavor synthesis of strong-flavor Baijiu, but their dynamics and associated metabolites across different vertical Jiupei layers have not yet been characterized in detail. This study employed metagenomic sequencing combined with metabolomic techniques to investigate the complex relationship between microbial succession and metabolite formation in Jiupei of strong-favor Baijiu fermentation. Results demonstrated that a total of 2940 compounds were identified and classified into 13 classes; of which over 94.7% of amino acids and derivatives, 57.5% of organic acids, and certain sugar alcohols increased during fermentation, whereas more than 81.8% of flavonoids decreased, particularly in the lower Jiupei layer. The volatile compounds, including ethyl caproate and ethyl lactate, showed a significant increase. Meanwhile, microbial diversity and richness dropped sharply from day 0 to day 30, with a recovery by day 60 in the middle and lower layers. The early stage of fermentation is characterized by the fungi Paecilomyces variotii, Lichtheimia ramosa, Rhizopus arrhizus, and Aspergillus chevalieri, as well as the bacteria Saccharopolyspora rectivirgula, Lactiplantibacillus plantarum, Leuconostoc citreum, and Weissella confusa, which secrete amylases and glycosylases to hydrolyze starch into sugars via enrichment of carbohydrate-related pathways, such as starch and sucrose metabolism, glycolysis/gluconeogenesis, and fructose and mannose metabolism. Acetilactobacillus jinshanensis, Lentilactobacillus diolivorans, and Philodulcilactobacillus myokoensis sharply increased in the later stage of fermentation, alongside enriched pathways for fatty acid and secondary metabolite biosynthesis. Acetilactobacillus jinshanensis ‌might synergistically accumulate characteristic flavor compounds through transferase and ligase reactions. These findings reveal the stage-specific microbial metabolic characteristics and synergistic mechanisms in flavor formation, providing a scientific basis for optimizing Baijiu fermentation processes to enhance Baijiu quality.}, }
@article {pmid42116518, year = {2026}, author = {Zhou, H and Xu, B and Zhang, L and Yan, L and Wang, R and Xu, Q and Jiang, C and Chen, A and Wu, X and Li, X}, title = {Ecological dominance and genomic features of bacterial generalists during pit fermentation of three distinct baijiu types in Anhui Province.}, journal = {Food research international (Ottawa, Ont.)}, volume = {236}, number = {}, pages = {119296}, doi = {10.1016/j.foodres.2026.119296}, pmid = {42116518}, issn = {1873-7145}, mesh = {*Fermentation ; China ; *Food Microbiology ; *Bacteria/genetics/classification/metabolism ; *Wine/microbiology/analysis ; Lactobacillus/genetics/metabolism ; }, abstract = {Microbial generalists are pivotal for maintaining the stability of fermentation systems, yet their distribution across different Baijiu types remains poorly understood. This study identified generalists and specialists during the pit fermentation of strong-flavor, jian-flavor, and sesame-flavor Baijiu in Anhui Province, and further elucidated their genomic features. Results showed that bacterial communities in all three types are dominated by generalists, whereas fungal communities depend more on diverse specialists. Bacterial generalists were represented by OTUs classified as Acetilactobacillus, Lactobacillus, and Limosilactobacillus. Targeted removal of these generalists increased the robustness of time-series networks, as they correlated negatively with most other taxa and were strongly linked to physicochemical properties. The major species belonging to bacterial generalists included Acetilactobacillus jinshanensis, Lactobacillus acetotolerans, and Limosilactobacillus pontis. These generalists possessed specialized genomic features for niche dominance, characterized by: (i) a low-acquisition, high-growth life history strategy (A/Y < 1); (ii) a preference for sugar metabolism (SAP >0); (iii) a complete multi-layered defense system conferring tolerance to acid and ethanol; and (iv) a streamlined (< 2 Mb) and non-redundant (lacking the TCA cycle) genome that minimizes regulatory burden. This study provides a systematic analysis of generalists across distinct Baijiu types in Anhui Province, offering a theoretical framework for understanding the rules of microbial assembly in the brewing process.}, }
@article {pmid42116534, year = {2026}, author = {Veyrenche, N and Boluda, S and Pérot, P and Malissin, I and Leruez-Ville, M and Jamet, A and Ferroni, A and Regnault, B and Salmona, M and Feghoul, L and Robert-Capraro, L and Leroux, A and Grasland, B and Niqueux, E and Briand, FX and Plu, I and Seilhean, D and Megarbane, B and Fourgeaud, J and Dheilly, NM}, title = {One Health Investigation into Fatal Encephalitis Caused by Pigeon Paramyxovirus Type 1, France.}, journal = {Emerging infectious diseases}, volume = {32}, number = {5}, pages = {753}, doi = {10.3201/eid3205.251576}, pmid = {42116534}, issn = {1080-6059}, mesh = {Humans ; France/epidemiology ; *Newcastle disease virus/genetics/classification/isolation &amp; purification ; Fatal Outcome ; *Newcastle Disease/virology/diagnosis/epidemiology ; Animals ; Male ; Phylogeny ; Columbidae/virology ; *Encephalitis, Viral/diagnosis/virology/epidemiology ; }, abstract = {Pigeon paramyxovirus type 1 (PPMV-1) is a genotype of avian paramyxovirus type 1 that uses species of the family Columbidae as reservoir species. We report fatal PPMV-1 encephalitis in a human without immunosuppression or travel history outside metropolitan France. Postmortem analyses revealed PPMV-1 in tissues, underscoring that physicians should consider this potential diagnosis.}, }
@article {pmid42116592, year = {2026}, author = {Andreani, J and Boschi, C and Decoppet, A and Delerce, J and Penant, G and Karadeniz, A and Grimaldier, C and Jardot, P and Zangoli, L and Mandy, M and Vigroux, N and Polesso, F and Edouard, S and Cano, P and Lagier, JC and La Scola, B and Colson, P}, title = {Severe Respiratory Illness and Death Associated with Outbreak of Human Rhinovirus B14 among Older Adults, France, 2024.}, journal = {Emerging infectious diseases}, volume = {32}, number = {5}, pages = {768-773}, doi = {10.3201/eid3205.250981}, pmid = {42116592}, issn = {1080-6059}, mesh = {Humans ; France/epidemiology ; *Rhinovirus/genetics/classification/isolation &amp; purification ; *Disease Outbreaks ; *Picornaviridae Infections/epidemiology/virology/mortality ; Aged ; Male ; Female ; Aged, 80 and over ; *Respiratory Tract Infections/epidemiology/virology/mortality ; Phylogeny ; Genome, Viral ; }, abstract = {We investigated an outbreak of unknown respiratory disease and 8 deaths among older adults in a long-term care facility in France. We identified human rhinovirus (HRV) by quantitative PCR and HRV-B14 by metagenomics. We obtained 5 HRV-B14 genomes that diverged from 5 publicly available genomes. Real-time metagenomics could enable rapid clinical diagnoses.}, }
@article {pmid42116727, year = {2026}, author = {Kutter, JS and Cuevas-Lobato, O and Fernandez-Pacheco-Gonzalez-Echavarri, BE and Moreno-Gomila, C and Garcia-Ibañez, N and Camacho, J and Ruiz-Pedro, E and Cabrerizo, M and Alós, JI and Diez-Fuertes, F and Fernandez-Garcia, MD}, title = {Unraveling the Transmission Dynamics of a Novel Norovirus GII.17[P17] Lineage During Two Consecutive Outbreaks in a Spanish Hospital.}, journal = {Journal of medical virology}, volume = {98}, number = {5}, pages = {e70966}, doi = {10.1002/jmv.70966}, pmid = {42116727}, issn = {1096-9071}, support = {PI23CIII-00009//Instituto de Salud Carlos III/ ; }, mesh = {Humans ; *Caliciviridae Infections/epidemiology/transmission/virology ; *Norovirus/genetics/classification/isolation &amp; purification ; *Disease Outbreaks ; Spain/epidemiology ; Phylogeny ; *Cross Infection/epidemiology/virology/transmission ; Feces/virology ; *Genotype ; Male ; Female ; Middle Aged ; Adult ; Molecular Epidemiology ; Aged ; Hospitals ; High-Throughput Nucleotide Sequencing ; *Gastroenteritis/epidemiology/virology ; Young Adult ; Genome, Viral ; }, abstract = {Norovirus outbreaks in healthcare settings pose significant challenges to infection prevention and control (IPC). To prevent and control such outbreaks efficiently, identifying sources and transmission clusters (TCs) is crucial but often limited by traditional outbreak investigations. Here, we examined two consecutive hospital norovirus outbreaks employing a genomic epidemiology approach to elucidate transmission dynamics and guide IPC strategies. Stool samples of 54 symptomatic patients were analyzed with different diagnostic methods, and 26 norovirus-positive samples underwent metagenomic next-generation sequencing (mNGS) for phylodynamic and phylogenetic analyses. All infections belonged to the novel GII.17[P17] lineage, circulating globally since 2023/2024. LiquidArray® outperformed fluorescence immunoassay (FIA, 28.6%) and RT-PCR (85.7%) with FIA's low sensitivity leading to missed cases highlighting the need for molecular confirmation for accurate outbreak management. Genomic analysis revealed multiple introductions, with two TCs identified in Outbreak-1 and one in Outbreak-2, as well as inter-hospital-unit spread. Reconstruction of transmission trees indicated sustained person-to-person spread with 0-3 unobserved intermediate cases in both outbreaks. Identical sequences in patients without clear epidemiological links suggested possible fomite transmission. These analyses provided key insights into infection sources and TCs that would have remained unknown using epidemiological investigations alone, supporting more targeted IPC resource allocation and intervention strategies.}, }
@article {pmid42116832, year = {2026}, author = {Dawson, MN and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the moon jellyfish, Aurelia sp. 4 Dawson et al. 2005 (Semaeostomeae: Ulmaridae) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {11}, number = {}, pages = {189}, pmid = {42116832}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Aurelia sp. 4 Dawson et al., 2005 (moon jellyfish; Cnidaria; Scyphozoa; Semaeostomeae; Ulmaridae). The genome sequence has a total length of 462.10 megabases. Most of the assembly (99.99%) is scaffolded into 21 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.88 kilobases. From the metagenome data, we recovered 3 bins, of which 2 were high-quality MAGs.}, }
@article {pmid42116847, year = {2026}, author = {Williams, NLR and Bei, Q and Raut, Y and Fuhrman, JA}, title = {Converting relative amplicon abundances to absolute abundances via flow cytometry: metagenomic validation and application to long ocean transects.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag081}, pmid = {42116847}, issn = {2730-6151}, abstract = {With microbes critical for ocean ecological and biogeochemical processes, we need to understand their abundance and diversity distributions. While traditional amplicon sequencing provides only relative abundance data, and the strongly preferred absolute abundances can be determined from samples spiked with internal standards, few oceanographic studies with absolute abundances exist. However, many have flow cytometry (FCM) data that should allow us to retrospectively "anchor" the relative abundances into absolute abundances. We tested this hypothesis with data from the 29th Atlantic Meridional Transect (AMT29) cruise where we had FCM of Synechococcus and Prochlorococcus, amplicons corrected with internal standards, and absolute cell count estimates from single copy recA and radA metagenomics. Anchoring the AMT29 amplicon data with Synechococcus FCM (used because phycoerythrin in Synechococcus is reliably detected by FCM in surface waters) yielded results strongly correlated with amplicon data corrected with internal standards (Pearson's r = 0.94, slope = 0.73), FCM (r = 0.80, slope = 0.43), and recA-based genome counts (Pearson's r = 0.94, slope = 0.62). Seeing this method worked reasonably well, we then generated estimates of absolute rRNA gene abundances from the Global rRNA Universal Metabarcoding of Plankton (GRUMP) transects that had FCM data (Pacific ~65 N to ~40S). These FCM-anchored gene copy estimates also showed strong correlations to FCM data (i.e. anchor with Synechococcus and predict Prochlorococcus), with r values ranging from 0.48-0.86. While the results are clearly only reasonable estimates, we believe the approach has the potential to significantly enhance the value of amplicon data which have accompanying FCM data.}, }
@article {pmid42117813, year = {2026}, author = {Qi, W and Lü, L and Huang, K and Qi, J and Li, M and Shi, M and Wang, H}, title = {Effects of Rotary Tillage and Fertilization on Chemical Properties and Microbial Communities of Soil Under Continuous Morchella Mushroom Cultivation.}, journal = {Biology}, volume = {15}, number = {9}, pages = {}, doi = {10.3390/biology15090674}, pmid = {42117813}, issn = {2079-7737}, support = {2024XTCX0403//Liaoning Academy of Agricultural Sciences Collaborative Innovation Project/ ; 2026NYGG010//Key Core Technology Research and Development in Shaanxi Province Agriculture/ ; }, abstract = {The severe continuous cropping obstacles in Morchella cultivation, driven primarily by soil microecological imbalance, critically constrain the sustainable development of the industry. To address this challenge, this study evaluated the efficacy of rotary tillage, calcium cyanamide (CaCN2), and organic fertilizer, applied individually and in combination, in mitigating these obstacles and explored the underlying microbial mechanisms. The soil was treated on 5 August 2024, and soil samples were collected on 5 October 2024. Four treatments were established: continuous cropping control (CK), rotary tillage (XGX), rotary tillage combined with calcium cyanamide (MPD), and rotary tillage combined with calcium cyanamide and organic fertilizer (MPX). Soil chemical properties were analyzed in conjunction with metagenomic sequencing to characterize the responses of soil properties and microbial communities, including both eukaryotic and bacterial taxa. The results indicated that the MPD treatment showed a relatively pronounced effect in enhancing key soil fertility indicators, including soil organic matter (OM), total nitrogen (TN), available nitrogen (AN), available potassium (AK), and total phosphorus (TP). All amendments significantly altered microbial community structures. Specifically, the integrated MPX treatment effectively reduced the relative abundance of the pathogenic fungus Olpidium while maintaining higher overall microbial diversity. It also significantly promoted the abundance of Morchella itself and beneficial bacterial phyla such as Actinomycetota and Pseudomonadota. Redundancy analysis identified AN and AK as the primary drivers of eukaryotic community variation, whereas Availa-ble phosphorus (AP) and potential of hydrogen (pH) were the key factors shaping the bacterial community. The results indicated that MPD was the showed relatively pronounced effectiveness in rapidly improving soil fertility and suppressing pathogenic fungi. In contrast, MPX showed relatively better performance in optimizing microbial community structure, enhancing microbial diversity, and strengthening overall ecological stability. These two treatments exhibited distinct advantages in soil chemical improvement and microbial community regulation, respectively, thereby providing alternative practical strategies and a theoretical basis for the ecological management of continuous-cropping obstacles in Morchella cultivation. It should be noted that this study did not include treatments with calcium cyanamide alone, organic fertilizer alone, or their combined application without rotary tillage. This is primarily because rotary tillage is a standard land preparation practice in Morchella cultivation, and the use of soil amendments without accompanying tillage is rarely adopted under practical production conditions.}, }
@article {pmid42118424, year = {2026}, author = {Devi, P and Nath, SK and Barua, B and Saha, T}, title = {Big data and artificial intelligence in animal nutrition: a new era of precision feeding.}, journal = {Tropical animal health and production}, volume = {58}, number = {4}, pages = {}, pmid = {42118424}, issn = {1573-7438}, mesh = {Animals ; *Big Data ; *Artificial Intelligence ; *Animal Feed/analysis ; *Animal Husbandry/methods ; *Animal Nutritional Physiological Phenomena ; *Livestock/physiology ; Dairying/methods ; }, abstract = {The convergence of Big Data and Artificial Intelligence (AI) is redefining animal nutrition by enabling precision feeding systems that are individualized, data-driven, and sustainability-oriented. This review synthesizes recent advances in multi-omics technologies, sensor-based monitoring, and machine learning applications across feed formulation, health surveillance, and production optimization. Precision feeding in pigs has been shown to reduce production costs by more than 8%, decrease protein and phosphorus intake by approximately 25%, lower nutrient excretion by up to 40%, and reduce greenhouse gas (GHGs) emissions by 6%, while maintaining or improving performance. In dairy systems, precision feed management strategies have achieved approximately 9.7% lower dietary crude protein levels, 14% reductions in manure nitrogen excretion, and annual net income gains of USD 137 per cow. AI-driven models have enhanced prediction of milk yield, feed conversion ratio (R[2] = 0.74), and residual feed intake (R[2] = 0.76), while enabling 96.26% accuracy in detecting microplastics in poultry feed. Integration of genomic, phenotypic, and sensor-derived datasets supports real-time monitoring, with wearable and IoT technologies transforming livestock management through continuous tracking of feeding behavior, emissions, and welfare indicators. Despite significant progress, current systems remain constrained by data heterogeneity, limited interoperability, and insufficient prescriptive decision-support frameworks. This article identifies methodological, technological, and adoption-related gaps, while highlighting future directions including nutrigenomics- and metagenomics-informed diet design, adaptive precision nutrition, and cost-effective solutions for smallholder systems. Collectively, these innovations establish Big Data and AI-enabled precision nutrition as a cornerstone of sustainable livestock production, advancing food security, climate resilience, and ethical animal management.}, }
@article {pmid42118429, year = {2026}, author = {Tekin, B and Gurbanov, R}, title = {Taxonomic and functional remodeling of the gut microbiota during aging and implications for microbiota-derived biomarkers.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42118429}, issn = {1573-0972}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Aging/physiology ; Biomarkers/analysis ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Animals ; Host Microbial Interactions ; Fatty Acids, Volatile/metabolism ; }, abstract = {The gut microbiota represents a complex microbial ecosystem that contributes to host metabolic regulation, immune homeostasis, and intestinal barrier function. Across the lifespan, gut microbial communities exhibit marked taxonomic and functional variation driven by environmental exposures, dietary patterns, medication use, and age-associated immune alterations. These differences are closely linked to chronic inflammatory states and immune dysregulation that accompany aging. This review synthesizes current evidence on age-associated differences in gut microbiota composition and functional capacity, with a focus on microbial traits and metabolic pathways relevant to host-microbe interactions. Pathological aging is frequently associated with reduced microbial diversity, loss of short-chain fatty acid-producing commensal bacteria, and enrichment of opportunistic or pro-inflammatory taxa. In contrast, healthy aging and longevity are commonly associated with more stable, resilient, and metabolically adaptable microbial communities. At the functional level, recurrent alterations in short-chain fatty acid biosynthesis, bile acid transformation, and tryptophan- and choline-related metabolic pathways define conserved features across aging-associated microbial profiles. Across neurodegenerative, metabolic, and cardiovascular conditions, overlapping taxonomic and functional patterns indicate shared microbiota-associated signatures linked to inflammatory states. Advances in metagenomic sequencing, functional annotation, and microbiome-focused biotechnological approaches now enable integrated analysis of microbial structure and metabolic potential. These developments provide a robust framework for identifying reproducible microbiome-based indicators relevant to aging-associated physiological changes and for translating microbiome research into biotechnology-driven applications.}, }
@article {pmid42119030, year = {2026}, author = {Yu, J and Tang, SN and Lee, PKH}, title = {Host-Linked Virome Assembly and Turnover Predict Bacterial Community Structure in Wastewater Treatment Systems.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag120}, pmid = {42119030}, issn = {1751-7370}, abstract = {Viruses play crucial roles in bacterial ecology and evolution through virus-host interactions; however, their distribution, assembly mechanisms, and temporal turnover remain underexplored in engineered ecosystems. In the present study, we used activated sludge (AS) and anaerobic treatment (AT) reactors from four full-scale industrial textile wastewater treatment plants as model ecosystems, integrating metagenomics, macroecological modeling, and deep learning to characterize viral structure, dynamics, and host interactions. A total of 1,046 and 1,386 high-quality viral operational taxonomic units were recovered from AS and AT systems, respectively, and most were affiliated with Caudoviricetes. Viral composition and genetic microdiversity were highly plant-specific and shaped by environmental selection and host interactions. Lognormal species abundance distributions and deviations from neutral expectations indicated deterministic assembly. Virulent viruses exhibited faster temporal turnover than temperate viruses. Viral co-occurrence networks showed strong plant-specific modularity and greater temporal stability than bacterial networks, suggesting that they play a stabilizing role in community dynamics. Tight virus-host abundance coupling and gene-level signatures of host-linked selection indicated ongoing coevolutionary interactions. A deep learning model accurately predicted bacterial community dynamics from viral composition at both the taxon and sample levels, highlighting the ecological relevance of viral signatures. Together, these findings reveal dynamic, plant-specific viromes tightly coupled to bacterial communities and highlight viral signatures as potential indicators for monitoring engineered ecosystems. Incorporating viral ecology into microbial management could enhance the stability, resilience, and functional performance of engineered ecosystems.}, }
@article {pmid42119140, year = {2026}, author = {Bao, Y and Ho, YW and Shen, Z and Lam, EY and Fang, JKH and Leung, KMY and Lee, PKH}, title = {Seasonal Divergence between Microbiomes on Microplastics and Natural Particles Increases with Rising Water Temperatures in Urban Rivers.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c13903}, pmid = {42119140}, issn = {1520-5851}, abstract = {The "plastisphere," which comprises microplastics (MPs)-associated microbial communities, is an emerging component of urban river ecosystems. However, its seasonal dynamics remain poorly understood, especially compared with microbiomes on natural particles (NPs). We therefore conducted a year-long metagenomic study at 15 sites across 10 major urban rivers in Hong Kong to compare MP- and NP-associated microbiomes across four seasons. Representative high-quality metagenome-assembled genomes revealed significant seasonal variations in both taxonomic and functional compositions across particle types, with water temperature identified as the primary environmental driver. As temperatures increased, both MP and NP microbiomes exhibited increased taxonomic and functional diversity but reduced functional redundancy and network stability. Compared to NPs, MP microbiomes exhibited higher taxonomic and functional turnover, more complex and connected cooccurrence networks, and distinct taxonomic and functional traits along the temperature gradient. In MP microbiomes, warmer conditions were associated with a higher abundance of pollutant-degrading and putatively virulent taxa (particularly from Firmicutes and Actinobacteria), along with enhanced biosynthetic functions and increased potential microbial sharing and horizontal gene transfer with surrounding aquatic microbiomes. These findings highlight the temperature-dependent ecological impacts of MP microbiomes and underscore the need to consider climatic factors when assessing the long-term ecological risks of MPs in urban riverine ecosystems.}, }
@article {pmid42119184, year = {2026}, author = {Pilliol, V and Beye, M and Boualam, MA and Tellissi, L and Slimani, A and Drancourt, M and Aboudharam, G and Tassery, H and Grine, G and Terrer, E}, title = {Evidence of a millennia-old association between a methanogenic archaeon and a bacterium in dental calculus: A re-analysis of ancient and modern metagenomic datasets.}, journal = {Archives of oral biology}, volume = {188}, number = {}, pages = {106622}, doi = {10.1016/j.archoralbio.2026.106622}, pmid = {42119184}, issn = {1879-1506}, abstract = {OBJECTIVES: Granehäll et al. (2021) identified TS-2 as an unknown Methanobrevibacter lineage abundant in ancient dental calculus, less prevalent in modern samples, and not linked to any cultivated representative. We aimed (i) to determine whether TS-2 corresponds to the cultivated oral archaeon Methanobrevibacter massiliense using genome-based species delineation, and (ii) to assess the antiquity of the association between M. massiliense and Pyramidobacter piscolens in ancient and modern dental calculus.<br><br>DESIGN: This fully in silico study combined comparative genomics with re-analysis of 97 ancient and modern dental calculus metagenomic datasets. Species-level relationships were assessed using average nucleotide identity, digital DNA-DNA hybridization, and 16S rRNA phylogeny. Metagenomic associations were examined using Kraken2-based taxonomic profiling, with Methanobrevibacter sp. YE315 as a proxy because M. massiliense was absent from the classifier database, and direct competitive read mapping to M. massiliense. Associations with P. piscolens were evaluated using Spearman correlation and negative binomial regression.<br><br>RESULTS: Comparative genomics supported TS-2 and M. massiliense as the same species-level taxon, with >&#x202f;95% average nucleotide identity and >&#x202f;90% digital DNA-DNA hybridization. In metagenomic analyses, the YE315 proxy was positively associated with P. piscolens in Kraken2 Spearman analysis (&#x3c1; = 0.3506, q = 0.0026), and mapped M. massiliense reproduced this pattern (&#x3c1; = 0.2939, q = 0.0153). Negative binomial models showed concordant but weaker support, whereas the signal for M. oralis was less consistent.<br><br>CONCLUSION: These results identify M. massiliense as the cultivated representative of TS-2 and support an ancient, recurrent association between M. massiliense and P. piscolens in dental calculus.}, }
@article {pmid42119293, year = {2026}, author = {Li, H and Xu, Y and Lin, T and Hu, C and Yang, Z and Su, H}, title = {Overwintering waterbirds are important reservoirs for the spread of antibiotic resistance genes (ARGs): Shared patterns at the waterbird-environment interface and the risk of horizontal transfer.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142298}, doi = {10.1016/j.jhazmat.2026.142298}, pmid = {42119293}, issn = {1873-3336}, abstract = {The global spread of antibiotic resistance genes (ARGs) has become a critical challenge to public health. Long-distance migratory waterbirds are recognized as important biological vectors in the transregional spread of ARGs. However, the sharing patterns of ARGs and the horizontal transfer risks between these birds and their habitats during the wintering period remain poorly understood. This limits a comprehensive understanding of their role in ARG transmission. This study investigated a typical wintering wetland in southwestern China along the East Asian-Australasian Flyway, using metagenomic approaches to systematically characterize the distribution patterns, sharing profiles, and horizontal transfer risks of ARGs in the guts of overwintering waterbirds and their associated aquatic and terrestrial habitats. The results show that multidrug resistance genes are the predominant type of resistance observed both in the guts of overwintering waterbirds and in their habitats. Extensive sharing of ARGs occurs between the guts of overwintering waterbirds and their habitats, with approximately 50% of the 1250 identified ARG subtypes shared by both. We detected 55 high-risk ARG subtypes belonging to 10 resistance categories. Among these, β-lactam resistance genes (e.g., blaNDM-5 and blaCTX-M-15) were the predominant types. In addition, the co-localization of ARGs with mobile genetic elements (MGEs) (e.g., transposons and plasmids) suggests that the gut of waterbirds and aquatic environments may represent potential hotspots for horizontal transfer of ARGs. This study highlights the high connectivity of ARGs between overwintering waterbirds and their habitats, offering important insights into ecological and public health risks related to ARG spread.}, }
@article {pmid42119385, year = {2026}, author = {Pan, L and Huang, Y and Chen, Y and Peng, T and Yang, J and Qiu, Y and Ji, M and Wu, X}, title = {Responses of soil microbes to antimony stress and coupled nutrient cycling in karst mining areas of Southwest China.}, journal = {Ecotoxicology and environmental safety}, volume = {318}, number = {}, pages = {120248}, doi = {10.1016/j.ecoenv.2026.120248}, pmid = {42119385}, issn = {1090-2414}, abstract = {Persistent and poorly mobile heavy metals in soil present a widespread environmental challenge. Among these, antimony (Sb) is a contaminant of emerging concern whose transformation and migration in soil require further investigation to inform effective remediation strategies. Microbial processes are central to these dynamics, yet the mechanisms underlying Sb-microbe interactions remain poorly defined. In this study, we used integrated geochemical and metagenomic analyses to assess Sb contamination and microbial community responses systematically in an abandoned Sb mining area in Southwest China. The data reveal how microbial communities respond to low and moderate levels of Sb contamination. Contamination was highest in the mining area, followed by the smelting and tailings areas; the control area exhibited the lowest levels. Community structure analysis revealed significant enrichment of Thiobacillus, Geothrix, and Anaeromyxobacter in the mining area, while Nocardioides and Sphingomonas were more abundant in the smelting area. Bradyrhizobium dominated in the control area. These patterns reflect distinct microbial responses to the Sb contamination gradient. Critically, partial least squares path modeling revealed that Sb contamination did not directly affect microbial α-diversity. Instead, its influence was indirectly mediated through disruptions in sulfur cycling functions-a novel finding highlighting the indirect ecological impact of Sb. Sb, along with co-occurring copper, may drive adaptive microbial succession by interfering with sulfate respiration. This process enriches microbial groups with sulfur-cycling-related detoxification functions, resulting in simplified community structure and reduced diversity. Thus, the primary mechanism by which Sb alters microbial communities in karst soils is indirect, operating via perturbation of the sulfur cycle rather than direct toxicity. These findings offer a theoretical basis for developing targeted microbial remediation strategies and restoring ecological functions in Sb-contaminated environments by regulating key elemental cycles.}, }
@article {pmid42119482, year = {2026}, author = {Paula, MPO and Varani, AM and da Silva, VLC and Roesch, LFW and Tótola, MR and Ramos, AC and Pylro, VS}, title = {Genome-resolved characterization of microbial consortia driving glyphosate degradation in soil.}, journal = {Chemosphere}, volume = {405}, number = {}, pages = {144948}, doi = {10.1016/j.chemosphere.2026.144948}, pmid = {42119482}, issn = {1879-1298}, abstract = {Glyphosate is a widely used non-selective herbicide associated with ecological and human health concerns due to its environmental persistence, highlighting the need for effective remediation strategies. Among available approaches, microbial enzyme-mediated degradation represents a promising biological solution. This study aimed to enrich and characterize glyphosate-degrading microbial consortia from coffee plantation soils, validate glyphosate and aminomethylphosphonic acid (AMPA) degradation by chromatographic analyses, and integrate genome-based functional annotation with comparative structural analyses to investigate enzymatic systems involved in C-P and C-N bond cleavage. The enrichment process, followed by metataxonomic and metagenomic analyses, revealed dynamic shifts in microbial community composition. Achromobacter and Serratia were identified as key genera, harboring genetic potential for glyphosate and AMPA degradation. High-performance liquid chromatography with diode array detection confirmed efficient transformation of both compounds, with consortia Con_CC and Con_CC-G achieving the highest removal efficiencies under carbon- and phosphorus-limited conditions. Genome-based functional annotation showed that both genera encode gene clusters associated with the C-P lyase pathway, while only Achromobacter harbors the gene encoding glyphosate oxidoreductase (GOX), linked to oxidative C-N bond cleavage. Structural modeling indicated conservation of key catalytic residues in PhnJ, whereas GOX-related sequences in Serratia corresponded to partial homologs lacking a complete catalytic site. By integrating chromatographic, genomic, and structural analyses, this study provides a multi-level framework linking microbial community dynamics, functional potential, and molecular mechanisms underlying glyphosate degradation.}, }
@article {pmid42119567, year = {2026}, author = {Chen, C and Xing, Y and Xing, G and Zeng, F and Zheng, N and Sha, S and Zhao, L and Zhang, Y and Ling, Y and Yao, X and Liu, C and Zhang, Y and Mei, T and Guo, R and Kang, J and Cheng, L and Fan, S and Sun, W and Li, S and Yan, Q and Yao, X and Kong, X and Ma, W}, title = {Multi-faceted characterization of the gut microbiome and metabolome in patients with primary Sjögren syndrome.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {102777}, doi = {10.1016/j.xcrm.2026.102777}, pmid = {42119567}, issn = {2666-3791}, abstract = {The gut microbiome and its metabolomic potential in primary Sjögren syndrome (pSS) remain largely unexplored. Here, we perform whole-metagenome shotgun sequencing of fecal samples from 206 pSS patients and 355 non-pSS controls, integrating compositional and functional profiling with serum and fecal metabolomes. pSS is associated with extensive multi-kingdom alterations, including 49 bacterial (e.g., Streptococcus parasanguinis, Ligilactobacillus salivarius, and Veillonella parvula), 19 fungal (notably Candida albicans), and 1,323 viral species. These signatures form robust inter-kingdom correlations and achieve high diagnostic accuracy in an independent validation cohort. Functional and metabolomic analyses reveal enrichment of toxin-related and aromatic pathways and depletion of protective metabolites in patients. pSS-enriched bacteria harbor abundant immunogenic epitopes, virulence factors, and antimicrobial resistance genes, and induce proinflammatory responses ex vivo. Together, these findings outline a multi-faceted microbial framework for pSS and suggest mechanistic links between gut dysbiosis and immune dysregulation.}, }
@article {pmid42119613, year = {2026}, author = {Liu, Y and Cheng, C and Xie, H and Nie, W and Chen, Y and Yu, C and Pavlostathis, SG and Zhang, J and He, Q}, title = {New insights into nitrous oxide-driven anaerobic methane oxidation mediated by Methylococcales and Gemmatimonadales.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134844}, doi = {10.1016/j.biortech.2026.134844}, pmid = {42119613}, issn = {1873-2976}, abstract = {The simultaneous biogeochemical transformation of methane (CH4) and nitrous oxide (N2O) in anoxic environments is a recently proposed pathway for decreasing carbon emission in wetlands. However, the mechanisms underlying this coupled process have yet to be elucidated. Here, two systems with CH4 to N2O molar ratios of 1:1 (R1) and 1:2 (R2) were established. Isotopic tracing showed that the production rate of [13]CO2 in R2 consistently exceeded than that in R1, with a maximum N2O-driven AOM rate of 2.29 μmol∙g[-1]dw∙d[-1], demonstrating the superior performance of R2. Microbial community analysis revealed that Methylococcales and Rhizobiales were the dominant methanotrophs, whereas Gemmatimonadales and Sphingobacteriales represented the primary denitrifiers involved in N2O reduction. Metagenomic binning further indicated that Methylococcales and Gemmatimonadales harbor complementary genomic potentials for CH4 oxidation and N2O reduction, supporting a synergistic interaction driving N2O-dependent AOM. This cooperation appears to rely on electron transfer between the methanotrophic and denitrifiers. Collectively, these findings provide mechanistic evidence for N2O-driven AOM, advancing the understanding of coupled carbon-nitrogen transformations and offering new insights into microbial strategies for mitigating greenhouse gas emissions in wetland systems.}, }
@article {pmid42119614, year = {2026}, author = {Zhang, Y and Yu, W and Chen, B and Lu, D and Guo, R and Fu, S}, title = {Harnessing microbial resource Rhodopseudomonas palustris for saline-alkaline paddy soil amelioration: key role of extracellular polymeric substances.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134777}, doi = {10.1016/j.biortech.2026.134777}, pmid = {42119614}, issn = {1873-2976}, abstract = {Bioremediation offers an eco-friendly solution for soil salinization, yet few salt-alkali-tolerant microorganisms can adapt to redox fluctuations induced by wet-dry alternation in paddy soil. Rhodopseudomonas palustris (R. palustris) holds promise for addressing this challenge, while the mechanism is still poorly understood. This study established a microcosm experiment mimicking paddy wet-dry alternation by regulating redox conditions to investigate the mechanisms of R. palustris and its extracellular polymeric substances (EPS) in soil amelioration. R. palustris adapted well to redox alternation and significantly reduced soil pH and electrical conductivity (EC) by 3-7% and 7-28%. In anaerobic phase, R. palustris secreted organic acids and promoted EPS synthesis, which directly complexed salt ions and drove soil acidification. Upon transition to aerobic conditions, it accumulated glycogen and polyhydroxyalkanoate (PHA) to sustain growth and EPS secretion. In the subsequent aerobic phase, EPS gradually transformed into amino acids, fulvic acid, and humic-like substances, as revealed by excitation-emission matrix (EEM) spectra, thereby improving soil fertility. Metagenomic analysis further revealed R. palustris and its EPS reshaped the microbial community and regulated the expression of related functional genes. Collectively, this study demonstrates R. palustris serves as an effective microbial resource for sodic-saline paddy soil amelioration, with EPS acting as a key bioactive component that drives this process toward biotechnology-driven remediation strategies.}, }
@article {pmid42119617, year = {2026}, author = {Yang, C and Cao, Y and Yang, Q and Li, J and Dong, T and Liu, Y and Li, X and Liu, F}, title = {Hematite-enhanced denitrification in bioelectrochemical system at low current density: kinetics, biofilm chemistry and metagenomic mechanisms.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134852}, doi = {10.1016/j.biortech.2026.134852}, pmid = {42119617}, issn = {1873-2976}, abstract = {Nitrate contamination of groundwater threatens drinking-water safety and necessitates the development of sustainable, low-energy remediation technologies. Bioelectrochemical systems (BESs) can enhance denitrification; however, their performance is constrained by low cathodic electron efficiency and ammonium accumulation. We developed a hematite-enhanced BES (HBES) and evaluated denitrification at different current densities (0-400 mA/m[2]). Hematite shifted the optimal current density from 200 to 100 mA/m[2], achieving complete nitrate removal within 72 h while suppressing ammonium formation to 0.38 ± 0.02 mg-N/L. Mechanistically, hematite improved cathodic kinetics and minimized activation losses, increased nitrate reductase activity, and promoted extracellular polymeric substance (EPS) enrichment with higher redox-active fulvic- and humic-like fractions. Community profiling revealed hematite-associated enrichment of Thauera, Acinetobacter, Hydrogenophaga, and Alishewanella, consistent with enhanced denitrification and electroactivity. Metagenomic analyses further revealed enhanced modules for sequential nitrate reduction to N2, suppression of dissimilatory nitrate reduction to ammonium (DNRA) marker genes, and elevated potentials for cytochrome-associated extracellular electron transfer (EET) and oxidative phosphorylation. Overall, hematite restructures electron-transfer networks and microbial metabolism at the mineral-biofilm-electrode interface, facilitating efficient and cleaner denitrification at relatively low current density and offering operational insights for BES-based groundwater nitrate remediation.}, }
@article {pmid42108251, year = {2026}, author = {Yin, M and Chen, X and Lu, R and Dong, Y and Luo, W and Tang, Z and Zeng, M and Xu, Y and Qing, Y and Xi, C and Feng, X and Guo, H and Mo, S and Luo, J}, title = {Diversity of fecal viromes and zoonotic risk assessment in captive wild felids using viral metagenomics.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-52077-7}, pmid = {42108251}, issn = {2045-2322}, support = {(Grant No. HX2023115P).//This research was supported by the grant for "Metagenomic Analysis of Viruses Carried by Amur Tigers and Leopards" (Grant No. HX2023115P)./ ; }, abstract = {Emerging viral diseases-particularly zoonotic pathogens-affect the health and conservation of endangered felids, including Panthera tigris altaica (Amur tiger) and Panthera pardus (leopard). To address this challenge, we employed a viromics approach to investigate the diversity of the fecal virome in wild felids and assess its zoonotic potential. Using in-depth metagenomic sequencing and analysis of fecal samples from captive wild felids housed in a wildlife institution, this study characterized the enteric virome and evaluated associated risks. A total of 18 viral families and 48 viral genera were identified. The DNA virus community exhibited stability in abundance and composition, dominated by the phyla Heunggongvirae and Bamfordvirae. Within Heunggongvirae, the class Caudoviricetes was the core component, with its abundance aligning with the intestinal bacterial community, suggesting a potential role of these bacteriophages in regulating microbial ecology. Additionally, sequences of the family Poxviridae, homologous to Variola virus (VARV), were detected. In contrast, the RNA virus community displayed higher diversity and variability, with the order Ortervirales as the predominant group. Sequences highly homologous to feline leukemia virus (FeLV) were repeatedly identified, suggesting potential latent infections. The detection of sequences related to rare environmental viruses, such as Casadabanvirus, highlights the potential risk of cross-species virus transmission under captive conditions. Stability analysis revealed that dominant DNA virus groups exhibited low abundance variability across samples. In contrast, unclassified RNA viral taxa showed higher abundance variability. KEGG functional annotation mapped DNA viral contigs primarily to microbial metabolic modules. Conversely, RNA assemblies extensively mapped to eukaryotic pathways (e.g., arachidonic acid and energy metabolism); due to the total nucleic acid extraction methodology, these mappings primarily reflect co-extracted host transcriptomic background rather than viral-encoded functions, providing an indirect snapshot of the concurrent enteric microenvironment. These baseline data delineate the virome structure in captive environments and provide practical targets for zoological biosecurity and proactive veterinary surveillance.}, }
@article {pmid42108276, year = {2026}, author = {Saha, PK and Sar, P and Sarkar, S and Mukherjee, D and Kazy, SK}, title = {Deep subsurface rock-hosted chemolithotrophic bacterial communities exhibited differential CO2 assimilation and bioconversion potential under varying oxygen level.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-51641-5}, pmid = {42108276}, issn = {2045-2322}, support = {MoES/P.O.(Seismo)/1(383)/2020 dated February 10, 2022//Ministry of Earth Sciences (MoES), Government of India/ ; }, abstract = {Deep continental subsurface hosts diverse microbial ecosystems that are primarily driven by chemolithoautotrophy. In this study, we investigated deep continental igneous rock-hosted bacterial populations enriched under microoxic (ME) and anoxic (AE) conditions. Metataxonomic, metagenomics and metabolomics approaches, along with physiological analyses, were performed to elucidate community composition, CO2 utilization and possible bioconversion potential of subsurface rock enrichment cultures under chemolithoautotrophic conditions. Following prolonged incubation, ME enrichments resulted in higher microbial growth with greater species diversity than the AE cultures. Ralstonia and unclassified Comamonadaceae were predominant in both the enrichment conditions. On the other hand, Cellulomonas, Phenylobacterium, Deinococcus, Desulfurispora, etc. were relatively abundant in ME, and Solimonas, Curvibacter, Caulobacter, Novosphingobium, Anaeromyxobacter, unclassified Clostridia, etc. were abundant in AE communities. CO2/H2 utilization and organic acids production were greater in ME enrichments. Shotgun metagenomics and predictive metabolic profiling revealed CBB cycle as the predominant carbon fixation pathway in ME, whereas WL pathway was prominent in AE. Genes for hydrogen, sulfur, and nitrogen metabolisms were observed in both the enrichment cultures. HRLC-MS based untargeted metabolomics indicated the presence of valuable metabolites (organic acids, osmolytes, lipids/amides) in rock cultures, reflecting the potential of deep subsurface microorganisms for CO2 utilization and possible bioconversion to valuable biomolecules.}, }
@article {pmid42108288, year = {2026}, author = {Yan, C and Zhang, F and Long, C and Yin, Y and Wang, L}, title = {A Brief Review of Microbial Omics: Methods and Perspectives.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {1-20}, pmid = {42108288}, issn = {1940-6029}, mesh = {*Genomics/methods ; *Metabolomics/methods ; *Proteomics/methods ; *Microbiota/genetics ; *Computational Biology/methods ; Single-Cell Analysis/methods ; Artificial Intelligence ; Transcriptome ; Metagenomics/methods ; }, abstract = {Microbial omics has progressed from isolated genomic analyses into a comprehensive, integrated multi-omics framework, profoundly advancing our understanding of microbial complexity and functionality. This mini-review systematically outlines the core technologies within microbial omics-including genomics, transcriptomics, proteomics, and metabolomics-by introducing their fundamental principles, common experimental workflows, and state-of-the-art bioinformatic strategies. We particularly highlight the emergence of single-cell microbial omics as a transformative methodology that resolves molecular and functional heterogeneity within communities, enabling the identification of rare taxa, strain-level microdiversity, and specialized functional roles that are obscured in bulk analyses. Furthermore, we discuss how artificial intelligence (AI)-driven tools are revolutionizing the interpretation of high-dimensional omics data, uncovering latent biological patterns, improving predictive modeling of microbial behavior, and facilitating the translation of microbiome insights into clinical and environmental applications. The review concludes by comparing the strengths, limitations, and optimal use cases of each omics layer and single-cell approach while also addressing ongoing technical challenges and future directions in the field.}, }
@article {pmid42108290, year = {2026}, author = {Li, B and Xu, J and Zhao, T and Yang, X and Yin, Q and Zou, Y}, title = {Metagenomic Data Preprocessing and Quality Control.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {43-61}, pmid = {42108290}, issn = {1940-6029}, mesh = {*Metagenomics/methods/standards ; Quality Control ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Software ; Workflow ; *Metagenome ; *Computational Biology/methods ; }, abstract = {Accurate metagenomic analysis relies on clean and well-processed sequencing reads. This chapter presents a concise four-step workflow for preprocessing: raw data assessment, adapter and quality filtering, host DNA removal, and final clean-read evaluation. By standardizing these essential procedures, researchers can minimize contamination, reduce technical bias, and ensure reliable inputs for assembly and downstream metagenomic analyses.}, }
@article {pmid42108291, year = {2026}, author = {Li, B and Yang, X and Zhao, T and Xu, J and Meng, Q and Yin, Q and Zou, Y}, title = {Metagenomic Assembly and Gene Prediction.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {63-89}, pmid = {42108291}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Metagenome ; *Computational Biology/methods ; Molecular Sequence Annotation ; Contig Mapping/methods ; Software ; Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenomic assembly and gene prediction connect quality-controlled reads to downstream microbiome analyses. This chapter outlines core assembly strategies, including per-sample versus co-assembly and short-read versus hybrid approaches, and highlights key parameters and metrics for evaluating assembly quality. Gene prediction from contigs and the construction of nonredundant gene catalogs are introduced as fundamental steps for representing community coding potential. The resulting contigs and gene sets provide essential input for metagenome-assembled genome (MAG) reconstruction, as well as taxonomic and functional annotation in subsequent chapters.}, }
@article {pmid42108292, year = {2026}, author = {Guo, JX and Gao, YZ}, title = {Absolute Quantification of Bacteria in the Microbiome and Its Application.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {91-103}, pmid = {42108292}, issn = {1940-6029}, mesh = {*Microbiota/genetics ; *Bacteria/genetics/isolation &amp; purification/classification ; High-Throughput Nucleotide Sequencing/methods ; Humans ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; }, abstract = {The advent of genomics and deep sequencing technologies has facilitated the development of absolute quantification techniques, which offer researchers more objective and precise sequencing outcomes. Unlike traditional relative quantification methods, which provide comparative data, absolute quantification delivers definitive measurements of genes or taxa. This analytical approach mitigates the potential for extraneous influences when comparing disparate samples, thereby reducing analytical errors. The implementation of absolute quantification techniques enhances our comprehension of microbial community structures, ecological dynamics, and their associations with host health or disease conditions. This chapter emphasizes a straightforward and broadly applicable method for genomic quantification, which necessitates the incorporation of a specified amount of internal standard DNA into the samples, eliminating the need for subsequent adjustments during library construction and sequencing. By assessing the proportion of internal standard DNA across various samples, sequencing data can be transformed into absolute quantification metrics. The internal standard method for absolute quantification is versatile and can be effectively utilized across multiple domains, including disease diagnosis, microbial ecology research, the fermentation industry, and environmental monitoring. Overall, absolute quantification methods furnish a more accurate and holistic perspective for microbiome research.}, }
@article {pmid42108294, year = {2026}, author = {Xia, H and Zhou, C and Fu, B and Han, H}, title = {Unlocking Enzyme Discovery: Leveraging Multi-Omics, Machine Learning, and De Novo Design.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {117-146}, pmid = {42108294}, issn = {1940-6029}, mesh = {*Machine Learning ; *Proteomics/methods ; Metagenomics/methods ; *Enzymes/genetics/metabolism/chemistry ; Lignin/metabolism ; Genomics/methods ; Multiomics ; }, abstract = {Enzymes are fundamental protein catalysts essential to life processes and widely applied in industrial and healthcare sectors. However, the broader application of natural enzymes is constrained by their inherent catalytic limitations, and traditional discovery methods such as microbial enrichment are often slow and low-throughput. Driven by advances in multi-omics and artificial intelligence, a range of novel screening strategies has been developed, enabling significant enhancements in both catalytic efficiency and stability of enzymes. This chapter assesses high-throughput approaches, such as metagenomics, metaproteomics, machine learning, and de novo design, comparing their respective advantages and limitations for enzyme discovery. Furthermore, we discuss the application potential of lignocellulose-degrading and plastic-degrading enzymes in biomass conversion and plastic waste recycling.}, }
@article {pmid42108295, year = {2026}, author = {Peng, B and Chang, X}, title = {Omics Approaches to Unraveling the Complexity of the Gut-Lung Axis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3033}, number = {}, pages = {147-164}, pmid = {42108295}, issn = {1940-6029}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Lung/metabolism ; *Metabolomics/methods ; Lung Diseases/metabolism/microbiology ; Metagenomics/methods ; Dysbiosis ; Animals ; *Genomics/methods ; Proteomics/methods ; }, abstract = {The complex, bidirectional communication between the gut and the lungs, known as the "gut-lung axis," profoundly influences host immune homeostasis and the pathogenesis of respiratory diseases. In recent years, multi-omics approaches, including metagenomics, metabolomics, and metatranscriptomics, have emerged as the core driving force for unraveling the complexity of this interorgan cross talk network. This review aims to systematically summarize the current omics-based evidence in the field of the gut-lung axis. We highlight key communication mechanisms discovered through multi-omics integration, particularly how gut microbiota-derived metabolites, exemplified by short-chain fatty acids (SCFAs), mediate distal immune regulation. Concurrently, we consolidate omics evidence from the contexts of respiratory infectious diseases, chronic lung disorders, and aging, systematically delineating the impact of gut dysbiosis on pulmonary pathophysiology via the gut-lung axis and emphasizing the feasibility of disease management in patients with lung diseases by modulating the gut microbiota. Although omics technologies have significantly advanced our understanding of this field, the challenge of effectively integrating vast, heterogeneous data and transitioning from "correlation" to "causation" remains a primary hurdle. By reviewing and discussing the current omics evidence in the gut-lung axis, this paper aims to provide new perspectives for future mechanistic explorations and clinical translation strategies.}, }
@article {pmid42109826, year = {2026}, author = {Sun, A and Jin, SL and Liu, JG}, title = {A practical guide for characterization of novel CRISPR-Cas systems with Pro-CRISPR factors.}, journal = {Biophysics reports}, volume = {12}, number = {2}, pages = {85-99}, pmid = {42109826}, issn = {2364-3420}, abstract = {The emergence of advanced genome editing technologies has revolutionized research in life sciences, offering an unprecedented way to uncover unknown biological functions and innovative therapeutic strategies. Among all genome editing tools, CRISPR-Cas-based technologies play a pivotal role in this revolution, particularly Class 2 effectors such as Cas9 and Cas12, owing to their high efficacy and ease of programmability. With the advancements in genome sequencing and metagenomics, an increasing number of novel CRISPR-Cas systems have been discovered, including those found in extreme environments and viruses. Furthermore, recent studies have revealed an unexpected role of non-Cas accessory genes, such as the Tn7-like transposon and Pro-CRISPR factors (Pcr), in conferring additional functionalities to the CRISPR system, providing new insights into the understanding of CRISPR-mediated bacterial immunity and advancing the development of genome editing technologies. Therefore, it is essential to develop comprehensive methods for characterizing the Cas proteins and Pro-CRISPR factors with a growing diversity. In this protocol, we provide a method encompassing protein purification, biochemical characterization, validation of protein-protein interactions, and preliminary in vivo functional assays in bacteria for Cas nuclease and its associated Pro-CRISPR factor. We hope this protocol will not only assist in the characterization of the CRISPR-Cas system, but also provide valuable guidance for the characterization of other nucleases or nucleic acid modification systems.}, }
@article {pmid42109869, year = {2026}, author = {Gao, Y and Zhu, T and Jiang, Y and Tian, F and Li, Y and Liu, W and Xu, S and Tong, Y and Qin, Z and Hu, F}, title = {Genomic characterization of two duck-origin picornaviruses with seven putative 2A peptides.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1753959}, pmid = {42109869}, issn = {2297-1769}, abstract = {INTRODUCTION: The Picornaviridae family is a large group of viruses comprising 68 genera. Duck-origin picornaviruses are categorized into four genera, however, the taxonomic status of some recently identified strains remains to be determined.<br><br>METHODS: In this study, two virus strains isolated from breeding ducks experiencing reduced egg production were identified and characterized through viral metagenomic analysis.<br><br>RESULTS: Two viral strains (NC0246 and PX0394) exhibiting the typical picornavirus-like genomic structure were identified and characterized. Notably, both strains exhibit extended 2A sequences that each possesses seven distinct 2A polypeptides considered rare in Picornaviridae family. Specifically, NC0246 exhibits a deletion of 73 amino acids (aa) in the region corresponding to 2A4-2A5 when compared to PX0394 indicating the genetic diversity of picornaviruses. Homology analysis revealed that the P1 region of NC0246 was most closely related to duck aalivirus A1, with aa identity of 37.37%. Conversely, the P1 region of PX0394 was most closely related to duck egg-reducing syndrome virus (DERSV), with aa identity of 64.44%. Furthermore, the 2C and 3D proteins of NC0246 and PX0394 was most closely related to DERSV. Phylogenetic analyses indicate that NC0246 and PX0394 form a sister clade to DERSV and duck aalivirus A1 and display marked heterogeneity in the P1 protein. While NC0246 and PX0394 branch nearest to DERSV and duck aalivirus A1, duck hepatitis A virus types 1 and 3, sharing secondary homology, occupy a separate lineage.<br><br>CONCLUSION: Two picornaviruses were identified and characterized from breeding ducks that exhibited decreased egg production. Through genomic structure and homology analysis, these viruses were most closely related to DERSV and duck aalivirus A1. NC0246, PX0394, and the previously reported DERSV show a close evolutionary relationship with the genus Aalivirus based on genomic and phylogenetic analyses, suggesting a potential affiliation with this genus.}, }
@article {pmid42110882, year = {2026}, author = {Mayne, R and Smith, DB and Brown, K and Chen, YP and Firth, AE and Katayama, K and Knowles, NJ and Simmonds, P}, title = {Comprehensive hallmark gene sequence, genomic and structural analysis clarifies new and established taxa within the Picornavirales.}, journal = {Virus evolution}, volume = {12}, number = {1}, pages = {veag023}, pmid = {42110882}, issn = {2057-1577}, abstract = {The order Picornavirales is a group of highly diverse RNA viruses that includes many pathogens of significance to human and veterinary health, agriculture, and the wider environment. However, the wide range of viruses assigned to the order, together with their genomic variability, and the recent description of numerous 'picorna-like' viruses derived from metagenomic analyses of environmental samples, challenge the established taxonomic classification of members of the order and the criteria for their classification. Here, we combine the existing gold standard, hallmark RNA-directed RNA-polymerase (RdRP) gene sequence-based analysis with helicase sequence-based phylogeny, RdRP structural prediction through the use of ColabFold and Fold Tree, and analysis of coding-complete genomes using GRAViTy-V2, to genetically classify 525 picornaviral genomes and recently described 'picorna-like' viruses. All analyses were conducted with a bespoke, fully automated pipeline for retrieval of genome sequences, domain prediction and extraction, phylogenetic analysis, and output conditioning, which is available as open-source software. Our results reveal broad support for established families as well as for 6 novel families, and 32 new genera. In instances where inconsistencies were found between classification methods, we demonstrate how examination of the pipeline's output may be used to reconcile differences with respect to the genomic features quantified by the analysis. Automated multimodal taxonomic analysis may save significant resources over manual methods and better define demarcation criteria for families and genera.}, }
@article {pmid42111070, year = {2026}, author = {Zurdo-López, M and Sagredo Del Rio, M and Cháfer Rudilla, M and Ibarra, A and Doncel-Pérez, E}, title = {Microbiota and Guillain-Barré syndrome: role of microbial metabolites, biomarkers, and emerging therapeutic strategies.}, journal = {Frontiers in neurology}, volume = {17}, number = {}, pages = {1815899}, pmid = {42111070}, issn = {1664-2295}, abstract = {Guillain-Barré syndrome (GBS) is an acute autoimmune polyradiculoneuropathy that follows infection and is characterized by immune-mediated demyelination or axonal injury of the peripheral nervous system. While established triggers such as Campylobacter jejuni are well recognized, increasing evidence implicates the gut microbiota as a key modulator of immune responses relevant to GBS pathogenesis. The intestinal microbiota produces a diverse array of bioactive metabolites, including short-chain fatty acids (SCFAs), tryptophan-derived indoles, and neurotransmitter-like molecules, which influence immune tolerance, gut barrier integrity, and neuroinflammatory signaling. SCFAs, particularly butyrate, exert anti-inflammatory effects and support epithelial and blood-nerve barrier function. Microbial tryptophan metabolites regulate astrocyte and microglial activity via aryl hydrocarbon receptor (AHR) signaling, thereby restraining central and peripheral neuroinflammation. In contrast, dysbiosis-associated metabolites such as lipopolysaccharide (LPS) may enhance systemic inflammation, disrupt immune tolerance, and promote autoantibody production through mechanisms including molecular mimicry. Studies suggest that specific microbial taxa and metabolite signatures may serve as diagnostic or prognostic biomarkers in GBS, offering insights into disease susceptibility and progression. Microbiota-targeted therapeutic strategies are emerging as promising adjuncts to immunotherapy. Probiotics and prebiotics may restore beneficial microbial communities and rebalance immunoregulatory metabolite production, while host-directed metabolic interventions such as creatine supplementation may further support mitochondrial function, immunometabolic homeostasis, and neuroprotection. Fecal microbiota transplantation (FMT), though still experimental in GBS, has shown benefit in related neuroinflammatory disorders by reestablishing eubiosis and dampening immune activation. Future studies integrating metagenomic, metabolomic, and immunologic profiling in well-characterized GBS cohorts are essential to validate these findings and advance personalized microbiota-based interventions.}, }
@article {pmid42111291, year = {2026}, author = {Marcos, S and Odriozola, I and Aizpurua, O and Eisenhofer, R and Mak, SST and Martin-Bideguren, G and Kale, V and Baldi, G and Richardson, LJ and Finn, RD and Tarradas, J and Estonba, A and Gilbert, MTP and Alberdi, A}, title = {Functional gut microbiota dynamics of generalist and specialist bacteria in association with chicken growth.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag091}, pmid = {42111291}, issn = {2730-6151}, abstract = {The early-life development of the gut microbiome in broiler chickens is a dynamic ecological process with significant implications for host physiology and productivity. Using 388 genome-resolved metagenomic and 61 metatranscriptomic samples across two replicated trials, we analysed the compositional and functional succession of the caecal microbiome in chickens from hatching to slaughter age. We reconstructed 822 bacterial genomes and distilled gene annotations into comprehensive metabolic traits that captured the functional capacities of each genome. We observed that the increase in microbial diversity with chicken age was accompanied by a decline in community-level average metabolic capacity, driven by a shift from metabolically versatile generalists (Lachnospiraceae) to hitherto uncultured, genome-reduced specialists (RF39, RF32, and UBA1242). However, the specific identity of the dominant genome-reduced specialists varied among individuals, resulting in contrasting associations with host body weight. At slaughter age, only 10 UBA660 (RF39) bacteria were positively associated with body weight, while other genome-reduced lineages, such as UBA1242 (Christensenellales), were among 190 negatively associated bacteria. Gene expression analyses revealed that despite their reduced functional repertoire, UBA660 exhibited greater metabolic activity than UBA1242, particularly in the production of two key metabolites for host nutrition and intestinal homeostasis: the essential amino acid lysine and the signaling molecule indole-3-acetate. These findings provide new insights into the functional ecology of the chicken gut microbiome and highlight the relevance of cultivation approaches to retrieve underexplored and uncultured bacterial taxa, which could open new avenues for microbiome-based strategies aimed at improving poultry growth and health in intensive production systems.}, }
@article {pmid42111294, year = {2026}, author = {Yergaliyev, T and Enokela, SO and Eberhardt, G and Flisikowski, K and Hornburg, SC and Reyer, H and Tetens, J and Wimmers, K and Zentek, J and Camarinha-Silva, A}, title = {Toward reproducible pig gut microbiome profiling through standardized methodologies.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag097}, pmid = {42111294}, issn = {2730-6151}, abstract = {Reproducible microbiome profiling is essential for linking microbial communities to host health, yet methodological variation continues to undermine reproducibility across studies. This problem is acute in pig microbiome research, where no standardized DNA extraction protocols exist despite the species' importance in agriculture and biomedicine. Here, we benchmark how 12 widely used extraction kits influence microbiome outcomes in 16S rRNA gene amplicon sequencing and shotgun metagenomics of pig fecal samples. We demonstrate that extraction choice biases 16S rRNA gene datasets, affecting DNA yield, diversity, community composition, and spike-in recovery, whereas metagenomic taxonomy and functional profiles are comparatively robust. Kit-dependent recovery of Gram-positive versus Gram-negative taxa revealed systematic biases with direct consequences for biological interpretation. By integrating spike-in controls, taxonomic resolution, and metagenome-assembled genomes, we establish a framework for evaluating DNA extraction methods in animal microbiome research. Our findings demonstrate that 16S rRNA gene amplicon sequencing is more susceptible to extraction-driven artifacts than metagenomics, highlighting the need for standardized protocols to ensure reproducibility and comparability across pig microbiome studies. Moreover, while shotgun metagenomics was comparatively robust to DNA extraction choice, the number of assembled good-quality metagenome-assembled genomes recovered was strongly dependent on the extraction kit selection.}, }
@article {pmid42111296, year = {2026}, author = {De Chiara, L and Doughty, R and Estévez-Gómez, N and Gallego-García, P and Alvariño, P and Díez-Martín, A and Dávila Piñón, P and Treangen, TJ and Cubiella, J and Posada, D}, title = {A comparison of methods for the optimal recovery of the human fecal virome.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag090}, pmid = {42111296}, issn = {2730-6151}, abstract = {Human virome research is gaining increasing attention as viruses are recognized as critical modulators of microbial communities and human health. Viral metagenomics, however, faces unique challenges, including the low abundance and diversity of viruses in biological samples, the absence of universal marker genes, and biases introduced by experimental protocols. While various virome protocols have been benchmarked using viral particles or nucleic acids from mock communities, these approaches often fail to capture the complexity and heterogeneity of natural viromes. In this study, we systematically evaluated modifications to key methodological steps in the metagenomic analysis of human fecal samples, including viral enrichment, nucleic acid extraction, genome amplification, and library preparation. Using gold-standard bioinformatic approaches on sequencing datasets generated after amplification, we assessed the impact of these modifications on relative viral taxonomic assignment, contig quality, richness, diversity, and inferred genome structure. Our findings reveal striking trade-offs between recovery of viral genomes and retention of nonviral sequences, demonstrating how methodological choices can shape the inferred virome composition. Based on these observations, we propose an optimized protocol that enhances viral genome recovery while reducing contamination from nonviral sequences. This refined workflow provides a more robust and reliable framework for gut virome studies, paving the way for a deeper exploration of the role of viruses in human health and microbial ecosystems.}, }
@article {pmid42111477, year = {2025}, author = {Gudenkauf, JC and Wagstaff, E and Arneson, EJ and Gill, C and Gillman, AN and Haim, H and Tan, CS}, title = {Successful Recovery from Meningoencephalitis Associated with Archetype-like JC Virus in a Lung Transplant Recipient: Case Report and Review of the Literature.}, journal = {Annals of clinical case reports}, volume = {10}, number = {1}, pages = {}, pmid = {42111477}, issn = {2474-1655}, abstract = {Meningoencephalitis due to JC polyomavirus (JCV) is rare and delays in diagnosis could lead to potentially fatal outcomes in immunosuppressed patients. We present a case of an HIV-negative lung transplant recipient who presented with neurological deficits, including aphasia and right-sided weakness. Brain imaging lacked demyelination usually diagnostic of progressive multifocal leukoencephalopathy (PML), the disease most often associated with JC virus, however cerebrospinal fluid (CSF) metagenomic analysis confirmed a high JC viral load, suggestive of JCV-associated meningoencephalitis. After reducing immunosuppression, the patient showed significant neurological improvement within three months and full recovery by 6 months. The JCV genome sequenced from patient's plasma and CSF were identical and resembled the "nonpathogenic" archetype in the non-coding region but shared homology in the coding region with the classically-considered neurotropic strains detected in those with PML. These findings suggest that mutations in the virus's noncoding region are not necessary for neuropathogenesis. We also review other cases of JCV-associated meningitis and encephalitis, which, in contrast to our case, were all fatal. Clinicians should consider JCV testing in immunosuppressed patients with encephalopathy and focal neurological deficits, even in the absence of significant brain radiographic abnormalities.}, }
@article {pmid42111802, year = {2026}, author = {Belkina, DD and Vinogradova, SV}, title = {Plant virome analysis by high-throughput sequencing: concepts and approaches.}, journal = {Vavilovskii zhurnal genetiki i selektsii}, volume = {30}, number = {2}, pages = {311-320}, doi = {10.18699/vjgb-26-35}, pmid = {42111802}, issn = {2500-0462}, abstract = {The metagenomic approach based on high-throughput sequencing is becoming increasingly prevalent for the detection of viral infections in plants. This method allows us to study the species composition of viruses associated with the plant, including novel species, describe their population genetic structure, and develop genetic test systems for routine diagnostics. A metagenomic approach to phytosanitary monitoring can help to determine the cause of unknown plant diseases, which is particularly important for preventing the spread of pathogens, such as viruses. Furthermore, as it is impossible to eliminate plant viruses in field conditions, comprehensive diagnostics using high-throughput sequencing is becoming an effective tool for complying with quarantine regulations on the import of foreign material, as well as for producing high-quality local planting material. High-throughput sequencing is becoming more affordable every year, with both the instrumentation and analytical capacity improving. This review summarizes key approaches to analyzing plant virome using high-throughput sequencing. The analysis process, from sample collection to bioinformatic data processing, validation and interpretation, is described in detail. The features of sequencing platforms and the factors affecting sequencing quality, including contamination, are discussed. Three complementary approaches to processing bioinformatic data are described: mapping reads to reference viral sequences; assembling and annotating contigs; taxonomic classification of reads without assembly. The importance of carefully interpreting the results is emphasized, considering the bioinformatic analysis and the validation by molecular genetic methods. This review will be useful for both researchers and specialists who have no experience with high-throughput sequencing, and those who have used this method for other applications.}, }
@article {pmid42111813, year = {2026}, author = {Mubaraki, FA}, title = {From sequencing to intelligence: how AI is transforming metagenomics.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e21137}, pmid = {42111813}, issn = {2167-8359}, mesh = {*Metagenomics/methods ; *Artificial Intelligence ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; Machine Learning ; Deep Learning ; Metagenome ; }, abstract = {Microbial communities are critical in advancing human health. Metagenomics is a technique that analyzes these communities and allows for investigating their composition and functions. Metagenomic shotgun sequencing enables to capture all of the genetic material in environmental samples, such as water, soil, or the human gut. Despite this advantage, one of the main challenges of this technique is the assembling and interpreting of its data, as it produces many short, fragmented reads. Though long-read technologies may change this in the future, artificial intelligence (AI), machine learning (ML) and data science (DS) offer a powerful solution now, enabling scientists to efficiently process and analyze these large and complex datasets. This review explores the latest advancements in AI and ML applications across the metagenomic pipeline. First, it examines the impact of deep learning (DL) on next-generation sequencing, particularly for long-read technologies. Then, it discusses how ML is automating and improving quality control processes, as well as the use of AI applications in metagenome-assembled genome (MAG) assembly, with a focus on contig binning. Finally, this article looks at how AI and ML can improve predictive modeling for phenotype prediction.}, }
@article {pmid42112348, year = {2026}, author = {Hua, M and Luo, J and Li, P and Zhang, Y and Zhang, X and Wu, Y and Dong, H}, title = {The microbiota-systemic lupus erythematosus axis: mechanisms, diagnostics, and therapeutic frontiers.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1782828}, pmid = {42112348}, issn = {1664-3224}, mesh = {Humans ; *Lupus Erythematosus, Systemic/therapy/diagnosis/immunology/microbiology ; Dysbiosis/immunology ; Animals ; *Microbiota/immunology ; *Gastrointestinal Microbiome/immunology ; Autoimmunity ; }, abstract = {Systemic lupus erythematosus (SLE) is a prototypical autoimmune disease in which host-microbiota crosstalk plays a pivotal role in immune dysregulation. Recent metagenomic studies have revealed that disease-specific dysbiosis--characterized by the expansion of pathobionts and depletion of immunoregulatory commensals--occurs across the gut, oral cavity, skin, and genital tract. Integrative multi-omics analyses have identified three mechanistic pathways linking microbial imbalance to autoimmunity: (1) microbial peptides trigger molecular mimicry and epitope spreading, activating autoreactive lymphocytes: (2) microbial metabolites disrupt redox homeostasis, impair epithelial barriers, and skew the AhR-mediated Th17/Treg balance; and (3) dysbiosis alters epigenetic regulation by inhibiting DNA methyltransferases, leading to hypomethylation of SLE-risk genes. Translational studies have shown that microbiome-targeted interventions, including probiotics, prebiotics, fecal microbiota transplantation, and even B cell-depleting chimeric antigen receptor T-cell (CAR-T) therapy, can restore microbial balance, reduce autoantibody levels, and modulate the gut-immune axis. Furthermore, microbial signatures are emerging as potential biomarkers for disease activity and treatment response. Despite this promise, challenges remain, such as the impact of immunosuppressants on the microbiota, spatial heterogeneity in host-microbe interactions, and limitations in causal inference. Looking forward, integrating single-cell metagenomics, microbiota-directed diets, and engineered microbial consortia may pave the way for personalized microbiome-based therapies. Reframing SLE as a "meta-organismal imbalance" positions microbial ecology at the forefront of precision medicine.}, }
@article {pmid42112399, year = {2026}, author = {Wang, Y and Dong, W and Qin, J}, title = {Fatal AA-like bone marrow failure and invasive pulmonary aspergillosis after long-term pembrolizumab in squamous NSCLC: a case report.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1800904}, pmid = {42112399}, issn = {1664-3224}, mesh = {Humans ; Male ; Middle Aged ; *Antibodies, Monoclonal, Humanized/adverse effects/therapeutic use ; *Carcinoma, Non-Small-Cell Lung/drug therapy/complications ; *Lung Neoplasms/drug therapy/complications ; *Invasive Pulmonary Aspergillosis/etiology/diagnosis ; *Anemia, Aplastic/chemically induced/diagnosis/etiology ; Fatal Outcome ; *Immune Checkpoint Inhibitors/adverse effects ; *Antineoplastic Agents, Immunological/adverse effects ; }, abstract = {Immune checkpoint inhibitors (ICIs) such as pembrolizumab have substantially improved outcomes in advanced non-small cell lung cancer (NSCLC), including squamous histology, but prolonged exposure may be complicated by immune-related adverse events (irAEs) and opportunistic infections. We report a 58-year-old man with advanced squamous NSCLC who achieved durable tumor control after six cycles of pembrolizumab plus platinum-based chemotherapy, followed by pembrolizumab maintenance monotherapy (18 cycles). During the later course, he developed severe bacterial pneumonia, invasive pulmonary aspergillosis (IPA), and subsequent aplastic anemia (AA)-like bone marrow failure. Despite systemic antifungal therapy and supportive measures, he experienced progressive pancytopenia complicated by massive hemoptysis and ultimately died. This case underscores the dual nature of ICIs: while providing meaningful and sustained antitumor benefit, they may rarely precipitate life-threatening hematologic toxicity and facilitate severe opportunistic infections in a complex immunologic milieu. Close surveillance of blood counts and infectious complications is warranted during long-term ICI therapy; unexplained cytopenias or new/worsening radiologic abnormalities should prompt early bone marrow evaluation and comprehensive microbiologic work-up. Metagenomic next-generation sequencing (mNGS) may offer useful adjunctive evidence in diagnostically challenging infections, particularly when invasive sampling is not feasible, but results should be interpreted in conjunction with clinical and radiologic context within a multidisciplinary framework.}, }
@article {pmid42112463, year = {2026}, author = {Guo, L and Luo, X and Luo, M and Zhang, M and Wang, B and Fu, Y and Wu, X and Yu, Y and Bai, L and Xu, Z}, title = {Diagnosis and treatment of a patient with mediastinal infection caused by Emergomyces orientalis and Mycobacterium fortuitum.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1778930}, pmid = {42112463}, issn = {2235-2988}, mesh = {Humans ; Female ; Young Adult ; *Mycobacterium Infections, Nontuberculous/diagnosis/drug therapy/microbiology ; *Coinfection/diagnosis/microbiology/drug therapy ; *Mycobacterium fortuitum/isolation &amp; purification/genetics ; Antifungal Agents/therapeutic use ; High-Throughput Nucleotide Sequencing ; Tomography, X-Ray Computed ; *Mediastinum/microbiology/pathology/diagnostic imaging ; Amphotericin B/therapeutic use ; China ; Treatment Outcome ; *Eurotiales/isolation &amp; purification ; }, abstract = {BACKGROUND: Emergomycosis, an emerging dimorphic fungal infection caused by Emergomyces species, primarily affects immunocompromised individuals. Emergomyces orientalis has been reported in China, including rare cases in immunocompetent individuals. Diagnosis remains challenging due to the lack of typical clinical manifestations and radiological features. Co-infection with other pathogens further complicates management, with no prior global reports of concurrent E. orientalis and non-tuberculous mycobacterial (NTM) infections.<br><br>CASE PRESENTATION: A 21-year-old immunocompetent woman with occupational exposure to soil presented with cough, fever, and a mediastinal mass on chest CT. The initial biopsy specimens revealed granulomatous inflammation and yeast-like fungi. Metagenomic next-generation sequencing (mNGS) of endobronchial ultrasound (EBUS)-guided specimens confirmed E. orientalis (40 reads). Liposomal amphotericin B induction therapy initially relieved the symptoms. However, recurrence prompted repeat mNGS, which revealed elevated Mycobacterium fortuitum loads (791 reads). Combined with the patient's history of soil exposure, a diagnosis of mediastinal E. orientalis with M. fortuitum co-infection was established based on the clinical presentation, the chest CT findings, histopathological observations of yeast-like fungi, the mNGS results, and the therapeutic response. Following confirmation of the co-infection, tailored adjustments to the antimicrobial regimen led to successful clinical management.<br><br>CONCLUSION: To the best of our knowledge, this is the first study in which E. orientalis and M. fortuitum were documented to coexist in the mediastinum. The dual pathogens were identified through a combination of EBUS-guided biopsy and mNGS. Accurate pathogen identification followed by tailored, pathogen-directed therapy is essential for the effective management of an E. orientalis and M. fortuitum mixed infection.}, }
@article {pmid42112573, year = {2026}, author = {Liborio, MP and Peri, AM and Harris, PNA}, title = {Evaluating emerging molecular diagnostics for severe infections in neutropenic patients with hematological malignancies.}, journal = {Expert review of molecular diagnostics}, volume = {}, number = {}, pages = {}, doi = {10.1080/14737159.2026.2667917}, pmid = {42112573}, issn = {1744-8352}, abstract = {INTRODUCTION: Neutropenia significantly increases infection risk in hematologic malignancies patients, when clinical signs are often subtle and fever may be the only indicator. Molecular diagnostic methods promise faster, more sensitive pathogen detection compared to conventional methods, aiming to improve timely and appropriate therapy.<br><br>AREAS COVERED: This review summarizes emerging molecular diagnostics for severe infections in neutropenic hematological malignancies patients, focusing on microbiological performance and, where available, clinical impact. We conducted a search in PubMed and Embase using subject headings: 'molecular diagnosis,' 'neutropenic,' 'infections,' 'hematological malignancies,' supplemented by information from manufacturers of commercial assays. The technologies reviewed include multiplex polymerase chain reaction, microarray-based assays, metagenomic and targeted next-generation sequencing, host transcriptomics, and methods for diagnosing invasive fungal infections. For each, we describe key characteristics, diagnostic performance, and clinical utility when reported.<br><br>EXPERT OPINION: Emerging molecular diagnostics shorten time to pathogen and resistance identification and broaden detection of organisms in febrile neutropenic patients with hematological malignancies. These methods are best integrated as complements to culture-based methods within centers with antimicrobial stewardship programs, where they inform earlier targeted therapy and rational de-escalation of antimicrobials. Priority actions include prospective trials powered for measuring clinical outcomes and economic endpoints, with standardized workflows, reporting, and quality assurance to enable clinical implementation.}, }
@article {pmid42112737, year = {2026}, author = {Ji, G and Duan, J}, title = {Pharmacist-driven optimization of presumptive psittacosis management: a case report of rapid clinical resolution.}, journal = {Journal of infection in developing countries}, volume = {20}, number = {4}, pages = {596-600}, doi = {10.3855/jidc.22259}, pmid = {42112737}, issn = {1972-2680}, mesh = {Humans ; Female ; Middle Aged ; *Psittacosis/drug therapy/diagnosis ; *Anti-Bacterial Agents/therapeutic use/administration &amp; dosage ; Chlamydophila psittaci/isolation &amp; purification ; Community-Acquired Infections/drug therapy/diagnosis/microbiology ; Animals ; }, abstract = {INTRODUCTION: Chlamydia psittaci has a high incidence of pneumonia after infection, but clinical diagnosis still faces challenges due to the lack of specific clinical manifestations and low positive rates in routine testing.<br><br>CASE PRESENTATION: A 60-year-old female patient with community-acquired pneumonia (CAP) failed to respond to initial intravenous antimicrobial therapy with cefmetazole/ciprofloxacin followed by piperacillin-tazobactam/levofloxacin, exhibiting persistent fever and worsening symptoms. Serial laboratory testing revealed progressive elevation of inflammatory markers, with C-reactive protein (CRP) rising from 110.2 to 120.9 mg/L and procalcitonin (PCT) from 1.37 to 2.15 ng/mL. Essential bronchoscopic examination and metagenomic next-generation sequencing (mNGS) could not be performed due to patient refusal, creating a diagnostic deadlock. The clinical pharmacist identified avian exposure during medication rounds, enabling presumptive diagnosis of psittacosis. Immediate pharmacist-initiated interventions included discontinuation of levofloxacin and commencement of targeted oral minocycline therapy. Clinical resolution occurred within 48 hours with defervescence and symptomatic improvement. Subsequent minocycline-induced nausea and diarrhea were effectively managed through pharmacist-instructed co-administration with food. Continuous clinical improvement facilitated discharge on oral minocycline, with follow-up imaging confirming complete resolution of pulmonary infiltrates.<br><br>CONCLUSIONS: This case underscores the value of pharmacist-led pharmaceutical assessment in uncovering atypical infection etiologies and guiding targeted antimicrobial therapy.}, }
@article {pmid42112819, year = {2026}, author = {Wei, X and Song, W and Li, S}, title = {Seasonal variations drive microbial community structure and nitrogen cycling in sediments of tributary pumping station forebays.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0304725}, doi = {10.1128/spectrum.03047-25}, pmid = {42112819}, issn = {2165-0497}, abstract = {Discharge from tributary pumping stations often impacts mainstream water quality, yet microbial communities and nitrogen metabolism in pumping station forebays remain poorly understood. Therefore, this study investigated the microbial community structure and nitrogen cycling mechanisms in sediments of tributary pumping station forebays within the Qinhuai River Basin using 16S rRNA and metagenomic sequencing. Results showed significant seasonal variations in the diversity and structure of sediment microbial communities, with higher diversity in spring than in winter. Genes associated with denitrification (e.g., narG, nirS, and nosZ) showed the highest abundance, suggesting that denitrification may be a key nitrogen transformation pathway. Co-occurrence network analysis revealed tighter associations between microbial taxa and nitrogen-cycling genes in spring, indicating more complex potential interactions during this season. The shift of network hubs across seasons suggested a seasonal succession of potential core functions related to nitrogen cycling. Redundancy analysis revealed that nitrate nitrogen (NO3[-]-N), water temperature (WT), and ammonium nitrogen (NH4[+]-N) were the factors most strongly associated with microbial community variation, with WT showing the strongest association with functional gene distribution. Partial least squares path modeling revealed that seasonal variation had a significant positive association with denitrification gene abundance and a significant negative association with genes related to assimilatory nitrate reduction to ammonium and anaerobic ammonium oxidation. These findings improve our understanding of microbially mediated nitrogen cycling in pumping station forebays and provide a scientific basis for water quality management in river networks influenced by pumping station drainage.IMPORTANCEThis study is important because it reveals that pumping stations, which are key infrastructure in managed river systems, are not just hydraulic structures but dynamic bioreactors where microbial communities actively transform nitrogen. By demonstrating seasonal variations in microbial diversity and revealing a high denitrification potential, the research provides a mechanistic understanding of how nitrogen pollution is naturally mitigated in these engineered environments. Crucially, it pinpoints temperature as a primary regulator of these microbial functions. These insights allow water managers to proactively optimize pumping operations and design interventions that harness microbial activity, ultimately protecting downstream water quality from nutrient pollution in a changing climate.}, }
@article {pmid42112890, year = {2026}, author = {Sorokin, DY and Khot, V and Merkel, AY and Mosier, D and Bale, NJ and Koenen, M and Strous, M}, title = {Physiology, functional genomics, and proteomics of Verruconatronum alginivorum gen. nov., sp. nov., the first isolated haloalkaliphile within Verrucomicrobiota, representing a new family, Verruconatronumaceae fam. nov.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0047526}, doi = {10.1128/aem.00475-26}, pmid = {42112890}, issn = {1098-5336}, abstract = {Despite the successful cultivation of many microbes from rich bacterial communities inhabiting alkaline soda lakes, members of the bacterial phylum Verrucomicrobiota have so far been detected only through metagenomics. Here, we used alginate as a selective substrate to enrich and isolate two strains of haloalkaliphilic Verrucomicrobiota. The isolates share identical 16S rRNA gene sequences representing a new genus lineage, and, together with other metagenome assembled genomes, a new family within Opitutales. Cells of strains AB-alg1[T] (from soda lakes) and AB-alg4 (from soda solonchak soils) are small and motile cocci forming submerged colonies in soft alginate agar. They are saccharolytic heterotrophs growing aerobically on polysaccharides (alginate, starch, and inulin) and sugars (glucose, fructose, mannose, sucrose, melezitose, maltose, and cellobiose). They also grow anaerobically by fermentation of alginate and D-mannose and by coupling incomplete denitrification to oxidation of alginate. Both isolates are obligately alkaliphilic and moderately salt-tolerant. The dominant membrane phospholipids include phosphatidylcholines and diphosphatidylglycerols (cardiolipins). The genome of AB-alg1[T] features polysaccharide lyases of the PL6, 7, 15, 17, 38, and 39 families for depolymerization of alginate. Based on distinct phenotype and phylogeny, we propose classification of strains AB-alg1[T] (JCM 35393[T]=UQM 41574[T]) and AB-alg4 as Verruconatronum alginivorum gen. nov., sp. nov. within a new family Verruconatronumaceae.IMPORTANCEAlkaline soda lakes and soils are extreme habitats dominated by obligate haloalkaliphic prokaryotes, some of which can produce alkali- and salt-stable polysaccharide-degrading exoenzymes useful for industrial and domestic applications. However, so far, little was known about the microbial potential for mineralization of acidic polysaccharides, such as alginate, in these habitats. The described isolates are the first representatives of a new family within the phylum Verrucomicrobiota specializing in the degradation of alginate and related polysaccharides. We present the key enzymatic machinery for alginate breakdown. These enzymes are high-pH tolerant and have potential for industry applications, for example, in washing powders and biomass waste recycling. Furthermore, the new family is one of the most abundant taxa in alkaline environments, and these environments are not known to harbor signature alginate producing biota, such as brown algae. This way, our study opens a new window on polysaccharide turnover in alkaline environments.}, }
@article {pmid42112913, year = {2026}, author = {Krupovic, M and Koonin, EV}, title = {Organization and evolution of the virosphere and the replicator space.}, journal = {Comptes rendus biologies}, volume = {349}, number = {}, pages = {35-75}, doi = {10.5802/crbiol.193}, pmid = {42112913}, issn = {1768-3238}, mesh = {*Viruses/genetics ; *Biological Evolution ; Animals ; Virus Replication ; Humans ; Virion/genetics ; Genome, Viral ; }, abstract = {Viruses are obligate symbionts of cellular life forms that can replicate only within host cells and typically form virions (virus particles) to spread among host organisms. Virions numerically dominate the biosphere, exceeding the number of cells several-fold, and also comprise the main reservoir of genetic diversity on earth. Nearly all organisms host multiple, diverse viruses. Unlike cellular organisms, viruses have genomes (genetic information carriers incorporated into virions) that consist of all forms of RNA and DNA, suggesting an evolutionary connection between extant viruses and the primordial replicator pool. Lately, extensive mining of metagenomes and metatranscriptomes has dramatically expanded the world of viruses (virosphere), revealing an unsuspected and unprecedented diversity. Viruses share no universal genes and have multiple origins. However, about 15 viral hallmark genes each bring together multiple, diverse groups of viruses, and many other genes are shared within such groups. Evolution of viruses is inextricably intertwined with the evolution of their hosts. A key aspect of virus-host coevolution is the arms race resulting in accelerated evolution on both sides, especially of host defenses and viral counter-defenses. A complementary, prominent feature of this coevolution is exaptation, whereby viral genes are coopted by the hosts for antiviral defense and other roles, and conversely, viruses capture host genes for diverse functions in virus replication, virion morphogenesis and virus-host interaction. In this review, we attempt a synthesis of the current understanding of the global organization of the virosphere, the major trends and events in the evolution of viruses, and the high-level taxonomy of viruses.}, }
@article {pmid42113294, year = {2026}, author = {Cortez-Cervantes, J and Carrillo-Reyes, J and Cervantes-Avilés, P and Moreno-Andrade, I}, title = {A statistical framework for identifying microbial indicators of ammonia-induced process instability in food waste anaerobic digestion.}, journal = {Bioprocess and biosystems engineering}, volume = {}, number = {}, pages = {}, pmid = {42113294}, issn = {1615-7605}, support = {IN104825//DGAPA-UNAM PAPIIT/ ; IN105025//DGAPA-UNAM PAPIIT/ ; 2022 Core Lab Genomics Tec-BASE Seed Fund//Instituto Tecnol&#xf3;gico y de Estudios Superiores de Monterrey/ ; }, abstract = {Ammonia is an essential nutrient for anaerobic digestion (AD) but becomes inhibitory at elevated concentrations, leading to process instability. Although numerous microbial taxa and functional genes have been proposed as indicators of ammonia stress, most lack systematic validation across defined inhibitory thresholds. In this study, batch anaerobic digestion assays were conducted under increasing total ammonia nitrogen concentrations to experimentally characterize ammonia-induced inhibition. Methane yields obtained from batch tests were fitted using a Hill model to define non-inhibitory, inhibitory, and minimum inhibitory ammonia levels. Shotgun metagenomic sequencing was applied to samples representative of each inhibition level, and a statistical framework integrating differential abundance analysis, network topology, redundancy analysis, and metabolic relevance was used to identify robust microbial indicators. Key taxa, including Anaerolinea, Methanomassiliicoccus, and Syntrophobacter, along with functional genes involved in acetate and propionate metabolism (e.g., acs and fhs), showed consistent and threshold-dependent responses to ammonia stress. These microbial indicators provide mechanistic insight into ammonia-induced AD instability and offer a promising basis for early-warning monitoring and microbial management strategies to improve the operational stability of anaerobic digesters treating food waste.}, }
@article {pmid42113401, year = {2026}, author = {Bhattacharjee, A and Singh, AK}, title = {Ecological and genomic insights into Bacillus altitudinis as a potential indicator of resistance genes in soil antimicrobial resistance pools.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {42113401}, issn = {1614-7499}, support = {OLP-2035//CSIR/ ; OLP-2081//CSIR/ ; OLP-2503A//CSIR/ ; GPP-0423//DST-ANRF/ ; }, abstract = {Soil associated with intensive poultry farming serves as a seminal reservoir of antimicrobial resistance genes. This study employed an integrated approach that combined metagenomics, phenotypic analysis, and whole-genome sequencing to investigate the soil resistome of poultry farms in the Jorhat district, Northeast India, and to evaluate Bacillus altitudinis as an environmental potential indicator for antimicrobial resistance. Metagenomic analysis of poultry-affected soil revealed a diverse array of resistance genes, including 753 unique resistance ontologies related to β-lactam, glycopeptide, macrolide, aminoglycoside, chloramphenicol, and colistin resistance. Culture-based testing of soil and fecal isolates (400 isolates) showed high resistance rates to colistin and ciprofloxacin (~60%), as well as notable resistance to erythromycin and kanamycin, indicating strong antibiotic selection pressures in these ecosystems. Among multidrug-resistant strains, B. altitudinis S2 was particularly notable, exhibiting high minimum inhibitory concentrations for last-line antibiotics such as vancomycin (>50 µg/mL), colistin (>50 µg/mL), and fourth-generation cephalosporins. It also demonstrated multidrug β-lactam resistance supported by synergistic inhibitors. Whole-genome sequencing (3.7 Mb) uncovered a complex antimicrobial resistance gene (ARG) profile, including vanZ, mcr-1, catA, mph, aph, and oxa-type β-lactamase genes, alongside multiple SMR, MATE, and RND efflux mechanisms. Many of these genes were located within genomic islands, prophage traces, and mobile genetic elements, strongly indicating horizontal gene transfer from various bacteria, including gut-associated enterococci. The genome also contained genes for resistance to heavy metals and oxidative stress, suggesting co-selection processes that sustain ARGs in soil. The study tries to show B. altitudinis as a crucial environmental indicator for ARGs, serving a genetic bridge between poultry gut microbiota and soil antimicrobial resistance pools, highlighting its significance for One Health antimicrobial resistance surveillance.}, }
@article {pmid42113811, year = {2026}, author = {Mussa, AJ and Ruboha, JO and Kabota, SA and Martin, MJ and Mwatawala, MW}, title = {Elevation and land use shape soil entomopathogenic fungal communities in the Uluguru mountains, Tanzania: Insights from metagenomic and culture-based approaches.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0348781}, doi = {10.1371/journal.pone.0348781}, pmid = {42113811}, issn = {1932-6203}, mesh = {Tanzania ; *Soil Microbiology ; Animals ; *Fungi/genetics/classification/isolation &amp; purification ; *Altitude ; Biodiversity ; Soil/chemistry ; Metagenomics/methods ; *Mycobiome ; }, abstract = {BACKGROUND: Soil-borne entomopathogenic fungi (EPFs) support ecological regulation of pests, yet their distribution across tropical mountain agroecosystems is poorly characterized. The study conducted between April and December 2024, evaluated diversity and distribution of soil EPF along the Uluguru Mountains slopes in Morogoro, Tanzania.<br><br>METHODS: Twenty-four soil samples were collected from cultivated and fallow soils at low (518 m), medium (1100 m), and high (1700 m) elevations on the Uluguru slopes (Morogoro, Tanzania). Amplicon sequencing of the ITS region profiled fungal communities, and selective isolation with ITS barcoding confirmed cultivable taxa. Diversity indices, Bray-Curtis dissimilarity, Principal Coordinate Analysis (PCoA), and PERMANOVA evaluated patterns across elevation and land use.<br><br>RESULTS: Fourteen EPF species in 12 genera were detected, dominated by Ophiocordycipitaceae (56.1%) and Clavicipitaceae (37.8%). Purpureocillium lilacinum, Metarhizium anisopliae, Clonostachys rosea, and Pochonia chlamydosporia were widespread. Cultivated soils at medium- and high elevations showed greater richness and diversity (1.37 and 1.57) than fallows (0.64 and 0.48) respectively, while high-altitude fallows were strongly dominated by Metapochonia suchlasporia. Community composition clustered by land use, with elevation as a secondary driver (PERMANOVA p&#x2009;=&#x2009;0.06). Selected P. lilacinum and C. rosea species caused 10-50% mortality of Spodoptera frugiperda larvae in preliminary laboratory assays.<br><br>CONCLUSIONS: Elevation and land use jointly structure EPF communities in the Uluguru Mountains. Some taxa showed preliminary pathogenicity in laboratory assays, indicating potential for future evaluation as biological control agents in smallholder farming systems. Public deposition of sequencing reads will facilitate reuse and benchmarking.}, }
@article {pmid42113832, year = {2026}, author = {Cai, Y and Wei, Y and Du, G and Zhang, X and Wang, Z and Wang, Z and Han, Z and Zhang, Y and Xu, Y and Han, X and Li, J and Li, Q}, title = {Identification and genetic characterization of a distinct genotype of Puumala orthohantavirus in Hebei Province, China.}, journal = {PLoS neglected tropical diseases}, volume = {20}, number = {5}, pages = {e0014250}, doi = {10.1371/journal.pntd.0014250}, pmid = {42113832}, issn = {1935-2735}, abstract = {Orthohantavirus infections pose a significant threat to human health, while numerous orthohantaviruses have been identified, suspected viral infections remain undiagnosed in the world, which highlights the need for further identification and characterization of viruses circulating in humans and host animals. In this study, viral metagenomics was utilized to investigate orthohantaviruses present in tissue samples collected from rodents trapped at the Bashang Grassland of Hebei Province, China. A total of 145 wild rodents belonging to six species were captured in the study area, and 725 tissue samples (lung, liver, kidney, spleen, gut) were collected in 2024. A Puumala orthohantavirus (PUUV), named Guyuan strain, was identified in Myodes rufocanus, with a positive rate of 0.69%. The complete genomic sequences of the L, M, and S segments were obtained and confirmed by Sanger sequencing. Phylogenetic analysis of these genomic sequences with those of other orthohantavirus species showed that the L, M, and S segments clustered with PUUV genomic sequences, while sharing a nucleotide sequence similarity of 81.2%, 80.2%, and 84.3% with previously characterized reference viral strains Kitahiyama128L, Tobetsu_04, and Baltic/205 Cg, respectively. Amino acid homology analysis demonstrated that the sequences exhibited the highest identity to PUUV Hokkaido strain at a level of 95.4%, 94.6%, and 97.0% respectively. Viral particles were observed in lung and kidney tissues using transmission electron microscopy, and viral protein antigen was detected in viral RNA-positive lung, liver, and kidney tissues through immunofluorescence assay with antibodies against the PUUV nucleocapsid protein, thereby confirming the virus's multiorgan tropism. The results demonstrated that a distinct genotype of PUUV was circulating in rodents in the study areas, which may have implications for zoonotic transmission surveillance and public health management in Hebei Province.}, }
@article {pmid42103726, year = {2026}, author = {Goulet, L and Plaza Oñate, F and Famechon, A and Quinquis, B and Belda, E and Prifti, E and Le Chatelier, E and Gautreau, G}, title = {CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-72637-9}, pmid = {42103726}, issn = {2041-1723}, support = {ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-24-PESA-0004//Agence Nationale de la Recherche (French National Research Agency)/ ; }, abstract = {Metagenomic sequencing provides insights into microbial communities, but it can be compromised by technical biases, including cross-sample contamination. This phenomenon arises when microbial content is inadvertently exchanged among concurrently processed samples, distorting microbial profiles and compromising the reliability of metagenomic data and downstream analyses. Existing detection methods rely on negative controls, which are insufficiently used and do not detect cross-contamination within non-control samples. Meanwhile, strain-level bioinformatics approaches do not distinguish contamination from natural strain sharing and lack sensitivity. To fill this gap, we introduce CroCoDeEL, a decision-support tool for detecting and quantifying cross-sample contamination. Leveraging linear modeling and a pre-trained supervised model, CroCoDeEL identifies specific contamination patterns in species abundance profiles. It requires no negative controls or prior knowledge of sample processing positions, offering improved accuracy and versatility. Benchmarks across three public datasets demonstrate that CroCoDeEL can detect contaminated samples and identify their contamination sources, even at low rates (<0.1%), provided sufficient sequencing depth. Application of CroCoDeEL to several existing studies reveals previously undetected contamination.}, }
@article {pmid42103925, year = {2026}, author = {Anil,  and Ramesh, KB and Gouda, MNR and Subramanian, S}, title = {Microbial zonation and functional roles in the gut of white grub (Maladera insanabilis) larvae.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-52250-y}, pmid = {42103925}, issn = {2045-2322}, abstract = {Maladera insanabilis, a widespread and destructive agricultural pest in India, thrives in nitrogen-deficient subsoil environments due to its dependency on gut bacteria. In particular, the hindgut is an anaerobic fermentation chamber, supporting microbial-driven nitrogen transformations essential for larval development. Despite its ecological significance, detailed studies exploring gut bacterial diversity and functional role in M. insanabilis are lacking. This study integrates metagenomics, culture-based techniques, enzymatic assays, and gene expression analyses to characterize the nitrogen-cycling potential of gut microbiota along the different gut compartments. The culture-based analysis isolated 16 aerobic and 8 anaerobic bacterial strains, predominantly from Bacillota and Pseudomonadota. High-throughput 16 S rRNA Illumina sequencing revealed 134 shared amplicon sequence variants (ASVs), with distinct bacterial assemblages, Burkholderia and Pseudomonas in the foregut, Paenibacillus in the midgut, and anaerobic genera such as Bacteroides and Desulfovibrio dominating the hindgut. Functional annotation using the KEGG database indicated that anaerobic gut bacteria are actively involved in nitrification, denitrification, and nitrogen fixation. The Enzyme assays confirmed high nitrate and nitrite reductase activity, with Burkholderia contaminans and Bacillus cepacia showing the highest activities. Michaelis-Menten kinetics and Lineweaver-Burk analysis (R[2] = 0.9871) showed a higher capacity (Vmax) for nitrate and nitrite reduction; a small Km indicates a high affinity for nitrate and nitrite. Gene expression studies viz., hzo, nifH, amx, nirS, and nirK revealed a significantly high expression level in the hindgut, especially under vermicompost treatment. This study provides the first comprehensive insight into nitrogen-cycling gut bacteria in M. insanabilis, highlighting their role in host nutrition and nitrogen transformation. These findings lay a foundation for future microbiome-targeted pest control strategies aimed at disrupting nutrient acquisition in soil-dwelling grubs.}, }
@article {pmid42103932, year = {2026}, author = {Wang, F and Zeng, W and Zhang, Z and Li, N and Cui, Z and Bai, J and Yan, J and Zhang, Y and Miao, Y and Gu, L and Xiong, B}, title = {Gut microbiota-modulated glutamic acid rejuvenates the quality of oocytes deteriorated by advanced reproductive age.}, journal = {EMBO molecular medicine}, volume = {}, number = {}, pages = {}, pmid = {42103932}, issn = {1757-4684}, support = {2023YFD1300502//MOST | National Key Research and Development Program of China (NKPs)/ ; BYSYSZKF2023029//State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital/ ; KYCX25_1007//Postgraduate Research &amp; Practice Innovation Program of Jiangsu Province/ ; }, abstract = {The gut microbiota plays a vital role in maintaining the physiological function of host health and the pathogenesis of various diseases. However, its relationship with maternal age-associated decline in oocyte quality remains elusive. Here, we report that establishment of gut microbiota from young donors in aged mice by fecal microbiota transplantation (FMT) is an effective method to rejuvenate the quality of maternally aged oocytes. Specifically, young gut microbiota promoted the ovulation and maturation of aged oocytes, and inhibited occurrence of cytoplasm fragmentation and spindle/chromosome abnormalities, hence enhancing the oocyte quality and female fertility. By integrating metagenome and untargeted metabolome of intestinal digesta, as well as targeted metabolome of ovaries and micro-transcriptome of oocytes, we identified that Bacteroides_caecimuris-modulated glutamic acid levels mediated the restorative effects of young gut microbiota on the aged oocytes through strengthening the mitochondria function. In addition, we demonstrated that in vivo supplementation of glutamic acid also enhanced the quality of aged oocytes, and the improvement of oocyte quality by glutamic acid was conserved across species. Altogether, our findings highlight the importance of gut microbiota in the oocyte aging and provide potential improvement strategies for age-related decline in oocyte quality and female fertility.}, }
@article {pmid42104156, year = {2026}, author = {Minnaar, LS and Inokuma, K and Hasunuma, T and den Haan, R}, title = {Engineering natural Saccharomyces cerevisiae isolates for enhanced one-step cellulosic ethanol production.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-026-13830-0}, pmid = {42104156}, issn = {1432-0614}, abstract = {Engineering yeast strains for use as chassis organisms in second-generation (2G) bioethanol is a promising strategy to improve process economics. Natural isolates of Saccharomyces cerevisiae offer strain backgrounds with greater genetic diversity and enhanced robustness, with the potential for improved heterologous protein production capabilities. In this study, heterologous cellulase production using different expression strategies was evaluated in various process-relevant conditions. Enhanced cellulolytic activity was clearly demonstrated in a cell-tethered enzyme system, compared to a free enzyme system, across identical strain backgrounds. Superior secretory capacity was obtained for YI59_V2 for all individual enzymes across all process-relevant conditions tested. In addition, this strain exhibited improved hydrolysis efficiency and ethanol production from crystalline cellulose, achieving ~10 g/L after 96 h (~88% of the maximum theoretical yield) without the need for exogenous cellulase supplementation. Interestingly, enhanced strain robustness against process-relevant, secretion, and cell wall stresses was also observed in transformants with cell-tethered cellulase systems compared to those with free enzyme systems. This study highlights that the expression design strategy for cellulase-encoding genes in this natural isolate was pivotal for increasing protein titres and for influencing strain robustness. Strains exhibiting elevated cellulase activity and increased robustness represent a key step toward the industrial deployment of consolidated bioprocessing (CBP). KEY POINTS: • Cell-tethered expression greatly boosted cellulase activity and cellulose breakdown. • YI59_V2 yielded ~ 10 g/L ethanol from crystalline cellulose without added enzymes. • Tethered enzymes reshaped cell walls and altered stress tolerance.}, }
@article {pmid42104260, year = {2026}, author = {Nguyen, TT and Steen, IH and Bøe, MH and Otterlei, M and Stokke, R}, title = {Arctic deep-sea hydrothermal microbiomes as a natural niche for novel antimicrobial peptides.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05098-1}, pmid = {42104260}, issn = {1471-2180}, abstract = {BACKGROUND: The escalating threat of antimicrobial resistance (AMR) has created an urgent need for new antimicrobial agents. Antimicrobial peptides (AMPs) are promising alternatives to conventional antibiotics due to their broad-spectrum activity and reduced risk of resistance development. While most AMP discovery efforts have focused on terrestrial microbes, extreme environments remain largely untapped. Deep-sea hydrothermal vent biofilms, such as those from the Arctic Mid-Ocean Ridges (AMOR), are unique ecosystems characterized by high pressure, temperature gradients, and chemical extremes. These conditions select for microorganisms with specialized adaptations, including the production of bioactive compounds that confer survival advantages. Such peptides may exhibit enhanced stability and novel mechanisms of action, making hydrothermal biofilms an exceptional resource for next-generation antimicrobials.<br><br>RESULTS: Using metagenomic and metatranscriptomic datasets from nine recently published AMOR biofilms, we predicted 961 AMP sequences with Macrel, of which 873 were unique and showed no identity to entries in the Antimicrobial Peptide Database (APD). AMPs were distributed across 51 microbial phyla, including underrepresented archaeal groups such as Asgardarchaeota, Nanoarchaeota, and Micrarchaeota. Transcriptomic profiling detected AMP expression in 25 phyla, including low-abundance candidate taxa, highlighting active AMP production. In silico minimum inhibitory concentration (MIC) prediction using APEX 1.1 suggested that 16.7% of AMPs may inhibit at least one clinically relevant pathogen, with Acinetobacter baumannii emerging as the most susceptible. Four peptides were synthesized for experimental validation; AMP OLKFNNDA_52_10 exhibited moderate in vitro activity against Staphylococcus aureus and weak activity against Escherichia coli, while showing low cytotoxicity toward human HEK293 cells. Other tested peptides displayed weak or no activity, underscoring discrepancies between computational predictions and biological outcomes.<br><br>CONCLUSIONS: Our study reveals extensive taxonomic and structural diversity of AMPs in Arctic hydrothermal vent biofilms and identifies novel candidates withbioactive potential. These findings emphasize the importance of integrating metagenomics, transcriptomics, machine learning, and experimental validation to uncover bioactive compounds from underexplored microbial ecosystems. Overall, AMOR biofilms represent a rich and untapped source of AMPs, offering new opportunities for antimicrobial drug discovery in the fight against AMR.}, }
@article {pmid42104558, year = {2026}, author = {Luo, X and Lei, Z and Fang, D and Chen, H and Qian, L and Jin, C and Wang, X and Liu, X and Liu, H and Wang, Y}, title = {Integrated multi-omics decipher the complex nodule microbiota and distinct Frankiaceae symbiotic traits in wild actinorhizal plants.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71234}, pmid = {42104558}, issn = {1469-8137}, support = {32300265//Young Scientists Fund of the National Natural Science Foundation of China/ ; }, abstract = {Actinorhizal plants are ecologically important pioneer species in temperate regions, capable of nitrogen-fixing root nodule symbiosis with Frankiaceae bacteria. Despite their significance within the nitrogen-fixing clades (NFC), multi-omics studies of actinorhizal symbiosis remain scarce. We profiled prokaryotic communities in the rhizosphere, root, and/or nodule compartments from five phylogenetically representative actinorhizal species, three legumes, and four nonnodulated NFC species using 16S rDNA sequencing. Transcriptomic and metagenomic analyses were performed on actinorhizal roots and nodules, respectively. Metagenome-assembled genomes revealed four novel Frankiaceae species. Frankiae relative abundance levels in nodules were generally lower than rhizobia in legumes. Actinorhizal nodules harbour diverse bacterial taxa, which exhibit predominantly positive interactions, with Frankiae forming a tightly interacting subgroup. Actinorhizal plants engage actively with soil microbiota, recruiting a specific rhizosphere community enriched with beneficial microbes, including ammonia-oxidising archaea. Many symbiotic mechanisms in nodulating host plants are conserved and derived from pre-existing molecular modules. Our analysis suggests the phosphoinositide signalling likely functions in actinorhizal symbiotic signal transduction. However, Frankiae exhibit fundamentally different symbiotic functional characteristics compared to rhizobia, reflecting less intimate symbiosis, which might favour the life-history strategies of temperate perennial actinorhizal plants.}, }
@article {pmid42104576, year = {2026}, author = {Ii C, JF and Vidal, MJS and Dela Cruz, FSE and Tantengco, OAG and Menon, R}, title = {The Microbiome Signature of the Placenta and its Role in Spontaneous Preterm Birth: A Systematic Review and 16S rRNA Re-Analysis.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {95}, number = {5}, pages = {e70246}, doi = {10.1111/aji.70246}, pmid = {42104576}, issn = {1600-0897}, mesh = {Humans ; Female ; Pregnancy ; *Placenta/microbiology ; *Premature Birth/microbiology/immunology ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; }, abstract = {PROBLEM: The advent of high-throughput 16S rRNA sequencing has enabled deeper insights into microbial communities associated with adverse pregnancy outcomes, including spontaneous preterm birth (sPTB). While microbial dysbiosis in the cervicovaginal and oral-gut microbiomes has been implicated in sPTB, the existence of a placental microbiome remains contentious. Traditional paradigms of a "sterile womb" have been challenged by studies suggesting a low-biomass microbial community in the placenta, though recent evidence disputes this claim, attributing findings to contamination or transient microbial DNA signals.<br><br>METHOD: This study systematically reviewed placental microbiome studies employing 16S rRNA sequencing and re-analyzed publicly available datasets to determine microbial signatures in term and preterm placentas. Following a comprehensive search of three databases and stringent inclusion criteria, seven studies were included. The risk of bias was assessed using a modified Joanna-Briggs tool, revealing moderate-to-low risk across studies. Methodological heterogeneity, including differences in contamination controls, sequencing regions, and analytical platforms, was a significant limitation.<br><br>RESULTS: A re-analysis of sequencing data showed no consistent microbiome signature distinguishing the term from preterm placentas. Beta diversity analysis revealed no group clustering, while alpha diversity indices showed comparable species richness. Bacterial DNA in placental tissues was primarily attributed to contamination from the urogenital tract or laboratory processes.<br><br>CONCLUSION: Findings underscore the importance of robust contamination control and standardized protocols in low-biomass microbiome research. Future studies should employ advanced techniques, such as metagenomics and fluorescence in situ hybridization, to evaluate the functional relevance of microbial communities in the placenta, as well as rule out microbial DNA deposited in the placenta through circulating bacterial extracellular vesicles (EVs).}, }
@article {pmid42104663, year = {2026}, author = {Yang, KL and Zhai, JN and Ye, JW and Zhang, XN and Wei, QC and Wang, H and Wang, HM and Chu, LL and Yang, J}, title = {Dysbiosis of Gut Archaea is Associated with Obesity and Could be Recovered after Bariatric Surgery.}, journal = {Biomedical and environmental sciences : BES}, volume = {39}, number = {4}, pages = {437-446}, doi = {10.3967/bes2026.019}, pmid = {42104663}, issn = {2214-0190}, mesh = {Humans ; *Bariatric Surgery ; *Gastrointestinal Microbiome ; *Obesity/microbiology/surgery ; Male ; Female ; *Archaea/physiology/genetics/classification ; Adult ; Middle Aged ; *Dysbiosis/microbiology ; }, abstract = {OBJECTIVE: Obesity is closely associated with an altered gut microbiota; however, the role of archaea in obesity remains unknown. We aimed to delineate the alterations in gut archaea in obese subjects and explore the changes in bariatric surgery-associated gut archaeal composition.<br><br>METHODS: Metagenomic sequencing data from 191 obese subjects and 184 lean controls were retrieved from three public cohorts. Of these, 23 obese patients who underwent bariatric surgery were followed up for 3 months.<br><br>RESULTS: The gut archaea of obese subjects showed significantly lower Shannon diversity index than those of lean controls. Principal component analysis of the gut archaea revealed distinct clusters in obese subjects and lean controls. A model using the 20 top archaeal genera discriminated obese from lean controls with an area under the receiver operating characteristic curve (AUC) of 0.79, 0.83, and 0.86 in three cohorts. Ecological analysis showed decreased trans-kingdom correlations between archaea and bacteria in obese subjects compared to those in lean controls, with partial restoration observed after bariatric surgery.<br><br>CONCLUSION: This is the first study to demonstrate that obesity is characterized by gut archaeal dysbiosis across multiple cohorts. Bariatric surgery-induced weight loss is associated with significant changes in the gut archaea.}, }
@article {pmid42104937, year = {2026}, author = {Kang, X and Hu, L and Song, J and Zhang, Z and Li, Y and Zhang, Q and Luo, C and Pang, Y and Guo, P and Yue, B and Li, P and Fan, Z}, title = {Snake Gut Microbiota as a Source of Anti-Inflammatory Probiotics: Isolation and Functional Characterization of Two Novel Strains.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.70118}, pmid = {42104937}, issn = {1749-4877}, support = {2023NSFSC1935//Sichuan Science and Technology Program/ ; }, abstract = {The intestinal microbiome is fundamental to host physiological homeostasis, while deviations from its balanced state have been linked to inflammatory bowel diseases (IBD). To address the limitations of conventional antibiotic therapies, this study explored snake gut microbiota as a novel source of anti-inflammatory probiotics. We explored the gut microbiota of five snake species (Deinagkistrodon acutus, Trimerodytes annularis, Trimerodytes percarinatus, Lycodon rufozonatus, and Trimeresurus stejnegeri) through metagenomic sequencing. Community composition analysis revealed that the phylum-level composition was mainly Proteobacteria, Bacteroidetes, Actinomycetota, and Firmicutes. We further detected some potential probiotic species, such as Enterococcus, Lactobacillus, and Limosilactobacillus. From 196 isolated strains, Lactobacillus johnsonii DA0116 and Limosilactobacillus reuteri DA0218 were selected through rigorous safety and functional assessments, including acid/bile tolerance, pathogen inhibition, and adhesion capacity. In a DSS-induced murine colitis model, both strains significantly reduced disease activity index (DAI), pro-inflammatory cytokines (TNF-α, IL-6, and IL-8), and restored gut microbiota diversity. Additionally, whole-genome analysis identified bacteriocin synthesis clusters (gassericin-S/T) and carbohydrate metabolism genes, explaining their antimicrobial and immunomodulatory properties. This study not only emphasizes the untapped latent value of reptilian gut microbiota for probiotic discovery but also provides two candidate strains with therapeutic promise for IBD and functional food applications.}, }
@article {pmid42105239, year = {2026}, author = {Minich, JJ}, title = {Protocol for high-throughput processing of fecal samples for long-read metagenomic sequencing using PacBio HiFi or Oxford Nanopore Technologies.}, journal = {STAR protocols}, volume = {7}, number = {2}, pages = {104526}, doi = {10.1016/j.xpro.2026.104526}, pmid = {42105239}, issn = {2666-1667}, abstract = {Long-read sequencing, whether using PacBio (PB) or Oxford Nanopore Technologies (ONT), requires high-molecular-weight (HMW) DNA at high purity and free of contaminants. Here, we present a protocol for high-throughput processing of fecal samples for long-read metagenomic sequencing. We describe steps for microbial inactivation, nucleic acid stabilization, and HMW DNA extraction. We then detail procedures for DNA cleanup, shearing, library preparation, and DNA sequencing. For complete details on the use and execution of this protocol, please refer to Minich et al.[1].}, }
@article {pmid42105544, year = {2026}, author = {Li, T and Feng, K and Wang, S and Du, X and Li, J and Gu, S and Zhao, B and Yang, X and Peng, X and He, Q and Wang, Y and Wang, D and Wang, J and Wang, Z and Liu, M and Xiao, J and Men, J and Jin, D and Zhang, J and Deng, Y}, title = {Integrating digital PCR and metagenomics to quantify potential soilborne bacterial pathogens in urban ecosystem.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142312}, doi = {10.1016/j.jhazmat.2026.142312}, pmid = {42105544}, issn = {1873-3336}, abstract = {Understanding the environmental occurrence patterns of soilborne pathogens is essential for public health, yet a comprehensive and accurate assessment remains challenging. This study presents an innovative technical framework integrating metagenomic pathogen screening with quantitative validation using chip-based digital PCR (dPCR) targeting the overall bacteria community as well as three dominant species-Ralstonia pickettii, Saccharomonospora viridis, and Gordonia terrae. This approach enabled a comprehensive quantification of potential human-, plant-, and zoonotic pathogens and elucidation of their environmental drivers across urban soil habitats in Beijing. Farmland and hospital greenspaces exhibited higher potential pathogen richness (15.55 ± 5.87 and 10.70 ± 4.52) and abundance (22,475.52 ± 15,559.92 and 26,217.62 ± 19,299.90 copies g[-1] soil) compared with forests and campus greenspaces. The composition of potential pathogens varied among habitats, with farmlands containing the highest number of unique species, and four taxa were detected across all habitats, showing strong adaptive capacity. Pathogen diversity was positively correlated with total and available phosphorus and with total bacterial α- and β-diversity, while negatively associated with soil organic carbon, reflecting limited pathogen inputs in carbon-rich forest soils and the key role of phosphorus in pathogen enrichment. Climatic and soil physicochemical factors indirectly influenced pathogen diversity by modulating bacterial communities, whereas human activities directly increased pathogen abundance. Molecular ecological network analysis demonstrated that 81% of the associations between pathogenic and non-pathogenic taxa were significantly negative, suggesting competitive exclusion as a key regulatory mechanism. Collectively, these findings provide a precise monitoring framework and new insights into cross-species interactions, contributing to improved risk assessment and One Health strategies for the prevention of soilborne diseases.}, }
@article {pmid42105734, year = {2026}, author = {Zhang, J and Zeng, W and Meng, Q and Gong, Q and Lu, Y and Bi, Z and Peng, Y}, title = {Efficient amino acid capture from sludge fermentation by Tetrasphaera enhances simultaneous nitrification, endogenous denitrification and phosphorus removal.}, journal = {Water research}, volume = {301}, number = {}, pages = {126061}, doi = {10.1016/j.watres.2026.126061}, pmid = {42105734}, issn = {1879-2448}, abstract = {The simultaneous nitrification endogenous denitrification and phosphorus removal (SNDPR) process shows great potential for carbon, nitrogen, and phosphorus removal. However, its application is challenged by limited carbon availability and the strong reliance of glycogen-accumulating organisms (GAOs) and traditional polyphosphate-accumulating organisms (PAOs) on volatile fatty acids. This study first established a fermentative PAO Tetrasphaera-dominated SNDPR coupled with in-situ sludge fermentation process, achieving stable and efficient nitrogen (95.7 ± 0.6%) and phosphorus (92.6 ± 1.6%) removal using complex organics (e.g., amino acids and proteins) from wastewater and sludge as carbon sources. Extending the anaerobic duration (from 5 h to 17 h) regulated the phosphorus removal and fermentation capacity of Tetrasphaera, promoting its dominance at the genomic (10.89%), transcriptional (6.24%), and translational (24.0%) levels. For phosphorus removal, the denitrifying phosphorus removal (DPR) rate using nitrite increased from 0.98 ± 0.05 mgN/gVSS·h at 5 h to 2.70 ± 0.07 mgN/gVSS·h at 17 h, shifting the system from aerobic phosphorus uptake dominance to a cooperative pattern with DPR, effectively lowering carbon demand. For fermentation, metagenomic analysis revealed that efficient amino acid capture by Tetrasphaera facilitated the retention of substantial sludge hydrolysates for intracellular amino acid storage, improving nutrient removal and mitigating NH4[+]-N and PO4[3-]-P release. Additionally, anammox bacteria (Candidatus Brocadia, 2.67%) self-enriched and synergistically contributed to nitrogen removal. Overall, this study provides new insights into the metabolic shift between fermentation and phosphorus removal in Tetrasphaera, demonstrating the feasibility of stable and efficient carbon, nitrogen and phosphorus removal by the SNDPR process in VFA-limited wastewater.}, }
@article {pmid42106331, year = {2026}, author = {Davin, ME and Ortís Sunyer, J and Delgado, LF and Tavis, SL and Lowndes, T and Zafar, Z and Caussin, J and Halder, R and Hickl, O and Laczny, CC and Hanslian, E and Koppold, DA and Rajput-Khokhar, A and Steckhan, N and Schade, S and Schneider, J and Mollenhauer, B and Michalsen, A and May, P and Hettich, RL and Wilmes, P}, title = {High-resolution multi-omics enhances prediction and detection of smORF-encoded proteins in the human gut microbiome.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-72762-5}, pmid = {42106331}, issn = {2041-1723}, support = {863664//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; Graduate Research Fellowship Program//National Science Foundation (NSF)/ ; }, abstract = {Small open reading frames (smORFs), which encode proteins under 100 amino acids, represent an underexplored dimension of the human gut microbiome, despite growing evidence of their essential biological roles. Due to small size and poor annotation, smORFs are typically excluded from metagenomic/metaproteomic analyses. Here, we present a high-resolution multi-omic workflow that integrates smORF prediction into metaproteome searches and enables ultra-deep detection of smORF-encoded proteins (SEPs), without experimental size-based enrichment, utilizing state-of-the-art mass spectrometry instrumentation. Applied to human gut microbiomes, this approach resulted in the largest number of detected SEPs to date, allowing identification of over 25,000 SEPs in the metaproteome, alongside the measurements of the larger proteins. Our multi-omics integrative strategy is critical for advancing human metaproteome research. It also provides a generalizable strategy for comprehensive SEP discovery across diverse microbial ecosystems greatly expanding the previously hidden proteomic landscape.}, }
@article {pmid42106335, year = {2026}, author = {Xue, H and Godneva, A and Tang, F and Li, H and Li, Y and Hu, M and Li, R and Su, J and Segal, E and Razzak, I}, title = {Population-scale characterization of the oral microbiome and associations with metabolic health.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-72748-3}, pmid = {42106335}, issn = {2041-1723}, abstract = {The oral microbiome may capture system-specific information about host metabolic health, yet large-scale, multi-system evidence remains scarce. We analyzed 9,431 participants in the Human Phenotype Project (HPP), integrating buccal-swab oral whole metagenome profiles with 44 metabolic measures spanning liver ultrasound, continuous glucose monitoring (CGM), and dual energy X ray absorptiometry (DXA). Here we show that using a microbiome-wide association study (MWAS) framework, we constructed a multilayer map across strains, gene families and pathways, revealing widespread associations: 213 strains, 124,603 gene families and 299 pathways were significantly associated with metabolic measures. Prioritizing the strongest and cross-phenotype signals, we identified multiple oral features with most significant associations to metabolic health. For example, acyl carrier protein (ACP) was associated with lower liver inflammation and reduced adiposity, whereas polyamine biosynthesis and ceramide α oxidation tracked higher glucose variability and adverse liver and adiposity phenotypes. Leveraging these MWAS-derived signals, we trained disease classification models using phenotype-selected oral features, which outperformed full-feature oral models across six metabolic diseases. These association signals were also robust in oral-health sensitivity analyses in HPP, and key BMI and waist-circumference associations directionally replicated at the genus level in an independent cohort (n = 20, 293). Together, these findings provide a population-scale oral-metabolic association map and highlight the potential of oral microbial markers as non-invasive tools for metabolic risk stratification.}, }
@article {pmid42106361, year = {2026}, author = {Sun, Y and Wu, S and Wu, Z and Zhu, W and Gao, H and Xing, J and Zhao, J and Fan, X and Su, X}, title = {Instance-based transfer learning enables cross-cohort early detection of colorectal cancer.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-01001-y}, pmid = {42106361}, issn = {2055-5008}, support = {2021YFF0704500//National Key Research and Development Program of China/ ; 20251ZDYF020482//Innovation Yongjiang 2035 Key R&amp;D Programme/ ; }, abstract = {Colorectal cancer (CRC) continues to be a major global public health challenge. Extensive research has underscored the critical role of the gut microbiome for diagnostics of CRC. However, early-stage prediction of CRC, particularly at the precancerous adenomas (ADA) stage, remains challenging due to the instability of microbial features across cohorts. In this study, we conducted a systematic analysis of 2053 gut metagenomes from 14 globally-sampled public cohorts and a newly recruited cohort. Despite substantial regional and cohort-level heterogeneity in microbiome composition, we elucidated that the consistent differences between groups in microbial signatures provide the fundamental basis for CRC detection. These patterns enabled robust performance in both inter-cohort and independent validations using an optimized bioinformatics framework. In contrast, such basis was lacking in ADA-associated microbial markers, limiting the generalizability of early detection models. To address this, we developed an instance-based transfer learning approach, Meta-iTL, which effectively leveraged knowledge from existing datasets to detect CRC risk at the ADA stage in the newly recruited cohort. Thus, Meta-iTL overcomes challenges posed by cohort-specific variability and limited data availability and advances the application of non-invasive approaches for the early screening and prevention of CRC.}, }
@article {pmid42106412, year = {2026}, author = {Guo, L and Holyoak, GR and DeSilva, U}, title = {Insights from healthy mares reveal that mammalian uteri harbor a diverse virome.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-49532-w}, pmid = {42106412}, issn = {2045-2322}, abstract = {The Earth's estimated 10[31] virions, primarily phages, significantly impact microbial ecosystems. Despite their abundance, viromes remain relatively understudied-particularly in domestic animals. While recent studies have described a dynamic commensal microbiome in mammalian uteri, no research has yet characterized the commensal virome in a mammalian uterus. In this study, we report for the first time the presence of a sparse, but diverse native virome in the equine uterus. The resulting virome database consists of 513 non-redundant viral genomes (> 2 kb). Taxonomic annotations revealed the prevalence of taxadominated by the genera Gammaretrovirus, Mamastrovirus, Sapovirus and Rosenblumvirus. Notably, 75% of the assembled genomes represented novel species. Phylogenetic analysis revealed distinct clades suggesting unexplored viral diversity within the uterine environment. Furthermore, bacterial hosts for equine uterine phages were predicted, aligning with previous studies' findings. Most notably, the study identified antibiotic resistance genes within the virome, hinting at potential gene transfer mechanisms between bacteria and viruses. This study establishes the first uterine virome of any mammal, shedding light on a previously unexplored domain. The findings highlight the potential for phage therapy in reproductive infectious diseases and the importance of understanding the maternal gestational environment. Moreover, the study emphasizes the need for further research to expand the uterine virome databases and deepen our understanding of uterine microbiome and its implications for animal and human health.}, }
@article {pmid42106682, year = {2026}, author = {Wang, Y and Ma, Y and Yi, J and Li, X and Shao, Y and Cao, L}, title = {A case report of post-arthroscopic knee infection caused by Capnocytophaga sputigena in an anemic patient.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13507-z}, pmid = {42106682}, issn = {1471-2334}, support = {23ZR1480300//Science and Technology Innovation Action Program of the Shanghai Science and Technology Commission/ ; }, abstract = {BACKGROUND: Capnocytophaga sputigena (C. sputigena), a species of bacteria resident in the human oral cavity. Here, to the best of our knowledge, this is the first reported case of a post-arthroscopic knee infection caused by this organism in an anemic patient. We described the clinical characteristics, therapeutic intervention and outcome associated with knee joint infection induced by this bacterium. Furthermore, the treatment approaches and challenges in managing this particular pathogen were explored.<br><br>CASE PRESENTATION: A 58-year-old female patient presented with a knee infection following arthroscopy, caused by C. sputigena. The species C. sputigena was confirmed on the basis of the results of the joint fluid culture and metagenomics next-generation sequencing (mNGS). The infection was treated with arthroscopic debridement, in addition to intravenous and intra-articular meropenem irrigation. The initial therapy with meropenem resulted in clinical improvement, and was subsequently de-escalated to amoxicillin-clavulanate potassium. Following a period of observation, the patient was discharged, as her condition was stable.<br><br>CONCLUSIONS: The case of a post-arthroscopic knee infection caused by C. sputigena in an anemic patient resulted in surgeons developing a more profound clinical understanding of infections induced by the bacterium. The combination of arthroscopic debridement with meropenem therapy (subsequently followed by de-escalation to amoxicillin-clavulanate potassium) yielded favourable clinical outcomes, thereby establishing a practical reference point for the management and prognosis of such infections.}, }
@article {pmid42106812, year = {2026}, author = {Ottesen, A and Kocurek, B and Mammel, MK and Charles, SJ and Dietrich, J and Pauley, S and Cole, SD and Rankin, S and Ceric, O}, title = {Breaking the culture habit: Complementing culture-based veterinary diagnostics with metagenomic data -A case study of feline and canine skin infections.}, journal = {BMC veterinary research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12917-026-05476-x}, pmid = {42106812}, issn = {1746-6148}, abstract = {BACKGROUND: Skin infections have been described as the primary cause for veterinary small animal practice visits, frequently requiring topical and systemic antibiotics. These infections often represent secondary complications of underlying pathologies, that can lead to recurrent infections and multiple antibiotic exposures. This creates selection pressure toward antibiotic resistance at the intersection of skin, bloodstream, and shared human-animal environments. This case study integrates Veterinary Diagnostic Laboratory (VDL) aerobic culture results with metagenomic (MGX) data to evaluate the combined utility of these approaches in advancing One Health veterinary diagnostics. Simultaneous reporting of culture-recovered pathogens alongside infection microbiomes and resistomes could strengthen pathogen epidemiology, illuminate polymicrobial etiologies, and inform antimicrobial stewardship.<br><br>RESULTS: One feline and eight canine skin swabs were analyzed with aerobic culture and traditional antimicrobial susceptibility testing (AST) and compared with MGX profiles. VDL aerobic culture and AST identified Staphylococcus aureus, S. pseudintermedius, S. schleiferi, methicillin resistant (MR) S. schleiferi (MRSS), MR S. pseudintermedius (MRSP) and Pseudomonas aeruginosa. MGX data detected the identical bacterial pathogens and identified methicillin resistance genes (mecA, mecI, mecR1) in samples where AST had confirmed MRSP and MRSS. MGX data also detected mec genes in samples without culture confirmed MR phenotypes as well as describing multi-domain microbiota (bacteria, fungi, protists, viruses, phages), antimicrobial resistance genes (ARGs), plasmids, and metabolic features associated with the skin infection samples.<br><br>CONCLUSIONS: MGX data detected the identical VDL recovered pathogens and genes that confer the AMR phenotypes recovered by VDL AST. MGX data also detected additional uncultured pathogens, ARGs, multi-domain microbiota, mobile AMR elements, and metabolic features. Future applications for these methods used simultaneously could support monitoring programs, advance pathogen epidemiology, inform treatment strategy, advance judicious antimicrobial administration, and provide data for machine learning (ML) models to improve precision veterinary diagnosis and treatment.}, }
@article {pmid42106836, year = {2026}, author = {Navazesh, SE and Ter Horst, A and Wen, W and Liu, Y and Kiang, D and Li, Z and Yu, A and Brown, CT and Ji, P}, title = {Dietary iron and metal-based growth promoters differentially modulate the gut resistome and Escherichia coli virulome in weaned pigs.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42106836}, issn = {1674-9782}, support = {NNFSA210073688//Novo Nordisk Foundation/ ; NNFSA210073688//Novo Nordisk Fonden/ ; }, abstract = {BACKGROUND: High levels of zinc oxide (ZnO) and copper sulfate are widely used as alternative growth promoters in postweaning pig diet. However, excessive exposure to these metals may drive co-selection for heavy metal (HMR) and antibiotic resistance (AMR). Nursery diets also contain abundant iron to offset the low bioavailability of plant-derived iron, yet how dietary iron influence gut dysbiosis and microbial resistance in postweaning pigs remains unclear. This exploratory study examined the effects of dietary iron and metal-based growth promoters on the fecal resistome of postweaning pigs using shotgun metagenomics and whole-genome sequencing (WGS).<br><br>METHODS: Fifty weanling pigs were stratified and randomly assigned to five dietary treatments for 24&#xa0;d. Experimental diets included a control diet (Con) containing 25, 139, and 141&#xa0;mg/kg of Cu, Fe, and Zn, respectively, a low-iron diet (LFe, 19&#xa0;mg Fe/kg), a high-iron diet (HFe, 1,219&#xa0;mg Fe/kg), a high-copper diet (HCu, 257&#xa0;mg Cu/kg), and a high-zinc diet (HZn, 2,631&#xa0;mg Zn/kg, including 2,490&#xa0;mg Zn/kg from ZnO). All pigs were orally administered with F18 enterotoxigenic Escherichia coli (ETEC) on d&#xa0;13-16. Metagenome sequencing were performed on d&#xa0;24 fecal DNA (n&#x2009;=&#x2009;24) to identify HMR genes (BacMet Predicted database) and AMR genes (CARD database). Functional annotation was performed using HUMAnN3. Whole genome sequencing (WGS) was conducted on 120 E. coli isolates from fecal cultures on d&#xa0;1, 12, and 24, and AMR and virulence genes were identified from contig assemblies using ABRicate.<br><br>RESULTS: Dietary metal treatments significantly altered &#x3b2;-diversity of HMR genes compared with Con, with HZn differing from both HCu and LFe (P&#x2009;<&#x2009;0.05). Fecal iron levels correlated with sodB (&#x3c1;&#x2009;=&#x2009;0.64, P&#x2009;=&#x2009;0.075), an iron-containing superoxide dismutase, while fecal copper levels correlated with pcoC (&#x3c1;&#x2009;=&#x2009;0.66, P&#x2009;=&#x2009;0.075), a plasmid-mediated copper resistance gene. Across metagenomes, 172 AMR genes were identified, dominated by glycopeptide and tetracycline resistance. While dietary iron had minimal effects on fecal AMR profile, HZn induced the largest shifts in resistome, including increases of ant(9)-la, conferring aminoglycoside resistance on mobile genetic elements, and&#xa0;adeF, encoding a multidrug efflux pump (P&#x2009;<&#x2009;0.05).&#xa0;Functional profiling revealed enrichment of carbohydrate metabolism pathways in HZn group (P&#x2009;<&#x2009;0.05). WGS of E. coli isolates showed distinct AMR profiles under HZn on d 24 and distinct virulence profile under LFe on d 12, exhibiting increased prevalence of exotoxin and T3SS genes (P&#x2009;<&#x2009;0.05).<br><br>CONCLUSION: Dietary iron restriction enhanced E. coli virulence genes, whereas excessive ZnO induced the most pronounced changes in the gut resistome and microbial metabolism, highlighting a risk for AMR co-selection and marked influence on gut microbiota.}, }
@article {pmid42107247, year = {2026}, author = {Tan, T and Hu, T and Chen, B and Kuang, W and Yu, H and Xie, Y and Zhang, Z and Wang, H and Deng, Z and Zhang, C}, title = {Boosting anaerobic reductive dehalogenation with natural protein amendments to unlock cryptic organohalide-reducing bacteria.}, journal = {Marine environmental research}, volume = {219}, number = {}, pages = {108100}, doi = {10.1016/j.marenvres.2026.108100}, pmid = {42107247}, issn = {1879-0291}, abstract = {Deep-sea sediments host a rich yet largely unexplored reservoir of microorganisms capable of reductive dehalogenation. However, the activity of dehalogenating consortia is often limited even under carbon-rich conditions, impeding the identification of key functional players. In this study, we report that the addition of natural protein materials can dramatically stimulate reductive dehalogenation in an enrichment culture derived from deep-sea cold seep sediments. This stimulatory effect was clearly demonstrated by supplementation with bovine serum albumin (BSA), which significantly enhanced the degradation rates of 2,4,6-tribromophenol (2,4,6-TBP) and tetrachloroethene (PCE). Integrated metagenomic and metatranscriptomic analyses revealed that two candidate novel clostridial lineages-Romboutsia and Oxobacteraceae-present in BSA-amended cultures harbored distinct reductive dehalogenase (RDase) genes. Romboutsia harbored three RDase genes, with one being upregulated during the degradation of 2,4,6-TBP intermediates and another specifically responding to PCE, suggesting a substrate-dependent regulatory strategy. Oxobacteraceae encoded a cytosolic RDase that was highly expressed during 2,4,6-TBP transformation. Metabolic reconstruction further indicated that both lineages could utilize BSA-derived amino acids for growth. This work establishes an effective biostimulation strategy to activate dehalogenation in deep-sea microbial communities and expands the known diversity and functional versatility of candidate organohalide-reducing bacteria.}, }
@article {pmid42107339, year = {2026}, author = {Zhang, X and Lu, J and Bao, Q and Xu, K}, title = {Renal mucormycosis caused by Apophysomyces species: case report and literature review.}, journal = {Journal de mycologie medicale}, volume = {36}, number = {2}, pages = {101627}, doi = {10.1016/j.mycmed.2026.101627}, pmid = {42107339}, issn = {1773-0449}, abstract = {INTRODUCTION: Mucormycosis represents an uncommon yet aggressive and life-threatening fungal infection, typically occurring in immunocompromised individuals. Unlike most Mucorales infections, Apophysomyces frequently infects otherwise healthy hosts, raising significant clinical concern. Alarmingly its atypical manifestation, necrotizing fasciitis, is often misdiagnosed as a bacterial infection due to overlapping clinical features.<br><br>CLINICAL CASE: Herein we present a case of Apophysomyces infection in kidney in an immunocompetent 52-year-old man, whose condition deteriorated swiftly, leading to failure of several organs, culminating in death. All laboratory results, including serological assays and microbial cultures from blood, respiratory secretions, urine, and stool, showed no abnormalities. The diagnosis was confirmed through metagenomic next-generation sequencing (mNGS) which was highlighted as valuable for early diagnosis. We conducted a literature review of 13 cases previously reported from 1994 to 2025, implying a higher prevalence among immunocompetent individuals. Patients of Indian constituted the majority across all reported cases. PCR, fungal culture and histopathological examination served as the primary diagnostic methods. Systemic antifungal agents were administered to 13 individuals, while surgical intervention was performed in 8 cases. Complete recovery was achieved in 7 patients.<br><br>CONCLUSIONS: Therefore our report highlights Apophysomyces variabilis as a novel pathogen of clinical importance in China, emphasizing that mortality rates escalate substantially without timely detection and appropriate management.}, }
@article {pmid42107405, year = {2026}, author = {Guo, Y and Zhou, W and Dong, M and Qiu, W and Gao, X and Ahmad, T and Farid, B and Lyu, W and Sun, L}, title = {Root-secreted aminosalicylic acid and 4,6-dioxoheptanoic acid: Dual roles in enhancing 4-nonylphenol bioavailability and regulating rhizospheric microbiota community.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142282}, doi = {10.1016/j.jhazmat.2026.142282}, pmid = {42107405}, issn = {1873-3336}, abstract = {Root exudates and rhizospheric microorganisms are key drivers of organic pollutant degradation in soil. However, the mechanisms underlying their coordinated effects are not yet fully understood. This paper analyzes the changes in the composition of Astragalus sinicus root exudates induced by 4-nonylphenol (4-NP) exposure and investigates the effects of key exudate components on 4-NP sorption-desorption, rhizospheric degradation, and soil microbial community. Metabolomic analysis indicated significant alterations in profile composition induced by 4-NP exposure, with organic acids representing the major responsive category. Specifically, aminosalicylic acid and 4,6-dioxoheptanoic acid-two pivotal organic acids-markedly enhanced 4-NP desorption from soil at a concentration of 50 μmol/L. Their addition reduced the desorption coefficient by 6.4-fold and 3.2-fold, respectively, compared to the control. A pot experiment further validated that application of the two organic acids significantly increased rhizospheric dissipation of 4-NP by 20.0-23.0% compared to soils planted with A. sinicus alone. Metagenomic analysis demonstrated that the key root exudates selectively enriched pollutant-degrading microorganisms (Pseudoxanthomonas sp. A, Cupriavidus, Rhodococcus, and Penicillium), and increased the abundance of functional genes (Cox1, ligB, ligI, and pcaF) and pathways associated with xenobiotic biodegradation. These findings indicate that specific root exudates enhance microbial degradation capacity by improving 4-NP bioavailability, providing a mechanistic basis for the targeted optimization of phytoremediation strategies for 4-NP-contaminated soils.}, }
@article {pmid42107727, year = {2026}, author = {Ramesh, K and Chellam, PV}, title = {Comparative genomic surveillance of fluoroquinolone resistance markers across major riverine hotspots by leveraging public metagenomes.}, journal = {International journal of antimicrobial agents}, volume = {}, number = {}, pages = {107839}, doi = {10.1016/j.ijantimicag.2026.107839}, pmid = {42107727}, issn = {1872-7913}, abstract = {The global surge in fluoroquinolone resistance (FQR) underscores the urgent need for robust environmental surveillance. From a One Health perspective, rivers serve as critical conduits and hotspots for antimicrobial resistance (AMR) dissemination. To address this, we conducted a systematic metagenomic surveillance of FQR across spatially prioritized freshwater ecosystems using distribution data of five major markers (gyr, par, qnr, aac, qep) retrieved from the National Center for Biotechnology Information (NCBI) Pathogen Detection Isolate Browser. Among 164 riverine metagenomic datasets, 31 high-quality datasets from the Mississippi, Yukon, Saint Lawrence, Yangtze, and Pearl rivers were analyzed. FQR genes were detected in 12 datasets, with normalized abundances ranging from 0.01 to 1.22 copies per bacterial cell. Plasmid-mediated qnrS2 and efflux pump genes (qepA2, AbaQ) emerged as the most prevalent determinants. Multivariate analyses revealed river-specific clustering patterns and strong correlations with metal resistance genes, highlighting co-selection pressures. The predominance of conjugative mobile genetic elements indicated an elevated potential for horizontal gene transfer. Taxonomic profiling further revealed enrichment of clinically important and World Health Organization (WHO) priority pathogens. Community structure analyses (Permutational Multivariate Analysis, R[2] = 0.7598, p = 0.003) confirmed significant microbial variations across rivers. Collectively, this integrative approach identifies environmental reservoirs of FQR genes, supporting river-based AMR surveillance. These insights are pivotal for shaping evidence-driven mitigation strategies and informing both national and global AMR policies.}, }
@article {pmid42107869, year = {2026}, author = {Wang, L and Lin, F and Yuhan, Y and Li, S and Pan, Z and Wu, Y and Gao, Y and Zhu, L and Wang, J and Wang, J}, title = {Humic substances with different molecular weights independently increased antibiotic resistance in agricultural soils contaminated with sulfamethazine.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128302}, doi = {10.1016/j.envpol.2026.128302}, pmid = {42107869}, issn = {1873-6424}, abstract = {Humic substances (HS) are known to enhance soil structure, but their effects on the antibiotic resistance distribution in agricultural soils, especially under sulfonamide contamination, remain poorly understood. This study employed an indoor soil microcosm experiment combined with metagenomic sequencing to examine the effects of high molecular weight humic acid (HA) and low molecular weight fulvic acid (FA) on the dynamics of the antibiotic resistance in sulfamethazine (SM2) contaminated agricultural soil, with the aim of identifying key driving factors. The results revealed that both HA and FA, especially at 1 g/kg, increased the total abundance of antibiotic resistance genes (ARGs), including dominant genes, such as Sul1, Cmx, VanR, Sul2 and FloR. Additionally, HS application led to increased abundance of mobile genetic elements (MGEs) and potential ARG hosts, such as Actinobacteria. Notably, HA inhibited the growth of cultivable sulfonamide-resistant bacteria (SRB), while FA promoted their growth. However, the antibiotic resistance ratio of cultivable bacteria remained relatively high under both HS treatments, consistent with the elevated ARG abundance. This may be attributed to the enhanced competitiveness of Pseudomonas within the SRB community under HS exposure. Variance partitioning analysis (VPA) indicated that MGEs and microbial communities jointly contributed to ARG variation and were closely associated with the antibiotic resistome. This study provides new insights into the ecological risks associated with HS application in agricultural soils.}, }
@article {pmid42107880, year = {2026}, author = {Yao, L and Shen, L and Liu, X and Fu, J and Pan, D}, title = {Ventriculo-Abdominal Subcutaneous Tunnelled External Drainage as a Transition Therapy to Reduce Shunt Failure Rate in Post-infection Hydrocephalus Patients: A single-center retrospective cohort study.}, journal = {World neurosurgery}, volume = {}, number = {}, pages = {125037}, doi = {10.1016/j.wneu.2026.125037}, pmid = {42107880}, issn = {1878-8769}, abstract = {OBJECTIVE: Assess the clinical efficacy of Ventriculo-Abdominal Subcutaneous Tunnelled External Drainage (VASTED) as a transition treatment before ventriculoperitoneal shunting(VPS) in the management of post-infection hydrocephalus(PIH).<br><br>METHODS: This study enrolled 384 patients who developed PIH after craniotomy. Following external ventricular drainage(EVD) and combined intravenous antibiotic therapy, patients underwent VASTED as a transitional treatment measure before definitive VPS placement when they achieved three consecutive negative cerebrospinal fluid(CSF) bacterial cultures within two weeks and no pathogen detection by metagenomic next-generation sequencing (mNGS). The primary endpoint of the study was the shunt failure rate after one year of follow-up, with infection and catheter blockage as the evaluation criteria.<br><br>RESULTS: A total of 378 cases underwent VPS surgery, with 6 cases refusing or abandoning treatment. During a one-year follow-up period, 9 shunt failures occurred (2.38%, 95% CI: 0.43-3.05). Among these, 5 failures were infection-related (1.3%) and 4 were due to pure mechanical obstruction (1.1%). The shortest duration of VASTED was 14 days, while the longest was 387 days, with a median drainage time of 69 days (95% CI: 28-112 days).<br><br>CONCLUSION: In patients with PIH, implementing VASTED as a transitional surgical treatment approach is closely associated with an extremely low one-year failure rate of VPS. This transitional strategy can significantly reduce the high failure rate following VPS.}, }
@article {pmid42103024, year = {2026}, author = {Zhang, T and Li, S and Wu, Y and Leung, J and Jiang, H and Xu, Z and Ng, SC and Kwok, T}, title = {Gut microbial signatures for aging-related sarcopenia and dietary links among community-dwelling old-old adults: A metagenomic study.}, journal = {Experimental gerontology}, volume = {}, number = {}, pages = {113161}, doi = {10.1016/j.exger.2026.113161}, pmid = {42103024}, issn = {1873-6815}, abstract = {BACKGROUND AND OBJECTIVES: Sarcopenia, characterized by progressive loss of muscle mass, strength and function, poses a major aging-related health challenge. While a gut-muscle axis is implicated, microbiota-sarcopenia associations in the old-old (≥80 years) remain unexplored.<br><br>METHODS: This cross-sectional analysis included 315 community-dwelling adults aged &#x2265;80&#x202f;years from a longitudinal cohort at the 20-year follow-up timepoint, of whom 180 met the inclusion criteria. Gut microbiota was profiled by shotgun metagenomic sequencing alongside sarcopenia assessment. Microbial taxa associated with sarcopenia were identified using MaAsLin2, and dietary associations were assessed by partial Spearman correlation.<br><br>RESULTS: The prevalence of sarcopenia in this old-old cohort (mean age 86.8&#x202f;&#xb1;&#x202f;4.3&#x202f;years) was 51.7%. Sarcopenic individuals showed lower nutrition scores, reduced microbial richness and altered &#x3b2;-diversity (all P&#x202f;<&#x202f;0.05). Multivariable analysis identified six differentially abundant species associated with sarcopenia (FDR&#x202f;<&#x202f;0.10), including two positively associated (Ruthenibacterium lactatiformans and Catenibacillus scindens), and four negatively associated (Phascolarctobacterium faecium, Pyramidobacter piscolens, Lacrimispora saccharolytica and Limosilactobacillus mucosae). Random forest and LEfSe analysis validated R. lactatiformans and P. faecium as the most discriminative signatures for sarcopenia. After adjusting for obesity, these signatures remained significant (P&#x202f;<&#x202f;0.05). These alterations were linked to functional dysregulation, including increased purine degradation and reduced biotin biosynthesis potential. R. lactatiformans abundance negatively correlated with dietary maltose intake (P&#x202f;<&#x202f;0.05).<br><br>CONCLUSION: In old-old adults, we identified distinct gut microbiota signatures associated with sarcopenia. R. lactatiformans and P. faecium emerged as candidate features. The dietary-microbiota correlations suggest potential nutrition strategies. These findings provide a basis for exploring microbiota-based approaches in advanced aging.}, }
@article {pmid42103277, year = {2026}, author = {Yan, J and Jin, N and Xu, C and Wu, H and Jiang, Q and Liu, H and Yuan, J and Yin, D and Lin, F and Wang, R and Liang, Y and Feng, Y and Lan, Y and Lin, X and Wang, Y and Zhang, N and Dai, L and Li, T and Dong, S and Cheng, L and Sun, X}, title = {Multi-omics landscape and machine learning predictors of acute and chronic coronary syndrome diagnosis in young patients.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.05.015}, pmid = {42103277}, issn = {2090-1224}, abstract = {BACKGROUND: Acute coronary syndrome (ACS) is a leading global cause of death, and its incidence is increasingly rising in young adults, who exhibit distinct clinical characteristics from elderly patients. However, multi-omics studies focusing specifically on young coronary heart disease (CHD) patients remain scarce, hindering precise diagnosis and mechanism exploration.<br><br>METHODS: Here, we enrolled 206 young chest pain patients (18-45&#x202f;years old), including 122 ACS patients, 38 chronic coronary syndrome (CCS) patients, and 46 individuals with healthy coronary arteries (NC). We performed integrated analyses of peripheral blood mononuclear cell transcriptomics, serum metabolomics, stool metabolomics, and gut microbiome metagenomics to characterize CHD subtypes and develop targeted diagnostic tools.<br><br>RESULTS: Our results showed that single omics layers had limited ability to distinguish CHD subtypes, while multi-omics integration significantly improved diagnostic efficacy. We identified unique molecular signatures for different subtypes: STEMI was associated with abnormal amino acid and carbohydrate metabolism, CCS was dominated by amino acid metabolism disturbances, and both STEMI and ACS showed enriched inflammation-related pathways. Novel biomarkers including p-chlorobenzene sulfonamide, cotinine, and the gut bacterium Streptococcus parasanguinis were identified, with Streptococcus parasanguinis validated as an atherogenic pathogen in a murine model. We constructed three multi-omics fusion diagnostic models (ACS vs. NACS, CCS vs. NC, STEMI vs. NSTE-ACS) with AUC values of 0.99, 0.95, and 0.96, respectively, and integrated them into a comprehensive diagnostic pipeline. Furthermore, multi-omics functional analysis unraveled a synergistic "microbiota-metabolism-immunity" regulatory network underlying CHD subtypes, linked to disordered amino acid and carbohydrate metabolism and aberrant inflammatory activation.<br><br>CONCLUSION: This study provides a systematic molecular landscape of young CHD, a high-precision diagnostic strategy, and novel targets for mechanism research and targeted intervention, addressing the unmet clinical need for precise management of young CHD patients.}, }
@article {pmid42103708, year = {2026}, author = {Basler, N and De Smet, L and Bouras, G and Swinnen, J and Pranga, K and Brussaard, CPD and Vandamme, P and de Graaf, DC and Matthijnssens, J}, title = {The honey bee triad: a comprehensive catalogue of phages in the Apis mellifera gut microbiome.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-72757-2}, pmid = {42103708}, issn = {2041-1723}, support = {955974//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 817622//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; H2020//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G049521N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; }, abstract = {Honey bees (Apis mellifera) contribute to crop production and floral biodiversity via pollination, but their health is increasingly challenged by stressors including pathogens, parasites and agricultural practices. Although the honey bee gut microbiome is relatively simple, its phages are not well studied. Here, we conducted a metagenomic study, providing a comprehensive catalogue of honey bee gut phages from 450 virus-enriched samples from 63 hives, across eight European countries, three seasons and three gut sections. We describe a diverse phageome including many phages that appear to belong to novel taxa, as well as a core set of 97 highly prevalent phages. In addition, we identify potential auxiliary metabolic genes, such as a sulfur metabolism gene carried by phages that are predominantly temperate and likely infect mutualistic honey bee core bacteria. This gene is associated with land use around the sampled hives, indicating complex ecological interactions in the tripartite system of the honey bee, its microbiota and the phages therein.}, }
@article {pmid41866358, year = {2026}, author = {Deepthi, M and Vadakkadath Meethal, K}, title = {Bacterially expressed recombinant TMOF induces mortality and gut microbial alterations in Aedes albopictus larvae.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41866358}, issn = {2045-2322}, abstract = {UNLABELLED: Mosquitoes, as vectors of numerous diseases, pose significant threat to human health. Aedes mosquitoes transmit diseases such as dengue, yellow fever and chikungunya, with dengue fever alone responsible for approximately 40,000 deaths and more than 96 million symptomatic cases annually. Current mosquito control methods are inadequate and results in environmental health hazards and development of resistance. Therefore, targeted control strategies are essential. In this context, we cloned and expressed the Trypsin Modulating Oostatic Factor (TMOF), a decapeptide that inhibits trypsin biosynthesis in mosquitoes by binding to a receptor. The codon-optimized gene for the TMOF peptide was synthesised and cloned in to pFN29AHis6Halo vector and expressed in Escherichia coli. The supernatant from the bacterial lysate containing recombinant TMOF peptide exhibited larvicidal activity against Aedes albopictus mosquito larvae, with an LC50 (48 h) of 242.1 ± 6.04 µg/mL. However, lysate from BL21 cells alone or recombinant peptide expressed with a single base shift in reading frame did not cause any mortality. The recombinant TMOF peptide was purified using nickel affinity chromatography and showed an LC50 of 2.13 ± 0.02 µg/mL, exhibiting 113.6 times more efficacy than the bacterial lysate supernatant. The LC90 (48 h) for bacterial lysate and affinity purified TMOF was 340.41 ± 6.04 µg/mL and 4.39 ± 0.20 µg/mL, respectively. TMOF peptide released from the recombinant protein by trypsin digestion also showed larvicidal activity. Exposure of larvae to TMOF fusion protein resulted in inhibition of trypsin biosynthesis in-vivo. Metagenomic analysis of the gut microbiota from TMOF-treated larvae resulted in reduction in abundance of bacteria belonging to Pseudomonadota and Bacillota compared to that of untreated larvae. Recombinant TMOF is also effective against Culex mosquito larvae, but shows no effects on non-target organisms such as Drosophila melanogaster, Luprops tristis, and Aplocheilus lineatus. Thus, the use of TMOF expressed in E. coli offers a promising eco-friendly method of mosquito control. (Patent number: 554267).<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41440-3.}, }
@article {pmid41902972, year = {2026}, author = {Rodriguez-Cruz, UE and Ochoa-Sánchez, M and Sierra, JL and Pagaza-Straffon, EC and Hurtado-Ramírez, JM and Quispe-Ricalde, MA and Castelán-Sánchez, HG and Dávila-Ramos, S}, title = {Unveiling a Microbial Treasure Trove: Phylogenetic Diversity and Bioremediation Potential in a High-Altitude Andean Saline System.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {41902972}, issn = {1432-184X}, support = {227-2015-FONDECYT//Fondo Nacional de Desarrollo Cient&#xed;fico, Tecnol&#xf3;gico y de Innovaci&#xf3;n Tecnol&#xf3;gica/ ; Contract No. 23 2018 UNSAAC//UNSAAC/ ; grant No. 103.5/15/10446//Programa de Mejoramiento del Profesorado, Universidad Aut&#xf3;noma del Estado de Morelos, Secretar&#xed;a de Educaci&#xf3;n P&#xfa;blica/ ; }, abstract = {UNLABELLED: The reconstruction of metagenome-assembled genomes (MAGs) has improved our knowledge of how microbiomes perform biological and chemical processes in diverse ecosystems, including extreme environments. However, in Latin America, these ecosystems have received insufficient attention. In this study, we used shotgun metagenomics to reconstruct MAGs in Acos a high-altitude intermediate saline system in Cusco, Peru. Most of the MAGs detected were classified only at the phylum level, indicating significant phylogenetic novelty. Of particular note is the presence of two poorly characterized archaeal MAGs from the genus Methanonatronarchaeum, belonging to the phylum Halobacteriota. All reconstructed MAGs displayed a broad spectrum of metabolic pathways associated with the nitrogen and sulfur cycles, indicating metabolic versatility that allows them to cope with the harsh conditions of the saline environment. Both bacterial and archaeal MAGs are enriched in various metabolic processes related to the metabolism of amino acid and nitrogenous compounds; this could indicate a mechanism for adapting to osmotic stress. Among the genes detected, those involved in the degradation of the common herbicide atrazine were identified; this provides information on potential microbial mediation processes for the bioremediation of contaminated soils. Furthermore, and equally important, these habitats harbor a great diversity of viruses, many of which have unknown in current databases. Taxonomic classification revealed bacteriophages belonging to the class Caudoviricetes, specifically the families Myoviridae, Siphoviridae, and Podoviridae. Overall, our work provides high-quality MAGs that expand current knowledge of the diversity, function, and ecological dynamics of Bacteria, Archaea, and viruses in high-altitude intermediate saline environments.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00248-026-02712-7.}, }
@article {pmid42098310, year = {2026}, author = {Li, W and Ni, P and Xu, J and Zhao, X and Dou, A and Wang, Y and Peng, L and Huang, S and Chen, Y and Shi, Q and Xie, Y and Zhang, W and Pan, S and Zhou, C}, title = {HIV-driven virome dysbiosis unveils distinct virome features and inter-viral correlations in blood and respiratory niches.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10221-z}, pmid = {42098310}, issn = {2399-3642}, support = {No. 82550118//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {While systemic immune dysregulation is well-documented in HIV infection, its impact on blood and respiratory tract viromes remains poorly understood. This study characterizes HIV-associated alterations in viral communities and examines their clinical relevance. Using viral metagenomics, we compare 203 ART-treated HIV-positive individuals and 120 healthy controls. HIV infection significantly restructures the blood virome, shifting from bacteriophage dominance (96.2% in controls) to eukaryotic virus predominance (69.1%). Increased alpha diversity, significant β-diversity divergence, and heightened dispersion heterogeneity are observed in HIV cases. Consistent enrichment of Flaviviridae, Parvoviridae, and Anelloviridae is detected. Throat viromes maintain phage dominance (>90%) but exhibit strain-level diversification, including Microviridae proliferation. Network analysis reveals Retroviridae-Anelloviridae co-dynamics (r = +0.562) and identifies Picobirnaviridae as a key interactor. Functional analysis shows enriched viral replication and host modulation genes. Compartment-specific disruption patterns nominate Pegivirus C, parvovirus B19, and Anelloviruses as potential biomarkers. Cross-kingdom viral interactions suggest novel mechanisms influencing disease progression and support future virome-targeting adjunct therapies.}, }
@article {pmid42098386, year = {2026}, author = {Wei, X and Bashir, K and Tian, X and Farooq, A and Olimi, E and Cernava, T and Zhang, L and Yu, X and Chen, Q and Penttinen, P and Gu, Y}, title = {Microplastic and lead shift microbiomes enriching viral auxiliary metabolic genes for potential polylactic acid degradation.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10162-7}, pmid = {42098386}, issn = {2399-3642}, support = {41201256//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Biodegradable microplastics and heavy metals increasingly co-occur in soils through plastic mulching, organic amendments, and legacy metal contamination. Yet, their combined effects on soil-plant-microbiota interactions remain unclear, particularly for the virus. Here we evaluated the impacts of bio-MPs, polylactic acid (PLA), lead (Pb), and their combination on buckwheat and rhizosphere bacterial-viral communities. Co-contamination reduced soil pH and nutrient availability, increased Pb accumulation in plant tissues and suppressed buckwheat growth. Metagenomic analyses revealed that both bacterial and viral communities were altered under Pb-containing treatments. Bacterial genes associated with carbon and phosphorus metabolism were suppressed, while viral auxiliary metabolic genes (AMGs) related to carbon utilization were enriched, especially carbohydrate esterases that hydrolyze PLA ester bonds. A putative AMG-associated carbohydrate esterase gene (P9222_28545) was identified and the esterase activity confirmed via heterologous expression in E. coli. These findings highlight a potential role of viruses in mediating microplastic degradation in soils.}, }
@article {pmid42098439, year = {2026}, author = {Prendergast, PJ and Bishop, HV and Herbold, CW and Verdu, EF and Dobson, RCJ and Day, AS and Ogilvie, OJ}, title = {Comprehensive cross-cohort analysis reveals global gut microbiome signatures of celiac disease.}, journal = {Communications medicine}, volume = {}, number = {}, pages = {}, doi = {10.1038/s43856-026-01627-1}, pmid = {42098439}, issn = {2730-664X}, abstract = {BACKGROUND: Celiac disease affects ~1-2% of people and remains incurable, requiring lifelong dietary restriction. The gut microbiome is thought to contribute to the development and progression of celiac disease. However, findings across previous studies are fragmented, making it difficult to understand exactly how the gut microbiome is involved.<br><br>METHODS: We integrate over 900 samples from global datasets spanning different disease stages (before onset, during active disease, and after treatment), body sites, and research methods. Datasets produced using both 16S rRNA gene sequencing and shotgun metagenomics profile the gut microbiome. Alpha and beta diversity analyses and differential abundance testing identify consistent changes in bacterial communities linked to celiac disease. Machine learning tests how well microbiome data predicts disease status.<br><br>RESULTS: Here, we show that celiac disease is not marked by large changes in gut microbiome diversity. Instead, there are subtle, consistent changes in specific bacteria, including a reduction in beneficial butyrate producers (Faecalibacterium, Prevotella, Agathobacter, Gemmiger), changes in mucin-associated microbes (Akkermansia muciniphila), and an increase in potentially harmful bacteria (Helicobacter, Campylobacter, Haemophilus parainfluenzae). These changes are seen before and during active disease and persist on a gluten-free diet. Microbiome-based disease prediction is moderately accurate for active disease and weaker for prospective performance, likely constrained by training data.<br><br>CONCLUSIONS: Our findings suggest that celiac disease is linked to specific changes in gut bacteria that are not fully resolved by diet alone. Future treatments may need to focus on restoring healthy gut bacteria, not just avoiding gluten, to better manage the disease.}, }
@article {pmid42098757, year = {2026}, author = {Jiang, X and Zhang, C and Zhang, Y and Li, J and Ren, J and Wang, J and Hou, X and Zhang, Z and Wu, S and Yao, J}, title = {Multi-omics analysis of soy isoflavone-induced responses in rumen fermentation, endocrine status and milk production in cows with varying milk yields.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {42098757}, issn = {1674-9782}, support = {2024-KFKT-011//the National Center of Technology Innovation for Dairy/ ; 32272829//National Natural Science Foundation of China/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; }, abstract = {BACKGROUND: Improving milk yield and feed efficiency is pivotal for climate-smart dairy systems, as rumen mediated fermentation governs energy and nitrogen utilization and thereby greenhouse-gas emission intensity. Soybean isoflavones (SIF) may modulate rumen fermentation, yet their effects on rumen function, microbiome features, host endocrine/metabolic responses, and lactation performance-particularly across cows with divergent milk-yield phenotypes-remain unclear.<br><br>RESULTS: Fifty&#x2011;six lactating Holstein cows (28 high&#x2011;yield cows, HY; 28 low&#x2011;yield cows, LY) were divided into two categories by milk yield. Within each yield category, cows were randomly assigned to one of two dietary treatments: a basal diet (Control) or the basal diet supplemented with SIF at 0.01% of dry matter. This yielded a 2&#x2009;&#xd7;&#x2009;2 factorial design with four experimental groups (n&#x2009;=&#x2009;14 per group): high&#x2011;yield control (HCON), high&#x2011;yield SIF (HSIF), low&#x2011;yield control (LCON), and low&#x2011;yield SIF (LSIF). SIF increased milk yield by 8.75% and improved fat-corrected milk (+&#x2009;7.20%), dry matter intake (+&#x2009;3.20%), and feed efficiency (+&#x2009;3.26%), with larger gains in HY cows (milk yield&#x2009;+&#x2009;8.89%; feed efficiency&#x2009;+&#x2009;4.55%). Rumen fermentation shifted toward a more energetically favorable profile, with lower acetate (-&#xa0;2.70%), higher propionate (+&#x2009;4.55%), and a reduced acetate-to-propionate ratio (-&#xa0;7.02%), accompanied by increased microbial crude protein (+&#x2009;21.53%) without changes in pH or NH3-N. SIF altered endocrine status irrespective of phenotype, increasing estradiol and progesterone while decreasing prolactin and growth hormone, and reduced blood ALP, lactate, and triglycerides. Metagenomics indicated phenotype-dependent microbial and functional responses to SIF: HY cows showed enrichment of taxa (e.g., Caudoviricetes sp., Eubacterium sp., and Butyrivibrio sp.) associated with amino-acid, cofactor metabolism and propionate pathways, whereas LY cows exhibited enrichment of Prevotella sp. and Bacteroides sp. with functions favoring carbohydrate degradation. The HCON group exhibited greater abundances of Prevotella sp. and Hallella spp. with enhanced carbohydrate degradation functions, whereas the LCON group was enriched in Ruminococcus sp. and Methanobrevibacter sp., associated with methane metabolism.<br><br>CONCLUSIONS: In conclusion, this study highlights the potential of SIF supplementation to improve lactation efficiency, modulate rumen microecology and endocrine function in dairy cows. These findings establish a theoretical framework for achieving efficient and precise feeding management on large-scale dairy farms.}, }
@article {pmid42098796, year = {2026}, author = {Monteleone, E and Cianci, MA and Albano, A and Loperfido, F and Griffante, G and Brasi, L and Borella, F and Gallio, N and Preti, M and Marchi, A and Gardella, B and Molineris, I and Donati, G and Proserpio, V}, title = {Unleashing the potential of mRNA-seq to uncover the microbiome structure and their crosstalk with host cells: the vulvar ecosystem.}, journal = {Microbiome}, volume = {14}, number = {1}, pages = {}, pmid = {42098796}, issn = {2049-2618}, support = {IG 2023 - Id. 28831//Fondazione AIRC per la ricerca sul cancro ETS/ ; MFAG 2023 - ID. 29203//Fondazione AIRC per la ricerca sul cancro ETS/ ; CRT 2023 RF = 106089 / 2023.1841//Fondazione CRT/ ; COD. 2022CLTAYH//Ministero dell'Universit&#xe0; e della Ricerca/ ; 2025.0983//Compagnia di San Paolo/ ; }, abstract = {BACKGROUND: To describe both host gene expression and microbiome composition in a single sample, parallel experimental and computational workflows (mRNA-sequencing and either 16S rRNA gene or metagenomics) have been traditionally applied. The vulvar milieu represents an area of emerging research for its role in health and disease. Located at the interface between the vagina and the perineum, the vulvar microbiome displays an intermediate signature, with influx from both ecosystems.<br><br>RESULTS: Following validation of the reliability of poly(A)-enriched mRNA-sequencing in reconstructing the microbiota composition using both a quantitative microbial standard (mock) and metagenomic analysis, we analyze a full cohort of 30 healthy vulvar samples. Crucially, the analysis of the entire cohort relies solely on mRNA-sequencing without the use of parallel DNA metagenomics. This unified approach allows us to analyze not only the vulvar cell transcriptome, but also the composition and dynamics of microbial communities, including the microbial gene expression signatures. This three-level analysis (host-mRNA, individual bacterial species, bacterial gene pathways) on the very same specimens further enables a gene-level exploration of host-microbe molecular crosstalk. Using this unified framework, we reveal marked heterogeneity and high inter-individual variability in the vulvar microbiota, identifying community state types that mirror those described in the vagina. Importantly, we show that distinct microbial configurations are associated with specific host transcriptional programs: Lactobacillus crispatus correlates with epithelial differentiation and barrier integrity, whereas communities enriched in Gardnerella vaginalis, or other taxa associated with dysbiosis, exhibit transcriptional signatures linked to inflammation. Interestingly, Lactobacillus gasseri, which has been associated with lower protection, shows an intermediate effect on vulvar cells.<br><br>CONCLUSIONS: Beyond providing new biological insights into an understudied anatomical niche, our study introduces a broadly applicable strategy with substantial impact for the field. With tens of thousands of human RNA-seq datasets already available in public repositories, our approach enables retrospective extraction of microbiome information and host-microbe interaction signals from existing transcriptomic data, without the need for additional sequencing or specialized microbiome protocols. This unlocks a powerful and cost-effective opportunity to revisit archived RNA-seq studies across tissues, diseases, and low-biomass environments, revealing previously inaccessible layers of host-microbiome crosstalk and maximizing the scientific value of published data. Video Abstract.}, }
@article {pmid42098851, year = {2026}, author = {Dong, J and Cao, Y and Chen, X and Xie, T and Zhang, X and Zhao, Q and Shi, C and Miao, Q and Xu, Z and Yan, L and Dong, L}, title = {Buyang Huanwu Decoction promotes neurorepair after spinal cord injury through a Lactobacillus johnsonii-indole-3-lactic acid-AhR-PI3K/Akt axis.}, journal = {Chinese medicine}, volume = {21}, number = {1}, pages = {}, pmid = {42098851}, issn = {1749-8546}, support = {YSJ2025009//Postgraduate Research &amp; Practice Innovation Program of Yan'an University/ ; 22XYJ0002//Xi'an Innovation Capability Strong Foundation Plan - Medical Research Project/ ; 2025PT-01//Platform Construction Project of Shaanxi Province's Health and Wellness Scientific Research and Innovation Capacity Enhancement Program/ ; }, abstract = {BACKGROUND: Spinal cord injury (SCI) induces gut microbiota dysbiosis, which significantly affects recovery. Buyang Huanwu Decoction (BHD), a traditional Chinese medicine formula, has shown therapeutic effects on SCI. Although BHD is known to modulate gut microbiota, whether its benefits are mediated through the gut-spinal cord axis remains unclear.<br><br>METHODS: A rat SCI model was established. BHD was administered orally, and fecal microbiota transplantation (FMT) from BHD-treated rats (BHD-FMT) was performed to assess neuroprotective and gut-protective effects. Behavioral testing, histology, and immunofluorescence evaluated motor recovery, inflammation, and neuroregeneration. Gut microbiota profiling was performed using 16S rDNA sequencing and metagenomics, while targeted metabolomics quantified tryptophan metabolites. Transcriptomics validated key pathways, and a microbiota-metabolite-signaling network was constructed.<br><br>RESULTS: BHD significantly improved motor function, reduced spinal inflammation, and promoted neuronal survival and axonal regeneration. It restored gut function, reduced colonic inflammation, and enhanced ZO-1 and Occludin expression, which were further confirmed by FMT. BHD-FMT reshaped the gut microbiota and enriched Lactobacillus johnsonii, which correlated positively with recovery. Metabolomics showed increased tryptophan metabolites, including indole-3-lactic acid (ILA) and indole-3-propionic acid (IPA), with ILA strongly associated with functional improvement. Transcriptomic analysis and Western blot validation demonstrated that BHD-FMT activated the AhR-PI3K/Akt pathway, which was suppressed by an AhR antagonist.<br><br>CONCLUSION: BHD promotes neuroregeneration after SCI by reshaping gut microbiota and enhancing tryptophan metabolism, potentially exerting its effects through the L. johnsonii-ILA-AhR-PI3K/Akt network. These findings reveal a gut-spinal cord axis-mediated mechanism of BHD and highlight microecological targets for SCI therapy.}, }
@article {pmid42098871, year = {2026}, author = {Biswas, P and Ahmed, S and Mondal, S and Oladokun, S and Gundogdu, O and Mallick, AI}, title = {Recombinant LAB vector-based multicomponent vaccine against Campylobacter jejuni potentially promoting a healthier microbial balance in the poultry gut.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02421-w}, pmid = {42098871}, issn = {2049-2618}, support = {BB/Y007115/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; P409/2023-24//BactiVac, University of Birmingham, UK/ ; IC-12047(12)/2/2024-BP-IUCA//Indo-UK (DBT-BBSRC)/ ; }, abstract = {BACKGROUND: Diarrheal diseases remain the second leading cause of preventable death globally, particularly among children under the age of 5 in developing countries, accounting for an estimated 2-3 million deaths annually. Among bacterial pathogens causing diarrheal illness, Campylobacter jejuni (C. jejuni) remains a major contributor, particularly in low- and middle-income countries (LMICs). As a common gut pathogen, C. jejuni expresses several secretory or surface-expressed colonization proteins (SECPs), namely haemolysin co-regulated protein (Hcp), valine glycine repeats G (VgrG), Campylobacter adhesion to fibronectin (CadF), fibronectin-like protein A (FlpA), and jejuni lipoprotein A (JlpA). Most of these proteins play pivotal roles in bacterial self-survival, host-cell adhesion, and invasion of avian and non-avian hosts. To minimize C. jejuni adhesion and subsequent colonization in the avian gut, we explored the potential of a multicomponent mucosal vaccine composed of CadF, Hcp, and JlpA protein of C. jejuni.<br><br>RESULTS: For this purpose, we bioengineered a food-grade Lactic Acid-producing Bacterium, Lactococcus lactis (L. lactis), to express three key immunogenic subunits of C. jejuni, CadF, Hcp, and JlpA. Utilizing this live vector-based multicomponent mucosal vaccine platform, we investigated the immunoprotective potential of these antigens in chickens. Since the particular strain of L. lactis is non-colonizing, we used chitosan, a natural mucoadhesive, biodegradable polymer, to microencapsulate the engineered bacteria and increase their gut retention time for optimal interaction with local immune cells. Our in vivo immunization study demonstrated that oral administration of this multicomponent vaccine formulation elicited a strong local antibody response (sIgA) (p&#x2009;<&#x2009;0.0001) and upregulated key pro-inflammatory cytokines, leading to robust mucosal immune protection (~&#x2009;1.54 log10 reduction) against the cecal colonization of C. jejuni. Beyond targeting C. jejuni, we hypothesized that the vaccine may influence the overall gut microbiota, potentially promoting a healthier microbial balance in the poultry gut. To this end, gut metagenomic analysis of vaccinated birds revealed a marked reduction in the phylum Campylobacterota (~&#x2009;2-fold), accompanied by increased abundance of the phyla Bacteroidota, as part of a beneficial microbial community.<br><br>CONCLUSIONS: Together, this study underscores the potential of a live vector-based, multicomponent mucosal vaccine as a promising, cost-effective strategy to reduce the cecal load of C. jejuni, potentially limiting the risk of foodborne transmission in poultry production systems.}, }
@article {pmid42098876, year = {2026}, author = {Liu, Z and Guo, Y and Xiao, L and Guo, J and Chen, Y and Wang, H and Nan, X and Zhou, M and Zhang, F and He, Y and Yu, Z and Wang, R and Ren, Z and Wu, J and Wang, M and Tang, X and Xiong, B}, title = {Proanthocyanidins inhibit methane emissions by interacting with methyl-coenzyme M reductase and reshaping rumen microbiome function.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02406-9}, pmid = {42098876}, issn = {2049-2618}, support = {2023YFD2000703//National Key R&amp;D Program of China/ ; 2023YFD2000701//National Key R&amp;D Program of China/ ; 32525054//National Natural Science Foundation of China/ ; CAAS-CSSAE-202402//Innovation Program of Chinese Academy of Agricultural Sciences/ ; 2022YFD1301100//Integrated Demonstration of Scalable and Efficient Healthy Breeding for Cattle and Sheep/ ; }, abstract = {BACKGROUND: Enteric methane (CH4) emissions from ruminants are a major source of agricultural greenhouse gases and represent an energy loss to the host. Methyl-coenzyme M reductase (MCR) is the terminal enzyme in methanogenesis and represents a key target for CH4 mitigation. This study integrated computational screening, in vitro fermentation, and in vivo experiments to identify plant-derived compounds capable of reducing enteric CH4.<br><br>RESULTS: Molecular docking of 3,900 phytochemicals identified proanthocyanidins (PAC) as top candidate, exhibiting strong predicted affinity to the MCR active site (-8.150&#xa0;kcal/mol). In vitro rumen fermentation assays showed that PAC supplementation reduced CH4 production by 22% while increasing dry matter degradability. In lactating dairy cows, dietary PAC supplementation (10 or 20&#xa0;g/kg dry matter) decreased daily CH4 emissions by&#x2009;~&#x2009;8%, and improved ruminal nitrogen utilization without affecting milk yield or ruminal volatile fatty acid production. Amplicon sequencing and metagenomic analyses revealed PAC supplementation shifts in rumen microbial community, characterized by increased relative abundance of Bacteroidota taxa and a decreased relative abundance of methanogenesis-related genes. Functional genes associated with carbohydrate, lipid, and nitrogen turnover were more abundant, indicating potential improvements in nutrient utilization. Consistent with these changes, untargeted metabolomics likewise identified shifts in metabolite profiles that may associated with alternative routes for utilizing reducing equivalents.<br><br>CONCLUSIONS: This study provides integrated computational, microbial, and physiological evidence that PAC supplementation can reduce enteric CH4 emissions in lactating dairy cows, inducing rumen microbial and functional shifts and improving nitrogen utilization. These findings support the potential of PAC as a natural approach to lowering CH4 emissions and advancing sustainable dairy production. Video Abstract.}, }
@article {pmid42099457, year = {2026}, author = {Liu, Y and Zhang, Z and Wu, G and Li, B and Wang, L and Wang, J and Wei, Z and Wang, Z and Yang, J and Zhang, K and Zhang, T and Tao, X and Chen, T and Fan, J and Zhou, J and Yang, X and Zhao, L and Wei, Y}, title = {Two stable gut microbiome guilds predict liver tumor class and treatment responses.}, journal = {iMeta}, volume = {5}, number = {2}, pages = {e70123}, pmid = {42099457}, issn = {2770-596X}, abstract = {Gut microbiome alterations are increasingly associated with hepatocellular carcinoma (HCC), highlighting the gut-liver axis as a key contributor to tumor progression and prognosis. Taxon-based HCC microbiome studies have shown limited reproducibility because they are affected by database dependency, taxonomic ambiguity, and overlooked ecological interactions. The Two Competing Guilds (TCG) model, based on stable gut microbiome interactions, provides a structurally grounded framework for robust, generalizable biomarkers. Using shotgun metagenomic data from a newly recruited cohort of 120 surgically resectable HCC cases and 76 benign liver tumor controls, we constructed co-abundance networks to identify stably correlated genome pairs and assembled a hepatic cancer-TCG (HCC-TCG) model composed of 142 genomes. Functionally, one Guild had more genes for butyrate production from carbohydrate fermentation while the other Guild was enriched in genes for virulence factors and antibiotic resistance, highlighting its potential proinflammatory roles. Classifiers trained on the abundance profiles of HCC-TCG genomes successfully distinguished HCC from benign liver tumors (area under the receiver operating characteristic, AUROC = 0.70) and from colorectal liver metastases (CRLM) (AUROC = 0.78). In an external validation cohort, the model further discriminated against HCC from intrahepatic cholangiocarcinoma (iCCA) (AUROC = 0.72), and from healthy controls (AUROC = 0.79-0.85), demonstrating its broad applicability for tumor stratification across clinical contexts. Moreover, HCC-TCG profiles predicted post-resection recurrence risk and response to adjuvant therapies (AUROC up to 0.83). Importantly, external validation in two independent cohorts of advanced HCC patients treated with PD-1/PD-L1 inhibitors demonstrated consistent predictive performance (AUROC = 0.64-0.73), confirming the model's generalizability in nonsurgical and immunotherapy contexts. This genome-specific, ecologically structured, and database-independent framework identifies a conserved Guild-based microbiome signature for HCC. Our findings demonstrate that a fixed genome-resolved ecological structure retains transferable discriminatory signal across clinical contexts. The HCC-TCG framework provides a genome-specific, interaction-based foundation for future development of non-invasive microbiome stratification strategies requiring prospective validation.}, }
@article {pmid42099461, year = {2026}, author = {Wu, R and Wen, T and Shang, N and Xie, P and Wang, Z and Li, H and Li, S and Zhang, D}, title = {Chondroitin sulfate restores muscle mass via gut-muscle axis remodeling through sugar-bile acid metabolism reprogramming.}, journal = {iMeta}, volume = {5}, number = {2}, pages = {e70118}, pmid = {42099461}, issn = {2770-596X}, abstract = {Glucocorticoid-induced myopathy is characterized by progressive muscle atrophy and impaired regeneration, yet effective microbiota-oriented interventions for preserving muscle homeostasis remain largely unexplored. Here, we demonstrate that dietary chondroitin sulfate (DCS) restores muscle mass and function through a microbiota-dependent gut-muscle metabolic axis. DCS failed to confer protection in germ-free or antibiotic-treated mice, establishing gut microbiota as a prerequisite for its efficacy. Microbiota transplantation and mono-colonization experiments identified Lactobacillus johnsonii Z-RW as a functionally relevant mediator capable of recapitulating muscle protection under controlled microbial conditions. Integrated metagenomic, metabolomic, and proteomic analyses revealed coordinated reprogramming of intestinal sugar utilization and bile acid metabolism following DCS administration. Notably, DCS promoted bile acid deconjugation and enrichment of secondary bile acids, coinciding with restoration of muscle regenerative and energetic programs, including upregulation of NMRK2, PAX7, and SIRT1. Metabolite supplementation further implicated bile acids as candidate mediators linking microbial metabolism to muscle phenotypes. To quantitatively integrate these shifts, we introduce the sugar-bile acid ratio as a systems-level descriptor of microbiota-driven metabolic remodeling. Our findings delineate a microbiota-dependent metabolic framework through which a functional polysaccharide reshapes intestinal biochemistry to influence distal muscle physiology. This work highlights bile acid-associated signaling as a central relay within the gut-muscle axis and provides a conceptual foundation for microbiota-targeted strategies to mitigate muscle wasting.}, }
@article {pmid42099660, year = {2026}, author = {Leal, F and Filho, RM and Inoue, LT and Heidrich, V and Dos Santos, EX and Bastos, DA and Camargo, AA and Jardim, DLF}, title = {Urinary microbiota diversity and composition in patients with advanced renal cell cancer.}, journal = {BJUI compass}, volume = {7}, number = {5}, pages = {e70186}, pmid = {42099660}, issn = {2688-4526}, abstract = {OBJECTIVES: This study aims to investigate the role of urinary microbiota in renal cell carcinoma; we analysed urinary microbiota in kidney cancer patients and explored its potential role as biomarker.<br><br>SUBJECTS AND METHODS: Samples were collected from 49 males (28 patients planned to undergo systemic therapy and 21 healthy volunteers). Two samples were collected from each patient, one prior to treatment and one after 8 to 12&#x2009;weeks of systemic therapy. Microbiota was analysed by 16S rRNA sequencing. Microbiota diversity, taxonomic composition and relative abundance were compared between groups and longitudinal samples.<br><br>RESULTS: Amplicon sequence variant (ASV) richness was higher in renal cancer patients (p&#x2009;=&#x2009;0.042) than controls. Beta diversity also differed between patients and controls by means of Jaccard (p&#x2009;=&#x2009;0.001), Bray-Curtis (p&#x2009;=&#x2009;0.008), and nonweighted UniFrac metrics (p&#x2009;=&#x2009;0.001). Acetobacter, Lacticaseibacillus, Alloscardovia, Brevibacterium and the family Propicionibactericeae had higher relative abundance in cancer patients, while Prevotella, Microbacterium and Sphingomonas were more abundant in controls. Beta diversity differed between pretreatment and posttreatment samples (p&#x2009;=&#x2009;0.008). After systemic treatment, we found an increased relative abundance for Prevotella, Rothia, Bradyrhizobium, Methylobacterium/Methylobrum, Porphiromonas and Fusobacterium and a decreased one for the Burkeholderia-Caballeronia-Paraburkholderia group. Higher ASV richness was predictive of poor prognosis for RCC patients (p&#x2009;=&#x2009;0.043) but not of treatment response.<br><br>CONCLUSIONS: Urinary microbiota in patients with renal cell carcinoma differed from controls. Changes in microbiota composition were observed after systemic treatment. Urinary microbiota should be further investigated as a potential biomarker in renal cell carcinoma.}, }
@article {pmid42100218, year = {2026}, author = {Hussain, N and Muccee, F and Mirza, AF and Ashraf, NM and Al Haddad, AHI}, title = {Genomic insights into Solea solea gut-borne Enterococcus faecalis for the development of new probiotics in aquaculture.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1778532}, pmid = {42100218}, issn = {2297-1769}, abstract = {Dietary manipulations using probiotics may contribute to the sustainable development of aquaculture. For probiotic applications, their traits, safety profiles, and functional characteristics should be explored. Whole genome sequencing (WGS) can be an informative tool in this regard. We initiated this study to obtain genomic insights into S. solea gut-associated bacteria. Bacteria (n = 20) exhibiting probiotic characteristics were subjected to DNA extraction. A mixture comprising equimolar concentrations of each bacterial DNA was prepared and analyzed through WGS. BV-BRC, metaSPAdes, MetaBAT2, DAS Tool, and PATRIC were used for taxonomic profiling, metagenome assembly, genome binning, comprehensive genome annotation, and subsystem analysis, respectively. For tree construction, MUSCLE and RaxML were employed. Fourteen bins comprising Actinomycetota, Bacillota, Bacteroidota, and Pseudomonadota were generated. Among these, the bin comprising the genome of Enterococcus faecium was selected. Its genome comprises 129 contigs with 2,944 coding sequences (CDSs). Genes associated with metabolism, protein processing, stress response, defense and virulence, cellular processes, and cell envelope were identified. Pathways identified included fatty acid and ketone body biosynthesis, glycerolipid and glycerophospholipid metabolism, linoleic acid metabolism, and self-defense mechanisms. This study confirmed the probiotic efficiencies of E. faecium. Hence, this bacterium might be employed as a fish feed supplement in aquaculture.}, }
@article {pmid42100351, year = {2026}, author = {Hu, Y and Yan, X and Gao, F and Xu, D and Yang, Y and Cheng, J and Chen, S and Cui, Z}, title = {Probiotic-driven microbiome remodeling is associated with coordinated immune and metabolic responses, improving growth and disease resistance in farmed tongue sole (Cynoglossus semilaevis).}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100600}, pmid = {42100351}, issn = {2666-5174}, abstract = {In flatfish aquaculture, labour-intensive tank cleaning represents a major operational challenge, limiting sustainability due to its high labour requirements and associated costs. We tested a new semi-closed recirculating aquaculture system (RAS) protocol for Cynoglossus semilaevis (tongue sole), replacing manual cleaning with post-feeding water exchange (80% drained) and probiotic application. Compared with control groups, the probiotic-water exchange protocol significantly improved growth (+0.18%/day) and survival (+7.9%), while shifting the gut microbiota from a Vibrio-dominated configuration to a Photobacterium-dominated one. Metagenomics revealed that Photobacterium damselae became the predominant taxon (86%) in the probiotic group, accompanied by the enrichment of quorum sensing pathways, CAZymes (CEs, AAs), and nutrient metabolism functions. Histological examination showed improvements in the intestinal muscular layer and villi structure. Multi-tissue transcriptomics identified systemic changes in immune and metabolic pathways, including activation of intestinal immune networks (IgA production, NF-κB signaling) and antimicrobial peptide genes. Liver, gill, and skin transcriptomes revealed enhanced DNA repair, cytokine signaling, and barrier pathways. JAK-STAT pathway was also activated, linking microbial metabolite sensing to growth promotion (stat5b, igf2bp3). The probiotic-integrated protocol modifies the gut microbiome by shifting microbial composition through changes in competitive interactions and microbial signaling pathways. It also improves the intestinal wall, overall immunity, and nutrient absorption. These findings provide insights into the microbiome-host interaction under probiotic treatment and suggest that this strategy may offer potential benefits under farm conditions, but further studies are needed to validate its safety and ecological implications.}, }
@article {pmid42100652, year = {2026}, author = {Luo, J and Feng, Y and Chen, J and Xu, N and Zhang, G and Ni, J and Li, C}, title = {Functional metagenomic reconstruction of microbial pathways altered by probiotic supplementation in liver failure.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1799729}, pmid = {42100652}, issn = {2235-2988}, mesh = {Animals ; *Probiotics/administration &amp; dosage ; Rats, Wistar ; Male ; Metagenomics ; Rats ; Feces/microbiology/chemistry ; Disease Models, Animal ; *Gastrointestinal Microbiome ; *Liver Failure ; Cytokines ; Ammonia/blood ; Dysbiosis ; Galactosamine ; }, abstract = {INTRODUCTION: Liver failure is a severe condition marked by circulatory failure, systemic inflammation, and gut microbial dysbiosis. This dysbiosis worsens liver damage by reducing beneficial metabolites and increasing harmful products. This study investigates the effects of probiotics on gut microbial functional pathways in liver failure. The aim is to link microbial metabolic reprogramming with host biochemical, inflammatory, and gut barrier responses through functional metagenomic reconstruction.<br><br>METHODS: Acute liver failure was induced in male Wistar rats using D-galactosamine (700 mg/kg) and lipopolysaccharide (10 &#x3bc;g/kg). Probiotic treatment began 24 hours after induction and was administered daily for 14 consecutive days before euthanasia. Two doses were used: low (1&#xd7;10&#x2078; CFU/day) and high (1&#xd7;10&#x2079; CFU/day). Fecal samples underwent shotgun metagenomic sequencing, followed by functional pathway reconstruction. These predictions were validated using metabolite profiling, quantitative PCR of microbial genes, intestinal barrier assays, and immune cell cytokine analysis. Host phenotypic markers were correlated with microbial pathways.<br><br>RESULTS AND DISCUSSION: Liver failure significantly elevated serum ALT (42.6&#xb1;6.8 to 512.4&#xb1;48.9 U/L), AST (78.3&#xb1;9.5 to 684.7&#xb1;62.1 U/L), and plasma ammonia (38.9&#xb1;5.2 to 128.6&#xb1;14.3 &#x3bc;mol/L). Probiotic supplementation showed a dose-dependent improvement. ALT dropped to 382.7&#xb1;41.6 U/L (low dose) and 248.9&#xb1;32.4 U/L (high dose). Ammonia levels decreased to 86.4&#xb1;9.7 &#x3bc;mol/L and 59.8&#xb1;7.6 &#x3bc;mol/L, respectively. Metagenomic analysis revealed a 1.7- and 2.6-fold increase in short-chain fatty acid (SCFA) biosynthesis pathways and a 38% and 61% decrease in urease-associated nitrogen metabolism. These changes were confirmed by higher fecal SCFAs (31.8&#xb1;4.2 to 63.9&#xb1;6.4 mM), lower ammonia (8.9&#xb1;1.1 to 3.7&#xb1;0.5 mM), improved intestinal barrier integrity (TEER: 462&#xb1;38 to 721&#xb1;44 &#x3a9;&#xb7;cm&#xb2;), and reduced TNF-&#x3b1; (214.6&#xb1;22.8 to 74.9&#xb1;12.3 pg/mL). Probiotic supplementation significantly reprogrammed the gut microbiome in liver failure. This highlights its potential as a therapeutic modulator of the gut-liver axis.}, }
@article {pmid42100656, year = {2026}, author = {Li, T and Liu, J and Wang, X}, title = {Diagnostic performance and clinical utility of metagenomic next-generation sequencing in suspected pulmonary infections: a comparative study stratified by immune status.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1812778}, pmid = {42100656}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; Aged ; Adult ; *Respiratory Tract Infections/diagnosis/microbiology/immunology ; Sensitivity and Specificity ; Bacteria/genetics/isolation &amp; purification/classification ; Fungi/genetics/isolation &amp; purification/classification ; Aged, 80 and over ; Molecular Diagnostic Techniques/methods ; }, abstract = {BACKGROUND: Pulmonary infections represent a significant global health concern, contributing substantially to morbidity and mortality worldwide. Metagenomic next-generation sequencing (mNGS) represents an advanced, comprehensive, and unbiased diagnostic approach for pathogen identification, effectively overcoming many limitations inherent in conventional diagnostic methods. This study aimed to systematically evaluate the clinical performance of mNGS in the etiological diagnosis of pulmonary infections, with a particular emphasis on its utility across diverse immune statuses.<br><br>METHODS: This retrospective study included 136 patients with suspected pulmonary infections admitted to the Department of Respiratory Medicine at Shandong Provincial Hospital from June 2023 to April 2025. Bronchoalveolar lavage fluid (BALF) samples were collected from all patients and concurrently subjected to mNGS and conventional microbiological testing (CMT). The pathogen detection spectrum and diagnostic performance of mNGS were systematically compared against those of CMT.<br><br>RESULTS: mNGS exhibited a significantly higher overall pathogen detection rate compared to CMT (77.2% vs. 50.0%, P < 0.001). Regarding the pathogen spectrum, mNGS identified a broader array of microorganisms, encompassing 19 bacterial, 9 fungal, and 2 mycobacterial species, in contrast to the 11 bacterial, 5 fungal, and 1 mycobacterial species detected by CMT. Diagnostic performance analysis further revealed that mNGS sensitivity was significantly superior to that of CMT (74.6% vs. 46.7%, P < 0.001). Furthermore, mNGS demonstrated a distinct advantage in detecting mixed infections, with a detection rate of 19.1%, significantly exceeding that of CMT (8.8%, P < 0.05). Subgroup analysis indicated a significantly higher incidence of mixed infections in immunocompromised patients compared to immunocompetent patients (35.1% vs. 13.1%, P < 0.05). Additionally, immunocompromised patients were more frequently subjected to adjustments in antimicrobial therapy guided by mNGS results (56.8% vs. 35.4%, &#x3c7;&#xb2; = 5.094, P < 0.05).<br><br>CONCLUSIONS: In conclusion, mNGS offers superior sensitivity and broader pathogen coverage for the etiological diagnosis of pulmonary infections compared to conventional microbiological testing. Its enhanced capability to detect mixed infections significantly improves diagnostic accuracy in immunocompromised patients and effectively facilitates the dynamic optimization of antimicrobial therapy. Serving as a powerful complement to traditional diagnostic methods, mNGS holds particular value for the rapid diagnosis of complex and immunosuppression-associated pulmonary infections.}, }
@article {pmid42100705, year = {2026}, author = {Li, J and Liu, M and Yang, C and Fan, Z and Su, J and Hu, Y and Yang, Y and Li, J and Pu, Y and Ma, E and Deng, X and Sun, J}, title = {Preceding crops may reduce denitrification potential and enhance ammonium assimilation pathways.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1808894}, pmid = {42100705}, issn = {1664-302X}, abstract = {BACKGROUND: Soil microorganisms are pivotal to nitrogen (N) cycling in croplands, yet how preceding crops modulate their functional profiles remains unclear.<br><br>OBJECTIVE: This field study aimed to quantify the effects of barley (BT) and rapeseed (RT) preceding crops (vs. no preceding crop, CK) on soil microbial functions and N-metabolic pathways in tobacco fields.<br><br>RESULTS: High-throughput metagenomics revealed that BT and RT significantly increased soil microbial richness (Chao1 index) compared to CK. At the genus level, CK contained 64% and 24% fewer unique taxa than BT and RT, respectively. While the top five KEGG functional pathways (e.g., Metabolic pathways, Biosynthesis of secondary metabolites) were conserved across treatments, their relative abundances differed. Critically, preceding crops reduced soil denitrification rates and increased glutamine dehydrogenase activity. Redundancy analysis confirmed that ammonium-N concentration was the key edaphic factor strongly correlated with microbial community structure and function (P < 0.01).<br><br>CONCLUSION: Our findings demonstrate that barley and rapeseed preceding crops enhance microbial richness and activity, thereby inhibiting denitrification and promoting N fixation via altered ammonium-N dynamics.}, }
@article {pmid42100978, year = {2026}, author = {Ranade, AV and Hegde, PS and Agni, MB and Rai, P and Upadhyay, SS and Aravind, A and Keshava Prasad, TS and Gowda, KMD}, title = {Cardiometabolomic signatures and gut microbiota dynamics in perinatally undernourished F1 offspring: Decoding the metabolic footprint.}, journal = {Journal of biosciences}, volume = {51}, number = {}, pages = {}, pmid = {42100978}, issn = {0973-7138}, mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Animals ; Female ; Rats ; Pregnancy ; Rats, Wistar ; *Malnutrition/metabolism/microbiology ; Docosahexaenoic Acids/administration &amp; dosage/pharmacology ; Metabolome ; Fetal Development ; Male ; Metabolomics ; Maternal Nutritional Physiological Phenomena ; Dietary Supplements ; *Prenatal Exposure Delayed Effects/metabolism ; Xanthophylls ; }, abstract = {The Developmental Origins of Health and Disease (DOHaD) hypothesis asserts that detrimental prenatal conditions, such as dietary deficiencies, may lead to enduring health consequences. Perinatal undernutrition, an important concern during fetal development, may affect growth and metabolic programming, resulting in lasting health implications. Maternal nutrition is crucial in modulating fetal endocrine systems and metabolic functions, influencing the development, blood circulation, and nutrient absorption. The present study examines the impact of perinatal undernutrition on the composition of gut microbiota and metabolite levels in offspring of undernourished dams, using an Albino Wistar rat model. Furthermore, we investigated the combined impact of astaxanthin (AsX) and docosahexaenoic acid (DHA) supplementation on cardiometabolic outcomes in these progenies. Astaxanthin, a powerful antioxidant, and DHA, an omega-3 fatty acid, have shown the ability to favorably alter the gut flora and metabolic pathways. The direct influence of AsX on gut microbiota remains unexplored, whereas DHA's role in fostering beneficial microbes and regulating metabolite production is well documented. The current study used metabolomics and metagenomics to investigate the intricate relationship between metabolites and gut microbiota in health and disease, offering insights into fetal programming and possible strategies to improve offspring health. The results highlight the need to address perinatal undernutrition and enhance gut health through targeted dietary interventions to improve long-term health outcomes.}, }
@article {pmid42100992, year = {2026}, author = {Xu, X and Chen, D and Luo, N and Zhang, W and Lou, L}, title = {Metagenomic next-generation sequencing for pathology-suspected fungal infections at rare anatomical sites: a case series.}, journal = {Future science OA}, volume = {12}, number = {1}, pages = {2669032}, doi = {10.1080/20565623.2026.2669032}, pmid = {42100992}, issn = {2056-5623}, abstract = {OBJECTIVE: Histopathology for suspected fungal infections lacks species-level identification and is prone to morphological mimics. The utility of metagenomic next-generation sequencing (mNGS) at rare anatomical sites is underexplored.<br><br>METHODS: We retrospectively analyzed 10 cases with histopathology suggestive of fungal infection at rare sites (brain, cardiac valve, bone, etc.). All underwent mNGS testing on formalin-fixed paraffin-embedded samples.<br><br>RESULTS: mNGS detected fungal DNA in 8/10 cases (80%), providing species-level identification (e.g., Cryptococcus, Candida, Fusarium, Rhizopus, Histoplasma). Polymicrobial infections were identified in 70%. mNGS corrected two misdiagnoses: one confirmed neurocysticercosis; another revealed only bacteria in a suspected fungal lesion. Antimicrobial resistance genes (ErmB) were identified in two cases.<br><br>CONCLUSION: mNGS enhances diagnostic precision at rare sites by enabling species identification, uncovering polymicrobial infections, and correcting morphological misdiagnoses, supporting targeted therapy.}, }
@article {pmid42101034, year = {2026}, author = {Walker, JR and Bachand, PT and Turner, JW and Labonté, JM}, title = {Viral Assemblages of a Hypersaline Estuary Show Divergent Responses to Freshwater and Temperature Disturbances.}, journal = {Environmental microbiology reports}, volume = {18}, number = {3}, pages = {e70354}, doi = {10.1111/1758-2229.70354}, pmid = {42101034}, issn = {1758-2229}, support = {NA19NOS4190106//Texas General Land Office/ ; }, mesh = {*Estuaries ; *Fresh Water/chemistry/microbiology/virology ; Salinity ; *Viruses/genetics/classification/isolation &amp; purification ; Bacteria/genetics/classification/isolation &amp; purification ; Temperature ; Metagenomics ; Ecosystem ; }, abstract = {Hypersaline environments harbor extremely dense bacterial and viral populations unique from other aquatic ecosystems. Changes to the hydrologic cycle and anthropogenic disturbances have the potential to alter these poorly described communities. Here, we aimed to assess the variation within the viral and bacterial communities of one of the world's largest hypersaline estuaries over 13 months. Using metagenomics, we identified viruses associated with two different salinity regimes, and we showed how viruses responded to pulse disturbances including freshwater inundation and freeze events. We identified 17, 324 viral species, of which 12,132 were found in only one of the salinity regimes. Our results demonstrate a potential association between freshwater pulses throughout June 2021 and shifts in viral community composition. Freeze events showed a greater propensity to alter the auxiliary metabolic genes (AMGs), or genes carried by viruses to alter host metabolism during infection. Viruses associated with low temperatures led to higher incidences of AMGs associated with sulfur cycling and oxidative phosphorylation as opposed to photosynthesis with freshwater inundation and no extreme weather. The contrasting responses to different pulse disturbances make evident the need to better understand how different types of disturbances alter viral communities and their potential to modulate important biogeochemical cycles.}, }
@article {pmid42101202, year = {2026}, author = {Yashar, M and Thigale, UY and Karakus, S}, title = {Role of microbiome in ocular surface disease: interpreting biology in a low-biomass environment.}, journal = {Current opinion in ophthalmology}, volume = {}, number = {}, pages = {}, doi = {10.1097/ICU.0000000000001228}, pmid = {42101202}, issn = {1531-7021}, abstract = {PURPOSE OF REVIEW: Growing use of sequencing technologies has accelerated investigation of the ocular surface microbiome, yet this environment is characterized by extremely low microbial biomass, complicating data interpretation. This review assesses current evidence linking microbial communities to ocular surface disease, discusses methodological and biological factors influencing interpretation of microbiome-disease associations, and proposes a framework in which microbial roles may be considered as drivers, modifiers, or markers.<br><br>RECENT FINDINGS: Studies across multiple ocular surface diseases report alterations in microbial composition, including reduced &#x3b1;-diversity and shifts in dominant taxa. Genera such as Staphylococcus, Corynebacterium, and Cutibacterium are frequently reported as resident members of the ocular surface microbiome, although their abundance varies across individuals and sampling sites. Across diseases, microbial patterns often overlap and remain inconsistent between studies. Emerging mechanistic evidence has identified specific microbial products, such as lipoteichoic acid, that promote ocular surface inflammation through defined signaling pathways, providing initial support for a potential driver or modifier role. In low-biomass environments such as the ocular surface, contamination, host DNA predominance, and methodological variability can strongly influence detected microbial signals.<br><br>SUMMARY: Interpretation of ocular surface microbiome data remains inherently challenging in this low-biomass context. However, the emergence of mechanistic studies suggests a transition from purely associative observations toward functional and translational investigation. Future studies should be designed to better define microbial roles by integrating standardized methodologies with multiomics approaches and detailed clinical phenotyping. Until such evidence emerges, microbiome research is best viewed as advancing biological insight rather than informing clinical decision-making.}, }
@article {pmid42101460, year = {2026}, author = {Colmant, AMG and Parry, RH and Charrel, R and Coutard, B}, title = {Benchmarks for taxonomic classification of jingmenviruses and closely related viruses using newly identified genomic sequences.}, journal = {The Journal of general virology}, volume = {107}, number = {5}, pages = {}, doi = {10.1099/jgv.0.002254}, pmid = {42101460}, issn = {1465-2099}, mesh = {*Genome, Viral ; Phylogeny ; *Flaviviridae/classification/genetics/isolation &amp; purification ; Genomics ; Metagenomics ; }, abstract = {Jingmenviruses are a group of viruses related to orthoflaviviruses characterized by a segmented genome and multipartite organization that have been detected worldwide in a wide range of hosts. With the growing number of new jingmenvirus sequences identified in metagenomics data, it can be difficult to assess whether a new sequence is associated with a new virus species or with a strain of an existing species. The ICTV is about to ratify the reclassification of the Flaviviridae family, recognizing segmented viruses previously designated jingmenviruses as part of that family and proposing two genera to classify them: Jingmenvirus and Guaicovirus. These proposals do not include clear criteria to classify jingmenviruses and related sequences into species or genera. In order to determine such criteria, we generated a large sequence database from published and newly assembled sequences. Indeed, we screened public raw sequencing data from studies that did not search for or report jingmenvirus or related sequences, looking for new strains of previously described viruses. We then performed multiple sequence alignments and used the inferred percentage identity values to determine demarcation criteria based on the distribution of evolutionary distances upon pairwise comparisons. We report the identification of almost 60 libraries containing jingmenvirus and related sequences, in a wide range of sample types and geographical locations. Using these data and published sequences, we have determined that to be classified as a virus species, at least four segments are required, on which eight cut-off values in percentage identity (nucleotide and amino acid) are used for demarcation. The use of these criteria would enhance consistency in jingmenvirus taxonomy and provide a standardized framework for comparative genomics studies of these viruses, as they are still under-characterized.}, }
@article {pmid42101522, year = {2026}, author = {Yuan, C and Zhang, T and Huo, J and Liang, W and Wang, L}, title = {Comparative analysis of next-generation versus third-generation sequencing for pathogen detection in clinical samples: a diagnostic accuracy study.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42101522}, issn = {1573-0972}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; Prospective Studies ; *Communicable Diseases/diagnosis/microbiology ; *Bacteria/genetics/isolation &amp; purification/classification ; Viruses/genetics/isolation &amp; purification ; Bronchoalveolar Lavage Fluid/microbiology/virology ; Fungi/genetics/isolation &amp; purification ; *Molecular Diagnostic Techniques/methods ; }, abstract = {BACKGROUND: The rapid and accurate identification of pathogens is crucial for clinical management of infectious diseases. While Next-generation sequencing (NGS) has transformed pathogen detection, Third-generation sequencing (TGS) offers advantages in real-time analysis and long-read capabilities. This study comprehensively compares the diagnostic performance of NGS and TGS across diverse clinical samples.<br><br>METHODS: We conducted a prospective diagnostic accuracy study involving 105 clinical samples (58 bronchoalveolar lavage fluid, 28 whole blood, 19 other body fluids) from patients with suspected infections. All samples were analyzed using both NGS (BGI platform) and TGS (Nanopore platform). Diagnostic performance was evaluated against a composite reference standard incorporating clinical diagnosis, microbiological culture, and laboratory findings.<br><br>RESULTS: NGS demonstrated significantly higher sensitivity compared to TGS (95.9% vs. 82.4%, p&#x2009;<&#x2009;0.001), while TGS showed superior specificity (87.1% vs. 64.5%, p&#x2009;=&#x2009;0.012). The overall agreement between platforms was 85.7% (Kappa&#x2009;=&#x2009;0.702). NGS exhibited particular advantages in viral detection (32 vs. 8 detections, p&#x2009;<&#x2009;0.001) and fungal identification (28 vs. 18 detections, p&#x2009;=&#x2009;0.023), whereas both technologies showed comparable bacterial detection capabilities. The area under the ROC curve was 0.92 for NGS and 0.85 for TGS. Turnaround time was significantly shorter for TGS (median 8 h vs. 30 h, p&#x2009;<&#x2009;0.001).<br><br>CONCLUSION: NGS and TGS demonstrate complementary strengths in clinical pathogen detection. NGS offers superior sensitivity and enhanced detection of viral and fungal pathogens, making it suitable for comprehensive diagnostic evaluation. TGS provides rapid results with higher specificity, advantageous for time-critical clinical decisions. A combined or scenario-specific approach may optimize pathogen detection in clinical practice.}, }
@article {pmid42101699, year = {2026}, author = {Bharsakale, RD and Gubyad, MG and Jagannadham, PTK and Kokane, SB and Warghane, AJ and Kokane, AD and Ghosh, DK}, title = {Draft genome sequence CR-NGP1 strain of 'Candidatus Liberibacter asiaticus' (CLas) from the host Citrus reticulata (Nagpur mandarin) from Central India.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {6}, pages = {}, pmid = {42101699}, issn = {1573-0972}, support = {Grant No. F.No. 16-11/PP/ICAR-CRP/25-26//ICAR- Consortium Research Platform on Vaccine and Diagnostics/ ; }, mesh = {*Citrus/microbiology ; India ; *Genome, Bacterial ; *Plant Diseases/microbiology ; *Rhizobiaceae/genetics/isolation &amp; purification/classification ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Whole Genome Sequencing ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Base Composition ; Liberibacter ; }, abstract = {Huanglongbing (HLB, 'Candidatus Liberibacter asiaticus') is one of the most devastating pathogens in citrus domain. Here, we present the nearly complete genome sequence of a CR-NGP1 strain obtained a from symptomatic Nagpur Mandarin (Citrus reticulata) tree in the Nagpur region of Central India. High-throughput sequencing on the Illumina NovaSeq 6000 platform generated ~ 85.7 million paired-end reads, 63.5 million paired-end reads and 14.8 million paired-end reads for sample CLas_001, CLas_002 and CLas_003 each with 150 bp read length, respectively. Two assembly strategies were used: (i) reference-based assembly with SPAdes produced a draft genome of ~ 1.19 Mb with assembly comprised 149 contigs, with an N50 of 14,173 bp, longest contig of 39,711 bp, and an overall GC content of 36.27%. (ii) KBase CONCOCT binning v1.1 applied to all 3 samples produced a nearly complete CR-NGP1 genome of ~ 1,156,009 bases with assembly of 93 contig, with an N50 of 17,668 bp, a longest contig of 39,711 bp, and an overall GC content of 36.4%. This resource of a CLas genome from Central India provides important insights to understand genetic diversity of CLas strains and will facilitate comparative genomics and epidemiological studies of Huanglongbing.}, }
@article {pmid42101805, year = {2026}, author = {Li, Q and Yang, X and Zhu, H and Yang, S and Yin, G}, title = {A rare case of long-standing lupus vulgaris with psoriasiform manifestations diagnosed by mNGS: a case report.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42101805}, issn = {1435-4373}, abstract = {This report describes a rare case of lupus vulgaris mimicking psoriasis, undiagnosed for over 40 years. Conventional diagnostics, including histopathology and mycobacterial culture, failed to yield a definitive diagnosis. Ultimately, metagenomic next-generation sequencing (mNGS) of the skin tissue detected the Mycobacterium tuberculosis complex, confirming the infection. The patient showed marked clinical improvement following two months of dual-drug anti-tuberculosis therapy. This case highlights the clinical utility of mNGS for diagnosing atypical, long-standing cutaneous tuberculosis when conventional methods are negative, thereby preventing prolonged misdiagnosis and ensuring timely treatment.}, }
@article {pmid42102564, year = {2026}, author = {Long, Z and Zhang, B and Bing, H and Wu, Y}, title = {Identifying microbial candidates for assisted phytoremediation through long-term microbial succession and functional gene shifts across a 50-year chronosequence of vanadium-titanium magnetite tailings.}, journal = {Journal of hazardous materials}, volume = {512}, number = {}, pages = {142304}, doi = {10.1016/j.jhazmat.2026.142304}, pmid = {42102564}, issn = {1873-3336}, abstract = {Soil microorganisms are central to vegetation restoration in metalliferous wastes. However, within mine tailings restoration chronosequences, particularly those enriched with vanadium (V), the long-term successional dynamics of microbial communities, their functional potentials, and the functional partitioning between key microbial taxa and lower-abundance microbial lineages remain poorly understood. Here, we utilized metagenomic sequencing across a 50-year restoration chronosequence to investigate changes in the microbial community and functional genes related to plant growth-promotion (phosphorus, nitrogen, and iron acquisition) and V tolerance/bioreduction. The results demonstrated significant shifts in the microbial community after five years of restoration. At the phylum level, Actinobacteria, Acidobacteria, Pseudomonadota, and Gemmatimonadota were dominant. In early stages (< 15 years), nitrogen and phosphorus acquisition genes (e.g., nif, fix, phoD) were 1.3-2.5 times more prevalent than in later stages, whereas functional genes associated with V (e.g., napA, narG, nirS) increased 1.5- to 2-fold over time. Vanadium and nitrogen were the primary environmental factors regulating both community structure and the relative abundance of critical functional genes. Keystone taxa possessed more nitrogen and phosphorus acquisition genes (65% and 45%, respectively), while metagenome-assembled genomes (MAGs) were enriched in genes related to siderophore biosynthesis (71%) and denitrification (potential V bioreduction) (65%). Based on functional gene profiles, Bradyrhizobium, Allosphingosinicella, Baekduia, Sphingomicrobium, and Hylemonella were identified as promising microbial candidates for enhancing restoration in V-contaminated sites. This study enables the development of targeted microbial consortia to mitigate nutrient deficiency and V toxicity, directly informing the design of more efficient, stage-specific phytoremediation strategies in V-rich tailings.}, }
@article {pmid42102590, year = {2026}, author = {Feng, R and Wang, X and Zhang, X and Li, L and Gao, X and Li, J and Kang, J and Yu, X and Jia, S and Zheng, G and Shi, P}, title = {Hidden antibiotic resistance risks and key drivers during tertiary wastewater treatment deciphered by an integrated metagenomic framework.}, journal = {Environment international}, volume = {212}, number = {}, pages = {110281}, doi = {10.1016/j.envint.2026.110281}, pmid = {42102590}, issn = {1873-6750}, abstract = {Potential high-risk antibiotic resistance genes (ARGs) were considered as higher public health threats in wastewater treatment systems. While tertiary wastewater treatment processes (TWTPs) effectively remove conventional and emerging pollutants, their impact on ARGs with potential higher risk remains unclear. In this study, metagenomic assembly and binning were applied to profile potential-risk ARGs and identify key factors shaping their distribution during TWTPs. Results showed that potential-risk ARGs accounted for 34.32 ± 1.98% to 59.71 ± 1.55% of total ARGs, indicating their widespread persistence. Notably, DB significantly increased the relative abundance of potential-risk ARGs, particularly those conferring resistance to multidrug, bacitracin, and aminoglycoside. In parallel, DB treatment elevated the abundance of mobile genetic elements (MGEs), primarily transposase-related. DB treatment facilitated the co-occurrence of potential-risk ARGs and MGEs, especially multidrug and transposase/recombinase. Key bacterial hosts carrying potential-risk ARGs, such as Pseudomonas and Acinetobacter, were highly enriched after DB treatment, contributing substantially to the proliferation of these ARGs. In contrast, UV disinfection and CW treatment continuously reduced the abundance and risk levels of potential-risk ARGs, highlighting their complementary roles in mitigating antibiotic resistance risks during TWTPs. Variation partitioning analysis showed that bacterial community composition explained 36.15% of the variation in potential-risk ARG profiles, underscoring its primary role in ARG dynamics. Overall, this study provides genome-resolved insights into the hidden risks of ARGs and key drivers during TWTPs, highlights the necessity of optimizing operational parameters to mitigate antibiotic resistance dissemination.}, }
@article {pmid42102689, year = {2026}, author = {Wang, W and Jiang, H and Liang, C and Yang, Y and She, D and Cheng, G and Wang, H}, title = {Soil functional carbon fraction accrual in temperate forests is linked to understory herbs, soil nutrients and microbial alterations.}, journal = {Journal of environmental management}, volume = {407}, number = {}, pages = {129886}, doi = {10.1016/j.jenvman.2026.129886}, pmid = {42102689}, issn = {1095-8630}, abstract = {Enhancing stable soil organic carbon (SOC) storage is vital for climate change mitigation. This study challenges the tree-centric paradigm in forest carbon management by investigating the relative roles of trees and understory herbs in driving SOC sequestration in temperate forests of Northeast China. Analyzing 720 soil samples from a 7.2 ha experimental forest, we measured oxidizable SOC fractions and tested the hypothesis that the understory herb layer is a primary driver of SOC accrual, mediated by soil properties and microbial communities. Results strongly supported our hypotheses. Plots with dense, tall herbs exhibited significantly higher levels of active and passive carbon fractions (increases of 7%-16%, amplified to 21%-45% when accounting for soil nutrients, physiochemistry, and water-holding capacity), whereas tree size showed no significant effect. Soil nitrogen was the strongest predictor of SOC variation. Herbs intensified the positive SOC-nitrogen relationship and were positively associated with beneficial soil conditions (e.g., near-neutral pH), contrary to the weak or negative correlations observed for trees. Structural equation modeling revealed that herbs exerted significant direct and indirect positive effects on carbon fractions, while the effects of trees were nonsignificant. Metagenomic analysis identified two contrasting microbial phyla groups: "positive-SOC" phyla (e.g., Thaumarchaeota, Planctomycetes) associated with herbs and high SOC, and "negative-SOC" phyla (e.g., Chloroflexi, Gemmatimonadetes). These findings underscore the critical, underappreciated role of the understory herb layer in SOC sequestration, mediated through soil nutrient enhancement, soil acidity, water retention, and shifts in microbial communities. Forest management strategies aiming to maximize carbon storage should prioritize herb layer conservation alongside tree layer considerations.}, }
@article {pmid42102934, year = {2026}, author = {Chen, Y and Li, Y and Cheng, S and Ma, Y and Zhang, Y and Zhang, W and Xu, X and Liu, Z and Duan, X and Duan, H and Zhou, A and Li, X and Makinia, J}, title = {Brief aerobic pretreatment for stabilizing long-term caproate production from food waste via fungi-bacteria chain-elongating consortia.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134810}, doi = {10.1016/j.biortech.2026.134810}, pmid = {42102934}, issn = {1873-2976}, abstract = {Recovery of medium-chain carboxylic acids (MCCA) from food waste is constrained by low efficiency and instability. This study validated a short-term aerobic pretreatment (AP) strategy to enhance fungi-bacteria synergy. In batch tests, AP (0.2 vvm) achieved optimal caproate titers of 22.32 ± 1.56 g COD/L. The pretreatment enriched ethanol-producing yeasts and lactate-producing bacteria, establishing a robust co-electron donor pool. Metagenomic analysis revealed that this synergy suppressed the competing tricarboxylic acid cycle, redirecting carbon flux towards reverse β-oxidation (RBO) pathway and providing essential precursors for Clostridium_sensu_stricto_12. In a 134-day semi-continuous operation, AP sustained high titers (17.2-22.1 g COD/L) through a specialized guild dominated by the Ruminococcaceae bacterium BL-6, avoiding the systemic performance deterioration observed in controls. Life cycle assessment (LCA) confirmed a >60% carbon footprint reduction compared to conventional routes. Short-term aerobic pretreatment effectively regulates microbial succession to stabilize low-carbon MCCA production from food waste.}, }
@article {pmid42102935, year = {2026}, author = {Li, J and Wu, Y and Li, X and Gao, R and Chen, X and Zhang, S and Zhang, J and Zhang, L and Zhang, S and Peng, Y}, title = {Partial Denitrification-Mediated anammox Evolution in anoxic Compartments: Deciphering metabolic activity and microbial community.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134812}, doi = {10.1016/j.biortech.2026.134812}, pmid = {42102935}, issn = {1873-2976}, abstract = {The integration of partial denitrification (PD, NO3[-]→NO2[-]) with anaerobic ammonium oxidation (Anammox) in anoxic biofilm systems presents a transformative approach for enhanced nitrogen removal from municipal wastewater. Through a 7-month comparative analysis of spatially stratified anoxic zones in an anaerobic-anoxic-oxic bioreactor treating real wastewater (NH4[+]: 47.6 ± 4.7 mg N/L; COD: 154.8 ± 29.6 mg/L), this study achieved 71.8 ± 5.8% total nitrogen removal (effluent TN: 12.9 ± 3.9 mg N/L), aiming to propose optimization frameworks targeting biofilm carrier deployment in the anoxic zone. Test results showed that functional dominance partitioning emerged as a key determinant: the first anoxic zone (A1) exhibited peak anammox activity (0.034 kg N/m[3]/d) via rapid acetate-driven nitrate reduction, while the third zone (A3) sustained maximum Ca. Brocadia abundance (1.7%). Metagenomic sequencing further revealed that the highest ratio of NO3[-] reductase gene (narG) to NO2[-] reductase genes (nirS, nirK) was 2.06 in A3 compared to 1.39-1.68 in the other biofilms, indicating a stronger ability to supply NO2[-] to anammox. Carbon metabolic gene distribution revealed A1's acetate/glucose preference versus A3's endogenous metabolism dominance (elevated TCA cycle genes). This study proposes an innovative biofilm management framework for energy-efficient municipal wastewater treatment: front-positioned carriers maximize anammox nitrogen removal under moderate carbon-to-nitrogen ratios (3-5), while rear-positioned units secure anammox biomass retention during carbon surges.}, }
@article {pmid42102938, year = {2026}, author = {Wu, Y and Yang, X and Deng, Y and Zhao, S and Wang, D and Zhang, W}, title = {Performance of microbial deodorization on anaerobically digested biosolids and odor rebound under rewetting conditions.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134809}, doi = {10.1016/j.biortech.2026.134809}, pmid = {42102938}, issn = {1873-2976}, abstract = {Odor control is a critical bottleneck in the quality upgrade of anaerobically digested biosolids for land application. The efficacy of microbial deodorization on biosolids has been scarcely evaluated and the mechanisms behind remain unclear. This study applied a sensory-instrumental combined analysis approach to evaluate the deodorization efficiency of two microbial agents on biosolids and odor recurrence upon rewetting. Results show that treatment with microbial agent could reduce the odor intensity and mitigate ammonia emission, yet it failed to completely eliminate the odor. The volatile profile of biosolids is complex, including various N-, S-, O-containing organic and inorganic compounds that collectively contribute to the malodor of biosolids. Rewetting of biosolids induced a rapid odor rebound to varying degrees depending on the maturity of biosolids. Deodorization treatment enhanced the solubility, transformation of biosolids organic matter and increased the humic-like characteristics of WEOM and reshaped the bacterial community showing enrichment of functional taxa (e.g., Actinobacteriota and Chloroflexi). Metagenomic analysis revealed that the key nitrogen-cycling genes (ureC, narG) were suppressed, thereby limiting the generation of NH3 and other related odorants. These findings elucidate a mechanistic linkage between microbial dynamics and the odor generation potential of biosolids, and highlight the critical role of moisture management in governing odor generation and post-deodorization biological stability of biosolids.}, }
@article {pmid42102997, year = {2026}, author = {Li, Y and Yu, T and Li, Z and Peng, J and Zhang, Y and Wang, Q and Xie, S}, title = {From high- to low-risk resistomes: Dynamic shifts in antibiotic resistance during biofilm development in a full-scale biological activated carbon fluidized bed.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128291}, doi = {10.1016/j.envpol.2026.128291}, pmid = {42102997}, issn = {1873-6424}, abstract = {Antibiotic resistance genes (ARGs) in drinking water bioreactor biofilms pose significant public health risks, yet existing studies focus on mature biological activated carbon (BAC) biofilms, overlooking the early colonization stage critical for ARG origin and dissemination. This gap hinders understanding of ARG dynamics and resistance mechanisms during drinking water BAC biofilm development. Using metagenomics, we first systematically investigated ARG risk dynamics in a full-scale biological activated carbon fluidized bed (BACFB)-a state-of-the-art drinking water technology-across operational days 7-187. Microbial communities and ARG profiles clustered distinctively into early (days 7-37) and late (days 82-187) stages. Upon biofilm stabilization, total ARG abundance significantly decreased (P< 0.05), with high-mobility/high-risk ARGs (sulfonamide-, florfenicol-, aminoglycoside-type) replaced by low-mobility types (rifamycin-, fosfomycin-type). These shifts were correlated with reduced abundance of Pseudomonadota (P < 0.05), increasing trends in the abundance of Bacillota and Actinomycetota (P < 0.1), and decreased abundance of mobile genetic elements, particularly plasmids (P < 0.01). Pathogenic ARGs shifted from aminoglycoside/tetracycline to rifamycin, with Bacillus thuringiensis/Streptococcus pneumoniae (rphB-carrying) as key late-stage risks. Rank I/II and emerging ARGs (mcr, tet(X)) also declined. Our findings uncover the dynamics of ARG risks during BAC biofilm development and highlight the underlying ecological drivers, providing a robust scientific basis for targeted risk mitigation in drinking water treatment systems.}, }
@article {pmid42088457, year = {2026}, author = {Li, P and Kahsen, J and Olsson-Francis, K and Green, SJ}, title = {Using Carrier DNA in Ultra-Low Input Library Preparations for Next-Generation Sequencing.}, journal = {Journal of biomolecular techniques : JBT}, volume = {37}, number = {1}, pages = {18-26}, pmid = {42088457}, issn = {1943-4731}, mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Gene Library ; *DNA/genetics ; Polymerase Chain Reaction/methods ; *Metagenomics/methods ; Metagenome/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The purpose of this study was to evaluate the use of carrier DNA (i.e., exogenous DNA spike-in) for shotgun metagenome sequencing of ultra-low levels (less than 50 picograms) of metagenomic DNA. The study hypothesized that carrier DNA would improve the robustness of library preparation for samples with DNA concentrations that are below detection by providing a tangible amount of known DNA thereby bringing total DNA concentrations closer to recommended input ranges for metagenomic library kits. The study employed adaptive polymerase chain reaction (PCR) cycling using an iconPCR instrument (N6tec) to allow dynamic thermocycling until a sufficient library for sequencing was amplified, regardless of the input DNA concentration. Libraries were sequenced and mapped in order to reference genomes of Lambda and mock community organisms, and outcome measures included total reads, on-target reads, evenness of coverage across 10 organisms within each mock community, and PCR duplication rate. The study demonstrated that libraries can be prepared down to 50 fg of input DNA, but there is a strong correlation between input DNA concentration and PCR duplication rate. The utility of spiking in carrier DNA is equivocal as it has mild negative impacts on the observed distribution of mock communities and serves as a loss of sequencing output. Although the loss of sequencing capacity due to carrier DNA can be partially offset by a reduced loss of data from PCR duplication, carrier DNA spike-in is not recommended for routine library preparation of ultra-low input samples. Adaptive cycling allows for appropriate cycling conditions when input DNA concentrations are below detection.}, }
@article {pmid42089121, year = {2026}, author = {Bhagat, S and Kushwaha, S and Singh, S}, title = {Targeted Gut Delivery of Zn, Cu, and Mn Nanominerals Alleviates Oxidative Stress by Activating Endogenous SOD Enzymes.}, journal = {Advanced healthcare materials}, volume = {}, number = {}, pages = {e71209}, doi = {10.1002/adhm.71209}, pmid = {42089121}, issn = {2192-2659}, support = {C0046//National Institute of Animal Biotechnology, Hyderabad/ ; }, abstract = {Trace minerals such as Zn, Cu, and Mn are essential for maintaining cellular redox balance as cofactors of key antioxidant enzymes, including SOD1 and SOD2. However, their oral supplementation is often limited by poor stability in the acidic gastric environment and low intestinal absorption. Here, we report the synthesis of methionine-coated-ZnO (Met-ZnO), ascorbic acid-coated Cu2O (AA-Cu2O), and dextran-coated MnO2 (Dex-MnO2) nanominerals, followed by encapsulation into pH-responsive microcapsules (NMs-MCap) for targeted intestinal delivery. The nanomineral mixture demonstrated strong antioxidant activity at physiological pH by scavenging superoxide radicals, hydrogen peroxide, and ABTS[•+] radicals. In intestinal epithelial (IEC-6) cells, nanominerals significantly alleviated BSO-induced oxidative stress, reducing apoptosis, necrosis, and intracellular ROS accumulation. Oral administration of NMs-MCap in Zn, Cu, and Mn-deficient rats elevated mineral levels in blood and liver, mitigated BSO-induced oxidative damage, reduced lipid peroxidation and pro-inflammatory cytokines, and preserved tissue architecture. Importantly, oral supplementation restored SOD1 and SOD2 expression in key organs, supporting enhanced endogenous antioxidant defense. Metagenomic analysis revealed that mineral deficiency, combined with oxidative stress, caused gut dysbiosis, reducing beneficial taxa and enriching opportunistic ones. Nanomineral supplementation restored microbial balance, increased SCFA-producing bacteria, and improved antioxidant and metal-handling functions, establishing NMs-MCap as a safe, targeted antioxidant strategy supporting host health.}, }
@article {pmid42089290, year = {2026}, author = {Banday, MM and Banday, S and Rahman, M and Harrison, AO and Singh, N and Moore, RM and Khan, MM and Shankar, S and Goda, Y and Coppolino, A and Movval, N and Stutts, S and Woolley, A and Dishaw, L and Goldberg, H and Mebratu, Y and Polson, SW and Patel, KN and Gaggar, A and Hayes, D and Krishnamoorthy, N and Gewurz, BE and Washko, G and Tesfaigzi, Y and Rehman, R and Sharma, NS}, title = {Anellovirus-Mediated Interferon Dysregulation Enhances Virus-Induced Lung Injury.}, journal = {American journal of respiratory cell and molecular biology}, volume = {}, number = {}, pages = {}, doi = {10.1093/ajrcmb/aanag048}, pmid = {42089290}, issn = {1535-4989}, abstract = {BACKGROUND: The lung virome (LV) and its interactions with the host-immune system leading to allograft injury after lung transplantation are not well characterized.<br><br>METHODS: Shotgun metagenomics and qPCR was performed on a multicenter BAL/serum cohort from lung transplant recipients (LTRs). Viral constructs from betatorquevirus clade and group 2 TTVs were transfected in primary bronchial epithelial cells (PBECs) or airways of C57BL/6 mice with and without exposure to Influenza A (IAV) or RSV.<br><br>RESULTS: LV in LTRs was dominated by viruses from the family Anelloviridae. CLAD LV was characterized by the enrichment of betatorquevirus clade (BTV). Validation in an independent cohort confirmed BTV abundance in CLAD BAL, serum and lung tissues. BTV ORF1 protein (kV1) suppressed PBEC IFN&#x3b1; and IFN&#x3b3; responses by preventing intranuclear STAT translocation. Co-culture of IAV or RSV in kV1 transfected PBECs significantly augmented replication of RSV and IAV and increased cellular injury. Likewise, in-vivo transfection of kV1 increased replication and lung injury associated with IAV.<br><br>CONCLUSION: Our work illuminates a novel virus-associated dysregulation of host interferon responses that promote lung injury associated with respiratory viral infections and, in part, explain differential host responses to viral infections after lung transplantation.}, }
@article {pmid42089622, year = {2026}, author = {Mustajab, M and Basler, N and De Smet, L and de Graaf, DC and Matthijnssens, J}, title = {Coding-complete genome sequence of a divergent black queen cell virus strain identified from honeybees (Apis mellifera) in Romania.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0012226}, doi = {10.1128/mra.00122-26}, pmid = {42089622}, issn = {2576-098X}, abstract = {We report the 8,451-nt coding-complete genome sequence of a divergent black queen cell virus strain (BQCV-Ro). This strain was identified via retrospective analyses of metagenomic virome data of Apis mellifera samples from Europe. The genome assembly is supported by extensive read mapping, with 100% horizontal coverage and a mean sequencing depth of ~338,171×. and shares 94.3% identity with the BQCV Yeongdeok isolate.}, }
@article {pmid42090957, year = {2026}, author = {Kämpfer, P and Lipski, A and Lawrence, KS and Olive, WR and Newman, MM and McInroy, JA and Viver, T}, title = {Pseudomonas corni sp. nov., Pseudomonas oplopanacis sp. nov., Pseudomonas salicis sp. nov., Pseudomonas rosaeacicularis sp. nov., Pseudomonas artemisiae sp. nov., Pseudomonas imperatae sp. nov. and Zestomonas ipomoeae sp. nov., isolated from rhizospheres showing plant growth promoting potential.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {4}, pages = {126719}, doi = {10.1016/j.syapm.2026.126719}, pmid = {42090957}, issn = {1618-0984}, abstract = {Several bacterial strains affiliated with the genera Pseudomonas and Zestomonas were isolated from rhizosphere samples and screened for plant growth-promoting (PGP) traits. Nine strains were analyzed polyphasically, showing ANI and dDDH values below or near species thresholds, together with phenotypic and biochemical traits supporting their differentiation. Genomic analyses revealed a repertoire of PGP-associated functions, including vitamin and cofactor biosynthesis (riboflavin, cobalamin, and thiamin), and high-affinity nutrient acquisition systems as phosphate transporters and phosphonate utilization. All strains encoded traits relevant to the rhizosphere inferred from genome annotation, including genes involved in auxin and cytokinin biosynthesis, oxidative stress tolerance, dissimilatory nitrate reduction, sulfur assimilation, and siderophore production. Metagenomic screening showed that most species are globally distributed across plant-associated, soil, freshwater, and animal-associated habitats. Based on phylogenetic, genomic, and phenotypic evidence, the strains represent seven novel species: Pseudomonas rosaeacicularis sp. nov., with AK-381[T] as the type strain (= LMG 34445[T] = CCM 9596[T]); Pseudomonas corni sp. nov., with AK-10[T] as the type strain (= CCM 9599[T] = LMG 34325[T]); Pseudomonas oplopanacis sp. nov., with AK-188[T] as the type strain (= CCM 9593[T] = LMG 34326[T]); Pseudomonas salicis sp. nov., with AK-309[T] as the type strain (= CCM 9595[T] = LMG 34328[T]); Pseudomonas artemisiae sp. nov., with DT-100[T] as the type strain (= LMG 32880[T] = DSM 115114[T] = CCM 9281[T]); Pseudomonas imperatae sp. nov., with ST-212[T] as the type strain (CCM 9594[T] = LMG 34330[T]); and Zestomonas ipomoeae sp. nov., with ST-55[T] as the type strain (LMG 32881[T] = CCM 9283[T] = DSM 115239[T]).}, }
@article {pmid42091967, year = {2026}, author = {Vinayagam, S and Bhowmick, IP and Rajendran, D and Arumugam, DK and Sekar, K and Renu, K and Kaur, H and Sattu, K}, title = {Genetic diversity and gut microbiome of Anopheles mosquitoes in Tamil Nadu by using COI DNA barcoding and 16S rRNA metagenomics.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-48529-9}, pmid = {42091967}, issn = {2045-2322}, support = {NER/85/2022-ECD-I//ICMR- Adhoc/ ; }, abstract = {Anopheles mosquitoes transmit infections to humans. Identifying the right mosquito species is crucial for vector control evaluation. This study uses COI gene DNA barcoding and 16S rRNA metagenomics to show the genetic diversity and gut microbial profile of undiscovered mosquito species. Three genera were found, including eight morphologically different Anopheles mosquitoes, and six mosquito species were molecularly validated, including An. moghulensis. The analysis of genetic diversity indicated that there is a state of balanced natural selection present. The species An. maculatus s.s. and An. stephensi exhibited nearly identical mutations, while An. moghulensis demonstrated evidence of purifying selection within the studied population. The gut microbiomes of An. moghulensis (149,377 reads), An. maculatus (51,016 reads), and An. dravidicus (33,126 reads) mosquitoes were also revealed. Afipia felis and Prevotella copri were the leading bacterial species, followed by other phyla including Proteobacteriota, Spirochaetes, and Firmicuteota. In An. moghulensis, alpha diversity assessments of Chao I incidence were dominating, whereas Shannon index was plentiful in An. maculatus s.s. mosquitoes. The mosquito's distinct bacterial species and shared microbial community are shown in the Venn diagram. These results suggest that the discovered bacterial taxa might be exploited to create vector control techniques for vector-borne illnesses.}, }
@article {pmid42092044, year = {2026}, author = {Loukas, A and Kalaentzis, K and Venetsianou, NK and Damianou, C and Paragkamian, S and Lagani, V and Jensen, LJ and Pafilis, E}, title = {CCMRI: a classification and curated database of climate change-related microbiome studies.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-51914-z}, pmid = {42092044}, issn = {2045-2322}, support = {2772//Hellenic Foundation for Research and Innovation/ ; }, abstract = {Climate Change (CC) is reshaping all ecosystem processes and structures. Microbial data provide valuable insights into how microbial processes contribute to CC and how CC, in turn, alters microbial communities. However, the growing volume of environmental genomics data makes identifying CC-related records challenging. The Climate Change Metagenomic Record Index (CCMRI) has been developed to harvest metagenomic/microbiome records pertaining to CC and to provide researchers with a curated database of CC-related microbiome studies (https://ccmri.hcmr.gr). To guide interpretation, the database's 169 metagenomic studies have been labelled according to their relation to CC as CC-caused, CC-causing, and CC-mitigating. They have also been annotated with the CC phenomena they explore, like methane production, temperature rise, permafrost thawing, greenhouse gas emission, methanotrophy, and ocean acidification. To ease navigation, they have also been classified according to their biome as aquatic, terrestrial, host-associated, and engineered. The CCMRI database was initially constructed through manual curation of all aquatic and terrestrial studies in the MGnify resource. It was then expanded with the help of the CCMRI curation-assistant system. This leveraged Large Language Models to scan the remaining MGnify studies, filtered them for relevance, and proposed candidates for inclusion. With a recall greater than 90%, the system achieved high accuracy in identifying CC-related studies. The final decisions on CC-relatedness and categorization were performed by a human curator. This approach combines the efficiency of automation with human oversight and greatly reduces the curation effort, ensuring sustainability and scalability.}, }
@article {pmid42092708, year = {2026}, author = {Ye, Y and Miao, H and Fang, W and Ni, J and Yang, K and Gu, P and Ren, X and Zhang, Z}, title = {Deciphering dual effects of humic substrates on anaerobic ammonium oxidation: from metabolic facilitation to systemic nitrogen flux interference.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134791}, doi = {10.1016/j.biortech.2026.134791}, pmid = {42092708}, issn = {1873-2976}, abstract = {Anaerobic Ammonium Oxidation (Anammox) is a promising strategy for nitrogen removal from landfill leachate due to its energy efficiency and independence from external carbon sources. However, continuous changes in recalcitrant organic compounds (i.e., fulvic acid (FA) and humic acid (HA)) at different landfill stages have potential effect on stability of anammox process. The present study systematically investigated the successive change of FA/HA concentrations and ratio that induced by different landfill age on anammox process in a laboratory-scale moving bed biofilm reactor operated over 200 days. Results showed a distinct dual-effect transition of FA and HA on the anammox process. 50-100 mg/L FA significantly improved nitrogen removal, achieving a peak total nitrogen removal efficiency (TNRE) of 91%. In contrast, the introduction of HA (100-200 mg/L) triggered a decline in TNRE to 80% and caused substantial nitrate (NO3[-]-N) accumulation. Microbial analysis revealed that FA-driven carbon abundance stimulated Candidatus Kuenenia and DNRA-functional Paracoccus and Bacillus, whereas HA suppressed DNRA bacteria in favor of nitrification. Metagenomic analysis showed that the electron shuttle and carbon source characteristics of FA enriched the relative abundance of energy metabolism genes (i.e., F-type ATPase) and quorum sensing genes (i.e., lamB), accelerating the anammox and denitrification process. However, HA interfered with the nitrogen metabolic flux via suppressing denitrification process (i.e., napA/B and nirS) and promoting nitrification genes (i.e., amoA and nxrA/B), leading to the accumulation of NO3[-]-N. These findings provide a mechanistic basis for optimizing anammox processes under varying humic substance conditions in landfill leachate treatment.}, }
@article {pmid42092716, year = {2026}, author = {Chai, Z and Chen, H and Cui, J and Song, C and Zheng, Y and Li, Y and Gao, T and Zheng, M}, title = {Micromolar chlorate sensitivity of wastewater-associated comammox Nitrospira: Endogenous toxification mechanism and implications for nitrification management.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134789}, doi = {10.1016/j.biortech.2026.134789}, pmid = {42092716}, issn = {1873-2976}, abstract = {Chlorate (ClO3[-]) is widely employed as a specific inhibitor of nitrite-oxidizing bacteria (NOB) to differentiate the contributions of ammonia-oxidizing microorganisms (AOMs). However, the discovery of completed ammonia oxidizing (comammox) Nitrospira, which performs both ammonia and nitrite oxidation, challenges the assumed specificity of chlorate, raising the question of whether it also inadvertently inhibits the ammonia oxidation activity of comammox Nitrospira, potentially leading to an underestimation of total ammonia oxidation activity in mixed communities. This study investigates the inhibitory kinetics and mechanisms of chlorate on wastewater-associated comammox Nitrospira. Batch assays revealed that comammox ammonia oxidation was hypersensitive to chlorate, with a half-maximal inhibitory concentration (IC50) of 9.11 µM, orders of magnitude lower than canonical NOB inhibition levels. Metabolic assays showed that 10 μM chlorate reduced ammonia oxidation activity to 49.1% during exposure, with recovery requiring multiple cultivation cycles. Integrated metagenomic and meta-transcriptomic analyses uncovered an endogenous toxification mechanism: chlorate is reduced by nitrite oxidoreductase (NXR) to cytotoxic chlorite, which triggers the upregulation of chlorite dismutase (CLD) and reactive chlorine species (RCS) defense genes, ultimately leading to metabolic arrest. This study confirms the inhibitory effect of chlorate on comammox Nitrospira and deciphers its RCS-mediated mechanism, emphasizing the need for caution when using chlorate-based assays to assess ammonia oxidation activity and providing a theoretical basis for selectively suppressing comammox Nitrospira in WWTPs.}, }
@article {pmid42092717, year = {2026}, author = {Fu, D and Ma, H and Zhang, J and Wang, H and Wu, Y and Ge, L and Fan, C and Wu, S and Zhang, S and Gao, H and Chen, Z}, title = {Interplay of quorum-sensing signals (homoserine lactone/penicillic acid) and nitrate in regulating microbial processes: As(III) immobilization, CH4 and N2O emission in constructed wetlands.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134788}, doi = {10.1016/j.biortech.2026.134788}, pmid = {42092717}, issn = {1873-2976}, abstract = {The concurrent mitigation of arsenic (As) pollution and greenhouse gas (GHG) emissions in constructed wetlands represents a significant challenge, largely due to the complex interactions within microbial-driven elemental cycles. This study investigated the regulatory roles of distinct quorum-sensing (QS) signals, i.e., C4-homoserine lactone (C4-HSL, a promoter) and penicillic acid (PA, a quencher), in concert with nitrate on the microbial-mediated transformation of As and GHGs (CH4 and N2O) in flooded paddy soil microcosms. The results revealed that the nitrate + C4-HSL treatment concurrently enhanced As(III) immobilization (increased by 8%) while suppressing CH4 and N2O emissions (by 7% and 56%) over a 24-day incubation period, compared to nitrate alone. Conversely, the nitrate + PA treatment inhibited As(III) oxidation (∼17.6 µM residual As(III) leaching) and promoted the accumulation of GHGs (increasing CH4 and N2O emissions by 8% and 77%). Mechanistically, C4-HSL activated the complete QS signaling network under nitrate amendment. This activation led to the enrichment of key functional microbial consortia (e.g., Pseudogulbenkiania, Streptomyces and Alicyclobacillus), an increase in relative abundance of critical metabolic genes (e.g., aox, pmo, nosZ, cpaF, tadA and cco), stimulated the secretion of protein-rich extracellular polymeric substances, and enhanced overall electron transfer system activity. These coordinated changes fostered coupled biogeochemical processes such as Fe(II)/Mn(II)-coupled denitrification and denitrifying AOM. In contrast, PA disrupted native QS communication, suppressed the aforementioned functional microbial groups and altered biofilm composition. Overall, the application of specific QS signals with nitrate exhibits the potential to directionally steer microbial community function, thereby highlighting a promising microbial-level strategy for the co-management of As and GHGs in engineered wetland systems.}, }
@article {pmid42092753, year = {2026}, author = {Palanisamy, M and Babalola, OO and Ramalingam, S}, title = {Shotgun metagenomic dataset of leaf endophytic microbiome of the garden sage (Salvia officinalis L.).}, journal = {BMC genomic data}, volume = {27}, number = {1}, pages = {}, pmid = {42092753}, issn = {2730-6844}, support = {CMRG2400927//Chief Minister`s Research Grant (CMRG), Government of Tamil Nadu, India/ ; }, mesh = {*Salvia officinalis/microbiology ; *Plant Leaves/microbiology ; *Metagenomics ; *Endophytes/genetics/classification ; *Microbiota ; *Metagenome ; Bacteria/genetics/classification ; Fungi/genetics ; }, abstract = {OBJECTIVES: Garden sage (Salvia officinalis L.) is a traditional medicinal plant known for its rich bioactive secondary metabolites. However, there is limited information about the diversity of endophytic microbial communities, including bacteria, fungi, archaea, and viruses. Therefore, the study employs shotgun metagenomics to generate and make publicly available a dataset representing the leaf endophytic microbiome of Salvia officinalis.<br><br>DATA DESCRIPTION: Metagenomic DNA was extracted from leaves of S. officinalis collected as three biological replicates and sequenced using the Illumina NovaSeq X platform. Host-derived and contaminant sequences were removed by mapping reads to the S. officinalis reference genome using BWA-MEM. The resulting high-quality FASTQ files were analyzed to characterize the taxonomic composition of the endophytic microbiome using Kraken2-based classification.}, }
@article {pmid42093069, year = {2026}, author = {Yuan, J and Li, J and Jin, L and Ye, J and Zhang, Z}, title = {Human herpesvirus-6B infection leading to hemophagocytic lymphohistiocytosis in an adult: a case report.}, journal = {Journal of medical case reports}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13256-026-06071-2}, pmid = {42093069}, issn = {1752-1947}, abstract = {BACKGROUND: Hemophagocytic lymphohistiocytosis (HLH) secondary to human herpesvirus-6B (HHV-6B) infection is rare in immunocompetent adults.<br><br>CASE PRESENTATION: We report the case of a 43-year-old East Asian (Chinese) woman who developed HLH, presenting with persistent fever, jaundice, and cytopenias. Metagenomic next-generation sequencing (mNGS) identified HHV-6B in both peripheral blood and liver tissue, thereby establishing the etiologic diagnosis. Prompt initiation of antiviral therapy with ganciclovir, combined with corticosteroids and intravenous immunoglobulin, resulted in rapid clinical remission.<br><br>CONCLUSIONS: This case highlights the critical importance of early pathogen identification using mNGS and timely immunomodulatory treatment for improving outcomes in adult patients with virus-associated HLH.}, }
@article {pmid42093272, year = {2026}, author = {Li, C and Zhang, X and Yang, Y and Zeng, H and Shi, Y and Zhang, J and Liu, L and Zhu, C and Zhang, Z and Li, C and Wang, X and Bai, X and Deng, H and Li, Q}, title = {Bifidobacterium animalis suppresses melanoma progression and activates anti-tumor immunity by inhibiting YAP1 expression in CD8+ T cells.}, journal = {Cancer biology &amp; medicine}, volume = {}, number = {}, pages = {}, doi = {10.20892/j.issn.2095-3941.2025.0652}, pmid = {42093272}, issn = {2095-3941}, support = {82403246//National Natural Science Foundation of China/ ; 2025A04J4030//Guangzhou Science and Technology Project/ ; }, abstract = {OBJECTIVE: The probiotic, Bifidobacterium animalis, (B. animalis) is known to provide health benefits in humans. This study investigated the role of B. animalis in suppressing malignant melanoma progression and modulating tumor immunity.<br><br>METHODS: Bifidobacterium spp. were isolated from human faeces and verified by whole-genome sequencing. The anti-tumor effects were assessed in B16-F10 melanoma cells. B. animalis efficacy was further evaluated in a syngeneic murine model. Immune profiling was performed with flow cytometry and CD8[+] T cell dependency was tested with antibody depletion. Functional metabolites were analyzed by liquid chromatography-mass spectrometry (LC-MS). Transcriptome sequencing elucidated the YAP1 mechanism in CD8[+] T cells. Gut microbiota composition was assessed via shotgun metagenomic sequencing.<br><br>RESULTS: Among the selected Bifidobacterium spp., B. animalis and its conditioned medium effectively inhibited melanoma cell proliferation. Oral administration of B. animalis significantly reduced the growth of B16-F10 allografts, accompanied by an increase in tumor-infiltrating effector T cells. The bioactive component of B. animalis was identified as a < 3-kDa non-protein fraction containing mannose, which phenocopied the anti-tumor and immunostimulatory effects of B. animalis. Microbiota profiling revealed probiotic enrichment in mannose-treated mice. CD8[+] T cell depletion abrogated mannose efficacy. Combination therapy with B. animalis and anti-PD-1 synergistically enhanced tumor control and T cell activation. Mechanistically, the bioactive fraction and mannose downregulated YAP1 expression in CD8[+] T cells.<br><br>CONCLUSIONS: B. animalis suppresses melanoma tumorigenesis in mice by restoring gut microbiota and secreting functional mannose. Mannose enhances anti-PD-1 efficacy by inhibiting YAP1 expression in CD8[+] T cells, thereby improving effector function. B. animalis may serve as a preventive measure for melanoma management.}, }
@article {pmid42093327, year = {2026}, author = {Wang, S and Li, S and Lyu, H and Zhi, W and Dang, Z and Guo, R and Zhu, X and Ji, G}, title = {Quantifying the Contribution of Cryptic Sulfide-Driven Autotrophic Denitrification to N2O Production in a Seasonally Hypoxic River-Reservoir System.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c03313}, pmid = {42093327}, issn = {1520-5851}, abstract = {Sulfur-autotrophic denitrification (S-ADN) has been frequently reported in inland waters, yet its quantitative contribution to nitrous oxide (N2O) productions remains poorly constrained. By combining field sampling, enrichment cultures, stable isotopes, and metagenomic analysis, we quantified S-ADN-derived N2O productions in an oligotrophic river-reservoir system and validated the universality of our approach across diverse aquatic ecosystems. A Thiobacillus-dominated S-ADN enrichment culture was successfully established over 218 days of continuous supplementation with reduced sulfur compounds, yielding critical isotopic signatures for source partitioning (δ[15]N[Bulk], average N isotopic composition; δ[18]O; and δ[15]N[SP], site preference). Then, the multi-isotope Bayesian model revealed that S-ADN (14.8%) and nitrifier denitrification (NDN, 21.1%) rapidly occupied the ecological niche of heterotrophic denitrification (HDN, 8.6%) to total microbial N2O sources under organic carbon-limited conditions. The cryptic sulfur cycle supplies a considerable pool of electron donors for S-ADN under low-sulfide conditions. Autotrophic denitrifiers (e.g., Thiobacillus, Sulfuritalea) exhibited significant synergistic interactions with ammonia-oxidizing archaea (AOA, Nitrosarchaeum), while ammonia-oxidizing bacteria (AOB, Nitrosomonas) and nitrite-oxidizing bacteria (NOB, Nitrospira) jointly completed nitrification─with Nitrosomonas further competing for nitrite to drive NDN. This study advances the quantitative assessment of S-ADN's role in N2O production and provides novel insights into microbial community interactions in oligotrophic aquatic systems.}, }
@article {pmid42093770, year = {2026}, author = {Niu, S and Guo, L and Li, Z and Liu, Y and Zhao, L}, title = {Clinical utility of metagenomic next-generation sequencing in the diagnosis of severe influenza complicated by invasive pulmonary aspergillosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1746504}, pmid = {42093770}, issn = {2235-2988}, mesh = {Humans ; *Invasive Pulmonary Aspergillosis/diagnosis/microbiology/complications ; Male ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Influenza, Human/complications/diagnosis ; Retrospective Studies ; Bronchoalveolar Lavage Fluid/microbiology ; Sensitivity and Specificity ; *Metagenomics/methods ; Mannans/blood ; Galactose/analogs &amp; derivatives ; Aged ; ROC Curve ; Adult ; China ; }, abstract = {OBJECTIVE: The incidence and mortality of severe influenza complicated by invasive pulmonary aspergillosis (IPA) have risen markedly in recent years. This study aimed to evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) for detecting IPA in patients with severe influenza.<br><br>METHODS: Severe influenza patients with suspected of having IPA admitted to Xinxiang Central Hospital, Henan Province, China, from March 2020 to September 2025 were retrospectively enrolled. Bronchoalveolar lavage fluid (BALF) and blood were collected for fungal culture, galactomannan (GM) assay, and mNGS. Final classification into IPA and non-IPA groups was based on composite clinical and microbiological criteria. Sensitivity, specificity, and receiver operating characteristic curves were used to compare the diagnostic performance of the three methods.<br><br>RESULTS: Comparison with traditional fungal culture and GM testing, mNGS provided significantly faster results. Among 189 patients suspected of severe influenza-associated IPA, mNGS demonstrated a sensitivity of 72.1% and a specificity of 80.2%. Its sensitivity was higher than that of fungal culture (28.6%), serum GM testing (37.6%), and BALF GM testing (44.1%); however, its specificity was slightly lower than that of fungal culture (89.5%), serum GM testing (84.3%), and BALF GM testing (81.3%). The area under the ROC curve (AUC) for mNGS was 0.76, which is higher than that for BALF GM testing (0.63), serum GM testing (0.61), and fungal culture (0.59). The combined diagnostic approach yielded an AUC of 0.83.<br><br>CONCLUSION: mNGS offers a rapid, sensitive and accurate solution for invasive pulmonary aspergillosis in severe influenza patients. It outperforms conventional fungal culture and galactomannan assays. Integrating mNGS with traditional diagnostic methods could substantially improve early detection and overall yield of IPA.}, }
@article {pmid42094492, year = {2026}, author = {Shan, Y and Pucci, N and Berns, C and Hoogendijk, R and Beijnvoort, M and Li, S and Sánchez-Cano, A and Kramer, G and Du, W and Mende, DR and Jan van Dijk, AD and Wortel, M and Zhang, J}, title = {A bifidobacterial enzyme orchestrates ecology and function of infant gut bacterial community.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.28.718440}, pmid = {42094492}, issn = {2692-8205}, abstract = {Human milk oligosaccharides (HMOs) are abundant and structurally diverse glycans that shape the development of infant gut microbiota. Yet, how individual HMOs and bacterial genes drive the community assembly remain elusive. Here, we reconstructed an eight-member infant Bacterial Community (iBaCo) from representing dominant taxa in human infant feces. When individual HMOs were the sole carbohydrate source, they showed deterministic effects on the iBaCo composition and metabolic output. Notably, the tetramer HMO lacto-N-tetraose (LNT), in spite of its identical monomer composition as lacto-N-neotetraose (LNnT), showed a strong effect on maintaining Bifidobacterium breve abundance in iBaCo, whereas LNnT did not. Monoculture growth profiling, proteomics, enzymatic kinetic assay, and molecular docking revealed that β -galactosidase D4BMY8 and the relevant downstream pathways are induced by LNT and that D4BMY8 has substrate preference on LNT over LNnT, enabling a faster growth of Bi. breve and accumulation of acetate and lactate in LNT compared to LNnT. Metabolic flux analysis indicated that the substrate-preference of β -galactosidase D4BMY8 drives the skewed energy cost toward lactate/acetate metabolic output. Finally, the D4BMY8-encoding gene lacZ5 is widely spread in all isolated Bi. breve genomes, but divergently distributed in infant metagenome-assembled Bi. breve genomes. Together, we demonstrated that a single enzyme-substrate interaction could orchestrate the composition and metabolic function of an infant bacterial community, which may contribute to the assembly of dynamic infant gut microbiota. Our integrative approach provides a mechanistic framework for understanding the interaction between diet, microbial community, and infant gut health.}, }
@article {pmid42094499, year = {2026}, author = {Majidian, S and Chalco, A and Zheng, X and Webby, RJ and Bowman, AS and Poulson, RL and Nemeth, NM and Sedlazeck, FJ and Agustinho, DP}, title = {Rapid phylogenomic analysis for viral surveillance and metagenomic profiling with Omni2Tree.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.29.721707}, pmid = {42094499}, issn = {2692-8205}, abstract = {Phylogenomic surveillance is limited not by sequencing throughput, but by the difficulty of converting heterogeneous raw data into reliable evolutionary inference, particularly for low-titer and contaminated viral field samples. Here we present Omni2Tree, an assembly-free framework that reconstructs viral phylogenies directly from raw sequencing reads and generates easily shareable interactive reports and genome-wide entropy profiles to identify diversification. In H5N1 benchmark analyses, Omni2Tree maintained accurate placement and topological stability even under low coverage, unlike assembly or reference based methods. Omni2Tree generated an annotated phylogeny for 64-sample H5N1 field surveillance dataset from the eastern USA in under 3 hours. Omni2Tree recovered known phylogenetic structure and key variability insights across 1,328 hepatitis C virus and 707 human cytomegalovirus datasets, and resolved co-infecting respiratory viruses in clinical metagenomic samples. By enabling direct analysis from raw reads, Omni2Tree supports faster, more portable, and more decentralized phylogenomic surveillance across outbreak, clinical, and resource-limited settings.}, }
@article {pmid42094537, year = {2026}, author = {Debray, R and Dickson, CC and Webb, SE and Ferretti, P and Meloimet, A and Gilbert, J and Alberts, SC and Blekhman, R and Archie, EA and Tung, J}, title = {Social microbiome transmission predicts microbial specialization and host lifespan in a wild primate.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.29.721577}, pmid = {42094537}, issn = {2692-8205}, abstract = {Social interactions are proposed to provide reliable routes for microbial transmission between animals, facilitating animal-microbiome co-evolution. However, microbiome transmission remains challenging to measure in wild populations. Here we combine behavioral observations of wild baboons with repeated strain-resolved metagenomic profiling to identify individual gut microbial species that follow a dominant mode of social transmission. In an 18-year metagenomic time series from the same population, baboons with higher levels of socially transmitted species lived longer than those with lower levels of socially transmitted species. Socially transmitted species were also more stable and persistent within baboons, yet had narrower host ranges outside of baboons. Thus, social transmission is not only detectable in free-living primates, but may play a special role in both host and microbial fitness.}, }
@article {pmid42094770, year = {2026}, author = {Tekere, M and Kalu, CM}, title = {Relative abundance of heavy metal resistance genes of three drinking water treatment plants unveiled through shotgun metagenomics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1822428}, pmid = {42094770}, issn = {1664-302X}, abstract = {INTRODUCTION: The occurrence and abundance of heavy metal resistance genes (HMRGs) in drinking water treatment plants (DWTPs) and the stages at which they occur are a global challenge due to the risk of consuming contaminated water.<br><br>METHODS: The present study identified HMRGs associated with raw water sources, treatment stages (disinfection and filtration), final treated water, and produced sludge in three DWTPs across three provinces (Gauteng, Limpopo, and Mpumalanga) in South Africa, using a shotgun metagenomic approach.<br><br>RESULTS: In total, five classes of heavy metals (copper, arsenic, mercury, chromate, silver) and 50 resistance genes were identified across the three DWTPs. Most of the genes were obtained from the disinfection stages of the DWTPs.<br><br>DISCUSSION: This genomic dataset provides valuable information on the impact of disinfection stages on the relative abundance of HMRGs in drinking water treatment processes. Additionally, the transfer of genes into the final treated water consumed by the populace is a significant human health concern.}, }
@article {pmid42094845, year = {2026}, author = {Olson, N and Thystrup, CAN and Smith, F and Mucache, H and Fafetine, J and Saíde, J and Mondlane-Milisse, A and Brito, DRA and Jesser, KJ and Brown, J and Hald, T and Freeman, M and Levy, K and Nadimpalli, ML}, title = {Strain-level analyses of public sequencing data to characterize Escherichia coli strain sharing between children and chickens in Mozambique.}, journal = {One health (Amsterdam, Netherlands)}, volume = {22}, number = {}, pages = {101429}, pmid = {42094845}, issn = {2352-7714}, abstract = {Escherichia coli causes diarrhea in children and can be transmitted from animals. Characterizing the scope of human-animal strain sharing is crucial for assessing potential health risks; however, conventional methods that assess single isolates are resource-intensive and lack sensitivity. Strain-level metagenomic analyses can reveal within-host strain diversity and between-host strain sharing. In this study, we aimed to determine whether E. coli strains we previously detected among chickens in Mozambique might pose meaningful risks to local children. To achieve this, we compared E. coli strains in chicken metagenomes to E. coli strains reported by others in children's stool in the same community during the same period (2014-2022) using the Strain Genome Explorer toolkit. At least one E. coli strain was shared between 37/23,937 (0.15%) chicken-human pairs. This approach represents a novel method for assessing the scope of bacterial strain sharing between human and animal populations within a community.}, }
@article {pmid42094906, year = {2026}, author = {Zeng, Q and Xie, L and Dai, W and Xu, F and Dai, Y}, title = {Extracorporeal Membrane Oxygenation Haemoperfusion for Leptospirosis Pulmonary Hemorrhagic Disease: Report of 1 Case.}, journal = {Respirology case reports}, volume = {14}, number = {}, pages = {e70565}, pmid = {42094906}, issn = {2051-3380}, abstract = {Severe pulmonary leptospirosis (SPFL), characterized by diffuse alveolar haemorrhage (DAH) and acute respiratory distress syndrome (ARDS), carries a high mortality, often due to diagnostic delays and complex management. We report a case of a 42-year-old male with outdoor occupational exposure who presented with fever and hemoptysis, rapidly progressing to severe respiratory failure and thrombocytopenia. Chest imaging confirmed DAH/ARDS. For refractory hypoxemia, veno-venous extracorporeal membrane oxygenation (VV-ECMO) was initiated without systemic anticoagulation due to active pulmonary haemorrhage. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid rapidly identified Leptospira interrogans, enabling targeted antimicrobial therapy alongside multidisciplinary support. The patient gradually improved, was successfully weaned from ECMO and ventilator support, and was discharged without residual organ dysfunction. This case demonstrates that early application of anticoagulation-free VV-ECMO combined with mNGS-based rapid diagnosis and multidisciplinary care can improve outcomes in SPFL, highlighting the importance of considering this diagnosis in febrile patients with DAH and environmental exposure.}, }
@article {pmid42094994, year = {2026}, author = {Vasselin, A and Scavazzin, V and Talarmin, JP and Lamoureux, C and Pérès, M and Le Bars, H and Fangous, MS and Beauruelle, C and Ansart, S and Héry-Arnaud, G}, title = {Granulicatella adiacens infective endocarditis in pregnancy: diagnostic contribution of metagenomic sequencing-a case report.}, journal = {ASM case reports}, volume = {2}, number = {3}, pages = {}, pmid = {42094994}, issn = {2996-2684}, abstract = {BACKGROUND: Granulicatella adiacens is a fastidious Gram-positive coccus and is a rare but recognized cause of infective endocarditis. Infective endocarditis during pregnancy is uncommon but carries substantial maternal and fetal risk. Plasma metagenomic analysis of microbial cell-free DNA has emerged as a complementary diagnostic tool in culture-negative infections.<br><br>CASE SUMMARY: We describe a 35-year-old pregnant woman with known mitral valve prolapse who presented at 21 weeks of gestation with an acute ischemic stroke. Initial etiological work-up, including transesophageal echocardiography, was unremarkable. Ten days later, she re-presented with left-arm pain and neurologic symptoms. Repeat echocardiography revealed multiple mitral vegetations compatible with infective endocarditis. Despite multiple sets of prolonged-incubation blood cultures and extensive serological testing, all microbiological investigations remained negative. Empirical intravenous ceftriaxone was initiated based on the working diagnosis of HACEK endocarditis. A plasma metagenomic cell-free DNA test ultimately identified G. adiacens, which was suspected to have entered the body through dental treatment received a few weeks earlier. Ceftriaxone was continued given the favorable clinical response, with vegetation resolution, troponin decline, and uncomplicated term delivery of a healthy infant.<br><br>CONCLUSION: This case illustrates the diagnostic challenges of culture-negative infective endocarditis in pregnancy and underscores the value of plasma microbial cell-free DNA sequencing as a complementary tool when conventional methods fail. It also emphasizes the need to repeat echocardiography when clinical suspicion remains high and raises the question of antibiotic prophylaxis for high-risk dental procedures in pregnant women with underlying valvular heart disease.}, }
@article {pmid42095002, year = {2026}, author = {de Araújo Butarelli, AC and Peres, FV and Pellizari, VH and Bendia, AG}, title = {Hot life in Antarctica: a novel metabolically versatile Pyrodictiaceae genus thriving at a volcanic-cryosphere-marine interface.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag080}, pmid = {42095002}, issn = {2730-6151}, abstract = {Deception Island fumaroles in Antarctica represent rare environments where extreme heat intersects with cryospheric and marine conditions, creating remarkable environmental gradients. From the near-boiling sediments, we reconstructed a high-quality metagenome-assembled genome affiliated with the Pyrodictiaceae. Phylogenomic analyses revealed that this genome, proposed to represent Ca. Pyroantarcticum pellizari, forms a distinct lineage separated from known genera in the family. Functional annotation uncovered a versatile metabolic repertoire, including pathways for sulfur and nitrogen cycling, peptide and amino acid transport, and mixotrophic energy conservation. Stress-response systems such as reverse gyrase, thermosome, and small heat-shock proteins were complemented by lineage-specific genes related to membrane stability, metal detoxification, and Pyrodictiaceae-specific cannulae. These adaptations likely support survival under sharp temperature gradients, hydrogen sulfide emissions, and high metal concentrations at the volcanic-cryosphere-marine interface. Our findings expand the phylogenetic and ecological scope of Pyrodictiaceae, highlighting Antarctic marine volcanoes as unique refuges for hyperthermophiles and as valuable models for investigating life's habitability under extreme temperatures.}, }
@article {pmid42095017, year = {2026}, author = {An, QT and Li, W and Ren, Y and Liu, X and Yao, L and Li, Y and Zhao, X and Zhang, Y and Feng, P and Du, X}, title = {A comparative study of gut microbiota and metabolites in Tibetan sheep during cold and warm seasons.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1768985}, pmid = {42095017}, issn = {2297-1769}, abstract = {Tibetan sheep, a vital livestock species adapted to the extreme hypoxia, low temperatures, and intense radiation of the Qinghai-Tibet Plateau, rely on gastrointestinal microbiota for ecological balance and host nutrition, metabolism, and immunity. However, the possible associations of gut microbiota and metabolites with seasonal phenology remain unclear. Integrating biochemical, metagenomic, and metabolomic analyses, this study investigated seasonal variations in serum indices, microbial communities, and metabolites to inform enhanced breeding strategies. Analysis of forage nutritional composition showed that warm-season forages had significantly higher concentrations of dry matter (DM), crude protein (CP), and ether extract (EE) (p < 0.01), whereas cold-season forages were characterized by significantly greater levels of neutral detergent fiber (NDF) and acid detergent fiber (ADF) (p < 0.01). Correspondingly, serum analysis revealed significantly higher warm-season concentrations of alanine aminotransferase, total cholesterol, creatinine, and urea nitrogen compared with the cold season (p < 0.01). Gut microbiota composition shifted seasonally, with Bacteroides dominating in warm seasons and Bacillus predominating in cold seasons. Functional metagenomics indicated cold-season enrichment in pathways related to carbon metabolism, ABC transporters, aminoacyl-tRNA biosynthesis, pyruvate metabolism, DNA replication, and methane metabolism (p < 0.01). Metabolomics identified elevated warm-season microbial metabolites (His-Met, leucylleucine, luteolin 7-glucoside, ursolic acid; p < 0.05) and higher cold-season compounds (melatonin, glabrol, prostaglandin E2; p < 0.05), with KEGG enrichment linking these to steroid hormone biosynthesis, fatty acid metabolism, bile acid synthesis, and propanoate pathways. These findings suggest possible associations between seasonal extremes and: (1) modulation of nutrient metabolism (e.g., secondary bile acids and short-chain fatty acids); (2) activation of stress-response pathways (e.g., pentose phosphate pathway, ABC transporters, and DNA replication); and (3) immune regulation mediated by bioactive metabolites. Cold-season enrichment in DNA repair and energy-production pathways may be associated with responses to oxidative stress, whereas warm-season shifts in lipid metabolism are consistent with increased nutrient availability. Fluctuations in key metabolites-such as elevated melatonin in cold seasons and elevated ursolic acid in warm seasons-likely reflect adaptations related to thermoregulation and antioxidant defense. This work provides foundational insights into microbiota-host interactions under extreme environmental conditions, supporting the optimization of supplementation, probiotic use, and sustainable husbandry on the Qinghai-Tibet Plateau.}, }
@article {pmid42095439, year = {2026}, author = {Williams, TGS and Umpleby, H and Fisayo, T and Rampling, T and Houlihan, CF}, title = {Clinician perspectives on patient consent for metagenomic next-generation sequencing of blood samples for the diagnosis of infection in clinical practice.}, journal = {Journal of medical microbiology}, volume = {75}, number = {5}, pages = {}, doi = {10.1099/jmm.0.002164}, pmid = {42095439}, issn = {1473-5644}, mesh = {Humans ; *Metagenomics ; *High-Throughput Nucleotide Sequencing ; *Informed Consent ; Surveys and Questionnaires ; United Kingdom ; *Communicable Diseases/diagnosis/blood ; }, abstract = {Introduction. Pathogen diagnostics based on metagenomic next-generation sequencing (mNGS) are now in clinical use. mNGS can identify unexpected pathogens or organisms of unclear significance and generate human genomic data. Given these features, it has been suggested that patients should provide specific informed consent for mNGS.Gap Statement. There is limited published guidance on the appropriate form of consent for clinical infectious disease mNGS to guide clinical implementation and current practice varies.Aim. To inform a pilot of mNGS for returning travellers delivered at a reference laboratory for use by specialist infection clinicians, we sought clinician perspectives on the form of consent required for mNGS and the information patients require to make an informed decision.Methodology. A national survey of infection specialists provided clinicians' opinions.Results. If consent for an infection screen including blood-borne virus testing had already been provided, only a minority of surveyed clinicians (22 out of 124, 18%) thought that mNGS should be discussed before it was performed on pre-existing blood samples.Conclusion. Most of the UK infection clinicians surveyed did not think that mNGS of blood from returning travellers required discussion before being performed when patients had already consented for infection diagnostics to find the cause of their illness. However, clinicians felt that patients should be aware of the potential for additional testing and wanted information on mNGS to be readily available.With the increasing availability of clinical infectious disease mNGS, engagement of non-specialist clinicians and patients is required to confirm the generalizability of these perspectives. The model of consent used for clinical infectious disease mNGS should be ethically adequate in addition to being acceptable to patients and clinicians.}, }
@article {pmid42095681, year = {2026}, author = {Muthamilselvi Sivabalan, SK and Vijayakumar, V and Sengupta, P and Palmal, S and Krishnamurthi, S and Kumar Singh, N and Kyrpides, NC and Raman, K and Venkateswaran, K}, title = {Unveiling hidden microbial diversity in Mars 2020 mission assembly cleanrooms with molecular insights into the persistence and perseverance of novel species defying metagenome sequencing.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0127325}, doi = {10.1128/spectrum.01273-25}, pmid = {42095681}, issn = {2165-0497}, abstract = {NASA cleanrooms, which are critical for assembling space mission components, are maintained under stringent decontamination protocols to minimize biological contamination. These environments are characterized by nutrient-poor and oligotrophic conditions, leading to low microbial loads. Despite extensive cleaning, oligotrophs capable of surviving in such conditions continue to persist, often remaining undetected due to their low abundance, resistance to environmental stresses, and difficulties in biomolecule extraction. Even with shotgun metagenome sequencing technologies, these microbes may go undetected or be underrepresented due to their robust cell walls and the absence of reference genomes in publicly available databases. Over a 6-month study of Mars 2020 mission cleanrooms, 182 bacterial strains belonging to 19 families were identified using a whole-genome sequencing (WGS) approach. Among these, 14 novel Gram-positive species were discovered, including eight spore formers. Though the novel species comprised only 0.001% of the sequencing data, their successful cultivation allowed for functional characterization. Through WGS data mining, genomic traits associated with resilience in extreme conditions were revealed. These species were found to be involved in nitrogen cycling, carbohydrate metabolism, and radiation resistance, traits essential for survival in extreme environments. Furthermore, 12 biosynthetic gene clusters were identified, including those linked to ectoine and [Formula: see text]-poly-L-lysine production, suggesting potential biotechnological applications. These findings highlight the hidden microbial diversity within cleanrooms and emphasize the necessity of advanced detection strategies. A better understanding of these microbes will provide insights into extremophiles with applications in biotechnology, medical research, and life support systems for future space exploration missions.IMPORTANCEDespite strict decontamination protocols, NASA cleanrooms harbor low-biomass microbial communities adapted to nutrient-poor environments. These oligotrophic microbes often go undetected in shotgun metagenomics methods due to their low abundance, resistance to lysis, and lack of reference genomes. Standard shotgun metagenome sequencing methods fail to retrieve them, as dominant microbial DNA overshadows rare species. Over 6 months of monitoring Mars 2020 mission cleanrooms, 182 bacterial strains from 19 families were identified, including 14 novel Gram-positive species, 8 of which were spore formers. Though present at 0.001% abundance in sequencing data, we successfully cultured them, enabling functional characterization. These microbes exhibited roles in nitrogen cycling, carbohydrate metabolism, and radiation resistance, with 12 biosynthetic gene clusters linked to ectoine and [Formula: see text]-poly-L-lysine production. These findings highlight the previously underestimated microbial diversity in cleanrooms and emphasize the need for advanced detection strategies to explore extremophiles with applications in biotechnology and space exploration.}, }
@article {pmid42096004, year = {2026}, author = {Huang, YJ and Shen, ZQ and Hu, DP and Huang, YY and Chen, GY and Lin, Y and Hu, BM and Yuan, XX and Deng, GP and Li, X}, title = {Multi-Omics Analysis Reveals Inflammatory Activation and Maternal-Fetal Interface Remodeling in Spontaneous Abortion.}, journal = {Current medical science}, volume = {}, number = {}, pages = {}, pmid = {42096004}, issn = {2523-899X}, abstract = {BACKGROUND: Spontaneous abortion (SA) is a common adverse outcome of early pregnancy, yet its underlying pathophysiological mechanisms remain incompletely understood. Accumulating evidence suggests that dysregulated inflammatory responses at the maternal-fetal interface play a critical role in pregnancy loss. However, the potential associations between alterations in gut microbiota, metabolic disturbances, and localized decidual inflammation in patients with SA have not been systematically characterized.<br><br>METHODS: Women with SA (n&#x2009;=&#x2009;30) and those with normal early pregnancy (NP, n&#x2009;=&#x2009;28) were enrolled in this study. Proinflammatory cytokines were quantified in decidual tissue homogenates, and histopathological and molecular analyses were performed to evaluate inflammatory activation at the maternal-fetal interface. The gut microbiota composition was profiled using shotgun metagenomic sequencing, while metabolic alterations in the feces were assessed by untargeted metabolomics. Integrated multi-omics analyses were conducted to explore associations among gut microbial dysbiosis, metabolic perturbations, decidual inflammatory signaling, and molecular alterations.<br><br>RESULTS: Compared with those from the NP group, the decidual tissues from the SA group exhibited significantly elevated levels of IL-1&#x3b2; and TNF-&#x3b1; (1.49-fold and&#xa0;1.51-fold, both&#xa0;P&#x2009;<&#x2009;0.0001), accompanied by pronounced histopathological abnormalities. Enhanced activation of the NF-&#x3ba;B signaling pathway was observed at the maternal-fetal interface in SA patients. Metagenomic analyses revealed distinct differences in the gut microbiota composition and community structure between the two groups, with differentially abundant bacterial taxa identified (LDA score&#x2009;>&#x2009;2.0). Consistent with these findings, fecal metabolomic profiling clearly revealed differences between SA and NP patients, with differentially abundant metabolites (VIP&#x2009;>&#x2009;1.0, adjusted P&#x2009;<&#x2009;0.05) predominantly enriched in lipid metabolism, amino acid metabolism, and immune-related pathways. In addition, the expression of leucine-rich repeat-containing G protein-coupled receptor 6 was significantly upregulated (P&#x2009;<&#x2009;0.0001) in the decidual tissue of SA patients.<br><br>CONCLUSIONS: These findings indicate that SA is associated with localized inflammatory activation at the maternal-fetal interface, dysregulation of decidual molecular activity, gut microbiota dysbiosis, and metabolic perturbations. Integrated multi-omics analyses suggest potential interactions among these factors that may be linked to decidual dysfunction during early pregnancy, providing new insights into the complex pathophysiology of SA.}, }
@article {pmid42096148, year = {2026}, author = {Zhu, D and Wang, S and Sun, X and Britton, RA}, title = {CRISPR-AsCas12a and dAsCas12a-Mediated Gene Knockout and Knockdown in Clostridioides difficile.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3046}, number = {}, pages = {47-55}, pmid = {42096148}, issn = {1940-6029}, mesh = {*Clostridioides difficile/genetics ; *CRISPR-Cas Systems/genetics ; Gene Editing/methods ; *Gene Knockout Techniques/methods ; *Gene Knockdown Techniques/methods ; Bacterial Proteins/genetics ; CRISPR-Associated Proteins/genetics ; }, abstract = {Clostridioides difficile (C. difficile) is a leading cause of antibiotic-associated diarrhea and severe colitis, yet its genetic manipulation has long been constrained by low DNA transfer efficiency and limited recombination systems. Recent advances in CRISPR-based technologies have revolutionized the genetic toolkit for this pathogen, enabling precise genome editing and transcriptional regulation. Among CRISPR nucleases, Cas12a offers distinct advantages over Cas9 for bacterial applications, including a smaller size, T-rich PAM recognition, single-crRNA requirement, and reduced toxicity, which enhances conjugation efficiency in genetically recalcitrant organisms. AsCas12a-based platforms have enabled large fragment deletions, multiplex editing, and rapid generation of marker-free mutants in C. difficile. Complementing these nuclease-active systems, nuclease-deactivated variants (dCas9 or dAsCas12a) support CRISPR interference (CRISPRi)-a reversible, tunable approach for transcriptional repression without altering genomic sequences. Compared to traditional mutagenesis, CRISPRi greatly accelerates functional genomics by enabling high-throughput screening and drug target discovery. Together, our lab has independently developed CRISPR-AsCas12a-mediated genome editing and dAsCas12a-based CRISPRi tools, providing complementary strategies to overcome longstanding genetic barriers in C. difficile. These tools open new avenues for system-level interrogation of virulence, antibiotic resistance, and host-pathogen interactions.}, }
@article {pmid42096157, year = {2026}, author = {Pizzini, J and McCullough, HC and Sidner, BS and Britton, RA and Piepenbrink, KH and Auchtung, JM}, title = {An In Vitro Model for Studying Interactions Between Gastrointestinal Microbes and Planktonic and Sessile Clostridioides difficile Populations.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3046}, number = {}, pages = {171-187}, pmid = {42096157}, issn = {1940-6029}, mesh = {*Clostridioides difficile/physiology ; *Gastrointestinal Microbiome ; Humans ; Mucins/metabolism/chemistry ; Bacterial Adhesion ; Bioreactors/microbiology ; *Plankton ; Intestinal Mucosa/microbiology ; Hydrogels/chemistry ; Biofilms/growth &amp; development ; }, abstract = {Interactions between Clostridioides difficile, the gastrointestinal microbiota, and the host mucosal epithelium play important roles in governing the ability of C. difficile to colonize and cause disease. Several in vitro tools have been developed to investigate C. difficile physiology in the presence of microbial communities. In this chapter, we describe a model for studying C. difficile-mucin interactions in the presence of a complex microbiota using continuous flow bioreactors. This model can facilitate mechanistic studies of specific microbes and mucin structures important for C. difficile colonization, complementing findings from animal models. The approach presented here builds upon the preceding chapter's protocol for generating mucin hydrogels on glass slides and extends it to examine C. difficile adhesion to mucosal surfaces.}, }
@article {pmid42096470, year = {2026}, author = {Hardick, J and Anantharam, R and Lu, J and Salzberg, SL and Rothman, RE and Fenstermacher, KZJ and Pekosz, A and Onzia, A and Nakiyingi, L and Manabe, YC and Kandathil, AJ}, title = {Comparison of unbiased metagenomic next generation sequencing to targeted multiplex diagnostic assays for the detection of respiratory viruses.}, journal = {PloS one}, volume = {21}, number = {5}, pages = {e0347750}, doi = {10.1371/journal.pone.0347750}, pmid = {42096470}, issn = {1932-6203}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Respiratory Tract Infections/virology/diagnosis ; Male ; Female ; Adult ; Nasopharynx/virology ; Middle Aged ; Multiplex Polymerase Chain Reaction/methods ; SARS-CoV-2/genetics/isolation &amp; purification ; *RNA Viruses/genetics/isolation &amp; purification ; Aged ; Child, Preschool ; Adolescent ; Child ; Young Adult ; }, abstract = {OBJECTIVES: Accurate diagnosis of existing and emerging respiratory pathogens is important. We evaluated the capability of unbiased metagenomic next generation sequencing (mNGS) to identify pathogenic RNA viruses from two cohorts of nasopharyngeal (NP) swabs previously tested by commercial multiplex respiratory diagnostics.<br><br>METHODS: NP swabs (N&#x2009;=&#x2009;100) in viral transport media (VTM) were assessed using mNGS for this study. Cohort 1 (N&#x2009;=&#x2009;52) consisted of symptomatic individuals who tested negative for SARS-CoV-2, influenza A/B, and RSV by the Xpert Xpress CoV-2/Flu/RSV Plus multiplex respiratory virus panel and were tested by mNGS for undetected pathogens. Cohort 2 (N&#x2009;=&#x2009;48) included symptomatic individuals who were positive (N&#x2009;=&#x2009;26) or negative (N&#x2009;=&#x2009;22) by the ePlex RP2 multiplex respiratory pathogen panel. Samples were positive for influenza A (N&#x2009;=&#x2009;8), rhinovirus/enterovirus (N&#x2009;=&#x2009;5), RSV (N&#x2009;=&#x2009;4), adenovirus (N&#x2009;=&#x2009;3), parainfluenza (N&#x2009;=&#x2009;2), seasonal coronaviruses (N&#x2009;=&#x2009;2), and human metapneumovirus (N&#x2009;=&#x2009;1), as well as a rhinovirus/enterovirus/human metapneumovirus co-infected sample (N&#x2009;=&#x2009;1). mNGS results were compared with ePlex RP2 findings, and symptomatic negative samples were evaluated for additional pathogen detection.<br><br>RESULTS: Cohort 1 contained 8% (4/52) viral and 19% (10/52) bacterial reads. In cohort 2, positive concordance between ePlex RP2 and mNGS was 31% (8/26). mNGS did not identify any viral reads in ePlex RP2-negative samples. However, it detected other microbial reads, such as Acanthamoeba castellanii, in 21% (10/48) of samples.<br><br>CONCLUSION: In this study, targeted multiplex amplification methods demonstrated better overall sensitivity in NPs of symptomatic respiratory individuals than mNGS. Other mNGS approaches may produce different results. This study suggests that mNGS may offer adjunctive information, including the detection of rare pathogens, which may be helpful in some clinical contexts.}, }
@article {pmid42096522, year = {2026}, author = {Zhao, D and Zhang, C and Li, M and Li, H and Su, S and Zhang, X}, title = {Characteristics of carbon-fixing microbial communities and pathways across different aquatic systems in the Tianjin Binhai region.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag112}, pmid = {42096522}, issn = {1365-2672}, abstract = {AIMS: Microbial carbon fixation is central to carbon cycling and carbon sink functioning in coastal aquatic ecosystems. Although carbon fixation pathways have been increasingly investigated across diverse aquatic environments, comparative evidence remains limited for hydrologically connected yet hydrochemically contrasting coastal groundwater and surface water systems. This study aimed to compare carbon-fixation-associated microbial communities and major carbon fixation pathways across groundwater, river water and reservoir water in the Tianjin coastal region.<br><br>METHODS AND RESULTS: We integrated metagenomic sequencing with hydrochemical analyses to characterise carbon-fixation-associated microbial communities and six representative carbon fixation pathways. Surface waters were dominated by bacteria and showed relatively stable community composition, whereas groundwater communities comprised both bacteria and archaea and displayed pronounced spatial heterogeneity. The Calvin-Benson-Bassham cycle was prevalent across all water types, and the reductive tricarboxylic acid (rTCA) cycle was also widely distributed. Groundwater showed higher contributions of the Wood-Ljungdahl pathway, the archaeal 3-hydroxypropionate/4-hydroxybutyrate and dicarboxylate/4-hydroxybutyrate cycles, together with the rTCA cycle, indicating coexisting carbon fixation strategies. Pathway abundance and module completeness further suggested differences in pathway integrity among water types. Total dissolved solids, HCO3&#x207b;, CO32&#x207b; and dissolved organic carbon were key correlates of carbon fixation gene distribution.<br><br>CONCLUSIONS: Carbon-fixation-associated microbial communities, pathway distributions, and pathway integrity differed markedly between coastal groundwater and surface waters. Groundwater exhibited enhanced non-CBB cycle potentials and more diversified carbon fixation strategies, highlighting the importance of groundwater processes in evaluating carbon sequestration potential and carbon cycling in hydrochemically heterogeneous coastal aquatic systems.}, }
@article {pmid42096753, year = {2026}, author = {Jin, B and Bai, Z and Yan, Y and He, H and Du, J and Xu, Y and Wang, L and Ji, J}, title = {Antibiotic-driven mechanisms in endogenous partial denitrification (EPD): Nitrite accumulation, microbial adaptation, functional gene responses and resistance gene proliferation.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142257}, doi = {10.1016/j.jhazmat.2026.142257}, pmid = {42096753}, issn = {1873-3336}, abstract = {The mechanisms by which antibiotics affect Endogenous Partial Denitrification (EPD) systems remain unclear. This study investigated the relationships between antibiotic type and pollutant removal, along with the underlying microbial metabolic mechanisms in an EPD system exposed to three antibiotics. The results showed that sulfadiazine (SD) and sulfamethoxazole (SMZ) exhibited higher chemical oxygen demand removal efficiency than tetracycline (TC). In the SD system, NO3[-]-N removal was 84.13%, whereas other systems achieved 97%, which was associated with a higher abundance of the n arG and nirS. Proteobacteria and Chloroflexi demonstrated strong adaptability to the antibiotics. TC inhibited the tricarboxylic acid cycle and organic matter degradation may be related to the reduced mdh. SD induced microorganisms to convert carbon sources into polyhydroxybutyrate instead of utilizing them directly, while SMZ optimized nitrogen metabolism by increasing the abundance of nirS and nirK, leading to higher NO2[-]-N accumulation in these two EPD systems. SD stress reduced the abundance of ppk2/ppx gene, inhibited the energy production and internal carbon reserve of denitrifying polyphosphate-accumulating organisms in anaerobic stage. Although the microorganisms had stronger phosphorus uptake potential by up-regulating ppk1 gene, the lack of ATP necessary to drive this process eventually led to the reduction of PO4[3] [-]-P removal ability. The abundance of resistance genes peaked in the SD system, significantly increasing the risk of antibiotic resistance. This study deciphers the metabolic mechanisms of the EPD system in response to three types of antibiotics and provides a scientific basis for its application in environments with fluctuating antibiotic stress.}, }
@article {pmid42096819, year = {2026}, author = {Kumar, K and Dutta, P}, title = {Integration of mass spectrometry and molecular biotechnology to study bioaerosols.}, journal = {Chemosphere}, volume = {405}, number = {}, pages = {144949}, doi = {10.1016/j.chemosphere.2026.144949}, pmid = {42096819}, issn = {1879-1298}, abstract = {Conventional culture-based and microscopic approaches yield limited information about the diversity, content, and real-time behaviour of biological aerosols. In recent years, mass spectrometry (MS) and molecular biotechnology have evolved as powerful and complementary analytical methods for detecting, identifying, and characterising air biological particles. This study critically reviews recent improvements in MS-based techniques for analysing bioaerosol chemical markers, proteins, metabolites, and toxins, including MALDI-TOF MS, GC-MS, LC-MS/MS, and real-time aerosol mass spectrometry. In parallel, contemporary advances in molecular biotechnology, including as PCR-based assays, metagenomics, and MS-driven proteomics and metabolomics, are described, with a focus on atmospheric applications. Special emphasis is placed on integrated analytical workflows that combine MS with molecular techniques to improve specificity, sensitivity, and source attribution. The current issues of low biomass concentrations, sampling artefacts, data interpretation, and standardisation are discussed, and future perspectives on portable MS systems, multi-omics integration, and AI-assisted data processing are presented. This study offers a thorough analytical chemistry viewpoint on next-generation methodologies for monitoring bioaerosols and promotes the development of enhanced instruments for assessing air quality and protecting human health.}, }
@article {pmid42097292, year = {2026}, author = {Hennecart, B and Belda, E and de Lahondès, R and Zucker, JD and Prifti, E}, title = {StrainMake: reproducible hybrid metagenomics with MAG recovery and strain-level resolution.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag212}, pmid = {42097292}, issn = {1367-4811}, abstract = {SUMMARY: Metagenomic workflows involve complex multi-step analyses, from quality control and assembly to binning, annotation, and strain-level profiling. Few existing metagenomic pipelines achieve the combination of flexibility, reproducibility, and hybrid assembly support within a unified workflow. We present StrainMake, a Snakemake-based workflow for de novo metagenomic analysis from short, long, or hybrid sequencing data. StrainMake integrates widely used tools across all major steps-quality control, assembly, binning, dereplication, taxonomic and functional annotation-while also providing non-redundant gene catalogues, community-scale metabolic models, and strain-level microdiversity metrics. The modular design enables the use of alternative tools, scalable execution on HPC systems, and full reproducibility through Snakemake and Conda.<br><br>RESULTS: Applied to the CAMI II strain-madness dataset, StrainMake&#x2004;&#x2004; produced high-quality assemblies and metagenome-assembled genomes (MAGs), while enabling strain-resolved comparisons across samples. Hybrid assemblies improved contiguity, whereas short-read assemblies offered faster runtimes, illustrating the workflow's benchmarking capacity.<br><br>StrainMake is open source and available at https://github.com/UMMISCO/strainmake, together with comprehensive documentation. Generated data are deposited in Zenodo (doi : 10.5281/zenodo.16950162).}, }
@article {pmid42097342, year = {2026}, author = {Yin, D and Chen, M and Chen, X and Feng, Y and Zhou, X and Guan, Y and Zhang, Y and Bai, S and Li, L and Ouyang, H and Cheng, J and Zhu, W}, title = {Integrative multi-omics reveals that Pueraria thomsonii Radix alleviates dyslipidemia by remodeling gut microbiota and regulating arachidonic acid metabolism.}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {121816}, doi = {10.1016/j.jep.2026.121816}, pmid = {42097342}, issn = {1872-7573}, abstract = {Pueraria thomsonii Radix (PTR, "Fen-ge") is a food-medicine herb widely used in China for metabolic complaints. Its putative lipid-modulating effects are supported by traditional practice, but the molecular basis remains incompletely understood.<br><br>AIM OF THE STUDY: To elucidate the active constituents and mechanisms by which PTR mitigates dyslipidemia.<br><br>MATERIALS AND METHODS: Chemical profiling and plasma exposure of PTR constituents were characterized by UPLC-Q-TOF-MS/MS. A high-fat-diet rat model was used to assess pharmacodynamic endpoints including serum lipid panel, hepatic histopathology, liver injury markers and inflammatory cytokines. Untargeted plasma metabolomics was performed in rats and patients; rat fecal 16S rRNA gene sequencing and hepatic transcriptomics complemented mechanism inference. Multivariate models were cross-validated and FDR-controlled; pathway and multi-omics correlation analyses integrated metabolite-microbe-gene relationships.<br><br>RESULTS: PTR significantly ameliorated dyslipidemia in high-fat diet-fed rats, as evidenced by improved serum lipid profiles, reduced ALT/AST levels, and alleviated hepatic steatosis and inflammation in histopathological examination. Integrated metabolomic analysis across rats and patients revealed that the restored metabolic pathways were primarily concentrated in arachidonic acid and unsaturated fatty acid metabolism. Gut microbiota analysis indicated that PTR remodeled microbial taxa correlated with arachidonic acid-related lipid metabolism. Meanwhile, hepatic transcriptomics data showed that differentially expressed genes were functionally enriched in biological processes such as lipid oxidation and were bioinformatically linked to the AMPK signaling pathway.<br><br>CONCLUSIONS: PTR may ameliorate dyslipidemia through coordinated modulation of the gut microbiota and arachidonic acid metabolic network. Based on integrated omics analysis, the hepatic AMPK signaling pathway may potentially be involved in this regulatory process; however, its direct mechanistic role requires further experimental validation. Future investigations employing targeted lipid-omics, protein phosphorylation assays, and microbiota-transfer experiments are warranted to elucidate the causal relationships.}, }
@article {pmid42097354, year = {2026}, author = {Kaliappa, GD and Palanisamy, H and Vidyalakshmi, S}, title = {Integrative Machine Learning Models to Unravel Gut Microbial Dysbiosis and Functional Disruption in Polycystic Ovary Syndrome.}, journal = {F&amp;S science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.xfss.2026.04.005}, pmid = {42097354}, issn = {2666-335X}, abstract = {OBJECTIVE: To study gut microbial diversity and metabolic pathway disruptions in women with PolyCystic Ovary Syndrome (PCOS) compared to healthy controls, and to evaluate the diagnostic potential of microbiome-driven machine learning models.<br><br>DESIGN: Case-controlled metagenomic data analysis SUBJECTS: Gut metagenomic data from women diagnosed with PCOS and age-matched healthy female controls EXPOSURE: Presence of PolyCystic Ovary Syndrome (PCOS) MAIN OUTCOME MEASURES: The primary outcome measures will include gut microbial alpha and beta diversity indices, microbial taxon abundance, functional pathway profiles, predicted metabolite levels, microbe-functional pathway-metabolite interaction networks, and the diagnostic accuracy of microbiome-based machine learning models.<br><br>RESULTS: Alpha and beta diversity analyses revealed marked gut microbial dysbiosis in women with PCOS, despite comparable species richness to healthy controls. Differential abundance analysis identified 41 significantly altered microbial species, including enrichment of pro-inflammatory taxa such as Bacteroides vulgatus and Ruminococcus gnavus, and depletion of beneficial commensals including Roseburia hominis and Prevotella copri. These compositional shifts indicate a pro-inflammatory microbial community structure in PCOS. Functional profiling demonstrated the upregulation of pathways involved in nucleotide turnover, lipid and carbohydrate metabolism, and neurotransmitter synthesis, potentially contributing to metabolic and neuroendocrine disruption. Network analysis revealed fragmented and unstable microbial-metabolite associations in PCOS compared with cohesive networks in controls. Microbiome based machine learning models achieved a diagnostic accuracy of 84.25% (AUC 0.93), underscoring their predictive potential.<br><br>CONCLUSION: The gut microbiome in PCOS is characterized by a pro-inflammatory community structure and disrupted metabolic pathways. These findings demonstrate the diagnostic potential of microbiome-based models and underscore the gut microbiome as a promising target for therapeutic interventions in the management of PCOS.}, }
@article {pmid42097759, year = {2026}, author = {Li, Z and Zhang, Q and Wang, H and Zhang, Z and Liu, J and Li, L and Lin, Y and Wang, Y and Yin, C and Wang, W and Shen, F and Han, Z and Hao, S and Cong, P and Tian, T and Liu, Q and Chen, X and Zhan, H and Peng, T and Yu, X and Pu, X and Lian, X and Wang, T}, title = {Diagnostic Value of Metagenomic Next-Generation Sequencing for Suspected Native Spinal Brucella Infection: A Multicenter Study.}, journal = {Neurospine}, volume = {23}, number = {2}, pages = {487-499}, doi = {10.14245/ns.2551698.849}, pmid = {42097759}, issn = {2586-6583}, support = {2023YFC2812004//National Key Research and Development Program/ ; 24-4-4-zrjj-154-jch//Qingdao Natural Science Foundation/ ; //Qingdao City Healthcare Key Discipline Construction Project/ ; 2023TSGC051l//Technological Innovation Capability Improvement Project/ ; ZR2024MH251//Shandong Provincial Natural Science Foundation General Project/ ; 202404070869//Shandong Province Medical and Health Science Project/ ; }, abstract = {OBJECTIVE: The aim is to study the diagnostic positive rates of metagenomic next-generation sequencing (mNGS), microbial culture, and serologic testing in suspected native spinal brucellosis, and to evaluate the clinical value of their combined application.<br><br>METHODS: In this multicenter, retrospective observational study, 128 patients with suspected native spinal brucellosis from 6 medical centers (February 2020 to February 2025) were enrolled. Specimens from infection sites were subjected to microbial culture, mNGS, and serological testing (agglutination test).<br><br>RESULTS: Of the 128 patients with suspected native spinal Brucella infections, 118 patients were diagnosed with Brucella spondylitis. Among the 118 confirmed Brucella spondylitis cases, mNGS demonstrated a positivity rate of 92.37% (109 of 118), significantly higher than that of culture (26.27%, 31 of 118) and agglutination test (83.05%, 98 of 118). In the 87 culture-negative samples, mNGS detected Brucella in 91.95% (80 of 87), compared to 82.76% (72 of 87) by agglutination test. mNGS confirmed Brucella infection in all 16 cases that were agglutination test negative. mNGS combined with agglutination tests can effectively complement each other, improving the sensitivity of diagnosis and thereby minimizing missed diagnoses to the greatest extent. Among the 10 nonbrucellar spinal pathologies, agglutination test showed a high false-positive rate of 90% (9 of 10), whereas mNGS had a 10% (1 of 10) false-positive rate. Therefore, the agglutination test has a relatively high rate of false positives.<br><br>CONCLUSION: mNGS detection represents an effective adjunct to microbial culture and the agglutination test. The concurrent use of all 3 methods enhances diagnostic accuracy and reduces the likelihood of missed and incorrect diagnoses, significantly improving patient prognosis and guiding personalized clinical treatment.}, }
@article {pmid42098163, year = {2026}, author = {Weng, Y and He, S and Luo, Z and Sun, J and Cheng, Q and Chen, Y and Tong, H}, title = {Keystone microbial taxa in the formation of stale aroma during pile fermentation of ripened Pu-erh tea.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00794-8}, pmid = {42098163}, issn = {2396-8370}, support = {CYB23127//Chongqing Graduate Student Research Innovation Project/ ; 2024J1110//Yunnan Provincial Department of Education/ ; 32272764//National Natural Science Foundation of China/ ; }, abstract = {Ripened Pu-erh tea is prized for its distinctive stale aroma. Methoxy-phenolic compounds, key contributors to this aroma, are produced during pile fermentation; however, the specific microorganisms responsible for their synthesis remain unclear. In this study, we identified the dominant taxa (Aspergillus luchuensis, A. fumigatus, Staphylococcus gallinarum, and S. kloosii) during pile fermentation through morphological analysis and metagenomic profiling. Gas Chromatography-Mass Spectrometry (GC-MS) analysis demonstrated the pivotal role of methoxy-phenolic compounds in the stale aroma. Moreover, using a metagenomic-based Weighted Gene Co-expression Network Analysis (WGCNA) combined with bivariate correlation network analysis, we identified key microbial taxa (Trichomonascus ciferrii, Heyndrickxia coagulans and Enterococcus sp.) involved in the generation of these compounds. Finally, we found that solid-state fermentation involving both dominant and keystone microbial taxa produced the highest levels of methoxy-phenolic compounds. Our findings reveal an inconsistency between dominant high-abundance taxa and keystone microbial taxa responsible for methoxy-phenolic compound synthesis during pile fermentation.}, }
@article {pmid42085838, year = {2026}, author = {ElHefnawi, M and Amin, DH and Elfiky, AM and Tamam, FMM and Elabiad, MA and Zada, S and Abu-Shahba, N}, title = {From culture to metagenomics: A paradigm shift in diagnosing infective endocarditis.}, journal = {Diagnostic microbiology and infectious disease}, volume = {116}, number = {1}, pages = {117449}, doi = {10.1016/j.diagmicrobio.2026.117449}, pmid = {42085838}, issn = {1879-0070}, abstract = {Infective endocarditis (IE) is a severe disease that damages heart valves and can lead to major complications, including heart failure, embolic events, and stroke. It is the third most common fatal infection worldwide. This review examines the clinical burden of IE, its microbial causes, and the ongoing challenges in diagnosis. Particular attention is given to the limitations of traditional blood cultures, especially in detecting culture-negative and fastidious organisms, and to the emerging role of metagenomic approaches. A comprehensive review of the literature was conducted, focusing on diagnostic methods such as blood cultures, molecular assays, and metagenomic sequencing. The role of bacterial biofilms in treatment failure and antibiotic resistance was also explored. Metagenomics, especially cell-free metagenomic DNA (cf-mDNA), shows promise as a non-invasive diagnostic tool that can overcome culture-based limitations. However, standardized protocols and prospective studies are needed to validate its routine clinical application in IE diagnosis and management.}, }
@article {pmid42085875, year = {2026}, author = {Amin, H and Šantl-Temkiv, T and M Wouters, I and Johannesen, A and Sigsgaard, T and Schlünssen, V and Malinovschi, A and Thorarinsdottir, H and Bertelsen, RJ}, title = {Urban indoor airborne antibiotic resistance genes: Role of antibiotic use and outdoor air pollution.}, journal = {The Science of the total environment}, volume = {1034}, number = {}, pages = {181854}, doi = {10.1016/j.scitotenv.2026.181854}, pmid = {42085875}, issn = {1879-1026}, abstract = {Antibiotic resistance genes (ARGs) in airborne dust represent an emerging concern for public health, particularly in indoor environments where human exposure is prolonged. While external environmental pressures are known to shape the abundance and diversity of microorganisms in indoor dust, their role in ARG dynamics remains underexplored. This study assessed the temporal and spatial patterns of airborne ARGs in indoor dust across four Nordic cities (Aarhus, Bergen, Reykjavik, and Uppsala) using electrostatic dust collectors (EDCs) in the same households at two time points: 2012 and 2022. Shotgun metagenomic sequencing was performed to profile ARGs. National antibiotic consumption data were obtained from the European Surveillance of Antimicrobial Consumption (ESAC-Net), outdoor air pollution data (PM2.5 and PM10) from the Copernicus Atmosphere Monitoring Service (CAMS), and meteorological parameters from the NASA POWER database. Beta diversity analysis revealed city-specific differences in ARG composition (PERMANOVA, R[2] = 0.18, P = 0.03), but no consistent temporal shift over the 10-year period. Macrolide, tetracycline, and aminoglycoside resistance genes were among the most abundant and persistent classes. A previously undetected macrolide resistance sequence was identified across all cities in 2022. Although national antibiotic consumption declined, cross-sectional correlations between national antibiotic consumption and ARG abundance strengthened from 2012 (Spearman's ρ = 0.25) to 2022 (ρ = 0.37), suggesting sustained ARG presence despite reduced antibiotic consumption. Several ARG classes showed associations with outdoor particulate matter, and these relationships were influenced by local meteorological conditions. For example, higher absolute humidity was associated with a weaker relationship between PM and polymyxin resistance genes, whereas stronger wind speeds were associated with stronger relationships between PM and Sulfonamide resistance genes. These findings highlight the complex environmental interplay between antibiotic consumption, air pollution, meteorological factors, and ARG dynamics in indoor air, emphasizing the need for integrated environmental and AMR surveillance, especially in the context of climate change.}, }
@article {pmid42085931, year = {2026}, author = {Wang, Z and Wang, Y and Peters, BA and Post, WS and Brown, TT and Palella, FJ and Rinaldo, CR and Witt, MD and Gange, SJ and Kuniholm, MH and Sha, BE and Chichetto, NE and Clish, CB and Gerszten, RE and Hodis, HN and Sharma, A and Anastos, K and Burk, RD and Kaplan, RC and Qi, Q and Hanna, DB}, title = {Multi-omics analysis of the gut microbiome and carotid artery atherosclerosis in men with and without HIV.}, journal = {EBioMedicine}, volume = {127}, number = {}, pages = {106281}, doi = {10.1016/j.ebiom.2026.106281}, pmid = {42085931}, issn = {2352-3964}, abstract = {BACKGROUND: How gut microbiota alterations may contribute to host inflammation and metabolomic profiles affecting atherosclerosis is not fully elucidated, especially in the context of HIV.<br><br>METHODS: We examined associations between gut microbial features (measured by shotgun metagenomics) and subclinical carotid atherosclerosis, as assessed by high-resolution B-mode ultrasound, in 359 men from the MACS/WIHS Combined Cohort Study. We measured 822 plasma metabolites using LC-MS/MS, and up to 2866 circulating proteins by the Olink Explore 3072/384 platform (with a primary focus on 617 proteins related to inflammation and immune function).<br><br>FINDINGS: Carotid artery plaque was detected in 115/359 men (32%). Adlercreutzia equolifaciens and Eubacterium sp3131 were associated with lower odds of plaque (OR [95% CI] = 0.57 [0.43, 0.77], 0.84 [0.76, 0.93], respectively), while Coprococcus sp13142 was associated with higher odds of plaque (OR [95% CI] = 1.14 [1.06, 1.23]). Results were consistent in men both with and without HIV. A. equolifaciens was positively correlated with HDL cholesterol and inversely correlated with systolic blood pressure. These plaque-associated microbial species were also associated with a range of circulating metabolites and inflammatory proteins. For example, A. equolifaciens positively correlated with the metabolites palmitoyl-EA and mesobilirubinogen, and inversely correlated with the pro-inflammatory chemokine CXCL9, the immune regulator CD160, and IL-24.<br><br>INTERPRETATION: We identified gut microbial features associated with carotid artery atherosclerosis, consistent across HIV status; these associations were partially explained by specific microbiota-related metabolites and inflammatory markers. If validated, these findings suggest gut microbiota-related targets for CVD prevention.<br><br>FUNDING: The study was funded by the National Heart, Lung, and Blood Institute (U01HL146204-04S1, K01HL169019).}, }
@article {pmid42086548, year = {2026}, author = {Lu, M and Jiao, JJ and Luo, X and Feng, X and Liang, W and Yu, S and Qi, Y and Wang, Z and Li, H and Li, M}, title = {Microbial drivers of ammonium accumulation in Holocene sediments of the Pearl River Delta.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-72058-8}, pmid = {42086548}, issn = {2041-1723}, support = {32225003, 32393970, 32393971, 92251306//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42407109//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42130702//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Elevated ammonium concentrations in deltaic groundwater pose a widespread environmental challenge, yet the microbial mechanisms linking depositional history to ammonium dynamics remain poorly understood. The Pearl River Delta, with the highest naturally occurring groundwater ammonium concentrations documented globally, provides a unique natural system to investigate these processes. Here, by integrating geochemical and metagenomic data, we show that fermentation-related genes are the most prevalent across all depositional zones, suggesting fermentation as the potential primary pathway for ammonium production, with the functional potential declining as sedimentary organic matter becomes increasingly recalcitrant with sediment age. Secondary mechanisms shift from nitrate reduction to nitrite ammonification across terrestrial-to-marine-dominated zones, reflecting salinity-driven metabolic partitioning. Notably, the marine-derived genus Brevirhabdus emerges as a key taxon linking depositional history to present-day biogeochemistry, demonstrating remarkable metabolic versatility. These findings demonstrate that paleo-depositional and hydrogeological evolution fundamentally shape microbial landscapes and dictate groundwater quality in deltaic systems worldwide.}, }
@article {pmid42086631, year = {2026}, author = {Moon, K and Kang, I and Cho, JC}, title = {Virome datasets and viral metagenome-assembled genomes from aquaculture-impacted freshwater environments.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07383-0}, pmid = {42086631}, issn = {2052-4463}, support = {NRF-2022R1A2C3008502//National Research Foundation of Korea (NRF)/ ; NA//Hankuk University of Foreign Studies (HUFS)/ ; }, abstract = {Bacteriophages in natural environments play a critical role in microbial ecology by regulating bacterial populations, mediating nutrient cycling, and facilitating horizontal gene transfer. Aquaculture operations, particularly inland fish farms, are major sources of anthropogenic influence on freshwater ecosystems. Here, we present three viral metagenomic datasets derived from freshwater samples collected at an inland aquaculture effluent site and adjacent upstream and downstream locations along the Sung-am River in Jincheon County, South Korea. The datasets were generated using the Illumina HiSeq X sequencing platform, yielding approximately 10.0-11.2 Gbp per sample. Quality assessments confirmed minimal bacterial contamination, with negligible proportions of rRNA and bacterial marker genes. Assembly using metaSPAdes and MEGAHIT, application of Phables to resolve high-quality phage genomes (viral metagenome-assembled genomes; vMAGs), viral identification with VirSorter2, and clustering using Vclust, resulted in 2,837-3,156 virus operational taxonomic units (vOTUs; ≥10 kb) per sample. Each vOTU sequence is analyzed for taxonomic assignment and putative host prediction. These datasets provide a valuable resource for further studies on viral diversity and microbial ecology in freshwater ecosystems affected by aquaculture.}, }
@article {pmid42086823, year = {2026}, author = {Ismaeil, M and Saeed, AM and Donia, SA and El-Sayed, WS}, title = {Predictive functional profiling of 16S rRNA genes amplicons reveals bioremediation and sulfur metabolism capacity in thermophilic hot spring bacteriomes.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42086823}, issn = {2045-2322}, mesh = {*Hot Springs/microbiology ; *Sulfur/metabolism ; *RNA, Ribosomal, 16S/genetics ; Biodegradation, Environmental ; *Bacteria/genetics/metabolism/classification ; Microbiota ; Phylogeny ; Soil Microbiology ; Hot Temperature ; Proteobacteria/genetics/metabolism ; }, abstract = {Thermophilic hot springs host highly specialized microbial communities critical for biogeochemical cycling and novel biotechnological applications. This study investigated the structure of the bacterial communities (bacteriomes) and predicted functional potential related to bioremediation and sulfur metabolism across three geochemically diverse soil sites within the Pharaoh's Bath Hot Springs ecosystem in South Sinai, Egypt. These sites were categorized by distinct thermal profiles: 70 °C (HS1), 75 °C (HS2), and 80 °C (HS3). Using 16 S rRNA gene amplicon sequencing and PICRUSt functional prediction, sequence analysis via the EzBioCloud server revealed that the HS2 site harbored the highest evenness and overall microbial diversity. Taxonomically, the HS1 and HS3 sites were dominated by Proteobacteria; in contrast, the HS2 site exhibited a more diverse profile, characterized by a reduced Proteobacteria presence and a high abundance of Rhodothermaeota. Predictive functional profiling identified 13 genes associated with biodegradation pathways (e.g., catechol and xylene degradation), suggesting an intrinsic genetic capacity to degrade complex aromatics and halogenated compounds across these thermal gradients. Regarding sulfur metabolism, functional predictions indicated that the HS2 site possessed the highest potential for dissimilatory sulfate reduction. Meanwhile, the HS1 site specialized in assimilatory sulfate reduction and, alongside the HS2 site, demonstrated a higher predicted capacity for sulfide oxidation. The distribution of heat-response genes varied by location: HspQ and Hsp33 were most prominent at the HS1 site, while HSP20 and DnaK reached their maximum abundance at the HS2 site. Overall, this study demonstrates the substantial intrinsic bioremediation potential of the studied bacteriomes and provides a predictive framework for understanding microbial functional potential in this system, with future studies offering opportunities to refine in situ functional validation and application.}, }
@article {pmid42087721, year = {2026}, author = {Pan, W and Tang, S and Wanek, W and Luo, Z and Chen, J and Yang, Y and Ge, T and Marsden, KA and Liang, G and Chadwick, DR and Chen, X and Gregory, AS and Wu, L and Liang, Y and Jones, DL and Ma, Q}, title = {Microbial Community Traits and Necromass Dynamics Shape Soil Carbon Accumulation.}, journal = {Global change biology}, volume = {32}, number = {5}, pages = {e70906}, doi = {10.1111/gcb.70906}, pmid = {42087721}, issn = {1365-2486}, support = {U24A20575//National Natural Science Foundation of China/ ; 32573140//National Natural Science Foundation of China/ ; 32402680//National Natural Science Foundation of China/ ; 2024M752818//China Postdoctoral Science Foundation/ ; 2026SNJF084//San Nong Jiu Fang Technology Cooperation Program of Zhejiang Province/ ; 2025SNJF025//San Nong Jiu Fang Technology Cooperation Program of Zhejiang Province/ ; 202303AC100013//Yunnan Key Research and Development Program/ ; 05//Smart Fertilization Project/ ; BBS/E/RH/23NB0007//UK Research and Innovation Biotechnology and Biological Sciences Research Council/ ; //Lawes Agricultural Trust/ ; }, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism/analysis ; Fertilizers/analysis ; *Microbiota ; *Carbon Sequestration ; }, abstract = {Soil organic carbon (SOC) sequestration is vital for food security and climate mitigation. However, its long-term response to fertilisation remains unclear. Using the 180-year Broadbalk Experiment (the world's longest-running fertilisation trial; Rothamsted, UK), combined with [14]C labelling and metagenomics, we identified fundamentally distinct mechanisms of SOC accumulation: a microbially mediated dual pathway under organic fertilisation versus a resource-limited pathway under inorganic fertilisation. Sustained organic inputs matched inorganic fertilisers in maintaining crop yields while increasing total SOC by 160% (relative to a no-fertilisation control), far exceeding the 26% gain under inorganic fertilisation. Mechanistically, the continuous supply of labile organic matter provided an energetic surplus, allowing copiotrophic microbial communities with high carbon use efficiency to reduce investment in energy-intensive enzyme synthesis. This metabolic efficiency facilitated a dual-pathway expansion, elevating dynamic particulate organic carbon (POC) from 1.4 to 7.5 g kg[-1], while microbial assimilation and necromass accumulation concurrently increased mineral-associated organic carbon (MAOC) from 6.8 to 21.5 g kg[-1]. Conversely, inorganic fertilisation induced an oligotrophic 'mining' strategy, in which microorganisms upregulated the degradation of complex organic matter under carbon-limited conditions, restricting sustained SOC accumulation primarily to the MAOC pool. A global meta-analysis of field experiments (0-120 years) corroborated these temporal trajectories across diverse soil types, showing that SOC under organic fertilisation increases in a time-dependent manner, reaching a 77% gain after 80 years (three-fold greater than under inorganic inputs). Overall, organic fertilisation enhances total SOC via POC and MAOC accumulation, whereas inorganic fertilisation mainly increases MAOC. Long-term SOC persistence depends not only on carbon inputs, but also on microbial community traits and necromass dynamics, suggesting that aligning nutrient inputs with these biological mechanisms is critical for sustainable carbon sequestration.}, }
@article {pmid42088021, year = {2026}, author = {Wang, A and Wang, Q and Zhang, T and Qi, G and Ren, W and Tian, W and Chen, J}, title = {Integrated multi-omics profiling reveals phenotype- and tissue-specific host-microbiota interactions in paired tumor and peritumoral tissues of advanced gastric cancer patients from Northwest China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1763765}, pmid = {42088021}, issn = {2235-2988}, mesh = {Humans ; *Stomach Neoplasms/microbiology/pathology/genetics ; China ; Female ; Male ; Middle Aged ; Gene Expression Profiling ; Gastric Mucosa/microbiology/pathology ; Aged ; Phenotype ; *Host Microbial Interactions/genetics ; Metagenomics ; *Microbiota ; Transcriptome ; Adult ; Helicobacter Infections/microbiology ; *Gastrointestinal Microbiome ; Helicobacter pylori ; Multiomics ; }, abstract = {BACKGROUND: Advanced gastric cancer (AGC) exhibits a high incidence in Northwest China, largely attributed to region-specific dietary patterns and environmental exposures. Its pathogenesis involves complex host-microbiota crosstalk, which has not yet been comprehensively elucidated through integrated multi-omics approaches. Herein, we employed trasncriptomic and shotgun metagenomic sequencing on paired tumoral and peritumoal mucosal tissues from 88 AGC patients in Northwest China. Our aim was to systematically characterize host gene expression profiles, the composition and functional potential of the gastric mucosal microbiota, and their intricate interrelationships.<br><br>RESULTS: Transcriptomic profiling clearly distinguished tumoral from peritumoral regions (PERMANOVA, R[2] = 0.24, P = 0.0001), with 8870 differentially expressed genes (DEGs) identified between the two tissue types. Tumor tissues harbored 8377 up-regulated DEG, which were enriched in extracellular matrix (ECM) organization, cell cycle regulation, signaling transduction, and inflammatory pathways (e.g., PI3K-Akt, IL-17 signaling). In contrast, peritumoral tissues showed 493 up-regulated DEGs primarily associated with metabolic processes. Host gene expression was significantly modulated by Lauren classification in tumoral mucosa (P = 0.025) and by Helicobacter pylori (Hp) infection in peritumoral tissues (P = 0.0424). Hp-infected tissues exhibited 65 up-regulated DEGs linked to transcriptional misregulation in cancer, inflammation, immune activation and mitochondrial pathways. Lauren subtypes displayed distinct transcriptomic signatures: intestinal-type AGC was enriched in metabolic processes, diffuse-type in immune and signal transduction pathways, and mixed-type in Ras/MAPK/ErbB and NF-&#x3ba;B signaling pathways. Correlation analysis between the 8870 DEGs and seven differentially abundant bacterial species (e.g., Serratia surfactantfaciens, Pseudomonas protegens, Prevotella jejuni, and Streptococcus infantis) revealed 13199 significant correlations. Among these, S. surfactantfaciens and P. protegens exhibited the strongest connectivity with host genes. Functionally, the correlated DEGs were involved in ECM structure, cell cycle progression, immune and inflammatory responses, cellular proliferation and differentiation, and metabolic processes.<br><br>CONCLUSIONS: Our findings demonstrated phenotype- and tissue-specific regulation of host gene expression in AGC and revealed extensive host-microbe interactions. This work fills a critical gap in multi-omics research on AGC in the Northwest Chinese population and suggests potential diagnostic and therapeutic targets for AGC.}, }
@article {pmid42082029, year = {2026}, author = {Hou, Y and Ren, B and Song, J and Li, P and Xue, Z and Zhao, Y and Dzakpasu, M}, title = {Antibiotics removal and nutrient transformation in constructed wetlands using novel aluminum Sludge-Derived Substrates.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134779}, doi = {10.1016/j.biortech.2026.134779}, pmid = {42082029}, issn = {1873-2976}, abstract = {The widespread use and environmental persistence of norfloxacin (NOR) and sulfamerazine (SMR) have raised concerns over their impacts on aquatic systems and biological nutrient removal. Constructed wetlands (CWs) offer a sustainable, low-cost approach for antibiotic abatement, yet the mechanisms by which NOR and SMR influence microbial nutrient transformation in CWs remain unclear. Here, alum sludge was repurposed as a novel substrate (NALS) in vertical flow CWs, providing a dual pathway for valorizing waste while targeting simultaneous antibiotic and nutrient removal. The systems effectively removed both NOR and SMR (70-77%) under environmentally relevant concentrations (3 and 10 mg/L) and maintained robust nutrient elimination, with COD removal of 75-81%, TP > 90%, and peak NH4[+]-N and NO3[-]-N removals of 93% and 88%, respectively. High antibiotic levels inhibited COD and TP removal, whereas low concentrations stimulated TP removal. Notably, elevated NOR impaired NH4[+]-N and TN removal, while SMR showed negligible effects on ammonium dynamics. Metagenomic analysis revealed that both antibiotics distinctly suppressed microbial communities across taxonomic levels and disrupted functional genes related to nitrification, denitrification, and nitrogen fixation. This work demonstrates the efficacy of NALS-based CWs in co-removing antibiotics and nutrients, while offering mechanistic insights into how antibiotic exposure reshapes microbial structure and function-advancing the design of sustainable treatment systems for antibiotic-laden wastewater.}, }
@article {pmid42082030, year = {2026}, author = {Li, D and Zhao, Z and Li, H}, title = {Achieving nitrogen removal in the integrated upper fixed-biofilm activated sludge reactor without recirculation: Differential protein and metagenomic analysis.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134774}, doi = {10.1016/j.biortech.2026.134774}, pmid = {42082030}, issn = {1873-2976}, abstract = {The Integrated Fixed-film Activated Sludge (IFAS) system emerges as an advanced nitrogen removal technology, particularly effective for treating high-nitrogen wastewater due to its sophisticated configuration. This research introduces an enhanced Integrated Upper Fixed-film Activated Sludge (IUFAS) reactor featuring a two-stage series design. By strategically positioning carrier media in the upper compartment and implementing controlled influent distribution with aeration in the lower section, the system achieves functional compartmentalization within a single reactor without liquid and sludge recirculation. Experimental results under influent conditions of chemical oxygen demand/total nitrogen (C/N) ratio (4 ∼ 5) and hydraulic retention time (10 h) confirmed effective nitrogen removal, evidenced by effluent total nitrogen consistently below 7 mg N/L and removal efficiency exceeding 87%. Notably, the optimized IUFAS configuration achieved functional zoning by establishing a pronounced dissolved oxygen gradient between the upper (0.1 ∼ 0.7 mg/L) and bottom compartments (0.3 ∼ 3.6 mg/L). This oxygen stratification facilitated distinct nitrogen removal pathways, including stable anaerobic ammonium oxidation (Anammox) as evidenced by successful Candidatus Brocadia enrichment in the secondary reactor's upper zone. Microbial analysis further indicated potential modulation of electron flow by sulfate-reducing bacteria and sulfur-driven denitrifying bacteria, whose synergistic activity optimized electron transfer pathways and enhanced denitrification efficiency. Additionally, microalgae reduced aeration demand, lowering energy consumption. These findings propose novel strategies for optimizing carbon source allocation in nitrogen removal processes, supporting the development of energy-efficient wastewater treatment systems.}, }
@article {pmid42082383, year = {2026}, author = {Asthana, S and Bhat, AD and Mahadevan, G and Kothegala, L and Negi, S and Yadav, S and Sudhakaran, A and Roy, A and Makwana, M and Patel, R and Rao B, H and George, CE and Gayen, S and Shukla, S and Jhunjhunwala, S and Sen, P and Kaur, P and Bhat, R and Saini, DK and ,  and , }, title = {The BHARAT study: a multi-modal, multi-omics investigation of aging signatures in the Indian population.}, journal = {Aging}, volume = {18}, number = {1}, pages = {380-396}, doi = {10.18632/aging.206373}, pmid = {42082383}, issn = {1945-4589}, mesh = {Humans ; India ; Male ; *Aging/genetics/metabolism ; Cross-Sectional Studies ; Female ; Middle Aged ; Aged ; Adult ; Biomarkers ; Adolescent ; Young Adult ; Metabolomics ; Proteomics ; *Healthy Aging ; Life Style ; Multiomics ; }, abstract = {India is undergoing a rapid demographic transition, with its elderly population projected to exceed 347 million by 2050. Although aging is the primary risk factor for multiple chronic diseases, most biological age (BA) models have been developed for Western populations, with limited applicability to Indian demographics. The BHARAT study (Biomarkers of Healthy Aging, Resilience, Adversity, and Transitions) aims to develop and validate composite signatures of aging in the Indian population by integrating multi-omics, biochemical, clinical, and lifestyle data. The BHARAT study is a multi-center, cross-sectional observational study designed using a hub-and-spoke model, with the Indian Institute of Science (IISc) serving as the central hub for omics analyses, biobanking, and data integration. Participants are stratified into five age groups (18-29, 30-44, 45-59, 60-74, ≥75 years) with balanced rural-urban and gender representation. The study primarily includes healthy participants, excluding those with chronic diseases that are not resolved by medication. Data collection encompasses comprehensive clinical and cognitive assessments, lifestyle and quality-of-life questionnaires, and biological sampling (including blood, urine, stool, cheek swabs, and hair). Multi-omics profiling spans epigenomics, proteomics, metabolomics, lipidomics, metagenomics, and immune phenotyping, integrating untargeted discovery-based Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) with targeted assays under harmonized protocols and quality-controlled biobanking standards. As the first large-scale, discovery-driven aging cohort in India, BHARAT will generate population-specific reference datasets, (re)train and calibrate biological clocks, develop a data-driven framework for organ-specific clocks, and identify biomarkers of physiological resilience and decline. Given that presently this study is cross-sectional in design, it will help establish a scalable framework for subsequent longitudinal and translational research to develop context-specific diagnostics, predictive models, and therapeutic targets for healthy aging in India.}, }
@article {pmid42082531, year = {2026}, author = {An, K and Wang, D and Qu, Y and Yu, H and Liang, H and Mao, Z and Xue, Z and Li, J}, title = {Branched-chain amino acids ameliorate CD4[+] T-cell-associated gut immune inflammation in Parkinson's disease.}, journal = {NPJ Parkinson's disease}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41531-026-01375-y}, pmid = {42082531}, issn = {2373-8057}, support = {81901303//National Natural Scientific Foundation of China/ ; 82471273//National Natural Scientific Foundation of China/ ; 82301621//National Natural Scientific Foundation of China/ ; }, abstract = {Previous studies have shown that alterations in the gut microbiota and its derived metabolites, branched-chain amino acids (BCAAs), are correlated with T-cell-associated immune imbalance and Parkinson's disease (PD). However, the associations among BCAAs, gastrointestinal dysfunction and T-cell-related gut inflammation remain unclear. This study showed that the constipation symptoms in the PD mice persisted after chronic MPTP treatment. An imbalance in the CD4[+] T-cell subtypes was observed in the colonic lamina propria (cLP), mesenteric lymph nodes (mLNs), and spleen. Metagenomic and metabolomic analyses showed that microbial dysbiosis promoted BCAA degradation rather than biosynthesis, and reduced BCAA levels were confirmed in the serum. BCAA supplementation alleviated constipation symptoms and increased Th1 and Th17 cell infiltration in the cLP, mLNs and spleen were significantly attenuated after BCAA treatment. This study highlights the therapeutic value of BCAAs in mitigating gut immune inflammation-associated constipation symptoms in PD.}, }
@article {pmid42082533, year = {2026}, author = {Tamang, S and Sherpa, MT and Najar, IN and Kumar, S and Das, S and Sharma, P and Das, N and Chowdhury, R and Thousen, R and Ranjan, RK and Pandey, P and Thakur, N}, title = {Metagenomic analysis of bacterial diversity, antibiotic resistance, and functional profiles in the ice core samples from two glaciers of Sikkim Himalaya.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-40915-7}, pmid = {42082533}, issn = {2045-2322}, support = {BT/PR41644/NER/95/1718/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; BT/PR41644/NER/95/1718/2021//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, abstract = {Glaciers cover a substantial portion of the world and are home to various biological populations. The Himalayas constitute the largest glaciated region outside the poles; hence, they are regarded as "The Third Pole" of the World. There are around 84 glaciers in the Teesta basin (Sikkim Himalaya). There is substantially less data available on the microbial diversity embedded in the glacial ice core samples of the Sikkim Himalaya, as well as their physico-chemistry and potential geomorphological hazards related to their retreat or decrease in snow-line cover. The present study aims to evaluate the microbial diversity in the glacier ice core region and the study area; therefore, two glaciers in the Sikkim Himalaya were chosen: Frey-Peak and Rathong Glacier. The bacterial diversity analysis reveals the prevalence of various phyla, including Pseudomonadota, Actinomycetota, Bacillota, and Bacteroidota. The random forest model reveals the significant contributions of various elements, including Na, Mg, K, Ca, and Zn, to the alpha diversity of the studied glaciers. Among physicochemical parameters, pH was found to contribute the most in shaping bacterial diversity. Cluster of Orthologous Groups (COG) analysis underscored a predominance of genes associated with amino acids (23.5%), carbohydrates (18.93%), lipids (10.88%), energy (17.26%), coenzymes (9.38%), and ion transport/metabolism (14.71%). KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology (KO) analysis revealed the presence of 4,915 to 96,954 genes. Interestingly, the metagenomic analysis revealed the presence of specific species of Bradyrhizobium, Beijerinckia, Burkholderia, and Corynebacterium, which are associated with nitrogen metabolism, suggesting their potential involvement in biogeochemical processes. Additionally, a total of 59 to 419 bacterial genes related to sulphur metabolism were deduced through the KEGG functional analysis. The study detected the presence of various antibiotic resistance genes corresponding to different classes of antibiotics, including aminoglycoside, tetracycline, fluoroquinolone, macrolide, and erythromycin. Network analysis reveals that antibiotic resistance genes primarily interact with the phyla Pseudomonadota, Bacillota, and Actinomycetota. The melting of glaciers, a significant effect of climate change, may release contaminants, antibiotic resistance genes, and pathogenic bacteria into free-flowing rivers, potentially impacting human health.}, }
@article {pmid42082982, year = {2026}, author = {Li, J and Guo, S and Yu, H and Hong, X and Nie, J and Sun, H}, title = {Thyroid functional state-dependent dysbiosis of gut microbiota in Hashimoto's thyroiditis: a cross-sectional metagenomic profiling study.}, journal = {Thyroid research}, volume = {19}, number = {1}, pages = {}, pmid = {42082982}, issn = {1756-6614}, abstract = {BACKGROUND: Hashimoto's thyroiditis (HT) is a prevalent autoimmune thyroid disease (AITD) closely linked to genetic predisposition and environmental factors. Gut microbiota dysbiosis has recently been implicated as a critical contributor to AITDs' pathogenesis. Our study aims to systematically investigate the dynamic alterations in gut microbial communities under varying thyroid functional statuses and elucidate their underlying mechanisms.<br><br>METHODS: 67 HT patients with varying thyroid functional statuses and 23 healthy controls were enrolled. Fecal 16&#xa0;S rDNA sequencing and analyses (alpha diversity, LEfSe, correlation, functional pathways) assessed microbiota-thyroid function links.<br><br>RESULTS: HT patients with hypo/hyperthyroidism had lower gut microbiota richness than euthyroid patients (more reduced in hyperthyroidism). The hyperthyroid group exhibited enrichment of Fusobacterium, the hypothyroid group was dominated by Clostridium sensu stricto_1, and the euthyroid group showed a predominance of short-chain fatty acid (SCFA)-producing bacteria (e.g., Lactobacillus). Clostridium sensu stricto_1 positively correlated with TPO-Ab levels but negatively correlated with FT3.Pro-inflammatory genera(e.g., Escherichia-Shigella, Streptococcus) demonstrated negative correlations with FT3.Functional prediction analysis revealed potential associations with L-tyrosine degradation in the hyperthyroid group, reduced proportions of bile acid metabolism pathways in the hypothyroid group, and enriched proportions of fatty acid metabolism pathways in the euthyroid group.<br><br>CONCLUSIONS: This study revealed that gut microbiota dysbiosis is closely associated with thyroid functional statuses in HT. Specific bacterial genera, such as Clostridium sensu stricto_1 and Fusobacterium, may contribute to immune regulation and disease progression. The dynamic alterations in gut microbial profiles provide potential biomarkers for precision diagnosis and treatment of HT.}, }
@article {pmid42083021, year = {2026}, author = {Han, Y and Cui, J and Huang, X and Guo, P and Yang, S}, title = {Microbial inoculants with straw mediate degradation-level-specific changes in soil carbon cycling genes and microbial community.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00898-4}, pmid = {42083021}, issn = {2524-6372}, support = {2022YFD1500600//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: Enhancing soil organic carbon (SOC) sequestration in degraded lands is critical for climate mitigation and sustainable agriculture. While straw amendment combined with microbial inoculants holds great promise, the underlying mechanisms governing its impact on soil microbiome and carbon cycling genes remain poorly understood.<br><br>RESULTS: Here, we employed metagenomic sequencing to analyze responses in soil carbon (C) cycling genes, microbial community structure, and functional profiles across three degradation levels (severely, moderately, and non-degraded) of cinnamon soils under straw application alone or in combination with microbial inoculants. Results showed that both straw and straw-microbial inoculants treatments significantly improved soil properties, with improvements in available nitrogen and microbial biomass carbon (severe degradation), SOC (moderate degradation), and available nutrients (non-degradation). The combined application notably reshaped microbial communities by enhancing bacterial alpha diversity while reducing fungal diversity, and strengthened the relationship of relevant key soil C genes in severely degraded soils. Soil pH exhibited significant positive correlations with soil C cycling genes. Key bacterial genera (Sphingomonas, Bradyrhizobium) showed strong associations with ABC transporters and glycoside hydrolases, and fungal genus (Chaetomium) linked to pyruvate and purine metabolism. Importantly, we observed degradation-level specificity: straw addition significantly increased the abundance of the amylase gene K01214 (encoding &#x3b1;-amylase for starch hydrolysis) in severely degraded soils, whereas the straw-inoculant combination enriched the chitinase gene K01207 (encoding chitinase for chitin hydrolysis) in moderately degraded soils.<br><br>CONCLUSIONS: Accordingly, we propose targeted application of straw with a customized chitinolytic-cellulolytic synthetic microbial community (1-5% of straw mass) to restore carbon cycling functions in degraded soils, while adopting optimized agronomic management to preserve microbiome stability in non-degraded soils. Our findings provide novel insights into microbial-mediated carbon cycling and a foundation for targeted soil restoration.}, }
@article {pmid42083059, year = {2026}, author = {Diop, K and Benlaïfaoui, M and Hunter, S and Méndez-Salazar, EO and Hakozaki, T and Richard, C and Prifti, DK and Kourtian, S and Proulx-Rocray, F and Naimi, S and Ponce, M and Messaoudene, M and Cauchois, F and Belkaid, W and Bataille, V and Lee, K and Mihalcioiu, C and Watson, IR and Elkrief, A and Routy, B}, title = {Metagenomics and culturomics reveal the dual role of the gut microbiome in the development of immune-related toxicities and the efficacy of immune checkpoint inhibitors in cancer.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02419-4}, pmid = {42083059}, issn = {2049-2618}, support = {284894//Fonds de recherche du Qu&#xe9;bec/ ; }, abstract = {BACKGROUND: Despite their major impact on cancer treatment, immune checkpoint inhibitors (ICI) are frequently associated with immune-related adverse events (irAE). Growing evidence suggests that the occurrence of irAE may be correlated with enhanced ICI efficacy, although the underlying mechanisms remain unknown. Most studies investigating the role of the gut microbiome in oncology have relied on sequencing approaches, particularly shotgun metagenomics. Although microbiome profiling revealed strong associations between specific bacterial taxa and clinical outcomes, it has limitations, including an inability to detect low-abundance bacteria and to recover live cultivable bacteria. To overcome these limitations, we combined shotgun metagenomics and culturomics on fecal samples collected from patients with melanoma and non-small cell lung cancer (NSCLC), at baseline and at the onset of immune related (ir)-colitis.<br><br>RESULTS: We first validated across three independent cohorts of 589 patients with melanoma or NSCLC treated with ICI that grade&#x2009;&#x2265;&#x2009;2 irAE were associated with significantly longer overall survival (OS) and progression-free survival (PFS). Complementary analysis using shotgun metagenomics and culturomics revealed that patients who developed grade&#x2009;&#x2265;&#x2009;2 irAE had a lower alpha diversity compared to those who did not develop grade&#x2009;&#x2265;&#x2009;2 irAE. Metagenomics results showed enrichment of Ruminococcus gnavus and Streptococcus vestibularis at baseline in grade&#x2009;&#x2265;&#x2009;2 irAE patients, while Clostridium paraputrificum and Streptococcus spp. were isolated by culturomics from baseline stool samples from ir-colitis patients. Longitudinal analysis of paired stool samples revealed a shift in microbiome composition with enrichment of Paraclostridium bifermentans and Clostridium paraputrificum, lower lipopolysaccharide and higher flagellin concentrations at baseline compared with the time of ir-colitis. Fecal microbiome transplantation from a patient with ir-colitis into mice induced surrogate markers of colonic inflammation and enhanced the anti-tumor activity of combined anti-PD-1/CTLA-4. P. bifermentans isolated from this patient sample demonstrated direct epithelial barrier disruption in Caco-2 monolayers, characterized by decreased ZO-1 and Occludin&#xa0;immunofluorescence signal and increased TNF-&#x3b1; and IL-1&#x3b2; expression. Moreover, in the dextran sodium sulfate (DSS) colitis model, P. bifermentans worsened weight loss. In a separate tumor model, it amplified the anti-tumor effect of dual ICI. This beneficial effect was also&#xa0;maintained after treatment with P. bifermentans&#x2009;<&#x2009;3&#xa0;kDa filtered supernatant.<br><br>CONCLUSION: Altogether, our results suggest that P. bifermentans promotes subclinical colitis while increasing the efficacy of dual ICI. This provides a potential microbiome-derived link between irAE and improved anti-tumor responses. Video Abstract.}, }
@article {pmid42083116, year = {2026}, author = {Onohuean, FE and Onohuean, M and Olot, H and Onohuean, H}, title = {Poor Glycemic Control in East Africa: Prevalence, Risk Factors and Public Health Implications in Diabetes Management.}, journal = {Endocrinology, diabetes &amp; metabolism}, volume = {9}, number = {3}, pages = {e70233}, doi = {10.1002/edm2.70233}, pmid = {42083116}, issn = {2398-9238}, mesh = {Humans ; *Glycemic Control/statistics &amp; numerical data ; Africa, Eastern/epidemiology ; Risk Factors ; Prevalence ; *Public Health ; *Diabetes Mellitus/epidemiology/therapy/blood ; Cross-Sectional Studies ; Blood Glucose/analysis ; Glycated Hemoglobin/analysis ; *Diabetes Mellitus, Type 2/epidemiology/blood/therapy ; }, abstract = {BACKGROUND: Diabetes mellitus remains a major public health concern in East Africa, and poor glycaemic control continues to drive avoidable complications, deaths and pressure on already stretched health systems.<br><br>OBJECTIVE: To estimate the prevalence of poor glycemic control and describe the main factors associated with it among people living with diabetes in East Africa.<br><br>METHODS: This review synthesized evidence from observational studies, cross-sectional surveys and regional health databases identified through PubMed, Scopus and Web of Science, following PRISMA guidance. Sociodemographic, clinical and behavioural indicators were examined to identify common patterns and predictors of poor glycaemic control. The review also considered how measurement approaches shaped reported estimates.<br><br>RESULTS: Fifty records were identified across PubMed (10), Scopus (23) and Web of Science (17). After screening, 37 records were eligible for full-text review, and 15 studies met the inclusion criteria for evidence synthesis. Across the region, poor glycemic control was consistently high, ranging from 60% to 85%. Most studies were facility-based and cross-sectional. Glycemic control was assessed mainly using HbA1c, commonly defined as &#x2265;&#x2009;7% or >&#x2009;7.5%, and less frequently by fasting blood glucose, typically &#x2265;&#x2009;7.2&#x2009;mmol/L or&#x2009;>&#x2009;130&#x2009;mg/dL. Type 2 diabetes was the dominant population studied, with fewer mixed cohorts and only one study focused on type 1 diabetes. Factors repeatedly linked to poor control included older age, longer duration of diabetes, poor medication adherence, limited access to care, low health literacy, inadequate diabetes education, insulin use, comorbidities, diabetic complications, unhealthy diet, physical inactivity, sedentary behaviour, substance use and limited self-management support.<br><br>CONCLUSION: Poor glycemic control is alarmingly common among people with diabetes in East Africa and reflects intertwined clinical, behavioural and health-system challenges. Region-specific strategies are needed to strengthen primary care, improve diabetes education, expand affordable monitoring and treatment and enhance surveillance to guide policy and resource allocation.}, }
@article {pmid42083299, year = {2026}, author = {Qin, R and Wang, C and Cong, M and Tian, L and Li, N}, title = {Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pneumonia in Patients With Cancer.}, journal = {Cancer medicine}, volume = {15}, number = {5}, pages = {e71915}, doi = {10.1002/cam4.71915}, pmid = {42083299}, issn = {2045-7634}, support = {JYKY2024-0050409022//Beijing Vlove Charity Foundation/ ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Retrospective Studies ; *Neoplasms/complications ; Aged ; *Pneumonia/diagnosis/microbiology ; Sputum/microbiology ; Adult ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: With the development of new sequencing technologies, metagenomic next-generation sequencing (mNGS) has become a diagnostic tool for respiratory tract infections. Patients with cancer may develop pneumonia caused by infections or antitumor therapy. Therefore, pneumonia in patients with cancer is more complex than that in healthy individuals. Currently, few reports are available on the use of mNGS for diagnosing pneumonia in patients with cancer.<br><br>METHODS: In this retrospective study, 14 patients with cancer diagnosed with pneumonia in March 2023 were enrolled from the Emergency Department of the Chinese Academy of Medical Sciences Cancer Hospital. Sputum samples from the patients were examined using conventional tests and mNGS to identify pathogens. The mNGS and conventional test results were compared to assess the diagnostic yield in patients with cancer.<br><br>RESULTS: The overall pathogen detection rate of mNGS was 64.29% (9/14), with corresponding diagnostic sensitivity, specificity, false-negative rate and false-positive rate of 90.00%, 25.00%, 10.00% and 75.00%, respectively. Among 13 paired sputum specimens, mNGS exhibited a numerically higher pathogen detection rate (61.54%, 8/13) than conventional diagnostic assays (38.46%, 5/13). McNemar's paired chi-square test demonstrated no statistically significant difference between the two detection methods (p&#x2009;=&#x2009;0.37), and Kappa concordance analysis generated a coefficient of 0.27 (p&#x2009;=&#x2009;0.23), suggesting poor inter-method consistency. Compared with conventional tests, mNGS detected additional pathogens in 8 specimens and identified a greater number of pathogens in 9/14 (64%) samples. Moreover, mNGS results led to diagnostic revisions and subsequent antimicrobial therapy adjustments in 64% (9/14) of enrolled patients. Additionally, mNGS detected antibiotic resistance genes in five patients, which provided guidance for antibiotic selection.<br><br>CONCLUSIONS: Metagenomic next-generation sequencing (mNGS) showed potential value in pathogen detection, as it appeared to identify pathogens more rapidly and comprehensively than conventional methods. It may provide auxiliary support for the diagnosis and treatment of pneumonia in this vulnerable population.}, }
@article {pmid42083599, year = {2026}, author = {Kozlova, AS and Zgoda, AV and Petushkova, NA and Bolochenkov, NA and Zgoda, VG and Salnitska, MA and Kazakov, DV and Lisitsa, AV}, title = {The Microbiomic Metaproteome of the Taiga Tick Ixodes persulcatus from the Tyumen Region.}, journal = {Acta naturae}, volume = {18}, number = {1}, pages = {55-63}, pmid = {42083599}, issn = {2075-8251}, abstract = {Metagenomic studies have revealed the taxonomic composition of the taiga tick (Ixodes persulca tus) microbiome, whereas metaproteomic data has provided information on the biochemically active fraction of the microbial community residing in the tick. The aim of this study was to characterize the biological pro cesses taking place within the microbiome of the taiga tick I. persulcatus using a metaproteomic approach. To expand the range of identifiable proteins, we used two trypsin concentrations in sample preparation for mass spectrometric analysis. The metaproteomes of unfed female and male ticks were analyzed, which ena bled identification of protein products encoded by 2,100 genes from microorganisms belonging to 203 bacteri al and fungal species. Increased abundance of proteins associated with Ascomycota fungi, particularly abun dant in females, were detected. Proteins from the pathogenic Rickettsia and Borrelia species were identified. These findings enable a transition from a taxonomic metagenomic description to a functional analysis of the microbial consortium role in the physiology of the vector tick, particularly given the identified microbiota differences related to the tick sex.}, }
@article {pmid42084116, year = {2026}, author = {Qi, J and Liang, C and Zhang, C and Wang, M and Wei, G and Jiao, S}, title = {Intensifying Aridity Undermines the Role of Soil Biodiversity in Supporting Ecosystem Stability.}, journal = {Global change biology}, volume = {32}, number = {5}, pages = {e70903}, doi = {10.1111/gcb.70903}, pmid = {42084116}, issn = {1365-2486}, support = {42477129//National Science Foundation of China/ ; JYB2025XDXM706//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; }, mesh = {*Biodiversity ; *Soil Microbiology ; *Climate Change ; China ; *Soil/chemistry ; *Ecosystem ; *Desert Climate ; }, abstract = {Biodiversity is widely recognized for enhancing ecosystem stability, yet its contribution is highly sensitive to climate change. However, whether and how climatic factors, particularly aridity, modulate the role of soil biodiversity in stabilizing ecosystems remains poorly understood. Here, we integrated a comprehensive soil survey of 265 dryland agricultural fields along a 3800 km east-west transect in China with a global meta-dataset encompassing 996 sites across six continents. Our analysis revealed a positive association between soil biodiversity and ecosystem stability, quantified using 11-year Normalized Difference Vegetation Index (NDVI) data (2012-2022). Critically, both our field data and global synthesis revealed that increasing aridity significantly weakened this biodiversity-stability relationship. The decline in soil microbial network complexity with increasing aridity partially explains this decoupling. Metagenomic analyses further showed that as aridity increased, microbial life history strategies shifted toward greater investment in stress tolerance at the expense of growth yield and resource acquisition. Together, our findings represent a substantial advance in revealing how intensifying aridity undermines the role of soil biodiversity in supporting ecosystem stability, and highlight the importance of microbial network complexity and life history strategies as key predictors of biodiversity-stability relationships under global change.}, }
@article {pmid42084385, year = {2026}, author = {Rodríguez, P and Simon, SA and Probst, AJ and Magnabosco, C}, title = {Depth-associated selection and drift shape persistent microbial populations in Holocene lake sediments.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0150025}, doi = {10.1128/msystems.01500-25}, pmid = {42084385}, issn = {2379-5077}, abstract = {Cosmopolitan microbial lineages are found in anoxic sediments worldwide, but the details about their ecology and evolution remain underexplored. In this study, we identified persistent populations from these cosmopolitan lineages belonging to Planctomycetes, Chloroflexi Atribacteria, and Candidatus Bathyarchaeia from an ~8,000-year sedimentary sequence. To investigate the genomic variations within these persistent populations, a pangenome of each population was constructed using all non-redundant metagenome-assembled genomes (MAGs) recovered from the sedimentary sequence and was screened for enriched functional genes, single-nucleotide polymorphism (SNP) density, dN/DS ratios, and pseudogene content. Our results show that the majority of persistent populations studied possess large variable genomes enriched for energy conservation and transcriptional regulation functions with increasing depth, whereas Planctomycetes retain a highly conserved, SNP-poor core genome. Analysis of SNPs across depths indicates progressive isolation with burial, while a subset of core genes shows signatures of positive selection. Collectively, the data support depth-associated selection acting alongside drift across Lake Cadagno's persistent sedimentary lineages.IMPORTANCEThroughout the subsurface, multiple examples of "evolutionary stasis" have been reported in microbial lineages that exhibit lower rates of metabolic activity and cellular turnover. This study uses an ~8,000-year sedimentary record of Lake Cadagno to evaluate how persistent populations of cosmopolitan bacteria and archaea have changed with burial and identifies signals of progressive genetic isolation along with positive selection of population-specific subsets of core genes with depth. Together, these changes show that Lake Cadagno's persistent populations are not in stasis but diverge over time and burial.}, }
@article {pmid42084478, year = {2026}, author = {Wang, C and Dou, P and Wang, Y and Li, X and Zhang, Y and Ma, X}, title = {A wolf in sheep's clothing: An unusual zoonotic pathogen in peritoneal dialysis effluent and an important diagnostic strategy.}, journal = {Peritoneal dialysis international : journal of the International Society for Peritoneal Dialysis}, volume = {}, number = {}, pages = {8968608261448060}, doi = {10.1177/08968608261448060}, pmid = {42084478}, issn = {1718-4304}, abstract = {Brucellosis is an infectious disease characterized by a natural foci, caused by Brucella, a genus of Gram-negative bacilli known for its obligate aerobic growth and capability for intracellular parasitism. This pathogen can be transmitted zoonotically between animals and humans. Due to its mechanism of intracellular survival, monotherapy with a single antibiotic often proves ineffective in eradicating Brucella. Therefore, clinical management necessitates the implementation of multidrug combination therapy alongside extended therapeutic regimens to achieve optimal bacteriological clearance. Conventional diagnostic methods, such as bacterial culture and serological testing, are frequently hindered by the fastidious growth requirements of the pathogen and the risk of false-positive serological cross-reactivity. These limitations may result in delayed diagnosis or unnecessary interventions. Recent advancements in molecular biology-particularly genomic analysis technologies-have revolutionized pathogen detection by facilitating rapid and precise identification of elusive pathogens. This study reports the first documented case of refractory peritoneal dialysis-associated peritonitis caused by Brucella diagnosed via metagenomic next-generation sequencing (mNGS). By employing mNGS to identify the pathogen, we summarize the clinical characteristics of this case and highlight the diagnostic advantages of this technology. Our findings aim to guide clinicians in selecting appropriate diagnostic approaches for similar cases, avoiding unnecessary delays and optimizing resource utilization in clinical practice.}, }
@article {pmid42084497, year = {2026}, author = {Leech, J and Obafemi, YD and Breselge, S and Aremu, T and Obadina, AO and Itohan, ME and Ezekiel, CN and Parkouda, C and Tankoano, A and Traoré, K and Banwo, K and Kunadu, AP and Madilo, FK and Sanni, AI and Ogunremi, OR and Onipede, G and Odeny, DA and Otieno, C and Claesson, MJ and Cotter, PD}, title = {Characterizing microbiomes of African fermented foods in a global context.}, journal = {Microbiology (Reading, England)}, volume = {172}, number = {5}, pages = {}, doi = {10.1099/mic.0.001695}, pmid = {42084497}, issn = {1465-2080}, mesh = {*Fermented Foods/microbiology ; *Microbiota/genetics ; Metagenomics ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Food Microbiology ; Metagenome ; Fermentation ; Africa ; Kenya ; Burkina Faso ; Ghana ; }, abstract = {Fermentation plays a vital role globally, shaping traditional diets and enhancing food preservation, nutrition and flavour. With over 5,000 varieties of fermented foods globally, the microbiomes of many of these have yet to be explored, particularly with respect to those produced in some regions of Africa. To begin to address this knowledge gap, we conducted a shotgun metagenomics-based analysis of 91 fermented foods produced in Burkina Faso, Ghana, Kenya and Nigeria and compared them to a larger, global curated Food Metagenomic Database (cFMD). As for other studies of fermented food microbiomes in general, the substrate that was fermented emerged as the primary determinant of microbial beta diversity within the current African dataset and between the broader cFMD dataset. However, it was notable that the newly studied samples showed a small but statistically significant geographic signal. The African samples also displayed more alpha diversity than the global dataset, with cassava-, seed- and grain-based samples having the highest alpha diversity among the African foods. We also characterized the functional and antimicrobial profiles of all food-derived metagenome-assembled genomes (MAGs), noting the prevalence of pathways associated with carbohydrate metabolism across both African and non-African MAGs and an absence of known antimicrobial resistance genes in numerous genera. These findings not only expand our fundamental understanding of Africa's under-studied fermented food microbiomes but also lay the foundation for starter culture development tailored to local substrates and conditions, fostering opportunities to enhance product safety, quality and scalability while retaining key characteristics associated with the original, artisanal product.}, }
@article {pmid42084683, year = {2026}, author = {Maurya, S and Shukla, AK and Reddy, B and Singh, AK and Singh, VK and Tripathi, M}, title = {Metagenomic insights into microbial community, antibiotic resistance genes, and virulence factor in Saryu River water, India.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {42084683}, issn = {1614-7499}, abstract = {A river confluence is an important ecosystem to investigate the microbial community and functional profile. Even after the enormous applications of trace elements and antibiotics, their release into the environment causes pollution and selective pressure that facilitate the proliferation and dissemination of resistance genes against antibiotics, metals and biocides among bacterial communities. Metagenomic exploration plays a pivotal role in deciphering riverine ecosystems and offers valuable insights for the mitigation of pollution and the dissemination of resistance genes. Monitoring microbial diversity could aid in identifying various prokaryotes, pathogens, and pollutants, including dyes and their associated resistance genes. Therefore, we aimed to elucidate the occurrence of resistance genes and virulence factors in the microbial community of Saryu River water using high-throughput metagenomics coupled with bioinformatic analyses. The highly dominant antibiotic resistance gene (ARG) types identified were rifampin, tetracycline, macrolide, polymyxin and rifampicin multidrug/efflux. ARGs such as rpoB2, Txr, adeF, tetB(P), and acrB were found to be abundant in Saryu River water. Among the detected MRG subtypes, namely, ruvB and arsB, the most abundant are in water. Further, the biocides against which the resistance was identified were ethidium bromide, triclosan, sodium dodecyl sulfate, etc. Among the virulence factors, tufa, htpB (adherence), Gmd (immune-modulation), cheD (motility), and clpV1 (effector-delivery-system) were found to be highly prevalent. Taxonomic classification revealed that Cyanobateriota, followed by Pseudomonadota (Proteobacteria) and Bacteroidota were the dominant phyla in the river water. Microcystis was the most dominant genus, followed by Desulfomicrobium and Dechloromonas. The present study shows that antibiotics and metals are the major sources of resistance genes development and dissemination in the environment.. Further, this is a preliminary study based on a single composite sample, representing a "snapshot" at a specific time and location. The present study highlights the persistence of ARGs, MRGs, biocides, and virulence factors in Saryu River water and provides valuable baseline data for risk assessment.}, }
@article {pmid42084764, year = {2026}, author = {Joshi, G and Khannam, KS}, title = {Marine microbiomes and their expanding role in biotechnological potential: a systematic review.}, journal = {Archives of microbiology}, volume = {208}, number = {7}, pages = {}, pmid = {42084764}, issn = {1432-072X}, mesh = {*Microbiota ; *Biotechnology ; *Seawater/microbiology ; *Bacteria/metabolism/classification/genetics/isolation &amp; purification ; Ecosystem ; Biodegradation, Environmental ; }, abstract = {Marine bacteria are present almost everywhere in the ocean environment and are essential to many biogeochemical processes. The perspectives of ecologists and evolutionary biologists on the significance of microbes in ecosystem function are shifting as a result of exploring the marine microbiomes. This is especially true in ocean habitats, where microbes comprise the bulk of the biomass and are responsible for the majority of the planet's key biogeochemical cycles, including those that influence the global climate. Emerging research suggests that many ecosystem services provided by coastal marine environments depend on intricate interactions between groups of microbes and the environment or their hosts. The structure, variety, and functional capability of marine microbial populations have been revealed on a global scale thanks to recent developments in molecular ecology techniques. Over-recent-decades, industrialization and urbanization have led to widespread contamination of oceans. These contaminants accumulate in seawater and sediments, particularly in coastal areas, posing risks to marine ecosystems and human health. Marine microorganisms possess diverse catalytic abilities and extreme environmental tolerance, making them suitable for bioremediation of toxins. Effective-degradation of pollutants often depends on syntrophic-interactions within microbial communities, highlighting the importance of understanding their collaboration and communication for marine resource management. Here, we assess the current level of knowledge about marine microbiome research and highlight key issues within this developing field of study. The review aims to enhance understanding of marine microbiome's roles and potential uses in biogeochemical analysis, biotechnology, and environmental remediation, which could support sustainable and circular business models for future generations.}, }
@article {pmid42085791, year = {2026}, author = {Besharati Fard, M and Ahmadi, N and Chen, Y and How, SW and De Vrieze, J and Wu, D}, title = {Tetracycline and ciprofloxacin reduce nitrification and denitrification activity and alter microbial community composition and activity in microalgal-bacterial aerobic granular sludge.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142255}, doi = {10.1016/j.jhazmat.2026.142255}, pmid = {42085791}, issn = {1873-3336}, abstract = {Microalgal-bacterial aerobic granular sludge (MB-AGS) systems offer promising potential for wastewater treatment under chemical stress. However, their performance in the presence of antibiotics remains poorly understood. This study evaluated the response of MB-AGS to 1000 µg/L of tetracycline and ciprofloxacin in two separate bioreactors operated under alternating dark (60 min) and light (170 min) cycles at 20 °C. Chemical oxygen demand (COD) removal remained stable at 90 ± 4% (tetracycline) and 91 ± 6% (ciprofloxacin) over 80 days, suggesting that COD conversion was not impacted by antibiotic exposure. However, phosphate removal declined from ∼63% (antibiotic-free bioreactors) to 45 ± 6% (under tetracycline exposure) and 38 ± 8% (under ciprofloxacin exposure) after addition of antibiotics. Ciprofloxacin inhibited nitrification (declined to ∼50% NH4[+] removal), associated with reduced abundance of Nitrosomonas, while tetracycline impacted denitrification, evidenced by a lower Thauera abundance. Despite these impacts, the system removed 88.3 ± 5.6% of tetracycline and 69.5 ± 12.4% of ciprofloxacin, primarily through biosorption (for both antibiotics were more than 80%). Extracellular polymeric substances content increased by ∼19% under antibiotics exposure. Metagenomic analysis indicated changes in microbial community composition and function, while the overall antibiotic resistance gene profile remained relatively stable despite dynamic changes in individual resistance genes under antibiotic exposure. These findings demonstrate the strong potential of MB-AGS systems for effective organic carbon removal, while also highlighting opportunities to further enhance nutrient removal and mitigate antibiotic resistance genes under antibiotic stress.}, }
@article {pmid42070841, year = {2026}, author = {Li, S and Yan, X and Ndayishimiye, JC and Smirnov, A and Tsyganov, AN and Nassonova, E and Mazei, NG and Mazei, YA and Yang, J}, title = {Urban park metagenomics highlights sediments as a potential hotspot for CH4 and N2O emission across diverse habitats.}, journal = {Journal of environmental sciences (China)}, volume = {164}, number = {}, pages = {481-491}, doi = {10.1016/j.jes.2025.07.053}, pmid = {42070841}, issn = {1001-0742}, mesh = {*Methane/analysis ; Metagenomics ; *Geologic Sediments/microbiology/chemistry ; Parks, Recreational ; *Nitrous Oxide/analysis ; Ecosystem ; *Environmental Monitoring ; *Air Pollutants/analysis ; Greenhouse Gases/analysis ; Microbiota ; }, abstract = {Urban areas contribute the vast majority of greenhouse gas (GHG) emissions, and urban greenspaces, including urban parks, are being established to promote environmental health by mitigating GHG emissions. However, the diversity of CH4 and N2O cycling genes and microbiomes in urban park ecosystems remains poorly understood. Here, we sampled five types of habitats in subtropical urban parks, including moss, sediment, soil, tree hole, and water, to explore the microbial communities and microbially mediated CH4 and N2O cycling processes using metagenomic sequencing. We found strongly positive biodiversity-ecosystem-functioning (BEF) relationships in nitrogen cycling functions, as well as in CH4 cycling, except in sediment, indicating the microbial community in the sediment had reached function saturation for CH4 cycling. CH4 cycling was driven by a few specific microbial genera, whereas many microorganisms participated in the denitrification process. Microbes in sediment exhibited the highest CH4 and N2O metabolic potential among the five habitats, especially for methanogenesis and N2O production processes. Significant positive correlations were observed between the mcrA and N2O cycling genes, suggesting methanogenesis could be coupled with denitrification. Environmental factors, such as dissolved oxygen, total nitrogen, and total carbon greatly affected microbial community composition and functional gene families. These results highlight that pond sediments are an overlooked potential source of CH4 and N2O emissions, which may undermine the role of urban greenspace in reducing GHG emissions. Reducing nitrogen pollution and eutrophication is recommended to mitigate CH4 and N2O emissions from pond sediments in urban environments.}, }
@article {pmid42070844, year = {2026}, author = {Wu, C and Wu, Y and Pan, J and Lv, Y and Li, W and Hu, M and Wang, J and Su, S and Zou, Q and Xue, S}, title = {Evolution and role of manganese-transforming bacterial microorganisms during natural manganese-tailing succession.}, journal = {Journal of environmental sciences (China)}, volume = {164}, number = {}, pages = {516-525}, doi = {10.1016/j.jes.2026.01.018}, pmid = {42070844}, issn = {1001-0742}, mesh = {*Manganese/metabolism ; *Bacteria/metabolism ; Biodegradation, Environmental ; *Soil Microbiology ; *Soil Pollutants/metabolism ; Mining ; }, abstract = {The natural succession of tailings is critical for reducing their adverse environmental impacts. However, the current knowledge of the Mn-transforming microorganisms involved in the natural vegetation succession of Mn tailings is very limited. This study reveals for the first time the evolution of Mn-transforming microorganisms during vegetation succession in Mn tailing. The results revealed that the amount of reducible Mn increased during the succession process (divided into nake-land, bryophyte, herb and woody-plant stages), which is the most important geochemical property driving bacterial community diversity. Metagenomic functional profile analysis revealed that the abundance of genes involved in nutrient uptake, metal tolerance, and metal detoxification increased during succession. A total of 51 metagenome-assembled genomes (MAGs) were reconstructed, in which 6 encoding multicopper oxidase (cotA)-containing MAGs were identified. The relative abundance of these cotA-containing MAGs first increased but then decreased during succession. Notably, genes associated with carbon fixation and denitrification were also identified in these cotA-containing MAGs, indicating their roles in coupling the cycling of manganese, carbon and nitrogen. These results suggest that Mn(II)- oxidizing bacteria could be crucial for lowering Mn toxicity, obtaining nutrients, and potentially contributing to the ecological succession of Mn tailings. The investigation of Mn-transforming microorganisms (cotA-MAGs) has also contributed to understanding the succession mechanisms and restoration of Mn tailing ecosystems.}, }
@article {pmid42070845, year = {2026}, author = {Yan, S and Li, R and Shen, X and Zhu, Y and Li, Y and Xu, M and Xie, S}, title = {Unveiling the role of bacterial communities in carbon fixation of mangrove wetlands: Insights into the redox potential and biogeochemical interactions.}, journal = {Journal of environmental sciences (China)}, volume = {164}, number = {}, pages = {526-537}, doi = {10.1016/j.jes.2025.08.024}, pmid = {42070845}, issn = {1001-0742}, mesh = {*Wetlands ; *Carbon Cycle ; Oxidation-Reduction ; *Soil Microbiology ; *Bacteria/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Mangrove wetlands are crucial for carbon sequestration, however, the contributions of bacterial carbon fixation in these ecosystems are often overlooked, and the predominant pathways remains unknown. This gap seriously hinders the understanding and precise assessment of carbon sequestration. This study systematically investigates the pathways, rates, and influential factors of bacterial carbon fixation in mangrove wetlands, utilizing soils from various tidal zones and depths. Through an integrated approach that combines in situ metagenome sequencing, [13]CO2 tagging experiment, functional gene abundance measurement, and 16S rRNA sequencing, we provide the first evidence that the reverse tricarboxylic acid cycle is the predominant pathway for carbon (C) fixation in mangrove soils. The mangrove ecosystem was identified as a significant hotspot for bacterial carbon fixation, with rates in topsoil ranging from 15 to 63 mmol C/(m[2]·day), significantly influenced by environmental variables such as oxidation-reduction potential, and ammonium and nitrate concentrations. In deep soils, high carbon fixation rates were detected in low tidal zones but not in middle and high tidal zones, which did not align with the abundance of carbon fixation functional genes. Notably, we found a strong correlation between carbon fixation rates and nitrogen metabolism processes, underscoring the ecological interactions between these biogeochemical cycles. These findings greatly enhance our understanding of microbial contributions to carbon cycling in mangrove ecosystems and offer novel insights into blue carbon sequestration and the management of coastal wetlands under varying environmental conditions.}, }
@article {pmid42070879, year = {2026}, author = {Xin, Y and Liu, L and Chen, SH and Zhao, QB and Zheng, YM}, title = {Enhancing urban river self-purification through riverbed substrates configuration: A nature-based solution for nutrient removal and restoration planning.}, journal = {Journal of environmental sciences (China)}, volume = {164}, number = {}, pages = {95-108}, doi = {10.1016/j.jes.2026.01.038}, pmid = {42070879}, issn = {1001-0742}, mesh = {*Rivers/chemistry ; *Water Pollutants, Chemical/analysis ; Nitrogen/analysis ; *Environmental Restoration and Remediation/methods ; Nutrients ; Phosphorus/analysis ; }, abstract = {Appropriate riverbed substrates, as nature-based engineering components, are critical for enhancing nutrient mitigation and ecosystem sustainability in urban rivers. However, their role in regulating hydrologically mediated nutrient fluxes and biofilm functions remains unclear, limiting substrate-optimized design for urban river restoration. This study integrated machine learning modeling, scenario simulations, and metagenomic analysis to quantify substrate-driven interfacial nutrient removal efficiencies and uncover microbial regulation mechanisms. A back propagation neural network could accurately predict interfacial ammonium and total organic carbon removal efficiencies (RMSE: 0.59-6.92 mg/(L·h·m[2]), R[2]: 0.66-0.97), with retention time, temperature, dissolved oxygen, and nutrient load identified as key predictors. Building upon the model-predicted scenario results, analysis of similarity tests confirmed that substrate type significantly influenced interfacial nutrient removal efficiencies (R > 0.05, P < 0.001). Scoring metrics demonstrated fine sand (1295) and gravel (1281) gained higher total scores than other substrates (1110-1182), indicating higher interfacial nutrient removal capacities. Metagenomic analyses revealed that these differences were driven by divergence in microbial functional potential. Substrate type selectively enriched functional genes related to nitrogen and carbon cycling (R > 0.18, P < 0.05), with gravel microcosms showing significantly higher gene abundance (8.00 × 10[-4]-2.08 × 10[-3]), despite similar community compositions governed by stochastic assembly (R[2] > 0.84). Topological analysis revealed that redundancy of functional gene network significantly influenced ammonium removal efficiency (P < 0.05), with fine sand and gravel enhancing ammonium removal, while lower clustering coefficients in artificial filler and gravel microcosms significantly promoted total organic carbon removal. This study suggested that fine sand and gravel should be more effective riverbed substrates for enhancing interfacial nutrient removal in urban river restoration.}, }
@article {pmid42071059, year = {2026}, author = {Gajjar, K and Panchal, D and Chaudhary, M and Raval, I and Chaudhary, D and Patel, CK and Bagatharia, S and Joshi, C and Patel, A and Dharajiya, D}, title = {Multi-omics characterization of microbial and metabolite profiles of Jeevamrit and Ghanjeevamrit cow-based bioformulations used in sustainable agriculture.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-50831-5}, pmid = {42071059}, issn = {2045-2322}, support = {GSBTM/JD(R&amp;D)/661/2022-23/00172688//Gujarat State Biotechnology Mission (GSBTM)/ ; GSBTM/JD(R&amp;D)/661/2022-23/00172688//Gujarat State Biotechnology Mission (GSBTM)/ ; GSBTM/JD(R&amp;D)/661/2022-23/00172688//Gujarat State Biotechnology Mission (GSBTM)/ ; }, abstract = {Jeevamrit (JV) and Ghanjeevamrit (GH) are traditional cow-based bioformulations used in natural farming practices, and this study provides a comprehensive characterization of their microbial profiles via 16 S rRNA amplicon metagenomics and metabolite profiles via GC-MS and LC-MS analysis, with two different groups of samples: experimental preparation (EP) and farmer preparation (FP). JV and GH harbored diverse and functionally rich microbial communities, including Lactiplantibacillus, Arcobacter, Comamonas, Planifilum, Pseudomonas, Gp6, etc., associated with nutrient cycling, microbial activity, and plant growth promotion. Untargeted metabolomics revealed ~ 222 (GC-MS) and ~ 1049 (LC-MS) metabolites in Jeevamrit and ~ 96 (GC-MS) and ~ 1208 (LC-MS) metabolites in Ghanjeevamrit. These metabolites were primarily classified as organoheterocyclic compounds, organic acids, lipids, benzenoids, and organic oxygen/nitrogen compounds, and are functionally associated with nutrient solubilization, microbial metabolism, regulation of plant growth, and enhancement of stress tolerance. Multi-omics analysis revealed a clear separation of EP and FP groups with high inter-omics correlations (Jeevamrit up to r = 0.92; Ghanjeevamrit up to r = 0.91). Jeevamrit exhibited dense connectivity with predominance of positive microbial-metabolite associations, while Ghanjeevamrit displayed fewer and more balanced positive and negative correlations. Overall, the study demonstrates that Jeevamrit and Ghanjeevamrit are microbially diverse and metabolically rich bioformulations, reinforcing their roles in enhancing soil health and plant growth. Future works on strain-level diversity, functional pathways analysis, and field trials across different crops and soil types are needed for the standardization and optimization of natural farming inputs.}, }
@article {pmid42071227, year = {2026}, author = {Guo, S and Cao, M and Wu, J and Ma, W and Liang, D and Xie, H and Xie, Y and Luo, Z and Lai, P and Liu, D and Zeng, W and Zheng, J and Xing, M and Yin, X and Xia, M and He, Z}, title = {Parvimonas micra promotes carcinogenesis of colorectal cancer through phenyllactic acid-induced DNA damage.}, journal = {Clinical and translational medicine}, volume = {16}, number = {5}, pages = {e70667}, doi = {10.1002/ctm2.70667}, pmid = {42071227}, issn = {2001-1326}, support = {2022YFA1304000//National Key R&amp;D Program of China/ ; 2024B1111150001//Guangdong S&amp;T Program/ ; //National Key Clinical Discipline/ ; U21A20344//National Natural Science Foundation of China/ ; 82273346//National Natural Science Foundation of China/ ; 2020B1111170004//Guangdong Provincial Clinical Research Center for Digestive Diseases/ ; 2021B1212040017//Science and Technology Program of Guangdong Province, China/ ; 2024A04J4086//Science and Technology Program of Guangdong Province, China/ ; B2302036//Shenzhen Medical Research Special Fund Project Target disease/ ; 2023WST03//Key Laboratory Start-Up Project (Sixth Affiliated Hospital of Sun Yat-Sen University)/ ; }, mesh = {*Colorectal Neoplasms/microbiology/genetics/pathology/etiology ; Humans ; Animals ; *DNA Damage/drug effects ; Mice ; Male ; *Lactates/metabolism/adverse effects ; Gastrointestinal Microbiome ; *Carcinogenesis ; Female ; Feces/microbiology ; Middle Aged ; }, abstract = {Recent studies have demonstrated the significance of gut microbiota in the colorectal cancer (CRC) pathogenesis. But their role in carcinogenesis remains to be established. Thus, we established a clinical cohort and the faecal samples from CRC and healthy control were collected. Our metagenomic analysis found that the presence of Parvimonas micra exhibited the most significant relationship with the occurrence of CRC. Increased colonisation of P. micra in CRC was validated with analysis of 1379 faecal metagenomes from eight public cohorts. Untargeted metabolomics subsequently identified an accumulation of phenyllactic acid (PLA) in faecal samples from CRC patients. Higher concentration of PLA was detected in the supernatant from our isolated P. micra. Whole-genome sequencing confirmed that a series of genes associated with PLA biosynthesis such as pdhD were observed in the P. micra genome. Importantly, both P. micra and PLA-induced carcinogenesis in Apc[Min/+] and azoxymethane/dextran sulphate sodium salt mice model. The roles of P. micra and PLA in CRC development were associated with DNA damage. Engineered Escherichia coli BL21 that encoded the heterologous pdhD from P. micra could also induce DNA damage. Mechanically, PLA-induced DNA damage and CRC carcinogenesis were significantly alleviated in Ahr[-/-] mice. Aryl hydrocarbon receptor (AHR) inhibitor exhibited a therapeutic potential to reduce mice carcinogenesis. These findings established the role of P. micra and its metabolite, therefore providing diagnostic and therapeutic targets for treating CRC.}, }
@article {pmid42071909, year = {2026}, author = {Corrigan, A and Stockdale, S and Mackenzie, AM and Wilkinson, RG and Warren, H and Taylor-Pickard, J and Murphy, R}, title = {Rumen Microbiome Development in Lambs Following Maternal and Early-Life Prebiotic Mannan-Rich Fraction (MRF) Supplementation.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {8}, pages = {}, doi = {10.3390/ani16081137}, pmid = {42071909}, issn = {2076-2615}, support = {NA//Alltech (Ireland)/ ; }, abstract = {The early-life rumen microbiome is highly dynamic, shaped by dietary transitions and maternal influences. Several dietary additives have been studied during the pre- and post-weaning periods to improve animal welfare, growth performance, and farming efficiencies. This study investigated microbial community assembly and growth performance of lambs provided with a mannan-rich fraction (MRF) supplement, either through maternal supplementation, directly, or via a combination of both. Using metagenomic sequencing and gas chromatography, we found differences in rumen microbial alpha and beta diversity related to both sampling time point and MRF supplementation (p < 0.05). At week 8, lamb microbiomes showed greater variance in their Shannon alpha diversity, with direct MRF supplementation only to the lamb resulting in a significantly greater diversity (p < 0.05). At week 20, combined maternal and lamb supplementation resulted in the highest Shannon diversity and was different compared to all other groups (p < 0.05). Beta diversity analyses combined with differential abundance analyses revealed that microbial community structures are driven by both diet and time, with maternal MRF supplementation associated with enrichment of taxa involved in carbohydrate fermentation and succinate metabolism, including Succiniclasticum ruminis, Succinovibrio dextrinosolvens, and Fibrobacter succinogenes. Generalized linear modeling identified significant associations between microbial alpha diversity metrics and total volatile fatty acids in lambs, particularly butyrate and valerate. Furthermore, at week 8, there was a significant positive correlation between alpha diversity metrics and propionate and valerate. In this study, lambs receiving MRF through maternal and direct supplementation had the highest growth performance, measured as the median average daily gains (kg) and final weights (kg) of lambs. These findings suggest that MRF supplementation, especially when provided both maternally and directly, may influence the lamb rumen microbiome and alter its metabolic potential with potential implications for optimizing early-life nutrition strategies in ruminant production systems.}, }
@article {pmid42072313, year = {2026}, author = {Alamri, A and Almutairi, AK and AlSinan, F and Alramadhan, A and Aldehalan, F and Almutairi, H and Alghuraybi, M and AlHarbi, NM and Alghannam, SF and Alotaibi, SS and AlOmary, M and AlKhater, S}, title = {Functional and Resistome Profiling of Paediatric Airway Microbiota in Asthma Using Shotgun Metagenomics.}, journal = {Biomedicines}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/biomedicines14040772}, pmid = {42072313}, issn = {2227-9059}, support = {IF-2020-016-CAMS//This work was funded by the Deputyship for Research &amp; Innovation, Ministry of Education in Saudi Arabia (IF-2020-016-CAMS) and approved by the deanship of scientific research (DSR) at Imam Abdulrahman bin Faisal University (IAU)./ ; }, abstract = {Background/Objectives: Asthma affects millions of patients worldwide and impacts their quality of life, particularly among children. Colonisation or an imbalance within natural resident microbiota may drive inflammatory responses in asthma; antibiotic resistance genes (ARGs) have also been investigated in asthma microbiome studies. However, research on the association between airway microbiota and ARGs remains limited. Therefore, we elucidated functional-level characterisation at the level of ARGs, virulence factors, and active pathways among a paediatric asthma cohort relative to a healthy control. Methods: Overall, 29 children with asthma and 20 control subjects were enrolled, and 3 swabs (2 nasal and 1 oropharyngeal) were obtained from each participant. Genomic DNA was extracted and sent for shotgun sequencing, after which bioinformatic analysis was conducted to remove human reads and analyse the microbiota pattern in the samples. The abundance of antibiotic resistance genes was evaluated along with the distribution of virulence genetic markers. Functional investigation of the most prevalent metabolic pathways was also performed. Results: Upper airway microbiome functional capacity varied by anatomical location, with oropharyngeal communities exhibiting greater metabolic breadth than nasal communities, suggesting the sample source to be the dominant factor shaping gene content, pathway profiles, and community structure. Asthma-related functional differences were modest, and no biological pathways remained significant following false discovery rate correction. Enrichment of antimicrobial resistance genes was observed, particularly those conferring resistance to β-lactams, macrolides, and tetracyclines. Conclusions: Different anatomical niches exhibit differential activities, and further exploration in this direction could aid in the development of diagnostic and therapeutic biomarkers for asthma.}, }
@article {pmid42073328, year = {2026}, author = {Indio, V and Mekonnen, YT and Oliveri, C and Rubboli, S and Candela, M and Seguino, A and Serraino, A and De Cesare, A}, title = {Reducing Antimicrobial Resistance in Poultry Carcasses Extends Beyond Farm-Level Interventions.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {8}, pages = {}, doi = {10.3390/foods15081440}, pmid = {42073328}, issn = {2304-8158}, support = {Horizon 2020 "Controlling Microbiomes Circulations for Better Food Systems" (CIRCLES) no. 818290.//European Union/ ; }, abstract = {The aim of this study was to assess how raising chickens without the use of antimicrobials affects the microbiome of poultry carcasses. A total of 151 caeca and neck skin samples from chickens raised without antimicrobials were collected in the same slaughterhouse and submitted to shotgun metagenomic sequencing. Caeca were dominated by Bacillota and Bacteroidota, while carcasses by Pseudomonadota. The caeca microbiome was enriched in genes related to a proliferating and metabolically active microbial community. Carcass-associated microbiomes were enriched in functional genes linked to adaptation to nutritionally limited and oxidative environments. A significantly higher cumulative antimicrobial resistance gene abundance was detected in carcasses compared to caeca. Specifically, carcasses exhibited approximately 1.5 times more AMR genes, reflecting an increase of nearly 49%. While caeca showed enrichment of resistance determinants associated with Gram-positive anaerobic gut commensals, carcasses were characterized by a predominance of multidrug efflux systems and clinically relevant β-lactam resistance genes, commonly associated with environmental and opportunistic Gram-negative bacteria. In carcasses, carbapenem-associated genes, such as OXA-58-like and CphA, were detected. However, these genes have not been associated with carbapenemase-producing Enterobacterales. Overall, the findings of this study indicate that reducing antimicrobial resistance in food animal production systems extends beyond farm-level intervention. At present, the benefits of the interventions aimed at reducing antimicrobial resistance at farm level seem to be compromised during the post-harvest stages.}, }
@article {pmid42073366, year = {2026}, author = {Brasileiro, CG and Moreno, MTDC and Santos, EO and Saranraj, P and Cardoso, AM and Vieira, JMBD}, title = {Assessing Food Safety Risks in Homemade Fermented Beverages: A Case Study with Quinoa Rejuvelac.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {4}, pages = {}, doi = {10.3390/life16040556}, pmid = {42073366}, issn = {2075-1729}, support = {E2023//FAPERJ, CNPq, and CAPES/ ; }, abstract = {Spontaneous fermentation processes can promote uncontrolled microbial growth and increase the risk of foodborne contamination, making the characterization of artisanal beverages essential for consumer safety. This study investigated the microbial composition of quinoa-based rejuvelac, a homemade fermented drink often perceived as a functional food, with the objective of identifying potential microbiological hazards associated with its preparation. High-throughput sequencing of the 16S rRNA V3-V4 region was combined with shotgun metagenomics to profile bacterial communities and recover metagenome-assembled genomes. The analysis revealed a strong dominance of Pseudomonadales, mainly Pseudomonas, Acinetobacter, Enterobacter and Burkholderiales, while lactic acid bacteria typically responsible for stable and safe fermentations were not detected. Shotgun metagenomics recovered medium- to high-quality genomes from Burkholderiaceae and Clostridiales, supporting the overrepresentation of non-beneficial taxa and indicating deviations from expected fermentation microbiota. These results show that the spontaneous preparation of rejuvelac may favor bacterial groups associated with environmental contamination rather than fermentative pathways, underscoring the importance of hygiene practices, controlled starter cultures and monitoring strategies to mitigate microbiological risk. The study highlights the need for improved safety standards in artisanal fermented foods to prevent unintended microbial contamination and protect consumers.}, }
@article {pmid42073451, year = {2026}, author = {Cerreto, M and Maestri, M and Pallozzi, M and Cerrito, L and Stella, L and Ianiro, G and Gasbarrini, A and Ponziani, FR}, title = {Gut Microbiota Biomarkers in Patients with Hepatocellular Carcinoma in the Era of Immune Checkpoint Inhibitors.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {4}, pages = {}, doi = {10.3390/life16040641}, pmid = {42073451}, issn = {2075-1729}, abstract = {Immune checkpoint inhibitors (ICIs) have revolutionized the therapeutic landscape for hepatocellular carcinoma (HCC); however, a considerable proportion of patients do not achieve durable clinical benefits. This highlights the need for reliable predictive biomarkers, which are currently lacking. The accumulated evidence supports a relevant role of the gut-liver axis in modulating immunotherapy outcomes, and several studies have identified distinct microbial features associated with either responders or non-responders. Responders to immunotherapy frequently present with higher microbial diversity and enrichment of beneficial taxa, whereas the expansion of pro-inflammatory and pathogenic bacteria has been associated with primary resistance and increased treatment-related toxicity in non-responders. However, the available findings remain heterogeneous across cohorts, likely owing to differences in geography, diet, liver disease etiology, treatment regimens, and microbiome analytical methods. Machine-learning models integrating metagenomic and metabolomic data have shown encouraging results in defining microbial signatures associated with treatment outcomes, although variability among cohorts currently limits their clinical applicability and generalizability. Beyond microbial taxonomic composition, microbiota-derived metabolites-such as short-chain fatty acids, bile acids, inosine, and tryptophan catabolites-appear to play a crucial role in shaping the tumor microenvironment and host immune responses, thus representing additional candidate biomarkers, also due to the relative ease of their measurement. Finally, microbiota-targeted interventions are emerging as potential strategies to enhance immunotherapy efficacy. Overall, the gut microbiome and its metabolic activity represent promising tools, albeit still under investigation, for patient stratification and personalized management in HCC treated with ICIs. Therefore, this review aims to summarize and critically discuss the current evidence on gut microbiota-derived biomarkers of response and resistance to ICIs in HCC, with particular focus on microbial composition, microbiota-related metabolites, and emerging microbiome-based therapeutic strategies. This narrative review provides an updated overview of the role of gut microbiota as both a biomarker and a therapeutic target in patients with hepatocellular carcinoma (HCC) receiving immune checkpoint inhibitor (ICI) therapy.}, }
@article {pmid42073497, year = {2026}, author = {Carraturo, F and Salamone, M and Annunziata, M and Di Brizzi, EV and Giorgio, CM and Petrillo, A and Fedi, L and Maione, A and Guida, M and Galdiero, E}, title = {Preliminary Characterization of Skin Microbiota and Mycobiota in Atopic Dermatitis by Metagenomic and Culture-Based Analyses.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {4}, pages = {}, doi = {10.3390/life16040690}, pmid = {42073497}, issn = {2075-1729}, support = {PRIN2022//European Union-Next Generation EU location/ ; 2022HC3FRM//Serum metabolomics in atopic dermatitis (MetabAD)/ ; }, abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disease influenced by several factors, including immune system imbalance, impairment of the epidermal barrier, and alterations in the composition of the gut and skin bacterial and fungal microbiota. This study combines metagenomic sequencing and culture-based methods to explore the impact of probiotic supplementation on the cutaneous microbiota and mycobiota of AD patients. Twenty-five adults diagnosed with AD were enrolled, and skin swabs were analyzed to characterize microbial diversity and load. Culturomic analyses identified 42 bacterial and 6 fungal species, confirming Staphylococcus aureus and Candida parapsilosis as predominant taxa. High-throughput sequencing revealed Staphylococcus spp. and Malassezia spp. as dominant genera, with notable interindividual variability. While probiotic use did not significantly influence bacterial diversity, it was associated with higher richness and evenness in fungal communities, as shown by alpha and beta diversity metrics. Malassezia restricta was more prevalent among probiotic users, whereas Candida parapsilosis and Rhodotorula mucilaginosa were enriched in non-users. These findings indicate an association between probiotic use and differences in the composition and diversity of the skin mycobiota compared with the bacterial microbiota, suggesting that fungal communities may be more responsive to probiotic-associated factors. Integrating metagenomic and culturomic approaches offers valuable insights into the complex interactions among host factors, microbial communities, and probiotic use in AD, paving the way for targeted microbiome-based therapeutic strategies.}, }
@article {pmid42073729, year = {2026}, author = {Ren, L and Zhang, X and Xu, X and Qin, Q and Fan, H and Wang, Z and Wang, W}, title = {Enhancing Duck Manure Anaerobic Digestion with Hydrochar: Exploring Green Material Potential via Bidirectional AD-HTC Coupling.}, journal = {Materials (Basel, Switzerland)}, volume = {19}, number = {8}, pages = {}, doi = {10.3390/ma19081563}, pmid = {42073729}, issn = {1996-1944}, support = {Grant No. 52300163//National Natural Science Foundation of China/ ; Grant No. ZR2024QE099//Shandong Provincial Natural Science Foundation/ ; }, abstract = {The efficient resource utilization of duck manure and agricultural/forestry wastes (AFW) plays a significant role in environmental protection and promoting the sustainable development of the economy and society. This study examined the effects of hydrochar derived from AFW in the anaerobic digestion (AD) process, determining the optimal addition ratio. This research systematically investigated the impact of hydrochar on methane yield, as well as changes of short-chain fatty acids, microbial community dynamics, and metabolic pathways during AD of duck manure. The underlying mechanisms were clarified by metagenomic and metabolomic analyses. This experiment used duck manure as substrate and added hydrochar of four different dosage levels. Laboratory batch tests ran for 32 days at 37 ± 0.5 °C, with three parallel samples for each group. The results indicated that hydrochar additive significantly improved methane yield (p < 0.05), with a maximum increase of 27.13% at an optimal dosage of 10.91 g·L[-1]. This amendment enhanced the abundance of Firmicutes, Bacteroidota, Chloroflexota, Halobacteriota, and Methanosarcina significantly. Compared to the control group, the abundances of functional genes involved in hydrolysis, acidogenesis, and acetogenesis pathways increased by 28-254% in the optimal treatment group, with methanogenesis-related genes showing a 16-155% enhancement (p < 0.05).}, }
@article {pmid42074337, year = {2026}, author = {Liu, X and Chen, Y and Zhou, X and Xiao, Y and Yuan, X and Su, N and Chen, C and Yan, Q and Chen, X}, title = {Bacillus subtilis and Trichoderma harzianum Reshape Rhizosphere Microbiome and Reprogram Root Transcriptome to Promote Mungbean Growth Under Continuous-Cropping Conditions.}, journal = {International journal of molecular sciences}, volume = {27}, number = {8}, pages = {}, doi = {10.3390/ijms27083699}, pmid = {42074337}, issn = {1422-0067}, support = {2025YFE0121200//National Key R&amp;D Program of China/ ; CARS-08//China Agriculture Research System of MOF and MARA-Food Legumes/ ; JBGS[2021]004//Jiangsu Seed Industry Revitalization Project/ ; }, mesh = {*Bacillus subtilis/physiology ; *Rhizosphere ; *Vigna/growth &amp; development/microbiology/genetics ; *Plant Roots/microbiology/genetics/growth &amp; development ; *Transcriptome ; *Microbiota ; Soil Microbiology ; Metagenomics ; *Hypocreales/physiology ; Gene Expression Profiling ; }, abstract = {Mungbean (Vigna radiata) is an important cash crop, yet the production is significantly compromised by continuous cropping. Beneficial microbial inoculation offers a promising strategy to alleviate the stresses through rhizosphere modulation and host physiological reprogramming. This study evaluated the efficacy of two biological control agents, Bacillus subtilis (B. subtilis) and Trichoderma harzianum (T. harzianum), in promoting mungbean growth under continuous-cropping conditions. Both individual applications of B. subtilis and T. harzianum significantly improved plant biomass, root system architecture, and yield. Combined metagenomic and transcriptomic analyses were conducted to unravel the underlying mechanisms. According to metagenomic analysis, both B. subtilis and T. harzianum were responsible for significant changes in beta diversity without significantly affecting the alpha diversity of the rhizosphere microbial community. T. harzianum recruited Chitinophagaceae unclassified, Abditibacterium, Hydrogenophilaceae unclassified, Methylophilaceae unclassified, and Chimaeribacter, while Bs recruited Candidatus Saccharibacteria unclassified. Transcriptomic analysis indicated that T. harzianum induced more extensive transcriptional reprogramming than B. subtilis. The enrichment analysis revealed both shared and distinct responses triggered by the two treatments. These findings suggest that B. subtilis and T. harzianum alleviate continuous-cropping stress through distinct yet complementary mechanisms involving rhizosphere microbiome modulation and mungbean transcriptional reprogramming. This study provides a sustainable strategy for legume cultivation.}, }
@article {pmid42075183, year = {2026}, author = {van Essen, RRT and Kaur, J and Li, T and Sawbridge, TI}, title = {Isolation of N-Fixing Bacteria from Warm-Season Pasture Grasses and the Evaluation of Nitrogen Effects on the Bacterial Communities Present in Cenchrus clandestinus.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/microorganisms14040786}, pmid = {42075183}, issn = {2076-2607}, support = {DB F.2//DairyBio 21-26, Future Forages Program/ ; }, abstract = {Nitrogen is essential for plant growth. Reliance on synthetic nitrogen fertilisers, however, is costly and contributes to soil degradation. Utilising nitrogen-fixing bacteria as biofertilisers may offer a sustainable alternative, reducing fertiliser costs and environmental impact. In this study, we attempted to isolate nitrogen-fixing bacteria from 14 seed batches of warm-season pasture grasses and successfully isolated bacteria from three of these batches. Whole genome sequencing confirmed the presence of the nif operon within all three isolates. Two seed batches of Cenchrus clandestinus (Hochst. ex Chiov.) Morrone from which nif-containing bacteria were isolated, along with two 'nif'-negative C. clandestinus seed batches, were used in nitrogen-limiting growth assays. This was done to evaluate the effect of the presence of seed-associated nitrogen-fixing bacteria within a seed batch on nitrogen-limited plant growth and the associated plant microbiome composition, using 16S amplicon sequencing of root and shoot samples. Initial plant growth assays revealed significantly reduced root length between plants grown from seed batches harbouring nitrogen-fixing bacteria and those without, under limiting nitrogen availability, but no resulting shoot biomass reduction was observed. The plant microbiomes of these nif-positive seed batches were also statistically similar to each other, compared to the nif-negative seed batch plants. Plant microbiomes of all four C. clandestinus seed batches were significantly different from their original seed microbiomes, showing shifts in community composition. This study demonstrates the presence of potential nitrogen-fixing bacteria associated with warm-season pasture grass seeds at low abundance and reveals differences in plant-associated bacterial community composition between seed batches harbouring and lacking these bacteria.}, }
@article {pmid42075229, year = {2026}, author = {Lai, R and Wang, Z and Liu, P and Tong, J and Ahmed, Z and Cui, R and Gu, Y and Luo, G}, title = {Environmental Altitude and Host Genetics Shape Divergent Microbiota and a Conserved Resistome in Porcine Intestinal Niches.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/microorganisms14040832}, pmid = {42075229}, issn = {2076-2607}, support = {Grant No. RQD2025005//Southwest Minzu University Research Startup Funds/ ; 32472888//National Natural Science Foundation of China/ ; XZ202501ZY0147//Science and Technology Projects of Xizang Autonomous Region/ ; 2024YFHZ0373//Sichuan Science and Technology Program/ ; sccxtd-2026-08//Program for Pig Industry Technology System Innovation Team of Sichuan Province/ ; 2024MS150//he Sichuan Provincial Administration of Traditional Chinese Medicine Science and Technology Research Special Project/ ; }, abstract = {Environmental stressors and host genetics influence gut microbiota and antimicrobial resistance, but their combined effects across intestinal niches remain poorly unexplored. We conducted a metagenomic analysis of 60 jejunal and cecal samples from 30 native Chinese pigs across three altitudes (500 m, 1400 m, and 3850 m). The aim was to disentangle the interactive impacts of altitude, breed, and intestinal site on microbiome structure and antibiotic resistome dynamics. The cecal microbiota was taxonomically conserved and strongly associated with breed. Conversely, while jejunal communities exhibited structural variations among the sampled cohorts, differences in alpha diversity (Shannon index, p < 0.01) appeared to be primarily associated with breed differences rather than an independent altitudinal effect. High-altitude Tibetan pigs showed an enrichment of Bifidobacterium and Pseudomonas, which may be linked to hypoxia adaptation. Despite a shared core resistome (88 ARG types), the cecum harbored significantly higher ARG abundance than the jejunum within-breed comparisons of Tibetan pigs across altitudes; this revealed stable ARG profiles (p > 0.05) suggesting that, although some descriptive differences were observed, the independent effect of altitude weakens when the genetic effect is taken into account. Furthermore, carbohydrate-active enzymes (e.g., CBM13, GH33) correlated positively with ARG abundance. In conclusion, the jejunum appears to act as an environmentally responsive niche, while the cecum exhibits a higher ARG abundance that is closely associated with the host breed.}, }
@article {pmid42075233, year = {2026}, author = {Mousa, WK and AlShami, R and Ghemrawi, R}, title = {Shared Microbial Blueprints Underlying Symbiotic Plasticity in Desert Plant Endophytes.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/microorganisms14040836}, pmid = {42075233}, issn = {2076-2607}, support = {SWARD-F23-020.//Sandooq Al Watan/ ; }, abstract = {The desert ecosystem harbors a resilient microbial community that sustains plant life under extreme stress. Understanding the endophytic microbiota of desert flora provides key insights into how these microorganisms enable plant survival and maintain ecological balance in arid landscapes. To date, the endophytic bacterial communities of dominant desert plants in the Arabian Peninsula have not been comprehensively characterized. Here, we investigated the endophytic microbiota of five co-adapted desert species, namely, Schweinfurthia papilionacea, Sesuvium verrucosum, Ochtocloa compressa, Helianthemum nummularium, and Convolvulus arvensis. These plants coexist in hyper-arid habitats and exhibit exceptional tolerance to drought, salinity, and nutrient scarcity. We hypothesized that, despite their phylogenetic divergence, these plants host functionally convergent microbial communities shaped by desert selection pressures. Using 16S rRNA gene amplicon sequencing, we obtained 3.4 million high-quality reads from 25 samples. Clustering at 97% similarity revealed 35 phyla and 17 dominant genera, highlighting notable microbial richness and ecological complexity. Alpha-diversity indices showed comparable species richness across hosts, while beta-diversity indicated community differentiation driven by environmental filtering. The dominant phyla included Pseudomonadota, Actinomycetota, Cyanobacteriota, and Bacillota, reflecting microbial adaptation to extreme desert conditions. Functional pathway prediction revealed enrichment of genes associated with DNA repair and protein turnover, suggesting metabolic flexibility and enhanced survival under stress. Overall, this study provides a comparative metagenomic insight into the endophytic bacterial communities of five desert plant species, uncovering a consistent pattern of functional convergence across diverse hosts. The findings suggest the presence of shared functional traits among the endophytic microbiota examined here, offering preliminary evidence for microbial contributions to plant resilience in arid environments.}, }
@article {pmid42075236, year = {2026}, author = {Wang, Z and Ma, C and Huang, H and Ke, S and Lv, J and Hu, J and Wang, S and Bao, Z}, title = {Holo-2bRAD: A Hologenomic Method for High-Resolution Analysis of Coral Microbiomes During Bleaching.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/microorganisms14040840}, pmid = {42075236}, issn = {2076-2607}, support = {2025B1111180001//Guangdong S&amp;T Program/ ; 2025A04J3824//GCI Science &amp; Technology (China)/ ; SOLZSKY2025013//Department of Science and Technology of Hainan Province/ ; }, abstract = {Coral reefs are biodiversity hotspots increasingly threatened by climate-induced bleaching, yet profiling the coral holobiont-the host and its associated microbiota-remains technically challenging due to high host-DNA contamination (often >95%) and the lack of comprehensive reference databases. Here, we present holo-2bRAD, a type IIB restriction site-associated DNA sequencing approach. This method, strategically integrated with a meticulously curated hologenome database (comprising 404,946 microbial genomes and 56 coral-derived metagenome-assembled genomes), effectively overcomes overwhelming host contamination (~99%). We demonstrate its exceptional species specificity (99.92%) in profiling Galaxea fascicularis (Linnaeus, 1767; Order Scleractinia, Family Euphylliidae) holobionts across bleaching severities, thereby validating its technical feasibility. Leveraging this high-resolution tool, our hologenome analysis revealed significant restructuring of coral-associated microbiota during bleaching, where microbial shifts (e.g., depletion of beneficial Thermoanaerobacterium thermosaccharolyticum and enrichment of stress-responsive bacteria) correlated more strongly with bleaching phenotypes than host genetic variation. By providing cost-effective, multi-domain hologenome profiling at unprecedented resolution, holo-2bRAD offers a practical tool for investigating holobiont dynamics and developing microbiome-informed coral conservation strategies.}, }
@article {pmid42075252, year = {2026}, author = {Amin, H and Šantl-Temkiv, T and Finster, K and Schlünssen, V and Sigsgaard, T and Wouters, IM and Sørensen, MT and Malinovschi, A and Thorarinsdottir, H and Bertelsen, RJ}, title = {Airborne Movement of Antibiotic Resistance Genes Between Livestock Stables and Farmers' Homes.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/microorganisms14040855}, pmid = {42075252}, issn = {2076-2607}, support = {TMS2021TMT03//Trond Mohn stiftelse/ ; No. 137087//NordForsk/ ; }, abstract = {Antibiotic resistance genes (ARGs) are prevalent in livestock environments due to antimicrobial use, yet their airborne dispersal into human-occupied indoor spaces remains poorly characterized. We investigated whether airborne ARGs disperse from livestock stables into farmers' homes and surrounding outdoor environments. Electrostatic dust collectors were deployed in paired pig and cow stables and their associated homes in Jutland, Denmark, to collect settled airborne dust. Pooled samples were analyzed using shotgun metagenomic sequencing. ARG dispersal patterns were assessed using FEAST source tracking and ecological similarity metrics, including shared ARG ratios and Jaccard indices. Pig production systems exhibited higher antibiotic use and stronger resistome continuity with farmers' homes than cow systems, reflected by greater FEAST contributions (P = 0.029) and Jaccard similarity (P = 0.029). Beta-diversity analysis supported higher compositional similarity between pig stables and homes (PERMANOVA R[2] = 0.23, p = 0.052), whereas cow environments showed greater divergence (R[2] = 0.41, P = 0.035). Across environments, tetracycline, macrolide-lincosamide-streptogramin B, and aminoglycoside resistance genes dominated, consistent with livestock-specific antibiotic use patterns. Supplementary indoor-outdoor comparisons across cow, pig, and chicken stables (from an independent 2024 sampling campaign not directly comparable to the 2008 EDC-based survey) revealed contrasting dispersal dynamics, with higher bacterial species spillover from cow stables but stronger ARG overlap from pig stables. Collectively, these findings are consistent with airborne ARG connectivity across occupational and environmental interfaces and support consideration of air as a potential pathway in One Health AMR surveillance.}, }
@article {pmid42075269, year = {2026}, author = {Yang, J and Yue, Y and Li, X and Lv, R}, title = {Dynamics of Microbial Carbon Metabolism During Vegetation Restoration in Sandy Ecosystems.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/microorganisms14040873}, pmid = {42075269}, issn = {2076-2607}, support = {2024B04031-2//Research and Development of Efficient Utilization Technology for Brackish Water in Desert Photovoltaic Power Stations/ ; 2024AAC03102//Natural Science Foundation of Ningxia/ ; }, abstract = {Understanding the succession of soil microbial carbon metabolism functions is crucial for elucidating carbon cycling mechanisms during ecosystem restoration in sandy lands. Soils were collected from Caragana korshinskii shrubland sites across a restoration chronosequence (0, 10, 30, 50, and 70 years) in the Mu Us Sandy Land. Biolog carbon source utilization analysis and metagenomic sequencing were employed to characterize the successional patterns of microbial carbon metabolism functions-a shift in carbon metabolism strategies from acquisition to conservation, and a transition in functional diversity from generalism to specialization. The results indicated that microbial communities exhibited two associated successional shifts in functional characteristics: carbon source utilization tended to transition from simple to complex substrates, while functional gene expression showed a progressive shift from broad multi-pathway patterns toward pathway-specific specialization. AWCD values increased continuously with restoration duration, and carbon source utilization patterns diverged significantly around 30 years. Early-stage sites (0-30 years) primarily utilized simple carbon sources, whereas late-stage sites (50-70 years) shifted toward more complex and diverse substrates. Principal component analysis revealed that 27 carbon sources contributed 91.3% of the variance to PC1. Microbial community structure succession revealed that Actinobacteria peaked at 10 years (43.63%), Proteobacteria peaked at 30 years (45.66%), and taxa such as Bacilli and Solirubrobacter dominated at 50-70 years. Carbon metabolism pathways exhibited stage-specific succession: glycolysis and the ED pathway were active in early stages, acetate metabolism dominated with the 3HB cycle peaking in intermediate stages, and the CBB cycle increased in later stages while methane metabolism shifted from high to low contribution. These two associated successional shifts occurred along the same restoration chronosequence, with the progressive transition in substrate utilization accompanying the development of specialist functional characteristics. These findings provide insights into the successional dynamics of microbial carbon metabolism during vegetation restoration, offering a microbiological basis for optimizing ecological restoration practices and enhancing soil carbon sequestration in sandy lands.}, }
@article {pmid42075270, year = {2026}, author = {Oladipo, P and Kade, A and Onohuean, H and Ram, JL}, title = {From Cryptic Clade to Emerging Pathogen: Exploring the Evolutionary Divergence and Clinical Relevance of Escherichia marmotae.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/microorganisms14040869}, pmid = {42075270}, issn = {2076-2607}, abstract = {The Escherichia genus includes both commensal and pathogenic species and is characterized by its diversity and adaptability to the mammalian gut and other environments. Among these species, E. coli has facilitated many scientific advances as a model organism. Recently, a new member of the Escherichia genus, Escherichia marmotae, has been described as a phylogenetically distinct clade that shows the greatest genetic divergence from E. coli. This review explores E. marmotae, its cryptic evolution, distinct characteristics, and ecological niches. E. marmotae has recently gained scientific prominence due to its association with animal feces, environmental occurrence, human clinical samples, and emerging as a potential pathogen. While its pathogenicity remains understudied, growing evidence from clinical, environmental, and animal sources suggests the need for heightened surveillance. This review highlights current knowledge gaps, underscores the need for improved diagnostic tools, and proposes future research directions to elucidate the clinical and ecological implications of this emerging pathogen.}, }
@article {pmid42075274, year = {2026}, author = {Chen, L and Chen, Y and Peng, Q and Zhou, D and Feng, S}, title = {Metagenomics and Metagenome-Assembled Genomes Analysis of Highland Barley Baijiu Daqu.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/microorganisms14040877}, pmid = {42075274}, issn = {2076-2607}, abstract = {Highland barley Baijiu is a kind of fermented liquor with national characteristics produced in the Qinghai-Tibet Plateau, and its quality largely depends on the highland barley Baijiu Daqu (HBQ). HBQ contains abundant microbial resources and embedded unknown genomes that have not yet been decoded. In order to deeply understand the key contribution of microorganisms in HBQ, this study analyzed the microbial community structure of HBQ, inferred predicted functions and recovered high-quality metagenome-assembled genomes (MAGs) based on Metagenomics. The results indicated that Pantoea agglomerans was the most abundant species in HBQ, followed by Lichtheimia ramosa, Pichia kudriavzevii, Saccharomycopsis fibuligera and Wickerhamomyces anomalus. The predictive function of the HBQ was focused on annotating carbohydrate metabolism and amino acid metabolism. Meanwhile, six high-quality MAG strains were recovered and identified as Unclassified Kroppenstedtia, Erwinia persicina, Leuconostoc citreum, Saccharopolyspora rectivirgula, Levilactobacillus brevis, and Pantoea agglomerans. Genome annotation of the recovered genomes showed eggNOG predicted function as well as primary and secondary metabolites. The metabolic network diagram of the functional microorganisms in HBQ related to flavor compounds was also predicted. The results can help to understand the formation mechanism of flavor profiles in highland barley Baijiu.}, }
@article {pmid42075297, year = {2026}, author = {Li, X and Qin, Z and Wang, H and Tao, X and Xia, J and Zhao, Y and Yi, P and Ma, Y and Wang, X and Ma, X and Li, N and Zhong, Q and Yao, G}, title = {Seasonal Dynamics of Skin Microbiota and Metabolites in Transhumant-Grazed Altay Sheep.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/microorganisms14040901}, pmid = {42075297}, issn = {2076-2607}, support = {2022TSYCJC0026//the "Tianshan Talent" Youth Science and Technology Top Talent Project of Xinjiang Uygur Autonomous Region/ ; }, abstract = {To explore the seasonal variation patterns of the skin microecology of Altay sheep under transhumant grazing conditions, skin swabs were collected from 60 free-grazing Altay sheep at seasonal transition nodes in the Altay region. Metagenomic sequencing combined with untargeted metabolomics was used to characterize their bacterial community structure, functional pathways, and metabolite profiles. The results showed that the skin microecology of Altay sheep presented obvious seasonal variation patterns. In spring, 35 of the 39 highly abundant bacteria were environmentally derived, five proliferation-related pathways were significantly enriched, and the levels of five metabolites associated with microbial community regulation and skin barrier defense were elevated. In summer, the abundance of three skin symbiotic bacteria increased, the activities of eight pathways mainly related to biofilm formation were significantly enhanced, and the contents of five metabolites primarily associated with membrane lipid homeostasis and selective bacteriostasis increased. In autumn, the abundances of nine radiation-resistant and cold-tolerant strains increased, together with the elevated abundance of two opportunistic pathogens; five repair-related pathways were active, and the levels of four anti-inflammatory and repair-associated metabolites were synchronously increased. In winter, the abundance of two cold-tolerant strains increased, the activities of pathways related to nitrogen metabolism and energy synthesis were enhanced, and one lignan compound was identified as the key metabolite. These findings elucidate the seasonal dynamic patterns of the skin microecology of Altay sheep and provide a theoretical basis for research on the adaptive mechanisms and seasonal health management of Altay sheep and other sheep in alpine regions.}, }
@article {pmid42075311, year = {2026}, author = {Cruells, A and Eguren, C and Robainas Barcia, A and Martínez, H and Sharaf, M and Ruiz, C and Sánchez-Baos, A and Carrón, N and Bou, L and Pérez, M and De Lucas, R and Guerra-Tapia, A}, title = {Shotgun Metagenomic Characterization of Acne Microbiota Before and After Treatment with a Topical Biotechnological Phytocomplex: Understanding Skin Dysbiosis.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/microorganisms14040915}, pmid = {42075311}, issn = {2076-2607}, abstract = {This study assessed the impact of a topical phytocomplex on the acne skin microbiota, encompassing bacterial, fungal, and phage communities. Skin samples obtained from participants exhibiting a positive response to the treatment were analyzed using high-throughput sequencing and bioinformatic approaches including taxonomic profiling, metagenome assembly, functional annotation, and phage identification. Results showed that after treatment, microbial diversity increased, reflecting a more balanced microbial composition. Cutibacterium acnes levels were reduced, particularly virulent IA1/IA2 phylotypes, whereas non-pathogenic or unclassified strains increased. Opportunistic pathogens such as Klebsiella pneumoniae were no longer detected, and beneficial genera including Psychrobacter and Dermabacter were enriched. Functional analysis showed reduced virulence- and biofilm-related pathways, alongside enhanced tryptophan metabolism, SCFA production, lipid synthesis, and riboflavin and folate biosynthesis. Fungal populations, dominated by Malassezia, became more evenly distributed, with notable post-treatment reductions in M. arunalokei, Exophiala spinifera, and Wickerhamomyces anomalus. Phage populations mirrored bacterial changes, with enrichment of Cutibacterium-associated phages post-treatment. These findings demonstrate that the phytocomplex promotes functional rebalancing of the skin microbiota by reducing pathogenic features while maintaining ecosystem stability. The inhibition of quorum sensing, potentially mediated by N-acyl-homoserine lactone acetylation, emerged from metabolic pathway annotation as a hypothetic key mechanism impairing bacterial communication and virulence associated with acne vulgaris.}, }
@article {pmid42075321, year = {2026}, author = {Wang, W and Wang, Z and Zhang, P and Zhang, J}, title = {Environmental Regulation of Gut Microbial Networks Links to Growth Variation in Schizopygopsis younghusbandi Across Contrasting Aquaculture Systems.}, journal = {Microorganisms}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/microorganisms14040925}, pmid = {42075321}, issn = {2076-2607}, support = {XZ202501JD0019; XZ202402ZD0005; XZ202401ZY0059//Science and Technology Program of Tibet Autonomous Region/ ; XZ202501JD0019//the Base and Talent Program Projects of Science and Technology Program of Tibet Autonomous Region/ ; 42371170//National Natural Science Foundation of China/ ; //the Agricultural and Animal Husbandry Science and Technology Innovation Project/ ; }, abstract = {Schizopygopsis younghusbandi is an endemic and economically important fish in the Qinghai-Xizang Plateau, but its aquaculture is limited by harsh environmental conditions and incomplete understanding of host-microbiome-environment interactions. This study applied metagenomic sequencing to examine how different culture environments affect growth, water microbial communities, and gut microbiome network stability. Three-year-old juveniles (initial body weight 50.57 ± 1.88 g) were reared for 90 days in five systems: conventional pond (P), wetland (WL), concrete tank (G), river (R), and recirculating aquaculture system (RC). No significant differences in initial body weight or length were observed among groups (p > 0.05). Fish in the RC system achieved the highest final body weight, weight gain rate, and specific growth rate (p < 0.05), while survival rates were highest in the river and RC groups and lowest in ponds (p < 0.05). Microbial diversity and community composition differed significantly among culture modes, with bacterial and protozoan communities showing the strongest environmental responsiveness. Co-occurrence network analyses revealed that RC and G systems exhibited higher network complexity, density, and proportion of positive correlations, reflecting enhanced microbial interaction and ecological stability, whereas the WL system showed reduced network connectivity. Correlation analysis indicated that bacterial abundance was positively associated with total nitrogen, total phosphorus, and dissolved oxygen (p < 0.05), highlighting environmental regulation of microbial assemblages. Overall, the aquaculture environment shapes gut microbial networks, which closely relate to growth performance. Recirculating aquaculture systems can mitigate growth limitations in plateau fish by stabilizing the environment and reinforcing gut microbial communities, providing a sustainable strategy for high-altitude aquaculture development.}, }
@article {pmid42075340, year = {2026}, author = {Cheng, L and Shen, Q and Wang, Y}, title = {Root-Zone Nitrogen Fertilization Increases Oilseed Rape Yield: Reprogramming Rhizosphere N-Cycling and Strengthening Soil-Plant Coupling.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {8}, pages = {}, doi = {10.3390/plants15081137}, pmid = {42075340}, issn = {2223-7747}, support = {2024J0487//Scientific Research Fund Project of the Education Department of Yunnan Province/ ; 202304BQ040005//Project of Science and Technology Department of Yunnan Province/ ; }, abstract = {Root-zone nitrogen fertilization (RZF) can increase crop N uptake and yield, yet the underlying rhizosphere N-cycling functional mechanisms remain insufficiently resolved. In a field experiment with winter oilseed rape (Brassica napus L.), RZF was compared with conventional fertilization (CF) under the same N input rates, alongside a zero-N control (N0). Compared with CF, RZF significantly increased seed yield (by 0.44 t ha[-1]) and aboveground N uptake (by 20.45 kg ha[-1]), while simultaneously enriching rhizosphere mineral N pools (NH4[+]-N and NO3[-]-N by 54.50% and 56.02%, respectively). Shotgun metagenomics revealed that RZF reprogrammed rhizosphere N-cycling functional potential, characterized by enhanced nitrogen fixation, reduced nitrification and denitrification, and a tendency toward increased assimilatory nitrate reduction. These module-level shifts were supported by concordant changes in key functional genes, indicating greater genetic potential for N retention and assimilation (nifD, glnA, gltB, nasA, napB, nrfA) and reduced potential for nitrification- and denitrification-driven N losses (amoB/C, narI, nirK, norB). Taxonomic composition analysis showed enrichment of Bradyrhizobium and suppression of key nitrifier taxa (Nitrosospira and a Nitrososphaeraceae-affiliated taxon) under RZF. Rhizosphere pH exhibited the strongest Mantel correlation with multiple N-cycling modules, and rhizosphere available N (AN; sum of NH4[+]-N and NO3[-]-N) was positively associated with plant N traits and yield. Structural equation modeling supported a pathway in which a functional balance index (retention/assimilation vs. loss/oxidation) increased AN (0.22), and AN strongly promoted yield (0.90). Collectively, these results elucidate a rhizosphere-centered mechanism whereby localized N placement strengthens soil-plant N coupling and enhances crop productivity through reprogramming microbial N-cycling functional potentials, positioning rhizosphere N processes as a key mechanistic bridge for microbiome-informed optimization of root-zone fertilization.}, }
@article {pmid42075353, year = {2026}, author = {Aleynova, OA and Ananev, AA and Nityagovsky, NN and Suprun, AR and Beresh, AA and Dubrovina, AS and Kiselev, KV}, title = {Ability of Different Bacteria from Grapevine to Colonize Arabidopsis thaliana Plants.}, journal = {Plants (Basel, Switzerland)}, volume = {15}, number = {8}, pages = {}, doi = {10.3390/plants15081151}, pmid = {42075353}, issn = {2223-7747}, support = {22-74-10001-&#x41f;//the Russian Science Foundation/ ; }, abstract = {This study investigates the impact of inoculating seeds with bacterial endophytes isolated from Vitis amurensis Rupr. on endophytic community composition in Arabidopsis thaliana (L.) Heynh. Ten bacterial isolates of the genera Agrobacterium, Bacillus, Curtobacterium, Erwinia, Frondihabitans, Gordonia, Pantoea, Pseudomonas, Sphingomonas, and Xanthomonas were applied to seeds and some visible phenotypic effects were observed on plant growth after two weeks. High-throughput sequencing of 16S rRNA revealed that the native endophytic microbiome of A. thaliana was dominated by Gammaproteobacteria, Actinomycetes, Bacteroidia, and Alphaproteobacteria. The key families were Microscillaceae, Chitinophagaceae, Rhizobiaceae, Rhodanobacteraceae, Nocardioi-daceae, Nocardiaceae, Xanthomonadaceae, Devosiaceae, Microbacteriaceae, Crocinitomi-caceae, Pseudomonadaceae, Solimonadaceae, Comamonadaceae, Caulobacteraceae, and Micrococcaceae. Arabidopsis seed inoculation with Agrobacterium sp. R8SCh-B12, Curtobacterium sp. P7SA-B3, and Gordonia aichiensis P6PL2 significantly reduced alpha diversity (Shannon index) and altered beta diversity relative to controls, indicating strong community restructuring. These three isolates, along with Pseudomonas sp. R8SCh-B2, Sphingomonas sp. RA62c-B5, Xanthomonas sp. R7SCh-B6, and Bacillus velezensis AMR25, successfully colonized the plant tissues, as evidenced by significant increases in genus-specific amplicon sequence variants, ASVs (up to 17,820-fold for Curtobacterium sp. ASV33). In contrast, Pantoea sp. P7SCH-B5, Erwinia sp. R8SCh-B3, and Frondihabitans sp. RA62c-B2 failed to colonize A. thaliana, despite being applied to the seeds, suggesting the existence of mechanisms restraining colonization. These findings demonstrate that only a subset of grapevine-derived endophytes can effectively colonize A. thaliana, and that successful colonization correlates with significant shifts in the native microbiome, even in the absence of overt phenotypic changes. This emphasizes the importance of strain-specific compatibility in plant-endophyte interactions. Thus, we report the first descriptions of several novel endophytes that colonized Arabidopsis plants and establish a convenient model to investigate plant-bacterial interactions.}, }
@article {pmid42076876, year = {2026}, author = {Krupa, &#x141; and Schmarz, GP and Staroń, R and Schmidt, HH and Rehner, J and Becker, SL and Krawczyk, M}, title = {Metagenomic profiling of bile in malignant cholestasis: Analysis of samples collected during EUS-guided biliary drainage.}, journal = {European journal of clinical investigation}, volume = {56}, number = {5}, pages = {e70200}, doi = {10.1111/eci.70200}, pmid = {42076876}, issn = {1365-2362}, support = {Precision-BTC-Network CA22125//European Cooperation in Science and Technology/ ; //Saarland University and the UdS-HIPS TANDEM initiative/ ; 469073465//Deutsche Forschungsgemeinschaft/ ; 2022-784-024//European Union Horizon 2020 Transcan project/ ; 2024-040//Dr. Rolf M. Schwiete Stiftung/ ; }, }
@article {pmid42076937, year = {2026}, author = {Lundtorp-Olsen, CM and Andersen, SVR and Massarenti, L and Gürsoy, M and Splunter, AV and Bikker, FJ and Gursoy, UK and Markvart, M and Damgaard, C and Belstrøm, D}, title = {Probiotics Augment the Effect of Non-Surgical Periodontal Treatment-A Randomised, Double-Blinded, Placebo-Controlled Trial.}, journal = {Journal of clinical periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jcpe.70136}, pmid = {42076937}, issn = {1600-051X}, support = {1044-00093B//Innovationsfonden/ ; //Archer Daniels Midland/ ; }, abstract = {AIM: To determine the effect of probiotic lozenges containing Lacticaseibacillus rhamnosus PB01, Latilactobacillus curvatus EB10 and xylitol after non-surgical periodontal treatment (NSPT) on changes in microbial composition. The secondary aims were to assess the clinical and immunological impact of probiotic consumption.<br><br>MATERIALS AND METHODS: Eighty adults with stage II or III periodontitis were enrolled and received NSPT at baseline, followed by a 12-week consumption of probiotics or placebo. Microbial sampling and clinical examination were performed at baseline, Week 6 and Week 12. The subgingival microbiota was analysed using 16S sequencing, the salivary microbiota by metagenomic sequencing and selected cytokines and proteases in saliva by bead-based immunoassay.<br><br>RESULTS: Sixty-one participants completed the trial (probiotics n&#x2009;=&#x2009;32, placebo n&#x2009;=&#x2009;29). At Week 12, Treponema socranskii, Selenomonas sputigena, Dialister pneumosintes, Dialister invisus, Anaeroglobus geminatus and Fusobacterium nucleatum were significantly associated with the placebo group, while Streptococcus sanguinis, Neisseria elongata and Neisseria oralis were associated with the probiotic group. Bleeding on probing percentage (BoP%) and number of periodontal pockets (PPD) &#x2265;&#x2009;5&#x2009;mm decreased significantly more in the probiotic group compared to the placebo group (p&#x2009;<&#x2009;0.05).<br><br>CONCLUSION: The tested probiotic supplement resulted in an additional short-term decrease in periodontitis-associated species along with greater improvements in BoP% and PPD &#x2265;&#x2009;5&#x2009;mm 12&#x2009;weeks post-NSPT, compared to the placebo group.}, }
@article {pmid42077846, year = {2026}, author = {Pinheiro, GL and Lin, NJ and Parratt, KH and Hines, I and Hack, HR and Servetas, SL and Iyer, H and Da Silva, SM}, title = {The Integration of Focused Ultrasonication, ddPCR, and Flow Cytometry Effectively Estimates Genome Copies per Cell and Enhances DNA Extraction Efficiency in Escherichia coli Samples.}, journal = {ACS omega}, volume = {11}, number = {16}, pages = {23885-23899}, pmid = {42077846}, issn = {2470-1343}, abstract = {Microbiology researchers rely on nucleic acid measurement techniques, such as the quantitative polymerase chain reaction (qPCR) and DNA sequencing, to address diverse scientific and practical challenges. These applications range from detecting microbial contaminants in regenerative medicine and biotherapeutic products to advancing waste remediation, pathogen detection, biosurveillance, and microbiome studies. A critical step in these techniques is DNA extraction, which involves breaking cells to release their DNA as the required input for downstream analyses. The efficiency of this process, known as DNA extraction efficiency (DEE), directly impacts the accuracy of quantitative measurements and, therefore, the interpretation of results. Unfortunately, most DNA extraction methods suffer from suboptimal efficiency that varies across microbial strains, potentially leading to inaccurate results. In this paper, we present a highly efficient DNA extraction protocol leveraging adaptive focused acoustics (AFA) technology to achieve a balance between cell lysis and DNA integrity. Using Escherichia coli as the model organism, the protocol delivers nearly 100% DEE, setting a benchmark for performance. A key innovation in this protocol is the integration of focused ultrasonication, droplet digital polymerase chain reaction (ddPCR), and flow cytometry to estimate genome copies and the corrected DNA extraction efficiency (cDEE), which accounts for the number of genome copies. The proposed protocol addresses the need for an accurate assessment of DEE and DNA quantification, as demonstrated here with E. coli, for various DNA-based techniques, including metagenomic analysis of complex microbial communities and the development of new DNA extraction protocols. This novel protocol addresses a longstanding limitation in microbiological research and has the potential to significantly enhance accuracy and reproducibility across various applications. While there is significant potential for applying this approach, the authors acknowledge that further studies using microorganisms with thicker cell walls will enhance the utility of this framework. However, the knowledge generated in this study can be readily applied and tailored to the specific objectives of individual research groups.}, }
@article {pmid42078366, year = {2026}, author = {Sy, M and Ndiaye, T and Thakur, R and Gaye, A and Levine, ZC and Ngom, B and Bellavia, KL and Firer, D and Toure, M and Ndiaye, IM and Diedhiou, Y and Mbaye, AM and Gomis, JF and DeRuff, KC and Deme, AB and Ndiaye, M and Badiane, AS and Paye, MF and Sabeti, PC and Ndiaye, D and Siddle, KJ}, title = {Oral and plasma microbiome in the context of acute febrile illness.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.16.26351042}, pmid = {42078366}, abstract = {Emerging infectious diseases and antimicrobial resistance (AMR) have surfaced as two major public health threats over the past two decades. Consequently, integrative surveillance systems capable of detecting both emerging pathogens and resistance-carrying bacteria are crucial. With advances in next-generation sequencing, simultaneous detection of pathogens and AMR is increasingly feasible. In this study, we used short-read metatranscriptomics complemented by total 16S rRNA metagenomic long-read sequencing to analyze paired oral and plasma samples from a cohort of febrile individuals at two locations in Senegal. Oral microbiomes differed in community composition between locations, and reduced diversity and richness were significantly associated with high fever. We identified at least one known pathogen in 15.33 % (23/150) of samples, with Borrelia crocidurae as the most frequently detected pathogen. We detected both pathogenic and non-pathogenic viruses in oral (10/72) and plasma (09/78) samples. Finally, we observed a high frequency of genes associated with resistance and virulence: 10% of samples expressed at least one AMR gene (ARG), and 24% expressed virulence factor genes. Resistance to widely used beta-lactam antibiotics was the most prevalent. Our findings provide critical data on oral and plasma microbiomes in the context of acute febrile illness in Senegal while expanding understanding of circulating ARGs.}, }
@article {pmid42078431, year = {2026}, author = {Tang, J and Luo, Z and Li, Y and Jiang, W and Weng, Y and Zhang, G and Li, C and Liu, Y and Sun, X and Chen, L}, title = {Invasive pericardial and pulmonary aspergillosis by uncommon Aspergillus species in anti-interferon-γ autoantibody-associated immunodeficiency: a case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1760017}, pmid = {42078431}, issn = {2296-858X}, abstract = {This case report describes a 51-year-old female patient who presented with dyspnea and was diagnosed with invasive aspergillosis affecting the pericardium and lungs, secondary to immunodeficiency syndrome caused by anti-interferon-γ autoantibodies. Diagnosis was established by pericardial tissue metagenomic next-generation sequencing (mNGS) identifying Aspergillus udagawae and serum anti-interferon-γ autoantibody testing (titer 1:2,500). Despite sequential antifungal therapy with voriconazole, isavuconazole, and amphotericin B, the patient developed progressive multifocal infection, including an abdominal wall abscess and mediastinal infection caused by Aspergillus siamensis, and ultimately died of multiple organ failure. This case highlights the diagnostic challenges and poor prognosis associated with this rare immunodeficiency syndrome and emphasizes the importance of early recognition, precise pathogen identification, and consideration of immunomodulatory therapy.}, }
@article {pmid42078521, year = {2026}, author = {Meng, T and Shi, J and Zhang, X and Zhao, X and Liu, Y and Rong, M and Chen, L and Dai, Y and Wei, S and Liu, J and Lu, Z}, title = {Mechanistic insights into nitrogen fertilizer regulation of carbon-nitrogen cycling and greenhouse gas emissions: a metagenomics-based investigation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1808047}, pmid = {42078521}, issn = {1664-302X}, abstract = {Nitrogen (N) fertilizer application can regulate the structure of soil microbial community and influence the abundance of functional genes involved in carbon (C) and N cycling, thereby affecting greenhouse gas (GHG) emissions. This study was conducted in 2023-2024, setting up six nitrogen application rates: N0 (0 kg·ha[-1]), N120 (0 kg·ha[-1]), N180 (0 kg·ha[-1]), N240 (0 kg·ha[-1]), N300 (0 kg·ha[-1]), and N360 (0 kg·ha[-1]). Using 16S amplicon sequencing technology and metagenomic sequencing, the study analyzed the abundance of carbon and nitrogen cycling functional genes. Combined with measurements of CH4, N2O, and CO2 emission fluxes, the research elucidated the mechanism by which nitrogen fertilizer regulates microbial modulation of greenhouse gas emissions. The results indicated that nitrogen application significantly increased greenhouse gas (CH4, N2O, CO2) emissions, with the highest emissions observed under the N300 treatment. Nitrogen application regulated soil nutrients, increasing soil total nitrogen, nitrate nitrogen, and microbial biomass carbon content. Reasonable nitrogen application (N240) increased bacterial α-diversity (Shannon index, Chao index, PD index) in the soil by 10.82, 14.65, and 1.92%, respectively, compared to N0. It also increased the abundance of dominant nitrogen-fixing bacterial phyla, including Actinobacteria, Proteobacteria, and Nitrospirota. Furthermore, it regulated the abundance of microbial-mediated functional genes involved in dissimilatory nitrate reduction (nirB), assimilatory nitrate reduction (nasA), denitrification (narG, narH, nirS), nitrification (norC, nxrA, nxrB, hao, amoC), as well as those in the carbon cycle related to methane metabolism (pmoA, pmoC, mttC), carbon fixation (por/nifj, rbcl/cbbl), and hydrogenotrophic methanogenesis (mch, hdrA, frdE). This regulation further modulated greenhouse gas emissions. Therefore, this study clarifies the microbe-associated mechanisms underlying the N fertilizer-driven coupling of C and N cycles with GHG emissions through an integrated analysis of microbial diversity and metagenomics. Furthermore, it offers new insights for sustainable N fertilizer management and emission mitigation strategies in agricultural systems.}, }
@article {pmid42078528, year = {2026}, author = {Dai, Z and Lu, Q and Sun, M and Chen, H and Jiang, Y and Yu, T and Wang, Z and Wang, Y and Zhu, R and Han, Y}, title = {Identification of novel CRESS-DNA viruses in the human vaginal microbiome.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1790643}, pmid = {42078528}, issn = {1664-302X}, abstract = {INTRODUCTION: Circular replication-associated protein (Rep)-encoding single-stranded DNA (CRESS-DNA) viruses are widely distributed across diverse hosts and environments, yet their diversity within the human vaginal virome remains poorly characterized. This study aimed to investigate the presence, diversity, and evolutionary relationships of CRESS-DNA viruses in the human vaginal niche.<br><br>METHODS: Viral metagenomic sequencing was performed on 24 pooled vaginal swab libraries derived from women with and without vaginitis. After host sequence removal and quality control, de novo assembly and viral identification were conducted. Candidate viral genomes were curated based on genomic features, followed by functional annotation, phylogenetic analysis using Rep protein sequences, and genome-wide pairwise nucleotide identity comparisons.<br><br>RESULTS: A total of five CRESS-DNA viral genomes were identified, including four complete and one nearly complete circular genomes. All genomes exhibited canonical architectures, encoding Rep and Cap proteins and containing conserved HUH endonuclease and superfamily 3 helicase motifs. Phylogenetic analysis placed these viruses within the orders Rohanvirales, Ringavirales, Cirlivirales, and Cremevirales, representing multiple distinct evolutionary lineages. Genome-wide pairwise identity analysis showed that all identified viruses fell below established species- and genus-level thresholds, indicating that they represent novel taxa. Comparative analyses further revealed substantial divergence from known environmental and vertebrate-associated viruses.<br><br>DISCUSSION: These findings expand the known diversity of CRESS-DNA viruses in the human vaginal virome and highlight their broad evolutionary diversity. The detected viruses likely represent diverse ecological origins rather than stable host-specific infections, and no clear association with vaginitis was observed. This study provides new insights into the evolutionary landscape of CRESS-DNA viruses in the human reproductive tract and underscores the need for further investigation into their biological roles and potential health implications.}, }
@article {pmid42078532, year = {2026}, author = {Padmanabhan, C and Puig, A}, title = {Editorial: Metagenomic insights into microbial communities in fruits and vegetable plants.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1844864}, pmid = {42078532}, issn = {1664-302X}, }
@article {pmid42078537, year = {2026}, author = {Shen, T and Zhou, Y and Gao, J and Xiong, X and Chen, C}, title = {Gut microbiota regulates growth retardation in pigs through their metabolites of taurine and butyric acids.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1811659}, pmid = {42078537}, issn = {1664-302X}, abstract = {Growth retardation of piglets has always been observed in current pig production system. Here we defined these pigs as stunted pigs. Stunted pigs show normal feed intake, but exhibit extremely slow growth speed. This brings a big economic loss to pig industry. Many factors can lead to growth retardation, including gut microbiota which has been reported to play important roles in growth retardation of children. However, whether and which gut microbial taxa are associated with growth retardation of piglets are largely unknown. Here we used 16S rRNA gene and shotgun metagenomic sequencing to identify bacterial taxa associated with growth retardation in 126 pigs including stunted pigs and their pairwise littermates showing normal growth. We identified several Clostridium spp. significantly enriched in the gut of normal growing pigs, including Clostridium symbiosum which was the key biomarker distinguishing stunted pigs and normal growing pigs, while several Bacteroides spp. had higher abundances in stunted pigs. Clostridium spp. was significantly associated with the shifts of functional capacities of the gut microbiome between normal and stunted pigs, e.g., biosynthesis of unsaturated fatty acids. Untargeted serum metabolome analysis found that normal growing pigs had higher concentration of taurine in serum. Increased concentration of serum taurine was associated with increased abundance of Clostridium symbiosum. Furthermore, all metabolites having higher abundances in normal growing pigs were enriched in the pathway of taurine and hypotaurine metabolism. Short-chain fatty acids (SCFAs) analysis identified butyric acid having higher concentration in feces of normal growing pigs in both discovery and validation cohorts, and the changes in the abundances of Clostridium symbiosum was correlated with the shifts of the concentrations of fecal SCFAs. These results suggested that Clostridium spp., especially Clostridium symbiosum improved pig growth by increasing the concentrations of serum taurine and fecal butyric acid, and was an important biomarker associated with pig growth. This study provided important insights into the effect of the gut microbiome on pig growth retardation.}, }
@article {pmid42078542, year = {2026}, author = {Mao, Y and Lv, Q and Chen, S and Wang, L and Li, K and Xie, Z and Yin, F and Xu, L and Wang, Q and Zhao, C}, title = {Case Report: An imported severe case of paediatric scrub typhus with Karp B subgenotype in non-endemic Northern China, Beijing.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1733143}, pmid = {42078542}, issn = {2296-2360}, abstract = {Scrub typhus, a zoonosis caused by Orientia tsutsugamushi (O. tsutsugamushi), remains a significant public health threat in the Asia-Pacific region. This disease is transmitted through the bite of infected trombiculid mite larvae (chiggers) and typically manifests as acute undifferentiated fever during the early stage. Despite the availability of targeted antibiotic therapies, delayed diagnosis frequently leads to severe complications and fatal outcomes. Here, we report a severe imported paediatric case in Beijing, a city in China's temperate zone, involving a 12-year-old girl with a recent travel history to Yunnan Province. The patient presented with fever, characteristic eschar, regional lymphadenopathy, and septic shock, ultimately progressing to multiorgan dysfunction syndrome. Whole-genome metagenomic next-generation sequencing (mNGS) of blood, cerebrospinal fluid (CSF), and sputum samples revealed O. tsutsugamushi with high sequence read counts, whereas blood cultures remained negative for other bacterial pathogens. Subsequent PCR amplification and Sanger sequencing confirmed the mNGS findings. Phylogenetic analysis of the TSA56 gene classified the strain within the Karp cluster. Serological analysis revealed the presence of O. tsutsugamushi-specific IgM and IgG antibodies. This severe paediatric case highlights the importance of considering travel-associated scrub typhus in the differential diagnosis of febrile illnesses in non-endemic regions. This is particularly relevant for patients with a history of insect bites in areas known to be endemic for O. tsutsugamushi.}, }
@article {pmid42079098, year = {2026}, author = {Wucher, BR and Pardo-De la Hoz, CJ and Stamper, I and Sharma, S and Kaune, D and Bendale, P and Peled, J and Xavier, JB}, title = {Metabiosis underlies a microbiota permissive to Pseudomonadota and increases the risk of gut-borne bloodstream infection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.20.716137}, pmid = {42079098}, issn = {2692-8205}, abstract = {The gut microbiota contains trillions of bacteria essential to health, but also harbors potential pathogens. The phylum Pseudomonadota, which includes Escherichia coli , Klebsiella pneumoniae , and Pseudomonas aeruginosa , typically composes <1% of the microbiota but causes disproportionate numbers of gut-borne bloodstream infections. Identifying the ecological dependencies that enable Pseudomonadota to cause gut-borne disease is important for human health. Here, we studied microbiota dynamics in patients undergoing allogeneic hematopoietic cell transplantation (allo-HCT) to find that microbiota compositions permissive to Pseudomonadota had, following antibiotic prophylaxis, high levels of Bacteroides- a major reservoir of polysaccharide utilization loci (PULs). We tested the causality of this clinical association in a mouse co-colonization model and discovered that Bacteroides fragilis promotes Pseudomonas gut colonization and survival to ciprofloxacin, a drug commonly used as prophylactic in allo-HCT. In vitro experiments revealed a general mechanism by which diverse Pseudomonadota species depend on Bacteroides polysaccharide breakdown to grow better, form more biofilm, and survive ciprofloxacin treatment under anaerobic conditions, a type of ecological dependency termed metabiosis . Guided by this insight, we used metagenomics to identify the PUL-encoded functions underlying the metabiotic potential of a patient's microbiota and establish a link to gut-derived Gram-negative bacteremia in allo-HCT. Together, our findings translate mechanistically based microbiome ecology into a clinically actionable framework for early risk stratification and intervention.}, }
@article {pmid42079121, year = {2026}, author = {Qian, K and Abhyankar, V and Keo, D and Zarceno, P and Toy, T and Eskin, E and Arboleda, VA}, title = {Systematic evaluation of 24 extraction and library preparation combinations for metagenomic sequencing of SARS-CoV-2 in saliva.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.16.719115}, pmid = {42079121}, issn = {2692-8205}, abstract = {UNLABELLED: Sequencing the respiratory tract transcriptome has the potential to provide insights into infectious pathogens and the host's immune response. While DNA-based sequencing is more standard in clinical laboratories due to its stability, RNA assays offer unique advantages. RNA reflects dynamic physiological changes, and for RNA viruses, viral RNA particles directly represent copies of the viral genome, enabling greater diagnostic sensitivity. However, RNA's susceptibility to degradation remains a significant challenge, particularly in RNase-rich specimens like saliva. To address this, we conducted a systematic, combinatorial evaluation of 24 distinct mNGS workflows, crossing eight nucleic acid extraction methods with three RNA-Seq library preparation protocols. Remnant saliva samples (n = 6) were pooled and spiked with MS2 phage as a control. The SARS-CoV-2 virus was spiked into half of the samples, which were extracted using the eight different extraction methods (n = 3) and compared using RNA Integrity Number equivalent (RINe) scores and RNA concentration. The extracted RNA was then processed across the three library construction methods and subjected to short-read sequencing to assess all 24 combinations head-to-head. We compared methods based on viral read recovery and found that RINe and concentration did not correlate with viral detection. The Zymo Quick-RNA Magbead kit and the Tecan Revelo RNA-Seq High-Sensitivity RNA library kit were the extraction and library-preparation kits that yielded the most SARS-CoV-2 reads, respectively. Importantly, our combinatorial analysis revealed that any small variability attributable to different nucleic acid extraction methods was heavily overshadowed by differences in quality attributable to the RNA-Seq library preparation methods. These findings challenge the reliance on conventional RNA quality metrics for clinical metagenomics and underscore the need to redefine extraction quality standards for mNGS applications.<br><br>IMPORTANCE: mNGS is a powerful and unbiased approach towards pathogen detection that has mostly been applied to blood and cerebrospinal fluid samples. However mNGS has recently been applied to more areas including the respiratory pathogen detection space, with potential applications in both in-patient diagnostics and public health surveillance. Saliva samples are an ideal sample type for these use cases since they can be collected non-invasively. However, saliva is also a challenging sample type due to its high RNase activity and often yields low-quality nucleic acid. This study explores the feasibility of using saliva specimens in mNGS with contrived SARS-CoV-2 samples to optimize the combination of two factors: nucleic acid extraction and RNA-seq library preparation. Exploration in this area could enhance the sensitivity of saliva-based mNGS assays, with the goal of future expansion of this specimen type in clinical diagnostics and public health surveillance.<br><br>KEY POINTS: The choice of RNA-Seq library preparation kit has a greater impact on pathogen detection than the nucleic acid extraction method.The combination of Zymo Quick-RNA Magbead extraction kit and TECAN Revelo RNA-Seq High Sensitivity RNA library kit recovered the highest percentage of total SARS-CoV-2 reads.RNA quantity and RINe score do not correlate with viral read capture, indicating a need for an alternative metric to assess RNA quality for downstream mNGS clinical diagnostics.}, }
@article {pmid42079283, year = {2026}, author = {Brenner, E and Vang, C and Johnson, C and Ravi, J}, title = {Genotype-phenotype modeling of light ecotypes in Prochlorococcus reveals genomic signatures of ecotypic divergence.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2025.10.13.678797}, pmid = {42079283}, issn = {2692-8205}, abstract = {UNLABELLED: Prochlorococcus species are the most abundant marine photosynthetic bacteria. Despite broadly shared phenotypic traits and marine habitats, they exhibit remarkable genomic diversity. We ask what genomic signatures underlie its ecotypic divergence into high- and low-light adapted lineages, and whether these signatures can still be recovered from incomplete assemblies. From ∼1,000 publicly available Prochlorococcus genomes, we focused on those with information on their light adaptation ecotype (high-light/low-light), phylogenetic clades, and depth of isolation. Across these divisions, we calculated average nucleotide identity and constructed pangenomes to assess cyanobacterial core genes vs. those that separate ecotypes. Despite scant conservation, we observe a sharp taxon separation by light ecotypes. Classical machine learning models trained to predict ecotype achieve near-perfect binary classification accuracy even when predicting on partial genomes (Matthews Correlation Coefficient = 0.86 - 1.00), while regression models trained to predict the depth of isolation performed poorly, with high root mean square error values (37.6 - 42.0m). For ecotype prediction, we analyzed top gene features across model runs and classes; these features included photosynthesis-associated genes and pathways, as well as many novel markers of unknown function. When separating ecotypes further by previously described phylogenetic clades, genomic content and composition show even clearer separation among clades, supporting the taxonomic breadth of the Prochlorococcus collective. These results emphasize the genomic specialization underlying ecotypic divergence and support the utility of ML approaches for cyanobacterial ecotype prediction from metagenomic data. Expanded sampling will yield novel clade-specific biology. All data, models, and results are available on GitHub: https://github.com/JRaviLab/cyano_adaptation .<br><br>IMPORTANCE: Prochlorococcus are common aquatic cyanobacteria that can derive energy from light. They can be classified into high-/low-light ecotypes depending on how they use light. Prochlorococcus have small genomes compared to other bacteria, but the gene sets they carry are also remarkably flexible, which may help them survive and adapt to their harsh oceanic environment. We studied hundreds of Prochlorococcus genomes from around the world in an effort to predict ecotypes from partial genome sequences. We used comparative genomics, machine learning, and other statistical methods to identify genomic features associated with ecotypes. These statistical approaches predicted ecotypes accurately, reliably, and according to large differences in gene content and genome structure. Our results support that Prochlorococcus can be divided into different species or genera based on clades, and provide many gene targets for further research to understand cyanobacterial circadian rhythms or improve their bioengineering potential as chassis organisms.}, }
@article {pmid42079297, year = {2026}, author = {Cornman-Homonoff, J and Rajendran, KM and Kolandaivelu, S and Coon, SD and Kupec, JT and Wang, L and Hu, G and Jala, VR and Sandle, GI and Rajendran, VM}, title = {Dietary Sodium Restriction Reprograms Gut Microbial Fermentation and Reduces Host Energy Harvest.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.20.719706}, pmid = {42079297}, issn = {2692-8205}, abstract = {Diet is a major determinant of gut microbiome structure and function, yet the role of dietary electrolytes-particularly sodium-remains poorly defined. Here, we identify dietary sodium availability as a key regulator of gut microbial fermentation and host energy harvest. Using a controlled sodium-sufficient versus sodium-deprived dietary intervention in rats, we integrated shotgun metagenomic sequencing, functional pathway analysis, targeted short-chain fatty acid (SCFA) quantification, and host physiological phenotyping. Sodium deprivation induced a coordinated restructuring of the gut microbiome, characterized by depletion of classical saccharolytic Firmicutes, including multiple Lactobacillus species, and enrichment of stress-tolerant, metabolically flexible taxa. Functional profiling revealed a shift away from growth-associated metabolic programs toward stress-adaptive and nutrient-scavenging pathways. Consistent with these changes, fecal concentrations of key SCFAs-including acetate, butyrate, hexanoate, and valerate-were significantly reduced, indicating impaired microbial fermentative capacity. These microbiome-level alterations translated into measurable host phenotypes, including reduced cecal mass and attenuated weight gain, consistent with decreased microbial energy harvest. Together, these findings establish a functional link between luminal sodium availability, microbial metabolic efficiency, and host energy balance, extending the framework of diet-microbiome interactions beyond macronutrients to include dietary electrolytes. This work identifies sodium as a previously underappreciated ecological constraint shaping gut microbial metabolism and suggests that modulation of dietary sodium intake may influence host metabolic outcomes through microbiome-mediated mechanisms.}, }
@article {pmid42079427, year = {2026}, author = {Xolalpa-Aroche, A and Contreras-Peruyero, H and Delgado-Suárez, EJ and Hernández-Mena, DI and Moguel-Chin, WI and Rivero-Cruz, JF and Velarde, RA and Ortiz-Vázquez, E and Rivero-Cruz, BE and Lovaco-Flores, JA and Rodríguez Orduña, L and Licona-Cassani, C and Barona-Gómez, F and Sélem-Mojica, N}, title = {Genome-resolved metagenomics reveals a phylogenetically cohesive Acetilactobacillus-like species complex dominating stingless bee pot honey.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag063}, pmid = {42079427}, issn = {2730-6151}, abstract = {Pot honey, the honey produced by stingless bees, is valued for its antimicrobial capacity, which may be influenced by its microbial content. While Lactobacillaceae species are commonly associated with honeybees and honey microbiomes, most studies have focused on Apis mellifera, leaving pot honey microbial diversity largely unexplored. We present the first pot honey shotgun metagenomic analysis from bee species Melipona beecheii and Scaptotrigona mexicana. We reconstructed 24 metagenome-assembled genomes (MAGs), 15 of which lacked close matches to any described species, showing [Formula: see text]81% Average Nucleotide Identity (ANI) to available reference genomes. Phylogenetic analyses resolved these MAGs into four well-defined clades (intraclade ANI [Formula: see text], interclade ANI [Formula: see text]), consistent with four novel species within the family Lactobacillaceae. GTDB-Tk classification placed MAG clades 1 and 2 closest to Nicoliella, and clades 3 and 4 closest to Acetilactobacillus. We validated the presence of these lineages in honey by sequencing three isolates that clustered within MAG clade 2. Aminoacid similarity (AAI/cAAI) indicates the presence of two genus-level lineages: one occupying a transitional genomic space near Nicoliella, and a second representing an undescribed genus. The genomic similarity of our MAGs and isolates to those from pot honey or larval food in Malaysia, Brazil, and Australia suggests these taxa are closely associated with stingless bees and may contribute to honey properties. By reducing the genomic underrepresentation of evolutionarily divergent sister clades related to Nicoliella and Acetilactobacillus, our genome-resolved analyses reveal a globally distributed, phylogenetically cohesive Lactobacillaceae species complex dominating pot honey.}, }
@article {pmid42079429, year = {2026}, author = {Christensen, R and Wang, YHD and Arnoldini, M and Cremer, J}, title = {Abundance-weighted pathway mapping demonstrates family-level structure of butyrate and propionate production across the human gut microbiome.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag075}, pmid = {42079429}, issn = {2730-6151}, abstract = {Fermentation products released by bacteria in the large intestine, such as butyrate and propionate, play central roles in host physiology and health. While the metabolic pathways producing these short-chain fatty acids (SCFAs) are well-characterized, less is known about their relative prevalence across hosts and gut conditions. Here, we introduce a genome-resolved, abundance-weighted bioinformatics framework that integrates pathway-based gene identification with extensive literature validation to systematically quantify the potential for butyrate and propionate production across bacterial species and human gut microbiomes. By comparing pathway predictions against over 700 experimentally characterized strains, we demonstrate high concordance with reported metabolic phenotypes, validating our approach beyond prior purely computational studies. Weighted by species abundance across ~18 000 metagenomic samples, we find that dominant gut taxa disproportionately drive SCFA production, with butyrate pathways enriched in Bacillota and propionate pathways in Bacteroidota. This abundance-weighted analysis reveals that pathway presence is well conserved at the family level, highlighting the ecological relevance of dominant taxa for community-level fermentation potential. Our results further show pronounced inter-individual variation and associations with age, birthing method, and inflammatory bowel disease, emphasizing how shifts in microbiota composition influence SCFA availability. By combining pathway-level resolution, abundance-weighted inference, and literature-based validation, our framework provides a robust, scalable approach to link microbial functional potential with host-relevant outcomes.}, }
@article {pmid42079433, year = {2026}, author = {Batilong, LS and Traifalgar, RFM and Del Castillo, CS and Jore, KAG and Fantonalgo, IRL and Huervana, FH and Javellana, TF and Pagapulan, MJBB and Failaman, AN and Gayosa, VED}, title = {Gut-Derived Lactic Acid Bacteria, Pediococcus pentosaceus, Enhances Growth Performance and Resistance to Pathogenic Vibrio harveyi of Hatchery-Bred Milkfish (Chanos chanos) in Nursery Culture.}, journal = {International journal of microbiology}, volume = {2026}, number = {}, pages = {6489487}, pmid = {42079433}, issn = {1687-918X}, abstract = {Hatchery-bred milkfish (Chanos chanos) fry continue to face stocking challenges due to inferior growth performance and reduced resilience compared with wild-caught fry. Recent metagenomic studies have shown that wild fry harbor a higher relative abundance of bacterial taxa belonging to the phylum Bacillota. These include lactic acid bacteria (LAB), which are widely recognized for their probiotic potential in aquaculture. Building on this metagenomic insight, the present study adopted a targeted approach to isolate LAB with anti-Vibrio activity and evaluate its probiotic potential in hatchery-bred C. chanos nursery culture. Screening identified Pediococcus pentosaceus HLAB22 as a promising LAB candidate, which was subsequently assessed through in vivo probiotic trials. Probiotic supplementation significantly improved growth performance, survival, and reduced the incidence of opercular deformities in early juveniles. The most pronounced effects observed at 10[6] CFU, followed by 10[3] CFU g[-1] feed compared with the control group. Gut colonization experiment demonstrated that dietary supplementation with P. pentosaceus HLAB22 at 10[6] CFU g[-1] feed enabled intestinal colonization within 12 days. This also resulted in near-complete suppression of Vibrio populations, supporting the significant decrease in water and C. chanos gut Vibrio load during the feeding trial. Furthermore, during immersion challenge with pathogenic V. harveyi, the in vitro anti-Vibrio activity of P. pentosaceus HLAB22 was translated into enhanced in vivo protection, yielding a survival rate of 83.33% in treated fish compared with 33.33% in the control group. Collectively, these findings indicate that oral application of P. pentosaceus HLAB22 at 10[6] CFU g[-1] feed is an effective strategy for promoting growth and enhancing resilience in C. chanos nursery culture. This study supports the use of targeted, host-associated probiotics to improve the performance of hatchery-bred milkfish fry and mitigate key challenges in nursery production systems.}, }
@article {pmid42079444, year = {2026}, author = {Fang, T and Yuan, F and Chen, Y and Li, N and Zhang, Y and Liu, H and Liu, X and Miao, Q and Hu, B}, title = {Emerging role of metagenomic next-generation sequencing in infectious disease diagnostics: Clinical integration and future directions.}, journal = {mLife}, volume = {5}, number = {2}, pages = {148-163}, pmid = {42079444}, issn = {2770-100X}, abstract = {Infectious disease diagnostics has been transformed by metagenomic next-generation sequencing (mNGS), an unbiased approach that detects bacteria, viruses, fungi, and parasites in a single assay. By sequencing all nucleic acids in a sample, mNGS overcomes the narrow detection scope and slow turnaround of conventional tests, substantially improving pathogen detection. In conditions such as meningitis/encephalitis, sepsis, and pneumonia, mNGS frequently identifies etiologies missed by routine diagnostic tests, thereby facilitating earlier pathogen-directed therapy and, in selected settings, improving clinical management and outcomes. This approach is particularly valuable for immunocompromised, pediatric, and intensive care unit (ICU) patients with atypical infections. Currently, clinical mNGS workflows primarily rely on short-read sequencing platforms (e.g., Illumina), whereas long-read platforms (e.g., Nanopore, PacBio) offer advantages for rapid or high-resolution applications. Optimized bioinformatics and stringent quality control are essential for reliable results. Beyond clinical diagnostics, mNGS provides valuable genetic data on antimicrobial resistance (AMR) and pathogen phylogeny, supporting public health and outbreak surveillance (e.g., wastewater monitoring and variant tracking). Current challenges include distinguishing colonization from infection, interpreting sequencing data quantitatively, and reducing cost and turnaround time. Looking ahead, emerging strategies such as targeted panels, rapid automated workflows, and host‑response integration are expected to further shorten time‑to‑result and improve diagnostic specificity. Parallel progress in ethical and regulatory frameworks remains essential to ensure responsible implementation. To support clinical adoption, a standardized framework for clinical interpretation of mNGS results, together with associated training, has been developed and implemented. Overall, mNGS is likely to become an increasingly important component of infectious disease diagnostics, with ongoing innovations expected to broaden its clinical and epidemiological impact.}, }
@article {pmid42079557, year = {2026}, author = {Kujala, K and Kinnunen, V}, title = {Lactic acid bacteria dominate urban Bokashi: a participatory, culture-independent pilot study of microbial diversity and functional potential in household-scale food waste fermentation.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag018}, pmid = {42079557}, issn = {2633-6685}, abstract = {In recent years, concerns over declining biodiversity in urban spaces have increased. Urban Bokashi composting (i.e. microaerobic or anaerobic fermentation of food waste indoors) has been suggested as a possibility to promote microbial diversity in the domestic environment. However, studies on microbial communities in household-scale Bokashi and their potential impacts on health and environment are lacking. Thus, the present pilot study investigated microbial communities in different stages of the Bokashi composting process in collaboration with six Bokashi practitioners by looking into physicochemical characteristics as well as microbial community composition (16S amplicon sequencing, 34 samples) and functional potential (shotgun metagenome sequencing, 11 samples). The collective results indicate that i) microbial communities in Bokashi compost differed between stages, but also between households, ii) microbial communities were dominated by lactic acid bacteria like Lentilactobacillus or Lacticaseibacillus, iii) metabolic pathways for the production of diverse organic acids were detected, iv) application of Bokashi ferment or leachate to soil can supply nutrients and organic acids to promote plant growth but does not substantially affect soil microbial community composition, and v) potentially pathogenic organisms were detected in extremely low abundances. Thus, urban Bokashi is likely not associated with increased health risks and positive impacts are feasible.}, }
@article {pmid42079638, year = {2026}, author = {Han, X and Zang, D and Lin, M and Yin, Y and Liu, D and Sun, Q and Chen, J}, title = {Dynamic changes in gut microbiota and metabolites in advanced lung cancer patients with immune-related adverse events.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1731931}, pmid = {42079638}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; Male ; Female ; Middle Aged ; *Lung Neoplasms/drug therapy/immunology/metabolism ; Aged ; *Immune Checkpoint Inhibitors/adverse effects ; *Metabolome ; Metabolomics/methods ; *Drug-Related Side Effects and Adverse Reactions/metabolism/etiology ; Feces/microbiology ; }, abstract = {BACKGROUND: Immune-related adverse events (irAEs) represent an urgent clinical challenge. Although accumulating evidence suggests that irAEs are associated with the gut microbiota and its metabolites, our understanding of the dynamic alterations in the gut microbiota and related metabolic profiles throughout the onset and progression of irAEs remains limited.<br><br>METHODS: A total of 48 fecal samples were collected from 32 lung cancer patients treated with immune checkpoint inhibitors, including 16 patients who developed irAEs and 16 who did not. Fecal samples were collected at baseline and, in patients with irAEs, at the time of irAEs onset. Metagenomic sequencing and untargeted metabolomics analyses were performed to identify baseline differences in gut microbiota and metabolites, characterize longitudinal dynamic changes in gut microbiota and metabolite profiles in patients with irAEs, and construct a machine learning based random forest model to predict the occurrence of irAEs.<br><br>RESULTS: There were baseline differences in microbial communities and metabolites between the two groups. In the non-irAEs group, Phocaeicola coprocola was enriched and Micrococales decreased. At baseline, viomycin was positively correlated with irAEs, while metabolites such as calcitriol and L-isoleucine were negatively correlated with irAEs. The roles of valine, leucine and isoleucine metabolism and vitamin B6 metabolism pathways were downregulated in the irAEs group. Compared to baseline, there were significant changes in gut microbiota and metabolites during the onset of irAEs, and the abundance of Veillonella increased during irAEs onset. Dynamic monitoring of metabolic changes in irAEs revealed decreased levels of trypsin butylester, BQ 123, DL-o-tyrosine, and nicotinamide-beta-riboside during irAEs attacks. Lysine degradation, arachidonic acid metabolism, folate biosynthesis, nicotinate and nicotinamide metabolism, and C5-branched dibasic acid metabolism were downregulated during the progression of irAEs. A model for predicting the occurrence of irAEs based on differential microbiota and metabolites was constructed, and after robust validation, the model showed good performance and excellent discriminative power.<br><br>CONCLUSIONS: The occurrence and development of irAEs are associated with the composition of the gut microbiota and metabolites, as well as their dynamic changes over time. These findings highlight the potential of gut microbiota and metabolites as biomarkers for predicting the occurrence and progression of irAEs.}, }
@article {pmid42080299, year = {2026}, author = {Li, Z and Ren, M and Hu, A and Meng, F and Wang, J}, title = {Depth Stratification Shapes Viral Diversity, Interactions, and Metabolic Potential in a Deep Freshwater Lake.}, journal = {Molecular ecology}, volume = {35}, number = {9}, pages = {e70367}, doi = {10.1111/mec.70367}, pmid = {42080299}, issn = {1365-294X}, support = {U24A20578//National Natural Science Foundation of China/ ; 42507557//National Natural Science Foundation of China/ ; 42372353//National Natural Science Foundation of China/ ; BK20240111//Basic Research Program of Jiangsu Province/ ; }, mesh = {*Lakes/virology/microbiology ; *Viruses/genetics/classification ; Metagenomics ; Fresh Water/virology ; Microbiota/genetics ; Ecosystem ; Geologic Sediments/virology ; Biodiversity ; Metagenome ; }, abstract = {Deep freshwater lakes exhibit distinct microbial community stratification across depth gradients, which plays important roles in biogeochemical cycling and ecosystem stability. As crucial regulators of microbiome composition and function, viruses may play key ecological roles in these stratified systems, yet their distribution patterns and ecological significance in deep-lake surface sediments remain poorly understood. Here, we assessed viral community dynamics and functional potential across the entire water depth gradient (0-155 m) of Fuxian Lake using metagenomics from 44 surface sediment samples. A total of 11,523 viral OTUs were recovered, with only 18% annotated to the family level and approximately 93% classified as putatively lytic. Viral communities showed systematic depth-related shifts across multiple dimensions. Specifically, alpha diversity, community turnover, and stochastic assembly processes increased significantly with water depth, accompanied by enhanced lytic virus dominance and larger genome sizes. Predicted virus-host association networks transitioned from highly connected and generalized at shallow depths to increasingly sparse and specialized at greater depths. Virus-encoded auxiliary metabolic genes showed significantly increasing abundance with water depth, along with functional shifts from host defense to enhanced biosynthesis and energy metabolism, especially regarding carbon fixation and organic matter degradation. Collectively, these results highlight the importance of water depth gradients in structuring viral communities within surface sediments and expand our understanding of viral ecological functions in deep lake ecosystems.}, }
@article {pmid42080548, year = {2026}, author = {Zhang, X and Zhong, A and Liu, Y and Zou, J and Gu, M and Zhu, X and Xu, H and Yin, S}, title = {Chronic intermittent hypoxia exacerbates hepatic steatosis in a microbiota-dependent manner in lean mice.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0016326}, doi = {10.1128/msystems.00163-26}, pmid = {42080548}, issn = {2379-5077}, abstract = {Chronic intermittent hypoxia (CIH), a hallmark pathological feature of obstructive sleep apnea (OSA), is extensively linked to hepatic steatosis in high-fat-diet-induced mice. However, the association between CIH and hepatic steatosis in lean mice, as well as the potential involvement of gut microbiota-related mechanisms, remains poorly understood. Four hundred participants in the Shanghai Sleep Health Study were included to assess the association between apnea-hypopnea index (AHI) and hepatic steatosis index (HSI). To characterize CIH-associated phenotypes and explore microbiota-related alterations in lean mice, liver histology, inflammatory cytokine profiling, metagenomic sequencing with antibiotic intervention, plasma untargeted metabolomics, and liver transcriptomics were performed. As a result, AHI was positively associated with HSI in non-obese participants. In lean mice, 16-week CIH alone induced hepatic steatosis and inflammation, accompanied by significant alterations in gut microbiota composition. Antibiotic treatment attenuated hepatic steatosis and inflammation in 16-week CIH-exposed mice. Metagenomic analysis revealed CIH-associated depletion of Bacteroides uniformis, which was reversed by antibiotic treatment. Plasma metabolomic profiling identified deoxycholic acid as a metabolite exhibiting opposite, phenotype-aligned alterations between CIH and CIH plus antibiotic groups and showing the strongest correlation with Bacteroides uniformis abundance. In parallel, liver transcriptomics revealed coordinated alterations in bile acid-related metabolic pathways and PPAR signaling consistent with CIH-induced and antibiotic-sensitive metabolic remodeling. Together, these findings indicate that prolonged CIH exposure induces hepatic lipid accumulation in lean mice and is associated with coordinated, antibiotic-sensitive alterations in gut microbiota composition, bile acid metabolism, and hepatic transcriptional programs, suggesting a potential involvement of gut microbiota-bile acid-liver interactions in CIH-associated hepatic steatosis.IMPORTANCEObstructive sleep apnea (OSA) is increasingly recognized as a contributor to metabolic dysfunction, yet its role in hepatic steatosis independent of obesity remains incompletely understood. This study shows that chronic intermittent hypoxia (CIH), a defining pathological feature of OSA, is sufficient to induce hepatic steatosis and inflammation in lean mice, independent of dietary manipulation. These findings broaden current understanding of OSA-associated liver disease beyond the context of obesity and metabolic syndrome. By integrating metagenomic sequencing, plasma metabolomics, and liver transcriptomics, this work highlights coordinated alterations in gut microbial composition, bile acid profiles, and hepatic lipid-related transcriptional programs associated with CIH exposure. Depletion of Bacteroides uniformis and elevation of deoxycholic acid were linked to CIH-induced hepatic phenotypes and were sensitive to antibiotic intervention, supporting a contributory role of gut microbiota-bile acid interactions in this process. Together, these findings underscore the potential importance of gut microbiota-host metabolic crosstalk in OSA-associated hepatic steatosis and suggest that microbiota- or bile acid-targeted strategies may warrant further investigation as adjunctive approaches for risk stratification and therapeutic intervention in OSA-related liver disease.}, }
@article {pmid42080847, year = {2026}, author = {Terzi, I and Akinosoglou, K}, title = {More Detection, Better Decisions? Rethinking Pathogen-Driven Therapy in Diabetic Foot Infections.}, journal = {The international journal of lower extremity wounds}, volume = {}, number = {}, pages = {15347346261447707}, doi = {10.1177/15347346261447707}, pmid = {42080847}, issn = {1552-6941}, abstract = {Pathogen-driven therapy is central to the management of diabetic foot infections (DFIs), where antimicrobial selection relies on microbiological identification. Over the past decade, diagnostic capabilities have expanded from conventional cultures to high-resolution molecular sequencing, substantially increasing pathogen detection. Whether this expansion translates into better therapeutic decisions, however, remains uncertain. This narrative review examines the roles and limitations of culture-based methods, antimicrobial susceptibility testing, targeted polymerase chain reaction panels, 16S rRNA gene sequencing, and shotgun metagenomics in DFIs. Culture remains the cornerstone of pathogen-directed therapy because it identifies viable organisms and provides phenotypic susceptibility data that inform antibiotic selection and de-escalation. Molecular techniques broaden detection and reveal polymicrobial complexity and resistance genes, yet increased analytical sensitivity does not consistently clarify pathogen prioritization, distinguish colonization from infection, or improve patient-centered outcomes. Intensified diagnostic strategies often lead to antimicrobial modification without clear gains in healing or cost-effectiveness. These findings underscore a persistent interpretative gap: detection capacity has advanced more rapidly than frameworks linking microbiological data to meaningful therapeutic action. Microbiology is indispensable but insufficient in isolation. Improved outcomes will depend less on detecting additional organisms and more on integrating microbiological findings with surgical management, vascular status, and multidisciplinary care.}, }
@article {pmid42081091, year = {2026}, author = {Gui, C and Li, J and Wang, Q and Chen, L and Shao, Q}, title = {Robot-Assisted Incision and Drainage for a Polymicrobial Brain Abscess.}, journal = {The Journal of craniofacial surgery}, volume = {}, number = {}, pages = {}, doi = {10.1097/SCS.0000000000012848}, pmid = {42081091}, issn = {1536-3732}, abstract = {OBJECTIVE: To evaluate the clinical utility of robot-assisted incision and drainage in the management of a polymicrobial brain abscess located in the central region.<br><br>METHODS: We retrospectively analyzed a case of polymicrobial odontogenic brain abscess in a 71-year-old male who presented with stroke-like symptoms. The patient was admitted due to progressive right-sided weakness, initially mimicking an acute ischemic stroke. Gadolinium-enhanced T1-weighted magnetic resonance imaging (MRI) revealed ring-enhancing lesions in the left precentral gyrus and the right temporal lobe, with corresponding high signal on diffusion-weighted imaging (DWI), highly suggestive of a brain abscess. Following empirical antibiotic therapy (vancomycin and meropenem), the patient clinically deteriorated, and a repeat MRI demonstrated enlargement of the left central abscess. During the Remebot robotic navigation, the abscess was incised and drained, yielding thick, yellowish-white purulent material. Postoperative metagenomic next-generation sequencing (mNGS) of the pus identified a polymicrobial infection comprising Fusobacterium nucleatum, Streptococcus constellatus, Parvimonas micra, and Porphyromonas gingivalis.<br><br>RESULTS: Based on the microbiological findings, the antibiotic regimen was tailored to a triple combination of vancomycin, meropenem, and metronidazole for 2 weeks, followed by vancomycin plus meropenem for an additional 4 weeks, complemented by rehabilitation and hyperbaric oxygen therapy. The patient demonstrated remarkable neurological recovery. One month post-surgery, right limb muscle strength had returned to grade 5, with only mild residual impairment in fine-motor coordination of the right hand. Three-month follow-up MRI revealed complete resolution of the previously observed intracranial ring-enhancing lesions.<br><br>CONCLUSION: For eloquent-area brain abscesses that progress despite medical management, robot-assisted incision and drainage offers a safe, precise, and efficacious minimally invasive surgical option. Integration of mNGS technology for pathogen identification enables targeted antimicrobial therapy, a pivotal step toward achieving favorable outcomes in complex infections.}, }
@article {pmid42081443, year = {2026}, author = {Reddy, SP and Morgenroth-Rebin, J and Wang, S and Wilson, MR}, title = {Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid for the Detection of Central Nervous System Pathogens.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {230}, pages = {}, doi = {10.3791/70075}, pmid = {42081443}, issn = {1940-087X}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Central Nervous System Infections/cerebrospinal fluid/microbiology ; }, abstract = {Metagenomic next-generation sequencing (mNGS) has emerged as a powerful tool for unbiased pathogen detection and host transcriptional profiling in clinical and research settings. While its utility in diagnosing central nervous system (CNS) infections is increasingly recognized, cerebrospinal fluid (CSF) samples pose unique challenges due to low nucleic acid abundance and susceptibility to degradation. This study presents an optimized research-based protocol for Illumina sequencing platforms tailored to CSF mNGS, spanning sample handling, nucleic acid extraction, library preparation, sequencing, and bioinformatic analysis. Quality control approaches adaptable to both high and low-resource settings are also provided, including alternatives to capillary electrophoresis. This study demonstrates the protocol's robustness through two representative cohorts: a high-depth, NovaSeq-based workflow and a cost-conscious NextSeq-based workflow. Across these cohorts, pathogens were detected in over 50% of cases, underscoring the method's diagnostic potential even with resource-constrained adaptations. This protocol facilitates reproducible CSF mNGS, providing a foundation for diverse applications in neuroinfectious disease research and diagnostics.}, }
@article {pmid42081609, year = {2026}, author = {Wang, Y and Zhang, B and Shen, C and Cao, M and Wang, N and Chen, T and He, G and Sun, G and Li, C and Li, Y and Yin, X and Sun, Y and Li, C and Zhou, X}, title = {N- Carbamoylglutamate enhances bull spermatogenesis via Paraprevotella-Mediated vitamin B6 biosynthesis in rumen microbiota.}, journal = {Reproduction (Cambridge, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/reprod/xaag049}, pmid = {42081609}, issn = {1741-7899}, abstract = {N-carbamoylglutamate (NCG), a functional analog of the arginine precursor, shows strong potential in enhancing spermatogenesis in bulls. In this study, dietary NCG supplementation significantly increased sperm density and motility in XiangXi yellow bulls, the local beef cattle. Metagenomic and serum metabolomic analyses revealed that NCG altered the composition of rumen microbiota, notably increasing the abundance of Paraprevotella and elevating serum vitamin B6 levels (p < .05), suggesting a possible microbiota-associated metabolic modulation underlying its reproductive benefits. To explore this mechanism, a busulfan-induced mouse model of impaired spermatogenesis was established. Mice received transplants of either rumen microbiota from NCG-treated bulls or the differential genus Paraprevotella. Both treatments alleviated reproductive damage and increased vitamin B6 levels in serum and testis. Mechanistic investigation indicated that Paraprevotella was associated with upregulated expression of 3-phosphoserine aminotransferase (SerC), a key enzyme involved in vitamin B6 biosynthesis. Subsequent vitamin B6 supplementation experiments showed increased testicular glutathione levels and reduced thiobarbituric acid-reactive substances level (TBARS, expressed as MDA equivalents). These experiments supported a contributory role of vitamin B6 in promoting spermatogenesis, including increased sperm count and enhanced expression of spermatogenic cell markers. In summary, this study demonstrated that NCG enhanced spermatogenesis in bulls by reshaping the rumen microbiota, particularly through enrichment of Paraprevotella, which was associated with increased systemic vitamin B6 levels and contributed to reproductive improvement. These findings provide further insights into the application of NCG in improving fertility in ruminants.}, }
@article {pmid42082028, year = {2026}, author = {Zhang, Q and Hu, Y and Wang, G and Kong, L and Xu, Z and Ma, X and Chen, R}, title = {Deciphering the impact of chlortetracycline on methanogenesis, microbial properties and antibiotic resistance genes in an anaerobic ceramic membrane bioreactor treating swine wastewater.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134760}, doi = {10.1016/j.biortech.2026.134760}, pmid = {42082028}, issn = {1873-2976}, abstract = {The presence of chlortetracycline (CTC) in swine wastewater poses a threat to anaerobic treatment and ecological safety. This study investigated the concentration-dependent effects of CTC on methanogenesis, microbial properties, and antibiotic resistance genes in an anaerobic ceramic membrane bioreactor (AnCMBR). Batch assays identified a biological inhibition threshold at 50 mg/L CTC. During long-term operation, CTC at 10 mg/L (after a brief adaptation) increased methane yield by 28%, while 50 mg/L CTC inhibited methanogenesis and reduced COD removal from 97% to 86%. High-level CTC raised antibiotic resistance gene abundance and decreased acute toxicity removal from 68% to 46%. Biodegradation dominated CTC removal, but its contribution declined from 42% to 19% as CTC increased, lowering overall removal from 60% to 30%. Metagenomic analysis revealed that low-level CTC upregulated hydrolysis/fermentation-related genes (e.g., enolase, phosphoglycerate mutase, pyruvate kinase), enhancing substrate supply for methanogenesis. In contrast, high-level CTC markedly enriched Spirochaetes (from 3% to 66%), suppressed key methanogenic genes involved in methyl-CoM reductase and downstream acetyl-CoA metabolism, while preserving acetoclastic pathway genes (acsS1.2, ackA, pta), collectively shifting the pathway toward acetoclastic methanogenesis. Notably, the AnCMBR maintained stable filtration performance, with the transmembrane pressure remaining below 6.5 kPa over 160 days. These findings demonstrate that low CTC levels can be tolerated after acclimation, whereas high CTC stress severely impairs methanogenesis, detoxification, and biosafety.}, }
@article {pmid42066983, year = {2026}, author = {Rajabal, V and Ghaly, TM and Colombi, E and Russell, DH and Sia, C and Shah, B and McPherson, VJ and Qi, Q and Coleman, NV and Gillings, MR and Tetu, SG}, title = {Discovery of novel antimicrobial resistance genes: Integrons as a high-throughput gene capture and functional screening platform.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128228}, doi = {10.1016/j.envpol.2026.128228}, pmid = {42066983}, issn = {1873-6424}, abstract = {Integrons are genetic elements that drive bacterial adaptation by capturing and expressing mobile gene cassettes. They play a key role in dissemination of antimicrobial resistance (AMR) genes, particularly in Gram-negative bacteria. In addition to known AMR determinants, integron gene cassettes carry a vast reservoir of novel genes whose functions are largely uncharacterised, making it difficult to assess their full contribution to the resistome. Contributing to this are limitations in current sequence-based prediction methods which often lack the ability to identify unknown AMR or other adaptive genes with novel mechanisms. To address this, we developed a high-throughput gene cassette capture system that utilises site-specific recombination activity of integrons and a counter selection strategy to capture and express gene cassettes from metagenomes. Coupling this platform with a functional screening approach allowed us to rapidly assay large libraries of environmental gene cassettes. Using this system, we recovered previously unknown AMR determinants while also providing insights into the prevalence of known clinical AMR genes in a range of environmental samples, including food and fertiliser. Here we provide experimental data on multiple novel bleomycin resistance genes and a stress response gene conferring gentamicin and tobramycin resistance. Our sequence analysis of the captured library also highlighted the diversity of the environmental cassette pool, with 656 unique cassettes recovered, the majority of which encoded proteins with unknown functions. The cassette capture system is a powerful tool for accessing hidden elements of the resistome and discovering novel adaptive genes that may go undetected using current sequence-based approaches.}, }
@article {pmid42067165, year = {2026}, author = {Zong, K and Zhang, T and Li, Y and Ji, M and Lu, J and Guo, Y and Zhao, C and Lv, J and Kong, Q and Wang, Q and Zhang, J}, title = {Mechanism of magnetite coupled microbial enhancement in mariculture wastewater treatment: Dual edged role of magnetite.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134749}, doi = {10.1016/j.biortech.2026.134749}, pmid = {42067165}, issn = {1873-2976}, abstract = {Marine aquaculture wastewater treatment faces dual challenges of microbial inhibition and greenhouse gas (GHG) emissions under saline stress. This study investigates the synergistic effects of submicron magnetite and intertidal microorganisms on treatment efficiency in constructed wetlands (CWs). Three CWs were designed: "Mag" (magnetite composite microorganisms), "IWS" (microorganisms only) and "CK" (control). Nutrient removal and GHG emissions were evaluated, and microbial mechanisms under saline conditions were explored via metagenomics. Mag achieved the highest removal efficiencies for NH4[+]-N, total nitrogen (TN), COD, and total phosphorus (TP), with TP removal 20.1% and 43.7% higher than in IWS and CK, respectively. Biological iron redox cycling on magnetite surfaces continuously generated reactive sites that enhanced nutrient adsorption and forms conductive pathways that facilitate direct interspecies electron transfer through the upregulation of pilA and cytochrome c, thereby promoting the transformation of aqueous organic pollutants into inorganic gaseous products. IWS promoted sulfur-driven autotrophic denitrification, effectively removing nitrogen and suppressing CH4 through competition between sulfur oxidizers and methanogens. Plant uptake also contributed to high TN and TP removal with low GHG emissions. CK exhibited dominant glycolytic activity with energy directed toward osmotic regulation, resulting in low contaminant removal and high GHG emissions. This study offers practical guidance for balancing nutrient removal efficiency with reduced GHG emissions in the treatment of saline wastewater.}, }
@article {pmid42067590, year = {2026}, author = {Alasadi, GJ and Khakvar, R and Zirak, L}, title = {Metagenomic detection of novel bacterial combinations associated with citrus decline in Iraq.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-51185-8}, pmid = {42067590}, issn = {2045-2322}, abstract = {Citrus decline diseases pose significant threats to global fruit production, with complex bacterial pathogen interactions remaining poorly understood. In Iraq's Karbala governorate, severe citrus decline has affected orange orchards for 25 years, causing tree mortality within 3-5 years and substantial economic losses. PCR screening was performed on 75 symptomatic orange trees to detect phloem-limited bacterial pathogens, followed by whole-genome metagenomics on three selected PCR-positive samples to characterize associated microbial communities. Raw NGS reads from these three samples were quality-filtered, then MetaPhlAn2 was used to map reads to a curated marker database and identify bacterial, archaeal, viral, and eukaryotic taxa. The analysis revealed complex mixed infections involving three major plant bacterial pathogens: whereas PCR assays identified Candidatus Phytoplasma citri in 13.3% of the 75 samples, two additional phloem-limited pathogens, Ca. Liberibacter asiaticus and Spiroplasma sp., were exclusively detected via metagenomic sequencing across the three analyzed samples. Trimmed reads were assembled into contigs and analyzed phylogenomically against a global reference dataset. Genome assemblies yielded three for Ca. P. citri (576,881 bp, 424,689 bp, and 72,017 bp) and one each for Ca. L. asiaticus (1,151,288 bp) and Spiroplasma sp. (1,833,004 bp). These findings should be considered exploratory given the limited metagenomic sample size (n = 3); independent validation using targeted molecular approaches is required to confirm the presence of Ca. L. asiaticus and Spiroplasma sp. This is the first report documenting the metagenomic detection and characterization of a mixed infection involving Ca. Phytoplasma citri, Ca. Liberibacter asiaticus, and Spiroplasma sp. associated with citrus decline in Iraq. These findings provide crucial insights into pathogen populations and characterization and inform targeted management strategies for emerging bacterial diseases in Iraqi agricultural systems.}, }
@article {pmid42067625, year = {2026}, author = {Liu, X and Zhang, H and Wang, YZ and Tu, X and Wen, J and Lei, S and Liu, N and Wei, X and Li, C and Li, Y and Liu, B and Feng, YQ and Zhu, QF and Liu, X and Ning, K}, title = {Sulfated bile acid produced by a human gut commensal alleviates paediatric sepsis in mice.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {42067625}, issn = {2058-5276}, support = {2023YFA1800900, 2018YFC0910502//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 2022FYC3400800//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 32071465, 31871334, 31671374//National Natural Science Foundation of China (National Science Foundation of China)/ ; 22361132526, 22274119, 22474101//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Gut microbiota and bile acids have been reported to affect sepsis progression, but the underlying mechanisms remain largely unknown. Here we investigated gut microbiota-bile acid interplay in two paediatric sepsis cohorts. Integration of bile acid-targeted metabolomics with gut metagenome data from paediatric sepsis patients identified deoxycholic acid 3-sulfate (DCA-3S) as significantly associated with paediatric sepsis progression. In vitro and in vivo experiments identified Enterococcus raffinosus as the primary producer of DCA-3S, contributing at least 80% of its total production, challenging the conventional notion of hepato-centric bile acid sulfation pathways. Intervention experiments in mouse and intestinal organoid models revealed that DCA-3S administration effectively alleviated sepsis by improving intestinal barrier function and attenuating inflammatory response. Collectively, our findings highlight a previously unrecognized microbial contribution to bile acid sulfation and position DCA-3S as a promising diagnostic and therapeutic biomarker for paediatric sepsis.}, }
@article {pmid42067917, year = {2026}, author = {Fang, Q and Huang, S and Zhang, C and Li, M and Ye, Z and Guo, H and Xiao, M and Wang, S and Yu, L and Zhang, H and Zhao, J and Tian, F and Chen, W and Zhai, Q}, title = {Capsaicin ameliorates glycemic levels via gut microbiota-derived 5-aminolevulinic acid in mice.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02415-8}, pmid = {42067917}, issn = {2049-2618}, support = {BX20250339//Postdoctoral Fellowship Program and China Postdoctoral Science Foundation/ ; U23A20259//National Natural Science Foundation of China/ ; JUSRP622013//Fundamental Research Funds for the Central Universities/ ; }, abstract = {BACKGROUND: Capsaicin, a natural alkaloid in chili peppers, regulates glycemic levels; however, its mechanisms and therapeutic potential remain unclear. This study aimed to elucidate the role of gut microbiota and their metabolites in mediating capsaicin's glycemic regulatory effects. We conducted experiments in specific pathogen-free (SPF) and germ-free (GF) mice, transient receptor potential vanilloid 1 (TRPV1) receptor ablation studies, and fecal microbiota transplantation (FMT) to demonstrate the involvement of gut microbiota in capsaicin-mediated glycemic control. Metagenomics and metabolomics analyses were employed to identify key microbial strains and metabolic pathways. Keystone strains and metabolites were supplemented in GF mice without capsaicin intervention to validate their effects on glycemic regulation. In vitro co-culture experiments were performed to investigate the mutualistic relationships among keystone strains under capsaicin treatment.<br><br>RESULTS: Gut microbiota constitute an important component of capsaicin-mediated glycemic regulation, acting in concert with but not solely dependent on TRPV1 signaling. Gut microbiota altered by capsaicin promote the production of 5-aminolevulinic acid (5-ALA), which contributes to heme synthesis and enhances glycemic control. Supplementation with Akkermansia muciniphila, Ligilactobacillus murinus, or 5-ALA in GF mice recapitulates the glycemic benefits of capsaicin. Furthermore, capsaicin enriches Akkermansia muciniphila, which in turn supports the growth of Ligilactobacillus murinus.<br><br>CONCLUSION: Capsaicin-induced changes in the gut microbiota promote 5-ALA synthesis, leading to improved glycemic control. These findings suggest that dietary or probiotic interventions targeting gut microbiota, particularly Akkermansia muciniphila and 5-ALA, may offer promising strategies for managing glycemic disorders, including type 2 diabetes (T2D). Video Abstract.}, }
@article {pmid42068031, year = {2026}, author = {Chen, S and Feng, H and Wang, Y and Huang, J and Xu, S and Gong, Y and Liu, X and Ouyang, Y and Ye, Q and Zheng, D and Sun, K and Wang, A and Chen, Y}, title = {Intestinal epithelial Syndecan-1 maintains mucosal homeostasis in inflammatory bowel disease by enhancing Faecalibacterium prausnitzii biofilm formation.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2665870}, doi = {10.1080/19490976.2026.2665870}, pmid = {42068031}, issn = {1949-0984}, mesh = {Animals ; *Syndecan-1/genetics/metabolism ; *Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Mice ; *Intestinal Mucosa/microbiology/metabolism ; Gastrointestinal Microbiome ; *Biofilms/growth &amp; development ; Mice, Knockout ; Humans ; *Faecalibacterium prausnitzii/physiology/genetics/growth &amp; development ; Mice, Inbred C57BL ; Homeostasis ; Disease Models, Animal ; Dextran Sulfate ; Colitis/microbiology/chemically induced ; Male ; Fecal Microbiota Transplantation ; }, abstract = {Despite the rising global incidence of inflammatory bowel disease (IBD), curative therapies remain unavailable. While our previous work implicated the intestinal proteoglycan Syndecan-1 (SDC1) in IBD-associated barrier dysfunction and inflammation, the underlying mechanism was unclear. This study aimed to elucidate how SDC1 maintains intestinal barrier integrity through interactions with the gut microbiome. In DSS-induced colitis, global knockout of Sdc1 (Sdc1[-/-]) exhibited exacerbated inflammatory infiltration and greater impairment of barrier structure and function than wild-type (WT). Formation of intestinal organoids was independent of genotype, indicating that Sdc1[-/-] does not impair barrier function via disrupting epithelial development. The heightened colitis susceptibility in Sdc1[-/-] mice was abolished in the antibiotic-treated pseudo-germ-free models, and transmissible to WT mice via fecal microbiota transplantation. Similar results were reproduced in a germ-free mouse model. Metagenomic sequencing identified Faecalibacterium prausnitzii as the most significantly depleted species upon Sdc1 knockout. In vitro, SDC1-attached glycosaminoglycans (heparan sulfate (HS) and chondroitin sulfate (CS)) but not the SDC1 core protein promoted F. prausnitzii growth. Prokaryotic transcriptome profiling indicated that HS/CS induces cobalamin biosynthesis in F. prausnitzii. The critical role of cobalamin as a mediator was confirmed, as its synthetic inhibition significantly diminished the growth-promoting effect of HS/CS. Mechanism studies showed that HS/CS enhanced biofilm formation in F. prausnitzii, thereby facilitating cobalamin biosynthesis. Oral administration of HS ameliorated DSS-induced colitis and promoted mucosal colonization of F. prausnitzii, independent of the host genotype. Finally, human IBD biopsies revealed a positive correlation between epithelial SDC1 and mucosal F. prausnitzii, as well as an inverse correlation with bacterial translocation and the number of LPS‑positive cells. Our study elucidates a novel mechanism in which the glycosaminoglycan chains of SDC1 promote F. prausnitzii colonization and growth through enhanced biofilm formation and cobalamin synthesis, thereby highlighting the therapeutic potential of HS for IBD and offering a new basis for host-directed microbiota regulation.}, }
@article {pmid42068598, year = {2026}, author = {Xu, M and Cheng, K and Cai, Z and Chen, G and Zhou, J}, title = {Metagenomic and metatranscriptomic insights into Ruegeria profundi-driven protective responses in coral holobionts against Vibrio coralliilyticus infection.}, journal = {Microbiological research}, volume = {309}, number = {}, pages = {128530}, doi = {10.1016/j.micres.2026.128530}, pmid = {42068598}, issn = {1618-0623}, abstract = {In the context of climate-driven coral reef degradation, opportunistic pathogens such as Vibrio coralliilyticus are emerging as significant secondary threats, acting in synergy with thermal stress to accelerate coral bleaching and mortality. In this study, we investigated the role of Ruegeria profundi in mitigating V. coralliilyticus-induced bleaching. Specifically, the responses of coral holobiont members to pathogenic and probiotic influences were evaluated using metagenomics and metatranscriptomics. We found that the presence of V. coralliilyticus enhanced the metabolic potential of the coral-associated bacterial community, particularly regarding carbohydrate utilization and virulence. Conversely, R. profundi reduced the relative abundance of pathogenic Vibrio species by over 50% and broadly suppressed the expression of virulence genes within the coral-associated bacterial community, including a > 2-fold downregulation of genes involved in quorum sensing and flagellar assembly. Transcriptomic data indicated that immune-related genes in the host were upregulated, whereas photosynthesis-related genes in photosymbiotic microalgae were downregulated in response to V. coralliilyticus infection. R. profundi significantly promoted apoptosis resistance and antimicrobial peptide activity in the host and enhanced photosynthesis in photosymbiotic microalgae (p < 0.05). Furthermore, R. profundi significantly suppressed virulence gene expression in the coral-associated bacterial community (p < 0.05). Collectively, our results indicated that R. profundi orchestrates a tripartite defense mechanism involving the coral host, its associated bacterial community, and symbiotic microalgae, effectively mitigating pathogen-induced dysbiosis and bleaching. These findings have promising implications for microbiome-based strategies in coral reef restoration.}, }
@article {pmid42068877, year = {2026}, author = {Liao, W and Gao, J and Zhang, J and Wu, Y and Jiang, Y and Liu, H and Chen, S and Xiu, L and Zhong, G}, title = {Haizao Yuhu Decoction alleviates goiter via the gut-thyroid axis: Microbiota-derived SCFAs promote hormone synthesis and restore apoptosis.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {156}, number = {}, pages = {158256}, doi = {10.1016/j.phymed.2026.158256}, pmid = {42068877}, issn = {1618-095X}, abstract = {BACKGROUND AND PURPOSE: Haizao Yuhu Decoction (HYD) is a classic Traditional Chinese Medicine for goiter, but its mechanism related to the "gut-thyroid axis" remains unknown. This study investigates whether HYD treats goiter via this axis and elucidates the underlying mechanisms.<br><br>METHODS: A rat goiter model was induced with propylthiouracil (PTU), followed by two weeks of HYD treatment. Gut microbiota was analyzed by metagenomic sequencing; fecal and serum short-chain fatty acids (SCFAs) were quantified by targeted LC-MS/MS analysis. Thyroid function was assessed via iodine content and hormone levels. Key proteins in hormone synthesis and apoptosis were evaluated by Western blot and immunohistochemistry. Fecal microbiota transplantation (FMT) supported microbiota causality.<br><br>RESULTS: HYD alleviated goiter and hypothyroidism. It restored gut microbiota diversity and enriched SCFA-producing bacteria (e.g., Bifidobacterium pseudolongum), coincident with increased SCFAs including butyrate. These SCFA changes correlated with reduced HDAC1/2/3/8 in thyroid tissue, consistent with enhanced histone acetylation, and were accompanied by upregulation of NIS, TG, TPO, and DUOX2. Concurrently, elevated SCFAs were associated with AKT/Mdm2 pathway inhibition, p53 stabilization, downstream activation of P21 and Caspase-3, and suppression of Bcl-2, supporting a model of promoted thyroid cell apoptosis. FMT supported that HYD-modulated microbiota alone reproduced these effects.<br><br>CONCLUSION: HYD alleviates PTU-induced goiter in rats in a manner associated with gut microbiota remodeling and increased SCFA production, which correlate with enhanced thyroid hormone synthesis and restored apoptosis-a relationship supported by FMT experiments. However, direct interactions between HYD and PTU cannot be fully excluded. These findings are consistent with a model in which HYD acts through the gut-thyroid axis, providing mechanistic insights into its therapeutic effects.}, }
@article {pmid42069091, year = {2026}, author = {Jin, H and Meng, L and Yulug, B and Altay, O and Li, X and Cankaya, S and Hanoglu, L and Ji, B and Coskun, E and Idil, E and Nogaylar, R and Oktem, EO and Sayman, D and Karaca, R and Ozsimsek, A and Shoaie, S and Turkez, H and Nielsen, J and Borén, J and Zhang, C and Uhlén, M and Mardinoglu, A}, title = {Machine learning based multi-omics analysis reveals key molecular determinants of Parkinson's disease severity.}, journal = {Neurobiology of disease}, volume = {}, number = {}, pages = {107424}, doi = {10.1016/j.nbd.2026.107424}, pmid = {42069091}, issn = {1095-953X}, abstract = {While single-omics analyses of Parkinson's Disease (PD) have demonstrated their ability in revealing the underlying molecular mechanisms, they often fail to provide a comprehensive view of the complete disease mechanisms. In this study, we leveraged multi-omics data from 64 heterogeneous, well-phenotyped PD patients, generated plasma metabolomics data and Olink proteomics data together with the gut and saliva metagenomics data, and investigated the altered molecular mechanisms and their interactions in association with the severity of motor function disorders in PD patients. Based on our multi-omics approach, we identified a panel of 58 biomarkers comprising one clinical variable, 10 proteins, and 17 metabolites from plasma, 26 gut species, and 4 saliva species for PD severity. These biomarkers exhibited superior predictive performance for assessing PD severity compared to those derived from single-omics datasets. The predictive power of our machine learning models based on these biomarkers was validated using additional multi-omics data from the same group of PD patients after a 3-month follow-up. The contribution of each omics dataset was evaluated by both supervised and unsupervised machine learning approaches, highlighting the importance of plasma metabolomics in disease stratification. Our study unveiled disease-related molecular alterations across multiple omics datasets, offering potential diagnostic and therapeutic insights for PD. Moreover, it underpinned the significance of employing multi-omics analyses when studying complex diseases like PD.}, }
@article {pmid42069117, year = {2026}, author = {Makowska-Zawierucha, N and Trzebny, A and Mokracka, J and Bradley, JA}, title = {The high Arctic resistome: stress-response genes, virulence determinants, and microbial populations in human-impacted environments of Spitsbergen.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128242}, doi = {10.1016/j.envpol.2026.128242}, pmid = {42069117}, issn = {1873-6424}, abstract = {The high Arctic, particularly Spitsbergen, faces the combined challenges of climate change and other anthropogenic pressures - including waste and contaminant release from human activity - that influence microbial populations and the spread of antimicrobial resistance (AMR). This study presents a snapshot analysis of metagenomes from various environments across Spitsbergen, including untreated and treated wastewater outflows, fjords, and glacial ice cores, to explore the abundance of stress-response genes, including antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs), and virulence genes (VGs), alongside the compositions of the associated bacterial populations. We reveal varying levels of stress-response genes and VGs in environments exposed to differing levels of human influence. ARGs and MRGs dominate in raw sewage, while VGs are more prevalent in fjord waters receiving both raw sewage and effluent, indicating that specific environmental conditions favor different resistance and virulence traits. We detect high abundance of ARGs and VGs downstream of both untreated and treated wastewater. Our analyses indicate the presence of bacterial populations with resistance and virulence traits - including Enterobacteriaceae, Enterococcaceae, Bacillaceae, and Staphylococcaceae - in downstream ecosystems. While we do not directly assess effects on human health or ecosystem function, these observations point to potential ecological impacts in Arctic environments and highlight the importance of continued monitoring to understand and manage the possible effects of human activities and climate change.}, }
@article {pmid42069315, year = {2026}, author = {Wu, G and Du, J and Li, H and Dong, Y and Wang, Q and Hu, F and Ji, J}, title = {Synergistic integration of sustainable wastewater treatment and agricultural waste valorization: Rapid in-situ enrichment of anammox bacteria via corncob biocarriers.}, journal = {Bioresource technology}, volume = {454}, number = {}, pages = {134769}, doi = {10.1016/j.biortech.2026.134769}, pmid = {42069315}, issn = {1873-2976}, abstract = {The slow proliferation of anammox bacteria (AnAOB) limits the large-scale application of anammox technology in mainstream wastewater treatment. Here, an innovative strategy was proposed in which agricultural waste corncob was utilized as biocarriers for the rapid enrichment of AnAOB. This study systematically validated the feasibility of using corncob as biocarriers to enhance the self-enrichment of AnAOB. Results showed that corncob addition shortened the anammox startup time by approximately 64.0% and increased total inorganic nitrogen (TIN) removal efficiency by 28.4%. The anammox activity of the corncob biofilm and flocs was 3.2- and 1.1-fold higher, respectively, than that of the control. The microbial community analysis indicated that corncob biofilm harbored the highest relative abundance of AnAOB (23.9%). Within the corncob biofilm, lignocellulolytic microbes degraded macromolecular organics to provide electron donors for denitrifiers, which facilitated nitrogen metabolic couplingbetween denitrifiers and AnAOB, therebyestablishing favorable microenvironment for the enrichment of AnAOB. Furthermore, metagenomic revealed NO cross-feeding between AnAOB and their symbionts further offered an ideal niche for AnAOB. Concurrently, the upregulation of key carbon metabolism genes indicated heightened microbial activity within the biofilm, while quorum sensing (QS) mechanisms also played a significant role in maintaining the dynamic stability of microbial community. This work established a natural and highly efficient pathway for the self-enrichment of AnAOB, simultaneously providing a synergistic solution for agricultural wastes (AWs) valorization, advanced wastewater nitrogen removal, and carbon neutrality, demonstrating broad application prospects and significant ecological value.}, }
@article {pmid42069316, year = {2026}, author = {Zhao, X and Tian, X and Zhang, H and Dang, Y and Ma, J}, title = {Metagenomic understanding of the performance enhancement in anaerobic digestion by granular activated carbon coupled with riboflavin under high organic loading.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134752}, doi = {10.1016/j.biortech.2026.134752}, pmid = {42069316}, issn = {1873-2976}, abstract = {Anaerobic digestion (AD) often suffers operation failure from ammonia inhibition and volatile fatty acids (VFAs) accumulation under high organic loading rates (OLRs). To overcome these limitations, this study employed granular activated carbon coupled with riboflavin (RFGAC) by stimulating direct interspecies electron transfer (DIET). A semi-continuous AD experiment was conducted for 145 days with OLRs ranging from 2.25 to 11.25 kg COD/(m[3]·d). The results showed that the RFGAC group achieved the highest methane content of 78%, and maintained a COD removal rate above 95%, outperforming the GAC group and the control. At an OLR of 6.75 kg COD/(m[3]·d), the control collapsed due to severe acidification when the pH dropped lower than 6.5, while the RFGAC group stably operated with effluent COD of 2200-5300 mg/L and seldom VFAs accumulation. Microbial community analysis revealed that RFGAC selectively shifted microbial community composition especially at high OLR, promoting Methanosarcina to form a synergistic consortium. The Pearson correlation analysis of digestion performance and metagenome revealed that Methanosarcina had a stronger correlation with methanogenesis than Methanothrix, which was enriched in the presence of GAC alone. Metabolic pathway analysis confirmed key DIET-related functional genes, hdrA2 and methyl transfer-associated mtrH, were respectively upregulated by 7-fold and 5-fold. This study offers a viable strategy to improve chicken manure AD, and provides deep mechanistic insights on RFGAC modulation of microbial community succession and functional gene expression.}, }
@article {pmid42069539, year = {2026}, author = {Hagenbeek, A and Masukagami, Y and Palanichamy, P and Husnik, F}, title = {Genome-resolved metagenomics reveals unexpected diversity and host range of Candidatus Lariskella (Rickettsiales: Midichloriaceae).}, journal = {BMC genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12864-026-12881-x}, pmid = {42069539}, issn = {1471-2164}, support = {RGEC29/2024;DOI:https://doi.org/10.52044/HFSP.RGEC292024.pc.gr.194160//Human Frontier Science Program/ ; }, abstract = {The intracellular endosymbiont Candidatus Lariskella (Alphaproteobacteria, Candidatus Midichloriaceae) has been found across a wide diversity of terrestrial arthropods, including ticks, true bugs, beetles, fleas, wasps and moths. Despite its prevalence, little is known about the biology of Ca. Lariskella, nor do we grasp the full extent of its host range. Here, we report the first known occurrence of Ca. Lariskella infecting a population of free-living marine nematodes (Enoplida, Thoracostomopsideae). This novel nematode-infecting Ca. Lariskella was found to be closely related to insect-infecting strains, despite the drastic shift in both host taxonomy and habitat. TEM and FISH microscopy showed Ca. Lariskella is localized within both the nematode somatic cells and developing oocytes, confirming its status as a nematode endosymbiont and strongly suggesting maternal transmission. This finding led us to reassess the host range of Ca. Lariskella. We screened the SRA database for Ca. Lariskella sequences and performed genome-resolved metagenomics on SRA entries positive for Ca. Lariskella. We recovered 16 novel Ca. Lariskella metagenome-assembled genomes from SRA entries, including from novel hosts such as ants and treehoppers. However, we did not encounter further instances of Ca. Lariskella within nematodes or marine invertebrates, which we attribute to the relatively poor sampling of these groups. Overall, our findings illustrate the ability of Ca. Lariskella to infect both arthropods and nematodes as well as hosts from both terrestrial and marine environments.}, }
@article {pmid42069617, year = {2026}, author = {Yuan, H and Song, Y and Nie, L and Yang, Z and Yang, L and Yang, K and Yang, Y and Li, W and Wang, X and Zhang, XX and Hua, Y and Yuan, ZG}, title = {The gut metabolite arachidonic acid alleviates intestinal injury induced by a Toxoplasma gondii strain isolated from a wild rodent.}, journal = {Parasites &amp; vectors}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13071-026-07389-y}, pmid = {42069617}, issn = {1756-3305}, support = {2025A1515012622//Natural Science Foundation of Guangdong Province/ ; }, abstract = {BACKGROUND: Wild isolates of Toxoplasma gondii may exhibit different virulence characteristics and host adaptability compared with those of laboratory strains. In this study, we isolated a novel rodent-derived T. gondii strain, denoted TgRodGz1, and evaluated its pathogenic features.<br><br>METHODS: TgRodGz1 was isolated from T. gondii-positive wild rodents in Guangdong Province and compared with the RH and Me49 strains in C57BL/6 mice. Virulence and intestinal injury were evaluated by survival analysis, brain cyst quantification, histopathology, tight junction assessment and qPCR. Gut microbiota and metabolic alterations were analyzed by metagenomic sequencing and LC-MS/MS-based metabolomics.<br><br>RESULTS: Compared with theT. gondii laboratory strains RH and Me49, TgRodGz1 was associated with more pronounced intestinal injury, including villus atrophy, barrier disruption and downregulation of tight junction proteins and increased gut permeability and inflammation. Metagenomic analysis revealed significant intestinal flora dysbiosis, with a marked reduction in beneficial bacteria and expansion of pathogenic bacteria. Metabolomic analysis revealed suppression of arachidonic acid (ARA) metabolism during TgRodGz1 infection. Supplementation with ARA did not directly inhibit parasite growth but significantly alleviated intestinal lesions, reduced brain cyst burden and attenuated inflammatory responses, including microglial activation.<br><br>CONCLUSIONS: These findings suggest that TgRodGz1 represents a distinct T. gondii genotype associated with pronounced intestinal pathology and suggest that ARA supplementation may alleviate intestinal and neuroinflammatory changes associated with T. gondii infection.}, }
@article {pmid42069941, year = {2026}, author = {Singh, A and Bhattacharjee, S and Singh, Y and Kostova, I}, title = {Parabiotics as Next-Generation Microbiome Therapeutics: Insights into Mechanisms, Evidence, and Therapeutic Potential.}, journal = {Current microbiology}, volume = {83}, number = {6}, pages = {}, pmid = {42069941}, issn = {1432-0991}, mesh = {Humans ; *Prebiotics/administration &amp; dosage ; Animals ; *Gastrointestinal Microbiome/drug effects ; Probiotics ; *Microbiota ; }, abstract = {Parabiotics (also termed paraprobiotics) are defined as non-viable microbial cells or their components, including peptidoglycans, teichoic acids, surface proteins, that confer health benefits without requiring viability which distinguishes them from traditional probiotics. Their non-viable nature eliminates risks such as microbial translocation, bacteremia, and sepsis, making them suitable for vulnerable populations including immunocompromised, critically ill, paediatric and elderly individuals. In addition, parabiotic exhibit improved thermal stability, extended shelf life, and easier incorporation into functional foods, nutraceuticals, and pharmaceutical formulations without cold-chain requirements. Mechanistically, parabiotics retain immunomodulatory, anti-inflammatory and have barrier-enhancing activities through interactions with host pattern recognition receptors, including Toll-like receptors, modulation of cytokine responses, and reinforcement of gut epithelial integrity. Preclinical and clinical studies support their therapeutic potential such as in case of heat-killed Lactobacillus acidophilus LB (L. acidophilus) has shown efficiency in managing acute paediatric diarrhoea, while heat-inactivated Lacticaseibacillus paracasei PS23 (Lcb. paracasei) has demonstrated improvements in muscle strength and inflammatory markers, including reduced C-reactive protein and interleukin-6 and increased interlukin-10 in elderly individuals. Similarly, inactivated Lactiplantibacillus plantarum (Lpb. plantarum) and Bifidobacterium strains have been associated with benefits in irritable bowel syndrome, atopic dermatitis, respiratory infections, visceral fat reduction, and antibiotic-associated dysbiosis. Synergistic combinations with prebiotics, postbiotics and related bioactives further enhance therapeutic outcomes in inflammatory, metabolic and infectious conditions. Advances in metagenomics, next-generation sequencing, proteomics, metabolomics, CRISPR-Cas systems, and synthetic biology are accelerating strain characterization, functional evaluation, and scalable production. Despite ongoing challenges in standardization and regulated harmonization, parabiotics represent a safe and effective approach for microbiome-targeted interventions. This review synthesizes current evidence on their therapeutic applications, technological advancements, and translational potential, highlighting their role in precision health and next-generation functional nutrition.}, }
@article {pmid42070641, year = {2026}, author = {Wu, M and Liao, H and Luo, Y and Yao, Y and Yang, D and Hu, Z and Gao, L and Xia, X}, title = {Moisture transfer-driven quality enhancement in solid-state fermented Daqu: Synergistic effects of microbial community adaptation and functional enzyme metabolism.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134771}, doi = {10.1016/j.biortech.2026.134771}, pmid = {42070641}, issn = {1873-2976}, abstract = {Solid-state fermented Daqu exhibits a typical heterogeneous structure, where moisture regulates the microbial activity by driving gas diffusion in the pores and nutrient enrichment, playing a crucial role in the quality of the final product. However, there is a lack of clarity regarding how moisture transfer affects Daqu microbial assembly and metabolic flux. This study pioneered a real-time controllable fermentation platform, employing stoichiometry, nuclear magnetic resonance, and metagenomics to investigate microbial saccharifying metabolic functions under moisture transfer regulation. Comparing representative low (LM: 34%, 36%) and high (HM: 38%, 40%) moisture groups, we found that porosity exhibited a strong positive correlation with water activity (coefficient > 0.9, p < 0.01), serving as the primary physicochemical contributor governing moisture transfer priority. Furthermore, steady-state mass transfer in the HM group (≥ 38%) enhanced the transfer rate from free water (T23) to capillary water (T22: 10-100 ms), shaping a saccharifying functional microbial community dominated by Rhizopus and Bacillus. Weighted network and functional gene predictions indicated that this process strengthened the substrate preference of core microorganisms toward starch, significantly reinforcing the metabolic synergy between glucoamylase and α-amylase. Conversely, transient mass transfer in the LM group (< 38%) triggered microbial functional differentiation, promoting the redistribution of non-starch polysaccharide hydrolases. Our research revealed the effects of moisture transfer on nutrient availability, microbial adaptation, and metabolic functions in stack-fermented Daqu. This work ensures Daqu stability and presents novel strategies to optimize solid-state fermentation efficiency through moisture-driven microbial metabolic trade-offs.}, }
@article {pmid42070688, year = {2026}, author = {Shurigin, V and Lu, X and Khan, AR and Muhammad, M and Ullah, I and Egamberdieva, D and Yu, Y and Li, L}, title = {Unveiling the Plant Growth-Promoting and Antifungal Potential of Melissa officinalis Endophytes: the Integrative Culture-Dependent and Metagenomic Approaches.}, journal = {Plant science : an international journal of experimental plant biology}, volume = {}, number = {}, pages = {113182}, doi = {10.1016/j.plantsci.2026.113182}, pmid = {42070688}, issn = {1873-2259}, abstract = {Endophytic bacteria play a central role in plant health, yet their diversity and functions in medicinal plants remain poorly characterized. In this study, we integrated high-throughput sequencing, culture-based isolation, functional assays, and greenhouse validation to characterize the endophytic microbiome of Melissa officinalis L. High-throughput sequencing revealed 347 species with strong tissue-specific structuring. Paucibacter and Pseudomonas genera related to phylum Pseudomonadota dominated in all plant tissues. Nineteen culture-dependent strains representing Pseudomonas, Microbacterium, Plantibacter, Agreia, and Kocuria demonstrated various plant growth-promoting traits, including phosphate solubilization, nitrogen fixation, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, indole-related compounds (IRC) production, siderophore secretion, and hydrolytic enzyme activities (chitinase, protease, and lipase). Pseudomonas fluorescens XIEG-4RS14 showed antifungal activity against Fusarium graminearum (50%) and F. moniliforme (37%), P. marginalis XIEG-4RS15 showed 100 and 62%, P. baetica XIEG-4RS18 showed 28 and 42%, P. fluorescens XIEG-4RS32 showed 45 and 39%, and P. rhodesiae XIEG-4RS37 showed 58 and 27% respectively. Greenhouse assays demonstrated that strains Pseudomonas fluorescens XIEG-4RS14, P. fluorescens XIEG-4RS32, P. taetrolens XIEG-4RS19, and P. poae XIEG-4RS27 increased wheat root and shoot dry weight by up to 113% to 60% respectively. These findings revealed that M. officinalis harbors highly cooperative and functionally effective endophytes with strong potential as next-generation bioinoculants for sustainable crop production.}, }
@article {pmid41877145, year = {2026}, author = {Zhang, QN and Zhang, XH and Shi, SS}, title = {Tacrolimus-induced interstitial lung injury in a pediatric cardiac transplant recipient: a case report and literature review.}, journal = {BMC pediatrics}, volume = {26}, number = {1}, pages = {}, pmid = {41877145}, issn = {1471-2431}, abstract = {BACKGROUND: Tacrolimus-induced interstitial lung injury (TI-ILI) is a rare but potentially fatal adverse effect of calcineurin-inhibitor therapy. To our knowledge, TI-ILI has not previously been reported in a paediatric heart-transplant recipient.<br><br>CASE PRESENTATION: A 6-year-old boy with PLN-related dilated cardiomyopathy underwent orthotopic heart transplantation. Maintenance immunosuppression comprised tacrolimus, mycophenolate mofetil and prednisone. On post-operative day 13 he developed bilateral ground-glass opacities with interlobular septal thickening on chest CT. Broncho-alveolar lavage metagenomics showed only low-abundance Pseudomonas aeruginosa and Acinetobacter baumannii; extensive microbiological, cardiac work-up was negative. Infiltrates progressed despite targeted antibiotics, but resolved within 4 weeks after tacrolimus was replaced by cyclosporine and corticosteroids were doubled. No relapse occurred during 6 months of follow-up.<br><br>CONCLUSIONS: TI-ILI should be considered in any heart transplant recipient with unexplained progressive bilateral pulmonary infiltrates. Early tacrolimus withdrawal and prompt corticosteroid therapy are associated with complete recovery; re-exposure to tacrolimus is contraindicated.}, }
@article {pmid42066584, year = {2026}, author = {Xu, Q and Wang, Q and Hou, D and Zhang, F and Zhang, C and Qi, B and Wei, M and Chen, J and Zha, Q and Qin, H and Song, Y and Wu, X}, title = {Cryptococcal pneumonia susceptibility in immunocompetent patients: Role of pseudomonas aeruginosa via IL-2/IL-12/IL-17 pathways.}, journal = {Journal of infection and public health}, volume = {19}, number = {6}, pages = {103230}, doi = {10.1016/j.jiph.2026.103230}, pmid = {42066584}, issn = {1876-035X}, abstract = {BACKGROUND: While pulmonary cryptococcosis affects immunocompromised patients, it also occurs in immunocompetent individuals. However, underlying mechanisms contributing to susceptibility in immunocompetent patients remain poorly understood.<br><br>METHODS: We enrolled 43 patients with pulmonary cryptococcosis, including 19 apparently immunocompetent patients (ICPC) and 24 immunocompromised patients (IMCPC), compared with community-acquired pneumonia (CAP) controls. Bronchoalveolar lavage fluid (BLAF) microbiota composition was analyzed using metagenomic next-generation sequencing. Peripheral blood immune parameters were measured, and correlation analyses were performed to identify potential associations. Publicly available single-cell transcriptomic datasets were analyzed to explore immune pathway alterations associated with chronic Pseudomonas infection.<br><br>RESULTS: ICPC patients were predominantly male, less likely to present with fever, and showed normal inflammatory markers compared to CAP controls. Despite normal reference ranges, ICPC patients demonstrated significantly reduced CD4&#x207a; T lymphocyte percentages&#xff0c;accompanied by elevated IL-2 and reduced IL-12p70 and IL-17A levels. BALF analysis revealed a significant enrichment of nonfermenting gram-negative bacteria: Ralstonia, Sphingomonas, Acinetobacter, Stenotrophomonas, Burkholderi and Pseudomonas, in ICPC patients&#xff0c;whereas no such alterations were observed in the IMCPC group. Correlation analyses demonstrated inverse relationships between the relative abundances of Stenotrophomonas and Pseudomonas abundance and CD4&#x202f;+&#x202f;T lymphocyte percentages and CD4&#x202f;+&#x202f;/CD8&#x202f;+&#x202f;ratios. Furthermore, single-cell transcriptomic analysis of chronic Pseudomonas infection showed enrichment of IL-2 signaling genes and suppression of IL-12 and IL-17A signaling pathways.<br><br>CONCLUSIONS: ICPC patients exhibit decreased peripheral CD4&#x202f;+&#x202f;T lymphocyte percentage with elevated IL-2 and reduced IL-12p70/IL-17A levels. The observed enrichment of specific bacterial taxa, particularly Pseudomonas species, and its inverse correlation with immune parameters suggest potential microbiome-immune interactions that may contribute to cryptococcal susceptibility.}, }
@article {pmid41872905, year = {2026}, author = {Zhao, H and Hua, J and Lu, W and Lv, X and Chen, C and Liang, Y}, title = {Rubber seed cake supplementation alters meat quality, intestinal health, and gut microbiota in Hu sheep.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41872905}, issn = {2524-4671}, support = {880698//Key Technology Integration and Application of Standardized Rearing Management for Meat Sheep in Agricultural Areas/ ; }, abstract = {UNLABELLED: This study aimed to investigate the effects of rubber seed cake (RSC) supplementation on slaughter performance, intestinal health, and gut microbiota in Hu sheep. Forty-eight Hu sheep (17.01 ± 0.57 kg; 3 months old) were randomly allocated to four dietary treatments: 0% (CON), 6% (R6), 12% (R12), and 18% (R18) RSC. Following an 80-day feeding trial, six sheep per group were randomly selected for slaughter. Samples of the longissimus dorsi, small intestine, and intestinal mucosa were collected for meat quality, morphological, and intestinal health analyses. Additionally, ileal contents were harvested and frozen for metagenomic sequencing. Dietary supplementation with RSC reduced the shear force of the longissimus dorsi muscle (P = 0.043) and lowered meat color L* (P = 0.044) and b* (P = 0.035) values in the R6 group compared to the CON group. Quadratic effects were observed for the villus height to crypt depth (VH/CD) ratio in the duodenum (P = 0.006), jejunum (P = 0.006), and ileum (P = 0.001) with increasing RSC supplementation, and the VH/CD ratio was significantly increased in the R6 and R12 groups (P < 0.05). Ileal pro-inflammatory cytokine concentrations, including tumor necrosis factor-alpha (TNF-α), interleukin-1 beta (IL-1β), and interleukin-6 (IL-6), decreased both linearly and quadratically with increasing RSC supplementation (P < 0.05). Quadratic effects (P < 0.05) were observed for the concentrations of mucin 2 (MUC2) and tight junction proteins such as zonula occludens-1 (ZO-1), occludin, and claudin in the jejunal and ileal mucosa with increasing RSC supplementation. Specifically, the concentrations of MUC2 and tight junction proteins in the jejunum, as well as MUC2 and ZO-1 in the ileum, were significantly higher in the R6 group (P < 0.05). RSC supplementation significantly altered the relative abundance of specific taxa, including Stenotrophomonas, Piromyces, Lichinomycetes, and Syntrophobacteria, as well as CAZyme gene sequences such as GH119, GT39, and GH13-8 (P < 0.05). In conclusion, these findings indicate that a 6% dietary supplementation of RSC is optimal in Hu sheep, as it improves meat quality and intestinal health by modulating the ileal microbiota composition and CAZyme abundance, thereby strengthening mucosal barrier function and alleviating inflammation.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00556-7.}, }
@article {pmid42061404, year = {2026}, author = {Su, Q and Chen, S and Lau, LH and Lui, RN and Wang, Y and Xu, Z and Cheung, CP and Ching, JYL and Shen, X and Peng, Y and Tun, HM and Ianiro, G and Rubin, D and Chang, EB and Chan, FKL and Ng, SC}, title = {Artificial intelligence-driven donor-recipient gut microbiome matching for optimized fecal microbiota transplantation.}, journal = {Cell reports}, volume = {}, number = {}, pages = {117301}, doi = {10.1016/j.celrep.2026.117301}, pmid = {42061404}, issn = {2211-1247}, abstract = {Fecal microbiota transplantation (FMT) has emerged as a promising therapy for gastrointestinal diseases, yet its clinical efficacy remains individually variable. Here, we analyze multi-kingdom and functional profiles in pre- and post-FMT metagenomes from 515 FMTs across 30 cohorts and 12 diseases, in which 94 metagenomes from 44 FMTs are newly collected. We reveal a robust association between clinical efficacy and post-FMT microbiome convergence of recipients toward donors, across diseases. To predict post-FMT microbial convergence, we develop MOZAIC (Microbiome Matching Optimization via Artificial Intelligence), a framework that integrates multi-dimensional donor-recipient microbiota features. MOZAIC achieves an average area under the curve (AUC) of 0.88 and accuracy/recall >0.80 in forecasting microbiome convergence, with 78.7% accuracy in predicting clinical outcomes, and retrospectively simulates a 1.44-fold improvement (from 49.4% to 71.0%) in clinical response rates over baseline. This study establishes microbiome convergence as a key mediator of FMT and provides a scalable tool for precision matching in microbiota-based therapies.}, }
@article {pmid42061651, year = {2026}, author = {Neuhaus, S and Tausch, SH and Gulich, K and Körber, N and Grützke, J and Hensel, A and Dahouk, SA and Dieckmann, R}, title = {Kitchen sponges as reservoirs of foodborne pathogens: Microbial growth dynamics, surface cross-contamination, and hygiene implications.}, journal = {Journal of food protection}, volume = {}, number = {}, pages = {100794}, doi = {10.1016/j.jfp.2026.100794}, pmid = {42061651}, issn = {1944-9097}, abstract = {Foodborne pathogens pose a persistent risk to public health, with domestic environments representing a major but often underestimated source of contamination. In this study, we investigated the survival, proliferation, and transfer potential of Salmonella Enteritidis, Escherichia coli, and Staphylococcus aureus in kitchen sponges harboring an established core microbiota. Using culture-based, metagenomic, and fluorescence in situ hybridization approaches in combination with confocal laser scanning microscopy, we examined pathogen persistence, desiccation tolerance, cross-contamination potential, and spatial microbial organization over 14 days. All three pathogens persisted within the sponge matrix for at least 2 weeks, even at very low initial populations (approximately 2,5log10 colony-forming units (CFU) per sponge section). Escherichia coli and Salmonella Enteritidis rapidly established stable populations reaching approximately 9 log CFU per sponge section, whereas Staphylococcus aureus showed limited growth of approximately 4 log CFU per sponge section, indicating species-specific interactions with the resident microbiota. Notably, pathogen populations remained stable after 3 days of desiccation, confirming the role of sponges as long-term microbial reservoirs. Contact between colonized sponges and surfaces under mild pressure resulted in transfer of up to 5 log CFU to contacted surfaces, highlighting realistic domestic transmission pathways. Sensory changes such as odor or discoloration were not correlated with microbial load, indicating that visual assessment is unreliable for sponge replacement decisions. These results underscore the role of kitchen sponges as critical microbial reservoirs in households and emphasize the need for regular sponge replacement or the use of alternative cleaning utensils. The standardized sponge model developed in this study provides a valuable platform for evaluating sanitation strategies and for understanding microbial interactions relevant to domestic hygiene and public health.}, }
@article {pmid42061790, year = {2026}, author = {Zhang, Y and Zhang, G and Liang, J and Chang, J and Zhang, P and Fang, W and Wang, Q}, title = {Regulation of greenhouse gas emissions and carbon sequestration in wetland by submerged plant mowing time and potential mechanisms.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124621}, doi = {10.1016/j.envres.2026.124621}, pmid = {42061790}, issn = {1096-0953}, abstract = {Mowing is an important submerged plant growth management measure to maintain the balance of inland wetland ecosystems. However, systematic studies on plant mowing time affecting wetland greenhouse gas (GHG) emissions and carbon sequestration remain scarce. In this research a pilot-scale wetland system was established to investigate the effects of submerged plant Ceratophyllum demersum L. mowing time on GHG emissions and carbon sequestration, and metagenomic techniques were employed to explore the functional microorganisms and genes for carbon and nitrogen cycling in wetland. The results showed that C. demersum L. mowing resulted in CO2 flux reduction of 55.76%-79.34%, CH4 flux reduction of 83.54%-99.48%, and N2O flux reduction of 75.80%-82.88%. The optimal plant mowing time was July, achieving a better trade-off between carbon sequestration and carbon emissions. The C. demersum L. biomass showed obvious temporal dynamics, with the highest biomass for mowing in July, increasing by 12.12% compared with that of control. However, plant mowing slightly reduced the water purification capacity. Microbial analysis revealed that plant mowing downregulated the expression of key functional genes (mcrA, pmoA, norB, nosZ) and decreased the abundance of methanogens and denitrifying bacteria, explaining the reduction in CH4 and N2O fluxes. These findings provide a scientific basis for wetland plant growth management. Future research should explore long-term field validation and effects of environmental variables.}, }
@article {pmid42062403, year = {2026}, author = {Radwan, HM and El Menofy, NG and Tharwat, EK and Mysara, M and Radwan, SMR}, title = {Metagenomic profiling of microbial communities and the resistome within Egyptian hospital wastewater and tap water.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {42062403}, issn = {2045-2322}, mesh = {*Wastewater/microbiology ; Egypt ; *Metagenomics/methods ; Hospitals ; *Drinking Water/microbiology ; Humans ; *Microbiota/genetics ; Water Microbiology ; *Metagenome ; *Bacteria/genetics/classification/drug effects ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Antimicrobial resistance (AMR) is a worldwide health concern that compromises the successful treatment of a growing array of infectious diseases, particularly in low- and middle-income countries. AMR is exaggerated by the spread of antimicrobial resistance genes (ARGs) across humans, animals, and environmental reservoirs like water and soil. Hospital wastewater (HWW) is the main source of antimicrobial resistance in the environment. The current study used high throughput metagenomic nanopore sequencing to investigate the microbial abundance and ARGs associated with both HWW and tap water in five different hospitals in Cairo, Egypt. The bacterial community composition of the HWW microbiome identified 25 taxonomic families. The most abundant genera in HWW were Acinetobacter (6%) and Propioniciclav (5%) out of 101 unique genera while, the most abundant in tap water were Enterococcus (53%), Escherichia (15%), and Francisella (14%) out of 89 unique genera. Alpha diversity analysis revealed significantly greater microbial diversity in the HWW samples than in the tap water samples (P value > 0.05), moreover beta diversity analysis revealed a significant difference in the microbial community composition between the tap water and HWW samples (P value > 0.05) using Chao metric for richness estimation and Shannon metric for richness and evenness estimation. Total ARG analysis revealed absence of ARGs in tap water using the three databases, while comparable levels of ARGs were detected in HWW across the five hospitals. In total, 45, 28, and 28 ARG subtypes were identified in the HWW samples using ResFinder, CARD, and the NCBI AMRFinderPlus databases, respectively. The most abundant AMR mechanisms among the five hospitals were linked to the inhibition of protein synthesis. Using the ResFinder database, streptogramin resistance genes were most prevalent in Hospitals 1 and 5 (15% and 40%, respectively); using CARD, aminoglycoside, lincosamide, and macrolide resistance genes were most predominant (relative abundances 35-60%). Using NCBI AMRFinderPlus, streptomycin, tetracycline, and macrolide resistance genes were most prevalent (relative abundances 30.1-60%). Detection of plasmid replicons in HWW identified 39 different plasmid-associated replication genes via the PlasmidFinder database. The Col440l-1, colRNAI-1 and Col440ll-1 plasmid replicons were the most detected across the five hospitals with relative abundances of 16.6%, 10.9% and 9.6%, respectively. This study revealed different microbial communities among HWW and tap water in addition to the widespread occurrence of ARGs and AMR encoding plasmid replicons in the HWW in the five different hospitals in Cairo, Egypt indicating a significant risk associated with HWW, necessitating the implementation of preventative measures to avert their environmental diffusion. To our knowledge, this is one of the first Egyptian studies to apply Oxford Nanopore long-read metagenomic sequencing for simultaneous profiling of microbial communities and the resistome in HWW and tap water, using three ARG databases across five hospitals in two seasons.}, }
@article {pmid42062603, year = {2026}, author = {Xu, T and Yang, Y and Zhu, R and Lin, W and Li, J and Zheng, Y and Zhang, P and Zhang, G and Zhao, G and Jiao, N}, title = {DeepSeMS: revealing the hidden biosynthetic potential of the global ocean microbiome with a large language model.}, journal = {Nature computational science}, volume = {}, number = {}, pages = {}, pmid = {42062603}, issn = {2662-8457}, support = {32470098//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92251307//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82170542//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92451303//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92251307//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Microbial-derived secondary metabolites (SMs) hold great therapeutic potential but are predominantly discovered from cultured species, representing only a fraction of microbial biodiversity. Advances in metagenomics have unveiled reservoirs of biosynthetic gene clusters (BGCs), but translating genomic sequences into precise chemical structures remains challenging owing to the structural complexity of cryptic BGCs and the context-dependent substrate tolerance and cross-reactivity of modular biosynthetic domains. Here we present DeepSeMS, a transformer-based large language model that accurately predicts secondary metabolite chemical structures from BGC sequences. By encoding biosynthetic genes as functional domains and leveraging a feature-aligned data augmentation, DeepSeMS outperformed existing methods and successfully generated chemically valid predictions for 96.38% of cryptic BGCs. Applying DeepSeMS to a global ocean metagenome, we characterized over 60,000 secondary metabolites, revealing chemical diversity, ecological specificity and considerable biomedical potential, especially as antibiotics. This study underscores the capability of deep learning-driven approaches in revealing hidden biosynthetic potential of Earth's largest, yet largely unexplored, microbial ecosystem.}, }
@article {pmid42062664, year = {2026}, author = {Kieliszek, M}, title = {Selenium: From Redox Signaling to Interactions with the Gut Microbiome.}, journal = {Biological trace element research}, volume = {}, number = {}, pages = {}, pmid = {42062664}, issn = {1559-0720}, abstract = {Selenium is an element that plays a crucial role in the proper functioning of the body. It is a component of selenoproteins, which exhibit strong antioxidant properties. This allows it to neutralize reactive oxygen species and protect cells from oxidative stress. It also plays a crucial role in supporting the proper functioning of the immune system. In this context, particular importance is attributed to its influence on the Th1/Th2 immune response and the activity of T lymphocytes and NK cells. There is a mutual relationship between selenium and the intestinal microbiota. Microorganisms in the gastrointestinal tract participate in the accumulation, transformation, and differentiation of selenium's chemical forms. These processes influence selenium's bioavailability and its activity in the host organism. The development of metagenomic methods has enabled the identification of specific selenium-dependent metabolic pathways within the microbiome. This represents an important research direction in the development of this field of biotechnology. In turn, appropriate selenium levels and selenoprotein activity influence the composition of the intestinal microbiota and the metabolite profile it produces. It is worth emphasizing that in the context of the development of microbiome engineering, there are also emerging concepts of designing probiotics capable of controlled selenium biotransformation. The beneficial properties of selenium for organisms depend on its appropriate chemical form and dose. It is worth noting that selenium deficiency can impair the antioxidant system, leading to a redox imbalance. Such processes can weaken the integrity of the intestinal barrier, leading to the development of various gastrointestinal diseases. Therefore, the interaction with intestinal microflora is such a crucial element of selenium's action. Microorganisms inhabiting the digestive tract participate in the processes of accumulation and transformation of various chemical forms of this element. These biochemical properties of microorganisms are crucial for the bioavailability of selenium in the human body. Therefore, the appropriate form of selenium is crucial for the proper functioning of the intestinal barrier. This article discusses the importance of selenium in redox processes and in the function of the gut microbiota. It highlights the potential role of this element in the prevention and treatment of gastrointestinal diseases. Future research should focus on further understanding these interactions and developing targeted approaches that utilize selenium-dependent pathways to restore intestinal homeostasis.}, }
@article {pmid42062918, year = {2026}, author = {Guo, P and Zhang, S and Huang, Z and Zhu, J and Zhang, W}, title = {Potential drug-drug interactions and 30-day mortality in ICU patients with bloodstream infection: a single-center retrospective study.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13426-z}, pmid = {42062918}, issn = {1471-2334}, abstract = {BACKGROUND: Patients in intensive care units (ICUs) with bloodstream infection (BSI) commonly receive multiple antimicrobials and supportive drugs, which increases the likelihood of potential drug-drug interactions (pDDIs). Evidence focused specifically on ICU patients with BSI remains limited.<br><br>OBJECTIVES: To describe the prevalence and severity of pDDIs in ICU patients with BSI and to examine whether pDDI exposure was associated with 30-day mortality.<br><br>METHODS: We performed a single-center retrospective cohort study of 90 adult ICU patients with an index episode of BSI between January 2019 and December 2024. Time zero was defined as the sampling time of the first qualifying positive blood culture or a clinically accepted positive blood metagenomic next-generation sequencing result for the index episode. Medication administration records, rather than prescription orders alone, were used for pDDI ascertainment. pDDIs were screened with the Micromedex Drug Interactions database (Merative, web-based version updated daily; accessed January 15, 2025). Exposure was defined within a fixed 48-hour window after time zero; a pDDI required actual administration of both interacting agents within the same 24-hour period during this window. Severity was standardized as mild, moderate, or severe. The primary outcome was 30-day all-cause in-hospital mortality. Because only 18 deaths occurred, the primary multivariable model included any pDDI exposure and SOFA score.<br><br>RESULTS: Seventy of 90 patients (77.8%) had at least one pDDI within the fixed exposure window. Based on the highest patient-level severity, 13/70 (18.6%) had mild, 22/70 (31.4%) moderate, and 35/70 (50.0%) severe pDDIs. The most frequent combinations were vancomycin plus amikacin (18/90, 20.0%) and piperacillin/tazobactam plus vancomycin (15/90, 16.7%). The clinical consequences listed for common pairs were reference-predicted interaction consequences rather than adjudicated observed toxicities. In the parsimonious multivariable model, any pDDI exposure was associated with higher observed 30-day mortality (adjusted OR 4.23, 95% CI 1.27-14.09; P&#x2009;=&#x2009;0.02), and each 1-point increase in SOFA score was also associated with mortality (adjusted OR 1.32, 95% CI 1.07-1.64; P&#x2009;=&#x2009;0.01).<br><br>CONCLUSIONS: pDDIs were common in this ICU BSI cohort and were associated with higher observed 30-day mortality. These findings should be interpreted cautiously given the retrospective single-center design, limited event count, residual confounding, and incomplete control of time-dependent exposure. Structured pDDI screening may still support medication safety in critically ill patients.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid42063196, year = {2026}, author = {Liu, Z and Meng, C and Shen, J and Wang, H and Guo, J and Zhao, J and Mu, C and Zhu, W}, title = {Dietary regulation on gut resistome linked with microbial amino acid metabolism in pigs.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {42063196}, issn = {2524-4671}, support = {National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; National Natural Science Foundation of China (32030104)//Weiyun Zhu/ ; }, }
@article {pmid42063256, year = {2026}, author = {Liu, Y and Wu, J and Yang, Y and He, Y and Zhou, R and Li, Y and Sun, J and Gong, M and Mei, X and Li, Y and Huang, H and Du, F and Deng, W and Ye, C and He, X and Li, L and Hao, J and Yang, M and Zhu, Y and Zhu, S}, title = {Decoupling the 'Attract-and-Kill' Strategy: Independent Functions for Zoospore Attraction and ROS-Executed Killing Synergize in Disease-Suppressive Intercropping.}, journal = {Plant communications}, volume = {}, number = {}, pages = {101876}, doi = {10.1016/j.xplc.2026.101876}, pmid = {42063256}, issn = {2590-3462}, abstract = {Soilborne Phytophthora diseases pose a major threat to agricultural sustainability. How non-host roots disrupt the transmission of soilborne Phytophthora pathogens without relying on classical antimicrobial exudates remains unknown. Through a decade-long field study, we demonstrate that strip intercropping achieves sustainable disease suppression (up to 46.85%) by leveraging non-host roots as ecological barriers that intercept zoospore transmission. Moving beyond the conventional focus on antimicrobial exudates, we decouple the 'attract-and-kill' strategy into two discrete functions: a broad-spectrum attraction function widespread among non-host plants (13 of 15 genera), which alone reduces disease by 9.2-24.4%; and a specialized killing function restricted to few species (e.g., garlic), where elevated root-interface concentrations of sulfur compounds induce cystospore rupture and germination inhibition, delivering 42.9-49.3% field suppression. The synergy of universal attraction and targeted killing intensifies efficacy at the rhizosphere interface. Mechanistically, killing is executed through a conserved ROS-PCD pathway, with pathogen sensitivity determined by intrinsic redox-buffering capacity. Metagenomic profiling further revealed that garlic roots and sulfur compounds enrich microbial motility genes and apoptosis pathways, adding a complementary mechanistic layer to the 'attract and kill'framework. We thus propose this two-component, ecology-based strategy for sustainable Phytophthora management in diversified cropping systems.}, }
@article {pmid42063433, year = {2026}, author = {Chen, L and Li, J and Liu, X and Chen, X and Li, H and Xie, D and Chen, Y and Yuan, J and Tao, E}, title = {Case Report: Beyond commensal: Staphylococcus epidermidis as a novel cause of NARDS.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1631683}, pmid = {42063433}, issn = {2296-2360}, abstract = {Staphylococcus epidermidis (S. epidermidis), usually a harmless skin bacterium, can become an opportunistic pathogen in newborns, particularly those with risk factors like premature membrane rupture. Although it commonly causes late-onset sepsis, its association with neonatal acute respiratory distress syndrome (NARDS) is rare. This report describes a unique case of NARDS in a full-term newborn caused by S. epidermidis. The infant, born via cesarean at 40 2/7 weeks with a 30.5-hour membrane rupture, developed severe respiratory failure shortly after birth, necessitating mechanical ventilation. Initial treatment with penicillin and cefotaxime was ineffective, and by day 3, the infant's condition worsened, showing respiratory distress, petechial rashes, and high inflammatory markers. Treatment was changed to vancomycin and meropenem, with the addition of intravenous immunoglobulin and two doses of pulmonary surfactant. Metagenomic next-generation sequencing (mNGS) confirmed S. epidermidis in the airway secretions. The patient was discharged after 19 days with a diagnosis of NARDS, intrauterine infectious pneumonia, neonatal air leak syndrome, type II respiratory failure, neonatal sepsis, and congenital heart defects. In conclusion, S. epidermidis is a novel pathogen capable of causing NARDS in high-risk infants with prolonged membrane rupture. The proposed mechanisms-including surfactant dysfunction and biofilm-associated virulence-are supported by experimental literature and are consistent with the clinical phenotype observed in our patient, though direct confirmation requires further study. Notably, skin symptoms like erythematous rash and petechiae may indicate invasive S. epidermidis infection, especially in cases of respiratory distress with skin symptoms following premature rupture of membranes. Moreover, mNGS is vital for pathogen identification when traditional cultures fail.}, }
@article {pmid42063498, year = {2026}, author = {Xiang, L and Wang, X and Wen, M and Wang, X and Zhang, Y and Tian, W and Liu, M and Zhang, W}, title = {Metagenomic insights into the rhizosphere microbiome dysbiosis associated with tobacco bacterial wilt.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1809980}, pmid = {42063498}, issn = {1664-302X}, abstract = {Tobacco bacterial wilt, caused by Ralstonia solanacearum, threatens global tobacco production. While the rhizosphere microbiome defends against soil-borne pathogens, mechanisms underlying how bacterial wilt reshapes microbial community structure, function, and ecological interactions remain poorly understood. Here, we employed metagenomic sequencing to investigate taxonomic and functional alterations in the rhizosphere microbiome of symptomatic (S) and asymptomatic (A) tobacco plants across two locations (Fenggang and Bozhou), establishing four groups: FA, FS, BA, and BS. Quality control of sequencing data showed no technical bias between groups (p > 0.05). Contrary to the paradigm that pathogen invasion reduced microbial diversity, alpha diversity analysis revealed higher species richness (Sobs) in symptomatic soils, whereas community evenness (Shannon and Simpson indices) remained unchanged, suggesting selective reshuffling rather than microbiome collapse. Beta-diversity analysis revealed significant compositional shifts associated with disease status (PERMANOVA, R [2] = 0.713, p = 0.001), with symptomatic communities displaying greater heterogeneity. Taxonomic profiling revealed consistent enrichment of the pathogen R. solanacearum and opportunistic bacteria (including Stenotrophomonas and Pseudomonas) in symptomatic rhizospheres, concomitant with depletion of putative beneficial taxa (Candidatus_Solibacter, Luteitalea, and Metarhizium). Functional annotation indicated a metabolic shift from homeostatic maintenance to stress adaptation and pathogenicity. Symptomatic soils exhibited significant enrichment of virulence factors, including motility and secretion system genes, microbial defense mechanism genes (COG), and antibiotic resistance genes (CARD). Additionally, increased abundance of carbohydrate-active enzymes (CAZy)-particularly glycoside hydrolases-suggested intensive nutrient acquisition from decaying tissues. Co-occurrence network analysis revealed that asymptomatic communities formed denser, competition-driven networks characterized by a higher proportion of negative correlations. Disease destabilized these networks by reducing connectivity and, crucially, rewired interactions of R. solanacearum from negative to positive associations with taxa such as Sphingobium, thereby reflecting erosion of competitive constraints and pathogen incorporation into cooperative networks. Our findings revealed that bacterial wilt drove multi-layered dysbiosis, encompassing pathogen-driven taxonomic selection, functional shifts toward stress adaptation and intensified competition, and collapse of stable antagonistic networks associated with plant health. This study provided mechanistic insights into microbiome-mediated disease progression and identified specific microbial taxa and network properties as candidate targets for ecological disease management and early diagnostic indicators.}, }
@article {pmid42063509, year = {2026}, author = {González de Figueras, C and Gómez, S and Lamprecht-Grandío, M and Mirete, S and Díaz-Rullo, J and Martínez-Rodríguez, P and Sánchez-Costa, M and González-Pastor, JE}, title = {Enhancing UV-C and perchlorate resistance in Arabidopsis thaliana through the introduction of microbial genes from hypersaline environment.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1789302}, pmid = {42063509}, issn = {1664-302X}, abstract = {Ultraviolet (UV) radiation reaching the Earth's surface affects all living organisms. Recent reports show a trend of increasing exposure levels due to stratospheric ozone depletion and contamination. UV-B radiation (280-315 nm), previously largely absorbed by the ozone layer, now reaches the surface in higher doses, posing a particular threat to plants, which are sessile organisms and cannot escape adverse conditions. The intrinsic protective and repair mechanisms in plants may be insufficient to counteract this increase, potentially impacting crop productivity, distribution, and quality, with serious implications for agriculture and ecological stability. This study aims to enhance plant resistance to UV radiation by introducing genes derived from extremophilic microorganism, which have previously shown to confer UV-protective effects in UV resistance to a radiation-sensitive Escherichia coli strain (recA mutant). Extremophile microorganisms have been discovered in high-irradiation environments, such as hypersaline lakes, where survival relies on unique genetic adaptations. In our laboratory, four genes were selected from metagenomic libraries derived from high-altitude hypersaline lakes in Argentina (Diamante and Ojo Seco, at 4,589 m and 3,200 m respectively) and from the Es Trenc salt flat (Mallorca, Spain). Based on these promising results, the genes were introduced into Arabidopsis thaliana to evaluate their potential to enhance UV-B tolerance in plants. The selected genes included one encoding a TATA-box binding protein, and three hypothetical proteins. Each gene was independently transformed into Arabidopsis thaliana lines and subjected to UV-B and UV-C irradiation (4.5 kJ·m[-2]), with UV-C (100-280 nm) ultimately chosen for its higher damaging potential to test the limits of plant tolerance. Additionally, cross-resistance was evaluated using sodium perchlorate, a common soil contaminant and oxidative stressor. Plants were exposed to concentrations between 3.67 and 7.34 g/L, exceeding those used in previous studies. As a result, the plants obtained were more resistant to UV radiation and were also capable of growing in environments containing higher levels of perchlorate in the growth medium. Thus, the expression of these genes in the plant appears to contribute to enhanced stress resistance.}, }
@article {pmid42063777, year = {2026}, author = {Zhu, M and Sun, C and Zhang, Y and Na, Y and Wang, Y and Zhao, Q and Gu, Y}, title = {Blepharitis driven by microbiome dysbiosis and Demodex infestation: possible pathogenic mechanisms.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1801375}, pmid = {42063777}, issn = {2296-858X}, abstract = {Blepharitis is a chronic inflammation of the eyelid margin that is mediated by the immune system. It is one of the common ocular surface diseases and often leads to serious sequelae that threaten vision, such as dry eye syndrome due to insufficient tear secretion, corneal neovascularization, and stubborn chalazion. Elucidating its precise etiology is therefore imperative. Emerging high-throughput sequencing and metagenomic analyses have unveiled a quantitative and qualitative disruption of the periocular microbiome (dysbiosis), characterized by the expansion of specific bacterial species such as Staphylococcus aureus, coupled with episodic blooms of Demodex. These perturbations are no longer considered epiphenomena. In this review, we reveal the possible mechanisms of the role of blepharitis and microbiota dysbiosis.}, }
@article {pmid42063778, year = {2026}, author = {Wu, S and Wu, M and Li, W and Zhang, C and Bi, Y and Fan, Y and Xu, Y and He, D}, title = {Case Report: Diagnosis of leptospirosis presenting as aseptic meningitis using metagenomics CAPture sequencing.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1734396}, pmid = {42063778}, issn = {2296-858X}, abstract = {BACKGROUND: Leptospirosis is a globally prevalent zoonotic disease caused by pathogenic Leptospira species. The manifestation of leptospirosis can range widely, from being asymptomatic to causing severe multi-organ failure with a high mortality rate. It is uncommon for leptospirosis to present primarily with neurological complications. In this context, we discuss a notable case of Leptospira borgpetersenii infection manifesting as aseptic meningitis in China.<br><br>CASE PRESENTATION: In this study, we describe a primary case of neuroleptospirosis leading to symptomatic aseptic meningitis following exposure to Leptospira borgpetersenii. Initially managed for viral meningitis, the diagnosis of leptospirosis was subsequently confirmed through cerebrospinal fluid (CSF) analysis using metagenomic next-generation sequencing (mNGS) and Metagenomics CAPture Sequencing (MetaCAP), both of which identified Leptospira borgpetersenii. Following a course of antibiotics and methylprednisolone therapy, the patient fully recovered.<br><br>CONCLUSION: This case underscores the importance of considering leptospirosis in differential diagnoses for aseptic meningitis, especially in individuals with occupational risks related to water or animal exposure. MetaCAP's extensive coverage, sensitivity, and early pathogen detection capabilities can significantly enhance patient outcomes.}, }
@article {pmid42063908, year = {2026}, author = {Kateete, DP and Lubega, C and Nasinghe, E and Mbabazi, M and Galiwango, R and Jjingo, D}, title = {Gut microbial profiles of COVID-19 patients in Uganda.}, journal = {African health sciences}, volume = {26}, number = {1}, pages = {1-15}, pmid = {42063908}, issn = {1729-0503}, mesh = {Humans ; *COVID-19/microbiology/epidemiology ; Uganda/epidemiology ; *Gastrointestinal Microbiome ; Female ; Male ; Adult ; Middle Aged ; SARS-CoV-2 ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Severity of Illness Index ; Bacteria/isolation &amp; purification/genetics ; }, abstract = {BACKGROUND: The role of the microbiome in COVID-19 outcomes remains an area of exploration. We comprehensively explored the gut microbiome of Ugandan COVID-19 patients and inferred potential implications.<br><br>METHODS: Stool and demographic data were collected from 100 COVID-19 confirmed cases at the covid isolation and treatment centers in Kampala during the first and second waves of the pandemic in Uganda (2020 and 2021, respectively). 16S rRNA sequencing was performed on the DNA extracted from stool, followed by bioinformatics analysis. Machine-learning techniques were used to determine microbes that were associated with disease severity.<br><br>RESULTS: We observed differences in microbial composition between COVID-19 patients and healthy controls. Pathogenic bacteria such as Klebsiella oxytoca, Salmonella enterica and Serratia marcescens had an increased presence in COVID-19 disease states, especially severe cases. Additionally, there was an increase in opportunistic pathogens like Enterococcus species, along with a decrease in beneficial microbes, such as Alphaproteobacteria, when comparing mild and severe cases. Machine-learning identified age and microbes like Ruminococcaceae, Bacilli, Enterobacteriales, porphyromonadaceae and Prevotella copri as predictive of severity.<br><br>CONCLUSION: The microbiome likely plays a role in the dynamics of SARS-CoV-2 infection in Ugandan patients. The shift in abundance of specific microbes can moderately predict severity of COVID-19 in this population.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid42064023, year = {2026}, author = {Liu, Y and Wang, W and Peng, Y and Feng, L and Li, C and Zhang, Z and Zhao, J and Yang, C and Mu, T and Wang, J and Li, C and Yang, C}, title = {Sources of Microbial and Organic Contaminants in the Production of Soybean Whey Protein for Feed and Potential Food Applications.}, journal = {Food science &amp; nutrition}, volume = {14}, number = {5}, pages = {e71709}, pmid = {42064023}, issn = {2048-7177}, abstract = {Soybean whey wastewater (SWW), a rich source of soybean whey protein (SWP), is prone to microbial rancidity, posing environmental and resource challenges. This study explores the causes of rancidity-characterized by a pungent, sour, and putrid odor-in the effluents of sealed buffer tank during SWP recovery via pneumatic flotation. Metagenome, bacterial diversity, and HPLC analyses showed the obligate anaerobe Megasphaera spp. dominated rancid effluents (up to 44% abundance), consumed lactate (decreasing from 10.2 g/L in influent to 2.7 g/L in effluent), and produced malodorous propionate and butyrate (up to 3.6 and 4.3 g/L, respectively). Three mitigation strategies were assessed: (1) full-scale high-throughput aeration-likely effective but energy- and cost-intensive; (2) local aeration-low-cost but weakly inhibitory; and (3) microbial intervention using the probiotic Enterococcus faecium LBSW, which colonizes the buffer tank, with localized aeration used only if microbial control fails. Strategy (3) was adopted for its energy and cost efficiency, successfully reducing pollution and supporting SWP recovery. Although the biosafety of E. faecium LBSW in food applications requires caution, the recovered SWP is primarily intended for animal feed, and subsequent high-temperature drying and sterilization (> 120°C) also offer potential for food-grade use.}, }
@article {pmid42064333, year = {2026}, author = {Reider, KE and Fannin, C and Hannah, KA and Gelona, AR and Anderson, C and Barnard-Kubow, K and Enke, RA}, title = {16S rRNA amplicon metabarcoding dataset from a retreating glacier forefield in the high tropical andes.}, journal = {Data in brief}, volume = {66}, number = {}, pages = {112758}, pmid = {42064333}, issn = {2352-3409}, abstract = {Glaciers are retreating rapidly worldwide, particularly at high elevations, changing the environments and habitats of microorganisms, plants, and animals drastically and leaving behind nutrient-poor sediment. We sought to explore seasonal, elevational, and soil age differences in microbial community diversity found in moraine deposits exposed by recent deglaciation and previously exposed during the Little Ice Age in the Cordillera Vilcanota of southeastern Peru. In the wet and dry seasons of 2023, JMU students and other researchers collected soil samples from 35 sites across a 2.5 square kilometer range in the Andes mountains. Each sample was assigned to the season collected, elevation of collection, and age of exposure. Total DNA was extracted from samples and the 16S rRNA gene was amplified and sequenced on an Illumina MiSeq platform. The data were then processed and analyzed using the QIIME2 bioinformatics pipeline. This dataset will be useful to the field for studying ecological community and ecosystem formation in glacier forefields emerging from climate change.}, }
@article {pmid42064443, year = {2026}, author = {Niyomvong, N and Wongsorn, D and Pitiwittayakul, N}, title = {Metagenomics of a Photo-Fermentative Bacterial Solution and Its Effect on the Growth And Yield of Mini Green Cos Lettuce.}, journal = {Tropical life sciences research}, volume = {37}, number = {1}, pages = {85-108}, pmid = {42064443}, issn = {1985-3718}, abstract = {Photosynthetic bacteria (PSB) are widely utilised in agriculture to enhance plant growth and crop quality by improving nutrient uptake and phytohormone production. This study aimed to analyse the metagenomic composition of a photo-fermentative bacterial solution derived from fermentation and assess its effects on the growth and yield of Mini Green Cos lettuce. Metagenomic analysis revealed that Bacteroidota (38%) was the most abundant phylum, followed by Proteobacteria (23%), Thermotogota (17%) and Firmicutes (15%). Within Proteobacteria, Alphaproteobacteria was dominant followed by Gammaproteobacteria. At the genus level, Petrimonas (22%), uncultured clones belonging to family Petrotogaceae (17%), Rhodopseudomonas (11%), Rubrivivax (6%), and an unidentified genus from Lentimicrobiaceae (4%) were the most prevalent. These findings highlight the microbial diversity of PSB solution, suggesting its potential role in plant growth promotion. A plant growth experiment was conducted using a Completely Randomised Design (CRD) with four treatments: control (T1), chemical fertiliser (T2), undiluted PSB solution (T3) and PSB solution diluted at a 1:1 ratio (T4), with 10 replicates per treatment. Among all treatments, lettuce irrigated with undiluted PSB solution (T3) exhibited the highest growth rate, yield and total chlorophyll content. However, its performance was not significantly different from that of the chemical fertiliser treatment (T2). These results suggest that PSB can effectively promote plant growth and yield, yielding results comparable to chemical fertilisers. Therefore, photo-fermentative bacterial solutions offer a sustainable and eco-friendly alternative to chemical fertilisers, supporting environmentally conscious agricultural practices.}, }
@article {pmid42065019, year = {2026}, author = {Behera, S and Gupta, S and Kale, A and Yadav, A and Rao, GP}, title = {Draft genome of a 'Candidatus Phytoplasma trifolii' -related strain BLL-Delhi associated with brinjal little leaf disease.}, journal = {3 Biotech}, volume = {16}, number = {5}, pages = {173}, pmid = {42065019}, issn = {2190-572X}, abstract = {The draft genome sequence of the brinjal little leaf (BLL) phytoplasma strain BLL-Delhi, related to 'Candidatus Phytoplasma trifolii' (16SrVI group), was recovered using a metagenome-resolved assembly strategy from Illumina HiSeq data. The genome comprises 476,098 bp assembled into 12 contigs, with a G+C content of 21.86%, encoding 421 predicted protein-coding sequences, 27 tRNAs, one tmRNA and one additional non-coding RNA, and shows 94% completeness. Genome annotation revealed a reduced yet functionally coherent gene repertoire, including putative effector-like proteins and genes associated with mobile genetic elements. This genome provides a resource for high-resolution taxonomic placement, comparative genomics within the 16SrVI phytoplasma group, and genome-based diagnostics for brinjal little leaf disease.}, }
@article {pmid42065375, year = {2026}, author = {Ding, SC and Yu, J and Liao, T and Ahmann, L and Yao, Y and Ho, C and Wang, L and Pinsky, BA and Gu, W}, title = {Adapting clinical chemistry plasma as a source for liquid biopsies.}, journal = {eLife}, volume = {14}, number = {}, pages = {}, doi = {10.7554/eLife.108708}, pmid = {42065375}, issn = {2050-084X}, support = {CA230156//NIH Office of the Director/ ; CAMS//Burroughs Wellcome Fund/ ; }, mesh = {Humans ; *Cell-Free Nucleic Acids/blood ; Liquid Biopsy/methods ; *Plasma/chemistry ; *Blood Specimen Collection/methods ; *Specimen Handling/methods ; }, abstract = {Circulating cell-free DNA (cfDNA) is valuable for molecular testing, but typically requires specialized collection tubes or immediate processing. We investigated whether residual plasma from heparin separators, routinely used in clinical chemistry, could serve as an accessible and underused source for cfDNA. We analyzed matched plasma samples from healthy volunteers in two experiments: an immediate-processing comparison across EDTA, Streck, and heparin separator tubes (n=5), and a clinical-handling simulation comparing EDTA and heparin separator tubes under delayed processing at room temperature or 4°C (n=6). We also analyzed matched plasma samples from viral PCR-positive patients in a hospital cohort (n=38). Whole-genome sequencing and enriched methylation sequencing were performed to assess concordance across metagenomics, copy number, methylation, and fragmentomic features. Under immediate processing, heparin separator plasma showed high concordance with EDTA and Streck plasma for methylation patterns (Spearman's ρ=0.65-0.70) and fragmentation features. In the Hospital Cohort, heparin separator plasma showed strong concordance with matched EDTA plasma for viral detection (Spearman's ρ=0.95), copy number alteration profiling (Spearman's ρ=0.72-0.96), and methylation patterns (Spearman's ρ=0.50-0.83). These findings support the feasibility of using refrigerated, promptly processed residual plasma from routine clinical chemistry as a supplementary source for cfDNA biobanking and molecular analyses.}, }
@article {pmid42066399, year = {2026}, author = {Yang, X and Chen, M and Song, B and Liu, T and Zhao, YG and He, Q and Chen, Y}, title = {Micro(nano)plastics reshape constructed wetlands: Linking biofilm succession's role to key biogenic substance transformation.}, journal = {Water research}, volume = {301}, number = {}, pages = {126024}, doi = {10.1016/j.watres.2026.126024}, pmid = {42066399}, issn = {1879-2448}, abstract = {Constructed wetlands (CWs) are increasingly recognized as terminal sinks for micro- and nanoplastics (MNPs), yet how chronic MNPs accumulation reshapes biofilm-mediated biogenic substance transformation remains poorly understood. Here, using a 300-day CW experiment integrating process analysis, biofilm microstructure characterization, and metagenomics, we demonstrate that plastic particle size acts as a decisive ecological switch governing biofilm succession and multi-element cycling. Long-term microplastics (MPs) exposure unexpectedly enhanced denitrification and sulfate reduction, whereas nanoplastics (NPs) persistently suppressed carbon, nitrogen, phosphorus, and sulfur transformations. Mechanistic analyses reveal that these divergent outcomes arise not from direct metabolic toxicity but from size-dependent reorganization of biofilm architecture, regulatory gene networks, and microbial cooperation. MPs promoted extracellular polymeric substance synthesis, reinforced anaerobic redox stratification, and strengthened electron-transfer-driven microbial clustering, while NPs disrupted biofilm integrity, downregulated succession-related genes, and fragmented functional interactions. This study challenges the prevailing assumption that MNPs accumulation uniformly degrades treatment performance and establishes a mechanistic framework linking particle size, biofilm succession, and ecosystem functioning. Our findings provide new insights into the long-term ecological effects of emerging particulate pollutants and offer guidance for designing resilient biofilm-based treatment systems under increasing plastic pressure.}, }
@article {pmid42066496, year = {2026}, author = {Río-López, R and Vourlaki, IT and Clavell-Sansalvador, A and Valdés, A and Padilla, L and García-Gil, LJ and Xifró, X and Ballester, M and Quintanilla, R and Ochoteco-Asensio, J and Prenafeta-Boldú, FX and Dalmau, A and Ramayo-Caldas, Y}, title = {Integrative metagenomic and metabolomic profiling identifies faecal biomarkers of prolonged social stress in pigs.}, journal = {Animal : an international journal of animal bioscience}, volume = {20}, number = {5}, pages = {101823}, doi = {10.1016/j.animal.2026.101823}, pmid = {42066496}, issn = {1751-732X}, abstract = {Stressors significantly impact human and animal health, increasing the risk of physical and mental disorders, in part by affecting the gut-brain axis. Although a link between stress, alterations in gut microbial composition, and the serum metabolite profile has already been established in humans, multiomics studies integrating the faecal microbiome and untargeted metabolomics remain unavailable. The objectives of the present study were twofold: first, to identify microbial and metabolic signatures associated with prolonged stress, and second, to evaluate the potential of integrative multiomics approaches to predict key metabolites and discover non-invasive faecal biomarkers of stress in pigs (n = 60). Gut microbial profiles were obtained by shotgun metagenomic sequencing, while faecal metabolites were analysed by untargeted reverse-phase liquid chromatography quadrupole time of flight mass spectrometry, followed by partial least squares discriminant analysis. Metabolite prediction from microbial features was performed using the machine learning method based on neural ordinary differential equations. Eleven discriminant metabolites were identified. In the control group, neurotransmitters such as serotonin and metabolites such as 2-acetamidophenol and sinapine (which possess anti-inflammatory and antioxidant properties) were the most prominent. Conversely, the stressed group exhibited elevated levels of xanthosine, pyrimidine bases (thymine and uracil), n-octadecylamine, and N-α-acetyl-L-lysine. N-octadecylamine (r = 0.37) showed a positive, and serotonin (r = -0.32) a negative correlation with hair cortisol. The results revealed interspecific interactions that modulated microbial and metabolic shifts between the control and stressed pig groups. Feature selection further identified 64 microbial genes that improved classification accuracy between control and stressed pigs to 91.06% and enhanced the prediction of key metabolites, including serotonin and xanthosine. Overall, this integrative multiomics framework elucidates complex microbiome-metabolite interactions and identifies non-invasive biomarkers of prolonged stress-induced metabolic dysregulation, providing valuable insights for animal welfare and translational human health research.}, }
@article {pmid42066541, year = {2026}, author = {Li, L and Chi, Y and Kong, Y and Zheng, D and Shi, Z and Kang, X}, title = {Rapid species-level discrimination of pulmonary TB and NTM by metagenomic next-generation sequencing with concurrent respiratory microbiome profiling.}, journal = {Diagnostic microbiology and infectious disease}, volume = {116}, number = {1}, pages = {117442}, doi = {10.1016/j.diagmicrobio.2026.117442}, pmid = {42066541}, issn = {1879-0070}, abstract = {INTRODUCTION: Rapid discrimination between Mycobacterium tuberculosis (MTB) and nontuberculous mycobacteria (NTM) remains clinically challenging, especially when conventional microbiological evidence is limited. Whether metagenomic next-generation sequencing (mNGS) can provide rapid species-level identification while simultaneously characterizing the respiratory microbiome remains to be systematically evaluated.<br><br>METHODS: Bronchoalveolar lavage fluid from 74 retrospectively enrolled patients with clinically diagnosed pulmonary mycobacterial disease (62 TB, 12 NTM-pulmonary disease (NTM-PD)) was analyzed by mNGS. Conventional test results were extracted from medical records. A supplementary assessment excluding mNGS from diagnostic review was additionally performed to reduce potential incorporation bias. Microbial diversity and between-group differences in the respiratory microbiota were evaluated.<br><br>RESULTS: In the clinically diagnosed cohort, mNGS was positive in 61/62 TB cases (98.4%) and 12/12 NTM-PD cases (100%). Mycobacterial cultures were negative in all tested patients in routine clinical practice. By comparison, AFB (8.82%, 3/34), T-SPOT.TB (71.43%, 10/14), and Xpert MTB/RIF (69.23%, 9/13) showed lower positivity among tested patients. In the supplementary assessment, 45/46 independently classified TB cases were mNGS-positive (97.8%). mNGS additionally detected non-mycobacterial pathogens in 62.16% (46/74) of patients, facilitating recognition of polymicrobial infection. Microbiome analysis revealed that the TB group showed relatively higher abundance of Streptococcus parasanguinis besides MTB, whereas NTM group was relatively enriched in opportunistic pathogens including Pseudomonas aeruginosa and Stenotrophomonas maltophilia.<br><br>CONCLUSION: In this retrospective real-world cohort, mNGS achieved rapid species-level discrimination of MTB and NTM with high positive detection rates, and simultaneously provided clinically relevant microbiome information, supporting its value as an adjunctive diagnostic tool for pulmonary mycobacterial infection.}, }
@article {pmid41862790, year = {2026}, author = {Amir, A and Zhong, J and Yao, Y and Chen, T and Li, M and Yan, H}, title = {Seasonal diet shifts alter the gut microbiome and resistome of captive geriatric giant pandas (Ailuropoda melanoleuca).}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41862790}, issn = {1471-2180}, support = {2024CPB-B18//Chengdu Research Base of Giant Panda Breeding/ ; 2024CPB-B18//Chendu Research Base of Giant Panda Breeding/ ; }, abstract = {UNLABELLED: The nutritional changes of giant pandas (Ailuropoda melanoleuca) in response to the seasonal variations from bamboo shoots (rich in proteins) to fibrous leaves trigger significant alterations in the structure and functions of the gut microbiome. However, the effect these dietary changes have on the gut resistome, especially in older adults, is not well characterized. In this study, shotgun metagenomic sequencing and quantitative PCR (qPCR) were used to investigate the microbial composition, functional potential, and profiles of antibiotic- and metal-resistance genes (ARG and MRG) in feces of adult (n = 11) and geriatric captive pandas (n = 11) that were fed on bamboo shoots or leaves. The microbes varied considerably among diet and age groups, with diet becoming the main source of taxonomic and functional disparity (P < 0.05). Shoot-fed pandas exhibited higher alpha diversity at the genus level and distinct clustering in principal coordinate analyses, whereas leaf-fed groups showed enrichment of taxa associated with fiber degradation and stress tolerance (P < 0.05). Functional annotation of bacterial responses to diet showed changes in carbohydrate processing pathway, carbohydrate transport, and cellular process pathways by changes in the KEGG pathway (P < 0.05). Changes depending on diet were also identified with significant changes in carbohydrate-active enzyme (CAZy) family during changes in the composition of the bamboo parts. Metagenomics and qPCR revealed that several antibiotic resistance genes, such as aac(3)-Xa, bcrA, tet44, sul2 and macB, were highly interacting between diet and age and the most diverse resistome was found in geriatric pandas (P < 0.05). Correlation analysis demonstrated that there is a positive co-occurrence pattern of Enterobacteriaceae and several ARGs. Collectively, our findings demonstrate that seasonal dietary shifts and host aging jointly restructure the gut microbiome and resistome of giant pandas, suggesting diet-mediated modulation of microbial adaptation, resistance dissemination, and ecological resilience in captivity.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04966-0.}, }
@article {pmid42010622, year = {2026}, author = {Goldstein, C and Lavy, I and Sun, T and Ennis, D and Shreffler, WG and Yuan, Q and Virkud, YV and Martin, VM and Yassour, M}, title = {Strain-level microbial signatures and inferred functional alterations in infants with food protein-induced allergic proctocolitis.}, journal = {Genome medicine}, volume = {18}, number = {1}, pages = {}, pmid = {42010622}, issn = {1756-994X}, support = {1685-3680//Gerber Foundation/ ; 230465//Demarest Lloyd Jr Foundation/ ; 229711//the Food Allergy Science Initiative/ ; K23AI151555//National Institute of Allergy and Infectious Diseases of the US/ ; K23AI130408//Artificial Intelligence/Machine Learning Consortium to Advance Health Equity and Researcher Diversity/ ; }, abstract = {BACKGROUND: The complex relationship between the gut microbiome and immune system development during infancy is considered a key factor in the rising rates of pediatric allergic diseases. Food protein-induced allergic proctocolitis (AP), the earliest identified form of non-IgE-mediated food allergy in infants, occurs at the mucosal surface where dietary proteins, intestinal microbes, and immune cells directly interact, and increases the risk for life threatening IgE-mediated food allergy, making it an important model for understanding early food allergic disease development. The question of how specific microbial compositions and functional pathways contribute to AP development and progression remains poorly understood.<br><br>METHODS: We performed metagenomic sequencing on 740 longitudinal stool samples from 163 infants (84 with AP, 79 without AP) enrolled in the prospective GMAP cohort. Taxonomic profiling, functional pathway analysis, strain-level characterization, and machine learning-based classification were applied to identify microbial differences across disease stages.<br><br>RESULTS: Here we show that infants with AP exhibit different microbial compositions, characterized by enrichment of Escherichia coli and Bifidobacterium bifidum during early life, including pre-symptomatic stages, while species like Bifidobacterium breve and Klebsiella species are more abundant in infants without AP. These findings suggest the presence of microbial signatures that may be detectable before clinical symptoms emerge, and demonstrate that strain-level differences within E. coli populations may represent AP-associated lineages with distinct gene content profiles that were not previously recognized. For example, biofilm formation and cell adhesion genes in E. coli were particularly enriched in AP-associated clades. Short chain fatty acid (SCFA) and other functional pathways were also associated with AP, including reduced SCFA production during the symptomatic phase, and then a potentially compensatory increased production following AP resolution.<br><br>CONCLUSIONS: Our results provide the first comprehensive strain-level characterization of the gut microbiome in AP, and functional implications, and generate new hypotheses to be tested regarding candidate microbial features associated with AP for future biomarker discovery and/or intervention targets. This work advances our understanding of how specific microbial taxa and functional pathways may contribute to non-IgE-mediated food allergies and opens new avenues for microbiome-targeted therapeutic approaches as well as novel prevention targets for IgE-mediated food allergies.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13073-026-01646-6.}, }
@article {pmid42055803, year = {2026}, author = {Auwal, AM and Matthews, R and Cook, C and Sargent, B and Easton, A and Ray, STJ and Ellul, MA and Michael, BD}, title = {Suspected encephalitis in adults.}, journal = {Practical neurology}, volume = {}, number = {}, pages = {}, doi = {10.1136/pn-2024-004299}, pmid = {42055803}, issn = {1474-7766}, abstract = {'Query encephalitis' is one of the most common reasons for inpatient neurology referral in the context of an acutely confused patient. Growing evidence suggests that time to treatment is a key determinant of outcome in both infectious and autoimmune encephalitis; hence, these two causes should be considered simultaneously at presentation. However, under-recognition and the existence of several mimics make a rapid diagnosis of encephalitis challenging. Appreciation of clinical syndromes can guide aetiological investigation and consequent treatment. In this article, we discuss clinical phenotypes associated with both infectious and autoimmune encephalitis, as well as a systematic approach to their investigation and up-to-date treatment strategies. We also highlight ongoing areas of research, such as metagenomics and therapeutic trials.}, }
@article {pmid42056322, year = {2026}, author = {Thakkar, S and Rathour, R and Rana, SS and Samant, S and Kikani, BA and Madamwar, D and Desai, C}, title = {Biochar-augmented microaerophilic fixed-film bioreactor integrated with an aerobic membrane bioreactor effectively reduces persistent, mobile chemicals in the CETP effluent treatment.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {5}, pages = {}, pmid = {42056322}, issn = {1573-0972}, support = {File No. GSBTM/JD(R&amp;D)/662/2022-23/00292469//Gujarat State Biotechnology Mission (GSBTM), Department of Science and Technology, Government of Gujarat/ ; }, mesh = {*Bioreactors/microbiology ; *Charcoal/chemistry ; Aerobiosis ; *Water Pollutants, Chemical/metabolism ; *Waste Disposal, Fluid/methods ; Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Membranes, Artificial ; *Water Purification/methods ; Biodegradation, Environmental ; Wastewater/chemistry/microbiology ; Biological Oxygen Demand Analysis ; }, abstract = {Different classes of chemical compounds including persistent, mobile chemicals (PMCs) often bypass the conventional treatment processes of common effluent treatment plants (CETPs), resulting in their unmonitored release into aquatic environments. In this study, an integrated treatment system comprising a microaerophilic fixed-film bioreactor (MFB) and an aerobic membrane bioreactor (Ae-MBR) was engineered to treat secondary CETP effluent. Two types of packing materials in the engineered MFBs were evaluated: one with wood charcoal (C-MFB) and another with 30% (w/w) biochar-augmented charcoal (BAC-MFB). The BAC-MFB showed better treatment efficiency, achieving 69.17% colour (Pt-Co units) removal and 93.01% COD removal at an optimal 3d hydraulic retention time (HRT). Integration with Ae-MBR further enhanced the treatment, achieving > 95% COD and > 94% colour removal, with an overall > 85% reduction in total number of parent chemical compounds and a specific > 83% reduction in PMCs from CETP effluent. At 3d HRT, bacterial community analysis revealed dominance of Campylobacterota and Bacillota in BAC-MFB under microaerophilic conditions, whereas Bacillota dominated in the Ae-MBR under aerobic conditions. The predicted metagenome analysis revealed significant enrichment of benzoate and aminobenzoate degradation pathways in the integrated system. While the BAC-MFB treatment alone achieved sufficient COD removal, its integration with Ae-MBR markedly enhanced the reduction in overall chemical complexity including PMCs from the CETP effluent. This study demonstrates that the engineered hybrid BAC-MFB-Ae-MBR system is a sustainable solution for the treatment of industrial CETP effluents.}, }
@article {pmid42056687, year = {2026}, author = {Wedell, E and Shen, C and Warnow, T}, title = {Phylogenetic Placement Using SCAMPP and Batch-SCAMPP.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2981}, number = {}, pages = {37-52}, pmid = {42056687}, issn = {1940-6029}, mesh = {*Phylogeny ; *Software ; *Metagenomics/methods ; Algorithms ; Likelihood Functions ; *Computational Biology/methods ; }, abstract = {Phylogenetic placement is the problem of adding sequences to an existing phylogenetic tree. While many techniques have been developed for this problem, methods based on optimizing maximum likelihood, such as pplacer and EPA-ng, have been shown to provide the highest accuracy. Unfortunately, these methods are limited to at most moderately large placement trees due to their design. SCAMPP and Batch-SCAMPP are two methods that have been developed to improve the scalability of both pplacer and EPA-ng to very large trees, while maintaining high accuracy. Here, we describe these methods and show how to use them in two applications: metagenomics, including taxon identification and abundance profiling, and incrementally growing large trees. SCAMPP and Batch-SCAMPP are available in open-source form on GitHub and PyPI.}, }
@article {pmid42056742, year = {2026}, author = {Zhang, X and Li, Q and Yang, H and Li, H and Hu, C}, title = {Active responses of cyanobacterial crusts directly exposed to the extreme stratospheric environment.}, journal = {Life sciences in space research}, volume = {50}, number = {}, pages = {133-145}, doi = {10.1016/j.lssr.2026.01.001}, pmid = {42056742}, issn = {2214-5532}, mesh = {*Cyanobacteria/physiology/metabolism ; *Extraterrestrial Environment ; Mars ; Exobiology ; *Extreme Environments ; Indoles ; Phenols ; }, abstract = {The stratosphere's highly hostile environment offers a unique and relatively accessible setting to evaluate extremophilic adaptation for extraterrestrial colonization. The accelerating pace of the Martian project has underscored the need for a better understanding of the synergistic responses of microbial communities in Mars-like habitats. Here, we loaded the cyanobacterial crust, a model system with multiple trophic levels, onto a balloon-borne astrobiology platform for a direct-exposure experiment in the stratosphere, aligned with the ground-control and indoor-simulated groups. After short-term in-situ exposure, we performed multi-omics analyses to delineate alterations in community composition and the community-level metabolic response. We observed a significant shift in the community composition of active members, with the relative abundance of photoautotrophs (except Scytonema) declining while that of chemotrophs increased. However, we demonstrated the unique thriving of the cyanobacterial genus Scytonema, attributed to its synthesis of the anti-ultraviolet compound scytonemin, its diverse material, and its energy acquisition. Meanwhile, the distinct metabolic profiles exhibited by various species and their interspecies metabolic interactions synergistically facilitated the retention of organic carbon and nitrogen, ultimately sustaining the stability of the biocrust community. Our study underscores the adaptive resilience of cyanobacterial crusts under stratospheric stresses. Notably, the robustness of Scytonema, particularly its unique survival capabilities, highlights its potential for extraterrestrial applications.}, }
@article {pmid42056812, year = {2026}, author = {Fu, Y and Zhuang, H and Shi, J}, title = {Reshaping of the electron transport chain and carbon metabolism by low-loading Fe3O4@PU for enhanced phenolic compounds degradation in an algal-bacterial biofilm system.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142207}, doi = {10.1016/j.jhazmat.2026.142207}, pmid = {42056812}, issn = {1873-3336}, abstract = {While previous algal-bacterial biofilm systems without magnetite have shown limited resilience to high concentration phenolic compounds, this study demonstrates that introducing low loading (5%) nano-Fe3O4 substantially enhances degradation stability by optimizing electron transfer pathways. Four algal-bacterial reactors with varying Fe3O4 loadings (5-50%) were constructed using polyurethane carriers to treat phenolic wastewater under increasing total phenol (TPh) concentrations (50-300 mg/L). The 5% loading reactor (R1) demonstrated outstanding performance, achieving > 80% TPh removal and approximately 76% COD removal even at the highest loading. Compared to without magnetite systems, R1 achieved 13-15% higher TPh degradation at 300 mg/L. R1 also exhibited the highest electron transfer system activity (0.487 μg O2·gVSS[-1]·h[-1]) and cytochrome c content (72.12 mg/g VSS), indicating that Fe3O4 serves as an electron shuttle, compensating for endogenous electron carrier limitations. Metagenomic analysis revealed that the enhanced performance stemmed from robust carbohydrate metabolism, particularly the upregulation of key glycolytic enzymes (pfkA) and glycogen degrading enzymes (GH13), ensuring efficient NADH/ATP production. This metabolic advantage supplied reducing power to the Fe3O4 optimized electron transport chain, synchronizing electron generation with respiratory utilization. These findings demonstrate that low-dose Fe3O4 optimizes natural electron transfer pathways by coupling metabolic flux with respiratory chain activity, offering a cost effective strategy for treating high strength industrial wastewater.}, }
@article {pmid42057074, year = {2026}, author = {de Oliveira, LG and Lopes Mechler-Dreibi, M and Storino, GY and Moreira Petri, FA and Carvalho Abreu Fantini, M and Silva Martins, T}, title = {Respiratory microbiota dynamics in piglets under nanotechnology-based and conventional vaccination protocols against Mycoplasma hyopneumoniae.}, journal = {BMC veterinary research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12917-026-05458-z}, pmid = {42057074}, issn = {1746-6148}, abstract = {Mycoplasma hyopneumoniae is a key pathogen in porcine enzootic pneumonia (PEP) and plays an important role in the porcine respiratory disease complex (PRDC). Understanding how vaccination strategies relate to the respiratory microbiota in piglets may provide insights into host-microbiota interactions and vaccine performance. This study evaluated the temporal dynamics of the respiratory microbiota in piglets subjected to different vaccination protocols, including a nanotechnology-based oral vaccine formulated with mesoporous silica (SBA-15), alone or combined with a commercial vaccine, on the respiratory microbiota of piglets. Forty-eight piglets from M. hyopneumoniae-free sows were divided into four experimental groups receiving different vaccination protocols: CV + SBA received the pure silica-based adjuvant (SBA-15) orally and a commercial vaccine at 24 days of life; OV3 + CV received an oral vaccine (OV) at 3 days and an intramuscular commercial vaccine at 24 days; CV received only the intramuscular commercial vaccine at 24 days; and OV + CV received both the oral and commercial vaccines at 24 days. Microbiota composition was assessed at 3, 41, and 71 days of life using 16S rRNA gene sequencing from nasal swabs and bronchoalveolar lavage fluid (BALF). Significant differences in nasal microbiota diversity were observed at early life stages. At D3, CV exhibited the highest diversity, while OV3 + CV had the lowest (Shannon index, p < 0.05 between CV and OV3 + CV). At D41, microbiota differences between groups had diminished, with only OV + CV showing higher richness compared with OV3 + CV (Chao1 index, p < 0.05). At D71, no significant differences were observed in overall diversity or bacterial composition among groups. As no treatment had been administered prior to sampling, these differences likely reflect baseline variability between groups. Additionally, no consistent associations were detected between microbiota diversity patterns and vaccination outcomes assessed by lung lesion scores and bacterial DNA load. These findings indicate that early-life differences in nasal microbiota were observed, but these were not sustained over time, and the respiratory microbiota converged toward a more stable community structure regardless of vaccination protocol.}, }
@article {pmid42057154, year = {2026}, author = {Mahmud, MR and Uddin, MK and Kareljärvi, P and Jalasvuori, M and Peräkylä, J and Eklund, T and Biström, M and Hasan, S and Vatanen, T and Kiljunen, S and Oliviero, C}, title = {Impact of phage therapy in post-weaning piglets challenged with ETEC strain in a controlled minitrial.}, journal = {Porcine health management}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40813-026-00516-2}, pmid = {42057154}, issn = {2055-5660}, abstract = {Enterotoxigenic Escherichia coli (ETEC) is a pathogen responsible for post-weaning diarrhea (PWD) in piglets, which results in economic losses in pig production. The rise of antibiotic-resistant ETEC strains together with restrictions on addition of zinc oxide in pig feed require alternative management approaches. Our research examines bacteriophage therapy as a solution to control ETEC infections in newly weaned piglets. A cocktail of phages targeting a strain of ETEC F4LT1ST2 was identified and subsequently multiplicated in laboratory. We conducted a trial including nine piglets divided into three groups. The negative control group was exposed to the phage cocktail by administration with the bedding material (saw dust) on the floor of their pen. The treatment group was exposed to the ETEC strain and to the phage cocktail, and the positive control group was exposed to the ETEC strain only. Shotgun metagenomic sequencing was performed on fecal samples to characterize bacterial and phage dynamics. Throughout a 10-day period we monitored daily the rectal temperature and the diarrheal score of piglets. Subsequently we evaluated phage and bacterial counts in fecal samples to determine phage therapy effect on gut microbiota dynamics and piglet health. The PHAGE+ETEC group showed 19.2% lower cumulative diarrhea burden (p = 0.044) and 61.9% higher average daily gain (p = 0.065). Rectal temperature correlated significantly with diarrhea severity (per-piglet Spearman's ρ = 0.727, p = 0.027). Alpha diversity did not differ between treatment groups across timepoints, suggesting that phage administration did not cause major shifts in microbial diversity. Metagenomic analyses showed significant reduction of E. coli abundance in PHAGE+ETEC group compared to PHAGE groups (p = 0.009). Consistent with these observations, plaque assay results confirmed active phage-bacteria interactions: no plaque formation was detected in the feces of the ETEC-only group, whereas the PHAGE+ETEC group showed phage replication, reaching 10[6] PFU/ml. This pilot study highlights the potential of phage therapy as an alternative to antibiotics for ETEC infections in piglets. Additional research with larger pig population and longer duration is required to confirm these findings and develop optimal phage application methods for swine production.}, }
@article {pmid42057164, year = {2026}, author = {Cabello, AM and Salles, S and Domínguez-Huerta, G and Capo, E and Camarena-Gómez, MT and García-Gómez, C and Sánchez, A and Mangot, JF and Cerezo, I and Bautista, R and Pérez, P and García, R and Ruiz, JM and Mercado, JM and Ferrera, I}, title = {Environmental disturbances and cyanobacterial traits shape prokaryotic dynamics in a eutrophic Mediterranean coastal lagoon.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00893-9}, pmid = {42057164}, issn = {2524-6372}, abstract = {BACKGROUND: Coastal ecosystems face increasing threats from eutrophication, driven by excess nutrient inputs that lead to ecosystem-disruptive algal blooms (EDABs). The Mar Menor coastal lagoon, located in the south-eastern Iberian Peninsula, has experienced severe ecological disruption since 2015, beginning with a Synechococcus‑dominated cyanobacterial bloom and followed by major shifts in eukaryotic phytoplankton composition. However, the mechanisms that affect phytoplankton dynamics in this coastal environment remain unknown. Here, we investigate the spatiotemporal dynamics of prokaryotic communities in the lagoon after the initial Synechococcus bloom using three years of 16S rRNA gene sequencing data and evaluate how environmental factors shape these patterns. In addition, we examine the fine‑scale diversity and dynamics of Synechococcus variants through metagenomics (petB gene) and use genome‑resolved analyses to identify functional traits associated with their succession in the lagoon. Finally, to investigate the role of biotic interactions in regulating cyanobacterial growth, we examine the temporal dynamics of cyanophages.<br><br>RESULTS: Microbial communities in the waters of the Mar Menor responded rapidly and consistently to short&#x2011;term environmental fluctuations and showed a weak seasonal signal in alpha and beta diversity. Prokaryotic assemblages associated with two deoxygenation events following extreme weather conditions (intense rainfall in autumn 2019 and unusually high temperatures in summer 2021) illustrated how episodic disturbances can drive substantial shifts in microbial composition; notably, Synechococcus became particularly prevalent after the intense rainfall event. Fine&#x2011;scale analyses of 16S rRNA and petB gene variants revealed that a restricted set of Synechococcus lineages dominated throughout the study period. Comparative genomic analyses of these cyanobacterial populations highlighted distinct functional repertoires, including genes involved in osmoprotectant biosynthesis, diverse toxin-antitoxin systems, herbicide resistance, and multiple viral defense mechanisms, present only in specific variants. Finally, temporal analyses of viral assemblages indicated that cyanophages played a key role in modulating Synechococcus population dynamics.<br><br>CONCLUSIONS: The temporal dynamics of prokaryotic communities in the Mar Menor indicate that the lagoon remains in an altered, non&#x2011;equilibrium state, likely sustained by recurrent anthropogenic and climatic pressures. The contrasting microbial responses observed during two different deoxygenation events underscore the ecosystem's complexity. This study highlights the importance of incorporating microbial community analyses into long&#x2011;term monitoring of threatened coastal systems, and the power of comparative genomics for identifying functional traits that enable cyanobacterial proliferation in disturbed ecosystems.}, }
@article {pmid42057198, year = {2026}, author = {Dikareva, E and van Best, N and Bervoets, L and West, CE and Rossel, C and Driessen, C and Mommers, M and Penders, J}, title = {The impact of the COVID-19 pandemic and associated lifestyle changes on early-life microbiome development.}, journal = {Genome medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13073-026-01660-8}, pmid = {42057198}, issn = {1756-994X}, support = {09150162410022/ZONMW_/ZonMw/Netherlands ; 2021-01637//Vetenskapsr&#xe5;det/ ; 967569//V&#xe4;sterbotten L&#xe4;ns Landsting/ ; 529051010//The Netherlands Organization for Health Research and Development (ZonMw) through the European Union Joint Programming Initiative-A Healthy Diet for a Healthy Life/ ; }, abstract = {BACKGROUND: The COVID-19 pandemic triggered rapid, population-wide behavioral and environmental changes, offering a unique natural experiment to study how early-life microbiome development responds to abrupt shifts in social and hygiene-related exposures.<br><br>METHODS: Using longitudinal data from 139 infants in the Dutch LucKi Gut study, we compared gut microbiome development in fecal samples collected before and during the pandemic. Whole metagenome sequencing of 808 stool samples was performed across nine time points in the first 14 months of life. An exposure index (EI) capturing variation in household-level pandemic-related behaviors was constructed for the 36 infants with samples collected during the COVID-pandemic to quantify variations in social distancing, lifestyle and hygiene measures.<br><br>RESULTS: Microbial richness and diversity increased with age, following established developmental trajectories. However, from 6 months onward, the COVID-19 pandemic independently shaped gut microbial composition, explaining up to 2.7% of variation by 11 months of age (Q-value&#x2009;=&#x2009;0.006). Forty-four species were differentially abundant in pandemic-era samples, including depletion of Gordonibacter pamelaeae and several Actinomyces species. Notably, greater environmental exposure (higher EI scores) was associated with lower abundance of G. pamelaeae, a microbe implicated in bile acid and immunomodulatory metabolism.<br><br>CONCLUSIONS: This is the first longitudinal whole-genome sequencing study to demonstrate that pandemic-related behavioral changes measurably altered infant gut microbiota maturation. These findings highlight the sensitivity of microbiome development to societal-level environmental disruptions and suggest that early-life microbial exposures, modulated by hygiene and social behavior, may carry long-term implications for child health.}, }
@article {pmid42057295, year = {2026}, author = {Klaps, J and Lemey, P and Bletsa, M and ,  and Kafetzopoulou, LE}, title = {nf-core/viralmetagenome: A Novel Pipeline for Untargeted Viral Genome Reconstruction.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag187}, pmid = {42057295}, issn = {1367-4811}, abstract = {MOTIVATION: Reconstructing eukaryotic viral genomes from metagenomic data is challenging due to their extensive diversity and potential genome segmentation. Current approaches often rely on labor-intensive manual curation for reference selection and scaffolding, limiting scalability for large studies or rapid outbreak response. We address the critical need for an automated, scalable pipeline for efficient viral metagenomic analysis without manual intervention.<br><br>RESULTS: We present nf-core/viralmetagenome, a comprehensive Nextflow pipeline for the untargeted reconstruction and variant analysis of eukaryotic DNA and RNA viruses from short-read metagenomic or hybridisation capture enriched samples. The pipeline automates the entire process from read preprocessing to consensus generation, integrating multiple de novo assemblers, automated reference selection, and iterative consensus refinement. It features robust quality control, extensive documentation, and seamless portability via Docker and Singularity. We validated the pipeline on diverse simulated and real datasets, demonstrating its ability to recover high-quality genomes from complex metagenomic samples and resolve co-infections, making it a powerful tool for viral surveillance.<br><br>AVAILABILITY: nf-core/viralmetagenome is freely available at https://github.com/nf-core/viralmetagenome with comprehensive documentation at https://nf-co.re/viralmetagenome. Archival code repository snapshots are published at zenodo with doi: https://doi.org/10.5281/zenodo.17524074.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at https://github.com/Joon-Klaps/nf-core-viralmetagenome-manuscript online.}, }
@article {pmid42057740, year = {2026}, author = {Wang, JL and Huang, SY and Chen, ZT and Zhou, Y and Kuzyakov, Y and Chen, JH and Ma, XM}, title = {Functional Resistance of Microbiome to Differently Charged Nanoplastics in Rhizosphere Hotspots Soil.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c17636}, pmid = {42057740}, issn = {1520-5118}, abstract = {Nanoplastics (NPs) pose greater soil ecological risks than microplastics due to their surface charge-dependent uptake, transport, and accumulation in plants. However, how differently charged NPs affect maize growth and microbial functional resistance in rhizosphere hotspots remains unclear. Here, we investigated the effect of positively (PS-NH2) and negatively (PS-SO3H) charged NPs on maize growth, enzyme activities and gene abundance, microbial resistance, and functional properties in acidic soil using soil zymography, 16S rRNA sequencing, and metagenomics. PS-NH2 showed stronger inhibitory effects on maize growth than PS-SO3H, mainly through reducing microbial diversity and weakening N and P cycling-related enzyme activities and resistance. Conversely, PS-SO3H maintained higher microbial resistance. Functional hotspots microbial species (particularly in Actinobacteria) alleviated NPs toxicity by accelerating N and P cycling to meet the demand for nutrients limiting maize growth. This study provides a mechanistic basis for assessing soil NPs risk with implications for agricultural sustainability and food safety.}, }
@article {pmid42057783, year = {2026}, author = {Harshvardhan,  and Kaur, M and Grover, V and Pinnaka, AK and Korpole, S}, title = {Metagenomic insights into oral microbiota dynamics in diabetic and non-diabetic periodontal disease: a pilot study.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1799124}, pmid = {42057783}, issn = {1664-302X}, abstract = {INTRODUCTION: Subgingival microbial dysbiosis is one of the key reasons behind periodontitis, a chronic inflammatory disease, which is further get severe in the presence of type 2 diabetes mellitus (T2D). Although changes in taxonomic composition have been well established, the functional interactions and metagenomic profiles across different stages of the disease remain unclear.<br><br>METHODS: A shotgun metagenomic analysis was performed on subgingival dental plaque samples from 16 individuals, divided into healthy, staged periodontitis, and diabetic periodontitis groups. Group-wise DNA pooling was done for maximum DNA yield. Further, Alpha/beta diversity, taxonomic profiling, pathogen-probiotic ratios, and metabolic pathway abundance were analyzed and studied.<br><br>RESULTS: The healthy group showed the highest alpha diversity, especially in the core biosynthetic pathways. On the other hand, the earlier stages of periodontitis showed a unique community structure and the lowest alpha diversity. Early periodontitis also showed the highest abundance of commensals like Actinomyces and Bifidobacterium, along with increased UMP/guanosine and L-arginine biosynthesis pathways. The advanced periodontitis group had an increase of red complex bacteria and loss of probiotics. An increase of the degradative pathways, such as L-histidine degradation, had also been observed in this stage. The diabetic periodontitis group had a distinct microbial profile that included Capnocytophaga and a considerable metabolic shift toward lipid metabolism and glycolysis, with higher overall microbial diversity than the other periodontitis groups.<br><br>CONCLUSION: The results clearly show that the subgingival microbial and functional patterns are different across the stages of the disease and metabolic status, which can be developed for underscoring the importance of targeting early metabolic shifts to prevent dysbiosis.}, }
@article {pmid42057917, year = {2026}, author = {Szentiványi, T and Bruszniczky, B and Biró, Z and Katona, K and Klein, &#xc1; and Bende, A and Bánáti, L and Vass, G and Lehotzky, P and Kovács, D and Földvári, G and Csivincsik, &#xc1; and Nagy, G and Nagy, RR and Miklós, M and Szabadi, KL and Szabó, &#xc9;S and Garamszegi, LZ}, title = {Unwelcome guests: Nematodes of zoonotic and animal health importance in native and invasive carnivores of Hungary.}, journal = {Current research in parasitology &amp; vector-borne diseases}, volume = {9}, number = {}, pages = {100380}, pmid = {42057917}, issn = {2667-114X}, abstract = {Wild carnivores are important reservoirs of parasitic nematodes, several of which have veterinary and zoonotic significance. In Europe, the role of invasive carnivores in parasite circulation remains poorly understood. Here, we screened 371 individuals of six wild carnivore species from Hungary (red foxes, badgers, golden jackals, raccoons, raccoon dogs, and beech martens), using molecular markers (cox1 and S12), and detected five nematode parasites: Dirofilaria immitis, Crenosoma vulpis, Angiostrongylus vasorum, Thelazia callipaeda, and Spirocerca lupi. The highest prevalence was observed in badgers (32.0%) and red foxes (15.7%), while invasive raccoons also showed a relatively high infection rate (13.2%). Dirofilaria immitis was one of the most common nematode species detected: it was found in four host species, including the first confirmed cases in Hungarian badgers and invasive raccoons, extending the known host range of this parasite in central Europe. Importantly, T. callipaeda was recorded in red foxes and an invasive raccoon dog, representing the first invasive host records of this zoonotic eyeworm in Hungary. Crenosoma vulpis was identified in raccoons, suggesting invasive species may act as incidental carriers of endemic parasites. Both C. vulpis and D. immitis showed low host specificity. These findings indicate that invasive carnivores, particularly raccoons, may harbour unexpectedly high prevalence and play a greater role in local parasite networks than previously assumed. Our results highlight the epidemiological significance of both native and invasive carnivores in sustaining nematodes of zoonotic and veterinary importance in central Europe, stressing the need for continued surveillance in wild carnivores.}, }
@article {pmid42058175, year = {2026}, author = {Zhong, H and Sun, C and Lu, Y and Cai, X and Cao, M and Wang, L and Feng, C and Song, M and Sun, W and Shi, M and Tao, Y and Zhou, J and Chen, C and Lu, X and Li, Y and Ni, Y and Cai, Y and Zhong, J and Li, Y and Wu, W and Shi, Y and Wang, M and Su, X}, title = {The clinical value of metagenomic next generation sequencing in the diagnosis of non-neutropenic invasive pulmonary aspergillosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1731736}, pmid = {42058175}, issn = {2235-2988}, mesh = {Humans ; Male ; *Invasive Pulmonary Aspergillosis/diagnosis/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Sputum/microbiology ; Mannans/analysis/blood ; Aged ; Sensitivity and Specificity ; Adult ; *Aspergillus/genetics/isolation &amp; purification/classification ; Galactose/analogs &amp; derivatives ; }, abstract = {BACKGROUND: This study aims to explore the performance of metagenomic next generation sequencing (mNGS) in the diagnosis of non-neutropenic invasive pulmonary aspergillosis (IPA) and its clinical application value.<br><br>METHODS: This multi-center study enrolled 293 suspected IPA patients who conducted mNGS from October 2020 to February 2024. These cases were classified into IPA group and non-IPA group according to IPA diagnostic criteria. We analyzed the diagnostic value of mNGS by comparing with sputum culture, BALF culture, serum and BALF GM test.<br><br>RESULTS: A total of 118 IPA patients (4 proven/113 probable/1 possible diagnosis) were included in our study. The most common Aspergillus species was A. fumigatus (63.4%), followed by A. flavus (23.2%), A. oryzae (7.1%), A. niger (3.6%) and A. terreus (2.7%). The sensitivity of bronchoalveolar lavage fluid (BALF) mNGS was significantly higher than BALF culture (81.9% vs. 27.0%, p<0.001) and BALF galactomannan (GM) (81.9% vs. 55.8% (GM&#x2265;1.0 cutoff value), p<0.001). The specificity of BALF mNGS was 92.2%, which was similar with BALF culture (98.5%) and BALF GM (94.7%). The combination of BALF mNGS and GM could increase the sensitivity to 88.7%, and had great negative predictive value (NPV, 92.3%). The sensitivity of blood mNGS was significantly higher than serum GM (58.8% vs. 16.7%, p<0.001). And the sensitivity of sputum mNGS was 66.7%, which was significantly higher than sputum culture (30.0%, p=0.025).<br><br>CONCLUSION: mNGS demonstrated significant diagnostic value for IPA, exhibiting significantly higher sensitivity compared to current conventional microbiological tests while maintaining equivalent specificity. The combination of BALF mNGS with GM performed great sensitivity and negative predictive value. BALF specimens seemed to be superior to blood and sputum samples. However, for patients unable to undergo bronchoscopy, sputum and blood mNGS were still superior to other methods.}, }
@article {pmid42058649, year = {2026}, author = {Kwarteng, A and Amedorme, D and Addy, HPK and Amewu, EKA and Osei-Poku, P and Larbi, A}, title = {Brukina in Focus: A Narrative Review on Metagenomic Approaches to Fermentation and Food Safety.}, journal = {International journal of microbiology}, volume = {2026}, number = {}, pages = {6677609}, pmid = {42058649}, issn = {1687-918X}, abstract = {Brukina, a traditional fermented beverage smoothie made from milk and millet, is popular in Ghana and other West African countries due to its tasty flavor, high nutritional content, and affordability. Despite its widespread consumption, the nature of its production through artisanal fermentation processes presents concerns regarding microbial consistency, nutritional optimization, and food safety. This literature review explores the potential of metagenomic approaches to uncover microbial diversity, functional capacity, and safety profiles of Brukina. By integrating insights from amplicon-targeted and shotgun whole-genome sequencing studies on fermented foods, we highlight how next-generation sequencing technologies can characterize lactic acid bacteria, yeast, and other microorganisms that drive fermentation. Additionally, we discuss how metagenomics can identify functional genes influencing carbohydrate metabolism, flavor and aroma generation, and production of antimicrobial resistance compounds. Thus, metagenomics provides a powerful framework for assessing public health risks and nutritional benefits. Bioinformatic tools have also been highlighted, and their relevant application in analyzing sequenced data to achieve taxonomic classification, identification of biochemical pathways, and functional profiling of microbial ecology of fermented foods. This review outlines key research gaps and recommends future directions, including starter culture development, standardization of Brukina production, multi-omics integration in metagenomics, and microbiome-informed food safety standards. Metagenomic profiling of Brukina holds promise for improving product quality, consumer safety, and scientific understanding of traditional fermented foods. By tackling the challenges raised, metagenomic techniques can be extremely helpful in maximizing Brukina fermentation, guaranteeing food safety, and maintaining the customs that give this product its distinctive character.}, }
@article {pmid42058681, year = {2026}, author = {Budai, M and Rák, G and Wenner, B and Móré, A and Bancsik, B and Nagy, B and Kovács, G and Szabolcs, M and Ladnyik, Z and Molnár, C and Guller, ZE and Lengyel, A and Vadász, C and Mizsei, E}, title = {The Influence of Plant Species Composition on an Endangered Grassland Specialist Reptile, the Hungarian Meadow Viper.}, journal = {Ecology and evolution}, volume = {16}, number = {}, pages = {e73579}, pmid = {42058681}, issn = {2045-7758}, abstract = {The Hungarian meadow viper (Vipera ursinii rakosiensis) is one of the most threatened vertebrates in Hungary, whose populations are not growing significantly despite enormous conservation efforts. Previous studies suggested an influence of vertical vegetation structure on habitat use, while the role of horizontal vegetation structure is still poorly understood. In the present study, we used vegetation survey data to investigate the effects of variables related to the horizontal structure and functional composition of vegetation on the occupancy and density of the Hungarian meadow viper. During a spring survey period, we collected viper occurrence data in 59 sampling quadrats alongside plant community samples, then used single-season occupancy models and N-mixture models for analysis. After model selection, the best models included the moisture-related vegetation gradient, species richness, graminoid-forb ratio, and height of plants as explanatory variables for both occupancy and density. Wetter meadows with fewer plant species, a higher graminoid/forb ratio, and habitats with characteristically lower-growing plant species were more probable to be used by the vipers. Our results suggest that the horizontal structure of the vegetation influences the habitat use of vipers and also draw attention to the threats posed by more frequent droughts and heatwaves.}, }
@article {pmid42059272, year = {2026}, author = {Damian, R and Katarzyna, J and Sebastian, W and Piotr, J and Joanna, G and Małgorzata, C and Monika, H and Edyta, K}, title = {Native Aquatic Plastispheres in a River-Wastewater Catchment: Carbapenem-Resistant Bacteria Isolation and Microscopy-Based Structural Analysis.}, journal = {Environmental microbiology}, volume = {28}, number = {5}, pages = {e70312}, doi = {10.1111/1462-2920.70312}, pmid = {42059272}, issn = {1462-2920}, support = {2021/43/B/ST10/01076//Narodowe Centrum Nauki/ ; }, mesh = {*Rivers/microbiology ; *Biofilms/growth &amp; development ; *Wastewater/microbiology ; *Carbapenems/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/isolation &amp; purification/drug effects/genetics/classification ; Drug Resistance, Bacterial ; Plastics ; *Carbapenem-Resistant Enterobacteriaceae/isolation &amp; purification ; }, abstract = {Plastispheres, microbial biofilms formed on plastic surfaces, are increasingly recognised as ecological niches capable of transporting pollutants and antibiotic-resistant microorganisms. However, mechanistic insights into antimicrobial resistance (AMR) dynamics in natural plastispheres remain limited, particularly for priority pathogens such as carbapenem-resistant Enterobacterales (CRE). Here, we evaluated plastispheres as environmental reservoirs and vectors of carbapenem-resistant bacteria, comparing wastewater (secondary settling tanks, representing the final stage before environmental discharge) and riverine environments. Using a combined SEM-CFM approach, we resolved plastic surface topography and the spatial organisation of biofilm-associated bacteria. Although CRE were not detected, carbapenem-resistant bacteria constituted a stable fraction of heterotrophic communities in both environments and were primarily associated with intrinsic resistance mechanisms. Carbapenem-resistant isolates included Aeromonas spp. (blaCphA), Stenotrophomonas maltophilia (blaL1), and Pseudomonas putida (efflux-based resistance). Microscopy revealed dense bacterial clusters on plastic surfaces, suggesting microenvironments that may facilitate cell-cell interactions, including horizontal gene transfer. These findings highlight plastispheres not only as vectors of AMR but also as potential evolutionary hotspots shaping resistance persistence and dissemination in aquatic systems. Future integrating metagenomic and genomic data on resistance gene mobility with spatially resolved microbial community structure will provide critical insights into the mechanisms and risks of AMR dissemination in plastisphere environments.}, }
@article {pmid42059388, year = {2026}, author = {Mejia, ME and Bowman, S and Lee, J and El-Halwagi, A and Ferguson, K and Maliekel, M and Zhou, Y and Serchejian, C and Robertson, CM and Ballard, MB and Lu, LB and Khan, S and Oladunjoye, OO and Huang, S and Agarwal, SK and Patras, KA}, title = {A cross-sectional analysis of the vaginal microenvironment in rheumatoid arthritis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0360225}, doi = {10.1128/spectrum.03602-25}, pmid = {42059388}, issn = {2165-0497}, abstract = {The human microbiota is implicated in the development and progression of rheumatoid arthritis (RA). Given the increased RA burden in women and well-known correlations between the vaginal microbiota and local inflammation, we seek to understand the vaginal microenvironment in the context of RA pathology. Self-collected vaginal swabs and questionnaires on dietary, menstrual, and health information were obtained from 36 RA and 50 demographically-matched control women, 18-63 years of age. Medication regimen, along with disease activity and severity, was captured for the RA cohort. Vaginal swabs were subjected to long-read 16S rRNA gene sequencing, multiplex cytokine analyses, and quantification of rheumatoid factor, C-reactive protein, and anti-citrullinated protein antibodies (ACPAs). Vaginal microbial richness and Peptoniphilus and Prevotella, among other rare taxa, were elevated in RA versus control samples. Vaginal interleukin (IL)-18 and epidermeal growth factor (EGF) levels were increased in the RA group; IL-18 correlated with multiple microbial features, whereas EGF levels were not associated with bacterial composition or other host factors. When faceted by diet and menopausal status, several immune markers were increased in the RA vaginal environment. Vaginal ACPAs were higher in the RA group and positively correlated with Streptococcus and multiple vaginal inflammatory cytokines. We describe vaginal microbial and immunological differences in women with RA, particularly when accounting for diet and menopausal status, and disease activity and severity. This work opens a new avenue in the multidisciplinary approach to RA patient care.IMPORTANCERheumatoid arthritis (RA) is a debilitating autoimmune disease that disproportionately impacts women. Although it is widely recognized that microbial factors can trigger or aggravate RA symptoms and alter disease progression, it is unknown whether RA impacts the microbiota and immune responses within the vaginal tract. In this study, we compare the vaginal microbial communities and immune (cytokine) profiles in women with RA and healthy controls. Within RA patients, we also evaluate how these factors relate to clinical RA symptoms, RA biomarkers, and RA-related medications. Overall, we found that RA was associated with increased microbial diversity and multiple inflammatory markers, some of which were also associated with RA biomarkers and disease activity. These findings suggest that the vaginal tract may be an additional tissue impacted by RA disease, and further research is needed to understand mechanisms and potential for therapeutic intervention.}, }
@article {pmid42059394, year = {2026}, author = {Murphy, MM and Pinnell, LJ and Doster, E and Wolfe, CA and Baker, LA and Machado, VS and Morley, PS}, title = {Early-life development of the microbiome and resistome in antibiotic-naïve dairy calves.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0251025}, doi = {10.1128/spectrum.02510-25}, pmid = {42059394}, issn = {2165-0497}, abstract = {This study aimed to characterize early-life changes in the fecal microbiome and resistome of calves. Fecal samples were collected from 49 Holstein heifers born and raised at a large organic dairy in Texas without antimicrobial drug exposures. Samples were collected from five age groups: early pre-weaning at 2-3 days old (Pre 1), late pre-weaning at 5 weeks old (Pre 2), prior to weaning at 12-13 weeks old (Pre 3), post-weaning in group hutches at 12-13 weeks old (Post 1), and later post-weaning at 13-14 weeks old (Post 2). Fecal samples were analyzed using 16S rRNA gene sequencing to characterize microbial communities and target-enriched shotgun sequencing to characterize antimicrobial resistance genes in the resistome. Richness of microbial communities increased as calves aged through the Pre 1, 2, and 3 samplings, before plateauing in the Post 1 and 2 groups. Diversity also increased in the Pre 1 and 2 groups, remaining similar thereafter. In contrast, resistome richness and diversity decreased during early life and then stabilized at around 5 weeks of age (Pre 2). Changes in microbial community structures were dramatic during the first 12 weeks, largely due to a significant decrease in the relative abundance (RA) of Pseudomonadota (Proteobacteria) and an increase in the RA of Bacillota (Firmicutes) and Bacteroidota. The resistome changed with an increased RA of tetracycline resistance genes, while drug and biocide resistance genes decreased. The apparent stabilization of microbial community features after 12 weeks of age may reflect a period when gut microbiome structure begins to establish greater stability.IMPORTANCEEarly-life development of the gut microbiome can have lasting effects on animal health, immune maturation, and productivity. Using 16S rRNA gene sequencing together with target-enriched metagenomic sequencing, we provide an in-depth characterization of the fecal microbiome and resistome of antibiotic-naïve dairy calves during early life. We demonstrate that microbiome diversity increased with age while resistome diversity decreased, revealing distinct temporal trajectories and suggesting ecological succession as a potential driver of resistance gene dynamics independent of antimicrobial drug exposure. Major resistome features appeared to stabilize earlier than overall microbiome structure, highlighting critical windows in early development when resistance gene composition may be most dynamic. These findings establish an important baseline for interpreting microbiome-resistome interactions and for evaluating how management practices and antimicrobial exposures may influence calf health and antimicrobial resistance ecology in dairy production systems.}, }
@article {pmid42059571, year = {2026}, author = {Čepić, A and Rausch, P and Geese, T and Dempfle, A and Grassl, GA and Baines, JF}, title = {Host genetics shapes the recovery of the gut microbiome after antibiotic treatment: the role of the blood group related B4galnt2 gene.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0164025}, doi = {10.1128/msystems.01640-25}, pmid = {42059571}, issn = {2379-5077}, abstract = {UNLABELLED: The intestinal microbiota is integral to host health, metabolism, and colonization resistance. Antibiotics can disrupt microbial homeostasis, leading to dysbiosis and altered colonization resistance. While antibiotic-induced microbiota disruption is well-documented, less is known about how host genetics shapes post-antibiotic recovery. Here, we investigate the impact of B4galnt2, a blood-group-related glycosyltransferase gene, on microbiota recovery following antibiotic treatment. Using a longitudinal, multi-omic approach-including 16S rRNA gene sequencing, metagenomics, and metatranscriptomics-we compare the microbiota dynamics of B4galnt2[+/-] and B4galnt2[-/-] mice after treatment with streptomycin, kanamycin, and vancomycin. Our findings reveal that B4galnt2[-/-] mice exhibit faster recovery of microbial diversity and composition following streptomycin treatment compared to their B4galnt2[+/-] counterparts. This accelerated recovery is associated with higher relative abundance of taxa such as Blautia, Dorea, and other Lachnospiraceae, and increased expression of motility-related genes, and differential regulation of antibiotic resistance genes (ARGs), including the aminoglycoside nucleotidyltransferase genes aadA and aadE. Genotype-dependent differences in recovery were most pronounced following streptomycin and were not consistently observed with kanamycin or vancomycin, indicating an antibiotic-by-genotype interaction shaped by the B4galnt2-associated microbiota. These results underscore the role of host genetics in shaping microbiota response and recovery following antibiotic exposure. By demonstrating the interplay between glycosylation-mediated microbiota composition, antibiotic response, and microbial recovery, our study may provide insights into the potential for personalized approaches to mitigate dysbiosis-related health outcomes.<br><br>IMPORTANCE: Antibiotic treatments disrupt the gut microbiome, often leading to long-term alterations that potentially affect host health. While much is known about how antibiotics cause microbial dysbiosis, little is understood about the factors that could influence the speed of microbial community recovery, such as host genetic differences. Using a mouse model, this study reveals that genetic variation at the blood group-related B4galnt2 gene significantly alters recovery after streptomycin treatment. Mice lacking intestinal B4galnt2 expression recover faster, with distinct changes in microbial composition, activity, and antibiotic resistance gene expression. These findings highlight how a single host gene can shape microbiota dynamics following antibiotic-induced disruption. The work emphasizes the importance of considering host genetic factors when predicting microbiome responses to antibiotics and suggests potential for genotype-guided strategies to reduce the adverse effects of microbiome-targeted therapies.}, }
@article {pmid42059616, year = {2026}, author = {Moidu Jameela, R and Kedare, MM and Khan, R and Dhankad, N and Sinha, RK and Zade, A and Shah, S and Chatterjee, A}, title = {Whole genome sequence of Tsukamurella tyrosinosolvens extracted from metagenome of human pleural fluid enriched in Mycobacteria Growth Indicator Tube.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0151825}, doi = {10.1128/mra.01518-25}, pmid = {42059616}, issn = {2576-098X}, abstract = {Misdiagnosis of emerging pathogen Tsukamurella tyrosinosolvens is common due to phenotypic similarity with Mycobacterium tuberculosis (MTB). We report a high-quality, near-complete genome of T. tyrosinosolvens from pleural fluid enriched in Mycobacteria Growth Indicator Tube. The genome of this clinically successful strain can be studied to understand pathogenesis and diagnostic challenges.}, }
@article {pmid42059625, year = {2026}, author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Spatial ecology of the Capnocytophaga genus in the human oral cavity.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0362625}, doi = {10.1128/spectrum.03626-25}, pmid = {42059625}, issn = {2165-0497}, abstract = {UNLABELLED: The human oral microbiome, a complex ecosystem of niche-specific communities influenced by local ecological factors, plays a critical role in health and disease. Capnocytophaga species are prevalent in the human mouth, often abundant in dental plaque and linked to both commensalism and pathogenicity, motivating a detailed study of their ecological and functional diversity. This study employs metapangenomics to reveal Capnocytophaga strain-level distributions and functional adaptations across distinct sites in the human oral cavity. Pangenomic, phylogenetic, and average nucleotide identity analyses enabled classification of unnamed genomes and identified 13 groups, of which 8 include validly named species, and the remainder are named using Human Microbial Taxon (HMT) designations in the Human Oral Microbiome Database (HOMD; https://www.homd.org/). Mapping metagenomic reads to the pangenome revealed a strong preference of most Capnocytophaga genomes for dental plaque (both supra- and subgingival), yet identified strain-level variants of C. sputigena, C. gingivalis, C. granulosa, and C. leadbetteri detected more often on the tongue. Among dental plaque-abundant taxa, functional analyses uncovered two clades: one with cbb3-type cytochrome oxidase that is tied to enhanced denitrification and could help the organism adapt to hypoxic zones, and another with bd-type ubiquinol oxidase, more suited to aerobic metabolism. Carbohydrate and amino acid metabolism pathways also differed between these clades. These findings identify metabolic adaptations that may underlie sub-specialization within the plaque habitat and highlight the strain-level diversity of Capnocytophaga, including low-prevalence strains that are preferentially detected in sites outside the primary plaque habitat of this taxon.<br><br>IMPORTANCE: Understanding the ecological roles of Capnocytophaga in the oral microbiome is critical for deciphering its contributions to health and disease, including periodontal and systemic infections. This metapangenomics study reveals a pronounced specialization by Capnocytophaga to dental plaque (including supragingival, subgingival, and periodontal pockets) and identifies metabolic adaptations, such as distinct respiratory, carbohydrate, and amino acid pathways, that may drive niche-specific survival. These findings support the site-specialist hypothesis and enhance our understanding of oral microbial community structure, laying a foundation for future research into microbial interactions and targeted therapies for oral health.}, }
@article {pmid42059663, year = {2026}, author = {Liu, C and Mao, Z and Yu, F and Ni, J and Bao, J and Qu, W and Huang, M and Shen, Y and Zheng, S and Chen, Y}, title = {Integrative multi-omics analysis reveals microbiota alterations and clinical indicators predictive of pulmonary fibrosis progression following SARS-CoV-2 infection.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {2}, pages = {}, doi = {10.1093/bib/bbag173}, pmid = {42059663}, issn = {1477-4054}, support = {82300005//National Natural Science Foundation of China/ ; 82072377//National Natural Science Foundation of China/ ; 81971919//National Natural Science Foundation of China/ ; LR23H200002//Zhejiang Provincial Natural Science Foundation/ ; }, mesh = {Humans ; *COVID-19/complications/virology/microbiology ; Male ; *SARS-CoV-2 ; Female ; Middle Aged ; Disease Progression ; *Pulmonary Fibrosis/microbiology/etiology/virology/pathology ; *Microbiota ; Aged ; Gastrointestinal Microbiome ; Bronchoalveolar Lavage Fluid/microbiology ; Transcriptome ; Metagenomics ; Multiomics ; }, abstract = {Pulmonary fibrosis (PF) following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is a life-threatening complication. Despite growing concerns about PF after SARS-CoV-2 infection, early recognition remains challenging. Additionally, the role of changes in respiratory and intestinal microbiota in PF progression remains insufficiently understood. To address this gap, this study uses a multi-omics approach to analyze microbiota and clinical changes in PF patients following SARS-CoV-2 infection, developing a predictive model for PF progression with risk stratification to enable early interventions and improve outcomes. A total of 68 patients with confirmed SARS-CoV-2 infection were included in the study, divided into two subgroups: patients with PF (COVID-PF) and patients without PF (COVID-non PF). Metagenomic sequencing of bronchoalveolar lavage fluid (BALF) and fecal specimens was performed to profile respiratory and intestinal microbiota. Peripheral blood mononuclear cells (PBMCs) were collected for transcriptome sequencing. A random forest classifier was developed to predict PF risk based on integrated respiratory-intestinal microbiota profiles as well as clinical indicators. Our findings suggest that there are significant differences in the respiratory and intestinal microbiota between COVID-non PF and COVID-PF patients. Transcriptomic analysis of PBMCs revealed significant activation of immunomodulatory pathways associated with PF development. The machine learning model further allowed early PF risk stratification, demonstrating that changes in both microbiomes, along with clinical indicators, can predict the progression and prognosis of PF. Overall, these results offer new insights into disease and suggest options for early detection and personalized treatment strategies for PF in SARS-CoV-2-infected patients.}, }
@article {pmid42059780, year = {2026}, author = {Wolfe, BE}, title = {Metagenomes enriched with Virgibacillus are associated with a pink paste defect in an unpasteurized blue cheese.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0002726}, doi = {10.1128/mra.00027-26}, pmid = {42059780}, issn = {2576-098X}, abstract = {Shotgun metagenomes were used to identify microbes associated with a pink discoloration of an unpasteurized blue cheese made in the United States. Taxonomic assessments of individual reads and metagenome-assembled genomes revealed that the genus Virgibacillus was present in the pink paste, but not in unaffected paste.}, }
@article {pmid42059891, year = {2026}, author = {Pang, H and Peng, B and Yan, X and Wang, J and Lu, Y and Yuan, X and Zhang, Y and Zhang, L and Huang, J and Zhang, Y and Yang, R and Ma, X and Wang, X and Fan, C and Zhang, L and Song, W and Cheng, Y and Liang, S and Wang, Y and Zheng, W and Li, G}, title = {Pregnancy-induced hypertension are preceded by prenatal perturbations of the gut microbiome and metabolome.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00018-026-06221-1}, pmid = {42059891}, issn = {1420-9071}, support = {2024ZD0532100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; No. Lingjunrencai-02-02//High-level construction project of public health technical personnel in Beijing Municipal Health System/ ; }, }
@article {pmid42060200, year = {2024}, author = {Demirci, T}, title = {Highlighting the Microbial Community of Kuflu Cheese, an Artisanal Turkish Mold-Ripened Variety, by High-Throughput Sequencing.}, journal = {Food science of animal resources}, volume = {44}, number = {2}, pages = {390-407}, doi = {10.5851/kosfa.2023.e59}, pmid = {42060200}, issn = {2636-0780}, abstract = {Kuflu cheese, a popular variety of traditional Turkish mold-ripened cheeses, is characterized by its semi-hard texture and blue-green color. It is important to elucidate the microbiota of Kuflu cheese produced from raw milk to standardize and sustain its sensory properties. This study aimed to examine the bacteria, yeasts, and filamentous mold communities in Kuflu cheese using high-throughput amplicon sequencing based on 16S and ITS2 regions. Lactococcus, Streptococcus, and Staphylococcus were the most dominant bacterial genera while Bifidobacterium genus was found to be remarkably high in some Kuflu cheese samples. Penicillium genus dominated the filamentous mold biota while the yeasts with the highest relative abundances were detected as Debaryomyces, Pichia, and Candida. The genera Virgibacillus and Paraliobacillus, which were not previously reported for mold-ripened cheeses, were detected at high relative abundances in some Kuflu cheese samples. None of the genera that include important food pathogens like Salmonella, Campylobacter, Listeria were detected in the samples. This is the first experiment in which the microbiota of Kuflu cheeses were evaluated with a metagenomic approach. This study provided an opportunity to evaluate Kuflu cheese, which was previously examined for fungal composition, in terms of both pathogenic and beneficial bacteria.}, }
@article {pmid42060748, year = {2026}, author = {Xie, F and Jiang, C and Li, Z and Feng, J and Yan, X and Hu, C and He, J and Chai, X and Huang, Z and Xu, Q and Wang, Y and Xiao, Y and Chen, K and Qin, W and Xiao, Y and Zhang, J and Wang, G and Jin, W and Guo, K and Lin, L and Liu, Y and Gao, X and Zheng, L and Shu, X and Wang, R and Wang, M and Si, H and Du, R and Zhu, W and Guan, LL and Wang, W and Qiu, Q and Mao, S and Xiong, J and Miao, W}, title = {Rumen ciliates modulate methane emissions in ruminants.}, journal = {Science (New York, N.Y.)}, volume = {392}, number = {6797}, pages = {eadv4244}, doi = {10.1126/science.adv4244}, pmid = {42060748}, issn = {1095-9203}, mesh = {Animals ; *Methane/biosynthesis/metabolism ; *Rumen/parasitology/metabolism ; *Ciliophora/genetics/classification/metabolism/ultrastructure/enzymology/physiology ; Hydrogen/metabolism ; Cattle/parasitology ; Hydrogenase/metabolism/genetics ; Oxygen/metabolism ; }, abstract = {Rumen ciliates are major contributors to enteric methane emissions from ruminant animals, yet the underlying mechanisms remain poorly understood. We present a catalog of 450 rumen ciliate genomes, with 87% newly generated. Using this resource, we quantified methane emissions from 100 cows and analyzed 1877 rumen metagenomic and metatranscriptomic datasets, which revealed correlations among ciliate abundance, methanogen abundance, and methane emissions. We further demonstrated that taxon-specific effects of rumen ciliates on methane production arise from a single-membrane, hydrogen-producing organelle called the hydrogenobody (HB), which is distinct from canonical hydrogenosomes in other protists. HBs are positioned near ciliary basal bodies and harbor specific hydrogenases and oxygen reductases. We found that Vestibuliferida ciliates, which have more abundant HBs than do Entodiniomorphida, exhibit enhanced hydrogen production and oxygen-scavenging capacity, thereby strongly promoting methanogenesis.}, }
@article {pmid42060822, year = {2026}, author = {Poretsky, RS and Dhiman, VK and Hendricks, DL and Lin, CY and Sanchez Gonzalez, D and Greenwald, S and Owens, SM and Williams, CH and Leslie, MT and Bemis, K and Frias, M and Kaufman, JT and O'Connor, DH and Johnson, MC}, title = {Detection of a Single Measles Infection Using Untargeted Ultra-Deep Metagenomic Sequencing of Wastewater in Cook County, Illinois.}, journal = {NEJM evidence}, volume = {}, number = {}, pages = {EVIDpha2600079}, doi = {10.1056/EVIDpha2600079}, pmid = {42060822}, issn = {2766-5526}, abstract = {AbstractMeasles is a contagious, vaccine-preventable viral disease that can be shed into wastewater by infected individuals. In September 2025, as part of an ongoing, nontargeted, ultra-deep metagenomic sequencing effort of wastewater in Cook County, Illinois, we detected measles reads from a facility serving more than 1 million people. Out of more than 900 million reads sequenced from wastewater collected on September 14, 2025, 43 matched measles virus genotype B3. Subsequent genomic analysis linked these reads to a confirmed measles infection that was present in the community on that day, demonstrating that untargeted metagenomics appeared to detect a single measles infection in a large municipal wastewater stream.}, }
@article {pmid42060994, year = {2026}, author = {Huang, D and Sun, X and Lin, W and Lan, X and Tan, Z and Ren, Y and Huang, Y and Cao, Y and Sun, W}, title = {Hydrogen oxidation coupled to dissimilatory arsenate reduction: A potentially widespread pathway associated with arsenic mobility in anoxic sediments.}, journal = {Water research}, volume = {301}, number = {}, pages = {125984}, doi = {10.1016/j.watres.2026.125984}, pmid = {42060994}, issn = {1879-2448}, abstract = {In aquatic environments, the arsenic (As) mobilization from anoxic sediments is an important process affecting water quality and associated health risks, as sediment-bound As can serve as a persistent secondary source to overlying waters and groundwater systems. Dissimilatory arsenate reduction (DAsR) is a key microbial process releasing dissolved As(III), yet the role of inorganic electron donors in this pathway remains poorly constrained. Although hydrogen (H2) is thermodynamically favorable for arsenate respiration, its role in arsenate reduction in natural sediments remains insufficiently resolved. In this study, hydrogen oxidation coupled to arsenate reduction (HOAsR) was investigated using sediments from an As-contaminated, mining-impacted river system. Microcosm incubations showed that H2 amendment stimulated As(V) reduction under anoxic conditions. DNA-stable isotope probing combined with metagenomics identified Sulfuritalea, Dechloromonas, and a Moorellia-related lineage as putative HOAsR-associated populations. Corresponding metagenome-assembled genomes encoded both H2 uptake [NiFe]-hydrogenases and the dissimilatory arsenate reductase gene (arrA). Comparative genome analysis further revealed that ∼75% of arrA-containing genomes harbor H2 uptake [NiFe]-hydrogenases, suggesting that H2 oxidation represents a phylogenetically widespread metabolic trait among DAsR bacteria. Analysis of public riverine metagenomes further indicated that HOAsR-associated genetic configurations are broadly distributed across sediment microbial communities. Together, these results indicated that HOAsR is a biologically plausible and geographically widespread potential pathway contributing to arsenic mobilization in anoxic sediments.}, }
@article {pmid42061080, year = {2026}, author = {Chen, C and Hao, H and Hao, R and Yu, N and Li, X}, title = {Microbial driving mechanisms of sludge reduction in modular wastewater treatment systems under surplus aeration regulation.}, journal = {Journal of environmental management}, volume = {406}, number = {}, pages = {129816}, doi = {10.1016/j.jenvman.2026.129816}, pmid = {42061080}, issn = {1095-8630}, abstract = {The treatment and disposal of residual sludge pose a critical bottleneck to the sustainable development of wastewater treatment plants (WWTPs). Modular wastewater treatment systems have garnered significant interest due to their high efficiency and operational flexibility, making them well-suited for small-scale community applications. This study aims to investigate the microbial driving mechanisms underlying sludge reduction in such field-based systems under surplus aeration regulation. By comparing treatment performance, microbial community structure, and metabolic functions between the Surplus Aeration (SA) group and the Conventional (Conv.) group-coupling 16S rRNA high-throughput sequencing and metagenomic analysis -the microbiological basis of sludge reduction was systematically elucidated. Results demonstrated that the SA group achieved a 63.7% reduction in residual sludge while maintaining compliant effluent quality (GB 18918-2002), with COD and NH4[+]-N removal rates both reaching more than 85%. 16S rRNA profiles indicated higher alpha diversity in the SA group and clear community separation from the Conv. group (PERMANOVA, p < 0.001). The SA group was enriched in taxa with documented extracellular polymeric substance (EPS) degradation potential, including Saccharimonadales, Saprospiraceae, and Caldilineaceae, whereas the Conv. group showed relatively higher abundance of taxa often associated with proliferation and EPS production (e.g., OLB17, Acinetobacter). Metagenomic functional annotation suggested higher representation of genes and pathways related to carbohydrate processing and energy metabolism in the SA group. As these omics results primarily reflect functional potential rather than confirmed in situ activity, we present a conceptual mechanism in which surplus aeration improves DO distribution and substrate utilization in the field system, thereby favoring EPS breakdown and energy-use efficiency-consistent with the observed reduction in sludge yield.}, }
@article {pmid41857781, year = {2026}, author = {Alexander, JE and Appleton, C and Beatty, SSK and Brown, DC and Carvell-Miller, L and McKee, TS and Morrison, J and Patterson-Kane, JC and Reynolds, R and Wadulack, S and , }, title = {Cohort profile of the first 2,000 canine enrolees in the Mars Petcare Biobank: demographic, hematologic and serum biochemistry results from March 2022 to December 2024.}, journal = {BMC veterinary research}, volume = {22}, number = {1}, pages = {}, pmid = {41857781}, issn = {1746-6148}, abstract = {BACKGROUND: The MARS PETCARE BIOBANK™ (MPB) is a study recruiting pets visiting Mars Veterinary Health hospitals in the USA over a ten-year period, with the aim of analysing longitudinal data from thousands of otherwise healthy dogs and cats at their first presentation to identify novel and actionable pet health insights . The present study summarises the baseline demographic, haematologic, and serum biochemistry data recorded for the first 2000 dogs enroled in the MPB study between March 2022 and December 2024 and considers how representative they are of the general population in the United States.<br><br>RESULTS: The median enrolment age was 3.0&#xa0;years (0.5&#x2013;10.0 yrs). The population was 52% male and 48% female with approximately 84% of the population having undergone neutering by their initial study visit. The median enrolment body weight was 20.0&#xa0;kg (2.5 &#x2013; 71.5&#xa0;kg) and the median body condition score was 5/9 (range 3&#x2013;7). One hundred and twenty eight breeds were represented and 47% of the population were described as mixed breed. The median values for all serum biochemistry and complete blood count parameters were within the applicable reference interval. For certain analytes including serum glucose, amylase, cholesterol, phosphorus, creatine phosphokinase, precision pancreatic lipase, platelet count, haematocrit, and haemoglobin more than 5% of dogs had results outside the reference intervals. On review only 0.25% of dogs were subsequently excluded from continuing the MPB study because the results were considered of clinical significance.<br><br>CONCLUSIONS: The MPB aims to enable research to deliver insights applicable to the general dog population accessing primary veterinary care in the USA, and recruits accordingly. These data suggest that the first 2,000 dogs recruited in the MPB are comparable in demographics to other studies of the US population. The number of blood test results falling outside of reference intervals (up to 17% depending on analyte), for dogs deemed by veterinarians to be healthy in the context of the clinical history and examination, raises questions around the definition of health and how reference intervals are used. Data gathered during the study is expected to provide valuable information to studies pertaining to genetic, metagenomic, metabolic, dietary, and environmental risk factors associated with early signals of transition to various common diseases.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12917-026-05419-6.}, }
@article {pmid41959053, year = {2026}, author = {Midani, FS and Lee, DH and Moon, Y and Seale, M and Horvath, TD and Ardis, AK and Cantú, J and Coles, E and Pizzini, JD and Zhu, D and Dooling, SW and Ahern, GJ and Ardis, CK and Beckford, A and Ruggiero, NM and Shin, J and Joos, R and Stanton, C and Ross, RP and Dai, DLY and Mandhane, PJ and Petersen, C and Turvey, SE and Kiely, ME and Murray, DM and Costa-Mattioli, M and Tolias, KF and Britton, RA and Danhof, HA}, title = {Infant gut microbiomes contribute to metabolic states that impact brain function.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41959053}, issn = {2692-8205}, abstract = {Alterations in the gut microbiome are associated with neurodevelopmental disorders, but causal mechanisms and therapeutic strategies remain undefined. Here, we demonstrate that human infant microbiomes isolated during the first six months of life drive behavioral impairments in mice and that microbiota-based interventions restore mice to normal behavior. Early-life microbiomes from twelve infants who later exhibited cognitive deficits at 2 years old (low-scoring) transferred adverse metabolic, brain, and behavioral phenotypes to mice, in contrast to microbiomes from twenty-three cognitively typical or high-scoring infants. Deficits in mice were rescued by fecal microbiota transplant from high-scoring infants or a rationally designed consortium that promoted amino acid levels. We confirmed lower fecal amino acid concentrations in low-scoring infants and replicated the association between early-life microbiome composition and cognitive outcomes in a second geographically independent infant cohort. Altogether, we discovered an early-life microbiome-mediated metabolic state causally linked to cognitive deficits and amenable to microbial intervention.}, }
@article {pmid42043697, year = {2026}, author = {Lomelí-Álvarez, MF and Escamilla-Montes, R and Diarte-Plata, G and Guo, X and Fierro-Coronado, JA and Rubio-Luque, AM and Vega-Carranza, AS and González, AL}, title = {Dietary and water probiotics enhance immunity, modulate microbiota, and increase survival of Penaeus vannamei challenged with V. parahaemolyticus.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {57}, number = {1}, pages = {}, pmid = {42043697}, issn = {1678-4405}, abstract = {This study evaluated the effects of Bacillus licheniformis and Pediococcus pentosaceus administered in both culture water and feed to Penaeus vannamei over a 47-day experiment. Treatments in triplicate were as follows: (I) Commercial Feed (CF); (II) CF + P. pentosaceus in the water (3 × 10[6] CFU/L); (III) CF + B. licheniformis in the water (3 × 10[6] CFU/L); (IV) P. pentosaceus in fermented feed (51 × 10[5] CFU/g); (V) B. licheniformis in fermented feed (147 × 10[6] CFU/g); (VI) Mix of P. pentosaceus (140 × 10[5] CFU/g) + B. licheniformis (180 × 10[5] CFU/g) in fermented feed + Mix of P. pentosaceus + B. licheniformis (3 × 10[6] CFU/L) in the water. Growth, immune effectors (phenoloxidase and superoxide anion), and gut bacterial profiles via 16S metagenomic sequencing were assessed. Survival was determined after a challenge with Vibrio parahaemolyticus. Probiotics did not affect growth. Only B. licheniformis in water and fermented feed elicited a significant immunostimulatory response, increasing superoxide anion production and phenoloxidase activity, respectively. Probiotic administration also modulated the gut microbiota, significantly increasing the relative abundance of beneficial genera like Ruegeria and Haloferula. Measures of both alpha and beta diversity indicated a significant restructuring of the microbial community in response to probiotics. Most major bacterial groups showed predominantly positive intra-group interactions, while Psychromonadaceae solely exhibited negative interactions with other families. Shrimp survival was significantly higher in shrimp treated with probiotics, excluding treatment II. These results demonstrate that probiotics strengthen innate immunity and improves disease resistance in shrimp by enhancing immunocompetence and enriching beneficial gut microbes, offering a viable strategy for sustainable aquaculture health management.}, }
@article {pmid42049248, year = {2026}, author = {Jose, A and Apewokin, S and Ollberding, NJ and Duan, Q and Trannguyen, J and Prisco, SZ and Thenappan, T and Hemnes, AR and Elwing, JM}, title = {Lactobacillus Is Associated With Disease in Pulmonary Arterial Hypertension: A Prospective Cohort Study.}, journal = {Comprehensive Physiology}, volume = {16}, number = {3}, pages = {e70161}, doi = {10.1002/cph4.70161}, pmid = {42049248}, issn = {2040-4603}, support = {K23HL16497/HL/NHLBI NIH HHS/United States ; HL168166/HL/NHLBI NIH HHS/United States ; 23CDA1049093//American Heart Association/ ; 2022 Research Award//Team Phenomenal Hope/ ; }, mesh = {Humans ; Male ; Female ; *Gastrointestinal Microbiome/physiology ; *Lactobacillus/physiology ; Prospective Studies ; Middle Aged ; *Pulmonary Arterial Hypertension/microbiology/physiopathology ; Adult ; Aged ; *Hypertension, Pulmonary/microbiology ; Ventricular Dysfunction, Right ; }, abstract = {BACKGROUND: Gut dysbiosis and gut-derived metabolites have been linked to pulmonary arterial hypertension. However, associations between specific microbes, and corresponding metabolites, with pulmonary arterial hypertension disease severity is limited.<br><br>METHODS: This was a prospective cohort study of patients with pulmonary arterial hypertension undergoing right heart catheterization, with pulmonary artery blood subject to nuclear magnetic resonance metabolomics, and simultaneous stool sample shotgun metagenomics. Validation of metabolite levels with disease severity was done in an independent cohort of pulmonary arterial hypertension patients with blood samples from right heart catheterization testing.<br><br>RESULTS: The presence of Lactobacillus species in the gut microbiome of pulmonary arterial hypertension patients was associated with less severe pulmonary hemodynamics and echocardiographic right ventricular dysfunction. Higher threonine levels were associated with more favorable pulmonary hemodynamic characteristics in both prospective and independent validation cohorts of pulmonary arterial hypertension patients.<br><br>CONCLUSIONS: Detectable Lactobacillus species in the gut microbiome of pulmonary arterial hypertension patients are associated with more favorable pulmonary hemodynamic and right ventricular characteristics. Circulating gut-derived metabolites may also be involved. Further investigation into the relationship between gut microbial Lactobacillus, circulating metabolites, disease severity, and clinical outcomes in pulmonary arterial hypertension may be warranted.}, }
@article {pmid42049488, year = {2026}, author = {Lan, K and Bai, D and Yuan, L and Luo, H and Jin, J and Li, SC and Wu, LF and Sun, XS and Liu, SL and Chen, QY and Mai, HQ and Liu, YX and Tang, LQ}, title = {Metagenomic identification of gut microbiome signatures for accurate diagnosis and prognostic prediction of Epstein-Barr virus-associated nasopharyngeal carcinoma.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2026-338223}, pmid = {42049488}, issn = {1468-3288}, abstract = {BACKGROUND: Nasopharyngeal carcinoma (NPC) is strongly associated with Epstein-Barr virus (EBV) infection. The gut microbiome can influence outcomes of viral infections but the potential links among the gut microbiome, EBV infection and NPC remain unclear.<br><br>OBJECTIVE: To characterise gut microbiome alterations in EBV-associated NPC, evaluate microbiome-based diagnostic performance (alone and in combination with EBV markers), and explore associations between microbial features, EBV DNA burden, prognosis and the tumour microenvironment.<br><br>DESIGN: We conducted a large-scale shotgun metagenomic study including 516 patients with EBV-associated NPC and 263 healthy controls. Microbiome dysbiosis, functional pathways and associations with plasma EBV DNA were assessed. Species-level markers were used to build a random forest classifier for NPC diagnosis, and performance was evaluated alone and in combination with EBV-specific markers. Survival analyses were performed to identify microbial features associated with NPC-related mortality and relationships with an immune-suppressive tumour microenvironment were explored.<br><br>RESULTS: NPC was characterised by gut microbiome dysbiosis, including depletion of short-chain fatty acid-producing species and reduced butanoate metabolism, which were significantly associated with plasma EBV DNA. A random forest classifier based on species-level markers distinguished NPC from controls with an area under the curve (AUC) of 0.917; performance improved to an AUC of 0.984 when combined with EBV-specific markers. Specific microbial species were associated with NPC-related mortality and prognostic microbial features were linked to an immune-suppressive tumour microenvironment.<br><br>CONCLUSION: EBV-associated NPC is associated with distinct gut microbiome and functional alterations that correlate with plasma EBV DNA. Microbial markers show strong diagnostic potential, particularly when integrated with EBV-specific markers, and prognostic microbial features may be linked to an immune-suppressive tumour microenvironment, supporting a potential role of the gut microbiome in NPC tumourigenesis.}, }
@article {pmid42049592, year = {2026}, author = {Pailhoriès, H and Velo-Suarez, L and Moalic, Y and Alcoforado-Diniz, J and Gouriou, S and Bessou, A and Cambau, E and Burgel, PR and Herrmann, JL and Héry-Arnaud, G and , }, title = {A disrupted microbial network and an ecological shift towards anaerobes in NTM-infected cystic fibrosis patients.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2026.04.005}, pmid = {42049592}, issn = {1873-5010}, abstract = {Nontuberculous mycobacteria (NTM) are increasingly recognized as opportunistic pathogens in people with cystic fibrosis (pwCF), but the ecological factors shaping their presence remain poorly understood. This study characterized the airway microbiota associated with NTM-positive culture using 16S rRNA gene sequencing of sputum from 108 pwCF (36 NTM-positive and 72 NTM-negative), matched by age, sex at birth, and CFTR genotype. Analyses integrated diversity metrics, differential-abundance modeling, multivariate regression, and microbial network inference, while accounting for Pseudomonas aeruginosa colonization. NTM-positive individuals exhibited slightly higher α-diversity and enrichment in strictly anaerobic taxa such as Alloprevotella tannerae, Stomatobaculum spp., and Prevotella nanceiensis, alongside reduced network connectivity. P. aeruginosa remained the dominant ecological driver, strongly reducing community diversity and structure. Partial Least Squares regression revealed that CFTR modulators (lumacaftor/ivacaftor) use and lung function (FEV1%) were associated with distinct, commensal-enriched communities. In contrast, NTM status was associated with a distinct axis, indicating an independent ecological niche. Overall, NTM-positive cultures were associated with an anaerobe-enriched but less structured microbiota, likely reflecting localized hypoxia and biofilm-associated microenvironments rather than a direct effect of disease severity or modulator therapy. These findings highlight the role of airway microecology in NTM presence and provide a framework for understanding host-microbe interactions in chronic CF airway infections.}, }
@article {pmid42049781, year = {2026}, author = {Manohar, CS and Ghose, M and Parab, AS}, title = {Integrated metagenomic analysis of bacteriomes associated with beach-cast seaweeds reveals metabolic potential for biotechnological and environmental applications.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-46393-1}, pmid = {42049781}, issn = {2045-2322}, support = {MLP2019//Council of Scientific and Industrial Research, India/ ; }, }
@article {pmid42050358, year = {2026}, author = {Zhu, F and Wang, T and Wang, Z and Shan, Y and Ren, P and Bie, X and Wang, D and Gao, Z and Guan, Q and Ge, L and Chen, Y}, title = {Bacillus cereus T146 Enhances Wheat Salt Tolerance by Restructuring the Rhizosphere Microbiome and Activating TaPIN1-Dependent Auxin Transport.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70567}, pmid = {42050358}, issn = {1365-3040}, support = {2024CXPT072//Key R&amp;D Program of Shandong Province/ ; ZR2025QC186//Shandong Provincial Natural Science Foundation/ ; ZR2023QC067//Shandong Provincial Natural Science Foundation/ ; }, abstract = {Salinity stress disrupts rhizosphere homoeostasis and inhibits root development. Although PGPR are known to alleviate such stress, critical knowledge gaps remain regarding the specific mechanisms by which they enhance tolerance under moderate to high salinity, particularly within the wheat rhizosphere -root interface. Here, we show that Bacillus cereus T146, isolated from saline-alkali soil, enhances wheat salt tolerance through two integrated mechanisms. Metagenomic and culturomic analyses further revealed that T146 enriches IAA-producing Pseudomonas in the rhizosphere, and co-inoculation experiments demonstrated that these recruited bacteria contribute synergistically to salt tolerance. On the host side, transcriptomic and cell biological analyses demonstrated that T146 reactivates salt-suppressed auxin pathways. Specifically, inoculation upregulates key regulators of lateral root development (PLT3, PLT7, GLV6) and increases PIN1, PIN2, and PIN3 abundance, leading to elevated auxin accumulation as indicated by DR5::GFP signals. Importantly, silencing TaPIN1 largely compromised T146-induced tolerance and transcriptional reprogramming, demonstrating a functional interplay between microbiome modulation and host hormonal regulation. These results reveal that T146 synergistically promotes salinity resilience by coordinating rhizosphere microbiome remodelling with auxin-mediated root development, offering a mechanistic framework for microbiome-based strategies to improve crop stress tolerance.}, }
@article {pmid42050656, year = {2026}, author = {Zakharevich, N and Strokach, A and Shitikov, E and Klimina, K}, title = {Correction: Bacteriophages in gut metagenomes: from analysis to application.}, journal = {Virology journal}, volume = {23}, number = {1}, pages = {}, pmid = {42050656}, issn = {1743-422X}, }
@article {pmid42050727, year = {2026}, author = {Ivanova, M and Svensmark, B and Bruun Jensen, EE and Aarestrup, FM and Vigre, H and Otani, S}, title = {Metagenomics provides broad detection of pathogens, antimicrobial resistance, and virulence genes in pig diarrhoea and complement conventional methods.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00577-2}, pmid = {42050727}, issn = {2524-4671}, }
@article {pmid42050730, year = {2026}, author = {Seppey, M and Benavides, A and Berkeley, MR and Manni, M and Zdobnov, EM}, title = {LEMMIv2: benchmarking framework for metagenomic and 16S amplicon profilers with a catalogue of evaluated tools.}, journal = {Genome biology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13059-026-04089-9}, pmid = {42050730}, issn = {1474-760X}, support = {ESKAS No. 2022.0531//Federal Commission for Scholarships for Foreign Students for the Swiss Government Excellence Scholarship/ ; 310030_189062//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; }, abstract = {Metagenomics enables culture-independent investigation of microbial communities without prior knowledge of sample composition. However, sequence analysis is complex, and many computational strategies exist. Selecting among them is challenging, and novel tools face visibility issues. Here, we present LEMMIv2, an updated platform for continuous benchmarking of metagenomic profilers, providing developers with impartial benchmarks and offering users a catalogue of evaluated tools. New features include support for alternative taxonomies and long-read applications, and a standalone pipeline for local benchmarking. We also extend the approach to 16S amplicon profiling with LEMMI16S, which evaluates methods across several reference databases.}, }
@article {pmid42051014, year = {2026}, author = {Memon, FU and Ahmad, S and Mo, Q and Liu, S and Xie, X and Nabi, F and Huang, Z and Tettamanti, G and Tian, L}, title = {Probiotic-based fermentation of watermelon waste: Effects on bioconversion efficiency, microbial shifts, and expression profiles of black soldier fly larvae.}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.70280}, pmid = {42051014}, issn = {1744-7917}, support = {//Guangxi Key Laboratory of Sericulture Ecology and Applied Intelligent Technology/ ; //Special Project of Guangxi Collaborative Innovation Center of Modern Sericulture and Silk/ ; //Natural Science Foundation of Guangdong Province/ ; }, abstract = {Insects such as black soldier fly larvae (Hermetia illucens, BSFL) are efficient bioconverters whose growth and physiological performance are strongly influenced by diet composition, gut microbiota, and the molecular regulation. This study investigated how a probiotic-based fermentation strategy modulates larval physiology, microbiome dynamics, and gene expression when BSFL are reared on fermented watermelon waste. Watermelon waste was fermented for 14 d using a consortium of Bacillus subtilis, Enterococcus faecalis, and Aspergillus oryzae, resulting in a nutritionally enhanced substrate. BSFL fed on fermented diet exhibited significantly increased growth performance, biomass yield, and nutritional content of the insect biomass. Metagenomic analysis revealed marked enrichment of gut microbes belonging to genera known to include beneficial and commensal species (Enterococcus, Vagococcus, Carnobacterium, Tetragenococcus, and Blautia) along with a reduction in genera containing species previously associated with opportunistic or pathogenic traits (Mycobacterium, Pseudomonas, Morganella, Pedobacter, and Serpula), indicating diet-induced modulation of host-microbe interactions. Transcriptomic profiling highlighted an upregulation of key genes involved in growth and development (CK1, HIB, and PDK1), protein and fat biosynthesis (DVL, GSK3, and Lpin), and immune defense (PGRP-SA, Spz, Toll, and Cactus). Functional enrichment analysis further confirmed their participation in critical signaling pathways, including Hedgehog, Wnt, mTOR, Toll and Imd, and MAPK. Overall, this study demonstrates that probiotic fermentation improves nutrient utilization, regulates host-microbe interactions, and activates molecular pathways associated with growth and immune resilience in BSFL, providing new insights into the physiological and molecular basis of dietary adaptation in insects.}, }
@article {pmid42051699, year = {2026}, author = {Du, Y and Guo, Z and Yao, D and Wang, Y}, title = {Hemophagocytic lymphohistiocytosis secondary to Pneumocystis jirovecii pneumonia: a rare case report.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1795567}, pmid = {42051699}, issn = {2296-858X}, abstract = {Hemophagocytic lymphohistiocytosis (HLH) secondary to Pneumocystis jirovecii pneumonia (PJP) is extremely rare in children. We present the case of a 10-year-old girl with a history of idiopathic thrombocytopenic purpura (ITP) on long-term oral prednisone, who was admitted for progressive fever, cough, and dyspnea. Metagenomic next-generation sequencing of blood and bronchoalveolar lavage fluid confirmed PJP. Despite targeted antifungal therapy and respiratory support, she developed persistent high-grade fever, pancytopenia, hyperferritinemia, hypofibrinogenemia, and hemophagocytosis on bone marrow aspirate by day 10, meeting diagnostic criteria for HLH. Genetic testing was declined by the parents. Management included dexamethasone, continuous renal replacement therapy, and plasmapheresis. Unfortunately, her condition deteriorated, and she was discharged upon parental request on day 22, succumbing on the same day. To our knowledge, this is the first reported pediatric case of HLH secondary to PJP in China. This case highlights that in children with PJP-especially those on immunosuppressive therapy-the development of persistent fever and cytopenia should prompt immediate evaluation for secondary HLH to enable timely intervention.}, }
@article {pmid42052210, year = {2026}, author = {Qu, HL and Li, JN and Gao, Y and Xu, XM and Zhang, XB and Yang, SD}, title = {From microscopy to antimicrobial decisions: a clinically grounded roadmap for critical care infectious diseases.}, journal = {Frontiers in artificial intelligence}, volume = {9}, number = {}, pages = {1807400}, pmid = {42052210}, issn = {2624-8212}, abstract = {In the intensive care unit (ICU), antibiotics often begin under extreme uncertainty. Fever, leukocytosis, hypotension, and organ dysfunction may signal bacterial infection, but the same findings are common with aspiration, post-operative inflammation, drug reactions, or sterile systemic inflammation. Cultures take time and their yield falls after antibiotics. Rapid molecular tests and metagenomics can add actionable information, but they also raise the burden of interpreting complex results. Microscopy is one of the few inputs that can shift management within minutes to hours: Gram-stain patterns from positive blood-culture bottles, respiratory specimens, cerebrospinal fluid, and wound material can reshape initial coverage and support early de-escalation when negative. Tissue and cytology help distinguish invasion from key mimics. The gap is consistency-reads vary across observers, workflows differ, and results do not always translate into reliable bedside actions. This review focuses on infectious-disease artificial intelligence (AI) as ICU bedside decision support, rather than as a survey of models. Using ICU sepsis as the primary use case-and neurocritical care as a challenging setting where sedation, brain injury, and noninfectious inflammation often mimic infection-we separate evidence into pathogen signals and host-response signals. We then map both streams to six decisions over the first 72 hours: start now versus pause, choose initial spectrum, reassess and narrow, escalate diagnostics and source control, act on high-risk resistance or invasive pathogens, and stop safely. We summarize where AI is most credible today (Gram-stain assistance, culture-plate triage, urine-culture screening, infection-focused digital pathology, host-response classifiers, and selected metagenomics) and what makes outputs actionable: calibrated probabilities, explicit confidence with safe deferral when uncertain, validation across hospitals and instruments, and endpoints tied to stewardship and safety (time to appropriate therapy, antibiotic days, de-escalation within 72 hours, missed bacteremia). Evidence was updated through February 28, 2026.}, }
@article {pmid42052392, year = {2026}, author = {Suenaga, H and Fujihara, H}, title = {Molecular basis for adaptive evolution of aromatic degradation enzymes in bacteria revealed by metagenomics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1795400}, pmid = {42052392}, issn = {1664-302X}, abstract = {Aromatic hydrocarbons, including persistent polycyclic aromatic hydrocarbons (PAHs), impose strong selective pressures that drive the adaptive evolution of bacterial degradation systems. Metagenomic studies have revealed extensive diversification of key catabolic enzymes, such as ring-hydroxylating and ring-cleavage dioxygenases, through the accumulation of single-nucleotide polymorphisms (SNPs) and structural modifications that increase substrate range and enhance catalytic efficiency in polluted environments. These findings demonstrate that gene mutations that change enzyme properties collectively shape the evolution of aromatic-degrading bacteria. Metagenomics is powerful tools for elucidating these evolutionary processes and advancing applications in bioremediation and industrial biocatalysis.}, }
@article {pmid42052398, year = {2026}, author = {Crippen, TL and Kim, D and Swiger, SL and Anderson, RC and Arsenault, RJ}, title = {Capturing the fungal diversity in manure, lagoons, troughs, and flies at a commercial dairy.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1794875}, pmid = {42052398}, issn = {1664-302X}, abstract = {The microbiomes within dairy facilities that could serve as reservoirs for beneficial and pathogenic fungi have not been extensively explored. Though fungi can cause food safety and animal health issues, they also represent species contributing to bovine digestion and environmental nutrient cycling. This study investigated whether fungal communities from specific elements at a working dairy differed between cross-vent or flow-through, free stall barn management systems and defined the possible pathogen locations. Shotgun metagenomics was carried out on manure, lagoons, troughs, and fly samples from the barns. The diversity of species was not significantly affected by management systems, except between lagoon communities. Flies carried the highest number of unique fungal species and the most abundant potential mammalian pathogens, but there was a lack of overlapping pathogen profiles between flies and the other dairy components. Thus, it remains unclear whether the species are being efficiently exchanged between these different components of the dairy environment, mechanically or biologically. Manure harbored the most opportunistic pathogenic species, lagoons harbored the most plant pathogens and beneficial species, and troughs had the most innocuous or understudied species. The results allow dairy managers to consider advantageous management systems and focus on fungal mitigation efforts at appropriate locations within the dairy.}, }
@article {pmid42052556, year = {2026}, author = {Chu, T and Liu, J and Zhang, Y and Yang, K and Li, S and Yan, Q and Li, Y}, title = {Metagenome-based virome analysis identifies the oral viral signatures for periodontitis.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2662091}, pmid = {42052556}, issn = {2000-2297}, abstract = {BACKGROUND: Periodontitis (PD) is a chronic infectious disease driven by bacterial biofilms, yet the oral virome's role in pathogenesis remains poorly understood.<br><br>OBJECTIVE: This cross-cohort meta-analysis aims to define PD-associated viral signatures, characterize predicted virus-host interactions, and evaluate the diagnostic potential of viral biomarkers.<br><br>METHODS: We integrated 89 saliva (44 PD, 45 healthy) and 86 subgingival plaque (48 PD, 38 healthy) metagenomes from six public cohorts for a unified virome analysis.<br><br>RESULTS: We identified 156 viral operational taxonomic units (vOTUs) significantly associated with PD (105 in saliva, 66 in subgingival plaque and 15 shared). PD-enriched vOTUs were predicted to target periodontal pathogens including Porphyromonas gingivalis, whereas Streptococcus-targeting phages were decreased. PD-associated vOTUs harbored diverse bacterial defense and anti-defense systems, with those enriched in PD overrepresenting lysozyme and replication-associated genes. Diagnostic models based on key viral markers achieved robust performance, with AUCs of 0.95 (saliva) and 0.92 (subgingival plaque) for classifying PD.<br><br>CONCLUSION: This study delineates a distinct oral virome profile in PD, highlights predicted virus-host interactions, and underscores the potential of viral biomarkers for PD diagnosis,providing a basis for future investigations into viral ecology and phage-based interventions.}, }
@article {pmid42052831, year = {2026}, author = {Li, Y and Gao, H and Liao, Z and Chen, Z and Song, Z and Xiong, W and Dai, Y and Li, W and Luan, S}, title = {Metagenomic Analysis Reveals Gut Microbiota Features in Membranous Nephropathy.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {31}, number = {4}, pages = {48982}, doi = {10.31083/FBL48982}, pmid = {42052831}, issn = {2768-6698}, support = {JCYJ20240813153002004//Shenzhen Foundation of Science and Technology/ ; JCYJ20250604191024032//Shenzhen Foundation of Science and Technology/ ; 2025A1515012512//Guangdong Basic and Applied Basic Research Foundation/ ; 2022041//Shenzhen Longhua District Healthcare Institutions Scientific Research Project/ ; //Key Medical Discipline Construction Fund of Shenzhen Longhua District/ ; JZ2025107//Guangdong Yiyang Healthcare Charity Foundation/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Glomerulonephritis, Membranous/microbiology ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Feces/microbiology ; Adult ; *Bacteria/genetics/classification ; Case-Control Studies ; }, abstract = {BACKGROUND: Membranous nephropathy (MN) is one of the most common forms of primary glomerulonephritis worldwide and is closely associated with immune dysregulation. Increasing evidence suggests that the gut microbiota plays a critical role in regulating renal disease through the gut-renal axis. However, the use of metagenomic sequencing to analyze changes in the gut microbiota in patients with MN has not yet been reported.<br><br>METHODS: This study employed a metagenomic approach to comprehensively analyze the gut microbiota in patients with MN (n = 10) and normal controls (NCs; n = 10). Shotgun metagenomic sequencing was performed on fecal samples. Microbial diversity, taxonomic composition, and functional pathways were assessed, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. In addition, correlations between gut microbial characteristics and clinical indicators were also evaluated.<br><br>RESULTS: The gut microbial community in the MN group showed distinct differences from the control group, particularly with an increased abundance in phylum: Proteobacteria, Firmicutes_C, and Cyanobacteria; the genera Dialister, Selenomonadales, Clostridium, Bacillus, Megamonas, Romboutsia, and Inesitibacter; the species Bilophila_wadsworthia, Enterococcus_C, Megamonas funiformis, and Clostridium_perfringens. Furthermore, Bacillus_A showed a significant positive correlation with both serum creatinine and the protein-to-creatinine ratio. Conversely, higher levels of Victivallis were associated with lower blood urea nitrogen, while increased Fusicatenibacter was correlated with lower phospholipase A2 receptor levels. KEGG analysis indicated that the MN gut microbiota was enriched for pathways related to tryptophan metabolism, oxidative phosphorylation, and pathogenic Escherichia coli infection. Additionally, receiver operating characteristic analysis revealed that a four-genus model comprising enriched Dialister, Enterococcus_C, and Clostridium_P, and reduced Fusicatenibacter yielded an area under the curve of 0.90 &#xb1; 0.12, suggesting promising discriminatory potential that warrants further validation.<br><br>CONCLUSION: These findings demonstrate alterations in the composition and functional potential of the gut microbiota in patients with MN compared with the control group. Given the cross-sectional design of this study, these observations should be interpreted as associative, and further studies are required to validate these findings and explore any associated biological relevance.}, }
@article {pmid42053312, year = {2026}, author = {Chung, B and Wang, S and Hao, Z and Allison, SD and Malik, AA}, title = {Plant litter chemistry and associated changes in microbial decomposition under drought.}, journal = {mBio}, volume = {}, number = {}, pages = {e0043826}, doi = {10.1128/mbio.00438-26}, pmid = {42053312}, issn = {2150-7511}, abstract = {UNLABELLED: Drought has consequences for microbial decomposition rates, including indirect effects through changes in plant litter chemistry. Here, we studied the impact of a decade-long drought on plant litter chemistry and microbial decomposition traits in a semi-arid ecosystem during an 18-month litter bag experiment. We investigated litter sourced from four conditions: grass and shrub vegetation under ambient and reduced precipitation. We hypothesized that litter chemistry drives microbial decomposition capabilities and enzyme activity due to vegetation differences and drought effects on litter chemistry. We found that carbohydrate-rich grass litter had a higher abundance of decomposition genes detected using metagenomics and enzyme activity than more recalcitrant shrub litter, which was richer in lignin and lipids; these patterns were related to substrate supply. Drought decreased some carbohydrate fractions in grass litter but did not change the lignin fraction in grass and shrub litter, suggesting that drought does not make litter more recalcitrant. Most decomposition genes and enzyme activities were not significantly affected by drought, thereby maintaining decomposition rates. Microbial community succession patterns-decreasing fungal abundance and increasing bacterial abundance with time-corresponded with decreasing chitin gene abundance and increasing peptidoglycan gene abundance over time, indicating microbial necromass recycling. We demonstrate minimal litter chemistry-mediated effects of drought but show significant changes in community composition and their decomposition capabilities over time, highlighting that complex microbial-chemical interactions under climate change can influence ecosystem-scale processes.<br><br>IMPORTANCE: Climate change is causing more severe and frequent droughts in semi-arid ecosystems, affecting soil microbes breaking down plant litter. Our research focuses on understanding the less studied pathway of drought impact on microbes via changes in plant litter chemistry. Drought can alter the plant litter chemistry by changing the composition and physiology of plants, which can alter microbial decomposition and ecosystem-level carbon cycling. We investigated litter decomposition traits of microbial communities in grass and shrub litter under long-term drought. There were significant changes in litter chemistry under drought but no increase in lignin fraction. Despite this, microbial communities maintained their decomposition capabilities under drought, highlighting the ability of microbes to adapt and continue functioning. We also demonstrate unique microbial community succession patterns and dead biomass recycling, which can have implications for carbon cycling rates in the ecosystem. This study sheds light on the complex microbial interactions that affect ecosystem functioning under climate change.}, }
@article {pmid42053608, year = {2026}, author = {Çağatay, NS and Dageri, A and Saruhan, I and Tuncer, C and Guz, N}, title = {Diversity and Composition of the Microbiome Associated with Adult of the Green Shield Bug Palomena prasina (Hemiptera: Pentatomidae).}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02779-2}, pmid = {42053608}, issn = {1432-184X}, support = {Project number: 116O328//T&#xfc;rkiye Bilimsel ve Teknolojik Ara&#x15f;t&#x131;rma Kurumu/ ; }, }
@article {pmid42053852, year = {2026}, author = {Peng, Q and Lin, Y}, title = {A case report of infective endocarditis caused by Mycoplasma pneumoniae in a child.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {42053852}, issn = {1435-4373}, abstract = {OBJECTIVE: This study aimed to investigate the clinical features and management strategies for infective endocarditis(IE) caused by Mycoplasma pneumoniae(M. pneumoniae) in children, in order to enhance understanding of this rare extrapulmonary complication of M. pneumoniae infection and provide clinical insights for its diagnosis and treatment.<br><br>METHODS: We retrospectively analyzed the clinical data and management process of a pediatric patient diagnosed with IE who was admitted to our hospital in September 2025.<br><br>RESULTS: A 9-year-old male patient was admitted with initial symptoms of fever and cough and was diagnosed with M. pneumoniae pneumonia. Subsequently, prompted by the detection of a faint blowing murmur on auscultation, transthoracic echocardiography was performed, which revealed a vegetation in the right ventricle. Empirical antibiotic treatment with doxycycline combined with vancomycin and ceftriaxone was initiated. M. pneumoniae was detected in two blood specimens using metagenomic next-generation sequencing (mNGS), while all three conventional blood cultures remained negative. Treatment was subsequently adjusted to doxycycline monotherapy. On hospital day 11, follow-up echocardiography examination showed resolution of the vegetative, with no evidence of thromboembolic events. After discharge, the patient continued oral doxycycline for a total treatment duration of 4 weeks. Follow-up revealed good recovery.<br><br>CONCLUSIONS: M. pneumoniae pneumonia in children may be complicated by IE. Antimicrobial agents should be guided by regional antimicrobial resistance patterns and resistance gene testing. The addition of anti-inflammatory and anticoagulant therapies should be considered when clinically indicated. mNGS is a valuable diagnostic tool for identifying pathogens in cases of blood culture-negative IE.}, }
@article {pmid42053938, year = {2024}, author = {Jang, YJ and Moon, JS and Kim, JE and Kim, D and Choi, HS and Oh, I}, title = {Blending Three Probiotics Alleviates Loperamide-Induced Constipation in Sprague-Dawley (SD)-Rats.}, journal = {Food science of animal resources}, volume = {44}, number = {1}, pages = {119-131}, doi = {10.5851/kosfa.2023.e61}, pmid = {42053938}, issn = {2636-0780}, abstract = {BIOVITA 3 bacterial species (BIOVITA 3), a probiotic blend powder containing Clostridium butyricum IDCC 1301, Weizmannia coagulans IDCC 1201 and Bacillus subtilis IDCC 1101, has been used as a food ingredient for gut health. However, its efficacy in improving constipation has not been reported. Therefore, we aimed to investigate the functional effects of oral administration of BIOVITA 3 as well as its component strains alone (at 1.0×10[9] CFU/day) in Sprague-Dawley (SD) rats with loperamide-induced constipation. The study included fecal analysis, gastrointestinal transit ratio, histopathological analysis, short chain fatty acids (SCFAs), and metagenome analysis. As results, the BIOVITA 3 group showed significant improvements in fecal number, water content, gastrointestinal transit ratio, and thickening of the mucosal layer. In the SCFAs analysis, all probiotic-treated groups showed an increase in total SCFAs compared to the loperamide-constipated group. Changes in microbial abundance and the diversity index of three groups (normal, constipated, and BIOVITA 3) were also defined. Of these, the BIOVITA 3 showed a significant improvement in loperamide-constipated SD-rats. This study suggests the possibility that BIOVITA 3 can be applied as an ingredient in functional foods to relieve constipation.}, }
@article {pmid42054100, year = {2026}, author = {Mellor, SA and Bloomfield, SJ and Palau, R and Savva, GM and Wain, J and Mather, AE}, title = {Metagenomic analysis of UK retail foods finds limited evidence for associations between food production method and antimicrobial resistance gene burden.}, journal = {Microbial genomics}, volume = {12}, number = {4}, pages = {}, doi = {10.1099/mgen.0.001705}, pmid = {42054100}, issn = {2057-5858}, mesh = {Animals ; *Metagenomics/methods ; *Food Microbiology ; Chickens/microbiology ; *Bacteria/genetics/classification/drug effects/isolation &amp; purification ; *Drug Resistance, Bacterial/genetics ; *Meat/microbiology ; Cattle ; Sheep ; Salmon/microbiology ; United Kingdom ; Microbiota/genetics ; Anti-Bacterial Agents/pharmacology ; Swine ; }, abstract = {Food is produced by a range of methods including extensive (organic and free range), intensive (conventional) and wild-caught production systems. Antimicrobial use varies between different food production systems, which may affect the microbial populations as well as the prevalence and diversity of antimicrobial resistance genes (ARGs) found on food at retail. In this study, shotgun metagenomics was used to investigate the microbial and ARG composition of 25 pork, 33 beef, 33 lamb, 60 chicken, 31 salmon and 41 leafy green samples collected in Norfolk, England, and labelled as extensive, wild caught or intensive. Food microbiomes consisted predominantly of spoilage-associated organisms including Pseudomonas, Lactococcus and Psychrobacter. Significant differences in bacterial diversity were found between intensive and extensive systems on chicken, and 22 differentially abundant genera were identified between production systems across beef, chicken and salmon. Genes conferring resistance to tetracyclines and beta-lactams comprised the majority of the food resistome across all commodities. Across most measures used to compare food resistomes between production methods, no significant differences were detected, except on chicken and salmon where differences in beta-diversity between production methods were detected, albeit with low effect sizes. Overall, these results suggest that differently produced foods, at least when tested at retail and in this region, may present a similar risk of antimicrobial resistance across the commodities investigated within this study. However, specific associations were identified with the microbial composition across chicken, beef and salmon, suggesting that production method may drive some variation in the microbial population structure on food products. Additional work at the farm or food processing levels is required to identify the drivers of these differences between production systems.}, }
@article {pmid42054312, year = {2026}, author = {Revel, J and Leroy, J and Delbecq, S and Constant, O and Marty, F and Naili, C and Barthès, A and Nagy, A and Schmidt-Chanasit, J and Cadar, D and Abd Rahaman, NY and Lajoix, AD and Desmetz, C and Simonin, Y}, title = {Differential Properties of NS1 Glycoproteins in West Nile and Usutu Viruses.}, journal = {Emerging microbes &amp; infections}, volume = {}, number = {}, pages = {2667565}, doi = {10.1080/22221751.2026.2667565}, pmid = {42054312}, issn = {2222-1751}, abstract = {AbstractWest Nile virus (WNV) and Usutu virus (USUV) are neurotropic orthoflaviviruses of the Flaviviridae family, transmitted primarily by Culex mosquitoes and maintained in enzootic cycles involving birds. While WNV is a well-established human pathogen causing hundreds of neuroinvasive cases annually in Europe, USUV has emerged more recently, with fewer documented human infections but increasing evidence of neurovirulence. The viral nonstructural protein 1 (NS1) plays a central role in orthoflavivirus pathogenesis by modulating host immune responses, disrupting endothelial barrier integrity, and facilitating viral dissemination. However, the functional and biochemical properties of NS1 from WNV and USUV remain poorly characterized. We combined in vitro, in vivo, and clinical approaches to compare NS1 secretion, stability, and its impact on blood-brain barrier. Our results show that WNV NS1 is secreted at significantly higher levels, exhibits greater thermal stability, and disrupts brain endothelial barrier integrity in vitro. In contrast, USUV NS1 is secreted less efficiently, is slightly less stable, and does not compromise blood-brain barrier integrity, despite inducing distinct transcriptional responses in brain endothelial cells. In mice, WNV infection led to higher serum NS1 levels and stronger systemic inflammation than USUV. Clinically, WNV NS1 was detected mainly in patients with neurological symptoms, whereas USUV NS1 remained undetectable in all cases. Altogether, these findings reveal differential NS1 properties between these closely related viruses, with key implications for orthoflavivirus diagnosis and neurovirulence mechanisms.}, }
@article {pmid42054365, year = {2026}, author = {Santos-Júnior, CD and Escobar, MC and Huber, P and Niño-Garcia, JP and Cardona, GI and Costa-Pereira, R and Sarmento, H}, title = {Resource availability structures microbial competition through genomic niche partitioning.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {18}, pages = {e2526391123}, doi = {10.1073/pnas.2526391123}, pmid = {42054365}, issn = {1091-6490}, support = {862923//EC | Horizon 2020 Framework Programme (H2020)/ ; 304655/2025-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico (CNPq)/ ; 22/15842-6//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; 23/02850-3//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; 20/11953-2//Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de S&#xe3;o Paulo (FAPESP)/ ; 2025hsqd014//Hubei Hongshan Laboratory/ ; }, mesh = {Humans ; Ecosystem ; Metagenome ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; Biodiversity ; Bacteria/genetics/classification ; Metagenomics/methods ; Soil Microbiology ; Genomics ; Microbiota/genetics ; *Microbial Interactions ; }, abstract = {Microbial competition for scarce resources shapes biodiversity patterns and ecosystem function across global biomes, yet quantifying this process from genomic data has remained elusive. Here, we introduce CaCo, a scalable metric that transforms metagenomic carbohydrate-active enzyme profiles into precise measures of niche overlap and competition potential (Resource Partitioning Score, RPS). Analyzing 14,691 high-quality metagenome-assembled genomes spanning Ocean, freshwater, soil, and human gut microbiomes, we reveal a striking macroecological pattern: Niche overlap increases from partitioned specialists in oligotrophic oceans to overlapping generalists in carbon-rich environments, including the human gut. This gradient aligns with classic niche theory, as phylogenetic signals indicate that closely related taxa may compete most intensely. Multitiered validation, spanning BIOLOG phenotypes, synthetic cocultures, and interaction gradients, confirms CaCo's predictive power and captures competitive exclusion. CaCo bridges genomic potential and ecological reality, providing niche-breadth metrics and enabling testable predictions of how resource availability shapes microbial competition and community structure.}, }
@article {pmid42054706, year = {2026}, author = {Vilaseca, A and Toledano, M and Flanagan, EP}, title = {Complexities in evaluation and management of infectious myelopathies.}, journal = {Current opinion in infectious diseases}, volume = {39}, number = {3}, pages = {227-239}, doi = {10.1097/QCO.0000000000001204}, pmid = {42054706}, issn = {1473-6527}, mesh = {Humans ; *COVID-19/complications ; *Spinal Cord Diseases/diagnosis/virology/therapy/etiology ; SARS-CoV-2 ; *Myelitis/diagnosis/virology ; Magnetic Resonance Imaging ; }, abstract = {PURPOSE OF REVIEW: To review recent advances in infectious myelopathies and integrate them into a practical, syndrome-based approach that supports early recognition, guides testing, and avoids pitfalls.<br><br>RECENT FINDINGS: Advances in MRI pattern recognition and pathogen-specific diagnostics have refined the evaluation of infectious myelopathies, with strategies tailored to geographic epidemiology, host susceptibility, and distinction from immune-mediated causes. During the COVID-19 pandemic, SARS-CoV-2-associated myelopathy emerged as a rare para- or postinfectious cause of myelitis. The pandemic coincided with a decline in enterovirus outbreaks and acute flaccid myelitis, which are now re-emerging, underscoring the importance of epidemiologic surveillance. Metagenomic next-generation sequencing is useful in suspected infectious myelopathy because it can identify unexpected pathogens from cerebrospinal fluid, but its imperfect sensitivity and contamination risk mean it should complement rather than replace conventional testing. Growing recognition of compartmentalized central nervous system inflammation and cerebrospinal fluid viral escape in HIV myelopathy has shifted management toward antiretroviral resistance patterns and treatment optimization. Therapeutic advances remain limited and largely pathogen-specific, although targeted approaches such as mogamulizumab for HTLV-1-associated myelopathy are promising.<br><br>SUMMARY: Recent progress in infectious myelopathies has been driven by improved pathogen detection and more tailored diagnostic strategies, although treatment advances are beginning to emerge.}, }
@article {pmid42055201, year = {2026}, author = {Lu, L and Pan, C and Fu, L and Zhao, L and Wang, HY and Yao, W and Yang, M}, title = {Subchronic exposure to environmental levels of fluoxetine disturbs gut microbiota-mediated intestinal barrier homeostasis and triggers delayed feeding response in zebrafish (Danio rerio).}, journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP}, volume = {}, number = {}, pages = {110551}, doi = {10.1016/j.cbpc.2026.110551}, pmid = {42055201}, issn = {1532-0456}, abstract = {Fluoxetine (FLX), a selective serotonin reuptake inhibitor, is frequently detected in aquatic environments because of its widespread use and inefficient removal by sewage treatment. Long-term FLX residues may induce chronic effects in non-target aquatic organisms. The intestine is a key metabolic and immune organ in fish, and may be affected by prolonged FLX exposure. However, studies on FLX-induced intestinal toxicity and its underlying molecular mechanisms are scarce. In the present study, adult female zebrafish were exposed to environmentally relevant FLX concentrations for 28 days, and subchronic toxic effects were assessed using an integrated approach combining physio-biochemical, behavioral, pathological, and multi-omics analyses. The results showed that the 28-day FLX exposure reduced the adult fish condition factor and altered feeding behavior. Notably, maternal FLX increased F1 offspring mortality and decreased the hatching rate, body length, and heart rate. In FLX-exposed adult intestines, goblet cell villus height was reduced and oxidative stress was induced, and transcriptome analysis revealed differentially expressed genes enriched in metabolism, neurodegenerative disease, and circadian rhythm pathways. Additionally, 16S rRNA and metagenomic sequencing showed FLX decreased gut microbiota α-diversity, altered community composition and assembly process, and enhanced antibiotic resistance genes. These findings highlight the dual threats of pharmaceutical pollution to ecological and public health, and provide support for the formulation of environmental and health protection measures.}, }
@article {pmid42055262, year = {2026}, author = {Trinh, HP and Lee, SH and Park, HD}, title = {Mitigating nitrite stress and restoring functional redundancy in anammox reactor via acetate-driven DNRA-anammox coupling.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134732}, doi = {10.1016/j.biortech.2026.134732}, pmid = {42055262}, issn = {1873-2976}, abstract = {Frequent fluctuations in nitrite concentrations and unstable control of partial nitritation often lead to excessive NO2[-] accumulation, resulting in performance deterioration in anammox-based systems. To address this challenge, an anammox reactor was operated for 180 days to investigate the inhibitory effects of elevated NO2[-]/NH4[+]ratios on anammox activity and to evaluate the effectiveness of external carbon supplementation in promoting dissimilatory nitrate reduction to ammonium (DNRA)-related pathways that contribute to NO2[-] reduction. Increasing NO2[-]/NH4[+]ratio from 1.3 to 3.0 decreased the nitrogen removal efficiency from 96.7% to 26.6%, reduced the relative abundance of anammox bacteria (Ca. Kuenenia and Ca. Jettenia) from 41.5% to 7.0% and promoted Nitrospira to 7.7%. In contrast, acetate supplementation at a C/N ratio of 0.2 suppressed Nitrospira to 0.2% and enhanced the abundance of anammox and DNRA-performing bacteria (e.g., Fimbriimonadaceae, Mycobacterium, Anaerolineales, Caldilineaceae, and Ignavibacteriaceae) to 31.2% and 15.7%, respectively. Metagenome-assembled genome analysis confirmed the enrichment of functional genes associated with anammox (hzsABC and hdh) and DNRA metabolism (nirBD and nrfAH), corresponding to the recovery of nitrogen removal efficiency to 82.3%. Quantitative microbial network analysis further revealed that functional redundancy index declined from 0.56 to 0.42 under nitrite stress but recovered to 0.53 following acetate supplementation, indicating the restoration of a functionally buffered microbial community. Overall, these results demonstrate that low-level acetate supplementation, (C/N = 0.2) effectively stimulated DNRA-mediated NO2[-] reduction to NH4[+] by both DNRA-performing bacteria, thereby supporting anammox activity and providing an energy-efficient strategy to mitigate NO2[-] accumulation and stabilize nitrogen removal in anammox-based systems.}, }
@article {pmid42055314, year = {2026}, author = {Zhang, Y and Xia, J and Qiu, Z and Tian, S and Wang, J and Ren, X and Chen, M}, title = {Successful Treatment of Balamuthia Mandrillaris Amebic Encephalitis Diagnosed by MetaCAP in China: A Case Report and Review of 25 Survival Cases.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108745}, doi = {10.1016/j.ijid.2026.108745}, pmid = {42055314}, issn = {1878-3511}, abstract = {Balamuthia mandrillaris, a free-living amoeba, can cause Balamuthia amebic encephalitis (BAE), a rare and often fatal cerebral infection. The reported mortality rate is >90%, largely attributable to the absence of specific clinical manifestations, sensitive diagnostic methods and effective therapeutic interventions. We herein describe a middle-aged, male patient diagnosed with BAE using Metagenomic Capture sequencing (MetaCAP) who achieved full recovery following early medical therapy without neurosurgical treatment. Our findings indicate that MetaCAP serves as a rapid and sensitive diagnostic approach, and sulfasalazine may confer a potential anti-inflammatory benefit in the management of BAE. In addition, we reviewed 25 survival cases of BAE reported in the PubMed database up to now.}, }
@article {pmid42044793, year = {2026}, author = {Zhou, Y and Hu, X and Du, L and Gu, Y and Li, J and Jia, M and Zhang, G and Wang, Y}, title = {Antibiotic Resistance Genes Across Divergent Wetland Types: Profiles, Driving Mechanisms, and Risk Assessment.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124601}, doi = {10.1016/j.envres.2026.124601}, pmid = {42044793}, issn = {1096-0953}, abstract = {Wetlands are critical reservoirs and hotspots of antibiotic resistance genes (ARGs). Metagenomic sequencing was employed to profile the ARG and mobile genetic element (MGE) abundance and diversity in coastal (B), constructed (R), and swampy (W) wetlands. In total, 560 ARGs were detected across all sites, primarily conferring resistance to cephalosporins and tetracyclines, with antibiotic efflux being the dominant mechanism of resistance. ARG richness was significantly higher in wetlands R and W than in wetland B (p < 0.001). Non-metric multidimensional scaling (NMDS) further indicated significant differences in ARG β-diversity among the wetlands. Pseudomonadota were identified as the primary hosts of both ARGs and MGEs. Soil salinity and Cr content were the key environmental factors regulating ARG profiles, with salinity exhibiting the broadest influence and linearly correlating with multiple ARG types. In addition, plasmid and insertion sequence (IS) richness positively correlated with ARG richness, showing the strongest explanatory power for ARG richness variation. Risk assessment revealed that rank I and II ARGs were significantly enriched in wetland W (p < 0.05), whereas rank IV ARGs were dominant across most sites. This study demonstrated that soil physicochemical properties, plasmids, and ISs jointly and differentially shaped ARG abundance and diversity in wetlands, accompanied by an assessment of their risk. These findings support the development of targeted strategies to mitigate ARG dissemination in wetland ecosystems.}, }
@article {pmid42044853, year = {2026}, author = {Weng, H and Wang, H and Zhang, Q and Li, X and Zhang, L and Peng, Y}, title = {Enrichment of comammox Nitrospira with urea: comparative genomics reveals divergent urea response mechanisms among ammonia-oxidizing microorganisms.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134722}, doi = {10.1016/j.biortech.2026.134722}, pmid = {42044853}, issn = {1873-2976}, abstract = {Urea is a major nitrogen form in natural and engineered ecosystems, yet the traits driving niche partitioning among nitrifiers during urea nitrification remain poorly understood. In this work, a stable urea nitrification microbial community was successfully established over prolonged cultivation characterized using 16S rRNA gene amplicon sequencing, qPCR and genome-resolved metagenomics coupled with comparative genomics. A clade A comammox Nitrospira closely related to Candidatus Nitrospira nitrosa became dominant (OTU330, 13.9%) and yielded the most abundant nitrifier metagenome-assembled genome (MAG). Genomes indicate comammox Nitrospira couples ATP-dependent urea ABC uptake to a streamlined urease-only module characterized by slow substrate turnover, whereas Nitrosomonas relies on passive urea channels and redundant urease/urea-amidolyase pathways, enabling rapid urea metabolism. These contrasting urea acquisition strategies suggest an affinity-capacity trade-off that underpins niche partitioning in urea-fed, oligotrophic nitrifying systems and provide targets for enhancing urea-based wastewater treatment processes.}, }
@article {pmid42045408, year = {2026}, author = {Kutuzova, S and Piera Líndez, P and Danielsen, LS and Nielsen, KN and Olsen, NS and Riber, L and Gobbi, A and Forero-Junco, LM and Erdmann Dougherty, P and Westergaard, JC and Browne, PD and Christensen, S and Hestbjerg Hansen, L and Nielsen, M and Nybo Andersen, J and Rasmussen, S}, title = {Improving metagenome binning by integrating intrinsic features and taxonomy.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {42045408}, issn = {1546-1696}, support = {NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF21SA0072102//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 7076-00129B//Innovationsfonden (Innovation Fund Denmark)/ ; }, abstract = {A common procedure for studying the microbiome is binning the sequenced contigs into metagenome-assembled genomes. State-of-the-art binning methods use coabundance and sequence-based motifs such as tetranucleotide frequencies, whereas taxonomic labels derived from alignment based classification have not been widely used. Here we propose TaxVAMB, a metagenome binning tool based on semisupervised bimodal variational autoencoders, combining tetranucleotide frequencies and contig coabundances with taxonomic information. TaxVAMB outperformed all other binners on CAMI2 human microbiome datasets, returning on average 29% more high-quality assemblies than the next best binner, and performed on par with the best binners on short-read datasets. On a human gut long-read dataset, TaxVAMB recovered 29% more high-quality bins. In a typical single-sample setup, TaxVAMB on average returns 83% more high-quality bins compared to VAMB. Lastly, TaxVAMB binned incomplete genomes better than any other tool, returning on average 300% more high-quality bins of incomplete genomes than the next best binner.}, }
@article {pmid42045553, year = {2026}, author = {Wei, D and Xing, C and Zeng, S and Hou, D and Deng, Z and Long, X and Wang, H and Zhou, R and Yu, L and Shu, N and Tao, Z and Zhou, X and Weng, S and He, J and Huang, Z}, title = {The crayfish-rice coculture model contributes to regulating the soil fertility of rice fields and maintaining the stability of soil microbial community composition and function.}, journal = {Advanced biotechnology}, volume = {4}, number = {2}, pages = {}, pmid = {42045553}, issn = {2948-2801}, support = {2023YFD2401705//National Key Research and Development Program of China/ ; 2024YFD2401202//National Key Research and Development Program of China/ ; AA23062047//Earmarked Fund for CARS-48-20; Guangxi Science and Technology Major Special Project/ ; SML2021SP203//Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; }, abstract = {Rice-fish coculture represents a classic sustainable agricultural paradigm; however, the microecological mechanisms underlying its capacity to maintain soil fertility and microbial community stability remain poorly understood. We conducted a 13-month field experiment comparing three cultivation systems:crayfish-rice coculture (CRCE), crayfish-waterweed coculture (CWCE), and rice monoculture (RME)-by integrating physicochemical analysis, 16S rRNA sequencing, metagenomics, microbial network analysis, and null model simulations. Our results demonstrated that coculture systems, particularly CRCE, enhanced soil fertility through carbon sequestration (total carbon: 25.0-45.0 mg/g; total organic carbon: 15.0-35.0 mg/g) and sustained redox homeostasis (consistently low oxidation-reduction potential: - 150 to - 50 mV), in stark contrast to the extreme redox fluctuations observed in RME. These stable edaphic conditions imposed deterministic selection on microbial communities (homogeneous selection contribution: 30%-50% in CRCE vs. 10%-20% in RME), shifting community assembly from stochastic drift dominance toward predictable succession. This assembly shift enriched functionally coupled keystone taxa, including iron reducers (Geobacter), sulfur oxidizers (Sulfuricurvum), and nitrifiers (Nitrospira), which formed ecological networks characterized by 98.6% positive interactions and enhanced functional gene repertoires associated with carbon, nitrogen, and sulfur biogeochemical cycles. Metagenomic analysis corroborated these findings, revealing enrichment of functional genes involved in polymer degradation, nitrification, and sulfate reduction in CRCE, supporting enhanced nutrient cycling capacity. We establish a hierarchical causal pathway in which bioturbation-induced environmental stabilization drives deterministic community assembly, which in turn promotes keystone taxon enrichment and functional integration. This framework provides a mechanistic explanation for how crayfish-rice coculture regulates soil fertility and sustains microbial community compositional and functional stability in anthropogenically designed agricultural ecosystems.}, }
@article {pmid42045683, year = {2026}, author = {Boppana, LKT and Bag, R}, title = {Metagenomic Microbial Next-Generation Gene Sequencing as a Noninvasive Diagnostic Tool in Adult Lung Transplantation: A Retrospective Case Series.}, journal = {Lung}, volume = {204}, number = {1}, pages = {}, pmid = {42045683}, issn = {1432-1750}, }
@article {pmid42046358, year = {2026}, author = {Chen, K and Huang, L}, title = {[Metagenomic next - generation sequencing for diagnosis of infection of unknown origin in intensive care units: a bibliometric analysis].}, journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control}, volume = {38}, number = {1}, pages = {79-83}, doi = {10.16250/j.32.1915.2026077}, pmid = {42046358}, issn = {1005-6661}, mesh = {*Bibliometrics ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; *Intensive Care Units ; *Metagenomics/methods ; }, abstract = {OBJECTIVE: To investigate the scientific outputs of metagenomic next-generation sequencing (mNGS) for diagnosis of infection of unknown origin in intensive care units (ICUs), and to decipher the latest advances, frontier trends and spatiotemporal evolution of research hotpots in mNGS for diagnosis of infection of unknown origin in ICUs.<br><br>METHODS: Publications pertaining to the application of mNGS in diagnosis of infection of unknown origin in ICUs were retrieved from Web of Science Core Collection (WOSCC) from January 1, 2015 to December 31, 2024. The software Scimago Graphica 1.0.30 was employed to generate the network maps of collaboration relationships between countries, international collaborative relationships, author collaborations, institutional collaborative relationships, and a heatmap of journals, and the software VOSviewer 1.6.18 was used to create a heatmap of keywords, and maps of keyword co-occurrence clustering and keyword clustering timelines. In addition, the keyword burst map was created using the software CiteSpace 6.3.R3.<br><br>RESULTS: A total of 1 707 publications were included in the final analysis, and the number of publications appeared an overall tendency towards a rise from 2015 to 2024, with the largest number of publications seen in 2024 (545 publications). The largest number of publications was recorded in China (1 390 publications), followed by in USA (190 publications) and United Kingdom (31 publications), and China led the global research in this field, with 81% of global related researches linked with China. Frontiers in Cellular and Infection and Microbiology published the largest number of articles (212 publications, 12.42%), and Joseph Derisi was the most productive author (33 publications). Author collaborations occurred within groups; however, there was a lack of close inter-group collaborations, with University of California, San Francisco and Chan Zuckerberg Biohub-based group seen as the largest collaborative group. High-frequency co-occurrence keywords included mNGS, infection, diagnosis, case report, community-acquired pneumonia and bronchoalveolar lavage fluid, and the 100 most common high-frequency co-occurrence keywords were assigned into four clusters. Keyword clustering timeline analysis revealed that the research hotspots in this field shifted from virus sequencing and sequence alignment to severe pulmonary infections, and keyword burst analysis showed identification, mNGS and virus as top three keywords with the highest burst intensity.<br><br>CONCLUSIONS: mNGS was mainly used for identification of viruses among patients with infections of unknown origins in ICUs from 2015 to 2024, and future research priority shifted to pathogen detection for severe pulmonary infections.}, }
@article {pmid42046871, year = {2026}, author = {Yang, Y and Tan, X and Zhang, Z and Liang, L and Wu, Z and He, J and Wang, Y and Dong, M and Zheng, J and Zhang, H and Feng, S and Cheng, W and Cui, B and Wei, H and Li, Q}, title = {Metagenomic sequencing reveals high reproducibility of human donor microbiota transplanted into germ-free mice via lower gut route.}, journal = {Journal of Zhejiang University. Science. B}, volume = {27}, number = {4}, pages = {375-389}, doi = {10.1631/jzus.B2400495}, pmid = {42046871}, issn = {1862-1783}, support = {2021YFA0805904//the National Key Research and Development Program of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Humans ; Mice ; Germ-Free Life ; *Fecal Microbiota Transplantation/methods ; Feces/microbiology ; *Metagenomics ; Reproducibility of Results ; High-Throughput Nucleotide Sequencing ; Male ; *Metagenome ; Mice, Inbred C57BL ; Female ; }, abstract = {Human flora-associated (HFA) mice are often used to simulate the structure of human intestinal microbiota and to study the causal relationships between diseases and gut microbiota. However, several factors affect the colonization efficiency of human microbiota in germ-free (GF) mice, and the differential effects of gavage and lower gut transplantation on colonization are still unclear. In this study, we explored the reproducibility of the recipient-to-donor gut microbiota community structure and function under different transplantation routes and the differences in microbial colonization between recipients via gavage transplantation (GT_mice group) and lower gut transplantation (LGT_mice group). High-throughput sequencing of the metagenome was performed on the feces of each subject, and the composition of microbiome of each group was analyzed. As expected, the introduction of human fecal microbiota into GF mice via lower gut transplantation had a high transfer efficiency, which was evident from the similar species community structure to that of the donor (Adonis R[2]=0.713 960 for LGT_mice group‒donor group; Adonis R[2]=0.774 095 for GT_mice group‒donor group) and a higher bacterial colonization rate. The findings provide unique insights into improving the accuracy of constructing humanized microbiota transplantation models, aiding our understanding of the relationships between the human gut microbiota and disease.}, }
@article {pmid42047611, year = {2026}, author = {Capone, K and Kuller, J and Durand, DJ and Tierney, NK and Lund, C}, title = {Exploration of Changes in the Human Skin Microbiome by Mode of Birth and Following First Bath.}, journal = {Pediatric dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/pde.70219}, pmid = {42047611}, issn = {1525-1470}, support = {UL1 TR000004/TR/NCATS NIH HHS/United States ; //Johnson &amp; Johnson Consumer Inc./ ; }, abstract = {BACKGROUND/OBJECTIVES: Microbes colonize the skin soon after birth, and the skin microbiome changes over time. However, the effects of bathing and hygiene products on the infant skin microbiome are not well studied. This randomized, single-center trial analyzed the skin microbiome in neonates born vaginally or via cesarean section (c-section), before and after their first bath with or without a mild baby cleanser.<br><br>METHODS: One hundred healthy full-term neonates were randomized to baths with water alone or with mild baby cleanser, stratified by delivery mode. Volar forearm swabs of neonates (before and after first bath) and their mothers were analyzed by 16S rRNA metagenomic sequencing.<br><br>RESULTS: At birth, neonates born vaginally had greater overall richness of the skin microbiome versus those born via c-section. Vaginally delivered neonates had similar species richness as their mothers, while neonates delivered via c-section had much lower species richness. Shannon diversity was similar regardless of birth mode, but community structure varied. Species richness was similar before and after bath in vaginally delivered neonates, but those born via c-section had higher species richness after their first bath and showed larger changes in community structures, compared with the vaginal group. Whether water alone or baby cleanser was used for the first bath did not greatly affect skin microbiome composition.<br><br>CONCLUSIONS: The mode of birth had the largest effect on the skin microbiome composition, richness, and structure. Neonates born via c-section showed the largest post-bath changes in the skin microbiome, while the use of water or baby cleanser had little effect.}, }
@article {pmid42047812, year = {2026}, author = {Zhu, R and Zhang, J and Shen, HL}, title = {Hip joint infection by Prevotella denticola in rheumatoid arthritis : A case diagnosed with metagenomic sequencing.}, journal = {Wiener klinische Wochenschrift}, volume = {}, number = {}, pages = {}, pmid = {42047812}, issn = {1613-7671}, abstract = {BACKGROUND: Infection, as a complication of rheumatoid arthritis (RA), has attracted increasing attention from rheumatologists. Here, we present the first case of RA with hip joint infection, which was driven by infection with Prevotella denticola. Anaerobic bacterial infection was identified by metagenomic next-generation sequencing (mNGS).<br><br>METHODS: We describe the case of a&#xa0;56-year-old woman with a&#xa0;history of RA who was admitted for intense hip joint pain and intermittent fever following long-term oral glucocorticoid (GC) treatment.<br><br>RESULTS: Although blood and hip joint effusion cultures for aerobic and anaerobic organisms were negative, we considered the possibility of a&#xa0;clinical diagnosis of hip joint infection; therefore, empirical antibiotic treatment was initiated but it was ineffective in this case. Prevotella denticola was identified by mNGS from the hip joint effusion obtained via ultrasound-guided puncture and the organism was resistant to the initial antimicrobial treatment. Finally, the adjustment of antimicrobial treatment led to successful treatment.<br><br>CONCLUSION: Patients with RA have a&#xa0;significantly greater risk of infections than the general population; however, Prevotella denticola infection of the hip joint has not been previously reported. The combination of ultrasound-guided puncture and mNGS to accurately recognize and treat joint infection in patients with RA in a&#xa0;timely manner is necessary to prevent the development of complications, a&#xa0;strategy worthy of further clinical application.}, }
@article {pmid42048337, year = {2026}, author = {Bernal Hernández, N and Rodríguez Cabal, HA and Pino, NJ and Ramírez Restrepo, S and Múnera Porras, LM}, title = {Metagenomic and taxonomic profiling of phyllosphere bacteria from Mangifera indica in response to urban air pollutants in Medellín, Colombia.}, journal = {PloS one}, volume = {21}, number = {4}, pages = {e0347959}, doi = {10.1371/journal.pone.0347959}, pmid = {42048337}, issn = {1932-6203}, mesh = {Colombia ; *Mangifera/microbiology ; *Bacteria/genetics/classification/drug effects ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Air Pollutants/metabolism ; Microbiota/genetics ; *Metagenome ; Phylogeny ; Cities ; }, abstract = {Urban trees and their phyllosphere-associated microbiota constitute a promising nature-based solution for mitigating urban air pollution. In this study, we characterized the taxonomic composition, diversity patterns, and functional potential of bacterial communities inhabiting the phyllosphere of Mangifera indica in two urban sites of Medellín, Colombia, with contrasting pollution levels and across two time points, analyzing a total of 12 samples. We integrated 16S rRNA gene amplicon sequencing, performed on the Illumina MiSeq platform, with shotgun metagenomic sequencing generated on the Illumina NovaSeq 6000 platform to assess community structure and the presence of genes involved in the degradation of airborne organic pollutants. Bacterial assemblages were dominated by Pseudomonadota (Proteobacteria), Actinomycetota, and Bacteroidota, with genera such as Methylobacterium, Pseudomonas, and Serratia consistently prevalent. Alpha diversity was higher in the highly polluted downtown, while beta diversity was shaped primarily by temporal variation. Functional annotation of metagenome-assembled genomes (MAGs) uncovered genes encoding complete aromatic hydrocarbon degradation pathways, including naphthalene, toluene, xylenes, and benzoate. Both ortho- and meta-cleavage routes for catechol degradation were detected, with temporal shifts in pathway dominance linked to changes in the abundance of key degraders taxa. These results reflect genetic potential for xenobiotic degradation within the M. indica phyllosphere microbiota, modulated by environmental conditions. Our findings highlight the ecological role of phyllosphere bacteria as contributors of inferred functional capacity relevant to atmospheric bioremediation and supports their integration into microbiome-informed green infrastructure strategies.}, }
@article {pmid42048878, year = {2026}, author = {Shi, W and Qin, Y and Li, W and Xu, J and Xu, H and Liu, Y}, title = {The dual role of phosphorus regeneration in controlling arsenic speciation: Iron-reducing bacteria in a seasonally ice-covered lake.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142206}, doi = {10.1016/j.jhazmat.2026.142206}, pmid = {42048878}, issn = {1873-3336}, abstract = {While the reductive dissolution of iron (hydro)oxides by dissimilatory iron‑reducing bacteria (DFeRB) can mobilize sediment bound arsenic (As), the role of concomitant phosphorus (P) regeneration in actively governing As speciation transformation, rather than mere release, remains mechanistically unclear, especially under seasonally contrasting redox regimes of ice-covered lakes. This study demonstrated that DFeRB mediated P regeneration exerts a dual, season‑dependent control over As speciation in lacustrine sediments. Through microcosm experiments simulating ice‑bound and summer periods, combined with sequential extraction, X‑ray diffraction, metagenomics, and structural equation modeling (SEM), and partial least-squares path modeling (PLS-PM), resolved that regenerated P not only promote As desorption via competitive adsorption but also redirect a substantial speciation of released As into a stable, pyrite‑coprecipitated pool (As‑S7). This sequestration pathway was particularly pronounced under ice‑bound anoxia, where DFeRB sustained a low‑rate, long‑duration reduction mode, as evidenced by persistent iron‑reduction gene (K02650, K17230) abundance and delayed As(III) peak release. SEM/PLS-PM quantified the seasonal shift in dominant mechanisms: summer release was driven by intensive P competition (including organic phosphorus), whereas ice‑bound conditions favored Fe‑S‑As co‑precipitation, effectively coupling prolonged microbial iron reduction to long‑term As immobilization. These findings establish P regeneration as a decisive switch between As mobility and stability in anaerobic sediments and define the seasonal microbial‑mineral feedbacks that modulate this switch. This work provides a predictive basis for assessing As fate in seasonally stratified water bodies under changing climatic conditions and a process-based basis for risk assessment and eutrophication management.}, }
@article {pmid42049031, year = {2026}, author = {Wong, O and Zheng, Z and Wang, M and Cao, A and Chan, FKL and Ng, SC and Su, Q}, title = {Microbiome biomarkers in autism spectrum disorder: Toward prediction, diagnosis, and prognosis.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {102780}, doi = {10.1016/j.xcrm.2026.102780}, pmid = {42049031}, issn = {2666-3791}, abstract = {Autism spectrum disorder (ASD) is a heterogeneous condition that lacks objective diagnostic biomarkers, often resulting in delayed intervention. Evidence increasingly links gut microbiota dysregulation to ASD pathophysiology via the microbiota-gut-brain axis, suggesting plausible translational applications. This review outlines mechanistic insights from preclinical and clinical studies to illustrate how microbial disturbances affect neurodevelopment. It examines the evolution of biomarker research from early 16S rRNA sequencing to advanced shotgun metagenomics incorporating functional integration, multi-omics, and genomic variants. Such advancements enhance diagnostic accuracy and generalizability. Although clinical causal evidence remains indirect, these microbial signatures show potential for early diagnosis, presymptomatic risk prediction, and tailored therapies. Key challenges include prospective validation in diverse cohorts, specificity testing against comorbidities, and addressing clinical heterogeneity. By summarizing methodological gaps and providing future guidance, this review aims to bridge mechanistic research and clinical practice to improve outcomes across the spectrum.}, }
@article {pmid42049067, year = {2026}, author = {Khandelwal, S and Mishra, A and Pandey, SK}, title = {Integrating microbial bioremediation, multi-omics, and emerging technologies for polycyclic aromatic hydrocarbon (PAHs) detoxification.}, journal = {Journal of microbiological methods}, volume = {}, number = {}, pages = {107519}, doi = {10.1016/j.mimet.2026.107519}, pmid = {42049067}, issn = {1872-8359}, abstract = {Environmental organic pollutants, identified as Polycyclic Aromatic Hydrocarbons (PAHs), are widespread and toxic. These hydrocarbons are commonly produced by industrial activities, burning fossil fuels, and crude oil discharges. Their high hydrophobicity, tendency to bioaccumulate, and mutagenic, carcinogenic, teratogenic, and genotoxic properties lead to significant environmental and human health risks. Additionally, their low bioavailability and chemical stability complicate PAHs remediation. In recent years, various methods have been explored to reduce their impact, including conventional physical and chemical treatments; however, these often face issues such as inadequate removal, high costs, lengthy processes, and environmental concerns. Bioremediation has emerged as a promising, environmentally friendly solution. This approach involves microorganisms such as bacteria, fungi, algae, and archaea utilizing specific enzymatic pathways-like dioxygenases, monooxygenases, peroxidases, and laccases-to transform PAHs into less toxic substances. Advances in genomics and metagenomics have identified key catabolic genes (e.g., nah, Phn, nid, pah) and regulatory mechanisms that enhance microbial resistance in PAH-contaminated environments. Since PAHs' low bioavailability and solubility often limit bioremediation alone, integrated strategies are gaining prominence. In-situ and ex-situ methods-including bioaugmentation, bio-stimulation, composting, and phytoremediation-boost microbial degradation of PAHs. Furthermore, advanced technologies such as multi-omics platforms, CRISPR-based genetic engineering, and artificial intelligence (AI) are transforming the field by enabling the development of targeted microbial strains, improving bioremediation efficiency, and creating predictive models. This review offers a recent, comprehensive outline by unifying PAHs toxicity, microbial degradation, traditional remediation, and advanced biotechnological tools into a single framework. A comprehensive and recent update of microbial and biotechnological approaches for sustainable PAHs bioremediation is offered by this review.}, }
@article {pmid41436515, year = {2025}, author = {Algarni, AD and Abd El-Samie, FE and Soliman, NF and Emara, HM and Algarni, F and Abd-Alhalem, SM and Marie, HS}, title = {Exploiting fuzzy weights in CNN model-based taxonomic classification of 500-bp sequence bacterial dataset.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {44733}, pmid = {41436515}, issn = {2045-2322}, mesh = {Datasets as Topic ; *Fuzzy Logic ; *Convolutional Neural Networks ; DNA, Bacterial/genetics ; *Bacteria/classification/genetics ; Deep Learning ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Computational Biology/methods ; }, abstract = {Taxonomic classification plays a crucial role in understanding the diversity and evolutionary relationships among bacteria. Accurately classifying bacterial DNA sequences based on a limited 500-bp segment remains challenging. This paper presents an improved Fuzzy-weighted Convolutional Neural Network (F-CNN) for taxonomic classification of bacterial DNA sequences, specifically focusing on the 500-bp segments. The proposed model aims to overcome the limitations of traditional classification methods by leveraging the power of deep learning and fuzzy logic processing. The improved fuzzy deep learning model is proposed to handle the problem of classifying samples with similar probabilities in the classification layer. It incorporates a feature selection stage using various techniques and a fuzzy weighting system to handle the uncertainty associated with similar classes in the classification layer and optimize parameters using fuzzy weights. The experimental results on the Ribosomal Database Project Release 11 (RDP 11) sequences dataset show the superiority of the proposed model, especially at the 500-bp region. Experimental results on the RDP 11 dataset, which includes over 1.4 million bacterial gene sequences, demonstrate the superior performance of the proposed model, achieving a classification accuracy up to 84.03% at the genus level for 500-bp segments and demonstrating high generalization when applied to longer sequences. This paper has significant implications for various fields, including microbiology, epidemiology, and environmental science, where accurate classification of bacteria is crucial for understanding their roles in different ecosystems and disease outbreaks.}, }
@article {pmid42035799, year = {2026}, author = {Chen, S and Zhu, B and Lu, X and Huang, Y and Wang, S and Wang, W and Chen, G and Wu, X and Zhou, J and Wu, F and Wu, K}, title = {Integrative multi-kingdom gut microbiome analysis uncovers clinical signatures of major depressive disorder.}, journal = {Journal of affective disorders}, volume = {}, number = {}, pages = {121858}, doi = {10.1016/j.jad.2026.121858}, pmid = {42035799}, issn = {1573-2517}, abstract = {BACKGROUND: Accumulating evidence indicates that gut microbiome is significantly altered in major depressive disorder (MDD). However, most studies have focused on bacteria, while the functional and ecological contributions of eukaryotes, archaea, and viruses in MDD remain poorly understood.<br><br>METHODS: Fecal samples were collected from 121 first-episode, drug-na&#xef;ve young adults with MDD and 117 healthy controls (HC) with matched demographic characteristics for shotgun metagenomic sequencing. Clinical data included the Hamilton Depression Scale (HAMD) and the MATRICS Consensus Cognitive Battery (MCCB). We systematically explored the multi-kingdom gut microbiome, functional genes, and metabolic pathways in MDD and their clinical associations, further assessing their diagnostic potential via machine learning.<br><br>RESULTS: MDD patients showed significant alterations in multi-kingdom microbiota diversity, accompanied by coordinated diversity relationships across microbial kingdoms relative to HC. In addition, we further identified 19 bacterial, 16 eukaryotic, 15 archaeal, and 10 viral species, as well as 22 functional genes and 32 metabolic pathways, that differed between groups. Importantly, five bacterial and four viral species were significantly associated with cognitive function, such as a positive correlation between Bifidobacterium pseudocatenulatum and attention/vigilance in MDD. Finally, validation demonstrated that a Random Forest model integrating multi-kingdom microbiota and functional features achieved superior diagnostic performance, significantly outperforming models based solely on bacterial features.<br><br>CONCLUSION: This study revealed extensive multi-kingdom microbial dysbiosis in MDD, providing deeper insight into disease-associated ecological disruption and highlighting the potential of microbial markers for enhancing clinical auxiliary diagnosis.}, }
@article {pmid42035921, year = {2026}, author = {Liu, H and Xie, B and Zhuo, H and He, B and Dai, J and Zhou, Z and Shen, G and Chen, B and Tang, J and Ren, H and Jiang, X}, title = {Molecular Traces of Microbial Cross-Kingdom Migration: From the Gut Ecosystem to the Intervertebral Disc Microenvironment.}, journal = {The spine journal : official journal of the North American Spine Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.spinee.2026.04.027}, pmid = {42035921}, issn = {1878-1632}, abstract = {BACKGROUND CONTEXT: Low back pain is a leading cause of disability worldwide, and lumbar intervertebral disc degeneration (IVDD) is strongly associated with its development. Recent studies have shown that the gut microbiota (GM) and its metabolites may be involved in the occurrence and development of IVDD through the gut-disc axis. However, the key microbes mediating this process and their specific molecular mechanisms remain unclear.<br><br>PURPOSE: This study aimed to identify the gut microbes that play a key role in the progression of IVDD using multi-omics approaches and clarify the specific mechanisms by which these microbes participate in IVDD by regulating host cell functions.<br><br>STUDY DESIGN/SETTING: A single center, prospective cross-sectional study.<br><br>PATIENT SAMPLE: We prospectively included 113 patients who underwent surgical treatment for symptomatic lumbar degenerative diseases from May 2022 to May 2023, and their degenerated lumbar intervertebral disc (IVD) tissues as well as paired feces samples were collected.<br><br>OUTCOME MEASURES: Metagenomic next-generation sequencing (mNGS), modified Pfirrmann typing, Single-cell RNA sequencing (scRNA-seq), Bulk RNA sequencing (Bulk RNA-seq).<br><br>METHODS: Clinical IVD samples and paired fecal samples were prospectively collected and subjected to multi-omics bioinformatics analysis. mNGS was used to analyze the microbial composition in IVD and paired fecal samples. scRNA-seq was employed to resolve the cellular heterogeneity of IVD tissues. Bulk RNA-seq was utilized to identify the characteristics of host response genes related to microbial exposure. Subsequent AUCell scoring was performed to evaluate the abundance of microbes in cell subsets. The CellChat algorithm was applied to analyze the microbe-mediated intercellular communication network of host cells.<br><br>RESULTS: The raw detection rate of mNGS in IVD tissues was 100%, with a positive rate of 60.2% (68/113) after excluding background bacteria. A total of 505 genera and 1,528 microbial species were detected, with dominant species including Stutzerimonas stutzeri and Moraxella osloensis. The mNGS detection rate in fecal samples was 100% (322 genera and 789 species), among which Phocaeicola vulgatus (PV) was a dominant species. A total of 7 bacterial species shared by GM and IVD were identified; however, only the relative abundances of PV and Bacteroides thetaiotaomicron (BT) increased gradually with the severity of IVDD. Single-cell RNA-seq identified 10 cell clusters, annotated as chondrocytes, macrophages, fibroblasts, and endothelial cells, with the proportions of the latter three non-chondrocyte populations being significantly higher in the severe IVDD group. Chondrocytes were further divided into subsets. Subsets MDC1 and MDC5 were related to mild degeneration with high expression of ACAN and SOX9, whereas SDC2, SDC3, SDC4, SDC6, and SDC7 were related to severe degeneration. AUCell scoring revealed that PV showed a significantly higher abundance in these pathological subsets, while BT was evenly distributed. Furthermore, chondrocytes with high PV abundance significantly upregulated matrix degradation genes including MMP13 and COL1A1, as well as cell adhesion genes such as POSTN and SPARC. These upregulated genes were significantly enriched in LPS-associated inflammatory cascades, extracellular matrix degradation, and metabolic reprogramming pathways. Crucially, LPS signaling genes including TLR4, MYD88, NFKB1, and RELA were upregulated in chondrocytes with high PV abundance, while short-chain fatty acid receptor genes were minimally expressed with no significant group differences. Finally, CellChat analysis revealed that high PV abundance amplified the communication between chondrocytes and macrophages, fibroblasts, and endothelial cells, which was mediated by the CXCL pathway for immune recruitment, the VEGF and ANGPT pathways for angiogenesis, and the TGF-&#x3b2; pathway for pro-fibrotic remodeling.<br><br>CONCLUSION: This study suggests that gut-derived PV may activate the inflammatory response of chondrocytes through the LPS-mediated TLR4-MYD88 signaling axis and reshape the intercellular communication network, thereby potentially contributing to the process of IVDD. These findings provide novel mechanistic insights into the gut-disc axis theory and offer new perspectives on IVDD therapeutic strategies targeting microbe-host interactions.}, }
@article {pmid42036057, year = {2026}, author = {Stem, AD and Alayyoub, M and Aalizadeh, R and Nikolopoulou, V and Lisgara, A and Shvartsman, A and Anitha, M and Patterson, A and Coble, R and Rushing, B and Sumner, S and Vasiliou, V}, title = {Integrated Multi-Omics Reveals Synergistic Hepatotoxicity of Ethanol and PFOS Co-Exposure.}, journal = {Chemico-biological interactions}, volume = {}, number = {}, pages = {112101}, doi = {10.1016/j.cbi.2026.112101}, pmid = {42036057}, issn = {1872-7786}, abstract = {Alcohol-associated liver disease (ALD) and exposure to per- and polyfluoroalkyl substances (PFAS) share key mechanisms of hepatotoxicity, yet their combined effects remain poorly characterized. We evaluated the impact of concurrent ethanol and perfluorooctanesulfonic acid (PFOS) exposure using a murine Lieber-DeCarli model characterized via multi-omic, spatial lipidomic, and metagenomic analyses. Exposure to PFOS resulted in rapid weight loss, while co-exposure led to decreased survival and pronounced hepatomegaly exceeding the effects of either exposure alone despite reduced cumulative ethanol intake. Histological analysis revealed enhanced hepatocellular injury with combined macrovesicular and microvesicular steatosis, consistent with impaired lipid handling and mitochondrial dysfunction. Transcriptomic and metabolomic profiling demonstrated disruption of xenobiotic metabolism, fatty acid β-oxidation, mitochondrial function, and bile acid transport, with PFOS acting as a dominant driver of metabolic stress and ethanol amplifying injury-related responses. Spatial lipidomics revealed hepatocyte-scale remodeling of membrane phospholipids, characterized by increased phosphatidic acid and depletion of phosphatidylinositol and phosphatidylserine under PFOS-containing conditions. Plasma metabolomics indicated systemic metabolic disturbance, including altered amino acid and redox pathways and depletion of microbiome-derived indole metabolites. Metagenomic analysis revealed reduced bacterial load and severe dysbiosis characterized by loss of commensal anaerobes, expansion of opportunistic taxa, and decreased microbial biosynthetic capacity. These findings indicate that PFOS increases susceptibility to alcohol-induced liver injury potentially through coordinated disruption of hepatic metabolism and gut-liver crosstalk, highlighting environmental PFAS exposure as a potential modifier of ALD severity.}, }
@article {pmid42036452, year = {2026}, author = {Byun, HR and Ji, SR and Frank, LE and Kipp, EJ and Larsen, PA and Chae, JS}, title = {Application of nanopore adaptive sampling for metagenomic detection of tick-borne RNA viruses.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-50572-5}, pmid = {42036452}, issn = {2045-2322}, support = {550-20250009//Seoul National University/ ; }, abstract = {Nanopore sequencing is a powerful tool for real-time pathogen detection and genomic characterization; however, its application to individual ticks is limited by abundant host-derived nucleic acids and low viral RNA levels. In this study, we applied nanopore adaptive sampling (NAS) to sequence viral RNA from individual Haemaphysalis (H.) ticks collected in the Republic of Korea (ROK). By combining NAS with long-read sequencing, high-resolution genome assembly can be achieved from samples containing low-abundance viral RNA and relatively short complementary DNA (cDNA) fragments generated during library preparation. These results indicate that NAS remains effective under suboptimal fragment-size conditions and improves genome assembly compared to conventional nanopore workflows. Phylogenetic analyses revealed that the detected Dabieshan tick virus (DTV) sequences were clustered with isolates from China and Japan, suggesting regional circulation facilitated by the widespread distribution of H. longicornis. Unlike previous studies relying on pooled samples without selective sequencing, NAS allowed high-resolution viral genome assembly from single ticks. These findings confirm the presence and genotypes of DTV for the first time in the ROK and demonstrate NAS as a practical, scalable approach for tick-borne RNA virus surveillance in single ticks, improving genomic assembly and supporting the monitoring of emerging tick-borne viruses in endemic regions.}, }
@article {pmid42036496, year = {2026}, author = {Tow, WK and Teh, CSJ and Ooi, CW and Lee, RFS and Krishnasamy, M and Palanisamy, UD and Sundralingam, U}, title = {Metagenomic insights into urolithin formation from rambutan rind extract by rat faecal-derived microbiome.}, journal = {Applied microbiology and biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00253-026-13841-x}, pmid = {42036496}, issn = {1432-0614}, abstract = {Ellagitannins and ellagic acid are microbially converted into urolithins, metabolites associated with antioxidant, anti-inflammatory, and mitochondrial-related activities. Although several human-derived urolithin-producing strains and their associated enzymes have recently been characterised, the diversity of microbial strategies across host systems remains poorly understood. This study investigated urolithin production in the Sprague-Dawley rat faecal-derived microbial communities supplemented with rambutan rind extract, an ellagitannin-rich agricultural by-product containing 35-40% geraniin. Rambutan rind extract supplementation was associated with reduced isobutyric acid levels at study endpoint. Ex vivo anaerobic fermentation of hydrolysed rambutan rind extract (113 µM ellagic acid equivalent) resulted in the formation of urolithin C (9.4 ± 0.6 µM) and Isourolithin A (12.5 ± 0.6 µM) by day 9. Shotgun metagenomics analysis revealed very low relative abundance of Actinobacteria (< 0.009%), despite this phylum encompassing most previously characterised urolithin-producing taxa. Canonical ellagic acid degradation genes and the MetaCyc EA degradation pathway were not detected. Comparative pathway analysis indicated overlap in general metabolic pathways with Ellagibacter isourolithinifaciens DSM 104140[T] reflecting shared metabolic frameworks rather than conserved urolithin biosynthetic pathways, with highly divergent homologues (Eadh1, Eadh2, Eadh3, and Ucdh). Together, these findings demonstrate that rambutan rind extract can support urolithin formation in rat faecal-derived microbial consortia and highlight functional associations consistent with alternative or yet-uncharacterised microbial strategies for ellagitannin biotransformation. These findings support a discovery-driven framework for investigating urolithin biotransformation in non-human gut microbiomes using ellagitannin-rich agricultural substrates. KEY POINTS: • Rambutan rind extract supports urolithin formation in rat-derived gut microbiota. • Substrate concentration influences urolithin production under ex vivo conditions. • Rat gut microbiota shows homologues' divergence in urolithin-associated proteins.}, }
@article {pmid42036837, year = {2026}, author = {Yancey, CE and Brumfield, KD and Buss, JA and Colwell, RR and Ettwiller, L}, title = {A Bait-and-Switch Strategy Links Phenotypes to Genes Coding for Polymer-Degrading Enzymes in Intact Microbiomes.}, journal = {Microbial biotechnology}, volume = {19}, number = {4}, pages = {e70359}, doi = {10.1111/1751-7915.70359}, pmid = {42036837}, issn = {1751-7915}, support = {//New England Biolabs/ ; OCE1839171//National Science Foundation/ ; CCF1918749//National Science Foundation/ ; CBET1751854//National Science Foundation/ ; R01ES030317A/ES/NIEHS NIH HHS/United States ; 80NSSC20K0814/NASA/NASA/United States ; 80NSSC22K1044/NASA/NASA/United States ; }, mesh = {*Microbiota ; *Chitin/metabolism ; Soil Microbiology ; *Bacteria/enzymology/genetics/classification ; Phenotype ; Chitinases/genetics/metabolism ; Genetic Association Studies ; }, abstract = {Natural microbial communities, with their vast diversity and complexity, are among the richest sources of untapped novel enzymes. Identifying novel enzymes can be challenging because microbiomes often lack clear, measurable phenotypes, unlike laboratory cultures where enzymatic activity can be linked to genetic elements. These constraints have left much of the functional diversity within microbiomes inaccessible to enzyme discovery efforts. Here, we present a genotype/phenotype association framework directly on microbial communities for enzyme discovery. For this, we developed a 'bait-and-switch' treatment strategy that generates measurable dual phenotypes directly within intact microbiomes. Using soil microbiomes as a test system, we applied chitin-rich compost as 'bait' to enrich chitin-degrading organisms, followed by glucose addition to functionally 'switch' the community. This treatment produced a distinct phenotypic signature: prevalence of known chitin degradation genes increases during the bait phase, and their transcripts are rapidly downregulated during the switch phase. By performing hypothesis-free association analysis of protein domains with this dual phenotype, we identified the glycoside hydrolase 18 as the most significantly associated protein domain. Experimental validation confirmed chitinase activity in 63% of tested enzymes, including candidates from unculturable bacteria and those with previously uncharacterized domain architectures. This species-independent, reference-free approach to discover novel enzymes has broad applications in microbiome engineering, biopolymer processing and systems biology, offering a generalizable strategy for functional gene discovery in complex microbial systems.}, }
@article {pmid42037322, year = {2026}, author = {Thouvenot, K and Serrat, F and Lenclume, V and Doussiet, E and Belda, E and Taïlé, J and Alili, R and Rondeau, P and Clément, K and Meilhac, O and Le Moullec, N and Gonthier, MP}, title = {Periodontitis in Patients With Severe Obesity: From the Oral and Gut Microbiota Dysregulation to the Visceral Adipose Tissue Inflammatory and Metabolic Disorders.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {40}, number = {9}, pages = {e71828}, doi = {10.1096/fj.202600054R}, pmid = {42037322}, issn = {1530-6860}, support = {APIDOM-BACTERIOB//CHU de La R&#xe9;union/ ; //Institut National de la Sant&#xe9; et de la Recherche M&#xe9;dicale (Inserm)/ ; //University of La R&#xe9;union/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Periodontitis/microbiology/metabolism/complications/pathology ; Male ; Female ; *Intra-Abdominal Fat/metabolism/pathology ; Middle Aged ; Adult ; *Obesity, Morbid/microbiology/complications/metabolism ; *Inflammation/metabolism/microbiology/pathology ; *Metabolic Diseases/microbiology/metabolism ; Dysbiosis/microbiology ; Porphyromonas gingivalis ; *Mouth/microbiology ; }, abstract = {During periodontitis, pathogenic oral bacteria like Porphyromonas gingivalis may exert systemic effects directly by translocating into the bloodstream and indirectly by deregulating the gut microbiota, aggravating obesity-related complications. This study aimed to evaluate the links between the periodontal infection, the oral and gut microbiota composition, and the inflammatory and metabolic profile during obesity. Thirty-nine patients suffering from severe obesity, with (n = 23) or without (n = 16) periodontitis, were enrolled. We examined the subgingival microbiota composition, periodontal status and salivary inflammatory response. The fecal microbiota composition was assessed by metagenomic analysis. Inflammatory and metabolic markers were measured in the plasma and epiploon visceral adipose tissue collected during bariatric surgery. Results show that patients with periodontitis exhibited an oral microbiota dysbiosis characterized by an increased abundance of bacteria from the red and orange complexes, worsened periodontal parameters (plaque index, bleeding index, gingival recession, probing depth and clinical attachment level), and higher IL-6 salivary levels. In fecal samples of patients with periodontitis, a higher proportion of the Proteobacteria phylum and changes in functional profile of bacteria were detected. Periodontitis was also linked to higher circulating concentrations of anti-P. gingivalis IgG, total cholesterol and lipoprotein (a). Moreover, periodontitis was associated with an enhanced production of TLR2, MyD88 and TGFβ, as well as higher activities of SOD and catalase antioxidant enzymes in the adipose tissue. Overall, these findings demonstrate that during obesity, the periodontal infection correlates with deregulated oral and gut microbiota composition, higher levels of pro-inflammatory mediators, and altered markers of oxidative stress and lipid metabolism.}, }
@article {pmid42037351, year = {2026}, author = {Chakraborty, S and Mukherjee, D and Sar, P}, title = {Genome-resolved insights into arsenic-impacted paddy soil and microcosm-derived microbiomes from West Bengal, India.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0005926}, doi = {10.1128/mra.00059-26}, pmid = {42037351}, issn = {2576-098X}, abstract = {This study reports 32 metagenome-assembled genomes (MAGs) reconstructed from arsenic (As)-impacted paddy soils of West Bengal, India, and microcosms from these soil samples. These MAGs, represented by 10 bacterial and 2 archaeal phyla, provided critical insights into the metabolic and biogeochemical potential of microbiomes in a highly As-impacted agroecosystem.}, }
@article {pmid42037384, year = {2026}, author = {Yang, K and King, S and Marshak, A and D'Mello-Guyett, L and Grignard, L and Knee, J and Wong, G and Zhao, L and Lamaka, NG and Save, D and Gose, M and Myers, A and Trehan, I and Cumming, O and Stobaugh, H and Schwartz, DJ}, title = {Gut microbiome associations with acute malnutrition relapse in South Sudan.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0358725}, doi = {10.1128/spectrum.03587-25}, pmid = {42037384}, issn = {2165-0497}, abstract = {Severe acute malnutrition (SAM) is a leading cause of childhood morbidity and mortality that is defined by anthropometric measurements, weight-for-height z score, and mid-upper arm circumference (MUAC) falling significantly below healthy standards. While treatments for SAM and our understanding of this disease have advanced, children experiencing SAM frequently relapse to acute malnutrition (AM) following anthropometric recovery. Little is known about the contribution of the gut microbiome to AM relapse. We hypothesized that features of the gut microbiome, including microbial composition, antimicrobial resistance gene carriage, and predicted microbial functional pathways, of children discharged from treatment for uncomplicated SAM in South Sudan, may be associated with AM relapse at 1-month follow-up. Overall, broad microbiome profiles at discharge were not associated with AM relapse. We evaluated the associations of microbiome features with AM relapse 1-month post-recovery using mixed linear effect models. We identified associations between higher MUAC, which may be a proxy for future health trajectories, and increased Sutterella wadsworthensis and trimethoprim-resistant dihydrofolate reductase antimicrobial resistance genes. These findings suggest that the gut microbiome at discharge of children treated for uncomplicated SAM has limited predictive value as a standalone diagnostic tool for identifying relapse risk at 1 month.IMPORTANCESevere acute malnutrition (SAM) is a devastating illness that impacts the morbidity and mortality of millions of children worldwide. Community-based management of acute malnutrition (CMAM) is the standard of care in South Sudan and many other low-resource settings for children presenting with SAM. Despite this intervention, children treated for SAM under CMAM frequently relapse to acute malnutrition (AM) following treatment. With advancements in our understanding of malnutrition, there has been a strong and growing interest in developing microbiome-based strategies to treat, prevent, and predict relapse to AM following treatment for SAM. Our work characterizes gut microbiome features of children from a geographic area that is traditionally underrepresented in gut microbiome research and shows that in isolation, a child's gut microbiome at discharge likely holds low predictive value for relapse to AM post-CMAM treatment; however, we identified key microbes and microbial features meriting further research.}, }
@article {pmid42037401, year = {2026}, author = {Wu, Q and Wu, D and Wang, J and Wang, H and Peng, J and Zhao, Y and Chen, J and Yuan, Q}, title = {Lytic viruses drive the decrease in polyphosphate-accumulating and phosphate-solubilizing potential of microbial communities with increasing reservoir age.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0248125}, doi = {10.1128/aem.02481-25}, pmid = {42037401}, issn = {1098-5336}, abstract = {River damming often leads to significant phosphorus enrichment in reservoir sediments and increases the risk of eutrophication with reservoir age. Microorganisms mediate critical steps of phosphorus cycling in ecosystems, and viruses are recognized as key regulators of microbial community structure and function. However, their influence on phosphorus-cycling microorganisms (PCMs) in freshwater environments remains poorly understood. In this study, surface sediment samples were collected from nine reservoirs (12-59 years old) of southwest China and analyzed using metagenomic and metatranscriptomic approaches to profile both PCMs and viral communities. The results demonstrated that the diversity of lytic viruses was the primary factor governing both shifts in the community stability of PCMs and the restructuring of P-cycling gene patterns with increasing reservoir age. Specifically, viral lysis reduced the relative abundance of dominant PCMs, thereby enhancing community diversity and stability. Concurrently, viral activity diminished PCMs' functional potential for phosphate solubilization and polyphosphate accumulation, while stimulating high-affinity inorganic phosphate (Pi) transport. Furthermore, viruses encoded auxiliary metabolic genes (AMGs) related to phosphate solubilization, mineralization, accumulation, and transport, underscoring the viral role in regulating phosphorus retention and release. Compared to polyphosphate-accumulating microorganisms, phosphate-solubilizing microorganisms may be more susceptible to viral infection. Additionally, viral activity was associated with an increase in the relative abundance of Cyanobacteria. Taken together, our results suggest viruses are key regulators of PCMs, highlighting that they should be incorporated into future strategies for assessing and mitigating reservoir eutrophication.IMPORTANCESediment microorganisms are regarded as the engine for endogenous phosphorus release in reservoirs. Therefore, understanding their dynamics and key driving factors is essential for effective eutrophication mitigation. Viral lysis and virus-encoded auxiliary metabolic genes (AMGs) may constitute a critical yet understudied mechanism influencing microbial phosphorus cycling. Our study provides unique, time-series-based mechanistic insights into how viral activity, in the context of large-scale artificial projects (river damming), restructures microbial phosphorus cycling and its potential ecological effects over decades.}, }
@article {pmid42037579, year = {2026}, author = {Virtuoso, FAS and Boekhorst, J and van Ravenstein, S and Schouten, D and Juanpere-Borràs, M and Broekhuis, F and Vissia, S and Mazebedi, R and Araldi, A and van Langevelde, F}, title = {DIY: A Practical Field-to-Sequencer Workflow for Metabarcoding the Diet of Terrestrial Carnivore Species.}, journal = {Molecular ecology resources}, volume = {26}, number = {4}, pages = {e70144}, doi = {10.1111/1755-0998.70144}, pmid = {42037579}, issn = {1755-0998}, support = {//Wageningen University and Research/ ; }, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Feces/chemistry ; *Diet ; *Carnivora/physiology/classification ; Workflow ; *Metagenomics/methods ; }, abstract = {Metabarcoding of faecal samples is a powerful, non-invasive approach for investigating the feeding ecology of carnivores, revealing prey diversity and unexpected dietary components with greater resolution than traditional methods. However, the approach remains technically demanding, as challenges and potential biases arise at every stage, from scat collection and DNA extraction to primer selection, sequencing, and data interpretation. Methodological details for these steps are often scattered across studies, limiting reproducibility and accessibility for ecologists. Here, we present a comprehensive field-to-sequencer workflow for dietary metabarcoding of terrestrial carnivores using Oxford Nanopore Technologies (ONT), covering all stages from sample collection to ecological interpretation. Drawing on field-collected scats of brown (Parahyaena brunnea) and spotted hyenas (Crocuta crocuta) across arid and semi-arid savannas in Botswana, we illustrate practical decisions, technical considerations, and common pitfalls encountered throughout the process. By integrating field, laboratory, and bioinformatic components into a single, accessible framework, this paper provides a pragmatic reference for ecologists aiming to design robust, transparent, and comparable studies of carnivore diet composition.}, }
@article {pmid42038227, year = {2026}, author = {Fu, L and Zhang, Y and Wang, L and Li, X}, title = {Primary amoebic meningoencephalitis caused by Naegleria fowleri in a 6-year-old girl: case report.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1801355}, pmid = {42038227}, issn = {2296-2360}, abstract = {BACKGROUND: Primary amoebic meningoencephalitis (PAM) is caused by Naegleria fowleri, a rare but highly fatal central nervous system infection with a mortality rate exceeding 95%. Early diagnosis is challenging due to the close similarity of its clinical manifestations and cerebrospinal fluid (CSF) findings to those of acute bacterial meningitis. Metagenomic next-generation sequencing (mNGS) has become a vital tool for identifying rare or unexpected pathogens.<br><br>CASE PRESENTATION: A previously healthy 6-year-old girl was admitted with fever, vomiting, and headache of 1 day's duration. Six days before symptom onset, she had played in natural freshwater bodies. After admission, she developed persistent high fever and rapidly progressive altered mental status, followed by two episodes of generalized tonic-clonic seizures, hemoptysis, acute respiratory failure, and circulatory shock. Initial cranial magnetic resonance imaging showed no abnormalities. CSF analysis revealed marked inflammatory changes: a white blood cell count of 3,072&#x2009;&#xd7;&#x2009;10[6]/L, markedly elevated protein (3,667.6&#x2005;mg/L), and significantly decreased glucose (0.08&#x2005;mmol/L). Despite administration of broad-spectrum antibiotics, glucocorticoids, osmotherapy, and comprehensive intensive care unit management, the patient died approximately 11&#x2005;h after admission following three cardiac arrests. Two days postmortem, CSF mNGS confirmed infection with Naegleria fowleri (copy number 3&#x2009;&#xd7;&#x2009;10[5]&#x2005;copies/mL), establishing the diagnosis of PAM.<br><br>CONCLUSIONS: This pediatric case serves as a warning that PAM should be considered in children with a history of freshwater exposure and rapidly progressive meningoencephalitis, even when early imaging is normal and CSF findings resemble bacterial meningitis. Early lumbar puncture, rapid molecular diagnostics, and heightened clinician vigilance are critical for the timely initiation of targeted therapy.}, }
@article {pmid42038247, year = {2026}, author = {Li, X and Jiang, Y and Dai, R and Yang, Y and Wang, W}, title = {Rickettsia felis meningoencephalitis in a child: a case report and literature review.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1763281}, pmid = {42038247}, issn = {2296-2360}, abstract = {Rickettsia felis (R. felis) infection occasionally invades the central nervous system, causing encephalitis or meningoencephalitis. Although the disease typically presents as mild to moderate illness, delayed diagnosis and treatment may increase the risk of adverse prognosis in pediatric patients. This article reports a case of R. felis meningoencephalitis in a child diagnosed by metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid. mNGS analysis detected high-confidence R. felis-specific sequences, and potential background microbial contamination was effectively excluded through a bioinformatics pipeline, thereby providing critical evidence for etiological confirmation. Due to insufficient clinical awareness, limited pathogen detection methods, and the self-limiting nature of the disease, R. felis infection is prone to missed diagnosis and misdiagnosis in febrile children. The clinical manifestations are nonspecific; even with central nervous system involvement, routine laboratory tests are unlikely to suggest the microbial etiology, contributing to the underrecognition and underreporting of pediatric R. felis meningoencephalitis. Therefore, enhancing diagnostic awareness and achieving early precise diagnosis and treatment may help shorten the disease course and improve patient outcomes.}, }
@article {pmid42038299, year = {2026}, author = {Liu, HJ and Wang, LF and Li, XY and Li, L}, title = {Toxicity-guided dose modification for disseminated Nocardia farcinica brain abscess in a patient with pneumoconiosis: a brief research report.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1805920}, pmid = {42038299}, issn = {1663-9812}, abstract = {BACKGROUND: Optimal antimicrobial strategies for disseminated nocardiosis with central nervous system (CNS) involvement remain poorly defined, particularly regarding trimethoprim-sulfamethoxazole (TMP-SMX) dosing in immunocompromised patients with severe drug intolerance.<br><br>METHODS: This observational case study analyzed the clinical course and pharmacological management of a 55-year-old male gold miner with pneumoconiosis and chronic corticosteroid use who developed Nocardia farcinica brain abscess. Diagnosis was established via metagenomic next-generation sequencing (mNGS) and phenotypic culture. An individualized antimicrobial regimen was designed based on toxicity monitoring.<br><br>RESULTS: Diagnosis of N. farcinica was confirmed by mNGS within 48&#xa0;h. The patient initially failed empirical meropenem but responded to combination therapy with imipenem, amikacin, and TMP-SMX. Due to grade III gastrointestinal toxicity (CTCAE v5.0), TMP-SMX was de-escalated from 15&#xa0;mg&#xb7;kg[-1]&#xb7;d[-1]-11.25&#xa0;mg&#xb7;kg[-1]&#xb7;d[-1], with maintenance at 7.5&#xa0;mg&#xb7;kg[-1]&#xb7;d[-1]. Clinical improvement was observed at Day 120, though durable cure remains unconfirmed.<br><br>CONCLUSION: In extreme circumstances of severe dose-limiting toxicity, temporary TMP-SMX dose reduction with intensive monitoring may be feasible as a bridge to complete guideline-concordant therapy, though this approach falls below current recommendations and requires robust therapeutic drug monitoring. Species-directed antimicrobial selection and early molecular diagnosis facilitated initial clinical resolution in this high-risk immunocompromised host.}, }
@article {pmid42038409, year = {2026}, author = {Nousias, O and Duffy, FG and Duffy, IJ and McCauley, M and Whilde, J and Duffy, DJ}, title = {Long-read nanopore shotgun metagenomic DNA sequencing for river biodiversity, wildlife, pollution, and environmental health monitoring.}, journal = {NAR genomics and bioinformatics}, volume = {8}, number = {2}, pages = {lqag040}, pmid = {42038409}, issn = {2631-9268}, mesh = {Animals ; *Rivers/microbiology ; *Biodiversity ; *Metagenomics/methods ; *Environmental Monitoring/methods ; Humans ; *Nanopore Sequencing/methods ; DNA, Environmental/genetics ; Environmental Health ; Animals, Wild/genetics ; Metagenome ; }, abstract = {As the human population expands and global temperatures rise, species, populations, and biodiversity decline at unprecedented rates, while the frequency of infectious disease emergence increases. Therefore, it is more vital than ever to accurately understand the current state of natural habitats and their constituent species. We assess the feasibility of a single assay: long-read shotgun metagenomic sequencing of environmental DNA (eDNA), to monitor species from across the tree of life, from viruses to complex multicellular organisms, across a representative Irish river system (Avoca River, Co. Wicklow). We conducted aquatic eDNA sampling and long-read shotgun metagenomic sequencing from a mountain tributary through to the sea. This approach could detect and quantify organismal DNA present in environmental samples, from microbes (including DNA viruses) to mammals. Rather than the traditional siloing of microbial and multicellular studies of DNA recovered from environmental samples, simultaneously considering viruses, microbes, and eukaryotes (animals, plants, and fungi) can provide deeper insights. This single assay can simultaneously quantify differences in DNA abundance for a broad range of species and pathogens across sites and sample types, enabling wide-ranging biodiversity assessments. This included human, wildlife, plant, and microbial pathogens and parasites with health, agricultural, and economic importance. The environmental genomic data enabled animal phylogeny and transmissible cancer analysis (blue mussel, Mytilus edulis) even from natural complex community settings. Oxford Nanopore sequencing provides a quantitative approach for river biodiversity, pollution, and environmental health monitoring. Long-read shotgun metagenomic sequencing of environmental samples offers the means to assess whole ecosystems and the ecological, trophic, and host-pathogen interactions occurring within them.}, }
@article {pmid42038418, year = {2026}, author = {Vlasovets, O and Schaipp, F and Simpson, L and Bolyen, E and Caporaso, JG and Mueller, CL}, title = {Sparse regression, classification, and microbial network estimation in QIIME2 with q2-classo and q2-gglasso.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {42038418}, issn = {2331-8422}, abstract = {MOTIVATION: Statistical analysis of microbial count data derived from 16S rRNA or metagenomics sequencing poses unique challenges due to the sparse, compositional, and high-dimensional nature of the data. While QIIME 2 already provides many tools for data pre-processing and analysis, plugins for statistical regression, classification, and microbial network estimation tailored to compositional count data are relatively scarce.<br><br>RESULTS: We present q2-classo and q2-gglasso, two novel QIIME 2 plugins that implement penalized regression, classification, and graphical modeling approaches for microbial compositional data. q2-classo enables the prediction of a continuous or binary outcome of interest using compositional microbiome data as predictors. Both sparse log-contrast regression and classification, as well as tree-aggregated log-contrast models are available. q2-gglasso enables the estimation of taxon-taxon association networks through sparse graphical model estimation, such as, e.g., the SPIEC-EASI framework, as well as adaptive and latent graphical models. The latent model can decompose taxon-taxon associations into a sparse direct interaction matrix and a latent (low-rank) matrix which enables robust principal component embedding of a data set. Within the QIIME 2 ecosystem we demonstrate their application on the Atacama soil microbiome dataset, illustrating robust model selection, classification, and microbial network estimation with covariates and latent factors.<br><br>AVAILABILITY: The software is freely available under the BSD-3-Clause License. Source code is available at https://github.com/bio-datascience/q2-gglasso and https://github.com/bio-datascience/q2-classo-latest, with installation through QIIME 2 and Docker.}, }
@article {pmid42038553, year = {2026}, author = {Rodríguez-Rodríguez, Y and Disla, AMM and Ortega, MER and Gandini, G and Tejada-Tejada, P and Guevara, M&#xc1; and Franco, EF and Dantas, CWD and Ramos, RT and Jáuregui-Haza, UJ}, title = {Microbial Profiling and Biosafety Assessment of a Sargassum-Based Liquid Biofertilizer Using 16S rRNA Metagenomics.}, journal = {International journal of microbiology}, volume = {2026}, number = {}, pages = {3219583}, pmid = {42038553}, issn = {1687-918X}, abstract = {Sargassum seaweed is increasingly abundant in the Caribbean, creating ecological disruption but also providing biomass for agricultural inputs. This study compares the microbial diversity and safety of a Sargassum-based liquid biofertilizer (SBLB-INTEC) with those of a conventional product (LB-BANELINO) using 16S rRNA amplicon sequencing, rather than culture-dependent methods. Both formulations contained key nutrients (K, Ca, and Mg) and low levels of heavy metals. They harbored dense but relatively simple bacterial communities dominated by Firmicutes, particularly Bacilli, with Proteobacteria and other phyla at lower abundances. Staphylococcus (Staphylococcaceae) was highly abundant in both products, while SBLB-INTEC showed a somewhat more balanced community, including Delftia and other Comamonadaceae. Shannon diversity tended to be higher in SBLB-INTEC, but differences in alpha- and beta-diversity between formulations were not statistically significant. Because 16S data cannot distinguish viable from nonviable cells or resolve strain-level pathogenicity, these results do not prove the absence of pathogens; instead, they provide a genus-level baseline to guide targeted culture, qPCR, and functional assays. Overall, the combination of a favorable chemical profile and microbial groups commonly associated with nutrient cycling and plant-associated functions suggests that SBLB-INTEC could become a valuable component of integrated nutrient management in tropical agriculture, offering hope for a more sustainable future pending confirmatory plant-response and biosafety studies. We recommend integrating these microbial data into a national biofertilizer monitoring framework, combining metagenomic surveys with targeted qPCR and resistance gene screening.}, }
@article {pmid42038636, year = {2026}, author = {Ryder, JH and Turbett, SE}, title = {Mindful diagnostics: a central nervous system infection case study.}, journal = {Antimicrobial stewardship &amp; healthcare epidemiology : ASHE}, volume = {6}, number = {1}, pages = {e96}, pmid = {42038636}, issn = {2732-494X}, abstract = {A clinical case is presented to discuss a framework for use of advanced diagnostics for central nervous system infections. Advantages, limitations, and diagnostic stewardship strategies are discussed for each modality: multiplex molecular meningitis/encephalitis panel, plasma microbial cell-free DNA sequencing, and cerebrospinal fluid metagenomic next generation sequencing.}, }
@article {pmid42039195, year = {2026}, author = {Liu, Y and Liao, X and Chen, Q and Wang, H and Dai, H}, title = {What is the impact of the virome and mycobiome on female reproductive tract health? A systematic scoping review.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1749584}, pmid = {42039195}, issn = {1664-3224}, mesh = {Female ; Humans ; *Virome ; *Mycobiome ; *Vaginosis, Bacterial/microbiology/virology ; *Microbiota ; Papillomavirus Infections/microbiology/virology ; Vagina/microbiology/virology ; *Reproductive Health ; *Genitalia, Female/microbiology/virology ; Bacteriophages ; }, abstract = {BACKGROUND: Traditional research on the female reproductive tract (FRT) microbiome has focused on the dominance of bacteria, particularly Lactobacillus, as a marker of health. This bacteriocentric paradigm, however, cannot fully explain clinical enigmas like the high recurrence of bacterial vaginosis (BV) or the persistence of HPV infection. This review introduces a new pan-microbiome framework that highlights the overlooked roles of the virome and mycobiome as the ecosystem's neglected components.<br><br>METHODS: We conducted a systematic scoping review following the PRISMA-ScR guidelines. We searched PubMed, Embase, and Web of Science databases for studies published up to October 2025. Inclusion criteria focused on original research and metagenomic studies examining the female reproductive tract (FRT) virome, mycobiome, and bacteriome, specifically their interactions and clinical associations with bacterial vaginosis (BV) and HPV persistence. Data were extracted and synthesized to evaluate the pan-microbiome framework.<br><br>RESULTS: The virome and mycobiome, despite their low biomass, are increasingly recognized as potential ecosystem modulators. Bacteriophages, for instance, are proposed to act as community "modulators," either through lytic cycles that maintain bacterial diversity or lysogenic cycles that may contribute to stabilizing pathogenic biofilms in dysbiosis like BV by introducing virulence genes. Similarly, fungi like Candida can transition from harmless commensals to pathogens when the protective bacterial balance is disturbed.<br><br>CONCLUSION: FRT health is an emergent property of the complex interactions among bacteria, viruses, and fungi. A comprehensive understanding requires a pan-microbiome perspective. Future therapeutic strategies should move beyond a "one-bug, one-drug" approach toward "ecosystem restoration," using targeted methods like phage therapy or vaginal microbiota transplantation to attempt to restore the balance of the entire microbial community.}, }
@article {pmid42039480, year = {2026}, author = {Liu, J and De Paolis Kaluza, MC and Bromberg, Y}, title = {16S rRNA k-mer composition encodes microbial functional potential.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.16.718937}, pmid = {42039480}, issn = {2692-8205}, abstract = {16S rRNA amplicon sequencing is widely used to profile microbiome taxonomic composition and functional potential. Most 16S rRNA-based analysis methods depend on comparing sequenced reads against reference marker genes from previously characterized organisms. Thus, method accuracy declines in environments dominated by uncharacterized microbes. We uncovered a direct link between 16S rRNA and genome-encoded functions. Using fully sequenced bacterial genomes, we show that (i) whole-genome k-mer composition is predictive of functions encoded in the genome and (ii) 16S rRNA k-mer profiles reflect their source genome k-mer compositions. Leveraging these relationships, we developed embeRNA, a neural network-based framework that predicts functions directly from 16S rRNA k-mer embeddings, without taxonomy assignment or phylogenetic placement. Furthermore, by producing per-function probability scores rather than categorical assignments, embeRNA allows users to adapt decision thresholds to match study goals and sample characteristics, e.g. balancing precision vs. recall or accounting for community novelty. We trained embeRNA on a large collection of bacterial function-omes and evaluated it using a stringent "novel microbes" benchmark, where all test 16S rRNA sequences were dissimilar to those seen in training (all <97% identical). On this test set of phylogenetically novel organisms, embeRNA outperformed reference-based methods overall and achieved significantly better performance for the "hard to label" set of functions. In testing on soil metagenomes with paired 16S rRNA amplicon and whole metagenome shotgun (WMS) sequencing data, embeRNA recovered most WMS-inferred functions and yielded abundance profiles strongly correlated with WMS results. Together, our results indicate that 16S rRNA k-mer composition carries substantial functional signal and that 16S amplicon data can be used to complement WMS-based inference to broaden functional characterization of microbiomes, particularly in understudied environments.}, }
@article {pmid42039609, year = {2026}, author = {Maldonado Pereira, L and Mutawi, TMA and Singh, A and Sanderson, B and Rekowski, MJ and Barnaba, C and Medina Meza, IG}, title = {Dietary Oxysterols Reprogram Hepatic Lipid Metabolism and Reshape the Gut Metabolome-Microbiome Interface.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.12.717948}, pmid = {42039609}, issn = {2692-8205}, abstract = {Dietary oxysterols are biologically active cholesterol oxidation products ubiquitous in Western diets, yet their systemic effects on host metabolism and the gut microbiome remain largely unexplored. Here, we employed an integrated multi-omics approach - shotgun metagenomics, quantitative proteomics, untargeted metabolomics, and bulk RNA-seq - to characterize the impact of DOxS exposure on the gut-liver axis in rats fed a Western diet (WD vs. WD-DOxS). Hepatic proteomics revealed near-complete suppression of the mevalonate/cholesterol biosynthesis pathway, particularly in males, while de novo lipogenesis enzymes (Scd1, Fasn, Plin2) were paradoxically upregulated, consistent with dual oxysterol signaling through SREBP inhibition and LXR activation. Bile acid synthesis was concurrently suppressed, confirmed by metabolomics. Strikingly, RNA-seq across liver, heart, and brain detected virtually no differentially expressed genes, establishing that DOxS act predominantly through post-transcriptional mechanisms. In the gut, DOxS increased microbial α-diversity while depleting Limosilactobacillus reuteri, with concomitant loss of the barrier-protective metabolite 3-indoleacrylic acid. Tissue-specific responses were widespread, with liver and colon frequently mounting opposing metabolic and immune responses to the same dietary challenge. Cross-omics integration revealed convergent microbiome-metabolite axes connecting microbial remodeling to both hepatic lipid reprogramming and colonic barrier disruption. These findings reposition dietary oxysterols from food-quality markers to active modulators of the gut-liver axis, with implications for metabolic disease and intestinal barrier integrity.}, }
@article {pmid42039751, year = {2026}, author = {Chen, XG and Zhou, L and Duan, K and Shi, SY and Subi, A and Sun, HW and Lu, YM and Hu, L and Yang, ZT}, title = {Integrative analysis of pathogen detection, antimicrobial resistance, virulence, and host response in severe infections using metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1786413}, pmid = {42039751}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Retrospective Studies ; Male ; Virulence Factors/genetics ; Female ; Middle Aged ; Virulence/genetics ; Aged ; Intensive Care Units ; *Bacteria/genetics/drug effects/pathogenicity/isolation &amp; purification/classification ; *Drug Resistance, Bacterial/genetics ; *Bacterial Infections/microbiology/diagnosis ; *Host-Pathogen Interactions ; Anti-Bacterial Agents/pharmacology ; Adult ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) offers unbiased pathogen detection. However, its integrative value in simultaneously revealing resistance, virulence, and host-response interplay in Intensive Care Unit(ICU)-infected patients remains underexplored.<br><br>METHODS: In this retrospective cohort study of 156 ICU-infected patients, we compared the diagnostic performance of mNGS against conventional microbiological testing (CMT). We analyzed mNGS-derived antibiotic resistance genes (ARGs) and virulence factors (VFs) and correlated them with host immune-inflammatory markers and clinical outcomes.<br><br>RESULTS: mNGS demonstrated a significantly higher positive detection rate (89.7% vs. 67.3%, P < 0.001) and clinical concordance (75.6% vs. 35.9%, P < 0.001) than CMT. It revealed a high mixed-infection rate (72.1%). ARGs were detected in 49.0% of bacterial infections, predominantly &#x3b2;-lactamase genes, showing 72.0% concordance with phenotypic susceptibility. Key VFs (e.g., rmpA in K. pneumoniae) were identified. Based on mNGS results, 47.4% of patients had their antimicrobial therapy adjusted.<br><br>CONCLUSION: mNGS provides a comprehensive diagnostic tool by integrating pathogen identification, resistance and virulence profiling, and host-response context, enabling more precise and timely management of ICU-infected patients.}, }
@article {pmid42039753, year = {2026}, author = {Li, X and Fang, J and Li, D and Cai, B and Yin, J and Zheng, Y and Yin, G}, title = {Performance evaluation of mNGS in pathogen diagnosis of skin and soft tissue infections and its optimization effect on antibiotic decision-making.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1771148}, pmid = {42039753}, issn = {2235-2988}, mesh = {Humans ; *Soft Tissue Infections/diagnosis/microbiology/drug therapy ; Retrospective Studies ; Male ; Female ; *Anti-Bacterial Agents/therapeutic use ; Middle Aged ; Adult ; *High-Throughput Nucleotide Sequencing/methods ; Antimicrobial Stewardship ; Aged ; *Metagenomics/methods ; *Bacteria/genetics/isolation &amp; purification/classification/drug effects ; *Skin Diseases, Bacterial/diagnosis/microbiology/drug therapy ; Young Adult ; Coinfection/diagnosis/microbiology/drug therapy ; Adolescent ; Clinical Decision-Making ; }, abstract = {BACKGROUND: Skin and soft tissue infections (SSTIs), often caused by polymicrobial pathogens, pose diagnostic challenges due to the limitations of conventional methods, including low sensitivity and prolonged turnaround time. This diagnostic gap has perpetuated empirical antibiotic use in clinical practice. Metagenomic next-generation sequencing (mNGS), with its unbiased pathogen detection capability, offers a transformative approach for rapid and precise microbial identification in SSTIs.<br><br>OBJECTIVE: To evaluate the clinical utility of mNGS compared to conventional microbiological testing in guiding antibiotic stewardship for complex SSTIs.<br><br>METHODS: A retrospective cohort study was conducted at the First Affiliated Hospital of Zhengzhou University from April 2023 to May 2025, enrolling 69 patients with clinically diagnosed complex SSTIs. All patients underwent concurrent mNGS testing, conventional bacterial culture, and pathological examination. The diagnostic performance of mNGS was systematically compared with culture methods, with emphasis on culture-negative cases and polymicrobial infections. The impact of mNGS-guided antibiotic adjustments was assessed.<br><br>RESULTS: mNGS demonstrated significantly higher pathogen detection rates than conventional culture (P < 0.001), with a concordance of 37.5% between the two methods. Among 24 culture-negative patients, mNGS identified pathogens in 20 cases (83.3% detection rate). For polymicrobial infections (n = 20), culture detected pathogens in only 2 cases, whereas mNGS successfully identified multiple pathogens in the majority. Antibiotic therapy was adjusted based on mNGS results in 11.9% (8/69) of patients.<br><br>CONCLUSION: mNGS substantially improves pathogen detection in complex SSTIs compared to conventional methods. Beyond diagnostic accuracy, its clinical value lies in enabling targeted antibiotic therapy, thereby optimizing antimicrobial stewardship and potentially reducing healthcare costs.}, }
@article {pmid42039757, year = {2026}, author = {Wu, Y and Zhang, J and Su, W and Zhang, Z}, title = {Global epidemiology of tick-borne Alpharhabdovirinae: a meta-analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1791903}, pmid = {42039757}, issn = {2235-2988}, mesh = {Animals ; Phylogeny ; *Ticks/virology ; Humans ; *Tick-Borne Diseases/epidemiology/virology ; Genome, Viral ; }, abstract = {INTRODUCTION: The Alpharhabdovirinae subfamily of the family Rhabdoviridae encompasses a diverse and expanding group of tick-borne viruses, some of which pose potential risks as emerging human pathogens. Despite increasing detection through metagenomic surveillance, the global diversity, phylogenetic relationships, and taxonomic framework of tick-borne Alpharhabdovirinae (TBA) remain poorly characterized.<br><br>METHODS: This study conducted a comprehensive meta-analysis of all publicly available TBA sequences based on phylogenetic analysis of five structural proteins (N, P, M, G, L), combined with host associations and geographic distributions.<br><br>RESULTS: 345 TBA strains were classified into 12 distinct phylogenetic clusters, each exhibiting unique evolutionary and ecological characteristics. These clusters include: (1) seven species-level lineages within the genus Alpharicinrhavirus, predominantly associated with Hyalomma and Haemaphysalis ticks across Eurasia; (2) a cluster related to Manly virus, widely distributed in Amblyomma, Haemaphysalis, and Rhipicephalus ticks acrossAustralia and China, exhibiting additional protein-coding genes of unknown function; (3) the genus Ledantevirus (21 species), characterized by broad host tropism including bats, rodents, and humans, with some members displaying phosphoprotein phylogenetic anomalies suggestive of recombination; (4) the genus Lostrhavirus, together with Tongliao Rhabd tick virus 1, forming a cluster associated with Hyalomma and Amblyomma ticks; (5) a Mononegavirus cluster comprising Alpharicinrhavirus heilongjiang, Alpharicinrhavirus skanevik (Norway mononegavirus 1), and Mononegavirales sp. specifically associated with Ixodesticks in Eurasia; and (6) one clusters with incomplete protein repertoires and uncertain taxonomic positions, including Tahe rhabdovirus 3 and Yanbian Rhabd tick virus 1 which lacks phosphoprotein entirely. This study provide a refined phylogenetic framework for TBA viruses, clarify their evolutionary relationships, and highlight critical knowledge gaps, including numerous uncharacterized hypothetical proteins and incomplete genomes that warrant further investigation.<br><br>DISCUSSION: This study underscores the importance of enhanced global surveillance and genomic characterization to assess the emergence potential and public health threat posed by this diverse group of tick-borne viruses.}, }
@article {pmid42039802, year = {2026}, author = {Adhikary, K and Selim, S and Sarkar, R and Ganguly, K and Das, J and Almuhayawi, MS and Alruhaili, MH and Gattan, HS and Karak, P}, title = {Synthetic microbiomes in bioengineered rhizospheres: new frontiers for climate-resilient agriculture.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1780132}, pmid = {42039802}, issn = {1664-302X}, abstract = {Climate change poses significant threats to global agricultural productivity, necessitating innovative strategies to ensure food security and ecological sustainability. One promising avenue lies in the deliberate design and deployment of synthetic microbiomes and engineered rhizospheres to enhance plant resilience under environmental stress. This review places particular emphasis on multi-kingdom microbial interactions including bacteria, fungi, protists, and archaea and their potential for tailored, stress-specific applications within engineered rhizosphere systems. By integrating knowledge from microbial ecology, genomics, and systems biology, researchers have begun to unravel the complex interactions between plants and their associated microbial communities. Engineered microbial assemblies tailored to specific host plants and environmental conditions have shown potential in stabilizing crop performance during drought, salinity, and nutrient limitations. Moreover, the manipulation of root exudation patterns and soil physicochemical properties can be harnessed to recruit beneficial microbes and suppress harmful ones. The review also examines the role of synthetic biology tools, such as CRISPR-based genome editing and metabolic pathway engineering, in optimizing microbial traits for enhanced plant support. However, knowledge gaps remain in understanding multi-kingdom dynamics, optimizing SynComs for specific environmental contexts, and translating laboratory successes to reliable, field-scale applications. Additionally, advances in high-throughput screening, machine learning, and metagenomic profiling are accelerating the identification of key microbial taxa and functions relevant to plant health. Despite these promising developments, challenges remain in scaling these approaches for field applications and ensuring their ecological safety and consistency. This review explores the need for interdisciplinary efforts to translate laboratory insights into field-ready technologies, ultimately contributing to the development of climate-resilient and sustainable agricultural systems.}, }
@article {pmid42039826, year = {2026}, author = {Gini, C and Tiezzi, F and Jiang, J and Byrd, MH and Wen, H and Johnson, JS and Brito, LF and van Vliet, S and Maltecca, C}, title = {Data-driven enterosignatures link gut microbiome reorganization to heat stress responses in lactating sows.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1797687}, pmid = {42039826}, issn = {1664-302X}, abstract = {BACKGROUND: Heat stress (HS) can disrupt the gut microbiome, yet most livestock studies rely on taxonomic summaries that overlook the ecological structure of microbial communities. Enterosignatures (ES) as latent, co-occurring microbial assemblages learned from metagenomic data, offer a framework to capture these dynamics but have scarcely been applied in livestock HS research.<br><br>METHODS: Shotgun metagenomes were obtained from 25 lactating sows, belonging to two genetic lines (TOL, n = 13; SEN, n = 12), which were divergently selected based on genomic breeding values (GEBVs) for heat tolerance, and exposed to HS conditions. Results were decomposed using non-negative matrix factorization (NMF), yielding 8 taxonomic (T-ES) and 5 functional (F-ES) subcommunities. Functional profiles (based on KEGG Orthology, KOs) were mapped to metagenome-assembled genomes (MAGs) to integrate metabolic attributes within each ES.<br><br>RESULTS: Temporal shifts dominated T-ES variation, with limited genetic-line effects. T-ES 1 (p = 5.42 &#xd7; 10[-4], Cohen's d = 0.723) and T-ES 7 (p = 0.007, Cohen's d = 0.303) showed increases from day 4 to day 14. Despite modest overall genetic line effects, TOL animals progressively transitioned toward phylogenetically diverse and balanced communities, whereas SEN animals shifted toward imbalanced states characterized by enrichment of taxa with pathobiont potential or single-taxon dominance. Other T-ES displayed small to moderate effects, and T-ES 8 showed a potentially noteworthy genetic line-specific effect size at late lactation (Cohen's d = 0.960; 95% CI: -1.80 to -0.10), though omnibus tests were non-significant (p = 0.757), and the wide confidence interval underscores substantial uncertainty at this sample size. No F-ES reached statistical significance (p > 0.05); moderate effect sizes (up to d = 0.638) suggest possible functional restructuring warranting investigation in larger cohorts.<br><br>CONCLUSION: This work presents the first use of ES to track microbiome responses to HS in lactating sows. ES revealed latent taxonomic and functional subcommunities with clear temporal reorganization, offering insights not detectable with standard clustering or diversity metrics. Although genetic-line effects were modest, several ES showed biologically relevant shifts, supporting ES as a hypothesis-generating exploratory framework for linking microbial ecology to physiological adaptation under HS conditions, while warranting validation in larger, controlled trials.}, }
@article {pmid42039832, year = {2026}, author = {Sola, L and Candeliere, F and Busi, E and Raimondi, S and Amaretti, A and Rossi, M}, title = {A genomic atlas of gut clostridia: phylogeny, butyrate, and propionate production.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1761627}, pmid = {42039832}, issn = {1664-302X}, abstract = {INTRODUCTION: Clostridia is a major microbial class in the human gut, crucial for fermenting undigested carbohydrates and proteins, which produce short-chain fatty acids essential for gut health and immune balance. This study revised the taxonomic classification and phylogeny of all the species of intestinal Clostridia catalogued in the Unified Human Gastrointestinal Genome database using a whole-genome approach and assessed butyrate and propionate producing species.<br><br>METHODS: A total of 1,897 Clostridia species, including those with recognised binomial nomenclature and those lacking formal taxonomic classification, were retrieved and reclassified using GTDB-Tk. Their phylogeny was determined by identifying, concatenating, and aligning the 120 ubiquitous single-copy proteins defined in the GTDB. Average amino acid identity (AAI), percentage of conserved proteins (POCP), and phylogenetic relationships were used to organize the species into genera and families. The presence of enzymes belonging to the biosynthetic pathways for butyrate and propionate production was investigated in all genomes with the tool GapSeq.<br><br>RESULTS: Reclassification of the genomes resulted in 404 recognised species and 1,493 species lacking formal taxonomic classification. Oscillospirales and Lachnospirales encompassed most of the species. The pathways leading to butyrate and propionate production were analyzed in their entirety, revealing 519 species as potential butyrate producers, 257 as potential propionate producers and 77 capable of producing both. To assess the abundance of each species, 151 faecal metagenomes of healthy subjects were profiled, indicating that butyrate producing Clostridia accounted on average for 28.0% of each microbiome.<br><br>CONCLUSIONS: This study offers a comprehensive overview of intestinal Clostridia diversity, emphasising their role in gut ecosystems and their potential for butyrate and propionate production.}, }
@article {pmid42040306, year = {2026}, author = {Yang, R and Zhu, J and Zhang, Y and Liu, Y and Li, Z and Zhang, H and Li, Q and Wang, X and Chen, X and Chen, D and Liu, Q}, title = {Organic amendments boost maize yield (Zea mays L.) in karst soils via a hierarchical process driven by soil phosphorus enhancement and microbial-mediated nutrient cycling.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1782544}, pmid = {42040306}, issn = {1664-462X}, abstract = {INTRODUCTION: Sustainable food production in fragile karst landscapes requires moving beyond input-intensive agriculture.<br><br>METHODS: This study investigated how long-term organic amendments affected maize yield, using a 15-year field trial on karst yellow soil. Integrating soil analysis, metagenomics, and causal modeling, revealed that adding farmyard manure or bio-organic fertilizer to mineral NPK increased yield by 12.08% and 11.48%, respectively, and improved key soil properties, most notably available phosphorus.<br><br>RESULTS: Organic inputs shifted the soil microbiome toward copiotrophic taxa and enriched genes for organic matter decomposition and phosphorus mobilization. However, statistical modeling revealed that these biological changes did not directly drive yield. Instead, the primary pathway was hierarchical: amendments first enhanced the soil's chemical habitat, which then directly boosted crop growth while simultaneously shaping the microbial community and its functional potential. The interaction of soil, microbes, and genes together explained 81% of the yield variation.<br><br>DISCUSSION: Our findings demonstrate that in phosphorus-limited karst soils, organic amendments act foremost as soil conditioners. Microbial processes, though crucial, are secondary mediators that translate improved soil conditions into efficient nutrient cycling. Therefore, sustainable intensification in these vulnerable agroecosystems should prioritize managing soil health over directly targeting microbial processes.}, }
@article {pmid42040505, year = {2026}, author = {Collado, C and Romero-Tena, P and Wegener, G and Elvert, M and Menapace, W and Laso-Pérez, R}, title = {Anaerobic oxidation of methane supports a minimal microbial community in a subsurface biofilm at Ginsburg mud volcano.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag072}, pmid = {42040505}, issn = {2730-6151}, abstract = {Deep marine sediments generate large amounts of methane, but most of this gas is consumed by the anaerobic oxidation of methane (AOM) mediated by microscopic consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). In this study, we investigated the AOM within a sulfate-methane transition zone (SMTZ) at a depth of ~9.6 m at the rim of the Ginsburg mud volcano in the Gulf of Cádiz. The SMTZ is supplied with sulfate from both overlying seawater and an underlying evaporitic deposit, and it coincides with a fracture zone that hosts a visible biofilm. Here, carbon dioxide shows the strongest [13]C-depletion, indicating intense methane consumption. Metagenomic and lipid biomarker analysis of the biofilm revealed an exceptionally simple microbial community dominated by ANME-1b archaea (63%), which predominantly produce strongly [13]C-depleted glycerol dialkyl glycerol tetraethers and, to a lesser extent, the less common macrocyclic archaeols. The putative partner bacterium Seep-SRB1c (Desulfobacterota) is less abundant (9%). Additionally, the biofilm contained five low-abundance heterotrophs that likely rely on biomass or metabolites released from the ANME-SRB consortium. Our study highlights the presence of active methanotrophic biofilms in subsurface sediments and suggests that these communities may play an overlooked role in mitigating seafloor methane emissions.}, }
@article {pmid42040506, year = {2026}, author = {Zhang, T and Pan, J and Palomo, A and Ouyang, Z and Wen, X and Li, J and Wang, C and Zheng, M}, title = {Unique characteristics of acid-tolerant comammox bacteria revealed by multi-omics analyses.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag070}, pmid = {42040506}, issn = {2730-6151}, abstract = {Complete ammonia oxidation (comammox) is a critical biogeochemical process in the nitrogen cycle. In this study, we utilized comammox Nitrospira to convert urine wastewater into ammonium nitrate by operating a laboratory-scale membrane bioreactor at pH 3 ~ 4. During the process, the acid-tolerant comammox Nitrospira was highly enriched. The metagenomic and metatranscriptomic analyses were applied to reveal its unique characteristics. Comparative genomic analysis among previously reported comammox Nitrospira demonstrated that this species was phylogenetically novel, named Candidatus Nitrospira aciditolerans. Key mechanisms were further identified to enable this species to thrive in acidic environments. These include active proton efflux, regulation of proton consumption, inhibition of proton influx, and cellular strategies for acid stress management and repair. Remarkably, different from other comammox Nitrospira and acid-tolerant ammonia-oxidizing bacteria (AOB), Candidatus Nitrospira aciditolerans possesses highly expressed V-type ATPases that are typically associated with acidophilic ammonia-oxidizing archaea (AOA). This may indicate an ecologically significant role for comammox bacteria and AOA in co-maintaining ammonia oxidation activity in low pH environments. Kinetic characterization revealed an apparent ammonium half-saturation coefficient K m of 0.50 ± 0.05 μM NH3 and an apparent ammonium inhibition constant K i of 241.43 ± 45.64 μM NH3. The enrichment culture demonstrated optimal ammonia oxidation activity at neutral pH but maintained functionality across a broader pH range between 4 and 8. Like other nitrifying bacteria, this comammox culture was sensitive to temperature and salinity changes. The findings enhance our understanding of the nitrogen cycle under acidic conditions and also present opportunities for engineering applications of acid-tolerant ammonia oxidizers.}, }
@article {pmid42040549, year = {2026}, author = {Chen, Q and Yang, Z and Ren, D and Bao, C and Zhao, Y and Shi, Z}, title = {Case Report: Pulmonary tuberculosis with pneumocystis jirovecii colonization in a non-HIV patient: a cautionary tale on interpreting mNGS results.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1782843}, pmid = {42040549}, issn = {2296-858X}, abstract = {The diagnosis and treatment process of this case highlights that mNGS, as a powerful pathogen detection tool, provides a rapid method for the early detection of Pneumocystis jirovecii. However, mNGS testing of lavage specimens alone cannot distinguish between colonization and infection by the pathogen, particularly when a high number of sequences are present. Clinicians should therefore interpret laboratory results with caution to avoid unnecessary treatment that may cause adverse effects to the patient. CT scans offer strong evidence for differentiating between Pneumocystis jirovecii infection and/or Mycobacterium tuberculosis infection. Performing a biopsy at the site of infection, collecting pathological samples, and submitting them for mNGS testing can further assist clinicians in making a definitive diagnosis.}, }
@article {pmid42040584, year = {2026}, author = {Li, CB and Tang, S and Wen, Y}, title = {Case Report: The complete radiological resolution of diffuse cholangitis in a HIV-positive patient with cryptosporidium infection after anti-retroviral therapy.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1686336}, pmid = {42040584}, issn = {2296-858X}, abstract = {We present a case of an HIV-positive patient with AIDS cholangiopathy secondary to Cryptosporidium infection. Imaging examination showed intrahepatic and extrahepatic cholangitis without papillary stenosis and extrahepatic bile duct strictures, indicating mild bile duct disease. However, it failed to obtain positive results in fecal microscopy examinations. Alternatively, metagenomic next-generation sequencing (mNGS) of a blood sample identified Cryptosporidium infection. The diagnostic power of mNGS is highly sensitive and can simultaneously identify various pathogens. To avoid irreversible damage to the biliary system, the rapid initiation of anti-HIV therapy restored the function of the immune system and led to the clinical resolution of cryptosporidiosis.}, }
@article {pmid42040837, year = {2026}, author = {Sander, MM and Stoof-Leichsenring, KR and Liu, S and Shen, W and Lisovski, S and Herzschuh, U}, title = {Sedimentary Metagenomics Reveal Avian Community Transitions From the Last Glacial Maximum to the Holocene.}, journal = {Ecology and evolution}, volume = {16}, number = {4}, pages = {e72064}, pmid = {42040837}, issn = {2045-7758}, abstract = {The transition from the Last Glacial to the Holocene was marked by significant warming. This forced a compositional turnover of terrestrial plant and mammal communities discovered by diverse palaeoecological techniques. In this study, we analysed ancient environmental DNA with shotgun metagenomics from eight lake sediment cores, collected in northern Eurasia and Alaska, to elucidate the relationship of past bird communities and vegetation structure across the last 21,000 years. We leveraged all DNA reads assigned to the class 'Aves' to characterise the compositional changes of the bird community. The dominance of chicken birds (Galliformes, mainly ptarmigans) during the Last Glacial Maximum turned into a higher taxonomic bird diversity with increased numbers of songbird, raptor and waterfowl abundances and genera. This went along with the late glacial loss of the steppe-tundra and the increase of shrub and tree cover. Compared to the northern boreal areas, vegetation and bird communities were more stable in the northern tundra sites, where open landscapes prevailed throughout. Metagenomics significantly contribute to the reconstruction of past avian community changes and thus have high potential to support the predictions of distribution changes in the course of future ecosystem change.}, }
@article {pmid42041249, year = {2026}, author = {Marroquin, SM and Cohen, S and Neely, MN and Doran, KS}, title = {Akkermansia muciniphila impacts group B Streptococcus vaginal colonization.}, journal = {mBio}, volume = {}, number = {}, pages = {e0286825}, doi = {10.1128/mbio.02868-25}, pmid = {42041249}, issn = {2150-7511}, abstract = {Streptococcus agalactiae, or group B Streptococcus (GBS), is an opportunistic pathogen that asymptomatically colonizes the vaginal tract of up to 30% of healthy individuals. However, during pregnancy, it is associated with adverse pregnancy outcomes, and GBS can be transmitted to the fetus in utero or the newborn during vaginal birth, resulting in invasive neonatal disease. Previously, we identified that Akkermansia muciniphila increases GBS vaginal persistence in a cohort of human vaginal microbiome samples collected throughout pregnancy and promotes GBS vaginal colonization in a murine model. However, the mechanisms responsible for these observations are unknown. Here, we analyze additional vaginal shotgun metagenomic data sets and show that across independent studies with diverse populations, A. muciniphila-positive samples had higher GBS abundance. We determined that A. muciniphila aggregates with human vaginal isolates of GBS across all serotypes and promotes GBS attachment to human vaginal epithelial cells (hVECs). RNA-sequencing analysis reveals that A. muciniphila changed the expression of 281 unique GBS genes during hVEC co-colonization, many of which are involved in cell wall/membrane/envelope biogenesis. We demonstrate the importance of the GBS capsule and pili for direct interaction with A. muciniphila and increased attachment to hVECs, respectively. Lastly, we found that A. muciniphila promoted GBS aggregation in the murine vaginal lumen and that continual treatment with A. muciniphila reduced GBS vaginal persistence. Our results provide mechanistic insights and further evidence of the impact of A. muciniphila on GBS vaginal colonization and also demonstrate a beneficial potential of A. muciniphila treatment in the vaginal environment.IMPORTANCEGroup B Streptococcus (GBS) is a frequent colonizer of the vaginal tract of healthy people; however, during pregnancy, maternal colonization is associated with adverse pregnancy outcomes. GBS is a leading cause of neonatal sepsis and meningitis, with transmission to neonates occurring either during vaginal delivery or through ascension into the uterus during pregnancy. The influence of the vaginal microbiota on GBS pathogenesis remains greatly underappreciated. We have found that GBS is associated with the mucin-degrading intestinal commensal Akkermansia muciniphila, a newly identified colonizer of the vaginal tract. Our research identifies the mechanistic impact of this commensal organism on GBS aggregation, cell adherence, and gene expression, as well as its therapeutic potential during GBS vaginal colonization. Unraveling relationships between GBS and the vaginal microbiota will improve maternal-fetal health and may facilitate the development of alternative methods to reduce GBS in utero complications and neonatal disease.}, }
@article {pmid42041251, year = {2026}, author = {Gador-Whyte, AP and Sherry, NL and Brischetto, A and Andersson, P and Bond, KA and van Hal, SJ and Harris, PNA and Howden, BP and , }, title = {Implementation of pathogen genomics in clinical microbiology laboratories.}, journal = {Clinical microbiology reviews}, volume = {}, number = {}, pages = {e0017725}, doi = {10.1128/cmr.00177-25}, pmid = {42041251}, issn = {1098-6618}, abstract = {SUMMARYPathogen genomics, including whole-genome sequencing (WGS) and clinical metagenomics, is a transformative technology increasingly being implemented in clinical microbiology, including in hospital laboratories. Pathogen genomics can improve the control of healthcare-associated infections, provide rapid infection diagnosis, and could enable replacement of laborious microbiology tests. To date, real-world implementation of pathogen genome sequencing has primarily been limited to public health laboratories, but sequencing in the clinical microbiology setting has the potential to provide advantages, including turnaround time and ability to focus on local priorities. In this review, we consider the factors that represent barriers to, and potential enablers of, the implementation of pathogen genomics in clinical microbiology, including the availability of funding and genomics-trained staff. We outline key use cases and implementation models of pathogen genomics in clinical microbiology and suggest a broad framework for labs commencing sequencing. Finally, we consider future opportunities, including direct-from-specimen sequencing, the role of machine learning in genomics analysis, and the application of pathogen genomics to clinical decision support.}, }
@article {pmid42041878, year = {2026}, author = {Carlone, J and Ribeiro, &#xc1;CDS and Parisi, A and Giampaoli, S and Fasano, A}, title = {Profiling the Athletes' Gut Microbiome: A Critical Methodological Perspective on 16S Metabarcoding and Shotgun Metagenomics.}, journal = {Biology}, volume = {15}, number = {8}, pages = {}, doi = {10.3390/biology15080600}, pmid = {42041878}, issn = {2079-7737}, abstract = {The growing interest in the role of the gut microbiome in athletic performance has led to the application of various sequencing technologies in this field. This review critically examines the sequencing methodologies used in microbiome studies on physical performance and sport, comparing their advantages, limitations, and applicability. In particular, the focus is on 16S metabarcoding and shotgun metagenomics, evaluating how these methodological approaches influence the interpretation of results in sports contexts. Close attention is directed toward technical challenges, methodological biases, and future perspectives, including emerging technologies and multi-omics approaches. This review aims to bridge the gap between methodological rigor and sports-specific applicability, providing evidence-based methodological guidance to support researchers in designing robust athlete microbiome studies and translating sequencing-derived findings into concrete applications for performance and sports health.}, }
@article {pmid42041929, year = {2026}, author = {Ma, Y and Hu, Y and Zhang, J and Sun, Q and Wang, H and Liu, X and Tian, W and Wang, W and Ma, X and Shao, D and Liu, K and Li, B and Qiu, Y and Ma, Z and Li, Z and Wei, J}, title = {The Gut Microbiome and Metabolome of Domestic Cats Were Altered by the Oral Administration of Complex Probiotics.}, journal = {Biology}, volume = {15}, number = {8}, pages = {}, doi = {10.3390/biology15080652}, pmid = {42041929}, issn = {2079-7737}, abstract = {Probiotics are commonly applied to maintain the balance of gut microbiota and regulate the intestinal metabolic function of companion animals. In the present study, complex probiotics (Bacillus coagulans SNZ-1969, Bacillus subtilis, and Bacillus licheniformis) were added into the basal diet of domestic cats to investigate their influence on the intestinal microbiome and metabolic characteristics. Results revealed that the alpha diversity of the gut microbiota in the probiotic group was enhanced when compared to the control group. The beta diversity of the gut microbiota was also altered by the oral consumption of the complex probiotics. Compared to the control group, the relative abundance of beneficial microbes (such as Clostridium, Bacteroides, Phocaeicola, and Ruminococcus) in the probiotic group was enhanced, while the relative abundance of opportunistic pathogens (such as Escherichia, Gallibacter, Corynebacterium) was decreased. Additionally, the intestinal metabolic characteristics of domestic cats were also changed. The metabolomic analysis identified 408 differential metabolites between the two groups, and the KEGG function pathway analysis proved that the dominant pathway related to the differential metabolites were the amino acid metabolism, lipid metabolism, carbohydrate metabolism, energy metabolism, endocrine system, digestive system, immune system, and other metabolic pathways. Spearman's correlation analysis revealed that the beneficial microbes had positive correlations with the differential metabolites. In conclusion, the current study demonstrated that oral administration of complex probiotics could regulate overall health and well-being in domestic cats through modulating the gut microbiome and metabolic characteristics.}, }
@article {pmid42043232, year = {2026}, author = {Geng, M and Wang, X and Huang, X and Li, Y and Wei, Y and Cai, Y and Li, J and Jiang, C and Wu, W and Liu, S and Guo, N and Zhang, X and Wu, W and Han, G and Han, X and Liu, T and Li, Q and Wang, S}, title = {Metatranscriptomic Analysis of Tick Virome Diversity in Hebei Province, China.}, journal = {Viruses}, volume = {18}, number = {4}, pages = {}, doi = {10.3390/v18040443}, pmid = {42043232}, issn = {1999-4915}, support = {ZDGWNLJS25-25//Surveillance and Early Warning Technologies for Unknown and Emerging Pathogens/ ; 20260864//Hebei Provincial Medical Science Research Project/ ; }, mesh = {Animals ; China ; Phylogeny ; *Virome/genetics ; *Ticks/virology ; Genome, Viral ; *RNA Viruses/genetics/classification/isolation &amp; purification ; Metagenomics ; }, abstract = {Ticks serve as primary vectors for a wide array of RNA viruses, yet the diversity and distribution of tick-associated RNA viruses remain incompletely characterized in Hebei province. To address this gap, we conducted a systematic metatranscriptomic investigation of 986 ticks representing six species, collected from the diverse ecological landscapes of Hebei Province in northern China. Our analysis recovered 25 complete or near-complete viral genomes spanning 12 families, including Phenuiviridae, Flaviviridae, and Nairoviridae. Of critical public health significance, we identified Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) in both Haemaphysalis longicornis and Dermacentor nuttalli. Phylogenetic reconstruction revealed marked geographic stratification where strains from the coastal plains clustered with the dominant Genotype F, while those from the mountainous north formed a characteristic and divergent lineage phylogenetically linked to isolates from Inner Mongolia. Furthermore, a novel viral agent provisionally named Zhangjiakou Hepacivirus was discovered in Haemaphysalis japonica. This virus shared less than 80% nucleotide identity with the rodent-associated Hepacivirus P, consistent with a rodent origin and possible cross-species transmission. Collectively, these findings reveal descriptive variation associated with vector identity, physiological status, and ecological context in shaping viral evolution and underscore the need for continuous metagenomic surveillance to mitigate emerging tick-borne disease risks within a One Health framework.}, }
@article {pmid42043279, year = {2026}, author = {Rūmnieks, J and Baltā, I and Šišovs, M and Tārs, K}, title = {ssRNA bacteriophage metagenomes reveal a diverse set of novel protein families.}, journal = {Protein science : a publication of the Protein Society}, volume = {35}, number = {5}, pages = {e70582}, doi = {10.1002/pro.70582}, pmid = {42043279}, issn = {1469-896X}, support = {5.2.1.1.i.0/2/24/I/CFLA/001//European Commission/ ; }, mesh = {Open Reading Frames ; *Viral Proteins/genetics/chemistry ; *Metagenome ; Genome, Viral ; *Bacteriophages/genetics ; }, abstract = {The bacteriophages with single-stranded RNA (ssRNA) genomes (class Leviviricetes) are among the simplest known viruses that encode only three core proteins: a receptor-binding protein, a capsid protein, and an RNA-dependent RNA polymerase. The number of isolated ssRNA phages has remained very low, but the accumulating RNA metagenome data have uncovered a large variety of these viruses in many environments. Besides the core proteins, many of these genomes putatively encode additional proteins, which up to now have remained uncharacterized. We looked for non-conserved open reading frames (ORFs) in Leviviricetes sequences from the IMG/VR virus metagenome database and used sequence- and structure-based clustering to organize them into similarity groups. Potential ORFs were found throughout the ssRNA phage genomes but almost exclusively on the positive-sense RNA strand, suggestive of their protein-coding potential. The prevalence of the non-conserved ORFs varied in various phage lineages, and their distribution among different genome positions was markedly uneven. Most of the identified ORFs encode all-α proteins, a portion of which contain transmembrane segments that resemble a group of known ssRNA phage lysis proteins, while many others represent previously uncharacterized families of globular or semi-globular α-helical proteins. We additionally uncovered a major class of globular α/β proteins and experimentally determined the structure of a representative protein of this group. These results pave the way for further functional studies of novel ssRNA phage proteins for a better understanding of this diverse virus group.}, }
@article {pmid42044527, year = {2026}, author = {Rabasco, JT and Bolyen, E and Caporaso, JG and Sapers, H and Callahan, BJ}, title = {Identify contaminants with decontam on the QIIME 2 Framework.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0126125}, doi = {10.1128/mra.01261-25}, pmid = {42044527}, issn = {2576-098X}, abstract = {Here, we present the integration of the decontam method for contaminant identification and a supplemental approach for identifying the source of contaminants in sequencing data within the QIIME 2 Framework for microbiome data science. We demonstrate its use in a tutorial based on the QIIME 2 "Moving Pictures Tutorial" data.}, }
@article {pmid42044543, year = {2026}, author = {Zhang, X and Chen, J and Li, Y and Tang, R and Zhu, T and Yuan, Y}, title = {Aerobic biodegradation of acesulfame by sediment-enriched microbial consortia: Kinetics, pathway, and microbial mechanism.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129734}, doi = {10.1016/j.jenvman.2026.129734}, pmid = {42044543}, issn = {1095-8630}, abstract = {Artificial sweetener acesulfame (ACE), an emerging pollutant frequently detected in aquatic environments, exhibits potential ecological toxicity and risk accumulation effects. However, its environmental fate and microbial degradation mechanisms within sedimentary environments remain inadequately characterized. Herein, we established a sediment-based microcosm system to quantitatively characterize the degradation kinetics of ACE, track associated shifts in microbial community structure and function, and decipher the underlying molecular mechanisms. The results showed that successive enrichment cycles significantly augment the aerobic biodegradation of ACE by sediment microbial communities. Under aerobic conditions, the degradation rate constant increased from 0.58 to 3.60 d[-1] following enrichment, significantly exceeding the rate under the anoxic conditions. Metagenomic analysis revealed that ACE treatment reshaped the microbial community structure, with Pseudomonadota remaining the dominant phylum (60.2-65.8%). Genes encoding ACE-degrading sulfatase and amidase were linked to Chelatococcus and Devosia, both of which showed dramatic enrichment in treated samples, underscoring their critical contribution to ACE degradation. A two-step hydrolytic pathway for ACE degradation via sulfonate ester and amide bond hydrolysis was elucidated through combined product analysis. This biodegradation process coincided with significant changes in the abundance of genes governing carbon, nitrogen, and sulfur metabolism, reflecting a functional restructuring of the microbial community. Toxicity assessment indicated that most transformation products exhibited lower toxicity than the parent compound, suggesting an overall reduction in environmental risk. These findings elucidate the microbial degradation mechanisms of ACE, facilitating the assessment of its environmental risks and the development of effective bioremediation strategies.}, }
@article {pmid42044779, year = {2026}, author = {Zhang, Y and Zeng, M and Guo, P and Zhang, Z and Chen, X and Li, X and Hao, F and Jiao, X and Wu, Y and Feng, W and Zheng, X}, title = {Effects of Rehmannia glutinosa Libosch. Rhizome Water Extract and Rehmapicrogenin on Pulmonary Hypertension: Multi-Omics Insights into Epidermal Growth Factor Receptor/Pyruvate Kinase M2 Pathway and Metabolic Regulation.}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {121775}, doi = {10.1016/j.jep.2026.121775}, pmid = {42044779}, issn = {1872-7573}, abstract = {Rehmannia glutinosa Libosch. (RG), as one of the 'Four Famous Chinese Medicinal Herbs', has a long history of medicinal use and is classified as belonging to the meridians of the heart, liver, and kidney. RG has the effects of clearing heat and cooling blood, nourishing yin, and generating fluids. Pulmonary hypertension (PH) is a cardiovascular disease, and its pathogenesis can be summarized as 'yin deficiency', 'blood stasis', and 'qi deficiency'. The efficacy of RG is highly compatible with this disease, and the compounds isolated from RG can significantly inhibit the proliferation of pulmonary arterial smooth muscle cells (PASMCs). However, the mechanism by which it intervenes in PH remains unclear.<br><br>OBJECTIVE: In this study, the mechanisms and active components of RG were investigated for treating PH by using multi-omics analysis and surface plasmon resonance (SPR) technology, providing experimental support for clinical application.<br><br>METHODS: A PH mouse model was established through 5 weeks of hypoxia, with RG administration starting in week four. Cardiorespiratory function was evaluated after treatment. The therapeutic targets of RG were identified via 16S rDNA sequencing, metagenomics, and metabolomics. SPR ligand fishing was performed to isolate rehmapicrogenin (Reh), an RG-derived compound that targets the epidermal growth factor receptor (EGFR). The effects and mechanisms of Reh were assessed by measuring cardiac and pulmonary function, oxidative stress, apoptosis, immune cell activity, and glycolysis. An in vitro model of hypoxia-induced PASMC proliferation was used to validate Reh's mechanism with an EGFR agonist (NSC).<br><br>RESULTS: RG extracts improved cardiorespiratory function and regulated gut microbiota, correcting the Firmicutes/Bacteroidetes (F/B) ratio in PH mice. RG also mitigated metabolic disturbances and inhibited glycolysis through pyruvate kinase M2 (PKM2) regulation, as confirmed using immunofluorescence analysis, western blotting, and PCR. SPR identified Reh as the active ingredient, which improved cardiorespiratory function, reduced oxidative stress and apoptosis, and suppressed EGFR and PKM2 expression and glycolysis. In vitro, Reh inhibited PASMC migration and proliferation, alleviated oxidative stress, and reduced mitochondrial damage. These effects were reversed upon NSC addition, confirming the role of EGFR in the mechanism.<br><br>CONCLUSION: RG and its active compound Reh mitigate hypoxia-induced PH by targeting the EGFR/PKM2 pathway, reducing glycolysis, and regulating gut microbiota dysbiosis.}, }
@article {pmid42044791, year = {2026}, author = {Dai, Y and Li, J and Wang, X and Xia, F and Zheng, J and Shen, C}, title = {Synergistic Mechanisms of Bacteria and Fungi in the Biodegradation of Benzo[a]pyrene: Insights from Metagenomic and Metabolomic Analyses.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124602}, doi = {10.1016/j.envres.2026.124602}, pmid = {42044791}, issn = {1096-0953}, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are pervasive organic pollutants, with benzo[a]pyrene (BaP), a prominent heavy-weight PAH, drawing considerable attention due to its high toxicity and resistance to degradation. While both bacteria and fungi have been demonstrated to effectively remediate BaP, their synergistic mechanisms remain poorly understood. In this study, we employed Pseudomonas nicosulfuronedens DY-8 (bacterium) and Arthrinium acutiapicum DL-5 (fungus) to explore the mechanisms underlying PAH bioaugmentation using metagenomic and metabolomic approaches. Although both strains individually enhanced BaP degradation, their combined application significantly reduced BaP residuals. qPCR analysis revealed that the bacteria promote BaP dissipation by stimulating the abundance of PAH-RHD GP genes in the soil. Correlations between metabolite abundance, enriched microbial populations, functional gene abundance, and fungal growth suggest that fungi enhance the growth of indigenous bacteria, further boosting the degradation of BaP metabolites. Additionally, the synergistic treatment of bacteria and fungi further altered the diversity of soil functional microorganisms, metabolic products, and functional genes. These findings provide insights into potential synergistic mechanisms by which bacterial-fungal interactions drive the degradation of high-molecular-weight PAHs, underscoring the potential of microbial consortia in the bioremediation of persistent organic pollutants in soil environments.}, }
@article {pmid41850677, year = {2026}, author = {Mi, X and Liu, R and Jiang, Z and Tang, M and Yan, J and Liu, J and Li, Y and Zheng, J and Yang, W and Gong, L and Shi, J}, title = {Gut Microbiota-Derived Propionate Governs Hepatic N2 Neutrophils in Wilson's Disease.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {20}, number = {7}, pages = {101770}, doi = {10.1016/j.jcmgh.2026.101770}, pmid = {41850677}, issn = {2352-345X}, abstract = {BACKGROUND &amp; AIMS: Neutrophil functions play a pivotal role in hepatic pathogenesis. Our previous work has established that N2-polarized neutrophils promote hepatic fibrogenesis in Wilson's disease depends on hepatic transforming growth factor-β1 (TGF-β1) production. However, the regulators governing TGF-β1 production in orchestrating disease-associated N2 neutrophils remain elusive. In this study, we investigated the immunomodulatory effects of gut microbiota-derived short-chain fatty acids (SCFAs) on neutrophil polarization.<br><br>METHODS: Fecal metagenomic sequencing and short-chain fatty acid (SCFA) profiling were performed on ATP7B-knockout (ATP7B-KO) mice and their wild-type (WT) littermate controls. Fecal microbiota transplantation (FMT) experiments were conducted by transferring feces from WT mice or Akkermansia muciniphila into recipient mice. Additionally, propionate or trichostatin A (TSA) was administered to both ATP7B-KO and WT groups. Mice were assessed using histological analyses, Sirius Red staining, flow cytometry, biochemical assays, immunohistochemistry, measurement of TGF-&#x3b2;1 levels, immunofluorescence, and quantitative real-time polymerase chain reaction (qRT-PCR) for gene expression profiling. To elucidate the underlying molecular mechanisms, 4D label-free quantitative acetylated proteomics, site-directed mutagenesis, plasmid transfection, co-immunoprecipitation (IP), and luciferase reporter assays were employed.<br><br>RESULTS: We report that Akkermansia muciniphila was markedly reduced in the gut microbiota of mice with Wilson's disease, accompanied by decreased SCFA levels, especially propionate. Additionally, transplantation of fecal bacteria from wild-type mice or A muciniphila could promote an antifibrotic effect, elevate propionate levels, reduce TGF-&#x3b2;1 secretion, and decrease hepatic N2 neutrophils in mice with Wilson's disease. Moreover, administration of propionate also significantly enhanced antifibrotic immunity. Mechanistically, propionate reduced the production of TGF-&#x3b2;1 in hepatocytes by inhibiting histone deacetylase activity, increasing the acetylation of DNAJA3 at sites K134 and K385, thus decreasing expression of DNAJA3. Consistently, gut-derived propionate inversely correlated with hepatic injury severity in patients with Wilson's disease, which could be functionally mediated by TGF-&#x3b2;1.<br><br>CONCLUSIONS: Gut microbiota are pivotal for hepatic neutrophil polarization and liver fibrosis in Wilson's disease. Our findings suggest that therapeutic modulation of gut microbiota, SCFA profiles, and TGF-&#x3b2;1 production, particularly when combined with histone deacetylase inhibitors, may represent promising therapeutic approaches for Wilson's disease.}, }
@article {pmid42032279, year = {2026}, author = {Ducarmon, QR and Karcher, N and Giri, S and Tytgat, HLP and Delannoy-Bruno, O and Pekel, S and Springer, F and Wörz, P and Schudoma, C and Typas, A and Zeller, G}, title = {Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {42032279}, issn = {2058-5276}, support = {LUMC Fellowship//Leids Universitair Medisch Centrum (Leiden University Medical Center)/ ; 395357507//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 01KD2102A//Bundesministerium f&#xfc;r Bildung und Forschung (Federal Ministry of Education and Research)/ ; ALTF 1030-2022//European Molecular Biology Organization (EMBO)/ ; }, abstract = {Carbohydrate-active enzymes (CAZymes) are crucial for digesting glycans, but tools for CAZyme profiling and interpretation of substrate preferences in microbiome data are lacking. Here we develop a CAZyme profiler called Cayman (Carbohydrate Active Enzymes Profiling of Metagenomes) and a hierarchical substrate annotation scheme for use with genomic or shotgun metagenomic datasets. Using these tools, we systematically surveyed CAZymes in human gut microorganisms (n = 107,683 genomes) and identified several putative mucin-foraging bacteria, including Hungatella and Eisenbergiella species, which were confirmed experimentally. We compared CAZymes in gut metagenomes (n = 3,960) from high-income settings versus low- and middle-income settings and found that low- and middle-income setting metagenomes are enriched in fibre-degrading CAZymes, while CAZyme richness is generally higher in high-income setting metagenomes. Additional analysis (n = 1,998) indicated that metagenomes of individuals with colorectal cancer are depleted in fibre-targeting and enriched in glycosaminoglycan-targeting CAZymes. Finally, we inferred CAZyme substrates from genomic co-localization of CAZyme domains. Cayman is broadly applicable and freely available from https://github.com/zellerlab/cayman .}, }
@article {pmid42032281, year = {2026}, author = {Tonkin-Hill, G and Shao, Y and Zarebski, AE and Mallawaarachchi, S and Xie, O and Mäklin, T and Thorpe, HA and Davies, MR and Bentley, SD and Lawley, TD and Corander, J}, title = {Strain-level transmission inference across multi-kingdom metagenomic data using TRACS.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {42032281}, issn = {2058-5276}, support = {2025515//Department of Health | National Health and Medical Research Council (NHMRC)/ ; DE240100316//Department of Education and Training | Australian Research Council (ARC)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; }, abstract = {Coexisting strains of the same species within metagenomic data pose a substantial challenge to inferring transmission of pathogenic and commensal microbes. Here we present TRAnsmision Clustering of Strains (TRACS), a highly accurate algorithm for estimating genetic distances between strains at the level of individual single nucleotide polymorphisms, which is robust to intra-species diversity within the host. Analysis of faecal microbiota transplantation datasets and extensive simulations demonstrates that TRACS outperforms existing methods. We use TRACS to infer transmission networks in patients colonized with multiple strains, including severe acute respiratory syndrome coronavirus 2 amplicon sequencing data, deep population sequencing data of Streptococcus pneumoniae and single-cell genome sequencing data from patients infected with Plasmodium falciparum. Applying TRACS to gut metagenomic samples from a mother-infant cohort revealed species-specific transmission rates and identified increased the persistence of Bifidobacterium breve in infants, a finding previously missed owing to the presence of multiple strains. Our study shows that TRACS can be used across microbial kingdoms to uncover strain dynamics.}, }
@article {pmid42032282, year = {2026}, author = {}, title = {Benchmarking shotgun metagenomics.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {42032282}, issn = {2058-5276}, }
@article {pmid42032888, year = {2026}, author = {Wu, S and Wang, Y and Li, H and Fang, X and Guo, J and Luo, X and Li, M and Song, F and Tan, Q and Deng, X and Xiao, S and Liu, H and Hu, C and Pan, Z}, title = {Rhizosphere microbiome influences fruit quality in citrus.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71159}, pmid = {42032888}, issn = {1469-8137}, support = {2023YFD2300603//The National Key Research and Development Program of China/ ; 2017YFD0202001//The National Key Research and Development Program of China/ ; 2019YFD1000103//The National Key Research and Development Program of China/ ; }, abstract = {Fruit quality is shaped by both crop genetics and cultivation environments, with soil conditions driving rhizosphere microbiome assembly. While rhizosphere microbes are known to enhance nutrient utilization and plant metabolism, their direct contribution to fruit quality regulation remains poorly understood. In this study, we demonstrate that the Satsuma mandarin (Citrus unshiu Marc.) and Navel orange (Citrus sinensis L. Osbeck) rhizosphere microbiome influence fruit sugar concentration, a key determinant of fruit quality. The rhizosphere core microbiota and soil mineral nutrients were positively correlated with fruit quality indices. Fruit quality-correlated bacterial operational taxonomic units (OTUs) explained an average of 32.6% of the observed variation in quality parameters. Inoculation with three bacterial strains (affiliated with Burkholderia, Pseudomonas, Rhizobium) and two bacterial consortia significantly increased fruit sugar concentrations. Metagenomic analysis linked sugar-associated microbes to iron (Fe) utilization, revealing genomic enrichment of siderophore biosynthesis gene clusters. Consistently, the selected bacterial strains exhibited siderophore secretion capabilities, increased leaf Fe content by 23.3-47.8% in citrus rootstock. Further field application of chelated-Fe fertilizer also increased fruit sugar concentration. Collectively, our results revealed an influence of the rhizosphere microbiome on fruit quality that is related to Fe acquisition optimization and subsequent sugar accumulation in citrus.}, }
@article {pmid42032992, year = {2025}, author = {Huang, Z and Wei, J and Luo, J and Pan, X and Wei, C and Zhou, Y and Xiao, S and Xu, N and Zhong, Y and Luo, M}, title = {[Comparison of 16S rRNA gene hypervariable regions V3-V4 and V4 sequencing results of gut microbiota in obese children with non-alcoholic fatty liver disease].}, journal = {Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences}, volume = {50}, number = {12}, pages = {2312-2324}, pmid = {42032992}, issn = {1672-7347}, support = {2022JJ40668//the Natural Science Foundation of Hunan Province/ ; }, mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; Child ; Feces/microbiology ; Male ; Female ; *Pediatric Obesity/microbiology ; *Obesity/microbiology/complications ; Adolescent ; }, abstract = {OBJECTIVES: 16S rRNA gene sequencing is an important method for studying microbial structure in samples. However, whether selecting different hypervariable regions for sequencing in the same sample affects the results remains unclear. This study aims to compare the sequencing results of 16S rRNA gene hypervariable regions V3 to V4 and V4 in children with obesity-related non-alcoholic fatty liver disease (NAFLD), and to provide evidence for scientifically evaluating gut microbiota detection results in obese children with NAFLD.<br><br>METHODS: Obese children with NAFLD and children with simple obesity who visited Hunan Children's Hospital between January 2019 and September 2021 were selected as study subjects. Fecal samples were collected, and total DNA was extracted. After PCR amplification of the gut microbiota V3 to V4 region and V4 region, sequencing was performed. &#x3b1;-diversity, &#x3b2;-diversity, and microbial community structure differences between the 2 hypervariable regions were compared. Seven samples were selected for metagenomic sequencing as the gold standard to evaluate the performance of V3 to V4 and V4 region sequencing.<br><br>RESULTS: A total of 145 participants were included, including 92 in the case group and 53 in the control group. The number of operational taxonomic units (OTUs) obtained by V3 to V4 sequencing (16 977) was higher than that obtained by V4 sequencing (3 362). &#x3b1;-diversity analysis showed that in the overall population, the Shannon index (5.49&#xb1;1.11) and Chao1 index (1 843.04&#xb1;580.78) in the V3 to V4 region were higher than the Shannon index (4.98&#xb1;0.65) and Chao1 index (379.59&#xb1;47.27) in the V4 region (all P<0.001). &#x3b2;-diversity analysis showed overall differences in microbial community structure between the V3 to V4 and V4 regions, and the intergroup differences were greater than the intragroup differences (P<0.05). Welch's t-test results showed that in the overall population, the numbers of differential taxa detected by V3 to V4 and V4 sequencing at the phylum, class, order, family, and genus levels were 2, 9, 35, 33, and 72, respectively; in the case group, the numbers were 1, 9, 32, 35, and 66; and in the control group, the numbers were 0, 7, 27, 21, and 0. Linear discriminant analysis effect size (LEfSe) analysis showed that V3 to V4 sequencing identified 29 differential taxa between the case group and control group, whereas V4 sequencing identified 7 differential taxa. Sensitivity analysis showed that the Shannon index obtained by V3 to V4 sequencing (5.41&#xb1;1.62) was not significantly different from that of metagenomic sequencing (6.39&#xb1;0.42) (P=0.169), while the Chao1 index (1 889.92&#xb1;781.73) was lower than that of metagenomic sequencing (3 092.71&#xb1;505.89), with a statistically significant difference (P<0.01). The Shannon index and Chao1 index obtained by V4 sequencing were both lower than those of metagenomic sequencing, with statistically significant differences (4.89&#xb1;0.94 vs 6.39&#xb1;0.42, 362.41&#xb1;35.22 vs 3 092.71&#xb1;505.89, respectively, both P<0.01).<br><br>CONCLUSIONS: Sequencing of the V3 to V4 and V4 regions of the 16S rRNA gene affects the results of gut microbiota structure analysis in obese children. The V3 to V4 region is more likely to detect differential taxa between case and control groups and provides a more accurate estimation of &#x3b1;-diversity. It may therefore be considered a preferred region for gut microbiota sequencing in children with NAFLD. However, there is currently no unified standard for selecting V regions in 16S rRNA gene sequencing, and the detection region and method should be selected comprehensively according to research objectives and sample characteristics.}, }
@article {pmid42033828, year = {2026}, author = {Liu, X and Li, N and Wu, WM and Ambrosini, R and Zhong, B and Mei, X and Liu, R and Zhou, L and Yi, S and He, Y}, title = {Freeze-thaw aging and microbial colonization converts microplastics into nitrogen cycling hotspots.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142170}, doi = {10.1016/j.jhazmat.2026.142170}, pmid = {42033828}, issn = {1873-3336}, abstract = {As global warming intensifies, the frequency of freeze-thaw events increases, significantly impacting microbial metabolism and biogeochemical cycling. However, the synergistic effects of freeze-thaw cycles (FTCs) and pervasive microplastics (MPs) on microbial community assembly and nitrogen cycling remain poorly understood. Here, we conducted a microcosm experiment integrating metagenomic and random forest model to elucidate the co-regulatory mechanisms of FTCs and MPs on plastisphere microbial communities and nitrogen metabolism. Results revealed that FTCs accelerated the environmental aging of MPs, inducing surface cracking and oxidation, thereby creating microenvironments favorable for microbial colonization. In the experimental microcosms, the combined effects of FTCs and presence of MPs increased microbial richness and diversity, promoted community differentiation between sediment and plastisphere, and increased microbial niche specialization. Functional analyses showed that FTCs induced a functional reconfiguration of the plastisphere nitrogen metabolism, with a selective enrichment of key enzyme genes, such as nitrite reductase, which may enhance nitrite redox activity and N2O emission capacity. In the plastisphere, the contribution of Acinetobacter to nitrogen cycling increased, whereas Nitrospira declined, possibly due to oxygen limitation. Overall, our findings suggested that FTCs may facilitate transformation of MPs from inert pollutants into potentially metabolically active microhabitats, providing critical insights for assessing emerging pollutants and climate change.}, }
@article {pmid42033834, year = {2026}, author = {Su, S and Lin, M and Li, K and Lin, J and Chen, Z}, title = {Soil aggregates as functional units for cadmium sequestration: Differential regulation by nitrogen enrichment and labile carbon inputs.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142196}, doi = {10.1016/j.jhazmat.2026.142196}, pmid = {42033834}, issn = {1873-3336}, abstract = {While cadmium (Cd) speciation in soil is known to control its environmental risk, how nitrogen (N) enrichment and labile organic carbon (LOC) inputs redistribute Cd fractions within soil aggregates remains unclear. This study examined how ammonium enrichment (AT), nitrate enrichment (NT), and glucose input (CT) altered carbonate-bound Cd (CB-Cd) and organic matter-bound Cd (OM-Cd) within soil aggregates. Both N enrichment and glucose input enhanced CB-Cd formation, with CT increasing CB-Cd by 39.19% via stimulated microbial activity and carbonate precipitation. Different sources of enriched N regulated OM-Cd, with AT decreasing OM-Cd by 15.55%, and NT increasing OM-Cd by 24.61%. This was attributed to competitive adsorption and suppressed microbial decomposition of recalcitrant organic matter. Aggregate hierarchy was also crucial in determining Cd speciation, where macroaggregates, with higher LOC and genes involved in carbonate precipitation, favored CB-Cd partitioning, whereas microaggregates, with greater surface area and enriched alkyl/aromatic C, served as the major OM-Cd sink. Microbial community analysis revealed that glucose reshaped communities, enriching r-strategists like Amycolatopsis and Trichoderma, which were positively correlated with CB-Cd and OM-Cd. Metagenomic data indicated that glucose stimulated genes for labile C degradation, reinforcing CB-Cd formation, while N addition suppressed C-degradation genes. Random forest and PLS path models identified alkyl C, O-alkyl C, and polysaccharide derivatives as primary SOC components regulating CB-Cd, while alkyl C, phenolic, and aromatic compounds regulating OM-Cd. These findings reveal a mechanism for stabilizing Cd in less bioavailable fractions via SOC and N management, leveraging soil aggregates' role in long-term metal sequestration.}, }
@article {pmid42033969, year = {2026}, author = {Tian, J and Wang, L and Wang, Y and Zheng, M and Sun, C}, title = {Distribution characteristics of emerging contaminants and microbial communities in Bohai Sea sediments.}, journal = {Marine environmental research}, volume = {219}, number = {}, pages = {108068}, doi = {10.1016/j.marenvres.2026.108068}, pmid = {42033969}, issn = {1879-0291}, abstract = {As a semi-enclosed marginal sea in China, the Bohai Sea has long been influenced by substantial pollutant inputs from surrounding rivers, making it an important region for investigating the distribution patterns of pollutants and microbial communities. In this study, the concentrations of emerging contaminants (ECs) in 19 sediment samples were determined, and metagenomic sequencing was employed to systematically analyze the structure and functional characteristics of microbial communities. The results showed that the detected ECs included synthetic musks (SMs, 7.96-22.85 ng/g dw), dominated by tonalide (AHTN) and galaxolide (HHCB); organophosphate esters (OPEs, not detected-282.27 ng/g dw), were not detected in most samples, but relatively high concentrations were observed at the NS-33 station; and polyhalogenated carbazoles (PHCZs, 0.70-4.36 ng/g dw), with 3,6-dichlorocarbazole (36-CCZ) constituting 61.87% of PHCZs. The microbial community was dominated by Proteobacteria (68.36%). Further network analysis indicated significant correlations between PHCZs and nitrogen metabolism genes, suggesting that PHCZs may inhibit nitrogen fixation and nitrification, while enhancing denitrification. Overall, this study reveals the distribution patterns of ECs and microbial communities in Bohai Sea sediments and their potential associations, providing insights into their interactions in coastal ecosystems.}, }
@article {pmid42033990, year = {2026}, author = {Wu, Q and You, J and Li, D and Tang, S and Wu, S and Wang, Q and Teng, W}, title = {Oxygen vacancy-rich nanosystems eradicate stubborn periodontal biofilms by synergistic EPS degradation, metabolic activation and microbiome restoration.}, journal = {Biomaterials}, volume = {333}, number = {}, pages = {124234}, doi = {10.1016/j.biomaterials.2026.124234}, pmid = {42033990}, issn = {1878-5905}, abstract = {Periodontitis-associated biofilms pose a severe public health threat due to a dual defense mechanism. This involves a protective physical matrix barrier and biological interference from persistent bacteria and microbial dysbiosis. Current strategies often fail to penetrate deeply, eradicate dormant persisters and resolve microbial dysbiosis, leading to biofilm resistance and disease recurrence. In this study, we develop a multifunctional nanoplatform combining photothermal, photodynamic therapy and peroxidase-like catalysis to execute a sequential strategy. This system integrates molybdenum oxide nanodots rich in oxygen vacancy (MoO3-x) with the photosensitizer indocyanine green (ICG). It exhibits improved optical and enzymatic performance due to the introduced oxygen vacancies. Upon irradiation, the system produces localized hyperthermia and ROS storms to destabilize the biofilm matrix and promote ultrasmall nanodots penetration. The thermal and oxidative stress increase membrane permeability and reactivate metabolism of dormant persisters. Metagenomic analyses confirms that MoO3-x/ICG-treated biofilms show decreased abundance of key persistence-related genes and great enrichment in metabolic pathways. Additionally, the platform exhibits therapeutic effects and a successful shift towards a healthier oral microbiota in periodontitis model. Overall, MoO3-x/ICG demonstrates excellent biofilm eradication and successfully prevents biofilm regrowth or secondary infection. This work targets the entire biofilm lifecycle and presents a nanoplatform for long-term management of periodontal infections.}, }
@article {pmid42034087, year = {2026}, author = {Liao, S and Lin, X and Wang, X and Lin, J and Lu, Y and Deng, W and He, Q and Chi, Y and Xu, Z}, title = {Insights into the salt-dependent mechanisms of physicochemical changes, microbial succession, and biogenic amine formation during Doubanjiang fermentation.}, journal = {Food chemistry}, volume = {516}, number = {}, pages = {149287}, doi = {10.1016/j.foodchem.2026.149287}, pmid = {42034087}, issn = {1873-7072}, abstract = {Excessive biogenic amine formation is a major safety concern in salt-reduced Doubanjiang fermentation. This study compared high- (12%), medium- (9%), and low-salt (6%) systems to elucidate physicochemical dynamics, microbial succession, and mechanisms promoting biogenic amine accumulation. Salt reduction accelerated acidification and proteolysis, with the low-salt system showing the highest total acidity (0.73 g/100 g) and free amino acids (2684.86 mg/100 g), accompanied by excessive biogenic amine accumulation (1456.95 mg/kg). Microbial communities responded strongly to salinity, with Weissella and Bacillus dominating under low-salt conditions, whereas Tetragenococcus and Millerozyma prevailed at higher salinities. Metagenomic and culturomic analyses further identified key functional strains associated with biogenic amine metabolism. Microbially driven acid accumulation and increased amino acid availability, together with activation of decarboxylases induced by acid stress, jointly promoted biogenic amine formation in the low-salt system. These findings clarify salt-dependent mechanisms of biogenic amine formation and provide guidance for designing safe reduced-salt fermentation strategies.}, }
@article {pmid42034426, year = {2026}, author = {Zhou, N and Wei, R and Yang, S and Hu, F and Feng, Y and Zheng, H}, title = {Antibiotic resistance gene profiles in the gut microbiomes of Apis cerana, Apis mellifera, and Bombus terrestris.}, journal = {Pesticide biochemistry and physiology}, volume = {220}, number = {}, pages = {107059}, doi = {10.1016/j.pestbp.2026.107059}, pmid = {42034426}, issn = {1095-9939}, mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Metagenome ; China ; }, abstract = {The gut microbiota of honeybees has been increasingly recognized as a reservoir of antibiotic resistance genes (ARGs). However, comprehensive comparisons of ARG profiles between honeybees and bumblebees inhabiting the same environments are limited. Moreover, the diversity of mobile genetic elements (MGEs) in bee gut microbiomes and their potential role in mediating the horizontal transfer of ARGs have not yet been fully elucidated. In this study, metagenomic sequencing of 48 gut samples from farmed Apis mellifera, Apis cerana, and Bombus terrestris across four regions in China revealed 127 ARG subtypes, which collectively conferred resistance to nine major antibiotic classes. We found that A. mellifera, which carried the highest load of ARGs, concurrently harbored the greatest abundance of MGEs among the three species. Although ARG abundance varied significantly by region, no consistent geographical pattern emerged across the bee species. Importantly, strong positive correlations were detected between the abundances of ARGs and MGEs, particularly between the insertion sequence gene Tn3 and plasmid gene IncQ1. Metagenome-assembled genome analyses further confirmed the co-occurrence of ARGs (sul2, aph(3″)-Ib, and aph(6)-Id) with MGEs (Tn3 and IncQ1) across the three bee species, providing direct evidence that horizontal gene transfer mediated by MGEs contributes to the dissemination of ARGs within bee gut microbiomes. Overall, these findings highlight the critical role of the bee microbiome as a reservoir for ARGs and as a bioindicator for environmental pollutants, providing important insights into the mechanisms of ARG dissemination in ecosystems.}, }
@article {pmid42034448, year = {2026}, author = {Zhang, Y and Zhao, L and Zhang, P and Yang, Y and Wang, A and Xue, C and Yao, Y and Zhang, J and Zhao, M}, title = {Paenibacillus polymyxa EP-4 can effectively control southern corn leaf blight and affect the selectivity of Spodoptera frugiperda to corn.}, journal = {Pesticide biochemistry and physiology}, volume = {220}, number = {}, pages = {107047}, doi = {10.1016/j.pestbp.2026.107047}, pmid = {42034448}, issn = {1095-9939}, mesh = {Animals ; *Zea mays/microbiology ; *Plant Diseases/microbiology/prevention &amp; control ; *Spodoptera/physiology/microbiology ; *Paenibacillus polymyxa/physiology ; *Pest Control, Biological/methods ; Plant Leaves/microbiology ; Ascomycota ; Biological Control Agents ; }, abstract = {Southern corn leaf blight (SCLB) and Spodoptera frugiperda pose serious threats to corn yield. In recent years, an increasing number of studies have investigated biological control agents to control plant diseases and insect pests. However, research on the use of one biocontrol bacterium to control plant diseases and insect pests simultaneously is very limited. In this study, the bacterium EP-4, which can significantly inhibit the growth of Bipolaris maydis, was identified as Paenibacillus polymyxa. EP-4 metabolites inhibited hyphal growth, caused hyphal deformities, significantly reduced the spore germination of B. maydis, and damaged cell membranes, leading to DNA leakage. In the greenhouse, EP-4 significantly reduced the disease index of SCLB and the feeding and oviposition preferences of S. frugiperda to corn. Metabolite analysis revealed that inoculation with B. maydis and S. frugiperda after EP-4 pretreatment affected the production of corn resistance-related substances such as brassinolide, quercetin, 2-undecanone and naringin. Metagenomic analysis revealed that EP-4 pretreatment and subsequent inoculation with pests and diseases could induce the recruitment of Pseudomonas, Burkholderia, Azotobacter and Mesorhizobium in corn. EP-4 could significantly reduce the occurrence of SCLB and significantly affect the feeding and oviposition of S. frugiperda on corn. The mechanism of action of EP-4 on pests and diseases has been shown to differ. This strain has great application potential in corn.}, }
@article {pmid42034850, year = {2026}, author = {Gupta, E and Sharma, S and Dash, PK and Parida, M}, title = {Metagenomic profiling unveils the viral diversity in field-collected Aedes larvae from Central India employing nanopore sequencing.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-49112-y}, pmid = {42034850}, issn = {2045-2322}, }
@article {pmid42034975, year = {2026}, author = {Wang, H and Chen, Z and Qi, L and Wang, Z and Xu, D and Mao, Y and Shen, Z and Chen, K}, title = {Metagenomic profiling of Poa alpigena rhizosphere and bulk soil microbiomes across differing land-use contexts in the Qinghai lake alpine wetland.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04999-5}, pmid = {42034975}, issn = {1471-2180}, support = {This work was supported by the Natural Science Foundation Project of Anhui Provincial Universities (No. 2022AH052150 and 2024AH051553). Research on Ecosystem Changes in the Qinghai Lake Littoral Zone Under Water Level Rise and Their Impacts on Carbon Cycle (2023-ZJ-905T).//This work was supported by the Natural Science Foundation Project of Anhui Provincial Universities (No. 2022AH052150 and 2024AH051553). Research on Ecosystem Changes in the Qinghai Lake Littoral Zone Under Water Level Rise and Their Impacts on Carbon Cycle (2023-ZJ-905T)./ ; }, }
@article {pmid42034994, year = {2026}, author = {Chen, Y and Bao, R and Jin, W and Yin, X and Qin, L and Pan, J and Yao, Y and Shen, J and Fang, T and Ma, Y and Zhou, C and Miao, Q and Hu, B}, title = {Metagenomic and genomic characterization of extrapulmonary Mycobacterium abscessus infections: a comparative cohort study.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13117-9}, pmid = {42034994}, issn = {1471-2334}, support = {SHDC22024315//Shanghai Shen Kang Hospital Development Center/ ; }, }
@article {pmid42035444, year = {2026}, author = {Lopez, C and Banker, A and Venkatasamy, V and Garcia, J and Mattiazzi, A and Eidam, L and Preczewski, L and Anjan, S and Nasrallah, A and Vianna, R and Morsi, M and Natori, Y}, title = {Diagnosing Hyperammonemia Syndrome in Non-Lung Solid Organ Transplant Recipients With Metagenomic Next-Generation Sequencing: Utility and Limitations From Two Clinical Cases.}, journal = {Clinical transplantation}, volume = {40}, number = {4}, pages = {e70550}, doi = {10.1111/ctr.70550}, pmid = {42035444}, issn = {1399-0012}, }
@article {pmid42032005, year = {2026}, author = {Gladkikh, AS and Naydenov, DD and Sharova, AA and Popova, MR and Arbuzova, TV and Klyuchnikova, EO and Sbarzaglia, VA and Gibitova, EA and Forghani, M and Tokarevich, NK and Lunina, GA and Ramsay, ES and Dedkov, VG}, title = {Metaviromic analysis of Ixodes ticks in Northwestern Russia reveals high viral diversity and novel RNA virus lineages.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-50087-z}, pmid = {42032005}, issn = {2045-2322}, support = {N. 24-45-20005//RSF grant/ ; }, abstract = {Ticks of the genus Ixodes are recognized as important vectors of a wide range of viral pathogens with potential implications for public and veterinary health. Recent advances in metagenomic sequencing have uncovered an unprecedented diversity within tick-associated viromes, yet much of the global tick metavirome remains unexplored, particularly in vast and ecologically diverse regions such as Northwestern Russia. In this study, we present a comprehensive metaviromic and phylogenetic characterization of viruses detected in Ixodes persulcatus and Ixodes ricinus ticks collected from five regions in Northwestern Russia between 2021 and 2023. Using high-throughput RNA sequencing, we identified viral sequences representing families Nairoviridae, Partitiviridae, Phenuiviridae, Flaviviridae, Chuviridae, and Narnaviridae, Orthototiviridae. Putative novel viral lineages were identified. Phylogenetic analyses revealed strong geographic structuring of some viral lineages. This suggests either the presence of local genotypes, or underrepresentation of Eurasian tick-associated viromes, in current databases. In addition to TBEV, other viruses previously associated with human illness were detected in ticks in Northwestern Russia (Beiji nairovirus, Mukawa virus). Our findings provide the first high-resolution snapshot of the tick virome in Northwestern Russia. They emphasize the importance of continued viral surveillance in underrepresented biogeographic zones. These data contribute to the growing global virome map and may inform the development of region-specific vector-borne disease countermeasures.}, }
@article {pmid42032049, year = {2026}, author = {Zhang, X and Li, W and Wu, H and Cai, T and Chen, H and Zeng, S}, title = {Enhanced pathogen identification in fungal endophthalmitis by metagenomic next-generation sequencing: a retrospective clinical evaluation.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-50225-7}, pmid = {42032049}, issn = {2045-2322}, support = {LHGJ20220091//Henan Province Medical Science and Technology Key Project/ ; 2023A1515012220//Guangdong Basic and Applied Basic Research Foundation/ ; 2024ZDJS120//Guangdong Province Research Capability Improvement Project for Key Construction Disciplines/ ; 2025XSJ013&#xff1b;2024XK003&#xff1b;2021BQ011//Nanfang College Guangzhou/ ; }, abstract = {Fungal endophthalmitis (FE) is a vision-threatening emergency that requires rapid pathogen identification. Conventional microbial culture demonstrates limited sensitivity in FE, warranting improved diagnostic approaches. We evaluated the detection performance of unbiased metagenomic next-generation sequencing (mNGS) in 31 clinically diagnosed FE cases, including 16 vitreous humor (VH) and 15 aqueous humor (AH) specimens. mNGS showed a positivity rate of 90.3% (28/31, 95% CI: 74.2%-98%), outperforming culture (9.1%, 2/22, 95% CI: 1.1%-29.2%). The positivity rates were 100% for endogenous FE and 85% for exogenous FE, while VH and AH specimens achieved 100% and 80% positivity, respectively. mNGS identified polymicrobial infections in 5 exogenous cases, and a total of 15 fungal species across 9 genera, dominated by Aspergillus flavus, Candida albicans, and Aspergillus niger. Candida albicans and Aspergillus flavus were the predominant pathogens in endogenous and exogenous FE, respectively. Notably, mNGS enabled detection of rare fungal species including Aspergillus niger, Aspergillus welwitschiae, Fusarium oxysporum, Memnoniella echinata, Rhizopus oryzae, Rhizopus microsporus, Chaetomium globosum, and Debaryomyces fabryi. Sequencing results were supported or supplemented by culture, beta-D-glucan, and galactomannan testing in selected cases. Among mNGS-positive cases, 82.1% (23/28) experienced clinical management changes guided by fungal identification. We further propose a laboratory workflow integrating mNGS with conventional assays, tailored to the obtained specimen volume of intraocular fluids.}, }
@article {pmid42025876, year = {2026}, author = {Stamatopoulou, P and Scarborough, MJ}, title = {Impacts of organic loading rate fluctuations and division of labor on sugar-based chain elongation revealed through metatranscriptomics.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134687}, doi = {10.1016/j.biortech.2026.134687}, pmid = {42025876}, issn = {1873-2976}, abstract = {Medium-chain carboxylates (MCCs) can be produced using open, mixed cultures of microorganisms in a process termed "chain elongation." Chain elongating bacteria can increase ATP yield by producing six-carbon caproate rather than four-carbon butyrate. Therefore, requiring chain elongating bacteria to maximize ATP yield for cell synthesis may be a way to increase production of the more valuable caproate. To test this, duplicate bioreactors were operated, and the impact of organic loading rate (OLR) fluctuations were assessed with glucose and xylose as substrates in media that did not include amino acids, vitamins, or other growth factors. Increasing the OLR did not reliably improve caproate production despite several known caproate-producing bacteria being present. 16S rRNA gene amplicon sequencing and shotgun metagenomics revealed that the same chain-elongating and sugar-degrading species were enriched in both bioreactors, including members of the Caproiciproducens, Caproicibacter, Olegusella, and Tractidigestivibacter genera. Further, metatranscriptomic results suggest a distinct division of labor associated with critical growth factors, including amino acids, folate, and pantothenate. This division of labor, while potentially beneficial to the microbial community, may result in low caproate production.}, }
@article {pmid42026082, year = {2026}, author = {Human, ZR and Štursová, M and Odriozola, I and Větrovský, T and Howe, A and Navrátilová, D and López-Mondéjar, R and Žifčáková, L and Brabcová, V and Mundra, S and Thoen, E and Morgado, L and Fiore-Donno, AM and Bonkowski, M and Adamczyk, B and Kohout, P and Lipton, MS and Calhoun, S and LaButti, K and Lipzen, A and Keymanesh, K and Tejomurthula, S and Pennacchio, C and Grigoriev, IV and Martin, F and Kauserud, H and Baldrian, P}, title = {Seasonality of composition, genomic potential and activity of coniferous forest soil microbiomes.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07163-w}, pmid = {42026082}, issn = {2052-4463}, support = {240859//Norges Forskningsr&#xe5;d (Research Council of Norway)/ ; }, abstract = {Coniferous forest soils represent a globally important carbon sink, where the microbiome is essential for carbon flux between tree roots, rhizosphere, litter and soil. Soil habitats, such as roots, rhizosphere, bulk soil and litter differ in physicochemical properties and composition of highly specialized microbial communities, whose activity reflects the seasonality of temperature and tree activity of these mid- to high-latitude biomes. Here we present a multi-omic dataset encompassing 160 samples collected from four coniferous forest soil habitats in the Czech Republic and Norway, sampled in early summer, late summer, early winter and late winter that characterize the composition, genomic potential and activity of tree roots and microbiome. For each sample, we provide metabarcoding-based composition of bacterial, fungal and eukaryotic communities, results of shotgun DNA sequencing (metagenomes) and shotgun RNA sequencing (metatranscriptomes) illustrating the functional potential and activity within habitats. This dataset enables analyses of the temporal variation of taxonomic composition, functional potential and transcription across seasons in a temperate and boreal coniferous forest.}, }
@article {pmid42026126, year = {2026}, author = {Miravet-Verde, S and Cacace, E and Mores, CR and Rutschmann, C and Lin, CW and Ruscheweyh, HJ and Cuénod, A and Barazzone, EC and Marrec, E and Vershynina, K and Schumann, R and Bower, DJ and Schubert, M and Egli, A and Fiebig, T and Slack, E and Sunagawa, S and Keys, TG}, title = {In silico typing maps the natural diversity of Escherichia coli transporter-dependent capsules.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {42026126}, issn = {2058-5276}, support = {51NF40_225148//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; CRSK- 3_228959//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 117.143 IP-LS//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; LT0050/2023-L//Human Frontier Science Program (HFSP)/ ; FN24-0000000703//Novartis Stiftung f&#xfc;r Medizinisch-Biologische Forschung (Novartis Foundation for Medical-Biological Research)/ ; 865730//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, abstract = {Serotyping identifies bacterial variants based on surface antigens, traditionally using antibody-based assays, but has been increasingly replaced by in silico methods that infer serotypes from genomic sequences for faster, scalable and more reproducible analyses. However, traditional Escherichia coli capsule serotyping has largely fallen out of use since the 1990s, leaving gaps in our knowledge of capsule genetics, diversity, distribution and epidemiology. As capsules influence bacterial interactions with phages, host immune systems and the environment, this gap limits our understanding of E. coli ecology and pathogenicity as well as vaccine and diagnostic development. Here we established a definitive genotype-serotype map for 35 serologically identified and structurally characterized transporter-dependent capsules. We then surveyed 37,723 E. coli genomes, cataloguing 85 transporter-dependent capsule types (K-types), including 55 types that were not part of the reference collection. We leveraged this catalogue to develop a hidden Markov model-based in silico serotyping tool, kTYPr, and applied it to curated sets of 24,015 E. coli genomes and 2,762 metagenome-assembled genomes spanning diverse environmental and clinical sources. We found previously uncharacterized K-types enriched in undersampled environments and associated with E. coli disease. This study expands our understanding of E. coli surface structures, supporting efforts for precision targeting with phage therapy or vaccines.}, }
@article {pmid42026467, year = {2026}, author = {Luo, C and Yao, H and Xian, Y and Yang, T and Xiao, X and Ying, L and Xu, J and Luo, X and Qiu, D and Liu, Y and Liu, B and Li, F}, title = {Functional remodeling of the gut microbiome and metabolome in primary idiopathic male infertility.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05064-x}, pmid = {42026467}, issn = {1471-2180}, support = {2024NSFSC0647//Sichuan Provincial Science and Technology Support Program/ ; 24SYJS01//Health Commission of Sichuan Province Medical Science and Technology Program/ ; SCU2025J4183//the Fundamental Research Funds for the Central Universities/ ; }, }
@article {pmid42026490, year = {2026}, author = {Pan, J and Kong, H and Liang, M and Fang, X}, title = {Pneumonia caused by co-infection with Mycobacterium tuberculosis and Pneumocystis jirovecii leading to acute respiratory distress syndrome in an HIV-negative immunocompromised patient: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13398-0}, pmid = {42026490}, issn = {1471-2334}, }
@article {pmid42026803, year = {2026}, author = {Zhang, F and Hu, K and Sun, C and Chen, R and Ni, G and Liu, X and Wei, L and Su, R}, title = {Gene-level gut microbiome signatures as predictive biomarkers for response to immune checkpoint inhibitors across multiple cancer types.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2662690}, doi = {10.1080/19490976.2026.2662690}, pmid = {42026803}, issn = {1949-0984}, mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use ; *Gastrointestinal Microbiome/genetics/drug effects ; *Neoplasms/drug therapy/microbiology ; Deep Learning ; Biomarkers, Tumor/genetics ; *Bacteria/classification/genetics/isolation &amp; purification ; Female ; Male ; Metagenomics ; }, abstract = {Targeting programmed cell death protein 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) with immune checkpoint inhibitors (ICIs) has improved survival across multiple cancer types, but the variability in patient response highlights the need for better predictive biomarkers. Existing studies rely on taxonomic abundance derived from reference genome databases, limiting the discovery and functional interpretation of uncharacterized microbes. Here, we integrated metagenomic data from multiple ICI-treated cohorts spanning diverse cancer types and geographic regions and developed a deep learning model, named BioP-VAE, that incorporates biological prior knowledge via protein sequence embeddings and uses gene-level microbial abundance features as input. Gene-level microbial abundance outperformed taxonomy abundance in predicting both ICI response and 12-month progression-free survival (PFS). In patients receiving combination immune checkpoint blockade (CICB), BioP-VAE achieved a mean AUC of 0.89 in intracohort and 0.88 in cross-cohort evaluation. Notably, in the monotherapy-treated intracohorts, BioP-VAE achieved a mean AUC of 0.97. Feature attribution analysis revealed key microbial genes. Additionally, we identified distinct predictive microbial signatures via age-stratified analysis, suggesting that host age may modulate microbiome‒immune interactions. Importantly, this is the first large-scale study to evaluate gene-level microbial abundance features for ICI response prediction across multiple cancer types by deep learning. Our findings demonstrate that incorporating biological prior knowledge into deep learning models can improve the discovery of microbial biomarkers that can be generalized across cancer types and treatment settings, offering a novel strategy for patient stratification in immunotherapy.}, }
@article {pmid42027256, year = {2026}, author = {Lu, S and Xia, Y and Sun, Q and Sun, Y and Chen, R and Jin, H and Zhang, J and Liu, W and Huang, J}, title = {Characterization of the Gut Virome in Patients with Inflammatory Bowel Disease and Non-Alcoholic Fatty Liver Disease.}, journal = {Journal of inflammation research}, volume = {19}, number = {}, pages = {581751}, pmid = {42027256}, issn = {1178-7031}, abstract = {OBJECTIVE: The dysbiosis of the gut microbiota is a well-known correlate in the pathogenesis of inflammatory bowel disease (IBD). However, the microbiome characteristics of patients with IBD who also have non-alcoholic fatty liver disease (NAFLD) are understudied, particularly the potential pathogenic mechanisms of the gut virome.<br><br>MATERIALS AND METHODS: In this study, we conducted a comprehensive gut virome correlation study, along with serum metabolomics analysis, by performing virus-like particle (VLP) and metagenomic sequencing on fecal samples from patients with inflammatory bowel disease and non-alcoholic fatty liver disease (IBD-NAFLD) and NAFLD (MASLD) controls without gastrointestinal diseases.<br><br>RESULTS: The results showed that changes in the fecal virome were associated with IBD-NAFLD (MASLD), particularly with an increase in the abundance of Caudovirales in IBD-NAFLD (MASLD) patients. Subsequent analysis of the gut virome identified Bacteroides as the top predicted host for the viruses. Additionally, we identified the pathways involved in all differential metabolites through KEGG annotation analysis, with the highest correlation being the galactose metabolism pathway.<br><br>CONCLUSION: In conclusion, by using a customized integrated gut virome catalog tailored for IBD, we revealed the fundamental changes in the gut virome of IBD-NAFLD (MASLD) patients. This study is the first to uncover the specificity of the gut virome in IBD-NAFLD (MASLD) patients and predict Bacteroides as a potential host, suggesting a microbial signature primarily influenced by intestinal inflammation.}, }
@article {pmid42027295, year = {2026}, author = {Sangodkar, N and Gonsalves, MJ and Nazareth, DR}, title = {Methanotrophy dominated symbiosis in novel species Gigantidas niobengalensis from the cold seeps of Krishna-Godavari basin.}, journal = {FEMS microbes}, volume = {7}, number = {}, pages = {xtag014}, pmid = {42027295}, issn = {2633-6685}, abstract = {Bathymodiolus mussels, which are prominent invertebrates at cold seeps and hydrothermal vents, are known for hosting symbiotic microbes within their gills. In this study, the microbial communities associated with the gills of novel bathymodioline mussel Gigantidas niobengalensis from an active cold seep site of Krishna-Godavari (K-G) basin was investigated by 16S rRNA amplicon sequencing. The average abundance of culturable methanotrophs in the gill tissues was 3.4 ± 0.9 × 10[4] CFU g[-1] with average methane oxidation rates of 1.71 ± 0.04 to 1.89 ± 0.02 µM g[-1] d[-1] under aerobic and 1.86 ± 0.001 to 1.98 ± 0.005 µM g[-1] d[-1] under anaerobic conditions. Metagenomic analysis revealed dominance of methanotrophs within the microbial communities comprising of >55% bacterial and >28% archaeal methanotrophs; with phyla Proteobacteria, Firmicutes, Bacteroidetes, Verrucomicrobia, Actinobacteria, Euryarchaeota, and Crenarcheaota being prevalent. Functional classification highlighted methane metabolism (20%) and carbon fixation (22%) as major energy metabolism pathways. This study represents the first metagenomic characterization of gill-associated symbionts in the novel cold seep mussel G. niobengalensis from the Indian Ocean. The findings fill a knowledge gap on chemosynthetic symbioses in Indian cold seep ecosystems and provide insights into metabolic adaptation of G. niobengalensis in the cold seep ecosystem.}, }
@article {pmid42027454, year = {2026}, author = {Chen, X and Gong, L and Lu, Y and Liu, W and Liu, F and Li, Q and Wang, L and Qiu, L and Zhang, D and Ye, X}, title = {Epidemiological characteristics and environmental surveillance of human psittacosis in Lishui City, Zhejiang Province, China (2021-2024).}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1769696}, pmid = {42027454}, issn = {1664-302X}, abstract = {INTRODUCTION: Psittacosis, caused by Chlamydia psittaci, is an underdiagnosed zoonosis that can lead to severe pneumonia and fatal outcomes. In China, traditional poultry farming poses substantial risks for avian-to-human transmission, yet comprehensive epidemiological evidence is scarce. To address this gap, we aimed to define the local epidemiology, risk factors, and environmental reservoirs of human psittacosis in Lishui City, Zhejiang Province.<br><br>METHODS: We conducted a multi-source epidemiological study (2021-2024) integrating surveillance data, clinical records, contact investigations, and environmental sampling. Cases were confirmed by quantitative polymerase chain reaction (qPCR) or metagenomic next-generation sequencing (mNGS).<br><br>RESULTS: We identified 28 laboratory-confirmed cases, showing annual fluctuations in reported case numbers. Infections, mostly confirmed by mNGS, were predominantly sporadic among elderly agricultural workers (mean age 62.6 years), with 96.4% reporting recent poultry exposure. All patients presented with pneumonia; 64.3% developed severe disease, resulting in three deaths. The median diagnostic delay-from symptom onset to diagnosis-was 12 days. A household cluster of three cases was detected; however, no secondary transmission occurred among 205 close contacts outside the household. C. psittaci DNA was detected in 14.79% (21/142) of environmental samples, with the highest number of cases detected in duck manure samples, with the highest positive rate (26.7%). Phylogenetic analysis of 20 ompA gene sequences revealed a predominantly genotype A and the waterfowl-TW genotype, which are closely related to strains from southern China.<br><br>DISCUSSION: Psittacosis in Lishui presents as a sporadic but clinically severe disease in older rural residents. The high frequency of severe pneumonia and prolonged diagnostic delay underscores an urgent need to improve clinical suspicion and access to molecular diagnostics. Detection of C. psittaci nucleic acid in environmental samples suggests possible environmental contamination; however, viability and transmissibility were not assessed.}, }
@article {pmid42027830, year = {2026}, author = {Chen, L and Ding, Y and Liu, Y and Xie, Q and Hu, J and Wang, M and Zeng, X and Zou, D}, title = {Case Report: Ultrasound guided puncture for type 2 diabetes mellitus combined with psoas abscess-a report of two cases.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1773238}, pmid = {42027830}, issn = {2296-858X}, abstract = {BACKGROUND: Psoas abscess (PA) is a rare infectious disease, with type 2 diabetes mellitus (T2DM) serving as a significant risk factor. The combination of metagenomic next-generation sequencing (mNGS) and ultrasound offers innovative approaches for the rapid and precise treatment of PA.<br><br>CASE PRESENTATION: Case 1: A 77-year-old woman presented with lumbar pain was initially misdiagnosed with lumbar disc herniation based on CT scan. Subsequent CT scan and ultrasound-guided puncture confirmed a left lumbar PA. mNGS detected the presence of Streptococcus agalactiae, which was negative on conventional culture. The patient was successfully treated with vancomycin for 5 weeks, with no recurrence at 3-year follow-up. Case 2: A 56-year-old woman with a 10-year history of T2DM presented with poor appetite and fatigue. CT imaging identified a left lumbar PA along with perirenal infection. Pus from ultrasound-guided puncture for conventional culture and mNGS detected the presence of Staphylococcus aureus. Treatment with oxacillin and vancomycin led to clinical resolution. The follow-up CT scan in 2024 indicated complete resorption of the lesion.<br><br>CONCLUSION: mNGS combined with ultrasound-guided puncture overcomes conventional culture limitations. This approach suggests clinical feasibility.}, }
@article {pmid42028026, year = {2026}, author = {Heinzelmann, D and Reuss, F and Zeh, N and Nilson, R and Walker, E and Fieder, J and Lindner, B and Renner, B and Schulz, P and Fischer, S and Schmidt, M}, title = {Discovery of a chimeric transposase-transposon system for advanced genome engineering.}, journal = {iScience}, volume = {29}, number = {5}, pages = {115548}, pmid = {42028026}, issn = {2589-0042}, abstract = {Transposases have transformed genetic engineering, yet functional systems remain scarce. In response, an unknown transposase system from Acyrthosiphon pisum was identified by metagenomic screening. Through systematic optimization, we enhanced nuclear localization, transposon architecture, and created a hyperactive transposase variant to boost efficiency. Intriguingly, the combined application of the newly discovered transposase with inverted terminal repeat sequences from a related pea aphid species, Aphis craccivora, further enhanced transposition activity, resulting in the first chimeric transposase system reported so far. We investigated the genomic integration events following transposition in mammalian cells to understand the underlying mechanisms and optimize the efficiency of transgene integration. This optimized system can expedite the generation of recombinant protein-producing Chinese Hamster Ovary (CHO) cell lines, even surpassing the hyperactive piggyBac system with regard to cell-specific productivity. These findings introduce a significant addition to the field of semi-targeted transgene integration technologies, offering substantial potential for enhancing biologics manufacturing.}, }
@article {pmid42028145, year = {2026}, author = {Chen, Y and Zhang, L and Wang, T and Pan, X and Chen, D and Liu, J}, title = {Characteristics of CD4[+]T-cell reduction and pulmonary infections in critically ill immunocompromised patients.}, journal = {Journal of intensive medicine}, volume = {6}, number = {2}, pages = {157-165}, pmid = {42028145}, issn = {2667-100X}, abstract = {BACKGROUND: The CD4[+]T-cell count is a key indicator for evaluating immunosuppression. Infections significantly influence the survival and prognosis of critically ill patients. This study aims to systematically evaluate the association between reduced CD4[+] T-cell counts and lung infections in immunosuppressed ICU patients, offering clinical evidence to guide the management of lung infections in this population.<br><br>METHODS: This retrospective, single-center study included 40 immunocompromised patients admitted to the ICU from January 1, 2021, to June 30, 2023. All participants underwent metagenomic next-generation sequencing. Patients with suspected lung infections based on their CD4[+]T-cell counts were divided into mild (350/&#xb5;L<CD4[+]T-cell count<500/&#xb5;L), moderate (200 /&#xb5;L<CD4[+]T-cell count &#x2264; 350/&#xb5;L), and severe (CD4[+]T-cell count &#x2264;200/&#xb5;L) groups. Microecological analysis was performed on each group. Intergroup comparisons were conducted for 28-day mortality, hospital length of stay, and ICU length of stay.<br><br>RESULTS: Amang these forty immunosuppressed patients, 8 were assigned to the mild group, 16 to the moderate group, and 16 to the severe group. Streptococcus pneumoniae was almost all distributed in moderate patients (75.0%), while severe patients had a higher proportion of fungi detected (25.7%). Respiratory microbiome analysis identified Acinetobacter baumannii, Human alphaherpesvirus 1, and Klebsiella pneumoniae as the most abundant species. Although no significant difference in the alpha diversity index was found among the groups, index values were lower in the severe group than in the moderate group. Beta diversity analysis showed that the microbial community structure did not significantly differ among the three groups. A total of 27 microbial markers were obtained, with multiple streptococcal species showing enrichment in moderate group and Candida tropicalis in severe group. By day 28, four patients (50.0%) in the mild group had died compared with six (37.5%) in the moderate group and nine (56.3%) in the severe group. There were no significant difference in the duration of ICU or hospital stays.<br><br>CONCLUSIONS: This study on ICU-admitted immunocompromised patients identified the prevalent pathogens and microbiome features associated with pulmonary infections, as well as their relationship with CD4[+]T-cell depletion. These findings are valuable for optimizing clinical diagnosis and treatment strategies and may contribute to improving patient outcomes.}, }
@article {pmid42028191, year = {2026}, author = {Hariharamohan, M and Chindarkar, M and Swain, HS and Rajesh, N and Rajesh, V}, title = {Integrating physicochemical and microbial characterization of red rice broth fermented over an 18-hour period augmented with metagenomic and metabolomic approaches.}, journal = {RSC advances}, volume = {16}, number = {23}, pages = {21129-21141}, pmid = {42028191}, issn = {2046-2069}, abstract = {Fermentation enhances the nutritional properties of foods. Fermented water of Kerala red rice (Oryza sativa L. subsp. indica), traditionally consumed in South India remains underexplored scientifically. This study characterizes the nutritional, microbial, and metabolite profiles of Kerala red rice water (broth) after 18 hours of natural fermentation using biochemical assays, shotgun whole-genome metagenomic sequencing (Illumina NovaSeq X Plus), untargeted gas chromatography-mass spectrometry (GC-MS) metabolomics, and a phytase-mediated mineral release assay. Fermentation enhanced nutritional quality with increase in carbohydrates by 22.7%, protein by 163.52%, and free amino acids by 35.47% compared to unfermented controls. Phytase activity rose from negligible levels to 0.12 U mL[-1]. Metagenomics identified 50 taxa, dominated by Proteobacteria (59.63%) and Firmicutes (40.12%), with ∼34% of the community carrying phytase-encoding genes. Dominant genera included Pantoea, Saccharibacillus, and Bacillus. Fermentation also enhanced mineral release, with calcium, iron, and zinc in the fermented rice water showing increases of approximately 1190%, 566%, and 93%, respectively, relative to unfermented controls over a 360 min in vitro digestion period. These findings provide the first integrated insight bridging traditional dietary practice with modern analytical science.}, }
@article {pmid42028978, year = {2026}, author = {Xiao, L and Liu, J and Noyce, GL and Lee, J and Duarte, CM and Zhou, M and Luo, M and Sun, R and Dang, R and Zhou, L and Zhang, L and Fu, C and Tan, Y and Yu, J and Han, G}, title = {Microbial Responses to Warming Reduce Deep Blue Carbon Storage.}, journal = {Global change biology}, volume = {32}, number = {4}, pages = {e70883}, doi = {10.1111/gcb.70883}, pmid = {42028978}, issn = {1365-2486}, support = {U2106209//National Natural Science Foundation of China/ ; 42077025//National Natural Science Foundation of China/ ; 42277236//National Natural Science Foundation of China/ ; 42071126//National Natural Science Foundation of China/ ; 2021213//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; XDA23050202//Strategic Priority Research Program of Chinese Academy/ ; YICE3510303//Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences/ ; }, mesh = {*Soil Microbiology ; *Carbon Cycle ; *Carbon/metabolism ; *Global Warming ; Soil/chemistry ; *Carbon Sequestration ; Wetlands ; *Climate Change ; Plants/metabolism ; }, abstract = {Coastal wetlands are critical blue carbon reservoirs, yet the depth-resolved impacts of warming on belowground carbon dynamics remain poorly understood. Over the course of an 8-year in situ experiment, we investigated plant-derived carbon inputs, soil carbon losses via respiration, and microbially mediated carbon fixation across a 60 cm soil profile under a projected 2°C atmospheric warming scenario. Plant carbon fixation (above- and belowground net primary productivity) and soil respiration exhibited synchronized responses to warming, with an initial increase, followed by a decline in the mid-term, and no significant response in the later stages. Soil and microbial respiration stabilized after prolonged exposure to elevated temperatures, as these processes were constrained by substrate availability. In contrast, phospholipid fatty acid profiling, amino sugar biomarkers, and metagenome-assembled genomes consistently indicated a greater than one-third reduction in microbial carbon fixation within subsoils (40-60 cm). Our fully factorial, depth-stratified warming design reveals the particular vulnerability of deep soil microbial carbon retention to long-term climate warming, independent of shifts in plant input or respiratory carbon loss. This work highlights underappreciated pathways influencing soil blue carbon dynamics in a changing world.}, }
@article {pmid42028995, year = {2026}, author = {Liu, M and Du, M and Xi, Z and Tastambek, KT and Bao, Y and Song, X and Zhou, A and Wang, Y}, title = {Bacillus aerius synergizes with coal gangue to enhance Medicago sativa growth via soil microbiome and gene regulation.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0026826}, doi = {10.1128/aem.00268-26}, pmid = {42028995}, issn = {1098-5336}, abstract = {UNLABELLED: The extensive accumulation of coal gangue poses significant environmental threats through water contamination, soil degradation, and atmospheric pollution, necessitating the urgent development of ecological utilization strategies. This study elucidates the mechanistic basis by which the thermophilic bacterium Bacillus aerius (B. aerius) enhances plant growth in coal gangue-amended sandy soils. Through integrated analysis of nutrient dynamics, phytohormonal activities, soil enzymatic profiles, and metagenomic functional profiling, we demonstrate significant synergy between coal gangue and B. aerius. When applied together in sandy soils, the germination rate, plant height, root length, and fresh biomass of Medicago sativa (alfalfa) increased by 1.18-2.06 times. The levels of soil nitrogen, phosphorus, and potassium also significantly increased, resulting in notable improvements in soil fertility. The bacterial treatment enhanced the activities of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and various soil enzyme activities while also optimizing the microbial community structure and increasing the abundance of beneficial bacteria, including Bacillus. Metagenomic analysis revealed the upregulation of growth-promoting genes such as acdS, nifK, and phnG, which collectively drive plant growth through multiple pathways, including enhanced soil nutrient availability, hormone regulation, soil enzyme activities, and nutrient cycling. Collectively, this work deciphers molecular-scale bacteria-gangue synergism, providing a theoretical foundation for sustainable coal gangue utilization and ecological restoration of degraded soils.<br><br>IMPORTANCE: The accumulation of coal gangue poses significant environmental challenges, necessitating the development of eco-friendly utilization strategies. This study demonstrates that the thermophilic bacterium Bacillus aerius acts synergistically with coal gangue to promote alfalfa growth in sandy soils while improving soil fertility. The combined treatment enhanced plant morphological traits, soil nutrient availability, beneficial microbial communities, and associated biological activities, with these effects supported by molecular evidence. As the first study to verify this growth-promoting mechanism, our findings address a critical knowledge gap and provide a theoretical foundation for the sustainable utilization of coal gangue in the ecological restoration of degraded soils.}, }
@article {pmid42029028, year = {2026}, author = {Valdez-Nuñez, LF and Chávez, IJ and Sekerci, F and Ayala-Muñoz, D and Straub, D and Kappler, A and Fischer, S and Mansor, M}, title = {Desulfosporosinus and Acididesulfobacillus dominate an acidophilic sulfate-reducing bacteria consortium during acid mine drainage bioremediation.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0030826}, doi = {10.1128/aem.00308-26}, pmid = {42029028}, issn = {1098-5336}, abstract = {Acid mine drainage (AMD) is an environmental threat due to its low pH and high metal content. Biological treatment of AMD using acidophilic sulfate-reducing bacteria (aSRB) represents a potential solution for this problem, but their substrate specificity and low tolerance to extreme acidity (pH ≤3.0) and toxic metals limit their application. Here, we used an indigenous aSRB-containing consortium to remove metals and neutralize a synthetic AMD (sAMD) system starting at pH 2.9. The consortium was enriched from acidic sediments of an abandoned mine tunnel in Peru. A bioremediation experiment (pH 2.9) was set up with Fe[2+] (40.25 mM), Al[3+] (5.39 mM), and Zn[2+] (3.97 mM) as the main dissolved metals. Glycerol and yeast extract were used as carbon sources. Physicochemical parameters, mineral formation, microbial communities, and dissolved metals were monitored for 160-200 days. At the end of the incubation, the final pH reached 6.1 and 100% of Zn[2+], >99% of Fe[2+], and >94% of Al[3+] were removed by the aSRB consortium as X-ray diffraction-amorphous minerals. The aSRB Desulfosporosinus and Acididesulfobacillus dominated the bioremediation experiment. Two high-quality metagenome-assembled genomes taxonomically affiliated to the aforementioned aSRB showed metabolic potential related to sulfur compounds reduction as well as to organic carbon degradation (e.g., glycerol and acetate). Differences related to carbon degradation during AMD bioremediation suggest a synergy between Acididesulfobacillus and Desulfosporosinus, thus avoiding toxic waste product accumulation. Overall, we obtained a novel aSRB-containing microbial consortium that can be used for acidity neutralization and metal removal, suitable for more robust AMD treatment technologies.IMPORTANCEAcid mine drainage (AMD) remains one of the biggest environmental challenges of the mining industry. Treatment technologies based on the application of microbial consortia are gaining popularity, taking advantage of synergistic interactions between different species to widen substrate specificity and to limit toxicity. Our research work here shows two acidophilic sulfate-reducing bacteria, Desulfosporosinus and Acididesulfobacillus, working together in AMD bioremediation. Desulfosporosinus initiated sulfate reduction at pH ~3.0 with glycerol as the carbon source and acetate as the waste product. Once pH rose to ~4.0, Acididesulfobacillus continued with sulfate reduction with acetate as a carbon source, thus avoiding acetate accumulation and cell toxicity. In the end, this synergistic interaction neutralized acidic pH and removed metals to a great extent, making it suitable for biological treatment of AMD.}, }
@article {pmid42029155, year = {2026}, author = {Perlas, A and Reska, T and Sánchez-Cano, A and Mejías-Molina, C and Gygax, D and Martínez-Puchol, S and Rusiñol, M and Eger, E and Schaufler, K and Höfle, U and Croville, G and Le Loc'h, G and Guérin, J-L and Urban, L}, title = {Real-time genomic pathogen, resistance, and host range characterization from passive water sampling of wetland ecosystems.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0254325}, doi = {10.1128/aem.02543-25}, pmid = {42029155}, issn = {1098-5336}, abstract = {UNLABELLED: Wetland ecosystems provide interfaces for the transmission of microbial pathogens and antimicrobial resistances (AMR) between migratory birds, wild and domestic animals, and human populations. The efficient surveillance of wetlands is, however, challenging, since the typically low concentration of pathogens requires the sampling of large volumes of water and subsequent targeted detection, which is inherently limited to a few pathogens or AMR genes of interest. Here, we present a holistic, accessible, and cost-efficient framework to characterize the pathogen and resistance load of water sources together with their potential associated hosts by combining passive water sampling through torpedo-shaped devices with nanopore sequencing technology. We used this framework to characterize anthropogenically influenced and natural wetland ecosystems along the East Atlantic Flyway, where we obtained robust assessments of the microbial communities from long-read metagenomic and RNA virome data and showed that anthropogenically impacted wetland ecosystems consistently exhibited higher relative abundances of pathogens and AMR genes. By focusing on avian influenza viruses (AIV), we finally highlight the additional need for targeted screening and whole-genome sequencing of pathogens of interest; we detected and characterized AIV at a third of the monitored sites and used environmental DNA to explore potential animal hosts to better understand the role of wetland ecosystems as One Health interfaces, where the health of animals, humans, and the environment are interconnected and pathogen transmission can occur across these domains.<br><br>IMPORTANCE: Wetlands connect wildlife, livestock, and people, making them key places to watch for pathogens and antibiotic resistance. Yet potentially harmful microbes are easy to miss in water because they represent only a small fraction of the abundant microbial life in water, making them hard to detect. We paired 3D-printed passive torpedo-shaped samplers with a portable genetic sequencer to analyze all microbes captured. We deployed this approach at 12 wetlands in Germany, France, and Spain. It revealed local microbial communities, identified disease-causing bacteria, and linked many antibiotic resistance genes to likely bacterial hosts. By comparing locations, we observed that sites near cities, farms, or wastewater had higher levels of pathogens and resistance than protected natural sites. Our analysis also recovered all viruses present, including those from mammals, birds, fish, insects, and plants. We also specifically looked for the virus that causes avian flu, found it at several sites, and classified it as low pathogenicity. Because our method is non-invasive to wildlife, affordable, and practical to deploy, it can provide early warnings to conservation and public health agencies and guide action where risks are present.}, }
@article {pmid42029954, year = {2026}, author = {Gao, J and Li, HL and Li, MS and Shao, ZJ and Yang, ZF and Li, CJ and Zhang, ZX and Zhu, D and Lv, ZH and Song, RH and Li, JL and Hu, W and Yin, YR}, title = {Cloning, heterologous expression, and characterization of a metagenome-derived GH10 xylanase with salt and alkali tolerance from Xinjiang saline-alkali soil.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {5}, pages = {}, pmid = {42029954}, issn = {1572-9699}, support = {YWLCYXZX2023300075//the Yunnan Provincial Clinical Medical Center for Emergency Traumatic Diseases/ ; 32560004//the National Natural Science Foundation of China Regional Program/ ; }, mesh = {*Metagenome ; Cloning, Molecular ; *Endo-1,4-beta Xylanases/genetics/metabolism/chemistry ; *Soil Microbiology ; *Alkalies ; Hydrogen-Ion Concentration ; *Soil/chemistry ; Enzyme Stability ; Salt Tolerance ; Escherichia coli/genetics ; Xylans/metabolism ; Recombinant Proteins/genetics/metabolism/isolation &amp; purification ; Temperature ; Amino Acid Sequence ; China ; Sodium Chloride ; Phylogeny ; }, abstract = {Xylanases are widely used in baking, seafood processing, and paper production, but their performance is often compromised under high-salt, acidic, or alkaline conditions, limiting broader industrial deployment. Identifying robust xylanases from saline-alkali environments is therefore of practical importance. Here, we report a GH10 xylanase gene, XynE102, mined from a saline-alkali soil metagenome from Karamay, Xinjiang. The deduced amino acid sequence shares 69.17% identity with a xylanase from Cellvibrionaceae bacterium (GenBank accession HEY7885703.1). XynE102 was cloned and heterologously expressed in Escherichia coli, and the recombinant enzyme was purified by Ni-NTA affinity chromatography. Using beechwood xylan as substrate, XynE102 exhibited optimal activity at 50 °C and pH 7.0. It retained ≥ 50% relative activity between 30 and 55 °C and pH 5.6-8.6, and ≥ 75% activity in 2.0 M NaCl. Notably, after preincubation at 40 °C for 60 and 120 min, its activity increased to 130% and 165% of the initial value, respectively. Following 24 h preincubation at pH 7-10, residual activity remained ≥ 80%, indicating pronounced alkaline stability. At 1 mM, Mn[2+], Co[2+], and Fe[3+] activated the enzyme, whereas Mg[2+], Cu[2+], and Cd[2+] inhibited it; 1% SDS had no measurable effect. XynE102 primarily hydrolyzed xylan to xylobiose and xylotetraose. It also hydrolyzed alkali-treated corn stalk and hot-water-pretreated wheat bran, yielding reducing sugar concentrations of 5.44 mM and 4.18 mM, respectively, after 24 h. Taken together, these results indicate that XynE102 is a neutral-pH xylanase with notable salt and alkali tolerance, supporting its potential for prebiotic XOS production and food-processing applications under moderate temperature conditions.}, }
@article {pmid42030718, year = {2026}, author = {Chen, L and Zhong, J and Deng, N and Lin, H and Zhang, L}, title = {Spatiotemporal patterns of arsenic and its microbial arsenic transformation in the Pearl River Estuary.}, journal = {Journal of hazardous materials}, volume = {510}, number = {}, pages = {142145}, doi = {10.1016/j.jhazmat.2026.142145}, pmid = {42030718}, issn = {1873-3336}, abstract = {Estuarine ecosystems are critical zones for arsenic (As) biogeochemical cycling, yet the spatiotemporal distribution and microbial transformation mechanisms of As in these dynamic environments remain poorly understood. This study integrated geochemical analyses with metagenomic and metatranscriptomic approaches to investigate As distribution and microbial transformation mechanisms in Pearl River Estuary (PRE). Our results revealed distinct spatiotemporal patterns of As in the PRE. As in sediment were significantly higher in the western region and exhibited a clear decreasing gradient from upstream to downstream. As(V) was the dominant species in both sediments and water, while organic As remained below detection limits. Seasonally, As concentrations peaked in winter and spring. Microbial community analysis showed that highly diverse microbial taxa capable of transforming As were detected, with Proteobacteria identified as the dominant phylum. Among key functional genes, arsM exhibited the highest abundance and transcription level, indicating substantial methylation potential throughout the estuary. Notably, metagenome-assembled genome (MAG) analysis uncovered a previously undocumented metabolic transition along the estuarine gradient, shifting from As(V) reduction coupled with methylation and efflux in upstream to As(III) oxidation with a more diversified strategy in mid-downstream. This systematic study clarified the distribution and microbial transformation mechanisms of As in the PRE, advancing our understanding of As biogeochemical cycling in estuarine ecosystems.}, }
@article {pmid42030844, year = {2026}, author = {Zhao, H and Che, W and Tan, X and Shen, Y and Xu, Y and Man, Y}, title = {Distribution characteristics and potential microbial degradation mechanisms of microplastics in oyster aquaculture areas of southern China.}, journal = {Journal of hazardous materials}, volume = {511}, number = {}, pages = {142136}, doi = {10.1016/j.jhazmat.2026.142136}, pmid = {42030844}, issn = {1873-3336}, abstract = {Microplastic (MP) pollution in coastal aquaculture is a growing environmental and public health concern. Despite increasing reports, the cross-regional and cross-media pollution patterns, ecological risks, and microbial degradation potentials in aquaculture ecosystems remain poorly understood. We investigated oyster farming systems in South China: Zhanjiang Bay (ZJB, semi-enclosed) and Xuwen (XW, open coast). MP abundances ranged from 20 to 54 items/L in seawater and 950-6483 items/kg in sediment, with particles < 50 μm and granular shapes dominant in both media, as determined by Laser Direct Infrared Imaging. MP spatial patterns differed markedly between regions; XW exhibited higher seawater MP levels attributed to larger farming scales, whereas ZJB showed greater sediment MP accumulation owing to weaker water exchange and a longer farming history. Source apportionment identified aquaculture facilities as the primary source (44.86%). Notably, while the overall pollution load was relatively low, the potential ecological risk index reached 866.51 (classified as "dangerous"), driven predominantly by highly toxic polymers such as polyurethane (PU) and polyvinyl chloride (PVC). The distribution of plastic-degrading genes (PDGs) and their host microbial communities was primarily determined by these aquaculture facilities and the environmental medium (sediment vs. seawater), rather than by localized water-quality conditions. Metagenomic analysis identified sediments as key metabolic hotspots, harboring diverse functional genes involved in polyethylene β-oxidation, polystyrene aromatic ring cleavage, and PU hydrolysis. These findings bridge the gap in understanding MP dynamics between diverse aquaculture habitats and highlight the potential of indigenous microbes in natural attenuation, providing critical insights for MP risk management.}, }
@article {pmid42030878, year = {2026}, author = {Saini, K and Prajapati, A and Kumar, SS and Kumar, V and Bajar, S}, title = {Performance assessment of sulfate-reducing bacterial consortium for the treatment of real landfill leachate under anaerobic conditions.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129743}, doi = {10.1016/j.jenvman.2026.129743}, pmid = {42030878}, issn = {1095-8630}, abstract = {Landfill leachate contains complex organic pollutants, ammonia, sulfate, and toxic metals, posing major environmental challenges. This study evaluated a sulfate-reducing bacterial (SRB) consortium isolated from electroplating wastewater for the treatment of real landfill leachate under anaerobic conditions. Physicochemical characterization revealed a Leachate Pollution Index (LPI) of 63.16, confirming the high hazardous nature of the leachate. The acclimatized SRB consortium exhibited strong metabolic activity and rapidly degraded pollutants. Within 10 days of treatment, the system achieved 82.84% removal of chemical oxygen demand (COD) and 97.83% removal of biochemical oxygen demand (BOD5), demonstrating efficient biodegradation of both biodegradable and persistent organic compounds. The concentrations of heavy metals were reduced to below the detection limit (BDL), primarily due to sulfide-mediated precipitation. Thus, SRB provide dual benefits of organic degradation and metal detoxification. Metagenomic profiling (16S rRNA sequencing) revealed dominant sulfate-reducing species, including Desulfovibrio vulgaris, Desulfotomaculum nigrificans, Desulfobulbus propionicus, and Desulfosporosinus orientis. Kyoto Encyclopedia of Genes and Genomes (KEGG) based functional annotation was performed to elucidate the metabolic potential of the SRB consortium. Scanning electron microscopy (SEM) analysis before and after treatment confirmed microbial colonization and sulfide-mediated metal precipitation. Overall, SRB-based anaerobic processes demonstrate significant potential as a sustainable and efficient treatment for high-strength landfill leachate with strong potential for scale-up and integration into waste management systems. Although the treated effluent did not meet CPCB (India) and EPA COD discharge standards, this bioremediation approach provides a cost-effective alternative to conventional physicochemical treatments. Further optimization of operational parameters and microbial activity could enhance treatment efficiency and facilitate regulatory compliance.}, }
@article {pmid42030912, year = {2026}, author = {Hua, Y and Xu, X and Chen, Y and Li, Y and Dai, X}, title = {Making waves: Wastewater sludge holds untapped antimicrobial potential.}, journal = {Water research}, volume = {300}, number = {}, pages = {125989}, doi = {10.1016/j.watres.2026.125989}, pmid = {42030912}, issn = {1879-2448}, abstract = {Wastewater treatment plants are widely recognized as critical nodes in the environmental dissemination and control of antimicrobial resistance (AMR). This risk-focused view is warranted, but incomplete. Wastewater sludge is one of the largest engineered and repeatedly accessible microbiomes on Earth, continuously shaped by diverse microbial inputs and exposure to antimicrobial compounds and other stressors. These conditions may also harbor underexplored antimicrobial functions. Here we propose framing sludge as a dual-function node within AMR stewardship: a resource for routine surveillance and risk management, and a source material for an offline, containment-first workflow to identify antimicrobial candidates, particularly antimicrobial peptides. We summarize recent advances in metagenomics and machine-learning-enabled peptide prioritization and outline an evidence ladder that links sequence signals to functional validation. A central principle is to decouple discovery from plant operations and to apply explicit decision gates early in the pipeline, including cross-resistance screening and resistance-evolution assays, to prevent inadvertently increasing selection pressure or AMR risks. Finally, we call for shared benchmarks to improve comparability across studies, including curated datasets, standardized validation panels, and routine reporting of negative findings and resistance-related outcomes. Together, these steps can help translate sludge-enabled discovery into environmentally responsible innovation aligned with AMR stewardship.}, }
@article {pmid42030968, year = {2026}, author = {Brown, JR and Chiu, CY and López-Labrador, FX and de Vries, JJC}, title = {The impact of clinical metagenomic testing on patient management: facts versus fantasy.}, journal = {The Lancet. Infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/S1473-3099(26)00106-4}, pmid = {42030968}, issn = {1474-4457}, abstract = {Clinical metagenomic testing by agnostic, unbiased next-generation sequencing is a diagnostic approach with the broad-based capacity to detect all known and novel pathogens in a single assay. After the discovery of this potentially transformative method decades ago, the availability of clinical metagenomic testing in the daily practice of the infectious disease specialist is accelerating. Prospective metagenomic studies have supplemented the substantial existing body of retrospective, exploratory literature, and these reports offer us a glimpse into the real-world use of clinical metagenomic testing for the diagnosis of infections in patients. In this Review, we examine the evidence collected from the prospective reports published to date, focusing on their impact on patient management, treatment, and outcomes.}, }
@article {pmid42031746, year = {2026}, author = {Yang, Y and Zhang, H and Herbold, CW and Huang, Y and Wang, R and Liu, J and Zhang, D and Ou, J and Zheng, F and Mao, C and Huang, J and Yu, Y and He, J and He, Z and Yan, Q}, title = {Trophic status strongly regulates nitrous oxide but not methane production in global freshwater lake sediments.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42031746}, issn = {2041-1723}, support = {92051120//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32030015//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32470097//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32100086//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Nitrous Oxide/metabolism/analysis ; *Methane/metabolism/analysis ; *Lakes/chemistry/microbiology ; *Geologic Sediments/chemistry/microbiology ; Denitrification ; Nitrification ; Eutrophication ; Greenhouse Gases/metabolism/analysis ; Metagenomics ; }, abstract = {Freshwater lakes are globally significant sources of potent greenhouse gases (GHGs), but how their GHGs emissions respond to changing nutrient levels remains unclear. Here, we demonstrated that nitrous oxide (N2O) production pathways in lake sediments are tightly linked to trophic state, whereas methane (CH4) production appears to be multifactorial Through global metagenomics and controlled batch experiments. In eutrophic sediments, N2O is efficiently removed through complete denitrification, with nitrification serving as the main production pathway, whereas oligotrophic sediments produce N2O primarily via incomplete denitrification. By simulating nutrient transitions using an innovative cross-inoculation experiment, we further revealed that lake sediments systematically shift between these N2O production pathways as their trophic state changes, from denitrification-driven to nitrification-dominated during eutrophication, with the inverse pattern during oligotrophication. Consequently, N2O emissions can be effectively mitigated by inhibiting nitrification in eutrophic lakes and restricting incomplete denitrification in oligotrophic ones. Our findings establish trophic status as a key driver of N2O production sources in lake sediments.}, }
@article {pmid42031750, year = {2026}, author = {Hallgren, J and Dharamshi, JE and Rodríguez-Gijón, A and Nuy, J and Garcia, SL and Jonas, K}, title = {Addendum: Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42031750}, issn = {2041-1723}, }
@article {pmid42012708, year = {2026}, author = {Kværner, AS and Birkeland, E and Avershina, E and Botteri, E and Bucher-Johannessen, C and Knudsen, MD and Hjartåker, A and Page, CM and Hov, JR and Song, M and Randel, KR and Hoff, G and Rounge, TB and Berstad, P}, title = {Alcohol consumption and colorectal carcinogenesis: an exploration of the gut microbial pathway as a potential mediator.}, journal = {European journal of nutrition}, volume = {65}, number = {4}, pages = {}, pmid = {42012708}, issn = {1436-6215}, abstract = {BACKGROUND: Alcohol consumption is one of the major risk factors of colorectal cancer (CRC), yet the mechanisms underlying this relationship, particularly the role of gut microbes, are not fully understood.<br><br>OBJECTIVE: To study associations of alcohol intake with the gut microbiome and colorectal lesions among CRC screening participants. Of particular interest was the potential role of gut microbes in mediating the association between alcohol intake and colorectal lesions.<br><br>METHODS: Screening participants with a positive faecal immunochemical test at ages 55&#x2013;77 were eligible for the CRCbiome study. Alcohol intake was assessed using a validated, semi-quantitative food frequency questionnaire and linked with shotgun metagenome based gut microbial profiles to study associations with screen-detected colorectal lesions. The potential role of alcohol-associated gut microbes in mediating the association between alcohol intake and colorectal lesions was examined using causal mediation analysis.<br><br>RESULTS: Of 1468 participants with dietary data, 414 were diagnosed with advanced lesions. Alcohol intake was positively associated with advanced lesions in a dose-dependent manner (ptrend&#x2009;=&#x2009;0.008), with odds ratio of 1.09 (95% confidence interval, 1.00, 1.19) per 10&#xa0;g/day increase. Compared to non-consumers, those consuming alcohol were characterized by a distinct microbial profile, manifested as modest, but consistent, shifts in &#x3b1;- and &#x3b2;-diversity, and differentially abundant bacteria. A causal mediation analysis showed that 12% of the association between alcohol intake and advanced lesions was mediated by alcohol-associated gut bacteria.<br><br>CONCLUSION: Alcohol consumption was associated with a distinct microbial profile, which partly explained the association between alcohol intake and advanced colorectal lesions. Trial registration: The BCSN is registered at clinicaltrials.gov (National clinical trial (NCT) no. 01538550).<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00394-026-03960-6.}, }
@article {pmid42020421, year = {2026}, author = {Shahzadi, I and Xue, W and Ubaid Ullah, H and Maddamsetti, R and You, L and Wang, T}, title = {Integrating theory and machine learning to reveal determinants of plasmid copy number.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-72303-0}, pmid = {42020421}, issn = {2041-1723}, support = {12401660//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32470701//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Plasmids are extrachromosomal mobile genetic elements whose copy numbers (PCNs) critically influence microbial evolution, antibiotic resistance and pathogenicity. Despite their importance and immense diversity, the ecological, evolutionary and molecular factors determining PCN remain poorly understood. Here, we present a theoretical model to explain the empirical power-law relationship between plasmid size and copy number, one of the fundamental quantitative principles governing PCN control. However, this relationship alone has limited predictive power. To improve PCN prediction, we introduce a data-driven approach incorporating diverse features. Trained and tested on 11,051 plasmids, our machine learning model achieves significantly enhanced accuracy, with plasmid-encoded protein domains emerging as key predictors. Applying this framework, we conduct a large-scale analysis of PCN distributions across hundreds of thousands of metagenomic plasmids (IMG/PR database) and tens of thousands of clinical isolates, revealing putative niche specific taxonomic PCN hotspots and hypothesis-generating ecological trends. These results provide valuable insights into plasmid ecology, antibiotic resistance genes (ARGs) surveillance and shed lights on the gut plasmidome, a "dark matter" in human microbiome.}, }
@article {pmid42020426, year = {2026}, author = {Seki, D and Pollak, S and Kujawska, M and Kiu, R and Acuna-Gonzalez, A and Crouch, LI and Bakshani, CR and Chivers, PT and Mommers, M and van Best, N and Penders, J and Hall, LJ}, title = {Human milk oligosaccharide mediates mutualism between Escherichia coli and Bifidobacterium bifidum.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {42020426}, issn = {2041-1723}, support = {220876/Z/20/Z//Wellcome Trust (Wellcome)/ ; }, mesh = {*Milk, Human/chemistry/metabolism ; Humans ; *Oligosaccharides/metabolism ; *Escherichia coli/physiology/growth &amp; development/genetics/metabolism ; *Symbiosis/physiology ; Female ; *Bifidobacterium bifidum/physiology/genetics/metabolism/growth &amp; development ; Gastrointestinal Microbiome ; Feces/microbiology ; Infant, Newborn ; Infant ; Breast Feeding ; Trisaccharides/metabolism ; Male ; Metagenomics ; Adult ; }, abstract = {Infant gut microbiota development involves frequent colonization by Enterobacteriaceae, particularly Escherichia coli, yet their ecological role in healthy infants is unclear. Here, we analyse longitudinal stool samples from healthy, term-born, breastfed infants (n = 41) and related mothers (n = 30) using shotgun metagenomics and novel computational approaches. Strain-resolved profiling indicates that Bifidobacterium species are frequently shared within families, whereas E. coli derive from external sources, but often persist within individuals. Despite differing ecological strategies, these genera co-exist and share evolutionary adaptations related to lactose acquisition in the infant gut. In vitro, we demonstrate that interactions between E. coli and Bifidobacterium bifidum are mutualistic in co-culture, where E. coli supplies cysteine to its auxotrophic partner, facilitating cooperative degradation of 2'-fucosyllactose, the predominant human milk oligosaccharide. In turn, the liberated monosaccharides sustain E. coli growth, highlighting a cooperative cross-feeding interaction that may contribute to regulating E. coli abundance within the infant host.}, }
@article {pmid42020430, year = {2026}, author = {Zhou, L and Li, D and Huang, Y and Kang, J and Lu, Y and Zhang, L and Liu, SQ}, title = {Lactiplantibacillus plantarum-mediated modulation of volatile flavor and quality in low-salt spontaneously fermented yellow capsicum sauce.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00854-z}, pmid = {42020430}, issn = {2396-8370}, support = {32302036//National Natural Science Foundation of China/ ; NHXXRCXM202312//'Nan Hai Xin Xing' Science and Technology Innovation Talent Platform Project Funding of Hainan Province, China/ ; 202407560053//China Scholarship Council/ ; KYQD(ZR)-21122//Scientific Research Foundation of Hainan University, China/ ; }, abstract = {Yellow capsicum sauce (YCS) is a special fermented condiment in Hainan province, China, and its fermentation typically occurs in a high-salt environment. In this study, the effects of different salt contents (5, 10, 15, and 20%, w/w) on microbial communities and volatile flavor profiles in YCS were systematically investigated by metagenomic approach and HS-SPME-GC-MS. The results revealed that Lactiplantibacillus (54.66%) was the dominant genus in low-salt samples (SF5), while its abundance was less than 6% in higher salinity levels (SF15 and SF20). A total of 48 volatile flavor compounds (VFCs) were detected in the naturally fermented YCS, with alcohols and esters being the primary VFCs. Low-salt fermentation facilitated the accumulation of VFCs, and the total VFCs content in SF5 was the highest. Aroma compounds showed a strong correlation with Lactiplantibacillus plantarum. To further validate the findings, L. plantarum MA1 isolated from SF5 was inoculated into the low-salt YCS substrate for bioaugmented fermentation. This strain significantly increased key aroma components, such as cis-3-hexenyl isovalerate, hexyl 3-methylbutanoate, and ethyl acetate. Moreover, it significantly increased the lactic acid content while reducing the nitrite content, thereby more effectively preserving the fresh yellow color of capsicum sauce and the stability of its spiciness.}, }
@article {pmid42020464, year = {2026}, author = {Bergo, NM and Peres, FV and Vieira, DC and Modolon, F and Moreira, JCF and Lizárraga, RGM and Romano, RG and Bendia, AG and Lemos, LN and de Moura Emilio, A and Amendola, AM and Castano, DCD and Chuqui, MG and Paula, FS and Brandão, WSG and Fonseca, G and Vasconcelos, ATR and Jonck, CR and Moreira, DL and Brandini, FP and Pellizari, VH}, title = {Microbial signatures define the ecosystem functions of the pelagic microbiome in a basin-scale, Southwest Atlantic Ocean.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-37419-9}, pmid = {42020464}, issn = {2045-2322}, support = {5850.0109317.18.9 and 21167-2//Petr&#xf3;leo Brasileiro S.A. (PETROBRAS)/ ; E-26/201.046/2022//Funda&#xe7;&#xe3;o Carlos Chagas Filho de Amparo &#xe0; Pesquisa do Estado do Rio de Janeiro/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, abstract = {The pelagic environment represents a mosaic of biogeographical domains shaped by regional oceanographic processes. Here, a coastal-to-open ocean microbiome investigation was conducted from 64 water samples of the Santos Basin (SB), located in the subtropical South Atlantic Ocean. We combined shotgun metagenomics with a hybrid machine learning workflow to investigate the taxonomic diversity, community structure, and ecosystem functions of pelagic microbiomes. The workflow integrated self-organizing maps (unsupervised) for pattern discovery and Random Forest (supervised) for predictive modeling. Unsupervised machine learning revealed a clear spatial and vertical (light-driven) distribution, with indicator taxa reflecting biogeochemical patterns consistent with global surveys. Supervised learning identified phosphate, salinity, and nitrate, influenced by local upwelling and La Plata River plume, as the primary environmental drivers of microbial community structure. In terms of functionality, the SB microbiome displayed depth- and region-specific patterns: photoautotrophs and nitrogen fixers dominated photic waters (with differences between coastal and oceanic stations), whereas chemolithoautotrophs and mixotrophs prevailed in the aphotic zone. Notably, nitrification signatures were more frequent in northern mesopelagic communities, while sulfur-oxidation pathways were enriched toward the south. Genes for CO bio-oxidation and dimethylsulfoniopropionate (DMSP) degradation were present across all depths. Furthermore, potential non-cyanobacterial diazotrophs were detected in the deep waters, underscoring previous underappreciated to nitrogen cycling. Our findings indicated that the Santos Basin hosts a functionally diverse microbiome including putative novel lineages. The taxonomic and functional patterns observed in the SB might provide insights into potential ecological responses to shifts in nutrient dynamics and physical processes. This investigation provides an ecogenomic baseline for understanding the microbial ecosystem services in subtropical oceans and reveals the potential of machine learning to uncover ecological patterns in underexplored marine regions.}, }
@article {pmid42020750, year = {2026}, author = {Grieshop, MP and Behr, AA and Bowden, S and Lin, JD and Molari, M and Reynolds, GZ and Brooks, EF and Doyle, B and Moore, AA and Rodriguez-Nava, G and Salinas, JL and Banaei, N and Bhatt, AS}, title = {Transposable elements are driving rapid adaptation of Enterococcus faecium.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {42020750}, issn = {1476-4687}, abstract = {Bacterial pathogens adapt rapidly to clinical and within-host selective pressures[1]. Insertion sequences (IS) are transposable elements that can contribute to pathogenic adaptation[2], but their activity and consequences in contemporary clinical populations are not well characterized. Here, combining large-scale genomic surveys with long-read sequencing of clinical isolates and longitudinal gut metagenomes, we quantify pathogen IS dynamics from global patterns to within-host evolution. Across 19,485 publicly available high-contiguity ESKAPEE pathogen genomes, Enterococcus faecium genomes are the most IS dense, dominated by replicative ISL3 family elements, which have proliferated in clinical lineages over the past 30 years. We find extensive chromosomal structural variation, largely involving ISL3, within a new single-hospital collection of bloodstream isolates. Long-read metagenomic sequencing of 28 longitudinal stool samples from 12 haematopoietic cell transplantation (HCT) recipients demonstrates within-host IS dynamics and their regulatory consequences. In one patient, an ISL3 insertion upstream of a folate transporter formed a strong promoter, increasing transcription and improving relative fitness under folate limitation. Enhanced folate scavenging may enable E. faecium to thrive in the setting of microbiome collapse, which is common in HCT and other critically ill patients[3]. Together, these results show that a recent ISL3 expansion is driving rapid evolution in healthcare-associated E. faecium, with consequences for its metabolic fitness that may help explain its increasing clinical burden. Several other pathogens also show elevated IS loads in our survey, which suggests that IS expansion-mediated evolution might be more broadly relevant.}, }
@article {pmid42020953, year = {2026}, author = {Flatau, R and Bickley, CD and Altamia, MA and Gasser, MT and Distel, DL}, title = {Metabolic potential structures gill symbiont communities in two common shipworm species.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag089}, pmid = {42020953}, issn = {1751-7370}, abstract = {Shipworms (Bivalvia: Teredinidae) are the most prolific wood consumers in marine environments. These wormlike marine bivalves digest wood using carbohydrate-active enzymes (CAZymes) produced by intracellular bacterial endosymbionts housed within their gills. Although several shipworm species are known to host multiple co-occurring symbiont species, the factors that influence symbiont community assembly, including the phylogenetic identity and metabolic capabilities of the symbionts, remain poorly understood. We sequenced gill symbiont metagenomes from multiple specimens of two shipworm species, Teredo bartschi (22 specimens) and Lyrodus pedicellatus (14 specimens), which have sympatric distribution in the wild, and which were reared together in laboratory co-culture. From these metagenomes, we assembled 90 metagenome-assembled genomes (MAGs) representing seven distinct symbiont species. The metagenome of each host specimen contained between 1 and 5 symbiont species, with each including at least one nitrogen-fixing symbiont. Six of the seven identified symbiont species were found in both host species, demonstrating a lack of host species specificity in these symbioses. We identified patterns of symbiont occurrence and co-occurrence in these two hosts and used these patterns to constrain the core set of CAZyme and nitrogen-fixation gene classes necessary to support host survival. Our results indicate that, in these two host species, symbiont community composition reflects the symbionts' capabilities for carbohydrate degradation and nitrogen fixation, rather than strict species-specific mechanisms of host and symbiont sorting.}, }
@article {pmid42021075, year = {2026}, author = {Ishikawa, R and Nakamura, M and Sakurai, A and Nakayama-Imaohji, H and Kuwahara, T and Ichimura-Shimizu, M and Shishibori, M and Kataoka, K}, title = {Influences of ampicillin exposure in early life on the murine gut microbiota and steatotic liver disease associated with western diet.}, journal = {The journal of medical investigation : JMI}, volume = {73}, number = {1.2}, pages = {186-207}, doi = {10.2152/jmi.73.186}, pmid = {42021075}, issn = {1349-6867}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Ampicillin/adverse effects/pharmacology ; Mice, Inbred C57BL ; Mice ; *Fatty Liver/etiology/microbiology ; *Diet, Western/adverse effects ; Female ; *Anti-Bacterial Agents/adverse effects ; Male ; Dysbiosis/chemically induced ; }, abstract = {Dysbiosis of gut microbiota is one of the important factors associated with metabolic dysfunction-associated steatotic liver disease (MASLD). Antibiotic use, especially in early life, could profoundly disrupt an establishing process of stable gut microbiota, and the influence on gut environment may persist throughout life. In this study, we examined effects of ampicillin exposure (AMP) in early life on the temporal changes of fecal microbiota and severity of MASLD in western diet-fed C57BL/6J mice. Histological evaluation of MASLD showed that steatosis in female mice and lobular inflammation was significantly influenced with AMP, and that NAS (MASLD activity score constituting from score of steatosis, lobular inflammation, and ballooning degeneration) tended to be high in female of AMP-treated group. 16S metagenome analyses of fecal microbiota showed significant decrease of α-diversity and remarkable shift to normally minor bacterial species at 4 weeks of age in AMP-treated mice, and the influence was continuously observed even after finishing the western diet feeding period. α-Diversity at 4weeks of age negatively correlated with combined scores of steatohepatitis and fibrosis. These results suggest that AMP in early life induced dysbiosis of gut microbiota and could promote the development of western diet-associated steatotic liver disease. J. Med. Invest. 73 : 186-207, February, 2026.}, }
@article {pmid42021418, year = {2026}, author = {Ravi, A and Shestivska, V and Thiago Dobbler, P and Sechovcová, H and Maixnerová, M and Semerád, J and Nehasilová, A and Vadroňová, M and Odriozola, I and Šubrtová Salmonová, H and Větrovský, T and Musilová, &#x160; and Cajthaml, T and Pěchoučková, E and Nemec, A and Kyselková, M}, title = {Cattle feces are a reservoir of diverse Acinetobacter species with potential to spread antibiotic resistance genes.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00568-3}, pmid = {42021418}, issn = {2524-4671}, }
@article {pmid42021724, year = {2026}, author = {Batra, N and Rout, PR and Dey, P}, title = {Modulation and adaptation of gut microbial metabolic functions under probiotic and postbiotic treatment using a novel in vitro anaerobic pseudo-colon system.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5fo04976h}, pmid = {42021724}, issn = {2042-650X}, abstract = {Probiotic and postbiotic compounds found in food influence gut microbiota to attenuate chronic metabolic diseases; however, the underlying mechanisms are not yet fully understood. This study employed a customized in vitro anaerobic pseudo-colon system (AMMR) to evaluate the impacts of Lactiplantibacillus plantarum (probiotic) and butyrate (postbiotic) on gut microbial composition and functionality, using human fecal samples. Metagenomic (16S rRNA) profiling and untargeted metabolomic (GC-MS) analysis were conducted after 48 h treatments. The results showed that butyrate supplementation markedly enhanced microbial diversity, inhibited opportunistic pathobionts (e.g., Enterococcus and Klebsiella), and selectively enriched butyrate producers (e.g., Lachnoclostridium), while diminishing the Firmicutes : Bacteroidetes ratio. It increased indole levels metabolically and redirected pathways towards amino acid synthesis and energy metabolism, while suppressing fatty acid formation. In contrast, L. plantarum exhibited modest alterations in microbial diversity while enhancing Bacteroides and Klebsiella and preserving elevated Enterococcus levels. It elevated saturated fatty acids (octanoic/capric acid) and enhanced amino acid catabolic pathways (valine/leucine) and redox regulators (taurine metabolism). Correlation analysis revealed that butyrate was associated with fiber-degrading microbes, whereas L. plantarum was associated with lactic acid bacteria, suggesting distinct ecological niches and interaction patterns. These findings collectively indicate that butyrate and L. plantarum elicit complementary microbial alterations, i.e., butyrate directly transforms the microbial structure and metabolism towards an anti-inflammatory phenotype, while L. plantarum largely influences via metabolic byproducts and niche adjustment. The complementary actions highlight the therapeutic potential of integrated probiotic-postbiotic approaches for the enhancement of gut health.}, }
@article {pmid42021875, year = {2026}, author = {Li, H and Song, Z and Zhao, Y and Li, M}, title = {[Advances in the Application of Artificial Intelligence in Clinical Microbiological Testing].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {57}, number = {2}, pages = {313-318}, pmid = {42021875}, issn = {1672-173X}, mesh = {*Artificial Intelligence ; Humans ; Deep Learning ; *Microbiological Techniques/methods ; Algorithms ; Microbial Sensitivity Tests ; }, abstract = {Traditional microbiological detection methods have inherent limitations in detection speed, sensitivity, and specificity, making them increasingly unable to meet growing clinical demands. In recent years, artificial intelligence (AI) has been rapidly integrated into clinical microbiological testing, with numerous studies demonstrating its significant potential to enhance pathogen identification, predict antimicrobial susceptibility testing, and advance laboratory automation. This article systematically reviews classical AI algorithms and their latest advancements in this field. For visual data applications, deep learning-based models are used to automatically analyze microscopy images or colony morphology, significantly improving recognition efficiency and diagnostic accuracy. For non-visual data, AI has achieved breakthroughs in analyzing multi-omics data such as genomics, transcriptomics, and metagenomics, and is widely used for rapid pathogen identification and prediction of antimicrobial resistance. Despite its promising prospects, the application of AI in clinical microbiological testing remains in the early stages of transitioning from scientific research to clinical practice. This paper further discusses the key challenges and opportunities encountered during this technological translation, aiming to help clinical professionals comprehensively understand the current status, future trends, and potential impact of AI in this field, thereby promoting its development into reliable and scalable routine diagnostic methods.}, }
@article {pmid42021890, year = {2026}, author = {Zhang, W and Zhong, S and Lu, S and Xiao, X and Xie, Y}, title = {[Diagnostic Performance of Metagenomic Next-Generation Sequencing for Mucormycosis: A Retrospective Cohort Study].}, journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition}, volume = {57}, number = {2}, pages = {411-418}, pmid = {42021890}, issn = {1672-173X}, mesh = {Humans ; *Mucormycosis/diagnosis/microbiology ; Retrospective Studies ; Female ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Middle Aged ; Mucorales/genetics/isolation &amp; purification ; *Metagenomics/methods ; Adult ; Aged ; ROC Curve ; Sensitivity and Specificity ; }, abstract = {OBJECTIVE: Mucormycosis is a life-threatening invasive fungal infection with high mortality, yet traditional diagnostic methods are limited by low positivity rates. This study aims to evaluate the diagnostic performance and clinical utility of metagenomic next-generation sequencing (mNGS) in mucormycosis.<br><br>METHODS: A retrospective analysis was conducted on 135 patients with mNGS results positive for Mucorales fungi at West China Hospital of Sichuan University from November 1, 2022, to October 31, 2024. Based on comprehensive clinical diagnostic criteria (including proven and probable cases), patients were classified into a confirmed mucormycosis group and a non-mucormycosis group. Receiver operating characteristic (ROC) curve analysis was used to evaluate the diagnostic performance of normalized read counts (lgRPM) from different specimen types. Fungal species distribution and laboratory parameters were compared between the two groups.<br><br>RESULTS: Among the 135 patients with positive mNGS results for Mucorales, 100 (74.1%) were ultimately diagnosed with mucormycosis. ROC curve analysis revealed that the diagnostic performance of mNGS varied by specimen type. For blood specimens, the area under the curve (AUC) was 0.772, with a specificity of 87.5% at the optimal cutoff value of 0.11 RPM. For bronchoalveolar lavage fluid specimens, the AUC was 0.717, with a sensitivity of 76.5% at the optimal cutoff value of 0.02 RPM. Combined analysis of all specimens showed that at the optimal cutoff value of 0.08 RPM (approximately 8 reads/100M), the sensitivity and specificity were 62.0% and 71.4%, respectively. Species distribution analysis showed that the proportions of Cunninghamella elegans (11.0% vs. 2.9%) and Rhizomucor pusillus (9.0% vs. 2.9%) were significantly higher in the confirmed group than in the non-mucormycosis group (P < 0.05). Levels of C-reactive protein and interleukin-6 were also significantly higher in the confirmed group (P < 0.05). Notably, all seven renal perfusion fluid samples yielded false-positive mNGS results.<br><br>CONCLUSION: mNGS technology can effectively improve the diagnostic yield for mucormycosis. However, results should be interpreted in conjunction with specimen type, read count, and clinical characteristics. BALF specimens offer high sensitivity, making them suitable for screening, while blood specimens demonstrate high specificity, making them valuable for confirmation. Positive results from low-biomass samples such as renal perfusion fluid warrant caution against false positivity. Fungal species identification and inflammatory markers may serve as adjunctive evidence for clinical diagnosis.}, }
@article {pmid42022012, year = {2026}, author = {Conrad, RE and Rodriguez-R, LM and Lindner, BG and Gerhardt, K and Konstantinidis, KT}, title = {An ANIr-based methodology to determine if two sequence-discrete populations are identical and identify cosmopolitan prokaryotic populations.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag068}, pmid = {42022012}, issn = {2730-6151}, abstract = {Although sequence-discrete species appear to dominate microbial communities, readily distinguishing between distinct populations of a species recovered from different short-read metagenomic samples is challenging due to technical limitations associated with read length. To close this gap, we developed a novel algorithm to evaluate which reads in a metagenome belong to a target population based on the distribution of sequence identities of reads aligned to a reference sequence, which are filtered using a Kernel density estimation (KDE) as a flexible alternative to the commonly used static 95% nucleotide identity cutoff. Subsequently, we employed the average nucleotide identity of reads (ANIr) aligning above the KDE threshold, and resampling techniques for estimating the confidence intervals of ANIr values, to quantify intrapopulation sequence diversity and compare populations across globally representative marine samples. Most populations showed high ANIr in only a few samples at similar depths and decreased ANIr and increased gene-content difference between samples where a closely related population is detected (e.g. same 95% ANI-based species). Accordingly, ANIr correlated with the physical distance between the samples, and only a few truly cosmopolitan populations were identified. Among the latter, Alteromonas macleodii [97% average amino-acid identity (AAI) to the type genome] and Prochlorococcus marinus (79% AAI) showed high relative abundance in both surface (0-200 m) and deep (>1000 m) samples. These results suggest that microbial communities under different environmental conditions share very few identical and abundant populations and provide a highly needed methodology to track such populations over space and time, in marine or other habitats.}, }
@article {pmid42022013, year = {2026}, author = {Franco, MEE and Singer, E and Roux, S and Meredith, LK and U'Ren, JM}, title = {Genomic and metagenomic survey of microbial carbonic anhydrase genes reveals novel clades, high diversity, and biome specificity.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag054}, pmid = {42022013}, issn = {2730-6151}, abstract = {Carbonic anhydrase (CA) enzymes catalyze the interconversion of carbon dioxide and bicarbonate with an efficiency exceeded only by superoxide dismutase. CA enzymes have evolved convergently in phylogenetically distant organisms, forming eight structurally unrelated classes that share physiological functions involved in photosynthesis, respiration, pH homeostasis, CO2 transport, and carbonyl sulfide hydrolysis that play central roles in medicine and the environment. Here, we leverage the recent surge in publicly available genomes and metagenomes to re-examine our understanding of the abundance, diversity, and phylogenetic relationships of the three major CA classes in Bacteria/Archaea and microbial Eukaryotes (Fungi, algae). We recovered a total of 57 218 α-, β-, and γ-CA sequences from 24 184 metagenomes and genomes, including the first putative α-CA from an archaeal species. CA sequences formed 3859 protein clusters (1188 with three or more sequences). Sequences within a cluster were typically taxonomically conserved only at higher levels (i.e. Superkingdom, Phylum). When viewed within a phylogenetic framework, the majority of subclades for each CA class contained CAs representing multiple Superkingdoms, although numerous novel β-CA clades appear unique to Fungi. Queries of CA Hidden Markov models against all public metagenome and metatranscriptome datasets revealed that CA is a ubiquitous enzyme present in virtually all sampled environments. However, CA clusters that were taxonomically conserved also appeared more environment-specific, which may explain high CA diversity. This work represents an important contribution to our understanding of the evolution, diversity, and environmental distribution of an enzyme that is key to life and has broad environmental and industrial applications.}, }
@article {pmid42022196, year = {2026}, author = {Yan, Z and Xie, J and Jin, L and He, T and Zhang, X and Li, X}, title = {Steam Cooking Methods Promote the Transfer of Viable Antibiotic-Resistant Pathogens from Water into Air.}, journal = {Environment &amp; health (Washington, D.C.)}, volume = {4}, number = {4}, pages = {730-741}, pmid = {42022196}, issn = {2833-8278}, abstract = {Steam cooking is an ancient and widely used method for sterilizing water and food globally. However, its effectiveness may be compromised by the ubiquitous presence of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in these media. Here, we combined metagenomic sequencing, quantitative PCR analysis, plate culture, and Sanger sequencing to examine the effects of steam cooking on the profiles of antibiotic resistance in cooked fish, tap water, and indoor air in real cooking environments (i.e., a canteen and a home kitchen) and a laboratory chamber. We found that while steam cooking eliminated over 92.0% of bacteria and ARGs in both tap water and fish, it significantly increased the absolute abundance of bacteria and ARGs in indoor fine particulate matter (PM2.5) across all settings. Tap water was identified as the primary contributor to the increase, transferring 14.6% of bacteria and 33.2% of ARGs into indoor PM2.5 during steam cooking. This process also elevated the relative abundance of certain putative human pathogens in indoor PM2.5, containing ARGs and heat shock proteins and mainly originating from tap water. To test if these transferred ARGs hosts were viable, we conducted plate culture experiments and identified a viable heat-resistant ARB, Bacillus cereus, transferred from water to indoor PM2.5 via water vapor. Our results highlight the cross-medium transport of ARB and ARGs via steam cooking and underscore the potential microbial safety issues to cooking personnel through inhalational exposure.}, }
@article {pmid42022320, year = {2026}, author = {Zhang, W and Huang, R and Yuan, J}, title = {Case Report: HHV8-positive multicentric Castleman disease in an HIV-positive patient :diagnostic challenges arising from atypical histology and the role of metagenomic sequencing.}, journal = {Frontiers in oncology}, volume = {16}, number = {}, pages = {1779973}, pmid = {42022320}, issn = {2234-943X}, abstract = {BACKGROUND: Multicentric Castleman disease (MCD), especially the HHV8-positive subtype, is a rare lymphoproliferative disorder that presents considerable diagnostic and therapeutic difficulties, particularly among HIV-positive patients. The co-occurrence of other infections, such as syphilis, may further complicate its clinical picture and management.<br><br>CASE DESCRIPTION: A 65-year-old man with well-controlled HIV presented with persistent fever, fatigue, and disseminated lymphadenopathy,. Through histopathological examination, molecular testing (including mNGS for HHV8), and PET-CT imaging, HHV8-positive MCD was diagnosed, along with latent syphilis. The patient was successfully treated with R-VP16 (rituximab and etoposide) for MCD and benzathine penicillin for syphilis, showing a positive clinical response. Throughout 36 months of continuous monitoring, the patient has maintained sustained complete remission with no evidence of disease recurrence.<br><br>CONCLUSION: This case underscores the importance of considering HHV8-driven lymphoproliferative disorders in HIV patients with unexplained lymphadenopathy and systemic symptoms, particularly in HHV8-endemic regions. It also highlights the essential roles of advanced diagnostics and multidisciplinary management in such complex presentations. The favorable outcome demonstrates the effectiveness of timely and targeted treatment, though long-term follow-up remains necessary due to the potential for relapse or progression.}, }
@article {pmid42022392, year = {2026}, author = {Abedien, ZU and Lean, IJ and Djordjevic, SP and Hick, PM and Westman, ME and Mckay-Demeler, J and Webster, J and Brito, BP}, title = {Next-generation detection in bovine respiratory and enteric diseases: metagenomic and amplicon sequencing insights into microbial diversity.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1788101}, pmid = {42022392}, issn = {2297-1769}, abstract = {Respiratory and enteric diseases are major contributors to morbidity, mortality, and economic loss in cattle production, with significant implications for animal welfare, particularly in calves. Traditional diagnostic approaches have laid the foundation for pathogen detection in cattle, providing essential tools for disease surveillance and control. However, their targeted nature limits the capacity to identify unexpected, novel, or polymicrobial infections that often underlie complex respiratory and enteric syndromes. Recent advances in molecular technologies, particularly amplicon sequencing (metataxonomics), metagenomics, and metatranscriptomics, enable untargeted, high-resolution profiling of microbial communities directly from clinical samples, offering transformative potential for research and diagnostics. This review synthesises current applications of these approaches in bovine respiratory and enteric disease research, highlighting key findings across virology, bacteriology, and parasitology. Collectively, these studies have expanded the catalogue of the microbial diversity, yet their interpretation remains challenged by the still-evolving understanding of microbial contributions to pathogenesis. Progress toward clinical integration is further hindered by the need for methodological standardisation, validation, and improved interpretive frameworks. Looking ahead, advancing these technologies will require harmonised protocols, integration of multi-omics datasets, and robust experimental and epidemiological studies to establish causal links between microbial signatures and disease outcomes. By bridging discovery and application, these approaches hold the potential to enhance diagnostic accuracy, strengthen surveillance, and support sustainable cattle production systems. As these technologies continue to evolve, they are likely to play an increasingly central role in bovine disease research and diagnostics.}, }
@article {pmid42022531, year = {2026}, author = {Wang, Y and Fu, J and Zhan, J and Liang, Y and Chen, R and Su, L and Zhou, Q and Zhang, Y and Cong, W and Xu, F}, title = {Panax ginseng-Polygonum cuspidatum is beneficial for alleviating atherosclerosis in ApoE[-/-] mice by modulating the composition of gut microbiota and related metabolites.}, journal = {Frontiers in cardiovascular medicine}, volume = {13}, number = {}, pages = {1773819}, pmid = {42022531}, issn = {2297-055X}, abstract = {BACKGROUND: Atherosclerosis (AS) is a central pathological driver underlying most cardiovascular diseases. Gut microbiota and related metabolites participate in regulating atherosclerosis. Panax ginseng and Polygonum cuspidatum (GP) herb pair has traditionally been used for cardiovascular diseases. Some active compounds in GP have shown anti-atherosclerotic effects and the effects of GP still needs more evidence-based supports. Therefore, this study aims to investigate the potential effects of GP on atherosclerosis and explore the underlying mechanisms.<br><br>METHODS: Fifty C57BL/6J ApoE[-/-] mice were randomly assigned to five groups: model, statin, low-dose GP, medium-dose GP and high-dose GP. They were fed a high-fat diet (HFD) to induce atherosclerosis. Ten wild-type C57BL/6J mice were given chow diet and served as controls. After 12-week intervention, their aortic tissues were collected for Oil Red O staining, colon tissues for Alcian staining and immunofluorescence, and serum samples for measurement of lipid levels and inflammatory cytokines. Then, their fecal DNA was extracted for metagenomic sequencing, while cecum and ileocecal valves were for untargeted metabolomics. Finally, fecal microbiota transplantation was performed to assess the contribution of gut microbiota to observed effects. Twenty additional ApoE[-/-] mice were randomized to two groups: FMT-Mod and FMT-GPH, given feces from the model or high-dose GP group.<br><br>RESULTS: Atherosclerotic plaques accumulated in the aorta and aortic sinus after HFD, while statin and high-dose GP alleviated this burden. TC, TG, LDL-C, MCP-1, MCP-3 and IL-2 showed significant increase after HFD, while statin and GP decreased LDL-C, MCP-1 and MCP-3. The goblet cells, ZO-1 and Occludin decreased after HFD, while statin and GP increased them, indicating that the intestinal barrier integrity was improved. Additionally, the composition of gut microbiota was modulated by GP. Some candidate taxa were identified, such as Bifidobacteriales, Bacteroidetes and Escherichia coli. Twenty-two metabolites were differentially abundant among the control, model and GP groups. Nineteen of them were modulated by HFD and reversed by GP, including 1-methylnicotinamide, dopamine and lysoPA (0:0/18:0). Mice given fecal transplants from the high-dose GP group showed less aortic plaques, lower levels of some lipid and inflammatory cytokines, more goblet cells, more expression of ZO-1 and Occludin, and more 1-methylnicotinamide than those given fecal transplants from the model group.<br><br>CONCLUSION: This study suggests that GP is beneficial for alleviating atherosclerosis in HFD-induced ApoE[-/-] mice, potentially by modulating the composition of gut microbiota and related metabolites.}, }
@article {pmid42022543, year = {2026}, author = {Yang, P and Meng, Y and Ma, Y and Xu, M and Zhang, X}, title = {Fermented cotton stalks preserve colonic epithelial integrity in Hu sheep via the microbiota-metabolite-NF-κB/MLCK axis and mitigate the adverse effects of direct feeding.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1777023}, pmid = {42022543}, issn = {2296-861X}, abstract = {BACKGROUND: This study aimed to compare three cotton-stalk processing strategies-grinding (FS), steam explosion (PH), and microbial fermentation (FJ)-and to clarify whether fermented cotton stalks preserve colonic epithelial integrity through a microbiota-metabolite-NF‑κB/MLCK axis in Hu sheep.<br><br>METHODS: Fifteen clinically healthy Hu sheep (26.7 &#xb1; 1.76 kg body weight; 115 &#xb1; 4 days of age) were used after a 14&#x2011;day adaptation period and randomly assigned to one of three diets (n&#x202f;= 5 per treatment) containing 40% processed cotton stalks (FS, PH, or FJ) for 8 weeks.<br><br>RESULTS: PH and FJ increased final body weight compared with FS, and average daily gain increased progressively from FS to PH to FJ (206.07, 282.50, and 322.14 g/d, respectively; p&#x202f;< 0.05). Colonic fermentation profiles were markedly improved by FJ, evidenced by lower pH, ammonia nitrogen, free gossypol, and acetate (p&#x202f;< 0.05), alongside higher total VFAs with elevated propionate and butyrate (p&#x202f;< 0.05), whereas LPS was not different among treatments (p&#x202f;> 0.05). Histology and scanning electron microscopy indicated that FJ maintained intact crypt architecture and epithelial surface continuity, while FS exhibited epithelial detachment and surface erosion. Metagenomic analysis revealed distinct community structures among groups, with FJ showing higher richness and enrichment of taxa associated with carbohydrate utilization and butyrate&#x2011;producing guilds (e.g., Lachnospiraceae&#x2011;related genera such as Anaerostipes, Blautia, and Coprococcus). Consistently, FJ suppressed colonic mucosal inflammation, as reflected by reduced IL&#x2011;1&#x3b2;, IL&#x2011;6, IL&#x2011;8, and TNF-&#x3b1; at both mRNA and protein levels (p&#x202f;< 0.05). Mechanistically, FJ attenuated NF&#x2011;&#x3ba;B activation and downstream MLCK signaling, shown by decreased p&#x2011;p65/p65, p&#x2011;I&#x3ba;B/I&#x3ba;B, MLCK abundance, and p&#x2011;MLC/MLC ratio (p&#x202f;< 0.05), while upregulating tight&#x2011;junction proteins (ZO&#x2011;1, occludin, claudin&#x2011;1, and claudin&#x2011;4; (p&#x202f;< 0.05).<br><br>CONCLUSION: Fermentation&#x2011;based processing of cotton stalks enhanced growth performance and promoted a favorable hindgut fermentation and microbial-metabolic milieu, thereby reinforcing colonic barrier integrity via inhibition of NF&#x2011;&#x3ba;B/MLCK&#x2011;associated inflammatory signaling, supporting fermented cotton stalk as a practical strategy to valorize cotton residues for ruminant feeding while mitigating gossypol&#x2011;related hindgut stress.}, }
@article {pmid42022809, year = {2026}, author = {Tian, YP and Li, QH and Li, YM and Zhao, JY and Wei, XX and Wang, JY and Zhou, YL and Yang, SB and Li, W and Guo, P and Wang, LX and Dai, TT and Hu, SF and Zhong, ZQ and Xie, YM and Lv, ZH}, title = {Gut microbiota and metabolome signatures in preterm infants with high versus low risk for neurodevelopmental impairment: a prospective, matched, longitudinal multi-omics study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1799859}, pmid = {42022809}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Infant, Premature ; Prospective Studies ; *Metabolome ; Longitudinal Studies ; Female ; Male ; Infant, Newborn ; Feces/microbiology ; *Neurodevelopmental Disorders/microbiology ; Metagenomics ; Infant ; Metabolomics ; Bacteria/classification/genetics/isolation &amp; purification ; Biomarkers ; Dysbiosis/microbiology ; Multiomics ; }, abstract = {Preterm birth is a leading global cause of neurodevelopmental impairment (NDI), yet early predictive biomarkers remain elusive. The gut microbiome, developing in parallel with the brain and communicating via the microbiota-gut-brain axis, holds potential as a source of such biomarkers. However, specific longitudinal multi-omics signatures predictive of NDI risk in preterm infants are poorly defined. We conducted a prospective, matched, longitudinal study of 60 preterm infants, classified at 3 months corrected age (CA) into high-risk (HR, n=30) or low-risk (LR, n=30) groups for NDI based on combined motor (TIMP) and neurological (GMs) assessments. Fecal samples from birth (meconium) and 3 months CA underwent shotgun metagenomic sequencing and untargeted metabolomics. Groups were rigorously matched for gestational age, birth weight, sex, and clinical exposures. While α- and β-diversity did not differ between groups, profound taxonomic and functional divergence emerged. At 3 months CA, the LR gut was enriched with Akkermansia muciniphila, whereas the HR gut was dominated by Klebsiella variicola. Functional metagenomics revealed a dysbiotic HR trajectory, enriching pathways for bacterial virulence, stress response, and-notably-multiple pathways annotated for human neurodegenerative diseases, contrasting with LR expansion of core biosynthesis. Metabolomics confirmed a dysfunctional HR state, showing impaired amino acid metabolism and aberrant neuroactive pathway enrichment. Critically, meconium features correlated with 3-month neurobehavioral scores, demonstrating ultra-early predictive potential. Integrated networks at 3 months directly linked Akkermansia muciniphila and co-varying glycerophospholipids to superior neurodevelopmental scores, forming a beneficial "Akkermansia-lipid" axis, while Klebsiella variicola and triterpenoids formed a dysbiotic hub. Our study defines a high-risk gut ecosystem trajectory in preterm infants, characterized by early commensal depletion, pathobiont expansion, and a functional shift towards inflammation and neuroinflammation. These signatures offer novel targets for early risk prediction and microbiome-targeted interventions.}, }
@article {pmid42022943, year = {2026}, author = {Fu, F and Zhang, C and Xu, Z and Ji, P and Zhang, Z}, title = {Gastric Microbiome Alterations in Sepsis-Related Gastrointestinal Bleeding: Two Case Reports and Literature Review.}, journal = {JGH open : an open access journal of gastroenterology and hepatology}, volume = {10}, number = {3}, pages = {e70318}, pmid = {42022943}, issn = {2397-9070}, abstract = {Sepsis, characterized by life-threatening organ dysfunction resulting from an uncontrolled response to infection, can impact various systems of the body, including the digestive system. Prior research has identified sepsis as a significant risk factor for gastrointestinal bleeding. However, there is limited reporting on the gastric microecology of individuals with sepsis complicated by gastrointestinal bleeding. This paper presents the cases of two patients, shedding light on this issue. The first case was a 29-year-old female who developed sepsis during perioperative liver transplantation, while the second case features a 34-year-old female with acute pancreatitis complicated by septic shock. Both patients underwent gastroscopy following gastrointestinal bleeding, revealing evident gastric mucosal injuries. Notably, the second patient exhibited suppurative gastritis. Metagenomic Next-Generation Sequencing (NGS) of gastric juice from these two patients unveiled microecological alterations in the stomach. The sequencing results indicated a substantial presence of pathogenic sequences, underscoring the role of direct gastric mucosal injury due to infection as a significant contributor to gastrointestinal bleeding. This study not only introduces a novel approach to pinpointing the causes of gastrointestinal bleeding in sepsis but also provides valuable insights for clinical diagnosis and treatment.}, }
@article {pmid42022944, year = {2026}, author = {Zhao, Z and Ling, J and Chen, J}, title = {Oral Microbiome and Constipation: A Causal Link Revealed by Mendelian Randomization.}, journal = {JGH open : an open access journal of gastroenterology and hepatology}, volume = {10}, number = {3}, pages = {e70390}, pmid = {42022944}, issn = {2397-9070}, abstract = {BACKGROUND: Constipation affects approximately 15.3% of the global population. While the gut microbiome's role in constipation has been studied, the causal relationship between the oral microbiome and constipation remains unexplored.<br><br>METHODS: We utilized Mendelian randomization (MR) and large-scale GWAS data to investigate the causal relationship between the oral microbiome and constipation. Oral microbiome data were sourced from a metagenome-wide association study (mgGWAS) on 2984 individuals, while constipation GWAS data came from 176&#x2009;629 samples in the Japan Biobank. Statistical methods included inverse variance-weighted (IVW) analysis, weighted median, and MR-Egger regression.<br><br>RESULTS: The MR analysis revealed significant associations between specific oral microbiome and constipation. Treponema denticola, found in saliva, was positively associated with an increased risk of constipation (OR&#x2009;=&#x2009;3.961, 95% CI&#x2009;=&#x2009;1.085-14.453, p&#x2009;=&#x2009;0.037). Conversely, certain bacteria like Pauljensenia sp000308055 showed protective effects (OR&#x2009;=&#x2009;0.409, 95% CI&#x2009;=&#x2009;0.167-0.999, p&#x2009;=&#x2009;0.0496). In the tongue coating, Neisseria sicca exhibited a significant positive association with constipation (OR&#x2009;=&#x2009;4.864, 95% CI&#x2009;=&#x2009;1.293-18.302, p&#x2009;=&#x2009;0.019), while Aggregatibacter segnis demonstrated a protective effect (OR&#x2009;=&#x2009;0.400, 95% CI&#x2009;=&#x2009;0.188-0.854, p&#x2009;=&#x2009;0.018).<br><br>CONCLUSION: This study is the first to explore the potential causal relationship between oral microbiome and constipation. The findings suggest that specific oral bacteria may influence the risk of constipation, highlighting the need for further research to validate these relationships and understand the mechanisms involved. Moreover, the study underscores the importance of considering both oral and gut microbiome in the context of gastrointestinal health and disease management.}, }
@article {pmid42023092, year = {2026}, author = {Li, X and Chen, D and Xiao, Y and Lei, Z and Yang, X and Zhang, Y and Li, L and Zheng, Y and Zhang, Y and Huang, Z and Lin, B}, title = {Metagenomic next-generation sequencing improves diagnosis of Talaromyces marneffei and mixed infections in HIV/AIDS patients: a retrospective study.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1800314}, pmid = {42023092}, issn = {2296-858X}, abstract = {BACKGROUND: Opportunistic infections remain a leading cause of morbidity in people living with HIV (PLWH). Talaromyces marneffei (T. marneffei) accounts for up to 15% of HIV-related hospitalizations in endemic regions. Metagenomic next-generation sequencing (mNGS) offers rapid pathogen detection; however, its utility in diagnosing HIV-associated coinfections is uncertain.<br><br>METHODS: This retrospective study enrolled 56 hospitalized PLWH with coinfections at the Third Affiliated Hospital of Sun Yat-sen University from March 2022 to October 2024. All patients underwent pathogen detection using both mNGS and CTM, with their diagnostic performance compared. Clinical data, treatment adjustments, and outcomes were analyzed.<br><br>RESULTS: mNGS demonstrated significantly higher detection rate (84.4%, 54/64; 95% CI: 73.1-92.2%) than CTM (28.1%, 18/64; 95% CI: 17.6-40.8%; p&#x202f;<&#x202f;0.0001), especially for T. marneffei detection (100% vs. 45.5%, p&#x202f;<&#x202f;0.0001). mNGS identified T. marneffei in 39.3% (n&#x202f;=&#x202f;22/56) of patients, including two rare cases (urinary and intracranial infections) missed by CTM. mNGS revealed mixed infections in 82.1% (46/56) of patients, substantially higher than the 5.4% detected by CTM. Notably, mNGS-guided therapy adjustments occurred in 74.1% of cases, compared with 22.2% for CTM (p&#x202f;<&#x202f;0.001), correlating with clinical improvement in 90% (36/40) of adjusted regimens.<br><br>CONCLUSION: Our data demonstrated that mNGS had a higher positive detection rate than CTM for detecting coinfections among PLWH, especially for T. marneffei and mixed infections. These results highlight the clinical value of mNGS as a complementary tool for pathogen identification in this vulnerable population.}, }
@article {pmid42023515, year = {2026}, author = {Shang, J and Peng, C and Guan, J and Cai, D and Wang, D and Sun, Y}, title = {PhaBOX2: an enhanced web server for discovering and analyzing viral contigs in metagenomic data.}, journal = {Nucleic acids research}, volume = {}, number = {}, pages = {}, doi = {10.1093/nar/gkag382}, pmid = {42023515}, issn = {1362-4962}, support = {//Hong Kong Research Grants Council/ ; 11209823//General Research Fund/ ; //City University of Hong Kong/ ; 9667256//Institute of Digital Medicine/ ; 9678241//Institute of Digital Medicine/ ; }, abstract = {Metagenomic sequencing has transformed virus discovery; however, downstream bioinformatic analyses for viral identification, classification, and host prediction remain fragmented across multiple tools. Here, we present PhaBOX2, a major upgrade that extends the platform from a specialized bacteriophage identification tool to a comprehensive and integrated suite for viral sequence analysis. PhaBOX2 broadens its detection, taxonomic, and host prediction scope beyond phages to enable the characterization of archaeal and eukaryotic viruses. The updated workflow incorporates rigorous quality control and quantitative analyses, automatically removes host contamination, clusters sequences into viral operational taxonomic units, and performs phylogenetic analysis based on marker genes. In contrast to traditional "black-box" deep learning approaches, PhaBOX2 combines alignment-based strategies with machine-learning models under a "glass-box" design philosophy, providing interpretable intermediate evidence alongside final predictions to improve transparency and biological interpretability. Powered by a dedicated high-performance computing infrastructure, the server delivers a fully automated, end-to-end workflow, while achieving an ~80% reduction in processing time. PhaBOX2 thus provides a robust and user-friendly ecosystem for viral metagenomic analysis and is freely available at https://phage.ee.cityu.edu.hk/.}, }
@article {pmid42023591, year = {2026}, author = {Lei, P and Qi, Z and Ma, Q and Zhao, B and Wen, B and Jiang, W and Xi, W and Liu, Y and Xun, Y and Zhang, S and Wang, Y and Guo, Y and Wang, W and Ma, X and Jia, M and Fan, Y}, title = {Gut microbiota reshapes host energy metabolism to modulate depressive behaviors.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2662556}, doi = {10.1080/19490976.2026.2662556}, pmid = {42023591}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Energy Metabolism ; Male ; Animals ; *Major Depressive Disorder/microbiology/metabolism/therapy ; Mice ; Female ; Fecal Microbiota Transplantation ; *Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Middle Aged ; Adult ; Mice, Inbred C57BL ; Disease Models, Animal ; Metabolomics ; Mitochondria/metabolism ; }, abstract = {Disturbances in energy metabolism are a key pathophysiological feature of major depressive disorder (MDD). The gut microbiota, as a critical regulator of host metabolism, may influence systemic energy homeostasis and contribute to depression. To investigate this, we performed a multi-omics analysis integrating targeted metabolomics and shotgun metagenomics on samples from 100 MDD patients and 68 healthy controls. MDD patients exhibited significant disruptions in central energy pathways (glycolysis, TCA cycle, and ornithine cycle), which correlated with symptom severity and cognitive impairment. We identified 36 bacterial species whose abundances were linked to mitochondrial fatty acid synthesis, ketogenesis, and amino acid metabolism, and were associated with altered levels of core metabolites like lactate and L-glutamic acid. Mediation analysis established a "gut microbiota-energy metabolites-depressive phenotype" axis, where metabolites mediated the effects of specific bacteria (e.g., Dorea_formicigenerans) on symptoms. To validate causality, we used a chronic social defeat stress mouse model with simultaneous autologous fecal microbiota transplantation (FMT). FMT effectively reshaped the gut microbiota, ameliorated depression-like behaviors, and reversed the stress-induced shift toward anaerobic glycolysis in serum and the central nervous system. Critically, FMT restored mitochondrial morphology and structural integrity in the prefrontal cortex and hippocampus, renormalizing the relationship between metabolism and behavior. Our findings elucidate the gut microbiota's role in MDD pathogenesis via host energy metabolism regulation and posit early autologous FMT as a novel strategy to correct central energy imbalances.}, }
@article {pmid42023670, year = {2026}, author = {Santillan, E and Neshat, SA and Wuertz, S}, title = {Predicting microbial community responses to disturbance using genome-resolved trait-based life-history strategies.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag099}, pmid = {42023670}, issn = {1751-7370}, abstract = {Understanding how microbial communities respond to disturbance remains a fundamental question in ecology, with broad implications for biodiversity, ecosystem function, and biotechnology. Trait-based approaches offer general rules to predict community responses by linking ecological strategies to measurable traits. Whereas life-history strategy frameworks such as the competitor-ruderal-stress-tolerant (CSR) model are well established in plant and animal ecology, their application to microbial communities has been limited. Here, we experimentally tested how microbial communities shift across a gradient of disturbance frequency in replicated bioreactors treating synthetic wastewater. We applied six conditions by doubling the organic loading rate at different frequencies, from undisturbed to press disturbance, and monitored changes over 42 days using genome-resolved metagenomics, 16S rRNA gene sequencing, biomass quantification, and effluent chemistry. By integrating ordination, network analysis, and machine learning, we identified emergent community-level life-history strategies, with competitor-dominated communities under undisturbed conditions, ruderal-associated strategies at intermediate disturbance frequencies, and stress-tolerant strategies under sustained high-frequency (press) disturbance. These strategies were reflected in functional trade-offs, shifts in community composition, and genomic trait distributions. A simulation-based approach was used to generate a CSR classification of metagenome-assembled genomes, which was consistent with patterns observed in other microbial ecosystems. Our results demonstrate that life-history frameworks can capture predictable microbial dynamics across disturbance regimes. This approach provides a unifying tool for linking microbial structure, function, and traits across scales, helping to reconcile ecological theory with microbial resource management in natural and engineered ecosystems.}, }
@article {pmid42023843, year = {2026}, author = {Olagoke, O and Zheng, X and Chung, S and Mengistie, HD and Asfaha, K and Read, TD and Dean, D}, title = {Phylogenetic diversity, functional pathways, and network interactions of ocular chlamydia-like organisms (CLOs) in trachoma-endemic Ethiopia.}, journal = {mBio}, volume = {}, number = {}, pages = {e0053426}, doi = {10.1128/mbio.00534-26}, pmid = {42023843}, issn = {2150-7511}, abstract = {Trachoma is the leading infectious cause of blindness worldwide and classically attributed to Chlamydia trachomatis (Ct). However, other members of the phylum Chlamydiae, particularly environmental chlamydia-like organisms (CLOs), may modulate ocular ecology and influence disease outcomes. Here, we investigated CLO distribution, phylogeny, and microbiome associations among 1,059 individuals from trachoma-endemic communities in Ethiopia using targeted 16S rRNA sequencing and metagenomic shotgun sequencing. CLOs were detected in 249 (23.3%) participants of all ages and sexes and were significantly less likely to be associated with Ct or trachomatous scarring (TS) and trichiasis (TT). Phylogenetic analyses revealed extensive CLO diversity with six novel phylotypes, the most abundant of which was ancestral to Sorochlamydiaceae-a family linking pathogenic Chlamydiaceae, which includes the genus Chlamydia, and symbionts of protists. CLO-positive microbiomes exhibited significantly greater species richness and evenness with distinct differences in community composition relative to CLO-negative microbiomes. These effects were most pronounced among males and older adults. Functional profiling revealed widespread depletion of biosynthetic and metabolic pathways in CLO-positive microbiomes, particularly in participants with TS/TT, suggesting reduced community biosynthetic capacity and niche modification. Species interaction network analyses demonstrated substantial reorganization of microbial associations in the presence of CLOs with increased connectivity and centrality compared to CLO-negative networks. These findings identify CLOs as prevalent, phylogenetically diverse, and ecologically influential members of the microbiome. Their inverse association with Ct and TS/TT underscores the importance of considering intracellular symbionts beyond Ct in understanding conjunctival microbial ecology, resilience, and trachoma pathogenesis and for designing novel control strategies.IMPORTANCETrachoma caused by Chlamydia trachomatis (Ct) remains the leading infectious cause of blindness globally. While control efforts focus exclusively on Ct, other members of the phylum Chlamydiae, such as chlamydia-like organisms (CLOs), inhabit mucosal surfaces but remain understudied in the eye. Using targeted 16S rRNA and metagenomic shotgun sequencing of conjunctival samples from villagers in trachoma-endemic Ethiopia, CLOs were prevalent (23.3%; 249/1,059), phylogenetically diverse, including novel Chlamydiae phylotypes, and inversely associated with both Ct infection and severe scarring disease. CLO microbiomes had increased microbial diversity, altered community composition, depleted metabolic pathway abundance, and reorganized species interaction networks compared to CLO-negative microbiomes. These findings challenge the singular focus on Ct in trachoma control and research and suggest that CLOs represent ecologically significant members of the conjunctival microbiome. Further research on their interactions with ocular microbial communities could reveal new insights into trachoma pathogenesis and inform more holistic approaches to disease control.}, }
@article {pmid42023878, year = {2026}, author = {Conte, CA and Rivarola, M and Gonzalez, S and Milla, FH and Soria, C and Giardini, MC and Segura, DF and Handler, AM and Bourtzis, K and Ragoussis, J and Lanzavecchia, SB}, title = {De novo whole-genome assembly of the Wolbachia sp. endosymbiont from Anastrepha fraterculus using long- and short-read metagenomic data.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0042526}, doi = {10.1128/mra.00425-26}, pmid = {42023878}, issn = {2576-098X}, abstract = {A whole-genome assembly and annotation of Wolbachia sp. infecting Anastrepha fraterculus sp. 1 were generated by a metagenomic analysis of sequencing reads from a host genome project. This study contributes to the characterization of this endosymbiotic bacterium and provides valuable insights for research on host-symbiont interactions and pest management strategies.}, }
@article {pmid42024170, year = {2026}, author = {Jiang, L and Tang, Y and Xu, L and Wei, Y and Liu, M and Che, X and Xin, R and Zhu, Y}, title = {Microbiome in adult severe caries and cross-kingdom biofilms validation.}, journal = {Clinical oral investigations}, volume = {30}, number = {5}, pages = {}, pmid = {42024170}, issn = {1436-3771}, support = {ZDXX25182//Nanjing Medical Science and Technique Development Foundation/ ; ZKX23053//Nanjing Medical Science and Technique Development Foundation/ ; 0224C010//High-Level Hospital Construction Project of Nanjing Stomatological Hospital, Affiliated Hospital of Medical School, Institute of Stomatology, Nanjing University/ ; }, mesh = {*Biofilms/growth &amp; development ; Humans ; *Dental Caries/microbiology ; Candida albicans ; Adult ; Saliva/microbiology ; *Microbiota ; Streptococcus mutans ; Male ; Veillonella ; Female ; Microscopy, Electron, Scanning ; Microscopy, Atomic Force ; Microscopy, Confocal ; Metagenomics ; Middle Aged ; }, abstract = {OBJECTIVES: Adult severe caries (ASC) is a form of rampant caries that develops in adulthood, causing severe impairment of oral function and reducing quality of life. However, the pathogenic mechanism of ASC remains unclear. This study aimed to identify the core microbiota in patients with ASC and preliminarily investigate the microbial interactions and pathogenicity of key ASC-associated core microorganisms.<br><br>MATERIALS AND METHODS: Saliva samples were collected from 7 adult patients with severe caries and 6 caries-free volunteers for metagenomic analysis. Based on microbiome profiling results, an in vitro cross-kingdom biofilm model composed of Streptococcus mutans (S. mutans), Candida albicans (C. albicans) and Veillonella parvula (V. parvula) was established to simulate a high caries-risk microenvironment. Scanning electron microscopy (SEM), crystal violet (CV) staining, and live/dead bacterial staining were used to evaluate biofilm formation. Acid production assays, acid stress challenge tests, confocal laser scanning microscopy (CLSM) and qRT-PCR were performed to analyze the acidogenicity and synthesis of extracellular polysaccharides (EPS). Additionally, atomic force microscopy (AFM) was used to assess the surface roughness of demineralized dentin slices.<br><br>RESULTS: Metagenomic analysis revealed significant enrichment of C. albicans and V. parvula in the saliva of patients with high caries susceptibility. The in vitro cultured cross-kingdom biofilms exhibited enhanced growth and EPS synthesis compared with single-species S. mutans biofilms. Moreover, cross-kingdom biofilms significantly increased surface roughness of demineralized samples, with a stronger effect than single- and dual-species biofilms.<br><br>CONCLUSIONS: Colonization by C. albicans and V. parvula increases biofilm biomass, enhances microbial survival under stress, and elevates biofilm virulence, which induces demineralization of dentin slices in vitro.<br><br>CLINICAL RELEVANCE: This study demonstrates that the interspecies interactions among caries-related microorganisms in ASC patients confer enhanced virulence and cariogenicity, providing novel insights for the investigation and prevention of high caries susceptibility.}, }
@article {pmid42025071, year = {2026}, author = {Waseem, H and Feng, K and Zhao, B and Yang, X and Liu, M and Wang, J and Li, J and He, Q and Wang, S and Lu, Y and Örmeci, B and Deng, Y}, title = {Diversity and geographic distribution of antibiotic resistance in food waste anaerobic digestion systems.}, journal = {Journal of hazardous materials}, volume = {510}, number = {}, pages = {142168}, doi = {10.1016/j.jhazmat.2026.142168}, pmid = {42025071}, issn = {1873-3336}, abstract = {Antibiotic resistance genes (ARGs) present in food waste pose a significant environmental and public health challenge, with anaerobic digestion emerging as a promising technology to reduce ARG abundance during waste treatment. In this study, we analyzed the resistomes in 64 anaerobic digestion sludge samples from seven full-scale food waste treatment facilities representing seven Chinese provinces. Across all facilities, a small core set of glycopeptide (van clusters), β-lactamase, aminoglycoside, and macrolide-lincosamide-streptogramin genes accounted for most ARG abundance (70.3%), marking them as critical targets for monitoring and post-treatment at high-risk sites such as Wenzhou. Resistome composition differed significantly among facilities and exhibited moderate correlation with bacterial taxonomic composition, with Firmicutes (Bacillota), Chloroflexota, and Proteobacteria as the major carriers associated with multiple resistance classes. ARG abundance was positively correlated with mobile genetic elements (r = 0.54, p < 0.0001), driven by integrases, transposases, and Tn916. Horizontal gene transfer was largely constrained within phylogenetic boundaries, particularly within Firmicutes (66.67%), limiting cross-phyla ARG dissemination. Resistome variation was driven predominantly by deterministic processes.; these deterministic filters together with regional differences in food-waste composition and MGEs, collectively select for a glycopeptide-dominated, Firmicutes-anchored resistome that is distinct from those in activated sludge and manure digesters.}, }
@article {pmid42025084, year = {2026}, author = {Xu, GL and Tan, S and Hu, Y and Cheng, M and Hou, J and Cui, HL}, title = {Five novel Haloarchaeobius species from coastal tidal flats and saline-alkali soil in China using integrated culture-dependent and culture-independent approaches.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {3}, pages = {126718}, doi = {10.1016/j.syapm.2026.126718}, pmid = {42025084}, issn = {1618-0984}, abstract = {Six novel halophilic archaeal strains, DFWS5[T], DT45[T], DYHT-AS-18[T], HRN-SO-5[T], TZWSO28, and TZWWS8[T] were isolated from tidal flats and saline-alkali soil collected from the eastern coastal region of China. Amplicon sequencing and metagenomic analyses indicated that these strains were present at low abundance in their original habitats, with only three strains detected by culture-independent approaches. These six strains constituted an independent clade alongside members of the genus Haloarchaeobius based on the 16S rRNA gene phylogeny. Except for the comparison between strains DYHT-AS-18[T] and TZWSO28, the average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity values among these strains and existing members of the genus Haloarchaeobius were 76.60-89.50%, 21.00-38.50%, and 67.99-88.76%, respectively, below the proposed thresholds for species delineation. In contrast, these three values between strains DYHT-AS-18[T] and TZWSO28 were 97.36%, 76.30%, and 97.25%, respectively, exceeding the proposed thresholds. Phylogenomic analysis revealed that the six strains clustered with members of the genus Haloarchaeobius, but formed distinct branches separate from the current species. The optimal growth conditions for these six strains in terms of NaCl, MgCl2, temperature, and pH were 0.9-4.8 M, 0-1 M, 20-50 °C, and 5.0-9.5, respectively. According to phenotypic differences in nutrition and biochemical activity, these six strains can be distinguished from their related species. On the basis of polyphasic taxonomic evidence, five novel species within the genus Haloarchaeobius are proposed to accommodate strains DFWS5[T], DT45[T], DYHT-AS-18[T], HRN-SO-5[T], TZWSO28, and TZWWS8[T], respectively.}, }
@article {pmid42025086, year = {2026}, author = {Islam, A and Han, Z and Rana, ML and Qiao, W and Guruge, SK and Zhang, Y and Yang, M}, title = {Removal of protozoa, opportunistic pathogens with virulence factors in swine manure using anaerobic digestion: Full-scale investigation and lab-scale optimization.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129728}, doi = {10.1016/j.jenvman.2026.129728}, pmid = {42025086}, issn = {1095-8630}, abstract = {Swine manure serves as a significant reservoir of zoonotic protozoa and opportunistic pathogens, posing environmental and public health risks when inadequately treated. In this study, multiple molecular approaches, including quantitative PCR, nested PCR with gp60-based phylogenetic analysis, virulence factor profiling, and metagenome-assembled genome (MAG) reconstruction, were employed to investigate the abundance, diversity, and treatment responses of Cryptosporidium, Giardia, twelve opportunistic pathogens, and associated virulence factors (VFs) in swine manure. Three full-scale anaerobic digestion (AD) systems were investigated, and thermophilic and hyperthermophilic pretreatments were applied to lab-scale AD systems to evaluate the efficiency of biological risk control. Cryptosporidium parvum was identified as the dominant species, with subtype IIaA17G4R1 and related zoonotic subtypes detected in both lab-scale and full-scale samples. Phylogenetic clustering of swine-derived sequences with human and cattle isolates indicates a potential risk of zoonotic transmission through manure-associated environmental contamination. In lab-scale AD, a significant reduction in Cryptosporidium, particularly under hyperthermophilic conditions, was observed, while Giardia was undetectable in both influent and effluent samples. In full-scale systems, persistence of Escherichia coli, Clostridium perfringens, Enterococcus, Salmonella, and multiple VFs was confirmed in the effluents. The hyperthermophilic-mesophilic (70 °C-37 °C) lab-scale treatments achieved a substantial reduction in overall pathogen abundance from 3.40 × 10[8] to 1.21 × 10[8] copies/g dry weight and in virulence gene loads from 5.24 to 2.35 copies/cell (P < 0.001), along with the significant removal of pathogenic MAGs such as Enterococcus, Escherichia, Pseudomonas, and Streptococcus. These findings demonstrate the effectiveness of AD for reducing microbial risks and underscore the potential of thermophilic phase digestion as a scalable, biologically effective method for reducing microbial risks associated with livestock manure reuse.}, }
@article {pmid41807604, year = {2026}, author = {Santacroce, M and Baranek, J and Adamski, Z and Trzebny, A and Dabert, M and Bufo, SA and Scrano, L}, title = {Prevalence of Bacillus species in the lytic cultural heritage of Santa Lucia alle Malve Rupestrian Church.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41807604}, issn = {2045-2322}, abstract = {UNLABELLED: Santa Lucia alle Malve (SLM) is a unique rupestrian heritage site, entirely carved into limestone. This monument, which was a church in the ancient settlement of Benedictine nuns over a millennium ago in southern Italy, holds exceptional value not only from an architectural and cultural perspective but also in terms of its microbial ecology. Until now, the specific microbiota of this site had remained unexplored. In this study, the bacterial community inhabiting the interior walls of Santa Lucia alle Malve was investigated using a metagenomic approach, alongside the isolation and comprehensive characterization of cultivable strains from various sampling sites. Both methodologies consistently revealed a dominance of spore-forming bacteria from the phylum Bacillota, particularly the genus Bacillus. Notably, most of the cultivable strains belonged to the Bacillus cereus sensu lato group and the Bacillus. licheniformis clade. Despite the high genetic similarity among these microorganisms, each strain exhibited a unique set of phenotypic traits, highlighting the potential complexity of the SLM metabolome. Additionally, two isolates were identified as Bacillus thuringiensis, entomopathogenic bacteria with possible applications in biological pest management. Finally, Staphylococcus warneri, a human skin commensal found in the church, suggests human influence on the microbial landscape.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41655-4.}, }
@article {pmid42014006, year = {2026}, author = {Liu, H and Luo, J and Yang, Y and Yang, R and Li, W}, title = {Spleen metabolomics coupled with gut microbiome analysis to elucidate the immunomodulatory mechanisms of longan polysaccharides against cyclophosphamide-induced immunosuppression in mice.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {152109}, doi = {10.1016/j.ijbiomac.2026.152109}, pmid = {42014006}, issn = {1879-0003}, abstract = {Longan polysaccharide (LP) has exhibited excellent immunomodulatory activities by modifying gut microbiota but the specific regulatory mechanism remains unclear. Therefore, spleen metabolomics and metagenomic sequencing of gut microbiota were combined to investigate the immunomodulatory mechanism of LP in cyclophosphamide (CPA)-induced immunosuppressed mice with an intact and antibiotic-depleted microbiota. The results indicated that LP significantly restored thymic and splenic indices, increased lymphocyte proliferation, and mitigated damage to immune organs. LP up-regulated the ratio of CD4[+]/CD8[+] in the mouse spleen to modulated cytokine secretion, thereby increasing serum concentrations of IFN-γ, TNF-α, IL-12, and IL-6. The metabolomic analysis indicated that LP alleviated CPA-induced splenic disturbance by coordinately improving amino acid metabolism, unsaturated fatty acid metabolism, and pyrimidine metabolism. Furthermore, LP significantly reshaped the CPA-induced gut microbiota imbalance, particularly by increasing the relative abundance of unclassified_f__Muribaculaceae and Bacteroides. However, antibiotic intervention almost offset the LP-mediated alleviation of immunosuppression. Our findings provide novel insights into the mechanisms underlying the immunosuppression-alleviating effects of natural polysaccharides.}, }
@article {pmid42014453, year = {2026}, author = {Treichel, NS and Pauvert, C and Séneca, J and Pjevac, P and Berry, D and Penders, J and Hitch, TCA and Clavel, T}, title = {Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {42014453}, issn = {2058-5276}, support = {460129525//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 445552570//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 10.55776/DOC69//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; 10.55776/COE7//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; }, abstract = {Shotgun metagenomics can provide both taxonomic and functional insights, but benchmarking is necessary to determine the sequencing depth appropriate for specific analyses. Here we used complex mixtures of DNA from cultured bacteria and analysed taxonomic composition, strain-level resolution and functional profiles at up to 11 sequencing depths (0.1-50.0 Gb). Reference-based analysis provided accurate strain-level taxonomy at 0.5-1.0 Gb. By contrast, de novo metagenome-assembled genome (MAG) reconstruction required deep sequencing (>10 Gb), and even MAGs deemed high quality by standard metrics were chimeric, with 54.5-81.8% accurately representing original strains, depending on the bioinformatic approach. Functionally, 2 Gb provided reliable insights at the pathway level for each of the mock communities tested, but sufficient proteome coverage was achieved only at or above 10 Gb. Library preparation and host DNA contamination were identified as confounders in shallow metagenomic analysis. This analysis highlights the potential and limitations of shallow metagenomics and provides guidance to accurately capture strain-level diversity using MAGs.}, }
@article {pmid42014512, year = {2026}, author = {Vijayasimha, M and Srikanth, M and Trivedi, NS}, title = {From Diagnostic Accuracy to Decision-Grade Respiratory Nanopore Metagenomics: Minimum Standards, Stewardship Endpoints, and Equitable Implementation.}, journal = {Current microbiology}, volume = {83}, number = {6}, pages = {}, pmid = {42014512}, issn = {1432-0991}, }
@article {pmid42014682, year = {2026}, author = {Lee, EM and McNulty, NP and Hibberd, MC and Cheng, J and Ahsan, K and Chang, HW and Cohen, BA and Gordon, JI}, title = {Enhancing inference of differential gene expression in metatranscriptomes from human microbial communities.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71871-5}, pmid = {42014682}, issn = {2041-1723}, support = {DK30292//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; }, abstract = {Metatranscriptomic (MTX) sequencing quantifies gene expression from the collective genomes of microbial communities (microbiomes), enabling assessment of functional activity rather than functional potential. While differential expression testing is essential for RNA-sequencing analysis, current metatranscriptomic approaches have only been benchmarked on simulated data, resulting in a lack of standard practices for analysis of real datasets. Here, we use mock communities (defined mixtures of microbial cells with known properties) to quantitatively assess robustness and susceptibility of current approaches to various confounders including organisms' low relative abundance, differential abundance, low prevalence, global transcriptional output changes, and compositional effects. We show that no current method is robust to all confounders and method performance on simulated data does not generalize to real datasets. We then apply the same approaches to MTX datasets generated from gnotobiotic mice colonized with defined consortia of human bacterial strains and show that the method nominated by the mock community comparisons successfully inferred cross-feeding dynamics that were subsequently validated in vitro. Finally, using metagenome-assembled genomes from a human clinical study, we leverage genome-level sequencing depth and detection of genes to exclude low information samples on a per-organism basis to overcome confounding low prevalence and enhance differential expression inference. We conclude that MTX benchmarking on real, non-simulated datasets can and should guide choice of methods and their implementation, enabling inference and validation of microbial metabolic strategies and interactions in vivo.}, }
@article {pmid42014730, year = {2026}, author = {Wang, Y and Yu, P and Huang, ES and Lu, DC and Zhang, W}, title = {Decoding a Microbial Community for Healthy Kelp: 403 MAGs from the World's Largest Kelp Farming Region.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07250-y}, pmid = {42014730}, issn = {2052-4463}, support = {2023-004//2023 Weihai Key Postdoctoral Research Funding Program/ ; }, abstract = {Kelp is economically and ecologically significant, with its organic nutrient-rich aquaculture water harboring diverse microbial communities that critically influence kelp health and productivity. To characterize these communities, we collected ten water samples from major kelp farming areas and reconstructed 403 medium- to high-quality Metagenome-Assembled Genomes (MAGs). Of these, 110 (27.3%) met high-quality criteria (completeness >90%, contamination <5%). Phylogenomic analysis classified these MAGs into 21 archaeal and 382 bacterial species across 19 phyla, with Pseudomonadota (n = 217), Bacteroidota (n = 74), and Patescibacteria (n = 24) as the dominant groups. UpSet plot analysis revealed the presence of a core set of 30 MAGs across all sampling sites. Notably, diseased samples exhibited a marked increase in Pseudomonadota MAGs, suggesting their potential as biomarkers for disease monitoring. Together, these findings provide foundational insights into the microbial ecology of kelp aquaculture systems, supporting improved disease management and sustainable practices.}, }
@article {pmid42014993, year = {2026}, author = {Dong, X and Yi, J and Wang, Y and Zhou, A and Zhang, J and Shi, L and Wang, C}, title = {Multi-omics integration analyses reveal microbiome and metabolome features in pregnant sow diarrhea induced by porcine epidemic diarrhea virus.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05043-2}, pmid = {42014993}, issn = {1471-2180}, }
@article {pmid42015023, year = {2026}, author = {Peng, Z and He, H and Zhou, S and Qiao, L and Wang, Q and Li, M and Zhao, Y}, title = {Rhino-orbito-cerebral Rhizopus delemar infection in a patient with anti-melanoma differentiation-associated-5-positive dermatomyositis diagnosed by metagenomic next-generation sequencing: a case report.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13359-7}, pmid = {42015023}, issn = {1471-2334}, }
@article {pmid42015434, year = {2026}, author = {Wang, S and Deng, F}, title = {Clinical Features and Coinfection Factors of Severe Community-Acquired Pneumonia with &lt;em&gt;Mycoplasma Pneumoniae&lt;/em&gt; in Children.}, journal = {Journal of the College of Physicians and Surgeons--Pakistan : JCPSP}, volume = {36}, number = {4}, pages = {483-488}, doi = {10.29271/jcpsp.2026.04.483}, pmid = {42015434}, issn = {1681-7168}, mesh = {Humans ; *Community-Acquired Infections/microbiology/epidemiology/diagnosis ; Male ; Female ; *Coinfection/epidemiology/microbiology/diagnosis ; Child ; Retrospective Studies ; *Pneumonia, Mycoplasma/epidemiology/diagnosis/microbiology ; *Mycoplasma pneumoniae/isolation &amp; purification/genetics ; Child, Preschool ; China/epidemiology ; Infant ; Adolescent ; Anti-Bacterial Agents/therapeutic use ; Severity of Illness Index ; Community-Acquired Pneumonia ; }, abstract = {OBJECTIVE: To characterise the clinical features of children with severe community-acquired pneumonia (CAP) associated with Mycoplasma pneumoniae (Mp) infection and to identify factors influencing polymicrobial coinfections.<br><br>STUDY DESIGN: A descriptive study. Place and Duration of the Study: Department of Internal Medicine, Anhui Provincial Children's Hospital, Anhui, China, from January to December 2023.<br><br>METHODOLOGY: A retrospective cohort study was conducted on 207 hospitalised children aged <16 years with confirmed CAP who underwent BALF testing due to severe symptoms, antibiotic-unresponsive fever, or unclear aetiology. Those with chronic comorbidities were excluded. BALF pathogens were detected via multiplex PCR and metagenomic next-generation sequencing (mNGS). Patients were divided into Mp mono-infection and coinfection groups; demographic, clinical, and laboratory data were compared, and logistic regression analysis was performed to identify factors associated with coinfection.<br><br>RESULTS: The coinfection group was significantly younger (4.12 &#xb1; 2.83 vs. 6.56 &#xb1; 2.47 years, p = 0.013) and had longer hospital stays (11.21 &#xb1; 4.26 vs. 9.90 &#xb1; 3.68 days, p = 0.049) than the mono-infection group. Inflammatory markers differed significantly: the coinfection group had higher IL-6 (28.64 &#xb1; 8.03 vs. 15.86 &#xb1; 14.21 pg/mL, p <0.001), but lower IL-2R (1774.15 &#xb1; 104.18 vs. 2157.39 &#xb1; 382.76 U/mL, p <0.001) and ESR (30.31 &#xb1; 14.79 vs. 40.08 &#xb1; 13.66 mm/h, p <0.001). Logistic regression confirmed IL-6 (p <0.001), IL-2R (p <0.001), and complications (p = 0.0281) as independent factors associated with coinfections, while chest CT findings showed no correlation (p >0.05).<br><br>CONCLUSION: Younger age, elevated IL-6 levels, reduced IL-2R levels, and the presence of complications are closely correlated with polymicrobial coinfections in children with severe Mp-associated CAP.<br><br>KEY WORDS: Pneumonia, Mycoplasma pneumoniae, Paediatrics, Coinfection, Metagenomic sequencing, Clinical characteristics.}, }
@article {pmid42015472, year = {2026}, author = {Song, M and Zhang, Z and Huang, H and Zou, Z and Wen, S and Cui, Y and Liu, S}, title = {Spinal Tuberculosis Diagnosed by Metagenomics Capture (MetaCAP) in a Patient Undergoing Maintenance Hemodialysis: A Case Report.}, journal = {The American journal of case reports}, volume = {27}, number = {}, pages = {e951840}, doi = {10.12659/AJCR.951840}, pmid = {42015472}, issn = {1941-5923}, mesh = {Humans ; Female ; Middle Aged ; *Tuberculosis, Spinal/diagnosis/drug therapy ; *Renal Dialysis ; *Metagenomics/methods ; *Kidney Failure, Chronic/therapy/complications ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND Spinal tuberculosis is difficult to diagnose in patients undergoing maintenance hemodialysis (MHD) because of immunosuppression, atypical clinical manifestations, and the limited sensitivity of conventional microbiological assays. Rapid and accurate pathogen identification is essential to distinguish spinal tuberculosis from other causes of vertebral destruction, including metastatic malignancy and bacterial spondylitis. This report aims to illustrate the diagnostic value of capture-based targeted sequencing for detecting Mycobacterium tuberculosis in extrapulmonary infection when routine tests and metagenomic next-generation sequencing (mNGS) yield inconclusive or misleading results. CASE REPORT A 64-year-old woman with end-stage renal disease secondary to IgA nephropathy, receiving long-term MHD, presented with progressive low back pain. Imaging revealed multilevel vertebral involvement with pathological fractures, raising suspicion of metastatic disease or infectious spondylitis. Histopathological examination demonstrated granulomatous inflammation, while acid-fast staining and routine cultures were negative. Initial mNGS of spinal tissue identified Staphylococcus aureus, leading to targeted antibacterial therapy. Although inflammatory markers declined, the patient's symptoms worsened and pancytopenia developed. Subsequent analysis of spinal pus using metagenomic capture (MetaCAP)-based targeted sequencing detected the Mycobacterium tuberculosis complex with high confidence. Anti-tuberculosis therapy was promptly initiated, resulting in rapid clinical improvement and radiological resolution. CONCLUSIONS This case shows the limitations of conventional microbiological methods and unbiased mNGS in diagnosing extrapulmonary tuberculosis in immunocompromised patients. Capture-based targeted sequencing offers enhanced sensitivity for Mycobacterium tuberculosis detection and may facilitate timely diagnosis and appropriate treatment of spinal tuberculosis in patients undergoing MHD.}, }
@article {pmid42016528, year = {2026}, author = {Xu, H and Guo, J and Chen, C and Pang, Z and Zhang, G and Zhang, W and Kan, H and Shao, X}, title = {Metagenomics reveals the functional profiles of soil microorganisms and nutrient cycling under long-term grass vegetation cropping.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100583}, pmid = {42016528}, issn = {2666-5174}, abstract = {Soil microbes are crucial for biogeochemical cycles and their functional potential is greatly affected by ecosystem management. Yet, how does grass vegetation affect the composition of soil microbial communities and the abundance of key nutrient-cycling functional genes? In this study, based on an experimental plot built for 7 years, the long - term influence of two grass vegetation types (Carex breviculmis and Festuca arundinacea Schreb) on soil microbial community structure and C, N, P, and S cycles were explored by metagenomics. The results showed that both plants significantly increased the diversity and richness of soil bacteria and fungi, and the abundance of Pseudomonadota and Ascomycota in Carex breviculmis increased significantly, while those of Actinomycetota and Mucoromycota decreased. Microbial network analysis shows that Carex breviculmis forms a highly modular, low - complexity microbial interaction network, indicating specialized and stable microbial community functions. Conversely, Festuca arundinacea Schreb has a more complex and less modular network, suggesting enhanced microbial interactions. Carex breviculmis significantly increased the abundance of genes related to carbon fixation (fumA/B, pps, ppc) and phosphorus mineralization (phoR/P/B, phnF/P), and also enhanced soil denitrification potential. In contrast, Festuca arundinacea Schreb showed a enrichment of soil nitrogen fixation genes (nifh). Additionally, growing Carex breviculmis and Festuca arundinacea Schreb induced the growth of sulfur - oxidizing bacteria (e.g., Thiobacillus), enriching the abundance of sulfur - metabolism - related genes (apr, sox). Genes related to microbial C, N, P, and S cycles are positively correlated with soil pH, available P, and alkali-hydrolyzed nitrogen. Overall, this study reveals how different grass vegetation types regulate microbial community structure and functional gene abundance to drive nutrient cycling differentiation in grassland ecosystems, thereby providing a theoretical basis for optimizing grass vegetation configuration in managed and restored grasslands to enhance soil ecological functions.}, }
@article {pmid42016568, year = {2026}, author = {Liu, L and Xu, C and Liu, Y and Yang, J and Ye, Y and Yao, Z and Lin, D and Qiu, H and Ruan, D and Qiu, Y and Wang, S and Lin, M and Zhang, Z and Huang, S and Meng, F and Zheng, E and Cai, G and Wu, Z and Wu, JJ}, title = {Restoring low-fiber diets-induced Lachnospiraceae bacterium loss partially recovers fiber digestion and immune function in mammals.}, journal = {Current research in food science}, volume = {12}, number = {}, pages = {101401}, pmid = {42016568}, issn = {2665-9271}, abstract = {Mammals rely on their gut microbiota to degrade cellulose, the major component of dietary fiber. Westernized populations harbor a depleted microbiome with reduced fiber-digesting capacity and impaired immune regulation due to prolonged consumption of low-fiber diets. Comparable patterns are evident in other mammals, including Western commercial pigs raised on high-energy, low-fiber diets, exhibiting reduced diversity and abundance of fiber-degrading bacteria. In contrast, semi-free-ranging Chinese indigenous pigs consuming fiber-rich diets retain a more diverse and functionally resilient microbiota, reflecting divergent trajectories of host-microbiota co-evolution. However, the specific cellulose-degrading species lost and strategies to restore these functions remain unclear in mammals. By analyzing 473 human stool metagenomes spanning non-westernized and westernized diets, together with 251 fecal 16S rRNA datasets and 95 metagenomes from Western commercial pigs, Chinese indigenous pigs, and their crossbred progeny, we identified the Lachnospiraceae bacterium as a key symbiont enriched in non-westernized guts. This bacterium possesses an extensive Carbohydrate-Active Enzymes repertoire conferring strong fiber-degrading capacity. Notably, low-fiber diets leave a genetic signature on this keystone gut symbiont, which cannot be reversed by short-term dietary interventions alone. Reintroduction of Lachnospiraceae bacterium to germ-free mice improved feed efficiency and increased acetic acid production. Intestinal transcriptomics and peripheral blood flow cytometry revealed that it activates a broad adaptive immune response, promoting CD4[+] T cell accumulation, B cell activation, and anti-inflammatory cytokine induction. Reintroduction of this bacterium also alleviated dextran sodium sulfate-induced colitis. These findings highlight the preclinical functional potential of this Lachnospiraceae bacterium in mitigating low-fiber diets-induced dysfunction in mammals.}, }
@article {pmid42016597, year = {2026}, author = {Srinivas, M and O'Sullivan, O and Cotter, PD and van Sinderen, D and Kenny, JG}, title = {Investigating the role of bacterial raw milk community members in chlorate reduction.}, journal = {Access microbiology}, volume = {8}, number = {4}, pages = {}, pmid = {42016597}, issn = {2516-8290}, abstract = {Chlorine-based detergents, used in the dairy industry for cleaning, often degrade into chlorate, contaminating milk and dairy products. Consumption of chlorate has been linked to thyroid dysfunction in adults and impaired neurological development in infants. Despite the ban on chlorine-based detergents in Ireland since 2021, chlorate contamination remains a problem in the dairy supply chain. A recent study identified chlorate-reducing bacteria naturally present in raw milk, highlighting their potential for mitigating chlorate. In this study, shotgun metagenomic sequencing was applied to determine the effects of chlorate concentration and incubation conditions on the raw milk microbiome, specifically focusing on chlorate-reducing bacteria within the community. Chlorate-spiked milk samples from different farms showed reductions in chlorate levels over time, from day 10 onwards when stored at 4 °C and after 24 h when incubated at 25 °C. Pseudomonas and Lactococcus were observed as the most dominant taxa in raw milk samples stored at 4 °C and 25 °C, respectively. High abundances of ydeP and narG genes were observed for 4 °C samples and were attributed to Pseudomonas and various low-abundance genera, respectively. High abundances of the napA gene were noted in 25 °C samples and were attributed to the Lactococcus genus. Overall, this study highlights the presence of naturally occurring chlorate-reducing bacteria as part of the raw milk microbiome and identifies multiple genes linked to various pathways potentially involved in chlorate reduction. Furthermore, incomplete pathways potentially involved in chlorate reduction were found, suggesting metabolic cross-feeding and underscoring the community roles bacteria play in chlorate reduction in raw milk. Additionally, a few previously uncharacterized genes, such as ydeP, belonging to the DMSO reductase gene family were identified at high abundances in samples that showed chlorate reduction, emphasizing the need for further biochemical characterization of these genes to better understand the pathways involved in chlorate reduction in milk.}, }
@article {pmid42016660, year = {2026}, author = {Qu, Y and Liu, Y and Zhou, X and Xu, P and Wang, L}, title = {Polymicrobial Pasteurella multocida-Anaerobic Coinfection Followhing a Cat Bite: Limb Salvage Through Metagenomic Next-Generation Sequencing-Guided Diagnosis and Multidisciplinary Management.}, journal = {Clinical case reports}, volume = {14}, number = {3}, pages = {e72304}, pmid = {42016660}, issn = {2050-0904}, abstract = {Successful management of a Pasteurella multocida and polymicrobial infection following a cat bite on the left leg entailed debridement, split-thickness skin grafting with vacuum-sealing drainage, and targeted antibiotic treatment. This approach enabled successful incorporation of the skin graft, preserving the limb and eliminating the necessity for amputation.}, }
@article {pmid42016731, year = {2026}, author = {Chen, G and Tang, S and Wang, H and Liang, Z and Lv, X and Han, J and Ni, L}, title = {Integration of volatile flavor metabolomics and metagenomics reveals microbial-enzymatic pathways governing key aromatic volatile compound biosynthesis in Hongqujiu fermentation.}, journal = {Food chemistry: X}, volume = {35}, number = {}, pages = {103811}, pmid = {42016731}, issn = {2590-1575}, abstract = {The anabolic pathways of key volatile flavor compounds (VFCs) in Hongqujiu (HQJ) remain insufficiently elucidated. In this study, dynamic changes in volatile flavor profiles and microbial communities throughout HQJ brewing, were systematically investigated using an integrated multi-omics strategy combining metabolomics, flavoromics and metagenomics. The results demonstrated that the ethanol content, titratable acidity, amino nitrogen and higher alcohols increased progressively throughout fermentation. Quantitative flavor metabolomic profiling identified 18 key VFCs, maining comprising ethyl esters, acetate esters and higher alcohols. Metagenomic sequencing revealed that Weissella, Lactobacillus, Saccharomyces, Aspergillus, Talaromyces and Monascus were the predominant microbal genera throughout HQJ fermentation. Functional gene annotation further indicated that key enzymes involved in flavor metabolism are primarily associated with Lactobacillus, Aspergillus, Talaromyces, Saccharomyces, Cyberlindnera and Monascus. Overall, this study elucidates the microbial-enzymatic basis of VFC biosynthesis and establishes a comprehensive flavor metabolic framework for HQJ fermentation, providing a theoretical foundation for aroma quality improvement.}, }
@article {pmid42016742, year = {2026}, author = {Funada Barbosa, MR and Ramos, EDSF and Villanova, F and Oliveira Silva, RL and Garcia, SC and de Araújo, RS and Mendes-Correa, MC and Tozetto-Mendoza, TR and Zhang, W and Pandey, RP and Luchs, A and Sato, MIZ and da Costa, AC and Leal, E}, title = {Exploring the Genomics of Marnaviridae Family: Identification, Characterization, and Taxonomic Implications.}, journal = {International journal of microbiology}, volume = {2026}, number = {}, pages = {7188239}, pmid = {42016742}, issn = {1687-918X}, abstract = {In this study, we characterized sequences similar to Marnaviridae obtained from water samples in the state of São Paulo, Brazil. Sixteen complete or nearly complete genomes were determined, all of them positive-sense single-stranded RNA, with lengths between 7074 and 10,198 base pairs, containing one or two open reading frames (ORFs). The amino acid sequences derived from the ORFs showed similarity and protein domains typical of the Marnaviridae family. Phylogenetic analysis based on RNA-dependent RNA polymerase (RdRp) revealed clusters closely related to viruses that have not yet been classified by the International Committee on Taxonomy of Viruses (ICTV). Some sequences showed proximity to established genera such as Salicharnavirus, Locarnavirus, and Labynarvirus, while others formed three distinct clades, suggesting the presence of new genera. Furthermore, one sequence displayed an RdRp identity of less than 90% and a capsid identity of less than 75%, indicating that it represents a novel species related to Marnaviridae. These findings expand current knowledge of Marnaviridae diversity, contributing to a better understanding of evolutionary relationships and emphasizing the need for taxonomic reorganization.}, }
@article {pmid42016964, year = {2026}, author = {Sun, X and Peng, Y and Hao, X and Dong, R and Wang, Z and Wang, L and Wang, C and Wu, X and Chen, Z and Zhang, W and Tang, X}, title = {Safeguarding a Flagship Species: Integrated Surveillance of Cross-Species Pathogen Transmission in Giant Panda Ecosystems.}, journal = {Ecology and evolution}, volume = {16}, number = {3}, pages = {e73260}, pmid = {42016964}, issn = {2045-7758}, abstract = {Emerging infectious diseases, driven by increasing interactions among humans, wildlife, and livestock, pose an escalating threat to global health, biodiversity, and economies. As a flagship endangered species, the giant panda (Ailuropoda melanoleuca) plays a pivotal role in biodiversity conservation in China. This review synthesizes current knowledge on pathogens threatening giant panda health, including viruses, bacteria, and parasites alongside their potential transmission pathways within nature reserves. We emphasize the roles of domesticated animals, sympatric wildlife, and ectoparasites as reservoir hosts or vectors. Special focus is placed on cross-species transmission dynamics and the critical need for integrated monitoring systems utilizing metagenomics and viromics. We propose a framework for establishing early warning systems and surveillance networks at the domestic-wild animal interface to enhance pathogen detection, disease prevention, and biodiversity conservation.}, }
@article {pmid42016980, year = {2026}, author = {De Panis, D and Priotto, O and Padró, J}, title = {Mitogenomic and Metabarcoding Resources for the Study and Conservation of Keystone Neotropical Raptors.}, journal = {Ecology and evolution}, volume = {16}, number = {3}, pages = {e73262}, pmid = {42016980}, issn = {2045-7758}, abstract = {Neotropical raptors are among the most threatened birds, facing increasing extinction risks due to habitat loss and human persecution. Despite their importance for ecosystem stability, basic data on their distribution, abundance, and genetic diversity remain scarce. To address these gaps, we assembled and annotated the mitochondrial genomes of nine high-priority raptors from the Neotropics, including the threatened Chaco Eagle (Buteogallus coronatus), Black-and-Chestnut Eagle (Spizaetus isidori), Rufous-tailed Hawk (Buteo ventralis), and Harpy Eagle (Harpia harpyja), as well as the Near Threatened Orange-breasted Falcon (Falco deiroleucus), Crested Eagle (Morphnus guianensis), Ornate Hawk-Eagle (Spizaetus ornatus), Plumbeous Hawk (Cryptoleucopteryx plumbea), and Solitary Eagle (Buteogallus solitarius). Mitogenome sizes ranged from 17,848 to 20,449 bp, with consistent gene content and a Control Region architecture common in Falconidae and Accipitridae. Phylogenetic analyses provided strong support for most relationships, highlighting the value of mitogenomic data for phylogeographic studies. We further designed metabarcoding primers for environmental DNA applications. Primers targeting the 12S rRNA gene and a mini-barcode for the Harpy Eagle's Control Region showed high resolution using short, conserved sequences ideal for combining degraded DNA with next-generation sequencing. Our study provides essential molecular tools for monitoring and protecting these ecologically vital yet threatened raptors across the Americas.}, }
@article {pmid42017035, year = {2026}, author = {Yang, Y and Ren, Y and Ma, T and An, J and Jin, S and Dong, Y}, title = {Research advances in the role of circulating microorganisms in gastrointestinal tumors (Review).}, journal = {Molecular and clinical oncology}, volume = {24}, number = {6}, pages = {40}, pmid = {42017035}, issn = {2049-9469}, abstract = {Gastrointestinal tumors are common malignant tumors of the digestive system, which globally threaten human health. Notably, it has been discovered that blood and other circulating body fluids are not completely sterile; instead, they harbor complex and dynamic microbial DNA and signatures [circulating microorganisms (CM)]. These microorganisms primarily originate from the microbial translocation (including bacterial fragments, DNA and metabolites) through a compromised intestinal barrier, and are closely associated with the initiation and progression of gastrointestinal tumors, thus providing novel perspectives for early tumor diagnosis and prognosis. Although there is currently no evidence that CM can directly cause cancer, their metabolites and exosomes may contribute to tumor microenvironment remodeling. On one hand, they activate pattern recognition and inflammatory signaling pathways, such as Toll-like receptor/signal transducer and activator of transcription, potentially inducing and maintaining low-grade chronic inflammation. On the other hand, they may facilitate immune evasion, potentially promoting the 'inflammation-cancer' transition. With the development of metagenomic technologies and the maturation of next-generation high-throughput sequencing technologies, CM have shown potential as liquid biopsy biomarkers for the early diagnosis of gastrointestinal tumors. Interventions targeting specific CMs have also shown prospects for enhancing efficacy in early clinical trials. However, the field still faces numerous challenges, including insufficient depth of mechanistic validation and a lack of standardized detection protocols. Future efforts should aim to conduct further systematic research to clarify the biological functions and clinical translational value of CM in gastrointestinal tumors.}, }
@article {pmid42017731, year = {2026}, author = {Su, DM and Ni, T and Yu, XL}, title = {Invasive streptococcus pneumoniae infection in the hip joint and thigh muscle group of an adult diagnosed by Q-mNGS: a case report.}, journal = {JPMA. The Journal of the Pakistan Medical Association}, volume = {76}, number = {3}, pages = {451-454}, doi = {10.47391/JPMA.22494}, pmid = {42017731}, issn = {0030-9982}, mesh = {Humans ; Male ; Adult ; Thigh ; *Hip Joint/microbiology ; *Pneumococcal Infections/diagnosis/therapy/microbiology ; *Streptococcus pneumoniae/isolation &amp; purification/genetics ; Debridement ; *Soft Tissue Infections/microbiology/therapy/diagnosis ; *Abscess/microbiology/therapy/diagnosis ; Anti-Bacterial Agents/therapeutic use ; *Myositis/microbiology ; *Arthritis, Infectious/microbiology/diagnosis ; Muscle, Skeletal/microbiology ; Drainage ; }, abstract = {Joint infections and myositis due to S. pneumoniae are rare. We report the case of a young adult male presenting with right hip joint infection complicated by thigh muscle abscess, successfully treated by surgical debridement, drainage tube placement, and aggressive antimicrobial therapy. A 38-year-old male presented with right buttock and thigh swelling, pain, night sweats, and limited mobility for 45 days. Imaging examination indicated soft tissue infection around the right hip joint with abscess formation. Quantitative meta-genomic next-generation sequencing (Q-mNGS) of joint fluid confirmed S. pneumoniae as the pathogen. Surgical intervention was performed due to lack of significant improvement after six days of anti-inflammatory therapy. The patient recovered well post-operatively and was discharged with medication after a total hospital stay of 31 days. This case highlights the importance of considering S. pneumoniae as a potential pathogen in joint and soft tissue infections in adults.}, }
@article {pmid42018084, year = {2026}, author = {Han, D and Pan, X and Pan, F and Han, B and Wu, Q and Zhou, Y and Liu, H and Xu, H and Sun, W and Cheng, H and Liu, W and Wan, R and Weng, W and Zhang, H}, title = {Translating Host-Derived Signals from Cerebrospinal Fluid Metagenomic Sequencing into a Diagnostic Tool for Autoimmune Encephalitis in Children.}, journal = {Journal of clinical immunology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s10875-026-02023-z}, pmid = {42018084}, issn = {1573-2592}, support = {82471882//National Natural Science Foundation of China/ ; 21ZR1452900//Natural Science Foundation of Shanghai Municipality/ ; GWVI-3//Three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai (2023-2025)/ ; shslczdzk06902//Shanghai Municipal Key Specialty/ ; }, }
@article {pmid42018438, year = {2026}, author = {Sun, X and Jiang, X and Zhang, L and Li, M}, title = {Extensive individual and microorganism-specific circadian oscillations of the upper respiratory tract microbiome.}, journal = {Cell reports}, volume = {45}, number = {5}, pages = {117284}, doi = {10.1016/j.celrep.2026.117284}, pmid = {42018438}, issn = {2211-1247}, abstract = {The upper respiratory tract microbiome (URM) influences host susceptibility and respiratory disease outcomes, but its normal temporal dynamics remain poorly understood. We conducted temporal metagenomic profiling of the URM by collecting oropharyngeal swabs from 22 healthy adults at 4-h intervals over 48 h. We identify significant 24-h cyclic variations in microbial composition and biomass, with two predominant oscillation patterns: "evening-peak" and "morning-peak" patterns. Temporal variation introduces substantial shifts in microbial profiles, leading to false positives in differential analyses. Microbial rhythmicity is linked to phenotypic traits such as oxygen and nutrient requirements. Nonetheless, rhythmic patterns differ across individuals, and regression analysis reveals that host identity contributes more substantially to microbial rhythmicity than species identity. Functional pathway analysis based on metagenomic sequencing data shows similar circadian fluctuations. Additionally, although anatomically adjacent, the oral cavity and oropharynx exhibit divergent rhythmic behaviors, highlighting local environmental influences on microbial rhythmicity. These findings reveal previously unrecognized temporal dynamics of the URM and provide a temporal framework for more accurate biomarker discovery.}, }
@article {pmid42018637, year = {2026}, author = {Reynolds, RC and Weiss, ACB and James, CC and Kojima, CY and Weissman, JL and Thrash, JC and Levine, NM}, title = {Defining metabolic niches for marine microbial heterotrophs.}, journal = {Science advances}, volume = {12}, number = {17}, pages = {eadz0537}, doi = {10.1126/sciadv.adz0537}, pmid = {42018637}, issn = {2375-2548}, mesh = {Phytoplankton/metabolism ; *Heterotrophic Processes ; Ecosystem ; Carbon Cycle ; *Microbiota ; *Aquatic Organisms/metabolism ; Biomass ; *Seawater/microbiology ; Metagenomics ; }, abstract = {Ocean microbial communities are made up of thousands of diverse taxa whose metabolic demands set the rates of both biomass production and degradation. Thus, these microscopic organisms play a critical role in ecosystem dynamics, global carbon cycling, and climate. While we have frameworks for relating phytoplankton diversity to rates of carbon fixation, our knowledge of how variations in heterotrophic microbial populations drive changes in carbon cycling is in its infancy. Here, we leverage global metagenomic datasets and metabolic models to identify a set of metabolic niches with distinct growth strategies. These groupings provide a simplifying framework for describing microbial communities in different oceanographic regions and for understanding how heterotrophic microbial populations function. This framework, predicated directly on metabolic capability rather than taxonomy, will enable us to tractably link heterotrophic diversity directly to biogeochemical rates in large scale ecosystem models.}, }
@article {pmid42019101, year = {2026}, author = {Ramírez-Arenas, PJ and López-Cortés, A and Martínez-Mercado, MA}, title = {Novel Methanosarcinaceae species Methanohalophilus methylutens sp. nov., Methanolobus methylotrophicus sp. nov., and Methanococcoides guerreronegronense sp. nov. from Guerrero Negro hypersaline microbial mats in accordance with the SeqCode.}, journal = {Systematic and applied microbiology}, volume = {49}, number = {3}, pages = {126716}, doi = {10.1016/j.syapm.2026.126716}, pmid = {42019101}, issn = {1618-0984}, abstract = {The Methanosarcinaceae family is the most versatile among methanogenic archaea, utilizing a wide variety of substrates for methanogenesis. It includes all known halophilic, methylotrophic methanogens. Despite evidence of their presence and even dominance over other methanogenic taxa in Guerrero Negro hypersaline microbial mats, no archaeal species have been cultured or described to date. Consequently, a significant gap remains in our understanding of their metabolic potential and diversity. In this study, seven high-quality metagenome-assembled genomes (MAGs) affiliated with the Methanosarcinaceae family were reconstructed. Three MAGs (E22BA4_117[TS], E22_A5_bin58[TS], and E22bin_1538[TS]) serve as the nomenclatural type for the novel proposed species Methanohalophilus methylutens, Methanolobus methylotrophicus, and Methanococcoides guerreronegronense, according to the SeqCode rules and representing the first Methanosarcinaceae species described from microbial mats of Guerrero Negro. Based on genomic content and phylogenetic features, we infer that these MAGs are cytochrome-containing methanogens supported by the presence of core methanogenesis genes (fwd/fmd, ftr, mch, mtd, mer, mtr and mcr). They exhibit distinct metabolic strategies: E22BA4_117[TS] is a generalist with broad substrate versatility, E22_A5_bin58[TS] is an expanded methylotrophic specialist, and E22bin_1538[TS] is a narrow-range methylotroph. All three MAGs encode the complete set of genes for the methylotrophic pathway, multiple Na[+]/H[+] antiporters and both transport and biosynthesis genes for compatible solutes, collectively indicative of their adaptations to hypersaline conditions. These novel species enrich the phylogenomic resolution of Methanosarcinaceae and expand current understanding of the diversity and ecological relevance of these methanogenic archaea in hypersaline ecosystems, while providing genomic evidence that clarifies their metabolic potential and adaptations.}, }
@article {pmid42019198, year = {2026}, author = {Zhang, C and Geng, H and Li, X and Dai, X and Xu, Y}, title = {Magnetically controlled non-conductive microbial carrier-mediated anaerobic digestion of sewage sludge.}, journal = {Water research}, volume = {300}, number = {}, pages = {125963}, doi = {10.1016/j.watres.2026.125963}, pmid = {42019198}, issn = {1879-2448}, abstract = {Magnetic porous microspheres (MPMs) have been used to enhance the anaerobic digestion (AD) of sludge. However, the feasibility of using MPMs as magnetically controlled microbial carriers in long-term AD remains unclear. Herein, without replenishment of MPMs, the methanogenic performance, main physicochemical properties of sludge and methanogenic metabolomics in 150-day MPM-mediated AD were comprehensively investigated. A substantial highly active anaerobes were found to adhere to MPMs, which maintained strong magnetic controllability and structural stability and significantly enhanced methane production (P < 0.001) and the methane proportion in biogas (P < 0.05) from AD at different hydraulic retention times (HRTs). The significant positive correlations between the interfacial Lewis acid-base (AB) interaction (R[2] > 0.79, P < 0.01) and daily methane production (R[2] > 0.52, P < 0.01) with water-mediated proton-coupled electron transfer (PCET) indicate that MPM-enhanced AB interactions can accelerate electron transfer by promoting proton movement in interfacial water molecules, thus enhancing methanogenesis during AD. Statistical analyses of variations in activities or contents of key bioenergetic substances on and within anaerobic cell membranes in AD confirmed this observation and simultaneously indicated that MPMs significantly enhanced the bioenergetics of CO2-reduction methanogenesis by promoting intracellular water-mediated PCET. Microbial community changes show that during the AD under different HRTs, MPMs significantly enriched bacteria capable of decomposing complex organics into acetate and hydrogen in an attached state, as well as free acetotrophic methanogens and attached hydrogenotrophic and hydrogen-dependent methylotrophic methanogens, thereby optimising the spatial distribution of methanogenic consortia. Metagenomics and genome-centric metagenomic analyses confirmed that MPMs significantly enhanced the hydrogen-dependent methanogenesis pathways of the attached methanogenic consortia and promoted energy-conserving metabolic cooperation between free and attached methanogenic consortia, reducing resource competition. Basic economic and environmental analyses revealed that the annual economic benefit increased by 112.2% and carbon emissions decreased by approximately 1.34 × 10[5] tons CO2/year with MPM-mediated AD relative to conventional AD. These findings can provide an important reference for the development of exogenous material-mediated AD technology.}, }
@article {pmid42019199, year = {2026}, author = {Liu, S and Wei, W and Wang, C and Ni, BJ and Zhu, S}, title = {Persulfate-driven sludge biorefinery toward value-added medium-chain fatty acids.}, journal = {Water research}, volume = {300}, number = {}, pages = {125935}, doi = {10.1016/j.watres.2026.125935}, pmid = {42019199}, issn = {1879-2448}, abstract = {Transforming waste activated sludge (WAS) into high-value biofuels is a key pathway toward sustainable waste management and carbon neutrality, yet the recalcitrance of extracellular polymeric substances (EPS) and microbial cell walls severely limits medium-chain fatty acids (MCFAs) production during anaerobic fermentation. Here, we propose a persulfate (PDS)-based pretreatment strategy that enhances MCFAs synthesis by driving sludge disintegration and substrate transformation. Treatment with 7.5 mM PDS increased MCFAs yield by ∼50%, reaching 13,341.4 mg COD/L. Mechanistic investigations reveal that SO4·[-] and ·OH radicals preferentially degrade tightly bound EPS, reducing protein and polysaccharide content by 38% and 46%, respectively, and increasing soluble chemical oxygen demand (SCOD) 5.05-fold. This transformation produces nitrogen-rich, low-molecular-weight dissolved organic matter (DOM). The resulting DOM exhibited high H/C ratios, low O/C ratios, and low aromaticity indices (AImod), significantly enhancing its bioavailability during anaerobic fermentation. Integrated metagenomic functional annotation and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) revealed that EPS-derived DOM reshaped the microbial metabolic network, stimulating glycolysis, amino acid metabolism, and carbon chain elongation. Moreover, the formation of unsaturated and aromatic-like fermentation products indicated enhanced DOM humification, which facilitated carbon chain elongation and microbial metabolic activity. Life cycle assessment and techno-economic analysis confirmed the environmental sustainability and economic feasibility of this radical-driven strategy. By elucidating the radical-EPS-DOM-metabolism cascade, this study provides mechanism-guided strategies for efficient sludge biorefinery, advancing the field from empirical operation toward targeted, high-efficiency design.}, }
@article {pmid42019232, year = {2026}, author = {Xu, B and Zhou, H and Xu, S and Wang, R and Xu, Q and Wu, X and Mu, D and Li, X}, title = {AI-2-mediated quorum sensing marks the ecological transition from collective cooperation to individual survival during Daqu storage.}, journal = {International journal of food microbiology}, volume = {456}, number = {}, pages = {111785}, doi = {10.1016/j.ijfoodmicro.2026.111785}, pmid = {42019232}, issn = {1879-3460}, abstract = {Quorum sensing (QS) is a central system reflecting microbial collective behavior; however, its role in shaping functional microbial communities within complex solid-state fermentation matrices such as Daqu remains insufficiently understood. Here, we integrated amplicon sequencing, metagenomics, proteomics, and metabolomics to investigate autoinducer-2 (AI-2)-mediated quorum sensing dynamics during Daqu storage. Storage induced a directional succession of the microbial community, revealing two distinct ecological stages. The rapid adjustment stage (0-2 months) was characterized by strong homogeneous selection and rapid species turnover, whereas the slow stabilization stage (3-9 months) was dominated by gradual shifts in microbial relative abundances. Notably, the LuxS/AI-2 pathway, the only QS system detected during Daqu storage, declined rapidly and then stabilized, coinciding with the transition between the two ecological stages. During the early stage, the core QS protein LuxS was tightly associated with the dominant taxon Lactobacillaceae and the methyl donor S-adenosylmethionine, forming a synergistic functional module. In contrast, during the late stage, LuxS became decoupled from stress-tolerant taxa and showed weakened associations with resistance-related metabolic networks. This shift was accompanied by a metabolic transition, with carbon flux gradually redirected from active glycolysis toward the pentose phosphate pathway and amino acid biosynthesis during later stages. Collectively, these findings demonstrate that temporal modulation of the LuxS/AI-2 quorum sensing system represents a critical regulatory node reflecting the transition of the Daqu microbial community from cooperative growth to stress-resilient survival, ultimately shaping metabolic phenotypes and ecosystem functions during storage.}, }
@article {pmid42019335, year = {2026}, author = {Sabatino, R and Pulina, S and Sbaffi, T and Kamburska, L and Titocci, J and Cherchi, M and Pittalis, C and Piscia, R and Vaccarelli, I and Rosati, I and Padedda, BM and Allemanno, F and Casiddu, P and Di Cesare, A}, title = {Lakes and lagoons used for drinking water supply and fisheries as sources of potentially pathogenic bacteria and antimicrobial resistance.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129718}, doi = {10.1016/j.jenvman.2026.129718}, pmid = {42019335}, issn = {1095-8630}, abstract = {Drinking water supplies and water basins used for fisheries represent two essential water sources for humans. Despite the growing accessibility of metagenomic approaches, their routine use for water quality monitoring is still limited. Many key water resources have yet to be fully characterized in terms of microbiome, pathobiome, and antimicrobial resistome. In this study, surface water samples were collected over one year from the artificial Lake Bidighinzu (drinking water supply) and the coastal lagoon Cabras (fisheries) located in the western Mediterranean area. Samples were analyzed for physical and chemical properties, and 16S rRNA gene amplicon and shotgun sequencing were used to characterize bacterial communities, pathobiomes, and antimicrobial resistomes. Physical and chemical properties were generally similar between sites, except for higher salinity in Cabras Lagoon. In Cabras Lagoon, richness of the bacterial community and pathobiome was generally higher in the largest trophic fraction (>20 μm), while in both sites the abundance of potentially pathogenic bacteria (PPB) increased at this fraction. PPB, including ESKAPE pathogens, were more abundant in Lake Bidighinzu. The overall antimicrobial resistome was similar across sites, with high-risk antimicrobial resistance genes (ARGs) such as emrB prevalent. Lake Bidighinzu also had more contigs where ARGs co-occurred with mobile genetic elements. This study highlights microbiological risks in two aquatic systems, particularly Lake Bidighinzu, and underscores the need to integrate metagenomic approaches, possibly with cultivation-based methods, to monitor water quality and assess health risks in drinking water supplies and fisheries.}, }
@article {pmid42019341, year = {2026}, author = {Zhao, Y and Chen, Y and Dang, Z and Li, K and Zhu, Y and Xu, C and Wan, X and Jia, B and Cao, G and Shen, Q and Zhao, Z}, title = {Metagenomic and transcriptomic insights into microbial activity maintenance strategies in a pilot-scale biosorption-biodegradation system for in situ sewer overflow treatment.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129750}, doi = {10.1016/j.jenvman.2026.129750}, pmid = {42019341}, issn = {1095-8630}, abstract = {Sewer overflow is a widely recognized issue in urban water environment pollution. Traditional in situ treatment technologies based on filtration and flocculation often fail to remove soluble pollutants effectively. Conventional in situ biological systems also struggle to maintain activity under fluctuating and nutrient-imbalanced influent conditions. Here, a compact in situ biological treatment process based on biosorption-biodegradation technology with a shortened hydraulic retention time (HRT) is proposed. During a 180-day pilot-scale experiment integrating ballasted flocculation, the system achieved average removal efficiencies of 75-94% for CODCr, NH4[+]-N, TP, BOD5, and SS. Effluent concentrations met Chinese surface water quality standards. The system maintained stable performance during wet weather events and after multiple dry periods of up to 30 days, demonstrating effective microbial activity maintenance. Based on the metagenomic and transcriptomic analyses, this stability is potentially related to nutrient supplementation through carbon metabolism of mixotrophic organisms and pollutant adsorption by biosorption sludge. Additionally, the reduced HRT prevents endogenous respiration and sludge degradation. The compact biosorption-biodegradation process offers an efficient and space-saving strategy for maintaining microbial activity during dry periods. It provides a promising solution for mitigating sewer overflow pollution in high-density urban areas.}, }
@article {pmid42019423, year = {2026}, author = {Xu, C and Feng, Y and He, S and Wu, M and Hu, S}, title = {Mining of FDRs-carrying microbes involved in aflatoxin B1 degradation.}, journal = {Food chemistry}, volume = {515}, number = {}, pages = {149316}, doi = {10.1016/j.foodchem.2026.149316}, pmid = {42019423}, issn = {1873-7072}, abstract = {Aflatoxin B1 (AFB1), a potent hepatocarcinogenic mycotoxin commonly found in food and feed, poses significant threats to food safety and public health. Microbes reduce AFB1 via biotransformation, so mining degrading strains is key. In this study, a novel AFB1 degrader, Mycobacterium sp. strain HM-7, was isolated from an AFB1-degrading bacterial consortium (designated A-2). Genomic analysis of the reconstructed metagenome-assembled genome (MAG) 12 and strain HM-7 revealed six putative F420H2-dependent reductases (FDRs), which are essential for the biotransformation of AFB1. When strain HM-7 was applied to animal feed, it achieved a significant reduction in AFB1 levels. Furthermore, bioinformatics mining based on the Genome Taxonomy Database (GTDB) identified a wide diversity of FDRs-carrying microbes involved in AFB1 degradation, mainly those belonging to the phylum Actinomycetota, highlighting their potential for bioremediation applications. This study provides valuable insights into the diversity of FDRs-carrying microbes involved in AFB1 degradation.}, }
@article {pmid42019451, year = {2026}, author = {Wei, ZW and Li, HQ and Wang, XH and Yang, XR and Su, JQ}, title = {Non-biodegradable microplastics amplify antibiotic resistance and pathogen spread in bay plastisphere.}, journal = {Journal of hazardous materials}, volume = {510}, number = {}, pages = {142147}, doi = {10.1016/j.jhazmat.2026.142147}, pmid = {42019451}, issn = {1873-3336}, abstract = {Microplastics (MPs) serve as reservoirs that facilitate the dissemination of antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs), posing significant threats to public health. However, quantitative evaluations of high-risk ARGs in the plastisphere and comprehensive assessments of their associated health implications are still scarce. In this study, we employed in-situ incubation combined with high-throughput quantitative PCR and metagenomic sequencing to systematically compare the prevalence of ARGs, virulence factor genes (VFGs), mobile genetic elements (MGEs), and HBPs between biodegradable and non-biodegradable MPs. Our findings revealed a marked enrichment of ARGs, VFGs, MGEs, and HBPs in non-biodegradable MPs (polypropylene, polyethylene, and polystyrene) relative to the biodegradable MPs (polyhydroxyalkanoates, polylactic acid, and polybutylene adipate terephthalate). Furthermore, an integrated risk assessment combining high-risk ARGs quantification with a Projection Pursuit Regression model revealed significantly elevated microbial risks associated with non-biodegradable MPs. Taxonomic analysis further indicated that Pseudomonas and Aeromonas act as key HBP vectors carrying ARGs and VFGs in the plastisphere, underscoring their role in facilitating the spread of antimicrobial resistance and virulence. These results highlight how plastic properties mediate microbial colonization patterns under complex field conditions, providing a robust framework for environmental risk evaluation and the targeted management of plastic-associated biological hazards.}, }
@article {pmid42019469, year = {2026}, author = {Peng, F and Zeng, YY and Chang, L and Huang, YX and Deng, JT and Liu, YX and He, X and Song, ZH}, title = {Gut microbiota-derived taurolithocholic acid modulates myofiber-type switching via p38 MAPK/PGC-1α signaling underlying breed differences between Arbor Acres and Taoyuan chickens.}, journal = {Poultry science}, volume = {105}, number = {7}, pages = {106914}, doi = {10.1016/j.psj.2026.106914}, pmid = {42019469}, issn = {1525-3171}, abstract = {It is well-established that the gut microbiota plays a crucial role in skeletal muscle development and homeostasis. However, the contribution of the gut microbiome to the distinct meat quality phenotypes observed between fast-growing commercial broilers and slow-growing local chicken breeds remains poorly understood. Therefore, this study aims to elucidate how the gut microbiota modulates pectoral muscle development by comparing muscle growth phenotypes and gut microbiome dynamics across these breeds. Using the fast-growing commercial Arbor Acres (AA) broiler and the slow-growing local breed Taoyuan (TY) chicken as models, we investigated how breed-specific gut microbiota modulate pectoral muscle fiber composition. AA broilers exhibited faster muscle growth but lower oxidative type I fiber proportion than TY chickens. While small intestinal microbiota succession was similar, cecal communities diverged markedly between breeds. Integrated metagenomic sequencing and metabolomics revealed that cecal Phocaeicola dorei abundance was strongly correlated with serum taurolithocholic acid (TLCA) levels and type I fiber content, especially in TY chickens, which prompted the selection of TLCA for functional validation. Reciprocal intestinal microbiota transplantation (IMT) shifted recipient muscle fiber phenotypes toward those of donors, confirming a causal role of the cecal microbiota. Furthermore, in vitro assays using AA-derived myoblasts demonstrated that TLCA promotes mitochondrial biogenesis and type I fiber formation by enhancing p38 MAPK phosphorylation and PGC-1α activation; this effect was abolished by the p38 inhibitor SB203580. Our study demonstrated that gut microbiota-derived TLCA modulates muscle fiber type transformation via the p38 MAPK/PGC-1α signaling pathway. This finding reveals an intricate mechanism whereby the gut microbiota regulates host muscle development through a metabolite-signaling axis, providing critical insights into the gut microbe-myofiber relationship.}, }
@article {pmid42019695, year = {2026}, author = {Liu, X and Wang, H and Zhou, S and Xie, Y and Wang, J and Wang, X and Xu, S and Wang, L and Jiang, C and Zhuang, X}, title = {Nanobubbles drive advanced anaerobic treatment of swine wastewater for efficient methane recovery: Performance gains and multi-pathway enhancement.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134692}, doi = {10.1016/j.biortech.2026.134692}, pmid = {42019695}, issn = {1873-2976}, abstract = {Swine wastewater contains recoverable energy, but anaerobic digestion is often limited by complex organics and slow hydrolysis. To overcome this limitation, this study introduced nanobubble technology using three gas media (air, O2, and O3) and systematically studied their effects on methane recovery during the anaerobic digestion of swine wastewater. Batch experiments showed that O3 nanobubbles achieved the strongest enhancement, increasing cumulative methane production by 87.5% compared with the control. This improvement may result from the strong oxidative capacity of O3 nanobubbles to degrade recalcitrant organics, as indicated by the second methane production peak observed only in the O3 nanobubbles. In contrast, O2 nanobubbles provided the weakest improvement, potentially because excess dissolved oxygen stimulated facultative aerobic respiration, converting substrates to CO2 and lowering availability for methanogenesis. Further analysis revealed that all nanobubble treatments accelerated volatile fatty acid turnover and enriched key hydrolytic and acidogenic microbes, particularly under O3 nanobubbles. The enrichment of Methanothrix and downregulation of the energy-intensive PilA gene suggest promoted electron transfer. Negatively charged nanobubbles may act as abiotic mediators that facilitate direct interspecies electron transfer. Metabolic analysis indicated enhanced hydrogenotrophic, methylotrophic, and acetoclastic methanogenesis, implying strengthened synergy among pathways. Overall, O3 nanobubbles show promise for resource recovery from organic waste.}, }
@article {pmid42019770, year = {2026}, author = {Xie, M and Kong, L and Hou, L and Chen, Y and Hou, J}, title = {Atopic Dermatitis: Multi-omics Insights into Microbiota-Driven Modulation of the Gut-Skin Axis.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108504}, doi = {10.1016/j.micpath.2026.108504}, pmid = {42019770}, issn = {1096-1208}, abstract = {Atopic dermatitis (AD) is a heterogeneous inflammatory skin disease resulting from complex interactions among host genetics, immune dysregulation, and microbial imbalance. Recent advances in multi-omics technologies have revealed distinct AD endotypes characterized by specific genetic variants, microbial enterotypes, and metabolite profiles. Emerging evidence highlights the gut-skin axis as an important regulatory pathway, in which alterations in gut microbiota influence the production of key microbial metabolites, including short-chain fatty acids (SCFAs) and tryptophan-derived aryl hydrocarbon receptor (AHR) ligands, thereby modulating Th2-dominant inflammatory responses. Integrated analyses combining metagenomics, metabolomics, and single-cell transcriptomics have further identified endotype-specific signatures, such as Bacteroides-enriched profiles associated with lipopolysaccharide-driven inflammation and Prevotella-dominant clusters linked to enhanced AHR activation and epithelial barrier repair. These findings provide a basis for precision stratification and the development of targeted therapeutic strategies, including genotype-guided biologics, microbiota modulation, engineered probiotics, phage therapy, and fecal microbiota transplantation. This review summarizes current evidence integrating host genetics, microbiota networks, and multi-omics biomarkers to provide a comprehensive framework for understanding AD endotypes and to highlight potential avenues for precision diagnosis and targeted interventions.}, }
@article {pmid42020064, year = {2026}, author = {Peters, BA}, title = {Evidence grows for the gut-kidney axis, but questions still remain.}, journal = {Kidney international}, volume = {109}, number = {5}, pages = {832-834}, doi = {10.1016/j.kint.2026.02.015}, pmid = {42020064}, issn = {1523-1755}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Kidney/microbiology/metabolism ; Metabolomics ; Cross-Sectional Studies ; Metagenomics ; }, abstract = {Lin et al. presented the largest cross-sectional study to date on the gut microbiome and kidney health. Their use of a vast sample size, discovery and validation approach, shotgun metagenomics, and integration with serum metabolomics represents a significant advance. In this commentary, we place these new findings into context with prior research and highlight the need for studies with a prospective design to identify true temporal relationships of the gut microbiome with kidney health.}, }
@article {pmid41814236, year = {2026}, author = {Xiao, H and Zhang, Y and Zhu, L and Guo, M and Yao, K and Dong, F and Duan, X and Liu, G}, title = {Meningitis and subdural empyema caused by group A streptococcal infection.}, journal = {BMC pediatrics}, volume = {26}, number = {1}, pages = {}, pmid = {41814236}, issn = {1471-2431}, support = {2024-1-2092//Capital's Funds for Health Improvement and Research/ ; 2-1-2-6-15//2022 Beijing Major Epidemic Prevention and Control Specially Construction Project/ ; }, abstract = {BACKGROUND: Group A streptococcus (GAS) could lead to various disease types in children, but central nervous system (CNS) infections are uncommon. In this paper, we analyzed the clinical features of a GAS case with meningitis and subdural empyema, and characterized the GAS clone.<br><br>CASE PRESENTATION: A thirteen-year-old boy complained of fever, headache, and left hemiplegia. Physical examination also showed central facial palsy of left side. The examinations of blood and cloudy cerebrospinal fluid (CSF) showed bacterial meningitis. Blood cultures and metagenomic sequencing (mNGS) of CSF showed GAS, and GAS antigen of throat swab was positive. The first anti-streptolysin (ASO) was negative, but increased obviously after 2 weeks. The examination of emm type showed emm 12.0 isolate. The head MRI showed restricted diffusion in the right frontal lobe, subdural empyema in the right side of cerebral falx, and meningitis. The CT revealed rhinosinusitis and mastoiditis. Bacterial meningitis, subdural empyema, sepsis, and sinusitis were diagnosed, and vancomycin and ceftriaxone were given. The patient also received dexamethasone in the beginning. Gradual improvement was seen in the patient&#x2019;s clinical status, laboratory parameters (blood/CSF), and radiographic manifestations.<br><br>CONCLUSIONS: The contiguous spread from rhinosinusitis could lead to meningitis and intracranial abscess in adolescent. GAS infection could be the pathogen for subdural empyema in patients with an abrupt onset of symptoms and rapidly deteriorating clinical course.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12887-026-06722-9.}, }
@article {pmid41814258, year = {2026}, author = {Zhou, Y and Yu, D and Li, S and Ruan, S and Ye, J and Zhou, D and Chen, Q and Jin, J and Song, K}, title = {Case Report: diagnosis of mixed Scedosporium apiospermum infection assisted by bronchoalveolar lavage fluid morphology.}, journal = {BMC pulmonary medicine}, volume = {26}, number = {1}, pages = {}, pmid = {41814258}, issn = {1471-2466}, support = {2025HZZD01//The Construction Fund of Key Medical Disciplines of Hangzhou, Laboratory Diagnostics/ ; 2025JK256//Zhejiang Science and Technology Plan for Disease Prevention and Control/ ; }, abstract = {BACKGROUND: Scedosporium apiospermum is a highly aggressive opportunistic pathogen, widely distributed in natural environments. Infections predominantly occur in immunocompromised individuals but may also affect immunocompetent individuals with predisposing factors such as trauma, drowning, exposure to contaminated water, diabetes, or malnutrition.<br><br>CASE PRESENTATION: In the reported case, morphological abnormalities were initially identified in bronchoalveolar lavage fluid (BALF). Subsequent microbial culture identification and metagenomic next-generation sequencing (mNGS) confirmed a mixed infection involving S. apiospermum.<br><br>CONCLUSIONS: This case highlights the importance of improving laboratory personnel&#x2019;s morphological recognition of S. apiospermum in routine examinations. The combined use of multiple diagnostic methods enhances detection rates, shortens the time to identification, ensures timely and effective treatment for patients, and ultimately reduces mortality.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12890-026-04215-0.}, }
@article {pmid41814359, year = {2026}, author = {Lai, C and Zhang, J and Xiong, Y and Wang, Y and Liu, Z and Shi, M and Ye, S and Zeng, J}, title = {Multi-omics analysis reveals the association of cesarean delivery with altered gut microbial profiles and a Th2-biased immune response in neonates.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {41814359}, issn = {1479-5876}, support = {Z-A20241044//Guangxi Zhuang Autonomous Region Health Department/ ; Z20210019//Guangxi Zhuang Autonomous Region Health Department/ ; Z-A20240946//Guangxi Zhuang Autonomous Region Health Department/ ; 2024GXNSFBA010112//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; }, abstract = {BACKGROUND: The gut microbiota plays a crucial role in providing essential stimulatory signals for the development of the immune system during the early stages of life. Cesarean delivery is associated with altered vertical microbial transmission and may affect early immune priming. Currently, only a limited number of studies have investigated the interactions among gut microbiota, fecal metabolites, and immune function in neonates delivered by cesarean section, which underscores the necessity for further research.<br><br>METHODS: We performed metagenomic sequencing and untargeted metabolomics to compare the gut microbiota and fecal metabolites of neonates born through cesarean delivery (n&#x2009;=&#x2009;18) and vaginal delivery (n&#x2009;=&#x2009;20). RNA sequencing (RNA-Seq) was utilized to identify differentially expressed genes (DEGs) in peripheral blood mononuclear cells (PBMCs). Immune profiling involved flow cytometry analysis to determine the proportions of Th1 and Th2 cells, ELISA-based quantification of plasma IFN-&#x3b3;, IL-12p70, IL-4, and IL-10, and assessment of STAT4 and STAT6 expression via ELISA and Western blot. Multi-omics integration was applied to elucidate the systemic impact of cesarean delivery on the neonatal gut microbiome, metabolome, and immune system.<br><br>RESULTS: The composition and functional features of the gut microbiota, and fecal metabolite profile, were significantly altered in Cesarean group. PBMC gene expression also showed marked differences, presenting a Th2-biased immune response and enrichment of genes associated with systemic lupus erythematosus and primary immunodeficiency. Flow cytometry and ELISA confirmed a Th1/Th2 imbalance, while Western blot revealed decreased STAT4 and increased STAT6 expression in the Cesarean group. Multi-omics analysis indicates that Bacteroides sp. is associated with alterations in fecal metabolite in neonates delivered via cesarean section. The reduced abundance of Bacteroides sp. and Bacteroides fragilis correlated with Th1/Th2 dysregulation. Additionally, gut microbiota changes were correlated with variations in the host oxidative phosphorylation pathway via fecal phosphate levels.<br><br>CONCLUSIONS: This multi-omics study reveals an association between the mode of delivery and distinct gut microbiota structure, fecal metabolite profiles, and immune development during early life. This provides a framework for investigating the potential connection between early-life immune programming and mode of delivery.<br><br>CLINICAL TRIAL NUMBER: Not applicable.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07988-4.}, }
@article {pmid42006125, year = {2026}, author = {Azuma, N and Wada, N and Aoki, R and Sampei, M and Mawatari, T and Saito, Y}, title = {Administration of bifidobacteria and dietary fiber improves cognitive function by increasing short-chain fatty acid-producing bacteria and reducing inflammation.}, journal = {Bioscience of microbiota, food and health}, volume = {45}, number = {2}, pages = {139-148}, pmid = {42006125}, issn = {2186-6953}, abstract = {Bifidobacterium animalis subsp. lactis GCL2505 (GCL2505), commercially known as the "BifiX" strain in Japan, reaches the intestine alive, proliferates after a single intake, and is associated with several positive health effects. A randomized, double-blind, placebo-controlled, parallel-group clinical trial of this probiotic strain in combination with inulin (a prebiotic) reported an improvement of cognitive function in the elderly. In the present study, a follow-up analysis was performed to elucidate the underlying mechanism, using a multi-omics approach that integrated a high-throughput assay of blood inflammatory markers and metagenomic analysis of the fecal bacterial composition. After probiotic and prebiotic administration, short-chain fatty acid producers such as Faecalibacterium and Bifidobacterium were increased in the gut. Moreover, in the subgroup with greater improvement in cognitive function scores, the levels of inflammatory markers were decreased. Subgroup analysis revealed that the improvement of cognitive function was associated with a reduction of inflammation and an increase of Faecalibacterium. These results suggest that GCL2505 and inulin can improve cognitive function by alleviating inflammation via an increase of short-chain fatty acid-producing bacteria, which appears to elevate levels of short-chain fatty acids, particularly acetate and butyrate, in the gut. The present results contribute to a deeper comprehension of the gut-brain axis and propose new avenues for potential therapeutic intervention in cognitive disorders.}, }
@article {pmid42006869, year = {2026}, author = {Li, Y and Zhu, H and Zhan, Z and Li, G and Zhou, Q and Zheng, C and Huang, F}, title = {Clinical features and prognostic factors of Chlamydia psittaci pneumonia: a retrospective study.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1804156}, pmid = {42006869}, issn = {2296-858X}, abstract = {BACKGROUND: Chlamydia psittaci pneumonia (CPP) is frequently misdiagnosed and can progress to severe illness. A deeper understanding of its clinical and imaging features is crucial for early detection and effective treatment.<br><br>METHODS: This retrospective study analyzed 74 patients diagnosed with CPP via metagenomic (mNGS) and targeted next-generation sequencing (tNGS) between January 2022 and September 2025. Patients were categorized into severe (n&#x202f;=&#x202f;21) and non-severe (n&#x202f;=&#x202f;53) groups based on established criteria for severe community-acquired pneumonia. Data on demographics, clinical manifestations, laboratory findings, and imaging characteristics were collected and compared.<br><br>RESULTS: The cohort had a median age of 60&#x202f;years, with a male predominance (62.2%). A history of poultry/bird exposure was reported by 87.8% of participants. Common symptoms included fever (94.6%), cough (63.5%), and fatigue (29.7%), with no significant differences between groups. Hospitalization was significantly longer in the severe group (12.95&#x202f;&#xb1;&#x202f;6.08&#x202f;days) than in the non-severe group (8.13&#x202f;&#xb1;&#x202f;3.30&#x202f;days) (p&#x202f;<&#x202f;0.001). Chest CT revealed consolidation and ground-glass opacities in all patients. Pleural effusion was significantly more common in the severe group (76.2% vs. 45.3%, p&#x202f;=&#x202f;0.016), as was bilateral lung involvement (52.4% vs. 22.6%, p&#x202f;=&#x202f;0.013). Multivariate analysis identified elevated D-dimer (OR&#x202f;=&#x202f;2.737, p&#x202f;=&#x202f;0.007) and reduced lymphocyte percentage (L%) (OR&#x202f;=&#x202f;0.813, p&#x202f;=&#x202f;0.026) as independent predictors of severe disease. ROC curve analysis showed an AUC of 0.765 for D-dimer and 0.739 for L% reduction. Following tetracycline or quinolone therapy, 94.6% of patients recovered, with an overall mortality rate of 5.4%.<br><br>CONCLUSION: Severe CPP is associated with prolonged hospitalization, bilateral pulmonary infiltrates, and pleural effusion. D-dimer and lymphocyte percentage are valuable prognostic indicators for disease severity. Early targeted antibiotic therapy is effective, but timely respiratory support is critical for severe cases.}, }
@article {pmid42006894, year = {2026}, author = {Cui, T and Huang, M}, title = {Case Report: A case of refractory tuberculous peritonitis mimicking and complicating suspected encapsulating peritoneal sclerosis in a long-term peritoneal dialysis patient.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1777805}, pmid = {42006894}, issn = {2296-858X}, abstract = {BACKGROUND: Tuberculous peritonitis (TBP) is a rare but severe complication in peritoneal dialysis (PD) patients, often presenting with non-specific symptoms. Its diagnosis is particularly challenging in patients with pre-existing or co-existing peritoneal pathology, such as changes suggestive of encapsulating peritoneal sclerosis (EPS).<br><br>CASE PRESENTATION: A 59-year-old male on PD for 14&#x202f;years with no prior history of peritonitis presented with recurrent abdominal pain, fever, and cloudy effluent, following a recent episode of Staphylococcus caprae peritonitis. Initial contrast-enhanced computed tomography (CT) revealed diffuse peritoneal thickening, omental "caking," and localized ascites, raising strong suspicion for EPS. However, the patient's condition relapsed despite broad-spectrum antibiotic therapy. Metagenomic next-generation sequencing (mNGS) of peritoneal fluid definitively identified Mycobacterium tuberculosis complex. The diagnosis was thus revised to TBP manifesting with secondary peritoneal inflammatory changes mimicking EPS. Management involved laparoscopic PD catheter removal, transition to hemodialysis, and initiation of a renal-adjusted anti-tuberculous regimen (levofloxacin and linezolid), leading to gradual clinical and biochemical improvement.<br><br>CONCLUSION: This case highlights that TBP can clinically and radiologically mimic EPS in long-term PD patients, leading to diagnostic delay. High clinical suspicion and the utilization of advanced molecular diagnostics like mNGS are crucial for accurate diagnosis. Catheter removal combined with appropriate anti-tuberculous therapy forms the cornerstone of management in such complex scenarios.}, }
@article {pmid42007374, year = {2026}, author = {Jeong, UJ and Ali, M and Park, YJ and You, JS and Yoon, SS}, title = {A responder-informed gut microbial consortium enhances anti-PD-1 efficacy in a mouse cancer model.}, journal = {Microbiome research reports}, volume = {5}, number = {1}, pages = {2}, pmid = {42007374}, issn = {2771-5965}, abstract = {Aim: Immune checkpoint inhibitors (ICIs), particularly anti-programmed cell death protein 1 (PD-1) therapy, have improved cancer treatment outcomes, yet durable benefit is achieved in only a subset of patients. Growing evidence implicates the gut microbiome as a modulator of ICI responsiveness, but defined and experimentally validated microbial strategies remain limited. This study aimed to identify responder-associated gut microbes and to evaluate a defined bacterial consortium for enhancing PD-1 blockade efficacy. Methods: Publicly available shotgun metagenomic datasets from anti-PD-1-treated cancer patients were re-analyzed to compare gut microbiome profiles between responders and non-responders. Bacterial taxa reproducibly enriched in responders were selected based on consistency across analytical criteria and cultivability and assembled into a four-strain consortium (UJ-04). The immune-adjuvant potential of UJ-04, alone or combined with anti-PD-1 therapy, was evaluated in a B16-F10 melanoma mouse model, with tumor growth and immune responses assessed by flow cytometry. Results: Metagenomic re-analysis identified four commensal bacterial taxa consistently enriched in responder patients, forming the defined UJ-04 consortium. While UJ-04 alone showed minimal antitumor activity, combination treatment with anti-PD-1 significantly enhanced tumor growth inhibition compared with anti-PD-1 monotherapy. This effect was accompanied by increased intratumoral CD8[+] T cells and natural killer cells, with concordant immune trends in peripheral compartments. Conclusion: A responder-informed, defined microbial consortium functionally translates clinical microbiome associations into in vivo validation and enhances PD-1 blockade efficacy by modulating host antitumor immunity. These findings support defined bacterial consortia as microbiome-based immunomodulatory adjuncts for immunotherapy.}, }
@article {pmid42007699, year = {2026}, author = {Carroll, AC and Hinz, A and Hicks, AMA and Khov, E and Van Bakel, T and Doukhanine, E and Fralick, M and Nott, C and Kassen, R and Thampi, N and Hug, LA and MacFadden, D and Wong, A}, title = {Targeted metatranscriptomic detection of viruses from floors for simultaneous evaluation of respiratory disease burden and viral variant identification.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0008626}, doi = {10.1128/msphere.00086-26}, pmid = {42007699}, issn = {2379-5042}, abstract = {UNLABELLED: Built environment surveillance is a proven approach for tracking disease burden of some viruses within hospitals and long-term care facilities. However, studies in clinical settings are lacking for simultaneously surveying targets in a built environment using targeted metatranscriptomics. We swabbed six discrete floor locations within an acute care center's emergency department (ED) in Ottawa, Canada, and sequenced cDNA using a 132 viral taxa panel, identifying viral burden across sampling locations and time. The determined SARS-CoV-2 variant profile across time was matched to provincial variant prevalence. The correlation between metatranscriptomic read abundances and reported cases of influenza A, SARS-CoV-2, and RSV was assessed. We quantified these via qPCR and assessed the correlation of Cq versus metatranscriptomic reads for these viruses. We sequenced a median of 1,302,882 reads per sample from 38 floor swabs collected during peak respiratory viral season (November 2022-February 2023). Diversity of viral communities varied significantly across locations in the ED. SARS-CoV-2 variant abundance shifts matched the changing infection landscape concurrently reported in Ontario. Relationships between targeted metatranscriptomic read ratios and clinical burden were not statistically significant, although we found modest correspondence between qPCR signal and read depth for RSV and SARS-CoV-2. This approach characterized the viral communities and the within-species diversity within an ED. Correlating sequencing-derived data with disease burden for three key respiratory viruses was inconsistent, with the exception of significant correlation between metatranscriptomic reads and Cq data for SARS-CoV-2. We were able to recover the distribution of clinically reported SARS-CoV-2 variants from the floor swab data.<br><br>IMPORTANCE: Environmental surveillance is useful for estimating the disease burden for certain viruses. qPCR is commonly used for surveillance of wastewater and built environments, including during the COVID-19 pandemic, but single, multiplexed reaction targets are limited. Targeted metagenomic or metatranscriptomic approaches can accurately quantify microbial populations of interest in an environment, reduce off-target sequencing, and evaluate a broader number of targets than qPCR assays. Here, we assessed the capacity of a targeted viral metatranscriptomic panel to correlate viral abundance in the hospital built environment with key pathogens of interest, including influenza A, RSV, and SARS-CoV-2. Our results suggest that targeted metatranscriptomics may identify viral communities in healthcare facilities, including strain-level detection capability. However, this approach must be validated for its effectiveness in viral surveillance that accurately reflects disease burden. This work contributes to a growing toolkit for pathogen surveillance, a critical endeavor to safeguard against outbreaks of known and emerging pathogens.}, }
@article {pmid42007817, year = {2026}, author = {Chen, M and Kang, Y and Cheng, M and Li, X and Keng, J and Zhao, P and Sui, H and Dong, J and Sun, L and Liu, B and Hu, Y and Jiang, J and Yang, F}, title = {Co-circulation of multiple arboviruses in acute febrile patients in Yunnan, China, identified by metagenomic sequencing.}, journal = {Journal of clinical microbiology}, volume = {}, number = {}, pages = {e0167025}, doi = {10.1128/jcm.01670-25}, pmid = {42007817}, issn = {1098-660X}, abstract = {UNLABELLED: Arboviruses such as dengue virus (DENV), chikungunya virus (CHIKV), and Zika virus (ZIKV) are transmitted by Aedes mosquitoes and mainly circulate in tropical and subtropical regions. With global warming, their geographic range is expanding, increasing their threat to public health. Yunnan Province, China, bordering Southeast Asia, is a hotspot for viral importation due to intensive cross-border mobility. However, systematic surveillance for these arboviruses among acute febrile patients remains insufficient. We performed metagenomic sequencing on serum specimens from 990 acute febrile patients at the China-Myanmar border between 2017 and 2023. The pathogens were confirmed by PCR and viral isolation. Phylogenetic and spatiotemporal analyses were used to infer viral origins and transmission dynamics. In this study, a CHIKV outbreak was confirmed in 2019, with strains closely related to those from Myanmar and Thailand. Four DENV serotypes 1-4 were identified, with the predominant serotype varying annually. ZIKV was detected and closely related to strains from Myanmar. Co-infections were identified, including one case each of CHIKV with DENV-1, CHIKV with DENV-3, CHIKV with ZIKV, and DENV-1 with DENV-2. Bayesian spatiotemporal analysis of CHIKV reconstructed global transmission routes, indicating that the 2019 outbreak in China likely originated in India and spread sequentially through Bangladesh, Thailand, and Myanmar. In addition, we also detected enterovirus, hepatitis virus, Saffold virus, and rhinovirus. This study reveals a comprehensive spectrum of pathogens, including the co-circulation of DENV, CHIKV, and ZIKV, and underscores the potential risk of arbovirus importation into China, highlighting the need for strengthened border surveillance.<br><br>IMPORTANCE: Arboviruses, including dengue virus (DENV), chikungunya virus (CHIKV), and Zika virus (ZIKV), are expanding their range and threatening global public health. Yunnan, situated along the China-Southeast Asia border, is highly susceptible to viral introduction. By applying viral metagenomic sequencing to acute febrile patients, this study uncovered a comprehensive spectrum of pathogens and the co-circulation of DENV, CHIKV, and ZIKV. Phylogenetic analyses revealed that arboviruses were closely related to strains from Myanmar and Thailand, indicating possible frequent cross-border viral introductions. Meanwhile, we reconstructed the global transmission pathways of CHIKV through Bayesian spatiotemporal analysis, providing valuable insights for regional prevention and control of arboviruses. These findings demonstrate that Yunnan serves as a critical interface for viral importation and underscore the urgent need to strengthen border surveillance and early warning systems to mitigate the spread of arboviruses.}, }
@article {pmid42008001, year = {2026}, author = {Hu, C and Yu, J and Chu, T and Wang, Q and Chen, L and Yu, Y and Wang, Y}, title = {Uncovering novel virophages and giant viruses in high-altitude Lake Namtso: diversity and evolution of host-virus-virophage tripartite interaction systems.}, journal = {Archives of microbiology}, volume = {208}, number = {7}, pages = {}, pmid = {42008001}, issn = {1432-072X}, }
@article {pmid42008944, year = {2026}, author = {Liu, J and Li, Y and Wang, H and Wang, L and Wu, G and Zhao, B}, title = {Biphasic dynamics of N-nitrosodimethylamine precursors in effluent-receiving rivers: Insights from multi-omics into microbial nitrogen metabolism regulation.}, journal = {Water research}, volume = {300}, number = {}, pages = {125933}, doi = {10.1016/j.watres.2026.125933}, pmid = {42008944}, issn = {1879-2448}, abstract = {Wastewater effluent introduces substantial dissolved organic nitrogen into rivers, thereby increasing the risk of carcinogenic N-nitrosodimethylamine (NDMA) formation from its precursors. However, the microbial metabolic mechanisms governing dynamics of these precursors along receiving rivers remain unclear. Here, through a 21-day time-series incubation of sediments from upstream, outfall, and downstream areas of a representative wastewater treatment plant, combined with multi-omics analyses i.e., 16S rRNA gene sequencing, metagenomics, and metabolomics, the transformation of precursors and microbially mediated nitrogen metabolism were elucidated. A biphasic pattern of NDMA precursors measured as formation potential (FP) was observed during incubation, characterized by a rapid formation from days 0 to 3 followed by a remarkable degradation until day 7 and subsequent stabilization. Nitrate peaked paralleling NDMA FP, with nitrite accumulation following the onset of precursors degradation. Multi-omics analysis revealed that this turnover was driven by strong functional coupling between key nitrogen-cycling taxa and specific metabolites, particularly short-chain peptides. Community structure in the early phase was dominated by r‑strategists e.g., Bacillota, which promoted organic nitrogen degradation and nitrification, resulting in the accumulation of NDMA precursors. As anoxia developed, the community shifted toward K‑strategists such as Pseudomonadota and Chloroflexota, which likely degraded precursors through co-metabolism and consumption of ammonia source. Metabolomics revealed the conversion of precursors into short-chain peptides and amino acid analogues. Notably, effluent exposure established a functionally specialized legacy effect in downstream sediments, stabilizing into a microbial metabolic hotspot with a peak NDMA FP of 1285 ng/L, 158% and 80.7% higher than those in the upstream and outfall area, respectively. This study establishes a mechanistic framework for evaluating the transformation and risk of NDMA precursors in river systems, with direct implications for monitoring strategies and designing of the wastewater outfall location.}, }
@article {pmid42010118, year = {2026}, author = {Menozzi, E and Ren, Y and Geiger, M and Macnaughtan, J and Avenali, M and Toffoli, M and Gilles, M and Calabrese, R and Mitrotti, P and Gallo, L and Famechon, A and Del Pozo, SL and Mezabrovschi, R and Koletsi, S and Loefflad, N and Yalkic, S and Limbachiya, N and Clasen, F and Yildirim, S and Shoaie, S and Blottière, H and Morabito, C and David, A and Quinquis, B and Pons, N and Le Chatelier, E and Valzania, F and Cavallieri, F and Fioravanti, V and Toschi, G and Blandini, F and Almeida, M and Ehrlich, SD and Meslier, V and Schapira, AHV}, title = {Microbiome signature of Parkinson's disease in healthy and genetically at-risk individuals.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {42010118}, issn = {1546-170X}, support = {MR/T046007/1//EU Joint Programme - Neurodegenerative Disease Research (Programi i P&#xeb;rbashk&#xeb;t i BE-s&#xeb; p&#xeb;r K&#xeb;rkimet mbi S&#xeb;mundjet Neuro-degjeneruese)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; ASAP-000420//Michael J. Fox Foundation for Parkinson's Research (Michael J. Fox Foundation)/ ; }, abstract = {Parkinson's disease (PD) is a major cause of disability. GBA1 variants are the most common genetic risk factor for PD and increase the risk up to 30-fold. Why only approximately 20% of GBA1 variant carriers develop PD remains unknown. Here, by combining clinical and fecal metagenomics data from 271 patients with PD, from 43 carriers of GBA1 variants not manifesting PD symptoms (GBA-NMC) and from 150 healthy controls, and using an innovative microbiome analysis, combining differential abundance of species and coherence of differential abundance variation between the groups as assessed by Cliff's delta (δ), we show that the composition of a large component of the gut microbiome (approximately 25%) in GBA-NMC is intermediate between healthy controls and patients with PD. This component is strongly correlated with disease progression in patients and prodromal symptoms suggestive of future development of PD in both GBA-NMC and healthy individuals. We found microbiome alterations similar to those described here in three independent cohorts from the United States, Korea and Turkey, totaling 638 patients with PD and 319 healthy controls, and we conclude that gut microbiome alterations can identify both genetically and non-genetically at-risk individuals in the general population who may be progressing toward PD, thus serving as an early marker of disease development in the premanifest phase.}, }
@article {pmid42010313, year = {2026}, author = {Qi, YL and Zou, DY and Hou, JJ and Zhang, ZF and Du, H and Feng, XY and Pan, YP and Zhang, CJ and Liu, Y and Li, M}, title = {A seven-year metagenomic genome catalogue of mangrove and mudflat sediments from the Futian Reserve, China.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07291-3}, pmid = {42010313}, issn = {2052-4463}, support = {42430707//National Natural Science Foundation of China/ ; 32370055//National Natural Science Foundation of China/ ; 32225003, 32393970, 92251306//National Natural Science Foundation of China/ ; JCYJ20230808105711023//General Program supported by Shenzhen Natural Science Foundation in Basic Research Fund/ ; 2023B0303000017//Guangdong Major Project of Basic and Applied Basic Research/ ; 2022B002//Shenzhen University 2035 Program for Excellent Research/ ; 2024T001//Shenzhen University Special Funding Initiative/ ; }, abstract = {Mangrove wetlands are ecologically and biogeochemically important "blue-carbon" ecosystems, yet long-term genomic resources for their microbial communities remain scarce. Here we present a seven-year (2017-2023) metagenomic dataset from the Futian Mangrove National Nature Reserve, China, comprising 65 sediment samples collected from paired habitats (mangrove forest and adjacent mudflat) across multiple depths. Sequencing produced ~5.3 Tbp of data, from which 6,922 metagenome-assembled genomes (MAGs) were reconstructed and dereplicated into 3,404 representative genomes (336 Archaea and 3,068 Bacteria). Quality control ensured that all genomes achieved medium- or high-quality standards, with assembly statistics and read recruitment rates supporting robustness and representativeness. Taxonomic annotation revealed broad phylogenetic diversity spanning 13 archaeal and 69 bacterial phyla, with many lineages lacking formal nomenclature and representing potential novel taxa. All raw sequences, genome assemblies, and detailed metadata have been deposited in public repositories, providing a standardized, time-resolved resource for comparative genomics, microbial ecology, and ecosystem restoration studies in coastal wetlands.}, }
@article {pmid42010457, year = {2026}, author = {Guo, J and Liang, C and Cairang, L and Si, L and Yan, J and Liu, D}, title = {Metagenomics reveals gut microbial differences and ecological adaptation in plateau zokor (Eospalax baileyi) populations.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05069-6}, pmid = {42010457}, issn = {1471-2180}, support = {LHZX-2023-02//Sanjiangyuan National Park Joint Grant from the Chinese Academy of Sciences and the People's Government of Qinghai Province/ ; }, }
@article {pmid42010710, year = {2026}, author = {Long, L and An, Y and Zhu, LT and Xu, XL and Lin, JJ and Xu, WJ and Chen, JY and Liu, FY and Liu, XY and Huang, Q}, title = {Unveiling microbial risks in Chinese household dust: a comprehensive analysis from absolute abundance to virulence unit.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02353-5}, pmid = {42010710}, issn = {2049-2618}, support = {(42177362)//National Natural Science Foundation of China/ ; (2025J02030, 2025J01256)//Fujian Provincial Natural Science Foundation of China/ ; (NO. NBSDC-DB-21)//National Basic Science Data Center "Environment Health DataBase"/ ; }, abstract = {BACKGROUND: People spend the majority of their lives indoors, yet the risk and virulence potential of household microbiota remain largely unexplored, particularly in developing countries.<br><br>RESULTS: Here, we conducted a nationwide survey on both dust samples and health information across 118 Chinese households. The microbiota composition and its functional units were analyzed using absolute 16S rRNA/ITS sequencing, metagenomics, and metaproteomics. Cross-domain network analysis of the core microbial communities revealed robust co-occurrence patterns in household dust. The mean absolute abundance of potentially pathogenic bacteria and fungi in households was 2.39&#x2009;&#xd7;&#x2009;10[5] and 2.83&#x2009;&#xd7;&#x2009;10[6] DNA copies/g dust. The potentially pathogenic community was primarily influenced by latitude, relative humidity, and average temperature. Although total absolute abundance was substantially lower in urban areas, the relative abundance of potentially pathogenic bacteria was markedly higher compared to rural environments. While urban-rural differences existed, the underlying statistical drivers were the environmental variables. The absolute abundance of potential pathogens was significantly associated with the prevalence of rhinitis, wheeze, and dermatitis in 266 participants. Children were identified as the highest-risk group from inhalation exposure of average daily dose. A total of 170 bacterial, 223 fungal virulence factors (VFs), and 370 antibiotic resistance genes (ARGs) were detected in dust and dust extracellular vesicle (EV)-associated DNA. EV-associated cargoes contributed 47.13% to the bacterial VF profiles, 11.90% to fungal VF&#xa0;profiles, and 44.45% to ARG profiles. Metaproteomic analysis confirmed the presence of VF profiles in dust EVs, which was further verified by curated proteomics data from 35 household pathogens.<br><br>CONCLUSIONS: This study provides a comprehensive, quantitative framework linking indoor microbial exposure to health risks, highlighting EVs as a non-negligible, novel, extracellular mechanistic pathway for health impact in household environments. Video Abstract.}, }
@article {pmid42010711, year = {2026}, author = {You, C and Zhang, W and Guan, Y and Liang, Q and Nong, C and Yang, T and Li, M and Banerjee, S and Zhou, X and Wang, X and Xu, Y and Shen, Q and Wei, Z}, title = {Metabolome-driven rhizosphere microbiome assembly determining the health of medicinal herb (Angelica sinensis) against root rot.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02393-x}, pmid = {42010711}, issn = {2049-2618}, support = {2022YFC3501501//National Key Research and Development Program of China/ ; KJYQ2025034, KJYQ2024039//Fundamental Research Funds for the Central Universities/ ; BK20240194//the Natural Science Foundation of Jiangsu Province/ ; }, abstract = {BACKGROUND: The rhizosphere-associated microbiota plays a crucial role in plant responses to disease stress. Plant secondary metabolites are recognized as crucial mediators in the assembly of rhizosphere microbial communities, particularly by enhancing the colonization of beneficial microorganisms. Despite this recognized importance, a deeper understanding of how such metabolome-driven microbiome assembly specifically determines plant resistance against soil-borne diseases is still lacking.<br><br>RESULTS: Here, we focused on the widely planted medicinal plant Angelica sinensis and demonstrated that root rot-diseased rhizosphere soils (DRS) exhibited a higher relative abundance of Fusarium and a lower relative abundance of Streptomyces compared to healthy rhizosphere soils (HRS). Shotgun metagenomic sequencing revealed that metabolism-associated genes, particularly those related to steroid degradation, are significantly enriched in HRS samples. Subsequent genome and functional gene analysis of Streptomyces revealed that the steroid degradation-related genes are associated with rhizosphere colonization in hosts. Rhizosphere Streptomyces S15 directly antagonized Fusarium and enhanced the root resistance of A. sinensis. Comparative metabolomics showed that A. sinensis plants from HRS secreted more lipid and lipid-like molecules than those from DRS, especially sterol lipids and long-chain fatty acids, which promoted the growth of Streptomyces S15 isolates. Transcriptome analysis validated that the lipid hormones are essential for sporulation, biofilm formation, and streptomycin biosynthesis of S15 strain. Finally, exogenous application of synbiotics (lipid prebiotics and S15) to A. sinensis resulted in the enrichment of S15-homologous Streptomyces amplicon sequence variant (ASV), further establishing beneficial bacterial communities in Fusarium-stressed rhizospheres.<br><br>CONCLUSIONS: Our study proposes that A. sinensis recruits steroid-metabolizing Streptomyces species by exuding key lipid compounds (i.e., methyl jasmonate and brassinolide) to combat Fusarium root rot. This study provides novel insights into using functional synbiotics as a promising strategy for manipulating plant-microbiome interactions to promote sustainable agriculture. Video Abstract.}, }
@article {pmid42010713, year = {2026}, author = {Tang, J and Wang, L and Yang, Z and Song, Y and Wu, S and Liang, Q and Li, Z and Zhou, S and Xiong, H and Chen, D and Li, J and Li, F}, title = {Gut microbiota induces dysspermatogenesis via microbial-derived phenylacetylglycine in Ggt1-deficient mice.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02401-0}, pmid = {42010713}, issn = {2049-2618}, support = {32272874//National Natural Science Foundation of China/ ; 2021YFF1000601//National Key R&amp;D Program of China/ ; 2662025DKPY008//Fundamental Research Funds for the Central Universities/ ; }, abstract = {BACKGROUND: Male infertility represents a global health concern, with emerging evidence linking gut microbiota dysbiosis to dysspermatogenesis and subfertility. However, the molecular mediators and regulatory mechanisms by which gut microbiota influences testicular functions remain poorly defined.<br><br>RESULTS: This study demonstrates that male gamma-glutamyl transferase 1-deletion (Ggt1[-/-]) mice exhibits infertility phenotypes, including reduced germ and testicular Leydig cell numbers, increased rates of abnormal sperm, and altered reproductive hormone levels. Metabolomic analysis reveals elevated levels of the gut microbial-derived metabolite phenylacetylglycine (PAGly) in serum and testes of Ggt1[-/-] mice, with in vivo injection experiments indicating its role in impairing spermatogenesis. Moreover, blocking PAGly effectively restores the impaired spermatogenesis in Ggt1[-/-] mice. Fecal metagenomic and metabolomic analyses show that gut microbiota in Ggt1[-/-] mice induces elevation of phenylacetic acid, a precursor metabolite of PAGly. Strikingly, fecal microbiota transplantation from Ggt1[-/-] mice (Ggt1[-/-]-FMT) recapitulates the infertility phenotypes including reduced germ cells and increased rates of abnormal sperm. Mechanistically, integrated CUT&amp;Tag and ATAC-Seq analyses reveal that transcription factor STAT5B occupies regulatory elements near Klk1b transcription start sites&#xa0;(TSS), confirming that transcription factor STAT5B directly regulates Klk1b gene transcription. Concretely, PAGly activates &#x3b2;2-adrenergic receptor (&#x3b2;2AR) on Leydig cells, triggering STAT3 phosphorylation, subsequent SOCS3 upregulation, and STAT5B phosphorylation suppression; p-STAT5B with transcriptional activation function is reduced, then Klk1b gene transcription is compromised, and therefore spermatogenesis is disrupted.<br><br>CONCLUSION: Ggt1 deletion-induced gut microbiota dysbiosis disrupts spermatogenesis via &#x3b2;2AR-STAT3-SOCS3-STAT5B-Klk1bs signaling pathway. Specifically, PAGly-induced &#x3b2;2AR activation promotes STAT3 phosphorylation, which induces SOCS3 to suppress p-STAT5B&#xa0;dependent Klk1bs transcription. This mechanism underscores the critical role of gut-derived metabolites in regulating testicular function and identifies potential targets for microbiota-modulated male infertility. Video Abstract.}, }
@article {pmid42010746, year = {2026}, author = {Yun, CS and Kim, JK and Kwon, H and Her, M and Moon, JS}, title = {Metagenomic 16S rRNA amplicon and shotgun sequencing in investigation of granulomatous lesions in layer chickens: a case report.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00565-6}, pmid = {42010746}, issn = {2524-4671}, }
@article {pmid42010766, year = {2026}, author = {Combs, D and Landeros, K and Garza, K and Azari, H and Abdelrahman, M and Albracht-Schulte, K}, title = {Exercise intensity as a modulator of gut microbiota and host metabolic health in obesity.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2661415}, doi = {10.1080/19490976.2026.2661415}, pmid = {42010766}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Obesity/microbiology/metabolism ; Animals ; *Exercise/physiology ; Bacteria/classification/genetics/metabolism/isolation &amp; purification ; Physical Conditioning, Animal ; Fatty Acids, Volatile/metabolism ; }, abstract = {The gut microbiome is shaped by complex interactions among host, environmental, and lifestyle factors, with exercise emerging as a reported modulator. Growing evidence suggests that exercise intensity, ranging from low to high, can differentially influence gut microbial composition, diversity, and functional outputs relevant to metabolic health. This narrative review synthesizes current findings examining intensity-dependent microbial adaptations in the context of obesity. Across animal models (n = 17) and limited human studies (n = 5), moderate-intensity training (MIT) and high-intensity interval training (HIIT) produce the most consistent microbiota shifts, while low-intensity training (LIT) exerts minimal effects. Reported taxa associated with beneficial outcomes consistent across animal and human investigations include Akkermansia (G), and Christensenellaceae (F). Mechanistically, intensity-dependent alterations in microbial communities may influence obesity-related pathways through modulation of short-chain fatty acid (SCFA) and bile acid metabolism, gut barrier integrity, endotoxemia, and inflammatory signaling. HIIT and MIT are linked to improved expression of tight junction proteins (ZO-1, Claudin, Occludin), reducing circulating lipopolysaccharide (LPS), and increasing SCFA-producing taxa; thus, supporting a role for the gut microbiome in mediating exercise-induced metabolic benefits. However, inconsistent findings between species, interindividual variability, and considerable heterogeneity in exercise intervention duration across both animal (4-16 weeks) and human (3-12 weeks) studies, as well as limited longitudinal human studies, underscore the need for deeper mechanistic investigations. Future research should employ metagenomic and metatranscriptomic profiling, integrate sex- and diet-stratified longitudinal designs, and clarify causal links between exercise-responsive taxa, microbial metabolites, and host physiology. Collectively, these data highlight exercise intensity as a key determinant of gut microbiome dynamics and reinforce the need for integrative, translational approaches to define its therapeutic potential for obesity and metabolic disorders.}, }
@article {pmid42010993, year = {2026}, author = {Wu, Y and Guo, X and Wang, X and Guo, F}, title = {Fatal Non-Hepatic Hyperammonemia Post-Glofitamab: Ureaplasma and Genetic Susceptibility: A Case Report.}, journal = {Immunity, inflammation and disease}, volume = {14}, number = {4}, pages = {e70443}, doi = {10.1002/iid3.70443}, pmid = {42010993}, issn = {2050-4527}, mesh = {Humans ; Male ; *Hyperammonemia/etiology/chemically induced/diagnosis ; Middle Aged ; Fatal Outcome ; Genetic Predisposition to Disease ; *Antibodies, Bispecific/adverse effects/therapeutic use ; *Lymphoma, Large B-Cell, Diffuse/drug therapy ; *Ureaplasma Infections/complications ; *Ureaplasma ; }, abstract = {BACKGROUND: Although primarily reported in solid organ transplant recipients and patients undergoing chimeric antigen receptor T-cell immunotherapy (CAR-T), non-hepatic hyperammonemia (NHHA) is a rare but lethal complication in the broader context of post- chemo-immunotherapy hematologic malignancies. It often presents with unexplained encephalopathy that mimics primary central nervous system (CNS) progression, leading to diagnostic delays. With the expanding use of bispecific antibodies (e.g., glofitamab), the etiology of NHHA, particularly the complex interplay between opportunistic infections and potential metabolic susceptibility, remains poorly understood.<br><br>CASE PRESENTATION: We report a fatal case of NHHA in a 58-year-old male with diffuse large B-cell lymphoma (DLBCL) following glofitamab-based chemo-immunotherapy. The patient developed sudden onset altered mental status with extreme hyperammonemia (peak blood ammonia 638.9&#x2009;&#xb5;mol/L) despite preserved liver function. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified Ureaplasma urealyticum. Furthermore, post-mortem whole-exome sequencing (WES) identified a heterozygous variant of SLC25A13 (NM_014251.3:c.2&#x2009;T&#x2009;>&#x2009;C). As biochemical confirmation of citrin deficiency was not available, the clinical significance of this variant remains uncertain, though it may represent a contributory metabolic susceptibility factor. Despite aggressive ammonia-lowering strategies, including continuous renal replacement therapy (CRRT) and targeted antibiotics, the patient succumbed to fulminant cerebral edema.<br><br>CONCLUSION: This case highlights the Ureaplasma urealyticum infection as a critical precipitant of fatal NHHA following glofitamab therapy, occurring in the background of possible genetic metabolic susceptibility (an unverified heterozygous SLC25A13 variant of uncertain functional significance). These findings underscore the critical need for early blood ammonia monitoring and rapid mNGS screening in immunocompromised patients with unexplained encephalopathy. We propose a structured diagnostic algorithm to expedite the recognition and management of this reversible yet life-threatening condition.}, }
@article {pmid42011017, year = {2026}, author = {Sadia, H and Amin, A and Ahmed, I}, title = {Metagenomic and Phenotypic Insights Into Biofilm-Forming Pathogens in Patients With Nosocomial Sepsis.}, journal = {BioMed research international}, volume = {2026}, number = {1}, pages = {e8989667}, pmid = {42011017}, issn = {2314-6141}, mesh = {*Biofilms/growth &amp; development ; Humans ; *Sepsis/microbiology/genetics ; *Cross Infection/microbiology/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Male ; Female ; Phenotype ; }, abstract = {Biofilm-related infections significantly contribute to bacterial diseases, with estimates suggesting that at least 80% of such infections are associated with biofilms. These infections often involve opportunistic pathogens, which not only influence the type of infection but also impact the microenvironment by interacting with other polymicrobial pathogens, thereby altering microbial diversity within the infection site. The present study was designed to assess potential changes in bacterial communities across various infection types. The 50 samples were collected and pooled from different anatomical locations: II-H1 (calf), ul-H2 (thighs), ft-H3 (upper leg), ct-H4 (chest), and Ca-H5 (catheter). The 16S rDNA sequencing was performed on 10 representative samples using the Sanger method to identify bacterial taxa, whereas the metagenomic analysis was conducted on the Illumina MiSeq platform (Illumina, Inc., San Diego, California). Sanger sequencing identifying several bacterial strains including Bacterium MS-AsIII-61, Bacterium HB33-1, Mammaliicoccus sciuri SSB38, multiple Staphylococcus species (S. aureus DA101 and S8, Staphylococcus sp. C0021-01R and TSA25S, S. cohnii FC2265, and S. saprophyticus A), and Enterobacter hormaechei D15. The metagenomics analysis revealed variations and diversity in the different location across the organ by relative abundance of 5 bacterial phyla and 38 species. The Proteobacteria phylum was the most abundant phylum across all sites, with the highest prevalence observed in Ca-H5, followed by ul-H2, ct-H4, II-H1, and ft-H3 in the decreasing order. In contrast, the Bacteroidetes phylum exhibited the highest abundance in ft-H3. Catheter-associated infections (Ca-H5 site) show a homogeneous ARG profile, dominated by genes supporting biofilm formation and persistence. MSA samples reflect diversity in methicillin and multidrug resistance genes, consistent with surgical-site and opportunistic infections. Trypto samples may represent an environmental or experimental condition leading to alternative ARG expression, highlighting site- or condition-specific variations. The different virulence factor responsible for the boost in the establishment of biofilms in these pathogens includes, surface adhesion proteins, increasing resilience to environmental, efflux pumps, quorum-sensing regulators, stresses, and antibiotic treatments. The study demonstrates the dynamic nature and impact of biofilm-related infections at anatomical sites. It also focused on biofilm-associated infections at surgical sites, their progression into chronic conditions, and the corresponding treatment patterns. The integration of metagenomic analysis with phenotypic studies provided deeper insights into the roles of key genes and their mechanisms in biofilm formation.}, }
@article {pmid42011181, year = {2026}, author = {Li, Z and Zhang, Y and Xu, H and Wang, D and Yuan, L and Su, N and Lu, H and Li, W}, title = {Prosthetic Joint Infection Caused by Staphylococcus argenteus: mNGS-Guided Diagnosis and Whole-Genome Characterization of an ST2250 Strain.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {594406}, pmid = {42011181}, issn = {1178-6973}, abstract = {BACKGROUND: Staphylococcus argenteus, a member of the Staphylococcus aureus complex, has increasingly been recognized as a human pathogen but is frequently misidentified as S. aureus in routine clinical laboratories. Reports of prosthetic joint infection (PJI) caused by this species remain rare.<br><br>METHODS: We describe a case of delayed-onset PJI in a 71-year-old woman following total knee arthroplasty. Repeated conventional cultures were negative after empirical vancomycin therapy. Metagenomic next-generation sequencing (mNGS) of wound exudate detected S. argenteus, which guided extended culture and subsequent isolation of low-abundance colonies. Species identification was confirmed by whole-genome sequencing (WGS), multilocus sequence typing (MLST), and reinterpretation of MALDI-TOF MS results. Antimicrobial susceptibility testing (AST) was performed and compared with WGS-based resistance prediction. Phylogenetic analysis was conducted using 452 publicly available S. argenteus genomes.<br><br>AIM: This study aimed to describe the clinical diagnosis, microbiological identification, and genomic characterization of a Staphylococcus argenteus strain causing prosthetic joint infection.<br><br>RESULTS: The isolate was identified as sequence type ST2250 and lacked the staphyloxanthin operon, consistent with the non-pigmented phenotype. WGS and phenotypic AST showed 100% concordance across 11 clinically relevant antibiotics. Phylogenomic analysis revealed that the strain clustered closely with Southeast Asian lineages. Following targeted therapy with intravenous vancomycin and surgical wound management, the patient showed rapid clinical improvement with resolution of local inflammation and complete wound healing.<br><br>CONCLUSION: This is the first confirmed case of S. argenteus PJI in Suzhou, China. The case highlights the diagnostic value of mNGS in culture-negative PJI, the importance of molecular tools for correctly differentiating S. argenteus from S. aureus, and the potential of WGS to support resistance prediction for rare staphylococcal pathogens.}, }
@article {pmid42011762, year = {2026}, author = {Lu, J and Wang, HN and Wang, CM and Xu, J and Ikechukwu, CK and Li, W and Ning, SY and Wu, P and Liu, YW and Shen, Q and Ji, LK and Wang, XC and Yang, SX and Zhou, CL and Wang, XL and Zhang, W and Shan, TL}, title = {Comparison of gut viromes across captive mammals reveals extensive genetic diversity in bacteriophage dark matter and mammalian viruses.}, journal = {Zoological research}, volume = {47}, number = {2}, pages = {606-620}, doi = {10.24272/j.issn.2095-8137.2025.134}, pmid = {42011762}, issn = {2095-8137}, mesh = {Animals ; *Mammals/virology ; *Animals, Zoo/virology ; *Bacteriophages/genetics ; *Genetic Variation ; *Virome/genetics ; Phylogeny ; *Viruses/genetics/classification ; *Gastrointestinal Microbiome ; }, abstract = {Comprehensive characterization of mammalian gut viromes is essential for early detection of commensal and potentially zoonotic viruses and for reducing the risk of cross-species transmission. Viral metagenomics was applied to profile gut viral communities from zoo mammals maintained across multiple zoological institutions in China. Viral communities differed markedly among host dietary guilds, with herbivores exhibiting the highest viral species diversity. In total, 1 027 viral sequences representing five major viral groups were recovered, including multiple mammal-associated astroviruses, picornaviruses, and parvoviruses with potential infectivity. Phylogenetic reconstruction based on viral hallmark genes demonstrated extensive genomic diversification across recovered lineages. Hosts for most microviruses were predicted to belong to the bacterial family Bacteroidaceae. In addition, 10 previously unreported crAss-like phages were identified in mammalian samples and showed close evolutionary relationships with proposed crAssphages from the human gut virome. Antibiotic resistance genes identified in the mammalian gut viromes primarily belonged to tetracyclines. These findings substantially expand current understanding of viral community structure in captive animals in China and provide a foundation for proactive surveillance frameworks targeting emerging mammalian viruses with zoonotic potential.}, }
@article {pmid42011768, year = {2026}, author = {Oba, S and Okuno, K and Watanabe, S and Yamamoto, Y and Takaoka, A and Hanaoka, M and Yamauchi, S and Kagawa, H and Tokunaga, M and Ban, D and Kinugasa, Y}, title = {Intratumoral fungal burden of Candida tropicalis as a novel prognostic biomarker for recurrence and mortality in colorectal cancer.}, journal = {Cancer}, volume = {132}, number = {8}, pages = {e70408}, doi = {10.1002/cncr.70408}, pmid = {42011768}, issn = {1097-0142}, support = {JP23K19499//Japan Society for the Promotion of Science/ ; JP24K18571//Japan Society for the Promotion of Science/ ; 2023DI008//Kobayashi Foundation for Cancer Research/ ; }, mesh = {Humans ; *Candida tropicalis/isolation &amp; purification/genetics ; Female ; Male ; *Colorectal Neoplasms/microbiology/mortality/pathology ; Prognosis ; Middle Aged ; *Neoplasm Recurrence, Local/microbiology/pathology/mortality ; Aged ; Biomarkers, Tumor ; Adult ; Disease-Free Survival ; }, abstract = {BACKGROUND: The crucial role of gut fungus dysbiosis in the carcinogenesis and progression of colorectal cancer (CRC) has recently garnered increasing attention. In this study, the potential role of Candida tropicalis, commensal gut fungi, in predicting CRC prognosis was investigated.<br><br>METHODS: A total of 304 frozen surgical cancer tissue specimens were obtained from patients with CRC and evaluated the intratumoral C. tropicalis burden using quantitative polymerase chain reaction assays. Mycobial composition and diversity analyses were performed by analyzing publicly available metagenomic datasets.<br><br>RESULTS: Metagenomic dataset analysis revealed significant differences in fungal composition and diversity of Candida species among adjacent normal and CRC tissues. The 5-year recurrence-free survival and disease-specific survival rates were significantly worse in patients with a high intratumoral C. tropicalis burden than in those with a low burden (78.0% vs. 86.6%; p&#xa0;=&#xa0;.03 and 88.9% vs. 98.0%; p&#xa0;<&#xa0;.01, respectively). Furthermore, multivariate Cox regression analysis revealed that increased intratumoral C. tropicalis burden was a significant independent predictor for recurrence-free survival (hazard ratio [HR]: 1.92; 95% CI, 1.08-3.44; p&#xa0;=&#xa0;.03) and disease-specific survival (HR: 4.29; 95% CI, 1.36-13.5; p&#xa0;=&#xa0;.03).<br><br>CONCLUSIONS: These results have demonstrated, possibly for the first time, the potential of intratumoral C. tropicalis burden as a novel prognostic biomarker for recurrence and mortality in patients with CRC.}, }
@article {pmid42012066, year = {2026}, author = {Guo, R and Gao, J and Zhang, C and Chang, Z and Sun, Y}, title = {Multi-Omics Analysis Reveals Coordinated Adaptations in Genes, Metabolism, and Gut Microbiota Underpinning Herbivory in Lordiphosa Flies.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.70110}, pmid = {42012066}, issn = {1749-4877}, support = {202401BC070011//Yunnan Fundamental Research Projects/ ; 32060112//Natural Science Foundation of China/ ; }, abstract = {Herbivorous insects are among the most ecologically successful animal groups. However, the adaptive mechanisms that allow them to exploit plant hosts, which are often nutrient-poor (low in simple sugars, high in structural carbohydrates) and defended by toxic secondary metabolites, are not fully resolved. Here, we investigated the evolutionary basis of herbivory in Lordiphosa clarofinis, a drosophilid species feeding on living plant tissues, using multi-omics approaches. Behavioral experiments revealed a strong oviposition preference for Galinsoga parviflora (a host rich in secondary metabolites), accompanied by elevated expression of chemosensory genes linked to host discrimination. Comparative genomic analyses revealed lineage-specific expansions of gene families associated with detoxification (e.g., cytochrome P450s) and carbohydrate metabolism, alongside positive selection on genes involved in fatty acid utilization and glycogen synthesis. Transcriptomic data showed differential expression of energy metabolism pathways in response to low-sugar plant diets, with upregulation of genes linked to lipid oxidation and gluconeogenesis. Metagenomic profiling of gut microbiota identified key taxa (e.g., Bacteroidetes) capable of degrading plant polysaccharides and synthesizing essential vitamins, potentially complementing host nutritional intake. Our results demonstrate that herbivory in L. clarofinis is associated with coordinated genomic, transcriptional, and microbial changes, rather than being attributable to a single adaptive mechanism. This study highlights how multi-level biological features covary with plant-based feeding and provides a framework for investigating the complex evolutionary and ecological correlates of herbivory in insects.}, }
@article {pmid42012165, year = {2026}, author = {Werner, A and Chibani, CM and Schmitz, RA}, title = {Navigating prokaryotic viral genome analysis from metagenomic data.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0124925}, doi = {10.1128/msystems.01249-25}, pmid = {42012165}, issn = {2379-5077}, abstract = {Viruses play crucial roles in microbial ecosystems, yet viromic analysis remains challenging due to the field's complexity and rapid evolution. This minireview supports non-specialists through the evolving landscape of viromics, focusing on the analysis of bacterial and archaeal DNA viruses from metagenomic data. We address major challenges, including viral diversity, methodological biases, and the overwhelming array of available tools and pipelines. While describing a typical viromic workflow, we provide users with background information for each of the steps from data acquisition, preprocessing, and quality control to viral characterization and common downstream analyses. The included references and resources will provide users with the information needed to confidently start their own virome analysis.}, }
@article {pmid42012213, year = {2026}, author = {Couto-Rodriguez, M and Danko, DC and Wells, HL and Rey, S and Jirau Serrano, X and Fidler, G and Papciak, J and Combs, PF and Plourde, A and Augenbraun, M and Mason, CE and Otto, C and O'Hara, NB and Nagy-Szakal, D}, title = {Analytical validation of a highly accurate and reliable next-generation sequencing-based urine assay.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0202625}, doi = {10.1128/spectrum.02026-25}, pmid = {42012213}, issn = {2165-0497}, abstract = {Urinary tract infections (UTIs) are diagnosed based on symptoms and confirmed by urine culture, despite its limitations in sensitivity. False-negative cultures can lead to inappropriate antimicrobial use or urosepsis in high-risk patients. Next-generation sequencing (NGS)-based metagenomics offers a comprehensive and precise alternative but is rarely applied clinically. We developed and validated BIOTIA-ID, a clinical-grade NGS-based diagnostic pipeline for pathogen detection in urine. Remnant clinical and spiked urine samples underwent extraction, metagenomic library preparation, and Illumina NextSeq 550 sequencing. We trained and applied a bioinformatic pipeline that uses machine learning to identify pathogens and resistance markers. BIOTIA-DX was intentionally designed and trained to increase stringency and reduce false positive detection of urogenital commensals or opportunistic microbes present at colonization levels. Internal controls ensured standardized, high-stringency results. The assay was validated on 1,470 urine specimens evaluating over 14.5k analytes. The clinical validation achieved a 97.2% sensitivity and 99.6% specificity with a limit of detection (LoD) of <15,000 CFU/mL for most bacterial species and <5,000 CFU/mL for fungal species. Discordant results were reconciled by target-specific qPCR or 16S Sanger sequencing, and 87% of the NGS results were concordant with the comparator. A subset of 332 clinical specimens was tested and validated for antimicrobial resistance (AMR). sul and blaSHV genes were commonly associated with Escherichia coli and Klebsiella pneumoniae, while cfxA was found in Prevotella and Pseudomonas spp. detected by BIOTIA-ID. Overall, these data demonstrate that BIOTIA-ID is a comprehensive, highly accurate end-to-end diagnostic assay with notable advantages over current culture-based diagnostics.IMPORTANCEUrinary tract infections (UTIs) are among the most common infections, yet current diagnostic methods, including urine culture, often fail to detect pathogens accurately, leading to delayed treatment and inappropriate antimicrobial use. Clinical metagenomics offers a powerful alternative, especially in complicated cases. BIOTIA-ID is a validated, clinical-grade next-generation sequencing (NGS)-based assay that provides highly accurate pathogen identification and antimicrobial resistance profiling. By incorporating machine learning and stringent quality controls, BIOTIA-ID minimizes false positives and enhances diagnostic precision. Our study demonstrates its superior performance over culture, with potential to improve UTI diagnostics, guide targeted therapy, and support antimicrobial stewardship. The implementation of urine metagenomic diagnostics could support recurrent and complicated UTI patient management, providing a more reliable alternative to traditional methods.}, }
@article {pmid42012671, year = {2026}, author = {Noronha, JM and Hudson, SB and Sharma, G and Ghadi, SC}, title = {Correction to: Metagenomic Insights into Viral Diversity from an Underexplored Khazan Creek and a Tropical Freshwater Lake.}, journal = {Current microbiology}, volume = {83}, number = {6}, pages = {}, doi = {10.1007/s00284-026-04870-w}, pmid = {42012671}, issn = {1432-0991}, }
@article {pmid42012901, year = {2026}, author = {Bellanco, A and Yépez-Notario, C and Lozano, M and Martínez-Cuesta, MC and Requena, T}, title = {Human Gut Microbiome Can Degrade the Sweetener Acesulfame K with Potential Damaging Effects in the Intestinal Barrier Function.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.5c16498}, pmid = {42012901}, issn = {1520-5118}, abstract = {Acesulfame K (Ace-K) is a commonly consumed sweetener, although knowledge about the Ace-K-gut microbiota interaction remains limited. This study evaluates dose-dependent effects of Ace-K on metataxonomics, metagenomics, and metabolic activity of children gut microbiota developed in a dynamic gut simulator. An Ace-K-dose dependent increase in Anaerostipes, Coprococcus, Subdoligranulum, Blautia, Sutterella wadsworthensis, Alistipes, and Bacteroides thetaiotaomicron was observed. Butyrate showed a dose-response increase that correlated with Ace-K consumption, suggesting its microbial metabolism. Increasing bacterial taxa showed sulfatase and amidase activities potentially capable of degrading Ace-K, releasing sulfamate and acetoacetate, which species such as Anaerostipes hadrus and Intestinimonas can metabolize to produce butyrate via the butanoyl-CoA pathway. Furthermore, the Ace-K-microbiome interaction led to a dose-dependent decrease in Caco-2 epithelial integrity, possibly due to the release of sulfated metabolites. This study provides evidence of the potential risk of Ace-K consumption based on its metabolism by the human gut microbiome.}, }
@article {pmid42013836, year = {2026}, author = {Steinberg, R and Pust, MM and Arias-Rojas, A and Pishchany, G and Ramsey, KA and Kieninger, E and Moeller, A and Casaulta, C and Hilty, M and Latzin, P and ,  and ,  and Korten, I and Xavier, RJ}, title = {An infant nasal microbial gene atlas uncovers intervention-driven microbiome shifts and salt-resistant pathogen expansion.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.03.019}, pmid = {42013836}, issn = {1934-6069}, abstract = {Functional studies of how early-life interventions shape the airway microbiome remain scarce. Here, we performed metagenomic sequencing of 704 longitudinal nasal swabs from infants with and without cystic fibrosis (CF) to construct and characterize a non-redundant gene atlas of the infant nasal microbiome. We aimed to determine how the nasal microbiome is perturbed by early therapies, as CF is commonly treated with inhaled hypertonic saline to improve mucociliary clearance. We found functional and compositional microbiome changes linked to inhalation therapy, including an expansion of salt-associated transporter genes and a community shift toward CF-associated microbial opportunists, including Haemophilus influenzae and fungi, carrying the identified salt-associated transporter genes with high sequence and structural identity. Hypertonic, compared with isotonic, saline accelerates H. influenzae growth and induces efflux pumps linked to antibiotic tolerance in vitro. This study establishes a reference framework for functional airway microbiome research, enabling the examination of therapeutic perturbations and their impact on microbial adaptation.}, }
@article {pmid42013844, year = {2026}, author = {Bargheet, A and Bø, GH and Hetland, MAK and Justine, M and Moyo, SJ and Löhr, IH and Blomberg, B and Langeland, N and Klingenberg, C and Pettersen, VK}, title = {Metabolic reprogramming of the infant gut by bifidobacteria-based probiotics drives exclusion of antibiotic-resistant pathobionts.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {102752}, doi = {10.1016/j.xcrm.2026.102752}, pmid = {42013844}, issn = {2666-3791}, abstract = {Early-life probiotics that strengthen gut resilience in infants are a promising strategy to combat the global emergency of antibiotic resistance. Still, their effects on antibiotic-resistant opportunistic pathogens, i.e., pathobionts, remain unclear. We evaluate the effects of probiotic supplementation in 152 full-term Tanzanian infants enrolled in the ProRIDE trial. Oral probiotics during the first 4 weeks of life increase gut colonization by Bifidobacterium species, while suppressing pathobionts, including extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E). Integrated metagenomics and metabolomics show that probiotics reduce resistome load and mobilome richness at 6 weeks, accompanied by concurrent shifts in the fecal metabolome. Specifically, the intervention increases lactate and pyruvate and reduces cross-feeding pathways that lead to propionate and butyrate, which partly explains the reduction in ESBL-E carriage. Our study documents putative pathways by which probiotic-driven Bifidobacterium colonization modulates the infant gut toward a lower level of antibiotic resistance.}, }
@article {pmid42013850, year = {2026}, author = {Qin, Y and Zhang, YX and Liu, LP and Xie, YH and Ma, XY and Hao, Y and Zhao, LC and Dong, JJ and He, Y and Sun, K and Zhong, H and Zhu, S and Liu, M and Fang, JY and Zhou, CB}, title = {Distinct signatures in the human gut and oral microbiomes of gastric cancer.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {102761}, doi = {10.1016/j.xcrm.2026.102761}, pmid = {42013850}, issn = {2666-3791}, abstract = {Microbiome dysbiosis is increasingly recognized as a hallmark of gastric cancer (GC). Here, we analyzed gut and oral shotgun metagenomic data from 317 individuals across two independent cohorts, with validation in a Harbin cohort. We identify 20 oral-gut shared species enriched in the gut of GC, predominantly lactic acid bacteria (LAB). While most gut microbial markers are abundant in saliva, none are significantly altered in GC. Strain-level analysis of 87 matched saliva-stool metagenomes confirms oral-gut transmission of Streptococcus species. GC-enriched LAB form robust co-abundance networks in oral and gut microbiomes, suggesting synergistic interactions. Functional analysis reveals enriched lactate fermentation pathways in GC stool, aligning with LAB dominance and previous findings on gastric microbiota. Moreover, microbiome-based classifiers achieve high predictive accuracy (area under receiver operating characteristic curve [AUROC] = 0.85 for stool, 0.87 for saliva) for GC diagnosis, highlighting translational potential. Collectively, these findings underscore the critical role of the oral-gut microbiome axis in GC.}, }
@article {pmid42013936, year = {2026}, author = {Nie, Z and Wang, Y and Ya, T and Dang, T and Wang, X and Liu, C and Hu, Z and Wang, X}, title = {Rapid recovery from starvation stress in low-temperature anammox system: extracellular polymeric substances protection and dissimilatory nitrate reduction to ammonium synergistically promote nitrogen metabolism recovery.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134677}, doi = {10.1016/j.biortech.2026.134677}, pmid = {42013936}, issn = {1873-2976}, abstract = {Understanding the response of the anammox system to starvation disturbances under low-temperature conditions is of great importance. In this study, we explored the performance, microbial community structure, and microbial metabolic in a low-temperature anammox system following a 15-day starvation period with the aim of identifying their response and recovery mechanisms after starvation stress. It was found that the low-temperature anammox system was able to regain its initial performance within 5 days. After system stabilization, the total nitrogen removal efficiency increased from 85% to 88%. The upregulation of hydrazine synthase (hzs) and hydrazine dehydrogenase (hdh) genes involved in anammox process was identified as part of a response mechanism of anammox bacteria. During the starvation period, the increased secretion of extracellular polymeric substances (EPS) served as a protective mechanism. Additionally, the synergistic interaction between dissimilatory nitrate reduction to ammonium (DNRA) bacteria and anammox bacteria contributed to the enhancement of nitrogen removal efficiency. The EPS-mediated synergistic interaction between anammox bacteria and heterotrophic bacteria was conducive to the survival of microorganisms during starvation and their prompt recovery upon the restoration of substrate supply.}, }
@article {pmid42013937, year = {2026}, author = {Zhu, Y and Hou, Q and Hu, F and Zhuang, G and Ma, A}, title = {Functional activators-facilitated FeS transformation enhances petroleum hydrocarbon degradation by promoting functional microbial proliferation.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134631}, doi = {10.1016/j.biortech.2026.134631}, pmid = {42013937}, issn = {1873-2976}, abstract = {Bioremediation of total petroleum hydrocarbon (TPH)-contaminated sites often faces a major challenge in sulfur-rich environments, where ferrous sulfide (FeS) immobilizes pollutants and sharply reduces their bioavailability, thereby stalling remediation. This study demonstrates that the bottleneck can be overcome by applying a composite functional activator to induce a targeted shift of the site microenvironment. The activator first selectively suppresses competing iron- and sulfur-reducing bacteria, reducing their relative abundance by 92%, thereby shifting the microbial community structure. Concurrently, a controlled decrease in local pH converts FeS from a pollutant sink into an active catalyst. The transformed FeS then activates molecular oxygen (O2) to generate reactive oxygen species (•OH and SO4[•-]), which chemically mobilize and pre-oxidize TPH, producing a "priming effect". This priming effect subsequently restructures the indigenous microbial community. Consequently, under optimized niche conditions and increased nutrient availability, TPH-degrading Bacillus populations expand significantly in the remediation environment: their relative abundance increases by 57%, and their niche breadth widens by 34%. Metagenomic analysis confirms upregulation of genes related to pollutant degradation, substance transport, and energy metabolism, strengthening the metabolic network. Ultimately, the integrated chemical-biological process achieves 90% TPH degradation. This study realizes the functional shift of FeS from remediation barrier to degradation booster, offering an innovative chemo-biological synergistic strategy and engineering paradigm for long-term stable remediation of TPH-contaminated sites.}, }
@article {pmid42000726, year = {2026}, author = {Zhou, X and Zhou, D and Pu, Y and Kim, H and Sun, Z and Qi, W and Jin, J and Zhang, W and Xia, M and Wang, C and Hong, S and Nguyen, LH and Jiao, N and Zheng, Y and Liu, T}, title = {Multi-kingdom profiling reveals altered gut phage-bacteria-metabolite interactions in MASLD.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71981-0}, pmid = {42000726}, issn = {2041-1723}, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is increasingly linked to gut microbial dysbiosis, but most studies have focused on bacteria, neglecting viruses and fungi, and their interactions. Here we show that MASLD is characterized by coordinated disruption of bacterial, viral and fungal communities and by a disturbed phage-bacteria-metabolite axis associated with disease-related bile acid changes. Integrating shotgun metagenomics, fungal ITS2 sequencing, fecal metabolomics and clinical profiling in 210 patients with MASLD and 210 age- and gender-matched healthy controls, we find reduced microbial diversity and extensive remodeling of cross-kingdom ecological networks in MASLD. Ruminococcus gnavus emerges as an enriched central hub, while Faecalibacterium prausnitzii and its associated bacteriophages are depleted. Phage-host analyses further reveal reduced lytic activity against R. gnavus and loss of sulfur amino acid metabolism-related auxiliary metabolic genes, which may impair F. prausnitzii fitness. Diminished phage control may facilitate R. gnavus expansion, alongside increased fecal isodeoxycholic acid, a secondary bile acid implicated in hepatic steatosis. A diagnostic classifier integrating bacterial and viral features with clinical parameters distinguish MASLD from controls in our cohort and maintain predictive performance in two external datasets. Together, these findings uncover a disrupted phage-bacteria-metabolite axis in MASLD and provide a multi-kingdom framework for non-invasive biomarker discovery and microbiome-targeted therapies.}, }
@article {pmid42001033, year = {2026}, author = {Galgano, S}, title = {Genomica: linear mixed model based, multiple hypothesis testing corrected, ortholog functional enrichment analysis.}, journal = {BMC bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12859-026-06450-y}, pmid = {42001033}, issn = {1471-2105}, abstract = {BACKGROUND: The analysis of ortholog genes derived from metagenomic experiments provides an invaluable opportunity to assess the functional role of microbial communities towards, for example, antimicrobial resistance or biochemical pathways under different experimental conditions. Nevertheless, the integration of the statistical analysis of these complex data sets and the enrichment of the derived significantly differential abundant orthologs is not currently facilitated by existing software. Genomica is an R package that, with minimal input from the user, allows to perform a double-step analysis of functional orthologs from the KEGG Orthology. The pipeline is carried out via combining false discovery rate corrected linear mixed models to functional enrichment analysis through integrating established R pipelines (i.e., lme4 and MicrobiomeProfiler).<br><br>RESULTS: Only two data frames are needed as input to run Genomica, which contain data and metadata, respectively. The fast pipeline integrated within the function Genomica allows to analyze 4000 orthologs in circa 3 min. The outputs are collected in a single directory, containing publication-ready results from the linear mixed model and from the enrichment analysis. The Benjamini &amp; Hochberg correction is applied to the results from the linear mixed model, therefore only P adjusted significant comparisons are further included in the enrichment analysis.<br><br>CONCLUSIONS: Genomica is a simple-to-use R package to analyze complex datasets, integrating a well-founded statistical analysis, accounting for the calculation of the type I error under repeated testing, with the enrichment analysis of the significantly differential abundant orthologs across experimental conditions, all with minimal input from the user.}, }
@article {pmid42001152, year = {2026}, author = {Leroy, M and Cyriaque, V and Rattei, T and Laurion, I and Comte, J}, title = {Microbiome and plasmidome shifts drive carbon, nitrogen, and greenhouse gas dynamics within transitioning permafrost.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00892-w}, pmid = {42001152}, issn = {2524-6372}, support = {2021-PR-284297//Fonds de recherche du Qu&#xe9;bec - Nature et technologie/ ; RGPIN-2020-06876//Natural Sciences and Engineering Research Council - Discovery and Northern Research Programs/ ; RGPIN-2020-06874//Natural Sciences and Engineering Research Council - Discovery and Northern Research Programs/ ; 2021-PR-284297//Fonds de recherche du Qu&#xe9;bec - Nature et technologies/ ; }, abstract = {Thermokarst lakes contribute to greenhouse gas emissions but often experience constraints on available nitrogen. However, the interactions between carbon and nitrogen cycles in these systems, especially along the terrestrial-aquatic continuum, remain poorly understood. The increased soil-water connectivity in those systems affects organic matter processing, nutrient availability, and microbial transport. In Nunavik (Quebec, Canada), we sampled along a transect from a palsa (permafrost remnant) through an emerging thermokarst lake to peatland soils and mature lake. Using hybrid metagenome co-assemblies with gene-, plasmid-, and genome-centric approaches, we explored key biogeochemical cycles and the role of plasmids in microbial adaptation along the transect. Gene annotation, metagenome-assembled genome (MAG) reconstruction, and network analysis revealed a shift from potential for anaerobic ammonium oxidation (anammox) in palsa and emerging lake to potential for nitrification in mature lake. Potential for methanogenesis transitions from hydrogenotrophic in the palsa to methylotrophic in lakes, likely driven by a bacterial consortium degrading aromatic, peat-derived compounds. Sediments may support methane production via both hydrogenotrophic and acetoclastic potential for methanogenesis, partially fueled by the action of polysaccharide lyases. Anaerobic methane oxidation (AOM) potential seems important in both peat and the mature lake; and can be coupled with nitrification and sulfate-reducing partners through extracellular electron transfer, with cytochromes playing a central role. Notably, plasmidome shifts preceded metagenomic changes, especially in genes related to carbon and methane cycling, suggesting a role for plasmids in microbial adaptation to permafrost thaw. These findings highlight the complex microbial and plasmid dynamics that drive carbon, nitrogen, and greenhouse gas cycles in permafrost ecosystems.}, }
@article {pmid42001834, year = {2026}, author = {Ma, Z and Gao, L and Hou, W and Wu, J and Wen, X and Zhang, Y and Dong, N and Dou, X and Shan, A}, title = {(-)-Epigallocatechin-3-gallate alleviates diarrhea in piglets by suppressing the NMU-NMUR1-ILC2 axis and modulating microbiota-associated energy metabolism.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {155}, number = {}, pages = {158119}, doi = {10.1016/j.phymed.2026.158119}, pmid = {42001834}, issn = {1618-095X}, abstract = {BACKGROUND: Bacterial diarrhea is considered a global health crisis, accounting for approximately 20 % of deaths related to colorectal cancer. (-)-Epigallocatechin 3-gallate (EGCG), one of the most abundant plant-derived polyphenols in the human diet, has shown promise in managing gastrointestinal disorders. But, the systemic evidence for EGCG in alleviating the progression of diarrhea and the mechanisms involved remain unclear.<br><br>OBJECTIVES: This study aims to determine whether EGCG confers diarrhea resistance in piglets under Escherichia coli (E. coli) and what the fundamental mechanisms involved are.<br><br>METHODS: Weaned piglets were used to create a E. coli-induced intestinal disorder-diarrhea susceptibility model. Piglets were supplemented with EGCG to identify diarrhea rate and activity of enteric nervous system (ENS). The interaction between the neuromedin U receptor 1 (NMUR1) and type&#x2161;innate lymphoid cells (ILC2) was analyzed using RNA sequencing (RNA-seq) and fluorescence colocalization techniques. Metagenomic and metabolomic analyses were further performed to assess the involvement of NMUR1 and the underlying mechanisms of beneficial microbes enriched by EGCG. The effects of beneficial microbes in treating intestinal morphology were investigated through histopathology, Scanning electron microscopy (SEM) and ELISA analysis methods.<br><br>RESULTS: EGCG reduced diarrhea rate in piglets by inhibiting the NMU-NMUR1-ILC2 pathway, ameliorating gut microbiota structure, and stimulating intestinal barrier. Apparently, the enteric nerve-microbial axis is linked with EGCG conferring diarrhea resistance in piglets. Mechanistically, EGCG suppressed the NMU-NMUR1-ILC2 axis to reduce the secretion of inflammatory cytokines (TNF-&#x3b1;, IL-6, and IL-8), while concurrently increasing the abundance of beneficial gut microbes and altering signature microbial community functions (energy metabolism pathways); accordingly, EGCG maintained the energy supply balance in gut epithelial cells and promoted the activity of goblet cell and Paneth cell by activating the AMP-activated protein kinase (AMPK)-sirtuin 1 (Sirt1) signaling pathway.<br><br>CONCLUSION: EGCG confers diarrhea resistance in E. coli piglets by maintaining intestinal mucosal barrier via the enteric nerve-microbial axis; thus, this study provides a potential prevention strategy for young mammals at risk of diarrhea.}, }
@article {pmid42002156, year = {2026}, author = {Jeon, J and Nguyen, HT and Yeo, G and Lee, C and Cho, SK and Oh, S}, title = {Integrating metagenomics and explainable artificial intelligence for modeling of food waste treatment using full-scale anaerobic digestion.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134649}, doi = {10.1016/j.biortech.2026.134649}, pmid = {42002156}, issn = {1873-2976}, abstract = {Anaerobic digestion (AD), a biochemical process that can convert food waste (FW) into methane, offers great promise as a sustainable form of energy production. While several attempts have been made to optimize AD systems using various mathematical models, more precise modeling approaches that fully consider the complexity of the AD process are required, leading to the adoption of artificial intelligence (AI) as a suitable alternative to numerical modeling. In line with this, the present study tested 11 AI-based models on their prediction of the methane yield for a full-scale AD process using FW as a feedstock. The models incorporated operational parameters, environmental conditions, and microbial information to improve their predictive performance, and the most precise model was a one-dimensional convolutional neural network (1D-CNN) with optimized hyperparameters. Explainable AI (XAI) was then used to determine the most important input features contributing to the predictions of the optimal AI model, thus allowing for detailed model interpretation. Methanothrix was identified as a key predictor of methane yield, and metagenomic analysis provided independent genome-level evidence broadly consistent with the XAI results. Overall, this study proposes a novel approach to the interpretation and optimization of AD performance, rather than focusing only on enhancing the predictive performance of a discrete model.}, }
@article {pmid42002296, year = {2026}, author = {Yang, X and Zhang, L and Zhou, S and Wang, Z and Lv, Q and Zhao, M and Wang, C}, title = {Mechanisms Underlying Bioactive Compounds Decline in Medicinal Blaps rhynchopetera During Artificial Rearing.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70304}, doi = {10.1111/1462-2920.70304}, pmid = {42002296}, issn = {1462-2920}, support = {2022YFC2602500//National Key Research and Development Program of China/ ; JiaoWaiSiYa[2020]619//Lancang-Mekong Cooperation Special Fund Projects/ ; SAJC202402//Chinese Academy of Sciences/ ; 2025YKZY002//Yunnan Characteristic Plant Extraction Laboratory/ ; 202449CE340005//Yunnan Provincial Science and Technology Department/ ; 202305AH340007//Yunnan Provincial Science and Technology Department/ ; }, mesh = {Animals ; *Coleoptera/microbiology/metabolism/growth &amp; development ; *Gastrointestinal Microbiome ; Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Metabolome ; Biological Products/metabolism ; }, abstract = {Artificial rearing is essential for sustainable utilization of medicinal insects, yet its impact on bioactive compound production remains poorly understood. Here we provide preliminary evidence that rearing of the medicinal beetle Blaps rhynchopetera reshapes its gut microbiota and metabolome, beyond mere environmental effects. Metabolomic analysis revealed 727 significantly altered metabolites, with 436 compounds, many linked to analgesic and anti-inflammatory activities, markedly reduced under rearing. Network pharmacology analysis suggested that this metabolic remodelling alters the overall regulatory landscape, with reduced network complexity compared to wild counterparts. Metagenomic profiling uncovered a decline in Pseudomonadota, a phylum positively correlated with multiple bioactive metabolites. Preliminary reintroduction of four Pseudomonadota strains suggested their potential involvement in terpenoid backbone biosynthesis, a key pathway for natural product synthesis. These findings reveal an intrinsic trade-off between rearing-driven microbial homogenization and preservation of medicinal potency, highlighting the need for microbiome-informed rearing strategies.}, }
@article {pmid42002357, year = {2026}, author = {Li, Z and Li, Z and Chu, L and Hu, S and Xue, C and Lin, H and Luo, Y and Zhang, Y and Zhang, J and Wang, Z}, title = {A novel Curcuma wenyujin-derived fructan modulates gut microbiota and metabolic pathways to ameliorate DSS-induced colitis.}, journal = {Carbohydrate polymers}, volume = {382}, number = {}, pages = {125292}, doi = {10.1016/j.carbpol.2026.125292}, pmid = {42002357}, issn = {1879-1344}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Curcuma/chemistry ; Dextran Sulfate/toxicity ; *Fructans/pharmacology/chemistry/isolation &amp; purification/therapeutic use ; Mice, Inbred C57BL ; Male ; Metabolic Networks and Pathways/drug effects ; *Colitis, Ulcerative/drug therapy/chemically induced/metabolism ; *Colitis/chemically induced/drug therapy ; Disease Models, Animal ; }, abstract = {Ulcerative colitis (UC) involves epithelial barrier breakdown, dysregulated mucosal immunity, and dysbiosis of the gut microbiota (GM). Given the biotherapeutic potential of dietary fructans, this study aimed to isolate a neutral fructan (CWP-W-1) from Curcuma wenyujin and to characterize its chemical structure and anti-colitis effects. CWP-W-1 was purified by DEAE-Sepharose and gel-filtration chromatography. Its structure was established using HPGPC, monosaccharide profiling, FT-IR, GC-MS, and NMR. In a DSS-induced UC mouse model, CWP-W-1 treatment alleviated disease severity and weight loss, decreased the disease activity index and rectal bleeding, prevented colon shortening, and restored histological architecture, with increased goblet cells and mucin staining. Metagenomic sequencing showed that CWP-W-1 mitigated DSS-associated dysbiosis, recovering α-diversity and shifting β-diversity toward healthy controls, with decreases in Proteobacteria and enrichment of beneficial taxa. Metabolite analyses indicated that CWP-W-1 increased short-chain fatty acids (SCFAs) and remodeled the tryptophan metabolic pathway, shifting the pro-inflammatory kynurenine bias toward indole-derived aryl hydrocarbon receptor (AhR) ligands, consistent with epithelial barrier support and immune homeostasis. Collectively, these results demonstrated that CWP-W-1 was a structurally defined fructan with significant therapeutic potential for UC through coordinated modulation of barrier function, mucosal immunity, and the gut microbiota.}, }
@article {pmid42002784, year = {2026}, author = {Liu, T and Fan, S and Li, J and Wang, T and Zhang, J and Wang, C}, title = {Curcumin modulates hepatic pyroptosis-autophagy crosstalk induced by aflatoxin B1 via rumen microbiota-blood-liver axis.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02396-8}, pmid = {42002784}, issn = {2049-2618}, support = {2023YFD1301005//National Key Research and Development Program of China/ ; }, abstract = {BACKGROUND: Aflatoxins, fungal secondary metabolites from Aspergillus species, primarily causes liver and gastrointestinal damage in ruminant. Curcumin, a plant polyphenol, has been shown to possess both anti-inflammatory and antioxidant properties, in addition to regulatory effects on gut microbiota. However, research on curcumin's impact against AFB1 toxicity in ruminants is limited. This study aims to elucidate whether AFB1 induces hepatic pyroptosis and autophagy in ruminants via the rumen microbiota-blood-liver axis and the regulatory role of curcumin. The experimental design involves the administration of AFB1 and curcumin to sheep, followed by a comprehensive observation of alterations in rumen microbiota, barrier function, and the occurrence of hepatic pyroptosis and autophagy, with the aim of elucidating the mechanism of curcumin in ameliorating AFB1-induced liver injury in sheep.<br><br>RESULTS: In the experimental setup, 800&#xa0;mg/kg dry matter (DM) curcumin was administered as a dietary supplement to alleviate the adverse effects of AFB1 (500&#xa0;&#x3bc;g/kg DM) on the rumen and liver of sheep. AFB1 suppressed NH3-N and VFAs production, whereas curcumin improved VFA generation and fermentation efficiency. Curcumin mitigated AFB1-induced rumen barrier impairment by upregulating tight junction proteins (ZO-1, Occludin, Claudin-1) and reducing LPS levels, which was consistent with metagenomic data showing amelioration of microbiota dysbiosis and reduced lysis of Gram-negative bacteria. At hepatic level, curcumin downregulated the principal mediators of the TLR4-NF-&#x3ba;B-NLRP3 signaling pathway (TLR4, p65, and NLRP3), attenuating pyroptosis and reducing serum AST, ALT, and LDH concentrations, while reversing inflammatory infiltration and hepatic cord disruption. Furthermore, curcumin restored autophagic flux by increasing the LC3-II/LC3-I ratio and decreasing p62 accumulation, counteracting AFB1-induced autophagy inhibition.<br><br>CONCLUSIONS: Curcumin counteracts AFB1-induced rumen-liver axis dysfunction. It works by stabilizing the microbiota, maintaining barrier integrity, and dually regulating pyroptosis and autophagy. Video Abstract.}, }
@article {pmid42002835, year = {2026}, author = {Morineau, N and Tessoulin, B and Guimard, T and Papin, M and Roquilly, A and Le Gouill, S and Montassier, E}, title = {Longitudinal gut microbiome dynamics are associated with clinical outcome and toxicity during ibrutinib therapy.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2659397}, doi = {10.1080/19490976.2026.2659397}, pmid = {42002835}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Piperidines/adverse effects/therapeutic use ; *Adenine/analogs &amp; derivatives/adverse effects/therapeutic use ; Male ; Female ; Middle Aged ; Aged ; Longitudinal Studies ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism/drug effects ; Feces/microbiology ; Treatment Outcome ; *Antineoplastic Agents/adverse effects/therapeutic use ; Adult ; }, abstract = {Accumulating evidence indicates that the gut microbiome influences therapeutic efficacy and toxicity across cancer treatments; however, its longitudinal dynamics during targeted therapies remain poorly characterized. Here, we performed whole-genome shotgun metagenomic sequencing of 291 longitudinal stool samples collected over one year from 30 patients with hematologic malignancies treated with ibrutinib. Overall gut microbial diversity remained stable at the population level but exhibited markedly divergent temporal trajectories according to clinical outcome, with progressive recovery in responders and blunted or delayed restoration in non-responders. Longitudinal modeling revealed distinct species- and pathway-level microbial dynamics between patients with treatment response or nonresponse, including enrichment of saccharolytic, short-chain fatty acid-associated taxa and metabolic pathways in responders, and expansion of bile acid-modifying, proteolytic, and inflammation-associated microbial features in non-responders. Functional profiling further demonstrated opposing temporal trends in pathways related to carbohydrate fermentation, amino-acid metabolism, and secondary bile acid synthesis. In addition, both baseline microbiome composition and longitudinal remodeling were associated with the development of ibrutinib-associated diarrhea. Together, these findings reveal coordinated, outcome-specific remodeling of the gut microbiome during ibrutinib therapy and highlight longitudinal microbiome trajectories, rather than static baseline features, as potential biomarkers of treatment response and toxicity, as well as targets for microbiome-directed interventions. In conclusion, our findings highlight a potential role of gut microbiome dynamics in modulating response to BTK inhibition and support the need for larger, prospective studies to validate these observations.}, }
@article {pmid42003340, year = {2026}, author = {Tong, Y and Marcelino, VR and Turnbull, R and Verbruggen, H}, title = {ChloroScan: Recovering Plastid Genome Bins From Metagenomic Data.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70143}, doi = {10.1111/1755-0998.70143}, pmid = {42003340}, issn = {1755-0998}, support = {2023.06155//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; DE220100965//Australian Research Council/ ; RYC2023-042907-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; //The University of Melbourne's Research Computing Services/ ; }, mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Genome, Plastid ; *Eukaryota/genetics/classification ; *Software ; Phylogeny ; Metagenome ; }, abstract = {Genome-resolved metagenomics has contributed greatly to discovering prokaryotic genomes. When applied to microscopic eukaryotes (protists), challenges such as the high number of introns and repeat regions found in nuclear genomes have hampered the mining and discovery of novel protistan lineages. Organellar genomes are simpler, smaller, have higher abundance than their nuclear counterparts and contain valuable phylogenetic information, but are yet to be widely used to identify new protist lineages from metagenomes. Here we present "ChloroScan", a new bioinformatics pipeline to extract eukaryotic plastid genomes from metagenomes. It incorporates a deep learning contig classifier to identify putative plastid contigs and an automated binning module to recover bins with guidance from a curated marker gene database. Additionally, ChloroScan summarizes the results in different user-friendly formats, including annotated coding sequences and proteins for each bin. We show that ChloroScan recovers more high-quality plastid bins than MetaBAT2 for simulated metagenomes. The practical utility of ChloroScan is illustrated by recovering 16 medium to high-quality metagenome assembled genomes (MAGs) from four protist-size-fraction metagenomes, with several bins showing high taxonomic novelty. The ChloroScan code (v0.1.7) is available at https://github.com/Andyargueasae/chloroscan/tree/release_v0.1.7 under Apache-2.0 licence.}, }
@article {pmid42003642, year = {2026}, author = {Krausfeldt, LE and Subramanian, P and Doan, D and McCauley, K and Dolan, M and Hurt, DE}, title = {DiscoVir: an automated, web-based pipeline for viral metagenomics.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0008526}, doi = {10.1128/mra.00085-26}, pmid = {42003642}, issn = {2576-098X}, abstract = {DiscoVir is an automated pipeline for viral metagenomics available in National Institute of Allergy and Infectious Diseases (NIAID)'s free web application for microbiome analysis, Nephele. DiscoVir makes viral discovery, taxonomic and functional annotation, host predictions, and diversity analyses of the virome easily accessible to researchers at all levels of expertise.}, }
@article {pmid42003644, year = {2026}, author = {Iizuka, R and Moriya, T and Oshima, T and Uemura, S and Yohda, M}, title = {Amplicon sequence collection of putative polyethylene terephthalate hydrolases from two different composts in Japan.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0017326}, doi = {10.1128/mra.00173-26}, pmid = {42003644}, issn = {2576-098X}, abstract = {We report a collection of amplicon sequences of putative polyethylene terephthalate (PET) hydrolases from two different composts in Japan. Employing previously designed degenerate primers, we identified 31 and 22 sequences from industrial and agricultural composts, respectively, confirming the presence of highly homologous PET hydrolase genes across different compost environments.}, }
@article {pmid42003651, year = {2026}, author = {Kocakahya, &#x130; and Şahin, G and Büyükkahraman, E and Arıkan, M}, title = {Metagenome-assembled genomes from urban pigeon feces in Istanbul, Türkiye.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0140525}, doi = {10.1128/mra.01405-25}, pmid = {42003651}, issn = {2576-098X}, abstract = {We report herein about 101 metagenome-assembled genomes (MAGs) obtained from pigeon fecal samples collected in 2025 from the Beyazıt, Kadıköy, and Beşiktaş squares of Istanbul. The MAGs were predominantly composed of members of the phyla Firmicutes, Actinobacteria, and Proteobacteria, with a lower representation of Campylobacterota and Patescibacteriota.}, }
@article {pmid42004019, year = {2026}, author = {Yuan, G and Zhu, X and Zhang, L and Wang, X and Wang, Y and Guo, D and Zhang, T and Wang, G and Wang, N}, title = {Shading affects the nitrogen cycling process and plant nitrogen uptake by altering the rhizosphere microbial community.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1780344}, pmid = {42004019}, issn = {1664-462X}, abstract = {Plants adapt to environmental changes by affecting the rhizosphere environment and microbial pathways. Shading affects nitrogen absorption and accumulation in plants by directly or indirectly altering the light intensity. However, the effects this has on the rhizosphere micro-environment and especially the microbial community are not fully understood. Utilizing non-targeted metabolomics and metagenomics, we investigated the changes in the microbial community structure in the cigar tobacco rhizosphere and the nitrogen cycling process and its relationship with nitrogen absorption by the plants under artificial shading conditions. Shading significantly increased the rhizosphere soil organic carbon, hydrolyzable nitrogen, ammonium nitrogen, nitrate nitrogen, and nitrogen contents in tobacco plants. Metabolomics revealed that shading significantly affected the arginine biosynthesis pathway in the rhizosphere soil, with the expression levels of L-oxornithine, citrulline and L-arginine significantly increasing. Metagenomics analysis indicated that shading significantly altered the rhizosphere microbial community structure and the nitrogen cycling process. The abundances of organic nitrogen-decomposition (gdh A, ansB) and nitrification genes (amoA_B, amoB_B, amoC_B, hao) significantly increased. Flavobacterium and Stenotrophomonas may play important roles in the nitrogen cycle in the rhizosphere. Correlation analysis indicated that Flavobacterium and Stenotrophomonas were significantly positively correlated with L-glutamic acid, L-ornithine and L-arginine (p < 0.05). These results reveal the biological mechanism by which shading affects nitrogen absorption in crops via changes in the rhizosphere microbial community and the nitrogen cycling process, providing a scientific foundation for guiding nutrient management strategies in shaded cultivation.}, }
@article {pmid42004152, year = {2026}, author = {You, G and Wang, S and Hua, Y and Su, J and Yang, Y and Shi, B and Cen, S}, title = {A four-year misdiagnosis of spinal Burkholderia pseudomallei infection: A case report and literature review.}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02558}, pmid = {42004152}, issn = {2214-2509}, abstract = {Melioidosis, traditionally an endemic disease, is increasingly reported in non-endemic regions. Its causative pathogen, Burkholderia pseudomallei, exhibits distinct characteristics from common pathogens but is prone to misdiagnosis due to clinical overlap with other infections. Despite advances in diagnostics, metagenomic next-generation sequencing (mNGS) has not been featured in case reports. We present a case of melioidosis, misdiagnosed for four years, where mNGS proved pivotal for definitive diagnosis. Based on our findings and literature review, we advocate for mNGS in melioidosis diagnosis. Furthermore, we identify subtle distinctions between melioidosis and tuberculosis amidst their similarities and propose integrating these features into a differential diagnostic framework.}, }
@article {pmid42004164, year = {2026}, author = {Chong, KL and Liew, KJ and Salleh, FM and Chong, CS}, title = {Metagenomic insights into mangrove lignocellulolytic bacteria and functional analysis of a glucose-tolerant GH 1 β-glucosidase.}, journal = {3 Biotech}, volume = {16}, number = {5}, pages = {163}, pmid = {42004164}, issn = {2190-572X}, abstract = {UNLABELLED: Mangrove ecosystems contain abundant lignocellulosic biomass and mangrove microorganisms that are capable of degrading plant polymers. In this study, a shotgun metagenomic approach was employed to explore the bacterial communities from Tanjung Piai National Park, Malaysia and their genes involved in lignocellulosic biomass degradation. A total of 148 of carbohydrate active enzymes (CAZy) genes spanning GH, CE, and AA families were identified with lignocellulolytic abilities. These enzymes included 20 cellulases, 46 hemicellulases, and 82 lignin-modifying enzymes. Approximately 89.19% of these genes were found from underexplored bacterial lineages. A set of lignocellulolytic genes derived from diverse bacterial taxa highlighted the synergistic action of mangrove bacteria in lignocellulose degradation. To validate the functionality of these genetic resources, one of the genes (BGL3_GH1) encoding a β-glucosidase was selected for expression and characterisation. The recombinant enzyme showed optimal activity at 60 ℃ and pH 7, retained up to 75% activity at 10% (w/v) NaCl. The enzyme exhibited a 1.6 to 2.1-fold in enzyme activity with glucose concentration up to 2 M. In a two-step saccharification assay using sugarcane bagasse, supplementation with recombinant BGL3_GH1 enhanced the saccharification yield (0.0674 g g[- 1] biomass) compared with treatments using commercial cellulase or recombinant BGL3_GH1 alone. These findings reveal the functional diversity of lignocellulose-degrading genes in mangrove bacteria and identify recombinant BGL3_GH1 as a potential enzyme candidate for biomass conversion application.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04788-x.}, }
@article {pmid42004407, year = {2026}, author = {Chu, D and Liu, N and Liu, Q and Li, X and Yang, H and Zhu, N and Liu, Z and Wang, R and Yuan, S and Fu, H}, title = {Diet-Driven Divergence in Gut Microbiota Variation Between Two Sympatric Gerbil Species.}, journal = {Ecology and evolution}, volume = {16}, number = {}, pages = {e73367}, pmid = {42004407}, issn = {2045-7758}, abstract = {Gut microbiota provide various benefits to their mammalian hosts; however, knowledge regarding interspecific differences in gut microecology remains limited. This study employed 16S rRNA sequencing combined with metagenomic functional prediction (potential functions or functional potential) to conduct a comparative analysis of the gut microbial composition and functional adaptability of two sympatrically distributed gerbil species with distinct diets: the herbivorous Rhombomys opimus (RO) and the omnivorous Meriones meridianus (MM). The results revealed that the omnivorous MM exhibited a level of gut microbial alpha diversity comparable to that of the herbivorous RO, whereas RO showed significant enrichment of norank_f__Muribaculaceae, a taxon associated with fiber degradation, and demonstrated higher abundance of genes related to complex fiber degradation. Notably, bacterial genera significantly enriched in the gut of MM, such as Lachnospiraceae_NK4A136_group and Desulfovibrio, may play important roles in maintaining gut health and enhancing chitin degradation efficiency. Furthermore, the abundance of genes related to monosaccharide and chitin degradation was significantly higher in MM than in RO. Functional network analysis indicated that the cellulose degradation gene networks in both gerbil species were predominantly synergistic, but the synergistic effect was stronger in RO than in MM (ratios of positive to negative correlation edges: 2.44: 1.59). Further analysis revealed that the monosaccharide and chitin degradation gene networks in MM both exhibited synergistic interaction patterns (ratios of positive to negative correlation edges: 1.69 and 2.95, respectively), whereas these two networks in RO were primarily antagonistic (ratios of positive to negative correlation edges: 0.831 and 0.73, respectively). This suggests that the gut microbiota of RO are more conducive to digesting complex plant fibers, while those of MM are better adapted for digesting starch and chitin. This differentiation in gut microbiota optimizes the utilization of different food resources by the two species, thereby promoting their sympatric coexistence. This study enhances our understanding of the adaptive mechanisms of gut microecology in rodents with different diets and provides an important foundation for further research on the microbial ecology of wild rodents and the mechanisms underlying sympatric species coexistence.}, }
@article {pmid42004633, year = {2026}, author = {Monjardino, P and Azevedo, AR and Mendonça, D and Pozsgai, G and Borges, PAV and Frias, J and Toubarro, D}, title = {Metagenomic survey of fungal communities in compost from dairy plant wastewater sludge and garden trimmings.}, journal = {Biodiversity data journal}, volume = {14}, number = {}, pages = {e174893}, pmid = {42004633}, issn = {1314-2828}, abstract = {BACKGROUND: Composting converts organic residues into stable organic matter and nutrients under aerobic conditions, improving soil properties and microbiome balance, while mitigating environmental impacts. Although microbiomes of various compost types have been studied, information is still fragmented and often not tailored to specific raw material combinations. In particular, little is known about the fungal communities involved in composting dairy plant wastewater sludge mixed with garden trimmings. This data paper contributes to filling that gap by providing a comprehensive taxonomic inventory.<br><br>NEW INFORMATION: We provide a fungus-focused dataset from 18 compost samples generated from a 1:1 (w/w) mix of garden trimmings and dairy plant wastewater sludge, collected at three process stages (thermophilic start/end; mid-cooling and maturation) under two turning regimes. Shotgun metagenomes were taxonomically annotated against NCBI taxonomy (accessed 19 Feb 2025). Only Fungi were detected within Eukarya, spanning nine phyla; Ascomycota (60.8%), Mucoromycota (17.76%), Basidiomycota (8.50%) and Chytridiomycota (7.21%) comprised 94.27% of the taxonomic features. We report 417 genera (13 >1% relative abundance each); top: Aspergillus (17.93%), Rhizopus (8.61%), Chaetomium (4.83%), Aureobasidium (3.09%), Madurella (2.85%), Paramicrosporidium (2.71%), Rhizophagus (1.88%), Rasamsonia (1.81%), Hyaloraphidium (1.39%), Thermochaetoides (1.31%), Talaromyces (1.19%), Trichoderma (1.15%), Podospora (1.06%) comprised 49.81% of the taxonomic feature abundance. Overall 663 taxa were identified (578 species, 416 genera, 230 families, 106 orders, 48 classes and 9 phyla). The dataset (DwCA; 663 occurrences) is intended to serve as a reference for compost mycobiomes and will be available via GBIF (DOI 10.15468/nmpzwr).}, }
@article {pmid42004896, year = {2026}, author = {Pourghasem, M and Tabatabaii, SA and Modarresi, SZ and Jafari Nodoushan, A and Fadavi, N and Soflaee, M and Hosseini Vajari, A and Khazaii, F and Shahhosseini, B and Fakhimi Derakhshan, K and Sadat Mansouri, S}, title = {Fungal Infections in Pediatric Patients With Hematologic Malignancies and Stem Cell Transplantation: Impact on the Upper and Lower Respiratory Systems.}, journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2026}, number = {}, pages = {8766717}, pmid = {42004896}, issn = {1712-9532}, abstract = {Invasive fungal infections (IFIs) are a leading cause of morbidity and mortality in children with hematological malignancies as well as those undergoing hematopoietic stem cell transplantation (HSCT). Extreme immunological dysregulation secondary to severe neutropenia, T-cell lymphopenia, graft-versus-host disease (GVHD), intensive chemotherapy regimens, and conditioning therapy for HSCT, as well as primary immunodeficiencies (PIDs), render these patients highly susceptible to both opportunistic and pathogenic fungal infections. Despite advances in antifungal drugs and diagnostic tools, it is very difficult in these children to provide timely diagnosis and optimal management of IFIs because of the nonspecific clinical manifestations, the invasiveness of present diagnostic modalities in pediatric patients, and biomarker kinetics differences in various pediatric age groups, along with a lack of incorporation of immunological-pharmacological maturity-associated variability in the existing scoring systems borrowed from adults. This narrative review provides a comprehensive and contemporary assessment of the epidemiology, host-related risk factors, clinical presentations, diagnostic criteria, and management practices for IFIs in children with hematological malignancies and following HSCT. It also highlights the role of EORTC/MSGERC criteria in defining IFIs as probable, proven, and possible infections and explores the sensitivity and specificity of noninvasive methods such as the galactomannan index, polymerase chain reaction (PCR), ß-D-glucan assay, high-resolution CT scans (HRCTs), and the latest approaches including next-generation sequencing (NGS) and metagenomics. This review points out significant gaps in pediatric research studies and supports efforts to optimize healthcare use with risk-prediction models rather than just relying on current algorithms.}, }
@article {pmid42005541, year = {2026}, author = {Naitchede, LHS and Ihearahu, OC and Saha, K and Igwe, DO and Yan, J and Osano, AA and Ray, S and Ude, G}, title = {Microbial community characterization in semi-hydroponic systems of Starbor kale (Brassica oleracea L.) grown under normal gravity and simulated microgravity.}, journal = {Current research in microbial sciences}, volume = {10}, number = {}, pages = {100592}, pmid = {42005541}, issn = {2666-5174}, abstract = {Kale is a member of the Brassicaceae family and contains a range of beneficial compounds. Given the global context of climate change, various vegetable production systems using advanced technologies, such as hydroponics, are being explored to alleviate food insecurity. Herein, we characterized the comprehensive microbial community associated with Starbor kale cultivation systems under normal gravity and simulated microgravity in coco coir, representing an innovative approach compared to previous studies. The kale seedlings were planted in growth vessels set into custom 2D clinostats and placed in a CONVIRON growth chamber for 43 days. The microbial DNA from coco-coir and root samples of grown kale was extracted and subjected to shotgun metagenomic sequencing. Comparisons between components revealed a higher abundance of bacteria in the soilless, while the kale roots were dominated by Eukaryota and archaea. The phyla Pseudomonadota and Actinomycetota were highly prevalent across all samples, with relatively high abundance in the coco coir samples from horizontal clinostats (HCR) under simulated gravity and from rotating vertical clinostats (VCR). The HCR group was associated with the highest number of biomarkers (28). Both CAZymes, glycoside hydrolases and carbohydrate esterases, exhibited higher relative abundances in the coco coir samples under normal gravity, whereas carbohydrate-binding modules were more abundant in HCR and VCR. The root samples showed much higher abundances of polysaccharide lyases (ranging from 0.00088 to 0.00097) and carbohydrate esterases (ranging from 0.030 to 0.033). The top four prevalent antibiotic resistance genes were adeF, vanY, vanT, and qacG. The findings of this investigation are crucial for the cultivation of kale and leafy green agriculture in hydroponic systems.}, }
@article {pmid42005844, year = {2026}, author = {Ibañez-Lligoña, M and Colomer-Castell, S and Campos, C and González-Camuesco, &#xc1; and Llauradó, A and Garcia-Larroy, J and Sánchez-Tejerina, D and Rando-Segura, A and Andrés, C and Esperalba, J and Nadal, P and Ferrer, R and Cortese, MF and Tabernero, D and Gregori, J and Riveiro-Barciela, M and Ruiz-Cobo, JC and Ruiz, A and Del Barco, E and Buti, M and Goya, M and Antón, A and Cano, A and Juntas-Morales, R and Quer, J}, title = {Unveiling pathogens and contaminants: refining metagenomics for clinical diagnostics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1786985}, pmid = {42005844}, issn = {1664-302X}, abstract = {INTRODUCTION: Shotgun metagenomic sequencing (mNGS), an untargeted approach that sequences all nucleic acids in a sample, has emerged as a powerful tool for pathogen detection and genome characterization. However, its implementation in clinical diagnostics remains limited due to technical challenges such as contamination and reduces sensitivity, especially in low-biomass samples.<br><br>METHODS: We applied mNGS to 144 clinical samples representing chronic infections, acute infections, and respiratory co-infections. To address contamination, we established a framework integrating negative controls, lab-specific contaminant watchlists, and computational filtering. Viral detection performance and genome recovery were assessed across sample types and viral loads.<br><br>RESULTS: Viral load was shown to be the primary determinant of sensitivity, with reliable recovery achieved only at higher titers. Our framework substantially improved contamination management, reducing false-positive signals and enhancing viral genome recovery. mNGS enabled the detection of clinically relevant co-infections and refined viral classification beyond targeted diagnostics, while also revealing the substantial risk of spurious detections in the absence of contamination-aware workflows.<br><br>DISCUSSION: These findings define practical sensitivity thresholds for clinical mNGS and underscore the need for contamination-aware workflows, particularly for low-biomass samples, while providing an open-source contaminants watchlist that enhances reliability and utility of clinical metagenomics.}, }
@article {pmid42005864, year = {2025}, author = {Steindler, L and Durán Canché, MA and Ilan, M and Bar-Shalom, R and Lopez, JV and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the marine sponge Diacarnus erythraeanus Kelly-Borges &amp; Vacelet, 1995, and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {10}, number = {}, pages = {466}, doi = {10.12688/wellcomeopenres.24763.2}, pmid = {42005864}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Diacarnus erythraeanus (sponge; Porifera; Demospongiae; Poecilosclerida; Podospongiidae). The genome sequence has a total length of 140.86 megabases. Most of the assembly (98.57%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 19.34 kilobases in length. Sixty-four binned genomes were generated from the metagenome assembly, of which 46 were classified as high-quality metagenome assembled genomes (MAGs). The microbial signature is typical of HMA sponges, including the Pseudomonadota, Chloroflexota and Acidobacteriota as dominant phyla and several candidate phyla (Poribacteria, Binatota, Latescibacterota) as well as the archaeal clade Nitrosopumilaceae in lower abundance.}, }
@article {pmid42005923, year = {2026}, author = {Lafon, T and Weingart, M and Vaidie, J and Calfee, CS and Jacob, ST and Freund, Y and Shapiro, NI and Barraud, O and Monneret, G and van der Poll, T and Fromage, Y and François, B}, title = {Challenges in early detection and prognostication of sepsis: new approaches from the emergency department and intensive care unit.}, journal = {EClinicalMedicine}, volume = {94}, number = {}, pages = {103864}, pmid = {42005923}, issn = {2589-5370}, abstract = {In this narrative review, we aimed to provide a comprehensive overview of emerging diagnostic strategies and precision medicine approaches in sepsis, while explicitly acknowledging the heterogeneity of clinical contexts. In the Emergency Department (ED), timely recognition of infection and sepsis represents one of the most frequent and challenging tasks, which may delay management directly increasing morbidity and mortality. Even if very popular and widely used, traditional scores and routine biomarkers remain of limited interest to confirm diagnosis and predict deterioration. Nevertheless, emerging point-of-care tools hold promise such as "real-time microbiology", bedside immune profiling, and echocardiography for on-time hemodynamic phenotyping. More advanced strategies, such as omics technologies and transcriptomic signatures, offer deeper biological precision, while machine learning and artificial intelligence can integrate high-dimensional ED data to anticipate deterioration and capture the dynamic evolution of sepsis subphenotypes. Many of these tools are already feasible at the bedside and only await integration into routine ED workflows. Embedding them within dedicated sepsis pathways and multidisciplinary teams could optimize global patient care and accelerate the transition toward precision medicine in acute sepsis. Sustainable improvements in sepsis outcomes will most likely not come from isolated devices but from their integration into coordinated and sepsis-specific pathways.}, }
@article {pmid42006114, year = {2025}, author = {Dorobantu, S and Grigorescu, A and Fratea, A and Mirauta, B and Neghina, A and Bica, G and Neacsu, A and Dumitrescu, F and Streata, I and Netea, M and Riza, AL}, title = {Strength of Omics in Uncovering Sepsis Mechanisms-A Perspective.}, journal = {Current health sciences journal}, volume = {51}, number = {4}, pages = {425-436}, pmid = {42006114}, issn = {2067-0656}, abstract = {BACKGROUND: Sepsis is a significant life-threatening condition due to a dysregulated response to infection. Large datasets yield unprecedented views and transformative insights into processes through various computational frameworks. Our aim was to highlight significant contributions from genomics, transcriptomics, proteomics in the field of sepsis, as modeled from human data. We are showcasing key findings in each omics that have improved the understanding of sepsis pathophysiology, while presenting a perspective from the group's own contribution to the field.<br><br>DISCUSSION AND CONCLUSIONS: Each of the presented omics has advanced our mechanistic understanding on sepsis pathogenicity, biomarker identification for diagnosis, prognosis, and molecular stratification purposes. Multi-omics sepsis research shows strong input from genomics, transcriptomics, proteomics. These have revealed mechanistic links and produce robust endotypes but faces challenges on the path to clinical integration. Integrative sepsis studies combine large-scale omics, paired sampling, and computational multi-omics frameworks to link molecular layers to phenotype. Addressing gaps in standardization, and age/ethnicity representation could yield actionable biomarkers, stratified therapies and improved outcomes.}, }
@article {pmid41997245, year = {2026}, author = {Wang, X and Wang, X and Ai, S and Wu, F and Xi, J and Li, J and Liu, Z}, title = {Harnessing native microbes: Intermittent aeration for bioremediation of phenolic compounds contaminated freshwater.}, journal = {Bioresource technology}, volume = {453}, number = {}, pages = {134641}, doi = {10.1016/j.biortech.2026.134641}, pmid = {41997245}, issn = {1873-2976}, abstract = {Phenolic pollutants pose persistent risks to freshwater ecosystems due to their toxicity, structural diversity, and resistance to biodegradation. This study investigated microbial community dynamics, gene-level adaptation, and biostimulation strategies for phenolic removal using native microbial community. Metagenome analyses revealed marked taxonomic shifts under phenolic stress, with engineered systems favoring modular cooperative degradation, whereas the natural community relied on dominance of stress-resistant taxa and inter-phylum horizontal gene transfer (HGT). Functional profiling identified 28 candidate KEGG Orthologs (KOs), including oxidative, ring-cleaving, and energy-support genes, enriched across core degraders such as Pseudomonas, Sphingobium, and Bordetella. Biostimulation assays demonstrated oxygen availability as the primary limiting factor: intermittent aeration (IA) enhanced phenolic degradation by 29%, while IA combined with activated carbon (IA + AC) achieved up to 75% improvement, especially for complex compounds like bisphenol A (BPA) and nitrophenol. Predictive modeling based on KO abundance and stimulation methods (R[2] = 0.75-0.88) successfully predicted degradation performance across 50 natural samples. While IA + AC provided the most consistent improvement, 15 communities achieved comparable efficiencies under IA alone, highlighting context-dependent biodegradation capacities linked to HGT and metabolic pathway diversity. These findings establish a scalable predictive framework and emphasize the importance of tailoring biostimulation strategies to native microbial capacities, offering a practical route for in situ bioremediation of phenol-contaminated freshwater systems.}, }
@article {pmid41998153, year = {2026}, author = {Li, S and Zhu, D and Saha, K and Kundu, BB and Sonkusale, S and Britton, RA and Ajo-Franklin, CM}, title = {Synthetic microbial co-cultures for modular bioelectronic sensing in diverse environments.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41998153}, issn = {1546-1696}, support = {W911NF-22-1-0239//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; W911NF-22-1-0239//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; W911NF-22-1-0239//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; RR190063//Cancer Prevention and Research Institute of Texas (Cancer Prevention Research Institute of Texas)/ ; RR190063//Cancer Prevention and Research Institute of Texas (Cancer Prevention Research Institute of Texas)/ ; RR190063//Cancer Prevention and Research Institute of Texas (Cancer Prevention Research Institute of Texas)/ ; R01 AI173318/AI/NIAID NIH HHS/United States ; R01 AI173318/AI/NIAID NIH HHS/United States ; }, abstract = {Whole-cell bioelectronic sensors are particularly well-suited for environmental and health monitoring as they can be integrated into compact electronic devices for field deployment over extended periods. However, current engineering strategies lack modularity, are limited to a few microbial chassis and depend on specialized instruments for signal detection. We present the electroactive co-culture sensing system (e[-]COSENS), a plug-and-play system for whole-cell bioelectronic sensor development. Here a 'sender' bacterium produces electron mediators in response to analytes and a 'receiver' bacterium utilizes the electron mediators to generate electrical signals via extracellular electron transfer. Modularly swapping the sender bacterium and its associated genetic sensing elements achieved bioelectronic sensing of metals, small molecules and peptides in distinct environments, such as urban waterways, milk, saliva and microbial communities. We designed a centimeter-sized bioelectronic device for portable signal readout using a household digital multimeter. The e[-]COSENS system simplifies the whole-cell bioelectronic sensor design and expands the potential of bioelectronic sensor applications.}, }
@article {pmid41998361, year = {2026}, author = {Thiyagarasaiyar, K and Paul, D and Kerttula, J and Keski-Karhu, M and Soosaar, K and Mander, &#xdc; and Hallin, S and Machacova, K and Pumpanen, J and Siljanen, HMP}, title = {Genetic Potential for N2O Metabolism in Tree Tissues: Insights From Nitrogen Cycling Gene Prevalence and nosZ Diversity Across Tree Species.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02773-8}, pmid = {41998361}, issn = {1432-184X}, }
@article {pmid41998362, year = {2026}, author = {Parida, D and Dhali, SL and Bala, K and Nogueira, R}, title = {Early microbial colonization study of daily-use plastics exposed to river water.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {5}, pages = {}, pmid = {41998362}, issn = {1573-0972}, abstract = {UNLABELLED: In rivers, microorganisms colonize plastic surfaces, initiating processes that can lead to their microbial decomposition. Our study investigates the bacterial community composition and diversity on the surfaces of plastics used daily, such as polyethylene terephthalate (PET) and low-density polyethylene (LDPE), which were exposed to river water from the Aller and Fusche rivers. Glass was used for comparison purposes. 16s rRNA sequencing revealed that the type of surface and the native microbial community in the river water, including the water quality, significantly influenced biofilm community assembly. River water samples, especially from the Fusche site, supported the highest microbial richness, while plastic exhibited moderate diversity, and glass beads hosted the lowest richness and diversity. Proteobacteria and Bacteroidetes dominated across all samples, with notable enrichment of functionally relevant families such as Rhodobacteraceae and Comamonadaceae. Ecologically relevant genera such as Flavobacterium, Hydrogenophaga, Rhodoferax, Sediminibacterium, and Rhodobacter dominated across samples. Alpha diversity reflected the richness of taxa within each sample, while beta diversity revealed distinct clustering based on both plastic type and site, indicating the influence of ecological pressure and niche partitioning. These findings highlight the capacity of plastic surfaces to harbour diverse and specialised bacterial assemblages, with implications for biogeochemical cycling, pollutant interactions, and potential microbial degradation pathways. This work contributes to deciphering the ecological roles of biofilms in freshwater plastisphere micro-environments and underscores the importance of material-specific microbial dynamics in assessing environmental risks.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11274-026-04907-z.}, }
@article {pmid41998767, year = {2026}, author = {Rungrojn, A and Chaisiri, K and Thaipadungpanit, J and Batty, EM and Blacksell, SD}, title = {Bacterial communities in Thai ticks: revealing geographical and methodological gaps in surveillance-a 25-year scoping review.}, journal = {Tropical medicine and health}, volume = {54}, number = {1}, pages = {}, pmid = {41998767}, issn = {1348-8945}, support = {JCPET02//Royal Society of Tropical Medicine and Hygiene/ ; 220211/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Ticks serve as key vectors for a diverse range of bacterial pathogens that affect humans and animals worldwide. In Thailand, a comprehensive understanding of tick-associated bacterial diversity remains limited. This scoping review synthesises published data on tick-borne bacteria across Thailand from 2001 to 2025, focusing on bacterial diversity, host-vector associations, geographic distribution, and molecular detection methods. Literature searches in NCBI, Embase, and Web of Science identified 402 studies (272 after duplicate removal), of which 39 met the inclusion criteria. Ticks were collected from animals, humans, and the environment across four zoogeographical regions. Rhipicephalus, Haemaphysalis, Dermacentor, and Amblyomma were the most commonly studied genera. Eighteen bacterial genera, including both pathogens and endosymbionts, were identified, with Coxiella-like endosymbionts, Rickettsia, Anaplasma, and Ehrlichia being the predominant genera. Rhipicephalus ticks exhibited the highest bacterial diversity, while Rickettsia spp. were the most frequently detected pathogens. Conventional PCR remained the principal diagnostic method, with limited application of quantitative and metagenomic sequencing approaches. Geographic analysis revealed that most studies were concentrated in the Northern Peninsular and Central Peninsular regions, while the Continental section of the Indo-Chinese Mainland and Korat Plateau zones were under-represented, which may limit the accuracy of regional risk assessments, as surveillance gaps can underestimate both the diversity and prevalence of pathogenic organisms in these areas. This review emphasises the intricate nature of tick-host-pathogen interactions and highlights the importance of implementing standardised genomic surveillance nationwide within a One Health framework. The findings reveal key gaps in current surveillance efforts and advocate for incorporating genomic tick monitoring into Thailand's national One Health strategies to improve zoonotic disease preparedness.}, }
@article {pmid41998806, year = {2026}, author = {Tang, R and Wang, J and Zhang, Z and Li, Y and Lan, Y and Fan, Z}, title = {Temporal Shifts in Gut Microbiota and Host Immunity During Chronic Diarrhea in an Infant Rhesus Macaque: A Longitudinal Case Study Based on Multi-Omics.}, journal = {Journal of medical primatology}, volume = {55}, number = {3}, pages = {e70074}, doi = {10.1111/jmp.70074}, pmid = {41998806}, issn = {1600-0684}, support = {2023NSFSC1935//Sichuan Province Science and Technology Support Program/ ; 32370450//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Macaca mulatta/immunology ; *Gastrointestinal Microbiome ; *Diarrhea/veterinary/microbiology/immunology ; *Monkey Diseases/immunology/microbiology ; Longitudinal Studies ; Transcriptome ; Male ; Anti-Bacterial Agents/therapeutic use ; Female ; Chronic Disease ; Multiomics ; }, abstract = {Diarrhea remains a major health challenge in captive rhesus macaques (RMs; Macaca mulatta), particularly among infants, yet the dynamic interplay between gut microbiota and host immune responses during disease progression remains poorly understood. Here, we conducted a longitudinal multi-omics study on a captive infant RM, analyzing 25 fecal metagenomes and 18 blood transcriptomes across diarrheal, antibiotic treatment, and recovery phases. Our results demonstrated that disease state was the primary driver of gut microbiota variation. The diarrheal phase was characterized by a significant reduction in microbial α-diversity and marked expansion of multidrug-resistant Enterobacteriaceae, including Escherichia, Shigella, and Salmonella, accompanied by severe depletion of probiotic genera such as Lactobacillus and Bifidobacterium. Correspondingly, antibiotic resistance genes targeting fluoroquinolones and cephalosporins accumulated substantially during diarrhea, explaining the limited efficacy of empirical antibiotic therapy. Blood transcriptome analysis revealed heightened innate immune activation, evidenced by upregulation of interferon-related genes, alongside suppression of adaptive immune pathways including interleukin-5 signaling. Integrated correlation analysis uncovered synchronized host-microbiome interactions, with inflammatory gene expression positively associated with opportunistic pathogens and negatively correlated with beneficial commensals. Clinical recovery coincided with re-establishment of probiotic populations, reduction in resistance gene burden, and normalization of immune function. These findings demonstrate that infant macaque diarrhea profoundly disrupts both gut microbial ecology and systemic immunity, supporting management strategies that prioritize targeted antimicrobial intervention and microbiome restoration over prolonged empirical antibiotic use in captive primates.}, }
@article {pmid41999333, year = {2026}, author = {Tang, X and Lu, SY and Huang, JH and Cheng, ZW and Ke, YC and Ai, CF and Liu, C and Liao, HP and Zhou, SG}, title = {Phage-Encoded Metabolic Bypass Drives Herbicide Resistance in Soil Microbiomes.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c02641}, pmid = {41999333}, issn = {1520-5851}, abstract = {Phages reshape microbial community functions through auxiliary metabolic genes (AMGs) and are increasingly recognized as active drivers of microbial adaptation. Although herbicides such as glufosinate significantly inhibit soil microbes, these communities exhibit striking resilience; however, the role of phages in facilitating this rapid adaptation remains poorly understood. Here, we dissect the temporal dynamics (days 0, 15, 30, and 60) of phage-host interactions under two contrasting stressors: the microbially toxic glufosinate and the nontoxic dicamba. We find that glufosinate transiently suppresses microbial diversity, followed by a robust recovery on day 60. This successional shift coincides with an elevated proportion of putative temperate phages (74.1%) and a strategic attenuation of bacterial antiviral systems, signaling a transition from antagonistic predation to mutualistic lysogeny. Metagenomic analyses across 23 regions in China corroborate that this temperate phage recruitment is a generalized response to field-relevant glufosinate exposure. Selection for temperate phage infections arises from asymmetric fitness costs (burdening virulent phage-susceptible hosts) and prophage integration of AMGs like gdhA. Specifically, coevolution assays reveal that glufosinate selectively penalizes virulent phage-sensitive hosts, favoring the recruitment of temperate phage infections. Furthermore, in vitro validation confirms that phage-encoded gdhA provides a compensatory metabolic bypass for ammonia detoxification, directly mitigating herbicide toxicity. Collectively, these findings delineate a phage-mediated mechanism for herbicide resistance evolution in soil microbiomes, emphasizing the need for a microbiome-informed agrochemical design to manage long-term ecological resilience.}, }
@article {pmid42000179, year = {2026}, author = {Iakovides, IC and Vasileiadis, S and Christou, A and Karaolia, P and Mina, T and Rocha, J and Duan, Y and Beretsou, VG and Gallois, N and Changey, F and Michael, C and Coelho, LP and Manaia, CM and Merlin, C and Fatta-Kassinos, D}, title = {Storage and soil depth, in addition to wastewater treatment, govern microbiota, and mobile genetic element and antibiotic resistance markers during reclaimed water irrigation.}, journal = {Water research}, volume = {300}, number = {}, pages = {125889}, doi = {10.1016/j.watres.2026.125889}, pmid = {42000179}, issn = {1879-2448}, abstract = {Reclaimed water (RW) offers a sustainable solution for agricultural irrigation and freshwater conservation, but its microbial and chemical composition, shaped by treatment and storage processes, requires careful consideration for environmental and public health impacts. This study compared two RW types (conventional activated sludge with sand filtration and chlorination - CAS + SFC-RW - and membrane bioreactor - MBR-RW) with a tube well (TW) water control. The goal was to assess how storage influences the microbial composition, key antibiotic resistance and mobilome genes, and RW the impact on irrigated lysimeter soils during lettuce cultivation. Total bacteria were profiled using 16S rRNA gene sequencing and ddPCR, while antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were quantified by ddPCR and analysed by metagenomics. Initial RW samples had 1-1.5 orders of magnitude more 16S rRNA copies compared with the control, with significantly different bacterial and ARG/MGE profiles. Actinomycetota dominated CAS + SFC-RW, Bacteroidota the MBR-RW, and Pseudomonadota the TW water. Class 1 integrons and Tn916/Tn1545 were more abundant in CAS + SFC-RW compared with the MBR-RW. Storage reduced these differences toward convergence with the TW water profile, with putative pathogenic taxa, however, being more recalcitrant to change. RW irrigation altered soil bacterial composition, with MBR-RW having a greater impact as declared by the enhanced presence of Bacteroidota in the receiving soils. The RW influence was inversely related with vertical distance of the irrigation point, while the lettuce crop presence showed minimal/no impact. These results highlight the need for careful management of RW treatment and storage to ensure safe, resilient agricultural practices.}, }
@article {pmid42000463, year = {2026}, author = {Devika, NT and Jayaraman, K and Nadimuthu, S and Nathamuni, SP and Sreya, PS and Jangam, AK and Katneni, VK}, title = {Gut microbial restructuring in white spot syndrome virus-infected Penaeus vannamei: Insights from long-read metagenomics.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {59}, number = {}, pages = {101834}, doi = {10.1016/j.cbd.2026.101834}, pmid = {42000463}, issn = {1878-0407}, abstract = {Microbial community restructuring following White Spot Syndrome Virus (WSSV) infection is a critical determinant in modulating the disease progression in Penaeus vannamei. In this study, full-length 16S rRNA sequencing (V1-V9) was employed to delineate the microbial shifts in healthy and WSSV-infected shrimp. The analysis revealed a pronounced reduction in Firmicutes in the WSSV-infected shrimp, a dysbiosis signature reported in WSSV-associated amplicon studies. With the advantage of full-length sequencing, this study achieved species-level resolution, identifying Vibrio alginolyticus (a known pathogen) alongside putative beneficial taxa such as Ruegeria conchae, R. arenilitoris, Demequina litorisediminis, and D.globuliformis, which were not captured in earlier amplicon-based studies. Diversity analysis demonstrated that, rather than loss of species, substantial restructuring in the form of abundance was observed between healthy and WSSV-infected shrimp, while the overall evenness of the community remained stable. Concurrently, WSSV-infection has triggered an increased abundance of core opportunistic pathogens, namely, Photobacterium damselae and V. alginolyticus, which clustered distinctly from putative beneficial taxa such as Ruegeria and Demequina species, reflecting a clear microbial imbalance. Collectively, these findings demonstrated that mortality in WSSV-infected shrimp is associated with dysbiosis characterized by a depletion of beneficial taxa and concomitant abundance of opportunistic pathogens. These insights provide a basis for developing targeted probiotic or therapeutic strategies to mitigate pathogen overgrowth.}, }
@article {pmid42000510, year = {2026}, author = {Yu, Z and Song, S and Deng, W and Zhou, X and Wang, Y and Zhou, S}, title = {Metagenomics insights into humification improvement and antimicrobial resistance reduction during hyperthermophilic coupled with electric field composting process.}, journal = {Journal of hazardous materials}, volume = {510}, number = {}, pages = {142094}, doi = {10.1016/j.jhazmat.2026.142094}, pmid = {42000510}, issn = {1873-3336}, abstract = {Compared to conventional thermophilic composting, hyperthermophilic composting elevates fermentation temperature and electric field composting facilitates oxygen transfer, with both strategies promoting humification and reshaping the microbial community structure. This study coupled hyperthermophilic composting with electric field composting (HEC) to further enhance livestock manure humification while suppressing antimicrobial resistance. A composting strategy consisting of 12-day hyperthermophilic pretreatment and 28-day electric field composting was implemented. Integrating analyses of the humification process, metagenomics, metabolic pathways, and key microbiota linked to humification and antimicrobial resistance, this study indicated that HEC strategy triggered an initial hyperthermophilic surge and sustained thermophilic, with potential enhancement of aerobic metabolic activity under the applied electric field, thereby driving microbial succession from Proteobacteria to Firmicutes and Actinobacteria. The favorable conditions and microbiota shift enhanced metabolic activity, accelerated transformation of organic substrates, and increased aromatic precursor accumulation, resulting in a 2.5-fold increase in humic acid carbon compared with conventional thermophilic composting. Meanwhile, HEC reduced antibiotic resistance genes (ARGs) abundance and diversity by suppressing resistance-associated microbiota, particularly Proteobacteria and Bacteroidetes, which predominantly harbor antibiotic efflux genes (e.g., adeF). The attenuation of ARGs abundance and diversity reached 66.1% and 74.2%, respectively, compared with 43.3% and 48.8% in conventional thermophilic composting after 40d fermentation, and meanwhile, dominant humus-forming microbiota were relatively less associated with ARGs. This study elucidated the mechanisms underlying enhanced humification and ARG mitigation during the HEC process, thereby offering an effective strategy for resource recovery from livestock manure.}, }
@article {pmid42000517, year = {2026}, author = {Han, W and Liu, Y and Liang, X and Liu, J and Jiang, Q and Zhang, C and Zhang, Y}, title = {A Trojan Horse in the soil: Tetracycline hijacks plant organellar ribosomes to stunt growth and unbalance the rhizosphere microecology.}, journal = {Journal of hazardous materials}, volume = {510}, number = {}, pages = {141792}, doi = {10.1016/j.jhazmat.2026.141792}, pmid = {42000517}, issn = {1873-3336}, abstract = {Tetracycline, a widely used antibiotic, accumulates in agricultural soils and poses significant risks to crop development and soil health. This study elucidates novel mechanisms of TC phytotoxicity by demonstrating its specific binding to the structurally conserved A-site of ribosomal small subunit RNA (SSU rRNA) in plant mitochondria and chloroplasts-organelles of prokaryotic origin. Through integrated physiological, transcriptomic, and structural analyses, we show that TC disrupts ribosomal function, induces oxidative stress, and impairs photosynthesis and antioxidant defense in soybean, and unbalances the SSU/LSU (ribosomal large subunit RNA) rRNA ratio. We further developed a comprehensive Ecological Risk Index (ERI) framework that integrates soil physicochemical properties, enzyme activities, microbial metabolism, and community structure to evaluate soil microecological shifts under TC stress. Metagenomic analysis uncovered functional adaptations in microbial nitrogen/phosphorus cycling and emphasized the role of multidrug resistance genes-rather than tetracycline-specific resistance-via mobile genetic elements, including those from ssDNA viruses. Our findings provide unprecedented insights into the evolutionary conservation of ribosomal targets of antibiotics and establish a holistic framework for assessing the ecological impact of antibiotic residues in agroecosystems.}, }
@article {pmid42000556, year = {2026}, author = {Snipen, L and Stoeck, T and Angell, IL and Philip, M and Pettersen, R and Majaneva, S and Ray, JL and Stokkan, M and Keeley, N and Rudi, K}, title = {Predicting sediment ecological state from metagenomes shows equal performance for taxonomic and functional features.}, journal = {Marine environmental research}, volume = {218}, number = {}, pages = {108055}, doi = {10.1016/j.marenvres.2026.108055}, pmid = {42000556}, issn = {1879-0291}, abstract = {The use of environmental microbial DNA to monitor the ecological state in seafloor sediments has many advantages and efforts are being made to find reliable biomarkers from DNA-based taxonomic profiles. However, the taxonomic composition of microbial communities can vary over time and space, while their functional characteristics typically remain consistent. Furthermore, functionality may better capture the breadth of biological complexity. Therefore, we here tested whether functional attributes of microbial communities serve as more reliable indicators of environmental quality than their taxonomic composition. To test this, we analyzed a set of Metagenome-Assembled-Genomes (MAGs) from 41 different coastal locations in Norway and Iceland, characterized by environmental impact gradients resulting from salmon aquaculture. Functional and taxonomic features extracted from these MAGs were then used to predict the ecological state of the corresponding sample sites using several supervised machine learning models and stratified feature selection. Our findings indicate that both taxonomic and functional features demonstrated comparable effectiveness in predicting environmental quality. This outcome has direct relevance for eDNA-based regulatory compliance monitoring. However, the functional insights derived from the most significant functional features identified by machine learning models remain essential for deepening our understanding of the ecological processes underpinning practical biomonitoring tools.}, }
@article {pmid42000565, year = {2026}, author = {Wan, X and Zhan, J and Chen, Z and Wu, B}, title = {Ventilation-driven microbial and antimicrobial resistance divergence in intensive poultry houses and the associated public health risks.}, journal = {Research in veterinary science}, volume = {206}, number = {}, pages = {106196}, doi = {10.1016/j.rvsc.2026.106196}, pmid = {42000565}, issn = {1532-2661}, abstract = {Ventilation strategies in intensive poultry production systems play a critical role in shaping airborne microbial communities and the dissemination of antibiotic resistance, with potential implications for environmental and public health. In this study, bioaerosols from closed (mechanically ventilated) and open (naturally ventilated) chicken houses were systematically characterized using high-throughput metagenomic sequencing to compare microbial community composition and antibiotic resistance gene (ARG) profiles under contrasting ventilation regimes. Open chicken houses exhibited significantly higher microbial diversity (P < 0.05), reflecting increased environmental microbial inputs, while the relative abundance of the potentially antibiotic-resistant pathogen Staphylococcus aureus was also elevated. In contrast, closed chicken houses facilitated the accumulation of a core microbial community, including potential pathogens such as Helicobacter pullorum and Clostridium perfringens. Closed chicken houses showed a greater enrichment of macrolide resistance genes. In addition, the overall abundance of ARGs, expressed as ARG copies per 16S rRNA gene, was significantly higher in closed houses than in open houses (P < 0.05). Although total ARG abundance was lower in open chicken houses, the proportion of contigs harboring both ARGs and mobile genetic elements (MGEs) was significantly higher (P < 0.05), indicating increased potential for horizontal gene transfer. These findings reveal differences in microbial diversity and associated health risks between different poultry production systems and underscore the importance of optimizing ventilation strategies to control pathogen transmission and the spread of antibiotic resistance.}, }
@article {pmid41803433, year = {2026}, author = {Jalal, RS and Alshehrei, FM}, title = {Rhizospheric glycosyltransferase repertoires as a resource for enabling sustainable bioprocessing and green biocatalyst discovery.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41803433}, issn = {2045-2322}, support = {UJ-25-DR-1837//University of Jeddah/ ; }, abstract = {UNLABELLED: The rhizospheric microbiomes associated with wild plant species Moringa oleifera and Abutilon fruticosum, endemic to the arid northwestern Mecca region of Saudi Arabia, represent untapped reservoirs of genetic capability with significant implications for agriculture, biotechnology, medicine, and environmental sustainability. Leveraging high-throughput metagenomic sequencing and advanced bioinformatics, this study systematically cataloged carbohydrate-active enzymes (CAZymes), with a particular focus on glycosyltransferase (GT) families, within these root-associated microbial consortia. The analysis revealed pronounced compositional divergence between rhizospheric and bulk soil microbiomes, underscoring the influence of plant species and edaphic factors in shaping niche-specific microbial assemblages and functional repertoires. The two rhizospheric microbiomes were consistently enriched in all six CAZy classes, with lineage-specific CAZymes of GT families (GT2 and GT84 in M. oleifera and GT31, GT39, and GT66 in A. fruticosum). These lineage-specific CAZymes catalyze the synthesis of structurally diverse polysaccharides, including cellulose, chitin, β-glucans, mannans, and chondroitin, thereby positioning the rhizospheric microbiomes of Moringa oleifera and Abutilon fruticosum as promising reservoirs of biocatalysts for possible future applications in industrial applications, biomedical engineering, and environmentally sustainable technologies. The evolutionary history of these enzymes in hot, oligohydric soils suggests adaptation to thermal and water-limited conditions, which may render them particularly suitable for deployment in industrial and biotechnological bioreactors. These CAZymes are predicted to be positioned as pivotal assets for sustainable bioeconomy initiatives and possible therapeutic glycoengineering.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-42974-2.}, }
@article {pmid41997155, year = {2026}, author = {Yang, W and Lee, YJ and Silva, RMB and DeLiberto, A and Yancey, CE and McCallum, D and Buss, JA and Moncion, R and Ong, JL and Mabuchi, M and Hough, DM and Weigele, PR and Ettwiller, LM}, title = {The discovery of 5mC-selective deaminases and their application to ultra-sensitive direct sequencing of methylated sites at base resolution.}, journal = {Molecular cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.molcel.2026.03.027}, pmid = {41997155}, issn = {1097-4164}, abstract = {Mining phages for new enzymatic activities continues to be important for the development of new tools for biotechnology. In this study, we used MetaGPA-a method linking genotype to phenotype in metagenomic data-to identify deoxycytidine deaminases, a protein family highly associated with cytosine modifications in metaviromes. Unexpectedly, a subset of these deaminases exhibited a preference for 5-methylcytosine (5mC) over cytosine (C) in both mononucleotide and single-stranded DNA substrates. In a methylome-sequencing workflow, deamination of 5mC by these enzymes enabled direct conversion of methylated cytosine while completely eliminating any background deamination of unmodified cytosine. This direct conversion allows for precise identification of methylated sites at single-base resolution with unmatched sensitivity enabling broad applications for the simultaneous sequencing of genome and methylome.}, }
@article {pmid41803939, year = {2026}, author = {Fauszt, P and Mikolas, M and David, P and Szoke, Z and Gashi, N and Szilagyi-Tolnai, E and Szilágyi, E and Szarvas, MM and Fazekas, ME and Kun-Nemes, A and Stagel, A and Gal, F and Czegledi, L and Biro, S and Stundl, L and Remenyik, J and Paholcsek, M}, title = {Longitudinal source-sink dynamics of fecal litter and farm indoor environmental resistomes in broiler chicken and Cherry Valley ducks.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41803939}, issn = {2524-4671}, abstract = {BACKGROUND: Antimicrobial resistance is a major One Health threat, and intensive poultry systems function as amplifiers. Although broilers and ducks are reared under similarly controlled conditions, their microecologies diverge. Integrated, longitudinal source-sink analyses quantifying overlap and directional flux between host-associated and environmental resistomes remain scarce. A two-year (2022–2024), longitudinal, commercial-scale comparison was undertaken across 15 stocking cycles under harmonized husbandry in Ross 308 broiler and Cherry Valley duck. Parallel shotgun metagenomics profiled fecal litter and farm indoor environments across standardized production, with daily monitoring in one complete cycle per system; in total, 96 pooled samples were sequenced to quantify cross-compartment overlaps.<br><br>RESULTS: Antibiotic resistance gene (ARG) reservoir dominance proved to be system-specific, duck systems were environment-centric, whereas broiler systems were fecal litter-centric. Although overall ARG diversity was similar between systems (broiler 2,542; duck 2,494 types), ducks exhibited greater compartmental divergence, with ~&#x2009;2.6-fold more environment-unique ARGs than paired fecal litter and 1.15-fold higher environmental richness than broilers. Compartment coupling also differed: broilers showed tighter host-environment overlap, while ducks were more partitioned. A shared environmental ARG pool (57.5%) indicated substantial cross-system exchange potential. Temporally, shared ARGs accumulated across the grow-out and peaked pre-depopulation. The distribution of significant ARG carrier species revealed asymmetric host-environment coupling: overlap across compartments was 66.67% in broilers versus 45.45% in ducks, notably. The impact of antimicrobial use was nuanced: short, targeted courses were associated with lower aaAMR burden overall Collectively, the recurrent detection of clinically consequential carriers (P. aeruginosa, E. coli, A. baumannii, S. aureus, K. pneumoniae, S. maltophilia, toxigenic Clostridium spp.) underscored One Health risks of zoonotic spillover and food-chain contamination.<br><br>CONCLUSION: Reservoir behavior in intensive poultry systems should be treated as system-specific, and matrix-targeted, with biofilm and humidity management prioritized in duck operations, and litter/manure control emphasized in broilers. The finisher-depopulation window emerges as a critical intervention point, warranting intensified mitigation clean-out. Finally, mitigation should extend beyond individual farms to transport crates, vehicles, shared equipment, and supply chains.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00544-x.}, }
@article {pmid41827064, year = {2026}, author = {Yu, S and Yue, X and Yang, Q and Xu, P and Yuan, H and Tang, W and Luan, Y and Wang, Q}, title = {Omics integration reveals how the gut microbiota of Warmblood horses responds to equestrian show jumping-a short-duration, high-intensity technical exercise stress.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41827064}, issn = {2524-4671}, abstract = {BACKGROUND: Intestinal microbial homeostasis and metabolic balance play a crucial role in maintaining normal physiological function in horses. Exogenous stress involving abrupt turns and jumps during show jumping significantly impacts intestinal microbial homeostasis and metabolic balance in these animals.<br><br>RESULTS: By comparing rectal (faecal) samples from 10 Warmblood horses collected before and immediately after a show jumping competition on the same day, we observed substantial alterations in intestinal microbial homeostasis and metabolic balance post-exercise. Microbial evenness significantly increased following the competition, accompanied by enrichment of specific taxa such as Bacteroides, Ruminococcus, Prevotella, and Fibrobacter. Metabolite analysis revealed a marked decrease in antioxidant-related compounds, including orsellinic acid, 2,3-dimethyl-2-cyclohexen-1-one, and (1&#x2009;R,6&#x2009;R)-1,4,5,5a,6,9-hexahydrophenazine-1,6-dicarboxylate. Conversely, glucosan and thiamine pyrophosphate levels increased. Post-competition, membrane lipid metabolism pathways were significantly downregulated, while antioxidant responses and energy metabolism pathways were upregulated. Spearman correlation analysis indicated positive associations between Fibrobacter, Ruminococcus, and Prevotella with energy metabolism-related metabolites, whereas Lysinibacillus correlated positively with metabolites involved in antioxidant activity and intestinal mucosal protection.<br><br>CONCLUSION: Collectively, our findings demonstrate that show jumping induces shifts in intestinal microbial homeostasis and metabolic balance in Warmblood horses. These adaptations appear conducive to preserving epithelial integrity and enhancing energy provision to meet the demands of high-intensity exercise. This study provides novel insights into the impact of acute high-intensity exercise on equine gut microbial dynamics and metabolism, offering a theoretical basis for probiotic-based interventions to support intestinal health in sport horses.}, }
@article {pmid41990624, year = {2026}, author = {Wang, G and Yang, F and Xu, S and Lin, D and Yang, R and Yan, P and Chen, Y and Fang, F and Guo, J}, title = {Microbial niches and metabolism drive spatial heterogeneity of hydroxyapatite precipitation in aerobic granular sludge.}, journal = {Water research}, volume = {300}, number = {}, pages = {125923}, doi = {10.1016/j.watres.2026.125923}, pmid = {41990624}, issn = {1879-2448}, abstract = {Biologically induced phosphate precipitation (BIPP) in aerobic granular sludge (AGS) provides a promising approach to address phosphorus removal instability and granule structural fragility in practical applications. However, the roles of microbial communities, ecological niches, and metabolic activities in driving phosphate precipitation and shaping its spatial distribution within AGS remain underexplored. This study systematically investigates AGS physicochemical properties, reactor performance, phosphorus speciation, precipitation composition and distribution, microbial community structure, and metabolic activity using sodium propionate (RP) and sodium acetate (RA) as sole carbon sources. The findings reveal for the first time the mechanisms by which microbial communities, ecological niches, and metabolic functions regulate phosphate precipitation and determine its spatial heterogeneity. BIPP contributes 22.6% and 60.1% of total phosphorus removal in RP and RA, respectively, thereby enhancing phosphorus removal efficiency and granule structural stability. Multi-scale analyses-including Standards, Measurements and Testing, Raman spectroscopy, X-ray diffraction, scanning electron microscopy-energy dispersive X-ray spectroscopy, and micro-computed tomography-reveal that hydroxyapatite (HAP) predominantly accumulates in the outer region of RP granules but in the inner region of RA granules. Periodic water quality variations, fluorescence in situ hybridization, granule-stratified sequencing, and metagenomic analyses indicate that the spatial heterogeneity of HAP is driven by the ecological niche separation and metabolic activities of polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs). In RP granules, PAO‑driven anaerobic phosphate release creates a high‑phosphate microenvironment, which promotes HAP formation in the granule outer region. In RA, GAO‑mediated endogenous denitrification increases local pH, thereby inducing HAP precipitation in the granule interior. Overall, this study elucidates the mechanisms underlying the spatial heterogeneity of phosphate precipitation in AGS from the perspectives of microbial community structure, ecological niches, and metabolic pathways. These findings provide guidance for optimizing AGS systems to achieve efficient phosphorus removal and stable operation.}, }
@article {pmid41990657, year = {2026}, author = {Ye, YQ and Lin, D and Shen, LQ and Wu, D and Li, Y and Wang, YF and Zhu, D}, title = {Viral communities as mirrors and vectors: Tracing antibiotic resistome distribution and dissemination across diverse habitats in Macao.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {142056}, doi = {10.1016/j.jhazmat.2026.142056}, pmid = {41990657}, issn = {1873-3336}, abstract = {Virus-mediated transmission of antibiotic resistance genes (ARGs) is increasingly recognized as a significant threat to global human health. However, the role of viral communities in ARGs dissemination across highly urbanized coastal regions containing with diverse habitats remains poorly understood. Here, we conducted shotgun metagenomic analyses on 49 samples collected from four habitats (urban sewage, soil, sediment, and coastal water) in Macao China, to characterize their viral communities and resistome profiles. We identified 23,579 viral operational taxonomic units (vOTUs) and 965 ARGs subtypes across these habitats. Viral community composition and total ARGs profiles exhibited system-scale spatial concordance, with a distance-decay trend, together with a positive association between viral ARGs and total ARGs abundance. Approximately 62.80% of ARGs subtypes were shared among habitats, suggesting a high degree of compositional overlap in resistome profiles among habitats. Urban sewage and coastal waters showed enriched viral abundance and ARGs diversity, with high-risk ARGs in sewage being 10.3- and 24.7-fold greater than in soils and sediments. High-risk ARGs (e.g., macB, udg) showed co-occurrence with virulence factor genes (VFGs) on viral contigs, and prophages were identified within Pseudomonadota and Bacteroidota, the dominant groups for phages and ARGs. The co-occurrence of ARGs and auxiliary metabolic genes (AMGs) within these hosts suggests that phages may facilitate the propagation of ARGs while enhancing host adaptability, thereby promoting their enrichment. By integrating multi-habitat analyses in human-impacted coastal regions, this study highlights the potential role of viruses in ARGs dissemination and informs resistome surveillance.}, }
@article {pmid41991090, year = {2026}, author = {Lee, JS and Jeon, YJ and Kim, TH and Khan, W and Yun, YM}, title = {Multiscale destabilization of anaerobic digestion by chloramphenicol: Divergence between methanogen detectability and methane recovery.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134635}, doi = {10.1016/j.biortech.2026.134635}, pmid = {41991090}, issn = {1873-2976}, abstract = {Antibiotic residues in livestock waste streams can affect anaerobic digestion (AD), yet their functional impact on microbial viability and metabolic pathways remains unclear. This study evaluated concentration-dependent effects of chloramphenicol (CAP) by integrating process kinetics, cellular integrity, dissolved-phase responses, and functional gene profiles. Methane yield was maintained at ≤ 50 mg/L CAP but declined sharply at higher concentrations, reaching near-complete inhibition at 1,000 mg/L. Estimated inhibition thresholds were derived as IC30 = 285 mg/L, IC60 = 535 mg/L, and IC90 = 852 mg/L from the fitted concentration-response relationship. Severe inhibition coincided with residual organic acid accumulation, pH decline, and enrichment of propionate and butyrate fractions with undetectable acetate. Flow cytometry revealed a marked CAP-dependent decline in intact biomass, with live-cell (P2) counts decreasing from 4.8 × 10[6] cells/mL in the control to 1.0 × 10[5] cells/mL at 1,000 mg/L, accompanied by increased forward- (FSC-A) and side-scatter (SSC-A) area indicative of structural stress. Fluorescence excitation-emission matrix (FEEM) analysis showed concentration-dependent enrichment of soluble microbial products (SMPs) fluorescence, and inoculum-only incubation confirmed biomass-associated solubilization under CAP exposure. Although methanogens remained numerically detectable (76.0% vs. 81.1%), key genes related to cofactor synthesis and electron transfer (comD, frhB, fwdA/fwdC, mcr) declined substantially at 1,000 mg/L. These convergent signals were consistent with multiscale destabilization. Given that microbial activity was not directly measured, the observed discrepancy between methanogen detectability and methane recovery should be interpreted as indicative of a potential functional imbalance rather than definitive evidence of functional decoupling.}, }
@article {pmid41991504, year = {2026}, author = {Elhani, I and Bredon, M and Enea, D and Desmons, A and Arrive, L and Bazille, C and Lefevre, A and Aouba, A and Bigot, A and de Moreuil, C and Alonso, I and Blasco, H and Creusot, L and Dupuy, C and Emond, P and Krasniqi, P and Lamaziere, A and Oeuvray, C and Rainteau, D and Svrcek, M and Rolhion, N and Sokol, H and Georgin-Lavialle, S}, title = {Functional changes in the gut microbiota are associated with the intestinal phenotype in A20 haploinsufficiency.}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {37}, number = {4}, pages = {e70343}, doi = {10.1111/pai.70343}, pmid = {41991504}, issn = {1399-3038}, support = {//snfmi-remi/ ; //fai2r/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Haploinsufficiency ; Female ; Male ; *Tumor Necrosis Factor alpha-Induced Protein 3/genetics ; Child ; Phenotype ; Feces/microbiology ; Adolescent ; *Inflammatory Bowel Diseases/genetics ; Child, Preschool ; Bile Acids and Salts/metabolism ; }, abstract = {BACKGROUND: A20 haploinsufficiency (HA20) is an autoinflammatory disease driven by pathogenic variants in TNFAIP3, which plays a crucial role in regulating immune responses. The clinical manifestations of HA20 resemble those of inflammatory bowel disease (IBD), with prominent gastrointestinal (GI) involvement. Given the well-established association between gut microbiota alterations and IBD, this study aimed to describe the GI involvement of HA20 patients and to investigate their fecal microbiota using shotgun sequencing and metabolomics.<br><br>METHODS: This study included 16 HA20 patients and 22 healthy age and sex-matched controls. GI clinical phenotype, liver imaging, and liver and GI tissue histology were assessed. Shotgun metagenomic sequencing was performed on fecal DNA. Fecal metabolomic profiling of bile acids, short-chain fatty acids (SCFAs), and tryptophan metabolites was performed.<br><br>RESULTS: Liver imaging revealed chronic liver disease in 3/5 patients, showing as liver dysmorphia and portal hypertension. Histological analysis showed lymphoplasmocytic infiltrate of the GI tract and the liver. The fecal microbiota of HA20 patients was characterized by marked alterations, including a reduction in microbial diversity and an increase in the pro-inflammatory bacterium Ruminococcus gnavus. Microbial bile acid deconjugation and desulfation were impaired. Additionally, tryptophan metabolism was altered, with a shift towards the kynurenine pathway.<br><br>CONCLUSION: Our results show that HA20 is associated with gut microbiota alterations and significant disruptions in metabolic pathways, particularly involving bile acids. These alterations could contribute to the chronic inflammation observed in HA20. These findings highlight the role of the gut-liver axis and of mucosal barrier dysfunction in HA20.}, }
@article {pmid41991911, year = {2026}, author = {Liu, Y and Huang, P and Zhang, C and Dong, Q and Wang, X and Tian, F and Zhao, J and Sun, Z and Chen, L and Chen, W and Zhai, Q}, title = {A microbiome catalog of Chinese traditional artisanal cheeses provides insights into functional and microbial diversity.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71929-4}, pmid = {41991911}, issn = {2041-1723}, support = {32425044//China National Funds for Distinguished Young Scientists/ ; 2022YFD2100703//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; }, abstract = {Cheese has been consumed globally over millennia and serves as a natural reservoir of diverse microorganisms. Chinese traditional cheeses rely on natural fermentation and have unique physiochemical and microbial characteristics compared to European cheeses. However, there is a major knowledge gap in the understanding of Chinese cheese microbiome. Here, we present a curated Cheese microbiome catalog (cCMC) consisting of 3327 high-quality metagenome-assembled genomes, recovered from metagenomic sequencing of 235 Chinese cheese samples covering all traditional artisanal cheese-producing regions in China, together with 198 publicly available non-Chinese cheese metagenomic datasets. This catalog represents 395 nonredundant species spanning 50 families, including 85 putative novel species. We identified six lactic acid bacteria species enriched in Chinese cheeses, and confirmed that the unique presence of Acetobacteraceae contributes to improving the nutritional quality of Chinese cheese. A total of 8851 biosynthetic gene clusters were detected from cCMC, with over 57% classified as novel. We demonstrated that SNP-level variations among different Lactobacillus helveticus strains are associated with differences in β-galactosidase thermostability. Using the cCMC database, we developed a synthetic microbial community as the starter culture for Qula, a yak milk-based Chinese cheese produced by the Tibetans. Overall, the cCMC provides a comprehensive resource of cheese to enable future attempts on large-scale industrial production of naturally fermented cheeses with distinctive ethnic features.}, }
@article {pmid41992382, year = {2026}, author = {Cuteri, V and Preziuso, S and Li, Y and Laus, F}, title = {Fecal virome at the human-animal interface: a one health perspective on an uncharted frontier.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00569-2}, pmid = {41992382}, issn = {2524-4671}, }
@article {pmid41992389, year = {2026}, author = {Gu, S and Jiang, C and Zhang, P and Luo, S and Gong, Y and Feng, W and Xiong, J and Zhang, J and Chen, K and Ning, K and Miao, W}, title = {Unraveling the colonization process of microeukaryotic communities on artificial micro-ecological islands.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00897-5}, pmid = {41992389}, issn = {2524-6372}, support = {2022FY100400//the Science &amp; Technology Fundamental Resources Investigation Program/ ; 2022xjkk0204//the Third Xinjiang Scientific Expedition Program/ ; U22A20454//the National Natural Science Foundation of China/ ; SNJNP2022008//the Background Resources Survey in Shennongjia National Park/ ; SNJGKL2022008//the Open Project Fund of Hubei Provincial Key Laboratory for Conservation Biology of Shennongjia Snub-nosed Monkeys/ ; }, abstract = {BACKGROUND: Micro-ecological islands provide unique habitats for microbes and play a crucial role in the functioning of aquatic ecosystems. Microbes settle on these micro-ecological islands, forming distinct microbial communities. Previous studies have provided some understanding of the colonization processes and regulatory mechanisms of protozoa in microbial communities. However, these islands are also subject to colonization by a variety of microbes beyond protozoa, and comprehensive cross-kingdom studies and their potential mechanisms remain largely unexplored.<br><br>RESULTS: Using polyurethane foam units (PFU) to simulate micro-ecological islands, we studied the colonization dynamics of microbes in two distinct aquatic ecosystems, the Yangtze River and East Lake. Over 10-day colonization survey was conducted, we applied eDNA-PFU technology combined with metagenomic sequencing to comprehensively identify species present in the microbial communities, including bacteria, fungi, flagellates, protozoa, and metazoa. We found that microeukaryotes, rather than prokaryotes, were the primary colonizers in these two aquatic ecosystems. Our study reveals a colonization process of microeukaryotes in PFUs, profoundly influenced by their motility modes. Additionally, we propose a hypothetical food web framework within micro-ecological islands that maintains community stability, representing the most fundamental biological interactions.<br><br>CONCLUSIONS: Overall, this study enriches our understanding of micro-ecological islands and provides deeper insights into the colonization processes and regulatory mechanisms of microbial communities. It highlights the practical significance of micro-ecological islands in biological resource management, environmental protection, and biodiversity conservation.}, }
@article {pmid41993122, year = {2026}, author = {Saez-Torillo, SN and Danielsson, R and Nguyen, TQ and Lima, J and Cleveland, MA and Roehe, R and Martínez-Álvaro, M}, title = {Predicting beef diet nutritional composition and intake from rumen metagenomic profiles.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {25}, number = {}, pages = {297-309}, pmid = {41993122}, issn = {2405-6383}, abstract = {Knowledge of diet composition and intake levels in beef cattle is valuable for post hoc feed traceability and for more accurate modelling of the diet impact on methane emissions and performance traits. However, a direct measure of this information can be costly and labour-intensive and is not always feasible. In this study, rumen metagenomic data combined with machine learning algorithms were used to predict diet type, nutritional composition, and intake levels. An external validation to assess the generalizability of the models was also performed. Rumen samples were collected from 142 animals belonging to two breeds, Luing (n = 70) and Charolais crossbred (n = 72), with 425.6 ± 43.5 d old and 461.9 ± 70.2 kg body weight. The animals participated in a 56-d feeding trial and were assigned to diets differing in forage-to-concentrate ratio, with 72 animals receiving a concentrate-based diet and 70 receiving a forage-based diet. Liquid ruminal contents were collected immediately postmortem and subsequently subjected to metagenomic sequencing. Based on these sequences, the relative abundance of microbial genes (MGs), microbial genera (MTs), and phyla were determined. The log-ratio between the abundances of Verrucomicrobia and Chlorobi discriminated diet type with an average classification accuracy of 0.86 ± 0.05, while using the log-ratio transformed abundances of 4769 MTs and MGs as predictors reached 0.90 ± 0.05. All this microbiome information was used in a random forest model to predict continuous values for nutritional diet components starch, crude protein, neutral and acid detergent fibre, and metabolizable and gross energy with external validation prediction accuracy values between 0.77 and 0.83. Microbiome features important for prediction of diet components such as fibre and starch included Mitsuokella, Selenomonas, and MGs involved in flagellar assembly and aminoacyl-tRNA biosynthesis. Microbiome data were more informative for predicting the feed composition than the amount of feed consumed, which reached a prediction accuracy of 0.27 ± 0.12 for dry matter intake (DMI). However, microbiome data can still be used as a screening tool to classify DMI into low, medium, or high with a classification accuracy of 0.74. Incorporating dietary information into linear phenotypic and genetic models to predict methane production (MP) and DMI reduced root mean square error (RMSE) by 26.9% and 9.6%, respectively, in the phenotypic model. In the genetic model, only MP showed a reduction in RMSE, with a 31% improvement. These findings highlight rumen microbiome data as a valuable tool for the post hoc prediction of feed composition in beef cattle.}, }
@article {pmid41993390, year = {2026}, author = {Hutchinson, NT and Ye, N and Jennings, M and Fang, C and Qi, N and Li, J}, title = {Engineered Lactate Catabolizing Probiotics Reveal Timescale Dependent Microbiome-Host Metabolic Coupling.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.07.716956}, pmid = {41993390}, issn = {2692-8205}, abstract = {The exchange of lactate, a metabolic substrate and regulator, between the gut lumen and systemic circulation for use in host and microbial processes is well documented, but tools capable of uncovering whether this process influences host metabolic status across acute and chronic contexts are lacking. In our prior work, we engineered probiotic Bacillus subtilis PY79 to produce lactate oxidase (LOX) intracellularly, allowing it to rapidly convert intestinal lactate to pyruvate. Following oral administration, LOX reduced systemic lactate concentrations at rest and under challenge conditions, providing a platform for investigating lactate's influence on host metabolism and microbiota. In the present work, we demonstrate that acute LOX administration effectively rewired microbiota function and host energy balance, as revealed by 16S sequencing and indirect calorimetry. In silico microbial community modeling via MICOM and metagenomic inference via PICRUSt2 suggested that acute shunting of lactate to pyruvate induced microbiota remodeling towards anabolic processes, reflected by increased flux of pyruvate, acetate, and formate, alongside moderate to large increases (Cohen's d = 0.60-1.00) in pathways for fructan degradation, B-vitamin biosynthesis, and lipid synthesis. These anabolic shifts temporally aligned with transient increases in host energy expenditure (β = 1.08, p<0.05) via glucose oxidation (β = 0.01, p<0.05), hinting at functional coupling between microbial biosynthesis and host energy balance via lactate exchange. Of note, acute LOX administration also improved thermoregulation and survival following LPS-induced sepsis, demonstrating functional relevance of these metabolic effects during acute inflammatory challenge. To assess chronic effects, we administered LOX for 6 weeks during diet-induced obesity. LOX treatment persistently reduced blood lactate. However, this chronic lactate reduction did not curtail the progression of diet-induced obesity or induce sustained modulation of host energy expenditure. This disconnect between acute and chronic findings suggests that gut-centric lactate conversion affects energy balance through microbiome and/or host-dependent mechanisms, but cannot override homeostatic forces in the long term to produce clinical benefit during chronic disease. Our results validate LOX probiotics as a tool for acute metabolic augmentation, and highlight a clear homeostatic limit to gut-centric therapies. This platform may enable targeted design of probiotic interventions matched to therapeutic timescale and inform synbiotic formulations that overcome homeostatic compensation.}, }
@article {pmid41993414, year = {2026}, author = {Liu, S and Mehta, P}, title = {Ecology of metagenomes: incorporating genotype-to-phenotype maps into ecological models.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.07.717079}, pmid = {41993414}, issn = {2692-8205}, abstract = {UNLABELLED: A major theoretical problem in community ecology is to understand how genes, organisms, and environments combine to shape the structure and diversity of ecological communities. However, most classic ecological models work entirely with phenotypic parameters, neglecting the central role played by genes. This limitation is particularly acute in microbial ecology, where the widespread use of sequencing technologies allows researchers to directly measure the genomic and metagenomic properties of communities. Here, we bridge this gap by incorporating genotype-to-phenotype maps into classical ecological models, including the generalized Lotka-Volterra model (GLV) and consumer resource models (CRMs). We focus on the case where genotype-to-phenotype maps are linear, which provides a tractable yet powerful framework for analyzing complex traits. Even in this simple setting, the resulting ecological dynamics give rise to novel gene-level ecological dynamics that can be recast entirely in terms of genes, allowing us to develop an ecology of metagenomes. We find that ecological interactions between genes lead to pervasive "metagenomic hitchhiking" - low-fitness genes can survive in the ecosystem because they are integrated into genomes of high-fitness species. We also show that phylogenetic relationships between species mold the ability of closely related strains to stably coexist in complex communities. This highlights how lineage structure and competitive interactions jointly shape community composition. Our framework provides a principled foundation for interpreting metagenomic data through the lens of ecological theory.<br><br>AUTHOR SUMMARY: Recent advances in sequencing technologies have transformed our ability to characterize microbial communities at the genomic level. However, most classic ecological models work entirely with phenotypic parameters, neglecting the central role played by genes. Here, we address this gap by extending classical ecological models to explicitly include genotype-to-phenotype maps. We focus on complex traits where the genotype-to-phenotype map is approximately linear. We show that the resulting ecological dynamics that can be recast entirely in terms of genes, allowing us to develop an ecology of metagenomes. Our framework provides a novel perspective for interpreting metagenomic data through the lens of ecological theory.}, }
@article {pmid41993507, year = {2026}, author = {Coleman, I and Ma, J and Qian, G and Jiang, Y and Brown Kav, A and Korem, T}, title = {End-to-end evaluation of pipelines for metagenome-assembled genomes reveals hidden performance gaps.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.06.712906}, pmid = {41993507}, issn = {2692-8205}, abstract = {The generation of Metagenome Assembled Genomes (MAGs) has become a standard and basic step in the analysis of metagenomic data. This multi-step process, which includes assembly, binning, refinement, and quality control, has many alternative approaches, algorithms, and parameters. Determining the ideal approach for a given ecosystem and study, or highlighting algorithmic gaps in need of additional research and development, requires rigorous benchmarking. We present MAG-E (MAG pipeline E valuator), a generalizable and expandable framework for end-to-end evaluation of entire MAG pipelines: from assembly, through binning, to quality control and filtering. MAG-E relies on simulations that are built to match an ecosystem of interest and provide a ground truth for accurate evaluation. To demonstrate the capabilities of MAG-E, we benchmark two assemblers, six binning algorithms, three binning modes, and three quality control and refinement methods in the context of the human gut microbiome. Our findings offer multiple insights into optimal MAG generation in this context. We find that metaSPAdes consistently outperforms MEGAHIT in terms of recall (completeness), and that COMEBin overall outperforms alternative binning algorithms, but has lower precision than SemiBin2. While multi-sample binning results in higher precision, as previously shown, single-sample binning has higher recall and leads to better overall performance with modern binners. Binning refinement, which combines bins from multiple different algorithms, leads to reduced performance. We further show that CheckM2 systematically overestimates completeness and underestimates contamination, and that this is partially ameliorated when using GUNC. Finally, we analyze performance at the contig level, and demonstrate that binning algorithms systematically underperform for prophages and fail to bin contigs that are shared between genomes. Overall, MAG-E offers deep insights into successes and gaps in this important analytic process.}, }
@article {pmid41993555, year = {2026}, author = {Herzog, HM and Fang, C and Lam, L and Jin, K and Zamarioli, A and Dinh, E and Gupta, CL and Sharma, A and Moody, T and Pierce, JL and Hohl, MS and Takimoto, SW and Lyalina, S and Wentworth, KL and Yu, K and Lu, VF and Mamikunian, I and Hunt, NK and Lynch, S and Pollard, KS and Hernandez, CJ and Perrien, DS and Hsiao, EC}, title = {Gut microbiome-dependent IL-1 signaling is a mediator of ACVR1 [R206H] -driven heterotopic ossification.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.05.716562}, pmid = {41993555}, issn = {2692-8205}, abstract = {UNLABELLED: Inflammatory diseases cause significant morbidity and mortality, but their pathobiology is often difficult to dissect due to complex genetic-environmental interactions. Genetic forms of heterotopic ossification, such as fibrodysplasia ossificans progressiva (FOP), reduce genetic variability, allowing careful dissection of non-genetic drivers of inflammation. While >95% of FOP patients harbor the ACVR1 [R206H] mutation, patients exhibit significant variability in disease progression, suggesting a role of environmental drivers. Here, we identify the gut microbiome as a regulator of inflammation-driven HO in FOP. Metagenomic profiling of cohabitating FOP/unaffected sibling pairs revealed a pathogenic gut microbiome profile in FOP patients (Bray-Curtis, p < 0.05). In Pdgfrα-Cre/Acvr1 [R206H] (FOP) mice, gut microbiome ablation by antibiotics reduced spontaneous HO formation (47.4% reduction, p < 0.05) and reduced plasma IL-1 pathway activity. IL-1β blockade in FOP mice suppressed trauma-induced HO formation. These findings identify a gut microbiome-IL-1-HO axis with modifiable targets for developing treatments for HO and related inflammatory conditions.<br><br>ONE SENTENCE SUMMARY: Antibiotic disruption of the gut microbiome reduces HO in FOP mice via an IL-1 mediated pathway.}, }
@article {pmid41993727, year = {2026}, author = {Sun, Y and Qiu, JW and Chen, C and Martín-Durán, JM and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the tubeworm, Lamellibrachia columna Southward, 1991 (Sabellida: Siboglinidae).}, journal = {Wellcome open research}, volume = {11}, number = {}, pages = {127}, pmid = {41993727}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Lamellibrachia columna (tubeworm; Annelida; Polychaeta; Sabellida; Siboglinidae). The genome sequence has a total length of 879.73 megabases. Most of the assembly (99.96%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.78 kilobases. Gene annotation of this assembly by Ensembl identified 21 983 protein-coding genes.}, }
@article {pmid41993799, year = {2026}, author = {Yue, XL and Wu, YH and Zheng, DQ and Sun, C and Xu, L and Cui, L and Xu, XW}, title = {[13]C-labeled single-cell Raman sorting reveals sulfur-driven dark carbon fixation in coastal sediments.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag073}, pmid = {41993799}, issn = {2730-6151}, abstract = {Chemoautotrophs drive carbon fixation in coastal sediments, but most of them remain uncultured with poorly characterized in situ activities. In this study, a cultivation-independent single-cell approach combining Raman spectroscopy with [13]C-stable isotope probing was developed to enable direct identification of active chemoautotrophs in coastal sediments using function-specific spectral biomarkers, targeted metagenomic sequencing and pure culture verification. [13]C-induced shifts in cytochrome c (749, 1129, 1312, 1589 cm[-1]) and phenylalanine (1002 cm[-1]) Raman bands were systematically evaluated and applied as functional biomarkers through investigations of both representative chemoautotrophic strains and environmental samples. The combined analysis of targeted sorting of active chemoautotrophic cells and metagenomic sequencing revealed dominant species and a complete Calvin-Benson-Bassham (CBB) cycle pathway in sulfur-oxidizing guilds. Remarkably, a novel sulfur-oxidizing chemoautotroph, Guyparkeria sp. TX1, which showed ≥99% gene sequence similarity to contigs recovered from sorted-cell metagenomes, was isolated from enrichment cultures. Its significant carbon fixation capacity provided experimental validation for the effectiveness of Raman-based in situ functional screening. This study establishes Raman-based functional biomarkers applicable to chemoautotrophic carbon fixation, enabling in situ mapping of microbial carbon fluxes. By integrating single-cell phenotypic activity with genomic potential, this work advances the mechanistic understanding of sulfur-driven dark carbon fixation, which sustains coastal blue carbon ecosystems as a keystone process.}, }
@article {pmid41993915, year = {2026}, author = {Hoedt, EC and Burns, GL and Hedley, KE and Waller, S and Sanchez, TC and Chisolm, O and MacCallum, H and Richardson, S and Suthers, B and Pepper, E and Keely, S and Talley, NJ}, title = {Shared functional microbiome signatures in Parkinson's disease and constipation predominate irritable bowel syndrome despite taxonomic divergence.}, journal = {Brain, behavior, &amp; immunity - health}, volume = {53}, number = {}, pages = {101218}, pmid = {41993915}, issn = {2666-3546}, abstract = {BACKGROUND: Gastrointestinal dysfunction, including constipation, is a common non-motor feature of Parkinson's disease (PD) and often precedes motor symptoms. The gut microbiome interacts with the host through neural, hormonal, and immune pathways, yet whether constipation represents a cause or consequence of PD remains unclear. Therefore, we aimed to interrogate the associations between microbiome and immune alterations in relation to constipation to provide novel insight into microbiome-gut-brain axis mechanisms in PD.<br><br>METHODS: We analysed peripheral blood mononuclear cells (PBMCs) for circulating gut-homing T cell populations and used shotgun metagenomics to profile the stool microbiome composition and functional capacity in PD patients (n&#xa0;=&#xa0;18), healthy controls (n&#xa0;=&#xa0;21), and individuals with constipation-predominant irritable bowel syndrome (IBS-C; n&#xa0;=&#xa0;8). Associations between immune markers and microbial taxa were assessed, and functional pathway differences were evaluated.<br><br>RESULTS: Circulating gut-homing T cell frequencies did not differ significantly between PD and controls, but constipated PD patients showed a trend toward increased circulating gut-homing T cells. Microbiome beta-diversity analyses revealed distinct taxonomic shifts in PD and IBS-C, while functional capacity was largely conserved. Of the differential functional pathways tryptophan biosynthesis, polyamine production, and vitamin B metabolism, processes critical for neurotransmitter synthesis, epithelial integrity, and neuroimmune regulation were reduced in PD compared to IBS-C.<br><br>CONCLUSION: Our findings highlight unique microbial and immune signatures in PD, partially overlapping with IBS-C, and underscore the importance of microbial metabolic pathways in gut-brain axis disorders. Collectively our findings suggest a contribution to dopaminergic dysfunction, neuroinflammation, and impaired gut motility. Future longitudinal studies are needed to clarify causal relationships and inform targeted interventions for PD-related gastrointestinal dysfunction.}, }
@article {pmid41993958, year = {2026}, author = {Meng, H and Zhao, S and Jin, H and Zhang, H and Li, Q and Zhang, L and Hu, J and Kong, F and Du, X and Li, Q and Ajwad Rahim, M and Xu, L and Xue, Y}, title = {Unveiling the Role of Rumen Microbiome in Modulating Intramuscular Fat Deposition of Pingliang Red Cattle.}, journal = {Food science &amp; nutrition}, volume = {14}, number = {4}, pages = {e71681}, pmid = {41993958}, issn = {2048-7177}, abstract = {Pingliang Red cattle is renowned for its tender meat and symmetrical intramuscular fat (IMF) deposition. Rumen microbiota are crucial for energy metabolism and nutrient acquisition in cattle, significantly influencing IMF deposition. Therefore, this study aimed to explore how rumen microbiota impact IMF deposition in Pingliang Red cattle. 34 castrated Pingliang Red cattle were subjected to the same management for 2 months, followed by centralized and unified slaughtering. Based on the measured IMF content in the longissimus dorsi, 18 cattle were selected and divided into a high-intramuscular-fat group (HIMF, n = 9) and a low-intramuscular-fat group (LIMF, n = 9). Rumen fluid was subsequently collected for metagenomic sequencing. Results showed significant differences in taxonomic abundance at both the genus and species levels, the relative abundance of carbohydrate-active enzyme (CAZy) families, and functional profiles (p < 0.05). Specific rumen microbes, such as Limosilactobacillus panis (AUC = 0.765) and Fibrobacter succinogenes (AUC = 0.753), served as potential biomarkers for HIMF deposition in Pingliang Red cattle. With the exception of Bacillus, Fibrobacter succinogenes, Limosilactobacillus panis, Prevotella intermedia, and Streptomyces exhibited positive correlations with IMF content. Functional analysis based on KEGG orthology (KO) indicated that specific enzymes promote IMF deposition by regulating the metabolism of short-chain fatty acids (SCFAs), long-chain fatty acids (LCFAs), and lipopolysaccharides, as well as insulin signaling. These findings provide a theoretical reference for regulating rumen microbial communities to improve IMF deposition.}, }
@article {pmid41994130, year = {2026}, author = {Khan, D and Espinoza, JL and Tientcheu, PE and Otchere, ID and Mohammed, NI and Worwui, A and Nicol, MP and Kwambana-Adams, B and Antonio, M and Dupont, CL}, title = {Shotgun metagenomic profiling of bacterial microbiomes, metagenome-assembled genomes and antimicrobial resistance in respiratory and blood samples from Gambian children with pneumonia.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-8724320/v1}, pmid = {41994130}, issn = {2693-5015}, abstract = {Pneumonia is a leading cause of morbidity and mortality in children, with bacterial pathogens being important etiologic agents. Most microbiome studies in pneumonia use technologies with limited taxonomical resolution and few include lung aspirate or blood samples. In this study, we assessed the microbial communities of the nasopharynx, nasopharynx/oropharynx, induced sputum, lung aspirate and blood, and recovered metagenome-assembled genomes from the same sites using shotgun metagenomics sequencing of samples from children with severe and very severe pneumonia in The Gambia. Our data show that Proteobacteria and Firmicutes were the most common phyla across the body sites, and this was largely driven by S. pneumoniae, H. influenzae/aegyptius and M. catarrhalis. Furthermore, we observed species overlap of blood and respiratory samples with average Jaccard similarity index values ranging from 34% to 58%. We recovered 60 medium and 35 high-quality MAGs in these niches including 11 S. pneumoniae , 10 H. influenzae strains and a limosilactobacillus with less than 95% Average Nucleotide Identity to any known species in GTDB-TK. We also showed that the resistomes in our MAGs were highly species specific with more than 70% of the detected AMR genes found exclusively in a single species.}, }
@article {pmid41994193, year = {2026}, author = {Jiang, T and Yan, F and Liu, B and Li, Q and Wang, K and Ru, X and Hao, Y and Guan, Y and Wang, Y}, title = {Intraventricular hemorrhage, suspected EBV reactivation, and TBA-positive epilepsy after deep cervical lymphovenous anastomosis in Alzheimer's disease: a case report.}, journal = {Frontiers in aging neuroscience}, volume = {18}, number = {}, pages = {1791011}, pmid = {41994193}, issn = {1663-4365}, abstract = {Lymphovenous anastomosis (LVA) is emerging as a potential surgical intervention to ameliorate cervical lymphatic outflow and enhance glymphatic clearance in Alzheimer's disease (AD). However, the spectrum of neurological sequelae associated with this procedure remains poorly characterized. We report the case of a 67-years-old male with amyloid PET-confirmed AD who underwent bilateral deep cervical LVA. Twenty-three days postoperatively, he presented with high-grade fever and altered consciousness. Head CT revealed acute hemorrhage in the posterior horn of the left lateral ventricle (∼2 mL). Cerebrospinal fluid (CSF) analysis demonstrated lymphocytic pleocytosis and significantly elevated protein levels; the fluid was uniformly bloody, confirming intraventricular hemorrhage. Plasma metagenomic next-generation sequencing (mNGS) identified Epstein-Barr virus (EBV), with serology supporting reactivation. Following antiviral and empirical antibiotic therapy, the patient's condition stabilized, and the hemorrhage resolved. Four months postoperatively, he developed new-onset generalized seizures. Despite negative results from a conventional autoimmune encephalitis antibody panel in both serum and CSF, a tissue-based assay (TBA) proved positive in both samples. Seizures were successfully controlled with levetiracetam. This case suggests a potential association between invasive lymphatic procedures and a hemorrhage-infection-immune cascade in highly vulnerable AD patients with preexisting metabolic and neurodegenerative risk factors.}, }
@article {pmid41994268, year = {2026}, author = {Zhang, F and Chen, J and Yuan, Y and Chen, J and Jiang, W and Xiang, W and Wang, N and Wu, Z and Fan, S and Zhang, K and Ma, Y and Liu, T and Zhang, J and Yu, Q and Zhang, J}, title = {The enhancing therapeutic effect of neonatal jaundice by bifidobacterium through regulating inflammation and gut microbiota in combination with phototherapy-a randomized controlled trial.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1761245}, pmid = {41994268}, issn = {1664-302X}, abstract = {BACKGROUND: Hyperbilirubinemia is among the most common conditions in neonates, and phototherapy is currently the most widely used treatment. However, it can induce side effects such as skin rashes, diarrhea, and gut microbiota dysbiosis, particularly affecting Bifidobacterium levels. This study aimed to investigate whether the supplementation of Bifidobacterium can alleviate dysbiosis and improve clinical outcomes in jaundiced neonates.<br><br>METHODS: A total of 79 jaundiced neonates were enrolled and divided into four groups: Phototherapy Control, M-16V, Bb-12, and the combined M-16V+Bb-12 group. Probiotics were administered until 30 days post-discharge, and neurodevelopment was assessed at 1.5-2 years using the Griffith Development Scales. Fecal samples collected before, during, and after treatment were analyzed using metagenomic sequencing and non-targeted metabolomics.<br><br>RESULTS: Probiotic supplementation significantly increased daily defecation frequency, accelerated the reduction rate of transcutaneous bilirubin, and shortened hospital stays. Griffith scores indicated that Bb-12 supplementation improved scores in personal-social and performance domains. Metagenomic analysis revealed significant differences in beta diversity between the control and probiotic groups; specifically, M-16V and combined supplementation increased the abundance of Bifidobacterium breve. Pathway enrichment analysis showed up-regulation of pyrimidine-containing compound metabolic processes, intramolecular transferase activity, and DNA conformation change. Metabolomics further demonstrated that combined supplementation elevated levels of 5-methyltetrahydrofolate (linked to DNA synthesis), benzoic acid and indoleacetic acid (linked to growth and development), and the anti-inflammatory metabolite indole-3-lactic acid.<br><br>DISCUSSION: For neonates receiving phototherapy, the addition of M-16 V + Bb-12 probiotics can improve the diversity of microflora, reduce the fixed value of harmful bacteria in the intestine, and enhance the excretion of bilirubin from the intestine, to improve the inflammatory damage and microbiota disorder caused by phototherapy, and achieve the effect of clinically improving jaundice, reducing bilirubin, shortening the length of hospitalization, and promoting neurodevelopment. It provides a safer and more effective treatment for neonatal jaundice.}, }
@article {pmid41994275, year = {2026}, author = {Yu, T and Yu, Y and Zhao, J and Li, H and Lu, H and Li, Y and Peng, Y and Wang, S and Wei, W and Cheng, X}, title = {Qifuyin improves physiological frailty by regulating the intestinal flora in 3xTg-AD mice.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1753643}, pmid = {41994275}, issn = {1664-302X}, abstract = {OBJECTIVE: Alzheimer's disease (AD) is often accompanied by motor dysfunction, impaired limb strength, and gut microbiota disturbances. This study aimed to evaluate the effects of Qifuyin (QFY), a traditional Chinese medicine formula, on motor deficits, limb strength, aging, and gut microbiota composition in 3xTg-AD mice, a widely used model of AD.<br><br>METHODS: Male and female 3xTg-AD mice were administered QFY at low, medium, or high doses. Motor function was assessed using grip strength and rotarod tests. Aging was evaluated through aging scores. Gut microbiota composition was analyzed at the phylum, family, genus, and species levels. Functional profiling of microbiota was performed using KEGG, eggNOG, and carbohydrate-active enzyme (CAZyme) databases. Pearson correlation analyses were conducted to explore relationships between microbiota composition and motor performance.<br><br>RESULTS: QFY treatment significantly improved both absolute and normalized grip strength in male and female 3xTg-AD mice. Similarly, motor coordination, as assessed by latency to fall on the rotarod, was significantly enhanced in the groups of QFY. Aging scores were significantly reduced after the treatment of QFY. Microbiome analysis revealed that QFY treatment restored species diversity and improved the overall composition of gut microbiota, with significant increases in Muribaculaceae and decreases in Alcaligenaceae, Rhodanobacteraceae, and Spirochaetaceae. Principal component analysis (PCA) indicated that the gut microbiota composition of the QFY group resembled that of the control (Con) group. Functional analyses showed that treatment of QFY restored microbial pathways related to metabolism and genetic information processing, with significant correlations between microbial alterations and improved motor outcomes. Additionally, QFY modulated the abundance of key carbohydrate-active enzymes, including GH43 and GH35, which were positively correlated with grip strength and rotarod performance.<br><br>CONCLUSION: Qifuyin improves motor function, reduces aging-related deficits, and restores gut microbiota homeostasis in 3xTg-AD mice. These findings suggest that QFY may offer therapeutic potential for addressing frailty and motor dysfunction in AD, in association with alterations in gut microbiota composition and predicted microbial functions.}, }
@article {pmid41994276, year = {2026}, author = {Xian, J and Li, Y and Feng, Z and Jin, Y and Cai, T and Cao, M and Cao, Y}, title = {High-fat diet-driven gut microbial sphingolipid metabolic reprogramming is associated with stress susceptibility in CUMS rats.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1802003}, pmid = {41994276}, issn = {1664-302X}, abstract = {The escalating comorbidity between depression and metabolic syndromes induced by a high-fat diet (HFD) poses a substantial social and economic burden on society. However, the precise molecular mechanisms by which a HFD qualitatively alters the basal pathophysiology of chronic unpredictable mild stress (CUMS) remain unclear. In this study, the differential roles of microbial and metabolic pathways in the onset and exacerbation of depression were investigated using CUMS rat models fed a normal diet (ND-CUMS) or HFD (HFD-CUMS). Our findings indicated that HFD intervention showed a trend toward aggravating depressive behaviors and resulted in significantly more severe neuronal injury in the hippocampus relative to the ND-CUMS group. Notably, integrated multi-omics (metagenome and metabolome) analysis revealed a crucial pathway divergence: basal CUMS depression was strongly associated with the dysregulation of glycerophospholipid metabolism, linked to microbiota such as Bacteroides thetaiotaomicron and Terrisporobacter glycolicus, while HFD triggered a predominant disruption of the sphingolipid metabolism pathway. Exploratory mediation analysis suggested that a sphingolipid-related signature that may statistically connect HFD-associated microbial shifts with neural injury and behavioral readouts. Therefore, our findings reveal a distinct mechanistic shift underpinning metabolic-comorbid depression. HFD does not merely exacerbate stress-induced depression but fundamentally transitions the underlying pathology from glycerophospholipid to sphingolipid signaling, highlighting the potential of targeting specific lipid metabolic reprogramming as a promising therapeutic strategy for combating metabolic-comorbid depression.}, }
@article {pmid41994278, year = {2026}, author = {Dang, M and Tang, Y and Chen, J and Xie, W and Zhong, Y and Yu, B and Zhang, E and Wang, Z}, title = {Rhizospheric soil microbial community structure and metabolic characteristics of wild Cymbidium mastersii at different altitudes.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1720137}, pmid = {41994278}, issn = {1664-302X}, abstract = {INTRODUCTION: Cymbidium mastersii, a perennial orchid of high ornamental value, faces severe survival challenges due to extremely low natural seed germination rates (<15%), habitat degradation, and illegal harvesting. It is listed as a Category II Nationally Protected Plant Species in China.<br><br>METHODS: We examined the rhizosphere microbial communities and metabolomes of C. mastersii across elevation gradients. We investigated the rhizospheric soil microbial community composition and metabolic characteristics of C. mastersii across different elevations.<br><br>RESULTS: The dominant bacterial phylum was Pseudomonadota, with relative abundances of 38.22% (CmL, low elevation), 36.91% (CmM, mid-elevation), and 62.54% (CmH, high elevation). While the dominant bacterial genera varied significantly with elevation, taxonomic richness exhibited a consistent decline with increasing altitude (p&#x202f;<&#x202f;0.05, linear regression), indicating altitudinal filtering of microbial diversity. LC-MS/MS metabolomic profiling identified 1,516 metabolites, predominantly enriched in lipid and lipid-like molecules, carbohydrates and derivatives, and aromatic compounds. Functional contribution analysis revealed Bradyrhizobium as the most influential taxon (10% variance explained), displaying a nonlinear elevational response. Correlation analysis of differential metabolites confirmed significant species-metabolite correlations (P < 0.05, R > 0.7). Our findings underscore the critical role of trophic interactions in shaping rhizosphere community assembly in alpine plants, thereby contributing to the broader understanding of microbial biogeography along elevational gradients.<br><br>DISCUSSION: This study not only confirms that the altitudinal gradient serves as a key environmental filter shaping the rhizosphere microecology of C. mastersii, but more importantly, by integrating metagenomic and metabolomic approaches, we systematically reveal for the first time that altitude differentially selects for microbial taxa with specific functions, ultimately driving the restructuring of the rhizosphere metabolic environment. Moving beyond mere community description, our work aims to elucidate the underlying pathways responsible for these shifts and their potential functional implications for host plant adaptation.}, }
@article {pmid41994292, year = {2026}, author = {Sun, M and Lei, Z and Li, B and Gao, SH and Fan, L}, title = {Virus-encoded metabolism may support environmental stress adaptation of microbial hosts in an estuarine hypoxic zone.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1785655}, pmid = {41994292}, issn = {1664-302X}, abstract = {Hypoxic zones in estuaries threaten the ecological balance and the productivity in coastal areas. However, it is poorly understood how viruses regulate metabolic processes of their microbial hosts to adapt to the hypoxic environment, and consequently impact the biogeochemical cycles in hypoxic zones. In this study, the diversity and functional potentials of the bacterial, archaeal and viral communities of a hypoxic zone at the Pearl River Estuary was characterized along with local environmental factors, with a particular focus on viral auxiliary metabolic genes (AMGs). The viral community derived from the virion fraction and the cellular fraction of the seawater were distinctly different, with the cellular fraction generating fewer unique viruses, but more types of AMGs. Overall, more AMGs were identified in samples with higher dissolved oxygen levels. Globally conserved AMGs were infrequently observed in the current samples, suggesting a certain level of adaptation of AMGs to the local environment. There were strong correlations in abundances among cyanobacteria, cyanophages, and photosynthesis AMGs, suggesting potential viral participation in estuarine primary production. Many AMGs involved in nutrient limitation endurance were found, potentially assisting their host with phosphorus, iron and B family vitamin shortages. Although putative hosts were predicted for the viruses, the functionality of their AMGs appears to be a better predictor of their distribution than the hosts they infect. Our study provides a functional insight into the viral community in poorly researched estuarine hypoxic zones, and sheds light on the potential interactions of viruses with their microbial hosts for co-adaptation to this unique environment.}, }
@article {pmid41994309, year = {2026}, author = {Sarkar, P and Sarkar, S and Unnisa, M and Singh, AP and Inavolu, P and Rughwani, H and Jakkampudi, A and Jaggaiahgari, S and Reddy, DN and Talukdar, R}, title = {The Jejunal Microbiota in Patients With Chronic Pancreatitis: Results From a Pilot Study.}, journal = {Gastro hep advances}, volume = {5}, number = {5}, pages = {100907}, pmid = {41994309}, issn = {2772-5723}, abstract = {BACKGROUND AND AIMS: Chronic pancreatitis (CP) is associated with several systemic metabolic abnormalities including diabetes. While the colonic microbiota and its association with diabetes in CP have been reported, the specific composition of the small intestinal microbiota and its function in CP remains poorly understood. In this pilot study, we primarily aimed to characterize the jejunal microbiota in patients with CP and explore potential associations with diabetes.<br><br>METHODS: Jejunal aspirates were collected in a RNAlater-containing sterile container from 29 patients with CP and 10 controls. The samples were then snap lysed followed by metagenomic DNA extraction. Next-generation sequencing was performed for the variable region 3-4 of the 16SrDNA in Illumina MiSeq. After quality control, microbial profiling and functional analysis were conducted using standard bioinformatics pipelines. We also evaluated tight junction integrity in jejunal biopsy samples using immunofluorescence. Furthermore, we assessed for plasma and stool metabolites.<br><br>RESULTS: Patients with CP exhibited higher abundances of Prevotella vespertina, Prevotella oris, and Prevotella salivae, while controls demonstrated higher abundances of Prevotella scopos, Veillonella, Rothia, and Lachnospiraceae. Immunofluorescence showed decreased expression of the tight junction protein occludin in the jejunal mucosa of CP diabetic (CPD) patients compared to endoscopic controls (EC) (p.corr. CPD-EC = 0.012). No differences were seen between CP nondiabetic and endoscopic controls, and between the CP subgroups (CPND-EC = 0.29 and CPD-CPND = 1 respectively). Overall, there were significant plasma metabolomic abnormalities in patients with CP and a trend toward reduction of butyrate in the stool samples of the CP patients with diabetes.<br><br>CONCLUSION: Our observations suggest alterations in the jejunal microbiota and mucosal barrier function in CP. These were associated with lower fecal butyrate. This may contribute to the pathogenesis of associated metabolic complications in CP. Further large-scale longitudinal and mechanistic studies are needed to validate our findings.}, }
@article {pmid41994369, year = {2026}, author = {Bao, Q and Zhang, X and Guo, J}, title = {Enterovirus D68 and mycobacterial coinfection: case report.}, journal = {Therapeutic advances in infectious disease}, volume = {13}, number = {}, pages = {20499361261432918}, pmid = {41994369}, issn = {2049-9361}, abstract = {The threat of viral epidemics to long-standing diseases, such as mycobacterial infection, is constantly evolving. Enterovirus D68 (EV-D68) is an emerging cause of respiratory infection and has raised great interest since its first outbreak in 2014. Very few studies have been done to describe the clinical aspects of the coinfection of EV-D68 and mycobacteria, so this study was conducted to help round out the understanding of this coinfection pattern. We observed three adult cases of EV-D68 and mycobacteria, who were admitted to the first affiliated hospital of Zhejiang University in August/September 2024. Only one case had a definite past history of immunodeficient disease and received long-term corticosteroid treatment, and the other two were previously healthy. The diagnoses of EV-D68 and mycobacterial infection were all simultaneously confirmed through the metagenomic Next-Generation Sequencing in bronchoalveolar lavage fluid specimens. All three patients were presented with severe respiratory symptoms, such as fever, cough, dyspnea and tachypnea, without any manifestations of central nervous system involvement. The radiological findings in chest CT scans varied from patchy opacity to massive consolidation. The individualized anti-mycobacterium treatment showed little therapeutic effect, while the improvement of symptoms and pulmonary lesions in chest CT was observed after starting or intensifying the administration of corticosteroid. All patients had a marked clinical improvement when discharged from hospital, and it took about 6-9 months for the lung lesions of mycobacterial infections to nearly resolve. These cases illustrate the potential for EV-D68 coinfection to exacerbate pulmonary inflammation in patients with mycobacterial disease, highlighting the need for vigilance regarding possible viral coinfections in settings with a high tuberculosis burden, such as China.}, }
@article {pmid41994453, year = {2026}, author = {Zhang, W and Zhang, K and Liao, Y and Yang, Z and Xia, Z and Ke, X and Zhang, D and Chen, J and Wu, H and Hong, Y and Wang, H and Liu, Z and Suo, L and Zhang, Y and Zhang, C}, title = {Characterization of the aqueous humor microbiome in Posner-Schlossman syndrome: an exploratory metagenomic sequencing study.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1780981}, pmid = {41994453}, issn = {2296-858X}, abstract = {OBJECTIVE: This study aims to characterize the aqueous humor (AH) microbiome in Posner-Schlossman syndrome (PSS) patients and evaluate its potential as a diagnostic and therapeutic target.<br><br>METHODS: Metagenomic next-generation sequencing (mNGS) was performed on 59 AH samples from patients diagnosed with PSS (n&#x202f;=&#x202f;28) and myopia patients who underwent intraocular lens (ICL) implantation (n&#x202f;=&#x202f;31). Taxonomic profiling and diversity analyses were conducted to characterize the microbial communities. Interactions among microbial community members were evaluated using correlation analyses.<br><br>RESULTS: Key findings revealed that intraocular microbiomes existed in both normal and diseased eyes; however, PSS patients exhibited lower microbial diversity (Shannon index, p&#x202f;=&#x202f;0.066; Simpson index, p&#x202f;=&#x202f;0.065) and distinct community structures (PERMANOVA, p&#x202f;=&#x202f;0.05). Disease-specific microbial signatures were identified: Paeniglutamicibacter was uniquely enriched in the PSS group, whereas Escherichia coli dominated in the ICL group. Moreover, ecological network analysis demonstrated contrasting interaction patterns. The microbiomes in the PSS group formed stable, tightly connected networks with balanced positive/negative correlations, whereas those in the ICL group exhibited antagonistic relationships, suggesting competitive exclusion. These results challenge the traditional view of ocular sterility and reveal dynamic microbiome shifts associated with PSS pathogenesis. The enrichment of Paeniglutamicibacter in PSS may represent an associated microbial signature that could potentially reflect compensatory responses to chronic inflammation, although experimental validation is needed to confirm this hypothesis.<br><br>CONCLUSION: Our study provides preliminary evidence supporting the concept of intraocular microbiome dysbiosis in PSS, which requires validation in future studies. These findings suggest that potential microbial biomarkers warrant further investigation for their diagnostic and therapeutic implications.}, }
@article {pmid41994458, year = {2026}, author = {Jiang, L and Ye, T and Cai, H and He, F}, title = {Case Report: A rare case of Pneumocystis jirovecii infection with left hydropneumothorax following immunotherapy for stage IVB clear cell renal cell carcinoma.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1784855}, pmid = {41994458}, issn = {2296-858X}, abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) is an opportunistic infection that predominantly affects immunocompromised individuals, most commonly HIV-infected patients with significantly reduced CD4+lymphocyte counts, and is associated with high clinical mortality. Currently, there are few reports of pneumothorax secondary to PJP, and most cases occur in HIV-infected populations. However, PJP complicated by hydropneumothorax in cancer patients receiving immunotherapy is exceedingly rare, with limited reports in the literature. To our knowledge, this article reports a rare clinical case of Pneumocystis jirovecii infection complicated by left-sided hydropneumothorax in a patient with stage IVB clear cell renal cell carcinoma after immunotherapy, aiming to provide valuable insights for the early diagnosis and management of PJP and its complications in cancer patients undergoing immunotherapy.<br><br>CASE: A 57-year-old male patient had previously undergone surgical treatment for left renal clear cell carcinoma, and developed recurrent metastases to the descending colon, liver, and upper pole of the left kidney after surgery, with a clinical stage of T4NxM1 stage IVB. After receiving targeted combination immunotherapy with sequential PD-1 inhibitors (toripalimab) plus anti-angiogenic agents (sunitinib, axitinib)-a regimen that enhances anti-tumor immunity but may disrupt pulmonary immune homeostasis-the patient gradually developed progressive dyspnea, chest tightness, hypoxemia, and anuria. Multiple auxiliary examinations were performed clinically, including chest X-ray, bronchoalveolar lavage, and metagenomic sequencing of pathogenic microorganisms. Based on the above examination results, the final diagnosis was Pneumocystis jirovecii pneumonia complicated by left-sided hydropneumothorax.<br><br>CONCLUSION: Although PJP complicated by hydropneumothorax after immunotherapy is rare, it should be considered as a possible etiology when cancer patients develop progressive dyspnea with difficulty maintaining oxygen saturation after receiving immune checkpoint inhibitor-based therapy, particularly in the context of immune checkpoint inhibitor use. While biomarkers for predicting immunotherapy efficacy and irAEs are well-studied, the identification of specific biomarkers for predicting opportunistic infections like PJP in this context remains an area of active research.}, }
@article {pmid41994961, year = {2026}, author = {Sun, QG and Zang, D and Xin, Y and Cui, J and Han, X and Chen, J}, title = {Multi-omics Analysis Reveals the Correlation of Gut Microbiota and Metabolites With Thalidomide Treatment for Chemotherapy-Induced Nausea and Vomiting in Small Cell Lung Cancer.}, journal = {Biotechnology journal}, volume = {21}, number = {4}, pages = {e70228}, doi = {10.1002/biot.70228}, pmid = {41994961}, issn = {1860-7314}, support = {82203056//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Small Cell Lung Carcinoma/drug therapy ; *Lung Neoplasms/drug therapy ; Male ; Female ; Middle Aged ; *Thalidomide/therapeutic use/adverse effects/pharmacology ; *Vomiting/chemically induced/drug therapy ; *Nausea/chemically induced/drug therapy ; Aged ; *Antineoplastic Agents/adverse effects/therapeutic use ; Metabolomics/methods ; Metabolome/drug effects ; Feces/microbiology ; Multiomics ; }, abstract = {Small cell lung cancer (SCLC) is a highly aggressive malignancy, and chemotherapy frequently causes nausea and vomiting, which can impair treatment tolerance. Because thalidomide (THD) has shown potential clinical benefit in alleviating nausea and anorexia, we investigated whether its effects might be associated with changes in gut microbial composition and metabolite profiles. Fecal samples were collected from patients with SCLC and categorized into THD-treated and control groups. Metagenomic sequencing and nontargeted metabolomic profiling were performed to characterize microbial composition and metabolic signatures. THD treatment was also associated with higher microbial alpha diversity and increased abundance of genera such as Eubacterium and Prevotella. Metabolomic analysis identified several differential metabolites, including hydrogenated MDI, becocalcidiol, β-octylglucoside, and azelaic acid. Collectively, these findings suggest that the gut microbiota-metabolite axis may be associated with the potential effects of THD on CINV and anorexia in patients with SCLC. The identified microbial taxa and metabolites may serve as candidate biomarkers or potential therapeutic targets, although further validation in larger studies is necessary.}, }
@article {pmid41995327, year = {2026}, author = {Chen, Y and Tang, X and Lu, S and Guo, L and Wang, L and Min, L and Niu, T and Zhou, Y}, title = {The diagnostic and prognostic utility of blood metagenomic next-generation sequencing for invasive pulmonary aspergillosis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0338425}, doi = {10.1128/spectrum.03384-25}, pmid = {41995327}, issn = {2165-0497}, abstract = {UNLABELLED: Differentiating invasive pulmonary aspergillosis (IPA) from colonization in patients with Aspergillus-positive blood metagenomic next-generation sequencing (mNGS) remains a clinical challenge. This study aims to evaluate the diagnostic and prognostic value of blood mNGS-derived fungal load (reads per million [RPM]) and two key serological biomarkers (galactomannan [GM] and 1,3-β-D-glucan [BDG]) in distinguishing these two entities. This retrospective study enrolled 95 patients with Aspergillus detected by blood mNGS, stratified into infection (n = 60) and colonization (n = 35) groups using modified EORTC/MSGERC criteria. We analyzed clinical characteristics, co-infection spectra, and serological biomarkers (GM and BDG). Diagnostic performance was evaluated via receiver operating characteristic (ROC) analysis, and prognostic factors for 28-day mortality were identified using least absolute shrinkage and selection operator-Cox regression. Distinct co-infection patterns were observed between groups: the infection group was dominated by polymicrobial co-infections, including clinically significant pathogens such as Acinetobacter baumannii, Klebsiella pneumoniae, Mucor spp., and Human cytomegalovirus; in contrast, the colonization group primarily featured single viral co-infections. While mNGS effectively detected Aspergillus, RPM alone showed limited ability to discriminate infection from colonization, with area under the curves (AUCs) ranging from 0.406 to 0.657 across patient groups. The optimal RPM cutoff varied substantially by immune status, being highest in immunocompetent patients (RPM cutoff: 1.77). Diagnostic performance significantly improved when RPM was integrated with GM (AUC up to 0.900 at a cutoff of 0.36 optical density index) or BDG (AUC up to 0.881 pg/mL), particularly in immunocompetent individuals. RPM also correlated with albumin, hemoglobin, platelet counts, and lymphocyte counts (all P < 0.05). Multivariate analysis identified reversed halo sign (hazard ratio [HR] = 2.143), decreased ratio of partial pressure of arterial oxygen to fraction of inspired oxygen (PaO2/FiO2; HR = 1.361), and elevated lactate dehydrogenase (HR = 1.055) as independent predictors of 28-day mortality. Blood mNGS demonstrates high sensitivity for detecting Aspergillus but requires integration with serological biomarkers to differentiate IPA from colonization. The RPM can offer prognostic utility. A multimodal strategy is crucial for early diagnosis and improving outcomes in high-risk patients.<br><br>IMPORTANCE: First large-scale validation of blood mNGS for invasive pulmonary aspergillosis diagnosis-this study represents the first sizable cohort systematically evaluating blood metagenomic next-generation sequencing (mNGS) for distinguishing invasive pulmonary aspergillosis from colonization, addressing a critical gap in non-invasive diagnostic approaches for critically ill patients. Comprehensive Aspergillus co-infection profiling-we identified distinct co-infection patterns, with the infection group showing significantly higher rates of polymicrobial infections, providing crucial insights into co-infection dynamics in Aspergillosis. Optimized diagnostic integration strategy-our findings demonstrate that while mNGS-derived reads per million alone show limited diagnostic value, their integration with serological biomarkers significantly improves performance, establishing a clinically relevant multimodal diagnostic framework. Robust prognostic stratification model-through least absolute shrinkage and selection operator-Cox regression, we established a validated prognostic model identifying reversed halo sign, decreased PaO2/FiO2, and elevated lactate dehydrogenase as independent predictors of 28-day mortality, providing clinically actionable tools for risk stratification.}, }
@article {pmid41995478, year = {2026}, author = {Conley, TE and Duncan, A and Modasia, A and Ford, AC and Pritchard, DM and Hildebrand, F and Warren, FJ and Spiller, R and Probert, CS}, title = {The Emerging Short Chain Fatty Acid Enriched Metabotype in Irritable Bowel Syndrome and Its Potential Clinical Relevance.}, journal = {Alimentary pharmacology &amp; therapeutics}, volume = {}, number = {}, pages = {}, doi = {10.1111/apt.70677}, pmid = {41995478}, issn = {1365-2036}, abstract = {BACKGROUND: Metabolomic analysis in irritable bowel syndrome (IBS) has identified metabotypes enriched in faecal short-chain fatty acids (SCFAs), but it remains unclear whether this reflects rapid colonic transit or if these metabolites actively contribute to pathophysiology.<br><br>AIMS: We aimed to determine whether an SCFA metabotype could be identified within a cohort of patients with moderate-severe IBS-D and assess whether this metabotype associated with greater clinical severity, alterations in gut transit time and specific microbiome features.<br><br>METHODS: This was a post hoc cross-sectional exploratory analysis of baseline data from the multicentre, randomised, placebo-controlled trial of ondansetron in IBS-D (TRITON: ISRCTN17508514). Faecal volatile organic compounds were profiled by GC-MS. The microbiome was characterised by whole-genome shotgun metagenomic sequencing. Unsupervised hierarchical clustering was used to identify an SCFA-enriched metabotype and non-negative matrix factorisation (NMF) enabled the derivation of complementary metabosignatures by assessing continuous gradients in metabolite composition.<br><br>RESULTS: A SCFA-enriched metabotype was identified in 20/63 participants (31.7%). This metabotype was associated with more severe abdominal pain, urgency, increased stool frequency and faster whole-gut transit. NMF identified three metabosignatures: S3 was typified by a high proportion of SCFAs and captured the SCFA-enriched metabotype, while S1 and S2 corresponded to the non-SCFA ("Other") metabotype. SCFA relative abundance positively correlated with symptom severity and inversely correlated with transit time. The Other metabotype and S1/S2 signatures were enriched in taxa linked to slower transit, whereas S3 showed no overlapping taxa with the SCFA metabotype.<br><br>CONCLUSION: A faecal metabotype enriched in SCFAs associated with an IBS-D phenotype characterised by pain, urgency, rapid transit and higher stool frequency.}, }
@article {pmid41995796, year = {2026}, author = {Vial, M and Costil, K and Agogué, J and Eustache, S and Heighton, S and Gissat, L and Gueuné, H and Caplat, C}, title = {Spatial and temporal variability of biofouling communities during early development in three French harbors of the English Channel.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {5}, pages = {}, pmid = {41995796}, issn = {1573-2959}, mesh = {*Biofouling/statistics &amp; numerical data ; *Biofilms/growth &amp; development ; *Environmental Monitoring ; France ; Aquatic Organisms/physiology ; Chlorophyll A/analysis ; Seawater/microbiology ; }, abstract = {Biofouling, the colonization of submerged surfaces by marine organisms, causes major economic losses in maritime activities. Although non-biocidal surface coatings are promoted as environmentally friendly antifouling solutions, the respective roles of surface properties and environmental conditions in shaping biofouling stages remain unclear. We hypothesized that coating surface properties primarily control early biofilm formation, whereas local environmental conditions govern subsequent macrofouling development. To test this hypothesis, we studied biofouling on two non-biocidal coatings - an anticorrosion epoxy and a fluoropolymer foul-release coating (FRC) - immersed under static conditions in three French harbors along the English Channel during the spring bloom. Early biofilm formation was assessed after 2 weeks in April, May, and June 2023 using chlorophyll a and the carbohydrate/protein ratio of extracellular polymeric substances (EPS). Macrofouling development over 3 months was evaluated through biomass, surface coverage rate, taxonomic composition, and microorganism abundances. Metagenomic analyses complemented the visual observations in Cherbourg during April and May 2023. The FRC showed a higher EPS carbohydrate/protein ratio, indicating greater resistance to initial microbial colonization, but exhibited significantly lower macrofouling intensity than the epoxy. This decoupling supports the hypothesis that surface properties and settlement processes operate at different spatial and temporal scales. Spatial variability in biofouling patterns may largely be associated with differences in nutrient availability and anthropogenic pressure. These findings demonstrate that early biofilm metrics alone cannot predict long-term fouling and highlight that antifouling performance depends on both material properties and environmental context. Integrating surface physicochemistry with site-specific ecological drivers can improve both coating design and antifouling evaluation strategies.}, }
@article {pmid41996042, year = {2026}, author = {Myoung, K and Kim, S and Choi, EJ and Kim, HJ and Baek, HS and Park, WS and Hwang, JS}, title = {Integrated analysis of age-related microbiome and metabolites reveals youth-associated metabolites in young Korean women's skin.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41996042}, issn = {1618-1905}, abstract = {Alterations in the composition and functional potential of the skin microbiome are closely associated with aging. Nevertheless, integrative analyses that concurrently examine microbial composition, functional gene profiles, and skin surface metabolomics remain limited, particularly among Asian populations. In this study, we performed a comprehensive multi-omics analysis integrating skin microbiome and surface metabolomic data from Korean women to explore metabolites associated with youthful skin state. Twenty-three healthy female participants in their 20s and 60s were recruited. Skin physiological parameters were assessed, and microbiome and metabolite samples were collected from the cheek area. Unsupervised clustering of microbiome functional profiles revealed three microbial community patterns that were not strictly aligned with chronological age. Based on these patterns, samples were grouped into three functional groups. The cluster enriched in participants in their 20s showed higher relative abundance of Cutibacterium and enrichment of microbial pathways related to carbohydrate and energy metabolism. Metabolomic profiling showed that phenyllactic acid (PLA) and hydroxyphenyllactic acid were more abundant in participants in their 20s and in the functionally young cluster. These metabolite patterns were accompanied by higher abundance of genes associated with phenylalanine metabolism. In vitro experiments further showed that PLA increased procollagen production and reduced the secretion of collagen-degrading enzymes in human dermal fibroblasts under inflammatory conditions. Together, these findings suggest links between microbiome functional profiles, phenylalanine-related metabolites, and skin physiology. This study provides an integrated view of microbiome-metabolite relationships in Korean skin and identifies PLA as a candidate metabolite associated with youthful skin environments.}, }
@article {pmid41996045, year = {2026}, author = {Mohanty, A and Pavan-Kumar, A and Chaudhari, A and Kumari, K and Kumar, P and Maurye, P}, title = {Comparative performance of traditional and commercial DNA extraction methods for fish gut microbiota analysis.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {41996045}, issn = {1573-4978}, support = {FBT-PB1-01//Indian Council of Agricultural Research/ ; }, }
@article {pmid41996243, year = {2026}, author = {Lin, D and Ma, QX and Ye, YQ and Wanek, W and Gregory, AS and Jones, DL and Graham, DW and Zhu, D and Penuelas, J and Zhu, YG}, title = {Nutrient balance regulates soil microbial health under long-term fertilization.}, journal = {Cell reports}, volume = {45}, number = {4}, pages = {117274}, doi = {10.1016/j.celrep.2026.117274}, pmid = {41996243}, issn = {2211-1247}, abstract = {Fertilizer application in intensive agriculture critically influences microbial communities. It is still unclear how long-term input of different nutrients shapes microbial eco-evolutionary strategies and ecological functions. Through 180-year-old field fertilization experiment, alongside microbial culturing, pot experiments, and comprehensive metagenomic data analysis, we show that exclusive fertilization with inorganic chemicals causes carbon-nitrogen imbalances that increase microbial resource competition and antibiotic resistance gene (ARG) levels. Viruses further amplify this expansion through "piggyback the winner" strategy. The imbalanced use of nitrogen in chemical fertilizers disrupt ecological niche connections, leading to an increase in virulent viruses and reducing microbial nutrient cycling capacity. In contrast, more balanced nutrient supplies from organic fertilization reduced microbial competition and promoted microbial growth. However, responsible antibiotic use in livestock is essential to maximizing these benefits. Our research provides insights into enhancing agricultural sustainability through the management of soil nutrient conditions.}, }
@article {pmid41996362, year = {2026}, author = {Buni, D and Kovács, &#xc1;B and Wehmann, E and Grózner, D and Bányai, K and Nagy, EZ and Bradbury, J and Bottinelli, M and Stefani, E and Catania, S and Lysnyansky, I and Kovács, L and Gyuranecz, M and Kreizinger, Z}, title = {Identification and detection of genetic markers associated with antimicrobial susceptibility and evaluation of efflux pump mechanisms in Mycoplasma iowae.}, journal = {PloS one}, volume = {21}, number = {4}, pages = {e0347345}, doi = {10.1371/journal.pone.0347345}, pmid = {41996362}, issn = {1932-6203}, mesh = {Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; *Mycoplasma/genetics/drug effects/metabolism ; Genetic Markers ; *Drug Resistance, Bacterial/genetics ; *Bacterial Proteins/genetics/metabolism ; Promoter Regions, Genetic ; }, abstract = {Mycoplasma iowae is an economically significant pathogen that causes reduced hatchability, late embryo mortality and leg deformities, chondrodystrophy and skeletal lesions in poults. While prevention is essential in the control of infection, the appropriate administration of antibiotics may reduce economic losses during outbreaks. As a first step in the exploration of antimicrobial resistance mechanisms in M. iowae, target modification and efflux pump activity were examined in the present study. Point mutations were analyzed in previously described antibiotic binding sites in the whole genome sequences of 99 M. iowae strains. Mismatch amplification mutation assays (MAMAs) were designed and validated for the differentiation of mutations corresponding to elevated minimum inhibitory concentration (MIC) values for fluoroquinolones. Broth microdilution assays were performed to evaluate the effect of efflux pump inhibitors. In the presence of orthovanadate (OV), MIC values were significantly lower than in the absence of OV for spiramycin, tilmicosin, tylosin and oxytetracycline, which may indicate the presence of an active efflux system in M. iowae. Putative promoter regions of efflux-related genes were predicted and characterized. Genetic mutations, previously described in other bacteria, were described to be associated with elevated fluoroquinolone, macrolide and lincomycin MICs in M. iowae, although certain resistant phenotypes remained unexplained, promoting future examinations for deeper insights. The developed MAMAs may support rapid identification of M. iowae strains with elevated MIC values for fluoroquinolones. The better understanding of the efflux pump mechanisms enables the development of alternative methods for the support of therapy against this pathogen.}, }
@article {pmid41996550, year = {2026}, author = {Bechtner, J and Hosek, J and Schwab, C}, title = {Fecal Material of Captive Wild Animals as Source of CAZymes With Application Potential.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {27}, number = {8}, pages = {e70315}, doi = {10.1002/cbic.70315}, pmid = {41996550}, issn = {1439-7633}, support = {grant NNF22OC0079746//Novo Nordisk Fonden/ ; grant AU FF-F-2020-7//Aarhus Universitets Forskningsfond/ ; }, mesh = {Animals ; *Feces/microbiology ; *Animals, Wild/microbiology ; *Glycoside Hydrolases/metabolism ; Gastrointestinal Microbiome ; }, abstract = {Gastrointestinal systems of mammals and birds host taxonomically complex and functionally diverse microbial communities. Microbial activities contribute to community functioning and interaction with the host but can also be exploited as a source of novel enzymes or other industrially relevant microbial traits. With the overall goal to identify new resources for carbohydrate-active enzymes (CAZymes), we bioprospected fecal microbial communities of the little-explored source of captive wild animals. Using dbcan3, we identified a CAZyome dominated by glycosyl hydrolases (GHs) specialized in degrading oligo- and polysaccharides with much lower diversity and abundance of glycosyl transferases, carboxyl esterases, polysaccharide lyases, and redox enzymes with auxiliary activity. CAZyome profiles differed between animals depending on gut physiology and diet. Crude cell extracts conferred hydrolytic activity against compositionally and structurally diverse polysaccharides and nitrophenyl-sugar analogs. We identified five candidate GH68 and GH70 enzymes with the potential to produce oligo- and polysaccharides from sucrose, highlighting that fecal metagenomes are a source of rare CAZymes with industrial relevance. Taken together, we exemplify the functional potential captive wild animal fecal microbiota and suggest such a gene pool as a largely untapped resource for the discovery of novel biotechnological applications.}, }
@article {pmid41996772, year = {2026}, author = {Haydar, MS and Alzate Zuluaga, MY and Astolfi, S and Del Buono, D and Cesco, S and Pii, Y}, title = {Nanoparticle-rhizosphere crosstalk: Insights into transformation, microbial interaction, plant uptake and translocation.}, journal = {Chemosphere}, volume = {403}, number = {}, pages = {144936}, doi = {10.1016/j.chemosphere.2026.144936}, pmid = {41996772}, issn = {1879-1298}, abstract = {For soil-applied engineered nanomaterials, the rhizosphere is the critical frontline zone where they encounter crop roots, microbes, and soil, determining their agronomic potential and environmental risks. Within this dynamic interface, nanoparticles (NPs), depending on their surface chemistry, particle size, properties, and composition, undergo physicochemical and biological transformations that govern their stability, dissolution, mobility, availability, and ecotoxicological outcomes. This review synthesizes current mechanistic evidence linking root exudation patterns, microbial activity, and soil physico-chemical conditions to NPs aggregation, dissolution, redox conversions, and eco-/bio-corona formation. Microbial extracellular polymeric substances, low-molecular-weight metabolites, siderophores, and biofilms further reshape particle speciation, modulating ion release, immobilization, nutrient availability, and potential toxicity to soil biota and crops. Once inside roots, nanoparticles follow multiple uptake routes, including apoplastic diffusion, endocytosis, plasmodesmata-mediated transport, and vascular translocation, while undergoing in-planta transformations into ionic or ligand-bound forms with distinct physiological and agronomical consequences. These processes are strongly context-dependent, shaped by plant species, development stage, NPs concentration, and soil-climate conditions, and mediated by a tripartite molecular dialogue among NPs, microbes, and plant signalling pathways that regulate root system architecture, rhizosphere microbial recruitment, and nutrient acquisition efficiency. Advances in high-resolution and multi-omics tools-such as synchrotron-based spectroscopy, single-particle ICP-MS, NanoSIMS, stable-isotopic tracers, and metagenomics are offering new insights into these interactions under realistic agricultural scenarios. We propose an integrated agroecological framework linking rhizospheric NPs transformations to plant uptake and responses, emphasizing the need for standardized exposure metrics, realistic concentrations, and long-term field trials for safe and sustainable nanotechnology use in agriculture.}, }
@article {pmid41996801, year = {2026}, author = {Chen, Y and Sun, Y and Yang, Y and Hu, S and Cui, K and Zhu, C and Fu, XZ and Li, CX and Jiang, P and Huang, Q}, title = {Differential distribution characteristics of heavy metal resistance genes and driving mechanisms of heavy metal speciation in river-lake system sediments.}, journal = {Journal of hazardous materials}, volume = {510}, number = {}, pages = {142080}, doi = {10.1016/j.jhazmat.2026.142080}, pmid = {41996801}, issn = {1873-3336}, abstract = {River-lake systems are critical zones for heavy metal biogeochemical cycling, yet the mechanisms linking heavy metal pollution to heavy metal resistance genes (MRGs) across hydrological gradients remain elusive. This study selected the Chaohu Lake Basin as a representative river-lake system to investigate the distribution characteristics of MRGs and their driving mechanisms on heavy metal speciation. Based on metagenomic sequencing and ICP-MS analysis of 78 sediment samples collected in wet and dry seasons, we found that the resistome was dominated by multi-metal, Cu, and As resistance genes, with the arsenic resistance gene pstA identified as a consistent network hub. MRGs diversity and network complexity exhibited significant seasonal depletion and spatial heterogeneity along the river-lake gradient. Heavy metals were predominantly fractionated into the stable residual phase; however, the river-lake gradient significantly influenced the spatial distribution of bioavailable fractions. Crucially, Structural Equation Modeling (SEM) revealed a seasonal shift in the regulatory mechanisms controlling heavy metal speciation. In the wet season, the river-lake system operated under a "biologically mediated" mode, where MRGs directly facilitated the mobilization of the reducible fraction. In the dry season, it shifted to a "physicochemically driven" mode, governed primarily by basic physicochemical factors. These findings highlighted that seasonal dynamics and the river-lake gradient jointly coordinated heavy metal fate through a complex interplay of biotic and abiotic factors, providing molecular-level insights for pollution management in continuous aquatic systems.}, }
@article {pmid41996860, year = {2026}, author = {Ji, Z and Fu, Z and Miao, L and Hang, D and Gu, A}, title = {Relationship between pesticide exposure, gut microbiota, and hypertension.}, journal = {Environment international}, volume = {211}, number = {}, pages = {110250}, doi = {10.1016/j.envint.2026.110250}, pmid = {41996860}, issn = {1873-6750}, abstract = {BACKGROUND: Both pesticide exposure and gut dysbiosis have been independently linked to an elevated risk of hypertension. However, the extent of interaction between these two factors remains poorly characterized in human populations.<br><br>METHODS: In a population-based study involving 218 adults from Jiangsu Province, China, we quantified pesticides in serum using LC-MS/MS and analyzed the gut microbiome via metagenomic sequencing. An environmental risk score (ERS) was created to represent pesticide exposure. We also used Mendelian randomization (MR) to identify causal gut microbial genera, multivariable regression for associations, and mediation analysis for potential pathways. Machine learning models were applied to differentiate hypertensive from non-hypertensive individuals based on a combined set of features.<br><br>RESULTS: Fourteen pesticides, notably bentazone and perfluorohexanesulfonate, were significantly associated with increased hypertension risk, and the ERS based on these pesticides further corroborated this association. Additionally, the overall microbiota composition was significantly associated with both pesticide exposure and hypertension status. Observational and MR analyses consistently identified branches of Clostridium as potentially contributors to hypertension risk. An interaction was observed between pesticide exposure and specific bacterial taxa. Specifically, high ERS combined with high Catenibacterium (both defined using a median split) abundance increased hypertension risk nearly fourfold. A neural network model achieved the best differentiation performance (AUC&#xa0;=&#xa0;0.897) for hypertension.<br><br>CONCLUSIONS: Exposure to specific pesticides, particularly bentazone, is associated with increased hypertension risk. This relationship is influenced by interactions with gut bacteria and partially mediated through alterations in the gut microbiota. These findings highlight the role of environmental chemicals and the gut microbiome in the development of hypertension.}, }
@article {pmid41997101, year = {2026}, author = {Liu, W and Yang, Y and Bian, J and Li, X and Lu, Z}, title = {Niche adaptation of marine heterotrophic nitrification-aerobic denitrification bacterium in mariculture wastewater treatment: Synergistic mechanism of nitrogen removal and sulfamethoxazole biotransformation.}, journal = {Water research}, volume = {300}, number = {}, pages = {125914}, doi = {10.1016/j.watres.2026.125914}, pmid = {41997101}, issn = {1879-2448}, abstract = {Efficient removal of nitrogen from mariculture wastewater (MW) by marine heterotrophic nitrification-aerobic denitrification (MHNAD) bacteria is an innovative approach to overcoming salt inhibition. However, their performance and survival strategies under long-term antibiotics exposure in real wastewater conditions remain elusive, limiting practical implementation. Here, a bench-scale biofloc-biological aerated filter (BF-BAF) system treating real MW was operated for 100 days. Under long-term exposure to sulfamethoxazole (SMX) (1.3 ± 0.4 mg/L), the stabilized nitrogen removal system achieved removal efficiencies of 97.2 ± 2.5 % and 91.6 ± 4.1 % for NH4[+]-N and SMX, respectively. MHNAD bacteria, dominated by Marinobacter and Celeribacter, were enriched (2.3-67.7 %) and identified as habitat-specific genera, while the growth of Nitrosomonas (0.02-0.04 %)-the sole ammonia-oxidizing bacteria (AOB) detected-was severely inhibited. Metagenomic analysis revealed upregulation of nitrogen assimilation (glnA and nasA) and denitrification genes (nirK and norC), driving niche differentiation. A novel MHNAD strain, Marinobacter sp. LAN01, was isolated from the settleable bioflocs. Multi-omics analysis indicated that LAN01 adapts to SMX stress by reallocating intracellular resources via NH4[+]-N assimilation (glnA-driven) and facilitates SMX degradation via N-acetylation, S-N bond cleavage, and hydrolysis. Nucleotide metabolism was downregulated to suppress DNA synthesis, thereby reducing the accumulation and transfer of sulfonamide resistance genes (sul1 and sul2). Overall, this works revealed the mechanism of synergistic nitrogen removal and antibiotic degradation, and highlighted the long-term application potential of BFT, paving the way for sustainable MW treatment.}, }
@article {pmid41997104, year = {2026}, author = {Zhang, X and Weng, S and Zhen, Z and Tang, Z and Huang, X}, title = {Phage predation mitigates the spread of antibiotic resistance in anaerobic digestion under shortened solid retention times.}, journal = {Water research}, volume = {300}, number = {}, pages = {125921}, doi = {10.1016/j.watres.2026.125921}, pmid = {41997104}, issn = {1879-2448}, abstract = {Optimizing anaerobic digestion (AD) via shortening solid retention time (SRT) enhances methane recovery, yet the mechanistic impact of SRT reduction on antimicrobial resistance (AMR) dissemination remains underexplored. Herein, we employed metagenomics to investigate how reduced SRTs (from 60 to 5 days) regulated the dynamics of antibiotic resistance genes (ARGs) mediated by pathogenic hosts, plasmids, and phages in mesophilic and thermophilic AD systems. Shortened SRTs elevated ARG abundance by 5.9-388% under mesophilic conditions, driven by the SRT-elicited niche expansion of antibiotic-resistant bacteria (ARB) and the persistent dominance of ESKAPE pathogen Enterobacter hormaechei, the latter intrinsically harbored and transmitted high-risk ARGs (aadA, sul1, and qacEdelta1) via multi-resistant plasmids. Notably, plasmid-mediated and cross-phylum transmission substantially enhanced ARG mobility. Contrastingly, thermophilic conditions eliminated ARGs by 17.0-57.1% under shortened SRTs, driven by thermophilic ARB niche differentiation. Crucially, both homology search and phage-host prediction indicated the lack of ARGs matching between phages and hosts under reduced SRTs, denoting a negligible contribution of transduction to horizontal ARG transfer. The dominance of lytic phages (85.3%), intensified lytic phage-host interactions, and heightened abundance of lytic phages lysing ARB collectively imposed potent phage top-down control over ARG hosts, with the lytic phage predation on ARB being validated by laboratory assays. We also identified 9 high-risk digestate ARG biomarkers (ANT(6)-Ia, aadA, ermA, mel, qacEdelta1, sul1, tet44, tetM, tetQ) by integrating criteria of prevalence, gene mobility, clinical relevance, and host pathogenicity to inform monitoring. Overall, this study underlined the significance of phage predation in mitigating ARG propagation under shortened SRTs, informing the development of novel AMR control strategies in AD practices.}, }
@article {pmid41792614, year = {2026}, author = {Zhou, J and Gu, T and Zhou, J and Zeng, X and Liu, Y and Chen, F and Hu, Y and Li, S}, title = {Clostridium zhoujianii sp. nov., a novel gram-negative species isolated from bat feces and its genetic characteristics.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41792614}, issn = {1471-2180}, support = {Qiankehe Platform Talent-ZDSYS [2023] 004//Key Laboratory of Microbiol and Infectious Disease prevention &amp;Control in Guizhou Province/ ; Guo Jikong Zong Ren Han [2024] 122//Project for Public Health Talent Cultivation of China/ ; Qiankehe [2025] 024//The local science foundation of Guizhou Province guided by the Central Committee of China/ ; }, abstract = {UNLABELLED: A strictly anaerobic, rod-shaped bacterial strain, designated LP20ᵀ, was isolated from the intestinal contents of bats collected in Qiandongnan, China. Phylogenetic analysis of the 16 S rRNA gene revealed that strain LP20ᵀ shared its highest similarity with Clostridium paraputrificum ATCC 25780ᵀ (98.10%), a value below the accepted threshold for species delineation. Whole-genome sequencing further supported its taxonomic novelty, with ANI, dDDH, and AAI values to the closest relatives all falling well below species-level cutoffs. Strain LP20ᵀ exhibited unusual Gram-stain-negative morphology, grew optimally at 30–37℃ and pH 7.0–8.0, and possessed distinctive fatty acid and polar lipid profiles, including the presence of an unidentified aminophospholipid. Phenotypic assays revealed several metabolic and enzymatic traits that differentiated LP20ᵀ from its closest phylogenetic neighbors. 16 S rRNA amplicon sequencing and metagenomic screening confirmed the presence of this species in multiple bat hosts, suggesting a wider distribution within bat gut microbiomes. Functional genomic analysis indicated enrichment of genes involved in carbohydrate metabolism and a limited antibiotic resistance profile. Based on polyphasic evidence, strain LP20ᵀ represents a novel species within the genus Clostridium, for which the name Clostridium zhoujianii sp. nov. is proposed. The type strain is LP20ᵀ (= JCM 37970ᵀ = GDMCC 1.5627ᵀ).<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04884-1.}, }
@article {pmid41796297, year = {2026}, author = {Shi, K and He, Q and Wang, S and Guo, J}, title = {An adaptive weight self-distillation deep learning framework for phenotype prediction from longitudinal gut microbiome data.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41796297}, issn = {1471-2180}, support = {62562022//National Natural Science Foundation of China/ ; Guike ZY22096025//Special Funds for Guiding Local Scientific and Technological Development by the Central Government/ ; 2025JJA170175//Guangxi Natural Science Foundation/ ; Z-C20241570//Guangxi Health Commission Self-Funded Research Project/ ; }, abstract = {BACKGROUND: The gut microbiota plays a vital role in maintaining human health. In recent years, extensive researches has focused on phenotype prediction in relation to various diseases, with the gut microbiota as a key predictor. Nevertheless, most existing studies rely on single-time-point analyses, which are insufficient to capture the dynamic patterns of host states and temporal variations inherent in longitudinal data.<br><br>RESULTS: In this study, we propose a deep learning framework, AWSD-CNN-LSTM, designed to classify host phenotypes using longitudinal metagenomic data. Unlike conventional approaches that treat each time point as an independent sample, our method models the sequential samples of each individual as a whole, integrating convolutional neural network (CNN) and long short-term memory network (LSTM) to effectively capture temporal dependencies in longitudinal microbiome sequencing data. In addition, the model incorporates an adaptive point-wise self-distillation mechanism to more accurately characterize host-specific patterns. Compared with state-of-the-art methods, AWSD-CNN-LSTM demonstrates superior performance on the PROTECT, DIABIMMUNE, and Infants datasets, achieving area under the receiver operating characteristic curve (AUC) values of 0.896, 0.813, and 0.894, respectively.<br><br>CONCLUSIONS: For the task of disease phenotype classification based on temporal data, we propose a novel framework that effectively captures the characteristics of time-series data and achieves high accuracy across multiple datasets. Our approach holds promise as a potential new tool for microbial knowledge discovery.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04922-y.}, }
@article {pmid41986605, year = {2026}, author = {Sumithra, TG and Gayathri, S and Mannur, VS and Neethu, N and Ratheesh Kumar, R and Nair, AV and Ratheesh, L and Zainul Abid, PM and Sundari, BKR and Dharani, G and Krupesha Sharma, SR}, title = {Bathymetry and environmental features govern the microbial communities in mesopelagic sediments of the Lakshadweep Islands of India.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-48651-8}, pmid = {41986605}, issn = {2045-2322}, support = {Deep-sea Metagenomics for enhanced next-generation bioethanol production' under Deep Ocean Mission (DOM) [MoES/PAMC/DOM/176/2023 (E-14624)]//Ministry of Earth Sciences/ ; }, }
@article {pmid41986657, year = {2026}, author = {Luchen, CC and Piedade, GJ and Chibuye, M and Simuyandi, M and Chisenga, CC and Chilengi, R and Bosomprah, S and Schultsz, C and Mende, DR and Harris, VC}, title = {Distinct infant resistome trajectories shaped by country income and geography revealed through global metagenomics reanalysis.}, journal = {npj antimicrobials and resistance}, volume = {4}, number = {1}, pages = {}, pmid = {41986657}, issn = {2731-8745}, support = {2023159//Amsterdam University Medical Center Amsterdam Public Health Research Institute/ ; LSHM23007//Track-AMR/ ; LSHM23007//Track-AMR/ ; 09150161810022//Netherlands Organisation for Health Research and Development (ZonMw) VENI/ ; 219775/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; LSHM21033//Co-funding by PPP Allowance awarded by Health~Holland, Top Sector Life Sciences &amp; Health GLORIA/ ; AI173360/NH/NIH HHS/United States ; }, abstract = {Antimicrobial resistance (AMR) costs lives, diminishes antimicrobial effectiveness and increases health care costs. We conducted a re-analysis of pooled fecal metagenomes from individual participants to characterise AMR gene (ARG) distributions in 0-2 year-old healthy infants across income and geography. From 2275 screened studies, we included nine datasets and 1944 fecal metagenomes. Resistome gene identifier (RGI) was used to identify ARGs, and gut microbiomes were profiled using Sylph. We assessed associations between ARGs, Escherichia coli abundance, and national-level indicators. In the first 3 months of life, ARG abundance patterns were not significantly different across income groups; however, by 6 months of age, infants in LICs had higher ARG abundance, associated with increased E. coli carriage. Caesarean section rates, antibiotic use, and income inequality positively correlated with ARG abundance in younger infants; physician density negatively correlated with ARG abundance in older children. These descriptive age- and context-specific associations may inform interventions to mitigate the carriage and spread of ARGs and the rise of AMR in vulnerable pediatric populations.}, }
@article {pmid41986663, year = {2026}, author = {Luiken, REC and Prinsen, H and Dasari, SN and Zweerus, H and Timmerman, AJ and Speksnijder, DC and Dohmen, W and Wagenaar, JA and Heederik, DJJ and Zomer, AL}, title = {Changes in antimicrobial resistance profiles of Escherichia coli and the metagenome on Dutch pig farms after antimicrobial usage interventions.}, journal = {npj antimicrobials and resistance}, volume = {4}, number = {1}, pages = {}, pmid = {41986663}, issn = {2731-8745}, abstract = {The use of antimicrobials in livestock farming drives selection and dissemination of antimicrobial resistance (AMR), prompting implementation of veterinary stewardship programs to reduce antimicrobial usage (AMU). We evaluated changes in AMR on 45 Dutch pig farms before and after tailored, coaching-based interventions using phenotypic testing of Escherichia coli and metagenomic profiling of pooled faeces. Post-weaning pig farms, including nursery and fattening units, entered the intervention in a stepped-wedge design, with intervention periods ranging from 10 to 27 months. Across farms, AMU and abundances of several antimicrobial resistance gene classes declined over time, alongside reductions in overall resistome levels. Proportions of phenotypic AMR in E. coli were more variable, although decreased AMU was associated with lower resistance for specific antimicrobial classes, such as tetracyclines and beta-lactams. While longer follow-up is required to fully assess long-term impacts, these findings indicate that veterinary antimicrobial stewardship programs can yield measurable short-term reductions in AMR at farm level.}, }
@article {pmid41986664, year = {2026}, author = {Frey, B and Varliero, G and Rüthi, J and Alekseev, I and Qi, W and Povazhnyi, V and Zemlianskii, V and Stierli, B and Ermokhina, K and Schaepman-Strub, G and Cuartero, J}, title = {Metagenomic insights into viral and microbial genes of Russian High-Arctic soil microbiomes.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10050-0}, pmid = {41986664}, issn = {2399-3642}, abstract = {High-Arctic soils are extreme ecosystems where microbial and viral roles remain poorly studied. Climate-driven vegetation expansion may alter these environments, but its impact is unknown. We generate a shotgun metagenomic database from four High-Arctic islands, comparing vegetated and unvegetated sites at two depths (0-2 cm and 30-50 cm). We analyse the functional gene potential, including biosynthetic gene clusters (BGCs) and antibiotic resistance genes (ARGs) in metagenome-assembled genomes (MAGs), and assess viral diversity. Vegetated soils at 30-50 cm were enriched in genes for carbon/nitrogen cycling, energy production, and carbohydrate metabolism, indicating enhanced nutrient inputs. Conversely, unvegetated soils show higher BGC and ARG richness, reflecting microbial competition under nutrient limitation. Viral richness decreases in surface vegetated soils, while diversity and giant virus (Nucleocytoviricota) abundance increase with depth. These findings reveal how vegetation and soil depth modulate microbiomes and viromes, critical for predicting ecosystem trajectories in a warming world.}, }
@article {pmid41986859, year = {2026}, author = {Iñiguez-Luna, MI and Gómez-Godínez, LJ and Cadena-Zamudio, JD and Cadena-Zamudio, DA and Aguirre-Noyola, JL and Barrera-Guzmán, LA}, title = {Omics Sciences: Driving the Conservation and Characterization of Plant Genetic Resources.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {3011}, number = {}, pages = {345-364}, pmid = {41986859}, issn = {1940-6029}, mesh = {*Genomics/methods ; *Plants/genetics/metabolism ; Metabolomics/methods ; Plant Breeding/methods ; Proteomics/methods ; Genome, Plant ; Computational Biology/methods ; Crops, Agricultural/genetics ; *Conservation of Natural Resources/methods ; Metagenomics/methods ; }, abstract = {Omics sciences have revolutionized the conservation and characterization of plant genetic resources by enabling a comprehensive understanding of genetic diversity, molecular mechanisms, and adaptive traits. Advances in genomics, transcriptomics, proteomics, metabolomics, and metagenomics have facilitated the identification of genes and metabolic pathways associated with stress tolerance, nutritional value, and agronomic performance. These technologies have enhanced the efficiency of germplasm banks by improving genetic resource characterization, optimizing conservation strategies, and accelerating breeding programs for climate-resilient crops. Additionally, omics approaches contribute to biodiversity conservation by revealing evolutionary relationships, ecosystem dynamics, and the functional roles of microbial communities in plant health. The integration of multi-omics data with bioinformatics and artificial intelligence further enhances predictive capabilities, enabling targeted conservation and breeding efforts. This review highlights the pivotal role of omics sciences in securing plant genetic resources for sustainable agriculture and global food security.}, }
@article {pmid41987827, year = {2026}, author = {Bornbusch, SL and Thacher, PR and Francisque, M and DeCandia, AL and Bortner, R and Garelle, D and Kendrick, EL and Maslanka, MT and Muletz-Wolz, CR}, title = {How "pro" are probiotics for wildlife species? Novel data, lack of evidence, and future directions.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag036}, pmid = {41987827}, issn = {2730-6151}, abstract = {Treatments that aim to purposefully manipulate host-associated microbiomes are now prevalent in human and animal medicine. Probiotics that contain live bacteria are purported to improve microbiome function and host health. Although research is advancing, commercial probiotic development has outpaced empirical study of probiotic efficacy. Probiotics are widely used in ex-situ wildlife care despite a lack of empirical study or support. We interrogate the relevance of commercial probiotics in ex-situ wildlife by (a) sequencing the composition of commercial probiotics used to treat wildlife, (b) comparing the probiotic sequences to data on the microbiomes of >900 animal species, and (c) characterizing the effects of a commercial probiotic on probiotic colonization, prevalence of a potential enteric pathogen (Clostridium perfringens), and metagenomic function in endangered black-footed ferrets (Mustela nigripes). We found mislabeling and potential contaminants in probiotics marketed for a range of species. The probiotic bacteria were rare or absent in published animal microbiomes. In black-footed ferrets, probiotic treatment induced minimal probiotic colonization, negligible functional change, and limited influence on the potential enteric pathogen. Given our findings, which reiterate concerns about the efficacy of commercial probiotics across human and animal sectors, greater effort must be put towards identifying species-specific probiotic candidates and studying alternative microbial therapies for wildlife under human care.}, }
@article {pmid41987902, year = {2026}, author = {De, R and Kanungo, S and Mukhopadhyay, AK and Dutta, S}, title = {Comparative metagenomic analysis of diarrheal and non-diarrheal gut microbiome delineating the identification of prospective prognostic markers and probiotics to protect from diarrhea: a brief report.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1729497}, pmid = {41987902}, issn = {2235-2988}, mesh = {*Diarrhea/microbiology/prevention &amp; control ; *Gastrointestinal Microbiome/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Cross-Sectional Studies ; *Probiotics/therapeutic use ; Feces/microbiology ; Pilot Projects ; Female ; Prognosis ; Male ; High-Throughput Nucleotide Sequencing ; Adult ; *Bacteria/classification/genetics/isolation &amp; purification ; Middle Aged ; Prospective Studies ; Biomarkers/analysis ; DNA, Bacterial/genetics ; }, abstract = {INTRODUCTION: Diarrhea is a leading contributor of mortality globally. To mitigate its disease burden, improved prognosis and alternative therapeutic approaches must be deployed. A cross-sectional gut microbiome analysis of 23 non-diarrheal and 5 diarrheal fecal samples was conducted with the aim of meeting the WHO's GAPPD (Global Action Plan for Pneumonia and Diarrhea) goals.<br><br>HYPOTHESIS: Next-generation sequencing is a potent tool being increasingly used for epidemiological surveillance. It can help in the comparison of the structural diversity of the gut microbiome between diarrheal and non-diarrheal samples, thereby aiding in the identification of prospective prognostic and therapeutic candidates.<br><br>AIM: The pilot study was designed to identify prospective taxa that were comparatively enriched in non-diarrheal samples and to predict gut microbial community interactions.<br><br>METHODOLOGY: 16S rRNA amplicon sequencing and subsequent analysis were undertaken for taxonomic profiling and abundance interpretation of OTUs.<br><br>RESULTS: Significant differences between the two groups with respect to structural composition was revealed. Firmicutes was the most abundant phylum in the majority of the samples. The B/F ratio was consistently <1 in all diarrheal samples. A significant difference in the mean B/F ratio of the two groups was found. Proteobacteria was significantly more abundant in the diarrheal group. On the other hand, Prevotellaceae was the most abundant family in non-diarrheal samples and was suppressed significantly in diarrheal samples. Streptococcaceae was the most abundant family in 60% of diarrheal samples; where Streptococcaceae was suppressed, Bacteroideaceae and Nocardiaceae were the most abundant. In non-diarrheal samples, where Streptococcaceae was almost completely suppressed, Bifidobacteriaceae was the most abundant and significantly suppressed other families. A negative correlation was observed between Prevotellaceae and Bacteroideaceae in the non-diarrheal group. Prevotella copri was the most abundant species in 70% of non-diarrheal samples and was significantly suppressed in diarrheal samples. Proteus mirabilis was identified in all the non-diarrheal samples, while they were absent in diarrheal samples.<br><br>CONCLUSION: The OTUs associated with diarrheal dysbiosis can serve as prognostic markers. To our knowledge, this is the first report on the comparative analysis of diarrheal and non-diarrheal microbiome, distinctly addressing the gut microbiome dysbiosis from the context that can lead to the development of prognostic markers and probiotics to protect the endemic population from diarrhea and help in achieving Sustainable Development Goals 2 and 3.}, }
@article {pmid41988145, year = {2026}, author = {Liu, L and Wang, L and Zhang, P and Gan, M and Liujiang, R and Cheng, G and Ge, M}, title = {Neonatal herpes simplex virus encephalitis: a single-center retrospective study of 14 cases.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1740937}, pmid = {41988145}, issn = {2296-2360}, abstract = {BACKGROUND: This single-center retrospective study aims to analyze the clinical characteristics, treatment strategies, and outcome at discharge of neonatal-onset herpes simplex virus encephalitis (NHSE).<br><br>METHODS: We conducted a single-center retrospective case review of infants diagnosed with NHSE at the Children's Hospital of Fudan University between February 1, 2016, and February 1, 2024. Clinical data, including demographics, clinical symptoms, laboratory findings, neuroimaging results, treatment regimens, and outcomes at discharge, were collected and analyzed.<br><br>RESULTS: A total of 14 infants with NHSE (7 males, 7 females) were identified at our center, with a median age at diagnosis of 26 days (range: 7-51 days). Initial symptoms predominantly included fever and seizures, with neurological involvement (e.g., seizures, lethargy, irritability or altered mental states) in 13 cases. Physical examinations, such as bulging anterior fontanel, were noted. Herpes simplex virus (HSV)-DNA was detected in 13 cases (6 HSV-1, 7 HSV-2) through cerebrospinal fluid (CSF) polymerase chain reaction (PCR) or metagenomic testing. Among these, 9 cases were identified via CSF-PCR, with 7 testing positive on the initial examination and 2 on repeated testing. Notably, 6 cases were diagnosed using metagenomic next-generation sequencing (mNGS), all of which yielded positive results on the first test. Ten out of the 12 children often exhibited temporal lobe spikes on video electroencephalograms (VEEGs). Early magnetic resonance imaging (MRI) revealed cytotoxic edema, progressing to multicystic encephalomalacia. All received acyclovir antiviral treatment. Seven discontinued treatments, one was referred for ocular lesions, and six improved and were discharged.<br><br>CONCLUSIONS: In this single-center cohort, NHSE often presents with nonspecific fever and seizures, with late onset and absent indicative rashes, complicating early diagnosis. For newborns suspected of having NHSE, early CSF HSV-DNA testing and prompt antiviral treatment are essential to improve outcomes. Metagenomic sequencing is especially valuable for accurate, rapid diagnosis when conventional methods fail.}, }
@article {pmid41989131, year = {2026}, author = {Schön, ME and Schvarcz, CR and Malkewitz, SV and Hinner, FC and Koslová, A and Mersdorf, U and Schimm, F and Rickert, S and Pozhydaieva, N and McBeain, K and Hackl, T and Schneider, AC and Barenhoff, K and Höfer, K and Edwards, KF and Steward, GF and Fischer, MG}, title = {Strain-level diversity of giant viruses infecting chlorarachniophyte algae in the subtropical North Pacific.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag093}, pmid = {41989131}, issn = {1751-7370}, abstract = {Giant DNA viruses are ubiquitous among unicellular eukaryotes and occur in marine, freshwater, and terrestrial environments. Despite intense metagenomic data mining, their strain-level diversity remains largely unexplored. Here we introduce a model system comprising four isolates of a giant virus called ChlorV, which infects marine microalgae of the class Chlorarachniophyceae (Rhizaria) from station ALOHA, Hawai'i. The ChlorV genomes are 469 kbp to 493 kbp long and encode approximately 400 proteins, at least 106 of which are present in purified virions. Although the four viral genomes are highly syntenic, they differ by several insertions and deletions that often encode methyltransferases. We found that some of these methyltransferase genes correlated with specific DNA methylation patterns in the same ChlorV strain. Our study describes the first giant viruses infecting the eukaryotic supergroup Rhizaria and demonstrates how viral strain-level variation in gene content and epigenetic features may affect eco-evolutionary processes in marine microalgae.}, }
@article {pmid41989380, year = {2026}, author = {Hontelez, S and Guthrie, M and Stobernack, T and van Baarlen, P and Rousseau, C and Boks, MP and Pereira, RR and Boekhorst, J and Kleerebezem, M}, title = {Microbiome signatures correlate with diet-mediated ADHD symptom reduction.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2659400}, doi = {10.1080/19490976.2026.2659400}, pmid = {41989380}, issn = {1949-0984}, mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology ; Child ; Male ; *Gastrointestinal Microbiome ; Female ; Feces/microbiology ; *Diet ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Attention-deficit hyperactivity disorder (ADHD) is one of the most common childhood neuropsychiatric conditions. Both (epi)genetic and environmental factors are suggested to contribute to the etiology of ADHD. In the last decade, nutrition has received considerable attention as a potential environmental factor triggering ADHD behavior, particularly applying a few-foods diet (FFD) has been shown to elicit considerable behavioral improvements. These studies are observational rather than investigating underlying molecular mechanisms. The present study included 79 children (boys aged 8-10) with ADHD following a progressive, i.e., increasingly restrictive, FFD diet for 5 weeks. Minimally invasive samples (feces, urine, blood, and buccal swabs) were collected before and after the intervention to obtain a multi-omics perspective of the dietary responses in the participating children. For 63% of the participating children, a more than 40% behavior score improvement was observed, with an average improvement of 73%. The strength of diet-induced changes in ADHD symptoms among children was significantly associated with the gut microbiome composition, particularly when analyzing species-stratified abundance profiles of previously characterized gut-brain modules in the fecal metagenomic data. While integrative multi-omics analysis did not identify composite signatures linked to symptom changes, the strongest multi-omics signal confirmed compliance with the dietary intervention. Our findings implicate a role of the gut microbiome and its metabolic capacity to communicate with the central nervous system in children with food-associated ADHD.}, }
@article {pmid41989870, year = {2026}, author = {Zhu, YC and Deng, Y and Zeng, JQ}, title = {Effects of concurrent Helicobacter pylori infection and small intestinal bacterial overgrowth on the gut microbiota and metabolic profiles: A multi-omics study.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {}, number = {}, pages = {}, doi = {10.1556/030.2026.02894}, pmid = {41989870}, issn = {1588-2640}, abstract = {This study investigated the synergistic effects of Helicobacter pylori (Hp) infection and small intestinal bacterial overgrowth (SIBO) on the gut microbiota structure and metabolic profiles and elucidate the underlying pathophysiological mechanisms. Forty-two patients with gastrointestinal symptoms were recruited and assigned to group A (Hp+ SIBO+), B (Hp+ SIBO-), C (Hp- SIBO+), or D (Hp- SIBO-) based on their Hp infection and SIBO status. Fecal samples were collected for metagenomic sequencing and untargeted metabolomic analysis. The associations between microbiota and metabolites were evaluated using alpha/beta diversity analysis, differential species screening, metabolite identification, and Procrustes/Spearman correlation analysis. Neither Hp infection nor SIBO significantly altered the alpha or beta diversity of the gut microbiota (both P > 0.05). However, specific shifts in microbial abundance were observed. Specifically, the abundance of short-chain fatty acid-producing bacteria such as Megamonas was significantly decreased in the SIBO+ groups. Metabolomic analysis revealed significant enrichment of inflammatory metabolites (e.g., prostaglandin derivatives) in group A, disordered bile acid conjugates (e.g., chenodeoxycholylisoleucine) and nucleotide metabolism in SIBO+ groups, and abnormal lipid/carbohydrate metabolism pathways in Hp+ groups. Multi-omics integration analysis indicated a strong coupling between the microbial structure and metabolic profiles (Procrustes analysis, P < 0.05). In group A, the abundance of Faecalibacterium and Hominenteromicrobium was negatively correlated with bile acid levels, suggesting impaired bile acid transformation. Hp infection and SIBO might synergistically exacerbate gut ecological and metabolic disorders by reshaping specific microbiota and metabolic networks (enhanced inflammatory response, disrupted bile acid circulation). Their co-occurrence produces additive effects, which could explain the aggravated clinical symptoms. This study provides a theoretical basis for interventions targeting microbiota-metabolite interactions, such as probiotics and bile acid modulators.}, }
@article {pmid41990029, year = {2026}, author = {Sun, Y and Zhang, M and Wang, X and Huang, X and Yu, Y and Pan, H and Li, H and Shi, L and Yang, W and Zhang, C and Ding, B and Liu, X and Li, J and Qian, C and Cheng, B and Zhang, C and Ran, J and Li, M}, title = {Gut Microbiota of Gray Snub-Nosed Monkeys: Adaptation to Seasonal Variations Through Energy Compensation and Thermogenesis.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.70092}, pmid = {41990029}, issn = {1749-4877}, support = {32330015//National Natural Science Foundation of China/ ; 32070404//National Natural Science Foundation of China/ ; QLKH [2023] 11//Guizhou Forestry Administration Scientific Research Project/ ; QLKH [2025] 11//Guizhou Forestry Administration Scientific Research Project/ ; //Investigation of Nationally Protected Wildlife Species in Tongren Region/ ; GZKPC-2025-01//Guizhou Province/ ; QCZH [2023]82//Protection and Restoration of Forests and Grasslands in 2024 from the Central Finance/ ; [2023]188//Guizhou Science and Technology Support Plan Project/ ; QKHFQ [2023]009//Construction of Capacity for Ecosystem Optimization and Innovation in Key Ecological Zones of Guizhou Province/ ; YWZ[2024]005//Construction of Capacity for Ecosystem Optimization and Innovation in Key Ecological Zones of Guizhou Province/ ; QKHPT[2021]5625//Guizhou Outstanding Young Scientist Program/ ; QJJ[2024]337//Natural Science Research Projects of the Education Department of Guizhou Province/ ; [2022]031//Guizhou Provincial Department of Education/ ; 2024BS011//Doctoral Program of the Science Research Foundation of Guizhou Education University/ ; 2024BS006//Doctoral Program of the Science Research Foundation of Guizhou Education University/ ; }, abstract = {As an extremely endangered species, the gray snub-nosed monkey (Rhinopithecus brelichi) relies on its gut microbiota for adaptation to environmental changes, particularly in coping with fluctuations in energy and nutrient availability. In this study, we employed metagenomic, metatranscriptomic, and widely targeted metabolomic analyses to characterize the gut microbiota of gray snub-nosed monkeys. Based on metagenome-assembled genomes (MAGs), we recovered 1229 non-redundant MAGs. Among them, a total of 103 MAGs exhibited significant seasonal variation, primarily belonging to the phyla Bacillota_A, Bacteroidota, and Bacillota_I. During winter, metagenomic results indicated that the gut microbiota exhibited an enhanced capacity to produce energy substrates such as amino acids, short-chain fatty acids, pyruvate, and acetyl-CoA, with increased conversion of these substrates. Metatranscriptomic analysis further confirmed that key carbon cycle-related genes and metabolic pathways were significantly upregulated in winter. Additionally, metabolite analysis indicated significantly lower levels of amino acids in winter fecal samples, suggesting that gray snub-nosed monkeys efficiently absorb and utilize metabolites, with the gut microbiota likely contributing to energy compensation. Notably, the gut microbiota may also synergistically support the host's non-shivering thermogenesis, helping maintain physiological functions in extreme cold conditions. This study elucidates the cooperative role of the gut microbiota in helping gray snub-nosed monkeys adapt to seasonal environmental fluctuations, providing new insights into how gut microbiota optimize winter energy utilization-an understanding with important implications for the conservation of endangered wildlife.}, }
@article {pmid41990134, year = {2026}, author = {Chen, X and Wang, Y and Feng, J and Chen, H and Yao, B and Li, F and Yang, Q and Qu, J}, title = {Hypobaric hypoxia affects gut microbiota of rats through affected community assembly, reduced network resilience, and metabolic reprogramming.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag039}, pmid = {41990134}, issn = {1574-6941}, abstract = {In host-microbe interactions, host diet and environmental stress are key driving factors shaping the gut microbiota. Although previous studies have shown that hypoxia affects the structure and function of the gut microbiota in rodents, most have relied on 16S rRNA gene sequencing and lacked analysis of community assembly mechanisms, co-occurrence networks, and functional pathways. Here, we used metagenomic next-generation sequencing (mNGS) to examine the gut microbiota of rats exposed to hypobaric hypoxia (WH, simulated 6000 m altitude) compared to WL group (2100 m altitude). Hypoxia significantly altered β-diversity of gut microbiota, but did not affect its α-diversity. Community assembly was primarily governed by stochastic processes, with hypoxia stress reducing their impact. Microbial co-occurrence networks were dominated by positive correlations, although network resilience and stability declined under hypoxia. Helicobacter and Eubacterium were identified as high-abundance differentiating genera, and Akkermansia muciniphila was significantly enriched in WH group. Functional analysis revealed alterations in pathways related to protein synthesis and carbohydrate metabolism, suggesting that hypoxia may affect nutrient utilization by the host. Overall, these findings provide a comprehensive view of how hypoxic stress reshapes the gut microbiota of rats, offering new insights into microbial dynamics under environmental stress.}, }
@article {pmid41990403, year = {2026}, author = {Zhao, J and Li, T and Huang, H and Servellita, V and Sotomayor-Gonzalez, A and Yakovleva, O and Wang, X and Ragupathy, V and Biswas, S and Barilko, P and Sun, E and Huynh, S and Hunsicker, M and DeQuach, J and Morales, JD and Highbarger, H and Dewar, RL and Porth, C and Denny, TN and McGivern, DR and Chiu, CY and Hewlett, I}, title = {Development and genomic characterization of a diverse HIV-1 variant reference panel for nucleic acid-based testing.}, journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology}, volume = {184}, number = {}, pages = {105941}, doi = {10.1016/j.jcv.2026.105941}, pmid = {41990403}, issn = {1873-5967}, abstract = {BACKGROUND: The high worldwide genetic diversity of HIV poses significant challenges for its detection and diagnosis by nucleic acid testing (NAT). Well-characterized reference panels are important for evaluating the analytical performance of HIV tests.<br><br>OBJECTIVE: To develop a reference panel for HIV NAT that reflects the genetic diversity of circulating strains.<br><br>STUDY DESIGN: HIV was cultured from blood specimens collected from blood donor and clinical sites in Cameroon. Metagenomic next-generation sequencing in combination with spiked primer enrichment along with Sanger sequencing were used to sequence 101 cultured HIV-1 samples representing 59 strains. To establish an HIV-1 variant reference panel, a diverse subset of cultured viruses was analyzed in multiple laboratories with different assays to determine consensus viral loads.<br><br>RESULTS: Near full-length HIV-1 genomes, with an average of 9589 base pairs (bp), were recovered from 37 (62.7%) of the 59 strains. The whole genome sequences of 28 strains exhibited more than 95% similarity to our previously reported genomes obtained by Sanger sequencing. An HIV variant reference panel for NAT comprising 18 diverse HIV-1 strains was developed. The panel included four subtypes, four circulating recombinant forms, and eight unique recombinant forms. Strains were prepared at low (n&#x202f;=&#x202f;18, 2.53 log10 copies/mL), medium (n&#x202f;=&#x202f;18, 3.61 log10 copies/mL), and high viral loads (n&#x202f;=&#x202f;15, 4.66 log10 copies/mL), yielding 51 panel members in total.<br><br>CONCLUSION: This diverse HIV reference panel can be used to evaluate the performance of HIV NAT and is available upon request to developers and manufacturers of HIV tests.}, }
@article {pmid41990622, year = {2026}, author = {Liu, L and Wang, C and Qi, WK and Zhang, SJ and Li, YY and Peng, Y}, title = {Mechanisms of aerobic simultaneous nitrogen removal under low COD/N conditions: Diffusion-reaction coupling and particle size effects via self-recirculating microgranular system.}, journal = {Water research}, volume = {300}, number = {}, pages = {125937}, doi = {10.1016/j.watres.2026.125937}, pmid = {41990622}, issn = {1879-2448}, abstract = {Nitrogen removal from ammonium-rich, carbon-limited wastewater remains constrained in continuous-flow microgranular sludge systems. In this study, a three-stage up-flow self-recirculating microgranular sludge reactor was developed to investigate nitrogen removal mechanisms under low chemical oxygen demand to nitrogen ratios (COD/N < 2.5) and high influent total nitrogen (TN > 400 mg/L). During long-term operation, the system achieved stable removal efficiencies of ammonium (98%), TN (94%), and COD (95%). Under ammonium stress, particle size decreased to a mean diameter of 249.2 μm, forming stable, non-flocculent microaggregates. Microgranules < 0.2 mm exhibited pronounced simultaneous partial nitrification-denitrification (SPND) and simultaneous nitrification-denitrification (SND) activities under aerobic conditions. Simultaneous nitrogen removal (SNR) activity peaked at 0.52 g TN/(g VSS·d) at a DO of 2 mg/L. In contrast, microgranules > 0.2 mm primarily followed SND-dominated pathways. Their SNR activity increased with DO and reached a maximum of 0.46 g TN/(g VSS·d). Microbial community and metagenomic analyses revealed a redox-stratified functional structural organization. Rubrivivax (11.5%) dominated the surface layer, likely linking organic matter degradation with nitrogen oxide reduction. Hyphomicrobium (11.9%) was enriched in intermediate layers and was associated with SND. In the core, the co-enrichment of Hyphomicrobium (7.2%) and Methylotenera (6.1%) supported the coupling of SND and SPND processes. These findings provide a basis for improving nitrogen removal from ammonium-rich, carbon-limited wastewater.}, }
@article {pmid41965542, year = {2026}, author = {Priya, S and Sridhar, SB and Shareef, J and Wadhwa, T and Balusamy, B and Meenakshi, DU and Sundram, S and Malviya, R}, title = {Epidemiology, diagnosis and emerging therapies for Lyme disease of the Northern Hemisphere.}, journal = {International journal of emergency medicine}, volume = {19}, number = {1}, pages = {}, pmid = {41965542}, issn = {1865-1372}, abstract = {BACKGROUND: Lyme disease is the most widespread tick-borne infection in the Northern Hemisphere and is challenging to diagnose and treat due to its changing clinical presentation, antigenic variation, tissue tropism, and the expanding distribution of vectors. This review includes ecology, pathogenesis, diagnostics, treatment, post-treatment, prevention, and novel translational approaches.<br><br>METHODS: A literature review was conducted to include literature published between January 2000 and March 2026 in PubMed/MEDLINE, Scopus, and Web of Science, with landmark studies used where applicable. Original research, clinical trials, systematic reviews, and major public health reports were prioritised.<br><br>RESULTS: Two-tier serology is the most common diagnostic technique, but it has limited sensitivity in early infection and does not distinguish between active and past infection. Culture and PCR are only useful in a few instances. The use of new technologies such as multiomics biomarkers, metagenomics, T-cell assays, and AI-enhanced diagnostics is promising but has not yet been tested in a prospective multicentre study. Most of the early and disseminated disease can be treated with standard antibiotics, whereas the long-term therapy of PTLD is not justified and can cause more adverse effects. These preventive and curative advancements involve VLA15 vaccination, anti-tick and reservoir-specific approaches, microbiome-engineered vectors, and anti-persister/ biofilm.<br><br>CONCLUSION: Lyme disease requires combined prevention, improved diagnostics, enhanced biomarker research, and well-designed PTLD trials. The short-term benefits will be based on the optimisation of existing diagnostics and vector control, and the long-term benefits will be based on rigorous validation of vaccines, biomarkers, and specific therapies.}, }
@article {pmid41973308, year = {2026}, author = {Aydin, F and Çek, &#x15e;}, title = {Mineral-microbiota interactions in aquaculture: implications for fish gut health and nutrition.}, journal = {Veterinary research communications}, volume = {50}, number = {4}, pages = {}, pmid = {41973308}, issn = {1573-7446}, abstract = {Dietary minerals and gut microbiota engage in a dynamic, bidirectional relationship that shapes the health, immune competence, and productive performance of farmed fish and shrimp. This review explores the bidirectional interactions between mineral supplementation and microbial communities within the gastrointestinal tract of farmed fish and examines the effects of individual and combined mineral supplementation including iron, zinc, magnesium, selenium, manganese, and copper in inorganic, organic, and nanoparticle forms on the intestinal microbiota and histomorphology of farmed aquatic species. Minerals serve essential physiological roles while simultaneously modulating microbial diversity, composition, and metabolic activity; conversely, the gut microbiota influences mineral bioavailability and absorption through enzymatic transformations and competitive uptake. Studies conducted on yellow catfish, largemouth bass, golden pompano, grouper, Nile tilapia, Chinese tongue sole, Pacific white shrimp, channel catfish, zebrafish, and Oriental river prawn were comprehensively examined. Findings indicate that organic and nanoparticle mineral forms generally exhibit higher bioavailability and more favorable effects on intestinal health compared to conventional inorganic sources, with partial substitution strategies (e.g., ~ 50% organic mineral replacement) yielding optimal outcomes in combined formulations. Optimized mineral supplementation was further associated with enrichment of beneficial microbiota, enhanced mucosal barrier integrity through goblet cell proliferation, and reinforcement of innate immune responses, collectively supporting nutrient assimilation, growth performance, and disease resistance. However, the reviewed studies share critical limitations: species diversity was narrow, experimental durations were short (8–80 days), no trial encompassed a full reproductive cycle, and the mechanisms underlying mineral–microbiota crosstalk remain incompletely understood. Synergistic or antagonistic interactions among Zn, Cu, Mn, Fe, and Se are inadequately characterized, and dose optimization specific to species, age, and physiological status has not been achieved. Future research should incorporate long-term and multigenerational designs, metagenomic and metabolomic analyses, comparative multi-mineral trials, and the integration of microbiome-based diagnostics to tailor mineral interventions, alongside validation under commercial aquaculture conditions and ecotoxicological assessment of nanoparticles in aquatic environments.}, }
@article {pmid41981035, year = {2026}, author = {Faber, Q and Baker, CCM and West, JR and Doherty, SJ and Ernakovich, JG and Barbato, RA}, title = {Antimicrobial resistance varies with warming in active layer soil and permafrost.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-46295-2}, pmid = {41981035}, issn = {2045-2322}, support = {PE 0602144A Program "Defense Resiliency Platform Against Extreme Cold Weather"//United States Department of Defense/ ; }, }
@article {pmid41981202, year = {2026}, author = {Benedicenti, O and Strand, DA and Mohammad, SN and Gulla, S and Amundsen, MM and Sindre, H and Vrålstad, T}, title = {Integrated approaches for pathogen monitoring and shotgun metagenomic analysis in Atlantic salmon farming.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-48791-x}, pmid = {41981202}, issn = {2045-2322}, support = {328724//Norges Forskningsr&#xe5;d/ ; 328724//Norges Forskningsr&#xe5;d/ ; 328724//Norges Forskningsr&#xe5;d/ ; 328724//Norges Forskningsr&#xe5;d/ ; 328724//Norges Forskningsr&#xe5;d/ ; 328724//Norges Forskningsr&#xe5;d/ ; 328724//Norges Forskningsr&#xe5;d/ ; 101136346//European Commission/ ; 101136346//European Commission/ ; 901674//Fiskeri - og havbruksn&#xe6;ringens forskningsfond/ ; }, abstract = {Specific tools for detecting waterborne pathogens are essential for limiting disease spread in aquaculture. We evaluated a field-deployable workflow combining filtration of eDNA/eRNA with targeted (RT-)qPCR and complementary shotgun metagenomics to monitor pathogens and microbial community dynamics in a single-farm study following one Atlantic salmon production cohort from hatchery to slaughter. The primary aim was to assess workflow feasibility and performance under real farm conditions, while secondarily examining whether metagenomic profiles could contextualise microbial shifts associated with pathogen presence. ISAV was consistently detected in hatchery water at ~ 4 × 10[3]-9 × 10[3] copies/L, whereas PRV1 was detected only inside sea pens from August onward (~ 4 × 10[2]-1.5 × 10[4] copies/L) and increased by more than two orders of magnitude after wellboat delousing. Shotgun metagenomics yielded a median of ~ 1.5 × 10[5] reads per sample (mean read length ~ 2.5 kb; N50 > 2 kb), enabling broad taxonomic screening. PRV1-positive seawater samples showed modest decreases in richness and shifts in viral taxa, though patterns were subtle and should be interpreted cautiously given low pathogen loads. The workflow was practical for trained farm personnel, and this integrated approach offers a scalable system for routine pathogen surveillance and supports earlier, evidence-based biosecurity actions, providing broader microbial information than qPCR alone.}, }
@article {pmid41981426, year = {2026}, author = {Muzhabaier, K and Li, Y and Wang, F and Guo, X and Chen, Q and Zhang, X and Cao, L}, title = {[Differential analysis of gut microbiome in patients with periprosthetic joint infection, aseptic failure, and osteoarthritis].}, journal = {Zhongguo xiu fu chong jian wai ke za zhi = Zhongguo xiufu chongjian waike zazhi = Chinese journal of reparative and reconstructive surgery}, volume = {40}, number = {4}, pages = {548-556}, doi = {10.7507/1002-1892.202601002}, pmid = {41981426}, issn = {1002-1892}, mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *Prosthesis-Related Infections/microbiology ; Female ; Middle Aged ; Aged ; *Osteoarthritis/microbiology ; Dysbiosis/microbiology ; Prosthesis Failure ; Arthroplasty, Replacement, Knee/adverse effects ; }, abstract = {OBJECTIVE: To explore the differences in gut microbiota diversity and structural characteristics among patients with periprosthetic joint infection (PJI), aseptic failure (AF), and osteoarthritis (OA), and to analyze the association between gut microbiota dysbiosis and the occurrence of PJI, thereby providing a new theoretical basis for elucidating the pathogenesis and treatment strategies of PJI in clinical practice.<br><br>METHODS: The study enrolled patients with PJI and AF admitted between February 2024 and December 2024, as well as OA patients admitted in February 2024. A total of 52 PJI patients, 19 AF patients, and 29 OA patients who met the selection criteria were included in the analysis. Significant differences were observed among the three groups in terms of gender, age, surgical site, preoperative C-reactive protein levels, and erythrocyte sedimentation rate (P<0.05), while no significant difference was found in American Society of Anesthesiologists (ASA) classification and body mass index (P>0.05). Among the PJI patients, infection staging was as follows: 9 cases in the acute phase, 28 cases in the delayed phase, and 15 cases in the chronic phase; 23 cases were accompanied by sinus tract formation. Fecal samples were collected at different time points: for the PJI group, samples were obtained preoperatively and on postoperative days (7&#xb1;1) and (14&#xb1;1); for the AF group, preoperatively and on postoperative day (7&#xb1;1); and for the OA group, preoperatively only. Metagenomics next-generation sequencing were employed to analyze gut microbiota &#x3b1;-diversity indices (ACE index, Chao1 index, Shannon index, Simpson index, and observed_species index) and differential bacterial genera (screened using the LEfSe algorithm).<br><br>RESULTS: Analysis of gut microbiota diversity showed that the preoperative &#x3b1;-diversity indices (ACE index, Chao1 index, Shannon index, Simpson index, and observed_species index) in the PJI group were significantly lower than those in AF group and OA group (P<0.05). Compared with the AF group on postoperative day (7&#xb1;1), the &#x3b1;-diversity indices in the PJI group on postoperative day (7&#xb1;1) were lower, but the difference was not significant (P>0.05); by postoperative day (14&#xb1;1), these indices further decreased, and the difference was significant (P<0.05). In the PJI group, no significant difference was observed in any of the indices across different time points postoperatively (P>0.05). Analysis of gut microbiota structural characteristics revealed that the PJI group exhibited characteristic dysbiosis both before and after operation. Preoperatively, the PJI group was characterized by enrichment of Pseudomonadota (relative abundance 13.19%), Enterobacteriaceae (Escherichia 3.26%, Klebsiella 1.90%), and opportunistic pathogens such as Enterococcus faecium (0.43%), while the relative abundances of Firmicutes (51.83%) and Bifidobacterium (0.24%) decreased. Postoperatively, the &#x3b1;-diversity in the PJI group further declined, with increased relative abundances of Escherichia and Klebsiella, and the relative abundance of Firmicutes decreased to 40.24%. LEfSe analysis of preoperative gut microbiota composition between the PJI group and AF group indicated that the AF group was predominated by Firmicutes, Bifidobacterium, and Roseburia preoperatively, with greater postoperative microbial stability compared to the PJI group.<br><br>CONCLUSION: Patients with PJI exhibited a gut microbiota profile characterized by reduced diversity and enrichment of opportunistic pathogens. Postoperative antibiotic treatment further aggravated this dysbiosis, providing new clinical insights into the role of gut microbiota imbalance in the pathogenesis and progression of PJI.}, }
@article {pmid41981681, year = {2026}, author = {Brachmann, S and Kiesewetter, KN and Liddicoat, C and Wallace, KJ and Breed, MF and Eisenhauer, N and Barnes, AD}, title = {Urban forest restoration enhances soil microbial functional potential and functional insurance via shifts in β-diversity.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00896-6}, pmid = {41981681}, issn = {2524-6372}, support = {UOWX2101//Ministry of Business, Innovation and Employment/ ; UOWX2101//Ministry of Business, Innovation and Employment/ ; UOWX2101//Ministry of Business, Innovation and Employment/ ; }, abstract = {BACKGROUND: Forest restoration has primarily been evaluated through changes in aboveground communities, while belowground microbial communities-critical drivers of ecosystem functions-remain less understood. Moreover, studies of soil microbes have focused largely on community structure, which does not necessarily reflect the recovery of functional capacity and stability.<br><br>METHODS: To determine how forest restoration affects microbial community structure and function and how microbial diversity relates to ecosystem multifunctional potential and stability, we analysed soil microbial communities from 79 urban forest restoration sites across New Zealand, spanning 0-63&#xa0;years since initial plantings. Shotgun metagenomic sequencing was used to characterize taxonomic composition and functional potential, with diversity quantified using alpha and beta metrics. To evaluate links between diversity and ecosystem function, we assessed ecosystem multifunctional potential (EMF) which describes the ecosystem's capacity to simultaneously provide multiple functions, and we developed a novel functional insurance (FI) index grounded in ecological theory as an indicator of functional stability and resilience. To calculate FI in microbial systems from sequencing data, we quantified functional overlap by estimating over 250 million species-function correlations per sample.<br><br>RESULTS: Contrary to our expectations, only beta diversity, not alpha diversity, was positively associated with EMF and FI, indicating that community composition and dissimilarity rather than species richness underpins microbial functional capacity and stability. EMF and FI were positively correlated, showing that high functional diversity and functional overlap can co-occur in microbial systems. In addition, archaeal turnover increased with closing forest canopies, contributing to higher EMF and FI, while bacterial turnover was only weakly associated with restoration parameters. Notably, restoration time did not play a role in shaping microbial diversity, EMF and FI.<br><br>CONCLUSIONS: Our findings demonstrate that microbial compositional turnover, rather than increases in species richness, are critical for restoring soil ecosystem functions. Incorporating microbial functional metrics like the FI index into restoration frameworks that recognise both above and belowground dynamics could promote resilient and multifunctional urban forests.}, }
@article {pmid41981684, year = {2026}, author = {Clough, J and Mikac, KM}, title = {Metagenomic profiling of bacterial and fungal microbiota and putative pathogens of southern greater gliders (Petauroides volans).}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00564-7}, pmid = {41981684}, issn = {2524-4671}, }
@article {pmid41981860, year = {2026}, author = {Liu, B and Yang, J and Wang, J and Zhang, J and Wang, L and Qu, B and Guo, L and Zhang, X and Yang, X and Jiang, Y}, title = {Application of Whole-Genome Sequencing and Metagenomic Sequencing in Microbial Analysis of Milk Powder and Its Processing Environment: Current Findings and Challenges.}, journal = {Comprehensive reviews in food science and food safety}, volume = {25}, number = {3}, pages = {e70478}, doi = {10.1111/1541-4337.70478}, pmid = {41981860}, issn = {1541-4337}, support = {//Danone Asia-Pacific Management Co. Ltd./ ; }, mesh = {*Whole Genome Sequencing ; *Milk/microbiology ; Animals ; *Metagenomics ; *Food Microbiology ; Food Handling ; Powders ; Food Contamination/analysis ; }, abstract = {As dairy enterprises increasingly focus on microbial contamination, traditional detection technologies are gradually showing limitations in terms of detection capability, accurate source tracking, and rapid response, especially when dealing with microbial communities in complex processing environments. Fortunately, whole-genome sequencing (WGS) and metagenomic sequencing provide innovative alternative solutions. These technologies significantly improve the detection of harmful microbes by offering strain-level resolution, detecting low-abundance organisms, and uncovering previously undetectable microbes. This review discusses the application of WGS and metagenomic sequencing in microbial monitoring, contamination source tracking, and quality control across the entire milk powder production chain. In particular, it highlights the progress made in microbial typing and source tracking, as well as in the detection of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs). This review also compares microbial control standards for milk powder and its processing environment across different countries and international organizations, providing a regulatory perspective. Furthermore, the integration of emerging technologies is also discussed, particularly machine learning (ML) and deep learning (DL). Artificial intelligence (AI) enables more efficient, predictive, and accurate microbial monitoring, improving contamination control and contributing to safer and higher-quality milk powder production processes. This review provides critical insights that contribute to improving microbial safety management and control strategies in milk powder production.}, }
@article {pmid41982876, year = {2026}, author = {Ren, J and Lan, Z and Wang, C and Zhu, J and Li, M and Xu, J and Lu, Y and Tu, J and Zhang, X and Boskovic, L and Huang, J and Hu, X}, title = {Metagenomic next-generation sequencing and conventional microbiology for microbial profiling in biliary tract infections: a comparative study with clinical stratification.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1799474}, pmid = {41982876}, issn = {1664-302X}, }
@article {pmid41982885, year = {2026}, author = {Santiago-Rodriguez, TM and Toranzos, GA}, title = {Editorial: Advances in phage applications: deciphering phage biological and ecological mechanisms through metagenomics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1822387}, doi = {10.3389/fmicb.2026.1822387}, pmid = {41982885}, issn = {1664-302X}, }
@article {pmid41982959, year = {2026}, author = {Zhang, K and Zheng, J and Wei, A and Qin, M and Zhu, G}, title = {Pulmonary infection caused by Tropheryma whipplei in a child before hematopoietic stem cell transplantation: a case report.}, journal = {Translational pediatrics}, volume = {15}, number = {3}, pages = {91}, pmid = {41982959}, issn = {2224-4344}, abstract = {BACKGROUND: Tropheryma whipplei (TW) triggers Whipple's disease (WD), a rare, chronic multisystemic infection with heterogeneous clinical presentations that can be easily overlooked, particularly Whipple's pneumonia. The advent of metagenomic next-generation sequencing (mNGS) technology applied to bronchoalveolar lavage fluid (BALF) analysis has enabled the identification of an increasing number of patients with acute pneumonia due to TW. Most reports describe symptomatic middle-aged males with cough, while asymptomatic pediatric cases remain exceptionally rare. Without adequate antibiotic therapy, WD is invariably fatal, especially in patients undergoing hematopoietic stem cell transplantation (HSCT). There is no established consensus on the optimal treatment regimen or duration, particularly for pediatric patients.<br><br>CASE DESCRIPTION: An 8-year-old boy with primary immunodeficiency due to a genetic mutation presented without respiratory symptoms. Yet, high-resolution computed tomography (HRCT) revealed nodular lesions. Initially misdiagnosed as a fungal infection, subsequent mNGS analysis of BALF identified TW as the sole pathogen, leading to a diagnosis of TW-associated pneumonia. Following a combined anti-infective therapy regimen, the patient successfully underwent the myeloablative conditioning (MAC) regimen. Neutrophil and platelet engraftment occurred promptly, with no severe transplant-related complications.<br><br>CONCLUSIONS: This retrospective analysis describes a clinical scenario involving a pediatric patient who exhibited no respiratory symptoms prior to transplantation but showed characteristic nodular lesions on imaging studies, ultimately confirming acute pneumonia caused by TW. Under a combination anti-infection regimen consisting of intravenous ceftriaxone, oral doxycycline, and oral hydroxychloroquine, the child tolerated the MAC regimen well. Neutrophil and platelet engraftment proceeded without delay, and follow-up imaging confirmed complete resolution of the pulmonary lesions.}, }
@article {pmid41983569, year = {2026}, author = {Vogel, MA and Machairas, F and Ferchiou, S and Osvatic, J and Alzubaidy, H and Séneca, J and Hausmann, B and Klun, K and Petersen, JM}, title = {Symbiont diversity within Loripes orbiculatus and the case for multiple hosts.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag094}, pmid = {41983569}, issn = {1751-7370}, abstract = {Seagrasses support immense biodiversity and are critical for maintaining coastal ecosystem health. These foundation species benefit from a 'three-way' facultative relationship with one of the common inhabitants of seagrass meadows, lucinid bivalves, which host specific bacterial Ca. Thiodiazotropha symbionts. Relatives of the bivalve symbionts have been detected on seagrass roots raising the possibility that these symbionts may colonize both animals and plants; however, no study has yet compared bivalve- and seagrass-associated symbionts at the same site and time. Our combination of 16S rRNA gene amplicon and metagenome sequencing revealed a greater diversity than was previously observed within both lucinid bivalves and on seagrass roots from the Adriatic Sea and resulted in the closed genome of one prominent symbiont species. We show that two of the Ca. Thiodiazotropha ASVs found on seagrass roots are identical to those found in bivalve hosts at the same site. This suggests that symbiont sharing may occur in the seagrass habitat between these two host species, which has important evolutionary and ecological implications for both hosts and symbionts.}, }
@article {pmid41983714, year = {2026}, author = {Viguier, C and Mansuy, JM and Martin-Blondel, G}, title = {Recent advances in flavivirus encephalitis.}, journal = {Current opinion in infectious diseases}, volume = {}, number = {}, pages = {}, pmid = {41983714}, issn = {1473-6527}, abstract = {PURPOSE OF REVIEW: Flaviviruses are an increasing public health concern, responsible for a broad spectrum of human disease ranging from asymptomatic or mild febrile illness to severe neuroinvasive infections such as encephalitis. Flavivirus encephalitis is associated with substantial mortality and long-term neurological sequelae, yet no specific antiviral therapy is currently available. Diagnosis remains challenging because of transient viremia and serological cross-reactivity, and preventive strategies are unevenly implemented. This review summarizes recent advances in the diagnosis, prognostic assessment, treatment, and prevention of flavivirus-associated encephalitis.<br><br>RECENT FINDINGS: Recent studies have reshaped diagnostic strategies through improved viral detection, including multimatrix molecular testing and metagenomic approaches, alongside better characterization of host-response markers in cerebrospinal fluid. Recent work has substantially refined understanding of host susceptibility, highlighting preexisting antitype I interferon autoantibodies as a major driver of severe disease across neurotropic flaviviruses, and identifying several biomarkers with potential prognostic value. Neuroimaging work has refined MRI pattern recognition across flaviviral encephalitis, with limited but evolving prognostic implications. While management remains largely supportive, the therapeutic pipeline is increasingly diverse, with growing interest in host-directed strategies.<br><br>SUMMARY: Flavivirus encephalitis represents a major clinical challenge driven by host vulnerability, diagnostic complexity, and the absence of validated therapies. Integrating recent advances in diagnostics, risk stratification, and prevention is essential, while ongoing therapeutic development offers cautious optimism for future management.}, }
@article {pmid41983840, year = {2026}, author = {Ibadullayeva, A and Khamzina, A and Smagulov, D and Khamzin, K}, title = {An overview of the livestock microbiome: sheep, horses, cattle, camels, and chickens.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {86}, number = {}, pages = {e299936}, doi = {10.1590/1519-6984.299936}, pmid = {41983840}, issn = {1678-4375}, mesh = {Animals ; Cattle/microbiology ; *Livestock/microbiology ; Camelus/microbiology ; Sheep/microbiology ; *Microbiota/genetics/physiology ; Chickens/microbiology ; Horses/microbiology ; }, abstract = {The animal microbiome plays a crucial role in determining the health, productivity, and welfare of livestock species, including sheep, horses, cattle, camel, and chicken. These animal species were selected due to the high consumption of their products in Kazakhstan. Enhancing their productivity, while maintaining the safety and quality of meat and milk derived from them, represents a pressing research priority. This review article includes current research on the composition, diversity, and purposes of the microbiota found within different organ systems of these species. This study focuses on recent advancements in sequencing technology, including metagenomics, 16S rRNA sequencing, and multiomic methods, to combine data on microbial diversity, composition, and functionality within the gastrointestinal tract and other organs. The key findings show differences in microbial communities associated with breed, age, and diet, the impact of microbiota on methane emissions and feed efficiency in ruminants, and the possibility of using microbiome management techniques (e.g., probiotics, prebiotics, and feed additives) to enhance livestock production. The microbiome influences various species, extending its effects beyond digestion and immunity to reproductive health and behavior. Despite advancements, translating microbiome data into actionable interventions is interfered by variability resulting from genetic, environmental, and management factors. Integrating microbiome research more closely with animal genetics and livestock production methods could lead to innovative approaches for improving the health, efficiency, and welfare of farm animals, ultimately supporting sustainable livestock farming practices.}, }
@article {pmid41983925, year = {2026}, author = {El Zibaoui, R and Venkatesan, A}, title = {An update on infectious encephalitis: from epidemiology to management.}, journal = {Current opinion in infectious diseases}, volume = {}, number = {}, pages = {}, pmid = {41983925}, issn = {1473-6527}, abstract = {PURPOSE OF REVIEW: Infectious encephalitis (IE) is a serious neurological condition that poses a major global health threat. This review summarizes emerging pathogens, particularly arboviruses, updated diagnostic strategies, and evolving treatment approaches, emphasizing ongoing gaps in diagnosis and management.<br><br>RECENT FINDINGS: Established arboviruses such as West Nile virus, Japanese encephalitis virus, Powassan virus, and Eastern Equine virus have regained attention due to their geographic expansion and the appearance of distinct genotypes. In parallel, increasing reports of encephalitis by newly emerging pathogens such as Oropouche virus and scrub typhus speak to the evolving nature of the epidemiology of IE. Advances in diagnostics, including multiplex PCR and metagenomic next-generation sequencing, have enhanced the breadth and accuracy of pathogen identification. As treatment options remain scarce, the role of immunomodulatory agents and novel antiviral molecules in the management of IE is actively being investigated.<br><br>SUMMARY: The emergence of novel and reemerging pathogens highlights the need for rapid, accurate diagnostics. Advanced molecular techniques and the identification of novel therapeutic targets have the potential to change the landscape of IE. However, strengthening surveillance and vaccination strategies, along with ongoing efforts in vaccine development, remain crucial for optimizing patient outcomes, increasing public health preparedness, and mitigating future outbreaks.}, }
@article {pmid41984378, year = {2026}, author = {Tao, X and Du, Z and Wang, X and Lv, L and Zhang, G and Liang, J and Zou, W}, title = {Volatile Fatty Acid Production from Baijiu Distillers' Grains Via Anaerobic Fermentation with Rumen Microbes: Performance and Mechanism.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41984378}, issn = {1559-0291}, support = {52400160//National Natural Science Foundation of China/ ; 52360020//National Natural Science Foundation of China/ ; E2024202030//Natural Science Foundation of Hebei Province/ ; RKJH[2025]26//Renhuai Municipal Science and Technology Program/ ; Qiankehe Jichu QN [2025] 292//Youth Science and Technology Talent Project of the Guizhou Provincial Basic Research Program/ ; }, }
@article {pmid41984912, year = {2026}, author = {Fri, J and Njanje, I and Mahopo, TC and Mavhandu-Ramarumo, LG and Bessong, PO and , }, title = {The Gut Bacterial Resistome in the First Two Years of Life: Protocol for a Longitudinal Observational Birth Cohort Study.}, journal = {JMIR research protocols}, volume = {15}, number = {}, pages = {e86058}, doi = {10.2196/86058}, pmid = {41984912}, issn = {1929-0748}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Infant, Newborn ; Female ; Infant ; Longitudinal Studies ; Prospective Studies ; Birth Cohort ; South Africa ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Observational Studies as Topic ; Rural Population ; Milk, Human/microbiology/chemistry ; Male ; Risk Factors ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a global health threat that increases the burden of infectious diseases and disproportionately affects communities of low socioeconomic status. Despite the call for community-level AMR data, prospective studies from rural sub-Saharan African communities to inform appropriate targeted interventions remain scarce. Given the role of enteric bacteria in AMR transmission dynamics, there is a need to understand the timing, risk factors, and ecological drivers of gut resistome acquisition and development during infancy.<br><br>OBJECTIVE: This study aimed to characterize the temporal dynamics of enteric bacterial resistomes during the first 2 years of life and to identify drivers of AMR acquisition and development in a community-based, prospective, observational birth cohort study in a rural South African community.<br><br>METHODS: The study aims to enroll 200 newborns and their mothers within 17 days post partum. Data on key exposures and variables include sociodemographics; perinatal and anthropometrics; feeding practices and dietary exposures; illness, medication, and vaccination history; breast milk metabolomic profiles; household socioeconomic status; maternal psychosocial and behavioral factors; hygiene and sanitation practices; and environmental exposures including hydro-meteorological variables, in-house livestock and pets, and drinking water quality. Biological samples include stools from monthly collections and diarrhea episodes for metagenomic analysis and breast milk for metabolomics. Planned analyses include assessing the infant microbiome and resistome structure (diversity, abundance, and composition) across time points and modeling associations between risk factors and AMR outcomes. Additionally, a cross-sectional community survey on knowledge, attitudes, and practices regarding antimicrobial use is conducted to inform knowledge translation through responsive dialogues, thereby developing ethnographically relevant packages for community-level AMR stewardship.<br><br>RESULTS: Participant identification and enrollment began in August 2023. By October 2025, 167 newborns had been enrolled, with 20 having completed the 24-month follow-up. The characteristics of the enrolled participants are presented in this protocol.<br><br>CONCLUSIONS: This study will offer a unique opportunity to generate longitudinal resistome data from a rural sub-Saharan African setting. The study is expected to contribute knowledge on the microbiome and resistome structure dynamics and trajectories associated with key risk factors of acquisition and development. In addition, co-produced ethnographically tailored educational packages, informed by knowledge, attitudes, and practices and bacterial resistome data, will drive sustainable community-centered AMR awareness interventions.}, }
@article {pmid41985067, year = {2026}, author = {Sarmah, MP and Zoramthara, K and Manngaihsiam, R and Boro, HH and Baraka, AGA and Saeed, AL and Gurusubramanian, G and Kharat, KR}, title = {Microbiome Simplification During Metamorphosis in Larva and Adults of Armigeres subalbatus (Coquillett, 1898) (Culicidae) Revealed by Shotgun Metagenomics.}, journal = {Archives of insect biochemistry and physiology}, volume = {121}, number = {4}, pages = {e70159}, doi = {10.1002/arch.70159}, pmid = {41985067}, issn = {1520-6327}, support = {EM/Dev/11/SG/01993/2024//Indian Council of Medical Research/ ; DST/INSPIRE Fellowship/[IF240039]//Department of Science &amp; Technology, New Delhi, India (INSPIRE-JRF)/ ; }, mesh = {Animals ; Larva/microbiology/growth &amp; development ; *Microbiota ; Metagenomics ; *Culicidae/microbiology/growth &amp; development ; *Metamorphosis, Biological ; Bacteria/genetics/classification ; Metagenome ; }, abstract = {Armigeres subalbatus is medically significant vector for filarial worms and the Japanese encephalitis virus. Shotgun metagenomic sequencing was employed to investigate the bacterial communities in A. subalbatus mosquitoes. The diversity metrics (Shannon H', Simpson 1-D, Berger-Parker) were calculated for larval and adult stages. De novo assembly and binning were used to recover metagenome-assembled genomes (MAGs) with > 82% completeness and < 4% contamination. Functional profiling assessed gene expression via transcripts per million (TPM) and clusters of orthologous groups (COG) categories. Larval microbiomes showed high alpha diversity (Shannon H' ≈ 1.336 ± 0.163, Simpson 1-D = 0.684 ± 0.046), dominated by Gammaproteobacteria (Aeromonas, Morganella, and Yersinia) and Bacteroidota, with persistent Shewanella and Acinetobacter. Adult microbiomes exhibited low diversity (Shannon H' = 0.637 ± 0.100, Berger-Parker = 0.682 ± 0.026), near-monoculture dominated by Aeromonas hydrophila, alongside low-abundance Stenotrophomonas, Pseudomonas, and Microbacterium. Six high-quality MAGs were recovered: larval (Bacteroidota, Shewanella, and Acinetobacter); adult (Acinetobacter, Stenotrophomonas, and Shewanella), confirming persistence of Shewanella and Acinetobacter, absence of Bacteroidota, and emergence of Stenotrophomonas in adults. Adult microbiomes displayed metabolic hyperactivity, with 1.5-4 times higher transcriptional output across COG categories compared to larvae. Chemotaxis [Methyl-accepting chemotaxis protein (MCP), K03406: ~6000 TPM in adults vs. < 1000 TPM in larvae] and ABC transporters (PF00005: > 10,000 TPM in adults) dominated adults, while larval expression was balanced among housekeeping functions. The microbiome undergoes significant restructuring during mosquito development, shifting from diverse larval communities to metabolically active, low-diversity adult assemblages. Recovered MAGs provide a genomic basis for future studies on mosquito microbiota dynamics and functions.}, }
@article {pmid41985316, year = {2026}, author = {Ariaee, A and Hunter, A and Wignall, A and Bremmell, K and Prestidge, C and Joyce, P}, title = {Spray dried inulin-montmorillonite hybrids alleviate high-fat diet-induced inflammatory and metabolic dysregulation in rats.}, journal = {Biomaterials advances}, volume = {185}, number = {}, pages = {214878}, doi = {10.1016/j.bioadv.2026.214878}, pmid = {41985316}, issn = {2772-9508}, abstract = {Metabolic dysregulation is strongly associated with excessive dietary lipid absorption and gut microbiota imbalances under high-fat diet (HFD) conditions. This study evaluates a spray-dried inulin-montmorillonite (INU-MMT) hybrid designed to simultaneously restrict intestinal lipid digestion and modulate gut microbiota composition. In simulated intestinal digestion, INU-MMT maintained the strong lipid-inhibitory effect of montmorillonite, reducing free fatty acid release by 2.8-fold compared to HFD conditions, while exhibiting improved dispersion stability attributed to INU's ability to reduce clay platelet aggregation. In a 21-day HFD-fed rat model, INU-MMT supplementation (1 g/kg/day) attenuated cumulative weight gain by 4.7% compared to the HFD control, exceeding reductions with INU (2.0%) and MMT (1.5%) alone. 16S rRNA gene sequencing of fecal samples revealed improved gut microbial diversity (Simpson's index, p = 0.0161) and uniquely enriched health-associated taxa including Akkermansiaceae (2.5-fold), Eggerthellaceae (7.7-fold), Ruminococcaceae (3.5-fold), and Peptostreptococcaceae (8-fold). Beta diversity analysis highlighted that INU-MMT induced a distinct microbial composition from INU, suggesting the complimentary effects of the hybrid promote a more widespread microbial change than prebiotic alone. Predictive metagenomic analysis using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2) software demonstrated a 98% reduction in microbial triacylglycerol lipase abundance, consistent with the observed in vitro lipolysis suppression. These findings demonstrate that the INU-MMT hybrid preserves MMT's restriction of lipid digestion while delivering INU's prebiotic benefits, producing additive effects in diet-induced weight gain and microbiota modulation. The multifunctional nature of this spray-dried hybrid highlights its potential as a dietary strategy for metabolic dysregulation.}, }
@article {pmid41985330, year = {2026}, author = {Kwiendacz, H and Cembrowska-Lech, D and Skonieczna-Żydecka, K and Klimontowicz, K and Podsiadło, K and Wierzbicka-Woś, A and Styburski, D and Kaczmarczyk, M and Gumprecht, J and Łoniewski, I and Nabrdalik, K}, title = {Multi-strain probiotic enhances metformin tolerance by modulating gut microbiome and bile acid pathways: Insight from multi-omics post-hoc analysis (ProGasMet trial).}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {198}, number = {}, pages = {119370}, doi = {10.1016/j.biopha.2026.119370}, pmid = {41985330}, issn = {1950-6007}, abstract = {BACKGROUND: Metformin is the cornerstone therapy for type 2 diabetes, but gastrointestinal intolerance commonly limits dose escalation and long-term adherence. In the ProGasMet trial, multi-strain probiotic supplementation improved metformin tolerability. However, the underlying microbiome-metabolome mechanisms remain unclear.<br><br>METHODS AND ANALYSIS: We performed an exploratory multi-omics analysis using Period 1 of a randomized, double-blind, placebo-controlled trial. Participants with metformin intolerance received a multi-strain probiotic or placebo for 12 weeks. Paired stool samples collected at baseline and end of treatment were available from 34 participants (68 samples). We integrated shotgun metagenomic species profiles, predicted gut metabolic modules, and untargeted faecal LC-MS metabolomics using multi-block sparse PLS (DIABLO), complemented by longitudinal covariate-adjusted feature-level analyses and associations with gastrointestinal symptom burden (QACSMI and a simplified GI score).<br><br>RESULTS: In multi-omics integration at 12 weeks, bile acid-related metabolites were among the strongest contributors to group separation, with hyodeoxycholic acid and related compounds enriched in the probiotic arm. Global biodiversity and community-wide turnover did not differ between groups. Feature-level analyses suggested modest, directionally coherent changes in selected taxa, functional modules, and metabolites. Higher hyodeoxycholic acid concentrations were associated with lower gastrointestinal symptom burden in probiotic-treated participants, a pattern not observed under placebo.<br><br>CONCLUSION: Probiotic supplementation may be associated with coordinated microbiome-metabolome shifts in metformin-intolerant type 2 diabetes, highlighting bile acid remodelling, particularly hyodeoxycholic acid, as a plausible candidate for improved tolerability. These results support prioritising secondary bile acid-microbiome pathways for confirmation in larger trials incorporating targeted bile acid quantification and causal modelling.}, }
@article {pmid41985671, year = {2026}, author = {Wang, Y and Liu, X and Li, Z and Kang, A and Bai, Y and Wang, Y and Liu, Y and Zhang, C and Yang, J and Cai, Q and Feng, Y and Yi, H and Zhang, M and Zhang, F and Liu, H and Xu, C}, title = {Oligofructose alleviates hyperandrogenism in polycystic ovary syndrome through gut microbiota-derived bile acids.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.04.036}, pmid = {41985671}, issn = {2090-1224}, abstract = {INTRODUCTION: Polycystic ovary syndrome (PCOS) is a common endocrine disorder in reproductive-age women, characterized by hyperandrogenism and metabolic dysfunction. Dietary interventions are recommended as one of the first-line therapies. Oligofructose (OFS), a prebiotic fiber, has demonstrated clinical benefits in PCOS; however, its underlying mechanism remains unclear.<br><br>OBJECTIVES: To determine whether OFS alleviates PCOS-like phenotypes through bile acid-dependent mechanisms and to identify downstream ovarian steroidogenic responses.<br><br>METHODS: Letrozole-induced PCOS-like mice received OFS supplementation. Microbiota dependence was assessed using antibiotic depletion and fecal microbiota transplantation (FMT). Bile acid involvement was evaluated using cholestyramine. Gut microbial composition and function were profiled by 16S rRNA and metagenomic sequencing, and bile acids were quantified by UHPLC-MS/MS. Ovarian transcriptomics, ex vivo ovarian explants, and primary granulosa cells were used to examine steroidogenic changes, with pharmacological inhibition applied to assess TGR5-related signaling.<br><br>RESULTS: OFS improved reproductive and metabolic abnormalities in PCOS-like mice. These benefits were abolished by microbiota depletion and bile acid sequestration, indicating microbiota- and bile acid-dependent effects. OFS was associated with increased circulating hyodeoxycholic acid (HDCA), which negatively correlated with serum testosterone. HDCA supplementation partially reproduced endocrine improvements under microbiota-depleted conditions. Ovarian transcriptomic and functional analyses demonstrated enhanced aromatization following OFS treatment. In ex vivo ovarian explants and primary granulosa cells, HDCA increased estradiol production, reduced testosterone, and upregulated CYP19A1 (encoding aromatase). Under androgen stimulation, pharmacological inhibition of TGR5 attenuated HDCA-associated increases in estradiol and aromatase activity, supporting involvement of TGR5-related signaling.<br><br>CONCLUSION: OFS alleviates PCOS-like phenotypes in a microbiota- and bile acid-dependent manner and enhances ovarian aromatization. These findings move beyond descriptive bile acid alterations in PCOS by providing functional evidence that dietary fiber-induced bile acid remodeling is associated with modulation of ovarian steroidogenic regulation.}, }
@article {pmid41986005, year = {2026}, author = {Ansari, A and Shete, O and Ghosh, TS}, title = {Artificial intelligence in microbial metagenomics.}, journal = {Progress in molecular biology and translational science}, volume = {221}, number = {}, pages = {255-276}, doi = {10.1016/bs.pmbts.2026.01.009}, pmid = {41986005}, issn = {1878-0814}, mesh = {*Metagenomics/methods ; *Artificial Intelligence ; Humans ; Microbiota/genetics ; Machine Learning ; }, abstract = {Rapid advancements in genomic sequencing technologies and similar technological advancements in the area of accessing, isolating, extracting and functional probing of microbes residing in diverse environments has resulted in a deluge of microbiome sequencing and microbial genomic sequencing data. Concomitant developments in the area of data science, specifically in the domains of advanced statistics, and artificial intelligence (AI) can facilitate mining this data to answer complex biological questions and developing translational applications in diverse areas, ranging from health-care to industrial microbiology. For most researchers, information on which AI tools address specific biological questions is scattered across disparate sources. In this chapter, we explore the various applications of AI-based methodologies (using case-studies) in answering different biological questions using microbial genomics and metagenomic data. We also discuss different AI and machine-learning (ML) based approaches to integrate metagenomic data with other "omics" data. Finally, we highlight both challenges and possibilities with this rapidly progressing field.}, }
@article {pmid41986051, year = {2026}, author = {}, title = {Correction to 'Clinical Value of Metagenomic Next-Generation Sequencing in Early Diagnosis of Peritoneal Dialysis-Associated Peritonitis: A Randomised Controlled Observational Trial'.}, journal = {Nephrology (Carlton, Vic.)}, volume = {31}, number = {4}, pages = {e70203}, doi = {10.1111/nep.70203}, pmid = {41986051}, issn = {1440-1797}, }
@article {pmid41975041, year = {2026}, author = {Stepanyan, A and Kotsafti, A and Rosato, A and Castagliuolo, I and Scarpa, M and Scarpa, M and , }, title = {Gut microbiota-associated predictors as biomarkers of neoadjuvant treatment response in rectal cancer-a systematic review.}, journal = {British journal of cancer}, volume = {}, number = {}, pages = {}, pmid = {41975041}, issn = {1532-1827}, support = {IG 2019 - ID. 23381//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; }, abstract = {BACKGROUND: The gut microbiome is increasingly recognized as a modulator of cancer therapy outcomes and a potential predictive biomarker. This systematic review synthesizes current evidence on microbial biomarkers associated with neoadjuvant treatment (NT) response in rectal cancer (RC).<br><br>METHODS: PubMed, Embase, and Ovid Medline databases were searched through March 2025. Eligible studies included RC patients treated with NT with baseline microbial analysis stratified by treatment response. Two reviewers independently performed screening, data extraction, and quality assessment (NIH and STORMS tools). Due to substantial heterogeneity, a structured qualitative synthesis without meta-analysis was conducted following SWiM guidelines, using a direction-of-effect vote-counting approach.<br><br>RESULTS: Sixteen observational studies (842 patients) were included, covering chemoradiotherapy (nCRT), total neoadjuvant therapy, chemotherapy, and immunochemoradiotherapy. Microbiota composition was investigated by 16S rRNA sequencing, metagenomics, or metatranscriptomics on fecal or tissue samples. While microbial diversity showed inconsistent associations, specific taxa&#xa0;-notably Bacteroides, Fusobacterium and Akkermansia- emerged as recurrent biomarkers of poor response to nCRT. Twelve predictive models reported AUROC values from 0.73 to 0.97, with limited external validation.<br><br>CONCLUSIONS: Specific microbial taxa show a consistent association with nCRT resistance across independent cohorts. However, methodological heterogeneity and limited reproducibility warrant standardized prospective validation before clinical implementation.<br><br>PROSPERO: CRD42023433704.}, }
@article {pmid41975095, year = {2026}, author = {Guan, K and Ocampo, RF and Matheus Carnevali, PB and Castelle, CJ and Gonzalez-Osorio, L and Castanzo, DT and Thomas, NC and Brothers, M and Dangerfield, TL and Hooper, MM and West, MS and Appleby, NM and Krudop, I and Lamothe, RC and Aliaga Goltsman, DS and Alexander, LM and Butterfield, CN and Johnson, KA and Brown, CT and Taylor, DW}, title = {Comparative characterization of Cas12f orthologs reveals mechanistic features underlying enhanced genome editing efficiency.}, journal = {Nature structural &amp; molecular biology}, volume = {}, number = {}, pages = {}, pmid = {41975095}, issn = {1545-9985}, abstract = {Miniature CRISPR-Cas12f nucleases are attractive candidates for therapeutic genome editing because of their compact size and compatibility with adeno-associated virus (AAV) delivery. However, editing efficiencies in mammalian cells are lower than those of larger systems. The extensive phylogenetic diversity of Cas12f suggests unexplored mechanistic variation with the potential for optimization. Here we identify and characterize a naturally occurring Cas12f ortholog discovered through metagenomics, Alistipes sp. Cas12f (Al3Cas12f), which supports robust genome editing in human cells. Through structural, biochemical and kinetic analyses, we compare Al3Cas12f to two recently described orthologs, Oscillibacter sp. Cas12f and Ruminiclostridium herbifermentans Cas12f. These orthologs present divergent architectures and regulatory features governing protospacer-adjacent motif recognition, guide RNA (gRNA) binding, dimerization and DNA cleavage. Notably, Al3Cas12f achieves efficient R-loop formation through a stable dimer interface and a naturally optimized gRNA. Leveraging these structural insights, we generate an engineered Al3Cas12f variant (RKK) that increases editing and improves activity across several tested genomic loci. By overcoming locus-dependent variability and an apparent potency threshold, this engineered compact editor seems to expand the feasibility of low-dose, AAV-compatible therapeutic genome editing. Our results elucidate mechanistic determinants of Cas12f activity and offer a framework for engineering compact genome editors that may bear therapeutic potential.}, }
@article {pmid41975182, year = {2026}, author = {Kleinbölting, N and Fiore, A and Cangioli, L and Visca, A and Huang, L and Hett, J and Costanzo, M and Sevi, F and Tabacchioni, S and Aprea, G and Mengoni, A and Pihlanto, A and Neuhoff, D and Sczyrba, A and Schlüter, A and Bevivino, A}, title = {Impact of microbial consortia and fertilization regimes on the soil microbiome in maize field trials.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-47528-0}, pmid = {41975182}, issn = {2045-2322}, support = {818431//Horizon 2020 Framework Programme/ ; }, abstract = {Beneficial microbial consortia provide an eco-friendly alternative to conventional inorganic fertilizers and can serve as a complementary management tool for enhancing soil fertility and crop productivity. This study aimed to assess the impact of microbial consortia application on the indigenous maize rhizosphere microbiome under different fertilization regimes in organically managed fields in Germany. Three experimental microbial consortia (MC_B, MC_C, MC_C_AMF) and one commercial product (Micosat F) were tested in combination with three fertilization levels (unfertilized, 110 kg nitrogen ha[- 1], and 200 kg nitrogen ha[- 1]) in a split plot design. The diversity, composition and functional potential of the maize rhizosphere microbiome were analyzed at different maize growth stages. Fertilization levels exerted a stronger influence than microbial consortia, significantly shaping community composition and functional traits of the indigenous soil microbiome. Increasing fertilization intensity altered the abundance of specific plant growth-promoting (PGP)-determinants, either stimulating or suppressing potential PGP bacteria. In contrast, microbial consortia application did not impact PGP-associated abundance profiles. Overall, the results indicate that multifunctional microbial consortia can act as effective biofertilizers in sustainable maize cultivation without compromising resident microbiome diversity, thereby reducing long-term ecological risks on natural biodiversity.}, }
@article {pmid41975253, year = {2026}, author = {Aquino, CI and La Vecchia, M and Pasolli, E and Sala, G and Ligori, A and Boldorini, R and Ferrante, D and Dianzani, I and Aspesi, A and Surico, D and Remorgida, V}, title = {Decoding the microbial landscape of endometrial cancer: a case-control study.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05017-4}, pmid = {41975253}, issn = {1471-2180}, support = {IG 2021-ID. 25886//Associazione Italiana per la Ricerca sul Cancro/ ; }, }
@article {pmid41975274, year = {2026}, author = {Nikolaidis, M and Hu, C and Juran, BD and McCauley, BM and Schlicht, EM and Bianchi, JK and Ali, AH and Tragaki, V and Atkinson, EJ and Johnson, S and Mars, RA and Eaton, JE and Carey, EJ and Franke, A and Schramm, C and Kashyap, PC and Go, YM and Tran, V and Teeny, S and Jones, DP and Grant, CW and Athreya, AP and Miller, GW and LaRusso, NF and Gores, GJ and Karlsen, TH and Hov, JR and Amoutzias, GD and Lazaridis, KN}, title = {Compositional and functional differences of gut microbiome and metabolome inform pathogenesis of cholestatic liver disease.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2655793}, doi = {10.1080/19490976.2026.2655793}, pmid = {41975274}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolome ; Female ; Male ; Middle Aged ; Feces/microbiology/chemistry ; Adult ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; *Liver Cirrhosis, Biliary/microbiology/metabolism/pathology ; *Cholangitis, Sclerosing/microbiology/metabolism/pathology ; Aged ; }, abstract = {Primary sclerosing cholangitis (PSC) and primary biliary cholangitis (PBC) are rare, idiopathic, chronic cholestatic liver diseases that respond differently to limited medical therapies and often lead to liver transplantation. We examined the compositional and functional differences in the gut microbiome, mycobiome, and metabolome of these diseases to better understand their impact on pathogenesis and outcomes. Stool sample metagenomes and metabolomes from patients with PSC (n = 245), PBC (n = 280) and matched controls (n = 245 and n = 278, respectively) were analyzed by shotgun sequencing and ultrahigh-resolution mass spectrometry. Comparisons were conducted with covariate-adjusted linear models. The gut microbiomes of patients with PSC and PBC were characterized by reduced diversity and increased abundance of pathobionts and virulence factors, coupled with altered microbial metabolism, including a reduction of short-chain fatty acids and B-vitamins. Untargeted stool metabolomics supported these results. Patients were stratified into groups using their microbial signatures, and each group had distinct patterns of microbiome-related changes. Cox regression analysis revealed that pathogenic microbial species were predictive of hepatic decompensation, whereas beneficial species had a protective effect. Based on previous groundwork and our new results, microbiome-based interventions such as probiotics, short-chain fatty acid supplementation, and phage therapy represent promising therapeutic options for cholestatic liver diseases.}, }
@article {pmid41975427, year = {2026}, author = {Zhang, Z and Bai, J and Liu, Y and Wang, J and Lv, Z and Tang, L and Wang, R and Gao, L and Liu, C and Lu, S and Fu, X and Ni, J and Wan, P}, title = {Effects of synthetic breast milk on the gut metagenome and whole blood transcriptome in lambs.}, journal = {BMC veterinary research}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12917-026-05460-5}, pmid = {41975427}, issn = {1746-6148}, support = {NYHXGG.2023AA206-3//Agricultural GG Project of Xinjiang Production and Construction Corps/ ; 2025AB5012//Tacheng Talents Project/ ; 2025AA01504//Project of Major Science and Technology Project of the Corps/ ; 2022TSYCCX0124//Young Science and Technology Top Talent Program of Tianshan Talent Training Program in Xinjiang Province/ ; XJARS-09-26//Xinjiang Agriculture Research System/ ; CARS-39-07//China Agriculture Research System/ ; }, }
@article {pmid41975703, year = {2026}, author = {Rong, R and Long, Y and Li, Y and Lin, L and Yang, J and Hu, Z and Liu, D and Chen, P}, title = {Metagenomic and Targeted Next-Generation Sequencing in Infectious Disease Diagnostics: Current Applications, Challenges, and Future Perspectives.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {16}, number = {7}, pages = {}, pmid = {41975703}, issn = {2075-4418}, support = {2024ZD0533100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 2024ZD0533106//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; P12220011-230148//Undergraduate teachingquality and teaching reform licensing project SYSU/ ; }, abstract = {Metagenomic and targeted next-generation sequencing (NGS) technologies are rapidly transforming diagnosis and management for infectious diseases. This review comprehensively examines the current applications of metagenomic NGS (mNGS) and targeted NGS (tNGS) in clinical microbiology, highlighting their roles in pathogen detection, antimicrobial resistance profiling, virulence characterization, and outbreak investigation-particularly in complex cases such as pneumonia, critical illness with pulmonary infections, and pediatric acute respiratory illnesses. We discuss the diagnostic performance, advantages, and limitations of these approaches, including challenges related to sensitivity, specificity, standardization, bioinformatic complexity, and cost-effectiveness. Furthermore, we explore emerging opportunities for integrating NGS-based surveillance with public health strategies, such as wastewater epidemiology, to monitor healthcare-associated infections (HAIs) and antimicrobial resistance (AMR) at the population level. Finally, we outline key steps needed to translate these powerful genomic tools from research settings into routine clinical and public health practice.}, }
@article {pmid41975975, year = {2026}, author = {Szala, &#x141; and Staninska-Pięta, J and Piotrowska-Cyplik, A}, title = {Microbiome of Bovine Milk and Factors Influencing Its Composition.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {7}, pages = {}, pmid = {41975975}, issn = {2076-2615}, support = {MEiN/2023/DPI/2870//Ministry of Science and Higher Education/ ; }, abstract = {The bovine milk microbiome is a complex and dynamic microbial ecosystem, comprising both commensal and pathogenic bacteria. Its composition is shaped by endogenous factors, including udder physiology, lactation stage, and health status, particularly mastitis, as well as by exogenous factors, such as housing conditions, farm infrastructure, milking practices, and post-milking processing. Mastitis not only alters milk quality but also induces persistent dysbiosis that may persist even after clinical recovery, highlighting the need for continuous microbiome monitoring to ensure milk safety. Advances in molecular and metagenomic techniques have enabled the detection of microbial taxa that are difficult to identify using traditional culture-based methods. However, challenges remain due to low microbial biomass, reagent contamination, and the inability to distinguish live from dead bacteria, all of which complicate accurate characterization. Environmental contamination from skin, air, and equipment, along with microbial shifts during transport, storage, pasteurization, and product separation, further modulate microbial communities. While mastitis-related changes in milk microbiota have been extensively studied, the effects of other bovine diseases and systemic health conditions remain largely unexplored, constituting a critical knowledge gap. Understanding the factors that shape milk microbial communities is essential for ensuring dairy product safety, optimizing herd management, and developing microbiome-based innovations in milk production.}, }
@article {pmid41976452, year = {2026}, author = {Li, X and Li, Y and Li, Q and Jin, Y and Chen, Y}, title = {Rumen Metagenomic and Muscle Metabolomic Characterization of Meat Quality in Duolang Sheep at Different Ages.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, pmid = {41976452}, issn = {2304-8158}, support = {2022TSYCLJ0014//Program for Science and Technology Innovation Talents/ ; 2023B02015//Key Research and Development Program Project of Xinjiang Uygur Autonomous Region/ ; }, abstract = {This study aimed to investigate the changes in the meat quality characteristics of Duolang sheep using rumen metagenomic and muscle metabolomic analyses across different age groups. A total of 24 three-month-old male Duolang sheep were selected and reared, and samples of longissimus thoracis muscle and rumen contents were collected at 4, 6, and 8 months of age to evaluate meat quality, metabolites, rumen metagenome, and volatile fatty acids (VFAs). The results indicated that the lightness (L*45min) and yellowness (b*45min) of the longissimus thoracis muscle at 45 min post-slaughter were significantly higher at 4 and 6 months than at 8 months of age (p < 0.05). In terms of ruminal VFAs, butyrate concentration was significantly higher at 6 months than at 4 months (p < 0.05), and valerate concentration exhibited a quadratic relationship with age (p = 0.02). With increasing age, the relative abundances of Prevotella and Fibrobacter increased, whereas those of Methanobrevibacter and Bacteroides decreased (p < 0.05), leading to shifts in functional pathways related to amino acid, lipid, and carbohydrate and energy metabolism. Untargeted metabolomics revealed that muscle betaine and inosine peaked at 4 months of age, whereas L-arginine, L-proline, and inosinic acid were most abundant at 6 months of age (p < 0.05). Correlation analysis revealed that the b*45min was positively associated with ruminal concentrations of propionate, butyrate, and valerate, as well as with the relative abundances of key Selenomonadales taxa (p < 0.05). Inosinic acid exhibited a positive correlation with the abundance of the genus Sodaliphilus and ruminal butyrate concentration (p < 0.05), while Sodaliphilus abundance was negatively correlated with inosine (p < 0.05). In summary, this study demonstrates that age-related variations in the meat quality of Duolang sheep are closely associated with rumen microbial ecology and muscle metabolites, offering novel insights into the molecular mechanisms underlying meat quality formation and identifying potential biomarkers.}, }
@article {pmid41976454, year = {2026}, author = {Olupot, CK and Sheehan, O and Kampff, Z and McDonnell, B and Woods, DF and Lugli, GA and Ventura, M and Reen, FJ and Sinderen, DV and Mahony, J}, title = {Raw Milk Cheese Microbiomes: A Paradigm for Interactions of Lactic Acid Bacteria in Food Ecosystems.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, pmid = {41976454}, issn = {2304-8158}, abstract = {While industrial-scale dairy fermentations often employ pasteurized milk as the substrate, many farmhouse and traditional production practices apply raw milk derived from a variety of mammals. Certain artisanal production systems rely on the autochthonous microbiota of the milk, fermentation vessels, equipment and/or environment to initiate milk coagulation. While the technological properties of lactic acid bacteria associated with dairy fermentations are well described, their interactions with other organisms during fermentation and cheese ripening are poorly investigated. This study presents an overview of the microbial ecology of raw and pasteurized milk used in the production of Irish farmhouse cheeses using metagenomic and culture-based approaches. Metagenomic analysis of four raw milk-derived cheeses established the dominant presence of either lactococci or Streptococcus spp. and with a secondary population of various lactobacilli. Interestingly, the Brie sample was also demonstrated to possess significant proportion of Hafnia spp. This was corroborated in culture-based analysis where Hafnia isolates were also identified. Furthermore, we report on the motility phenotype, lactose utilization ability and metabolic products of isolates of Hafnia paralvei and Hafnia alvei, and determine that these strains could grow in a non-antagonistic manner on plates with strains of Lactococcus lactis and Streptococcus thermophilus. As artisanal and farmhouse production systems are often associated with protected or regionally significant products, it is essential to develop a clear understanding of the microbial communities within and the complex relationships between the community members.}, }
@article {pmid41976504, year = {2026}, author = {Buranavanitvong, N and Thanthithum, C and Kanyakam, K and Azzout-Marniche, D and Jouan-Rimbaud Bouveresse, D and Chotechuang, N and Prakitchaiwattana, C}, title = {Diet-Associated Gut Bacterial Microbiota and Metabolome Signatures Linked to Fermented Food Intake in Healthy Postmenopausal Women.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, pmid = {41976504}, issn = {2304-8158}, support = {FOOD_FF_68_290_2300_073//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; GCUGR1125671022D//the 90th Anniversary of Chulalongkorn University Scholarship under the Ratchadapisek Somphot Endowment Fund/ ; NA//the Second Century Fund (C2F), Chulalongkorn University/ ; }, abstract = {Long-term adherence to plant-based diets can modify gut bacterial microbiota composition and metabolite profiles, which may be particularly relevant for postmenopausal women who frequently adopt such diets and experience age-related changes in nutrient absorption and metabolism. Fermented foods, commonly consumed in vegetarian diets, enhance dietary diversity and nutritional quality. This study compared gut bacterial microbiota and fecal metabolomes between vegetarians (VGs) and omnivores (OMs) and evaluated the contribution of fermented food intake. Thirty-two healthy postmenopausal Thai women (>55 years; 16 VGs, 16 OMs) were enrolled. Gut bacterial microbiota and fecal metabolites were analyzed using 16S rRNA metagenomic and untargeted [1]H-NMR metabolomics. The five most frequently consumed fermented foods were microbiologically characterized. Fermented food consumption was found to be significantly different between groups. OM participants reported infrequent consumption (<10% per week), whereas VG participants consumed fermented foods daily, often in multiple forms (>60% of weekly meals). VG participants exhibited enrichment of Prevotella, Faecalibacterium, and Blautia, while OM participants showed higher abundances of Bacteroides and Escherichia-Shigella. LEfSe identified Weissella as a bacterial taxon associated with the VG group. Functional prediction and metabolomic analyses indicated enhanced carbohydrate fermentation and increased short-chain fatty acid (SCFA) production in VGs, whereas OM profiles reflected greater protein catabolism. Fermented foods consumed by VGs shared microbial biomarkers with the VG gut bacterial microbiota and were rich in SCFAs and essential amino acids, supporting their potential role as microbial and metabolic contributors within the gut ecosystem and nutritional adequacy in postmenopausal vegetarians.}, }
@article {pmid41977149, year = {2026}, author = {Liszkowska-Walisiak, W and Motyl, I and Płacheta-Kwiatkowska, B and Wlaźlak, M and Ruman, T and Nizioł, J and Wilkowska, A and Maher, A and Berłowska, J}, title = {Apple Pomace Fermented with Non-Saccharomyces Yeast as a Factor Modulating Gut Microbiota.}, journal = {International journal of molecular sciences}, volume = {27}, number = {7}, pages = {}, doi = {10.3390/ijms27072960}, pmid = {41977149}, issn = {1422-0067}, mesh = {*Malus/metabolism/chemistry ; *Gastrointestinal Microbiome ; *Fermentation ; Humans ; *Yeasts/metabolism ; Fatty Acids, Volatile/metabolism ; Bacteria/classification/genetics ; }, abstract = {The valorisation of agro-industrial by-products through fermentation offers an opportunity to develop functional ingredients with targeted effects on gut microbiota. This study evaluates the impact of apple pomace fermented at a low temperature (15 °C) by cold-adapted yeast on the structure and metabolic activity of human gut microbiota, simulated using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]). The fermented apple pomace preparation was characterised by high stability under gastrointestinal conditions, supporting its potential applicability as a functional food ingredient. Supplementation with fermented apple pomace induced distinct changes in the composition and activity of gut microbiota compared to the non-fermented substrate, including increased abundance of the genera Akkermansia, Coriobacteriaceae, and Parabacteroides, and reduced abundance of Bifidobacterium, Klebsiella, Serratia, and Raoultella. The fermented preparation was associated with reduced accumulation of metabolites typically linked to proteolytic fermentation and a more stable metabolic profile throughout the supplementation and washout phases. Short-chain fatty acid analysis indicated that fermentation influenced both the quantity and proportional balance of microbial fermentation products, promoting profiles closer to physiological reference ranges. Overall, fermentation of apple pomace at 15 °C enhanced its functional properties and modulated gut microbiota metabolism in a manner consistent with improved ecosystem stability. These findings highlight the potential of fermented fruit by-products as sustainable ingredients for dietary strategies aiming to support gut microbial functionality.}, }
@article {pmid41977414, year = {2026}, author = {Wang, C and Hou, L and Wang, Y and Gao, G and Geng, Y and Pan, J}, title = {Preliminary Study on the Synergistic Degradation Mechanism of the Microbial Community on the Wood of the Dingtao M2 Tomb.}, journal = {International journal of molecular sciences}, volume = {27}, number = {7}, pages = {}, doi = {10.3390/ijms27073233}, pmid = {41977414}, issn = {1422-0067}, support = {2024YFF0907700//National Key R&amp;D Program of China/ ; N/A//Fundamental Research Funds for the Central Universities/ ; N/A//Preservation Research Center of the Mausoleum of the Dingtao King/ ; }, mesh = {*Wood/microbiology/metabolism ; *Microbiota ; Lignin/metabolism ; *Penicillium/metabolism/genetics ; Metagenomics/methods ; }, abstract = {According to our investigation carried out in July 2023, the wood of the Western Han Dynasty Dingtao M2 Tomb, stored in the preservation room, exhibited signs of microbial degradation. Our metagenomic analysis first revealed Penicillium as the dominant genus on the end of the wrapped wood. Furthermore, functional annotations demonstrated that the resident microbial community possessed cellulolytic and ligninolytic capabilities. Targeted metabolomic analysis evaluated the degradation capacity of Penicillium charlesii DTP_1, a strain isolated from the wrapped wood. We hypothesize that DTP_1 provides an acidic microenvironment via the production of organic acids; the functional microbial community then decomposes lignin into small metabolites via enzymatic action, and these products are then utilized by the microbial community, including DTP_1. Finally, we verified that liquid cinnamaldehyde and volatile gaseous allicin and carvacrol exhibit better inhibitory efficacy. Nevertheless, further optimization of plant-derived agents and application methods are still required. This study proposes a putative mechanism underlying the degradation of the Dingtao M2 Tomb wood by the microbial community, thereby providing theoretical support for the conservation of wooden cultural heritage and relics.}, }
@article {pmid41978025, year = {2026}, author = {De Nat, M and Boscolo, S and Gallo, SP and Nanni, L and Fusaro, D}, title = {Ensemble Deep Learning Models on Raw DNA Sequences for Viral Genome Identification in Human Samples.}, journal = {Sensors (Basel, Switzerland)}, volume = {26}, number = {7}, pages = {}, doi = {10.3390/s26072238}, pmid = {41978025}, issn = {1424-8220}, mesh = {*Deep Learning ; Humans ; *Genome, Viral/genetics ; Neural Networks, Computer ; *Sequence Analysis, DNA/methods ; Metagenomics/methods ; Base Sequence ; *Viruses/genetics ; }, abstract = {Detecting highly divergent or previously unknown viruses is a critical bottleneck in clinical diagnostics and pathogen surveillance. While alignment-based methods often fail to classify sequences lacking homology to known references, deep learning offers a powerful alternative for signal extraction from 'viral dark matter.' In this work, we present a high-performance ensemble of deep convolutional neural networks specifically designed to identify viral contigs in complex human metagenomic datasets. Our framework processes sequences acquired from high-throughput biological sensors and integrates complementary architectures to capture both local motifs and global genomic signatures. The proposed ensemble achieves state-of-the-art performance, reaching an AUROC of 0.939 on 300 bp contigs and significantly outperforming existing models such as transformer-based approaches, ViraMiner, and DeepVirFinder. Crucially, our results demonstrate high robustness to data degradation, maintaining stable predictive power even with a 10% random nucleotide substitution rate, a common challenge in degraded clinical samples. Furthermore, the model generalizes to 'unseen' viral families not present during training, demonstrating its utility for emerging threat detection. To ensure full reproducibility and facilitate further research in clinical sensing, the complete code and datasets are publicly available on Github.}, }
@article {pmid41979145, year = {2026}, author = {Alderete, TL and Holzhausen, EA and Liang, D and Jones, RB and Lurmann, F and Goran, MI and Chang, HH and Sarnat, JA}, title = {Early-Life Air Pollution Exposure Is Associated with the Infant Gut Microbiome and Fecal Metabolome in the First Two Years of Life.}, journal = {Research report (Health Effects Institute)}, volume = {}, number = {237}, pages = {1-58}, pmid = {41979145}, issn = {1041-5505}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Feces/chemistry/microbiology ; Female ; *Metabolome/drug effects ; Infant ; Male ; *Air Pollution/adverse effects/analysis ; *Air Pollutants/adverse effects/analysis ; Pregnancy ; Particulate Matter/adverse effects/analysis ; *Environmental Exposure/adverse effects ; California ; Prenatal Exposure Delayed Effects ; Infant, Newborn ; }, abstract = {INTRODUCTION: Obesity is a major public health concern because it increases the risk of numerous diseases, including cardiovascular disease and type 2 diabetes. Ambient and near-roadway air pollution has been associated with childhood obesity risk, independent of diet and physical activity. However, the biological mechanisms underlying these relationships remain unclear. Based on our previous work and existing literature, we hypothesized that exposure to air pollutants alters the developing infant gut microbiome and fecal metabolome, with implications for childhood obesity risk. In this study, we aimed to determine whether prenatal or early-life exposure to ambient air pollution and near-roadway air pollution is associated with the gut microbiome and fecal metabolome during the first 2 years of life.<br><br>METHODS: Our analysis had two components, both of which examined participants from the Southern California Mother's Milk Study, a Latino cohort in which we collected detailed information regarding maternal and child health during the first 24 months of life. Residential-based estimates of exposure to ambient particulate matter (particulate matter &#x2264;2.5 &#xb5;m and &#x2264;10 &#xb5;m in aerodynamic diameter: PM2.5 and PM10, respectively), nitrogen dioxide (NO2), and ozone (O3), as well as near-roadway air pollution (NOx), were modeled using residential address histories. High-throughput metagenomics and metabolomics were performed on stool samples collected at 1, 6, 12, 18, and 24 months of age. Overall, our sample included 207 unique individuals with gut microbiome data and 127 unique individuals with fecal metabolomics data. In the first analysis component, we examined the cross-sectional associations of pre- and postnatal exposure to ambient and near-roadway pollutants with the infant gut microbiome and fecal metabolome at 1, 6, 12, 18, and 24 months of age. In the second analysis component, we examined the longitudinal associations of pre- and postnatal exposure to air pollutants with the trajectory of the developing infant gut microbiome and fecal metabolome.<br><br>RESULTS: Our findings indicate that exposure to air pollutants during prenatal and postnatal periods is associated with significant changes in the developing gut microbiome and its metabolic output, as evidenced by perturbations in the fecal metabolome. These molecular alterations were evident in both cross-sectional and longitudinal analyses. The results suggest that early-life exposure to air pollution can disrupt the developmental trajectory of the gut microbiome, potentially leading to changes with substantial health implications. These findings underscore the importance of mitigating air pollution exposure during critical developmental periods to protect and promote gut health and overall well-being in infants.<br><br>CONCLUSIONS: We identified gut microbes and fecal metabolites associated with early-life exposure to air pollution. Many of these markers of gut bacterial composition and function have been linked to childhood obesity. These findings contribute to our understanding of mechanisms underlying the obesogenic effects of air pollutants in early life. Future work in this cohort will include integrated mixture and multi-omics analyses to explore the joint impact of air pollution exposure on the gut microbiome and fecal metabolome.}, }
@article {pmid41979617, year = {2026}, author = {Li, G and Dan, N and Lu, T}, title = {Two Cases of Severe Chlamydia psittaci Pneumonia with Respiratory Failure and Literature Review.}, journal = {Clinical laboratory}, volume = {72}, number = {4}, pages = {}, doi = {10.7754/Clin.Lab.2025.250675}, pmid = {41979617}, issn = {1433-6510}, mesh = {Humans ; *Chlamydophila psittaci/genetics/isolation &amp; purification ; *Respiratory Insufficiency/microbiology/diagnosis/etiology ; *Psittacosis/diagnosis/drug therapy/microbiology/complications ; Male ; Anti-Bacterial Agents/therapeutic use ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Female ; Treatment Outcome ; }, abstract = {BACKGROUND: Chlamydia psittaci pneumonia is a zoonotic disease with non-specific clinical manifestations, often leading to delayed diagnosis. Metagenomic next-generation sequencing (mNGS) can help us identify pathogens in a timely manner and quickly adjust treatment strategies.<br><br>METHODS: We reported two cases of severe Chlamydia psittaci pneumonia with respiratory failure and reviewed relevant literature.<br><br>RESULTS: Both patients were diagnosed with Chlamydia psittaci infection through mNGS after routine pathogen testing failed. After using Omadacycline based treatment, the patients' clinical and radiological characteristics improved significantly and were successfully cured.<br><br>CONCLUSIONS: For patients infected with Chlamydia psittaci pneumonia, timely identification of the pathogen is crucial. mNGS can quickly detect Chlamydia psittaci in critically ill patients, guide clinical timely targeted treatment, and improve patient symptoms.}, }
@article {pmid41979623, year = {2026}, author = {Xie, BX and Chen, Y and Tan, YR and Jiang, T and Huang, MH and Zhu, YM and Chen, S}, title = {Challenges in the Diagnosis of Hematogenous Disseminated Pulmonary Tuberculosis with Multiple Organ Involvement.}, journal = {Clinical laboratory}, volume = {72}, number = {4}, pages = {}, doi = {10.7754/Clin.Lab.2025.250640}, pmid = {41979623}, issn = {1433-6510}, mesh = {Humans ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Pericardial Effusion/microbiology ; Male ; Tomography, X-Ray Computed ; High-Throughput Nucleotide Sequencing ; Middle Aged ; *Tuberculosis, Miliary/diagnosis/microbiology ; Antitubercular Agents/therapeutic use ; }, abstract = {BACKGROUND: Tuberculosis is a public health problem worldwide, and China is a high-burden country. Hematogenous disseminated pulmonary tuberculosis is one of the most serious forms of tuberculosis, and diagnosing hematogenous pulmonary tuberculosis is a challenge, even for the most experienced clinicians, who may also feel perplexed. We report a case of hematogenous disseminated tuberculosis involving multiple organs that was initially misdiagnosed as metastatic malignancy. The diagnosis was finally confirmed by metagenomic Next-Generation Sequencing (m-NGS) of peritoneal and pericardial effusions, which detected Mycobacterium tuberculosis complex.<br><br>METHODS: Appropriate laboratory tests, m-NGS, Chest and abdominal CT, Pericardiocentesis, and Peritoneal puncture.<br><br>RESULTS: Chest and abdominal CT showed diffuse nodules in both lungs, pericardial effusion, bilateral pleural effusion, and abdominal pelvic effusion. Tuberculosis bacillus antibody was negative, erythrocyte sedimentation rate increased to 42 mm/H, and the carcinoembryonic antigen (CEA) increased to 7.1 ng/mL, peritoneal effusion adenosine deaminase increased to 65.17 U/L, pericardial effusion adenosine deaminase increased to 142.39 U/L. m-NGS of pericardial effusion and peritoneal effusion detected 886,963 M. tuberculosis complex.<br><br>CONCLUSIONS: Miliary tuberculosis is a severe and rare form of tuberculosis. Delayed diagnosis may be the most important factor leading to death from miliary tuberculosis. We report a case where Mycobacterium tuberculosis was identified through mNGS of pericardial and peritoneal effusions, enabling rapid diagnosis of disseminated tuberculosis. This case provides a new approach for the rapid diagnosis of disseminated tuberculosis.}, }
@article {pmid41980062, year = {2026}, author = {Zhan, J and Yang, W and Guo, J and Yu, Y and Lai, S and Liu, X and Zhou, S}, title = {Iron plaques as terminal electron acceptors optimize clostridial fermentation and nitrogen fixation in rice rhizospheres.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag088}, pmid = {41980062}, issn = {1751-7370}, abstract = {Fermentative Clostridium species associated with rice roots can contribute substantially to biological nitrogen fixation in anoxic paddy soils, yet whether their biological nitrogen fixation is regulated by the redox chemistry of rhizosphere remains unclear. Here we show that iron plaques on rice roots function as terminal electron acceptors that reprogram Clostridium fermentation and thereby enhance biological nitrogen fixation. In nitrogen-fixation microcosms, Clostridium sensu stricto I was selectively enriched under plaque-associated Fe(III)-reducing conditions, coinciding with elevated nitrogen fixation. Metabolomic profiling coupled with metabolic flux analysis revealed that Fe(III) reduction redirects a portion of carbon and electron flow from low-energy-yield solventogenesis toward high-energy-yield acidogenesis. This shift increases cellular ATP generation and expands the reductant pool, thereby benefiting the energetic and reductant demands of nitrogenase. Integrated transcriptomic and metagenomic analyses further identified NosR, a flavin mononucleotide-binding protein that is upregulated during Fe(III) reduction and may facilitate electron delivery to plaque-associated Fe(III). Our findings establish a mechanism in which iron plaque reduction optimizes fermentation for biological nitrogen fixation, providing fundamental insights into coupled Fe-N cycling in rice rhizospheres and suggesting potential strategies for sustainable nitrogen management in flooded agroecosystems.}, }
@article {pmid41980294, year = {2026}, author = {Paulí, S and Rosell-Díaz, M and Moreno-Navarrete, JM and Pons Tamarit, J and Pérez-Brocal, V and Moya, A and Puig, J and Garre-Olmo, J and Ramos, R and Fernández-Real, JM and Mayneris-Perxachs, J}, title = {Glucose metabolism's impact on Blastocystis presence in the human gut.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {61}, number = {}, pages = {106647}, doi = {10.1016/j.clnu.2026.106647}, pmid = {41980294}, issn = {1532-1983}, abstract = {BACKGROUND AND AIMS: The role of Blastocystis spp. parasite in human health remains debated. Recent literature associates it with a healthy gut and lifestyle. Evidence suggests that Blastocystis spp. could enhance glucose homeostasis, although Blastocystis spp. is considered to be epiphenomena for a lifestyle. Moreover, some subtypes seem to have a beneficial impact while others would hinder the host's health. Here, we explore the complex link between Blastocystis spp. and glucose metabolism parameters.<br><br>METHODS: We explored shotgun metagenomic profiles of the gut microbiota from fecal samples associated with glucose metabolism parameters in 4 independent cohorts (CGM, n = 65; IMAGEOMICS, n = 1030; PECT, n = 841 and MEIFLO, n = 22), using microbiome compositional analysis methodology. We leverage data from MEIFLO, a recent clinical trial conducted in patients recently diagnosed with type 2 diabetes (T2D), to investigate how metformin-induced improvement in glucose metabolism influences gut microbiota composition, using Linear Models for Differential Abundance. We studied possible associations of Blastocystis spp. with leukocyte telomere length.<br><br>RESULTS: We confirmed and extended the relationship between glucose homeostasis and Blastocystis spp. and subtypes ST1 and ST4, showing its association with glucose and insulin levels in all cohorts. Importantly, we observed that glucose homeostasis may shape Blastocystis spp. abundance in the gut, rather than the reverse, based on clinical trial data showing that metformin (not placebo) increased Blastocystis spp. in recently diagnosed T2D patients. We identify Blastocystis as one of the microbial genera most strongly and directly associated with telomere length in the IMAGEOMICS cohort.<br><br>CONCLUSIONS: The direct relation between Blastocystis and telomere length aligns with the observed inverse associations of glucose levels with telomere length, and glucose levels with Blastocystis. We propose that Blastocystis may be associated with healthy glucose metabolism as an outcome and potentially serve as an indicator of improved metabolic health.}, }
@article {pmid41980639, year = {2026}, author = {Li, R and Li, S and Yan, Y and Xie, Y and Liu, L and Zhao, J and Zhang, J and Cai, Z and Huang, X}, title = {Reductive soil disinfestation and hydrothermal biochar regulate antibiotic resistance mechanisms by reshaping soil bacterial functional traits and interaction patterns.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134622}, doi = {10.1016/j.biortech.2026.134622}, pmid = {41980639}, issn = {1873-2976}, abstract = {The health risk posed by antibiotic resistance genes (ARGs) in agricultural soils has become a growing concern. However, a systematic understanding of how microbial life history strategies, functional traits, and community interactions jointly shape ARG dynamics remains lacking. This knowledge gap not only constrains our ability to elucidate the evolutionary mechanisms underlying microbial resistance but also hampers the precise prediction and effective management of soil ARG risks. Here, we established distinct soil habitats through diverse soil managements, including control (CK), reductive soil disinfestation (RSD), and RSD combined with hydrothermal biochar application (HCR), to investigate how microbial traits and interactions shape ARG resistance mechanisms using metagenomic analyses. Our results showed that RSD and HCR treatments significantly reduced the overall abundance and ecological risk of ARGs compared to CK. In CK soils, microbial communities characterized by intensive interactions, high metabolic activity, and rapid growth efficiency promoted the enrichment of ARGs conferring resistance via antibiotic target alteration, protection, or replacement. In contrast, RSD/HCR treatments favored slow-growing, functionally complex, and competition-dominated communities, which were enriched in ARGs associated with antibiotic efflux mechanisms. Moreover, ARGs exhibited pronounced co-occurrence patterns with antimicrobial biosynthetic gene clusters in highly competitive environments. Collectively, this study reveals the selective responses of ARG resistance mechanisms to distinct microbial ecological strategies and provides new insights for the precise management of environmental antibiotic resistance risks.}, }
@article {pmid41980640, year = {2026}, author = {Yang, H and Peng, N and Fan, Y and Huang, J and Zhang, J and Li, L and Ding, J and Tang, Z and Song, J and Liu, D and Hu, R and He, Z and Wang, C}, title = {Genome-Resolved insights into significance of DNRA Microbes in N2O production during manure composting.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134617}, doi = {10.1016/j.biortech.2026.134617}, pmid = {41980640}, issn = {1873-2976}, abstract = {Nitrous oxide (N2O) production during manure composting has traditionally been attributed primarily to heterotrophic denitrification (HD), while the roles of alternative pathways remain poorly resolved. Using time-resolved multi-omics across 37 samples from various manure sources, our study investigated the transcriptional landscape of N2O-producing pathways during composting. Microorganisms associated with dissimilatory nitrate reduction to ammonium (DNRA), including Fermentimonas and JAHWKS01 lineages, accounted for 21.2-33.1% of N2O-producing gene expression-comparable to HD-revealing DNRA as a previously underappreciated source. DNRA-associated gene expression was regulated by viral factors, predominantly through lytic Caudoviricetes phages. Expanding our analysis to 174 public metagenomic datasets revealed that DNRA-derived N2O-producing gene abundance peaked under static and hyperthermophilic conditions, highlighting aeration and temperature as critical mitigation controls. Furthermore, our study identified a substantial proportion of microorganisms harboring both DNRA and HD pathways. These findings refine mechanistic understanding of composting N2O emissions and inform multi-pathway mitigation strategies.}, }
@article {pmid41980647, year = {2026}, author = {Song, M and Jiang, L and Lin, Z and Li, J and Luo, C and Qiu, R}, title = {Size-dependent effect of microplastics on sulfamethoxazole degraders in soil as revealed by integration of SIP and metagenomics.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134620}, doi = {10.1016/j.biortech.2026.134620}, pmid = {41980647}, issn = {1873-2976}, abstract = {Microbes related to antibiotic degradation in situ in agricultural soil with MPs and their response to different sizes of MPs are ambiguity. This study investigated the microbes participating in antibiotic degradation in soils with 4.5 mm and 0.1 mm MPs by using DNA-SIP with metagenomics, Raman-activated cell sorting (RACS) with sulfamethoxazole (SMX) and polyethylene as the model compound and MPs. The 4.5 mm MPs enhanced SMX degradation by promoting diversity and abundance of degraders benefiting from improved soil properties, relation between degraders and SMX, and bacteria with positive co-occurrence relationship with degraders. The 0.1 mm MPs inhibited SMX degradation by decreasing diversity, abundance of degraders, and intensifying bacteria mutually exclusive with degraders due to harsher soil conditions. Furthermore, DNA-SIP-RACS successfully acquired cells of SIP-identified putative degraders, and directly linked SMX degradation potential with metC1, metF1and luxS1, proving possibility of applying this approach in antibiotic-degrading microbes in soil.}, }
@article {pmid41980652, year = {2026}, author = {Back, JP and Klain, V and Pintro, VO and Lopes, FC and Marques, AL and Kray, J and Beys-da-Silva, WO and Santi, L and Schrank, A and Mayer, FQ and Vainstein, MH}, title = {Viral Diversity of Coastal Restinga Soils From Southern Brazil.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70343}, doi = {10.1111/1758-2229.70343}, pmid = {41980652}, issn = {1758-2229}, support = {441167/2023-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 382064/2025-9//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 383394/2024-4//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 314485/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 305705/2025-3//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 303971/2025-8//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 313620/2021-0//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; 303945/2025-7//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; }, mesh = {Brazil ; *Soil Microbiology ; *Biodiversity ; *Viruses/classification/genetics/isolation &amp; purification ; Phylogeny ; Metagenomics ; Soil/chemistry ; }, abstract = {Coastal ecotones are highly dynamic environments for viral studies due to their extreme abiotic conditions, transitional nature between marine and terrestrial domains and high biodiversity. In Brazil, the Restinga is a coastal ecotone along the shoreline, characterized by nutrient-poor sandy soils, high salinity, strong winds and intense solar radiation, hosting poorly explored microbial communities essential for ecological balance. This exploratory study provides a preliminary characterization of viral diversity across three Restinga localities in southern Brazil (Imbé, Cidreira and Mostardas) using metagenomics. We identified 261 viral families, 2023 genera and 6064 species, with 'Unknown' representing 44%-46% of families and ~9% of genera. Among known taxa, Mimiviridae was most frequent (15%-16%), followed by Phycodnaviridae (9%), Peduoviridae (5%) and Kyanoviridae (4%-5%). Genera such as Tupanvirus and Fadolivirus were abundant (~5%), with Fadolivirus algeromassiliense and Donellivirus gee among the most frequent species. Although alpha diversity and composition did not differ significantly among sites, landscape features influenced viral communities. Viral richness and abundance increased with urban land cover and isolation but decreased with Restinga cover and patch fragmentation.}, }
@article {pmid41980940, year = {2026}, author = {Lu, Z and Li, R and Zhou, K and Li, S and Sun, S and Liu, J and Zhao, L and Chen, S and Liu, K and Yuan, X and Shao, Z}, title = {Tick-vectored mobilization of antibiotic resistance genes: transboundary dissemination across wildlife-livestock-vector-environment interfaces.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00986-w}, pmid = {41980940}, issn = {2055-5008}, support = {2024SF-YBXM-289//Key Research and Development Projects of Shaanxi Province/ ; 82473689//National Natural Science Foundation of China/ ; 82273689//National Natural Science Foundation of China/ ; WW25Z01SF027//Wuwei City Science and Technology Plan Project/ ; }, abstract = {Antibiotic resistance genes (ARGs) are emerging as critical environmental contaminants across diverse ecological interfaces. To dissect evidence of microbiome and resistome in the different interconnected interfaces of ecotone, we conducted a field investigation of the microbiome and resistome of marmots, along with coexisting domestic sheep, ticks and their cave soils within the same ecological habitat. We used shotgun metagenomics with metagenome-assembled genomes (MAGs), species-resolved binning, ARG identification, source-tracker analyses, and horizontal gene transfer (HGT) network analysis to examine potential cross-interface dissemination. The composition of the mammalian gut microbiome was primarily comprised of Firmicutes, while ticks and soils exhibited distinct clusters that were predominantly dominated by Proteobacteria. The observed resistance mechanisms manifested niche-specific patterns, with target alteration predominating in mammals, whereas ticks exhibited elevated antibiotic inactivation/efflux strategies, and soils prioritized efflux mechanisms. Metagenomic assembly from these four groups yielded 5339 metagenome-assembled genomes (MAGs), of which 1481 met medium- or high-quality standards. Ticks exhibited 72% species similarity and 52% ARG concordance with marmots, while soils conserved 32% ARGs and >86% toxin genes with mammals. Our findings demonstrate that the transboundary dissemination of ARGs across different ecological interfaces, necessitates integrated surveillance of antimicrobial resistance at ecological boundaries to mitigate public health risks.}, }
@article {pmid41980943, year = {2026}, author = {Kim, J and Kim, N and Cha, JH and Ma, J and Lee, I}, title = {Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41980943}, issn = {2041-1723}, support = {2022R1A2C1092062//National Research Foundation of Korea (NRF)/ ; RS-2025-18362970//National Research Foundation of Korea (NRF)/ ; 2022M3A9F3016364//National Research Foundation of Korea (NRF)/ ; }, mesh = {*Metagenomics/methods ; *Metagenome/genetics ; Benchmarking ; Humans ; Neural Networks, Computer ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; }, abstract = {Metagenomic binning is essential for reconstructing prokaryotic genomes from metagenomic samples. We benchmarked various binning tools using Critical Assessment of Metagenome Interpretation (CAMI)-simulated, custom-simulated, and real metagenomic datasets, primarily focusing on short-read sequencing data. Our analysis highlights critical factors influencing binning efficacy: (i) Sequencing depth and taxonomic complexity strongly impact binning performance, while CAMI-simulated benchmarking datasets exhibit substantially lower complexity than human gut and environmental metagenomes, (ii) Chimeric genome rates vary widely across tools, (iii) Multi-sample binning is most effective with about 20 samples, as using too few or too many samples can reduce its benefits, and (iv) Binning efficacy was lower for single-end sequencing samples due to reduced contig quality and assembly fragmentation. Neural network-based tools consistently outperformed others in genome recovery from both real samples and simulated samples with realistic taxonomic complexity, though at higher computational cost. By integrating and refining genome bins from the top three binning tools, we recovered >30% more high-quality genomes than previous methods. This study provides practical guidance for improving metagenomic binning to facilitate the reconstruction of prokaryotic genomes.}, }
@article {pmid41980953, year = {2026}, author = {Luo, E and Pham, ND and Rogers, TJ and Sheam, MM and Benner, BE and Vallino, JJ and Trubl, G and Huber, JA}, title = {Quantitative stable isotope probing (qSIP)-informed metagenomics identifies viruses infecting chemoautotrophs.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71833-x}, pmid = {41980953}, issn = {2041-1723}, abstract = {Aquatic environments absorb ~2.5 gigatonnes of atmospheric carbon each year[1], more than the carbon stored in the atmosphere, soils, and all biomass combined. Primary producers transform this dissolved inorganic carbon into biomass that can subsequently flow into other trophic levels, or be released back into the environment through viral lysis. While there is substantial knowledge about the diversity and activity of viruses infecting photoautotrophic primary producers and the ecosystem impact, little is known about viruses infecting chemoautotrophs, representing a gap in our understanding of key processes driving microbial carbon cycling. Here, we combine metagenomics with quantitative [12/13]C stable isotopic probing (qSIP) mesocosm experiments in a marine-derived meromictic pond to quantify population-specific isotopic enrichment, identify key chemoautotrophic primary producers, and virus-host dynamics. Isotopically enriched carbon is tracked from the genomes of chemoautotrophs to putative viruses, showing that active populations of hydrogen/sulfur-oxidizing chemoautotrophs (Thiomicrorhabdus, Hydrogenovibrio, Sulfurimonas, Sulfurovum) are targeted by viruses. This work provides the foundation for revealing the diversity and activity of viruses infecting globally-widespread chemoautotrophs. Our study sheds light on trophic interactions that impact microbial carbon cycling in aphotic environments and builds toward biogeochemical models that incorporate viral impacts on chemoautotrophic microbial communities.}, }
@article {pmid41967340, year = {2026}, author = {Li, M and Yao, K and Harindintwali, JD and Qian, M and Wu, N and Kan, Y and Song, Z and Xiao, X and Liu, P and Zhao, Y}, title = {Alkali-organic synergy rewires microbial acid tolerance to restore nitrogen cycling in acidic soils.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129619}, doi = {10.1016/j.jenvman.2026.129619}, pmid = {41967340}, issn = {1095-8630}, abstract = {Soil acidification in global croplands is intensifying, yet the microbial mechanisms by which amendments restore soil nitrogen (N) cycling remain poorly understood. Here, we used a decade-long field experiment in strongly acidic soils to elucidate how alkali slag and organic manure, alone and in combination, regulate acid-tolerant microbial functions and N transformation processes. By integrating soil physicochemical analyses, 16 S rRNA gene sequencing, and shotgun metagenomics, we show that the combined application of organic manure and alkali slag (OM + AS) most effectively increased soil pH (from 4.18 to 5.42) and reduced inorganic N accumulation relative to single amendments (Ammonium nitrogen, nitrate nitrogen, and total organic nitrogen decreased by 15.66 mg/kg, 12.56 mg/kg, and 46.09 mg/kg respectively). Metagenomic profiling revealed that OM + AS consistently up-regulated acid-tolerance pathways (proton pump increased by 6.12%, alkali production increased by 9.75%, acid consumption increased by 5.12%) together with key N cycling genes, with the strongest enhancement observed for nitrification (increased by 84.54%). Network analysis demonstrated significant positive co-occurrence between acid-tolerance and nitrification genes across the microbial community. Correspondingly, bacterial taxa harboring these functions, including Sphingomonas and Nitrospira, were most abundant under OM + AS. We propose that alkali slag and organic manure act synergistically to elevate soil pH, relieve acid stress on microbes, and promote a community with dual capacities for acid tolerance and active N transformation. These findings mechanistically link soil acidity amelioration with enhanced microbial-mediated N cycling and offer a functional basis for designing targeted soil remediation strategies.}, }
@article {pmid41967439, year = {2026}, author = {Tang, C and Wan, C and Gan, J and He, Z and Wei, C and Tan, H and Wu, R and Yu, F and Li, Y}, title = {Rhizosphere phosphorus and iron cycling accelerates manganese phytoextraction by Polygonum lapathifolium.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {142033}, doi = {10.1016/j.jhazmat.2026.142033}, pmid = {41967439}, issn = {1873-3336}, abstract = {Manganese (Mn) contamination in mining soils poses persistent ecological risks due to its high mobility and potential accumulation in plants. Although exogenous microbial inoculation is increasingly used to improve phytoremediation, the mechanisms by which it regulates rhizosphere phosphorus (P) and iron (Fe) cycling, and thereby influences Mn bioavailability, remain poorly understood. We hypothesized that Enterobacter sp. inoculation would enhance Mn phytoextraction by stimulating rhizosphere P activation and Fe speciation transformation, thereby promoting nutrient acquisition and Mn mobilization. To test this hypothesis, we investigated the effects of Enterobacter sp. inoculation on rhizosphere P/Fe fractions, functional genes, and Mn phytoextraction. Enterobacter sp. significantly decreased rhizosphere soil pH and enhanced P-releasing enzyme activities, increasing available P by 26.7% under the C1.0 (3.8 ×10[7] CFU·g[-1] (soil)) treatment compared with the control (p < 0.05). Concurrently, Fe(II) and amorphous Fe increased by 11.9% and 15.1%, respectively (p < 0.05), indicating enhanced Fe transformation in the rhizosphere. These shifts facilitated plant P and Fe acquisition, promoted biomass production, enhanced Mn phytoextraction in Polygonum lapathifolium L. by strengthening rhizosphere redox conditions and mineral interfacial processes. Metagenomic analysis revealed that Enterobacter sp. inoculation increased the functional potential of genes related to P activation (e.g., gcd, phnP) and Fe biosynthesis/uptake (e.g., hemH, pchB), mainly associated with Pseudomonadota and Actinomycetota. Partial least squares path modeling further confirmed positive associations among P/Fe cycling genes, rhizosphere P/Fe fractions, enzymatic activities, and plant growth. Overall, microbial inoculation enhanced Mn phytoremediation by coordinating rhizosphere nutrient cycling processes, providing a promising strategy for the remediation of HMs-contaminated mining soils.}, }
@article {pmid41967476, year = {2026}, author = {Wang, H and Di, D and Du, S and Tateno, R and Peñuelas, J and Migliavacca, M and Chen, Q and Guan, J and Song, Y and Shi, W}, title = {Plant functional trait differentiation and microbial life-history strategy shifts drive soil respiration under long-term forest restoration.}, journal = {Tree physiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/treephys/tpag042}, pmid = {41967476}, issn = {1758-4469}, abstract = {Soil respiration (Rs) represents a major carbon (C) flux linking plant productivity with microbial decomposition; however, the mechanisms by which contrasting forest restoration pathways regulate Rs and its components remain insufficiently understood. We conducted a six-year field observation (2017-2022) across abandoned farmland (AF), Quercus liaotungensis forest (QF), and Robinia pseudoacacia plantation (RP) on the Loess Plateau, China, integrating measurements of Rs, autotrophic (Ra), heterotrophic (Rh), plant functional traits, soil physicochemical properties, and microbial C metabolic potential. Afforestation significantly increased Rs, with a stronger enhancement observed in QF than in RP. Although Ra did not differ significantly between the two forest types, Rh accounted for approximately 70% of Rs and primarily explained the significant differences in Rs between restoration pathways. Elevated Rh in QF was strongly associated with greater abundances of microbial functional genes involved in the degradation of C substrates. Integrated analyses further revealed that differentiation in plant functional traits between QF (conservative strategy) and RP (acquisitive strategy) indirectly amplified Rh contributions to Rs by reshaping soil substrate availability and coordinating shifts in microbial life-history strategies. Collectively, our findings identify plant functional trait differentiation as a key driver of long-term Rs dynamics, mediated by shifts in microbial life-history strategies.}, }
@article {pmid41967488, year = {2026}, author = {Du, M and Xue, P and Minasny, B and Jang, HJ and McBratney, A}, title = {Macroecological processes impact Australian soil resistomes and climatically stable regions with anthropogenic activities serve as ARG hotspots.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag079}, pmid = {41967488}, issn = {1751-7370}, abstract = {Soil antibiotic resistance genes (ARGs) pose a global health threat, but a critical knowledge gap remains regarding how macro-scale pedoclimatic constraints interact with land-use intensification to determine the spatial distribution of the soil resistome. To address this, we conducted a continental-scale survey of Australian topsoils and used metagenomic analysis to reveal the hierarchy of drivers shaping the soil resistome. Machine learning was applied to predict the spatial ARG distribution across Australia. We found that, at the continental scale, climatic variability acts as the dominant filter on ARG distribution, overriding local soil properties and human disturbance. Unexpectedly, climatically stable regions, characterised by sandy and low-carbon soils in Southwestern Australia, emerged as ARG hotspots. We also demonstrated that anthropogenic land use amplifies ARG abundance within these climatically stable regions. Furthermore, spatial modelling revealed distinct geographical patterns: although total ARG abundance was enriched in coastal regions, specific resistance mechanisms showed unique distributions. As a continental-scale investigation of soil ARGs in Australia, this study provides a framework to identify high-risk regions where lower climatic variability and intensive farming interact to enhance antimicrobial resistance.}, }
@article {pmid41968394, year = {2026}, author = {Zhao, B and Yang, X and Feng, K and Wang, J and Liu, M and Wang, Y and Wang, D and Peng, X and He, Q and Lu, Y and Waseem, H and Wang, S and Deng, Y}, title = {Phylogenetic assembly of methanogenesis regulates methane yield in food-waste anaerobic digestion.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag083}, pmid = {41968394}, issn = {1751-7370}, abstract = {Anaerobic digestion (AD) of food waste (FW) is a key wate-to-energy strategy, yet daily biogas yield is often challenging to sustain, partly due to a limited understanding of the internal methanogens and their functional divergence. Here, we investigated seven full-scale mesophilic FW-AD systems distributed across China along a broad latitudinal gradient (>2,800 km), linking methane production variations (0.38-2.11 m3/m3•d-1) with the phylogenetic distributions of methanogens and their methanogenic genes. We found that hydrogenotrophic and aceticlastic pathways were ubiquitous, whereas methylotrophic methanogenesis showed regional enrichment in warmer regions, reflecting persistent influences of climate-associated upstream conditions on downstream methanogenic communities. Gene-level phylogeny of methanogenesis-related alleles, rather than species-level phylogeny, closely tracked biogas yield variation (Mantel's P < 0.05) and showed consistently stronger associations than gene-level compositions (mean standardized total effect: 0.491 vs. 0.298, P < 0.01). Higher methane yields (1.61 vs. 0.61 m3/m3•d-1 in high- vs. low-performing systems, P < 0.01) were significantly associated with reduced Faith's phylogenetic diversity (1.82 vs. 2.30, P < 0.01) and tighter clustering (mean pairwise phylogenetic distance, MPD: 0.25 vs. 0.30, P < 0.01) of methanogenic gene variants, suggesting that phylogenetic coherence may reflect ecological filtering favoring efficient methanogenesis, albeit at the expense of functional redundancy. These findings highlight gene-level trait phylogeny as a potential proxy for functional robustness, offering a framework for ecological design of AD microbiomes.}, }
@article {pmid41968748, year = {2026}, author = {Hilpert, K}, title = {Peptidomics: A New Dimension in Microbiome Research.}, journal = {Protein and peptide letters}, volume = {}, number = {}, pages = {}, doi = {10.2174/0109298665436241260327111926}, pmid = {41968748}, issn = {1875-5305}, abstract = {The human gut microbiome is now recognised as a major determinant of health, with roles extending beyond digestion to influence neurodegeneration, metabolism, immunity, and pharmacological responses. Clinical studies link microbial imbalances to Alzheimer's disease, Parkinson's disease, depression, and cardiovascular disorders, yet the underlying mechanisms remain only partly understood. Methodological advances have progressively deepened our insight. DNA-based sequencing (metagenomics) catalogues microbial genes but reveals only potential functions. RNA-based sequencing (metatranscriptomics) highlights active gene expression, but instability of transcripts and poor correlation with protein activity limit its predictive value. Metabolomics measures small-molecule end products, providing direct evidence of microbial biochemistry and identifying disease-linked metabolites such as urolithin A, trimethylamine N-oxide, and equol. These approaches together have transformed microbiome science, but they remain incomplete. A critical and underutilised dimension is peptidomics: the systematic analysis of endogenous peptides in the gut and circulation. Enabled by peptide-enriching, protease-inhibiting workflows and high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS), peptidomics directly captures unstable signaling peptides and proteolytic fragments that are often invisible to conventional proteomics. Coupled with emerging gut-specific peptide databases, such as MetaPep, and Artificial Intelligence (AI) assisted de novo sequencing and spectral prediction for non-human peptides, this provides a concrete technical route to reading out the functional peptide layer of the microbiome. Peptidomics can capture functional signals of host-microbiome interaction, reveal context-specific biomarkers, and provide mechanistic insight into disease. Recent studies demonstrate that peptide-level resolution uncovers microbial contributions to gut inflammation, modulates the gut-brain axis, and enables peptide-based disease stratification in conditions such as inflammatory bowel disease. However, despite these promising examples, peptidomics remains largely absent from mainstream microbiome research, which needs to be changed. Integrating peptidomics with existing genomic, transcriptomic, and metabolomic approaches will generate a more complete and functional picture of the microbiome. This shift will accelerate biomarker discovery, refine diagnostics, and expand the search for peptide-based therapeutics, positioning peptidomics as an essential next step in microbiome science.}, }
@article {pmid41969349, year = {2026}, author = {Cheng, L and Wang, J and Sun, J and Xu, S and Zhao, G and Li, M}, title = {Integrated multi-omics of the ruminal microbiome and host metabolome reveals compensatory growth in response to dietary energy restriction and re-alimentation in growing beef bulls.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {25}, number = {}, pages = {265-281}, pmid = {41969349}, issn = {2405-6383}, abstract = {Understanding the mechanisms of dietary energy on compensatory growth in beef cattle is crucial for improving feed efficiency and mitigating the environmental footprint of beef production. The objectives of the study were to investigate the effects of dietary energy restriction and subsequent re-alimentation on growth performance, nutrient digestibility, ruminal microbiome, plasma metabolites, and nitrogen metabolism in growing beef bulls. Twelve 6-8-month-old Simmental crossbred bulls (initial body weight: 226 ± 24 kg) were randomly allocated to two groups (n = 6 per group): the dietary energy restriction group (REC) was fed a diet containing 9.25 MJ/kg metabolizable energy (ME) for 4 weeks (energy restriction period), followed by a 2-week re-alimentation period with a 10.29 MJ/kg ME diet, while the control group (CON) was fed the 10.29 MJ/kg ME diet consistently throughout the experimental period. Dietary energy restriction significantly decreased body weight and average daily gain (ADG) compared to CON (P < 0.05). However, no significant differences were observed by the end of the re-alimentation period (P > 0.05), demonstrating successful compensatory growth through dietary energy modulation. Ruminal propionate, total volatile fatty acids, ammonium nitrogen, and microbial crude protein (MCP) concentrations significantly decreased in the energy restriction treatment compared to CON (P < 0.05), but MCP exceeded the levels in CON after dietary energy re-alimentation (P < 0.05). Energy restriction also significantly increased urinary nitrogen excretion (P = 0.002), driven by imbalanced amino acid metabolism and significantly increased urinary urea (P = 0.038), which significantly reduced protein synthesis and nitrogen retention (P = 0.017). Metagenomics analysis revealed that energy restriction significantly increased the relative abundances of Limosilactobacillus, Enterococcus, and Aliarcobacter (P < 0.05), while decreasing those of Gemmatirosa and Mesorhizobium (P < 0.05). Dietary energy re-alimentation significantly increased the relative abundance of Gramella, Acetobacter, Phaeobacter, and Flammeovirga (P < 0.05). These bacteria are associated with pathways related to amination, transamination, and microbial protein synthesis. Integrated multi-omics revealed shifts in the ruminal microbiome and host metabolome, particularly in pathways related to ruminal urea hydrolysis, biosynthesis of glutamate, glutamine, and alanine, and post-absorptive amino acid metabolism, which collectively enhanced protein synthesis and compensatory growth. These findings establish a practical feeding strategy to optimize feed efficiency and enhance compensatory growth in beef bulls via short-term dietary energy manipulation.}, }
@article {pmid41969354, year = {2026}, author = {Dayan, J and De Cesare, A and Soglia, F and Zampiga, M and Indio, V and Antenucci, EL and Petracci, M and Sirri, F}, title = {Nutritional alternatives to commercial lipid sources: Impact of the dietary inclusion of black soldier fly (Hermetia illucens) larvae oil on broiler chicken productivity, breast meat quality traits and caeca microbiome.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {25}, number = {}, pages = {255-264}, pmid = {41969354}, issn = {2405-6383}, abstract = {Protein production from poultry, particularly broiler chickens, is considered a key component of future global food security, due to its relatively high sustainability. However, the use of resources such as soybean oil remains a concern. Black soldier fly (Hermetia illucens [HI]) larvae oil represents a promising alternative due to a relatively rapid rearing cycle and ability to utilize organic waste as growth substrates. This study investigated how replacing a commercial lipid source such as soybean oil, with HI larvae oil affects broiler growth performance, meat quality traits, fatty acid (FA) profile, and caeca microbiome. A total of 552 one-d-old male Ross 308 broilers, with equal initial weights (48.89 ± 0.18 g; P = 0.597), were allocated to three dietary treatments with 8 replicate pens per group (23 birds/pen). All birds received the same commercial basal diet, formulated to be isoenergetic and with the same amino acid profile, differing only in the source of the supplemented oil: 100% soybean oil group (CON), 50% soybean oil + 50% HI larvae oil group (MIX), or 100% HI larvae oil group (HIO). Growth performance parameters were recorded at the end of each feeding phase (14, 28, and 42 d). At slaughter (42 d), 10 breasts (pectoralis-major muscle) and thighs (extensor-iliotibialis muscle) samples per group were collected for meat quality assessment, and caecal content samples were obtained from 8 birds/group for microbiome analysis. Growth performance metrics showed an improvement in feed conversion ratio during the starter phase for HI larvae oil-fed groups (1.54 vs. 1.45 vs. 1.46 for CON, MIX, and HIO, respectively; P < 0.001) and comparable performance across the trial. Meat quality traits remained within commercially acceptable ranges, with minimal effects observed, apart from variations in breast fillet redness and thigh protein oxidation. FA analysis indicated higher levels of saturated FAs in the HI groups, with a concurrent reduction in omega (n)-6 levels and a more balanced n-6 to n-3 ratio (16.47 vs. 15.18 vs. 11.60 for CON, MIX, and HIO, respectively; P < 0.001). The caecal microbiome revealed stable diversity across groups, with only minor shifts in relative abundance. Overall, the findings showed that HI larvae oil is an effective alternative to conventional vegetable lipid sources in poultry nutrition, with added potential to enhance growth performance during the early growth stages.}, }
@article {pmid41969371, year = {2026}, author = {Ramos Peña, DE and Boussetta-Charfi, O and Antezack, A and Amroune, N and Colson, P and Monnet-Corti, V and Saia, RS and Guillemot, J and Pozzetto, B and Pillet, S and La Scola, B and Bourlet, T and Fragoso Motta, AC}, title = {Interplay Between Oral Microbiota and Mouth Health in People Living With HIV Under Antiretroviral Therapy With or Without Periodontitis.}, journal = {International journal of dentistry}, volume = {2026}, number = {}, pages = {8794149}, pmid = {41969371}, issn = {1687-8728}, abstract = {People living with HIV (PLWH) in combined antiretroviral therapy (cART) face microbiota shifts linked to immune status, ART regimen, and periodontal diseases, which are capable of inducing local and systemic inflammation. This study aimed to analyze the oral microbial community composition in PLWH under cART with (n = 24) or without (n = 25) periodontitis using shotgun metagenomic sequence analysis, and describe the interaction between bacterial species, clinical and immunological parameters, and the response to nonsurgical periodontal therapy (NSPT). Saliva samples were collected at baseline for both groups, and 30 days after NSPT for the periodontitis group. Within the periodontitis group, all periodontal parameters presented highly significant improvement after NSPT when compared to baseline. The gingival microbiota did not differ significantly between patients with periodontitis and controls; however, a wider range of bacterial species was found in the microbiota of the periodontitis group compared to the control group, while post-treatment the periodontitis group presented an alpha diversity intermediate between the two former groups. Regarding the distribution of the different bacterial species, Porphyromonas gingivalis was found significantly enriched in the periodontitis group, along with different Treponema sp., Fretibacterium fastidiosum, Campylobacter rectus, Bacteroides zoogleoformans, Tannerella forsythia, and Porphyromonas endodontalis. Correlations between seven inflammatory markers and seven periodontitis-related bacterial taxa were found for saliva in the group of periodontitis patients, which was not the case in controls; interestingly, the profiles after NSPT showed intermediate results. By contrast to saliva, the inflammatory markers of periodontitis patients showed no marked differences in blood plasma, except for TNF-alpha and partly IL-4. In view of the fact that oral microbial imbalance may contribute not only to local disease but also to systemic immune activation in the course of HIV-1 infection, reinforcing the importance of maintaining periodontal health represents a part not to be neglected for an optimal management of PLWH.}, }
@article {pmid41969565, year = {2026}, author = {Kavagutti, VS and Beavogui, A and Wiart, N and Wincker, P and Oliveira, PH}, title = {Defensomes, counter-defensomes, and the remodeling of microbial communities.}, journal = {PNAS nexus}, volume = {5}, number = {4}, pages = {pgag073}, pmid = {41969565}, issn = {2752-6542}, abstract = {Bacteria and mobile genetic elements (MGEs) have coevolved for billions of years in an enduring evolutionary arms race, leading to the emergence and diversification of a vast arsenal of defense and counter-defense systems. In the last recent years, high-throughput screening methods and genome-resolved metagenomics have markedly enhanced our understanding of the diversity and abundance of immune systems across cultured and uncultured microorganisms. This fueled subsequent interest in better understanding the dynamic tri-kingdom interplay between bacteria, bacteriophages, and eukaryotic cells, and led to renewed efforts to improve alternative antibacterial phage-based therapies. Here, we discuss the evolutionary and ecological dynamics underlying the bacteria-MGE arms race, recent findings on bacterial defensomes, MGE counter-defensomes, holodefensomes, and their key role in the development of microbiome-targeted therapies. To this end, we argue why and how highly conserved anti-MGE defense systems should be prioritized as promising targets for the development of next-generation bacterial inhibitors with broad biomedical relevance, supported by a comprehensive analysis of their distribution and diversity across bacteria.}, }
@article {pmid41969652, year = {2026}, author = {Zhang, H and Zhang, L and Yang, B and Gao, C and Liu, H and Zhang, Y and Chen, X}, title = {Correction: Metagenomic and metatranscriptomic profiling of bronchoalveolar lavage fluid identifies microbial and host biomarkers of drug-resistant tuberculosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1826950}, doi = {10.3389/fcimb.2026.1826950}, pmid = {41969652}, issn = {2235-2988}, abstract = {[This corrects the article DOI: 10.3389/fcimb.2025.1726935.].}, }
@article {pmid41969653, year = {2026}, author = {Dai, Z and Hu, Y and Tai, A and Lu, Y and Hu, S and Pan, J and Xiao, Y and Ma, X and Fu, Q and Zhao, H and Su, Z and Tong, P and Hao, Z and Yao, G and Wang, J}, title = {Characterization of a Klebsiella pneumoniae mutant strain wGF 1-2 with attenuated virulence, altered morphology, and reduced biofilm formation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1761564}, pmid = {41969653}, issn = {2235-2988}, mesh = {*Klebsiella pneumoniae/genetics/pathogenicity/virology/physiology ; *Biofilms/growth &amp; development ; Animals ; Mice ; Virulence ; Klebsiella Infections/microbiology/pathology ; Disease Models, Animal ; Mutation ; Proteomics ; Host-Pathogen Interactions ; Bacteriophages ; Gene Expression Profiling ; Gastrointestinal Microbiome ; Female ; Metagenomics ; }, abstract = {INTRODUCTION: The global rise of antimicrobial resistance has positioned multidrug-resistant Klebsiella pneumoniae as a critical health threat, necessitating alternative therapeutic strategies such as phage therapy. However, the long-term evolutionary consequences of phage-bacteria interactions remain poorly understood. This study characterizes a unique attenuated mutant, wGF 1-2, derived from a hypervirulent K. pneumoniae strain (GF) during phage isolation efforts.<br><br>METHODS: The wGF 1-2 mutant was serendipitously isolated during attempts to obtain lytic phages against the parental GF strain. We performed an integrated multi-omics and phenotypic characterization, including genomic sequencing, proteomic profiling, and transcriptomic analysis. Host-pathogen interactions were assessed using a murine infection model (evaluating survival and tissue colonization), and the impact on the gut microbiota was analyzed via metagenomics.<br><br>RESULTS: Compared to the parental strain, wGF 1-2 exhibited a significant reduction in biofilm formation and distinct morphological alterations. In a murine model, the mutant was avirulent, resulting in 100% survival even at a high challenge dose (10&#x2076; CFU), with minimal tissue colonization. Multi-omics analysis revealed extensive genomic structural variations (81 insertions and 64 deletions). Proteomic shifts included the downregulation of proteins involved in metal ion binding and metabolic pathways. Furthermore, infection with wGF 1-2 led to host inflammatory suppression and a restructuring of the gut microbiota characterized by an increase in beneficial Bacteroidota.<br><br>DISCUSSION: This study provides a comprehensive characterization of an attenuated K. pneumoniae mutant, wGF 1-2. The extensive genomic and phenotypic alterations observed highlight the significant evolutionary potential of bacterial pathogens during phage interactions. These findings underscore the necessity of thorough safety assessments, including evolutionary risk evaluations, for the future development of phage-based therapies.}, }
@article {pmid41970373, year = {2026}, author = {Duan, Y and Wang, L and Cui, H and Fang, Z and Lu, Y and Sun, Z}, title = {The effect of elastic-band resistance training on fecal microbiota and derived metabolites of aged individuals with possible sarcopenia.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1762454}, pmid = {41970373}, issn = {2296-858X}, abstract = {BACKGROUND: Individuals with possible sarcopenia exhibit altered microbiota profiles and poor intestinal metabolism. Exercise training is linked to changes in gut microbiota and has been proposed to enhance the quality of aging skeletal muscle.<br><br>AIMS: In older adults with possible sarcopenia, the study aimed to determine if elastic-band resistance training modulates gut microbiota and its generated metabolites and investigate the underlying relationships with physical function.<br><br>METHODS: Thirty-one volunteers with possible sarcopenia were randomly assigned to either the control group (CG, n&#x202f;=&#x202f;17) or the intervention group (RG, n&#x202f;=&#x202f;14), which underwent 24&#x202f;weeks of elastic-band resistance training. Physical function, body composition, and blood and fecal samples were collected from each patient at baseline and 24&#x202f;weeks. Enzyme-linked immunosorbent assay (ELISA) was used to evaluate protein metabolism regulatory factors, targeted metabolomics was used to quantify short-chain fatty acid (SCFA) levels, and metagenomic sequencing was used to analyze the composition of the fecal microbiota.<br><br>RESULTS: The gait speed (GS), arm curl test (ACT), 2-min step test (2MST), and timed up-and-go test (TUGT) all showed notable improvements in the RG. The RG also showed lower serum levels of tumor necrosis factor-&#x3b1; (TNF-&#x3b1;) and higher plasma concentrations of acetate and propionate. Following the intervention, the RG displayed decreased abundances of Eisenbergiella and Eggerthella and increased abundances of the genus Bacillus. Eggerthella abundance was inversely connected with 2MST performance, whereas the change in propionate level was positively correlated with 2MST, TUGT, GS, and appendicular skeletal muscle index (ASMI).<br><br>CONCLUSION: The elastic-band resistance training effectively improved physical function, modulates gut microbiota and SCFAs. The results revealed the physiological mechanisms by which gut microbiota and SCFAs regulate aging muscle health, providing scientific support for possible sarcopenia prevention and treatment via gut-muscle axis bidirectional crosstalk.<br><br>CLINICAL TRIAL REGISTRATION: https://www.chictr.org.cn/index.html.}, }
@article {pmid41971320, year = {2026}, author = {Wu, Y and Deng, L and He, X and Zhou, D and Ling, S and He, M and Wang, Q and Wang, C and Wang, M and Wu, H and Li, L and Li, D and Yun, L}, title = {Intestinal microbiome gone native: gut microbiome shift and resistome diversity in first homecoming giant panda family.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1737792}, pmid = {41971320}, issn = {1664-302X}, abstract = {INTRODUCTION: The world-famous giant pandas (Ailuropoda melanoleuca) often travel abroad for public exhibitions and international scientific cooperations. Previous research has reported alternations in the gut microbiome structure and enrichment of gut antibiotic-resistant genes (ARGs) in human international travelers, the latter of which is harmful to native residents and the environment. The microbiome and ARGs of these animal travelers, however, have not yet been investigated, even though they often interact with local keepers, visitors, and other pandas.<br><br>METHODS: In this study, we have clarified the dynamic microbiome composition and snapshot of ARGs (resistome) of the first panda family returning from overseas. Fecal samples were gathered for high-throughput sequencing for both amplicon and metagenomics sequencing, which were collected on the first day of their quarantine (Admission stage) and 3 days after the quarantine (Release stage). Feces from two native captive pandas were used as controls.<br><br>RESULTS AND DISCUSSION: The predominant Escherichia-Shigella proportion in the mother and father pandas decreased from 79.02 and 47.46% to 57.03 and 33.77%, while the Streptococcus abundance increased from 0.27 and 12.44% to 29.47 and 54.59%. The main genus of child pandas, Weissella, decreased from 45.24 to 0.02% after quarantine, and the Streptococcus ratio increased from 11.89 to 43.82%. Significant richness and bacterial diversities were found in these samples. The main ARG types are multidrug and polymyxin; the latter being an uncommon ARG in native pandas. Consequently, to protect local ecosystems from the introduction of novel ARGs, waste from translocated giant pandas should be managed under strict biosecurity protocols.}, }
@article {pmid41971325, year = {2026}, author = {Qi, L and Kang, H and Li, X and Wang, L and Lin, Y and Zhan, M and Zeng, F and Xiao, Z and Liu, X and Chen, Z and Liu, L}, title = {Multi-omics profiling implicates gut microbiota-sphingolipid interplay in the neuroprotective effects of semaglutide on diabetic cognitive impairment.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1705784}, pmid = {41971325}, issn = {1664-302X}, abstract = {BACKGROUND: The gut microbiome is a critical regulator of host health, but how it mediates the therapeutic effects of drugs targeting neurodegenerative diseases like diabetic cognitive impairment (DCI) is unclear. Here, we investigated whether the neuroprotective effects of the GLP-1 agonist semaglutide (SE) are linked to its modulation of the gut-brain axis.<br><br>METHODS: We used an integrative multi-omics approach in a mouse model of DCI. We combined fecal shotgun metagenomics and targeted bile acid profiling with cerebral proteomics and metabolomics to characterize the gut-brain crosstalk following a 12-week SE treatment. Animal behavior, neuronal survival and synaptic integrity were assessed to confirm therapeutic efficacy.<br><br>RESULTS: SE treatment reversed cognitive deficits, rescued hippocampal neuronal loss, and restored synaptic integrity in diabetic mice. At the ecosystem level, metagenomics revealed that SE treatment profoundly remodeled the gut microbiota, enhancing microbial &#x3b1;-diversity, enriched beneficial genera (Bacteroides, Barnesiella), and depleted the pro-inflammatory genus Desulfovibrio. This microbial shift was associated with normalized fecal and cerebral bile acid profiles. Mechanistically, our analysis implicated a dysregulated sphingolipid pathway in the DCI brain, characterized by the upregulation of the transporter ATP-binding cassette transporter A2 (ABCA2) and the enzymes sphingosine-1-phosphate phosphatase 1 (SGPP1) and ceramide synthase 2 (CERS2). SE treatment dynamically modulated this pathway: it downregulated ABCA2 in a potentially weight-independent manner and SGPP1 in a weight-dependent fashion, linked to the normalization of cerebral bile acid profiles. In contrast, CERS2, a robust marker of disease severity, was not altered by SE.<br><br>CONCLUSION: Our study uncovers a novel "gut microbiota-bile acid-sphingolipid" axis in DCI and suggests that SE acts via a dual mechanism. It drives a weight-dependent restoration of the gut-brain axis, normalizing microbial and bile acid profiles to regulate SGPP1, while also exerting weight-independent effects, potentially through direct modulation of targets like ABCA2. This work highlights the gut microbiome as a key component in the therapeutic action of SE and reveals the multifaceted nature of its neuroprotective effects.}, }
@article {pmid41971343, year = {2026}, author = {Qiao, YC and Jiang, XX and Zhan, JP and Cheng, XH and Liu, F and Zhang, WS and He, GP and Peng, JZ and Wu, YJ and Yang, SG}, title = {Correction: Effects of different mulching practices on soil microbial community structure, function, and interaction networks in a chieh-qua cultivation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1832275}, doi = {10.3389/fmicb.2026.1832275}, pmid = {41971343}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2026.1691984.].}, }
@article {pmid41971525, year = {2026}, author = {Adekoya, AE and Boggs, TE and Ibberson, CB}, title = {Revealing community dynamics in polymicrobial infections through a quantitative framework.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag061}, pmid = {41971525}, issn = {2730-6151}, abstract = {Laboratory models provide tractable, reproducible systems that have long served as foundational tools in microbiology. However, the extent to which these models accurately mimic the biological environments they represent remains poorly understood. A quantitative framework was recently introduced to assess how well laboratory models capture microbial physiology in situ. However, applications of this framework have been limited to characterizing the physiology of a single species in human infections, leaving a gap in our understanding of overall microbial community physiology in polymicrobial contexts. Here, we extended this framework to evaluate the accuracy of laboratory model systems in capturing community-level functions in polymicrobial infection. As a proof of concept, we applied the extended framework to a polymicrobial model of human chronic wound (CW) infection. CWs harbor metabolically diverse bacterial species that engage in a range of microbe-microbe interactions, ultimately impacting community dynamics and disease progression. However, studies on the mechanistic drivers of chronic wound infection have relied on single species or pairwise approaches. Here, we demonstrate that our adapted framework can be used to develop accurate polymicrobial models. Further, we demonstrate that this extended framework can evaluate the occurrence of known microbe-microbe interactions. Building on our prior work in large-scale metagenomic and metatranscriptomic analysis, we propose a highly accurate 6-member synthetic bacterial community model i.e. representative of the taxonomic and functional complexity of human CW infections. This approach will support the development of ecologically relevant polymicrobial models and better treatment strategies.}, }
@article {pmid41971531, year = {2026}, author = {Zhang, W and Han, N and Zhang, T and Qiang, Y and Peng, X and Li, X and Kan, B}, title = {Dynamic change patterns of the human gut microbiota-fluctuation, loss-acquisition, and turnover-and their underlying causes.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag046}, pmid = {41971531}, issn = {2730-6151}, abstract = {The temporal dynamics of the gut microbiome are critical to human health, yet their patterns and underlying drivers remain poorly characterized at a monthly resolution and strain level. This knowledge gap limits the development of targeted microbiome interventions. Here, we integrate longitudinal analyses across three human cohorts-a cross-sectional cohort (n = 190), an intensive 52-month time series (n = 7), and a paired 6-month cohort (n = 43)-together with a humanized mouse model under antibiotic perturbation. Using shotgun metagenomics (516 samples), we resolve microbial dynamics at species and strain resolution. We identify three distinct modes of temporal variation: relative abundance fluctuations, species loss-acquisition events, and strain turnover. Strain turnover contributes substantially to the dynamic reservoir of functional genes, including those associated with virulence and antibiotic resistance. These dynamics are influenced by antibiotic exposure and microbial interspecies interactions. Our work provides a month-scale atlas of gut microbiome variation, revealing widespread transient colonization and strain-level plasticity, thereby offering a refined framework for understanding microbiome stability and personalized microbial ecology.}, }
@article {pmid41971738, year = {2026}, author = {Ji, HL and Liu, CH and Nie, CX and Luo, JF and Li, XR and Fu, AS and Ge, YL}, title = {Metagenomic next-generation sequencing unveils invasive aspergillosis masquerading as miliary tuberculosis in a neutropenic leukemia patient: a case report.}, journal = {Frontiers in fungal biology}, volume = {7}, number = {}, pages = {1751760}, pmid = {41971738}, issn = {2673-6128}, abstract = {BACKGROUND: Empirical anti-tuberculosis therapy is a common strategy when patients with acute leukemia chemotherapy-induced neutropenia develop diffuse pulmonary small nodular and subsolid lesions. However, the absence of pathogenetic verification may lead to catastrophic consequences.<br><br>METHODS: Following negative conventional microbiological cultures (bronchoalveolar lavage bacterial culture, Gram/Gram-negative test) and ineffective anti-infective therapy, a second bronchoscopy revealed caseous obstructive lesions in the right upper lobe bronchus. Metagenomic Next-Generation Sequencing (mNGS) analysis of lavage fluid ultimately confirmed invasive pulmonary fungal disease.<br><br>RESULTS: The mNGS analysis of the bronchoalveolar lavage fluid (BALF) reported 6,750 Aspergillus fumigatus sequences, 43 Aspergillus complex sequences, and 81 Candida albicans sequences (considered airway colonization with no pathogenic significance), confirming probable invasive pulmonary aspergillosis (IPA) in line with the 2023 revised EORTC/MSGERC consensus criteria for invasive fungal diseases. Following discontinuation of anti-tuberculosis therapy, targeted antifungal treatment with amphotericin B (40 mg daily) was initiated. Post-treatment, the patient's temperature normalized. Follow-up CT demonstrated improved absorption of lesions in the left lung and right lower lobe, with stable cavitary nodules in the right upper lobe.<br><br>CONCLUSION: This case demonstrates that invasive pulmonary fungal infection can perfectly mimic the typical radiographic features of hematogenous disseminated pulmonary tuberculosis, including diffuse small nodular and subsolid lesions with a miliary distribution pattern predominantly in the upper lobes and extrapulmonary manifestations such as erythema nodosum. For unexplained pulmonary infections in immunocompromised hosts where conventional diagnosis and empirical treatment fail, the timely application of bronchoscopy combined with mNGS technology represents a critical breakthrough for achieving precise diagnosis.}, }
@article {pmid41971837, year = {2026}, author = {Du, S and Lin, D and Zhang, TL and Chu, HY and Zhu, D}, title = {Earthworm gut's potential positive impact on carbon cycle by influencing carbohydrate metabolism and microbial genome size.}, journal = {Fundamental research}, volume = {6}, number = {2}, pages = {837-846}, pmid = {41971837}, issn = {2667-3258}, abstract = {The earthworm microbiome significantly impacts global soil ecosystems. This study explores how earthworm gut eukaryome (fungi and protists) and functional genes respond to land use and climatic factors. Over 150 earthworm-soil sample pairs were collected from arable and forest ecosystems across China. High-throughput and shotgun metagenomic sequencing revealed lower fungal, protistan, and CAZyme gene diversities in the earthworm gut than in the soil (0.77-fold, 0.19-fold, and 0.74-fold compared to the soil, respectively), but higher proportions of parasitic protists (3.78-fold compared to the soil) and carbohydrate metabolism genes involved in glycosyl transfer (1.41-fold compared to the soil). Arable systems showed higher abundances of functional genes associated with carbon fixation, nitrification, phosphorus dissolution, and sulfite reduction compared to forest systems. This study highlights the associations between earthworm gut microeukaryotes and functional genes especially glycosyl transferases involved in carbohydrate biosynthesis. Furthermore, larger microbial genomes were found in the earthworm gut compared to the soil, which may harbor more functional genes involved in cellular processes, carbohydrate binding, and glycosyl transfer. These findings suggest that earthworm gut microeukaryotes may have a positive impact on their average genome sizes and carbohydrate metabolism within the carbon cycle. This study contributes to advancing our understanding of the functionality of microeukaryotes in the earthworm gut, especially for the carbon cycle.}, }
@article {pmid41971922, year = {2026}, author = {Zhu, W and Li, Y and Xu, Q and Lin, D and Zhou, T and Yang, F and Shi, M}, title = {Late-onset fungal infection of the bronchial stump post-lung resection: a report of two rare cases of Aspergillus flavus and mixed Candida/Cryptococcus coinfection diagnosed via metagenomic next-generation sequencing.}, journal = {AME case reports}, volume = {10}, number = {}, pages = {63}, pmid = {41971922}, issn = {2523-1995}, abstract = {BACKGROUND: Fungal infection of the bronchial stump is rare, characterized by insidious clinical manifestations and often misdiagnosed as bacterial infection or tumor recurrence. Most reported cases involve Aspergillus fumigatus, with Aspergillus flavus encountered far less frequently. Importantly, fungal colonization of the bronchial stump by Cryptococcus species has not been previously documented, nor has a mixed infection involving Cryptococcus and other fungi at this site. These rare presentations highlight diagnostic blind spots in postoperative airway management and underscore the need for heightened clinical awareness.<br><br>CASE DESCRIPTION: Case 1: A 53-year-old man underwent left upper lobectomy for adenocarcinoma four years prior. In 2024, he presented with hoarseness and chest tightness. Positron emission tomography-computed tomography (PET-CT) revealed a metabolically active soft-tissue nodule adjacent to the surgical suture line. Bronchoscopic biopsy combined with metagenomic next-generation sequencing (mNGS) confirmed the diagnosis of bronchial stump aspergillosis (BSA). The patient received posaconazole therapy for 7 months. Case 2: A 77-year-old woman underwent right lower lobectomy for adenocarcinoma six years earlier. In 2025, she developed cough with sputum production. CT demonstrated bilateral pneumonia with focal consolidation/atelectasis and bilateral pleural effusions. Bronchoscopy and mNGS identified a mixed infection with Candida albicans and Cryptococcus neoformans at the bronchial stump. Following treatment with caspofungin and fluconazole, her clinical symptoms improved, and follow-up CT imaging showed resolution of inflammatory changes.<br><br>CONCLUSIONS: Although fungal infection of the bronchial stump is rare, it warrants early consideration when post-lobectomy patients develop persistent symptoms unresponsive to antibiotics. Early radiological clues-such as unexpected metabolic activity around suture granulomas or localized nodular thickening at the stump-should prompt further evaluation. When conventional cultures remain negative and clinical deterioration continues, early initiation of mNGS can facilitate timely pathogen identification and guide targeted antifungal therapy.}, }
@article {pmid41972094, year = {2026}, author = {Yoshioka, I and Hayashi, C and Endo, Y and Sawada, A and Mori, Y and Ban, S and Yaguchi, T}, title = {Detection of fungal contamination on museum books stored under controlled environmental conditions: A discrepancy between culture-based and metagenomic analysis approaches.}, journal = {Mycoscience}, volume = {67}, number = {1}, pages = {20-26}, pmid = {41972094}, issn = {1618-2545}, abstract = {Mold contamination in library and museum collections poses risks to both cultural heritage and human health. This study examined fungal flora on books stored under controlled environmental conditions (temperature <20 °C, relative humidity <50%) in The University Museum, The University of Tokyo. Both culture-dependent methods and DNA-based metabarcoding targeting the internal transcribed spacer 2 region were used. DNA analysis revealed that Aspergillus halophilicus accounted for over 90% of the sequences from six books. In contrast, culture-based methods using standard media (e.g., PDA, DG18, M40Y) primarily isolated species such as Aspergillus, Penicillium, and Cladosporium, but not A. halophilicus. However, cultivation on CzA supplemented with 70% sucrose at lower temperatures enabled successful isolation of A. halophilicus from one sample. The strain was identified based on morphological features and β-tubulin gene analysis. These findings demonstrate a notable discrepancy between molecular and culture-based results, underscoring the limitations of conventional media for detecting xerophilic fungi in dry environments. The study suggests that desiccation-tolerant species like A. halophilicus can thrive even under strict storage controls and may evade standard integrated pest management (IPM) protocols. To better assess fungal risks in preservation settings, combining improved media with DNA-based methods is essential.}, }
@article {pmid41972101, year = {2026}, author = {Tong, W and Qiao, L and Yang, Y and Li, X and Zhang, Y and Huang, Z and Luo, H and Zhao, L and Zhang, S}, title = {Cross-kingdom metabolic cooperation drives vanillic acid biosynthesis: A spatiotemporal dissection of microbial functional networks in solid-state fermentation.}, journal = {Current research in food science}, volume = {12}, number = {}, pages = {101394}, pmid = {41972101}, issn = {2665-9271}, abstract = {Microbial self-organization into spatiotemporally structured consortia is key to metabolic specialization in natural environments, yet the principles governing this process in food fermentation are poorly understood. Here, we elucidate how cross-kingdom microbial cooperation drives the biosynthesis of vanillic acid (VA), a critical flavor and bioactive phenolic compound, during the solid-state fermentation of strong-flavor baijiu (SFB). Integrated metagenomic and network analyses across stratified pit layers and fermentation stages revealed a defined three-phase succession model. Early phase (D0-D12) was dominated by filamentous fungi (Aspergillus, Paecilomyces) in upper layers, initiating starch hydrolysis and phenylpropane precursor synthesis (e.g., contributing 22.6% to phenylalanine ammonia-lyase). A transitional bacterial-fungal consortium (Pichia, Klebsiella) then mediated intermediate conversion (D12-D45), with enzymatic hotspots shifting downward. The maturation phase (D45-D85) was defined by the dominance of acidophilic Acetilactobacillus (>80% relative abundance) in the lower layer, which executed the final synthesis steps (contributing 31.5% to caffeic acid O-methyltransferase) and concurrently suppressed vanillic acid degradation via downregulation of vanillate O-demethylase. Network analysis confirmed a spatial metabolic division of labor: fungi specialized in upper-layer lignin deconstruction, while bacteria dominated the completion of phenylpropanoid pathways in the lower layer. Critically, peak VA accumulation (0.375 mg/L at D45) coincided with synchronized enzyme expression across layers, demonstrating active metabolic coordination rather than passive environmental filtering. Our findings establish that functional succession and spatial compartmentalization are fundamental ecological principles enabling efficient biosynthesis in solid-state fermentation, demonstrating that flavor outcomes can be programmed through targeted microbial consortium design.}, }
@article {pmid41972180, year = {2026}, author = {Zhai, Y and Yu, M and Cheng, L and Liu, X and Yan, J}, title = {Orientia tsutsugamushi and Epstein-Barr Virus coinfection presenting with transient fluctuating hearing loss: a case report.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1750100}, pmid = {41972180}, issn = {1664-3224}, mesh = {Humans ; Female ; Middle Aged ; *Epstein-Barr Virus Infections/diagnosis/complications/drug therapy/virology ; *Scrub Typhus/diagnosis/complications/drug therapy/microbiology ; *Coinfection/diagnosis ; *Orientia tsutsugamushi/immunology ; *Herpesvirus 4, Human/immunology ; *Hearing Loss/diagnosis/etiology ; }, abstract = {Scrub typhus, caused by the obligate intracellular bacterium Orientia tsutsugamushi(O. tsutsugamushi), is an acute febrile illness. While neurological complications are known, hearing loss is an uncommon manifestation, and coinfection with Epstein-Barr virus(EBV) presents unique diagnostic and pathophysiological challenges. A 58-year-old woman presented with a 5-day history of high fever, severe headache, and constitutional symptoms. She reported transient, fluctuating bilateral hearing loss. Examination revealed characteristic eschars on her legs. Laboratory findings indicated hepatic impairment and systemic inflammation. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid detected O. tsutsugamushi and EBV. EBV serology profile (VCA-IgG+, VCA-IgM-, EBNA-IgG+) suggested viral reactivation. The patient failed to respond to initial beta-lactam antibiotic therapy but showed rapid and complete resolution of symptoms, including hearing loss, after initiation of doxycycline. At the 1-month and 3-month follow-up, audiological assessment confirmed normal hearing. This case highlights a rare presentation of scrub typhus with EBV coinfection involving fluctuating hearing loss. The dramatic response to doxycycline suggests this auditory symptom may be a reversible, immune-mediated complication of O. tsutsugamushi infection. Physicians should be aware of this potential manifestation in endemic areas. The immunological interplay between these pathogens warrants further investigation.}, }
@article {pmid41972428, year = {2026}, author = {Wang, YF and Wang, YN and Lin, D and Xu, JY and Qi, FY and Cui, HL and Lu, HJ and Qiao, M and Topp, E and Zhu, D and Rillig, MC and Zhu, YG}, title = {Diversity of Pharmaceuticals Enhances Antibiotic Resistance in the Invertebrate Gut via Biofilm-Mediated Mechanisms.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e18849}, doi = {10.1002/advs.202518849}, pmid = {41972428}, issn = {2198-3844}, support = {42307169//National Natural Science Foundation of China/ ; 42577136//National Natural Science Foundation of China/ ; U25A20803//National Natural Science Foundation of China/ ; 2023J02031//Fujian Provincial Natural Science Foundation of China/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; 2023321//Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; }, abstract = {The environmental accumulation of non-antibiotic pharmaceuticals is an emerging driver of antibiotic resistance. While individual compounds are known to shape the soil resistome, and contaminant diversity also plays a role, the impact of pharmaceutical diversity on the gut resistome of soil invertebrates remains unclear. Here, we combined metagenomics and metaproteomics to examine the collembolan gut and soil resistome across a gradient of pharmaceutical diversity under diurnal warming. Increasing pharmaceutical diversity at a constant total concentration significantly enriched antibiotic resistance genes (ARGs) in the gut microbiome, with no comparable effect in surrounding soils. This enrichment was mainly driven by multidrug resistance associated with efflux activity and biofilm-related processes, accompanied by increases in ARG-carrying taxa such as Gordonia and Ochrobactrum. Notably, Ochrobactrum encoded biofilm-related aryl polyene pathways. In vitro experiments confirmed that biofilm formation promotes resistance through coordinated cellular responses. Metaproteomic data indicated that Ochrobactrum initiates early biofilm formation by recruiting extracellular matrix producers such as Bacillus and Pseudomonas. Diurnal warming modulated these responses, indicating an interaction between chemical diversity and climate stress. These findings identify pharmaceutical diversity as an independent driver of ARG enrichment in host-associated microbiomes and establish chemical complexity as a key factor in assessing the ecological risks of pharmaceutical pollution.}, }
@article {pmid41972755, year = {2026}, author = {Langenfeld, K and Arts, P and Monahan, A and Criswell, A and Wigginton, KR and Duhaime, MB}, title = {Novel machine learning-based approach to identify viral biomarkers of human respiratory emissions from oral and nasal metagenomes.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0011326}, doi = {10.1128/msphere.00113-26}, pmid = {41972755}, issn = {2379-5042}, abstract = {Humans spend approximately 90% of their lives in built environments, making virus transmission indoors a key determinant of health. Environmental sampling of respiratory viral pathogens is often challenging because of frequent non-detect measurements. Non-detect measurements do not differentiate between samples containing low or no pathogens from samples that simply lack respiratory expulsions altogether. This ambiguity can be resolved by scanning samples for a biomarker of human respiratory emissions. To do so, reliable biomarkers for environmental monitoring need to be identified. Ideal biomarkers are prevalent across individuals, abundant, and unique to the human respiratory tract. Here, we present a new machine learning-based approach to query for suitable biomarker candidates from publicly available metagenomes and apply it to identify viral biomarkers of healthy oral and nasal microbiomes. Twelve viral biomarker candidates were selected from 1,232 curated viral operational taxonomic units. The viral biomarker candidates had as much as 63% prevalence across respiratory metagenomes, and prevalence was further increased to 77%-81% by combining two or three biomarkers. Real-time PCR confirmed that these viral biomarkers were prevalent and abundant in nasal swabs and saliva samples. Notably, top candidate biomarkers remained stable and detectable through multiple lab purification steps, increasing confidence in their viral origins and demonstrating their suitability for environmental monitoring. These findings demonstrate that existing metagenomes can be used to identify effective biomarker candidates for environmental sampling.IMPORTANCEDeveloping non-pharmaceutical interventions to reduce virus transmission indoors relies on robust environmental monitoring methods. Monitoring viral pathogens is challenging because of frequent non-detect measurements that introduce uncertainty. For instance, a non-detect measurement could indicate either the absence of the pathogen or simply the lack of human respiratory activity and, thus, exposure. To aid in distinguishing these scenarios, this study identifies viruses from the human respiratory tract using publicly available sequencing data that can be incorporated into environmental monitoring as biomarkers of human respiratory activity. These viral biomarkers will improve indoor monitoring to help enact interventions to mitigate virus transmission. Furthermore, our approach to identify biomarkers from existing metagenomes can be adapted for future biomarker identification in any system.}, }
@article {pmid41972785, year = {2026}, author = {He, X and Liu, J and Cheng, H and Zhu, X and Lin, H and Li, D-W and Yang, Y and Liu, R and Song, D and Zheng, Y and Lea-Smith, DJ and Pedentchouk, N and Todd, JD and Zhao, M and Zhang, X-H}, title = {Metabolically diverse microorganisms mediating hydrocarbon cycling in the subseafloor sediment of the Challenger Deep.}, journal = {mBio}, volume = {}, number = {}, pages = {e0394325}, doi = {10.1128/mbio.03943-25}, pmid = {41972785}, issn = {2150-7511}, abstract = {Hadal subseafloor sediments host abundant and active microbial biosphere with considerable heterotrophic activity. However, carbon and nutrient cycling processes and mechanisms driven by hadal subsurface microorganisms remain poorly understood. Using culture-dependent and culture-independent methods, we characterized the diversity, metabolism, and vertical dynamics of hydrocarbon-degrading (HYD) bacteria in a subsurface sediment core (MT20-750, ~750 cm below seafloor [cmbsf]) collected from the Challenger Deep (10,816 m below sea level) in the Mariana Trench. The sediment core contained high concentrations of mid- and long-chain n-alkanes (310-8,724 ng/g), although no <C18 n-alkanes at detectable levels were present, in contrast to proximal hadal seawater samples where these compounds were highly abundant. Metagenomic analysis identified diverse genes for aerobic and anaerobic degradation of n-alkanes and aromatic compounds, distributed across a wide range of taxa, dominated by Chloroflexota, Planctomycetes, Proteobacteria, and Actinobacteria, alongside six novel HYD phyla. Metabolic reconstruction of 120 HYD metagenome-assembled genomes (MAGs) suggests distinct hydrocarbon degradation preferences and metabolic strategies among different bacterial groups. Additionally, hadal bacterial isolates from Proteobacteria, Actinobacteria, and Firmicutes were able to degrade n-alkanes (C18-36), with Dietzia maris HXX048 removing ~50% of n-eicosane within 45 days under 5°C and 50 MPa. Predicted substrate binding of C10 and C20 with AhyA and heterologous expression of almA in Chloroflexota genomes supported their degradative capacity under anaerobic and aerobic conditions. The detection of putative hydrocarbon synthesis genes, specifically oleBC and oleC, suggests that hadal heterotrophic microorganisms may synthesize hydrocarbons. These findings provide evidence for microbial hydrocarbon production and thereby support a previously unrecognized sedimentary hydrocarbon cycle.IMPORTANCEOur findings suggest that hydrocarbon degradation may play an important role in organic matter decomposition and carbon cycling in the hadal subseafloor. This degradation capacity is likely distributed through diverse metabolic pathways across a wide range of phylogenetic taxa. The detection of genes likely encoding enzymes involved in aerobic and anaerobic hydrocarbon degradation, as well as the identification of novel hydrocarbon-degrading (HYD) phyla, highlights the complexity and significance of microbial processes in hadal subsurface sediment. The widespread distribution of hydrocarbon degradation capacity in different hadal sediments suggests hydrocarbons as a potential carbon source sustaining microbial life in this extreme environment. Moreover, the presence of genes associated with hydrocarbon synthesis suggests that hadal sediment microbes possess the genetic potential for both degrading and producing hydrocarbons, pointing to a dynamic and multifaceted hydrocarbon cycle within hadal subsurface sediment.}, }
@article {pmid41973542, year = {2026}, author = {Muurmann, AT and Rasmussen, JA and Limborg, MT and Gilbert, MTP and Bahrndorff, S}, title = {Functional gut microbiomes enhance performance in house fly larvae.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0001126}, doi = {10.1128/aem.00011-26}, pmid = {41973542}, issn = {1098-5336}, abstract = {UNLABELLED: In a world with an increase in human population, food consumption, and the generation of organic waste, insects are emerging as a promising tool to convert organic waste material into human food or animal feed. The insect microbiome is known to play a key role in the degradation of organic substrates, but little is known about the metabolic potential of the microbiome of industrially reared fly larvae. We investigated the microbial composition and metabolic potential of the house fly (Musca domestica) larva gut microbiome from larvae grown on three different waste and by-product-based substrates. We found that bacteria associated with the larval gut were enriched for functions related to microbial stress mechanisms, indicating strong selection of the gut microbiome by house fly larvae. In addition, the gut microbiome of larvae reared on sludge-based substrate had higher diversity when weighting for rare species and a higher coverage of "carbohydrate transport and metabolism" genes compared to brewery by-product-based substrate. A positive correlation between coverage of "pyridoxal-P synthesis" and larval survival and substrate conversion efficiency suggests that microbial synthesis of vitamin B6 could enhance larval performance. Additionally, a negative correlation between coverage of the "Entner-Doudoroff pathway" and "homoprotocatechuate degradation" and substrate conversion indicates microbial competition for sugars and aromatic amino acids. Together, these results reveal how the host selects on gut microbiomes with metabolic potential that is optimized toward the conversion of substrates that may be ultimately valuable for commercial insect production.<br><br>IMPORTANCE: Fly larvae are expected to play an important role in future food and feed production through the conversion of low-value biomass into high-quality protein. The gut microorganisms of fly larvae are expected to play an important role in bioconversion and could potentially be manipulated to improve biomass conversion. In this study, the importance of the gut bacteria of house fly larvae for bioconversion was investigated by metagenomic sequencing, which provided information on the bacterial abundance and potential functional roles in the larval gut. The results reveal that the functional potential of gut bacteria is affected by larval feed and correlates with larval performance, highlighting the importance of the gut microbiome for efficient biomass conversion.}, }
@article {pmid41973723, year = {2026}, author = {Denison, ER and Hillary, LS and Bolanos, HA and Anagu, HI and Emerson, JB}, title = {DNA Viral Size Fraction Metagenomics for Human Stool Samples.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {229}, pages = {}, doi = {10.3791/70187}, pmid = {41973723}, issn = {1940-087X}, mesh = {Humans ; *Feces/virology ; *Metagenomics/methods ; *DNA, Viral/genetics/isolation &amp; purification/chemistry ; *DNA Viruses/genetics/isolation &amp; purification ; }, abstract = {Understanding the healthy human virosphere (the viral component of the microbiome) requires accurate measurements of viral community composition across a diverse range of viral types. Building on prior experience with soil viral community ecology methods, here we demonstrate a series of laboratory approaches for enriching and extracting DNA from extracellular DNA viruses in human stool samples. A working primary protocol is presented, along with options for deviations at different steps. The general approach involves adding a liquid buffer (default: protein-enhanced phosphate buffered saline, PPBS) to facilitate removal of free viral particles from the stool matrix, centrifugation to separate the liquid fraction containing viral particles, filtration (default: 0.2 µm pore size) to remove most cells, concentration of viral particles (default: ultracentrifugation), removal of free nucleic acids with nucleases prior to virion lysis, and then DNA extraction for sequencing. Alternative techniques, including different buffers, filter sizes, and concentration methods, are also noted. Overall, multiple options for generating high-quality viromic DNA for sequencing are offered. Rather than tailoring the approach to specific equipment and resources, the protocol's flexibility should make it broadly applicable across labs with varying standard molecular biology equipment.}, }
@article {pmid41974680, year = {2026}, author = {Valverde, G and Sarhan, MS and Cook, R and Rota-Stabelli, O and Adriaenssens, EM and Zink, A and Maixner, F}, title = {An ancient genome of Streptococcus pyogenes from a pre-Columbian Bolivian mummy.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71603-9}, pmid = {41974680}, issn = {2041-1723}, abstract = {Streptococcus pyogenes, or Group A Streptococcus (GAS), is a human pathogen responsible for a range of diseases, from mild infections to severe illnesses. Despite its significance in modern clinical settings, little is known about the pathogen's evolutionary history or its presence in ancient human populations. Here, we present genomic evidence of S. pyogenes in the pre-Columbian Americas. We analysed a tooth from a naturally mummified individual dating to the Late Intermediate Period (1283-1383 cal AD), housed in the National Museum of Archeology (MUNARQ) in La Paz, Bolivia. Mitochondrial DNA analysis confirmed the host's Native American ancestry. Shotgun metagenomic sequencing and de-novo assembly enabled the near-complete reconstruction of an ancient S. pyogenes genome displaying close similarity to contemporary strains linked to pharyngitis. The genome contains core virulence genes, but prophages lack streptococcal pyrogenic exotoxins. Phylogenetic analyses place the strain at the base of modern S. pyogenes diversity, and Bayesian analyses indicate that most extant lineages diversified globally within the past ~5,500 years. Our results push back the confirmed presence of S. pyogenes in the Americas by several centuries and suggest that the pathogen circulated among Indigenous populations prior to the European contact.}, }
@article {pmid41974697, year = {2026}, author = {Espinosa, CA and Njunge, JM and Tickell, KD and Diallo, AH and Sayeem Bin Shahid, ASM and Gazi, MA and Kazi, Z and Yoshioka, E and Tigoi, C and Mburu, M and Ngari, M and Ngao, N and Omer, E and Gumbi, W and Gichuki, BM and Mitchel, A and Williams, J and Gogain, J and Janjic, N and Mandal, R and Jenkins, B and Browne, HP and Shao, Y and Rozday, T and Stares, MD and Dawson, NJR and Berson, E and Chang, A and Kim, Y and Mataraso, SJ and Shu, CH and Phongpreecha, T and Xue, L and Saleem, A and Singa, B and Ahmed, T and Voskuijl, WP and Wishart, DS and Houpt, ER and Liu, J and Ali, A and Mupere, E and Chisti, MJ and Bandsma, RHJ and Lawley, TD and Koulman, A and Lancioni, CL and Aghaeepour, N and Berkley, JA and Walson, JL and , }, title = {Multiomics characterization of acute child illness and mortality in Africa and South Asia.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-69754-w}, pmid = {41974697}, issn = {2041-1723}, abstract = {Childhood illnesses from infectious diseases in low- and middle-income countries contribute substantially to the global under-five mortality. Many hospitalized children experience incomplete recovery, readmission, and post-discharge mortality despite guideline-directed care. However, targeted interventions remain elusive due to limited understanding of underlying mechanisms. In this work, we employ multiomic profiling and multivariate modeling to investigate biological drivers of inpatient and post-discharge mortality in 3,101 acutely ill children across nine sites in sub-Saharan Africa and South Asia. In a nested case-cohort (N = 1008), we generate plasma proteomics, serum metabolomics and lipidomics, stool metagenomics, and fecal pathogen data at admission and discharge. Additionally, we profile 270 geographically matched community children for biological baselines. We identify a generalizable mortality signature marked by immune, inflammatory, and metabolic dysregulation with gut dysbiosis. We show that mortality-associated signals persist from admission through discharge, indicating unresolved disease and that malnourished children show greater baseline perturbations, explaining elevated risk. We also find some children with low clinical severity display high predicted mortality risk from targeted biomarkers. Finally, we distill predictive models to a clinically feasible biomarker panel and validate our findings in an independent cohort (N = 100). By linking inpatient and post-discharge mortality to specific biological mechanisms, our findings highlight why current care can fail and demonstrate how biomarker-guided risk stratification can identify vulnerable children currently missed by clinical assessments, enabling targeted interventions to reduce mortality in low- and middle-income countries.}, }
@article {pmid41974712, year = {2026}, author = {Zhao, N and Geng, P and Jimenez, D and Garcia, AC and Six, N and LaPlante, CI and Perez, AG and Silverman, GJ and Morel, L and Ge, Y}, title = {Multiomics-guided discovery of protective microbiome signatures in lupus-prone mice treated with Faecalibacterium prausnitzii.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71718-z}, pmid = {41974712}, issn = {2041-1723}, support = {R01AI143313//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01AI143313//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, abstract = {Gut microbiome dysbiosis has been implicated in the pathogenesis of systemic lupus erythematosus (SLE). However, microbiota-targeted therapeutic strategies have been lacking. Here, we report the potential of Faecalibacterium prausnitzii (strain UT1) to ameliorate gut dysbiosis and alleviate disease progression in the B6.Sle1.Yaa male mouse model of SLE. Fecal metagenomes of patients with SLE shifted carbohydrate catabolism from dietary fibers to host glycans, coinciding with depletion of F. prausnitzii. Oral administration of UT1 partially reversed lupus-associated microbiome alterations and rescued carbohydrate metabolic deficiency in lupus-prone mice. Using correlative metatranscriptomics and metabolomics, we observed restricted expression of bacterial genes related to mucin degradation, elevated pentose phosphate pathway and bile acid-modifying activities, and redirected tryptophan catabolism toward indoleacetic and indoleacrylic acids. Further host cell profiling showed that UT1 rebalanced colonic regulatory T (Treg) and T helper 17 (Th17) cell responses, suppressed systemic autoimmune activation and autoantibody production, and reduced renal pathology. Thus, our findings identify SLE-associated active microbiome signatures and provide a probiotic candidate for the treatment of lupus disease.}, }
@article {pmid41975031, year = {2026}, author = {Sepulveda, BJ and González-Recio, O and Chamberlain, AJ and Xiang, R and Cocks, BG and Wang, J and Prowse-Wilkins, CP and Marett, LC and Williams, SRO and Jacobs, JL and García-Rodríguez, A and Jiménez-Montero, JA and Pryce, JE}, title = {Reliable enteric methane prediction from the cattle (Bos taurus) rumen microbiome.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-10048-8}, pmid = {41975031}, issn = {2399-3642}, support = {DairyBio//Dairy Australia/ ; }, abstract = {The production of methane, a potent greenhouse gas, by ruminants during feed digestion is designated enteric methane emissions (EME) and is mainly produced by the rumen microbiome. Reliably recording EME in large populations is currently cost-prohibitive, hampering farming decisions aimed at reducing EME. Here, we perform comprehensive analyses on host genetics, KEGG orthology groups (KOs) from the rumen metagenome, and EME of more than 800 cows from Australia and Spain. We report that the rumen microbiome explains up to 34% of the EME variance, and when combined with the host genome, the variance explained is up to 59% with prediction accuracies of up to 0.40. The results support a recursive model, where both the host genome and rumen metagenome explain EME. The isometric log-ratio transformation of KOs may potentially better capture relationships between host genetics and the rumen microbiome than the centered log-ratio transformation, and BayesR yielded slightly higher microbe‑explained EME variance than best linear unbiased prediction. A forward simulation estimated to reach 90% of EME prediction accuracy with 6,000 animals with rumen microbiomes and host genomes, which could open opportunities for developing strategies to reduce EME. Our study contributes to the foundation for reducing EME, supporting global warming mitigation.}, }
@article {pmid41963805, year = {2026}, author = {Roslan, MF and Saad, MFM and Pau, SSN and Basir, S and Aziz, H and Akbar, MA and Bunawan, H}, title = {Bacterial community profiling of Malaysian drinking water reservoirs using metagenomic amplicon sequencing.}, journal = {BMC genomic data}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12863-026-01422-w}, pmid = {41963805}, issn = {2730-6844}, }
@article {pmid41963968, year = {2026}, author = {Zhou, N and Liu, J and Zhang, X and Xiao, G and Zhang, M}, title = {Vitamin K2 emerges as the key mediator: Cetobacterium somerae ZNN-1 increases muscle protein deposition and improves liver health in Nile tilapia (Oreochromis niloticus).}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {41963968}, issn = {1674-9782}, support = {32373145//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Cetobacterium somerae (C. somerae) is a common indigenous bacterium in the intestine of freshwater fish. Studies have shown that it has the potential to promote protein deposition, but the underlying mechanisms remain unclear.<br><br>RESULTS: Nile tilapia were fed with C. somerae ZNN-1 (10[8]&#xa0;CFU/g feed), which significantly increased the carcass ratio, reduced the hepatosomatic index, and decreased whole-body lipid content. Supplementation of C. somerae ZNN-1 significantly increased the crude protein content in muscle, promoted glucose uptake and utilization in muscle tissue, and activated the phosphorylation of S6K/S6 in muscle tissue. C. somerae ZNN-1 supplementation significantly decreased hepatic total lipid, triglyceride, and free fatty acid contents. Further analysis revealed that C. somerae ZNN-1 supplementation markedly activated the phosphorylation of hepatic AMPK and upregulated the expression of genes involved in hepatic lipolysis and fatty acid &#x3b2;-oxidation. Integrated serum metabolomic, bacterial genomic, and gut metagenomic analyses revealed that C. somerae ZNN-1 synthesized chorismate (CHA), which serves as a precursor for gut microbiota to produce vitamin K2 (VK2). In vitro experiments demonstrated that VK2 activated the S6K/S6 pathway to promote protein synthesis, while stimulating AMPK phosphorylation and activating lipid catabolism to reduce fat accumulation.<br><br>CONCLUSIONS: These findings provide a theoretical basis for the application of C. somerae ZNN-1 in enhancing edible protein content and reducing fat deposition of aquatic animals.}, }
@article {pmid41964024, year = {2026}, author = {Sosef, NP and Boxman, ILA and Dirks, RAM}, title = {Evaluation of two virome probe hybridization capture panels for food safety surveillance.}, journal = {Virology journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12985-026-03159-5}, pmid = {41964024}, issn = {1743-422X}, support = {WOT Food Safety Enforcement 002//Dutch Food and Consumer Product Safety Authority/ ; }, abstract = {In recent years, viromics has received growing attention for viral disease surveillance. This study set out to compare the VirCapSeq-VERT panel and the Comprehensive Viral Research Panel (CVR Panel) for probe hybridization capture of viral nucleic acids in oyster extracts, a main vehicle for the transmission of foodborne viruses. Using ten-fold serial dilutions of human norovirus (hNoV) GI.2 and GII.4 spike-in oyster extracts, both hybridization capture panels achieved detection levels down to 14 genome copies (gc) for hNoV GI.2 and 5 gc for hNoV GII.4. For hNoV GI.2, a genome coverage of ≥ 95% was achieved at 59 gc using the CVR Panel, whereas 724 gc were required for a similar coverage using VirCapSeq-VERT. For hNoV GII.4, a genome coverage of ≥ 97% was achieved at 87 gc with either panel. Next, the hybridization capture performance was compared for a mixture of various foodborne viruses (hNoV GI.2, hNoV GI.3, hNoV GII.4, hepatitis A virus and hepatitis E virus) in the absence of matrix and in the presence of oyster matrix. Sensitive detection of all added viruses was observed at low input levels (less than 200 gc/constructed library) in oyster extract. Taken together, the CVR Panel seems as good as, or slightly more sensitive than, VirCapSeq-VERT for the viruses tested. The availability of various viral enrichment panels, together with foreseen improvements regarding the cost-effectiveness and accessibility, is poised to facilitate broad hazard assessment and genomic profiling techniques in food virology, thereby enhancing food safety and improving early warning.}, }
@article {pmid41964077, year = {2026}, author = {Hernandez, LK and DiDonato, N and Pasa-Tolic, L and Chuckran, PF and Firestone, MK and Sieradzki, ET and Yuan, MM and Estera-Molina, K and Kimbrel, J and Dijkstra, P and Banfield, JF and Pett-Ridge, J and Blazewicz, SJ}, title = {Reduced legacy precipitation decreases microbial community growth efficiency and alters soil organic carbon in a California grassland.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02395-9}, pmid = {41964077}, issn = {2049-2618}, support = {DE-SC0020163//U.S. DOE Biological and Environmental Research Award/ ; SCW1589//U.S. DOE Biological and Environmental Research Award/ ; SCW1632//U.S. DOE Office of Biological and Environmental Research Genomic Science Program/ ; }, abstract = {BACKGROUND: Changes in global patterns can leave a lasting legacy in semiarid grasslands by reshaping microbial growth dynamics and carbon cycling during the first wet-up in the autumn-a period known for intense microbial activity and significant carbon emissions. To study the lasting impacts of decreased winter rain, we implemented two precipitation regimes (100% vs. 50% mean annual precipitation) in California Mediterranean-climate grassland field plots. After the dry season, soils were rewetted in the laboratory with H2[18]O and sampled at 0 h, 3 h, 24 h, 48 h, 72 h, and 168 h post rewet. We quantified CO2 efflux, measured microbial growth and mortality via quantitative [18]O stable isotope probing and 16S rRNA gene amplicon sequencing, and characterized the soil organic carbon chemical composition, metagenomes, and metatranscriptomes.<br><br>RESULTS: We found that reduced winter precipitation imposed a strong legacy effect on microbial turnover; despite maintaining similar respiration rates, microbial growth declined by&#x2009;~1 order of magnitude, yielding decreased community growth efficiency (CGE&#x2009;=&#x2009;new biomass growth/respiration), and microbial mortality declined by ~2 orders of magnitude. Soil organic carbon also shifted from lipid-like, amino-sugar-like, and protein-like compounds (indicative of microbial necromass) to more oxidized lignin-like and tannin-like compounds (indicative of decomposing plant-derived compounds). Meta-omics revealed distinct metabolic strategies linked to CGE. At high-CGE, microbes appeared to consume more energetically favorable N-rich necromass (released via high microbial turnover); this allowed for increased amino acids and peptidoglycan biosynthesis and greater aromatic compound degradation, fueling further energy production and growth efficiency. At low CGE, communities had elevated carbohydrate metabolism and lipid turnover, consistent with increased investment in plant detritus degradation and membrane repair and maintenance rather than growth.<br><br>CONCLUSIONS: Together, our findings demonstrate that reduced winter rainfall decreases microbial turnover following rewetting without a concurrent reduction in CO2 emissions. This shift results in persistently lower CGE, which has the potential to increase soil carbon loss as CO2. If such conditions are maintained over multiple years, these changes could reshape soil organic carbon stocks and alter the balance of grassland ecosystems under future climate scenarios. While our data suggest that sustained reductions in CGE may drive SOC decline, the magnitude and persistence of these effects depend on long-term environmental dynamics and warrant further investigation. Video Abstract.}, }
@article {pmid41964107, year = {2026}, author = {Zhang, Z and Chen, C and Zhang, M and Zhu, J and Xu, X and Wang, Z and Zhou, L and Wu, C and Zong, M and Yin, T and Cao, Z and Gao, A and Zhang, C and Su, T and Jiang, L and Zhou, W and Zhou, W and Zhou, Y and Wang, J and Ning, G and Jiang, Y and Liu, R and Wang, W}, title = {Gut microbiota signatures in primary aldosteronism and functional identification of an aldosterone-degrading gut bacterium.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2657047}, doi = {10.1080/19490976.2026.2657047}, pmid = {41964107}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome ; Humans ; *Hyperaldosteronism/microbiology/metabolism ; Animals ; *Aldosterone/metabolism/blood ; Male ; Mice ; Feces/microbiology/chemistry ; Middle Aged ; Female ; *Bacteria/classification/metabolism/genetics/isolation &amp; purification ; *Ruminococcus/metabolism/genetics ; Blood Pressure ; Aged ; *Eubacteriales/metabolism ; Metagenomics ; Essential Hypertension/microbiology ; }, abstract = {Primary aldosteronism (PA), a major cause of secondary hypertension, is characterized by autonomous aldosterone overproduction. Although the gut microbiota is closely linked to blood pressure regulation, its role in PA remains unclear. We performed metagenomic sequencing on fecal samples from 13 patients with essential hypertension (EH), 57 with unilateral PA (UPA), and 51 with bilateral PA (BPA). Despite comparable overall microbial diversity, gut microbial compositional differences were observed among EH and PA subtypes, particularly at finer taxonomic levels. We next identified 39 microbial species that were positively associated with plasma aldosterone concentration (PAC), and 29 that were negatively associated. In the co-abundance network, Ruminococcus gnavus emerged as one of the top three central nodes and was negatively correlated with PAC. Functionally, R. gnavus efficiently degraded aldosterone and multiple natural steroid hormones in vitro, and aldosterone degradation was accompanied by the generation of 3α,5β-tetrahydroaldosterone. R. gnavus-colonized germ-free mice showed reduced fecal aldosterone levels and downregulated expression of aldosterone downstream genes in the intestine. In an aldosterone infusion model, R. gnavus similarly decreased fecal aldosterone and improved systolic blood pressure (SBP) and serum potassium. Logistic regression further revealed that the presence of R. gnavus was associated with lower odds of having a historical highest SBP ≥ 160 mmHg in patients with PA. Collectively, this study reveals different gut microbial signatures in PA and highlights the aldosterone-metabolizing capacity and blood pressure regulation of R. gnavus. These findings advance our understanding of gut microbiota-steroid hormone interactions in PA and provide a basis for exploring microbiota-based stratification and intervention strategies in steroid hormone-related conditions.}, }
@article {pmid41964456, year = {2026}, author = {Lefebvre, CS and Salmona, M and Hamane, S and Dellière, S and Charlier, V and Huguenin, A and Bonnal, C and Legoff, J and Feghoul, L and Dutkiewicz, M and Caméléna, F and Berçot, B and Charvet, E and Battistella, M and Alanio, A and Ghelfenstein-Ferreira, T}, title = {Shotgun metagenomic sequencing improves cross-kingdom diagnosis of mycetoma.}, journal = {Journal of the European Academy of Dermatology and Venereology : JEADV}, volume = {}, number = {}, pages = {}, doi = {10.1111/jdv.70450}, pmid = {41964456}, issn = {1468-3083}, }
@article {pmid41964564, year = {2026}, author = {Zhao, S and Lin, S and Chen, M and Yan, J and Yang, D and Guo, F and Qu, H and Chen, Y}, title = {Iron-Cycling-Constructed Wetland-Microbial Fuel Cell-Enhanced Removal of Sartans: The Overlooked Singlet Oxygen and Functional Microorganisms.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c00492}, pmid = {41964564}, issn = {1520-5851}, abstract = {The global challenge of population aging has led to an increase in the utilization of cardiovascular drugs such as sartans, which are frequently detected in aquatic environments and necessitate advanced treatment. Current sartan removal technologies are limited by their requirement for strict reaction conditions and the potential formation of toxic byproducts. This study presents a novel iron-cycling-constructed wetland-microbial fuel cell (Fe-CWMFC) that combines biotic and abiotic processes to effectively degrade sartans (94.4 ± 3.5%-95.9% ± 3.3%). Mass balance analysis revealed that direct microbial degradation pathways made the highest contribution (40.7-44.5%), followed by ROS-driven degradation (20.3-21.8%), substrate adsorption (26.1-29.7%), and plant uptake (2.3-2.5%). Iron cycling enhanced ROS-driven degradation, with 11.3-13.3% derived from biotic [1]O2 and 7.0-9.3% derived from abiotic [1]O2. Metagenomic binning analysis identified 60 MAGs (e.g., Thiobacillus, Nitrosomonas) with sartan degradation potential, which harbor genes encoding functional enzymes (e.g., decarboxylase, dehydroxylase, and demethylase). By combining biodegradation and ROS-driven degradation to target functional groups (e.g., -COOH, -OH, and -CH3) in sartans, the toxicity was significantly reduced. This research enhances our understanding of the combined role of ROS and microorganisms in micropollutant removal and highlights Fe-CWMFC as a high-efficiency, sustainable, and low-toxicity treatment technology for complex environmental applications.}, }
@article {pmid41964658, year = {2026}, author = {Liu, H and Wang, C and Huang, Z and Wang, J and Cai, F and Tian, C and Feng, J and Shen, J and Wang, X}, title = {Progressive Decomposition of Algal Organic Matter Decouples Nitrogen Transformations in Lake Sediments: Evidence from Short-Term Incubation.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c08386}, pmid = {41964658}, issn = {1520-5851}, abstract = {Against the backdrop of global lake eutrophication, algal bloom decay is increasingly affecting ecosystems. Algal organic matter (AOM), a natural complex mixture, undergoes multiple release and transformation stages, yet its composition and pathways remain unclear. This study used spectroscopic, mass spectrometric, and metagenomic analyses to monitor a time-compressed algal decay experiment. Results showed that AOM release and transformation can be divided into three stages. Within 1 day, labile AOM consisting mainly of proteins (8.36%), lipids (8.22%), and unsaturated carbohydrates (7.72%) was rapidly released, reshaping nitrogen (N) cycling. Its high bioavailability promoted sediment mineralization and a positive priming effect, while anaerobic conditions reduced nitrification and denitrification rates by 88.7% and 34.5%. Within 3-7 days, semilabile AOM rich in tannins (19.2%) and carbohydrates (9.41%) was gradually decomposed, maintaining anaerobic conditions. The imbalance of excessive NH4[+] and depleted NO3[-] led to the decoupling of nitrification-denitrification. After 7 days, humic-like AOM dominated by lignins (56.8%) prevailed, reducing oxygen consumption and enabling rapid recovery of nitrification and slow rebound of denitrification. These findings clarify the phased transformations of AOM and their microbial interactions, providing mechanistic insights into the short-term fluctuations of lake water quality and microbial processes during bloom decay.}, }
@article {pmid41965517, year = {2026}, author = {Han, J and Zhou, X and Guo, M and Zhang, C and Liu, C and Cai, L and Zhao, H}, title = {Intestinal dysbiosis associates with silica-induced pulmonary fibrosis in mice via arginine and tryptophan pathways.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-05023-6}, pmid = {41965517}, issn = {1471-2180}, support = {2025QN03136//Natural Science Foundation of Inner Mongolia/ ; 2025MS03093//Natural Science Foundation of Inner Mongolia/ ; 62231013//National Natural Science Foundation of China/ ; 62261043//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Pulmonary fibrosis (PF) is a life-threatening interstitial lung disease with a lack of effective therapeutic approaches. Silicosis is a subtype of PF that is specifically caused by the inhalation of crystalline silica particles. In recent years, the gut-lung axis has been shown to be involved in the occurrence and progression of various respiratory diseases. However, the involvement and specific mechanism of action of the gut microbiome in silica-induced PF remain to be elucidated. Therefore, we established a silica-induced PF murine model using an inhalation exposure system, and combined gut metagenomic and untargeted metabolomics data to correlate microbial and metabolic changes with profibrotic cytokine levels.<br><br>RESULTS: In mice exposed to silica dust for 64 days and 128 days, Akkermansia muciniphila and Staphylococcus lentus were significantly enriched, whereas the abundance of Lactobacillus murinus was notably reduced. Relevant network analysis revealed that these gut microbiota changes were highly correlated with metabolic disorders of tryptophan and arginine. Moreover, changes in the gut microbiome composition corresponded with the fluctuations in the levels of profibrotic cytokines, including transforming growth factor-beta, tumor necrosis factor-alpha, fibroblast growth factor, and hydroxyproline.<br><br>CONCLUSION: We successfully established a murine model of PF induced by silica inhalation. Our results suggest that Lactobacillus murinus, Akkermansia muciniphila, and Staphylococcus lentus are key microorganisms involved in the development of silica-induced PF, while the arginine and tryptophan metabolic pathways serve as key regulatory pathways in the gut-lung axis contributing to disease development.}, }
@article {pmid41965741, year = {2026}, author = {Khangarot, R and Kumari, V and Mishra, R and Singh, A}, title = {Artificial intelligence in microbiology: implications for metagenomics, diagnostics, and AMR surveillance.}, journal = {Biomedical engineering online}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12938-026-01568-9}, pmid = {41965741}, issn = {1475-925X}, abstract = {Artificial intelligence (AI) is now a key player in modern microbiology, as it enables high-resolution analyses of genomic, metagenomic, and clinical data for the monitoring of infectious disease and antimicrobial resistance (AMR). Considerable advancements in deep learning, transformer-based sequence models, graph neural networks, and multimodal architectures have greatly improved microbial classification accuracy, antibiotic resistance gene (ARG) detection, and resistance prediction. Taking metagenomic sequencing into consideration, these advancements have contributed to the development of sensitive, scalable, and non-invasive methods to profile microbiomes, determine novel resistance, and monitor AMR trends at the population level. This review summarizes recent advances in AI-aided microbiology, with a particular emphasis on AMR surveillance. Specific topics include deep learning frameworks for ARG annotation, emerging approaches to identifying new resistance genes, and multimodal applications (genomic and clinical metadata) aimed at improving phenotype prediction. The role of metagenome-assembled genomes (MAGs) to enhance AMR surveillance efforts is noted, along with their noted limitations relative to isolate genomes. The discussion includes the examination of explainable AI (XAI) techniques including SHAP, attention mechanism approaches, and gradient-based attribution approaches, with the aim of increasing transparency and clinical explainability. We also cover potential applications including AI-enabled non-invasive fecal microbiome diagnostics, laboratory automation, and environmental surveillance. While there has been significant progress, unresolved issues exist relating to dataset variations, liability of models to datasets, interpretability, and regulatory approval. Overcoming these barriers, however, will require standardized frameworks for these workflows, privacy-preserving federated learning methods, and interpretable AI frameworks for clinical and public health tools. AI could fundamentally change AMR surveillance by allowing for earlier resistance detection, advanced risk assessment recommendation, and improved monitoring strategies globally.}, }
@article {pmid41965996, year = {2026}, author = {Wang, C and Shen, J and Liu, H and Huang, Z and Wang, J and Tian, C and Cai, F and Feng, J and Sha, F and Wang, X}, title = {DNRA dominates over denitrification during algal blooms in a mesotrophic lake: Implications for nitrogen retention and eutrophication risk.}, journal = {Journal of environmental management}, volume = {405}, number = {}, pages = {129621}, doi = {10.1016/j.jenvman.2026.129621}, pmid = {41965996}, issn = {1095-8630}, abstract = {Nitrogen (N) overloading threatens global lake ecosystems. However, how algal blooms affect the N balance in mesotrophic lakes by shaping N-cycling biogeographic patterns remains a critical knowledge gap. This study systematically elucidated N cycling patterns and microbial mechanisms driving N retention during algal blooms in Erhai Lake by integrating field monitoring,[15]N isotope pairing technique ([15]N-IPT), and absolute quantitative metagenomics. Results revealed that algal blooms shaped a N-cycling functional pattern in Erhai Lake characterized by organic degradation and synthesis (ODAS) dominance and dissimilatory nitrate reduction (DNR) as a key process. Notably, algal blooms disrupted traditional nitrification-denitrification coupling, shifting N cycling towards a retention mode dominated by dissimilatory nitrate reduction to ammonium (DNRA). Sedimentary DNRA contributed 69% (14.69 ± 5.57 μmol N L[-1] h[-1]) of total dissimilatory nitrate reduction (DNR) process, supported by significantly elevated NrfA (602.49 ± 121.04 μmol d[-1] g[-1]) and NirBD (361.29 ± 138.39 μmol d[-1] g[-1]) enzyme activities. Partial Least Squares Path Modeling (PLS-PM) identified the nitrogen retention index (NRI) as co-regulated by water depth and algal-mediated microbial activity/rates. High-NRI sediments were dominated by Bacteroidota (mainly orders Marinilabiliales and families Prolixibacteraceae) and Myxococcota (primarily families Anaeromyxobacteraceae), while low-NRI sediments were characterized by enrichment of Pseudomonadota (Thioalkalivibrio nitratireducens and Gallionellaceae) and Campylobacterota (Campylobacter sp. BCW_8712). DNRA outcompeted denitrification, diverting nitrate to ammonium rather than N2 gas and resulting in an internal N loading that was an order of magnitude higher than external inputs. This work challenges the denitrification-centric paradigm, revealing the microbial mechanisms of endogenous N accumulation under algal bloom conditions and providing a theoretical basis for the management of plateau lakes.}, }
@article {pmid41966291, year = {2026}, author = {Ashango, ZA and Seyum, EG and Nwogha, JS}, title = {Integrating metagenomics into legume breeding: A breeder-centered roadmap from core microbiomes to precision inoculation.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105941}, doi = {10.1016/j.meegid.2026.105941}, pmid = {41966291}, issn = {1567-7257}, abstract = {Metagenomics, culture-independent profiling of genetic material recovered from environmental samples, provides a powerful route to characterize microbial communities associated with legumes and to translate their functional potential into breeding targets that enhance resilience and productivity. Across analyses of rhizosphere, endosphere, and seed microbiomes, repeated studies consistently identify a conserved set of microbial functions linked to nutrient cycling, responses to abiotic and biotic stress, and biological control of pathogens, thereby offering mechanistic support that community-level functional capacities can shape host outcomes, including seedling vigor, nutrient-use efficiency, and stress tolerance. To move from descriptive discovery to actionable breeding, three complementary translational strategies have emerged: (i) synthetic microbial communities (SynComs) engineered to deliver targeted metabolic functions while enabling rigorous assessment of community stability and functional consistency; (ii) predictive model systems that integrate metagenomic features with phenotypic measurements to prioritize candidate taxa or functions for subsequent validation; and (iii) precision inoculation approaches that deploy validated microbes or consortia in agronomic settings to test whether metagenome-inferred functions confer robust performance under field-relevant conditions. A critical appraisal of metagenomic, multi-omics, and translational studies indicates that functional-phenotypic mappings are promising, yet substantial barriers continue to constrain reproducibility and scalability, including heterogeneity in sampling and experimental design, biases introduced by DNA extraction and sequencing, variability across bioinformatics workflows and reference databases, and overarching biosafety and regulatory constraints that can obscure true biological signals and weaken the reliability of functional inferences intended to guide selection decisions. To mainstream metagenomics in conventional legume breeding, we propose a breeders' roadmap centered on coordinated standardization and decision-ready analytics, encompassing standardized metagenomics-compatible sampling and sequencing platforms, harmonized computational frameworks and metabolic inference tools to ensure comparable functional calls, high-throughput phenotyping protocols aligned to microbiome-sensitive host traits, and selection frameworks that explicitly incorporate microbiome-oriented decision rules rather than treating microbial signals as ancillary. Finally, integrating machine learning with multi-omics datasets alongside precision delivery systems offers a practical route to generate actionable holobiont-level selection indices, and, when coupled with clearly defined translational pipelines and methodological standardization, metagenomics can broaden breeding gains beyond those achievable using host genomics alone, enabling more reliable, function-driven microbiome-assisted improvement of legume performance.}, }
@article {pmid41966300, year = {2026}, author = {Bojko, J and Abd-Alla, A}, title = {'Invertebrate-virome sequence detection: implications for invertebrate products trading and regulations' - An editorial for the special issue.}, journal = {Journal of invertebrate pathology}, volume = {}, number = {}, pages = {108623}, doi = {10.1016/j.jip.2026.108623}, pmid = {41966300}, issn = {1096-0805}, abstract = {Invertebrates can be infected by many viruses that may either cause disease (invertebrate‑pathogenic viruses) or be transmitted to vertebrates or plants. Viral infections may occur in natural invertebrate populations as well as in mass‑reared colonies. The significant recent advances in genome‑sequencing technologies have provided fast and relatively inexpensive tools for detecting invertebrate viruses in both wild and mass‑rearing settings, even at very low levels. The presence of such viruses raises important questions regarding the impact of covert infections on invertebrate health, sanitation, and overall colony performance. The articles in this special issue address viral sequence detection, viral sequence diversity, the impact of viruses on invertebrates, and the relationship between food and feed, and policy.}, }
@article {pmid41966314, year = {2026}, author = {Liu, S and Qin, Y and Ni, H and Hou, QY and Xu, C and Leng, X and Li, XM and Yang, MT and Tang, LY and Sun, YZ and Zhao, Q and Ni, HB and Zhang, XX and Jiang, J and Yang, LH and Ma, H}, title = {Genomic Characterization, Antimicrobial Resistance and Virulence Profiles of Klebsiella pneumoniae Isolated from Mink in Northern China.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108485}, doi = {10.1016/j.micpath.2026.108485}, pmid = {41966314}, issn = {1096-1208}, abstract = {Klebsiella pneumoniae is an important opportunistic pathogen of One Health concern, and its multidrug-resistant (MDR) and hypervirulent strains pose serious threats to public health. However, the epidemiological characteristics, antimicrobial resistance profiles, and virulence potential of K. pneumoniae circulating in farmed minks remain poorly understood. In this study, we integrated phenotypic antimicrobial susceptibility testing, whole-genome sequencing, and metagenomic analysis to investigate the epidemiology, resistance determinants, and virulence characteristics of K. pneumoniae isolated from farmed minks in northern China. A total of 41 K. pneumoniae strains from 325 fecal samples (isolation rate: 12.62%), including three hypervirulent strains. All isolates exhibited multidrug resistance, with complete resistance to florfenicol, azithromycin, and sulfisoxazole, but remained highly susceptible to carbapenems and polymyxin B. Whole-genome sequencing revealed that the isolates harbored 241 antibiotic resistance genes (ARGs), including ESBL-associated genes and the plasmid-mediated mcr-1.1, along with 7,111 virulence factor genes (VFGs) and 135 mobile genetic elements (MGEs). Metagenomic analysis further revealed a complex resistome and virulome, with 7,259 ARGs and 6,701 virulence-related genes identified across samples. Antibiotic target alteration and efflux were the dominant resistance mechanisms, while effector delivery systems, metabolic functions, and adherence were the major virulence categories. MGEs were abundant, especially transposases, indicating active genetic mobility within the microbial community. Overall, this study provides a comprehensive characterization of antimicrobial resistance and virulence features of mink-derived K. pneumoniae and highlights the potential role of farmed minks as reservoirs of multidrug-resistant bacteria within the One Health framework, offering important insights for antimicrobial resistance surveillance and public health risk assessment.}, }
@article {pmid41966472, year = {2026}, author = {Merkhan, K and Chaudhry, AS}, title = {Phytogenic feed additives mitigate in vitro methanogenesis and alter microbial community and functional pathways in the dairy cow rumen.}, journal = {Anaerobe}, volume = {98}, number = {}, pages = {103046}, doi = {10.1016/j.anaerobe.2026.103046}, pmid = {41966472}, issn = {1095-8274}, abstract = {OBJECTIVES: Using phytogenic feed additives (PFA) could be a promising strategy for mitigating enteric methane (CH4) emissions from ruminants. This study aimed to evaluate the efficacy of specific phytogenic additives on rumen fermentation, methanogenesis, microbial community, and functional pathways.<br><br>METHODS: This 2 x 4 x 3 factorial study was conducted using an in vitro rumen fermentation system for a period of 72&#xa0;h. Treatments included two silage-to-concentrate ratios (60:40 and 40:60), four PFA (great burnet leaves, GBL; oregano leaves, OL; cumin seeds, CS; and garlic bulbs, GB), and three inclusion levels (0, 10, and 20&#xa0;g&#xa0;kg[-1] DM) for each PFA.<br><br>RESULTS: The GB addition proved the most potent anti-methanogenic additive, reducing CH4 by up to 32.8% at 20&#xa0;g&#xa0;kg[-1] DM, followed by GBL with a 28.5% reduction at 10&#xa0;g&#xa0;kg[-1] DM, without impairing total volatile fatty acid production. Methane suppression was associated with a lower acetate-to-propionate ratio, decreased abundance of methanogenic archaea (particularly Methanobrevibacter), and reduced expression of the key methanogenesis gene mcrA and fmdB. While GB exhibited a strong anti-protozoal effect, OL effectively reduced ruminal ammonia concentrations. Additionally, metagenomic analysis identified Porcincola was among the core and most abundant genera in our bovine rumen dataset.<br><br>CONCLUSION: Optimising the inclusion of specific phytogenic additives can selectively manipulate the rumen microbiome, concurrently reduce methane production and influence nitrogen metabolism. Further research is warranted to evaluate potential synergistic interactions among these additives to enhance fermentation efficiency of ruminant diets.}, }
@article {pmid41966559, year = {2026}, author = {Jordán, M and Bustos-Caparros, E and Gago, JF and Zhang, Z and Tian, Z and Singleton, DR and Rossello-Mora, R and Grifoll, M and Vila, J}, title = {Unraveling acridine degradation mechanisms in PAH-contaminated soils using DNA-SIP combined with metagenomics and soil transcriptomics.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {142004}, doi = {10.1016/j.jhazmat.2026.142004}, pmid = {41966559}, issn = {1873-3336}, abstract = {Polycyclic aromatic nitrogen heterocycles (PANHs), also known as azaarenes, are common co-contaminants at sites contaminated with polycyclic aromatic hydrocarbons (PAHs). Recent non-target analysis of PAH-contaminated soil samples has revealed an unexpected abundance and diversity of PANHs, with acridine standing out as a predominant compound within this group. Despite its known toxicity and prevalence in contaminated soils, the microbial communities and biochemical mechanisms responsible for acridine degradation remain poorly understood. We conducted DNA-stable isotope probing (DNA-SIP) using newly synthesized uniformly labeled [13]C-acridine to comprehensively assess the bacterial taxa and functional genes involved in acridine biodegradation in a creosote-contaminated soil. Metagenomic analysis of [13]C-enriched DNA from soil incubations identified a member of the genus Sphingobium as the primary acridine degrader. Transcriptomic analysis based on its 16S rRNA gene expression demonstrated a strong correlation with acridine removal from the soil. Shotgun metagenomic sequencing enabled the reconstruction of one metagenome-assembled genome (MAG). Functional annotation of this MAG revealed five gene clusters potentially involved in acridine biodegradation, and their actual contribution was assessed by gene expression analysis in soil incubations. Based on these findings, we reconstructed the metabolic pathway for putative acridine degradation in PAH-contaminated soil.}, }
@article {pmid41966829, year = {2026}, author = {Tóth, AG and Paholcsek, M and Solymosi, N and Stágel, A and Gömbös, P and Posta, K and Lakatos, I and Nagy, S&#xc1; and Ferenczi, S and Szőke, Z}, title = {Protocol for the assessment of the impact of mycotoxins and glyphosate residues on the gut microbiome and resistome of European fallow deer.}, journal = {STAR protocols}, volume = {7}, number = {2}, pages = {104498}, doi = {10.1016/j.xpro.2026.104498}, pmid = {41966829}, issn = {2666-1667}, abstract = {Here, we present a protocol to describe the bacteriome of the intestinal content of toxin-exposed fallow deer. We describe steps for measuring fecal mycotoxin (deoxynivalenol, zearalenone, fumonisin B1, and aflatoxin B1) levels using liquid chromatography-mass spectrometry, as well as serum glyphosate. We then detail a short-read shotgun DNA sequencing-based bioinformatic pipeline for the toxin level-associated analysis of the bacteriome and resistome and the construction of metagenome-assembled bacterial genomes. This protocol has potential applications in further toxin level-associated metagenome studies. For complete details on the use and execution of this protocol, please refer to Tóth et al.[1].}, }
@article {pmid41967167, year = {2026}, author = {Okoye, CO and Okoye, KC and Ezenwanne, BC and Olalowo, OO and Andong, FA and Echude, D and Chukwudozie, KI and Emencheta, SC and Ezeonyejiaku, CD and Ikele, CB}, title = {Microbiome and multi-omics insights into sustainable aquaculture: A triennial systematic review.}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {59}, number = {}, pages = {101830}, doi = {10.1016/j.cbd.2026.101830}, pmid = {41967167}, issn = {1878-0407}, abstract = {Aquaculture is the fastest-growing food production sector, yet intensive practices drive disease outbreaks, antibiotic resistance, and environmental degradation, threatening long-term sustainability. The aquaculture microbiome, encompassing host-associated and environmental microbial communities, regulates nutrient cycling, pathogen suppression, immunity, and overall system resilience. This triennial systematic review (2023-2025), conducted according to PRISMA guidelines, synthesized 19 highly relevant peer-reviewed studies that applied multi-omics approaches (metagenomics, transcriptomics, metabolomics, SNP genotyping, and their integration) to aquaculture microbiomes across shrimp, finfish, and hybrid species. The studies collectively revealed diverse host-microbe-metabolite interactions underpinning growth, immunity, and disease resistance, with representative examples including microbial-metabolite-host signaling axes and microbiome-mediated immune modulation, as seen in Salinivibrio-AMP-mTOR axis, EHP-resistant shrimp via metabolic reprogramming and stable microbiota, and Bacillus-mediated diglyceride production. Beneficial taxa such as Cetobacterium and Salinivibrio, heritable microbiome traits, and sustainable interventions including insect-meal feeds, phytogenic additives, and organic copper consistently improved growth, immunity, and microbial stability while reducing dysbiosis under stress. Environmental stressors and pathogens induced reproducible shifts in microbial diversity, functional pathways, and host metabolism. These findings demonstrate that multi-omics integration is transforming aquaculture into a precision discipline, enabling microbiome-informed selective breeding, targeted probiotics, and environmentally sound nutrition. To translate these insights into practice, future research must emphasize functional validation, machine learning-driven predictive models, and ecosystem-level assessments to achieve resilient, antibiotic-reduced, and sustainable aquaculture systems.}, }
@article {pmid41967206, year = {2026}, author = {Moletta-Denat, M and Azam, O and Pourcher, AM and Manno, M and Zennaro, B and Bonin, E and Bonnafous, A and Chenon, P and Leboucher, A and Alvarez-Fraga, L and Godon, JJ and Wéry, N}, title = {Fate of pathogenic bacteria in five full-scale biogas plants monitored using cultivation, dPCR, and shotgun metagenomics: Insights from each approach.}, journal = {Waste management (New York, N.Y.)}, volume = {218}, number = {}, pages = {115505}, doi = {10.1016/j.wasman.2026.115505}, pmid = {41967206}, issn = {1879-2456}, abstract = {Current global standards for quantification of pathogenic or indicator bacteria in biogas plants primarily rely on culture-based methods using specific media. However, molecular techniques such as quantitative PCR, digital PCR (dPCR), and shotgun metagenomics are increasingly employed in research and may offer more effective pathogen monitoring for industrial applications. This study analyzed samples from five full-scale biogas plants using traditional culture-based methods, dPCR and shotgun metagenomics to monitor indicator bacteria (Escherichia coli, Enterococcus spp. and Clostridium perfringens) and pathogenic species (Salmonella enterica, Listeria monocytogenes, Staphylococcus aureus and Clostridium botulinum). The DNA extraction protocol was optimized to achieve quantification limits of 1.1 copies of gene g[-1] wet weight, compatible with regulatory thresholds. Comparing the three methods revealed that shotgun metagenomics detected a greater diversity of pathogenic species in biowaste, including S. aureus and C. botulinum. Acidophilic conditions in hydrolysis tank effectively hygienized the biowaste. In contrast, the four agricultural biogas plants showed limited effect on the three indicator bacteria, as indicated by dPCR. This study demonstrates, for the first time, the added value of combining dPCR and shotgun metagenomics to assess pathogen dynamics in biogas plants. Together, these methods provide a more comprehensive and specific view of microbial contaminants, as illustrated by the detection of Enterococcus cecorum in digestates.}, }
@article {pmid41864063, year = {2026}, author = {Jian, X and Yu, P and Zhang, Y and Pan, H and Wu, K and Zhang, H and Zhang, H and Huang, Y and Zhao, Y and Wang, Y and Wang, Y and Zhou, Q and Zhang, X and Zhao, G and Li, B and Guo, J and Xia, K and Tang, B and Li, J}, title = {Large-scale profiling of blood microbial signatures in patients with Parkinson's disease and its association with disease progression: a cross-sectional study.}, journal = {EBioMedicine}, volume = {126}, number = {}, pages = {106224}, pmid = {41864063}, issn = {2352-3964}, mesh = {Humans ; *Parkinson Disease/microbiology/blood/diagnosis ; Disease Progression ; Male ; Female ; Aged ; Biomarkers/blood ; Middle Aged ; Cross-Sectional Studies ; *Microbiota ; Whole Genome Sequencing ; *Bacteria/genetics/classification ; Metagenomics/methods ; }, abstract = {BACKGROUND: Emerging evidence supports the presence of microbial signatures in the blood, yet their clinical relevance remains poorly understood. In this study, we profiled blood microbial signatures in patients with Parkinson's disease (PD) and investigated their associations with disease progression.<br><br>METHODS: We analysed 4018 whole-genome sequencing (WGS) data of blood samples from two independent cohorts. The high-quality non-human reads were extracted for microbial annotation using Kraken 2 and Bracken software with the PlusPF database. To identify PD-associated signatures, we implemented a population-based, cross-cohort filtration process with resequencing validation to minimise noise and putative contaminants.<br><br>FINDINGS: Microbial DNA signals, predominantly bacterial, were extensively detected in the sequencing data and were more abundant in individuals with PD than in controls. Across the two cohorts, 126 bacterial species were identified as key signatures, nearly two-thirds of which are known to colonise human body sites. Among these, 19 species exhibited increased abundance and higher prevalence in PD, and could serve as features to discriminate effectively patients from controls. Furthermore, several microbial signatures were correlated with more severe clinical manifestations, such as motor dysfunction and cognitive impairment.<br><br>INTERPRETATION: Our findings supported blood microbial signatures as promising biomarkers in PD, although their origin and functional relevance remain to be validated. The analytical framework may facilitate future investigations into the potential clinical implications of blood microbial signatures in disease contexts.<br><br>FUNDING: This work was supported by Hunan Innovative Province Construction Project, National Natural Science Foundation of China, and Natural Science Foundation of Hunan Province.}, }
@article {pmid41956535, year = {2026}, author = {Cui, T and Huang, M}, title = {Tuberculous Peritonitis Diagnosed by Metagenomic Next-Generation Sequencing Progressing to Fatal Encapsulating Peritoneal Sclerosis in a Peritoneal Dialysis Patient: A Case Report.}, journal = {Seminars in dialysis}, volume = {}, number = {}, pages = {}, doi = {10.1111/sdi.70022}, pmid = {41956535}, issn = {1525-139X}, support = {SZSM202411016//Sanming Project of Medicine in Shenzhen/ ; }, abstract = {A 40-year-old woman on peritoneal dialysis for 3 years presented with febrile peritonitis. Metagenomic next-generation sequencing (mNGS) confirmed Mycobacterium tuberculosis complex in ascitic fluid, leading to prompt anti-tuberculosis therapy. She initially improved but developed ultrafiltration failure 15 months later and transitioned to hemodialysis. At 18 months, she developed bowel obstruction, bloody ascites, and characteristic imaging and laparoscopic findings of encapsulating peritoneal sclerosis (EPS). Despite supportive care, she deteriorated and died 30 months after tuberculosis peritonitis diagnosis. This case highlights that mNGS enables rapid diagnosis of tuberculous peritonitis when conventional tests are inconclusive, and that tuberculosis peritonitis may serve as a potent inflammatory trigger for EPS even after peritoneal dialysis cessation. Early recognition and timely intervention may improve outcomes.}, }
@article {pmid41956809, year = {2026}, author = {Li, X and Xie, M and Kang, JX and Chen, Y and Han, J and Chen, Y and Chen, Q and Yu, T and Liu, S and Ouyang, Z and Sun, Q and Li, K and Zhang, S and She, J and Yu, J}, title = {Bifidobacterium catenulatum boosts anti-PD-1 efficacy in microsatellite stable colorectal cancer via activating CD8[+] T cells.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-336025}, pmid = {41956809}, issn = {1468-3288}, abstract = {BACKGROUND: Certain gut bacteria are associated with improved responses to immunotherapy.<br><br>OBJECTIVE: We aim to identify bacteria that inhibit colorectal cancer (CRC) progression and enhance immunotherapy efficacy.<br><br>DESIGN: The abundance of bacteria in CRC patients was evaluated in our in-house cohorts and validated in published datasets. The effect of candidate bacterium with anti-PD-1 therapy was determined in two syngeneic mouse models of MC38 (microsatellite instability-high) and CT26 (microsatellite stable, MSS), transgenic Apc [min/+] mice and azoxymethane/dextran sulfate sodium (AOM/DSS)-induced CRC tumourigenesis model. Immune landscape changes were identified by multicolour flow cytometry and immunohistochemistry staining. Metabolomic profiling was performed on stool, serum and tumour tissues.<br><br>RESULTS: Bifidobacterium catenulatum was significantly depleted in stool samples of 110 CRC patients compared with 112 healthy controls, which was further validated in 3 published metagenomic datasets comprising 198 CRC patients and 176 normal subjects. Oral administration of B. catenulatum inhibited tumour growths in multiple CRC models including MC38 and CT26 syngeneic models, Apc[min/+] mice&#x2009;and AOM/DSS-induced CRC. Notably, B. catenulatum synergised with anti-PD-1 therapy through enhancing intratumoural CD8[+] T cell infiltration in MSS CRC models of Apc[min/+] mice&#x2009;and CT26 allografts. B. catenulatum-derived acetate was identified as the functional metabolite. Mechanistically, acetate directly bound to MCT-4 in CD8[+] T cells and activated mitogen-activated protein kinase signalling. Pharmacological and genetic MCT4 ablation abolished acetate-mediated CD8[+] T cell activation in vitro.<br><br>CONCLUSION: B. catenulatum suppresses colorectal tumourigenesis through generating acetate, which also improves anti-PD-1 efficacy through activating CD8[+] T cells in MSS CRC. B. catenulatum is a potential adjuvant to improve immunotherapy against CRC.}, }
@article {pmid41957175, year = {2026}, author = {Yang, S and Wang, X and Duan, J and Yang, S and He, J and Fang, C and Zhao, N and Huang, Y}, title = {Effects of replacing chemical fertilizer with organic fertilizer on organic carbon mineralization and carbon cycle functional genes in yellow soil.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-47725-x}, pmid = {41957175}, issn = {2045-2322}, support = {2022YFD1901500, 2022YFD1901505//National Key R&amp;D Program Project/ ; ZSYS[2025]035//Guizhou Key Laboratory of Cultivated Land Quality (Qian Ke He Platform)/ ; grant number BQW[2024]009//Construction of High Quality and Efficient Mechanized Scientific and Technological Innovation Talent Team of Characteristic Coarse Cereals in Guizhou Province/ ; }, abstract = {Fertilization-mediated soil organic carbon (SOC) mineralization is a key process in agroecosystem carbon cycling, yet the microbial mechanisms involved under different fertilization regimes remain unclear. This study, based on a three-year field experiment in acidic yellow soil (Ultisol) in Guizhou, integrated SOC mineralization incubation and metagenomic sequencing to compare SOC mineralization and functional gene profiles under no fertilization (CK), chemical fertilizer alone (NP), and replacing chemical fertilizer with 50% or 100% organic fertilizer (1/2NPM and M). Fertilization significantly increased cumulative mineralized SOC (Ct) (p < 0.05); NP showed high mineralization, whereas organic-fertilizer replacement reduced the cumulative mineralization ratio (Ct/SOC). Metagenomic analysis indicated NP did not substantially alter carbon-cycling genes but lowered the C/N ratio, increasing microbial diversity and driving "carbon-compensation" mineralization. Conversely, 1/2NPM and M improved soil pH, available phosphorus (AP), and nitrate nitrogen (NO3[-]-N), reshaped microbial community structure, up-regulated carbon-fixation genes (korA, facA, coxS), and suppressed carbon-degradation genes (pel, chi), enhancing carbon sequestration capacity. Partial least squares path modeling confirmed a "stoichiometry-community diversity" cascade significantly regulated SOC mineralization (p < 0.01), with organic-fertilizer replacement shifting functional profiles from carbon degradation to carbon fixation.}, }
@article {pmid41957291, year = {2026}, author = {Yang, M and Fang, J and Liao, Q}, title = {Comment on: "Exploring the gut microbiome in systemic lupus erythematosus: metagenomic and metabolomic insights into a new pro-inflammatory bacteria Clostridium scindens"-a call to disentangle clostridium scindens' bile acid metabolism from glucocorticoid modulation in SLE pathogenesis.}, journal = {Clinical rheumatology}, volume = {}, number = {}, pages = {}, pmid = {41957291}, issn = {1434-9949}, }
@article {pmid41957365, year = {2026}, author = {Kan, J and Spotton, K and Morales-Amador, A and Hernandez, Y and Burian, J and Panfil, C and Ternei, MA and Boer, RE and Bhattacharjee, A and Brady, SF}, title = {Mode of action guided metagenomic natural product discovery reveals convergent evolution of a ClpP-targeting motif.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71586-7}, pmid = {41957365}, issn = {2041-1723}, support = {R35GM122559//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; NIH T32 GM136640//U.S. Department of Health &amp; Human Services | National Institutes of Health (NIH)/ ; }, abstract = {The discovery of natural products with specific modes of action from metagenomes remains challenging. Here, we present resistance-CONKAT-seq, a pipeline that links biosynthetic gene clusters (BGCs) to self-resistance genes, enabling identification of metabolites with desired molecular targets. Using clpP-directed resistance-CONKAT-seq, we identify the calprotamides, which activate native ClpP and enhance its activity. Cryo-EM and bioinformatic analyses reveal that the calprotamides' medium-chain N-acylphenylalanine substructure is a convergently evolved ClpP-targeting motif and identify additional BGCs predicted to encode this moiety, including some with co-localized clp genes. The synthesis of structures bioinformatically inspired by two such clp-linked BGCs, desmethyl jomthonic acid C and tuscamide, reveals that both enhance ClpP activity. Extending our bioinformatically guided synthesis study to additional BGCs lacking nearby clp genes shows that ClpP activity enhancement correlated with antibacterial activity, with the strongest enhancers exhibiting narrow-spectrum antibiotic activity. These findings establish N-acylphenylalanine as a previously unrecognized but common natural motif for targeting ClpP, which should help guide the discovery of both natural and synthetic ClpP modulators for antibiotic and anticancer development. Resistance-CONKAT-seq offers a scalable method for exploring biosynthetic dark matter for metabolites with desired modes of action.}, }
@article {pmid41957864, year = {2026}, author = {Mawarda, PC and Speksnijder, A and Krijger, D and Berkhout, J and Hoogenboom, A and Duijker, DA and Khoiri, AN and Kraaijeveld, K and Stech, M and Wittink, F}, title = {Functional redundancy and stability support the resilience of the Evernia prunastri holobiont under urbanization.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00886-8}, pmid = {41957864}, issn = {2524-6372}, support = {NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.111//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; }, abstract = {BACKGROUND: Lichens are now recognized as holobionts comprising a mycobiont, photobiont, and diverse microbiomes, yet the functional roles of these additional microbial partners remain poorly characterized, especially under urbanization. Here, we used the epiphytic lichen Evernia prunastri from urban and natural areas to test the hypothesis that its resilience to urbanization is underpinned by functional stability and redundancy within its multi-kingdom consortium.<br><br>RESULTS: Using an integrated approach of amplicon and shotgun metagenomic sequencing, we found that the bacterial community structure and the functional potential of the mycobiont, bacteria, and fungi remained stable despite urbanization, highlighting stability and resistance to urban environmental stress. Furthermore, by focusing on symbiosis-related functions, we found that each partner shows tendencies toward certain roles, yet we discovered broad functional overlap, suggesting microbial contributions that buffer the symbiosis. Finally, we found that E. prunastri and its microbiome harbors diverse biosynthetic gene clusters with predicted ecological functions relevant for the symbiosis, spanning photoprotection, oxidative stress mitigation, nutrient acquisition, defense, and chemical communication.<br><br>CONCLUSIONS: Our study provides unprecedented genomic evidence that lichen resilience is an emergent property of the integrated holobiont, where functional complementarity and redundancy among diverse symbiotic partners maintain stability under urban environmental conditions.}, }
@article {pmid41957950, year = {2026}, author = {van der Heijden, M and Clubb, JHA and Erawijantari, PP and Ronkainen, A and Arias, V and Jirovec, E and Kudling, T and Pakola, SA and Ojala, N and Haybout, L and Basnet, S and Grönberg-Vähä-Koskela, S and Karoliina Raatikainen, S and Hemminki, O and Kanerva, A and Quixabeira, DCA and Cervera-Carrascon, V and Manuel Dos Santos, J and Lahti, L and Hemminki, A}, title = {Alistipes and Eggerthella shape the response to oncolytic adenovirus therapy in mice and humans through short-chain fatty acid metabolism.}, journal = {Oncoimmunology}, volume = {15}, number = {1}, pages = {2656514}, doi = {10.1080/2162402X.2026.2656514}, pmid = {41957950}, issn = {2162-402X}, mesh = {*Oncolytic Virotherapy/methods ; Humans ; Animals ; Mice ; *Adenoviridae/genetics ; *Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; *Oncolytic Viruses ; Feces/microbiology ; Female ; *Neoplasms/therapy/microbiology ; Male ; }, abstract = {Accumulating evidence implicates the microbiome as an important determinant of clinical outcomes in cancer therapies; however, the role of the microbiome in oncolytic virus therapy remains largely unexplored. We investigated the gut microbiome of cancer patients following treatment with the oncolytic adenovirus igrelimogene litadenorepvec (Ad5/3-E2F-d24-hTNF-IRES-hIL2; TILT-123). Baseline fecal samples from phase I clinical trials (NCT04695327 and NCT05271318) were analyzed using shotgun metagenomic sequencing and compared to treatment outcomes. A higher relative abundance of Alistipes was observed in patients with treatment benefit, while elevated Eggerthella was observed with reduced benefit. These associations were validated in a preclinical mouse model where administration of Alistipes shahii improved the efficacy of adenovirus therapy. In addition, enrichment analysis in patient samples showed a positive correlation between higher relative abundance of Alistipes and elevated short-chain fatty acids in both feces and serum, which in turn revealed higher circulating neutrophil counts. Finally, in a case study, we observed that adenovirus treatment resulted in increased Alistipes relative abundance and reduced Eggerthella relative abundance, indicating that adenovirus therapy may beneficially modulate the microbiome. Overall, our findings reveal a novel association between Alistipes, Eggerthella, and the therapeutic response to oncolytic adenovirus therapy, highlighting their potential as biomarkers or targets for microbiome-based interventions such as pre-, pro-, or postbiotics.}, }
@article {pmid41958036, year = {2026}, author = {Shin, H and Jeon, MK and Hur, HG}, title = {A Cautionary Case for Host Assignment Based on Broad Environmental blaOXA Carriers.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70327}, doi = {10.1111/1758-2229.70327}, pmid = {41958036}, issn = {1758-2229}, support = {RS-2023-NR076613//National Research Foundation of Korea/ ; }, mesh = {*beta-Lactamases/genetics ; Metagenomics/methods ; *Bacteria/genetics/drug effects/enzymology/isolation &amp; purification/classification ; Anti-Bacterial Agents/pharmacology ; Wastewater/microbiology ; Metagenome ; *Bacterial Proteins/genetics ; Microbiota ; Drug Resistance, Bacterial/genetics ; }, abstract = {Metagenomic analyses rely heavily on contig assembly and reference databases, which can introduce substantial bias when predicting the hosts of antibiotic resistance genes (ARGs) in complex environmental microbiomes. Reference-based metagenomic pipelines assign ARGs mostly to clinically important pathogens because publicly available genomic repositories are dominated by clinically relevant isolates. Motivated by this limitation, we investigated whether metagenomic inferences accurately reflect the true bacterial hosts of ARGs in a wastewater treatment plant, also integrating culture-based validation. Metagenomic screening suggested that ARGs (blaOXA) were primarily associated with clinical taxa. In contrast, culture-based screening identified a wider host distribution of blaOXA genes. Our results imply that environmental bacteria, rather than clinically important taxa, are also hosts of blaOXA genes. Phenotypic testing showed elevated cephalosporin minimal but no carbapenem resistance, consistent with the nature of carbapenem-hydrolysing class D β-lactamases. Our findings reveal that reliance on reference-based metagenomic host prediction can underestimate the diversity of environmental ARG reservoirs. This integrated approach highlights the need for cautious interpretation of metagenomic host assignments and the importance of coupling metagenomic pipelines with culture-dependent validation when assessing ARG ecology in the natural environments.}, }
@article {pmid41958322, year = {2026}, author = {Yang, D and Bao, C and Xia, Y and Ling, Y and Zhang, F and Ji, R and Zhong, J and Zhang, T and Tian, H and Xu, X and Sun, B}, title = {Insights Into Variations in the Gut Virome of Tibetan Macaques (Macaca thibetana) Across Wild, Captive, and Semi-Provisioned Environments.}, journal = {American journal of primatology}, volume = {88}, number = {4}, pages = {e70148}, doi = {10.1002/ajp.70148}, pmid = {41958322}, issn = {1098-2345}, support = {32171488//National Natural Science Foundation of China/ ; 32300400//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Macaca/virology/microbiology ; *Virome ; Tibet ; Male ; Animals, Zoo/virology ; Female ; }, abstract = {Viruses are integral components of the mammalian gut ecosystem, playing crucial roles in regulating the gut microbiome and maintaining host health. However, the impact of human activity on the gut virome of mammals remains poorly understood. This study investigated the gut viromes of Tibetan macaques (Macaca thibetana), a primate species endemic to China, under three distinct human-influenced environments (wild, semi-provisioned, and captive) using metagenomic sequencing. Our results revealed that semi-provisioned macaques supported the highest viral diversity, while captive and wild groups exhibited lower diversity, with distinct functional shifts among groups. Furthermore, the co-variation and highly coupled KEGG functional profiles between viral and bacterial communities suggest they function as an integrated synergistic network, where changes in one directly impact the metabolic output of the other. Co-occurrence network analysis further demonstrated that the virus-bacterium interaction network in the captive group was the most fragile, with a structure indicative of a high risk of micro-ecosystem imbalance. Microbial system imbalance is characterized by alterations in both community composition and function, resulting in diminished resilience and stability, which may ultimately compromise host intestinal health. Our results demonstrate that captivity and provisioning drive divergence in the Tibetan macaque gut virome. The fragile, skewed networks in captive individuals highlight a potential cost to microbial health, which may underlie broader health and adaptation risks such as heightened pathogen susceptibility and diminished capacity to cope with environmental perturbations. Thus, monitoring the virome offers a novel early-warning system, informing strategies to enhance welfare and conservation outcomes.}, }
@article {pmid41958469, year = {2026}, author = {Voigt, RM and Chaudhary, A and Naqib, A and Engen, PA and Adnan, D and Dhana, K and Green, SJ and Villanueva, M and Agarwal, P and Barnes, LL and Sacks, F and Keshavarzian, A}, title = {Weight loss and metabolic improvements dominate the microbiome response in the MIND diet intervention: a randomized controlled trial.}, journal = {Alzheimer's &amp; dementia (New York, N. Y.)}, volume = {12}, number = {2}, pages = {e70239}, pmid = {41958469}, issn = {2352-8737}, abstract = {INTRODUCTION: Observational studies link the MIND diet to reduced risk of Alzheimer's disease (AD) and slower cognitive decline. However, a recent randomized controlled trial found no differential cognitive benefit of the MIND diet over a control diet in the context of shared caloric restriction. Given that both groups achieved significant weight loss and metabolic improvements, this study aimed to disentangle the impact of the MIND diet and host metabolic improvements on the intestinal microbiome.<br><br>METHODS: A subset of participants (n = 213) from the MIND trial were analyzed in this study. Clinical data and stool samples were collected at baseline, Year 1, Year 2, and Year 3, and longitudinal changes in microbiome composition were assessed via shotgun metagenomics.<br><br>RESULTS: Both groups exhibited significant, transient microbiome remodeling at Year 1 (the period of most active weight loss). The control group demonstrated a broad range of altered metabolic pathways, whereas the MIND diet group showed only one, suggesting a functional buffering effect of the MIND diet. Prospective modeling independent of diet group revealed that a poorer cognitive trajectory was significantly associated with increased inositol degradation (PWY-7237) and purine nucleotide salvage (PWY66-409); conversely, a better cognitive trajectory was associated with increased degradation of deoxy sugars (FUC-RHAMCAT-PWY).<br><br>DISCUSSION: Caloric restriction, weight loss, and host metabolic improvement are the dominant factors shaping the intestinal microbiome, overshadowing diet-specific taxonomic shifts. The MIND diet appeared to provide a modest stabilizing effect on the microbial functional profile against perturbations during active weight loss; however, these dietary associations did not persist in covariate-adjusted models, suggesting that host metabolic improvements remained the primary driver of functional shifts.}, }
@article {pmid41958710, year = {2026}, author = {Nakamichi, K and Manandhar, A and Shrestha, S and Sundararajan, M and Poudel, MP and Karmacharya, BM and Bade, A and Banjara, P and Shrestha, A and Sandt, A and Turski, G and Buhr, ED and Chowdhary, A and Van Gelder, RN}, title = {Association of Seasonal Hyperacute Panuveitis Syndrome with S. pneumoniae Endophthalmitis.}, journal = {Ophthalmology science}, volume = {6}, number = {5}, pages = {101128}, pmid = {41958710}, issn = {2666-9145}, abstract = {PURPOSE: To identify potential infectious agents in cases of seasonal hyperacute panuveitis syndrome (SHAPU) from vitreous biopsies of patients with this disorder.<br><br>DESIGN: A retrospective cohort analysis.<br><br>SUBJECTS: Vitreous biopsies were obtained during the course of care from 53 subjects with SHAPU.<br><br>METHODS: DNA extraction and whole genome shotgun sequencing was performed using Oxford Nanopore long read sequencing. Sequences were matched against microbial and human databases. Visual outcomes at presentation and at 6 months were recorded.<br><br>MAIN OUTCOME MEASURES: Identification and characterization of metagenomic sequences in vitreous isolates from subjects with SHAPU.<br><br>RESULTS: Adequate DNA for sequencing was obtained from 32 SHAPU subjects. Fifteen samples yielded bacteria on culture, with 14 S. pneumoniae and 1 S. aureus isolate recovered. Bacterial DNA was detected by whole genome sequencing in 29 of 32 cases. S. pneumoniae was the predominant organism recovered. Bacterial genomic loads ranged up to 10&#x2009;000 bacteria/human cell, indicating active infection. No pathogens were detected in control samples. Reconstruction of bacterial genome was possible in 7 SHAPU cases and indicated diverse S. pneumoniae subtypes associated with individual cases. Sufficient DNA remained for analysis of torque teno virus by qualitative polymerase chain reaction in 17 cases, of which 13 were positive. Visual outcomes were mixed, with 7 patients having hypotonous eyes at 6 months, but 8 patients having better than 20/200 vision. No relationship could be discerned between presenting bacterial load and visual outcome.<br><br>CONCLUSIONS: The majority of SHAPU cases show molecular evidence for concurrent S. pneumoniae infection. Good visual results are possible in treating SHAPU as endophthalmitis.<br><br>FINANCIAL DISCLOSURES: The authors have no proprietary or commercial interest in any materials discussed in this article.}, }
@article {pmid41959051, year = {2026}, author = {Weng, Y and Moyne, O and Walker, C and Haddad, E and Lieng, C and Chin, L and Rahman, G and McDonald, D and Knight, R and Zengler, K}, title = {A Multi-Omics Processing Pipeline (MOPP) for Extracting Taxonomic and Functional Insights from Metaribosome Profiling (metaRibo-Seq) data.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.11.710980}, pmid = {41959051}, issn = {2692-8205}, abstract = {Metaribosome profiling (metaRibo-Seq) enables genome-wide measurement of translation across complex microbial communities by sequencing ribosome-protected mRNA fragments, but the short length of these footprints creates substantial nonspecific mapping against large reference genome collections, leading to spurious taxonomic and functional assignments. Here we present MOPP (Multi-Omics Processing Pipeline), a modular reference-based workflow that denoises metaRibo-Seq data by leveraging matched metagenomic coverage breadth to identify genomes likely to be truly present in a sample before aligning metatranslatomic and optional metatranscriptomic reads. MOPP generates taxon-by-gene count tables across genomic, transcriptional and translational layers, enabling integrated downstream analyses of microbial function. We evaluated MOPP using a defined 79-member synthetic human gut community profiled by metagenomics and metaRibo-Seq. Coverage breadth filtering markedly improved detection accuracy relative to a standard baseline workflow, with performance remaining robust across a broad intermediate threshold range and peaking at 92-95% coverage breadth. At a 92% threshold, MOPP reduced the number of distinct detected operational genomic units by 99.4% while retaining 87.8% of aligned metaRibo-Seq reads on average, and increased the F1 score from 0.02 to 0.61. Residual false positives were predominantly attributable to genomes with extremely high nucleotide similarity to true community members, whereas false negatives were enriched among low-abundance taxa, indicating that remaining errors are driven primarily by biological similarity and detection limits rather than widespread nonspecific mapping. Together, these results establish MOPP as a high-throughput workflow for robust processing of metaRibo-Seq in the context of matched metagenomics and position it as a scalable framework for integrated taxonomic and functional analysis of microbial communities across genomic, transcriptional and translational layers.}, }
@article {pmid41959121, year = {2026}, author = {Solomon, Z and Eno, M and Thompson, SC and Rager, SL and Jin, JC and Zeng, MY and Keerthy, D and Worgall, S and Johnson, EL and Heras, A}, title = {Increased S. epidermidis in the airway-gut microbiome of infants with bronchopulmonary dysplasia.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.03.715941}, pmid = {41959121}, issn = {2692-8205}, abstract = {RATIONALE: Bronchopulmonary dysplasia (BPD), the lung disease associated with premature birth, is a significant health problem, often with long-term respiratory consequences. Recent research has highlighted the potential role of the lung and gut microbiome in the development and progression of BPD, yet it is unclear what aspects of the microbiome may contribute to BPD susceptibility.<br><br>OBJECTIVES: To comprehensively characterize the lung and gut microbiomes of preterm infants and identify shared microbial taxa that are associated with BPD development.<br><br>METHODS: Tracheal aspirate and stool samples were collected from 39 premature infants over the first month of life. To assess the taxonomic microbial composition of the lung and gut, samples were analyzed using shotgun metagenomic sequencing. BPD classification was determined using the National Institute of Child Health and Human Development severity-based definition at 36 weeks postmenstrual age.<br><br>MEASUREMENTS AND MAIN RESULTS: Microbial communities of the lung and gut were significantly different between infants who went on to develop BPD and those who did not, with an enrichment of skin-associated microbial genera such as Staphylococcus, Corynebacterium, and Cutibacterium in infants who developed BPD. Specifically, Staphylococcus epidermidis was enriched in premature infants who developed BPD and was the most prominent species shared between lung and gut communities. Temporal changes in gut microbial communities co-occurred with feeding practices and antibiotic exposure, suggesting an influence of external factors on microbiome composition.<br><br>CONCLUSIONS: Our findings provide evidence that certain microbial colonization patterns among premature infants are closely associated with the pathogenesis and progression of BPD.}, }
@article {pmid41959210, year = {2026}, author = {Muller, E and Baum, S and Borenstein, E}, title = {MAAMOUL: Metabolic network-based discovery of microbiome-metabolome shifts in disease.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.27.714614}, pmid = {41959210}, issn = {2692-8205}, abstract = {MOTIVATION: A central goal in human gut microbiome research is to identify disease-associated functional shifts, an objective increasingly pursued through metagenomic and metabolomic assays. However, common differential abundance analyses of genes or metabolites often yield long and difficult-to-interpret feature lists. Aggregating features into predefined pathways can improve interpretability but relies on fixed pathway boundaries that may not reflect context-specific functional changes. Moreover, even when paired metagenomic-metabolomic data are available, they are often analyzed separately or linked only through simple statistical associations.<br><br>RESULTS: We introduce MAAMOUL, a knowledge-based computational framework that integrates metagenomic and metabolomic data to identify disease-associated, data-driven microbial metabolic modules. Leveraging prior knowledge of bacterial metabolism, MAAMOUL maps disease-association scores onto a global microbiome-wide metabolic network and identifies custom modules enriched for altered genes and metabolites. Applying MAAMOUL to inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) datasets revealed significant disease-associated modules not detected by conventional pathway-level analysis. In IBD, modules reflected disrupted sulfur and aromatic amino acid metabolism and enhanced microbial nucleotide salvage, whereas in IBS they linked purine and nicotinate/nicotinamide metabolism. These results demonstrate that network-guided multi-omic integration can uncover coherent functional shifts in the gut microbiome overlooked by single-omic or purely statistical approaches.<br><br>AVAILABILITY: MAAMOUL is available as an R package at https://github.com/borenstein-lab/MAAMOUL .}, }
@article {pmid41959308, year = {2026}, author = {Sakdinan, B and Sinha, A and Qadri, F and Khan, AI and Nelson, EJ and Shapiro, BJ}, title = {Species-specific prophage induction by ciprofloxacin in human gut metagenomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.11.711154}, pmid = {41959308}, issn = {2692-8205}, abstract = {UNLABELLED: Antibiotics are known to trigger prophage induction in controlled laboratory settings, but it remains unclear whether this also occurs within microbiomes in nature. Current methods investigating the link between antibiotics and prophage induction within the human gut rely on in vitro culturing of human gut bacterial isolates. Using a metagenomic approach, we aimed to measure prophage induction and whether it is associated with antibiotic exposure. Across two independent human cohorts, we compared prophage to bacterial host read depth ratios (P:H) across known or measured antibiotic exposures. We found that induction is not broadly associated with antibiotic exposures at the level of the overall microbiome, but that ciprofloxacin increases P:H ratios in specific bacterial species. We documented heterogeneous trajectories of P:H ratios over the course of antibiotic exposure, sometimes increasing and remaining high, or returning to baseline. This study complements experimental models by providing in vivo evidence of induction in the human gut.<br><br>IMPORTANCE: Bacteriophages are viruses that infect a bacterial host. The lytic and lysogenic cycles are the two classic outcomes of phage infection. In the lytic cycle, the phage immediately replicates and lyses its host to release new viral particles. In the lysogenic cycle, the phage, now called a prophage, integrates its genome into that of its host without killing it. Prophages can switch to the lytic cycle in a process called induction, in which the viral genome is replicated, the host cell is lysed, and viral particles are released. The most immediate consequence of induction is host cell death which can impact bacterial populations and communities. Since prophages are mobile genetic elements that can move between bacteria, they are also an important vehicle for horizontal gene transfer. While induction has been well studied in vitro , whether and how induction occurs within the complex microbial ecosystem in humans is less well characterized. Understanding prophage induction in vivo is therefore critical in corroborating in vitro observations.}, }
@article {pmid41959338, year = {2026}, author = {Kramer, AM and Zhang, A and Ayala, N and de Sanctis, B and Karim, L and Hinrichs, AS and Walia, S and Turakhia, Y and Corbett-Detig, R}, title = {Panmap: Scalable phylogeny-guided alignment, genotyping, and placement on pangenomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.29.711974}, pmid = {41959338}, issn = {2692-8205}, abstract = {Pangenomes capture population-level variation but remain computationally challenging at scale. We present Panmap, a tool that leverages evolutionary structure to place, align, and genotype sequencing reads against mutation-annotated pangenomes containing up to millions of genomes. Panmap introduces a phylogenetically compressed k -mer index that stores only sequence differences along branches, enabling efficient comparison of reads to both sampled genomes and inferred ancestors. This approach reduces index size by up to 600-fold and construction time by over three orders of magnitude relative to existing tools. Panmap places a 100× coverage SARS-CoV-2 sample onto 20,000 genomes in 0.4 seconds and onto 8 million genomes in under two minutes. Furthermore, it enables accurate haplotype identification and abundance estimation in metagenomic samples and sensitive placement of ancient environmental DNA without prior alignment. Our approach makes large-scale pangenomes directly amenable to read mapping, genome assembly, alignment-free phylogenetic placement, and metagenomic analysis.}, }
@article {pmid41959403, year = {2026}, author = {Maier, J and Gin, C and Rabasco, J and Spencer, W and Bass, A and Duerkop, BA and Callahan, B and Kleiner, M}, title = {TrIdent - An R package to automate transductomics analysis of virus-like particle mediated DNA mobilization.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.31.715651}, pmid = {41959403}, issn = {2692-8205}, abstract = {BACKGROUND: Transduction is a form of horizontal gene transfer in which bacterial DNA is packaged and transferred by virus-like particles (VLPs). Transductomics is a sequencing-based method used to detect DNA carried by VLPs. During transductomics analysis, reads from a sample's ultra-purified VLPs are mapped to metagenomic contigs assembled from the same sample's whole-community. The read mapping produces coverage patterns that require a time-consuming manual inspection and classification process which makes the method's use unfeasible for datasets with many samples.<br><br>RESULTS: We developed a novel algorithm, TrIdent (Transduction Identification), that uses pattern-matching to automate the transductomics data analysis and that is available as an R package (https://jlmaier12.github.io/TrIdent/). There is no software equivalent to TrIdent so we compared TrIdent's classifications of transductomics datasets to classifications made by human classifiers. TrIdent's classifications were generally comparable to the manual classifications on a previously generated, manually classified transductomics dataset. When applied to newly generated transductomics data from the murine microbiota, TrIdent agreed with two independent human classifiers as much as the two independent human classifications agreed with each other. TrIdent classified transductomics datasets in a fraction of the time needed by human classifiers, and the classifications produced by TrIdent are fully reproducible. We used TrIdent to explore three murine gut transductomes and found that bacterial DNA associated with the Oscillospiraceae and Turicibacteraceae families was highly enriched in the DNA packaged by VLPs as compared to the whole community metagenomes.<br><br>CONCLUSIONS: The TrIdent software is a more accessible, more efficient, and more reproducible alternative to the manual inspection of read coverage patterns previously required for transductomics data analysis. To demonstrate the application of TrIdent, we analyzed transductomics datasets from murine fecal pellets and showed that specific low abundance bacterial families appear to be heavily involved in transduction.}, }
@article {pmid41959459, year = {2026}, author = {Kim, M and Ardell, SM and Kryazhimskiy, S}, title = {Module-Selection Balance in the Evolution of Modular Organisms.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.04.01.715873}, pmid = {41959459}, issn = {2692-8205}, abstract = {The architecture of the genotype-phenotype-fitness map (GPFM) is a key determinant of evolutionary dynamics. One salient feature of biological GPFMs is variational modularity, where each mutation affects only a small subset of functional traits. Variational modularity may constrain the dynamics of trait evolution, but these constraints are not well understood. Here, we use several extensions of the Fisher's geometric model with two functional traits to investigate these constrains. We find that on GPFMs with universal pleiotropy, populations evolve along the fitness gradient, which implies that the trait under stronger selection is optimized exponentially faster than the trait under weaker selection. In contrast, on modular GPFMs, populations approach a quasi-steady state that we term a "module-selection balance" where both traits improve at the same rate and their ratio remains constant. We demonstrate that the existence of a module-selection balance is robust with respect to the details of evolutionary dynamics and GPFMs themselves, as long as they are variationally modular. Our theory predicts that variationally modular organisms should exhibit stereotypical bi-phasic dynamics of genome evolution, especially in the strong clonal interference regime, and we find support for this prediction in metagenomic data from Lenski's long-term evolution experiment in bacterium Escherichia coli . We propose that module-selection balance is an inherent feature of variationally modular GPFMs, which imposes an important constraint on long-term trait evolution.}, }
@article {pmid41959466, year = {2026}, author = {Sapoval, N and Treangen, TJ and Nakhleh, L}, title = {Leveraging spectrum of graph sheaf Laplacian as a genome-architecture-aware measure of microbiome diversity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.10.710879}, pmid = {41959466}, issn = {2692-8205}, abstract = {MOTIVATION: Measures of microbial diversity that can be derived directly from metagenomic sequencing data offer a valuable summary view of the underlying complex systems. Prior work has shown that both taxonomic composition and abundances that are captured by standard diversity measures (e.g., Shannon entropy), and structural variation within the metagenome due to gene duplications, losses and horizontal transfers (HGT), can correlate with the host's health. However, there are no diversity measures available that simultaneously account for the genome architecture and taxonomic composition within the sample. Thus, in this work we propose the spectral energy of a graph sheaf Laplacian as such a measure, and justify its applicability through a simulation study and analysis of biological data.<br><br>RESULTS: First, we describe a theoretical framework that allows us to combine the features of genome graphs with the taxonomic data. Then, we explore the sensitivity of the proposed diversity measure to genome rearrangements and HGT events in a simulation study. Finally, we explore applicability of our proposed measure to characterization of diversity of human gut metagenomes. We find our proposed measure to offer better discrimination between healthy controls and inflammatory bowel disease (IBD) patients' samples (n = 403) in the cohorts analyzed.<br><br>https://github.com/nsapoval/bd-gsl.}, }
@article {pmid41959535, year = {2026}, author = {Xue, J and Allaband, C and Zuffa, S and Zhou, D and Poulsen, O and Meadows, J and McDonald, D and Ambre, M and Ackermann, G and Birmingham, A and Cao, J and Mohanty, I and Dorrestein, PC and Knight, R and Haddad, GG}, title = {Farnesoid X receptor-dependent microbiome-bile acid signaling mediates obstructive sleep apnea-induced atherosclerosis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.31.715631}, pmid = {41959535}, issn = {2692-8205}, abstract = {Intermittent hypoxia and hypercapnia (IHC), a hallmark of obstructive sleep apnea (OSA), accelerates atherosclerosis, yet the underlying mechanisms remain unclear. The gut microbiota and metabolites, specifically bile acids, change with IHC and thus the bile acid receptor farnesoid X receptor (FXR) might mediate IHC-induced atherosclerosis. In this study, ApoE [-/-] and ApoE [-/-] FXR [-/-] mice were exposed to IHC or room air and fed with a high-fat, high-cholesterol diet for 10 weeks. Markers of atherosclerosis, fecal microbiome, and metabolome were then examined via Sudan IV staining, absolute abundance shotgun metagenomics, and untargeted liquid chromatography tandem mass spectrometry (LC-MS/MS). IHC markedly increased aortic atherosclerosis in ApoE [-/-] mice, an increase that was abolished by FXR deficiency. In addition, IHC reshaped gut microbial composition, promoting enrichment of bile acid-modifying taxa and increasing levels of microbial hydroxysteroid dehydrogenase (hsdh). The bile acid pool was also remodeled and associated with aortic atherosclerosis via FXR-dependent metabolic signals in ApoE [-/-] mice. Knockout of FXR disrupted microbiome shift under IHC and uncoupled microbial bile acid metabolism from vascular lesion development, thereby protecting against aortic atherosclerosis. These findings show that FXR has a central role in linking IHC, microbial bile acid metabolism, and cardiovascular pathology.}, }
@article {pmid41959658, year = {2026}, author = {Funauchi, A and Hashimoto, K and Fukushima, K and Matsumoto, Y and Hamada, N and Hara, R and Niitsu, T and Nii, T and Matsuki, T and Tsujino, K and Miki, K and Kumanogoh, A and Nakamura, S and Kida, H}, title = {Gastric Aspirate Isolate Demonstrates Strain-Level Concordance With Sputum Isolate in Nontuberculous Mycobacterial Pulmonary Disease.}, journal = {Open forum infectious diseases}, volume = {13}, number = {4}, pages = {ofag175}, pmid = {41959658}, issn = {2328-8957}, abstract = {The nontuberculous mycobacteria (NTM) isolated from gastric aspirate have demonstrated >85% strain concordance with those from the sputum, suggesting that they originate from the lungs rather than the environment. Gastric aspirate, although not yet internationally recognized, may be a useful supplementary specimen for diagnosing NTM pulmonary disease.}, }
@article {pmid41960427, year = {2026}, author = {Nuanmuang, N and Leekitcharoenphon, P and Njage, PMK and Jirakkakul, J and Dulsawat, S and Tachaleat, A and Svendsen, CA and Møller, FD and Otani, S and Cheevadhanarak, S and Aarestrup, FM}, title = {Comparative resistome from toilet waste in three different income areas, Bangkok, Thailand.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1790551}, pmid = {41960427}, issn = {1664-302X}, abstract = {Antimicrobial resistance (AMR) is a significant public health threat and is associated with millions of deaths worldwide each year. Besides antimicrobial usage, different socioeconomic factors have recently gained attention as being associated with increased AMR. Bangkok, a city with diverse income levels, provided a unique setting for this study, which aimed to explore the possible within-city association between income-level areas and the diversity and abundance of AMR. Twenty-seven toilet waste samples were collected from nine different sites (low-, middle-, and high-income) during March-April 2023, and metagenomic sequencing was performed. The sequencing data were quality checked, and sequences that passed quality control were mapped to antimicrobial, metal, and disinfectant resistance gene databases as well as bacterial taxonomy databases. We observed higher antibiotic resistance genes (ARGs), metal resistance, and disinfectant resistance abundance (fragments per kilobase per million mapped reads, FPKM) in low-income groups compared to middle- and high-income groups. This included both acquired ARGs and presumed intrinsic ARGs, including genes associated with completely novel antibiotics that have so far only been identified through functional cloning. Significant differences in individual ARGs were also observed between sites. Our study highlights the relative abundance of ARGs across different income groups, emphasizing how the development of resistance mechanisms revealed through metagenomic analysis can serve as a valuable tool for city-level surveillance of AMR from toilet waste, particularly in low-income settings.}, }
@article {pmid41960429, year = {2026}, author = {Freund, L and Topacio, TM and Miao, Y and Porter, WC and Swenson, M and Maltz, M and Botthoff, J and Aronson, EL}, title = {Weather conditions structure the taxonomic and functional diversity of the aeolian dust microbiome.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1691133}, pmid = {41960429}, issn = {1664-302X}, abstract = {INTRODUCTION: The aeolian dust microbiome is composed of uniquely adapted microorganisms that can withstand the harsh conditions of the atmosphere. Specific microbial taxa and survival strategies have been observed in dust microbiomes from around the world, yet the environmental processes that select for microbial composition and function are poorly understood.<br><br>METHODS: Here we explore the taxonomic and functional diversity of the aeolian dust microbiome from sites around the Salton Sea, a hypersaline lake in Southern California, and how dust sources and weather influenced the microbiome. Dust samples were collected from four locations around the Salton Sea in the summer and fall of 2020 and 2021, and 16S (V3-V4) rRNA amplicon sequencing and shotgun metagenomic sequencing was used to characterize the aeolian dust microbiome.<br><br>RESULTS: We observed significant differences in microbial composition between sites, and we were able to identify 13 microbial genera that were members of the core dust microbiome across samples. We also found that genes involved in sporulation, UV-radiation resistance, thermal resistance, osmotic stress resistance, quorum sensing, and antibiotic resistance were shared across the aeolian dust metagenomes. Lastly, local wind conditions and estimated dust source surface categories were significant predictors of the microbial adaptations we found in the aeolian dust metagenomes.<br><br>DISCUSSION: Our results demonstrate the ability of airborne dust microorganisms to readily adapt to their harsh environment and highlight the survival mechanisms that allow them to disperse across broad distances, thus posing a potential health risk to exposed communities.}, }
@article {pmid41960438, year = {2026}, author = {Zhao, Z and Xiang, L and Liu, Y and Xu, S and Chen, Y and Yu, M}, title = {Rare fungal keratitis caused by plant pathogens: report of two cases and review of the literature.}, journal = {Frontiers in fungal biology}, volume = {7}, number = {}, pages = {1785252}, pmid = {41960438}, issn = {2673-6128}, abstract = {Macrophomina phaseolina and Colletotrichum fructicola are notable plant pathogens, yet cases of keratitis from these fungi are rarely reported. Limited awareness of this keratitis etiology among ophthalmic professionals reduces the likelihood of accurate diagnosis and timely treatment. This report aims to improve the understanding of these rare infections in eye care. We present two cases of keratitis: one caused by M. phaseolina and another by C. fructicola, both of whom experienced a complicated treatment course. Traditional fungal exams yielded negative results, which limited disease identification and focused therapy. To determine the cause, we used metagenomic next-generation sequencing (mNGS) on clinical samples obtained from corneal scrapings. The mNGS report was received during therapy and quickly identified the pathogen. Based on this, we looked for treatment regimens for this kind of infection in previous literature, altered and implemented appropriate antifungal drug therapy, and the patient's condition improved. We review the literature from 1970 to 2025 on M. phaseolina and Colletotrichum spp. keratitis. We identified 10 cases of M. phaseolina keratitis from four studies and 72 cases of Colletotrichum spp. keratitis, including five of C. fructicola, in 43 articles. Misdiagnosis was common due to limited clinical and microbiologic suspicion. The rise of infections by rare pathogens highlights diagnostic challenges. Traditional methods often delay accurate diagnosis, while mNGS enables rapid identification of pathogen, crucial for effective treatment and vision preservation.}, }
@article {pmid41960830, year = {2026}, author = {Sun, S and Zhou, Y and Deng, F and Meng, Y and Zhu, X and Wang, H and Wei, D}, title = {Engineering an l-Threonine Aldolase from Staphylococcus epidermidis for Enhanced Diastereoselectivity in the Synthesis of a Chloramphenicol Intermediate.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.6c01578}, pmid = {41960830}, issn = {1520-5118}, abstract = {l-Threonine aldolase (LTA) is an attractive biocatalyst for the synthesis of l-syn-p-nitrophenylserine (l-syn-1b), a key intermediate in chloramphenicol synthesis. However, low diastereoselectivity has limited its broader application in stereospecific C-C bond formation. To overcome this limitation, a metagenomic library constructed from non-natural amino acid-enriched environments was screened, leading to the identification of an LTA from Staphylococcus epidermidis (SeLTA) that exhibits the highest diastereoselectivity toward l-syn-1b among naturally occurring LTAs reported to date. To further enhance its diastereoselectivity, structural comparison, alanine scanning, and tunnel analysis were employed to identify hotspots that modulate the diastereoselectivity of SeLTA. Subsequent saturation mutagenesis and iterative saturation mutagenesis at these positions yielded the quadruple variant A176G/Y202S/N7C/F129E (Mut4), which increased the diastereoselectivity from 32.5%syn to 92.7%syn. Furthermore, Mut4 exhibits markedly improved diastereoselectivity toward para- and meta-substituted benzaldehyde derivatives. Molecular dynamics (MD) simulations further elucidated the molecular basis underlying the enhanced diastereoselectivity of Mut4. This study provides a potential biocatalyst for the sustainable and efficient synthesis of a chloramphenicol intermediate.}, }
@article {pmid41961352, year = {2026}, author = {Cao, XY and Tian, JJ and Zhang, W and Chen, CL and Ma, H}, title = {Puerarin Alleviates Depression via Integrated Regulation of TLR4/MyD88/NF-κB Signaling and Gut Microbiota-Metabolic Axis.}, journal = {Neurochemical research}, volume = {51}, number = {2}, pages = {}, pmid = {41961352}, issn = {1573-6903}, }
@article {pmid41961522, year = {2026}, author = {Song, W and Li, M and Yue, X and Meng, Y and Xie, Y and Zhang, Y and Hu, Y and Zheng, Y and Yue, X}, title = {Microbial succession and metabolic mechanisms driving flavor evolution in Northeast Chinese dajiang: a comprehensive review integrating insights from East Asian fermented soybean pastes.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-22}, doi = {10.1080/10408398.2026.2644602}, pmid = {41961522}, issn = {1549-7852}, abstract = {This review systematically explores the spatiotemporal microbial succession and flavor evolution during the fermentation of northeast Chinese soybean paste (dajiang), with a focus on the jiangpei (solid-state starter) and jianglao (brine fermentation) stages. By integrating metagenomic, metabolomic, and sensory data, this review synthesizes evidence linking microbial community dynamics-featuring Lactobacillus spp., Zygosaccharomyces rouxii, and Aspergillus oryzae-to the biosynthesis of key flavor compounds. These include umami amino acids (e.g., glutamic acid, 1.5-2.0 g/kg), fruity esters (e.g., ethyl acetate, 124.67 μg/kg), and phenolic antioxidants. Cross-feeding interactions (e.g., yeast utilization of lactic acid for ester synthesis) and environmental stressors (12%-18% NaCl, 25 °C-30 °C) are shown to enhance flavor complexity by modulating metabolic pathways like amino acid degradation and lipid β-oxidation. Unlike prior studies focusing on fragmented fermentation stages, this review systematically addresses the full fermentation continuum, highlighting how aerobic-to-anaerobic transitions drive functional metabolite accumulation. The review concludes by outlining a roadmap to modernize dajiang production through standardized quality control, precision flavor modulation, and traditional process optimization, enabled by culturomics/MAGs, multi-omics integration, and AI-assisted fermentation monitoring and control.}, }
@article {pmid41961886, year = {2026}, author = {Cosma, BM and Pillay, S and Calderón-Franco, D and Abeel, T}, title = {Predicted meta-omics: A potential solution to multi-omics data scarcity in microbiome studies.}, journal = {PloS one}, volume = {21}, number = {4}, pages = {e0345919}, doi = {10.1371/journal.pone.0345919}, pmid = {41961886}, issn = {1932-6203}, mesh = {Humans ; *Metagenomics/methods ; Machine Learning ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Inflammatory Bowel Diseases/microbiology ; Neural Networks, Computer ; Multiomics ; }, abstract = {Imbalances in the gut microbiome have been linked to conditions such as inflammatory bowel disease, diabetes, and cancer. While metagenomics and amplicon sequencing are commonly used to study the microbiome, they do not capture all layers of microbial functions. Other meta-omics data can provide more insights, but these are more costly and laborious to procure. The growing availability of paired meta-omics data offers an opportunity to develop machine learning models that can infer connections between metagenomics data and other forms of meta-omics data, enabling the prediction of these other forms of meta-omics data from metagenomics. We evaluated several machine learning models for predicting meta-omics features from various meta-omics inputs. Simpler architectures such as elastic net regression and random forests generated reliable predictions of transcript and metabolite abundances, with correlations of up to 0.77 and 0.74, respectively, but predicting protein profiles was more challenging. We also identified a core set of well-predicted features for each meta-omics output type, and showed that multi-output regression neural networks performed similarly when trained using fewer output features. Lastly, our experiments demonstrated that predicted features can be used for the downstream task of inflammatory bowel disease classification, with performance comparable to that of experimental data.}, }
@article {pmid41962241, year = {2026}, author = {Lin, Z and Pang, S and Xu, T and Zhou, YL and Zhang, C and Qian, PY and Zhang, S}, title = {Marine plastisphere expands the ecological niche and evolutionary dynamics of nrfA-dependent nitrite ammonifying bacteria.}, journal = {Water research}, volume = {299}, number = {}, pages = {125879}, doi = {10.1016/j.watres.2026.125879}, pmid = {41962241}, issn = {1879-2448}, abstract = {The marine plastisphere affects nitrogen cycling processes, but its role in nrfA-dependent nitrite ammonification, a critical phase of dissimilatory nitrate reduction to ammonium (DNRA) with important implications for nitrogen retention and greenhouse gas dynamics, remains unexplored. In this study, we analyzed 269 plastisphere metagenomes and eight metatranscriptomes from global public datasets. The plastisphere contained elevated nrfA levels compared to seawater, and nrfA transcripts were consistently detected. A total of 285 putative nrfA-dependent nitrite ammonifying bacteria were identified, including 156 novel genera. Most plastisphere MAGs overlapped with other examined marine biofilms, whereas 109 MAGs were uniquely detected in plastisphere samples within the analyzed comparative datasets. Functional studies revealed diverse electron-donor utilization strategies supporting DNRA in plastisphere microorganisms. Evolutionary analyses showed that nrfA genes were distributed across different phyla through horizontal gene transfer, whereas purifying selection limited sequence divergence. These findings highlight a previously underappreciated genetic and transcriptional potential for DNRA in plastic-associated biofilms at the particle scale, with implications for nitrogen retention within plastisphere microhabitats.}, }
@article {pmid41962374, year = {2026}, author = {Zhou, LT and He, DH and Li, J and He, RX and Ma, SJ and Gong, GY and Zou, XS and Li, S and Zhou, YF and Hu, WJ}, title = {Dynamics and drivers of last-resort antibiotic resistance genes during pilot-scale aerobic fermentation of municipal sludge and subsequent bok choy pot trials.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {141891}, doi = {10.1016/j.jhazmat.2026.141891}, pmid = {41962374}, issn = {1873-3336}, abstract = {Sludge from wastewater treatment plants may exacerbate environmental dissemination of last-resort antibiotic resistance genes (LARGs) when applied to land. However, LARG behavior during aerobic sludge fermentation and subsequent soil-plant transfer remains poorly understood. This study specifically targeted LARGs beyond common ARGs and coupled pilot-scale fermentation with bok choy cultivation to resolve their dynamics and compartmentalization. Using metagenomic sequencing with correlation and network analyses, we identified environmental drivers and inferred potential hosts. Optimized fermentation conditions (maintaining >50 °C for 10 days) reduced moisture to 30%, lowered the C/N ratio to 24.7, and achieved germination indices of 85%-90%. Fermentation promoted microbial succession, enhanced metal passivation and organic matter humification, and reduced antibiotic and ARG abundance, with total antibiotic degradation reaching 49.19% in the thermophilic phase. LARG abundance increased by 47.6% in the mesophilic phase due to cell lysis and MGE release, then declined by 9.7% in the thermophilic phase and 47.8% during maturation. Although fermentation stabilized sludge, specific genes (e.g., KPC-22 and poxtA) rebounded, driven by horizontal gene transfer and physicochemical changes. Subsequent planting demonstrated that a 10%-15% sludge application rate optimized bok choy agronomic performance and improved soil antibiotic degradation. Across soil, rhizosphere, and phyllosphere, LARGs exhibited distinct compartmentalization patterns. Network analysis further indicated that LARGs were primarily associated with indigenous soil taxa (e.g., Streptomyces) rather than potential pathogens (e.g., Klebsiella). Consequently, the impact on the core transmission network was minor, suggesting that appropriately fermented sludge application presents a controllable ecological risk and supports its safe utilization under the studied conditions.}, }
@article {pmid41963033, year = {2026}, author = {Tzora, A and Nikolaou, K and Lagkouvardos, I and Voidarou, C and Intze, E and Fotou, K and Skoufos, I}, title = {A novel classification system based on cheese microbial profiles for the assessment of cheese typicity.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105049}, doi = {10.1016/j.fm.2026.105049}, pmid = {41963033}, issn = {1095-9998}, mesh = {*Cheese/microbiology/classification/analysis ; *Microbiota ; *Bacteria/classification/genetics/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; *Food Microbiology ; High-Throughput Nucleotide Sequencing ; Animals ; Milk/microbiology ; Phylogeny ; Greece ; }, abstract = {Cheese typicity reflects the unique characteristics influenced by raw ingredients, traditional tools employed, environmental and production conditions, the cheese-making process and the specific geographical region of origin. In the present study, the typicity of Greek cheeses was studied and compared with cheeses from various countries worldwide, based on microbiota profiles. The dataset included publicly available and 63 newly generated sequences, totaling 322 cheese samples, derived from seven different countries. The analysis incorporated next generation sequencing (NGS) technology, with Illumina sequencing of the 16S rRNA gene hypervariable regions V3-V4, followed by a standardized analytical pipeline process. Through de novo clustering, four main Cheese Microbial Profiles (CMP) - clusters and nine sub-clusters were identified. Core microbiota was identified within sub-clusters. The dominant bacterial genera were Lactobacillus in CMP1, Lactococcus in CMP2 and CMP3, and Streptococcus in CMP4. Distinct cheese types exhibited a statistically significant tendency for specific microbial profiles within clusters. However, no clear signatures of geographic origin were detected, nor were associations found between microbial communities and cheese production parameters such as cheese type, milk source, starter culture addition or milk pasteurization. Additionally, we developed a novel model capable of accurately classifying new cheese samples into clusters and sub-clusters, based on their bacterial ecological community structure. Our findings could support future initiatives, especially when combined with multi-omic approaches, to better identify cheese typicity, verify authenticity, potentially trace geographical origin, and ultimately enhance the quality and safety of cheeses.}, }
@article {pmid41963036, year = {2026}, author = {Hou, J and Li, Y and Liu, M and Li, L and Chen, H and An, Y and Xu, H and Yao, Y}, title = {Antibiotic resistance genes (ARGs) in rice: Source attribution and putative mobility patterns.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105055}, doi = {10.1016/j.fm.2026.105055}, pmid = {41963036}, issn = {1095-9998}, mesh = {*Oryza/microbiology/genetics ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Phylogeny ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Seeds/microbiology ; Microbiota ; Metagenome ; *Genes, Bacterial ; *Drug Resistance, Microbial/genetics ; }, abstract = {Rice grains can harbor antibiotic resistance genes (ARGs), yet the relative roles of seed-associated and environmental reservoirs remain unclear. We used shotgun metagenomics on rice tissues (grain, seed, leaf, stem, root) and surrounding matrices (bulk/rhizosphere soil, irrigation water, rainwater, PM10). In total, 1019 ARG subtypes were detected; grains contained 395, the largely overlapping with seeds (290) and environmental samples (322). FEAST source tracking revealed contrasting attribution patterns: seed sources explained nearly half of the grain microbiome (average contribution 49.49%) versus 8.45% from environmental sources, whereas environmental sources contributed more strongly to the grain resistome (20.68%). 747 metagenome-assembled genomes (MAGs) were reconstructed, including 275 ARG-carrying MAGs. Phylogenetic screening identified 39 near-identical (≥99%) ARG linkages across samples, operationally classified by host consistency (same vs different predicted hosts) into 11 putative VGT-like and 28 putative HGT-like patterns. For example, blaGOB-50 in grains and seeds shared near-identical sequences within Elizabethkingia anopheles (VGT-like), while APH(9)-Ic in grains (Burkholderia) matched PM10 (Comamonas), consistent with an HGT-like linkage. In selected cases, ARG-MGE co-localization (e.g., umuC, cca) further supported mobility interpretations. Together, these results indicate seedborne signatures in the grain microbiome but comparatively stronger environmental association for the grain resistome, informing efforts to trace ARG reservoirs in rice systems.}, }
@article {pmid41963043, year = {2026}, author = {Liu, G and Zhong, J and Yang, D and Zeng, Y and Cao, R and He, S and Bai, W and Qu, C}, title = {The mechanisms underlying ester enhancement and higher alcohol reduction in Chi-flavor base liquor brewing via Limosilactobacillus fermentum fortification: A multi-omics investigation.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105070}, doi = {10.1016/j.fm.2026.105070}, pmid = {41963043}, issn = {1095-9998}, mesh = {Fermentation ; *Limosilactobacillus fermentum/metabolism/genetics/isolation &amp; purification ; *Alcoholic Beverages/microbiology/analysis ; *Esters/metabolism/analysis ; *Flavoring Agents/metabolism/analysis ; Saccharomyces cerevisiae/metabolism/genetics ; Acetates/metabolism/analysis ; *Alcohols/metabolism/analysis ; Ethanol/metabolism/analysis ; Lactates/metabolism/analysis ; Taste ; Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Multiomics ; }, abstract = {Chi-flavor Baijiu is a unique liquor in the Pearl River Delta region. Ethyl lactate is the key flavor with low content in base liquor, affecting qualities of Chi-flavor Baijiu. To address this issue, Limosilactobacillus fermentum Y8 (Y8) isolated from sour mash, was used to fortify the fermentation. Results showed that contents of ethyl acetate and ethyl lactate reached to 663.55 mg/L and 604.25 mg/L, increased by 334.97% and 331.26%, respectively, with that of ethanol unchanged and main higher alcohols reduced significantly. Metagenomic analysis revealed that Lactiplantibacillus, Limosilactobacillus, Pediococcus, Levilactobacillus, and Lactobacillus were the top five abundance species. Metatranscriptomic data indicated that Saccharomyces cerevisiae, Lactobacillus brevis and L. fermentum were the dominant active species, the succession of which was significantly influenced by Y8 addition. Correlation analysis revealed that L. fermentum was positively related to reducing sugar, total acid and esters, while negatively to higher alcohols. Based on metatranscriptomic analysis, a new pathway for lactate synthesis from lactaldehyde was found with Y8 fortification, along with acyl-CoA thioester hydrolase gene ybgC upregulated significantly, providing more precursors for ester synthesis. At the same time, enzymes related to ester synthesis were upregulated with that of higher alcohols downregulated. Collectively, Y8 fortification could affect the succession of microbiota and promote the synthesis of ester precursors and ester synthesis pathway, and decrease higher alcohols synthesis pathway. This study not only provides a strain to fortify Chi-Flavor Baijiu brewing with improved qualities but also reveals mechanisms of flavor modulation and microbial community succession during the brewing process.}, }
@article {pmid41963048, year = {2026}, author = {Diaz, M and Wilson, N and Ponsero, AJ and Seecharran, T and Som, N and Al-Khanaq, H and Gutiérrez, AV and Gilmour, M}, title = {Microbial community succession and functional potential during processing and storage of cooked ham assessed by shotgun metagenomics.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105075}, doi = {10.1016/j.fm.2026.105075}, pmid = {41963048}, issn = {1095-9998}, mesh = {Metagenomics ; *Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Animals ; Swine ; Food Storage ; *Meat Products/microbiology/analysis ; Cooking ; *Microbiota ; Food Microbiology ; Food Handling ; }, abstract = {Wet-cured ham is a ready-to-eat meat product in which microbial communities contribute to desired product characteristics related to product quality, while also presenting as a spoilage risk. Microorganisms are introduced early during the live brining of raw meat, with the brine representing a long-standing, complex and active culture that influences nitrate generation, preservation, and flavour development. To support quality control and identify early indicators of spoilage, this study investigated taxonomic and functional microbiome changes across production stages, from brining and cooking to cold storage, slicing, and packaging under modified atmosphere. Using metagenomics, we characterised microbial community composition and functional profiles across 67 samples from raw ingredients, intermediate production steps, and final products. Microbial communities differed significantly between stages, despite sharing a related taxonomic structure. Brining markedly reduced diversity, and cooking further decreased richness and evenness. A set of 28 taxa was consistently detected across stages, though their relative abundance varied. Latilactobacillus curvatus was abundant prior to cooking but declined sharply afterwards, while Arthrobacter rhombi, initially rare, became dominant in the cooked product. During chilled storage, microbial succession continued, with some taxa re-emerging after being nearly eliminated by cooking. Functional gene profiling revealed distinct metabolic pathway shifts across stages, particularly involving respiration, amino acid metabolism, and fermentation. These findings provide a detailed baseline of microbial and functional dynamics in the production and storage of wet-cured ham. The results offer a foundation for spoilage risk assessment and contribute to the development of microbiological monitoring strategies to support product safety and shelf-life management.}, }
@article {pmid41963049, year = {2026}, author = {Zhai, WT and Zhao, H and Chai, LJ and Zhang, W and Zhang, XJ and Lu, ZM and Gao, CQ and Si, GR and Zhang, WQ and Wang, ST and Shen, CH and Xu, ZH}, title = {Microbial and environmental determinants of 1-propanol biosynthesis in Jiang-flavor Baijiu fermentation.}, journal = {Food microbiology}, volume = {138}, number = {}, pages = {105076}, doi = {10.1016/j.fm.2026.105076}, pmid = {41963049}, issn = {1095-9998}, mesh = {Fermentation ; *Flavoring Agents/metabolism ; *1-Propanol/metabolism ; *Wine/microbiology/analysis ; *Yeasts/metabolism/genetics/classification/isolation &amp; purification ; *Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Temperature ; Metagenomics ; Saccharomyces cerevisiae/metabolism ; Hydrogen-Ion Concentration ; }, abstract = {1-Propanol is a crucial flavor compound in Jiang-flavor Baijiu, yet the key microbial pathways and environmental factors controlling its synthesis have not been systematically investigated. Using an integrated approach of metagenomics and culture-dependent techniques, this study identified the key microbes, pathways, and factors controlling 1-propanol synthesis. The highest 1-propanol level was detected in first-round base Baijiu, with rapid accumulation during early pit fermentation. Metagenomics revealed the propanoate pathway as the dominant route, primarily contributed by Limosilactobacillus, while Pichia and Saccharomyces were key providers of pyruvate decarboxylase in the citramalate and threonine pathways. Pure-culture validation confirmed that L. panis MR32 predominantly utilizes 1,2-propanediol as the precursor, while yeasts such as P. kudriavzevii 2J2 and S. cerevisiae LB7A prefer the 2-ketobutyrate pathway. Environmental tests revealed optimal 1-propanol production by L. panis MR32 at pH 5.5 and increasing yields with temperature (25-45 °C). In contrast, most yeasts produced the most 1-propanol at 30 °C, beyond which yields declined, with only P. kudriavzevii 2J2 and I. orientalis IO tolerating high lactic acid. Our findings clarify the microbial division of labor and environmental drivers of 1-propanol formation, enabling targeted fermentation control.}, }
@article {pmid41963512, year = {2026}, author = {Matoba, R and Iijima, H and Sakamoto, Y and Kawabata, R and Ishiguro, A and Akamaru, Y and Kito, Y and Aizawa, M and Matsuyama, J and Takahashi, M and Makiyama, A and Suzuki, T and Tsuda, M and Yasui, H and Hihara, J and Okuda, H and Kawada, J and Yoshioka, T and Kawakami, H and Eguchi Nakajima, T and Muro, K and Ichikawa, W and Fujii, M and Sunakawa, Y}, title = {Metabolic and functional pathways of gut microbiota in patients with gastric cancer.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-47830-x}, pmid = {41963512}, issn = {2045-2322}, abstract = {We analysed the differences in bacterial composition between 475 Japanese patients with advanced gastric cancer (median age, 70 years; median BMI 20.0) and 106 healthy individuals using a comprehensive metagenome shotgun analysis. Among the patients with advanced gastric cancer, 71% were male, 37% had relapsed, and 55.5% previously underwent gastrectomy. Bifidobacterium, Anaerostipes, and Parabacteroides were predominant in healthy individuals, whereas Streptococcus, Lactobacillus, and Odoribacter were predominant in patients with advanced gastric cancer. Additionally, Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that butanoate and pyruvate metabolism was enriched in healthy individuals, whereas factors, such as ABC transporters and ribosomes, were enriched in patients with advanced gastric cancer. Cluster analysis broadly classified patients with advanced gastric cancer and healthy individuals into two clusters; however, clustering using pathway data more clearly classified patients with advanced gastric cancer and healthy individuals than clustering using flora analysis. Moreover, healthy individuals showed higher bacterial flora diversity than those with advanced gastric cancer. Although the dataset we used was limited and may be difficult to generalise, we identified some molecular characteristics and functional pathways of the microbial genera within the intestines of patients with advanced gastric cancer.}, }
@article {pmid41764595, year = {2026}, author = {Martínez-Murcia, A and Navarro, A and Miró-Pina, C and García-Sirera, A and Pérez, L and García-Román, V and Navarro-Gracia, JF}, title = {Early detection of nosocomial pathogens in air and surfaces using an innovative genetic approach for surveillance in healthcare settings.}, journal = {Antimicrobial resistance and infection control}, volume = {15}, number = {1}, pages = {}, pmid = {41764595}, issn = {2047-2994}, support = {INNCAD/2022/23//AVI/ ; }, abstract = {BACKGROUND: Healthcare-associated infections remain a major cause of morbidity, mortality, and financial burden worldwide, further exacerbated by the emergence of antimicrobial resistance. Environmental reservoirs of pathogens, including air and surfaces, play a critical role in nosocomial transmission. This study aimed to validate an integrated air and surface molecular surveillance system for the early detection of clinically relevant pathogens and resistance genes in hospital environments.<br><br>METHODS: Weekly air and surface samples were collected over 28 weeks from two hospitals in southeastern Spain. DNA and RNA were extracted and analysed by quantitative PCR (qPCR) targeting bacterial, fungal, and viral pathogens, as well as antimicrobial resistance genes. A subset of samples underwent shotgun metagenomic sequencing to confirm qPCR results and characterize microbial communities. Environmental findings were compared with clinical infection data from both hospitals.<br><br>RESULTS: Viral, bacterial and fungal pathogens were detected with similar patterns between air and surface samples and between hospitals. Carbapenem resistance genes showed distinct distribution profiles between hospitals. Respiratory viruses displayed strong temporal correlations with patient admissions, with viral RNA occasionally detected before clinical peaks.<br><br>CONCLUSIONS: This integrated molecular surveillance system allows sensitive detection of pathogens and resistance genes in hospital environments. Coupling air and surface sampling with qPCR provides a robust tool for identifying contamination sources and tracking temporal infection trends. Its scalability and adaptability make it suitable for implementation as an early warning system in infection prevention programmes, enhancing patient safety and supporting proactive control of nosocomial infections.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13756-026-01725-8.}, }
@article {pmid41771971, year = {2026}, author = {Deng, S and Wu, X and Xu, W and Wu, X and Cai, H and Wang, S and Liu, J and Cao, J}, title = {Multi-dimensional immunoprotection of Ganoderma lucidum spore oil in immunosuppressed mice via microbiome-proteome-metabolome network analysis.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41771971}, issn = {2045-2322}, support = {JCYJ20220530153201003//Science and Technology Planning Project of Shenzen Municipality/ ; GDRC202119//Natural Science Foundation of Top Talent of SZTU/ ; 82104362//National Natural Science Foundation of China/ ; 20211063010055//Research Founding of Post-doctor who came to Shenzhen/ ; SDAIT-20-05//Shandong Province Traditional Chinese Medicine Industry Project/ ; 2022ZDJS119//Guangdong Province Key Discipline Construction Research Project/ ; }, abstract = {UNLABELLED: Ganoderma lucidum has a long-standing history of use as a medicinal mushroom, with its spore oil (GLSO) extracted from broken cell walls using CO2 supercritical extraction. However, there is a notable scarcity of experimental studies on the protective effects and underlying mechanisms of GLSO on immune function impairment. The present study aims to explore the characteristics that GLSO contributes to protecting immune functions in cyclophosphamide-induced immunocompromised mice through a multi-omics analysis approach. GLSO administration significantly improved serum hemolysin levels, macrophage phagocytosis, and NK cell activity in immunosuppressed mice. Metagenomics, metabolomic, and proteomic analyses revealed that the immune protection mediated by GLSO was associated with structural rearrangements within gut microflora and shifts in microbial diversity. Specifically, there was an increase in beneficial microorganisms and a decrease in pathogenic organisms, accompanied by various alterations in metabolites and protein expressions. The identified 5 metabolites (propionic acid, beta-glycyrrhetinic acid, 3-aminosalicylic acid, creatine, and 2-phenylacetamide) and 5 proteins (Slc9a9, Blm, Hk3, AP1M2, and J chain) might serve as potential mediators of GLSO to alleviate immune dysfunction collectively caused by CYP in immunosuppressed mice.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-40137-x.}, }
@article {pmid41935036, year = {2026}, author = {Larsson, DGJ and Flach, CF and Kristiansson, E}, title = {Antibiotic resistance gene analyses in microbial communities: challenges and opportunities.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41935036}, issn = {2041-1723}, support = {2022-00945//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; }, abstract = {Culture-independent antibiotic resistance gene analyses enable broad explorations of microbial communities but often fail to link such genes to bacterial hosts and genetic contexts. This makes assessing prevalence of resistant pathogens and likelihood of further transmission or resistance evolution uncertain.}, }
@article {pmid41951362, year = {2026}, author = {Kariya, E and Tirard-Collet, P and Boulagnon-Rombi, C and Destras, G and Wallon, M and Menotti, J and Lapendry, A and Kaidi, N and Rabodonirina, M and Lievre, L and Depaquit, J and Villena, I and Trecourt, A and Huguenin, A}, title = {Integrated histomolecular diagnosis of mesenteric anisakiasis.}, journal = {Journal of clinical pathology}, volume = {}, number = {}, pages = {}, doi = {10.1136/jcp-2026-210635}, pmid = {41951362}, issn = {1472-4146}, abstract = {A 49-year-old woman was admitted with gastrointestinal symptoms and imaging consistent with duodeno-ileitis. Her clinical course was complicated by mesenteric ischaemia, requiring resection of a 45-cm ileal segment. A pre-adult Anisakis spp. larva was identified within a mesenteric nodule through an innovative diagnostic approach combining histopathological analysis with shotgun metagenomic analysis.}, }
@article {pmid41951635, year = {2026}, author = {Heng, YC and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Kittelmann, S}, title = {Metagenome-assembled genomes, and gene and protein catalogues from the global wild boar faecal microbiome.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07154-x}, pmid = {41951635}, issn = {2052-4463}, abstract = {Prophylactic antibiotic use in pig farming has contributed to the rise of antimicrobial resistance, spurring interest in probiotics to enhance pig gut health and immunity. Wild relatives of domestic pigs may harbour beneficial microbes, yet their gut microbiomes remain underexplored. In this study, we reconstructed 3,288 metagenome-assembled genomes (MAGs) from 89 wild boar faecal samples collected across four countries, all meeting at least MIMAG medium-quality standard (≥50% completeness, <10% contamination). These MAGs represented 968 distinct species, including 956 bacterial species from 113 families and 419 genera, and 12 archaeal species from 2 families and 7 genera, with half classified as novel. In addition, we also constructed catalogues of genes and proteins from the wild boar faecal metagenomes. Notably, most species (58%), genes and proteins (85%) identified in the wild boar faecal microbiomes were absent from equivalent catalogues of domestic pigs. Our catalogues highlight wild boars as a reservoir of previously untapped microbial resources for microbiome research and the exploration of biotechnological applications including probiotics.}, }
@article {pmid41951715, year = {2026}, author = {Wang, H and Wu, SH and Zhang, K and Chen, KH and Vilgalys, R and Liao, HL}, title = {Multiple hypervariable markers improve mycobiome classification in metatranscriptome and metagenome data.}, journal = {Communications biology}, volume = {}, number = {}, pages = {}, doi = {10.1038/s42003-026-09820-7}, pmid = {41951715}, issn = {2399-3642}, abstract = {Profiling the taxonomic and functional composition of mycobiome using metagenomic and metatranscriptomic sequencing is advancing our understanding of fungal functions in ecosystems. However, the sensitivity and accuracy of mycobiome classification using genome- or core protein-based approaches, is limited by the availability of reference genomes and the resolution of sequence databases. To address this, we propose the MicroFisher, a novel tool to identify taxonomically useful reads from metagenomic or metatranscriptomic data, enabling taxonomic identification of community members based on multiple hypervariable markers. We applied MicroFisher to profile the simulated fungal communities to assess the performance of the developed tool, and found higher performance in fungal prediction and abundance estimation compared to existing tools. In addition, we also used metagenomes from forest soil and metatranscriptomes of root eukaryotic microbes to test our method and found that MicroFisher provided more accurate profiling of environmental microbiomes compared to other classification tools. MicroFisher leverages high-resolution hypervariable marker gene databases and weighted integration algorithms to deliver more accurate fungal community classification compared to existing state-of-the-art tools. Additionally, it enables the detection of rare taxa, which is challenging with other available tools. Thus, MicroFisher serves as a novel pipeline for classification of fungal communities from metagenomes and metatranscriptomes.}, }
@article {pmid41951791, year = {2026}, author = {Somerville, TF and Kaye, SB}, title = {Comment on: 'Metagenomic next-generation sequencing: a game changer in the diagnosis of unique intraocular infections'.}, journal = {Eye (London, England)}, volume = {}, number = {}, pages = {}, pmid = {41951791}, issn = {1476-5454}, }
@article {pmid41951875, year = {2026}, author = {Wang, Y and Li, Y and Fang, J and Huang, Z and Zhang, C and Xu, B}, title = {A Novel Broad pH-Adaptive Bile Salt Hydrolase from Nomascus concolor Fecal Microbial Metagenome Facilitates the Cholesterol-Lowering Ability of Escherichia coli Nissle 1917.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41951875}, issn = {1867-1314}, support = {32360034//National Natural Science Foundation of China/ ; }, }
@article {pmid41952168, year = {2026}, author = {Shen, Y and Qu, S}, title = {Ganciclovir for severe neonatal varicella pneumonia when acyclovir is unavailable: a case report.}, journal = {Virology journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12985-026-03142-0}, pmid = {41952168}, issn = {1743-422X}, abstract = {BACKGROUND: Perinatal varicella is a rare and severe condition with a high mortality rate, particularly when it leads to complications such as pneumonia in neonates. Acyclovir is the standard treatment for varicella-zoster virus (VZV) infections; however, limited options exist when it is unavailable. This case report describes the successful treatment of neonatal varicella pneumonia with ganciclovir and provides insights into its potential as an alternative therapy. A female Asian neonate was admitted to our hospital on the 9th day of life with a rash, fever, and respiratory distress. Her mother developed varicella at 39 weeks of pregnancy, four days before delivery. The infant was diagnosed with VZV pneumonia based on clinical presentation and confirmed by detection of VZV DNA in blood(metagenomic next-generation sequencing detected 109,491 sequences with 100% relative abundance and 99% confidence).<br><br>INTERVENTION: Ganciclovir 5&#xa0;mg/kg every 12&#xa0;h for 8 days; intravenous immunoglobulin 400&#xa0;mg/kg once daily for 3 days.<br><br>OUTCOME: The infant was successfully weaned off mechanical ventilation, with normalized blood gas parameters (PaO&#x2082;/FiO&#x2082; ratio 346) and inflammatory markers (CRP decreased from 29.44&#xa0;mg/L to 2.87&#xa0;mg/L). She was discharged home with stable breathing and crusted skin lesions. Telephone follow-up at 2 and 4 weeks post-discharge confirmed the infant remained well with no respiratory symptoms or developmental concerns.<br><br>CONCLUSION: Ganciclovir may serve as a life-saving alternative for severe neonatal VZV pneumonia when acyclovir is unavailable. This case highlights the need for further research to establish its safety, optimal dosing, and efficacy in this population.}, }
@article {pmid41953110, year = {2026}, author = {Craddock, HA and Motro, Y and Winner, KM and Lotem-Michaeli, Y and Segal, E and Godneva, A and Grinstein, D and Moran-Gilad, J}, title = {Metagenomic analysis of antimicrobial resistance genes in domestic canines.}, journal = {One health (Amsterdam, Netherlands)}, volume = {22}, number = {}, pages = {101380}, pmid = {41953110}, issn = {2352-7714}, abstract = {A One Health approach is critical to addressing the spread of antimicrobial resistance (AMR). A key source of AMR in humans is companion animals, particularly canines. Recent investigation has shown that the canine fecal microbiome is rich in antimicrobial resistant genes (ARGs), yet few studies have studied the resistome of working canines. Our objective was to investigate the resistome of canines to elucidate associations between various exposures and demographic factors and ARG carriage. We performed resistome and microbiome analyses on previously-generated metagenomic sequence data from 126 Israeli working canines and 147 global canines. We found that the canine microbiome and resistome varied significantly with country of origin, and the resistome varied significantly with gastrointestinal disease state, canine job type, and microbiome composition. Tetracycline resistant genes were the most dominant across all canines. Extended-spectrum beta lactamase (ESBL) genes were observed in up to 33% of canines. Genes of concern, including potential carbapenemases (blaOXA-181 and blaOXA-347) and colistin resistance genes (mcr-10) were infrequently observed. The Inc family of plasmids, typically associated with ESBL genes, were frequently detected. Altogether our research suggests that canines, including working dogs, are a potential source of ARGs and plasmids which carry ARGs. Importantly, the abundance and identity of these ARGs is associated with various potentially modifiable factors such as microbiome composition. As canines are an important human exposure within the One Health paradigm, future work is necessary to understand the risk and transmission dynamics of ARGs between humans and their companion canines.}, }
@article {pmid41953529, year = {2026}, author = {Brown, JR and Ross, CS and Worth, A and Merve, A and Storey, N and Hacohen, Y and Mankad, K and Kaliakatsos, M and Shendi, HM and Atkinson, L and Gilmour, K and Hatcher, J and Lennon, A and Bamford, A and Kusters, M and Elfeky, R and Núñe, A and Brown, IH and Reid, SM and Cooper, J and Byrne, AMP and James, J and Lean, FZ and Banyard, AC and Breuer, J}, title = {Identifying virulent avian paramyxovirus type-1: A paediatric case of progressive encephalitis diagnosed by clinical metagenomics with case series review.}, journal = {IDCases}, volume = {44}, number = {}, pages = {e02555}, pmid = {41953529}, issn = {2214-2509}, abstract = {BACKGROUND: Immunocompromised patients presenting with encephalitis can present a diagnostic conundrum as infection can be caused by a broad range of pathogens, many of which are not detected by standard of care testing pathways. Untargeted metagenomics has proven utility in the diagnosis of such infections, particularly for immunocompromised patients.<br><br>METHODS: An immunosuppressed adolescent presented with idiopathic progressive muscle weakness resulting in respiratory failure, 16 years after haematopoeitic stem cell transplant for familial haemophagocytic lymphohistiocytosis type 5. Clinical and radiological findings suggested a diagnosis of isolated central nervous system haemophagocytic lymphohistiocytosis, however the patient demonstrated no improvement on immunosuppressive therapy. Untargeted metagenomics was performed on brain biopsy tissue.<br><br>RESULTS: Clinical metagenomics detected avian paramyxovirus 1 (APMV-1) in the brain tissue 12 days after biopsy, confirmed by targeted PCR and immunohistochemistry. The metagenomics results guided treatment; immunosuppression was stopped and medication with potential activity against RNA viruses started. The patient died 8 months after symptom onset.<br><br>CONCLUSIONS: We describe the third published case of fatal encephalitis caused by APMV-1, detectable only in brain parenchyma and only by clinical metagenomics, demonstrating the utility of brain biopsy and metagenomics when investigating encephalitis in immunocompromised patients. Case series review suggests profoundly immunocompromised patients are at risk of severe infection caused by AMPV-1.}, }
@article {pmid41953658, year = {2026}, author = {Song, J and Li, Y and Wang, L and Zhang, J and Shi, C and Zhong, L and Liu, C and Song, M and Yu, X and Zhang, W and Wen, P}, title = {Comparative study of the physicochemical properties, volatile compounds, and bacterial microbiota in commercial and traditional yak yogurt from the Qinghai-Tibet plateau.}, journal = {Food chemistry: X}, volume = {35}, number = {}, pages = {103771}, pmid = {41953658}, issn = {2590-1575}, abstract = {This study aimed to elucidate differences between the commercial starter culture (CK) and traditional starters from different Tibetan regions (Gannan (GN), Qinghai (QH), Tibet (XZ)) in fermenting yak yogurt by physicochemical properties, flavor, and bacterial community. Results indicated acidity, proline, arginine, alanine, and C6:0 contents were significantly higher in the traditional starter culture than CK (P < 0.05). Gas chromatography-ion mobility spectrometry analysis found the traditional starter culture group was dominated by alcohols and esters, whereas CK exhibited richer ketones. Metagenomic analysis revealed Lactobacillus delbrueckii (49.56% in XZ, 24.86% in GN) and Streptococcus spp. (18.30% in CK, 17.21% in QH) as the dominant. Moreover, pH and titratable acidity were primary factors affecting microbial diversity. Meanwhile, glutamic acid modulated ester biosynthesis like ethyl acetate, while C16:0 fatty acids inhibited off-odor ketones such as 2-pentanone. This study offers valuable insights into developing specialized fermentation agents and standardizing the quality of yak yogurt.}, }
@article {pmid41953764, year = {2026}, author = {Ivan, FX and Versi, A and Tiew, PY and Abdel-Aziz, MI and Kermani, NZ and Maitland-Van Der Zee, AH and Howarth, P and Koh, MS and Adcock, IM and Chotirmall, SH and Chung, KF}, title = {Multidrug-resistant Haemophilus influenzae cluster of severe asthma from sputum bacteriome-resistome.}, journal = {ERJ open research}, volume = {12}, number = {2}, pages = {}, pmid = {41953764}, issn = {2312-0541}, abstract = {BACKGROUND: Severe asthma encompasses heterogeneous inflammatory phenotypes and airway bacteriome diversity but the state of its airway resistome remains understudied. We therefore evaluated the link between the airway microbiome and the antibiotic-resistant genes by determining the clusters from a bacteriome-resistome integration from sputum samples of patients with severe asthma.<br><br>METHODS: Induced sputum samples from severe asthma (SA; n=96), mild-moderate asthma (MMA; n=23) and healthy controls (HCs; n=23) in the European U-BIOPRED asthma cohort were metagenomically sequenced. Respiratory bacteriome was evaluated by taxonomical and functional classification. The comprehensive antibiotic resistance database was used to determine airway resistome and Similarity Network Fusion to cluster integratively the bacteriome-resistome.<br><br>RESULTS: More multidrug-resistance genes were present in SA compared with MMA and HCs with the hmrM, encoded in Haemophilus influenzae chromosome, being highest. Two of the three defined clusters were dominated by commensals with resistance genes from different classes but different in &#x3b1;- and &#x3b2;-diversities. The third cluster was dominated by multidrug-resistant H. influenzae, with SA characteristics of increased asthma duration, reduced pulmonary macrophages and decreased lung function. It had the highest signature expression of neutrophil activation, NETosis and of interleukin (IL)-5, IL-6, IL-13, IL-17 and IL-33 signalling pathways. These clusters were reproduced in an Asian-Singapore SA cohort including the multidrug-resistant H. influenzae cluster, but with an additional cluster of multidrug-resistant Pseudomonas aeruginosa.<br><br>CONCLUSION: The demonstration of U-BIOPRED multiresistant H. Influenzae and of Asian-Singapore multiresistant P. aeruginosa clusters highlights the potential importance of antibiotic-resistant genes in driving severe asthma.}, }
@article {pmid41954112, year = {2026}, author = {Banerjee, M and Lahiri, A and Basak, S and DAS, S and Mukhopadhyay, S and Banerjee, R and Basak, K}, title = {StaLAENet: A stacked LSTM-nested deep-autoencoder network for identification of antimicrobial resistance of nosocomial pathogens.}, journal = {Journal of biosciences}, volume = {51}, number = {}, pages = {}, pmid = {41954112}, issn = {0973-7138}, mesh = {Humans ; Algorithms ; *Cross Infection/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Drug Resistance, Bacterial/genetics ; Computational Biology/methods ; Autoencoder ; }, abstract = {As various technological innovations are assisting medical science in a considerable way, rendering a significant leap towards 'lab-to-land' delivery, in a similar vein, algorithm development and concomitant framework-based approaches help the field to enrich its patient care. Although antimicrobial drugs revolutionized this particular area, antimicrobial resistance is a pressing global health concern as microbial strains are becoming resistant to conventional antibiotics, undermining the efficacy of these drugs and leading to increased illness and healthcare costs. To tackle this menace, apart from technological innovations such as diagnostic kits, an informatics-based framework approach is the call of the day. Despite the emergence of several computational approaches, they lack in generalization, scope, and scalability. Here, we have developed a novel framework StaLAENet (stacked LSTM-nested deep-autoencoder network) to predict antibiotic-resistant gene drug classes targeting ESKAPE pathogens. This framework comprises two modules: a feature representation module comprising a stacked LSTM-nested deep autoencoder and a classification module that leverages a dense network using latent features. StaLAENet demonstrated an efficient performance - accuracy: 0.938±0.043, specificity: 0.888±0.061, precision: 0.912±0.020, and recall: 0.881±0.021 - for Enterococcus faecium using 4-mer data, with similar results for other organisms using various k-mer data. Comparative analysis confirmed its superiority over existing pipelines. Further, independent evaluation with non-redundant sequences (sourced from another database) and with a metagenomic dataset highlighted its generalizability, robustness, and capability to analyze complex microbial communities. StaLAENet can offer a robust solution for combating AMR, enabling an efficient way of antimicrobial stewardship and patient care.}, }
@article {pmid41954388, year = {2026}, author = {Zhao, P and Liu, H and Dong, J and Su, H and Jin, Q and Yang, F}, title = {From hepatitis misdiagnosis to zoonotic false alarms: a metagenomic blacklist framework for the parvo-like hybrid viral group.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0015726}, doi = {10.1128/spectrum.00157-26}, pmid = {41954388}, issn = {2165-0497}, }
@article {pmid41954393, year = {2026}, author = {Shukla, N and Budhbhatti, U and Puvar, A and Raval, I and Pandit, R and Chavda, P and Chauhan, A and Jhala, D and Shah, D and Shah, T and Raval, J and Prajapati, H and Patel, N and Upadhyay, K and Joshi, M and Patel, AK and Bondre, V and Kumar, N and Joshi, C}, title = {Genomic and evolutionary characterization of Chandipura virus: a cause of the 2024 outbreak in Gujarat, India.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0157825}, doi = {10.1128/spectrum.01578-25}, pmid = {41954393}, issn = {2165-0497}, abstract = {UNLABELLED: Acute encephalitis syndrome (AES) caused by Chandipura virus (CHPV) is a rapidly progressive and often fatal neurological illness predominantly affecting children in India. However, limited research on CHPV disease progression and viral genomics has hindered a comprehensive understanding of its transmission dynamics and evolutionary behavior. CHPV is endemic in India, with previous outbreaks (2003-2004) reported case fatality rates (CFRs) ranging from 56% to 75%. In the current (2024) outbreak, the CFR declined to 46%, with an overall test-positivity rate of 18.6%, possibly reflecting improvements in supportive care. Despite advances in genomics and sequencing technologies, only a limited number of CHPV genomes are publicly available. To address this gap, we performed whole-genome sequencing of CHPV isolated from a pediatric patient aged 12 years from Patan, Gujarat. Comparative genomic analysis with previously reported Indian strain revealed approximately 293 mutations, including 24 non-synonymous. The estimated evolutionary rate of CHPV was ~1.62 × 10[-2] substitutions/site/year. Furthermore, the selective pressure analysis showed that, despite the virus being under strong purifying (negative) selection, several non-synonymous changes were identified. Nonetheless, as the present analysis is based on the single genome, further sequencing, validation, and broader comparative analysis are required to draw a definitive inference. However, these findings suggest that even under purifying selection pressure, CHPV retains the ability to infect and cause severe disease in children. This highlights the continued need to investigate virus-host interactions, particularly host immune responses, to better understand CHPV pathogenesis and its ability to cause disease in children.<br><br>IMPORTANCE: Chandipura virus (CHPV) is an etiological agent of acute encephalitis syndrome (AES) in children, characterized by rapid neurological decline; yet the viral and host factors governing its neuropathogenesis and sudden outbreak dynamics remain poorly defined. Despite minimal genomic variation indicative of strong purifying selection, which supports the continued efficacy of existing molecular diagnostics and candidate therapeutics, CHPV re-emerges unpredictably in human populations, as exemplified by the 2024 AES cluster in Gujarat. This outbreak underscores the importance of continuous genomic surveillance to elucidate viral behavior and immune-evasion mechanisms. Moreover, it highlights the utility of both amplicon-based and metagenomic next-generation sequencing approaches for future CHPV detection and comprehensive genome characterization.}, }
@article {pmid41954722, year = {2026}, author = {Kruis, T and Wassermann, M and Graf, B and Lührig, K and Menzel, P and Schwarzer, R and Ziegler, J and Isner, C}, title = {Correction: Unmasking the mimic: vertebral alveolar echinococcosis diagnosed by metagenomic next‑generation sequencing.}, journal = {Infection}, volume = {}, number = {}, pages = {}, doi = {10.1007/s15010-026-02771-5}, pmid = {41954722}, issn = {1439-0973}, }
@article {pmid41954798, year = {2026}, author = {Liu, P and Zhang, J and Liu, X and Li, B and Peng, Y and Li, B and Lyu, X and Tan, L and Guo, Z and Li, Z and Hu, M}, title = {Metagenomic next-generation sequencing for comprehensive pathogen detection in intraocular infection.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41954798}, issn = {1435-4373}, support = {Grant No.2023XQLH173//Central Universities of Central South University/ ; No. 82102499//National Natural Science Foundation of China/ ; No. 82270658//National Natural Science Foundation of China/ ; No. 2021JJ40840//the Hunan Natural Science Foundation/ ; No.202211003513//Scientific Research Project for Hunan Health Commission/ ; }, }
@article {pmid41954996, year = {2026}, author = {Prabhu, A and Rinke, C}, title = {ICTV Virus Taxonomy Profile: Krittikaviridae 2026.}, journal = {The Journal of general virology}, volume = {107}, number = {4}, pages = {}, doi = {10.1099/jgv.0.002239}, pmid = {41954996}, issn = {1465-2099}, mesh = {Genome, Viral ; Phylogeny ; *DNA Viruses/classification/genetics/ultrastructure/isolation &amp; purification ; Virion/ultrastructure/genetics ; DNA, Viral/genetics ; *Archaea/virology ; Virus Replication ; }, abstract = {The family Krittikaviridae includes dsDNA viruses associated with the marine archaeal lineage Poseidoniales. These viruses have been identified through metagenomic analysis of brackish estuarine samples and are closely related to other 'magroviruses'. The family belongs to the order Magrovirales and includes the genus Velanvirus and the species Velanvirus brisbanense. Viruses in the family have a genome of about 80 kbp that includes modules for DNA replication and virion morphogenesis. Krittikavirids are predicted to form virions with an icosahedral capsid and helical tail, characteristic of viruses belonging to the class Caudoviricetes. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Krittikaviridae, which is available at ictv.global/report/krittikaviridae.}, }
@article {pmid41955630, year = {2026}, author = {Wu, Z and Chen, H and Yao, Y and Wu, J and Li, H and Wang, W and Jiang, Q and Li, P and Zhou, H}, title = {Clinical evaluation of probe capture based targeted next generation sequencing for pulmonary infection in immunocompromised patients: a cross-sectional diagnostic accuracy study.}, journal = {Infectious diseases (London, England)}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/23744235.2026.2654559}, pmid = {41955630}, issn = {2374-4243}, abstract = {BACKGROUND: Timely aetiological diagnosis of pulmonary infection in immunocompromised patients (ICPs) remains challenging because clinical presentations may be atypical and conventional microbiological tests (CMTs) have limited sensitivity. Probe capture based targeted next generation sequencing (ptNGS) has emerged as a potential alternative to metagenomic next generation sequencing (mNGS), but its clinical performance in this population remains incompletely defined.<br><br>METHODS: In this cross-sectional diagnostic accuracy study, immunocompromised adults undergoing bronchoalveolar lavage for suspected pulmonary infection were enrolled. Bronchoalveolar lavage fluid (BALF) samples were analysed using CMTs, mNGS, and ptNGS. Composite clinical adjudication served as the reference standard. Diagnostic performance was compared at the case level, and pulmonary microbiota characteristics were explored.<br><br>RESULTS: Among 78 enrolled patients, 60 were classified as having pulmonary infection. Causative pathogens were identified in 52 cases, and fungal pathogens, particularly Pneumocystis jirovecii, were the most frequently detected. At the case level, ptNGS and mNGS demonstrated higher sensitivity than CMTs (80.0% vs 80.0% vs 26.7%) and showed high concordance in microorganisms identified (91.7%). Specificity was 72.2% for CMTs, compared with 44.4% for mNGS and 38.9% for ptNGS. Positive sequencing results were also observed in patients without pulmonary infection (n&#x2009;=&#x2009;18), predominantly involving viral or opportunistic microorganisms. Microbiota analysis of 65 samples revealed reduced microbial alpha diversity and altered community composition in patients with pulmonary infection.<br><br>CONCLUSIONS: In ICPs with suspected pulmonary infection, ptNGS substantially increases pathogen detection compared with CMTs and demonstrates diagnostic performance comparable to mNGS. Sequencing results require careful clinical interpretation, given the difficulty in distinguishing infection from colonisation in respiratory specimens. Exploratory microbiota analyses suggest infection associated alterations in lung microbial ecology that warrant further validation.}, }
@article {pmid41955710, year = {2026}, author = {Sahu, TK and Rathored, J and Patil, P}, title = {Tri-layer microbiology for LMIC Hospitals: linking syndromic panels with reflex culture and targeted sequencing for real world care - a narrative review.}, journal = {The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases}, volume = {30}, number = {3}, pages = {105808}, doi = {10.1016/j.bjid.2026.105808}, pmid = {41955710}, issn = {1678-4391}, abstract = {Rapid, syndromic molecular panels and high throughput sequencing have transformed the diagnostic landscape for sepsis, respiratory, gastrointestinal, and central nervous system infections, but their value in routine practice depends on how they are integrated with conventional microbiology and antimicrobial stewardship. This review synthesises recent high-quality evidence to propose a pragmatic three-tier hybrid framework. Tier 1 comprises syndrome specific rapid panels that provide organism and selected resistance markers within hours, primarily to accelerate early escalation or de-escalation rather than to replace culture. Tier 2 positions reflex culture and targeted adjunct tests as the non-negotiable specificity anchor, confirming molecular hits, distinguishing infection from colonisation or contamination, generating phenotypic susceptibility data and supplying isolates for infection prevention and public health surveillance. Tier 3 reserves targeted or metagenomic sequencing for a small, clinically critical subset of high suspicion, panel negative and culture negative cases, where additional breadth can realistically change management. Across sepsis/BSI, pneumonia, gastrointestinal infection and CNS disease, available data indicate that clinical benefit is driven less by any individual technology and more by disciplined implementation: clear indications, explicit reflex rules, close linkage to antimicrobial stewardship and systematic audit of key performance indicators such as time-to-targeted therapy, spectrum of antimicrobial use and cost per additional actionable diagnosis. The proposed tiered, syndrome wise algorithms provide a transferable conceptual scaffold that can be adapted to local resources, allowing laboratories in both high and low resource settings to introduce advanced diagnostics without abandoning culture-based anchors or stewardship accountability.}, }
@article {pmid41955799, year = {2026}, author = {Chen, Y and Zhuo, G and Liu, C and Zheng, Y and Guo, S and Lu, X and Zhen, G}, title = {Efficient cadmium removal and immobilization from acid mine drainage by composite sulfate-reducing consortia: Mechanistic insights from EPS characterization, key enzyme activities, and metagenomics.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {141956}, doi = {10.1016/j.jhazmat.2026.141956}, pmid = {41955799}, issn = {1873-3336}, abstract = {Bioremediation has gained increasing attention for remediating heavy-metal wastewater from mining activities, such as acid mine drainage (AMD). Cadmium (Cd) is of special concern due to its high mobility, bioaccumulation, and highly toxic with stringent discharge limits, yet community- and metabolism-level mechanisms that sustain remediation under metal stress remain insufficiently understood. Here, three lab-scale up-flow anaerobic sludge bed (UASB) reactors enriched with sulfate-reducing bacteria (SRB) were established with inocula containing 100% sludge, 75% sludge + 25% soil, and 50% sludge + 50% soil to evaluate Cd removal performance and microbial adaptation. All reactors achieved ≥ 97.5% Cd removal, with effluent Cd consistently below detection, demonstrating effective immobilization under tested conditions. Sequestration in the bottom layer helped maintain a more favorable metabolic environment in the upper zone. Integrated analyses of extracellular polymeric substances (EPS), enzyme activities, and metagenomic revealed inoculum-dependent trade-offs: moderate soil addition enhanced recovery resilience, whereas the pure-sludge inoculum retained stronger sulfur-cycling potential than soil-derived communities. Metagenomic profiling supported distinct roles of dissimilatory sulfate reduction in sulfide generation and metal sulfide precipitation and assimilatory sulfur pathways in cellular sulfur demand and stress buffering. Notably, direct interspecies electron transfer/extracellular electron transfer (DIET/EET) associated genes and electron-transport indicators were enriched in reactors with superior recovery, supporting an inferred sulfate reduction-DIET (SR-DIET) synergy whereby coupled sulfur cycling and enhanced interspecies/extracellular electron exchange may facilitate energy restoration and sustained Cd immobilization. These findings advance mechanistic understanding of SRB-based treatment and inform engineering of resilient anaerobic consortia for mine-impacted and industrial effluents.}, }
@article {pmid41955854, year = {2026}, author = {Luo, M and Fan, J and Wang, X and Ge, Y and Feng, D and Cao, S and Wang, J and Deng, H and Luo, J and Zhao, Y and Ge, C and Bu, H}, title = {Microplastics drive the reconfiguration of microbial sulfur cycling pathways in seagrass bed sediments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {398}, number = {}, pages = {128089}, doi = {10.1016/j.envpol.2026.128089}, pmid = {41955854}, issn = {1873-6424}, abstract = {Microplastics (MPs) pollution threatens marine biogeochemical cycles, but its impact on the sediment sulfur cycle remains unclear. A 112-day microcosm incubation experiment was conducted to investigate the effects of three common MPs, polylactic acid (PLA), polyethylene (PE), and polystyrene (PS), on sulfur speciation, microbial communities, and functional genes in seagrass bed sediments using integrated amplicon sequencing and metagenomics. MPs significantly altered sediment sulfur speciation, with PLA inducing the strongest shifts, including 111.2% accumulation of total inorganic sulfate (TIS) and a 163.3% increase in TIS/Sulfide ratios, indicative of enhanced sulfur oxidation, while PE and PS promoted sustained sulfide accumulation. Distinct polymer-specific changes in sulfur-cycling bacteria communities were observed, with PLA suppressing the dominant Bradymonas (31.3% decrease) while enriching heterotrophic Sulfitobacter (26.5% increase), PE driving a transition towards autotrophic pathways with Thiohalomonas increasing by 272.8%, and PS selectively enriching generalist sulfur-oxidizing genera such as Roseovarius and Methyloceanibacter. Metagenomic analysis highlighted a shift from assimilatory biosynthetic pathways to dissimilatory energy-generating processes. These findings suggest that MPs intensify sulfide stress and disrupt sulfur metabolism, thereby reducing sediment biogeochemical stability and potentially impairing carbon burial and ecosystem resilience. These results provide critical insights into the ecological consequences of MP exposure on biogeochemical cycles in seagrass bed sediments.}, }
@article {pmid41955934, year = {2026}, author = {Cornu Hewitt, B and Odendaal, ML and de Rooij, MMT and Bossers, A and Franz, E and Bogaert, D and Smit, LAM}, title = {Impacts of inhaled exposures on the upper respiratory tract microbiome: a systematic review.}, journal = {The Science of the total environment}, volume = {1030}, number = {}, pages = {181776}, doi = {10.1016/j.scitotenv.2026.181776}, pmid = {41955934}, issn = {1879-1026}, abstract = {BACKGROUND: Inhaled exposures can substantially affect human health. The upper respiratory tract (URT) microbiome forms a critical first point of interaction with inhaled agents (e.g. air pollutants and chemicals), yet its response to most inhaled exposures remains poorly characterised beyond the well-studied effects of tobacco smoking.<br><br>METHODS: We systematically reviewed research articles from 2005 to 2024 investigating the effects of inhaled exposures on the human URT microbiome, using sequencing-based approaches. Database searches in PubMed, Scopus, and EMBASE yielded 5263 unique publications. Following screening using ASReview, 66 studies met inclusion criteria, covering four exposure domains: urban outdoor, rural outdoor, household indoor, and occupational settings.<br><br>RESULTS: Inhaled exposures were consistently associated with alterations in the URT microbiome, often differing by anatomical niche (e.g. nasal, nasopharynx, oral, oropharynx). Outdoor air pollution and urbanisation were linked to reduced microbial diversity and depletion of commensals, whereas green space and agricultural exposures were associated with higher diversity, enrichment of health-associated taxa, and introduction of animal- and soil-associated microbes. Findings for other exposures (e.g. indoor pollutants, pesticides) were more heterogeneous.<br><br>CONCLUSIONS: Overall, the URT microbiome remains understudied as a mediator of respiratory health effects related to inhaled exposures, while methodological heterogeneity complicates comparability across studies. Future research should prioritise benchmarked protocols, longitudinal designs, and functional analyses (e.g. metagenomics) to clarify how inhaled exposures alter microbial activity, resilience, ecological interactions, and host outcomes. This synthesis highlights the need for integrated environmental health approaches and for assessing the long-term consequences of inhaled exposures.}, }
@article {pmid41955982, year = {2026}, author = {Besharati Fard, M and Guo, H and De Vrieze, J and Wu, D}, title = {Chronic ciprofloxacin exposure reduces anaerobic digestibility of waste microalgal-bacterial aerobic granular sludge: Metagenomics and metatranscriptomics overview.}, journal = {Water research}, volume = {299}, number = {}, pages = {125876}, doi = {10.1016/j.watres.2026.125876}, pmid = {41955982}, issn = {1879-2448}, abstract = {Microalgal-bacterial aerobic granular sludge (MB-AGS) is a promising wastewater treatment technology, but its long-term sustainability depends on whether its waste biomass (WMB-AGS) can be effectively stabilized through anaerobic digestion, particularly under antibiotic stress. Here, we compared the digestibility and ciprofloxacin response of WMB-AGS and conventional waste activated sludge (WAS) using 21-day biochemical methane potential (BMP) tests, 3-day hydrolysis-acidogenesis assays, and 90-day semi-continuous digesters, supported by enzyme activity, extracellular polymeric substances (EPS) characterization, and multi-omics profiling. The WAS produced substantially higher methane yields (302 ± 7 mL CH4/g VS) than WMB-AGS (62 ± 4 mL CH4/g VS), confirming the superior digestibility of WAS. Ciprofloxacin effects were exposure-regime dependent, a single initial dose up to 1000 µg/L did not affect methane production in BMP assays. However, continuous ciprofloxacin exposure in semi-continuous digesters significantly reduced daily biogas production, from 114 ± 9 to 96 ± 6 mL/day in WAS and from 23 ± 1 to 15 ± 2 mL/day in WMB-AGS. During the hydrolysis-acidogenesis, ciprofloxacin promoted volatile fatty acid accumulation and inhibited key hydrolytic, acidogenic, and methanogenic enzymes. Biotransformation was the dominant ciprofloxacin removal mechanism. The EPS acted as an initial protective interface but also contributed to hydrolysis limitation. Multi-omics analyses showed that chronic ciprofloxacin exposure did not suppress core methanogenesis genes, but reconfigured upstream electron-transfer and methyl-transfer functions, with enrichment of Corynebacterium and Methanobacterium. Overall, WMB-AGS is inherently less digestible than WAS. These findings highlight the need to consider substrate-specific matrix effects and long-term antibiotic pressure when evaluating the downstream anaerobic valorization.}, }
@article {pmid41955988, year = {2026}, author = {Wang, X and Xue, T and Li, J and Zhang, C and Hao, G and Xing, Y and Tao, R and Guo, L and Zhang, H and Chai, S and Zheng, L}, title = {Novel photoelectron-driven nitrate reduction in anammox granules using photosensitive semiconductor iron mineral for wastewater treatment.}, journal = {Water research}, volume = {299}, number = {}, pages = {125862}, doi = {10.1016/j.watres.2026.125862}, pmid = {41955988}, issn = {1879-2448}, abstract = {The accumulation of nitrate byproducts and limited electron availability fundamentally constrain the efficacy of anaerobic ammonium oxidation (anammox) processes. While iron minerals regulate electron transfer, their potential to drive anammox via semiconductive photoexcitation remains underexplored. Here, we establish a novel "Photo-Chemo-Bio" strategy to overcome these thermodynamic bottlenecks using light-excited hematite (α-Fe2O3). Among tested minerals, hematite exhibited superior band-structure suitability, achieving a 3.65-fold photocurrent enhancement (4.06 μA·cm[-2]) upon bio-hybridization, facilitated by the active recruitment of photo-electrons via upregulated outer-membrane c-type cytochromes. Crucially, this photo-enhanced electron supply boosted the total nitrogen removal rate by 27.4% while suppressing nitrate yield by 42.8%. Kinetic analysis revealed a precise metabolic decoupling: solar irradiation did not accelerate ammonia oxidation but specifically diverted electron flow toward nitrate reduction pathways. Genome-resolved metagenomics unraveled the molecular basis of this synergy, identifying a "hardwired" cooperative network: flanking Desulfobacillus-like species, characterized by a specific metabolic truncation (absence of nor genes), act as obligate "net NO providers" to fuel the anammox core; concurrently, heterotrophic Casimicrobiaceae unexpectedly encode Photosystem II (psbA), functioning as auxiliary "energy antennas" to harvest photons. These findings demonstrate how mineral-microbe hybrids can orchestrate electron flux to close the nitrogen loop, offering a sustainable, carbon-free strategy for high-efficiency wastewater treatment.}, }
@article {pmid41956026, year = {2026}, author = {Sorgato, AC and Kim, B and Papillon, J and Nivala, J and Silveira, DD and Lapolli, FR and Forquet, N}, title = {Microbial fuel cells inoculated with French vertical flow treatment wetland sludge: A step towards clogging biodetector development.}, journal = {Bioelectrochemistry (Amsterdam, Netherlands)}, volume = {171}, number = {}, pages = {109297}, doi = {10.1016/j.bioelechem.2026.109297}, pmid = {41956026}, issn = {1878-562X}, abstract = {Clogging is considered an operational challenge in French vertical flow treatment wetlands (VFTWs), causing hydraulics and aeration problems. The available monitoring methods are labor intensive. Microbial fuel cells (MFCs) have emerged as real-time biosensors, including for treatment wetlands (TW) systems. In this study, French VFTW sludge was investigated as inoculum in MFCs, to assessing its adaptation into electrochemical environment as a step for clogging MFC-based biodetector implementation in such systems. The results show that the inoculum was successfully adapted, with stable current generation at 0.4 mA. The electrochemical impedance spectroscopy (EIS) demonstrated the establishment of a biofilm with electroactive characteristics and non-limiting anode. Metagenomic analysis showed that the French VFTW harbor electroactive species, and the MFC created a selective pressure on the VFTW sludge inoculum and significantly shaped the microbial community and function, stimulating the enrichment of electroactive bacteria (EAB), such Geobacterales (4.11% to 5.83%), with potential expression of cytochrome-c for extracellular electron transference (EET). This study illustrates the feasibility of developing electroactive biofilms from French VFTW and suggests its use as an inoculum, improving the integration of TW-MFC systems. Considering these results, the well-adapted anodic biofilm could enable the detection of aeration limitations via cathodic reactions in future studies.}, }
@article {pmid41956515, year = {2026}, author = {Rober, AR and Reese, LC and Brown, SP and McMahon, KD and Louca, S and Cieslik, J and Kane, ES and Turetsky, MR and Wyatt, KH}, title = {Hydrologic History Regulates Microbial Biofilm Diversity and Ecosystem Function.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70300}, doi = {10.1111/1462-2920.70300}, pmid = {41956515}, issn = {1462-2920}, support = {MCB-2514370//National Science Foundation/ ; DEB-2141285//National Science Foundation/ ; DEB LTREB-2011286//National Science Foundation/ ; DEB LTREB-2011257//National Science Foundation/ ; DEB-1636476//National Science Foundation/ ; RJVA-PNW-01-JV-11261952-231//Pacific Northwest Research Station/ ; //USDA Forest Service/ ; }, mesh = {*Biofilms/growth &amp; development ; *Ecosystem ; *Biodiversity ; Bacteria/genetics/classification/isolation &amp; purification ; Fungi/genetics/classification/isolation &amp; purification ; Cyanobacteria/genetics/classification ; Hydrology ; Droughts ; Floods ; Metagenomics ; }, abstract = {Aquatic biofilms are an understudied component of northern peatlands and are expected to play a more prominent role in ecosystem processes in areas where aquatic habitat is expanding. The goal of this study was to investigate how hydrologic history influences biofilm diversity and functional genes. This study was conducted in a long-term water table manipulation that simulates drought (lowered water table treatment) and flooding (raised water table treatment) conditions relative to a control treatment (no manipulation). We used a combination of metabarcoding and metagenomic approaches to (1) examine the diversity of eukaryotic algae, cyanobacteria, bacteria and fungi within the biofilm and (2) identify functional genes associated with alternating wet-dry transitional states. Historical flooding, but not drought, led to broad changes in composition and functional genes, especially those associated with carbon metabolism and nitrogen cycling. Differences were related to changes in relative abundance rather than the presence/absence of individual taxa or genes. Hydrologic history influenced community diversity by reducing interspecific competition or by alleviating resource limitation. These findings show that hydrologic history regulates species membership of the community (and thereby associated genes) but differences in water chemistry and interspecific interactions alter the relative abundance of species and their functional potential.}, }
@article {pmid41946009, year = {2026}, author = {Sutaoney, P and Singh, P and Malakar, S and Arsi, L and Ghosh, P}, title = {Microbial lipases: Catalyzing sustainable solutions for industrial innovations.}, journal = {Enzyme and microbial technology}, volume = {198}, number = {}, pages = {110869}, doi = {10.1016/j.enzmictec.2026.110869}, pmid = {41946009}, issn = {1879-0909}, abstract = {Microbial lipases are multifaceted biological catalyst that have surfaced as a key driver in various industries and are both eco-friendly and cost efficient.In large scale applications, lipases produced from bacteria, fungi and yeasts function better than their equivalents generated from plants and animals due to their wide substrate specificity, catalytic efficacy and stability under physicochemical circumstances. Recent developments in microbial lipase research, including sources, screening techniques, assay procedures, production methods, purification tactics, and biochemical characterisation, are critically examined in this review.The structural and mechanistic elements that control lipase function-such as lid domains, interfacial activation, and catalytic triads-are given special attention since they all have an impact on the stability, specificity, and industrial performance of the enzyme.Large-scale screening is done to check for the production of lipase in Bacillus sp., Achromobacter sp., Alcaligenes sp., Arthrobacter sp., Pseudomonas sp., and Penicillium sp. Additionally, the combination of synthetic biology, metagenomics, CRISPR-Cas technologies, enzyme engineering, and AI-assisted modelling is emphasized as a revolutionary strategy for identifying and customizing lipases with desired characteristics, including extreme environment microbes and application-specific variants.The review also highlights the growing industrial uses of microbial lipases in the bio-fuel, food and beverage, detergent, textile, leather, pharmaceutical, and medical industries, highlighting their contribution to the development of economically feasible and ecologically safe bioprocesses. All things considered, microbial lipases are an important biotechnological tool for developing sustainable industrial innovation and green chemistry.}, }
@article {pmid41946242, year = {2026}, author = {Yang, Y and Wang, Y and Li, J and Long, Y and Xiao, X and Fang, C and Hu, L}, title = {Temperature-dependent demethylation of methylarsenic by methanogens: Linking carbon metabolism to arsenic speciation in landfills.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {141986}, doi = {10.1016/j.jhazmat.2026.141986}, pmid = {41946242}, issn = {1873-3336}, abstract = {The environmental risk posed by arsenic (As) in landfills, driven by its high concentrations and mobility, is a significant concern. While inorganic arsenate [As(V)] and arsenite [As(III)] are dominant, the microbial-mediated conversion of these inorganic species into less toxic methylated arsenicals (MAs) is a key attenuation pathway. However, the reverse process-the demethylation of MAs back to more toxic inorganic forms-and its microbial drivers in landfills are not well understood. The availability of substrates and temperature are important growth factors and environmental factors that affect the activity and community structure of MA. This study investigated the demethylation of dimethylarsinic acid (DMAs) by methanogenic communities enriched from the leachate saturated zone (LSZ) under different thermal fields (15℃, 35℃, 55℃). We found that methylotrophic methanogens were the primary agents of DMAs demethylation, with the highest efficiency observed at mesophilic temperature (35℃), followed by thermophilic (55℃) and psychrophilic (15℃) conditions. Interestingly, methane (CH4) release exhibited a distinct trend (55℃ > 35℃ > 15℃), indicating an inconsistency between methanogenic activity and MAs demethylation efficiency at higher temperatures. A partial least squares path model (PLS-PM) revealed that both the abundance of methanogenic functional genes and CH4 release had a significant negative effect on As species (path coefficients of -0.615 and -0.376, respectively). Metagenomic analysis identified Methanosarcina as the dominant methylotrophic genus at 35℃, while Methanosarcina thermophila and JAULTD01 sp. were key drivers at 55℃. Our findings demonstrate that methanogens dynamically couple carbon metabolism to As speciation, and this coupling can be reshaped by temperature-mediated shifts in the dominant methanogens and their functional genes distribution.}, }
@article {pmid41946252, year = {2026}, author = {Deng, B and Ren, ZH and Ren, CY and Zhao, HP}, title = {Inhibiting Cr(VI)-mediated ARG dissemination in wastewater: Synthetic antioxidant-, extracellular polymeric substance-, and nuclease-producing microbiome targeting ROS, MGEs, and ARG-MRG co-occurrence.}, journal = {Journal of hazardous materials}, volume = {509}, number = {}, pages = {141985}, doi = {10.1016/j.jhazmat.2026.141985}, pmid = {41946252}, issn = {1873-3336}, abstract = {Heavy metals (HMs) trigger the sustained enrichment and dissemination of antibiotic resistance genes (ARGs) by exerting selective pressure, and there is an urgent need for effective and environmentally friendly control strategies. Herein, we found that long-term (180 d) hexavalent chromium [Cr(VI)] stress (10 mg/L) could facilitate the enrichment of multidrug-resistant plasmids (e.g., blaTEM and sul1) and significantly increase (p < 0.05) the conjugative transfer frequency. Subsequently, we constructed a synthetic carotenoid- and extracellular nuclease gene exeM-producing microbiome centered on Deinococcus radiodurans R1, which synthesizes and secretes extracellular polymeric substances (EPS) via the Wzx/Wzy-dependent pathway, thereby alleviating environmental oxidative stress by adsorbing Cr(VI) (over 85%) and scavenging ROS (approximately 18-26-fold). qPCR results demonstrated that the synthetic microbiome effectively reduced ARG abundances, along with the mobile genetic elements traG and intI1 (by more than one order of magnitude, MGEs) and the metal resistance gene chrA (by more than two orders of magnitude, MRG). Electron microscopy and metagenomic analysis demonstrated that the synthetic microbiome could further reduce the co-occurrence of ARGs and MRGs (e.g., tetA, chrA, and chrB) by impairing plasmid integrity and preserving cell membrane integrity (ompC, oprC, plsB, and fabR), thus inhibiting horizontal gene transfer. In addition, it reduced the abundance of Pseudomonadota (the host harboring ARGs and MGEs, p < 0.05) by 33-48%. This study provides a sustainable bioremediation strategy for controlling the dissemination of ARGs in heavy metal-polluted wastewater.}, }
@article {pmid41946403, year = {2026}, author = {Bamanu, B and Liu, Y and Wan, H and Tian, Z and Zhao, Y}, title = {Deciphering β-lactam stress response in anammox systems: Off-target enzyme binding, electron transfer compensation and microbial collaboration.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134561}, doi = {10.1016/j.biortech.2026.134561}, pmid = {41946403}, issn = {1873-2976}, abstract = {The prevalence of antibiotics in pharmaceutical and municipal wastewater poses a critical threat to biological wastewater treatment, especially the anaerobic ammonium oxidation (anammox) process. This study investigated the inhibitory mechanism of cephalexin (CFX), a β-lactam antibiotic, on anammox performance. Exposure to 100 mg/L CFX reduced nitrogen removal efficiency to 48.5% and suppressed specific anammox activity and heme c content, while lower concentrations (≤10 mg/L) caused no significant inhibition. Molecular docking indicated strong binding affinities of CFX toward key functional enzymes, including nitrite reductase and hydrazine synthase, with binding energies of -7.6 and -7.4 kcal/mol, respectively, suggesting off-target enzyme interference rather than direct β-lactam-specific inhibition. The system showed reversible inhibition with multi-level adaptation, including enhanced extracellular polymeric substances secretion, strengthened antioxidant defense, elevated electron transport activity, and microbial community restructuring. Metagenomic analysis revealed enrichment of β-lactamase, efflux pump, and antioxidant-related genes during recovery, supporting detoxification and adaptive resistance. These insights establish a mechanistic framework for designing resilient anammox systems capable of recovering from β-lactam antibiotic shocks in practical wastewater treatment applications.}, }
@article {pmid41946559, year = {2026}, author = {Campo-Beamud, C and Adan Ruiz, A and Bastante Quijano, J and Campo Beamud, E and Gómez-Romero, FJ and Fernández Ruíz, AJ and Copete, S}, title = {Publicly available multimodal large language models for ocular surface infections: benchmarking against corneal specialists in triage, diagnosis and treatment.}, journal = {The British journal of ophthalmology}, volume = {}, number = {}, pages = {}, doi = {10.1136/bjo-2025-328867}, pmid = {41946559}, issn = {1468-2079}, abstract = {BACKGROUND/AIMS: Ocular surface infections remain a major cause of visual loss worldwide, yet diagnosis often relies on slow or insensitive microbiological techniques. Artificial intelligence may complement emerging molecular tools by supporting rapid triage and diagnostic reasoning. This study benchmarked publicly available multimodal large language models (LLMs) against corneal specialists for the diagnosis, treatment and urgency triage of infectious keratitis and conjunctivitis.<br><br>METHODS: A single-centre diagnostic-accuracy study included 60 microbiologically confirmed infectious keratitis and conjunctivitis cases, each comprising a slit-lamp photograph and a paired clinical vignette. Six multimodal LLMs (GPT-4o, GPT-5, Gemini, Claude, Perplexity and Grok) were evaluated for diagnosis, treatment and urgency triage under three input conditions (image-only, text-only and image+text). Outputs were compared with two corneal specialists.<br><br>RESULTS: LLM performance depended strongly on input modality. Image-only accuracy was lowest (best GPT-5, 61.4%; &#x3ba;=0.38) with frequent misclassification of fungal and Acanthamoeba keratitis and hallucinations confined to this setting. Text input improved results (GPT-5, 83.3%; &#x3ba;=0.78), though accuracy remained below specialists (87-90%; &#x3ba;&#x2248;0.8). Combined image+text achieved near-human accuracy without consistently surpassing corneal specialists (Perplexity 96.7%; &#x3ba;=0.95; GPT-5 91.7%; &#x3ba;=0.87). Treatment accuracy remained lower (81-85% vs 90-98%), while urgency triage matched experts in multimodal input.<br><br>CONCLUSION: Publicly accessible multimodal LLMs can approach expert-level performance in diagnosis and triage when provided with clinical context and slit-lamp images. Gaps in therapeutic reasoning and rare pathogen recognition underscore the need for targeted refinement and validation. These models may complement specialist care, supporting rapid triage and integration with molecular or metagenomic diagnostics, especially in resource-limited settings.}, }
@article {pmid41947210, year = {2026}, author = {Tang, G and Zhang, C and Zhang, X and Liu, H and Suen, G and Yao, J and Zhang, J}, title = {Multi-omics revealed the effects of rumen to blood path on early lactation performance in transition dairy cows.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02403-y}, pmid = {41947210}, issn = {2049-2618}, support = {2023YFE0111800//National Key Research and Development Program of China/ ; 2024-JSGG-021//the National Center of Technology Innovation for Dairy/ ; 2024BBF01006//Key Research and Development Project of Ningxia Hui Autonomous Region/ ; }, abstract = {BACKGROUND: The transition period is vitally important to the life cycle of dairy cows. However, the function of the microbiota during both pre- and post-partum and their relationship with ruminal, plasma, and milk metabolites still require systematic investigation. To address this, the 7 highest- and 7 lowest-performing animals among a cohort of 100 dairy cows were selected based on their postpartum energy-corrected milk yield. Rumen fluid and plasma samples were collected during both pre- and post-partum periods, whereas milk samples were obtained postpartum. Shotgun metagenomics of rumen contents in addition to metabolomics of rumen, plasma, and milk samples were performed to evaluate the associations between ruminal microbes and early lactation performance in transition dairy cows.<br><br>RESULTS: Compared with prepartum cows, postpartum high-yield cows had greater concentrations of ruminal volatile fatty acids and plasma total bile acid. Moreover, plasma urea nitrogen and most amino acids, peptides, and their derivatives in plasma and milk were increased in postpartum high-yield cows, relative to postpartum low-yield cows. Metagenomic analysis revealed that the relative abundances of several species within the Prevotella, Succinimonas, Succinatimonas, and Methanosphaera increased, while other bacteria belong to Alistipes and Bacteroides, and archaeal Methanobrevibacter species decreased in postpartum cows, particularly in postpartum high-yield cows. Co-occurrence network and correlation analysis suggested that Prevotella and Succinatimonas were negatively correlated to Alistipes, Bacteroides, and Methanobrevibacter, potentially contributing to the nutritionally efficient phenotype of postpartum high-yield cows. A metabolic pathway analysis of our metagenomic data revealed that postpartum high-yield cows possessed more microbial genes involved in starch utilization and amino acid synthesis, while a wide range of microbial genes involved in cellulose utilization, acetogenesis, and amino acid degradation were found in prepartum cows with low-yield in postpartum. A structural equation model analysis showed that the increased relative abundances of Prevotella tf.2-5 and Succinatimonas CAG_777 were related to greater concentrations of plasma chenodeoxycholic acid glycine conjugate, milk 5-Methoxytryptophan, and energy-corrected milk yield. Finally, pan-genomic analysis confirmed that Alistipes, Bacteroides, and Methanobrevibacter possess genetic conservation of both hydrogenases and dehydrogenases, which may contribute to energy loss in the rumen via hydrogen dissipation.<br><br>CONCLUSION: In summary, our findings provide a fundamental understanding of how microbiome-dependent mechanisms contribute to early lactation performance in dairy cows during the transition period. The increased abundance of Prevotella, Succinimonas, and Succinatimonas in postpartum cows suggest that they are important microbes during the transition period and may help in coping with metabolic challenges, while improving nutrient utilization efficiency during this period. Our study underscores the importance of the ruminal microbiome during the transition period and highlights the need for rumen-based nutritional intervention strategies to improve production efficiency in ruminants. Video Abstract.}, }
@article {pmid41947478, year = {2026}, author = {Yang, X and Zhu, C and Liu, B and Yang, P and Cao, Z and Liang, J and Hu, J and Yu, Q and Zhong, Y and Du, W and Chow, J and Yan, S and Liu, H and Li, L and Wang, T and Gu, Y and Ma, G}, title = {Astragaloside IV Exhibited Antidiabetic Effects by Improving Glucose Metabolism, Repairing Damaged Gut Barrier and Regulating Intestinal Microbiota.}, journal = {Phytotherapy research : PTR}, volume = {}, number = {}, pages = {}, doi = {10.1002/ptr.70205}, pmid = {41947478}, issn = {1099-1573}, support = {81374051//National Natural Science Foundation of China/ ; 81873078//National Natural Science Foundation of China/ ; 82074109//National Natural Science Foundation of China/ ; 82374133//National Natural Science Foundation of China/ ; }, abstract = {Astragaloside IV (AS-IV), a main active ingredient derived from Astragali Radix, displays a favorable effect in treating type 2 diabetes mellitus (T2DM). This study was aimed to figure out its antidiabetic mechanisms. The db/db mice were treated with AS-IV, and the metabolism phenotype and epithelial barrier permeability were tested. Trans-epithelial resistance assay was performed in Caco-2 cells. Metagenomic sequencing was used to determine the gut microbiota composition and function. The content of short-chain fatty acid (SCFA) in feces was determined using Agilent 8890-5977B GC-MS. Despite increasing mice body weight, AS-IV significantly reduced hyperglycemia in the db/db mice, decreased the ratio of liver weight/body weight, alleviated hepatic total cholesterol and triglyceride levels. AS-IV reduced inflammation through suppressing pro-inflammatory genes (Il1b, Tnf, Ccl2) and elevating anti-inflammatory genes (Il10, Il4, Il13, Il33) in the colonic epithelium. AS-IV also reversed the increased intestinal permeability and decreased expression of tight junction (TJ) proteins Claudin-1, ZO-1 in the db/db mice and Claudin-1, Occludin in Caco-2 cells. Additionally, metagenomic sequencing showed AS-IV altered composition and function of gut microbiota. The 80 species of gut microbiota were markedly changed, e.g., boosting of Alistipes spp. and Prevotella copri, decreasing of relative abundance of Ruminococcus gnavus and Enterocloster bolteae. AS-IV upregulated the SCFA related pathway, increased the content of SCFA, upregulated the transcription levels of SCFA receptors (i.e., GPR41, GPR43 and GPR109a), thereby improved glucose metabolism in the db/db mice. These findings demonstrate that AS-IV exhibited favorable antidiabetic effects by improving glucose metabolism and altering intestinal microbiota symbiosis via repairing the damaged gut barrier. This study will provide valuable reference for the development of new antidiabetic drugs and medication of T2DM.}, }
@article {pmid41947790, year = {2026}, author = {Sun, W and Li, Y and Su, J and Mao, S and Yang, S and Zhu, Y and Liu, Y and Ma, J and You, W and Zhang, Y and Guo, H and Xing, G and Li, S and Yan, Q and Ma, X}, title = {Multi-kingdom metagenomic characterization of the gut bacteriome, mycobiome, and virome in chronic functional constipation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1744020}, pmid = {41947790}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Virome ; *Mycobiome ; *Constipation/microbiology/virology ; Metagenomics ; Feces/microbiology/virology ; Female ; *Bacteria/classification/genetics/isolation &amp; purification ; Male ; Middle Aged ; *Fungi/classification/genetics/isolation &amp; purification ; Adult ; Dysbiosis/microbiology ; Viruses/classification/genetics/isolation &amp; purification ; Metagenome ; Chronic Disease ; Aged ; }, abstract = {BACKGROUND: Chronic functional constipation (CFC) is a common gastrointestinal disorder increasingly linked to gut microbiome dysbiosis. However, multi-kingdom metagenomic characterization of bacterial, fungal, and viral communities in CFC remains limited.<br><br>METHODS: Fecal samples from 53 CFC patients and 48 healthy controls were analyzed using whole-metagenome shotgun sequencing. Microbial composition, function, cross-kingdom interactions, and diagnostic potential were evaluated using diversity analyses, KEGG annotation, network analysis, and random forest modeling.<br><br>RESULTS: Compared with healthy controls, CFC patients exhibited marked alterations across multiple microbial kingdoms. The gut bacteriome showed significant community-structure shifts despite comparable &#x3b1;-diversity, characterized by depletion of health-associated Firmicutes (e.g., Faecalibacterium and Roseburia) and enrichment of Proteobacteria (e.g., Klebsiella). The mycobiome displayed selective changes in diversity and composition, with several potentially pathogenic fungal taxa enriched in CFC (e.g., Fusarium sp. c181). In the virome, community composition differed significantly between groups, with higher viral richness in CFC and widespread depletion of diverse bacteriophages in CFC patients. Functional profiling suggested feature-level functional differences without a clear global shift, including reduced carbohydrate transport and utilization pathways and relatively higher abundance of stress-response and metabolic adaptation modules in CFC. Cross-kingdom network analysis demonstrated substantially denser microbial interactions in CFC, dominated by viral associations, with Faecalibacterium prausnitzii and Faecalibacterium_SGB15346 acting as central hubs. Machine-learning models showed strong discriminatory power for CFC classification based on bacterial and viral features, whereas fungal features contributed less.<br><br>CONCLUSIONS: CFC is associated with coordinated multi-kingdom gut microbiome dysbiosis involving bacteria, fungi, and viruses, accompanied by functional shifts and intensified cross-kingdom interactions. Bacterial and viral signatures show strong potential as microbiome-based biomarkers for CFC, highlighting the importance of integrating multi-kingdom analyses to better understand disease-associated gut ecosystem alterations.}, }
@article {pmid41948038, year = {2026}, author = {Howells, AEG and Santana, M and Cook, EM and Orrill, B and Boyer, G and Debes, RV and Fecteau, KM and Colman, DR and Boyd, ES and Shock, EL}, title = {Pushing the upper temperature limit of methanotrophy in continental hydrothermal ecosystems, active biological methane oxidation in hot springs of Yellowstone National Park.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1736896}, pmid = {41948038}, issn = {1664-302X}, abstract = {Methane oxidation in terrestrial geothermal systems is an understudied process contributing to carbon cycling in extreme environments. We combined geochemical analyses, 16S rRNA gene amplicon sequencing, shotgun metagenome sequencing, and [14]CH4 microcosm assays across 61 Yellowstone hot springs spanning pH 1.9-9.0 and temperatures of 28.6-92.2 °C to survey hydrothermal systems for methanotrophy. Bacterial aerobic methanotroph phylotypes were detected at multiple sites, including Verrucomicrobia (order S-BQ2-57) and Alphaproteobacteria, with the family Methylocystaceae having the highest relative abundance among bacterial methanotroph phylotypes. No known archaeal anaerobic methanotrophs were observed. Biological methane oxidation was widespread, occurring at 14 of 17 experimental sites under both ambient and air-amended conditions. Rates were highest at CH4-rich, NH3-poor sites dominated by bacterial methanotrophs, consistent with energy supply predictions integrating CH4/O2 and CH4/NH3 concentration ratios. Conversely, NH3-rich, energy-rich sites exhibited lower methane oxidation rates (MOR) and were dominated by archaeal ammonia oxidizers, primarily Candidatus Nitrosocaldus, suggesting chemical competitive inhibition of NH3 on methanotrophy. Remarkably, significant methane oxidation occurred at eight sites where no known methanotrophs were detected, including a site at 89.9 °C-well above the previously reported upper growth temperature limit for methanotrophs from continental geothermal and hydrothermal systems-pointing to uncharacterized thermophilic lineages. These results suggest that biological methane oxidation in Yellowstone hot springs is influenced by the interplay of substrate availability and energy supply. By linking energy supply calculations with microbial distributions, we identify both known methanotrophs (Verrucomicrobia, Alphaproteobacteria) and archaeal ammonia oxidizers as potential active contributors, while highlighting the potential for novel thermophilic lineages, thereby expanding the ecological and thermal boundaries of methane oxidation in extreme terrestrial ecosystems.}, }
@article {pmid41948759, year = {2026}, author = {Zhu, G and Zou, Z and Fang, Z and Xu, B}, title = {Rare but Critical: Severe Tropheryma Whipplei Pneumonia-Induced Cardiopulmonary Failure in a Young Immunocompromised Adult-A Case Report and Literature Review.}, journal = {Clinical case reports}, volume = {14}, number = {4}, pages = {e72448}, pmid = {41948759}, issn = {2050-0904}, abstract = {Tropheryma whipplei, traditionally linked to classic Whipple's disease with gastrointestinal involvement, is increasingly recognized as a cause of pneumonia. Reports of T. whipplei-associated pneumonia progressing to respiratory failure with concurrent acute cardiac failure remain extremely rare. A 38-year-old man with poorly controlled diabetes presented to the emergency department with acute chest tightness, dyspnea, and impaired consciousness. Laboratory findings indicated type II respiratory failure and elevated inflammatory markers. Imaging revealed scattered patchy hazy opacities and increased density bilaterally, prompting emergent intubation and transfer to the intensive care unit. Despite empirical antibiotics for severe pneumonia, he developed acute cardiac failure on day 3, manifesting as bloody sputum and diffuse moist rales with rhonchi on auscultation, alongside an LVEF of 49% and a markedly elevated serum BNP level of 3100 pg/mL. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid detected abundant T. whipplei sequences. He was administered targeted therapy with meropenem, supported by mechanical ventilation, diuresis, and glycemic control. Cardiopulmonary function improved, and he was discharged on oral doxycycline plus hydroxychloroquine. Follow-up endoscopy and biopsy showed no gastrointestinal involvement (Periodic Acid-Schiff negative), restored cardiac function (LVEF 58.6%), and no recurrence. This case underscores T. whipplei as a potential cause of isolated pneumonia with cardiopulmonary failure in functionally immunocompromised hosts and highlights the critical role of mNGS in guiding timely targeted therapy to improve outcomes.}, }
@article {pmid41949195, year = {2026}, author = {Saini, G and Yadav, R and Bagga, R and Sharma, N and Sethi, S}, title = {Cervicovaginal microbiota in female sex workers with bacterial vaginosis: A metagenomic perspective.}, journal = {Indian journal of dermatology, venereology and leprology}, volume = {}, number = {}, pages = {1-3}, doi = {10.25259/IJDVL_1199_2025}, pmid = {41949195}, issn = {0973-3922}, }
@article {pmid41949263, year = {2026}, author = {Marriott, L and Martinez-Lopez, A and Liga, A and Horiba, K and Warr, A and Phulusa, JN and Kumar, RS and Carey, L and Ito, Y and Parcell, BJ and Leslie, NR and Feasey, NA and Jacob, ST and Rylance, J and Kersaudy-Kerhoas, M}, title = {An automated and portable platform for rapid cell-free DNA isolation and its application in microbial DNA metagenomic sequencing from human blood samples.}, journal = {Lab on a chip}, volume = {}, number = {}, pages = {}, doi = {10.1039/d5lc00876j}, pmid = {41949263}, issn = {1473-0189}, abstract = {The prompt identification of pathogens in human circulation in a clinically deployable format remains an unmet clinical need. The established test for infection diagnostics remains blood culture, which typically takes 2-4 days and is positive in less than 15% of cases, with many prevalent pathogens difficult or impossible to culture. While microbial cfDNA in blood could facilitate the diagnosis of sepsis, febrile and infectious conditions, sample preparation for cell-free DNA (cfDNA) analysis in decentralised settings presents challenges due to its complexity and the low concentration and fragmented nature of cfDNA in blood plasma. We developed a portable and automated platform and a consumable (CNASafe) for cfDNA isolation from human plasma samples. The platform-device performance was evaluated by comparing relative cfDNA yield against a reference (QIAGEN QIAamp Circulating Nucleic Acid Kit). cfDNA eluates from ten non-cultured blood samples from hospital patients were sequenced on a nanopore sequencer, and results compared to blood cultures. Extraction of cfDNA using the CNASafe device was completed in 40 minutes, compared to the 1 hour 15 min reference protocol. The device achieved an average relative cfDNA recovery of 100.5% over 333 unique extractions encompassing all parameter variations, demonstrating a performance equivalent to the reference kit. From the patient samples, a sufficient quantity of microbial cfDNA was extracted to either identify pathogens missed by blood cultures or confirm negative cultures. The CNASafe platform and real-time nanopore sequencing offer a promising solution for the rapid deployment of metagenomic diagnostics, enabling pathogen identification within a few hours in decentralised clinical environments.}, }
@article {pmid41949675, year = {2026}, author = {Chen, Y and Sun, N and Gan, B and He, Y and Luo, J and Pan, K and Zeng, Y and Jing, B and Zeng, D and Ni, X}, title = {Targeting Bifidobacterium animalis alleviates high-fluoride exposure-induced kidney injury in mice.}, journal = {AMB Express}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13568-026-02031-7}, pmid = {41949675}, issn = {2191-0855}, support = {2025YFHZ0278//Sichuan Science and Technology Program/ ; }, }
@article {pmid41949810, year = {2026}, author = {Adolph, JE and Pentek, C and Bauch, T and Held, C and Brenner, T and Felderhoff-Müser, U and Grumaz, S and Horvatek, P and Steindor, M and Asar, L and Voigt, S and Dziobaka, J and Dohna-Schwake, C and Goretzki, SC}, title = {Next-generation sequencing of cell-free microbial DNA in blood samples of critically ill children: a single-center experience.}, journal = {Molecular and cellular pediatrics}, volume = {13}, number = {1}, pages = {}, pmid = {41949810}, issn = {2194-7791}, abstract = {BACKGROUND: Rapid and accurate pathogen detection is critical for optimizing outcomes in pediatric sepsis. Next-generation sequencing (NGS) of cell-free DNA (cfDNA) from blood enables culture-independent identification of microbial DNA from bacteria, viruses, fungi, and parasites. We evaluated the diagnostic yield and clinical impact of cfDNA-based NGS in critically ill and predominantly immunocompromised pediatric patients (≤ 18 years) with suspected infection. This retrospective single-center study included pediatric patients who underwent plasma cfDNA-NGS at a tertiary care hospital in Germany. Following computational removal of human DNA, remaining sequences were aligned to curated microbial reference databases. Diagnostic performance was compared with blood cultures and viral PCR, and clinical relevance was assessed by pediatric infectious disease specialists.<br><br>RESULTS: 111 tests in 78 pediatric patients, mostly with systemic inflammatory response syndrome of unknown etiology, were performed. Overall, 61 tests (54.5%) were positive for pathogenic cfDNA. Compared with conventional microbiological diagnostics, NGS demonstrated a sensitivity of 64.7% and specificity of 88.2% when blood cultures and viral PCR served as the reference standard. NGS identified additional pathogens in a substantial proportion (41.1%) of cases that remained negative by standard testing. Of those pathogens only found by NGS, over 60% were deemed clinically relevant. In 14.8% of positive NGS results, a pathogen-specific therapy was started, while 40.2% of tests led to a discontinuation of therapy (51.0% of negative tests). Out of all positive NGS, 38 (62.3%) were classified as clinically relevant. NGS testing also detected rare infections with fungi and parasites in four cases each.<br><br>CONCLUSION: Detection of pathogenic cfDNA through NGS from blood shows promising results as an additional diagnostic tool in critically ill pediatric patients with suspected infections. Clinical utility is currently still limited by its high cost, undetermined diagnostic validity and limitations in testing for resistances and restricted availability of raw sequencing data due to data-protection constraints.}, }
@article {pmid41949970, year = {2025}, author = {Lerhzouli, H and Al Ibrahmi, B and Khal-Layoun, S and Bour, A}, title = {New therapeutic approaches based on modulation of the intestinal microbiota to correct dysbiosis in patients with type 2 diabetes.}, journal = {La Tunisie medicale}, volume = {103}, number = {11}, pages = {1707-1717}, doi = {10.62438/tunismed.v103i11.6101}, pmid = {41949970}, issn = {2724-7031}, mesh = {Humans ; *Diabetes Mellitus, Type 2/complications/microbiology/therapy ; *Dysbiosis/therapy/microbiology/etiology ; *Gastrointestinal Microbiome/drug effects/physiology ; Probiotics/therapeutic use ; Hypoglycemic Agents/therapeutic use ; Insulin Resistance ; }, abstract = {Type 2 diabetes is a chronic disease characterized by insulin resistance and reduced insulin production in pancreatic cells. Conventional treatment of type 2 diabetes relies on hypoglycemic drugs, physical activity and a balanced low-carbohydrate diet, but with technological advances in metagenomics and metabolomics researchers have developed new therapeutic approaches aimed to modulate, the gut microbiota to correct the dysbiosis confirmed in people with type 2 diabetes. This literature review provides an update on therapies aimed to modulate the gut microbiota to correct dysbiosis in type 2 diabetics and summarizes the latest advances in this field.}, }
@article {pmid41950191, year = {2026}, author = {Kador, SM and Shila, JF and Afrin, S and Jannat, J and Islam, KT and Rubaiyat, RN and Bhuiyan, MIU and Chakrovarty, T and Hasan, MS and Sakib, N and Rahman, MS and Islam, OK and Islam, MT}, title = {Microbial diversity, functional genomics and antibiotic resistance in integrated chicken and fish farming systems of Bangladesh.}, journal = {PloS one}, volume = {21}, number = {4}, pages = {e0344367}, doi = {10.1371/journal.pone.0344367}, pmid = {41950191}, issn = {1932-6203}, mesh = {Animals ; Bangladesh ; *Chickens/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Aquaculture ; *Drug Resistance, Microbial/genetics ; *Fishes/microbiology ; Genomics ; Anti-Bacterial Agents/pharmacology ; Biodiversity ; Microbial Sensitivity Tests ; Metagenomics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {The integrated chicken and fish farming system in Bangladesh is widely practiced for its resource efficiency, yet its microbial structure, functional potential, and associated antimicrobial resistance risks remain poorly understood. This study investigated microbial communities, metabolic functions, and antimicrobial resistance profiles across multiple components of integrated farming systems, including chicken gut, chicken droppings, feed, fish intestine, and pond sediment. Microbial profiling was performed using 16S ribosomal ribonucleic acid (rRNA) gene sequencing, functional metagenomic prediction, and culture-based isolation, complemented by antimicrobial susceptibility testing. A total of 2,838 operational taxonomic units were identified, with bacteria constituting the vast majority of detected microorganisms. Microbial community composition was strongly shaped by sample type, reflecting distinct ecological niches within the farming system. Chicken gut samples were dominated by Firmicutes, feed samples by Cyanobacteria, and sediment samples exhibited the highest microbial diversity, including taxa involved in biogeochemical cycling. Functional analysis revealed that pathways related to amino acid and carbohydrate metabolism were most abundant across all samples, while sediment and feed were enriched in pathways associated with xenobiotic degradation, suggesting a role in environmental detoxification. Culture-based methods isolated clinically relevant bacteria, including Escherichia coli and Proteus mirabilis, although metagenomic analysis indicated that these organisms represented only a minor fraction of the overall microbial community. Antimicrobial susceptibility testing demonstrated notable resistance, particularly to tetracyclines and fluoroquinolones. Metagenomic analysis further identified multiple antimicrobial resistance genes, with several showing strong associations with specific bacterial genera. This study provides the first comprehensive characterization of microbial diversity, functional capacity, and antimicrobial resistance within integrated chicken and fish farming systems in Bangladesh, highlighting potential environmental reservoirs of resistance and underscoring the need for improved management strategies to enhance sustainability and reduce public health risks.}, }
@article {pmid41950533, year = {2026}, author = {Cai, X and Yao, Y and Zheng, Y and Zhao, X}, title = {Multi-omics gut microbiome signatures for treat-to-target management in inflammatory bowel disease.}, journal = {Microbiological research}, volume = {309}, number = {}, pages = {128511}, doi = {10.1016/j.micres.2026.128511}, pmid = {41950533}, issn = {1618-0623}, abstract = {Inflammatory bowel disease (IBD) care now relies on an expanding portfolio of biologics and small molecules, yet symptom-driven phenotyping often misses molecular endotypes, contributing to primary non-response and loss of response. This review examines how gut microbiota-centered multi-omics can be translated into decision support within treat-to-target (T2T) management and therapeutic drug monitoring (TDM). We synthesize evidence from stool and mucosal metagenomics/metatranscriptomics, virome and bacteriophage signals, metabolomics, blood proteomics, and host transcriptomic/epigenomic and genetic layers, emphasizing analytical validity, external validation, calibration, and action-linked thresholds. Longitudinal data indicate that IBD-associated dysbiosis is predominantly functional and time-varying, enabling applications in diagnosis, prognosis, therapy-response prediction, and monitoring of inflammatory burden and remission depth. However, many reported predictors show limited transportability due to pre-analytical variation, batch effects, endpoint heterogeneity, and confounding by diet, antibiotics, and prior therapies. We propose a pragmatic, tiered workflow: deploy minimal, interpretable signatures at baseline and early induction, and interpret outputs alongside fecal calprotectin/CRP, endoscopy or imaging when indicated, and drug exposure/anti-drug antibodies to distinguish underexposure and immunogenicity from true mechanistic non-response, guiding dose optimization versus mechanism switching. Digital/remote monitoring can operationalize iterative reassessment while reserving deeper omics for decision-critical checkpoints. Overall, the microbiome is best framed as an actionable layer within a multi-signal IBD management system rather than a standalone biomarker; translation will depend on standardization, workflow integration, prospective validation, and demonstrated clinical and economic value.}, }
@article {pmid41950684, year = {2026}, author = {Cao, S and Liu, X and Tao, Y and Ren, J and Zhou, Z and Du, R}, title = {EPS-mediated mineralization drives granule densification and enhances denitratation-anammox coupling under alkaline conditions.}, journal = {Water research}, volume = {299}, number = {}, pages = {125888}, doi = {10.1016/j.watres.2026.125888}, pmid = {41950684}, issn = {1879-2448}, abstract = {The granular-based CANDAN (Complete Ammonium and Nitrate removal via Denitratation-Anammox over Nitrite) process offers a promising low-carbon and high-rate strategy for nitrogen removal; yet the mechanisms by which alkaline conditions regulate granule structure and functional coupling remain insufficiently understood. Here, a 9-L sequencing batch reactor (SBR) was operated for 130 days with stepwise pH elevation from 7.31 ± 0.03 to 8.52 ± 0.08 to elucidate alkaline condition-driven structural and functional adaptations in CANDAN granules. Moderate alkaline conditions significantly improved nitrogen removal, with total nitrogen removal efficiency increasing to 91.4 ± 0.1 %, accompanied by pronounced improvement in sludge settleability (sludge volume index after 30 min of settling, SVI30, decreased from 76.4 to 19.4 mL g[-1] SS) and stabilization of dominant granule sizes at 0.5-1 mm, accounting for approximately 69.8 % of the total granules, indicating progressive granule densification. Mineralogical analyses revealed that hydroxyapatite dominated the inorganic matrix, with co-precipitation of calcium carbonate (CaCO3) and transient magnesium ammonium phosphate formation reinforcing granule structure. Elevated pH also remodeled extracellular polymeric substances (EPS), increasing loosely bound EPS, raising the protein-to-polysaccharide ratio, and enriching tryptophan-like proteins that facilitated EPS-mediated mineral nucleation. Metagenomic analysis revealed streamlined carbon metabolism and enrichment of key nitrogen-cycling genes (napA, nosZ, hzsA), while downregulation of Ca[2+], Mg[2+], and phosphate transport genes favored extracellular mineral accumulation. Overall, moderately alkaline conditions drive EPS-mediated mineralization that densifies granules and stabilizes Denitratation-Anammox coupling, providing mechanistic insight for optimizing low-carbon nitrogen removal under alkaline wastewater conditions.}, }
@article {pmid41950685, year = {2026}, author = {Zuo, Z and Xing, Y and Qiao, L and Yang, S and Ren, D and Guo, M and Liu, Y and Huang, X}, title = {Unveiling in-pipe carbon-sulfur transformation and microbial function during urine transport for centralized management.}, journal = {Water research}, volume = {299}, number = {}, pages = {125840}, doi = {10.1016/j.watres.2026.125840}, pmid = {41950685}, issn = {1879-2448}, abstract = {Source-separated urine collection and centralized nutrient recovery at city-scale hold great potential for advancing sustainable resource management. As the critical link between urine collection systems and nutrient recovery facilities, urine-transporting sewer systems have recently been incorporated into life cycle assessments (LCA), yet their potential for biochemical transformations has not been explored. Here, for the first time, we experimentally unveil key pollutant transformations and microbial functions in a urine-fed bioreactor (representing urine transport), with a sewage-fed bioreactor serving as a control. Major urine nutrients (N, P, and K) remained largely stable during transport, whereas organic carbon and sulfate decreased markedly. Methane production was negligible over 160 days, while sulfide production initially declined but fully recovered by day 80, accompanied by elevated microbial activity and substantial sulfide accumulation in sediments. Microbial community analyses revealed that urine exposure reduced community richness and led to a pronounced community, with methanogenic archaea strongly inhibited and sulfate-reducing bacteria (SRB) becoming dominant under prolonged urine stress. A Desulfomicrobium-like SRB species was progressively enriched (∼35% of total metagenome-assembled genomes (MAGs)) and likely responsible for the sulfide rebound. Spatial heterogeneity of microbial communities in sediments further explains depth-specific sulfide accumulation. Overall, this study provides important insights into carbon-sulfur transformations and microbial adaptation in urine transport systems, informing improved system design, operation, and further LCA.}, }
@article {pmid41950966, year = {2026}, author = {Yan, S and Han, Q and Chen, L and Jin, D and Lu, Y and Zhou, J and Zhang, X}, title = {Simultaneous removal of Se(IV) and Cr(VI) from acidic wastewater using a Se(IV)-reducing internal circulation reactor: performance and microbial resistance mechanisms.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134537}, doi = {10.1016/j.biortech.2026.134537}, pmid = {41950966}, issn = {1873-2976}, abstract = {Acidic wastewater contaminated with selenite (Se(IV)) and chromate (Cr(VI)) poses elevated environmental risks due to the combined toxicity of metal(liod) and acidity. Metal(loid)-resistant consortia, such as Se(IV)-reducing sludge (SeRS), provide a promising strategy for treating such wastewater by converting Se(IV) and Cr(VI) into less toxic Se(0) and Cr(III), respectively. In this study, an internal circulation (IC) reactor loaded with SeRS and granular activated carbon was constructed to evaluate its performance in treating such wastewater. In the absence of Cr(VI), the reactor achieved 94.6-98.5% Se(IV) removal at influent pH 4.5-8.0 with 1-3 mM Se(IV). At optimal pH 5.5, nearly complete removal of both oxyanions was achieved at Se(IV)/Cr(VI) molar ratio of 5.2-10.4. Alkalinity generation from acetate oxidation buffered influent acidity at influent pH 4.5-5.5 and sustained microbial activity. Cr(VI) stress selectively enriched Brucella, Trichlorobacter, and Seleniivibrio for Cr(VI) reduction, while Pseudomonas accounted for Se(IV) and Cr(VI) reduction. Integrated extracellular polymeric substances (EPS), glutathione reductase (GOR), and metagenomic analyses revealed microbial resistance to Cr(VI) stress likely relied on intracellular glutathione-related detoxification, enzymatic Se(IV)/Cr(VI) reduction and antioxidant defenses, while extracellular EPS protection declined. Overall, it was demonstrated that the developed IC reactor process enabled robust and efficient removal of both Se(IV) and Cr(VI) from acidic wastewater.}, }
@article {pmid41951175, year = {2026}, author = {Rana, N and Angrup, A and Tiewsoh, K and Ray, P}, title = {Automating Microbial Community Analysis (AMCA): Development and application of as amplicon based graphical pipeline in patients with Chronic Kidney Disease.}, journal = {Indian journal of medical microbiology}, volume = {}, number = {}, pages = {101110}, doi = {10.1016/j.ijmmb.2026.101110}, pmid = {41951175}, issn = {1998-3646}, abstract = {INTRODUCTION: Amplicon sequencing is a targeted approach used to assess the diversity of microbial communities by amplifying and sequencing a specific genetic locus from DNA. QIIME2 is one of the most prevalent methods for metagenomics analysis due to its plugin-based design wherein distinct modules can be utilized to perform specific functions. However, QIIME2 data input, and plugin utilization is cumbersome to navigate. Previous amplicon pipelines also lack host depletion and statistical biomarker identification modules from upstream and downstream analysis.<br><br>METHODS: To this effect, we assembled a simple and customizable Zenity based GUI workflow for analysing amplicon data with Automating Microbial Community Analysis (AMCA). The analysis integrates key attributes of amplicon analysis: host depletion with Bowtie2 and biomarker prediction by LEfSe. The bash-based analysis guides and allows the user to select filtering parameters based on intermediate results while minimizing the need to navigate command-based plugins.<br><br>RESULTS: The outputs from the AMCA workflow include the filtered and host-depleted raw sequencing data, taxonomic abundances, alpha and beta diversity indices, alpha rarefaction analysis, phylogenetic tree (rooted and unrooted) and significant features which explain key microbial differences between conditions/classes of the experiment. The implementation of the designed workflow has been tested on a pilot study based on amplicon sequencing in 100 samples from patients of Chronic Kidney Disease and healthy controls. The exploratory LEfSE analysis revealed key taxa Streptococcus, Bacteroides and Faecalibacterium to vary between disease and control conditions. The source code related to the analysis can be assessed from the Github repository at https://github.com/Nitika-Rana/AMCA.<br><br>CONCLUSION: The study delivers an efficient, user-friendly, and customizable workflow for amplicon analysis, simplifying QIIME2 execution while enabling host depletion and biomarker characterization.}, }
@article {pmid41942205, year = {2026}, author = {Zhang, F and Wang, X and Wang, J and Fan, X and Kong, Y and Li, X and Zeng, X and Li, H and Liu, W and Zhang, A and Song, D and Gong, H}, title = {Revealing the microbial diversity and functional annotation during postharvest storage of sweet cherry using metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {233}, number = {Pt 1}, pages = {118955}, doi = {10.1016/j.foodres.2026.118955}, pmid = {41942205}, issn = {1873-7145}, mesh = {*Food Storage/methods ; *Prunus avium/microbiology ; *Metagenomics/methods ; *Food Microbiology ; *Microbiota ; Bacteria/classification/genetics ; *Fruit/microbiology ; }, abstract = {This study aimed to investigate the dynamic changes in the quality characteristics, microbial community diversity, functional annotation and metabolic pathways of sweet cherries stored at 25 °C for 0, 1, 3, 5 or 7 days. The results showed that the quality characteristics of sweet cherries gradually deteriorated with increasing storage time, and the abundance of Proteobacteria increased gradually. Mucoromycota appeared on D3 group, which may be one of the main microbial groups causing sweet cherry rot. In addition, 3D principal coordinate analysis showed that the species composition of sweet cherries stored for 1 day and fresh cherries was highly similar. The results of the Bray-Curtis distance analysis indicate a significant trend towards separation in species composition from the third day of storage. Moreover, KEGG annotations of metabolites and enzymes suggest that glycolysis and pyruvate metabolism are important in the storage of sweet cherries. Meanwhile, the pathway diagram shows that the main substances maintaining the pathway are pyruvate kinase and pyruvate dehydrogenase, which are detected in groups D5 and D7 groups. This study examines the changes in microbial communities and functional annotations that occur during the storage of sweet cherries after harvest. This provides a theoretical basis for developing new, efficient antibacterial agents for storing sweet cherries.}, }
@article {pmid41942425, year = {2026}, author = {Peña-Valencia, MF and Robaina-Estévez, S and Custer, GF and Turak, O and Sierra, F and Mendes, LW and Rubiano-Labrador, C and Gutiérrez, J and Vaksmaa, A and Dini-Andreote, F and Rosado, AS and Reyes, A and Jiménez, DJ}, title = {Lignocellulose-mediated selection of potential halophilic PET-degrading enzymes from mangrove soil.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71548-z}, pmid = {41942425}, issn = {2041-1723}, abstract = {Mangroves are ecosystems located at land-sea transition zones, where they are continuously exposed to plant biomass and plastic pollution. Their soils harbor extensive microbial diversity with potential for discovering polymer-degrading enzymes. Here, we perform a microcosm experiment to examine how mangrove soil microbial communities respond to inputs of lignocellulose or polyethylene terephthalate (PET) in the presence and absence of seawater, and to explore the selection of putative PET-active enzymes (PETases) using gene- and genome-resolved metagenomics. Incubation conditions lead to a gradual increase in salinity, resulting in the enrichment of halophilic taxa, including spore-forming bacteria and archaeal species, particularly in seawater-depleted treatments. Lignocellulose input is the primary driver of soil microbial community restructuring, followed by seawater presence. In dry, lignocellulose-amended microcosms (L treatment), microbial diversity is significantly reduced, while lignocellulolytic taxa within the phyla Bacillota and Actinomycetota are enriched. Twelve potential PETases are identified in the L treatment, sharing >70% sequence similarity with known PETases, and three are predicted to be thermostable. Two putative PETases from Microbulbifer species display distinct sequence and structural features, thereby expanding the currently limited PETase sequence landscape. This study demonstrates that perturbing environmental microbiomes with plant-derived polymers represents a promising strategy for capturing novel PETases.}, }
@article {pmid41942856, year = {2026}, author = {Liu, SW and Wang, XX and Xian, LY and Zou, DW and Huang, YF and He, XL and He, F and Wang, XT}, title = {Metagenomic analysis of intestinal microbiota characteristic differences between patients with ankylosing spondylitis and healthy individuals.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04996-8}, pmid = {41942856}, issn = {1471-2180}, support = {2023JH2/101700219//Liaoning Province Science and Technology Plan Joint Project (Applied Basic Research Project)/ ; }, }
@article {pmid41942925, year = {2026}, author = {Maimaitiming, A}, title = {Metagenomic next-generation sequencing (mNGS) for severe cat bite infections with negative aerobic culture: a single-center retrospective study in a rabies vaccination center.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13222-9}, pmid = {41942925}, issn = {1471-2334}, }
@article {pmid41943157, year = {2026}, author = {Bruna, P and Barra, PJ and García, M and Liachko, I and de la Luz Mora, M and Dutilh, BE and Abanto, M}, title = {Unraveling plasmid contributions to phosphorus acquisition in soil microbiomes.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00887-7}, pmid = {41943157}, issn = {2524-6372}, support = {2023-21230832//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; FONDECYT Regular 1241293//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; 1230084//Agencia Nacional de Investigaci&#xf3;n y Desarrollo (ANID)/ ; FONDECYT Regular 1251164//Agencia Nacional de Investigaci&#xf3;n y Desarrollo (ANID)/ ; Consolidator grant 865694/ERC_/European Research Council/International ; Germany's Excellence Strategy - EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; }, abstract = {BACKGROUND: Phosphorus (P) is a fundamental macronutrient for plant and microbial growth, but its availability in soils is often constrained by strong interactions with minerals and organic matter. While the role of bacteriophages in P cycling has gained attention, plasmids remain comparatively underexplored despite their central role in horizontal gene transfer. This study aimed to investigate the occurrence, diversity, and ecological relevance of plasmid-borne genes involved in P acquisition across soils with contrasting P availability.<br><br>RESULTS: Using curated plasmid databases and soil metagenomes from diverse biomes, we identified a broad repertoire of plasmid-encoded P-acquisition genes. These genes encompassed regulatory pathways, transport systems, organic P mineralization, and inorganic P solubilization. Regulatory and transporter genes were the most abundant categories, with phoB, phoP, and ugpC among the most frequently detected. When additional analyses were performed using habitat-specific P classifications and continuous P gradients, these associations appeared weak and were not significant after multiple-testing correction. These results suggest that plasmid-encoded P-acquisition genes are broadly distributed across environments rather than tightly constrained by measured soil P levels, while taxonomic assignment revealed that Pseudomonadota were the predominant plasmid hosts, followed by Bacillota and Actinobacteriota, suggesting broad host diversity.<br><br>CONCLUSIONS: This study provides a genomic overview of plasmid-borne genes associated with P acquisition in soils. Our results show that these genes are widespread across plasmids from diverse environments and host taxa, suggesting that the soil mobilome may represent an important reservoir of functions related to microbial P metabolism. While the presence and relative abundance of these genes indicate their potential ecological relevance, functional expression and ecological impact remain to be experimentally validated. These findings expand current knowledge of plasmid contributions to nutrient cycling and highlight the mobilome as a potential target for future studies aiming to better understand microbial strategies for P acquisition in soil ecosystems.}, }
@article {pmid41943240, year = {2026}, author = {Zhu, W and Qian, J and Peng, M and Li, Y and Hu, J}, title = {Post-COVID-19 Area Postrema Syndrome With SARS-CoV-2 in CSF: A Dual-Case Report and Review of the Literature.}, journal = {Immunity, inflammation and disease}, volume = {14}, number = {4}, pages = {e70421}, doi = {10.1002/iid3.70421}, pmid = {41943240}, issn = {2050-4527}, support = {ZDXM2024003//Wenshan Prefecture People's Hospital 2024 Annual Internal Scientific Research Key Projects/ ; }, mesh = {Humans ; Female ; *COVID-19/complications/cerebrospinal fluid/immunology ; *SARS-CoV-2 ; *Neuromyelitis Optica/cerebrospinal fluid/immunology/virology/etiology ; *Area Postrema/virology/pathology ; Middle Aged ; Adult ; Magnetic Resonance Imaging ; Immunoglobulin G/blood/cerebrospinal fluid ; Aquaporin 4/immunology ; Autoantibodies/blood ; }, abstract = {BACKGROUND: Neuromyelitis optica spectrum disorder (NMOSD) is a rare autoimmune astrocytopathy characterized by inflammatory demyelinating lesions in the central nervous system. Area postrema syndrome (APS), marked by intractable nausea, vomiting, and hiccups, is a recognized but less common initial manifestation. Post-infectious autoimmunity triggered by SARS-CoV-2 has been increasingly associated with NMOSD pathogenesis; however, the clinical significance of direct viral neuroinvasion and its relationship to divergent patient outcomes remains poorly understood.<br><br>METHODS: We report two female patients who developed isolated APS shortly after COVID-19 infection. Both patients underwent comprehensive neurological evaluation, including brain and spinal magnetic resonance imaging (MRI), cerebrospinal fluid (CSF) analysis with metagenomic next-generation sequencing (mNGS), and serological testing for aquaporin-4 immunoglobulin G (AQP4-IgG), myelin oligodendrocyte glycoprotein immunoglobulin G (MOG-IgG), and glial fibrillary acidic protein immunoglobulin G (GFAP-IgG) using cell-based assays. Clinical outcomes were compared in the context of antibody serostatus and treatment strategies. A review of the relevant literature on post-COVID NMOSD was also performed.<br><br>RESULTS: Both patients presented with intractable vomiting and hiccups following SARS-CoV-2 infection, and MRI demonstrated isolated T2/FLAIR hyperintense lesions in the dorsal medulla consistent with area postrema involvement. SARS-CoV-2 RNA sequences were detected in the CSF of both patients via mNGS, suggesting direct viral neuroinvasion or blood-brain barrier compromise. Despite similar initial presentations, their outcomes diverged dramatically. Patient 1 was AQP4-IgG negative, responded well to immunotherapy with intravenous immunoglobulin and corticosteroids followed by mycophenolate mofetil maintenance, and remained relapse-free at 12-month follow-up with significant lesion regression on MRI. Patient 2 was AQP4-IgG positive in both serum and CSF, and despite acute treatment, experienced a fatal relapse 6 months later with longitudinally extensive transverse myelitis while on low-dose prednisone monotherapy.<br><br>CONCLUSIONS: Isolated APS may represent an important yet under-recognized manifestation of post-COVID-19 autoimmune neuroinflammation. Detection of SARS-CoV-2 in CSF supports a role for direct viral neuroinvasion as a localized inflammatory stimulus. AQP4-IgG serostatus serves as a critical prognostic determinant: seronegativity is associated with a benign, monophasic course, whereas seropositivity mandates prompt initiation of potent immunosuppressive therapy to prevent devastating relapses. Clinicians should maintain a high index of suspicion for NMOSD in patients with unexplained persistent vomiting following COVID-19, and perform urgent neuroimaging and antibody testing for early risk stratification.}, }
@article {pmid41943413, year = {2026}, author = {Liu, F and Xie, F and Zhong, Q and Lin, X and Yang, Q and Li, Y and Huang, C and Huang, Q and Xu, L and Zhong, J}, title = {Application Value of Metagenomic Next-Generation Sequencing Using Bronchoalveolar Lavage Fluid and Blood Samples in Patients with Severe Pneumonia Complicated with Bloodstream Infection.}, journal = {Polish journal of microbiology}, volume = {75}, number = {1}, pages = {75-83}, doi = {10.33073/pjm-2026-008}, pmid = {41943413}, issn = {2544-4646}, mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; Retrospective Studies ; Middle Aged ; *Metagenomics/methods ; Aged ; Bacteria/genetics/isolation &amp; purification/classification ; *Pneumonia/microbiology/blood/complications/diagnosis ; Fungi/genetics/isolation &amp; purification/classification ; Aged, 80 and over ; Adult ; *Sepsis/microbiology/diagnosis ; }, abstract = {This study was designed to systematically evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) using blood and bronchoalveolar lavage fluid (BALF) samples in patients with severe pneumonia complicated by bloodstream infections. A retrospective analysis of 30 patients with severe pneumonia-bloodstream infection admitted to our hospital from January 2018 to December 2022 was conducted, and the potential pathogens in both BALF and blood samples were simultaneously detected by conventional microbial examination (traditional group) and mNGS tests (mNGS group), comparing the differences in pathogen species and detection rates between the two methods. There was no significant difference in the positivity of pathogen detection in BALF and blood samples using mNGS (p = 0.492). The proportion of bacteria (p = 0.005) and fungi (p = 0.037) detected by BALF mNGS was higher than that by blood mNGS, but there was no significant difference in the proportion of viruses (p = 0.121). In addition, the positive rate of pathogen detection by mNGS in BALF and blood samples was significantly higher than that by traditional methods (p < 0.01). BALF mNGS demonstrated superior diagnostic sensitivity for bacterial and fungal pathogen detection compared to blood mNGS and conventional culture methods. Notably, blood specimens retained distinct advantages in identifying specific viral infections. Future prospective studies with larger sample sizes are warranted to validate these findings.}, }
@article {pmid41943678, year = {2026}, author = {Zhou, G and Chen, L and Ma, L and Liu, J and Feng, B and Zhang, C and Ma, D and Zhang, H and Liang, Y and Zhang, J}, title = {Sodicity Thresholds Alter Biodiversity-Multifunctionality Relationships Through Fungal Dominance and Microbial Trait-Based Strategies.}, journal = {Global change biology}, volume = {32}, number = {4}, pages = {e70843}, doi = {10.1111/gcb.70843}, pmid = {41943678}, issn = {1365-2486}, support = {42277336//National Natural Science Foundation of China/ ; 42425703//National Natural Science Foundation of China/ ; BK20221561//Natural Science Foundation of Jiangsu Province/ ; CX(24)1003//Jiangsu Agricultural Science and Technology Innovation Fund/ ; NMKJXM202401-01//Key Special Projects of the "Science and Technology Revitalizing Inner Mongolia" Action Fund/ ; CARS-03//China Agriculture Research System/ ; CARS-52//China Agriculture Research System/ ; //Chinese Academy of Sciences/ ; }, mesh = {*Soil Microbiology ; *Biodiversity ; China ; *Soil/chemistry ; *Fungi/physiology ; Ecosystem ; *Sodium/analysis ; Salinity ; }, abstract = {Increasing soil sodicity represents a critical threat to global agroecosystem health, but how exchangeable sodium percentage (ESP) modulates relationships between biodiversity and ecosystem multifunctionality (BEF) is unresolved. We surveyed 378 soil samples from 189 paired saline-sodic lands and adjacent farmlands across four major saline-sodic regions of China spanning ~2000 km. Random forest models demonstrated that ESP emerged as the primary abiotic predictor of soil multifunctionality, defining sharp thresholds ~13% for cropped systems and ~44% for natural saline-sodic habitats beyond which BEF relationships undergo fundamental reorganization. These breaks coincide with significant shifts toward fungal dominance within microbial communities. Notably, under hyper-sodic conditions, fungal diversity emerges as essential for sustaining ecosystem functions. Metagenomic and trait-based analyses further characterized three functional dimensions of microbial trait-based strategies-environmental responsiveness, metabolic capacity, and nutrient recycling. We then mechanistically linked microbial life-history strategies to soil multifunctionality. Our results showed that in farmland soils, nutrient recycling was positively associated with multifunctionality, whereas metabolic capacity was negatively correlated with multifunctionality, and in saline-sodic soils metabolic capacity exhibited a positive association with multifunctionality. Collectively, this study establishes ESP as a key regulator of BEF relationships and microbial eco-evolutionary adaptations, providing mechanistic insights for managing saline-sodic soils under escalating climate change.}, }
@article {pmid41944124, year = {2026}, author = {Cai, S and Li, E and Sun, T and Huang, A and Zhang, Y and Xiong, X and Cheng, B and Chai, H and Zhang, J and Zhang, J and Hu, C and Zhang, W}, title = {Amine-Containing Micropollutants Exposure Reshapes Sludge Anaerobic Digestion via Enzymatic Inhibition and Stress-Mediated Alteration of Methanogenic Pathways.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c10074}, pmid = {41944124}, issn = {1520-5851}, abstract = {Amine-containing micropollutants (AMPs), a class of structurally diverse polar compounds characterized by one or more amine functional groups, are frequently detected in wastewater sludge. However, the anaerobic transformation of these compounds and their impacts on microbial metabolism during anaerobic digestion (AD) remain poorly understood. In this work, six representative AMPs were selected to cover 16 structurally diverse primary, secondary, tertiary amine, and quaternary ammonium functionalities. α-C hydroxylation and N-acetylation were identified as the dominant initial reactions among the detected transformation products (TP), collectively accounting for 42.6% of all identified TPs. Furthermore, compound-specific differences in metabolic disturbance were observed. Quaternary ammonium compounds, N-dodecyl-N-benzyl-N,N-dimethylammonium chloride (DDBAC) and N,N-Didodecyl-N,N-dimethylammonium chloride (DDDAC) markedly reduced acetate kinase activity by 10.69 and 14.28%, respectively, and resulted in methane production yield reductions of 88.97 and 88.19%. The genome-centric metagenome revealed that exposure to AMPs prompted the reassembly of the microbial community, altered its functional attributes, and disturbed interspecies cross-feeding interactions. Specifically, AMPs triggered a shift in the methanogenic consortium from mixotrophic Methanosarcina flavescens to hydrogenotrophic Methanobacterium sp., owing to the latter's metabolic versatility, vigorous proliferation, and superior energy conservation. These findings indicated that the chemical properties of amine functional groups have effects on anaerobic biotransformation pathways and microbial energy metabolism, providing mechanistic insight into AMPs toxicity and guiding mitigation strategies to enhance the stability and resilience of full-scale AD systems.}, }
@article {pmid41944276, year = {2026}, author = {Feng, Z and Lu, JN and Wang, G and Li, M and Chen, D and Chen, C and Jiang, Y and Yu, H and Chao, Y and Tang, YT and Jin, C and Baker, AJM and Morel, JL and Xu, Z and Wang, S and Qiu, R}, title = {Beyond Metal(loid) Immobilization: Redox-Stratified Biocrusts Shield Humid Mining Regions.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c13821}, pmid = {41944276}, issn = {1520-5851}, abstract = {Biological soil crusts (biocrusts) develop vertical redox-microbial-nutrient stratification that regulates hydrological and elemental cycles and contributes to ecological restoration in extreme environments, including mining regions. However, the roles of this heterogeneity in metal(loid) immobilization remain unclear, particularly in humid regions, where pronounced redox and microbial stratification may foster unrecognized stabilization mechanisms. We integrated physicochemical characterization with bioinformatic analysis to reveal stratified microbial communities and metabolic potentials in humid tailings biocrusts. Biocrusts exhibited stratified functionality through the upper photoautotrophic layer (PL) and the lower heterotrophic layer (HL). In the PL, Cyanobacteria and SWB02 formed a self-reinforcing oxygen barrier through clay-silt enrichment (2.8-fold higher than bare tailings sand) and extracellular polysaccharide accumulation (18-fold), which swelled upon hydration to physically hinder oxygen infiltration, confining Gammaproteobacteria-associated iron-manganese oxide immobilization to this layer. Beneath this barrier, the HL harbored sulfidogenic potential through microbes enriched in hydB (17.4-fold) and phsC (3.4-fold) genes, including Bacteroidota and Desulfobacterota, supporting a potential mechanism for metal(loid) sequestration via sulfide formation in underlying tailings, where sulfur occurred exclusively as sulfides at 5 cm depth. This barrier-mediated effect may outweigh metal(loid) immobilization within biocrusts. Our findings elucidate biocrust-mediated protection against metal(loid)s and provide theoretical support for remediation in humid mining regions.}, }
@article {pmid41944309, year = {2026}, author = {Wang, Z and Zhang, J and Lu, H and Ni, J and Yang, S and Shi, Y and Zhang, S and Zhang, P and Liu, L}, title = {Gemella morbillorum Promotes Colorectal Carcinogenesis: LPBDCP-Mediated Invasion Activates Ras Signaling and Destabilizes p53.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e17245}, doi = {10.1002/advs.202517245}, pmid = {41944309}, issn = {2198-3844}, support = {82473713//National Natural Science Foundation of China/ ; 82173602//National Natural Science Foundation of China/ ; }, abstract = {Gut microbiota dysbiosis promotes colorectal cancer (CRC) tumorigenesis. A global fecal metagenomic analysis identified Gemella morbillorum as a key contributor to the CRC-associated microbiota. Fluorescence in situ hybridization revealed that Gemella morbillorum is enriched in CRC tumor tissues compared to adjacent normal tissues. In vitro and in vivo experiments elucidated the oncogenic effects of Gemella morbillorum on human CRC cell lines and mouse models. Multimodal imaging shows that Gemella morbillorum can internalize into host cells. RNA sequencing, co-immunoprecipitation, and mass spectrometry identified that Gemella morbillorum invades host cells via interaction between its LysM peptidoglycan-binding domain protein (LPBDCP) and host cell surface transmembrane protein TMEM140. This invasion triggers Ca[2] [+] influx, downregulates RASA4, and activates the PI3K-AKT-NF-κB and RAF-MEK-ERK signaling pathways. Following invasion, Gemella morbillorum secretes NAD-dependent protein deacetylase (NDPD), which induces p53 deacetylation and degradation. Collectively, these events accelerate cell proliferation, shorten the cell cycle, and inhibit apoptosis, thereby promoting malignant transformation. Genetic knockout of LPBDCP or TMEM140 effectively inhibits bacterial invasion and abrogates the oncogenic effects of Gemella morbillorum. In tumor-bearing mice, knockout of LPBDCP or NDPD eliminates the tumor-promoting effects of Gemella morbillorum. These results underscore Gemella morbillorum's role in CRC and pinpoint potential intervention targets.}, }
@article {pmid41889817, year = {2026}, author = {Lu, T and Dietz, ZK and Ericsson, AC and Picking, WD and Picking, WL}, title = {Eco-tank Housing Maintains Wild-Type Microbiota and Rewilds the Laboratory Mouse Gut Microbiome to Restore Natural Immune Tone.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {41889817}, issn = {2692-8205}, abstract = {Laboratory mice housed under individually ventilated cage (IVC) conditions harbor simplified gut microbiota and immune phenotypes that diverge substantially from those shaped by environmental exposure, limiting translational relevance. To reintroduce controlled ecological complexity while maintaining biosafety and reproducibility, we developed the Eco-tank, a pathogen-monitored semi-natural housing system incorporating environmental substrates and dietary diversity. Longitudinal 16S rRNA sequencing revealed that even wild-caught Mus musculus rapidly lose microbial richness and predicted metabolic breadth under IVC housing. Eco-tank conditions stabilized diversity and preserved elements of wild-associated community structure during extended captivity. In parallel, standardized C57BL/6 mice housed in Eco-tanks underwent rewilding-like restructuring, with increased richness and community shifts toward a wild-associated configuration. Functional inference analyses indicated expansion of predicted pathways linked to short-chain fatty acid production, amino acid metabolism, and environmental substrate utilization. Eco-tank housing enhanced baseline resistance to pulmonary Pseudomonas aeruginosa (Pa) infection without compromising vaccine-induced protection, indicating that restoration of environmental microbial signals does not impair adaptive immunity. Together, these findings identify housing ecology as a dominant determinant of microbiome structure and functional potential. The Eco-tank provides a scalable and tractable framework for integrating environmental microbial complexity into laboratory models to better align preclinical immunology with ecologically conditioned immune systems.}, }
@article {pmid41936935, year = {2026}, author = {Wang, J and Bi, Y and Fu, Z and Qiao, H and Liu, F}, title = {Harvesting reed (Phragmites australis) for wetland nitrogen removal: Productivity, microbial communities, and underlying mechanisms.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134553}, doi = {10.1016/j.biortech.2026.134553}, pmid = {41936935}, issn = {1873-2976}, abstract = {Non-point source nitrogen (N) pollution is a primary driver of aquatic eutrophication. While reed (Phragmites australis) wetlands effectively intercept N, the optimal harvesting strategy for maximizing N removal while maintaining ecosystem function remains unclear. This study investigated the effects of different harvesting frequencies on N removal, plant productivity, and associated microbial mechanisms in wetland microcosms over a three-year period. Four treatments were evaluated: unplanted control (CK), planted with no harvest (T0), annual harvest (T1), and biennial harvest (T2). Results demonstrated that all planted treatments significantly enhanced N removal compared to CK. Although not statistically significant among planted groups, T1 consistently achieved the highest average removal efficiencies for total nitrogen, ammonium-nitrogen, and nitrate-nitrogen. Furthermore, T1 produced the greatest aboveground biomass, facilitating the largest export of N and other nutrients. Metagenomic analysis revealed that reed planting shifted the microbial community, suppressing Cyanobacteria (e.g., Stanieria) and Nitrospirota (e.g., Nitrospira F), while enriching Proteobacteria and Chloroflexota. These compositional changes were coupled with a functional shift that key dissimilatory pathways (denitrification and dissimilatory nitrate reduction) were upregulated, while assimilatory nitrate reduction was suppressed. Additionally, annual harvesting fostered a more complex and stable microbial co-occurrence network. Structural equation modeling indicated that harvesting enhanced N removal primarily through plant-microbe interactions, with increased plant N accumulation promoting microbial N-functional gene abundance, and ultimately driving N removal. Overall, annual harvesting optimally coupled high biomass production with microbial N removal, presenting a sustainable management strategy for wetlands that balances water purification with resource recovery.}, }
@article {pmid41936957, year = {2026}, author = {Ghaly, TM and Shah, BS and Coleman, NV and Elbourne, LDH and Le Roux, JJ and Gillings, MR and Paulsen, IT and Tetu, SG}, title = {Agriculture alters protein evolution of respiratory nitrate reductase in soil bacteria at a global scale.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124428}, doi = {10.1016/j.envres.2026.124428}, pmid = {41936957}, issn = {1096-0953}, abstract = {Humans are a major evolutionary force, yet our impacts on the evolution of Earth's microbiomes and their biogeochemical processes remain poorly understood. Notably, the overlooked potential for the intensive use of agricultural fertiliser to drive evolutionary changes in soil nutrient cycling genes warrants urgent attention. Here, analysing >2,500 soil metagenomes from across the globe, we identify increased rates of diversifying positive selection on genes involved in the reduction of nitrate (a key component of nitrogen fertilisers) in agricultural, but not natural land systems. Altered selection on genes encoding the respiratory nitrate reductase (Nar) were specific to Burkholderiales, a major group of denitrifying bacteria. Nar protein regions under positive selection flanked the enzyme's substrate channel, favouring smaller amino acids, likely resulting in the widening of the channel entrance. We present a novel hypothesis that this channel widening could increase rates of substrate turnover, which we propose would be evolutionarily advantageous under excess nitrate availability, ultimately enhancing growth rates despite potential enzymatic trade-offs. As Burkholderiales are dominant nitrate reducers globally, such evolutionary consequences of agriculture on this lineage could have cascading environmental impacts, including increased nitrous oxide emissions. These findings indicate that anthropogenic selection might be altering protein-level evolution of vital microbial biogeochemical processes.}, }
@article {pmid41937023, year = {2026}, author = {Field, CM and Keller, PM and Schultheiss, E and Gewitsch, B and Wiemer, DF and Schawaller, M and Halfter, M and Frickmann, H}, title = {Potential impact of antimalarial chemoprophylaxis with doxycycline on antimicrobial resistance genes in the enteric microbiome of deployed German soldiers - a case-control-study.}, journal = {Travel medicine and infectious disease}, volume = {}, number = {}, pages = {102978}, doi = {10.1016/j.tmaid.2026.102978}, pmid = {41937023}, issn = {1873-0442}, abstract = {BACKGROUND: Antimalarial chemoprophylaxis with doxycycline is taken by German soldiers on tropical deployments. In a case-control-assessment, diagnostic metagenomics was applied to comparatively assess antimicrobial resistance genes in enteric microbiomes of soldiers with and without medical history of doxycycline-based antimalarial chemoprophylaxis on deployment.<br><br>METHODS: Two groups of 26 military deployment returnees, each either exposed or non-exposed to antimalarial chemoprophylaxis with doxycycline, were matched by deployment site and period, age and sex in declining order of prioritization. Metagenomic analysis of stool samples was applied to detect resistance gene sequences within the sample materials.<br><br>RESULTS: In total, 3,770 different antibiotic resistance genes were detected across all samples. No significant differences were found in the frequency of antibiotic resistance genes in each sample compared between the doxycycline group and the control group. Approximately one third of metagenomically assembled genomes could be identified taxonomically at the species level (32.2%) and over half at the genus level (53.9%). The overall distribution of ABR genes at the species level showed that Escherichia coli was host for over a quarter of detected genes - 1,021 genes in only 42 identified genomes. Hosts with the next highest number of ABR genes were Escherichia marmotae (156 genes), Staphylococcus aureus (85 genes), Klebsiella michiganensis (63 genes) and Leclercia adecarboxylata (62 genes).<br><br>CONCLUSIONS: The study suggests - if any - only a low impact of doxycycline intake during military deployments on the enteric resistome of soldiers at post-deployment assessments. Reasons for Escherichia's high ABR gene load remain to be investigated.}, }
@article {pmid41937144, year = {2026}, author = {Bočaj, V and Pongrac, P and Likar, M}, title = {Microbial functional traits in the hyperaccumulating Noccaea praecox rhizobiome are metal-dependent and host-driven.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00890-y}, pmid = {41937144}, issn = {2524-6372}, support = {P1-0212//The Slovenian Research and Innovation Agency/ ; P1-0212//The Slovenian Research and Innovation Agency/ ; P1-0212//The Slovenian Research and Innovation Agency/ ; }, abstract = {BACKGROUND: Noccaea praecox is a zinc (Zn), cadmium (Cd), and lead (Pb) hyperaccumulating plant native to the Italian peninsula and Western Balkans, where it occurs naturally in both metalliferous and non-metalliferous soils. In the present study, we investigated the effects of soil metal concentrations and the plant host on microbial functional traits, specifically the resistome (i.e., microbial functions associated with metal tolerance and resistance) in two soil compartments: the roots and rhizosphere of N. praecox. For this, we collected four plants from each metalliferous and non-metalliferous site and used a metagenomic sequencing approach to characterise microbial functions from paired root and rhizosphere samples, with three root samples per site obtained due to limited biomass, and four rhizosphere samples.<br><br>RESULTS: The compartment was the primary driver of the general microbial functional structure. By contrast, the soil metal concentrations and root compartment significantly shaped the microbial resistome. Functions associated with the cobalt-zinc-cadmium efflux system and copper-transporting P-type ATPase V were significantly enriched at the metalliferous compared to the non-metalliferous site, with log2 fold change being 2.62 and 1.72, respectively. Transporters associated with manganese/iron and cobalt/nickel were shaped by the host, regardless of soil metal levels, consistent with host-mediated filtering of microbial functions. Notably, several Zn transporter-related microbial functions associated with the ZIP family were more abundant in the rhizosphere, potentially supporting the plant's high Zn demand.<br><br>CONCLUSION: Overall, our results demonstrate that both environmental conditions and plant host play interactive roles in shaping the microbial functional potential, with the host sometimes exerting a stronger influence than soil metal content. The enrichment of Zn transporters (Zrt-/Irt-like proteins) in the rhizosphere of the Zn-hyperaccumulating N. praecox suggests a specific microbial adaptation that may facilitate Zn uptake. These findings provide new insight into the functional dynamics of plant-microbe interactions that support the N. praecox lifestyle.}, }
@article {pmid41937169, year = {2026}, author = {Mullin, CE and Louca, S}, title = {Effects of heat-assisted sample desiccation on microbiome surveys.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00889-5}, pmid = {41937169}, issn = {2524-6372}, abstract = {Sample preservation remains a challenge in microbiome surveys, particularly in remote areas. Drying samples eliminates the need for cold chains and preservatives, but sophisticated desiccation tools such as lyophilization are impractical in the field. Further, the effects of sample drying on modern analyses, such as gene-centric metagenomics and metagenome-assembled genome (MAG) recovery, remain poorly understood. Here we explore heat-assisted sample desiccation followed by storage at room temperature as a cost-effective and practical solution in the field. We assess its effects relative to freezing on typical metagenomic and 16 S rRNA amplicon sequence analyses of bacterial and archaeal communities, using 60 samples from 6 different source materials (soils from 3 locations, feces from 3 animals). We consider multiple metrics related to the success of DNA extraction, sequencing, contig assembly, OTU clustering, gene annotation and MAG recovery, as well as impacts on inferred microbial community composition. We find that, while desiccation had a significant negative impact on multiple metrics related to DNA extraction success, its impacts on downstream metrics such as OTU richness, Shannon diversity, gene annotation and MAG recovery were more nuanced and often insignificant. Further, while the preservation method had a significant influence on the inferred microbial community composition, samples from different source materials (e.g., soils from different locations, or feces from different individuals) remained clearly distinguishable. We conclude that heat-assisted desiccation can be a viable sample preservation method for microbiome studies, when a high consistency with frozen samples is not a requirement.}, }
@article {pmid41937465, year = {2026}, author = {Do, TT and Le, VV and Nguyen, LTT and Nguyen, TTK and Vu, NTH and Trinh, HN and Lee, SA and Ngo, CC and Phi, QT}, title = {Metagenomic and Culture-Based Insights into Salinity-Driven Bacterial Community Dynamics throughout Crude Oil-Degrading Enrichment Cultivation.}, journal = {Journal of microbiology and biotechnology}, volume = {36}, number = {}, pages = {e2508050}, doi = {10.4014/jmb.2508.08050}, pmid = {41937465}, issn = {1738-8872}, mesh = {*Petroleum/metabolism ; *Bacteria/genetics/metabolism/classification/isolation &amp; purification ; *Salinity ; Soil Microbiology ; Metagenomics/methods ; Biodegradation, Environmental ; Soil Pollutants/metabolism ; Hydrocarbons/metabolism ; *Microbiota ; Phylogeny ; }, abstract = {Soil salinization and crude oil contamination are critical global threats to ecosystems, agriculture, and human health. Bioremediation is widely recognized as a cost-effective and eco-friendly strategy for removing petroleum pollutants from soil. In this study, we investigated salinity-driven bacterial community dynamics collected from crude oil-contaminated soil in Cam Ranh Bay, Khanh Hoa, over a 21-day enrichment cultivation, using shotgun metagenomic and culture-based approaches. The enrichment cultivation was performed in Bushnell-Haas mineral salts (BHMS) medium supplemented with 5% (v/v) crude oil-diesel mixture (5:95) and 1.5% NaCl. Shotgun metagenomic analysis revealed that after 21 days of enrichment, the relative abundance of crude oil-degrading genera increased markedly in the enriched samples compared to the native samples-for example, Pseudomonas rose from 0.44% to 3.51%, Gordonia from 0.03% to 78.68%, and Achromobacter from 0.03% to 3.77%. Functional analysis further identified metabolic pathways, including hydrocarbon degradation, osmoprotection, and heavy metal detoxification. In addition, 36 representative bacterial strains were isolated from the enriched cultures, predominantly belonging to the genera Pseudomonas, Bacillus, Stenotrophomonas, and Achromobacter. All isolates were able to degrade crude oil under salinity stress conditions of up to 4%. Notably, Rhodococcus sp. KH5 and Gordonia sp. KH53 maintained consistently high degradation efficiencies across 0-4% salinity, ranging from 17.67-35.00% and 28.67-36%, respectively. Overall, our findings demonstrate that saline enrichment shifts the bacterial community toward halotolerant hydrocarbon and crude oil degraders.}, }
@article {pmid41937665, year = {2026}, author = {Sizikova, TE and Lebedev, VN and Borisevich, SV}, title = {The Mengla virus (Filoviridae: Dianlovirus).}, journal = {Voprosy virusologii}, volume = {71}, number = {1}, pages = {7-12}, doi = {10.36233/0507-4088-356}, pmid = {41937665}, issn = {2411-2097}, mesh = {Animals ; *Chiroptera/virology/genetics ; *Filoviridae/genetics/classification/pathogenicity/isolation &amp; purification ; Humans ; Phylogeny ; Genetic Variation ; Genome, Viral ; *Filoviridae Infections/virology/epidemiology/genetics ; Asia, Southeastern/epidemiology ; Hemorrhagic Fever, Ebola/virology/genetics/epidemiology ; }, abstract = {INTRODUCTION: Filoviruses associated with various species of pteropodid bats (Chiroptera: Pteropodidae) are traditionally regarded as potential causative agents of hemorrhagic fevers with epidemic potential. The known agents of Ebola and Marburg fevers periodically cause sporadic cases and epidemic outbreaks in African countries. Recent discoveries of novel filoviruses associated with pteropodid bats in South and Southeast Asia highlight the necessity to investigate their genetic diversity and pathogenic potential. The aim of this study was to investigate the genetic diversity and pathogenic potential of new filoviruses associated with bats, based on literature data.<br><br>MATERIALS AND METHODS: This review is based on an analysis of published literature describing the detection and molecular characterization of novel filoviruses identified in different geographic regions, with a particular focus on filoviruses associated with pteropodid bats in South and Southeast Asia. The analyzed studies include data on virus discovery, genome organization, taxonomic classification, and experimental assessment of biological properties.<br><br>RESULTS: Several novel filoviruses have been identified by metagenomic RNA sequencing of tissues from pteropodid bats captured in South and Southeast Asia. Among them, Mengla virus was detected in tissues of pteropodid bats (Rousettus spp.) captured in Mengla County, Yunnan Province, People's Republic of China. Owing to a high level of genetic divergence, Mengla virus was classified as a representative of a new genus, Dianlovirus, within the family Filoviridae. Although a live isolate of Mengla virus has not yet been obtained, experimental studies using chimeric minigenome systems and virus-like particles suggest that the virus may exhibit tropism for tissues of various vertebrate hosts, including humans.<br><br>CONCLUSION: Members of the family Filoviridae are widely distributed within the geographic range of their natural reservoir-pteropodid bats-across South and Southeast Asia, including viruses evolutionarily related to Ebola and Marburg viruses. Although human disease caused by Mengla virus and other recently discovered filoviruses has not been documented, the potential for cross-species transmission and the emergence of novel filovirus infections in endemic regions remains.}, }
@article {pmid41937718, year = {2026}, author = {Chen, X and Xie, M and Feng, J and Zou, J and Shi, J and Xie, X}, title = {From Diet to Resistome: Habitat Fragmentation Rewires Gut Microbiomes To Elevate Antibiotic Resistance Gene Enrichment in a Horseshoe Crab Sentinel.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c17817}, pmid = {41937718}, issn = {1520-5851}, abstract = {Habitat fragmentation may amplify antibiotic resistance genes (ARGs), yet the ecological pathways linking landscape patterns to host resistomes in intertidal systems remain unclear. Macrobenthic organisms as potential reservoirs and dispersal nodes are ideal models. Focusing on the horseshoe crab (Tachypleus tridentatus), a food web hub and habitat indicator, we integrated landscape metrics, metagenomics, and path modeling (PLS-PM) to examine, across fragmented habitats, links among sediment physicochemistry, larval diet, gut microbiota, mobile genetic elements (MGEs), and ARGs. Results revealed that more fragmented habitats promoted individuals with higher ARG abundance and diversity, alongside stronger MGE enrichment and increased ARG-MGE co-occurrence, indicating enhanced mobility potential. Fragmentation also coincided with greater dietary diversity but higher among-individual convergence, selective assembly of gut microbiota with higher diversity, and tight ARG-MGE association. PLS-PM supported a diet-gut microbiota-MGE-ARG cascade, while the direct effects of sediment chemistry were not significant. Attributing ARG hosts at the MAG level, Enterobacteriaceae and Vibrionaceae dominated ARG abundance and enrichment, indicating lineage selectivity. Multidrug and polymyxin resistance was most prominent. These findings identify key AMR risk pathways and inform priority interventions for T. tridentatus and habitat conservation. The developed assessment framework is scalable and offers a paradigm for One Health management in mudflat systems.}, }
@article {pmid41937905, year = {2026}, author = {Cheng, Y and Peng, L and Liu, D and Zhong, L and Liu, Y and Yang, T}, title = {Case Report: A rare culprit of severe pulmonary infection in children: prevotella.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1782202}, pmid = {41937905}, issn = {2296-2360}, abstract = {BACKGROUND: To characterize the clinical features, diagnostic pitfalls, and treatment of severe pediatric pulmonary infection caused by Prevotella species.<br><br>METHODS: We retrospectively reviewed clinical data, the diagnostic workflow, antimicrobial regimens, and outcomes of two children with severe Prevotella pulmonary infection.<br><br>RESULTS: Case 1 was an 11-year-old boy with necrotizing pneumonia, and Case 2 was a 13-year-old boy with retained foreign-body aspiration. Both patients responded poorly to initial cephalosporin-based therapy. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage (BAL) fluid identified Prevotella nanceiensis (sequence count 299,022; relative abundance 92.24%) and Prevotella oralis (210,449; 67.98%) within 24&#x2005;h, whereas anaerobic culture (Case 1) became positive after 4 days. Based on mNGS results antibiotics were adjusted to metronidazole plus a carbapenem (meropenem for Case 1; imipenem-cilastatin for Case 2), and both children received adjunctive pulmonary rehabilitation before discharge. They subsequently recovered and were discharged.<br><br>CONCLUSION: Severe Prevotella pulmonary infection in children has non-specific manifestations and may respond poorly to conventional beta-lactam therapy, leading to delayed diagnosis. mNGS enables rapid pathogen identification and supports targeted anti-anaerobic treatment. For severe or complicated cases refractory to empirical therapy, metronidazole combined with a carbapenem may be an effective option.}, }
@article {pmid41937991, year = {2026}, author = {Halphen, J and Ahmadzade, M and Mankidy, B and Berenji, A and Ghasemi-Rad, M}, title = {Letter to the Editor: Evidence for a two-step species-level pulmonary nocardiosis diagnostic approach.}, journal = {World journal of radiology}, volume = {18}, number = {3}, pages = {118126}, pmid = {41937991}, issn = {1949-8470}, abstract = {Pulmonary nocardiosis, a rare and diagnostically challenging infection, usually presents with heterogeneous radiographic findings, compounded by the low sensitivity of traditional confirmatory cultures. In their most recent work, Wang et al analyzed 102 patients with pulmonary nocardiosis to address these concerns, investigating species-characteristic imaging patterns, pathological associations, and the role of metagenomic next-generation sequencing (mNGS) in the diagnostic approach. High-resolution computed tomography (CT) in adult patients with pulmonary infections caused by Nocardia wallacei was demonstrated to have a sensitive (85.71%) and specific (83.34%) presentation of bronchopneumonia in relation to the five Nocardia species in the sample with CT data. The authors also compared traditional cultures to mNGS, finding that traditional cultures and mNGS were concordantly positive in only 3.3% of cases. This letter supports a combined radiologic and molecular diagnostic approach, enabling earlier and more accurate species identification in pulmonary nocardiosis, thereby informing treatment decisions, and enhancing epidemiologic understanding.}, }
@article {pmid41938562, year = {2026}, author = {Ye, B and Liu, R and Li, R and Roduan, MRM and Noor, WSAWM and Sairi, F}, title = {Comparative gut microbiome composition and predicted microbial functions in captive and free-range yaks (Bos grunniens).}, journal = {Veterinary world}, volume = {19}, number = {2}, pages = {864-876}, pmid = {41938562}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: The gut microbiota is essential for nutrient digestion, immune function, and environmental adaptation in ruminants, particularly high-altitude species like yaks (Bos grunniens). Different husbandry practices (captive vs. free-range) can potentially alter the microbial communities and affect the yak health. However, comparative data on how these systems affect yak gut microbiomes remain limited, with most studies focusing on taxonomy rather than functional implications. This study aimed to compare gut microbiome composition, diversity, and predicted functional profiles between captive (CY) and free-range (FY) yaks using a 16S rRNA gene metabarcoding approach.<br><br>MATERIALS AND METHODS: Fecal samples were collected from healthy ~2-year-old yaks (n=5 CY, n=5 FY) in Litang County, Ganzi Prefecture, Sichuan, China, during summer. DNA was extracted, and the V4 region of the 16S rRNA gene was sequenced on Illumina NovaSeq 6000. Bioinformatic analyses included quality filtering, Operational taxonomic units (OTU) clustering (97% similarity), taxonomic annotation (SILVA database), &#x3b1;- and &#x3b2;-diversity analysis. The microbial function was predicted using PICRUSt2 (KEGG pathways), BugBase (community phenotypes), and FAPROTAX (ecological functions). Statistical comparisan used Welch's t-tests, Wilcoxon rank-sum tests, principal coordinates analysis (PCoA), and Analysis of similarities (ANOSIM) with significance set at p < 0.05.<br><br>RESULTS: &#x3b1;-Diversity indices (e.g., Shannon p = 0.5476) showed no significant differences between CY and FY. However, &#x3b2;-diversity revealed distinct community structures (PCoA: PC1 30.52%, PC2 12.25%; ANOSIM R = 0.976, p = 0.007), with FY samples more homogeneous. At the genus level, CY were enriched in Ruminococcaceae bacterium UCG-005, Streptococcus, Escherichia-Shigella, Treponema, Christensenellaceae R-7, and Clostridium sensu stricto 1 (many fermentative or potentially opportunistic). FY showed higher abundances of Bacillus, Arthrobacter, Rhodococcus, Candidatus Saccharimonas, Prevotellaceae UCG-001, and Paenibacillus. Predicted functions indicated FY had greater capacities for carbohydrate/amino acid metabolism, DNA repair, fatty acid biosynthesis, and vitamin B pathways, while CY favored fermentation and reductive acetogenesis. BugBase highlighted higher anaerobic phenotypes in CY.<br><br>CONCLUSION: Husbandry practices profoundly influence yak gut microbiome structure and inferred metabolic potential, with free-range systems promoting, homogeneous communities suited to natural high-fiber diets while captive systems promotes fermentative and opportunistic shifts. These microbiome differences suggest opportunities for probiotic interventions to enhance yak health, productivity, and sustainability in high-altitude pastoral systems. Future metagenomic and metabolomic validation is needed.}, }
@article {pmid41938867, year = {2026}, author = {Dai, Z and Lu, Q and Sun, M and Chen, H and Jiang, Y and Yu, T and Wang, Z and Wang, Y and Zhu, R}, title = {Discovery of a novel orthototivirus-like virus in patients with vulvovaginal candidiasis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1779554}, pmid = {41938867}, issn = {2235-2988}, mesh = {Female ; Humans ; Phylogeny ; *Candidiasis, Vulvovaginal/virology/microbiology ; Genome, Viral ; Vagina/virology/microbiology ; Metagenomics ; Capsid Proteins/genetics ; RNA, Viral/genetics ; RNA-Dependent RNA Polymerase/genetics ; Adult ; *Double Stranded RNA Viruses/genetics/isolation &amp; purification/classification ; }, abstract = {INTRODUCTION: Vulvovaginal candidiasis (VVC) is a common fungal infection affecting women worldwide. Although the vaginal microbiome has been extensively studied, the diversity of viruses present in the vaginal microenvironment remains poorly characterized.<br><br>METHODS: Vaginal swab samples from patients diagnosed with VVC were subjected to viral metagenomic sequencing using an Illumina NovaSeq platform. Viral contigs were assembled, annotated, and screened against public databases. Genome organization, pairwise sequence identity, and phylogenetic relationships were analyzed to determine the evolutionary position of the detected virus.<br><br>RESULTS: Here, we identified a novel double-stranded RNA virus, tentatively named Vaginal-associated orthototivirus-like 1 (VAOTV-1), in vaginal swab samples from patients with vulvovaginal candidiasis. VAOTV-1 was represented by a partial genome sequence of 4,332 bp, encoding a complete RNA-dependent RNA polymerase (RdRp; 729 amino acids) and a partial capsid protein (CP; 532 amino acids). The encoded RdRp protein shared a maximum amino acid sequence identity of 47.43% with Totiviridae sp. isolate 22AP502 (GenBank accession no. XTJ93729.1), reported from Bandicota indica. In contrast, the CP showed no significant similarity to any sequences currently available in public databases, and BLASTn searches against the NCBI nucleotide database did not yield any significant matches. Phylogenetic analysis, together with the relatively low amino acid sequence identity to known members of the genus Totivirus within the family Orthototiviridae, suggests that VAOTV-1 represents a distinct and highly divergent orthototivirus-like lineage.<br><br>DISCUSSION: These findings indicate that VAOTV-1 represents a highly divergent orthototivirus-like virus and expands the known diversity of totiviruses detected in human-associated mucosal environments. This discovery highlights previously unrecognized viral diversity in the vaginal virome and provides new insights into viruses associated with vulvovaginal candidiasis.}, }
@article {pmid41939082, year = {2026}, author = {Turner, ML and Nguyen, MT and Kung, Y and Doan, T and Seitzman, GD}, title = {Rhizopus angle abscess, scleritis and endophthalmitis following Kahook Dual Blade goniotomy and phacoemulsification.}, journal = {American journal of ophthalmology case reports}, volume = {42}, number = {}, pages = {102572}, pmid = {41939082}, issn = {2451-9936}, abstract = {PURPOSE: To describe a rare case of Rhizopus angle abscess progressing to scleritis and endophthalmitis after routine cataract surgery with Kahook Dual Blade (KDB) goniotomy in an immunocompetent patient.<br><br>OBSERVATION: A 79-year-old male developed hyphema and anterior chamber fibrin three days after uncomplicated phacoemulsification with KDB. Despite intravitreal vancomycin and ceftazidime, inflammation worsened, and by postoperative day nine vision was count fingers with intraocular pressure of 29&#xa0;mmHg. Slit-lamp exam showed an inferonasal corneal infiltrate with a purulent angle abscess at the goniotomy site and dense vitritis. Intravitreal and oral voriconazole were started for presumed fungal infection. Standard cultures and PCR were negative, but metagenomic RNA deep sequencing of aqueous fluid detected Rhizopus stolonifer. After two months of systemic and intravitreal voriconazole, the infection resolved and visual acuity improved to 20/70, leaving localized limbal thinning.<br><br>CONCLUSION AND IMPORTANCE: This case illustrates that Rhizopus angle abscess can occur in an immunocompetent host following anterior segment surgery and may masquerade as bacterial endophthalmitis. Early suspicion of fungal infection and use of metagenomic deep sequencing were critical for diagnosis and successful treatment, emphasizing the need to consider invasive fungal pathogens and advanced molecular diagnostics in culture-negative postoperative ocular infections.}, }
@article {pmid41939697, year = {2026}, author = {Bagul, SY and S, S and Saran, PL and Khadke, GN and Das, M}, title = {Deciphering genotype and geography dependent microbiome composition and its role in disease suppression in Ashwagandha.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1786817}, pmid = {41939697}, issn = {1664-302X}, abstract = {Ashwagandha, Withania somnifera (L.) Dunal is a perennial evergreen shrub widely used to treat mental health disorders and physical debility, and to enhance overall physiological function. Variations in genotype and geographic origin significantly influence rhizospheric microbial communities by altering soil physicochemical properties. This study applied shotgun metagenomic sequencing to investigate microbial community shifts in the rhizosphere of Nagori Ashwagandha (RN) from Rajasthan, Vallabh Ashwagandha-1 (GV) from Gujarat, and Nagori Ashwagandha from Rajasthan cultivated in Gujarat (GN). Fusarium wilt incidence was 67%, affecting the roots, which represent the most economically important part of ashwagandha. Taxonomic analysis identified Actinomycetota (46-60%) and Pseudomonadota (35-42%) as the predominant phyla, with Nocardioides (3.1-8.8%), Streptomyces (4.5-6.5%), and Bradyrhizobium (1-1.6%) as dominant genera across all groups in metagenomic analysis. Alpha-diversity analysis revealed higher species richness and Simpson's index in the GV group compared to the GN and RN groups. Beta-diversity assessment using Bray-Curtis distances showed partial clustering of GN and RN relative to GV in principal coordinate analysis and hierarchical dendrograms. Functional profiling based on KEGG annotation indicated that core metabolic and cellular pathways predominated across all genotypes, with no significant differences in Tier 1 and Tier 2 functional categories. To our knowledge, this represents the first shotgun metagenomic analysis of ashwagandha. Culturomics analysis yielded seventeen isolates from two rhizospheric locations; among these, Bacillus subtilis DMA1 exhibited the highest mycelial inhibition against Fusarium solani (64%), with a germination rate of 98%, root length of 2.1 cm, shoot length of 1.3 cm, seed vigor index of 333.2, and maximum fresh biomass of 1.12 g. Co-inoculation with F. solani and Bacillus subtilis DMA1 in pot trials significantly increased root length (20.1 cm), shoot length (39.5 cm), root girth (14.9 mm), and total biomass (51.1 g) compared to control and Fusarium-only treatments. These findings indicate that Bacillus subtilis DMA1 reduced wilt incidence by 70% and enhanced plant growth under pathogen-stress conditions.}, }
@article {pmid41939705, year = {2026}, author = {Rey-Mariño, A and Ruiz-Ruiz, S and Jiménez-Hernández, N and Pons, X and Artacho, A and Codoñer-Franch, P and Francino, MP}, title = {Patterns of gut microbiome composition, function and dynamics in toddlers, adolescents and adults over a three-year period.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1768977}, pmid = {41939705}, issn = {1664-302X}, abstract = {Despite their relevance, studies of the long-term stability of the gut microbiome are rare due to the difficulty in following the same individual through long periods of time, particularly during childhood and adolescence. Here, we have been able to analyze microbiome stability throughout a 3-year period in toddlers, adolescents, and adults of the same population, at the levels of taxonomic composition and functional profile. Our analyses show that stability is lower at taxonomical than at functional level in all three age groups, indicating the existence of functional redundancy through time. Considering the entire period of sampling, toddlers were significantly more unstable than the other two groups at the level of taxonomic composition. However, local analyses revealed that low stability for both composition and function was restricted to the time period between 20 and 24 months of age, whereas after this point stability levels in toddlers were similar to those of adolescents and adults. Although the microbiome stabilized at around two years of age in terms of large-scale, rapid changes in diversity, composition, and functional profile, further changes did occur both before and after adolescence. Therefore, adolescence remains a transitional period, in which the abundances of some taxa and functions still differ from adult levels. These include, among others, Bifidobacterium, Streptococcus, Bacteroides fragilis and several members of the Lachnospiraceae, as well as various functions related to energy metabolism. Overall, our results pinpoint the two-years mark as a point of significant stabilization for the gut microbiome, without precluding the further occurrence of important changes in the relative abundance of specific taxa and gene functions both before and after adolescence.}, }
@article {pmid41939707, year = {2026}, author = {Li, X and Jin, S and Hu, H and Lan, Y and Ni, B and Su, J and Luo, S and Tan, L and Zhang, Y and Huang, H and Xu, Y and Yang, J and Zhou, C and Chen, K and Li, S and Liang, B and Bai, S and Zhang, K and Pan, H and Dong, X and Yan, D}, title = {Feeding Diqing Tibetan pigs with 50% of soybean meal replaced by walnut meal can reduce subcutaneous fat deposition and promote intramuscular fat accumulation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1794046}, pmid = {41939707}, issn = {1664-302X}, abstract = {BACKGROUND: Protein feed resource shortage is a major constraint to the sustainable development of the livestock industry and a bottleneck problem hindering the growth of the Tibetan pig industry in China's Qinghai-Tibet Plateau region. Walnut meal, rich in protein, holds promise as a substitute for soybean meal. However, the effects and underlying mechanisms of walnut meal substitution on Tibetan pigs in Diqing remain unclear.<br><br>RESULTS: The study showed that substituting 50% of soybean meal with walnut meal in the diet of Diqing Tibetan pigs significantly reduced backfat thickness and increased intramuscular fat content (P < 0.05). Integrated multi-omics analyses, including metagenomics, transcriptomics, and lipidomics, revealed that walnut meal substitution significantly reduced the abundance of Clostridium butyricum in the cecum of Diqing Tibetan pigs. The reduction in Clostridium butyricum was linked to the lipolytic capacity of subcutaneous adipose tissue, potentially facilitating the breakdown of triglycerides into free fatty acids (FFAs), which are then released into the bloodstream. When these free fatty acids are transported to muscle tissue, the muscle exhibited inhibited oxidative metabolism (e.g., a decrease in acylcarnitine metabolites), while showing an upregulation in the expression of genes related to adipocyte differentiation (e.g., MEDAG, VDR) and triglyceride synthesis (e.g., PPARGC1A, ANGPTL4). Ultimately, these processes may contribute to the synthesis and storage of triglycerides in muscle, thereby facilitating intramuscular fat deposition.<br><br>CONCLUSION: This study reveals that walnut meal can serve as a substitute for soybean meal, and a 50% substitution ratio is conducive to intramuscular fat deposition in Diqing Tibetan pigs. The findings provide valuable insights for the development and application of unconventional protein feed resources, and offer new perspectives for the production of marbled pork.}, }
@article {pmid41939710, year = {2026}, author = {Alibrandi, A and Plewka, J and di Primio, R and Bartholomäus, A and Vuillemin, A and Probst, AJ and Kallmeyer, J}, title = {Microbial diversity and community shifts in a petroleum reservoir under production: effects of water breakthrough and anthropogenic alterations.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1741638}, pmid = {41939710}, issn = {1664-302X}, abstract = {Subsurface petroleum reservoirs host indigenous microorganisms that survive extreme conditions and long-term isolation. Microbial activity in these environments can contribute to adverse effects such as oil biodegradation and reservoir souring. Unlike the broader deep biosphere, oil reservoirs are frequently subjected to anthropogenic disturbances, particularly during production, when processes like water injection introduce external microbes and electron acceptors. In this study, we investigated microbial diversity, community structure, and the impact of water breakthrough using 16S rRNA gene and metagenomic sequencing of produced fluids, production water, and injection water samples from the Edvard Grieg oil reservoir offshore Norway. We found clear regional heterogeneity in community composition, characterized by overall low diversity, dominated by thermophilic, anaerobic, and halotolerant taxa. The southern region (wells A13, A17, A18, and A19) exhibited lower diversity, while the microbial community composition of well A07 showed a distinct signature. The prevailing genera included the strictly anaerobic bacterium Thermoanaerobacter and the hyperthermophilic archaeon Thermococcus. Water breakthrough triggered shifts in community structure, not because of widespread replacement by injected microbes, but due to the increase in sulfate-reducing bacteria. Comparison between sequence data from production fluids and water samples allowed the identification of microbial signatures that can act as cost-effective tools for monitoring oil reservoir processes and integrity.}, }
@article {pmid41939717, year = {2026}, author = {Navarro-Nieva, A and Martínez-Checa, F and Delgado, R and Párraga, J and Francino, MP and Jiménez-Hernández, N and Del Moral, A}, title = {Airborne microorganisms in muddy rain: microbe-mineral interactions and their ecosystem impact.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1772201}, pmid = {41939717}, issn = {1664-302X}, abstract = {The Sahara Desert and the Sahel region in North Africa contribute approximately 50-70% of global atmospheric dust emissions. Microorganisms can attach to dust particles and be dispersed into exogenous environments, being subsequently deposited by gravitational sedimentation (dry deposition) or through aqueous precipitation (wet deposition) also known as muddy rain. In the present work, five muddy rain samples were collected in Granada (Spain) during different episodes in 2021-2022. The SEM-EDX study demonstrated a high content of fine clay particles which may facilitate the atmospheric transport of microorganisms. The colonization of strategic microsites and the formation of mineral aggregates might be possible mineral-bacteria interactions. According to metagenomic analysis, Pseudomonadota (64%), Bacteroidota (13%), and Bacillota (6%) were the main phyla. At the genus level, extremophiles, plant-beneficial bacteria, and others involved in soil biogeochemical cycles have been described. Fourteen cultivable microorganisms were isolated and identified by means of 16S rRNA sequencing. Members of the phyla Pseudomonadota, Bacillota, Actinomycetota and Bacteroidota have been found. Among the isolates, Stenotrophomonas rhizophila and Brevundimonas bullata potentially exert beneficial effects at the ecosystem level. In general, muddy rain facilitates the transport and dispersal of microorganisms from different environments, with a potential positive influence on soils and vegetation in terrestrial ecosystems.}, }
@article {pmid41940150, year = {2026}, author = {Luo, H and Wang, Y and Hou, H and Yang, J and Liu, YX}, title = {Advances and applications in sequencing-based pathogen surveillance.}, journal = {aBIOTECH}, volume = {7}, number = {1}, pages = {100004}, pmid = {41940150}, issn = {2662-1738}, abstract = {The ongoing emergence of infectious diseases necessitates cutting-edge diagnostic methodologies. Traditional diagnostic methods are constrained by limited range, lengthy processing times, and inadequate sensitivity. High-throughput sequencing technologies, particularly multiplex polymerase chain reaction (PCR)-based targeted sequencing, have emerged as transformative tools for pathogen detection, offering enhanced sensitivity, specificity, and cost efficiency. However, challenges in primer design, such as dimerization and bias, limit the effectiveness of these approaches. This review explores advances in sequencing technologies, emphasizing the roles of culturomics, metagenomics, and metatranscriptomics in pathogen discovery. We spotlight innovative strategies for error-tolerant primer design that address existing limitations by balancing coverage and specificity, thereby optimizing the multiplex PCR process. Furthermore, integration of artificial intelligence enhances the precision and scalability of sequencing, enabling real-time diagnostics. Collectively, these advances offer promising pathways to bolster global health, food security, and ecological resilience through robust and sustainable pathogen-detection systems.}, }
@article {pmid41940273, year = {2026}, author = {Huang, F and Shi, X and Chen, P and Hu, Q and Zhao, Y and Chen, Z and Ma, W and Tan, Q and Feng, X and Zhang, X}, title = {Dietary drivers of gut microbiota diversity and function in wildlife of Wolong Nature Reserve: a metagenomic study.}, journal = {Current zoology}, volume = {72}, number = {1}, pages = {14-29}, pmid = {41940273}, issn = {1674-5507}, abstract = {While diet is known to regulate the composition, function, and diversity of the human gut microbiome, its effects on wildlife remain understudied. Here, noninvasive sampling methods were first used to conduct metagenomic analyses of the gut microbiomes of 10 protected wild animals in the Wolong Nature Reserve. There were significant differences in microbiota composition and function between herbivores and carnivores. Herbivores exhibited higher microbial diversity and evenness (Shannon and Pielou indices), with Bacillota and Acinetobacter predominating, whereas carnivores were enriched in Pseudomonadota and Escherichia. Cellulose-degrading bacterium Ruminococcus champanellensis was abundant in herbivores, while Rhodococcus and Pediococcus, which were associated with toxin degradation and pathogen inhibition, were more prevalent in carnivores. Carnivores showed higher lipid metabolism and protein degradation, as evidenced by the enrichment of leucyl aminopeptidase and oligopeptidase B, while herbivores demonstrated superior cellulose and starch digestion, characterized by the enrichment of cellulose 1,4-beta-cellobiosidase. Stochastic processes shaped gut microbiome assembly, especially in herbivores. Potential health risks from pathogens such as Escherichia and Listeria were identified, and Escherichia abundance was positively correlated with niche width. Furthermore, the findings suggest that high-altitude environments may promote the persistence and spread of pathogens. Overall, our findings underscore the intricate linkages between diet, gut microbiota composition, assembly processes, and host ecology in protected wildlife, address a key knowledge gap, and provide important theoretical and practical insights for ecological conservation, species restoration, and environmental management.}, }
@article {pmid41940285, year = {2025}, author = {Jeong, GH and Lim, KS}, title = {Exploring the potential of salivary small RNAs as non-invasive biomarkers in pigs.}, journal = {Journal of animal science and technology}, volume = {67}, number = {6}, pages = {1207-1214}, pmid = {41940285}, issn = {2055-0391}, abstract = {Saliva, a non-invasive potential source of circulating microRNAs (miRNAs) and microbiomes, is not well described in pigs. Salivary miRNA expression profiles and the functional significance in pigs were investigated in this study. Saliva samples were extracted from adult female pigs, and small RNA sequencing revealed 26 known and 223 novel miRNAs. The large number of novel miRNAs also demonstrates the differences between salivary miRNAs in pigs and other biological samples. Functional analysis of miRNA target genes indicated enrichments in molecular functions related to transcription regulator activity, cytoskeleton organization, and protein binding, suggesting roles for this interaction in gene expression and physiological control. Moreover, metagenomic analysis revealed microbial sequences representing around 39% of the total reads, with Corynebacterium genus, an important member of the oral microbiota, being the most prevalent. Combining miRNA with microbiome data indicates that porcine saliva is rich in molecular information that will be useful for salivary health monitoring and microbiome studies. This study underscores the potential of salivary miRNAs as biomarkers for physiological processes and microbiome interactions in pigs, paving the way for further research into their diagnostic and monitoring applications.}, }
@article {pmid41940335, year = {2026}, author = {Buysse, M and Ballinger, MJ and Bruley, M and Amoros, J and Grillet, J and Farassat, N and Serr, A and Lagrèze, WA and Wennerås, C and Grankvist, A and Schön, T and Berglund, J and Bell-Sakyi, L and Sprong, H and Duron, O}, title = {A human-associated Spiroplasma ixodetis lineage responsible for infantile cataracts and adult febrile illness.}, journal = {iScience}, volume = {29}, number = {4}, pages = {115233}, pmid = {41940335}, issn = {2589-0042}, abstract = {Bacteria of the Spiroplasma ixodetis clade are well characterized as reproductive parasites and defensive endosymbionts of arthropods. Nevertheless, clinical evidence indicates that they can also infect humans, causing neonatal ocular disease and acute febrile illness in adults. Using metagenomic assembly and phylogenomic analyses of Spiroplasma ixodetis-related human infections (SiRHIs), combined with a systematic meta-analysis of public datasets, we identified 25 human cases across ten European countries. Despite the frequent detection of multiple S. ixodetis strains in ticks, our data provide no evidence implicating tick-associated strains in human infections. Instead, SiRHI constitute a distinct monophyletic lineage within the S. ixodetis clade, consistent with a shared evolutionary origin with arthropod-associated relatives. Notably, SiRHI genomes harbor horizontally acquired chaperone genes absent from most arthropod-associated Spiroplasma, while retaining conserved effector genes typical of endosymbionts, suggesting the preservation of ancestral symbiotic traits alongside newly acquired molecular adaptations.}, }
@article {pmid41940665, year = {2026}, author = {Huang, C and Feng, Q and Yu, B and Zou, H and Cai, Y and Liu, J and Li, D and Zhang, H and Zou, X}, title = {Diabetes affects the composition of the respiratory tract microbiome and transcriptome in patients with viral pneumonia.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0191125}, doi = {10.1128/spectrum.01911-25}, pmid = {41940665}, issn = {2165-0497}, abstract = {UNLABELLED: Research shows that patients with viral pneumonia complicated by diabetes have a worse prognosis and higher mortality. Our study aimed to assess the effect of diabetes on respiratory tract microbes and the transcriptome in patients with viral pneumonia. We included 76 subjects from China-Japan Friendship Hospital, including 16 healthy people, 17 patients with viral pneumonia and diabetes (VD), and 43 patients with viral pneumonia without diabetes (VP). We collected their sputum samples for both metagenomic and 16S rRNA sequencing and collected blood samples for RNA sequencing. In transcriptome analysis, the VD group downregulated the expression of PTCH1 and upregulated the expression of ANK1, RBM38, BPGM, CRYM, TAL1, and HBD. The differential pathways are mainly reflected in the formation, development, and maintenance of red blood cells, the activity of immunoglobulins, and the membrane transport and transportation of substances. There is a significant difference in microbial diversity between the two groups. Both analysis methods demonstrate a significant increase in the abundance of g__Treponema, s__Treponema_denticola, and s__Campylobacter_rectus in the VP group. The host genes AGAP1, RNF182, and ANKRD9 are particularly closely associated with microorganisms. Our results suggest that diabetes may inhibit the expression of genes related to immune regulation, energy metabolism, and oxygen utilization in patients with viral pneumonia. Meanwhile, we predict that VD may be associated with a decrease in microbial diversity and a decline in microbial functions in cellular processes, environmental adaptation, metabolism, and genetic activity. These abnormalities can worsen the course of viral pneumonia and affect the prognosis of patients.<br><br>IMPORTANCE: We used 16S rRNA and metagenome sequencing to analyze the respiratory microbial composition of patients with viral pneumonia complicated by diabetes (VD) and patients with viral pneumonia without diabetes (VP) and used transcriptome sequencing to compare the gene expression of patients in VD, VP, and healthy people. Our results indicate significant differences in gene expression and respiratory microbiota profiles between VD and VP. VD may inhibit the immune regulatory response and affect cell energy metabolism and oxygen transport and utilization by regulating related gene pathways. The abundance of Treponema denticola in the VP group was significantly higher than that in the VD group. We predicted that the functions of differential microorganisms may be related to cellular processes, environmental information processing, genetic information processing, human diseases, and metabolism. This study found characteristic biomarkers related to viral pneumonia with diabetes, providing a new strategy for further research and clinical treatment.}, }
@article {pmid41940696, year = {2026}, author = {Li, Y and Zhang, H and Xiang, B and Zhang, Y and Zhang, M}, title = {Enhanced microbiota-derived mucinases in colorectal cancer patients revealed by gut metagenome probing coupled with functional validation.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0190325}, doi = {10.1128/aem.01903-25}, pmid = {41940696}, issn = {1098-5336}, abstract = {Mucinases produced by the gut microbiota play a dual role in regulating the integrity and renewal of the mucus layer, which is essential for maintaining gut homeostasis and human health. In this study, we constructed protein hidden Markov models based on 11 known mucinases and used them to systematically identify mucinase sequences from gut metagenome-assembled genomes derived from 80 colorectal cancer (CRC) patients and 86 healthy (Healthy) subjects. A total of 1,869 mucinases were detected, widely distributed across the studied cohorts, with the majority originating from Bacteroides, Phocaeicola, and Akkermansia species. Further analysis identified 42 mucinases that differed significantly in abundance between the two groups, all of which were enriched in CRC patients. Taxonomic attribution revealed that, in CRC patients, these mucinases were primarily derived from Bacteroides (36.0%), Phocaeicola (30.6%), Akkermansia (8.8%), Alistipes (8.6%), and Escherichia (6.4%), whereas in Healthy subjects, they mainly originated from Bacteroides (26.1%), Akkermansia (22.7%), and Phocaeicola (20.3%), with a notably higher proportion from Akkermansia. Among the 42 mucinases, WL42 and LLN1 exhibited significantly higher abundance levels compared to the others. Phylogenetic and predicted structural analyses suggested that these two mucinases belonged to the M60 and M98 families, respectively. Functional validation through co-incubation experiments demonstrated that both mucinases could cleave the glycosylated MUC1 and MUC2 substrates, but not the corresponding non-glycosylated proteins. These findings confirm the feasibility of discovering novel mucinases directly from gut metagenomic data and provide insights into their potential roles in health and disease.IMPORTANCEOur study established a feasible bioinformatics pipeline for the systematic identification of microbial mucinases within the gut microbiome, providing a methodological foundation for large-scale mining of functionally active mucin-degrading enzymes. We identified 42 mucinases significantly enriched in CRC patients, suggesting their potential involvement in CRC pathogenesis. Among them, two mucinases were experimentally validated for their ability to degrade mucin, offering direct functional evidence of their capacity to disrupt the mucosal barrier. Genus-level metagenomic profiling further identified Bacteroides, Phocaeicola, and Akkermansia as major mucinase-producing genera. Maintaining the secretory balance of these mucinase-producing bacteria might be crucial for ameliorating intestinal barrier dysfunction in CRC patients. The findings of this study offer critical insights into the microbial origins and potential mechanistic contributions of mucinases in colorectal cancer, underscoring their relevance in mucus barrier breakdown and disease progression.}, }
@article {pmid41940802, year = {2026}, author = {Yersin, S and Gody, JC and Mazel, F and Djimbele, E and Nigateloum, SN and Gondje, BP and Vondo, SS and Kaleb Jephté Estimé, K and Raub, A and Teo, Y and Djorie, SG and Kapel, N and Sansonetti, PJ and Vonaesch, P and , }, title = {Strain-level translocation and enrichment dynamics of oral bacteria in the lower gastrointestinal tract of stunted children.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2653550}, doi = {10.1080/19490976.2026.2653550}, pmid = {41940802}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; *Mouth/microbiology ; Female ; *Bacteria/classification/isolation &amp; purification/genetics ; Feces/microbiology ; Child, Preschool ; Saliva/microbiology ; Infant ; Cross-Sectional Studies ; *Bacterial Translocation ; *Growth Disorders/microbiology ; Child ; *Gastrointestinal Tract/microbiology ; Metagenomics ; }, abstract = {Emerging evidence suggests that ectopic colonization of oral bacteria in the lower digestive tract may exacerbate gastrointestinal disorders. Nevertheless, it remains unclear whether bacteria of oral origin are continuously translocating from the oral cavity to the lower gastrointestinal tract or are locally adapted and persist in their respective niches. We investigated strain translocation dynamics in 44 healthy and stunted children from Bangui, Central African Republic. Using cross-sectional shotgun metagenomic sequencing of saliva, gastric, duodenal, and fecal samples, and isolation and whole-genome sequencing of 87 Streptococcus salivarius isolates, we showed the translocation of members of the genera Streptococcus, Veillonella, Rothia, and Haemophilus. Fecal isolates were more closely related to oral isolates from the same individuals than to those from other individuals. Additionally, saliva showed higher S. salivarius nucleotide diversity compared to other compartments, which is consistent with frequent intraindividual translocations from the oral cavity to the lower gastrointestinal tract. Finally, we showed that overrepresentation of oral bacteria in the duodenum of stunted children is related to increased biomass, while in the colon, it is linked to depletion of overall biomass, including in butyrate-producing strains. Our study quantifies dynamics of oral-to-gut translocation and enrichment of oral taxa, providing key insights into microbiota disruption in stunted children.}, }
@article {pmid41940852, year = {2026}, author = {Jin, Z and Yuan, Q and Wang, J and Liao, H and Bol, R and Wu, D and Wu, Q and Tang, Y and Guo, W and Liu, Y and Chen, J}, title = {Recycling of Sedimentary Phosphorus Pools in Two Yunnan-Guizhou Plateau Lakes, Southwest China.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.6c00162}, pmid = {41940852}, issn = {1520-5851}, abstract = {Applying phosphate oxygen isotopes (δ[18]OP) to identify sediment phosphorus (P) sources and its recycling is still challenging due to poor understanding in δ[18]OP variations of sediment P pools and their driving mechanisms. Here, we analyzed the δ[18]OP in inorganic P (Pi) pools of sediment cores and varied P sources from Lake Dianchi and Lake Erhai in the Yunnan-Guizhou Plateau, Southwest China. The δ[18]OP values of sediment detrital Pi (Det-Pi, nonbioavailable P) were consistent with those of watershed soils (within ∼0.4-0.6‰), indicating that the δ[18]OP of sediment Det-Pi inherits the δ[18]OP of soil Det-Pi. The δ[18]OP values of aluminum-bound Pi (Al-Pi) and authigenic Pi (Auth-Pi) in sediment were close to or within the δ[18]OP equilibrium (δ[18]OP-eq) ranges, implying oxygen isotopic exchange equilibrium between phosphate and ambient water prior to the formation of sediment Al-Pi and Auth-Pi. However, the δ[18]OP of iron oxide-bound Pi (Fe-Pi) in sediment was lighter (∼3‰) than δ[18]OP-eq, retaining the negative isotopic signal of organic P (Po) remineralization. Furthermore, [31]P NMR and metagenomic analysis indicated that microbial-mediated Po mineralization and Pi recycling are the driving factors for δ[18]OP changes in sediment Fe-Pi, Al-Pi, and Auth-Pi. These integrated insights deepen our understanding of the biogeochemical cycling for sedimentary P.}, }
@article {pmid41940893, year = {2026}, author = {Liao, Y and Wang, B and Li, Y and Ni, W and Li, X and Hu, S}, title = {Establishment of the chromid database and analysis of evolutionary research.}, journal = {Molecular genetics and genomics : MGG}, volume = {301}, number = {1}, pages = {}, pmid = {41940893}, issn = {1617-4623}, mesh = {*Evolution, Molecular ; Phylogeny ; *Genome, Bacterial/genetics ; *Databases, Genetic ; *Bacteria/genetics/classification ; Polymorphism, Single Nucleotide ; Metagenomics/methods ; Computational Biology/methods ; }, abstract = {In bacterial multireplicon genomes, in addition to the main chromosome, there is a widespread class of secondary replicons with a distinct evolutionary status known as chromids. These elements possess plasmid-like replication and partitioning systems, while their nucleotide composition and gene functions are highly similar to those of the main chromosome. Therefore, chromids are considered to play important roles in the evolution of bacterial genome architecture and in environmental adaptation. With advances in long-read sequencing technologies and breakthroughs in bioinformatics methods, metagenomic data resources have been greatly expanded. Using our previously developed automated tool, "Chromid-Finder", we systematically identified and collected chromid sequences from large-scale metagenomic assemblies. These data were then uniformly curated, classified, and centrally managed to construct a public database platform dedicated to chromids-Chromid Database. On this basis, we conducted comprehensive analyses of the evolutionary and genetic characteristics of chromids. Phylogenetic analyses revealed the overall evolutionary landscape of chromids. Variation analyses showed that SNP distributions on chromids exhibit clear and well-organized patterns, depicting a dynamic population that is continuously adapting to the environment through fine-scale sequence tuning and non-coding regulatory mechanisms. Structural variation analyses further identified several hotspot regions significantly enriched in key genes related to metabolic functions, nutrient acquisition, and antibiotic resistance. The distribution patterns of recombination events suggest that their occurrence is likely driven primarily by non-phylogenetic factors such as environmental conditions and ecological niches. In addition, systematic quantification of heritable mobile genetic elements indicated that the number of integrative and conjugative elements (ICEs) largely determines the overall mobile element burden within chromids.}, }
@article {pmid41941835, year = {2026}, author = {Hennen, J and Ifrach, J and Morse, C and Charcos, I and Godil, SS and Mossop, CM}, title = {First reported case of Lawsonella clevelandensis brain abscess in the setting of invasive cutaneous squamous cell carcinoma identified via bedside stereotactic aspiration: illustrative case.}, journal = {Journal of neurosurgery. Case lessons}, volume = {11}, number = {14}, pages = {}, doi = {10.3171/CASE25887}, pmid = {41941835}, issn = {2694-1902}, abstract = {BACKGROUND: Brain abscesses associated with malignant skull base invasion pose unique diagnostic and management challenges for neurosurgeons, particularly when routine cultures remain negative. The authors report the first documented intracranial infection caused by Lawsonella clevelandensis, a recently described anaerobe that mimics Nocardia or Mycobacterium sp., diagnosed using bedside stereotactic biopsy as well as metagenomic next-generation sequencing.<br><br>OBSERVATIONS: A 74-year-old woman with recurrent, locally invasive facial squamous cell carcinoma presented with recent-onset shaking of her lower extremity and a large right frontal mass extending through the calvarium and orbit. Imaging revealed ring-enhancing lesions consistent with abscess. Bedside stereotactic biopsy and drainage were performed, and metagenomic sequencing identified L. clevelandensis. Antibiotics were narrowed to ceftriaxone and metronidazole, stabilizing her condition, although repeat drainage was required for radiographic progression. She subsequently underwent multidisciplinary skull base resection and reconstruction, with operative cultures isolating Enterococcus faecium but no further Lawsonella sp.<br><br>LESSONS: This case represents the first documented intracranial L. clevelandensis infection and demonstrates the diagnostic value of molecular sequencing in culture-negative brain abscesses. It also highlights bedside stereotactic biopsy and drainage as a safe, minimally invasive strategy for managing intracranial infection in medically complex patients. https://thejns.org/doi/10.3171/CASE25887.}, }
@article {pmid41942049, year = {2026}, author = {Chen, W and Zhang, Y and Tian, Y and Dai, W and Huang, D and Zhao, Z and Henawy, AR and Shao, Z and Cai, M and Huang, F and Zheng, L and Cheng, W and Zhang, J}, title = {Multi-cycle application of Virgibacillus dokdonensis induces a root-knot nematode-suppressive soil via specifically recruiting functional Pseudomonas.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2026.04.004}, pmid = {41942049}, issn = {2090-1224}, abstract = {INTRODUCTION: Inducing the development of disease-suppressive soils against root-knot nematodes (RKNs) represents a sustainable strategy for reducing pesticide dependence, with microbial management serving as a core approach. However, the formation mechanisms, key microbial drivers, and functional stability of RKN disease suppressive soil remain poorly understood.<br><br>OBJECTIVES: This study aimed to elucidate the ecological mechanisms underlying soil microbiome-mediated suppressiveness against RKNs induced by multi-cycle application of the deep-sea biocontrol bacterium Virgibacillus dokdonensis MCCC 1A00493.<br><br>METHODS: Using a three-cycle consecutive microcosm experiment, we tracked RKN disease incidence and soil microbial community dynamics. We combined microbiome sequencing with functional assays to identify key functional taxa, and constructed synthetic microbial communities (SynComs) to validate their synergistic suppression with V. dokdonensis.<br><br>RESULTS: Continuous application of V. dokdonensis significantly reduced RKN disease, with the control efficacy reaching 37.86%, 51.11%, and 65.85% over three cropping cycles. This suppressiveness was achieved through direct antagonism and the reshaping of the soil bacterial community, which involved the successful colonization of V. dokdonensis and specific enrichment of indigenous functional Pseudomonas. Metagenomic analysis indicated a significant upregulation of bacterial chemotaxis genes. Further chemotaxis assays confirmed that the fermentation supernatant of V. dokdonensis specifically attracts high-nematicidal Pseudomonas, achieving a relative chemotaxis index reaching 3.0 to 9.1. Based on this, we constructed synthetic communities of functional Pseudomonas with varying complexity levels. Among them, a simplified SynComV1, consisting of Pseudomonas monteilii, P. parafulva, P. fulva, P. plecoglossicida, and P. putida, exhibited the greatest disease suppression, reaching 48.38%. Notably, co-application of V. dokdonensis and SynComV1 demonstrated significant synergistic effects, enhancing the control efficacy to 58.33%.<br><br>CONCLUSIONS: Overall, this study revealed that multi-cycle application of V. dokdonensis induces a RKN-suppressive soil by specifically recruiting indigenous high-nematicidal Pseudomonas to synergistically suppress RKN disease. These findings provide a practical strategy for developing efficient and sustainable technologies for RKN management.}, }
@article {pmid41942192, year = {2026}, author = {Xia, Y and Kuda, T and Zhou, Q and He, Q}, title = {Bidirectional modulation of microbial communities by tea polyphenols and gallic acid enhances quality in dry fermented sausages.}, journal = {Food research international (Ottawa, Ont.)}, volume = {233}, number = {Pt 1}, pages = {118924}, doi = {10.1016/j.foodres.2026.118924}, pmid = {41942192}, issn = {1873-7145}, mesh = {*Gallic Acid/pharmacology ; *Meat Products/microbiology/analysis ; *Polyphenols/pharmacology ; Fermentation ; *Tea/chemistry ; *Food Microbiology ; *Microbiota/drug effects ; Antioxidants/pharmacology ; Animals ; *Fermented Foods/microbiology ; Humans ; Food Quality ; Taste ; }, abstract = {Tea polyphenols (TP) and its primary component gallic acid (GA) possess antibacterial and antioxidant properties, serving as natural additives to enhance the safety and quality of fermented meat products. This study investigated the bidirectional regulatory effects of TP and GA on microbial dynamics and quality attributes in dry fermented sausages. TP (1-4 mg/mL) enhanced the growth of Lactiplantibacillus plantarum while inhibiting Staphylococcus aureus and Escherichia coli, promoting lactic acid bacteria (LAB) dominance and reducing spoilage and pathogenic bacteria. Sausages treated with TP showed reduced levels of biogenic amines (291.06 vs. 376.22 mg/kg) and NDMA (0.86 vs. 1.32 μg/kg), improved texture (hardness and springiness), and better color stability, all without affecting sensory acceptability. Metabolomic and metagenomic analyses suggested that GA enriched beneficial Lactococcus garvieae and suppressed spoilage-associated Enterococcus faecalis and Citrobacter freundii. Besides, it promoted the microbial-mediated production of key antioxidant metabolites and flavor enhancers (e.g., purpurogallin, sesamol). These results indicated that TP and GA could serve as multifunctional additives that enhance fermentation efficiency, microbial safety, and sensory quality by precisely regulating microbial communities and their metabolic functions.}, }
@article {pmid41764528, year = {2026}, author = {Zhang, W and Su, Q and Shi, H and Sun, Y and Li, X and Li, M and Wang, H and Yu, J and Wong, N and Chan, FKL and Zhang, J and Ng, SC}, title = {Discovery and characterization of Christensenella hongkongensis as a novel bacterium in the adenoma-carcinoma progression.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {41764528}, issn = {1479-5876}, abstract = {BACKGROUND: Colorectal cancer (CRC) is one of the most prevalent malignancies worldwide and commonly starts from a pre-cancerous stage. This study aimed to identify potential fecal bacterial candidates associated with progression of CRC from the adenoma-carcinoma sequence and to explore underlying mechanisms of carcinogenesis.<br><br>METHODS: Publicly metagenomic datasets were analyzed using MaAsLin2 to identify bacterial species enriched in CRC patients compared to healthy controls. Additionally, we established a large cohort in mainland China, consisting of 686 subjects, including 285 CRC patients, 73 advanced adenoma patients (AA), 134 non-advanced adenoma patients (nAA), and 194 healthy controls (NC). Fecal samples from this cohort were analyzed by duplex quantitative polymerase chain reaction (qPCR) to validate the abundance of key bacterial candidate and its association with tumor node metastasis (TNM) stages. Receiver operating characteristic (ROC) curve analysis was performed to evaluate the diagnostic performance of Christensenella hongkongensis (C. hongkongensis) alone and in combination with fecal immunochemical test (FIT) across different CRC stages. In vitro experiments and transcriptome sequencing were performed to explore the effects of C. hongkongensis and its mechanisms in CRC progression.<br><br>RESULTS: MaAsLin2 analysis identified seven bacterial species were significantly more abundant in fecal samples of CRC patients than in healthy controls (p&#x2009;<&#x2009;0.05). Among them, C. hongkongensis, an obligately anaerobic, catalase-positive, motile, non-sporulating, gram-positive coccobacillus was distinguished by its lowest abundance in healthy controls and significant enrichment in CRC patients. Validation in our recruited cohort showed that the abundance of C. hongkongensis progressively increased from non-advanced adenomas to advanced adenomas and CRC. For classifying AA from nAA, C. hongkongensis yielded an area under the ROC curve (AUC) of 0.60 (95% CI 0.53&#x2013;0.68), with 45.2% sensitivity and 85.8% specificity. A combined model integrating C. hongkongensis abundance and FIT further improved diagnostic performance, increasing AUCs from 0.77 to 0.81 for AA vs NC (p&#x2009;<&#x2009;0.05) and from 0.76 to 0.82 for AA vs nAA (p&#x2009;<&#x2009;0.001). Linear regression analysis revealed a significant positive association between C. hongkongensis and TNM stages in CRC. In vitro experiments showed that C. hongkongensis promoted CRC cell proliferation, inhibited apoptosis, and enhanced the growth of patient-derived CRC organoids. RNA-seq analysis identified activation of the Wnt/&#x3b2;-catenin signaling pathway, which was further validated by elevated protein levels of active &#x3b2;-catenin, reduced phosphorylation of GSK3&#x3b2;, and the upregulation of downstream targets c-Jun and Cyclin-D1.<br><br>CONCLUSIONS: Our findings suggest that C. hongkongensis promotes colorectal tumorigenesis via Wnt/&#x3b2;-catenin activation, and highlight its potential as a novel non-invasive bacterial marker for early detection and monitoring of CRC progression.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07886-9.}, }
@article {pmid41933601, year = {2026}, author = {Chen, J and Yan, Y and Xie, K and Gao, M and Ma, Y}, title = {Effect of delivery mode and temperature control of microbial consortium-based compound enzyme on anaerobic digestion of food waste: Decipherment from engineering and energy angles.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134536}, doi = {10.1016/j.biortech.2026.134536}, pmid = {41933601}, issn = {1873-2976}, abstract = {Microbial consortium-based compound enzyme (MCE) has been developed as an alternative to commercial enzyme for food waste (FW) decomposition, yet how to deliver it to anaerobic digestion (AD) system for maximum energy recovery remains unclear. This study systematically compared the simultaneous hydrolysis and AD (Sim mode), as well as separate hydrolysis and AD (Sep mode) at mesophilic and thermophilic temperatures, and dissected their influencing mechanisms on methane production from FW. Results showed that Sep mode and mesophilic temperature were the optimal conditions for methane production, where over 70% of soluble COD and 96% of soluble carbohydrate were consumed within 1 d, and the highest cumulative methane yield reached 507.32 mL/g VS. Dynamics of microbial communities revealed that temperature exerted greater influence on bacterial and archaeal succession than delivery modes, and mesophilic temperature-driven transition from hydrogenotrophic archaea to acetotrophic archaea was a key factor in enhancing methane production. Metagenomic analysis further elucidated that key metabolic functions were temperature-dependent, and Methanothrix was identified as the dominant contributor to these metabolic functions. Moreover, energy balance unveiled that Sep mode respectively increased net energy recovery (ΔEtotal) and energy ratio (Er) by 68.33% and 25.90%, achieving concurrent maximization of quantity and efficiency of energy recovery.}, }
@article {pmid41933710, year = {2026}, author = {Huang, S and Zhang, S and Chen, Y and Su, X and Lu, X and Song, X and Li, W and Guo, Z and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Wang, X and Shan, T and Zhang, W}, title = {Viral metagenomic analysis of CRESS-DNA viruses in six wild herbivorous mammal species from the Qinghai-Tibet plateau.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105932}, doi = {10.1016/j.meegid.2026.105932}, pmid = {41933710}, issn = {1567-7257}, abstract = {As natural reservoirs for diverse viruses, mammals harbor complex and highly diverse viral communities. The Qinghai-Tibet Plateau, recognized as the "Third Pole" of Earth, exerts substantial evolutionary pressure on virions through its extreme environmental conditions characterized by high altitude, hypoxia, intense ultraviolet radiation, and dramatic diurnal temperature variation. Circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses represent a ubiquitous group of small viruses that play crucial roles in maintaining global ecological equilibrium. Through viral metagenomic analysis of 741 fresh fecal samples collected from six wild herbivorous mammal species across three geographical regions of the Qinghai-Tibet Plateau, we systematically characterized their virome composition, revealing distinct interspecies variations in viral community structure. Focusing on CRESS-DNA viruses, we identified 180 complete viral sequences containing intact replication-associated protein (Rep) genes, including: Circoviridae (2 sequences, 1 novel), Genomoviridae (48 sequences, 38 novel), Smacoviridae (106 sequences, 103 novel), and Unclassified CRESS-DNA viruses (24 sequences, 20 novel), collectively representing an 86% discovery rate of novel viral virus. These viral sequences exhibited remarkable genetic divergence, with the majority (73%) failing to cluster within established taxonomic units, suggesting the plateau may constitute an evolutionary hotspot for novel CRESS-DNA viruses. Our findings not only expand current understanding of CRESS-DNA viral diversity but also indicate potential long-term symbiotic virus-host relationships rather than purely pathogenic interactions in this extreme ecosystem. Notably, high viral detection rates in species such as the Pseudois nayaur suggest their potential role as key transmission vectors. These discoveries provide novel insights into virus-host coevolution mechanisms under extreme environmental conditions and establish a scientific foundation for early warning systems of viral transmission risks in high-altitude ecosystems.}, }
@article {pmid41933826, year = {2026}, author = {Ma, J and Zhang, H and Liang, S and Feng, X and Xia, Z and Li, H and Zou, S and Li, D}, title = {The health threat of wild animals by Rank I ARGs from habitat soils: Metagenomic and metabolomic evidence.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {398}, number = {}, pages = {128041}, doi = {10.1016/j.envpol.2026.128041}, pmid = {41933826}, issn = {1873-6424}, abstract = {Human disturbance (HD) leads to the enrichment of antibiotic resistance genes (ARGs), posing a threat to the health of wild animals. However, not all ARGs necessarily endanger wild animals' health. Therefore, this study used the golden snub-nosed monkeys (Rhinopithecus roxellana) as a sentinel species, and employed metagenomics to investigate the impact of high-risk ARGs (Rank Ⅰ ARGs) from habitats on wild animals' health. Subsequently, we studied the expression of metabolites within the metabolic network harboring homologous functional genes based on metabolomics. The results indicated that only 0.034% of ARGs in the habitat soils were classified as Rank I ARGs. HD not only increased the accessibility, mobility, pathogenicity and availability of Rank I ARGs in the soils of wild animals' habitats, thereby elevating the health risks to wild animals. Especially, the energy metabolism and carbohydrate metabolism functions of the gut microbiome were disrupted in wild animals. Multiple factors influence the health of wild animals posed by Rank I ARGs under HD: primarily, the strong correlation between ARGs and MGEs; the indirect impact of the content of AP in the soil; the increased proportion of the host bacteria Enterobacter; and the rise in the potential host bacteria of Rank I ARGs. We suggested that the use of aminoglycoside, glycopeptide, and peptide antibiotics should be strictly controlled in nature reserves, coupled with enhanced monitoring of soil nutrients, particularly available phosphorus.}, }
@article {pmid41934012, year = {2026}, author = {Moraïs, S and Mizrahi, I}, title = {Micro-scale spatial metagenomics opens a new era in microbiome ecology.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2026.03.005}, pmid = {41934012}, issn = {1878-4380}, abstract = {Understanding microbial communities requires moving beyond 2D representations toward a holistic view that couples 3D spatial organization with ecological function, integrating microbial inventories, genes, expression profiles, and interactions at scales and dimensions in which microbial life unfolds. In this opinion article, we synthesize recent findings and emerging approaches that enable the investigation of microbial interactions within their native 3D context. We propose conceptual frameworks for integrating spatial-functional information into comprehensive ecological maps, providing new avenues to interpret microbial interactions and to test ecological theory in situ. Together, these insights outline a new ecological paradigm for microbiome research and highlight how spatially resolved understanding can be harnessed to interpret and ultimately guide the modulation of microbial interactions and ecosystem function in natural settings.}, }
@article {pmid41934196, year = {2026}, author = {Alvarez-Sala, A and Jiménez-Hernández, N and Artacho, A and Ruiz-Pérez, S and Pascual, EC and Pons, J and Sorlí, JV and Corella, D and Gosalbes, MJ}, title = {Multi-Omic Insights Into Mediterranean Diet-Associated Microbiota.}, journal = {Molecular nutrition &amp; food research}, volume = {70}, number = {7}, pages = {e70450}, pmid = {41934196}, issn = {1613-4133}, support = {UGP-19-038//FISABIO/ ; UGP-21-205//FISABIO/ ; CIAICO/2022/27//Conselleria de Innovaci&#xf3;n, Universidades, Ciencia y Sociedad Digital/ ; Prometeo2021/021//Conselleria de Innovaci&#xf3;n, Universidades, Ciencia y Sociedad Digital/ ; CB06/03/0035//CIBEROBN/ ; }, mesh = {Humans ; *Diet, Mediterranean ; Male ; Female ; Adult ; Bacteria/genetics/classification ; *Microbiota ; Metagenomics ; Middle Aged ; Olive Oil ; *Gastrointestinal Microbiome ; Feces/microbiology ; Fruit ; Vegetables ; Multiomics ; }, abstract = {This study aimed to evaluate the gut microbiota and mycobiota composition, depending on the Mediterranean diet (MD) adherence, using metataxonomics. Combining metagenomics and metatranscriptomics, we also investigate the gene expression level in the bacterial community. Two groups of healthy subjects greatly differing in adherence were selected. Significant differences in microbiota composition were observed between individuals with high adherence (HAMD; mean 10.5 +/- 0.9 points) and low adherence (LAMD; 5.23 +/- 83 points). Notably, the olive oil, vegetable, and fruit consumption presented an important discriminant power between groups. Saccharomyces, Penicillium, and Candida were the most abundant genera. Mycobiota richness was higher in LAMD than in HAMD. Aspergillus was identified as a biomarker for LAMD, whereas Yarrowia, a potential probiotic, was a biomarker for HAMD. Metatranscriptomics indicated that Bacillota was the most metabolically active phylum in the gut microbiota. The low-abundant genus, Methanobrevibacter, showed high transcriptional activity, contributing to the crucial methanogenesis process. Gene expression analyses further highlighted functional differences. Overall, HAMD microbiota presented increased metabolic activity, protein synthesis, and cellular mobility. Overexpression of flagellin and urease genes may enhance immune response in HAMD. Further metatranscriptomic studies are necessary to deepen our understanding of intestinal microbiota transcriptional programs and their interactions with the diet and human health.}, }
@article {pmid41934511, year = {2026}, author = {Kumar, KS and Jeyabal, J and Yagoo, A and Vilvest, J and Vaishnika, AM}, title = {Dietary chitosan enhances gut microbial diversity and modulates beneficial and pathogenic communities in Channa striata fingerlings.}, journal = {Antonie van Leeuwenhoek}, volume = {119}, number = {5}, pages = {}, pmid = {41934511}, issn = {1572-9699}, mesh = {*Chitosan/administration &amp; dosage/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Animal Feed/analysis ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects ; RNA, Ribosomal, 16S/genetics ; Diet ; Dietary Supplements ; *Fishes/microbiology ; Biodiversity ; Aquaculture ; }, abstract = {Dietary modulation of the gut microbiome is a promising approach for improving fish health and sustainability in aquaculture. Chitosan, a biopolymer derived from Artemia shells, has gained attention as a functional prebiotic feed additive due to its antimicrobial and immunomodulatory properties. The effects of dietary chitosan on gut microbial diversity and community composition were evaluated in Channa striata (murrel) fingerlings. Fish were fed three experimental diets: a basal diet (Exp-1), a black soldier fly larvae (BSFL)-based control diet (in which BSFL meal was used as a primary protein ingredient, with its nutritional composition considered during formulation), and a chitosan-supplemented diet (Exp-2). Gut microbiota were characterized using high-throughput 16S rRNA gene sequencing, and microbial diversity, composition, and interaction networks were analyzed. Alpha diversity analysis demonstrated that the chitosan-based diet significantly enhanced microbial richness (Chao1 = 531.62) and promoted a more balanced gut microbial structure compared to the basal diet, which showed reduced diversity and relative dominance of certain taxa previously reported to include opportunistic species. Chitosan supplementation enriched genera such as Lactobacillus, Bacteroides, and Alloprevotella, along with members of Muribaculaceae, which are commonly associated in the literature with functions such as polysaccharide degradation and short-chain fatty acid production, although functional roles cannot be conclusively assigned at the genus level. In contrast, the basal diet group showed a higher abundance of taxa including Plesiomonas and Clostridium sensu stricto, which have been reported in some contexts to include opportunistic strains. Network analysis further revealed stronger clustering and connectivity among microbial taxa under chitosan supplementation, suggesting improved microbial stability. Overall, dietary chitosan appears to influence gut microbial composition and diversity, suggesting a possible role in influencing gut microbial balance. These findings highlight its possible application as a sustainable feed additive in aquaculture, although further functional validation is required.}, }
@article {pmid41934651, year = {2026}, author = {Zhang, N and Li, L and Chen, F and Kang, X and Liu, L and Kuang, D}, title = {Rapid Cavitary Pneumonia and Reversible Hepatic Injury in Burkholderia pseudomallei ST271 Infection.}, journal = {The American journal of case reports}, volume = {27}, number = {}, pages = {e951729}, doi = {10.12659/AJCR.951729}, pmid = {41934651}, issn = {1941-5923}, mesh = {Humans ; Male ; *Melioidosis/drug therapy/diagnosis/complications/microbiology ; Middle Aged ; *Burkholderia pseudomallei/isolation &amp; purification/genetics ; Anti-Bacterial Agents/therapeutic use ; *Pneumonia, Bacterial/microbiology/drug therapy/diagnosis ; }, abstract = {BACKGROUND Burkholderia pseudomallei is the causative agent of melioidosis, an infectious disease endemic to tropical and subtropical regions that displays highly variable clinical presentations, ranging from localized abscesses to severe septicemia. Sequence type (ST) 271 has been rarely reported; data concerning its clinical and epidemiological characteristics remain limited. This report describes a rare case of ST271 infection presenting with rapidly progressive cavitary pneumonia and reversible hepatic injury. CASE REPORT A previously healthy 50-year-old male construction worker from Haikou, China, presented with a 2-week history of intermittent fever, hemoptysis, and persistent cough. Chest computed tomography revealed a thick-walled cavitary mass in the right upper lobe. Laboratory findings demonstrated substantially elevated liver enzymes, indicating acute hepatic injury. Metagenomic sequencing of bronchoalveolar lavage fluid identified B. pseudomallei, and whole-genome sequencing classified the isolate as ST271. The strain was sensitive to imipenem, ceftazidime, and trimethoprim-sulfamethoxazole; preliminary in vitro bacteriophage susceptibility also was observed. After initiation of intravenous ceftazidime followed by oral trimethoprim-sulfamethoxazole, the patient showed rapid clinical improvement that included robust resolution of the pulmonary lesion and normalization of liver enzymes, consistent with reversible hepatic injury. CONCLUSIONS This case highlights the aggressive clinical course of the rare B. pseudomallei ST271 strain, characterized by rapidly progressive cavitary pneumonia and concurrent hepatic injury in an immunocompetent host. Early identification using sequencing techniques facilitated timely targeted therapy and a favorable recovery. The observed in vitro phage susceptibility may provide preliminary insight for future research into alternative management strategies for resistant strains.}, }
@article {pmid41934839, year = {2026}, author = {Dong, C and Sun, L and Liu, Z and Sun, C and Pan, D and Zhu, L and Hu, B}, title = {Seafood resistome across trophic levels: Tissue patterns, drivers, and potential dietary exposure.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141959}, doi = {10.1016/j.jhazmat.2026.141959}, pmid = {41934839}, issn = {1873-3336}, abstract = {Antibiotic resistance genes (ARGs) are recognized as emerging contaminants relevant to human exposure. They are widespread in seafood, but their distribution across trophic levels and tissues remains unclear. We analyzed 43 metagenomes covering five marine trophic levels, from seawater plankton to obligate piscivores, and examined muscle, gill, and viscera samples. Multidrug, tetracycline, bacitracin, and β-lactam genes together accounted for about 70% of total relative ARG abundance. ARG richness, diversity, and abundance increased with trophic level. In higher trophic taxa, edible muscle contributed a larger share of the total ARG signal, indicating greater relevance to dietary exposure. Procrustes and variation partitioning showed that ARG composition was mainly associated with microbial community structure and mobile genetic elements (MGEs). Contig analysis further showed co-occurrence of ARGs and MGE markers, suggesting mobility potential. A composite risk index that integrates abundance, mobility proxies, and host or pathogen association also increased with trophic position. These results show clear trophic and tissue patterns of ARGs in marine foods and support priority monitoring of high trophic taxa, edible tissues, microbiome and MGE features along seafood supply chains.}, }
@article {pmid41934858, year = {2026}, author = {Chen, Z and Zheng, M and He, J and Ye, C and Zheng, W and Liang, Y and Yu, X and Guo, F}, title = {Trait-mediated restructuring of gut microbiota under chlorinated drinking water exposure.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141965}, doi = {10.1016/j.jhazmat.2026.141965}, pmid = {41934858}, issn = {1873-3336}, abstract = {Chlorine residuals in drinking water are environmentally relevant oxidants regulated within distribution systems and ingested during routine consumption. Here, we use longitudinal, within-subject designs in humans (0.5 mg/L chlorine exposure) and a parallel mouse model (10 mg/L) to assess the ecological impact of chlorine residuals on gut microbiota under realistic conditions. Crucially, overall diversity, total bacterial biomass, antibiotic resistance genes, and phage communities remained largely unaffected. However, we report a lineage-independent de-dominance effect, where initially dominant taxa decline following exposure. Genome-resolution analysis reveals that microbes with larger genomes and functional enrichment in energy metabolism and membrane biogenesis are more likely to increase, enabling accurate prediction of microbial responses to chlorination. These patterns can be interpreted within the Competitor-Stress-tolerator-Ruderal life-history framework, in which disturbance of chlorine residuals transiently reduces the advantage of competitive dominant taxa and favors stress-tolerant taxa. Our findings demonstrate that chlorination residuals act as subtle, trait-mediated ecological stressors in the gut microbiome, producing selective yet predictable shifts. These insights frame chlorine residuals as hazardous environmental agents and inform microbiome-aware optimization of water disinfection and residual control.}, }
@article {pmid41935109, year = {2026}, author = {Zhang, M and Luo, K and Liu, D and Li, Y and Liu, Q and Li, J}, title = {The influence of human activities on the microbial community structure and function of a karst cave in southwest China.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-46434-9}, pmid = {41935109}, issn = {2045-2322}, support = {52560012//National Natural Science Foundation of China/ ; [2024]2-38//Science and Technology Plan Project of Guiyang City/ ; Qiankehe Chengguo [2025] Zhongda 103//Guizhou Provincial Science and Technology Achievement Transformation Plan Project/ ; }, abstract = {With human activities like exploration, geological investigation and tourism, the structure and function of karst cave microbial communities are prone to change. In this study, sediments from seven different spots in the Dushan Tian Cave in Guizhou Province, China were collected. And the structure and potential key metabolic functions of the microbial community were analyzed through metagenomics. The results showed that the structure of the microbial communities was associated with human-impacted environmental factors. Total phosphorus and Sulfide might promote the growth of Gemmatimonadetes_bacterium. However, Sulfide and organic matter might inhibit the growth of Gemmatimonadetes, Gemmatimonadetes_bacterium, Acidobacteria and Candidatus_Rokubacteria. Human activities triggered ecological effects. In terms of the abundance, denitrification genes increased but ammonia oxidation genes decreased in nitrogen metabolism, suggested there was an increasing trend in the potential of denitrification function. The sulfur metabolic potentials mainly involved assimilatory sulfate reduction where sulfates might be accumulated. The potential of carbon metabolism showed a trend towards the decomposition of exogenous carbon. The methane potential had changed. This study revealed the impact of human activities on cave microorganisms and clarified the response mechanism of cave microorganisms under human interference. It provided an important reference for the ecological protection and development and utilization of karst caves.}, }
@article {pmid41935274, year = {2026}, author = {Dastjerdi, A and Davies, H and Abu Oun, M and Navickaite, I and Karuna, S and Nevel, M and Comin, A and Williamson, S}, title = {Virome of post-weaned diarrhoeic pigs and healthy cohorts in England.}, journal = {Virology journal}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12985-026-03152-y}, pmid = {41935274}, issn = {1743-422X}, abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) is a disease syndrome that negatively impacts pig health, welfare and productivity. PWD typically occurs within two weeks of weaning and coincides with significant physiological changes, including villus atrophy and increased crypt depth in the gastrointestinal (GI) tract. The GI microbiome of healthy pigs is a complex ecosystem of commensal microorganisms. Disruption of the natural integrity of the GI tract has been associated with increased colonization by both viral and bacterial pathogens.<br><br>METHODS: In this study, metagenomic sequencing was used to assess the presence, load, and diversity of viruses in the GI tracts of PWD-affected pigs and age-matched healthy (AMH) cohorts on commercial pig farms in England. In addition, the viromes of archived faecal samples from post-weaned pigs between four and six weeks of age, collected from diagnosis-not-reached (DNR) and diagnosis-reached (DR) enteric cases were investigated through sequencing.<br><br>RESULTS: Viruses belonging to at least ten virus families were identified in both PWD and AMH pigs including astrovirus, enterovirus, kobuvirus, smacovirus, picobirnavirus, sapovirus, parvovirus, posavirus, teschovirus, sapelovirus, rotavirus, torovirus, anellovirus and adenovirus. Co-infection with four viruses, astrovirus, enterovirus, kobuvirus and smacovirus was detected in all samples from PWD and AMH pigs. No sequence reads matching porcine coronaviruses, porcine reproductive and respiratory disease virus, porcine circoviruses, swine influenza virus, atypical porcine pestivirus or porcine teschovirus-1 were detected in either PWD or AMH faecal samples. Metagenomic analysis also identified several viruses with a higher virus load in PWD cases (astro, entero, sapelo, sapo, posa, adeno and toro-viruses), but the differences from those in AMH cases were not statistically significant. No viruses were detected in samples from archived DNR and DR cases that were not found in the PWD and AMH pigs.<br><br>CONCLUSIONS: This study revealed the complexity of the virus element in the enteric microbiome in the post-weaned pigs. The role of the viruses detected and their interplay with the host and other bacterial or viral flora in inducing PWD, however, remains unclear and warrants further studies.}, }
@article {pmid41935328, year = {2026}, author = {Li, XX and Li, BY and Fu, GW and Zhao, H and Li, J and Zhou, YH and Zhang, X and Zhao, YC}, title = {Clinical impact of metagenomic next-generation sequencing on pathogen detection and outcomes in non-immunocompromised patients with severe pneumonia supported by veno-venous extracorporeal membrane oxygenation.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-12702-2}, pmid = {41935328}, issn = {1471-2334}, }
@article {pmid41935339, year = {2026}, author = {Castaldi, V and Wicaksono, WA and Criscuolo, MC and Gualtieri, L and Langella, E and Di Lelio, I and Monti, SM and De Filippis, F and Berg, G and Rao, R}, title = {Prosystemin-derived signals: bridging leaf microbiome dynamics and defense activation.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00885-9}, pmid = {41935339}, issn = {2524-6372}, abstract = {BACKGROUND: Plant-derived peptides can act as resistance inducers and represent promising tools for sustainable crop protection. Despite growing interest and application, their broader effects on plant-associated microbiomes remain insufficiently characterized. Here, we investigated the impact of an immunomodulatory peptide derived from the tomato defense protein Prosystemin on the tomato phyllosphere microbiome and leaf volatilome.<br><br>RESULTS: The peptide was applied as a foliar spray at biweekly intervals from planting to two months post-germination to approximate common agricultural practices. Shotgun metagenomic sequencing combined with qPCR revealed abundant bacterial communities (up to 4.6 log10 bacterial 16S rRNA gene copies) dominated by Actino-, Alphaproteo- and Gammaproteobacteria across all samples. Peptide treatment was associated with a significant shift in community structure, characterized by reduced alpha diversity and increased microbial associations. Several genera, including Acinetobacter, Sphingobium, Sphingomonas, Brevundimonas, and Massilia, increased in relative abundance following treatment. Functional profiling indicated rearrangements in gene categories related to stress response and metabolic adaptation. Notably, volatilome analysis further revealed elevated monoterpene emissions in peptide treated plants, consistent with activation of defense-associated metabolism. Members of the Sphingomonadaceae family, particularly Sphingobium yanoikuyae, appear well suited to persist under peptide-associated conditions and may therefore contribute to the observed community restructuring, although causal mechanisms remain to be tested.<br><br>CONCLUSION: Beyond its established role in protecting tomato against pests and necrotrophic fungi, the Prosystemin-derived peptide provides an opportunity to investigate peptide-triggered plant responses and their interactions with the plant microbiota.}, }
@article {pmid41935438, year = {2026}, author = {Bai, Y and Zhao, J and Wang, Z and Zheng, J and Zhu, X and Shao, Y and Zhang, X}, title = {A case of Rickettsia felis caused pneumonia and diagnosed by clinical analysis and Targeted Next-Generation Sequencing (tNGS) using Bronchoalveolar Lavage Fluid (BALF): A case report and literature review.}, journal = {Journal of infection and public health}, volume = {19}, number = {5}, pages = {103217}, doi = {10.1016/j.jiph.2026.103217}, pmid = {41935438}, issn = {1876-035X}, abstract = {Feline rickettsia pneumonia is a rare lung disease caused by feline R. felis infection, which is mainly transmitted by feline fleas. A 57-year-old male patient was hospitalized with pain in the back of the sternum. Chest CT showed bilateral diffuse interstitial lung disease with multiple nodules. After the empirical anti-infection treatment was ineffective, the second-generation meta-genome sequencing (mNGS) of bronchoalveolar lavage (BALF) was diagnosed as feline rickettsia infection. In terms of treatment, inject tegacycline intravenously and then sequentially take minocycline. The patient's symptoms were relieved quickly, and the imaging improved significantly. This report summarizes the clinical and imaging characteristics and diagnosis and treatment experience of the case, aiming to provide reference for the early identification and treatment of such rare infections.}, }
@article {pmid41935631, year = {2026}, author = {Keller, MI and de Zawadzki, A and Thiele, M and Suvitaival, T and Sulek, K and Kuhn, M and Schudoma, C and Podlesny, D and Nishijima, S and Fullam, A and Kim, CY and Niu, L and Wretlind, A and Hansen, JK and Israelsen, M and Johansen, S and Akanni, W and Hazenbrink, D and Juel, HB and Mann, M and Hansen, T and Krag, A and Bork, P and Legido-Quigley, C and , }, title = {Alcohol-Related Liver Disease Disrupts Bile Acid Homeostasis and Gut Microbial Bile Acid Metabolism.}, journal = {JHEP reports : innovation in hepatology}, volume = {}, number = {}, pages = {101848}, doi = {10.1016/j.jhepr.2026.101848}, pmid = {41935631}, issn = {2589-5559}, abstract = {BACKGROUND &amp; AIMS: Alcohol overuse disrupts liver function and alters gut microbial communities, with alcohol-related liver disease (ALD) causing half of all liver-related deaths worldwide. Bile acids (BAs) regulate liver and gut function, but their homeostasis becomes disrupted in ALD. Gut microbes transform primary BAs to secondary BAs, which are reabsorbed via enterohepatic circulation, but BA metabolism during ALD progression remains poorly understood.<br><br>METHODS: We investigated BA homeostasis in a cross-sectional ALD cohort (n=462), alongside matched healthy controls (n=148), and validated key findings in two independent ALD cohorts (n=34 and n=52). We integrated BA concentrations, measured by targeted mass spectrometry in feces and plasma, with liver proteomics and gut microbiome profiles from metagenomic and metatranscriptomic sequencing.<br><br>RESULTS: Advanced fibrosis states were associated with decreased hepatic BA synthesis, impaired hepatic BA uptake from blood but with increased levels of primary and secondary BAs in plasma (inprimis, taurocholic acid: F=69.9, p=8.6e-66) and feces (inprimis, cholic acid: F=5.5, p=1.4e-4). The abundance of microbial secondary BA dehydroxylation and epimerization pathways in the gut microbiome community increased with disease severity. Genes encoding the oxidation arm in the multi-step dehydroxylation pathway (e.b. baiB) increased, whereas those in the reduction arm (baiN) were depleted. In ALD patients, we suggest Eggerthella lenta, Mediterraneibacter torques, and Bacteroides thetaiotaomicron as relevant microbes for BA metabolism.<br><br>CONCLUSION: Fibrotic ALD is characterized by disrupted primary BA synthesis and hepatic uptake, leading to hepatotoxic BA accumulation in the gut and blood circulation. Altered microbial secondary BA metabolism reflects a functional shift in the gut microbiome throughout the fibrosis stages. Our findings highlight the gut-liver axis as an important factor influencing ALD progression, even in early, asymptomatic fibrosis stages.<br><br>CLINICAL TRIAL NUMBER: GALAXY main cohort: Danish Data Protection Agency nos. 13/8204, 16/3492 and 18/22692; and Odense Patient Data Exploratory Network under study identification nos. OP_040 and OP_239 Validation cohort 1: EudraCT number 20214-001856-51 Validation cohort 2: ClinicalTrial.gov ID NCT03863730 IMPACT AND IMPLICATIONS: This study shows that integrating different omics approaches provides insight into metabolic disruptions across the gut-liver axis that drive alcohol-related liver disease progression. Additionally, our study identifies specific bacterial species influencing bile acid concentrations in alcohol-related liver disease using data from human fecal metagenomics and metatranscriptomics. These findings could inform the design of future therapeutic targets focusing on either the liver or the gut for treating alcohol-related liver disease.}, }
@article {pmid41935814, year = {2026}, author = {Sambucci, KM and Samaš, P and Ssebide, B and Petrželková, KJ and Okello, RO and Nizeyimana, F and Bukamba, N and Smiley-Evans, T and Gilardi, K and Pafčo, B and Červená, B}, title = {Shifts in strongylid communities associated with chronic wasting in mountain gorillas.}, journal = {International journal for parasitology}, volume = {}, number = {}, pages = {104848}, doi = {10.1016/j.ijpara.2026.104848}, pmid = {41935814}, issn = {1879-0135}, abstract = {Host-parasite relationships are typically maintained in a dynamic equilibrium, but disruptions to this balance can lead to clinical disease and population-level health impacts. Chronic wasting, characterized by chronic loss of body condition, alopecia, a browning hair coat and pot belly, is an emerging health concern in mountain gorillas of Bwindi Impenetrable National Park, Uganda. Deworming of suspected cases has led to marked short-term health improvements, implicating intestinal helminths. To investigate, we analysed faecal samples from human-habituated gorillas collected in 2018 and 2021, and unhabituated gorillas in 2018, using high-throughput sequencing of strongylid nematodes (ITS-2) and gut bacteria (16S). Strongylid community composition varied with chronic wasting occurrence, with Oesophagostomum emerging as a key taxon driving this difference, while bacterial communities remained relatively stable. Strongylid diversity increased between 2018 and 2021, and habituated gorillas exhibited reduced strongylid genetic diversity, higher relative abundance of Oesophagostomum and lower relative abundance of Murshidia compared to unhabituated gorillas. These results suggest that a higher abundance of Oesophagostomum is associated with chronic wasting in mountain gorillas due to either a causative association or because of other genetic, immunological or environmental causes allowing Oesophagostomum, a common member of the gut eukaryote community of the Bwindi gorillas, to overpopulate.}, }
@article {pmid41935918, year = {2026}, author = {Lazarevic, V and Ruppé, E and Schrenzel, J}, title = {10th International Conference on Clinical Metagenomics (ICCMg10): meeting report.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2026.03.008}, pmid = {41935918}, issn = {1878-4380}, abstract = {The 10th International Conference on Clinical Metagenomics (ICCMg10) brought together clinicians, microbiologists, bioinformaticians, and industry partners to review progress and challenges in translating metagenomics into routine clinical practice. Discussions focused on advances in sequencing technologies, automation, clinically oriented workflows, and computational and reporting strategies. Clinical sessions addressed diagnostic implementation across infectious syndromes, including respiratory, prosthetic joint, bloodstream, and deep-seated infections, with attention to cell-free DNA assays, long-read sequencing, and antimicrobial resistance detection. Broader applications of metagenomics, spanning microbiota research and environmental systems, reflected the expanding scope of the field. Overall, ICCMg10 underscored the importance of multidisciplinary collaboration, harmonized practices, and clinically meaningful interpretation to support the broader implementation of clinical metagenomics.}, }
@article {pmid41936200, year = {2026}, author = {Uematsu, S}, title = {Programming systemic and mucosal immunity through co-adjuvant-based prime-boost vaccination.}, journal = {Current opinion in virology}, volume = {76}, number = {}, pages = {101525}, doi = {10.1016/j.coviro.2026.101525}, pmid = {41936200}, issn = {1879-6265}, abstract = {The development of effective mucosal vaccines has been limited by the limited availability of mucosal adjuvant approaches with established clinical track records and an incomplete understanding of how systemic and mucosal immunity are coordinated. Recent studies indicate that the priming phase of vaccination plays a decisive role in programming the quality, durability, and anatomical distribution of subsequent immune responses. This review discusses emerging evidence that co-adjuvant-based priming strategies can establish long-lasting immune programs that enable adjuvant-free mucosal boosting. Focusing on the combination of CpG DNA and curdlan as a prototypical example, this review highlights how coordinated activation of innate immune receptors during priming imprints dendritic cells, B cells, and T cells to support robust mucosal IgA and tissue-resident immunity. This review further discusses translational advances demonstrating that this immune programming paradigm can be maintained using translationally oriented formulations designed with clinical development in mind and validated in non-human primates. Independent studies using mRNA and protein-based vaccines support the general principle that the quality of priming, rather than the boosting modality, determines successful mucosal immunity. Together, these findings redefine vaccine adjuvants as tools for immune programming and provide a conceptual framework for next-generation vaccine design.}, }
@article {pmid41936930, year = {2026}, author = {Zhou, Z and Song, Y and Zhou, Y}, title = {Metagenomic Next-Generation Sequencing Profiling of Primary versus Iatrogenic Osteoarticular Infections: Unveiling Distinct Pathogen Spectra and Diagnostic Implications.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108688}, doi = {10.1016/j.ijid.2026.108688}, pmid = {41936930}, issn = {1878-3511}, abstract = {OBJECTIVE: To evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) versus microbial culture in primary osteoarticular infection (POI) and iatrogenic osteoarticular infection (IOI), and to analyze pathogen spectrum differences and clinical implications.<br><br>METHODS: Ninety-two patients with confirmed osteoarticular infection (POI, n=42; IOI, n=50) were retrospectively analyzed. All specimens were tested using both mNGS and conventional culture. The pathogen detection rates, pathogen spectrum composition, detection of mixed infections, and concordance of results between the two methods were compared.<br><br>RESULTS: mNGS demonstrated a significantly higher overall detection rate than culture (72.83% vs. 43.48%; P < 0.001), particularly in IOI (78.00% vs. 34.00%; P < 0.001). Pathogen profiling showed predominance of Staphylococcus aureus in POI, whereas IOI exhibited greater microbial diversity with increased detection of Staphylococcus epidermidis (31.03%) and anaerobes (13.79%). Polymicrobial infections were more frequently identified by mNGS (14.13% vs. 4.35% by culture; P&#x202f;=&#x202f;0.024), primarily in the IOI group. Concordance between mNGS and culture was substantial in POI (&#x3ba;&#x202f;=&#x202f;0.66; 95% CI: 0.42-0.89) but only slight in IOI (&#x3ba;&#x202f;=&#x202f;0.12; 95% CI: -0.12 to 0.35), largely attributable to the high rate of mNGS-exclusive positives in IOI (48.00%).<br><br>CONCLUSION: mNGS improves pathogen detection in osteoarticular infections, especially in IOI where it identifies complex and polymicrobial infections more effectively than culture, providing critical support for guiding antimicrobial therapy.}, }
@article {pmid41857392, year = {2026}, author = {Zhai, X and Jin, J and Yu, M and Liu, R and Li, J and Liu, Y and Zhang, XH and Liu, J}, title = {Spatial Heterogeneity of Microbial Communities and Biogeochemical Function in Water Column of Site F Cold Seep, South China Sea.}, journal = {Microbial ecology}, volume = {89}, number = {1}, pages = {}, pmid = {41857392}, issn = {1432-184X}, support = {202172002//the Fundamental Research Funds for the Central Universities/ ; LSKJ202203206//the Science &amp; Technology Innovation Project of Laoshan Laboratory/ ; ZR2022YQ038, ZR2024JQ006//Shandong Province Natural Science Foundation/ ; }, abstract = {UNLABELLED: Cold seep is a distinctive deep-sea environment mainly formed by methane-rich fluids leaking on the seafloor, gaps remain regarding the influence of seepage on microorganisms inhabiting water column across vertical and horizontal dimensions. Site F cold seep, located at 1,120 m depth on the northern South China Sea (SCS) slope, is one of the most active cold seeps in SCS. We performed 16S rRNA gene and metagenomic sequencing on samples collected by Niskin bottles mounted on Conductivity-Temperature-Depth profiler and Remote Operated Vehicle to analyze the structure and metabolic potentials of microbial communities throughout the water column at Site F. Microbial abundance generally decreased with depth at all sampling spots and was higher at sites adjacent to the seepage compared to those farther away, indicating a potential vertical and horizonal influence of methane seepage on water microbial community. High microbial abundance at deeper depths may attribute to a higher proportion of Gammaproteobacteria, comprised mainly of Alcanivoracaceae, Alteromonadaceae, Marinobacteraceae, methylotrophs represented by Methylophagaceae and Methylococcales (mainly Methylomonadaceae), and sulfur-oxidizing bacteria represented by SUP05 and Ectothiorhodospiraceae. Consistently, the aerobic methane oxidation gene pmoA was more prevalent in the deeper water and was found in four bacterial classes in addition to Gammaproteobacteria. Sulfur-oxidizing genes also exhibited higher abundances at depths and were primarily affiliated with Rhodobacteraceae. These microbes likely play important roles in aerobic oxidation of methane and sulfur, contributing to methane depletion during upward diffusion. By integrating sampling across vertical and horizontal dimensions, we demonstrate that seepage shapes the microbial community and biogeochemical functions in the water column at Site F.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00248-026-02722-5.}, }
@article {pmid41932913, year = {2026}, author = {Barbour, A and Bendayan, Y and Marks, C and Choi, YHK and Oveisi, M and Callaghan, M and Sun, C and Zargaran, S and Xia, M and Wood, D and Smith, L and McLean, JS and Mazzulli, T and Glogauer, M}, title = {Phosphorylated lantibiotics-producing commensals integrate into the human oral microbiome to suppress pathogens and promote microbiome homeostasis.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00976-y}, pmid = {41932913}, issn = {2055-5008}, abstract = {Commensal bacteria produce antimicrobial peptides (AMPs) to maintain microbiome homeostasis, yet the traits underlying this resilience and their translation into biotherapeutics remain understudied. Phosphorylated lantibiotics (pLANs) are a recently identified class of ribosomally synthesized and post-translationally modified peptides (RiPPs), with dual antimicrobial and pro-immune activities. In this manuscript, we explore the potential of commensals' pLANs biosynthesis as a mechanism for pathogen suppression and microbiome homeostasis. Subgingival metagenomics revealed that oral health correlates with Streptococcus salivarius enrichment and an increased prevalence of streptococcal RiPP biosynthetic gene clusters. Guided by these associations, we screened 80 S. salivarius isolates, identifying a small subset producing pLANs with potent activity against Porphyromonas gingivalis, vancomycin-resistant Enterococcus faecium, and multidrug-resistant Streptococcus pneumoniae. A representative lead strain, SALI-10, exhibited robust epithelial adhesion and a sorbitol-driven metabolic adaptation that enhances pLANs expression. In human-derived dysbiotic biofilms, SALI-10 stably engrafted, suppressed periopathogens, reduced antibiotic-resistance genes, and enriched acid-buffering pathways. In a first-in-human feasibility trial, daily oral administration of SALI-10 for one week yielded increased pLANs signals, pathogen depletion, and reduced oral neutrophil counts. Ultimately, pLANs-producing S. salivarius acts as a precision commensal to restore ecological balance, defining a mechanistically grounded and microbiota-mediated strategy to prevent oral and respiratory infections.}, }
@article {pmid41933095, year = {2026}, author = {Fu, Z and Sun, Y and Yao, H and Liu, Q and Zhang, Q and Hu, J and Zhou, Y and Jiang, N and Ai, J and Jin, J and Zhang, W}, title = {A diagnostic model based on pulmonary microbiota and host gene expression to distinguish colonization from pneumonia.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-44972-w}, pmid = {41933095}, issn = {2045-2322}, abstract = {Pneumonia remains a leading cause of global mortality. Conventional diagnostic approaches frequently fail to distinguish microbial colonization from true infection in the lower respiratory tract, complicating clinical decision-making and contributing to antibiotic overuse. Improved diagnostic strategies are urgently needed. In this prospective, single-center study, deep sputum specimens were collected from patients with respiratory colonization (n = 17) and infectious pneumonia (n = 27) admitted to the neurosurgical ICU of Huashan Hospital. Metagenomic next-generation sequencing (mNGS) and metatranscriptomic profiling were performed to characterize both the pulmonary microbiota and the host immune response. These features were subsequently integrated to construct a diagnostic model. Microbial community profiling revealed reduced alpha diversity and enrichment of metabolically active pathogenic taxa in the infection group, consistent with a dysbiotic state permissive to invasion. In contrast, the colonization group demonstrated a more balanced microbial ecosystem. Transcriptomic analyses identified 2232 differentially expressed host genes between the two groups. The colonization group showed marked activation of the Wnt, MAPK, chemokine, and focal adhesion pathways, which are functionally implicated in epithelial barrier maintenance and early immune homeostasis. A multi-omics diagnostic model incorporating seven gene features (ANKRD52, ZC3HAV1L, SERPINE3, CDPF1, ZNF720, TAGLN3, and LRRC15) achieved a discrimination between colonization and infection (AUC = 0.951 in the training cohort; 0.875 in the validation set). By jointly analyzing the pulmonary microbiome and host transcriptome, this study provides insight into host-microbe interactions distinguishing colonization from infection and presents a predictive model with potential clinical relevance.}, }
@article {pmid41933201, year = {2026}, author = {Prasoodanan Pk, V and Maistrenko, OM and Fullam, A and Mende, DR and Kartal, E and Coelho, LP and Spang, A and Bork, P and Schmidt, TSB}, title = {Unbinned contigs expand known diversity in the global microbiome.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41933201}, issn = {2058-5276}, support = {12/RC/2273-P2 (APC Microbiome)//Science Foundation Ireland (SFI)/ ; 947317 (ASymbEL)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 947317 (ASymbEL)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; FT230100724//Department of Education and Training | Australian Research Council (ARC)/ ; }, abstract = {The ongoing census of microbial life is hampered by disparate sampling across Earth's habitats, challenges in isolating uncultivated organisms, limited resolution in taxonomic marker gene amplicons and incomplete recovery of metagenome-assembled genomes. Here we quantify discoverable Bacterial and Archaeal diversity in a comprehensive, curated cross-habitat dataset of 92,187 publicly available metagenomes. Clustering 502 million sequences of 130 marker genes, we predict ~705,000 Bacterial and ~27,000 Archaeal species-level clades, the vast majority of which were hidden among unbinned contigs. We estimate that ten and 145 previously undescribed Archaeal and Bacterial phyla, respectively, are discoverable in this dataset. We identify soils and aquatic environments as hotspots of discoverable lineages, but predict that undescribed taxa remain abundant across all habitats. Finally, we show that prokaryotic diversity appears to arise within common evolutionary patterns, as clade size distributions follow power laws, consistently across the Tree of Life.}, }
@article {pmid41933302, year = {2026}, author = {Wu, L and Pu, J and Xi, X and Bao, Y and Luo, L}, title = {Streptomyces morookaense spinal suppurative infection: a case report.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13238-1}, pmid = {41933302}, issn = {1471-2334}, support = {2025M781412//The China Postdoctoral Science Foundation/ ; }, abstract = {PURPOSE: Streptomyces species are ubiquitous soil actinomycetes and a major source of antibiotics, but invasive human infection with spinal involvement is exceedingly rare and may mimic tuberculous or fungal spondylodiscitis. We report a thoracic suppurative vertebral infection caused by Streptomyces morookaense and highlight an integrated diagnostic approach.<br><br>METHODS: A 66-year-old woman with no known immunodeficiency developed progressive thoracic back pain one month after severe trauma with open wounds. CT/MRI showed osteolytic endplate destruction at T3-T4 with paravertebral abscess formation. Fluoroscopy-guided percutaneous biopsy of the T4 vertebral body was performed for histopathology, culture, and metagenomic next-generation sequencing (mNGS).<br><br>RESULTS: Histopathology demonstrated fibrinous exudate, necrosis, and inflammatory granulation tissue with fragmented trabeculae, without granuloma or caseous necrosis; acid-fast staining was negative. Vertebral tissue culture grew Streptomyces spp, and mNGS identified high-abundance sequences matching S. morookaense. Intravenous piperacillin/tazobactam led to rapid pain relief and normalization of inflammatory markers within one week, and no recurrence was observed during follow-up.<br><br>CONCLUSION: This case suggests that Streptomyces morookaense has the potential to involve the thoracic spine in immunocompetent individuals. For unexplained spinal infections with negative routine tests, percutaneous vertebral sampling with integrated interpretation of pathology, culture, and mNGS can improve detection of rare pathogens and help avoid inappropriate empirical therapy.}, }
@article {pmid41933424, year = {2026}, author = {Zhao, Y and Wang, Z and Fan, D and Zhang, J and Tu, Y and Diao, Q and Cui, K}, title = {Gut microbiota-driven IL-17/PPAR axis mediates epigallocatechin-induced intestinal repair in weaned lambs.}, journal = {Journal of animal science and biotechnology}, volume = {17}, number = {1}, pages = {}, pmid = {41933424}, issn = {1674-9782}, support = {2024YFD1300204//National Key Research and Development Program of China/ ; 32172764//National Natural Science Foundation of China/ ; 25036//Agricultural Science Technology Project of Shijiazhuang/ ; }, abstract = {BACKGROUND: Early weaning is a key strategy to improve lamb production efficiency; however, it inevitably compromises intestinal barrier integrity and function. This study aimed to investigate the effects of epigallocatechin (EGC) on growth performance and intestinal barrier function in weaned lambs, using metagenomics, metabolomics, and intestinal transcriptomics to elucidate the underlying mechanisms.<br><br>RESULTS: Weaning induced oxidative stress, inflammation, and metabolic disruptions in the jejunum. Supplementation with 12.5&#xa0;mg/kg EGC (LE) significantly improved growth performance, reduced diarrhea incidence (P&#x2009;<&#x2009;0.05), enhanced mucosal antioxidant capacity (P&#x2009;<&#x2009;0.001), and strengthened anti-inflammatory ability (P&#x2009;<&#x2009;0.001). Metagenomic analysis showed that the LE intervention enriched Ruminococcus spp. and reduced the abundance of Slackia. This microbial shift was associated with elevated luminal concentrations of valeric acid and microbial metabolites derived from EGC. Transcriptomic profiling revealed that the intervention upregulated the PPAR signaling pathway, which supports nutrient metabolism and barrier repair. Concurrently, it attenuated aberrant IL-17 signaling and promoted the restoration of mucosal immune homeostasis, indicating a resolution of excessive inflammatory responses.<br><br>CONCLUSIONS: Supplementation with 12.5&#xa0;mg/kg EGC alleviates weaning stress by fostering a beneficial gut microbiota and promoting the production of specific metabolites. These changes reactivate PPAR mediated epithelial repair and dampen pathological immune activation. Low-dose EGC is an effective nutritional strategy to improve intestinal health and growth in weaned ruminants.}, }
@article {pmid41663924, year = {2026}, author = {Li, B and Shi, X and Yao, X and Yan, Y and Wu, K and Zhang, C and Ren, Y}, title = {Association of the residual feed intake (RFI) with the rumen microbiota composition and metabolism in Dorper-Hu crossbred lambs.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41663924}, issn = {1471-2180}, support = {2020BQ53//The Science and Technology Innovation Program of Shanxi Agricultural University/ ; SXBYKY2021037//Shanxi Province Outstanding Doctor Award Fund/ ; J202011313//"1331 Project" Key Disciplines of Animal Sciences, Shanxi Province/ ; Modern Agro-industry Technology Research System in Shanxi Province//Modern Agro-industry Technology Research System in Shanxi Province/ ; }, abstract = {BACKGROUND: Improving feed efficiency in livestock is crucial for sustainable animal production. Residual feed intake (RFI) is a superior metric that accurately assesses feed efficiency. Animals with a low RFI (LRFI) usually consume less feed than animals with a high RFI (HRFI). Ruminal microbiota plays an important role in feed digestion in sheep. It is essential to elucidate the associations between rumen microbial composition, metabolic profiles, and growth performance of lambs with differing RFI by metagenomic sequencing and metabolomic profiling.<br><br>RESULTS: Although no significant differences were observed in growth performance, LRFI lambs exhibited significantly lower dry matter intake (P&#x2009;<&#x2009;0.05) and improved feed efficiency. Integrative metagenomic and metabolomics analysis revealed that the LRFI group showed enrichment of bacteria (Prevotella, Roseburia, and Pseudoscardovia) (P&#x2009;<&#x2009;0.05) and metabolites (N-Acetylneuraminic acid 9-phosphate, N-Succinyl-L-glutamate, 5-hydroxyindolepyruvate, pelargonidin, sinapic acid, and spermidine) associated with efficient nitrogen metabolism, enhanced microbial protein synthesis, and antioxidant activity. By contrast, the HRFI group was characterized by increased abundance of microorganisms (Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina) (P&#x2009;<&#x2009;0.05), coupled with elevated levels of metabolites (histidinal, tetrahydrocorticosterone, and sakuranetin). Correlation networks identified positive correlations among Prevotella, unclassified f_Prevotellaceae, several amino acid intermediates and specific flavonoids, and the host traits of reduced DMI and RFI. Conversely, the genera Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina were positively correlated with the increased DMI and RFI.<br><br>CONCLUSIONS: Efficient (low-RFI) animals exhibited a Prevotella-driven microbiome and a distinct metabolome characterized by enrichment of several amino acid intermediates and specific flavonoids, while a more diverse but methanogen-related microbial community (such as Methanobrevibacter, Ruminococcus, Butyrivibrio, and Sarcina) is present in inefficient (HRFI) sheep. The identified microbial and metabolic profiles provide potential biomarkers for breeding feed-efficient animals and developing targeted nutritional interventions to improve ruminant production sustainability.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04788-0.}, }
@article {pmid41666437, year = {2026}, author = {Kohsar, M and Haar, M and Schmidt-Chanasit, J and Ramharter, M and Buchholz, BM and Krasemann, S and Bernreuther, C and Cadar, D and Omansen, TF and Wichmann, D and Ko, LM and Jordan, S}, title = {Fatal Dengue Fever in a Traveler Returning from Togo to Germany.}, journal = {The American journal of tropical medicine and hygiene}, volume = {114}, number = {4}, pages = {720-723}, pmid = {41666437}, issn = {1476-1645}, mesh = {Humans ; *Travel ; *Dengue/complications/diagnosis ; Fatal Outcome ; Germany ; Togo ; Male ; *Liver Failure, Acute/virology ; Adult ; }, abstract = {A previously healthy traveler of Togolese origin visiting friends and relatives presented with severe dengue complicated by acute liver failure. Despite intensive care management and listing for high-urgency liver transplantation, the patient succumbed to the disease. This case highlights the risk for life-threatening travel-related complications of dengue.}, }
@article {pmid41927118, year = {2026}, author = {Huang, H and Liu, Z and Liu, X and Li, Q and Yang, X and Chen, L and Ye, W}, title = {Coinfection of Human Cytomegalovirus and Pneumocystis jirovecii Caused Severe Pneumonia in a Non-HIV Elderly Patient: A Case Report.}, journal = {Annals of clinical and laboratory science}, volume = {56}, number = {1}, pages = {122-129}, pmid = {41927118}, issn = {1550-8080}, mesh = {Humans ; *Pneumocystis carinii/isolation &amp; purification ; *Cytomegalovirus Infections/complications/virology/drug therapy ; *Pneumonia, Pneumocystis/microbiology/complications/drug therapy ; *Coinfection/virology/microbiology ; *Cytomegalovirus/isolation &amp; purification ; Male ; Aged ; *Pneumonia ; }, abstract = {OBJECTIVE: To present a case of a non-human immunodeficiency virus (HIV)-infected patient with human cytomegalovirus (HCMV) viremia and severe Pneumocystis jirovecii (PJ) pneumonia.<br><br>CASE REPORT: The patient was admitted in June 2024 for chronic dry cough and dyspnea. Sputum-targeted next-generation sequencing (tNGS) and blood pathogen metagenomic detection were used to identify concurrent infections of sputum HCMV and PJ, along with blood HCMV. The extensive treatment included intravenous ganciclovir, in conjunction with caspofungin and oral sulfamethoxazole, augmented by glucocorticoids and breathing assistance. After three weeks, the patient's oxygenation index markedly improved, accompanied by the significant resolution of imaging lesions, leading to patient discharge in June 2024.<br><br>CONCLUSION: This case underscores the diagnostic efficacy of tNGS on several opportunistic infections for older people with several comorbidities.}, }
@article {pmid41927536, year = {2026}, author = {Dong, Y and Wang, M and Zhou, X and Wang, P and Yan, K and Wang, S and Zhong, JC and Li, H and Zhao, L and Li, B and Li, J}, title = {Multi-cohort analysis of metagenome for type 2 diabetes identified universal gut microbiota signatures across populations.}, journal = {Nutrition &amp; diabetes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41387-026-00418-w}, pmid = {41927536}, issn = {2044-4052}, abstract = {BACKGROUND: Several studies have investigated the association between the gut microbiota and type 2 diabetes mellitus (T2D) in various populations. Nonetheless, noises specific to individual cohorts might distort the microbial dysbiosis characteristics and result in inconsistent findings across studies. Thus, we aimed to identify the universal features of perturbed gut microbiota across diverse populations.<br><br>METHODS: A total of 433 fecal shotgun metagenomic sequences were analyzed to profile and compare the gut microbiome shifts between patients with T2D and healthy controls from cohorts in Europe and Asia.<br><br>RESULTS: Based on cross-cohort integrative analysis, patients with T2D showed significantly higher microbial alpha diversity, and distinctive microbial structures compared to healthy individuals. By excluding bacteria exhibiting divergent directional changes, consistent characteristics with ten T2D-enriched bacteria, such as Clostridium bolteae and Clostridium citroniae and eight T2D-depleted bacteria, including Streptococcus thermophiles and Haemophilus parainfluenzae were revealed across populations. Particularly, these reliable bacterial markers, which were robust against demographic variation, distinguished patients with T2D from healthy controls with high accuracy (AUCs&#x2009;>&#x2009;0.8) in both European and Asian cohorts. Correlation analysis demonstrated that T2D-enriched and T2D-depleted bacteria, respectively, formed their own mutualistic networks that were negatively linked to each other. Moreover, T2D-enriched bacteria were dramatically positively associated with fasting blood glucose and glycated hemoglobin. Functionally, 10 KEGG pathways with consistent directional changes across European, Asian, and combined cohorts were identified. Specifically, the Nucleotide excision repair pathway was markedly downregulated in patients with T2D, while the AGE-RAGE signaling pathway in diabetic complications was consistently enriched in patients with T2D across cohorts.<br><br>CONCLUSIONS: Our results elucidated reproducible profiles of gut commensal bacteria in patients with T2D, which are robust across populations. Identifying the universal gut microbiome signatures of T2D in heterogeneous cohorts offers valuable insights for understanding disease development and is crucial for prevention and diagnosis across diverse populations.}, }
@article {pmid41927550, year = {2026}, author = {Oki, H and Takebe, K and Bonsu, A and Fujii, K and Masuda, R and Henderson, N and Mima, T and Koide, T and Moradi, M and Matsushita, O and Sakon, J and Kawahara, K}, title = {Bacterial collagenase harnesses collagen geometry for processive cleavage.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71099-3}, pmid = {41927550}, issn = {2041-1723}, support = {24K10218//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 23K14519//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 23K06545//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 2218054//Armenian National Science and Education Fund (Armenian National Science &amp; Education Fund)/ ; GM103429 and GM151696//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; }, abstract = {Collagen, the major structural protein in the animal extracellular matrix, forms a triple helix that resists proteolysis and requires specialised enzymes for degradation. Flesh-eating bacteria secrete collagenases that unwind the collagen triple helix and processively trim Gly-X-Y triplet repeats, yet the molecular basis of this process has remained obscure. Here, cryo-electron microscopy reveals how Hathewaya histolytica collagenase ColH engages its substrate and exploits the helix's architecture for catalysis. ColH encircles a single collagen triple helix in a closed-ring conformation and, through dynamic domain motions, dehydrates and destabilises it. The enzyme undergoes substrate-assisted twisting to adopt a rigid ratcheted conformation, in which one chain is bent into a tripeptide-long 'bight' and threaded into the active site for cleavage, while two uncut strands are partitioned to non-catalytic sites. Release of the bight appears to reset the enzyme, with the uncut strands serving as guiding tracks. Repeated cycling between dynamic and rigid states likely enables triplet-by-triplet translocation, allowing ColH to harness collagen's geometry for processive degradation. These findings reveal a bacterial strategy for collagen unwinding and cleavage distinct from that of mammalian collagenases, highlighting divergent evolutionary solutions for degrading one of nature's most intractable substrates.}, }
@article {pmid41927589, year = {2026}, author = {Jiang, P and Liang, Z and Kovacevic, V and Shi, J and Milicevic, N and Wang, F and Liu, L and Liu, Y and Jiang, Y and Han, M and Lin, X and Petronić, &#x10c; and Stanojevic, N and Wang, L and Wang, S and Cheng, H and Li, J and Chen, R and Zhang, Y and Li, Y and Li, J and Fang, X and Yue, Z and Xue, C and Yin, P and Chen, H}, title = {The Extreme Environment Microbiome Catalog (EEMC): a global resource for microbial diversity and antimicrobial discovery.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71145-0}, pmid = {41927589}, issn = {2041-1723}, abstract = {Microorganisms in extreme environments represent a promising source of novel metabolites, yet their global diversity and biosynthetic potential remain underexplored. Here, we reconstruct 78,213 bacterial and archaeal genomes from 2293 publicly available metagenomes and 3214 microbial isolates to establish a unified database, the Extreme Environment Microbiome Catalog (EEMC). The EEMC expands known global phylogenetic diversity, encompassing 32,715 representative species and nearly 4 billion non-redundant genes, 63.00% and 19.21% of which are previously unannotated, respectively. It also comprises 163,693 biosynthetic gene clusters, grouped into 64,733 gene cluster families, 58.68% of which are classified as novel, underscoring the functional diversity of microbial communities across various extreme habitats. We further develop protein large language models to predict genome-encoded candidate antimicrobial peptides (cAMPs) from the EEMC, identifying 3032 non-toxic candidates. Of 100 synthesized peptides, 84% demonstrate antibacterial activity, and all 50 tested cAMPs exhibit low cytotoxicity. Notably, six of the most potent cAMPs show significant efficacy against multidrug-resistant, Gram-negative pathogens in vitro, indicating their biomedical potential. Together, our study establishes the EEMC as a foundational resource for uncovering novel microbial lineages and biosynthetic capabilities, highlighting its substantial potential for drug discovery and laying the foundation for future advances in biotechnology and biomedicine.}, }
@article {pmid41927746, year = {2026}, author = {Akanmu, AM and Hassen, A and van Marle-Köster, E and Adejoro, FA}, title = {Dietary plant extracts reduce methane emission and modulate rumen microbial functionality in Merino lambs.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-46933-9}, pmid = {41927746}, issn = {2045-2322}, support = {SRUG2204254606//National Research Foundation/ ; }, abstract = {The formation of enteric methane from ruminants represents a significant loss of dietary energy that adversely affects growth and production while also contributing to the environmental footprint of livestock production through greenhouse gas accumulation. Phytogenic feed additives rich in bioactive compounds have been proposed as sustainable alternatives to synthetic additives for improving nutrient utilisation and reducing methane. This study evaluated the effects of Moringa oleifera, Jatropha curcas, and Aloe vera extracts on growth performance, nutrient digestibility, methane production, rumen fermentation in South African Mutton Merino lambs using an in vivo feeding trial while the microbial diversity and functionality was evaluated using shotgun metagenomic sequencing. Supplementation with Moringa and Jatropha improved dry matter and crude protein digestibility (P < 0.05). Methane emission decreased in all plant extract groups, with reductions of 17% (Jatropha), 9% (Moringa), and 12% (Aloe) relative to control (P < 0.05). Ammonia nitrogen concentrations were lower in supplemented groups, particularly Moringa and Aloe (P < 0.01), while volatile fatty acids and growth performance were unaffected. Metagenomic profiling revealed Bacteroidetes as the dominant phylum and showed enrichment of genes which may be associated with protein biosynthesis and carbohydrate metabolism in Moringa and Jatropha lambs, aligning with improved digestibility and reduced methane emissions. Dietary inclusion of M. oleifera, J. curcas, and A. vera extracts reduced methane emissions and improved dry matter and crude protein digestibility without compromising growth. These results suggest that these phytogenic extracts can serve as sustainable feed additives to improve efficiency and mitigate environmental impacts in ruminant production systems.}, }
@article {pmid41928235, year = {2026}, author = {Arzu, JL and Fleury, ES and Cecil, KM and Chen, A and Lanphear, BP and Yolton, K and Buckley, JP and Braun, JM and Laue, HE}, title = {Associations of the gut microbiome and cardiometabolic risk in adolescence: the HOME study.}, journal = {BMC medical genomics}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12920-026-02359-w}, pmid = {41928235}, issn = {1755-8794}, }
@article {pmid41928361, year = {2026}, author = {Heng, YC and Chua, JHX and Silvaraju, S and Fan, H and Low, A and Lim, ACH and Chen, B and Mane, L and Dagar, SS and Fliegerova, K and Moniello, G and Ikeda-Ohtsubo, W and Okuda, K and Seedorf, H and Lim, KJ and Kittelmann, S}, title = {Metagenomic insights into the global wild boar faecal microbiome reveal novel taxa and carbohydrate degraders distinguishing wild and domesticated Sus.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02392-y}, pmid = {41928361}, issn = {2049-2618}, support = {Project number CRG/2022/008319//Anusandhan National Research Foundation (ANRF), DST, Government of India/ ; FDS2223MONIELLO - CUP J83C22000160007//Fondazione di Sardegna, Italy/ ; University Research Fund 2020//University of Sassari/ ; WIL@NUS Corporate Laboratory, Singapore//Wilmar International/ ; }, abstract = {BACKGROUND: The inclusion of fibre in domestic pig diets is favourable from a digestive health, environmental, and socio-economic perspective. Unlike the highly optimized formulated diets of domestic pigs, wild boars feed opportunistically, consuming a broad range of foods that consist predominantly of plant materials. Consequently, the intestinal microbiota of wild boars is thought to be adapted to a versatile, fibre-rich diet and may represent a valuable source of probiotics for enhancing fibre degradation. However, comprehensive studies characterizing the wild boar gut microbiome, particularly its community structure and carbohydrate utilization potential, and comparison to that of domestic pigs are still lacking.<br><br>RESULTS: We collected 89 faecal samples from wild boars across four countries and analysed them primarily using metagenomic sequencing. De novo assembly yielded 3,288 high- and medium-quality metagenome-assembled genomes (MAGs) representing 968 distinct species, of which 538 were previously unknown. Incorporating these MAGs enabled robust microbiome comparisons with 125 previously published samples largely from domestic pigs, which revealed significant structural and functional differences. These differences resolved into two community types, determined not by host species but by diet and lifestyle: C1 comprising 81% of samples from free-ranging, foraging wild boars and C2 consisting of 93% of samples from captive, fed domestic pigs. The lower alpha-diversity observed in C1 likely reflected the impact of highly fluctuating dietary resources and environmental conditions, resulting in dominance of fewer resilient or adaptable taxa. Nevertheless, both community types maintained substantial carbohydrate utilization potential: while C2 exhibited a higher relative abundance of CAZyme[sub] genes associated with a broader range of carbohydrate substrate (CHO) classes, C1 was enriched in individual species that were generally richer in CAZyme[sub] genes and CHO classes. To leverage this potential, we curated a catalogue of carbohydrate degraders from both community types and identified 47 highly versatile species, with several novel species amongst them.<br><br>CONCLUSIONS: This study uncovered the previously untapped microbial diversity in the wild boar faecal microbiome and demonstrated that the faecal microbiome of Sus is primarily shaped by diet and lifestyle. The two community types identified, which differed both structurally and functionally, represent alternative states of microbiome homeostasis in wild versus domesticated Sus populations. The curated catalogue of carbohydrate degraders provides a valuable resource to guide tailored probiotic supplementation during dietary transitions to novel fibrous feedstocks. Video Abstract.}, }
@article {pmid41928791, year = {2026}, author = {Bajaj, J and Sommer, A and Auch, B and Khoruts, A}, title = {Proximity-ligation metagenomics reveals disease-specific mobilome dynamics in disrupted gut ecosystems.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-9142184/v1}, pmid = {41928791}, issn = {2693-5015}, abstract = {Distinct ecological pressures shape accumulation of antimicrobial resistance and virulence genes in the gut microbiome. Using proximity ligation shotgun metagenomics to resolve host-mobilome relationships, we analyzed microbiomes from two patient cohorts: recurrent Clostridioides difficile infection (rCDI) and cirrhosis. While rCDI reflects antibiotic-driven disruption, cirrhosis-driven microbiome changes result from altered gut physiology. We found increased chromosomal determinants of antibiotic resistance in both, but plasmid-mediated amplification was more evident in rCDI.}, }
@article {pmid41929040, year = {2026}, author = {Patabandige, DLJ and John, J and Ortiz, M and Campbell, BJ}, title = {Environmental Gradients Shape the Hydrocarbon-Degrading Microbiome in Two Mid Atlantic Bays.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.25.714183}, pmid = {41929040}, issn = {2692-8205}, abstract = {UNLABELLED: Hydrocarbons are recalcitrant organic matter that are released into the environment via natural and anthropogenic activities. We hypothesized that abiotic and biotic factors, including salinity, temperature, seasonality, microbial interactions, and functional redundancy, influence the abundance and activity of potential hydrocarbon degraders in the Delaware and Chesapeake Bays. We identified key genes in hydrocarbon degradation pathways in metagenomes, metatranscriptomes, and metagenome assembled genomes (MAGs) from these estuaries. Aerobic aromatic and alkane degradation pathways predominated in both estuaries, with higher gene abundances observed in low-salinity spring and summer samples. Hydrocarbon degrading MAG abundance were significantly structured by salinity, temperature, nitrate, and silicate concentrations. Metatranscriptomic analyses revealed consistently higher expression of aerobic alkane and aromatic degradation genes in the Delaware compared to the Chesapeake Bay, with the highest occurring under low-salinity spring conditions in the former. Catechol degradation pathways exhibited high functional redundancy, whereas the naphthalene degradation pathway showed restricted distribution. Co-expression analysis revealed that Burkholderiales displayed condition dependent metabolic coupling while Pseudomonadales integrated hydrocarbon degradation with fermentation and central metabolism, demonstrating complementary strategies that support multi-scale ecosystem resilience. In conclusion, environmental gradients and taxon-specific metabolic strategies together govern hydrocarbon degradation potential in these estuaries, with implications for predicting ecosystem responses to hydrocarbon inputs under changing conditions.<br><br>IMPORTANCE: Coastal estuaries are among the most contaminated aquatic environments on Earth, receiving continuous hydrocarbon inputs from industrial activity, urban runoff, and natural sources. Microorganisms are the primary agents of hydrocarbon breakdown in these systems yet predicting when and where this capacity is active and how resilient it is to environmental change remains a major challenge. Using paired genomic and transcriptomic data from microbial genomes across two major mid-Atlantic estuaries, we show that hydrocarbon degradation capacity is not uniformly distributed but is instead shaped by salinity, nutrients, and seasonality in pathway-specific ways. Critically, dominant degrader taxa employ fundamentally different metabolic strategies to sustain this function across fluctuating conditions, providing a form of community-level insurance against environmental disturbance. These findings advance our ability to predict microbial hydrocarbon degradation in coastal systems and inform nature-based approaches to bioremediation under increasing climate and anthropogenic pressures.}, }
@article {pmid41929113, year = {2026}, author = {Wang, S and Guitor, AK and Valentin-Alvarado, LE and Garner, R and Zhang, P and Yan, M and Shi, LD and Schoelmerich, MC and Steininger, HM and Portik, DM and Zhang, S and Wilkinson, JE and Lynch, S and Morowitz, MJ and Hess, M and Diamond, S and Banfield, JF and Sachdeva, R}, title = {Metagenomic strain-resolved DNA modification patterns link extrachromosomal genetic elements to host strains.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.27.714056}, pmid = {41929113}, issn = {2692-8205}, abstract = {DNA modification is central to microbial defense against extrachromosomal genetic elements (ECEs), consequently ECEs tend to adopt their host's modification patterns. Shared ECE-host modification patterns enable linking ECEs to their hosts, but modification detection tools are designed for single genomes and are ineffective at metagenome scale. Here, we present MODIFI, software for detecting DNA modifications in metagenomes. MODIFI assumes that each k-mer in a metagenome is mostly unmodified and calculates background signal levels for that k-mer from PacBio HiFi reads, eliminating the need for matched control experiments. MODIFI ECE-host linkages were validated using >1,000 isolate and mock microbiome datasets. Illustrating the approach, we identified 315 strain-resolved, non-redundant ECE-host linkages in environmental and human metagenomes. In infant gut microbiomes, a chromosomal inversion in Enterococcus faecalis alters host and associated plasmid methylation motifs simultaneously. Overall, MODIFI solves a major bottleneck in DNA modification analysis and provides a foundational tool for understanding microbial epigenomics.}, }
@article {pmid41929272, year = {2026}, author = {Biesheuvel, MM and Barkema, HW and Morley, PS and Pinnell, LJ and Doster, E and Valeris-Chacin, R}, title = {In silico performance of a targeted enriched metagenomics approach to infer Mycoplasma bovis strains in milk.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1770245}, pmid = {41929272}, issn = {2297-1769}, abstract = {Strain variation plays a key role in the microbial epidemiology of Mycoplasma bovis, yet its true diversity remains incompletely characterized, partly due to limitations of culture-based methods. This study evaluated the in silico suitability of a targeted enrichment (TE) shotgun sequencing approach to detect and classify M. bovis strains in milk metagenomic samples. As a proof of concept, the accuracy of this approach was assessed using milk-derived M. bovis strains. A total of 620 M. bovis whole-genome sequences were downloaded from NCBI, of which 162 (26.1%) originated from milk samples. Genomes were grouped into Genomically Clustered Sequence Variants (GSVs) using MashTree and TreeCluster to enable strain-level classification. To simulate TE sequencing data, genomes from different milk-associated GSVs were randomly selected and fragmented in silico into 150-bp reads. Mock milk samples were generated by sampling reads with replacement from these genomes. Sequencing depth was modeled using a Poisson distribution, while mixed-strain DNA samples were simulated by including 1, 3, 6, or 9 GSVs per sample. Enrichment proportions were set at 0.3, 0.5, 0.7, and 0.9. Two classification tools, Kraken2 and Themisto/mSWEEP, were evaluated for their ability to detect and classify the simulated TE reads. Themisto/mSWEEP consistently outperformed Kraken2, achieving an average read classification accuracy of 84.9% compared with 1.4% for Kraken2. Sensitivity for Themisto/mSWEEP was 100% with a single spiked GSV and declined slightly to 97.0% with nine GSVs, whereas Kraken2 achieved sensitivities of only 17.3% and 4.7%, respectively. Positive predictive value (PPV) showed a similar pattern: 98% for Themisto/mSWEEP vs. 4.7% for Kraken2 with a single GSV, and 65.5% vs. 10% with nine GSVs. While Kraken2's PPV increased slightly with additional GSVs, Themisto/mSWEEP's PPV decreased. Both methods maintained high specificity and negative predictive value (>91%) across all scenarios. Enrichment proportion had no measurable effect on performance. Overall, Themisto/mSWEEP demonstrated superior accuracy for GSV-level identification of M. bovis strains. Enrichment to at least 30% of total reads was sufficient to recover strain-level data. Further work is needed to assess the biological relevance and practical applications of these genomic clusters.}, }
@article {pmid41929449, year = {2026}, author = {Røsland, A and Amin, H and Lie, SA and Malinovschi, A and Bunæs, DF and Bertelsen, RJ}, title = {Effect of periodontal therapy on the oral microbiome and lung function: an intervention study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1725666}, pmid = {41929449}, issn = {2235-2988}, mesh = {Humans ; *Microbiota ; Male ; *Periodontitis/therapy/microbiology ; Female ; Middle Aged ; *Mouth/microbiology ; Longitudinal Studies ; Adult ; Bacteria/classification/genetics/isolation &amp; purification ; *Lung/physiology ; Metagenomics ; Aged ; }, abstract = {INTRODUCTION: The oral cavity harbors over 700 bacterial species, and disruption of this balance can lead to periodontitis, which has been linked to systemic conditions including respiratory disease.<br><br>METHODS: In this longitudinal clinical trial, 57 never-smoking adults with stage I-II periodontitis underwent full-mouth periodontal disinfection. Airway resistance and subgingival plaque sampling (analyzed by shotgun metagenomics) was measured at baseline and six weeks after therapy.<br><br>RESULTS: Periodontal treatment significantly improved clinical periodontal parameters, and was associated with reductions in airway resistance. Microbiome analysis showed a shift from periodontitis-associated taxa, including Prevotella, Porphyromonas, and Tannerella, toward health-associated species such as Actinomyces oris, and Rothia dentocariosa. Higher airway resistance was associated with a greater relative abundance of periodontitis-associated bacteria.<br><br>DISCUSSION: Together, findings suggest that periodontal therapy promotes a healthier oral microbiome and is associated with improved lung function in non-smokers with no prior lung disease.}, }
@article {pmid41929455, year = {2026}, author = {Geng, Y and Yuan, Y and Lin, X and Wei, J and Zhang, Q and Mao, X and Zhang, X and Zhang, X and Zhang, Y and Zhao, J and Guo, F and Zheng, P}, title = {Distinct characteristics on mixed infection of SARS-CoV-2 variants and other respiratory pathogens among patients with acute COVID-19 in central China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1653022}, pmid = {41929455}, issn = {2235-2988}, mesh = {Humans ; *COVID-19/virology/epidemiology ; China/epidemiology ; Male ; Female ; Middle Aged ; *SARS-CoV-2/genetics/isolation &amp; purification/classification ; *Coinfection/virology/epidemiology/microbiology ; Aged ; Adult ; Risk Factors ; Mycoplasma pneumoniae/isolation &amp; purification ; Severity of Illness Index ; Hospitalization ; High-Throughput Nucleotide Sequencing ; Pneumonia, Mycoplasma/epidemiology ; Respiratory Tract Infections ; }, abstract = {BACKGROUND: Reports on mixed infection with different severe acute respiratory syndrome coronavirus 2 variants and other respiratory pathogens in patients with acute coronavirus disease in China remain scarce. In this study, we analyzed the clinical characteristics of mixed infections involving different severe acute respiratory syndrome coronavirus 2 variants and other respiratory pathogens in patients with acute coronavirus disease in central China.<br><br>METHODS: Nested polymerase chain reactions and metagenomic next-generation sequencing were employed to identify severe acute respiratory syndrome coronavirus 2 variants. Clinical data, including hospitalization days, severity classification, outcomes, and laboratory data, were collected and analyzed.<br><br>RESULTS: Seven patients had mixed infections with different severe acute respiratory syndrome coronavirus 2 variants in samples collected on different dates. Overall, 54.6% (83/152) of patients had co-existing respiratory pathogen infection. The most common co-existing respiratory pathogen was Mycoplasma pneumoniae. Longer hospital stays, intensive care unit admission, and prolonged duration from admission to positive severe acute respiratory syndrome coronavirus 2 sample detection were independent risk factors for acute coronavirus disease infection with different respiratory pathogens. Severity classification, mixed infection, cerebral fraction, and fever were independent risk factors for failed treatment. Early detection of white blood cell count, procalcitonin, and D-dimer concentrations can help predict mixed respiratory infections and treatment outcomes.<br><br>CONCLUSIONS: The phenomenon of mixed infection with different variants in patients with coronavirus disease may have been underestimated. Therefore, active surveillance of severe acute respiratory syndrome coronavirus 2 variants should be performed in older patients with comorbidities.}, }
@article {pmid41929479, year = {2026}, author = {Pan, Y and Li, B and Liu, L and Wang, Z and Liu, X}, title = {Gut dysbiosis induces the development of asthenozoospermia through butanoate metabolism.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1760881}, pmid = {41929479}, issn = {1664-3224}, mesh = {Male ; *Dysbiosis/complications/microbiology/metabolism ; Animals ; *Gastrointestinal Microbiome ; *Asthenozoospermia/metabolism/etiology/microbiology ; Humans ; Mice ; Case-Control Studies ; Fecal Microbiota Transplantation ; Adult ; Fatty Acids, Volatile/metabolism ; Butyrates/metabolism ; Sperm Motility ; Metabolomics ; Testis/metabolism ; }, abstract = {BACKGROUND: Asthenozoospermia is a leading cause of male infertility with a rising incidence. While gut dysbiosis is implicated in metabolic disease, its role in asthenozoospermia pathogenesis remains unclear.<br><br>MATERIALS AND METHODS: We conducted a case-control study comparing the fecal microbiomes of men with isolated asthenozoospermia (n=60) and healthy controls (n=60) using shotgun metagenomic sequencing. Causality was assessed by fecal microbiota transplantation (FMT) from patients or controls into germ-free male mice. Metabolic perturbations were profiled by untargeted serum metabolomics and targeted short-chain fatty acid (SCFA) quantification in humans, alongside untargeted testicular metabolomics and serum SCFAs in recipient mice.<br><br>RESULTS: Metagenomic analysis (LEfSe) identified species-level differences, with marked depletion of butyrate-producing taxa in asthenozoospermia, most notably the prototypical butyrate producer Faecalibacterium prausnitzii. The relative abundance of F. prausnitzii was significantly positively correlated with sperm motility and progressive motility, linking gut composition to sperm quality in asthenozoospermia. Untargeted serum metabolomics identified 39 differential metabolites; KEGG enrichment prioritized butanoate metabolism. Targeted SCFA profiling confirmed significantly lower serum butyrate in asthenozoospermia versus controls. In germ-free males, FMT with patient-derived microbiota reduced sperm motility and progressive motility and induced histopathological abnormalities, including decreased interstitial Leydig cells, loss and atrophy of select intratubular cells, and an increased proportion of abnormal seminiferous tubules. Following patient FMT, recipient mice exhibited significantly reduced serum butyrate; testicular metabolomics revealed distinct profiles with 140 key differential metabolites, again implicating butanoate metabolism. Mechanistically, reduced F. prausnitzii-derived butyrate might impair Leydig cell steroidogenesis via disrupted PPAR signaling.<br><br>CONCLUSIONS: Asthenozoospermia is associated with gut dysbiosis characterized by loss of butyrate-producing bacteria, systemic and testicular disturbances in butyrate metabolism, and microbiota-mediated transmission of impaired sperm quality. These findings implicate the gut-testis axis in asthenozoospermia pathogenesis and nominate butyrate metabolism as a potential therapeutic target.}, }
@article {pmid41929693, year = {2026}, author = {Xue, H and Zhang, M and Tang, Y and Huang, W and Yu, X and Zhang, J and Pan, M and Liu, Z}, title = {Integrated metagenomic and metabolomic profiling of spontaneous preterm birth in Chinese women.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1729476}, pmid = {41929693}, issn = {1664-302X}, abstract = {BACKGROUND: Spontaneous preterm birth (sPTB) remains a major cause of neonatal morbidity and mortality. We used integrated metagenomics and untargeted metabolomics to identify vaginal microbial and host metabolic signatures associated with sPTB in Chinese women.<br><br>METHODS: Vaginal swabs (sPTB, n&#x202f;=&#x202f;37; term, n&#x202f;=&#x202f;62) and available maternal plasma were profiled by shotgun metagenomic sequencing and UHPLC-HRMS metabolomics. Group differences in microbial diversity/taxa and metabolite features were evaluated, followed by pathway enrichment and microbiome-metabolome correlation analyses.<br><br>RESULTS: Compared with term controls, sPTB was characterized by reduced Lactobacillus dominance, higher vaginal microbial alpha diversity (p&#x202f;<&#x202f;0.05), and distinct community structure (PERMANOVA p&#x202f;<&#x202f;0.001). Metabolomic profiles of plasma and vaginal fluid differentiated sPTB from term pregnancy and highlighted decreased pantothenic acid and increased 4-pyridoxic acid, together with lipid and amino-acid perturbations. Pantothenic acid showed good discrimination (AUC&#x202f;=&#x202f;0.82), and a multi-metabolite model improved classification (AUROC&#x202f;=&#x202f;0.9544). KEGG analysis implicated vitamin B6 metabolism, pantothenate/CoA biosynthesis, and glycerophospholipid metabolism. Microbiome-metabolome integration dentified exploratory an sPTB-associated pattern in which Lactobacillus (e.g., L. crispatus) was positively correlated with pantothenic acid, while dysbiosis-/pathogen-associated taxa (including C. trachomatis) correlated with 4-pyridoxic acid.<br><br>CONCLUSION: sPTB in this Chinese cohort is associated with concurrent vaginal dysbiosis and systemic/local metabolic disturbances, supporting integrated microbiome-metabolite markers for risk stratification and potential preventive targets.}, }
@article {pmid41929767, year = {2026}, author = {Peng, W and Yang, W and Ma, L and Wang, Q and Yang, R and Ji, A and She, M and Wang, T and Gong, W and Yan, L}, title = {Flower vinegar prepared from Yunnan large-leaved tea tree prevents high-fat diet-induced obesity in mice by regulating gut microbiota.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1749951}, pmid = {41929767}, issn = {2296-861X}, abstract = {Obesity and its metabolic complications are major public health concerns. The gut microbiota plays a pivotal role in regulating host adiposity. Fermented products from Camellia sinensisvar. Assamica (Yunnan large-leaved tea) flowers, a novel food ingredient, may offer therapeutic potential, but their effects on obesity and gut microbiota remain unexplored. We investigated the anti-obesity effects of vinegar fermented from Camellia sinensisvar. Assamica flowers (TTFV) in a high-fat diet (HFD)-induced obese mouse model. Body weight, glucose and lipid metabolism, hepatic injury, steatosis, inflammation, and oxidative stress were assessed. Metabolomic analysis and metagenomic sequencing of gut microbiota were performed. Key metabolic pathways were analyzed. TTFV supplementation significantly attenuated HFD-induced body weight gain, improved glucose and lipid profiles, alleviated hepatic steatosis and injury, and reduced systemic inflammation and oxidative stress. TTFV modulated host metabolite profiles and related metabolic pathways. Crucially, TTFV reshaped the gut microbiota structure: it increased the relative abundance of Bacteroidota and decreased the Firmicutes/Bacteroidota ratio at the phylum level. At the family level, it promoted beneficial bacteria (Oscillospiraceae, Eubacteriaceae) and suppressed potentially harmful ones (Erysipelotrichaceae). Metabolic pathway analysis indicated TTFV's positive role in maintaining cellular homeostasis and regulating metabolic disturbances. Our findings demonstrate that TTFV exerts protective effects against HFD-induced obesity in mice. These benefits are closely associated with the remodeling of gut microbiota composition and the modulation of key metabolic pathways. This study is the first to report the anti-obesity potential and microbiota-regulating effects of TTFV, suggesting its promise as a functional food ingredient for promoting intestinal health and mitigating obesity-related metabolic disorders.}, }
@article {pmid41929953, year = {2026}, author = {Oso, TA and Okesanya, OJ and Adebayo, UO and Obadeyi, KB and Ayelaagbe, OB and Talabi, OA and Adewole, PD and Anorue, CO and Ahmed, MM and Talabi, OT and Ogaya, JB and Lucero-Prisno, DE}, title = {Microbiome alterations in Alzheimer's disease: A systematic review of current evidence and global perspectives.}, journal = {Journal of Alzheimer's disease reports}, volume = {10}, number = {}, pages = {25424823261436287}, pmid = {41929953}, issn = {2542-4823}, abstract = {BACKGROUND: Growing evidence implicates the gut-brain axis in Alzheimer's disease (AD), with gut microbiome dysbiosis proposed to modulate neuroinflammation, amyloid pathology, and cognitive decline.<br><br>OBJECTIVE: To systematically synthesize human studies (2021-2025) profiling gut microbiomes in AD; identify consistent taxonomic and functional signatures; map geographic study distribution; and highlight translational gaps.<br><br>METHODS: A PRISMA-compliant systematic review of human studies using 16S rRNA, metagenomics, metatranscriptomics, or fecal microbiota transplantation (FMT)/probiotic designs was conducted. Two reviewers screened studies and assessed quality using Joanna Briggs Institute tools. Owing to heterogeneity, findings were narratively synthesized across microbiome diversity, taxonomy, function, metabolism, oral-brain links, causality, interventions, and predictive analyses.<br><br>RESULTS: Thirty-seven studies, mainly from Asia with some from Europe, North America, and Africa, revealed consistent gut dysbiosis in AD. Findings show reduced alpha-diversity, loss of short-chain fatty acid-producing bacteria (e.g., Faecalibacterium prausnitzii, Bifidobacterium), and enrichment of pro-inflammatory taxa (Escherichia/Shigella, Proteobacteria). Functional analyses indicate reduced butyrate synthesis, disrupted lipid and tryptophan-kynurenine metabolism, and links with apolipoprotein epsilon (&#x3b5;4) gene and cognition. Limited causal evidence arises from Mendelian randomization and small FMT trials, with randomized, longitudinal confirmation still needed.<br><br>CONCLUSIONS: Current evidence suggests a biologically plausible association between gut microbiota and AD pathogenesis, positioning microbiome-derived biomarkers and interventions as promising but still exploratory avenues. Harmonized, longitudinal, multi-omic, and geographically inclusive studies are urgently needed to clarify causal mechanisms and translate these correlational findings into validated diagnostics and therapeutics.}, }
@article {pmid41930262, year = {2025}, author = {Bertoldi, S and Klaes, S and Claus, S and Marsans, A and Heipieper, HJ and Eberlein, C}, title = {Cross-feeding drives degradation of phthalate ester plasticizers in a bacterial consortium.}, journal = {Frontiers in microbiology}, volume = {16}, number = {}, pages = {1757196}, pmid = {41930262}, issn = {1664-302X}, abstract = {Reports of plastic pollution across diverse ecosystems continue to emphasize the environmental risks associated with the increasing consumption of synthetic polymers. Plastics frequently contain additives such as phthalic acid esters, which are extensively employed as plasticizers to enhance flexibility in plastic materials and as constituents of numerous consumer products. These compounds are not chemically bound to polymers, allowing them to leach into the environment and have been implicated as potential endocrine disruptors in animals. In the present study, the bacterial degradation of selected phthalate esters was examined, with diethyl phthalate (DEP) utilized as a model compound. A bacterial consortium capable of degrading DEP was enriched from a biofilm of a polyurethane tubing. The consortium was capable to mineralize DEP as the sole carbon and energy source at concentrations of up to 4 mM, whereas concentrations above 6 mM inhibited its activity due to DEP toxicity. This degradation was only possible by the whole consortium and not by single isolates. The degradation of DEP as well as the timely occurrence of monoethyl phthalate as degradation intermediate was confirmed by UPLC analysis. Metagenomic sequencing identified the consortium as comprising a Microbacterium sp. strain and two Pseudomonas spp. Metaproteomic analyses of the consortium, performed under varying time points and carbon sources and integrated with complementary growth experiments, facilitated the reconstruction of the degradation pathway and the identification of putative enzymes involved in DEP metabolism. Microbacterium sp. DEP1M initiated the degradation by hydrolysis of DEP into ethanol and monoethyl phthalate, which is then taken up by the cells and further metabolized to ethanol and phthalate. The latter is subsequently oxidized by a dioxygenase and further transformed to the central intermediate 3,4-dihydroxybenzoic acid (protocatechuate). Protocatechuate is then exclusively degraded via the ortho cleavage pathway. Notably, the distribution of enzymatic functions among different community members strongly supports the occurrence of microbial cross-feeding, indicating that DEP mineralization is a cooperative process within the consortium.}, }
@article {pmid41930266, year = {2026}, author = {Marter, P and Brinkmann, H and Freese, HM and Ringel, V and Bunk, B and Jarek, M and Koblížek, M and Wagner-Döbler, I and Petersen, J}, title = {The microbiome of marine mat-forming cyanobacteria-a microcosm of taxonomic novelty and phototrophic diversity.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag041}, pmid = {41930266}, issn = {2730-6151}, abstract = {Intertidal biological mats are highly dynamic ecosystems typically dominated by filamentous cyanobacteria of the genus Coleofasciculus. These primary producers play important roles in primary production, biogeochemical cycling, and coastal protection. 16S rRNA gene profiling of non-axenic cultures has recently revealed an astonishing wealth of associated bacteria. We analyzed the microbiomes of 14 non-axenic Coleofasciculus cultures from nine globally distributed marine sampling sites, representing seven distinct phylogenomic lineages. Metagenome sequencing and binning resulted in 320 metagenome-assembled genomes (MAGs) representing a broad spectrum of "uncultivated" bacterial diversity mostly belonging to Pseudomonadota, Bacteroidota and Planctomycetota. Marinovum algicola, and Roseitalea porphyridii were found in 12 of the microbiomes studied, making them the most common housemates. The complex microbiome of Coleofasciculus sp. WW12 contained seven Planctomycetota MAGs from so far undescribed species, representing inter alia a new family in the order Phycisphaerales and an MAG from a deeply branching sister lineage of all cultivated planctomycetes. The discovery of 36 proteobacterial MAGs with photosynthesis gene clusters (PGCs) and 32 MAGs with proteorhodopsin or xanthorhodopsin operons documented the coexistence with many photoheterotrophic bacteria, indicating that the cyanosphere is a hotspot of phototrophic life. The presence of a PGC-containing Myxococcales MAG (Candidatus Photomyxococcus marinus) is of special interest because it paves the way to investigate photosynthesis in Deltaproteobacteria. In a Mediterranean Coleofasciculus culture, three alphaproteobacterial MAGs were found that have both a xanthorhodopsin operon and the PGC, suggesting that dual phototrophy is not restricted to alpine lakes or glaciers, and can also be found in marine habitats.}, }
@article {pmid41930333, year = {2026}, author = {Tan, H and Ding, Y and Gu, Z and Wang, X and Wang, J and Wei, T and Zhang, X and Pan, L and Shi, Y and Chang, S and Guo, C and Weng, J and Zheng, X and Yue, T}, title = {Microbiome-Based Clustering Identifies Glycemic Control-Related Subtypes in Youth With Recent-Onset Type 1 Diabetes.}, journal = {MedComm}, volume = {7}, number = {4}, pages = {e70705}, pmid = {41930333}, issn = {2688-2663}, abstract = {Type 1 diabetes (T1D) in children exhibits substantial heterogeneity in glycemic control, yet the biological mechanisms underlying this variation remain unclear. We aimed to explore endotype heterogeneity in youth with recent-onset T1D using unsupervised clustering based on multi-omics data, and to identify associated molecular signatures and underlying mechanisms. In a discovery cohort of 69 children and adolescents with recent-onset T1D, unsupervised clustering of fecal metagenomic profiles revealed two robust subgroups distinguished by hemoglobin A1c (HbA1c) levels. The High-HbA1c group was enriched in Bacteroidota, while the Low-HbA1c group was enriched in Firmicutes and certain Bacteroides species (Bacteroides ovatus, Bacteroides xylanisolvens, Bacteroides nordii, and Bacteroides cellulosilyticus). Metabolomics revealed significant enrichment of tryptophan-derived metabolites in the Low-HbA1c group. Bacteroides species signatures are positively correlated with tryptophan metabolite skatole. In an independent validation cohort, Bacteroides signatures discriminated individuals with good versus poor glycemic control (AUC = 0.854). Similar microbial patterns were observed in healthy children stratified by glycemic risk, indicating broader relevance of these signatures. Together, microbiome-based clustering identified glycemic control-related subtypes in T1D youth and suggested a potential role of Bacteroides and skatole in glycemic control. Mechanistic studies are warranted to confirm its role as a glycemic control-related endotype with distinct pathophysiology.}, }
@article {pmid41930475, year = {2026}, author = {Tan, Y and Zou, D and Ni, C and Zeng, Q and Li, M}, title = {From Field Metagenomes to Mutant Genomes: Coevolution of Cyanophages and Synechococcus in Estuarine Ecosystems.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c12277}, pmid = {41930475}, issn = {1520-5851}, abstract = {Picocyanobacteria, represented by Prochlorococcus and Synechococcus, are major photosynthetic organisms in aquatic ecosystems, and their viruses (cyanophages) significantly impact cyanobacterial ecology and evolution. Here, we combined metagenomics of Synechococcus communities along four representative estuaries in China and whole-genome analyses of laboratory-evolved Synechococcus mutants to link viral diversity to host adaptation and evolution. We assembled 83 cyanophage genomes (mainly cyanomyoviruses), with expanded auxiliary metabolic genes encoding glycosyltransferases and radical S-adenosyl methionine proteins involved in amino acid and lipopolysaccharide metabolism. Metagenome-assembled cyanobacterial genomes revealed mutations predominantly in membrane-associated functions linked to phage infection. In parallel, we identified genetic pathways conferring phage resistance in 18 evolved Synechococcus mutant strains that are resistant to phage infection. Notably, mutations in carbohydrate (rfbA) and photosynthetic energy transfer (cpeT) of Synechococcus mutants recurred in both cultured isolates and recovered metagenomes. These results indicate that cyanophages in estuaries leverage broader metabolic toolkits, while Synechococcus repeatedly evolves resistance. Together, these findings outline a reciprocal adaptive landscape that helps explain the persistence and turnover of picocyanobacterial populations in estuarine environments.}, }
@article {pmid41930516, year = {2026}, author = {Wang, W and Li, M and Liu, X and Li, Y and Yang, K and Tuovinen, OH and Wang, H}, title = {Anaerobic antimony oxidation by mine groundwater bacteria: The energy-detoxification trade off governed by carbon source and Sb concentration.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141926}, doi = {10.1016/j.jhazmat.2026.141926}, pmid = {41930516}, issn = {1873-3336}, abstract = {Microorganisms drive anaerobic antimony (Sb) oxidation and detoxification in groundwater, how carbon source (organic vs. inorganic) regulates this process and shapes microbial adaptive strategies remains unclear. To fill this knowledge gap, microcosms were conducted with groundwater from Xikuangshan mining-area, integrating with hydrochemistry, genes quantification, and metagenomics. The results demonstrated efficient anaerobic Sb(III) oxidation coupled with NO3[-] reduction, regulated synergistically by Sb concentration and carbon sources. The concentration of 0.5 mM Sb(III) served as a critical threshold that triggered changes in bacterial diversity, composition, and Sb(III)-oxidation behavior. Below this, NaHCO3 promoted higher oxidation rates (P < 0.05), linked to enrichment of Hydrogenophaga, Aquabacterium, Acidovorax, and aioA genes (Sb-oxidizing gene). Above 0.7 mM Sb(III), Na-lactate activated aioA and narrowed the rate gap, accompanied by increases in both abundance and niche of Dechloromonas. In addition, elevated Sb stress reshaped the metabolic networks across microcosms. The communities prioritized energy allocation to nitrogen fixation (nifH) with multiple benefits over redundant carbon fixation (cbbL). This research expands the known range of Sb and carbon drive microbial metabolic remodeling, advancing our predictive understanding of Sb biogeochemical cycling in contaminated aquifers.}, }
@article {pmid41930813, year = {2026}, author = {Liu, J and Mai, Y and Xie, Y and Zhou, X and Ye, Y and Jiang, D and He, L and Ye, Z and Li, D and Xia, C and Su, J and Huang, S}, title = {Dehydroandrographolide succinate alleviates ulcerative colitis via regulating RAB9A/NF-κB axis-mediated macrophage polarization and remodeling the gut microbiota.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {155}, number = {}, pages = {158039}, doi = {10.1016/j.phymed.2026.158039}, pmid = {41930813}, issn = {1618-095X}, abstract = {BACKGROUND: Dehydroandrographolide succinate (DAS), isolated from Andrographis paniculata, exhibits potent anti-inflammatory activity, yet its therapeutic potential and precise mechanism in ulcerative colitis (UC) remain unexplored.<br><br>PURPOSE: This study aims to investigate the efficacy and molecular basis that is responsible for the amelioration of DAS against UC.<br><br>METHODS: Effect of DAS against colitis was studied in a DSS-induced colitis model, and the critical role of macrophage was verified by the macrophage depletion and adoptive macrophage transfer (AMT) model. The anti-inflammation activity of DAS was investigated in the LPS/IFN-&#x3b3;-stimulated THP-1-derived macrophage model in vitro, followed by DARTS, CETSA, molecular docking/dynamics, and transcriptomics to elucidate the underlying mechanism. The effect of DAS on gut microbiota was analyzed with metagenomic sequencing.<br><br>RESULTS: DAS attenuated the colitis features, including weight loss, diarrhea, rectal bleeding, and colon shortening, together with reduced inflammatory infiltrates and restored crypt architecture. DAS down-regulated pro-inflammatory cytokines (IL-1&#x3b2;, IL-6, TNF-&#x3b1;) and up-regulated anti-inflammatory mediators (IL-10, IL-13), meanwhile restoring tight-junction proteins (ZO-1, Occludin) and goblet-cell mucins. Macrophage depletion abolished DAS's benefit, while AMT with DAS-treated macrophages relieved the colitis features, confirming the macrophage-dependency of DAS. Transcriptomics and the following verification revealed that the anti-inflammatory activity of DAS mainly relied on the NF-&#x3ba;B signaling pathway by suppressing p65 phosphorylation and downstream targets. DAS inhibited M1 polarization and protected epithelial monolayers from macrophage-mediated damage. Moreover, DAS exhibited high-affinity binding to RAB9A, and RAB9A knockdown abolished DAS-mediated suppression of TLR4/NF-&#x3ba;B signaling pathway in macrophages. Metagenomic analysis revealed that DAS treatment enriched Lachnospiraceae bacterium, Duncaniella freteri, Lachnospiraceae bacterium 10-1, Bacterium 1XD8-76, Schaedlerella arabinosiphila, while depleted Muribaculaceae bacterium, Bacteroides intestinalis and Clostridiaceae bacterium. Functional gene profiling indicated that DAS upregulated genes related to butyrate metabolism, amino sugar and nucleotide sugar metabolism, and starch and sucrose metabolism.<br><br>CONCLUSION: DAS alleviates DSS-colitis by targeting RAB9A to block the NF-&#x3ba;B signaling pathway-driven M1 macrophage polarization, and is accompanied by gut microbiota remodeling, highlighting the promising application of DAS against UC.}, }
@article {pmid41931872, year = {2026}, author = {Ren, Z and Wen, Y and Ma, Y and Li, M and Wang, L and Yu, R and Wu, L}, title = {Species-specific salinity adaptation mechanisms drive niche partitioning of nitrite-dependent anaerobic methane oxidation bacteria in a natural wetland gradient.}, journal = {Water research}, volume = {298}, number = {}, pages = {125791}, doi = {10.1016/j.watres.2026.125791}, pmid = {41931872}, issn = {1879-2448}, abstract = {Nitrite-dependent anaerobic methane oxidation (N-DAMO) is a key process regulating methane emissions from wetland ecosystems. However, the species-specific mechanisms that enable N-DAMO bacteria to adapt and occupy distinct niches along environmental gradients (such as salinity) remain largely unknown. This makes it difficult to predict the ecological function of these bacteria. In this study, the structure, functional diversity, and species-specific salinity adaptation mechanisms of N-DAMO bacterial community in the Ulansuhai Wetland along a natural salinity gradient were investigated. An integrated approach combining metagenomic sequencing, isotopic tracer experiment, quantitative PCR, and biogeochemical measurements was employed for this research. The results show that salinity significantly reshaped the community structure and diversity of N-DAMO bacteria, while their potential activity remained functionally stable. This functional resilience was underpinned by distinct niche partitioning among four dominant species of Candidatus Methylomirabilis, species. Each species exhibited unique genomic potential for exopolysaccharide biosynthesis, osmoregulation, and stress response. Furthermore, the N-DAMO process constituted a significant methane sink, representing 39.5% of the observed anaerobic methane oxidation activity. Path analysis further explained that salinity regulated N-DAMO bacterial communities directly and through indirect pathways mediated by soil carbon and nitrogen pools. This research provides the first mechanistic framework linking species-specific genomic traits of N-DAMO bacteria to salinity adaptation and niche partitioning. The study offers novel insights for predicting wetland methane emissions.}, }
@article {pmid41931886, year = {2026}, author = {Xiao, S and Han, Z and Tang, Y and Wu, X and Huang, J and Zeng, W}, title = {Dual roles of tetracycline-degrading bacteria in pollutant detoxification and resistome reshaping under tetracycline-copper co-contamination.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141951}, doi = {10.1016/j.jhazmat.2026.141951}, pmid = {41931886}, issn = {1873-3336}, abstract = {Combined contamination of soils with antibiotics and heavy metals represents a growing environmental challenge, yet remediation strategies addressing their synergistic toxicity remain limited. In this study, the bioremediation potential of a tetracycline-degrading bacterial consortium (Raoultella sp. XY-1 and Pandoraea sp. XY-2) was evaluated in tetracycline-copper (TC-Cu) co-contaminated soils by integrating chemical, biological, and ecological assessments. Soil column experiments demonstrated that bioaugmentation significantly enhanced TC degradation (48.57-53.71% after 90 days) compared to uninoculated controls (<12%), while simultaneously reducing copper bioavailability by shifting acid-extractable and reducible fractions toward more stable oxidizable forms. Inoculation further alleviated the strong inhibition of soil enzymatic activities (sucrase, urease, phosphatase), reflecting improved soil functional recovery. Metagenomic sequencing revealed that TC-Cu co-contamination reshaped microbial community composition, particularly increasing the relative abundance of Actinomycetota and Campylobacterota. Bioaugmentation further facilitated the establishment of Raoultella and indirectly stimulated indigenous resistant taxa through community interactions. Correlation network analysis further revealed that Raoultella was a highly connected genus in co-occurrence networks of antibiotic resistance gene (ARG)- and metal resistance gene (MRG)-hosting genera. LC-MS detection of intermediate products during TC microbial degradation proposed three microbial degradation pathways and inferred microbial resistance mechanisms under TC-Cu coexistence. Collectively, these findings highlight that TC-degrading bacteria not only reduce pollutant toxicity but also reshape microbial and genetic landscapes in co-contaminated soils, potentially suppressing the diffusion risk of resistance genes at low TC-Cu level. This work provides novel insights into the ecological trade-offs of bioremediation and supports the development of targeted, sustainable strategies for complex antibiotic-metal pollution scenarios.}, }
@article {pmid41931897, year = {2026}, author = {Zhang, K and Chang, S and Zhu, Y and Shang, H and Fu, Q and Tu, X and Yu, Y and Feng, Y}, title = {Metagenomic analysis of urban water systems uncovers the interplay between antibiotic resistance genes and microbial communities in response to PFAS contamination.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141890}, doi = {10.1016/j.jhazmat.2026.141890}, pmid = {41931897}, issn = {1873-3336}, abstract = {Urban water systems (UWS) are facing the severe challenge of coexisting emerging contaminants per- and polyfluoroalkyl substances (PFAS) and antibiotic resistance genes (ARGs). Herein, we analyze 15 PFAS at all key nodes within the UWS and the manufacturing plant park (MPP) in industrial clusters. Meanwhile, 16S rRNA and metagenomic approach were employed to annotate microbial community and ARGs, investigating their response to PFAS contamination. Fifteen PFAS were detected in MPP wastewater with total concentrations ranging from 30.28 to 3738.51 (557.68 ± 1072.03) ng/L, with short-chain accounting for 63.5%. Wastewater treatment plant (WWTP) serves as both sink and source of PFAS, with a negative average removal efficiency (mean = -158.6%) ultimately contributing to the prevalence of PFAS in the drinking water treatment plants (DWTPs) and tap water (17.64 -84.72, 36.06 ± 18.52 ng/L). 1141 ARGs subtypes were identified by metagenomic with significant differences in relative abundance between different nodes samples (p = 0.00). Additionally, the co-occurrence network revealed 14 genera may as potential hosts for 25 ARGs subtypes. However, significant differences in microbial diversity and abundance were observed at different nodes samples (R = 0.408, p = 0.00), with PFAS reducing microbial community diversity, particularly in river system (R = 0.723, p = 0.00). Finally, the structural equation modeling (SEM) revealed that PFAS exerted the greatest negative contribution to ARGs profiles (total effect = -1.39) through synergistic effects involving direct negative impacts on microbial diversity (-0.679) and mobile genetic elements (MGEs) (-0.121). This suggests that PFAS may influence the ARGs profiles by synergistically inhibiting gene-level transfer mediated by MGEs within potential host microbial. Additionally, physicochemical parameters (0.42), nutrient levels (-0.29), and ion concentrations (0.06) were also minor drivers of ARGs profiles.}, }
@article {pmid41932005, year = {2026}, author = {Parente, E and Pietrafesa, R and De Filippis, F and De Vivo, A and Labella, MG and Hidalgo, M and Lavanga, E and Ricciardi, A}, title = {A survey of bacterial and fungal communities of table olives.}, journal = {International journal of food microbiology}, volume = {455}, number = {}, pages = {111759}, doi = {10.1016/j.ijfoodmicro.2026.111759}, pmid = {41932005}, issn = {1879-3460}, abstract = {Table olives are produced from a large number of olive varieties subjected to different trade preparations, resulting in a highly heterogeneous family of fermented foods. To characterise the diversity of bacterial and fungal communities and its relationship with variety, ripeness, and trade preparation, we surveyed 363 samples from 40 producers across 6 countries, combining physicochemical measurements, viable counts, and amplicon-based metagenomics. This is the largest survey of table olive microbial communities to date and includes the first culture-independent characterisation of microbial communities for several Italian PDO and non-PDO varieties, most notably Oliva di Gaeta. The contrast between alkali-treated and naturally fermented olives was the dominant structuring factor, with HALAB (Halophilic and Alkalophilic Lactic Acid Bacteria) and other halophiles enriched in alkali-treated varieties and a diverse array of Lactobacillaceae and Pseudomonadota characterising naturally fermented olives. Despite these consistent signals, striking variability was observed within the same variety and even within the same producer, driven by stochastic colonization events, house microbiota, and the widespread use of small fermentation vessels. This variability obscured variety-specific microbial signatures and prevented reliable discrimination of Italian PDO varieties from similar non-PDO counterparts using amplicon-based approaches. The ecological and taxonomic complexity documented here, encompassing bacterial and fungal genera with largely untapped starter and flavour potential, provides the foundation for the development of variety-specific microbiome-based starter cultures.}, }
@article {pmid41932427, year = {2026}, author = {Bao, C and Ren, Y and Tang, C and Su, Y and Yue, H and Chen, X}, title = {Viral Isolation and Genomic Characteristics of the First Bovine Parainfluenza Virus Type 3 Isolated from Water Buffaloes (Bubalus bubalis) in China.}, journal = {Veterinary journal (London, England : 1997)}, volume = {}, number = {}, pages = {106655}, doi = {10.1016/j.tvjl.2026.106655}, pmid = {41932427}, issn = {1532-2971}, abstract = {Bovine parainfluenza virus type 3 (BPIV3) is an important pathogen associated with bovine respiratory disease. In this study, we report the isolation and genomic characterization of BPIV3 from a water buffalo with respiratory symptoms in China. Virus isolation was performed using susceptible cell cultures, followed by identification via RT-qPCR, transmission electron microscopy, and indirect immunofluorescence. Metagenomic sequencing of the near-complete genome showed that the isolate shared 89.9%-91.1% nucleotide identity with BPIV3 genotype A strains. Notably, several distinct mutations were identified in the structural protein genes, and phylogenetic analysis demonstrated that the isolate formed a separate cluster within genotype A, suggesting that it may represent a novel subtype within this genotype. To our knowledge, this is the first report describing the isolation and genomic characterization of BPIV3 from water buffaloes in China. These findings provide baseline molecular data for further studies on the genetic diversity and evolution of BPIV3.}, }
@article {pmid41932524, year = {2026}, author = {Qian, J and Li, X and Xu, X and Zhang, D and Xiang, G and Wang, Z and Zhang, Z and Liu, M and Hao, W and Wu, D}, title = {Thiosulfate-Driven redox buffering enables efficient nitrogen removal and norfloxacin degradation in mixed denitrifying systems.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134550}, doi = {10.1016/j.biortech.2026.134550}, pmid = {41932524}, issn = {1873-2976}, abstract = {Wastewaters often contain both conventional pollutants and recalcitrant antibiotics, posing challenges to biological treatment. This study investigated a mixed autotrophic-heterotrophic denitrification system driven by sodium acetate and sodium thiosulfate for simultaneous nitrate and norfloxacin removal. A sequencing batch reactor was operated in four stages, culminating in norfloxacin exposure (0.5 mg/L). Results showed stable nitrogen removal (>95%) and norfloxacin degradation (>90%) under sustained antibiotic stress. Batch tests confirmed that the co-presence of thiosulfate and acetate enhanced norfloxacin biodegradation via co-metabolic pathways, with negligible abiotic removal. Three-dimensional excitation-emission matrix spectroscopy revealed a shift toward humic-like extracellular polymeric substances under norfloxacin, supporting biofilm integrity. 16S rRNA sequencing and metagenomics indicated dynamic microbial restructuring, with persistent core taxa (Thauera, Desulfofustis) and enrichment of stress-tolerant groups (norank_o_SJA-15). Functional analysis showed upregulation of carbon metabolism (pta, ackA), denitrification (nirS, nosZ), and sulfur oxidation (SUOX, SoxX, SoxA) genes, alongside oxidative stress mitigation genes (catB, gst) and xenobiotic degradation genes (HGD, E1.13.11.4). Antibiotic resistance gene profiles shifted toward multidrug (>29%), peptide resistance (14.0%→15.4%), and glycopeptide resistance (7.0%→9.4%), dominated by multidrug efflux and target alteration mechanisms, enabling community resilience while minimizing energetically costly defenses. This work elucidates the synergistic roles of dual electron donors in pollutant co-removal and stress mitigation, offering a robust, sustainable strategy for treating antibiotic-laden wastewater.}, }
@article {pmid41932525, year = {2026}, author = {Liu, Q and Wei, S and Li, Y and Yu, X and Zhang, Z and Li, J}, title = {Synthetic microbial community drive methane oxidation coupled to Cr(VI) reduction via division of labor and extracellular electron transfer.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134546}, doi = {10.1016/j.biortech.2026.134546}, pmid = {41932525}, issn = {1873-2976}, abstract = {While methane oxidation coupled to Cr(VI) reduction has been widely investigated, the functional specialization and division of labor within microbial consortia remain insufficiently understood. In this study, a synthetic microbial community (SynCom) was constructed by controlling methane concentration and chromium load. The maximum Cr(VI) removal load of this system reached 20.63 mg/L/d. The metagenomic assembly genome analysis showed that under hypoxic conditions, Methylocystis (6.30%) was the core microorganism driving methane oxidation. It achieved extracellular electron transfer (EET) through multiheme c-type cytochromes and conductive pili, or jointly with dominant genera such as Hyphomicrobium and Thiobacillus, to couple methane oxidation with Cr(VI) reduction. Integrated multi-omics revealed significant enrichment of differentially expressed proteins involved in quorum sensing and methane metabolism, along with elevated expression of ABC transporter substrate-binding protein and porin. The primary metabolites included N-Methyl-l-Proline, l-Histidine, and Hypaphorin, with l-Glutamine serving as a central node connecting the highest number of pathways in the metabolic network. The inhibition experiments confirmed that inhibiting the methane oxidation would directly reduce the efficiency of Cr(VI) reduction. This study revealed the microbial division of labor and the microscopic process of EET driven by aerobic methanotrophs under hypoxic conditions, and expanded its application potential in bioremediation from the perspective of SynCom. It could be a scientific foundation for pollution control technologies of methane-based biotransformation and utilization.}, }
@article {pmid41932647, year = {2026}, author = {Wang, DY and Wang, YW and Yu, KC and Yang, X and Ma, J and Li, BH and Peng, YL and Deng, XY and Chen, ZX and Wang, L}, title = {Probiotic potential of Parabacteroides johnsonii in mitigating age-related ovarian functional decline.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2026.03.023}, pmid = {41932647}, issn = {1673-8527}, abstract = {The gut microbiota is increasingly recognized as a regulator of reproductive health, yet its role in ovarian aging remains unclear. Here, we combine Mendelian randomization (MR) analysis with experimental validation to investigate the causal relationship between gut microbiota and ovarian aging. MR analysis identifies four microbial taxa significantly associated with age at natural menopause. In mouse models, germ-free mice exhibit accelerated ovarian functional decline, including reduced ovarian reserve and impaired folliculogenesis. Fecal microbiota transplantation (FMT) from young donors alleviates ovarian aging phenotypes, whereas FMT from aged donors exacerbates functional decline. Metagenomic analysis reveals species-level differences between young and ovarian-aging mice, with Parabacteroides johnsonii (P. johnsonii) enriched in young mice. Administration of P. johnsonii to middle-aged mice improves ovarian reserve, reduces follicular atresia, enhances granulosa cell proliferation, and decreases systemic inflammation. These findings highlight a causal role of the gut microbiota in ovarian aging and support microbiota-targeted interventions as a potential strategy to preserve ovarian function.}, }
@article {pmid41932883, year = {2026}, author = {Silva, RMB and Slyvka, A and Lee, YJ and Guan, C and Lund, SR and Raleigh, EA and Skowronek, K and Kuska, MS and Bochtler, M and Weigele, PR}, title = {A single viral enzyme drives tRNA-dependent hypermodification of DNA at adenine.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-70671-1}, pmid = {41932883}, issn = {2041-1723}, support = {FNP, POIR.04.04.00-00-5D81/17-00//Fundacja na rzecz Nauki Polskiej (Foundation for Polish Science)/ ; }, abstract = {Nucleic acid modifying enzymes drive diverse defense and counter-defense measures in the evolutionary arms race between viruses and their cellular hosts. Abundant and widespread bacterial viruses (bacteriophage or phage) encode for biosynthetic pathways that install elaborate DNA hypermodifications which protect their genomic DNA from host endonucleases. Here, we establish the molecular basis for the multistep biosynthesis of 6-aminocarboxymethyl-2'-deoxyadenosine (6-NcmdA), a nucleobase hypermodification found in the virion DNA of bacteriophage Mu that leads to restriction evasion in the context of phage-host conflicts. In the first step, we show that Mu-encoded Mom enzyme catalyzes the formation of 6-NcmdA by transferring glycine from charged tRNA[Gly] to the N6 position of adenine within double-stranded DNA. We uncover a second step where the glycyl-dA intermediate undergoes an on-base rearrangement to form 6-NcmdA. Examination of the proposed reaction pathways by quantum chemical calculations confirms the instability of acyl exocyclic groups at N6-adenine and reveals an energetically favorable orientation of 6-NcmdA that restores canonical base pairing. An X-ray structure confirms Mom is a member of the GNAT superfamily and suggests binding sites for both tRNA and DNA. Guided by the Mom structure and patterns of sequence conservation across metagenomic space, we show residues R111 and S124 are essential for catalysis. This work demonstrates that the Mom enzyme defines a new category of acetyltransferases utilizing charged tRNA to modify DNA.}, }
@article {pmid41932890, year = {2026}, author = {Zhao, L and Zheng, J and Shen, Y and Xu, X and Liu, X and Yu, J and Li, J and Yang, B and Chen, L and Wang, F and Liu, S and Peng, X and Du, J and Dong, R}, title = {Composite polyphenols mitigate microplastic exposure-related immune disturbances: a two-phase population trial.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71167-8}, pmid = {41932890}, issn = {2041-1723}, abstract = {Microplastics (MPs) are widespread, making it urgent to elucidate their toxicity and identify intervention strategies. Here, we designed a two-phase population trial, comprising a baseline pilot population (n = 151) and a 28-day randomized, double-blind, placebo-controlled trial (n = 98). Primary outcomes include fecal MP concentration and blood parameters (complete blood count, glycemic and lipid, and cytokines), with exploratory outcomes comprising fecal metagenomics and plasma metabolomics. The median MP concentration in 151 participants' fecal samples is 158.28 μg/g dry weight, correlating with levels of 7 inflammatory indexes, 4 cytokines, and 2 lipid indicators. Composite polyphenols (CP) significantly reduced plasma levels of IL-1β (P = 0.045, effect sizes = -0.463), IL-6 (P = 0.023, effect sizes = -0.576) and IL-8 (P = 0.022, effect sizes = -0.529). 507 differentially expressed microbiotas (DEMs; P < 0.05) and 144 significantly different metabolites (SDMs; P-FDR < 0.25, VIP ≥ 1) are observed between the high and low MP exposure groups; 108 DEMs and 85 SDMs are identified following CP intervention. Notably, CP could mitigate the pro-inflammatory effects of high MP exposure by modulating gut microbiota and up-regulating glycerophospholipid metabolism and arginine biosynthesis. The gut bacteria Staphylococcus and the plasma metabolite PC (22:5/0:0) are identified as potential mediators in this protective effect. Trial registration: ClinicalTrials.gov: NCT06437119.}, }
@article {pmid41736110, year = {2026}, author = {Pirolo, M and Sherwani, MK and Espinosa-Gongora, C and Eriksen, E&#xd8; and Tassinato, C and Alberdi, A and Guardabassi, L}, title = {Faecal microbiome profiling uncovers putative biomarkers for piglets resilient to post-weaning diarrhoea.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41736110}, issn = {2524-4671}, abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) is a major health and economic concern in intensive pig production. In this study, we hypothesized that the faecal microbiome, sampled before disease onset, could provide early prognostic markers of PWD risk and applied a machine-learning framework to identify biomarkers predictive of piglet susceptibility or resilience to PWD. At two Danish commercial farms experiencing PWD outbreaks, four pens per farm were monitored for 14 days post-weaning, with daily clinical assessments and rectal swabs collected every other day. In a nested case–control design, we profiled 140 samples from 41 piglets that developed PWD and 82 samples from 16 piglets that remained healthy by 16S rRNA sequencing. Additionally, we performed shotgun metagenomics on 56 pre-diarrhoeic samples from susceptible piglets and 47 from resilient piglets. A random-forest classifier with recursive feature elimination identified metagenome-assembled genomes (MAGs) predictive of resilience or susceptibility, trained and cross-validated independently within each farm. Negative binomial zero-inflated mixed (NBZIM) models assessed associations with known PWD risk factors (e.g. birth/weaning weights, weaning age and dam parity).<br><br>RESULTS: Prior to diarrhoea onset, microbial community structures differed significantly between resilient and susceptible piglets at both farms (PERMANOVA, p&#x2009;<&#x2009;0.05). Feature-reduced models achieved high accuracy (AUC&#x2009;=&#x2009;0.94 and 0.82 in Farm A and Farm B, respectively) and identified 10 and 13 MAGs enriched in resilient piglets, and one and two MAGs enriched in susceptible piglets from the two farms, respectively. All MAGs were farm-specific, highlighting the multifactorial aetiology of PWD. NBZIM models indicated that most predictive MAGs were independent of established PWD risk factors. Temporally, these MAGs peaked in relative abundance early after weaning (day 4 in Farm A; day 0 in Farm B). In the farm with unclear aetiology, functional analysis showed that susceptibility-associated MAGs were depleted for arginine/ornithine and vitamin (cobalamin, thiamine) biosynthesis and lactate production traits, suggesting metabolic dysbiosis.<br><br>CONCLUSIONS: Our findings indicate that pre-diarrhoeic faecal microbiome signatures predict PWD risk and provide a foundation for early prognostic tools and targeted interventions, including probiotic development, to mitigate PWD and reduce reliance on antimicrobials in pig production.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00522-3.}, }
@article {pmid41742048, year = {2026}, author = {Zhang, Y and Wangjia, P and Yang, S and Liu, P and Xu, X and Han, H}, title = {Bartonella quintana endocarditis presenting with severe coombs-positive anemia: a case report.}, journal = {BMC cardiovascular disorders}, volume = {26}, number = {1}, pages = {}, pmid = {41742048}, issn = {1471-2261}, support = {XZ202501ZR0145//Natural Science Foundation of Tibet Autonomous Region/ ; XZZR202402030(W)//Natural Science Foundation of Tibet Autonomous Region/ ; XZZR202402105(W)//Natural Science Foundation of Tibet Autonomous Region/ ; }, abstract = {BACKGROUND: Bartonella quintana is a recognized cause of blood culture-negative endocarditis, often associated with predisposing social factors or pre-existing valvulopathy. Diagnosis is challenging and relies on advanced microbiological techniques.<br><br>CASE PRESENTATION: A 17-year-old Tibetan herdsman from a high-altitude region presented with a two-week history of fever, dyspnea, and lower limb edema. He had no history of homelessness or alcoholism but lived in poor sanitary conditions. Laboratory investigations revealed severe Coombs-positive hemolytic anemia and serological markers suggestive of systemic lupus erythematosus (SLE). Transthoracic echocardiography showed vegetations on both aortic (bicuspid) and mitral valves with severe regurgitation and rapid hemodynamic progression. All blood cultures were negative. Metagenomics Next-Generation Sequencing (mNGS) of peripheral blood identified B. quintana as the causative pathogen. Antibiotic therapy was adjusted to doxycycline (9 weeks) and gentamicin (3 weeks). Concurrently, immunomodulatory therapy with methylprednisolone and intravenous immunoglobulin was administered for the hemolytic anemia. Given the severe valvular insufficiency, the patient successfully underwent urgent aortic and mitral valve replacement. His clinical condition improved significantly post-operatively.<br><br>CONCLUSION: This case highlights the diagnostic utility of mNGS in confirming B. quintana endocarditis in a culture-negative scenario, especially when clinical presentation is complicated by concomitant autoimmune features mimicking Libman-Sacks endocarditis. A treatment strategy combining targeted antibiotics for the infection and immunomodulation for the hematologic complication, followed by definitive surgery, led to a successful outcome. It underscores that B. quintana infection should be considered in patients from disadvantaged backgrounds with endocarditis, even in the absence of classic risk factors.}, }
@article {pmid41749306, year = {2026}, author = {Liu, Z and Liu, M and Chen, H and Li, S and Zheng, N and Xing, G and Zhang, Y and Xu, J and Li, M and Xiao, C and Lu, T and Yan, Q and Lei, Z and Feng, M and Li, Y}, title = {Distinct gut virome profiles are associated with response to anti-PD-1 therapy in non-small cell lung cancer.}, journal = {Journal of translational medicine}, volume = {24}, number = {1}, pages = {}, pmid = {41749306}, issn = {1479-5876}, abstract = {BACKGROUND: The gut microbiota is a key modulator of immune checkpoint inhibitor (ICI) efficacy, yet the contribution of the gut virome remains poorly defined, particularly in advanced non–small cell lung cancer (NSCLC). Here, we characterized the gut virome and explored its potential role in shaping response to PD-1 blockade.<br><br>METHODS: We performed metagenomic virome profiling of fecal samples from 338 advanced NSCLC patients treated with PD-1 inhibitors and evaluated model generalizability in an independent external cohort (n&#x2009;=&#x2009;30). Viral diversity, taxonomic composition, and functional potential were analyzed. Virus&#x2013;bacteria co-occurrence networks were constructed, and random forest classifiers were developed to predict treatment response.<br><br>RESULTS: Viral Shannon diversity decreased progressively with poorer clinical response, and &#x3b2;-diversity analyses revealed distinct virome community structures between responders (R) and non-responders (NR). Differential abundance analysis identified 194 NR-enriched vOTUs, predominantly assigned to Peduoviridae and Inoviridae, and 594 R-enriched vOTUs, mainly from Herelleviridae and Microviridae. Host prediction indicated that NR-enriched vOTUs frequently targeted bacterial genera such as Clostridium_M, Bacteroides, and Escherichia, whereas R-enriched vOTUs targeted beneficial genera such as Faecalibacterium and Roseburia. Network analyses further revealed response-specific virus&#x2013;bacteria interaction modules. Functional profiling showed that NR-enriched vOTUs were associated with metabolic functions, including K01689 (eno; enolase). A virus-only random forest model outperformed a bacterium-only model in predicting response (area under the curve [AUC]&#x2009;=&#x2009;0.768 vs. 0.664) and maintained superior performance in the external cohort (AUC&#x2009;=&#x2009;0.742). In addition, Akkermansia muciniphila positivity was associated with a higher-diversity, responder-favorable virome configuration.<br><br>CONCLUSIONS: The gut virome undergoes marked remodeling during anti&#x2013;PD-1 therapy in advanced NSCLC and displays distinct taxonomic, ecological, and functional signatures associated with clinical outcome. These findings support the gut virome as a strong predictor of ICI response and highlight its potential as both a biomarker and a therapeutic target.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07900-0.}, }
@article {pmid41761072, year = {2026}, author = {Costa, J and Pascoal, F and Baptista, MS and Hop, H and Assmy, P and Wold, A and Magalhães, C and Duarte, P}, title = {Comparative analysis of prokaryotic communities, hydrography, and biogeochemistry in Atlantic vs non-Atlantic influenced Svalbard fjords.}, journal = {BMC microbiology}, volume = {26}, number = {1}, pages = {}, pmid = {41761072}, issn = {1471-2180}, abstract = {BACKGROUND: Fjords in Svalbard are undergoing significant changes due to climate warming. Those along the west coast of Spitsbergen are particularly affected by the increasing influence of “warm” Atlantic Water (AW), a process known as Atlantification. We compared Kongsfjorden, a relatively “warm” fjord on the west coast, with Rijpfjorden, a typical cold Arctic fjord on the north coast of Nordaustlandet, combining physical and biogeochemical data with 16S rRNA gene amplicon and shotgun metagenomic sequencing. We hypothesize that differences in fjords’ water masses and prokaryotic communities provide insight into the effects of Atlantification as it expands eastwards along the shelf north of Svalbard.<br><br>RESULTS: We found that warm AW dominated in Kongsfjorden, whereas Rijpfjorden was dominated by cold Arctic Water and Winter Cooled Water. Our results suggest that the Atlantic-influenced Kongsfjorden is a nutrient sink, whereas Rijpfjorden showed similar behavior only in 2016, a particularly warm year, otherwise no clear sink/source role could be identified. Analysis of 16S rRNA gene sequences revealed that Proteobacteria had higher relative abundances in Kongsfjorden while Bacteroidota dominated in Rijpfjorden. Ammonium and nitrite-oxidizing prokaryotes were most prevalent in deeper water masses of both fjords. The archaeal taxa of the ammonia-oxidizing community, mainly Nitrosopumilus and Nitrosopelagicus, were consistently more dominant than ammonium and nitrite-oxidizing bacteria. Denitrification and nitrogen fixation genes differed between the fjords, with Kongsfjorden having a higher coverage of diazotroph genes.<br><br>CONCLUSIONS: Kongsfjorden and Rijpfjorden displayed distinct hydrographic conditions, with Kongsfjorden being under a stronger influence of Atlantification. Our results suggest that warmer water masses are linked to higher nutrient uptake. The clear association between microbial communities and water masses offers insight into changes driven by Atlantification.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04821-2.}, }
@article {pmid41862737, year = {2026}, author = {Liu, L and Yu, QQ and Zhang, YL and Zhou, JT and Jin, Y and Jiang, CH and Zhuang, S and Wei, J and Li, P and Miao, H and Zhao, YY}, title = {Renal fibrosis is induced by hyperactive Wnt/β-catenin pathway via microbial-mediated tryptophan metabolism-driven AhR signaling in rodents and humans.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {83}, number = {1}, pages = {}, pmid = {41862737}, issn = {1420-9071}, support = {82274079//National Natural Science Foundation of China/ ; 82274192//National Natural Science Foundation of China/ ; 82474062//National Natural Science Foundation of China/ ; LHZSZ25H270001//Natural Science Foundation of Zhejiang Province/ ; 2023-ZDLSF-26//Key Science and Technology Program of Shaanxi Province/ ; }, abstract = {UNLABELLED: Renal fibrosis is a common pathological endpoint in progressive chronic kidney disease (CKD). Clinical evidence indicates that a decline in renal function is more closely associated with tubulointerstitial fibrosis (TIF) than with glomerular injury. Recent advances in multi-omics technologies have provided powerful tools for uncovering unrecognized disease molecular mechanisms. Metagenomic and metabolomic analyses were performed to profile the fecal microbiota and serum metabolites, respectively, and to identify tubulointerstitial damage (TID)-related bacterial taxa and metabolites. Identified serum metabolites were also determined in healthy controls and tubulointerstitial nephropathy (TIN) patients. The expression of aryl hydrocarbon receptor (AhR) and Wnt/β-catenin signaling–related genes and proteins was evaluated in obstructed kidney of unilateral ureteral obstruction (UUO) rats and AhR shRNA-treated UUO mice as well as in 1-hydroxypyrene (HP)-stimulated HK-2 cells untreated or treated with AhR shRNA. UUO induced progressive TID and TIF in rats. Alterations in gut microbiota composition, particularly changes in Enterocloster aldenensis (E. aldenensis) and Lactobacillus acidipiscis (L. acidipiscis), were strongly correlated with TID. In parallel, microbial-derived tryptophan catabolites (MDTCs), including tryptamine, indole-3-acetic acid (IAA), indole-3-lactic acid (ILA), indole-3-propionic acid (IPA), indole-3-acrylic acid, indole-3-aldehyde (IAld), and indoxyl sulfate were strongly associated with TID severity. Linear regression analyses revealed correlation coefficients exceeding 0.80 between E. aldenensis and IAA, ILA, and IPA, and between L. acidipiscis and IAld, indicating close relationships with progressive TIF. Similarly, the changes of 14 MDTCs were further demonstrated in TIN patients and they could separate TIN patients form healthy controls. Some MDTCs showed strongly correlation with estimated glomerular filtration rate in TIN patients and high values of area under the curve, sensitivity and specificity. These microbial and metabolic alterations were accompanied by activation of the AhR–Wnt/β-catenin signaling pathway. By contrast, AhR shRNA treatment inhibited mRNA expression of AhR and its downstream target genes, including cytochrome P450 family 1 subfamily A member 1 (CYP1A1), CYP1A2, CYP1B1 and cyclooxygenase-2 accompanied by suppressing nuclear AhR localization, retarded protein expression of Wnt1, β-catenin and Twist, enhanced E. aldenensis and L. acidipiscis abundances and reversed MDTC dysregulation in UUO mice. Bioactivity-directed isolation and identification demonstrated that polyporusterone A (PPA) from Polyporus umbellatus increased abundance of E. aldenensis and L. acidipiscis and normalized dysregulated MDTCs in UUO rats. PPA treatment suppressed intrarenal AhR signaling and Wnt1/β-catenin pathway. Consistent effects were observed in HP-induced HK-2 cells treated with PPA; however, AhR knockdown partially attenuated these inhibitory effects. Taken together, this study first demonstrated that the enrichment of pathogenic bacteria and depletion of probiotics-mediated dysregulation of MDTCs is closely linked to the activation of the AhR–Wnt/β-catenin signaling axis in UUO rat model. Targeting GM may represent a promising therapeutic strategy for CKD and renal fibrosis.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00018-026-06176-3.}, }
@article {pmid41921761, year = {2026}, author = {Nee, GW and Agrawal, K and Dalan, R and Kasahara, K and Xiang Darren, LY and Ali, Y and Wong, S}, title = {The oral-gut microbiome axis in diabetes mellitus: a systematic review and emerging clinical perspectives.}, journal = {Diabetes research and clinical practice}, volume = {}, number = {}, pages = {113232}, doi = {10.1016/j.diabres.2026.113232}, pmid = {41921761}, issn = {1872-8227}, abstract = {Emerging evidence suggests that diabetes mellitus (DM) is not only a metabolic disorder but also a mucosal disease shaped by microbial interactions across body niches. This review synthesizes current evidence on the oral-gut microbiome axis in DM, focusing on microbial transmission, functional overlap, and clinical relevance. A systematic search of six databases identified studies profiling paired oral and gut microbiomes in individuals with diabetes. Across included studies, consistent findings demonstrate concurrent dysbiosis in both niches. Notably, oral-associated taxa such as Streptococcus, Prevotella, Fusobacterium, and Porphyromonas were detected in the gut, suggesting ectopic colonization and inter-niche microbial transmission. Functional analyses revealed shared disruptions in key metabolic pathways, including short-chain fatty acid production and glycine betaine metabolism, with downstream effects on inflammation and insulin resistance. These microbial alterations correlated with established clinical markers such as HbA1c, fasting glucose, and inflammatory indices. Emerging machine-learning models integrating oral and gut microbiota demonstrated promising diagnostic performance (AUC > 0.83). Collectively, these findings support a potential bidirectional oral-gut axis associated with metabolic dysregulation in DM. Despite limitations including cross-sectional design and heterogeneity, this axis represents a novel target for biomarker development and therapeutic intervention. Future longitudinal and interventional studies are required to determine causal relationships and clinical utility.}, }
@article {pmid41921901, year = {2026}, author = {Möller, T and Kreft, A and Dennebaum, M and Hess, G and Michel, C and Kriege, O}, title = {Disseminated Strongyloides stercoralis Infection Diagnosed by Metagenomic Next-Generation Sequencing of a Cell-Free DNA blood sample in a Patient with Hematologic Malignancy in Germany: A Case Report.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108668}, doi = {10.1016/j.ijid.2026.108668}, pmid = {41921901}, issn = {1878-3511}, abstract = {BACKGROUND: Rare infections that are atypical for Central Europe are increasingly relevant due to global migration, climate change, and the widespread use of immunosuppressive therapies. Diagnosing such infections is often delayed or missed entirely because conventional testing relies on prior clinical suspicion and region-specific test panels. Hypothesis-free metagenomic next-generation sequencing (mNGS) offers a promising diagnostic strategy in these cases.<br><br>CASE PRESENTATION: We report a case of disseminated Strongyloides stercoralis (S. stercoralis) infection with hyperinfection syndrome in a man undergoing B-cell-depleting lymphoma therapy. The patient presented with gastrointestinal and pulmonary symptoms, weight loss, and eosinophilia. Conventional microbiological and serological testing failed to identify a cause. Diagnosis and relevant bacterial and fungal coinfection was established using mNGS (DISQVER&#xae;) from blood-derived cell-free DNA. Treatment with ivermectin and albendazole led to rapid clinical improvement, and the patient recovered completely.<br><br>CONCLUSION: This case illustrates the diagnostic challenges posed by rare infections in immunocompromised patients in non-endemic regions. It highlights the growing need for broad, rapid, and hypothesis-independent diagnostic tools such as mNGS, which can play a key role in identifying unexpected pathogens and guiding early targeted therapy in high-risk populations.}, }
@article {pmid41921920, year = {2026}, author = {Yang, MT and Qin, Y and Xu, C and Leng, X and Li, XM and Hou, QY and Sun, YZ and Zhao, Q and Liu, S and Tang, LY and Ma, H and Chen, BN and Zhang, XX and Li, ZY and Ni, HB}, title = {Virulence and Antimicrobial Resistance Profiling of Klebsiella pneumoniae Isolated from Foxes in Northern China.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108476}, doi = {10.1016/j.micpath.2026.108476}, pmid = {41921920}, issn = {1096-1208}, abstract = {Klebsiella pneumoniae is a significant opportunistic pathogen in animal farming. To investigate the occurrence of K. pneumoniae and associated antimicrobial resistance risk in foxes, this study collected 350 fecal samples from foxes across five northern Chinese provinces. A total of 163 K. pneumoniae isolates were recovered (isolation rate: 46.57%), and all isolates were classified as multidrug-resistant (MDR). All isolates were resistant to azithromycin and sulfisoxazole, with high resistance to enrofloxacin (98.16%), ciprofloxacin (87.12%), and tetracycline (70.55%). Resistance to tigecycline and polymyxin B was lower. Notably, all isolates were susceptible to meropenem. Antimicrobial resistance gene (ARG) analysis revealed high carriage rates of tet(E), aac(3)-IIa, and qnrS, alongside the colistin resistance genes mcr-1 and mcr-8. Whole-genome sequencing of 66 isolates revealed substantial genetic diversity: 45 sequence types (STs) were identified among 64 typeable isolates, with ST35 and ST603 being the most common (5/64, 7.81% each), and lineages previously reported in human clinical settings (e.g., ST307 and ST15) were also detected; however, no direct cross-host transmission was evaluated in this study. Capsular types KL22 (10/64, 15.63%) was the most common. Metagenomic analysis further showed that the fox gut microbiome harbored diverse ARGs, with 29 ARGs detected in both K. pneumoniae isolates and fox gut resistome datasets (descriptive overlap). Among these, 20 genes (e.g., blaCTX-M-55 and aac(3)-IIa) were located on predicted plasmids or transposons, suggesting potential mobility rather than confirmed transfer. Conjugation assays provided limited proof-of-concept evidence for plasmid-mediated transfer of tet(A) and tet(E). Collectively, these findings suggest that farmed foxes may serve as potential reservoirs of MDR K. pneumoniae and transferable resistance determinants, supporting the need for continued surveillance and prudent antibiotic use within a One Health framework.}, }
@article {pmid41922261, year = {2026}, author = {Adebayo, AA and Babalola, OO}, title = {Rhizosphere Microbiome as an Underexplored Resource for Agroecosystem Sustainability: Insights From the Carrot Root Zone.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70325}, doi = {10.1111/1758-2229.70325}, pmid = {41922261}, issn = {1758-2229}, support = {CRP/ZAF22-93//International Centre for Genetic Engineering and Biotechnology/ ; }, mesh = {*Daucus carota/microbiology/growth &amp; development ; *Rhizosphere ; *Plant Roots/microbiology ; *Microbiota ; *Soil Microbiology ; Agriculture ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; }, abstract = {Rhizosphere microbiome is critical for nutrient turnover, pathogen suppression, and stress modulation, forming the basis of microbial products relevant to agriculture. However, microbial communities associated with carrot root zone remain relatively underexplored, with limited studies focused beyond descriptive surveys. Here, we synthesise existing information on the structural, functional, and ecological dynamics of the carrot rhizomicrobiome, highlighting its emerging yet underdeveloped mechanistic profiling. Existing literature indicates that carrot-associated microbes may play a role in nutrient mobilisation, growth promotion, and antagonism. The early proof-of-concept works demonstrate that the microbes may gain potential applications in biofertilizers, biostimulants, and biocontrol agents. While these functions are strongly influenced by soil properties, genotype, and management, only a few carrot-specific isolates/consortia have been multi-environmentally validated. The limited progress partly reflects the overall underrepresentation of vegetables in microbiome-based studies, compared to other major crops. We explored the key characteristics, economic, and agricultural significance of the carrot rhizosphere, highlighting its richness with beneficial microorganisms. Among the gaps identified are inadequate functional-level and field trial, and insufficient multi-omics integration, which currently limit biotechnological translation. Addressing these gaps through targeted isolation, mechanistic functional and field validation could position carrot rhizosphere microbiome as a valuable yet underexplored resource for enhancing agroecosystem sustainability.}, }
@article {pmid41922337, year = {2026}, author = {Doni, L and Trinanes, J and Bosi, E and Vezzulli, L and Martinez-Urtaza, J}, title = {Deciphering the Hidden Ecology and Connectivity of Vibrio in the Oceans.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71231-3}, pmid = {41922337}, issn = {2041-1723}, abstract = {Long-range dispersals of marine bacteria in the oceans have remained largely indecipherable, which is particularly relevant for Vibrio, responsible for global epidemics in humans and animals. Here, we combine the analysis of 40 terabases of metagenomic data and satellite-tracked surface drifter data, from across the globe revealing that Vibrio are abundant members of the ocean surface and show a strong association with microplankton, which appears to govern their distribution and connectivity at a global scale. We identify long-distance biological corridors connecting Vibrio communities, including potentially pathogenic Vibrio. These corridors allow movement over thousands of kilometres in a fairly short time, with estimates of less than 1.5 years to cross an ocean basin. These findings have deep implications for the demography and community dynamics of Vibrio species and the epidemiology of associated diseases.}, }
@article {pmid41922358, year = {2026}, author = {Korchagina, MV and Mullin, CE and Soufi, HH and Lambert, S and Moran, IG and Porch, R and Albright, SE and Doran, AS and Jones, LM and Malamud, N and Jin, Q and Wood, AM and Louca, S}, title = {Genome-resolved metagenomic survey of 500 samples from 56 hot springs across the Western US.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07139-w}, pmid = {41922358}, issn = {2052-4463}, abstract = {Hot springs are natural laboratories for studying microbial diversity, evolution, and adaptation to extreme environments. Despite their abundance across the Western US, information about the functional and genomic structure of inhabiting microbial communities is restricted to a handful of locations. Here we present a dataset of 500 deep metagenomes, totaling 3.38 terabasepairs and collected from 56 remote hot springs across the US Great Basin and Yellowstone, with 25 of the hot springs surveyed annually over 4 consecutive years. Additionally, we present 780 bacterial and archaeal metagenome-assembled genomes (MAGs) binned from these metagenomes, with completeness ≥80% and contamination ≤5%, of which 149 are considered "high quality". Many of the MAGs likely represent entirely novel genera and even families, relative to the Genome Taxonomy Database. Our spatiotemporally extensive dataset yields insight into the microbial functional structure at dozens of previously unstudied locations, substantially expands our repertoire of extremophile microbial genomes, provides a new resource for high-temperature biotechnology, and enables future phylogenomic studies of these communities through space and time.}, }
@article {pmid41923365, year = {2026}, author = {Merritt, B and Ratcliff, JD and Ta, S and Osis, G and Mauldin, MR and Thielen, PM}, title = {TaxTriage: An Open-Source Metagenomic Sequencing Data Analysis Pipeline Enabling Putative Pathogen Detection.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag119}, pmid = {41923365}, issn = {1367-4811}, abstract = {MOTIVATION: TaxTriage is a comprehensive pathogen identification workflow designed for both short- and long-read untargeted DNA and RNA sequencing data. Combining read classification, mapping, and de novo assembly approaches, putative pathogens are identified through comparisons to curated pathogens and abundance expectations from healthy cohort data. Flexible installation options are enabled using Nextflow™ (NF), including cloud deployment via NF Tower (Seqera Platform) and local installation on a variety of systems, including standalone installations without external internet access. Final analysis summaries are compiled into an Organism Discovery Report, which lists likely pathogens and supporting data, including a custom confidence score.<br><br>RESULTS: Evaluation of published in silico, clinical, and outbreak datasets identified performance comparable to alternative cloud-based processing pipelines for expected pathogen and co-infection detection with similar sensitivity and increased specificity. To support both public health and veterinary diagnostics communities, customization options have been incorporated to enable improved performance for host species of interest.<br><br>Source code for TaxTriage is freely available at https://github.com/jhuapl-bio/taxtriage. TaxTriage v2.1.1 has been archived on Zenodo at https://zenodo.org/records/17081354 to permit reproducible analysis as described in this manuscript.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid41923466, year = {2026}, author = {King, Z and Buckley, HL and Lear, G and Seale, B and Lee, KC and Schwendenmann, L and Lacap-Bugler, DC}, title = {Comparative Amplicon and Shotgun Metagenome Profiling of Soil Microbial Communities in Kauri Forests Affected by Phytophthora agathidicida.}, journal = {Environmental microbiology reports}, volume = {18}, number = {2}, pages = {e70324}, doi = {10.1111/1758-2229.70324}, pmid = {41923466}, issn = {1758-2229}, support = {C09X1817//New Zealand's Biological Heritage/ ; //Ministry of Business, Innovation and Employment/ ; }, mesh = {*Phytophthora/genetics/isolation &amp; purification ; *Soil Microbiology ; New Zealand ; RNA, Ribosomal, 16S/genetics ; *Metagenome ; Forests ; *Microbiota ; Plant Diseases/microbiology/parasitology ; Metagenomics ; Bacteria/classification/genetics/isolation &amp; purification ; Nucleic Acid Amplification Techniques ; Phylogeny ; }, abstract = {Soil-borne pathogens can influence microbial communities and ecosystem function, making it important to understand their broader ecological impacts. We investigated interactions between Phytophthora agathidicida (the causal agent of kauri tree dieback) and soil microbial communities, while also comparing detection and community-profiling methods. Soils from 60 kauri trees across three sites in the Waitākere Ranges, New Zealand, were analysed using loop-mediated isothermal amplification (LAMP) for pathogen detection, and 16S rRNA gene/ITS gene amplicon sequencing alongside shotgun metagenomics for community characterisation. LAMP detected P. agathidicida in 39/60 samples, while shotgun sequencing detected Phytophthora-associated DNA at low abundance across all samples. Microbial community structure and functional potential showed weak association with pathogen presence, though differential abundance testing identified several genera enriched in pathogen-detected soils, including taxa previously linked to disease suppression. Amplicon and shotgun profiles indicated broadly comparable patterns at higher taxonomic and functional levels, while differences between approaches emerged primarily at finer taxonomic resolution. Importantly, functional predictions from PICRUSt2 closely matched shotgun-derived profiles at broader scales, indicating its suitability as a cost-effective tool for broad-scale monitoring. These findings suggest limited direct pathogen effects on microbial communities and highlight how integrating molecular approaches provides complementary insights into soil microbiome-pathogen interactions.}, }
@article {pmid41923582, year = {2026}, author = {Menezes, GA and Sekar, P and Akhter, A and Tayade, KD and Fathima, S and Hussain, ZFZ and Nigam, A}, title = {Gut Microbiota and Dyslipidemia in Type 2 Diabetes: A Pilot Study of 16S rRNA Profiles and Predicted Functional Shifts.}, journal = {Journal of diabetes research}, volume = {2026}, number = {1}, pages = {e9317962}, doi = {10.1155/jdr/9317962}, pmid = {41923582}, issn = {2314-6753}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/microbiology/complications/blood ; Pilot Projects ; Middle Aged ; *Dyslipidemias/microbiology/blood ; Male ; *RNA, Ribosomal, 16S/genetics ; Female ; Aged ; Adult ; Bacteria/genetics/classification ; }, abstract = {Hyperlipidemia is a major, modifiable driver of global cardiovascular risk. The intestinal microbiota, comprising bacteria, archaea, fungi, and viruses, modulates lipid metabolism through bile acid transformation, energy harvest, and inflammatory signaling. This study profiled the gut microbiota of 15 adults with type 2 diabetes mellitus (T2DM) and explored associations with fasting lipid measures using 16S rRNA gene sequencing (V3-V4 region) on the Illumina MiSeq platform and PICRUSt2 functional prediction. Overall α-diversity was reduced, and community composition was dominated by Firmicutes and Actinobacteria with relative depletion of Bacteroidetes. At lower taxonomic ranks, enrichment of Prevotella copri, Collinsella spp., Ruminococcus spp., and selected Bifidobacterium spp. was observed, alongside depletion of short-chain fatty acid (SCFA)-linked taxa, including Akkermansia muciniphila, Lactobacillus plantarum, and members of the Bacteroides and Parabacteroides lineages. Exploratory within-cohort trends indicated that higher triglycerides (TGs) and lower HDL-C tended to co-occur with increased Collinsella and clostridial signals and reduced SCFA-associated taxa. Predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog functions suggested shifts in lipid, carbohydrate, and secondary bile acid metabolism, consistent with a metabolically activated and proinflammatory intestinal milieu. In this single-arm cohort of adults with T2DM, a low-diversity, Firmicutes/Actinobacteria-weighted microbiome with depletion of SCFA-linked taxa paralleled an atherogenic lipid profile, supporting an association between gut microbial dysbiosis and lipid abnormalities in adults with T2DM. These findings suggest the potential of microbiota-informed adjuncts, including dietary fermentable fiber, targeted probiotics and next-generation biotherapeutics, and bile-acid-modulating strategies as supportive approaches to lipid management in T2DM. This was a pilot, single-arm, exploratory study without a nondiabetic control group, and findings should be interpreted as hypothesis-generating. Nevertheless, the cross-sectional design, small sample size, and 16S-based taxonomic resolution limit causal interpretation. Larger, longitudinal studies integrating shotgun metagenomics and metabolomics are needed to confirm these associations, validate biomarkers, and elucidate mechanistic pathways that could guide precision interventions for diabetic dyslipidemia.}, }
@article {pmid41923636, year = {2026}, author = {Xiong, C and Delgado-Baquerizo, M and Liang, J and Wang, J and Yan, Z and Jensen, SO and Gao, M and Sáez-Sandino, T and Guirado, E and Muñoz-Rojas, M and Román, R and Maestre, FT and Singh, BK}, title = {Soil microbial diversity associates with lower prevalence of human bacterial pathogens across global soils.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2026.03.011}, pmid = {41923636}, issn = {1934-6069}, abstract = {Soil-inhabiting pathogens threaten human health, but their biogeography and associations with soil biodiversity remain poorly understood. Here, we present global patterns of dominant human bacterial pathogens by integrating 1,602 soil metagenomes from 59 countries across continents. We show that dominant human pathogens are more prevalent (i.e., relative abundance) in wet (tropical and temperate) ecosystems and are particularly abundant in cropland soils. We find a global negative association between soil microbiome diversity and pathogen prevalence. We further reveal a significant and positive correlation between the abundance of dominant human pathogens and both disease virulence and global patterns of mortality associated with infectious diseases. Many dominant pathogens are likely to increase their proportion under global change scenarios. Our work provides a global atlas of dominant soil-inhabiting human pathogens and reveals their biogeography and ecology. These findings can guide the development of effective surveillance and risk management strategies to reduce outbreaks and pandemics.}, }
@article {pmid41923798, year = {2026}, author = {Ibisanmi, TA and Jiang, X and Willcox, M and Kumar, N}, title = {Recent advances in computational antimicrobial peptide discovery through big data, modeling, and artificial intelligence and their interplay in ushering the next golden era of drug development.}, journal = {Frontiers in bioinformatics}, volume = {6}, number = {}, pages = {1749404}, pmid = {41923798}, issn = {2673-7647}, abstract = {The accelerating antimicrobial resistance (AMR) crisis continues to render more and more conventional antibiotics ineffective. Antimicrobial peptides (AMPs) are promising alternatives to traditional antibiotics due to their broad-spectrum activity, diverse mechanisms of action, and lower propensity for resistance. Traditional discovery approaches face limitations arising from the vast sequence space and the challenge of balancing efficacy with low toxicity. Addressing these challenges is critical for developing next-generation antimicrobial agents, and computational methods are increasingly driving progress. Public repositories, and techniques such as molecular docking enable in silico evaluation of peptide target interactions, identifying candidates with strong binding potential. Molecular dynamics (MD) simulations offer deeper insights into how AMPs disrupt membranes, form pores, or act synergistically, while Steered MD extends this to probing membrane penetration. Artificial intelligence (AI) methods, including machine learning and deep learning, capture complex sequence activity relationships, predict novel AMPs from genomic and metagenomic data, and design new peptides de novo using generative models. Despite rapid advances, most existing reviews treat these approaches in isolation, leaving a fragmented understanding of their interplay. This paper addresses that gap by unifying computational strategies, highlighting synergies, and critiquing limitations. Ultimately, integrating these methodologies offers a path toward more efficient AMP discovery to fight AMR.}, }
@article {pmid41923934, year = {2026}, author = {Dhawi, F and Alsanie, SI}, title = {Contrasting leaf transcriptomic responses to drought and heat stress in the desert CAM species Mesembryanthemum forsskalii.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1805066}, pmid = {41923934}, issn = {1664-462X}, abstract = {INTRODUCTION: Dryland ecosystems are increasingly exposed to extreme heat and prolonged water limitation. Facultative crassulacean acid metabolism (CAM) enables certain desert plants to enhance water-use efficiency and adjust carbon assimilation under stress conditions. Mesembryanthemum forsskalii Hochst. ex Boiss. (Aizoaceae; locally known as Samh) is a hyper-arid adapted species native to Saudi Arabia, yet genomic and transcriptomic resources for this plant remain scarce. This study aimed to generate foundational genomic resources and characterize transcriptional responses to drought and heat stress.<br><br>METHODS: We integrated rhizosphere metagenomics and leaf transcriptomics. A genome-resolved rhizosphere metagenome was generated from mature field-grown plants. In parallel, micropropagated plants were exposed under controlled conditions to progressive drought (17 days without irrigation) or acute heat shock (55 &#xb0;C for 120 min), each compared with well-watered controls. RNA sequencing generated 123.77 Gb raw data and 121.96 Gb clean reads after quality filtering. Differential gene expression was identified using thresholds of |log2FC| &#x2265; 2 and FDR &#x2264; 0.05, followed by transcription factor profiling and KEGG pathway annotation.<br><br>RESULTS: Heat stress induced substantially broader transcriptional reprogramming than drought. A total of 1,348 genes were differentially expressed under heat stress, compared with 84 genes under drought. Heat exposure strongly increased the expression of transcription factor families including B3 (20.00-fold relative to drought), bHLH (22.65-fold), and bZIP (8.94-fold). KEGG pathway analysis revealed expanded representation of metabolic pathways under heat, including secondary metabolite biosynthesis, ribosome function, carbon metabolism, and endoplasmic reticulum protein processing. Rhizosphere binning recovered archaeal and bacterial genomes affiliated with stress-tolerant lineages, providing the first microbial genomic framework associated with M. forsskalii.<br><br>DISCUSSION: These results demonstrate a heat-dominant transcriptional response in M. forsskalii and provide the first integrated transcriptomic and rhizosphere metagenomic resources for this desert facultative CAM species. Heat-inducible transcription factors, particularly B3 and NAC families, emerge as promising targets for improving thermotolerance and water-use efficiency in crops.}, }
@article {pmid41924127, year = {2026}, author = {Booker, AE and Fei, C and Amin, SA and Custer, J and Watkins, K and Yaeger, W and Ahn, SH and Vidyarathna, NK and Burns, A and Klass, S and Glibert, PM and Heil, CA and Schulz, F and Martínez Martínez, J}, title = {Complex viral interactions revealed for the harmful bloom-forming dinoflagellate Karenia brevis.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag051}, pmid = {41924127}, issn = {2730-6151}, abstract = {Karenia brevis regularly forms harmful blooms along the West Florida Shelf that negatively affect marine and terrestrial organisms through toxin production. These blooms impose economic and environmental hardship, driving the need for research to understand the factors influencing their dynamics and to mitigate their impacts. A mostly unresolved issue is the potential role of viruses in bloom termination. We conducted an experiment incubating K. brevis cultures with size-fractionated bloom water samples. Flow cytometry revealed giant virus-like populations (VLPs) in replicate cultures with <1 μm-filtered and <0.2 μm-filtered bloom water. The VLPs' abundance was paralleled by declines in photoefficiency and culture lysis. Metagenomic analyses of the lysates revealed 11 giant virus genomes (35%-100% complete) representing 7 viral operational taxonomic units (vOTUs) within the order Imitervirales (Nucleocytoviricota). Ten of these vOTUs were more abundant in the incubations with <0.2 μm-filtered bloom water, coinciding with the absence or low abundance of algicidal bacteria. The vOTUs and K. brevis cell abundances showed a positive correlation at a coastal site during bloom and nonbloom periods. The most apparent association was to vOTU6, which may owe its competitive advantage to the presence of the auxiliary metabolic genes bacteriorhodopsin, carbonic anhydrase, and dinoflagellate viral nucleoprotein. The metagenomes also contained polinton-like virus (PLV) genomes. Since many PLVs are hypothesized to depend on co-infection with Nucleocytoviricota viruses for their propagation, our results suggest complex viral interactions within K. brevis blooms. Future research to elucidate virus-bacteria-K. brevis interaction mechanisms may be key to understanding bloom dynamics and developing management tools.}, }
@article {pmid41924306, year = {2026}, author = {Batacan, R and Rao, A and Bajagai, YS and Stanley, D and Briskey, D}, title = {Oleoylethanolamide supplementation enriches Akkermansia muciniphila and modulates intestinal barrier function in adults with obesity: A randomized, double-blind, placebo-controlled trial.}, journal = {Gut microbes reports}, volume = {3}, number = {1}, pages = {2622259}, pmid = {41924306}, issn = {2993-3935}, abstract = {Targeted modulation of the gut microbiome represents a promising nutritional strategy to support metabolic and intestinal health in overweight and obese adults. Oleoylethanolamide (OEA) is an endogenous lipid mediator that regulates satiety, lipid metabolism, and inflammation, but its effects on the human microbiome are not well defined. In this randomized, double-blind, placebo-controlled trial, 57 adults with obesity (BMI 30-40 kg/m[2]) received either 300 mg of TRPTI, providing 250 mg/day of OEA (n = 28), or placebo (n = 29) for 12 weeks. Outcomes included shotgun metagenomics, microbiome profiling, intestinal barrier and inflammatory biomarkers, and safety measures. OEA was safe and well-tolerated with no adverse changes in clinical biomarkers. Although overall microbial diversity remained stable, OEA induced selective, health-relevant compositional shifts. Notably, Faecalibacterium prausnitzii and Akkermansia muciniphila were enriched. These changes coincided with functional host benefits, including increased occludin at Week 12 and interleukin-2 at Week 6, while reducing interleukin-1β, consistent with improved epithelial barrier dynamics and reduced inflammation. Functional pathway analysis suggested enhanced microbial metabolic and redox capacity. These findings indicate OEA supplementation selectively enriches beneficial gut bacteria - particularly A. muciniphila, while improving gut barrier biomarkers and immune function without disrupting microbiome stability. These findings position OEA as a safe, targeted microbiome-modulating ingredient with potential applications for supporting gut and metabolic health.}, }
@article {pmid41924310, year = {2026}, author = {Chen, X and Wang, N and Jiang, C and Luo, S and Cheng, M and Chu, D and Hu, C and Zhang, P and Chen, K and Yang, F and Xiong, J and Ning, K and Miao, W}, title = {Data Mining of Sediment Microbiomes of the Tibetan Plateau Revealed a Genomic Repository of Ancient Lineages and Adaptive Evolution of Asgardarchaeota.}, journal = {Research (Washington, D.C.)}, volume = {9}, number = {}, pages = {1213}, pmid = {41924310}, issn = {2639-5274}, abstract = {The extreme climatic conditions of the Tibetan Plateau foster unique microbial communities, especially in the sediment ecosystem. A thorough understanding of these communities could facilitate revealing their microbial diversity, biological resources, and response to climate change. Here, we have constructed the Tibetan Plateau Microbial Catalog of Sediment (TPMC-S) based on 248 metagenomic sediment samples from the Tibetan Plateau. We identified 511,056,752 nonredundant genes and recovered 13,696 metagenome-assembled genomes with enormous phylogenetic novelty (over 90% novel species), far exceeding other contemporary Tibetan microbial catalogs and expanding the microbial functional diversity. We also revealed that similarities of sediment microbial communities followed the distance-decay relationship. Furthermore, sediments contained a high proportion of evolutionarily "possible ancient species (PAS)" compared with paired aquatic samples, especially ancient archaeal lineages, suggesting a microbial "sedimentary archive" in sediment. Finally and most importantly, Asgardarchaeota, including 2 potentially novel genera, were identified from the sediments, and their latest divergence predated the uplift of the Tibetan Plateau, while they still gained functions to adapt to extreme environments. Our findings positioned the Tibetan Plateau as both a genomic repository of microbial antiquity, especially Asgardarchaeota, and an active arena for modern extremophile innovation, providing insights for deciphering microbial resilience strategies in climate-sensitive ecosystems and informing novel bioprospecting efforts.}, }
@article {pmid41924424, 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 = {Correction: 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 = {1817909}, doi = {10.3389/fcimb.2026.1817909}, pmid = {41924424}, issn = {2235-2988}, abstract = {[This corrects the article DOI: 10.3389/fcimb.2026.1751074.].}, }
@article {pmid41924426, year = {2026}, author = {Pan, Y and Du, N and Liu, Y and Wu, M and Hao, S and He, Y and Jiang, Y}, title = {Clinical features of Tropheryma Whipplei in pediatric pneumonia: an mNGS and tNGS-based case-control study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1753963}, pmid = {41924426}, issn = {2235-2988}, mesh = {Humans ; Case-Control Studies ; Male ; Female ; *Tropheryma/genetics/isolation &amp; purification ; Child, Preschool ; Child ; Infant ; Bronchoalveolar Lavage Fluid/microbiology ; Metagenomics ; High-Throughput Nucleotide Sequencing ; *Whipple Disease/microbiology/pathology ; *Pneumonia/microbiology ; Mycoplasma pneumoniae/isolation &amp; purification ; Coinfection/microbiology ; Adolescent ; }, abstract = {INTRODUCTION: Tropheryma whipplei (TW), which causes Whipple disease, has recently been associated with respiratory diseases, particularly pneumonia. To understand its role in pediatric pneumonia, this study analyzed the clinical and pathogenetic characteristics of TW in pediatric pneumonia patients.<br><br>METHODS: We utilized metagenomic and targeted next-generation sequencing (mNGS/tNGS) data from 3,759 pediatric bronchoalveolar lavage fluid (BALF) samples (2023-2024). This case-control study included 103 TW-positive pediatric pneumonia patients (59 with severe pneumonia, SPTW+; 44 with mild pneumonia, MPTW+), along with 206 TW-negative pneumonia patients as controls (118 with severe pneumonia, SPTW-; 88 with mild pneumonia, MPTW-).<br><br>RESULTS: Through inter-group comparisons, the results showed that TW-positive patients were younger and had lower BMIs than controls, with shorter hospital stays and milder inflammation. Severe TW-positive cases showed more localized right-lung lesions, less pleural effusion, and more bronchial involvement. Mycoplasma pneumoniae co-detection was frequent (86.4%), along with Moraxella catarrhalis, human bocavirus type 1, and rhinovirus A.<br><br>DISCUSSION: TW-positive pediatric pneumonia presents with milder symptoms, suggesting that TW may act as a colonizer rather than a primary pathogen. Consequently, antimicrobial treatment specifically targeting TW may not be immediately warranted at detection. These results provide important insight for the individualized treatment of pediatric pneumonia with TW positive.}, }
@article {pmid41925105, year = {2026}, author = {Zu, S and Yu, X and Song, J and Xiao, Y and Yi, H and Li, H}, title = {The Role of Gut Microbiota and Their Derived Metabolites in Chemotherapy-Induced Nausea and Vomiting in Ovarian Cancer.}, journal = {Cancer medicine}, volume = {15}, number = {4}, pages = {e71752}, doi = {10.1002/cam4.71752}, pmid = {41925105}, issn = {2045-7634}, support = {2023QH1193//Startup Fund for Scientific Research, Fujian Medical University/ ; YCXH 22-10//Nursing Research Special Fund of Fujian Maternal and Child Health Hospital/ ; }, mesh = {Female ; *Gastrointestinal Microbiome ; Animals ; Humans ; Rats ; Middle Aged ; *Ovarian Neoplasms/drug therapy ; Rats, Sprague-Dawley ; *Vomiting/chemically induced/microbiology/metabolism ; *Nausea/chemically induced/microbiology/metabolism ; Dysbiosis/microbiology ; *Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Cisplatin/adverse effects/administration &amp; dosage ; Metabolomics ; Fecal Microbiota Transplantation ; Aged ; Carboplatin/adverse effects/administration &amp; dosage ; Feces/microbiology ; Paclitaxel/adverse effects/administration &amp; dosage ; Metabolome ; Adult ; }, abstract = {OBJECTIVE: This study aimed to investigate the relationship between gut microbiota and chemotherapy-induced nausea and vomiting (CINV) in patients with ovarian cancer undergoing platinum-based chemotherapy (carboplatin or cisplatin combined with paclitaxel).<br><br>METHODS: Clinical data and fecal samples were collected from patients with ovarian cancer after admission but prior to the initiation of their first chemotherapy cycle. Patients were divided into the CINV (n&#x2009;=&#x2009;25) and non-CINV (n&#x2009;=&#x2009;25) groups on the basis of symptoms occurring after chemotherapy. No additional samples were collected during chemotherapy. Integrated metagenomic sequencing and untargeted metabolomic profiling identified CINV-associated microbial taxa and metabolites. Additionally, fecal microbiota transplantation (FMT) in SD rats validated causal links between gut dysbiosis and CINV pathogenesis.<br><br>RESULTS: Bacteroides caccae, Corynebacteriales, and Corynebacterium were significantly enriched in the CINV group. KEGG enrichment revealed upregulated pathways in CINV, including focal adhesion, lysosome function, and eukaryotic cellular communities. Metabolomic analysis identified 19 significantly increased metabolites in the fecal samples of CINV patients versus 10 in non-CINV controls. KEGG enrichment revealed that the pentose phosphate pathway, glutathione metabolism, and lipoic acid metabolism were significantly implicated in CINV pathogenesis. Multi-omics integration revealed Bacteroides sp. A1C1 strongly correlated with hesperetin, arbutin, orciprenaline, and myristolic acid. In rats, cisplatin-induced CINV models showed higher kaolin consumption versus controls (p&#x2009;<&#x2009;0.05). FMT from non-CINV donors reduced kaolin consumption in cisplatin-treated rats (p&#x2009;<&#x2009;0.05). The expression of 5-HT3R, NK1R, and NK2R in the medulla oblongata and colon was significantly increased in the cisplatin model group (p&#x2009;<&#x2009;0.05) and partially reversed by non-CINV FMT (p&#x2009;<&#x2009;0.05).<br><br>CONCLUSIONS: Gut microbiota dysbiosis directly contributes to CINV pathogenesis. Bacteroides sp. A1C1 and its putatively identified metabolites (hesperetin, arbutin, orciprenaline, and myristolic acid) represent potential diagnostic biomarkers for CINV.}, }
@article {pmid41925202, year = {2026}, author = {Leibovitzh, H and Krongauz, D and Schlesinger, Y and Cohen, NA and Hirsch, A and Ron, Y and Thurm, T and Godneva, A and Weinberger, A and Segal, E and Maharshak, N}, title = {Phage-display immunoprecipitation sequencing reveals distinct antibody signatures against bacterial flagellins associated with treatment response in Crohn's disease.}, journal = {Clinical and translational gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.14309/ctg.0000000000001030}, pmid = {41925202}, issn = {2155-384X}, abstract = {OBJECTIVES: Enhanced immune response against bacterial flagellins among patients with Crohn's disease (CD) is associated with aggressive disease course. However, its association with response to biologic treatment is unknown. We aimed to assess whether treatment response among patients with CD is associated with antibody reaction to bacterial flagellins and related microbial alterations.<br><br>METHODS: Thirty-nine patients with active CD (Harvey-Bradshaw Index [HBI]>4 or fecal calprotectin [FCP]>150&#x3bc;g/g) commencing biologic treatment were included. Serum and stool samples were collected at baseline and during treatment at weeks 14, 22 and 52. Serum samples were analyzed using high-throughput phage-display immunoprecipitation sequencing (PhIP-Seq) and fecal samples by DNA shotgun metagenomic sequencing.<br><br>RESULTS: Using PhIP-Seq analysis, only the anti-flagellin antibodies library showed consistently attenuated antibody responses against bacterial flagellins in patients achieving remission (HBI&#x2264;4 and FCP&#x2264;150) versus non-remission at all time points (p<0.05). Of the 55 anti-flagellin antibodies analyzed, 15 showed consistent >1.5-fold over-representation in non-remission samples, with high conservation of amino-acid sequences and targeting of Clostridiales, Lachnospiraceae, or Roseburia species. Remission was associated with increased abundance of flagellin-target taxa including Roseburia intestinalis and decreased Ruminococcus_B gnavus and pathways involved in cellular oxidative stress, while non-remission showed increased Bacteroides species and pathways involved in 5-aminoimidazole ribonucleotide and semi-essential amino acids biosynthesis (q<0.05).<br><br>CONCLUSIONS: PhIP-Seq revealed that biologic treatment response in patients with CD associates with consistently decreased antibody responses against specific bacterial flagellins with conserved sequences. These findings identify potential biomarkers and therapeutic targets for improving treatment outcomes.}, }
@article {pmid41925227, year = {2026}, author = {Deng, F and Han, Y and Peng, Y and Xu, Z and Yang, J and He, J and Li, D and Dong, G and Zhang, P and Jiang, H and Chai, J and Wang, C and Zhao, J and Li, Y}, title = {Microoxic conditions promote Escherichia-associated cellulase expression in the giant panda gut.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag068}, pmid = {41925227}, issn = {1751-7370}, abstract = {Giant pandas possess a carnivore-like gastrointestinal tract yet subsist on bamboo, and their gut communities contain few canonical cellulolytic taxa. We investigated how fiber processing proceeds in this setting by building a species-resolved reference and linking community features to cellular transcriptional profiles and isolate phenotypes. Using culturomics and PacBio HiFi metagenomics, we assembled a species-resolved reference catalog for the panda gut microbiome (Pbac v2; 466 species-level genomes). Community profiling across 142 samples resolved three enterotypes dominated by Escherichia coli (ET-Ecoli), Clostridium SGBP116 (ET-Clos), and Streptococcus alactolyticus (ET-StreA), with ET-Ecoli enriched for tricarboxylic-acid and respiratory-chain modules and showing higher abundance of an endo-β-1,4-glucanase marker. Droplet-based microbial single-cell RNA-seq from four samples (16 659 cells) assigned a substantial share of cellulase-associated transcripts (GH1/GH3/GH5/GH9) in situ to Escherichia and revealed within-species heterogeneity: E. coli subpopulations segregated into respiration-enriched versus three-carbon/anaerobic-like programs, with cellulase/LPMO-linked transcripts concentrated in the former. Guided by these associations, panda-derived E. coli isolates assayed under defined atmospheres showed oxygen-dependent cellulolytic readouts in vitro. Although in vivo oxygen levels were not measured, the convergence of species-resolved community signatures, single-cell attribution and isolate phenotypes indicates that E. coli can contribute to cellulose processing under microoxic conditions in this cohort. The Pbac v2 resource and the integrated workflow (culturomics + HiFi metagenomes, multi-omics, microbial scRNA-seq) provide a template for species-level assignment of microbiome functions in hosts with unconventional diet-physiology combinations.}, }
@article {pmid41926886, year = {2026}, author = {Hoang, HG and Chacha, WE and Binh, QA and Mukherjee, S and Jiang, Y and Zhang, T and Van Tung, T and Tran, HT and Naidu, R}, title = {Biotechnologies for removal of per- and polyfluoroalkyl substances (PFAS) in biosolids: Current status and challenges.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129237}, doi = {10.1016/j.jenvman.2026.129237}, pmid = {41926886}, issn = {1095-8630}, abstract = {Per- and polyfluoroalkyl substances (PFAS), widely recognized as "forever chemicals," pose significant environmental management challenges due to their persistence, mobility, and bioaccumulative behavior. Biosolids derived from wastewater treatment plants represent an important pathway for PFAS redistribution into terrestrial environments, particularly through land application. This review provides a comprehensive assessment of the global distribution, environmental behavior, toxicity, and biodegradation potential of PFAS in biosolids. A bibliometric analysis was conducted using the Web of Science database, and keyword co-occurrence mapping with VOSviewer was applied to evaluate research trends from 2018 to 2024. The findings indicate that research activity is concentrated in China (31%), Europe (30%), and North America (16%), with limited data available from South America, Oceania, and Africa, highlighting regional knowledge gaps. The environmental fate of PFAS in biosolids is governed by pH, temperature, redox conditions, and organic matter content, which influence sorption-desorption processes, mobility, and long-term persistence in soils. Biodegradation pathways include anaerobic reductive defluorination and aerobic oxidative transformation. Certain bacterial genera, such as Dehalobacter spp. and Gordonia spp., have demonstrated degradation efficiencies approaching 80-90% under optimized laboratory conditions. Fungal-mediated oxidative processes may further promote partial mineralization through enzymatic defluorination. In phytoremediation systems, long-chain PFAS preferentially accumulate in plant roots, whereas short-chain compounds exhibit greater mobility and translocation potential. Emerging remediation strategies integrating metagenomics, functional gene characterization, and enzyme-based treatments show promise for enhancing PFAS attenuation. However, substantial uncertainties remain regarding long-term bioaccumulation, biomagnification, and regulatory risk thresholds. Addressing these gaps is essential for developing science-based management strategies for PFAS-contaminated biosolids and protecting environmental and human health.}, }
@article {pmid41926891, year = {2026}, author = {Duan, P and Guan, Y and Zhang, J and Han, Z and Li, H and Wang, S and Kong, F and Cui, Y}, title = {Enhanced performance and mechanism of nano-iron-nickel modified substrate in the treatment of compound antibiotic wastewater in constructed wetland.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129455}, doi = {10.1016/j.jenvman.2026.129455}, pmid = {41926891}, issn = {1095-8630}, abstract = {Nano zero-valent iron nickel (nZVI/Ni) was loaded on the walnut shell activated carbon (AC) and its spheres (ACS) to prepare nZVI/Ni-ACS and nZVI/Ni/AC-SAS composites. These were applied in constructed wetlands (CWs) to construct a "substrate-microorganism" synergistic system for treating tetracycline (TC) and sulfamethoxazole (SMX) in livestock and poultry wastewater. Adsorption experiments determined the optimal mass ratios were ACS:Fe:Ni = 2:1:0.05; AC:Fe:Ni = 1:1:0.05; nZVI/Ni/AC:SA = 6:1. At 500 μg/L influent concentrations, TC and SMX removal efficiencies in CWs with modified substrates (CW-LA: 86.96%/87.79%; CW-LB: 89.88%/86.94%) significantly exceeded gravel (CW-G: 26.07%/55.28%) and ACS (CW-Z: 39.90%/67.56%) systems. Mechanistically, the modified substrates strongly adsorbed TC and SMX, while Fe and Ni acted as electron donors and catalysts to drive their chemical reduction and stimulate biological co-metabolism. Metagenomic analysis revealed that the TC/SMX removal mechanisms were associated with an increased abundance of antibiotic-resistant microorganisms (Methanothrix, Desulfobacter, Thauera, Geobacter, Pseudomonas), which benefited efficient antibiotic degradation, while their immobilization within the tightly bound EPS (TB-EPS) matrix effectively minimized ecological risks. This study provided critical data for the enhanced CW treatment of TC and SMX in livestock and poultry wastewater by modified substrates.}, }
@article {pmid41736165, year = {2026}, author = {Wei, C and Chen, Z and Wang, Y and Huang, L and Chen, C}, title = {Large-scale genomic analysis of jumbo phages: coevolution, genome architecture, and host interaction mechanisms.}, journal = {Animal microbiome}, volume = {8}, number = {1}, pages = {}, pmid = {41736165}, issn = {2524-4671}, support = {32272831//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Jumbo phages are phages with comparatively large genome sizes. Jumbo phages have been identified in various microbial communities. However, their diversity, genome structure, potential function, and their interactions with hosts and other phages are largely unknown due to insufficient genomic data.<br><br>RESULTS: We collected 59,652,008 putative viral genomes from seven habitats by using 38 public metagenome datasets, an integrated public viral genome database (IGN), and pig gut viral genome databases. We obtained 10,754 jumbo phage genomes with sizes ranging from 200 to 831&#xa0;kb. Most (94.64%) of these jumbo phage genomes were classified into Caudoviricetes, and the results have expanded the known diversity of Caudoviricetes. We found 2,389 species-like operational genome clusters that contained 3,727 (34.69%) genomes without any known viral genomes in the IGN, suggesting potential novel species-like genomes. Genome analysis suggested the potential coevolution of jumbo phages with habitat types and highlighted the utilization of alternative genetic codes and their corresponding suppressor tRNAs for recoding stop codons. CRISPR spacer analysis revealed potential bacterial or archaeal hosts of jumbo phages and uncovered competitive networks among jumbo phages. Habitat type had an important effect on the variation in phage auxiliary metabolic genes.<br><br>CONCLUSIONS: This study provides an important resource and new knowledge for future studies on the interaction between jumbo phages and their bacterial or archaeal hosts.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00534-z.}, }
@article {pmid41915473, year = {2026}, author = {Zhao, Y and Li, J and Han, K and Chen, L and Zhuang, Q and Li, S and Hua, M and Li, N and Yue, J and Gu, C and Rong, C and Yang, D and Deng, Z and Huang, J and He, L and Zeng, H and Yu, Z and Chen, C}, title = {Phage-related symbiosis and antagonism shape gut ecosystem dynamics in Lachnospiraceae and Bacteroidaceae.}, journal = {Cell reports}, volume = {45}, number = {4}, pages = {117166}, doi = {10.1016/j.celrep.2026.117166}, pmid = {41915473}, issn = {2211-1247}, abstract = {The human gut microbiota is shaped by intricate, yet poorly resolved interactions among bacteria, as well as their relationship to bacteriophages. However, resolving this complex interaction and dynamics has been limited by the challenges in genome recovery and functional characterization. We develop culture-enriched metagenomic co-barcoding sequencing (cMECOS), obtain 5,006 high- or medium-quality (HMQ) metagenome-assembled genomes (MAGs) and reconstruct bacteria-phage interaction networks via CRISPR spacer mapping. This framework uncovers two ecologically distinct, inter-specific bacterial networks: a Lachnospiraceae-dominated community associates with temperate phages and is characterized by metabolic cross-feeding and a Bacteroidaceae-dominated community linked to virulent phages and marked by resource competition. Both network architectures are disrupted in both inflammatory bowel disease (IBD) and obesity (OB), underscoring their role in ecosystem stability. Our work establishes cMECOS as a powerful platform for deciphering complex microbiome interactions and identifies phage-related bacterial networks as critical regulators of gut homeostasis, providing a foundation for phage-informed therapeutic development.}, }
@article {pmid41915526, year = {2026}, author = {Xiao, Z and Wei, A and Jia, Y and Zhao, W and Jiang, X}, title = {Semantic fusion of dual perspectives on genomic sequences and quorum sensing for bacteriophage lifestyle prediction.}, journal = {IEEE journal of biomedical and health informatics}, volume = {PP}, number = {}, pages = {}, doi = {10.1109/JBHI.2026.3679001}, pmid = {41915526}, issn = {2168-2208}, abstract = {As the most ubiquitous and abundant viral community, bacteriophages (phages for short) play a vital role in regulating the ecological balance by infecting bacteria and archaea. Phages can be classified into two types based on their lifestyles: virulent phages and temperate phages, which are closely related to their functional characteristics and influence their interaction patterns with hosts. Therefore, identifying phage lifestyle is critical for understanding the mechanisms by which phages infect bacteria and represents a key step in mastering their functions and potential applications. In this paper, we propose a novel method for phage lifestyle identification by considering two perspectives. One perspective is based on the genomic sequences of phages, in which both local and global semantic features are integrated. The other perspective focuses on the host quorum sensing phenomena that influence phage lysogen-lysis decisions. Specifically, we first capture local sequence variation patterns by extracting the relative positional information of nucleotide fragments at different intervals, which enables robust representation of local genomic semantics. Secondly, the pretrained nucleotide language model DNABERT is applied to capture the semantics of genome sequences by considering the global contextual information. Finally, combined with quorum sensing signals from the bacterial host, a final fusion representation is obtained, which is fed into a predictive model to identify the phage's lifestyle. Experimental results show that our method has excellent and stable performance in both phage complete genome and short contigs from metagenomic data. We also investigate early-life viral colonization in the human gut metagenome, further validating the model's generalizability and real-world applicability.}, }
@article {pmid41915541, year = {2026}, author = {Yue, Y and Kang, YJ and Wang, H and Jiang, H and Zhou, H and Jiang, W and Li, K}, title = {Diagnosis of Cat-Scratch Disease by Metagenomic Next-Generation Sequencing.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {}, number = {}, pages = {15303667261435870}, doi = {10.1177/15303667261435870}, pmid = {41915541}, issn = {1557-7759}, abstract = {Cat-scratch disease caused by Bartonella henselae is a worldwide distributed zoonotic disease. Cats are the major reservoirs of B. henselae, and human infection cases are usually resulted from contact with pet cats. In this study, a 49-year-old woman presented to the hospital after 10 days of fever. She also complaint lymph node enlargement and pain. Laboratory tests indicated liver dysfunction and inflammation. Pathological examination of the lymph node suggested the possibility of cat-scratch disease, and then doxycycline was used. Metagenomic next-generation sequencing showed that 59496 sequences of B. henselae were identified, confirming the diagnosis of cat-scratch disease. Meanwhile, Acinetobacter towneri and Epstein-Barr virus were also identified. Doxycycline therapy was continued, and the enlargement of lymph node was apparently alleviated. Epidemiological investigation showed that she had a pet cat, and she was possibly infected through direct contact with the cat. Cat-scratch disease in China may be an underestimated disease. Although multiple methods for detecting B. henselae have been established, low bacteremia is still a key challenge to molecular diagnosis. mNGS is a preferable choice for the diagnosis of cat-scratch disease due to its feasibility, sensitivity, and timeliness.}, }
@article {pmid41916285, year = {2026}, author = {Makumbi, JP and Leareng, SK and Bezuidt, OK and Coelho, LP and Makhalanyane, TP}, title = {Persistence of high-risk antimicrobial resistance genes in extracellular DNA along an urban wastewater-river continuum.}, journal = {Cell reports}, volume = {}, number = {}, pages = {117128}, doi = {10.1016/j.celrep.2026.117128}, pmid = {41916285}, issn = {2211-1247}, abstract = {Inadequate wastewater treatment can drive the spread of antimicrobial resistance (AMR), threatening ecosystems and human health. Extracellular DNA (exDNA) stabilizes antimicrobial resistance genes (ARGs) in the environment and facilitates horizontal gene transfer, yet its taxonomic structure and influence on AMR ecology remain poorly understood, especially in African aquatic systems. We profile exDNA-associated resistomes across nine South African wastewater treatment plants and receiving rivers, comparing single-stage activated sludge process (ASP-only) and combined ASP-biofilter systems. exDNA harbors high-risk mobile ARGs conferring resistance to last-resort antibiotics, with enrichment in effluents and downstream rivers. Surprisingly, upstream river samples also carry abundant ARGs, indicating cumulative inputs from multiple environmental reservoirs. ARGs are mainly associated with Pseudomonadota and Bacteroidota, suggesting that exDNA constitutes an ecologically distinct AMR reservoir dominated by key taxa. These findings underscore the need to integrate exDNA into AMR surveillance and highlight its broader role in microbial adaptation within freshwater environments.}, }
@article {pmid41917109, year = {2026}, author = {Foresto, L and Radaelli, E and Leuzzi, D and Palladino, G and Scicchitano, D and Bejaoui, S and Turroni, S and Rampelli, S and Santolini, C and Pari, A and Marcellini, F and Danovaro, R and Corinaldesi, C and Candela, M}, title = {Metagenomic profiling reveals distinct signatures of pathogens, antibiotic-resistance genes and human viruses in urban river mouths of the north-western Adriatic coast.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-45229-2}, pmid = {41917109}, issn = {2045-2322}, }
@article {pmid41917329, year = {2026}, author = {Sun, Y and Hu, X and Han, J and Wang, Y and Luo, J and Yu, J and Duan, Y and Wang, X and Liu, J}, title = {Rapid and noninvasive artificial intelligence-assisted diagnostic method for oral squamous cell carcinoma.}, journal = {NPJ digital medicine}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41746-026-02527-3}, pmid = {41917329}, issn = {2398-6352}, support = {Grant No. 82272815//The National Natural Science Foundation of China/ ; Grant No. 62322114//The National Natural Science Foundation of China Outstanding Youth Fund/ ; Grant No. YG2023LC06//The Medical Engineering Cross Foundation of Shanghai Jiao Tong University/ ; }, abstract = {Oral squamous cell carcinoma (OSCC) remains the most common head and neck malignancy, for which early detection is critical yet challenging with current invasive methods. This study aimed to establish a comprehensive diagnostic framework for OSCC by integrating proton transfer reaction-time-of-flight mass spectrometry (PTR-TOF-MS) breath analysis and metagenomic sequencing with artificial intelligence (AI). Exhaled breath and saliva samples were collected from participants in a discovery cohort (n = 222) and an external validation cohort (n = 83). Samples were analyzed using PTR-TOF-MS and metagenomic sequencing, and multimodal diagnostic models were constructed and trained on the discovery cohort data. We identified OSCC-specific biomarkers, including methanethiol and Fusobacterium nucleatum, and developed an interactive online platform (https://bio.futurecnn.com/) enabling real-time predictions and biomarker interpretability. The AI-driven diagnostic model achieved excellent accuracy (ROC-AUC: 0.92) in distinguishing OSCC patients from healthy controls in the external set. This approach offers a practical, noninvasive solution for OSCC screening and establishes an adaptable framework for other breath-based diagnostics.}, }
@article {pmid41917792, year = {2026}, author = {Karnachuk, OV and Lukina, AP and Avakyan, MR and Panova, IA and Kadnikov, VV and Beletsky, AV and Mardanov, AV and Novikov, AA and Scherbakova, VA and Ravin, NV}, title = {A Novel Slowly Evolving Lineage of the Desulforudis Clade From the Deep Subsurface.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70293}, doi = {10.1111/1462-2920.70293}, pmid = {41917792}, issn = {1462-2920}, support = {24-14-00396//Russian Science Foundation/ ; 22-14-00178-&#x420;//Russian Science Foundation/ ; }, mesh = {Phylogeny ; Genome, Bacterial ; Siberia ; RNA, Ribosomal, 16S/genetics ; Evolution, Molecular ; DNA, Bacterial/genetics ; }, abstract = {Endemic to the deep subsurface biosphere sulphate-reducing 'Desulforudis audaxviator' has been called a living microbial fossil due to the high nucleotide sequence identity of its genomes across continents. Evolutionary stasis of this bacterium was established based on the analysis of metagenome assembled genomes, single cell genomes and a single axenic culture. The lack of high-quality reference genomes necessitates efforts to cultivate and isolate pure cultures that could shed light on the hypothetical slow evolution of Desulforudis-clade bacteria deep underground. Molecular signatures demonstrated the presence of Desulforudis-like phylotypes in subsurface environments worldwide. Here we report the isolation of four novel strains of the Desulforudis-clade, all belonging to Desulfosceptrum tomskiensis gen. nov. sp. nov. Four strains of the new species were isolated from deep boreholes in Western Siberia, separated by hundreds of kilometres. Genome comparisons revealed minimal differences between these strains, with average nucleotide sequence identity (ANI) values above 99.9%, low number of SNPs, and near-identical CRISPRs. The bacterium, together with Desulforudis audaxviator BYF[T] gen. nov. sp. nov., deposited in international culture collections, provides a bases for understanding the slow evolution of Bacillota endemic to the deep biosphere.}, }
@article {pmid41918091, year = {2026}, author = {Luo, S and Chen, X and Guo, S and Hu, S and Dong, Z and Geng, J}, title = {Temperature-driven metabolic adaptation in thermophilic microbial communities of Western Sichuan hot springs.}, journal = {BMC microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12866-026-04921-z}, pmid = {41918091}, issn = {1471-2180}, support = {2022YFC26023002//National Key Research and Development Program of China/ ; }, }
@article {pmid41918132, year = {2026}, author = {Gao, L and Fang, BZ and Yang, J and Lian, ZH and Chen, Y and Mohamad, OAA and Xu, QY and Liu, YH and Wu, D and Yuan, Y and Abdugheni, R and Li, MM and Wang, P and Ortúzar, M and Li, XY and Huang, JR and Liu, L and Jiang, HC and Shu, W and Hedlund, BP and Li, WJ and Jiao, JY}, title = {Microbial decomposer diversity and metabolic function during the decomposition of brine shrimp carcasses in a saline lake.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02361-5}, pmid = {41918132}, issn = {2049-2618}, support = {2022B0202110001//Guangdong S&amp;T Program/ ; }, abstract = {BACKGROUND: Decomposition of brine shrimp carcasses has a crucial role in carbon cycling of saline lakes, yet the microbial dynamics remain poorly understood.<br><br>RESULTS: Here we integrated metagenomics, metatranscriptomics, culturomics, metabolomics, and microcosm experiments to investigate microbial community succession and function during brine shrimp (Artemia sp.) carcass decomposition in Barkol Lake, a hypersaline lake in China. A total of 149 metagenome-assembled genomes (MAGs) and 77 pure culture genomes were recovered across 33 phyla, with 72.12% genomes representing species-level novel lineages. Our results reveal diverse bacterial and archaeal taxa, including novel lineages from CG03, T1Sed10-126 and rare archaeal taxa (Asgardarchaeota, Thermoplasmatota, Nanoarchaeota, and Halobacteriota), involved in degradation of biomacromolecules-proteins, carbohydrates, lipids, and nucleic acids-via extracellular hydrolysis, nutrient transport, and intracellular catabolism. These taxa exhibit substrate preferences, rapidly responding to the breakdown of polysaccharides and proteins, followed by lipids and nucleic acids. Hydrolyzed oligomers are further oxidized by various microbes through fermentation, sulfate reduction, and methanogenesis via metabolic handoffs. Additionally, viral auxiliary metabolic genes (AMGs) further enhance microbial host functions, contributing to key ecological processes such as carbon cycling and stress response. A temporally structured microbial decomposer network (MDN) was observed, driving mineralization cascades from fermentation to sulfate reduction and methanogenesis.<br><br>CONCLUSIONS: This study reveals microbial metabolic handoffs and virus-mediated modulation as critical mechanisms for organic matter turnover, expanding the known diversity and function of decomposers in saline ecosystems. Our findings offer new insights into biogeochemical processes in saline lakes and highlight a synergistic microbial decomposer network involving bacteria, archaea, and viruses that collectively drive nutrient cycling during brine shrimp carcass decomposition. Video Abstract.}, }
@article {pmid41918376, year = {2026}, author = {Yuan, H and Guan, T and Yuan, Q and Zeng, Q and Yu, J and Cai, Y and Liu, E and Li, Q and Wang, Y}, title = {Molecular-Microbial Cascades Regulate Organic Phosphorus Mineralization in Lake Sediments.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c15353}, pmid = {41918376}, issn = {1520-5851}, abstract = {Organic phosphorus (Po) mineralization is a major internal source of soluble reactive phosphorus (SRP) in lakes, yet the molecular and microbial mechanisms governing this transformation remain poorly understood. Here, we aim to elucidate these mechanisms by integrating excitation-emission fluorescence spectroscopy, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS), and metagenomics across two contrasting ecological niches in Taihu Lake, namely the Cyanophyta-dominated and macrophyte-dominated regions. We also supplement our results with the findings from a global meta-analysis. We found that fulvic-associated Po (Fu-Po) dominated sedimentary Po inventories, whereas Po extracted with NaHCO3 (NaHCO3-Po) and microbial biomass Po (biomass-Po) exhibited higher decomposition potential. Fluorescence indices indicated increasing lability with depth, and humic-like materials exhibited a higher tendency to be decomposed under anoxia, accompanied by the accumulation of fulvic-like fractions. FT-ICR-MS revealed proteins and lignins as key constituents of humic-associated Po and Fu-Po, supporting their bioavailability, while NaHCO3-Po was enriched in compounds with lipid-like CHOSP formulas, suggesting greater lability. Metagenomics identified phoD as the most abundant phosphatase-encoding gene, with rare but highly connected phoD-harboring taxa emerging as potential keystone regulators alongside abundant functional groups. Across global lake sediments, alkaline phosphatase activity, Po content, and phoD abundance were found to covary positively, and structural equation modeling highlighted Fu-Po as a disproportionate indirect driver of SRP replenishment via phoD-mediated phosphatase activity. These findings reveal a mechanistic cascade linking molecular composition to phoD-mediated enzymatic potential in Po mineralization, identifying Po bioavailability, rather than inorganic phosphorus pools alone, as a critical driver for reducing internal loading. Targeting this pathway could modulate Po mineralization mechanisms in sediments worldwide, offering valuable insights into the management of lake eutrophication under accelerating nutrient pressures.}, }
@article {pmid41918527, year = {2026}, author = {Yang, K and Huang, Y and Gu, L and Li, J and Ma, Y and Gao, P and Qiu, W and Liu, K and Zhang, Y and Liu, H and Xu, J and Xu, J and Liu, T}, title = {Er-Chen Decoction ameliorates metabolic dysfunction-associated steatotic liver disease via gut microbiota-barrier axis-driven hepatic metabolic reprogramming.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1768664}, pmid = {41918527}, issn = {1664-302X}, abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) constitutes a critical global health challenge, with gut-liver axis dysfunction and metabolic endotoxemia serving as key drivers. The traditional Chinese medicinal formula Er-Chen Decoction (ECD) has proven effective in treating metabolic disorders, yet the specific mechanisms by which it modulates gut-liver crosstalk have not been fully elucidated.<br><br>METHODS: A mouse model of MASLD was established via a high-fat diet (HFD). The therapeutic effects of ECD were evaluated using the glucagon-like peptide-1 (GLP-1) receptor agonist semaglutide (SE) as a positive control. A comprehensive analysis of the underlying mechanisms of ECD treatment was conducted by integrating fecal metagenomic sequencing, untargeted serum metabolomic profiling, hepatic transcriptomic analysis, and molecular biology assays.<br><br>RESULTS: Treatment with ECD markedly ameliorated hepatic steatosis, insulin resistance, and hyperlipidemia, demonstrating a therapeutic efficacy comparable to that of SE. Fecal metagenomic analysis indicated that whereas SE predominantly enriched the genus Akkermansia, the relative abundance of Bifidobacterium and Lactobacillus was markedly and specifically elevated following ECD treatment. Serum metabolomic profiling revealed that ECD specifically activated the tryptophan-indole metabolic pathway, as evidenced by elevated concentrations of indoleacrylic acid and indole-3-acetic acid. Correlation analyses established a strong positive correlation between these indole derivatives and the bacterial genera enriched by ECD. Mechanistically, our findings suggest that elevated indoles activate the aryl hydrocarbon receptor (AHR) in the colon, upregulating tight junction proteins ZO-1 and Occludin and restoring intestinal barrier integrity, thereby significantly reducing serum lipopolysaccharide (LPS) levels. In hepatic tissue, the diminished LPS influx alleviated the suppression of DNA methyltransferase 3B (DNMT3B), thereby promoting the epigenetic silencing of the lipid droplet fusion protein CIDEA and inhibiting pathological hepatic lipogenesis.<br><br>CONCLUSION: Our findings elucidate a novel mechanism through which ECD may ameliorate MASLD via the distinctive "gut microbiota-indole-barrier" axis. In contrast to SE, ECD modulates gut microbiota composition to boost indole production and subsequently activate AHR signaling. This activation inhibits endotoxin translocation and induces hepatic DNMT3B-mediated epigenetic reprogramming to reverse hepatic steatosis. These results offer scientific evidence supporting the potential of ECD as an effective therapeutic strategy for MASLD.}, }
@article {pmid41918743, year = {2026}, author = {Schröder Alvarez, L and Conejeros, I and Espinosa, G and Salinas-Varas, C and Ott, B and Weigel, M and Imirzalioglu, C and Fritzenwanker, M and Windhorst, AC and Hain, T and Taubert, A and Hermosilla, C and Wagenlehner, F}, title = {Presence of neutrophil extracellular traps (NETs) in different types of human urinary tract infections (UTI). A pilot study.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1745166}, pmid = {41918743}, issn = {1664-3224}, mesh = {Humans ; *Extracellular Traps/immunology/metabolism ; Female ; Pilot Projects ; Male ; *Urinary Tract Infections/immunology/microbiology/urine ; Middle Aged ; Adult ; *Neutrophils/immunology/metabolism ; Aged ; Biomarkers ; Pyelonephritis/immunology/urine ; Bacteriuria/immunology ; }, abstract = {INTRODUCTION: Activated polymorphonuclear neutrophils (PMN) release neutrophil extracellular traps (NETs) composed of a web-like DNA core, concomitant with nuclear histones, granular peptides and enzymes. NETs in human urine and their potential role in human urinary tract infections (UTI) pathogenesis is still understudied. This pilot study aimed to analyze presence of NETs in urine samples of patients with different types of UTI.<br><br>METHODS: Urine and blood samples were collected from three cohorts: group (A) included females (n = 24) with cystitis (n = 10), pyelonephritis (n = 6), and asymptomatic bacteriuria (n = 8); group (B) composed of males with catheter-associated UTI (n = 20) and a control group (C) consisting of healthy patients of mixed gender (n = 20). NETs in urine samples were confirmed by immunofluorescence-based detection of neutrophil elastase and citrullinated histone. The presence of granular enzymes (myeloperoxidase, cathelicidin), calprotectin (subunits S100A8, S100A9) and CD15[+] PMN were detected by ELISA, western blot and flow cytometry, respectively. To study potential associations of NETs with the respective UTI microbiome, bacterial spectrum of each urine sample was estimated by 16S rRNA gene analysis.<br><br>RESULTS AND DISCUSSION: On average, 23.29% &#xb1; 16.89% of PMN forming NETs were detected in group A [subgroups cystitis (27.72% &#xb1; 17.88%), pyelonephritis (22.75% &#xb1; 12.91%), asymptomatic bacteriuria (18.17% &#xb1; 17.14%)] and 30.63% &#xb1; 17.88% in group B, with no differences observed between UTI groups, including patients with asymptomatic bacteriuria. For the control group (group C), a low incidence of NET-releasing cells was observed (0.32% &#xb1; 1.42%), resulting in a significant difference (p < 0.05) when compared to all UTI groups studied. Furthermore, different NET-phenotypes [i. e. spread NETs (sprNETs), diffuse NETs (diffNETs) and aggregated NETs (aggNETs)] were detected in both UTI groups. The presence of NET-associated proteins was confirmed in all UTI groups, but absent in the control samples. Microbiome analyses revealed a reduced microbial variability within UTI samples with the predominance of the bacterial family Enterobacteriaceae. Overall, PMN-derived NETs were consistently found in all UTI samples, suggesting a role of NETs in diverse UTI pathologies. Future studies should investigate its utility as an inflammatory biomarker in clinical human UTI.}, }
@article {pmid41918857, year = {2026}, author = {Erözden, AA and Tavşanlı, N and Demirel, G and Sanli, NO and Çalışkan, M and Arıkan, M}, title = {MetaPepticon: automated prediction of anticancer peptides from microbial genomes and metagenomes.}, journal = {PeerJ}, volume = {14}, number = {}, pages = {e20990}, pmid = {41918857}, issn = {2167-8359}, mesh = {*Peptides/genetics/pharmacology ; *Antineoplastic Agents/pharmacology ; *Metagenome ; Humans ; *Genome, Microbial ; *Software ; High-Throughput Nucleotide Sequencing ; Algorithms ; Computational Biology/methods ; }, abstract = {BACKGROUND: Anticancer peptides (ACPs) are increasingly recognized as promising therapeutic candidates due to their ability to selectively target cancer cells. However, the systematic discovery of novel ACPs, particularly from high-throughput sequencing datasets, remains hindered by technical and methodological limitations. Current prediction frameworks require pre-extracted peptide sequences, involve manual preprocessing, and yield variable results, which restricts their applicability for large-scale, data-driven discovery.<br><br>METHODS: To address these limitations, we developed MetaPepticon, a modular, end-to-end pipeline for the discovery of ACP candidates from diverse sequencing inputs, including raw genomic, metagenomic, transcriptomic, and metatranscriptomic reads, as well as assembled contigs and peptide sequences. MetaPepticon automates quality control, filtering, assembly, small open reading frame prediction, ACP classification using multiple predictive algorithms, and in silico toxicity filtering.<br><br>RESULTS: MetaPepticon enables scalable and reproducible ACP prediction from raw sequences through integration of multiple predictors within a configurable agreement framework. Applied to 41,171 microbial genomes and 4,072,884 peptides, MetaPepticon identified 10,725 moderate-agreement ACP candidates, including 4,590 novel, non-toxic peptides. MetaPepticon expands the practical applicability of existing ACP prediction methods to high-throughput sequencing data and is freely available at: https://github.com/arikanlab/MetaPepticon.}, }
@article {pmid41918874, year = {2026}, author = {Su, X and Yang, J and Le, Z and Xiao, J and Zhao, D}, title = {Integrative multi-omics analysis reveals probiotic-induced microbiota shifts in women with gestational diabetes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1782744}, pmid = {41918874}, issn = {2235-2988}, mesh = {Humans ; Female ; *Probiotics/administration &amp; dosage ; *Diabetes, Gestational/microbiology ; Pregnancy ; *Gastrointestinal Microbiome/drug effects ; Adult ; Metabolomics/methods ; Metagenomics ; Multiomics ; }, abstract = {INTRODUCTION: Gestational diabetes mellitus (GDM) is a common pregnancy disorder. It is associated with impaired glucose tolerance and insulin resistance, increasing the potential risks for both maternal and fetal complications. GDM is associated with an increased risk of type 2 diabetes later in life. Management is a big issue in maternal health. New work has underscored the role of the gut microbiota in metabolism and immune function. This indicates that probiotics might exert their mode of action through modulating the microbiota and controlling metabolism.<br><br>METHODS: This study employs a multi-omics strategy to assess the impact of probiotic administration on gut microbiota composition, metabolomic profiles, and host gene expression in GDM women. Women with GDM received probiotics for 8 weeks. Metagenomic sequencing quantified alterations of gut microbiota composition and LC-MS provided untargeted metabolomics in serum and urine. Gene expression was analyzed by qRT-PCR in reference to other physiological factors such as insulin signaling, inflammation, oxidative stress, and gut barrier. Data integration was performed using Principal Component Analysis (PCA), Partial Least Squares Discriminant Analysis (PLS-DA), and network analysis, then pathway enrichment analysis was conducted with KEGG and MetaboAnalyst.<br><br>RESULTS: The supplementation of probiotics resulted in a significant change of gut microbiota (Lactobacillus 7.6-fold; Bifidobacterium 6.4-fold). Escherichia/Shigella was reduced. The amounts of short-chain fatty acids (SCFAs), especially butyrate and acetate, were increased 3.1 fold and 2.5 fold, respectively. In a gene expression assessment, the insulin receptor and AKT increased 2.5- and 1.9-fold higher, respectively, indicating greater insulin sensitivity. Levels of TNF-&#x3b1; and IL-6 decreased; however, genes related to gut barrier function (ZO-1, CLDN1) increased.<br><br>DISCUSSION: The administration of probiotic has a great impact on gut microbiome, metabolic activity, and host gene expression in women with GDM. Our data indicate that probiotics may represent a non-invasive and safe treatment for gestational diabetes through enhancing insulin sensitivity, anti-inflammatory environment, and gut health status. Larger confirmatory studies are needed to corroborate these findings and augment future clinical application of probiotics in GDM patients.}, }
@article {pmid41918946, year = {2026}, author = {Hsiao, CC and Chen, CH and Liu, CS and Wang, JY and Lin, CY and Yang, KD and Lee, CH and Lin, TT and Lin, CJ and Tsai, YG}, title = {Airway microbial dysbiosis and oxidative mitochondrial DNA damage in the development of bronchopulmonary dysplasia.}, journal = {ERJ open research}, volume = {12}, number = {2}, pages = {}, pmid = {41918946}, issn = {2312-0541}, abstract = {BACKGROUND: This study investigated the association between airway microbiome composition, oxidative mitochondrial DNA (mtDNA) damage and the development of bronchopulmonary dysplasia (BPD) in preterm infants.<br><br>METHODS: A prospective cohort study enrolled 82 very low birth weight preterm infants (<32&#x2005;weeks' gestation). Tracheal aspirates (TA) were collected at birth and on postnatal day 28. Airway microbial diversity and composition were assessed using 16S rRNA sequencing. Oxidative mtDNA damage was measured using 8-hydroxy-2'-deoxyguanosine (8-OHdG) levels in TA samples. We used PICRUSt2-based metagenome predictions from 16S rRNA gene sequencing of TA samples, with functional pathway annotations based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.<br><br>RESULTS: Infants who developed BPD (n=25) had lower gestational age, birth weight and prolonged ventilatory support (p<0.05). Oxidative mtDNA damage was significantly higher in infants with BPD, particularly in moderate-to-severe cases (p<0.05). BPD was associated with reduced microbial alpha diversity and distinct beta diversity clustering. Infants with BPD exhibited higher relative abundance of Proteobacteria and lower relative abundance of Firmicutes, with enrichment of Stenotrophomonas, Acinetobacter and Serratia (p<0.05). By day 28, KEGG-based functional predictions revealed enrichment in microbial pathways related to bacterial motility proteins, circadian rhythm signalling pathway, MAPK signalling pathway and &#x3b1;-linolenic acid metabolism. Proteobacteria abundance correlated positively with oxidative mtDNA damage (r=0.49, p<0.01).<br><br>CONCLUSIONS: Airway microbial dysbiosis and oxidative mtDNA damage are strongly associated with BPD severity. Targeting oxidative stress and microbiome modulation may offer potential strategies for BPD prevention and management.}, }
@article {pmid41919078, year = {2026}, author = {Fan, Y and Qin, H and Liu, J and Abbas, M and Yang, C and Cheng, H and Dong, X}, title = {Lactobacillus acidophilus alleviates slow transit constipation by modulating 5-HT pathway and gut microbial composition.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1775405}, pmid = {41919078}, issn = {2296-861X}, abstract = {INTRODUCTION: Slow transit constipation (STC) is a chronic disease characterized by delayed intestinal transit and weakened spontaneous contractions of colonic smooth muscle. Current pharmacological treatments are often associated with adverse effects, highlighting the need for safe and more effective therapeutic strategies. This study investigated the potential role of Lactobacillus acidophilus (L. acidophilus) in regulating intestinal motility and alleviating STC, as well as the underlying mechanism.<br><br>METHODS: A humanized mouse model was established by intragastric administration of fecal bacterial suspension from STC patients on alternate days, in order to evaluate the effect of L. acidophilus on constipation. The regulatory effect of L. acidophilus on intestinal motility was evaluated using defecation parameters. Colon histopathology was assessed by hematoxylin-eosin (H&amp;E) staining. Immunohistochemistry (IHC), RT-qPCR, ELISA, and in vitro cell experiments were performed to examine the inflammatory cytokine levels and changes in the 5-hydroxytryptamine (5-HT) signaling pathway. In addition, metagenomic sequencing was used to analyze changes in the intestinal microbial community.<br><br>RESULTS: The results showed L. acidophilus treatment significantly enhanced intestinal peristalsis and maintained the intestinal barrier by up-regulating Occludin expression and down-regulating inflammatory cytokines, including TNF-&#x3b1; and IL-1&#x3b2;, thereby suppressing inflammatory responses. Both in vivo and in vitro experiments showed that L. acidophilus affected the synthesis and release of 5-HT by regulating the expression of TPH1 and the mechanosensitive ion channel Piezo1. Additionally, L. acidophilus reshaped the intestinal microbial community structure and altered the inter-bacterial interaction network, which was closely associated with improved intestinal motility.<br><br>CONCLUSION: Our current research reveals that constipation symptoms by L. acidophilus through the gut microbiota composition, intestinal barrier, and the 5-HT signaling pathway. These findings provide a strong theoretical basis for the development of L. acidophilus as a potential therapeutic strategy for the treatment of STC.}, }
@article {pmid41919237, year = {2026}, author = {Zheng, D and Li, L and Qi, H and Jiao, XF and Wang, K}, title = {Successful azithromycin treatment of Chlamydia psittaci pneumonia in second-trimester pregnancy resulting in term delivery: a case report.}, journal = {Frontiers in pharmacology}, volume = {17}, number = {}, pages = {1780706}, pmid = {41919237}, issn = {1663-9812}, abstract = {Psittacosis pneumonia is a zoonotic infection caused by Chlamydia psittaci (C. psittaci), primarily transmitted via contact with infected avian species. Diagnostic challenges arise from the inherent difficulties of pathogen culture and serological testing, frequently resulting in misdiagnosis or underdiagnosis. Gestational psittacosis, in particular, is a rare but life-threatening condition, with delayed diagnosis conferring risk of severe maternal and fetal complications. We present a case of C. psittaci pneumonia in a 24-week pregnant woman, with the diagnosis confirmed by metagenomic next-generation sequencing (mNGS). Empirical intravenous azithromycin (0.5 g daily) was promptly initiated for 3 days, leading to rapid symptomatic resolution. After a 2-day interruption, targeted oral azithromycin (0.5 g daily) was restarted for an additional 3 days following pathogen confirmation via mNGS. The patient was successfully discharged after a 10-day hospital stay under multidisciplinary management. She finally gave birth to a healthy baby girl at 40 weeks and 3 days of gestation, with favorable maternal and neonatal outcomes. To our knowledge, this represents one of the few reported cases of full-term delivery following azithromycin monotherapy for gestational psittacosis. It provides valuable insights into the diagnosis and management of gestational psittacosis, emphasising the importance of multidisciplinary involvement in preserving maternal and fetal safety.}, }
@article {pmid41919563, year = {2026}, author = {Afridi, R and Ibrahim, M and Yaqoob, M and Ahmad, W}, title = {Synergistic Effect of Glyphosate and Polyethylene Microplastics on Culturable Gut Microbiota Alterations in Zebrafish.}, journal = {Environmental toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1002/tox.70091}, pmid = {41919563}, issn = {1522-7278}, abstract = {The coexistence of emerging pollutants, that is, microplastics (MPs) and pesticides poses significant threat to aquatic organisms. This study investigated the combined effects of polyethylene microplastics (PE-MPs) and glyphosate on the gut microbiome of zebrafish. Following a 21-day exposure, 16S rRNA sequencing revealed that co-exposure caused the most significant disruption, surpassing the individual effects of each stressor. Co-exposure resulted in the lowest alpha diversity and a distinct microbial community structure, characterized by the depletion of A. veronii and a marked enrichment of opportunistic pathogens like A. hydrophila. Clear separation of all exposed groups from controls, with the co-exposure group forming the most distinct cluster was observed in non-metric multi-dimensional scale analysis. Specifically, a higher number of ASVs were differentially abundant in the co-exposure group compared to the individual exposures. In the MPs group, Aeromonas species were markedly replaced by Enterobacter species. Glyphosate significantly enriched A. hydrophila species in the gut. Treatment-specific clustering, with Enterobacter species associated with MPs, and A. hydrophila with glyphosate and co-exposure groups were observed in Heatmap analysis. The findings indicate that microplastics not only act as direct stressors but also as glyphosate carriers, leading to amplified, non-additive shifts in the gut microbiome and posing a heightened ecological risk.}, }
@article {pmid41919955, year = {2026}, author = {Pan, W and Tang, S and Wanek, W and Liu, X and Zhou, J and Gregory, AS and Marsden, KA and Chadwick, DR and Liang, Y and Wu, L and Jones, DL and Ma, Q}, title = {Organic Fertilization Promotes the Microbial Formation of Moderately Active Soil Phosphorus Pools to Sustain Phosphorus Availability: Insights from 180 years of Fertilization.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c12810}, pmid = {41919955}, issn = {1520-5851}, abstract = {Phosphorus (P) fertilization is essential for crop production, but most applied P is rapidly fixed into mineral-associated forms. Although fertilization regulates P distribution in soils, its effects on microbe-mediated processes that regulate P availability and stabilization remain unclear. Here, we investigated P transformations under organic fertilization (FYM), inorganic fertilization (NPK), and no fertilization (NIL) using the 180 year Broadbalk experiment. Through [33]P isotopic tracing, metagenomics, and enzymatic profiling, we found that FYM and NPK stimulate distinct P transformation pathways. FYM, through sustained organic carbon inputs, enhanced microbial immobilization and phosphatase activity, causing a 41% reduction in stable P formation and 47% increase in moderately active P levels and shifting P dynamics toward more bioavailable forms. NPK fertilization reduced pH and limited microbial carbon availability; 33% of [33]P was recovered in the stable P fraction, indicating abiotic immobilization into inorganic P pools. The microbial community under NPK adapted to P fixation by enriching P-cycling-related genes and acid-tolerant taxa, enhancing P turnover relative to NIL but preventing long-term immobilization less effectively than FYM. Thus, organic fertilization maintains P in more biologically available forms and mitigates abiotic P fixation; our research provides a mechanistic foundation for more efficient and resilient P management in agroecosystems.}, }
@article {pmid41919968, year = {2026}, author = {Zhou, C and Wang, S and Zhao, H and Wang, S and Jiang, L and Yu, C}, title = {Metagenomic mining reveals extensive novelty, enhanced biodegradation potential, and untapped biosynthetic capacity in Chinese oilfield microbiomes.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0039226}, doi = {10.1128/aem.00392-26}, pmid = {41919968}, issn = {1098-5336}, abstract = {Oil reservoir microorganisms represent a vast and largely unexplored reservoir of biological diversity and functional potential, yet comprehensive studies on their genomic and metabolic characteristics remain limited. To address this gap, we collected 101 metagenomic sequencing samples from 13 distinct oilfields across China. Through extensive de novo assembly and binning processes, we successfully reconstructed 3,057 medium and high-quality metagenome-assembled genomes (MAGs), providing an unprecedented genomic resource for reservoir microbiome research. Strikingly, 73.77% of these MAGs correspond to novel taxa at the species level, highlighting the significant unexplored microbial diversity in these environments. Detailed genomic analysis revealed that MAGs classified under the class Planctomycetia exhibited notably larger genome sizes, primarily driven by the expansion of specific gene families, suggesting adaptive evolutionary strategies in hydrocarbon-rich environments. Furthermore, we identified 68 genes implicated in anaerobic alkane biodegradation pathways, with samples from the Shengli oilfield demonstrating particularly enhanced biodegradation potential, indicating site-specific functional adaptations. Beyond biodegradation, our study uncovered three MAGs assigned to the genus Tistrella, which harbored a remarkable abundance of biosynthetic gene clusters (BGCs) for secondary metabolites. Additionally, 14 candidate antimicrobial peptides (cAMPs) were detected, signifying the potential for novel bioactive compound discovery. Critically, both the Tistrella MAGs and cAMPs were identified for the first time within petroleum reservoir ecosystems, underscoring the unique biotechnological value of these environments. This research not only expands our understanding of oil reservoir microbial communities but also emphasizes their substantial implications for industrial applications, including bioremediation, antimicrobial development, and sustainable resource management.IMPORTANCEThis study provides a groundbreaking genomic exploration of oil reservoir microbiomes across 13 Chinese oilfields, reconstructing 3,057 medium and high-quality metagenome-assembled genomes (MAGs). Remarkably, 73.77% of these MAGs represent novel species, revealing vast unexplored microbial diversity. We observed genome expansion in Planctomycetia lineages and identified 68 genes involved in anaerobic alkane degradation, with heightened biodegradation potential in Shengli oilfield samples. Crucially, we discovered three Tistrella MAGs rich in biosynthetic gene clusters (BGCs) for secondary metabolites and 14 candidate antimicrobial peptides (cAMPs), both reported for the first time in petroleum reservoirs. These findings highlight the immense biotechnological potential of reservoir microbiomes, offering new pathways for bioremediation strategies in oil-contaminated environments and novel sources for antimicrobial discovery. This work underscores the critical need for continued investigation into these unique ecosystems to harness their functional capabilities for energy sustainability and pharmaceutical innovation.}, }
@article {pmid41920399, year = {2026}, author = {Hoque, MN and Rana, ML and Gilman, MAA and Pramanik, PK and Islam, MS and Punom, SA and Rahman, R and Hassan, J and Rahman, MS and Ramasamy, S and Schreinemachers, P and Oliva, R and Rahman, MT}, title = {Rooftop and surface garden soils in Bangladesh harbor diverse resistome profiles.}, journal = {Environmental monitoring and assessment}, volume = {198}, number = {4}, pages = {}, pmid = {41920399}, issn = {1573-2959}, support = {Grant ID: Proc-451-05//This work was conducted as part of the CGIAR Research Initiative on Resilient Cities Through Sustainable Urban and Peri-urban Agri-food Systems and is supported by contributors to the CGIAR Trust Fund (https://www.cgiar.org/funders)./ ; }, mesh = {*Soil Microbiology ; Bangladesh ; Soil/chemistry ; *Environmental Monitoring ; *Drug Resistance, Microbial/genetics ; Gardens ; Anti-Bacterial Agents ; *Drug Resistance, Bacterial/genetics ; }, abstract = {Despite the growing expansion of urban agriculture, the diversity, composition, and antimicrobial resistance (AMR) profiles (i.e., resistome) of microbial communities in rooftop and surface garden soils in Bangladesh remain insufficiently characterized, limiting our understanding of their potential role as reservoirs and disseminators of AMR. In this study, shotgun metagenome sequencing was applied to 27 soil samples, including 7 from Dhaka rooftop gardens (DRG), 6 from Dhaka surface gardens (DSG), 8 from Gazipur rooftop gardens (GRG), and 6 from Gazipur surface gardens (GSG) to comprehensively characterize their resistome profiles. We identified 88 antibiotic resistance genes (ARGs), of which 19 (21.6%) were shared across all sites, and found significant differences in resistome composition by garden type (p = 0.04). Rooftop soils harbored more ARGs (DRG, 50; GRG, 48) than surface soils (DSG, 40; GSG, 41) and were dominated by glycopeptide resistance genes, collectively representing 62.43-74.07% of ARGs. Rooftop garden soils were also enriched in efflux pumps (adeF, 45.21% of rooftop ARGs) and ribosomal-protection-related oxazolidinone resistance gene O23S (62.13% in GRG). Conversely, surface soils featured a higher abundance of genes mediating antibiotic inactivation, such as CATA (11.64% in DSG) and fosBx1 (5.94% of surface ARGs), as well as those conferring co-resistance to biocides (qacG) and metals. The efflux pump gene adeF also remained a significant component of the surface resistome (24.33% of surface ARGs). Geographic location also modulated resistome composition. Garden soils from Gazipur emerged as notable hotspots, characterized by extremely high abundances of tetracycline efflux pumps (TET45) and multiple copper resistance genes and regulators (e.g., COPA, YCNJ, CSOR). Key ARG carriers included Bacillus licheniformis, B. paralicheniformis, Pseudomonas sabulinigri, and Paenibacillus spp. Spearman correlation analyses revealed strong positive associations (r = 1.0) between specific taxa and resistance mechanisms, as well as co-occurrence patterns among antibiotic, biocide, and metal resistance genes. Collectively, these results indicate that garden soils represent important reservoirs of ARGs, with resistome architecture influenced by both garden type and location, highlighting the necessity for sustainable management practices and a One Health approach to environmental resistome surveillance.}, }
@article {pmid41921236, year = {2026}, author = {Lu, D and Ping, C and Jia, D and Liu, J and Wang, H and Song, Y and Cai, X}, title = {Mechanism of Legionella pneumophila-induced liver injury via gut microbiota translocation under immunosuppression.}, journal = {Pathology, research and practice}, volume = {282}, number = {}, pages = {156456}, doi = {10.1016/j.prp.2026.156456}, pmid = {41921236}, issn = {1618-0631}, abstract = {Legionnaires' disease presents substantial clinical challenges in immunocompromised patients, with the pathogenesis of multi-organ dysfunction remaining poorly understood. Through an immunosuppressed guinea pig model, we demonstrate that Legionella pneumophila (Lp) infection triggers a systemic pathological cascade that extends beyond pulmonary damage. Our results show that Lp infection not only induces severe pulmonary inflammation and endothelial barrier disruption but also initiates gut-liver axis injury mediated by intestinal microbiota dysbiosis. Metagenomic sequencing revealed specific enrichment of Anoxybacillus kestanbolensis and Geobacillus vulcani in both intestinal and hepatic tissues post-infection, indicating microbial translocation. This bacterial dissemination was associated with enhanced hepatocyte apoptosis and exacerbated liver injury. Mechanistically, we demonstrate that Lp infection compromises intestinal epithelial integrity, promotes translocation of enteric pathogens, and subsequently activates hepatic apoptotic pathways, thereby aggravating systemic inflammation and multi-organ failure. These findings elucidate the gut microbiota-gut-liver axis as a pivotal mechanism in Lp-induced systemic damage and suggest potential therapeutic targets for severe Legionnaires' disease in immunocompromised hosts.}, }
@article {pmid41921318, year = {2026}, author = {Wang, F and Shi, C and Zhang, W and Chen, Y and Chen, Z and Yang, S and Zhang, J and Liu, W and Cao, W}, title = {Fresh-seawater interface shapes nitrogen fate in a subtropical estuary: Insights from multi-isotopic and metagenomic analyses.}, journal = {Water research}, volume = {298}, number = {}, pages = {125836}, doi = {10.1016/j.watres.2026.125836}, pmid = {41921318}, issn = {1879-2448}, abstract = {Estuaries, the key transitional interface between freshwater rivers and saline seas, are hotspots of nitrogen (N) cycling processes. In this study, we integrated multi-isotope and metagenomic sequencing techniques to characterize nitrate (NO3[-]) sources, mixing and transformation processes, and the regulatory roles of microbial functional genes in different seasons and subzones in the Jiulong River estuary, a typical subtropical estuary. NO3[-]-N was the dominant form of dissolved inorganic N (70.31-91.70 %), with significantly lower concentrations in the seaward subzone than those in other subzones. Hydrochemical parameters, dual-isotope (δ[15]N-NO3[-] and δ[18]O-NO3[-]) signatures, and MixSIAR model indicated that soil N was the largest contributor to NO3[-] (44.7 %), followed by M&amp;S and groundwater in the riverward subzone. The upstream inflow from the riverward subzone accounted for 64.6 % of NO3[-] sources in the mixing subzone. Extensive aquaculture activities in the estuary were the dominant NO3[-] source (44.8 %), followed by M&amp;S and the upstream inflow from the mixing subzone in the seaward subzone. Nitrate reduction genes dominated the N-cycling functional genes and mediated the primary NO3[-] transformation pathways. The PLS-PM model indicated dissimilatory nitrate reduction to nitrite (DNRN) genes had a significant positive effect (0.892) on NO3[-] concentrations and influenced competition between dissimilatory nitrate reduction to ammonium (DNRA) and denitrification for substrates through the C/N ratios. The lower nosZ/narG ratios and higher nitrous oxide concentrations in the riverward and mixing subzones led to more susceptibility to incomplete denitrification, whereas the higher DNRA/DNRN ratios and the significant positive correlation between DNRA and the C/N ratios favored DNRA in the seaward subzone. The lower temperatures and river flows in winter were significantly lower than those in other seasons, which constrained N transforming capacity and resulted in the lowest dissolved nitrous oxide concentration. Therefore, salinity and temperature regulated the primary N-cycling processes by reshaping the composition of functional genes. Overall, this study clarifies the N sources and transformation pathways and provides a systematic theoretical foundation for the development of subzone-based management strategies for estuarine ecosystems.}, }
@article {pmid41921321, year = {2026}, author = {Sudarshan, AS and Konstantinidis, KT and Pinto, AJ}, title = {Gene-centric analysis of Raskinella chloraquaticus reveals a functionally conserved taxonomic group in global drinking water distribution systems.}, journal = {Water research}, volume = {298}, number = {}, pages = {125784}, doi = {10.1016/j.watres.2026.125784}, pmid = {41921321}, issn = {1879-2448}, abstract = {A recent metagenomic survey of drinking water systems revealed that a highly prevalent and dominant uncultured bacterial genus (Raskinella) was represented globally by a single species (Raskinella chloraquaticus). R. chloraquaticus comprises of two sub-species groups, Lineages 1 and 2, the former representing a globally prevalent genomovar. The objective of this study was to perform comparative analysis of the gene content of R. chloraquaticus to characterize the gene-level diversity and determine factors shaping the diversity of this species. Pangenome analysis revealed that R. chloraquaticus possesses a core set of genes that constitute a major portion (87.74%) of the known gene content of the genome. Furthermore, most of the gene diversity of R. chloraquaticus is associated with Lineage 2 organisms, which consists of at least four distinct genomovars. Lineage 1 organisms consist of a higher proportion of identical genes than would have been expected if changes primarily occurred through random mutations and thus is potentially indicative of recombination. In contrast, Lineage 2 organisms appear to have emerged through random mutations and display stronger geographic preference. These results indicate that homologous recombination and geographic isolation likely shape the genetic repertoire of R. chloraquaticus. Further, the high level of gene conservation in R. chloraquaticus may be reflective of highly selective environment in drinking water systems. Thus, R. chloraquaticus may represent a model organism to probe selective pressures shaping the drinking water microbiome.}, }
@article {pmid41921326, year = {2026}, author = {Liu, X and Li, C and Zhao, Y and Li, X and Zhang, Q and Zhang, L and Peng, Y}, title = {A novel approach for achieving high enrichment of anammox and nitrogen removal rate in municipal wastewater treatment: A pure biofilm process.}, journal = {Water research}, volume = {298}, number = {}, pages = {125838}, doi = {10.1016/j.watres.2026.125838}, pmid = {41921326}, issn = {1879-2448}, abstract = {Against the backdrop of global carbon neutrality goals and increasingly stringent pollutant discharge standards, the anammox nitrogen removal process has gained significant attention due to its high efficiency, energy-saving, and environmentally friendly characteristics. The current mainstream wastewater treatment technologies still encounter challenges in enriching anaerobic ammonium-oxidizing bacteria (AnAOB) and managing the disposal of substantial amounts of residual sludge. The pure biofilm process has garnered significant attention as the primary focus for autotrophic nitrogen removal transformation in wastewater treatment plants (WWTPs), owing to its ability to efficiently enrich AnAOB and produce low amounts of sludge. This study innovatively proposed a novel pure biofilm process and explored the self-enrichment mechanism of AnAOB in this system. Over 200 days of municipal wastewater treatment under a low C/N ratio (average of 3), the effluent ammonia nitrogen removal efficiency (ARE) and total nitrogen removal efficiency (NRE) achieved 97.72 ± 1.50 % and 94.27 ± 2.92 %, respectively. Long-term operation and batch experiments revealed that carbon source regulation is crucial for the performance of pure biofilm systems. Furthermore, the pure biofilm system demonstrates greater resilience to organic loading shocks compared to floc sludge and hybrid systems. QPCR and 16S rRNA sequencing confirmed the successful enrichment of AnAOB (pre-anoxic:8.94 %, post-anoxic:8.61 %), with anammox contributing to an impressive 81.10 % of nitrogen removal. Additionally, fluorescence in situ hybridization combined with confocal laser scanning microscopy (FISH-CLAM) technology demonstrated a spatially uniform distribution of AnAOB within the system, in contrast to hybrid systems. Metagenomic sequencing revealed the carbon and nitrogen metabolic pathways of functional bacteria in the pure biofilm system, showing that AnAOB's metabolic diversity and ecological niche adaptation within the biofilm structure drove their self-enrichment. Finally, microelectrode measurements of N2O production in the pure biofilm system confirmed its substantial potential for emission reduction. This work offers a practical solution for WWTPs aiming to reduce energy consumption and transition from heterotrophic to autotrophic nitrogen removal processes.}, }
@article {pmid41921531, year = {2026}, author = {Li, W and Lv, M and Cheng, M and Han, Y and Yu, H and Huang, Y and Meng, D and Xu, X and Sun, L and Lu, Z and Liu, QL}, title = {Feasibility of Low-Biomass Exhaled Breath Microbiome Sequencing Using a PDC-Sampler in Febrile and Healthy Individuals.}, journal = {Journal of breath research}, volume = {}, number = {}, pages = {}, doi = {10.1088/1752-7163/ae5a51}, pmid = {41921531}, issn = {1752-7163}, abstract = {Exhaled breath is a noninvasive and repeatable biological matrix offering new opportunities for respiratory microbiome analysis, yet its extremely low microbial biomass limits current high-throughput applications. Building on our previously developed phase-change drywall cyclone sampler (PDC-sampler), which integrates condensational growth with dry-wall cyclone separation, we established a validated workflow for efficient aerosol collection and multi-omics sequencing of exhaled breath. Using this platform, exhaled breath from 15 febrile patients and 6 healthy volunteers was analyzed via shotgun metagenomic and 16S rRNA sequencing to assess microbial composition, diversity, and functional features. The PDC-sampler significantly increased microbial DNA yield, enabling stable detection of bacterial taxa dominated by Pseudomonadota, Bacillota, Bacteroidota, and Actinomycetota. Functional annotations and diversity metrics revealed distinct microbial and metabolic patterns between individuals, confirming the platform's analytical sensitivity and biological representativeness. This work experimentally validates the feasibility of exhaled breath microbiome sequencing using the PDC-sampler, providing a practical and generalizable framework for noninvasive respiratory microecology studies and future diagnostic applications.}, }
@article {pmid41912071, year = {2026}, author = {Zhang, PP and Cui, MY and Shen, Y and Han, B and Yu, W and Wei, TT and Zeng, KW and Tu, PF}, title = {Ophiopogon japonicus Polysaccharide Ameliorates Pulmonary Fibrosis via Gut Microbiota-Metabolite Crosstalk.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108464}, doi = {10.1016/j.micpath.2026.108464}, pmid = {41912071}, issn = {1096-1208}, abstract = {Despite the clinical application of Ophiopogon japonicus in idiopathic pulmonary fibrosis (PF), its key anti-fibrotic components and underlying mechanisms remain poorly defined. Using a bleomycin-induced murine PF model, we systematically compared the efficacy of the total extract (OJTE), polysaccharides (OJTP), saponins (OJTS), and flavonoids (OJTF). The active component was further investigated via integrated metagenomics and metabolomics (serum/feces) to decipher the gut-lung axis mechanism. All O. japonicus components attenuated lung injury and collagen deposition, with OJTP demonstrating the most potent efficacy (reducing lung hydroxyproline content by 42.12% (p < 0.01) compared to the model group). Multi-omics analysis revealed that OJTP remodeled the gut microbiota, notably enriching probiotic strains such as Muribaculaceae bacterium (log2FC = 2.17) and Duncaniella muricolitica (log2FC = 2.06), as well as the polysaccharide-utilizing species Prevotella sp. MGM2 (log2FC = 2.79). Concomitantly, OJTP significantly altered host metabolism, upregulating key metabolites including urobilinogen (p < 0.0001) and 5-amino valeric acid betaine (5-AVAB, p < 0.002). These metabolites are implicated in porphyrin and amino acid metabolism, respectively. Correlation networks further established strong associations between these OJTP-modulated microbes and metabolites. Our study first identifies OJTP as the primary bioactive component of O. japonicus against PF. We propose a novel trans-organ mechanism wherein OJTP ameliorates PF via orchestrating a "gut microbiota-metabolite" axis, highlighting the therapeutic potential of targeting polysaccharide-probiotic synergy.}, }
@article {pmid41912361, year = {2026}, author = {Rathwell, C and Fuchsman, CA and Rocap, G}, title = {Hi-C Links Reveal Viral Activity and Infection Within the Free-Living Microbial Community of a Secondary Chlorophyll Maximum in the Eastern Tropical North Pacific.}, journal = {Environmental microbiology}, volume = {28}, number = {4}, pages = {e70274}, doi = {10.1111/1462-2920.70274}, pmid = {41912361}, issn = {1462-2920}, support = {DGE-2140004//National Science Foundation/ ; DEB-1542240//National Science Foundation/ ; OCE-2022911//National Science Foundation/ ; }, mesh = {Pacific Ocean ; *Bacteria/virology/genetics/classification/metabolism ; Phylogeny ; *Chlorophyll/metabolism/analysis ; *Microbiota ; *Seawater/microbiology/virology ; *Bacteriophages/genetics/classification/isolation &amp; purification ; Metagenomics ; }, abstract = {Oxygen-deficient zones (ODZs) influence global nitrogen cycling as key sites for the removal of bioavailable nitrogen through denitrification and anammox. Despite their importance, many microbes and viruses in ODZs remain uncultivated, limiting our understanding of their ecological roles. This study employed Hi-C proximity linkages, combined with long and short read metagenomic sequencing to characterise active viral interactions in the prokaryotic community at a secondary chlorophyll maximum in the Eastern Tropical North Pacific ODZ. Among the identified 861 assembled viral contigs over 10 kb, 75 showed significant links to microbial genomes. Virus-host linkages indicated 19 novel virus-microbe pairs that were likely infectious, and which conventional in silico host prediction methods largely missed. The virus-host relationships involved nine distinct microbial phyla, with previously unrecorded viral infections of Planctomycetes, Chloroflexota, Alphaproteobacteria, Gammaproteobactera, Myxococcota and Verrucomicrobia. Most hosts carried the genomic potential for denitrification. Phylogenetic analysis of the terminase large subunit (terL) genes from linked viruses suggested that many active phages resemble known temperate phages, indicating that lysogeny may be an ecological strategy in ODZs. Our comprehensive metagenomic approach offers new insights into viral-host interactions in this ecosystem, highlighting the importance of including proximity methods in viral ecology studies of uncultivated microbial populations.}, }
@article {pmid41912389, year = {2026}, author = {Wang, YY and Zhang, Q and Zhao, ZF and Zhao, YX and He, Y and Liu, PL and Li, YH}, title = {[Coexistence of lung cancer, brucellosis, and tuberculosis in a single patient: a case report].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {49}, number = {4}, pages = {421-424}, doi = {10.3760/cma.j.cn112147-20260105-00006}, pmid = {41912389}, issn = {1001-0939}, support = {H2024206551//Hebei Natural Science Foundation/ ; 20260411//Hebei Medical Research Project/ ; }, mesh = {Humans ; Male ; Middle Aged ; *Lung Neoplasms/complications/diagnosis ; *Brucellosis/complications/diagnosis ; *Tuberculosis, Pulmonary/complications/diagnosis ; Mycobacterium tuberculosis/isolation &amp; purification ; *Carcinoma, Squamous Cell/complications/diagnosis ; Coinfection ; }, abstract = {Lung cancer, pulmonary tuberculosis, and brucellosis are common clinical diseases. They share overlapping clinical manifestations and pulmonary imaging findings, and all may involve multiple organ systems, making differential diagnosis challenging. We reported a rare case of lung cancer, and co-infection with pulmonary tuberculosis and brucellosis. A 57-year-old male was admitted to our hospital, presenting with intermittent fever for 7 months and cough accompanied by shortness of breath for 1 month. He had previously sought medical care at multiple hospitals, where he was diagnosed with brucellosis and suspected of having pulmonary tuberculosis. Despite receiving anti-tuberculosis and anti-brucellosis treatments, his pulmonary imaging abnormalities and dyspnea progressively worsened. Pathological examination of mucosal biopsies obtained via bronchoscopy and cervical lymph node biopsy at our hospital confirmed squamous cell lung carcinoma. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid detected Mycobacterium tuberculosis. Although his pulmonary condition temporarily improved following standardized anti-tuberculosis treatment and chemotherapy for lung cancer, the lung cancer subsequently progressed, and the patient ultimately died.}, }
@article {pmid41912482, year = {2026}, author = {Shao, Y and Wang, J and Liu, Y and Ni, Y and Liu, Z and Li, Y and Jia, Q and Li, Q and Wang, X and Li, T and Liu, M and Zhang, S and Guo, Y and Guo, X and Wang, D and Liu, Y and Liu, C and Cai, H and Ning, Y and Zhang, J and Xu, G and Le, W}, title = {Distinct metabolomic and proteomic signatures in Parkinson's disease patients with REM sleep behavior disorder.}, journal = {Signal transduction and targeted therapy}, volume = {11}, number = {1}, pages = {}, pmid = {41912482}, issn = {2059-3635}, support = {82271524//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82401742//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024RY003//Dalian Science and Technology Bureau/ ; No. 2023-MS-262//Natural Science Foundation of Liaoning Province (Liaoning Provincial Natural Science Foundation)/ ; }, mesh = {Humans ; *Parkinson Disease/genetics/metabolism/complications/microbiology/pathology/blood ; Female ; Male ; *REM Sleep Behavior Disorder/genetics/metabolism/pathology/blood/complications/microbiology ; *Metabolomics ; Middle Aged ; Aged ; *Proteomics ; Gastrointestinal Microbiome/genetics ; }, abstract = {Rapid eye movement sleep behavior disorder (RBD) is the most specific prodromal marker of Parkinson's disease (PD), affecting 40-50% of PD patients. PD with RBD (RBD-PD) represents a clinically aggressive subtype characterized by more severe motor and nonmotor symptoms, prominent autonomic dysfunction, and accelerated disease progression; however, its underlying pathogenesis remains poorly understood. Here, we integrated multiplatform metabolomics and proteomics with precise clinical phenotyping to delineate molecular signatures in plasma across different PD subtypes. Our analyses demonstrated that PD patients exhibit significant metabolic reprogramming, characterized by a shift in energy metabolism from the tricarboxylic acid cycle toward glycolysis, a dysregulated urea cycle, and lipid remodeling, as well as extensive activation of inflammatory and immune responses involving the PI3K-Akt, IL-17, NF-kappaB, MAPK and TNF signaling pathways. Notably, the RBD-PD subgroup exhibited distinctive metabolic disturbances characterized by the accumulation of gut microbiota-derived toxic aromatic amino acid catabolites. Importantly, these alterations were also observed in idiopathic RBD (iRBD) patients, representing the prodromal stage of PD. By integrating metagenomic profiles, we further revealed that gut microbial dysbiosis in RBD-PD and iRBD drives a functional shift away from dietary fiber fermentation and toward enhanced degradation of protein, aromatic amino acids, glycine, and intestinal mucin glycans. This metabolic reprogramming is associated with exacerbated oxidative stress, neuroinflammation, and accelerated pathological progression. These findings provide multiomic evidence that clarifies the molecular heterogeneity in PD and highlights gut microbiota-driven dysfunction as a key contributor to both the iRBD and RBD-PD subtypes.}, }
@article {pmid41912529, year = {2026}, author = {Achudhan, AB and Narayanan, R and Madhavan, T}, title = {Metagenome Sequencing and Recovery of 52 Microbial Genomes from Plastic-Polluted Coastal Sediment.}, journal = {Scientific data}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41597-026-07068-8}, pmid = {41912529}, issn = {2052-4463}, abstract = {Plastic pollution is an escalating environmental concern, particularly in coastal regions where sediments serve as long-term sinks for plastic debris. Despite this, the microbial communities inhabiting plastic-contaminated sediments remain poorly characterized in highly polluted hotspots. In this study, we conducted a genome-resolved metagenomic investigation of sediment sample from plastic pollution hotspot in India. Using Illumina short-read sequencing and three high-performing binning tools we reconstructed 52 non-redundant metagenome-assembled genomes (MAGs) from 2,374 initial bins. All MAGs met the MIMAG criteria with 15% reaching near-complete genomes. Taxonomic classification revealed diverse representation of 18 different phyla. Interestingly, 90% of the MAGs could only be classified at intermediate taxonomic levels in the Genome Taxonomy Database (GTDB), suggesting the presence of novel microbial lineages. Taxonomic novelty was further confirmed using the Type Strain Genome Server (TYGS), which identified 3 novel orders, 16 families, and 28 genera. This study provides the first comprehensive genomic insight into microbial communities from plastic-polluted coastal sediments in India and lays the groundwork for exploring their ecological functions.}, }
@article {pmid41913056, year = {2026}, author = {Marques, LL and Pinho, AJ and Pratas, D}, title = {FALCON2: compression-based metagenomic classification of ancient viruses.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag155}, pmid = {41913056}, issn = {1367-4811}, abstract = {MOTIVATION: Ancient DNA (aDNA) sequences present unique challenges for taxonomic classification due to extreme fragmentation (reads 20-100 bp), end-biased cytosine deamination, and high contamination rates. Conventional metagenomic classifiers based on exact k-mer matching or alignment lose discriminative power on such short and damaged reads, limiting the analysis of paleogenomic samples.<br><br>RESULTS: We present FALCON2, a compression-based metagenomic classifier that leverages position-aware finite-context models to maintain high accuracy on degraded viral ancient viruses. FALCON2 consolidates the capabilities of its predecessor, FALCON-meta, into a unified executable with enhanced features including model persistence, direct processing of compressed inputs, multiple file handling, and optional pre-filtering methodologies for contaminated samples. Under controlled benchmarking with database, taxonomy, and thread parity on simulated viral datasets, FALCON2 achieved an Area Under the Curve of Receiver Operating Characteristic (AUC-ROC) of 0.999, an Area Under Precision-Recall Curve (AUPRC) of 0.968, and an F1-score of 0.918, substantially outperforming Centrifuge (AUPRC&#x2009;=&#x2009;0.625), Kraken2 (AUPRC&#x2009;=&#x2009;0.184), and CLARK-S (AUPRC&#x2009;=&#x2009;0.013) on pooled micro-averaged metrics. FALCON2's advantage is most pronounced on ultra-short reads (20-40&#x2009;bp), where exact k-mers become sparse. FALCON2 pre-filtering at threshold 0.7 improved precision by 10 percentage points with negligible recall loss. FALCON2 runs on systems with 4-8&#x2009;GB RAM for typical analyses.<br><br>AVAILABILITY: FALCON2 is freely available at https://github.com/cobilab/FALCON2 under GPL v3 license. Benchmarking data and scripts are archived at DOI: https://doi.org/10.5281/zenodo.17291214.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, }
@article {pmid41913289, year = {2026}, author = {Kieri, O and Narayanan, A and Jütte, BB and Svensson, P and Aleman, S and Sönnerborg, A and Ray, S and Nowak, P}, title = {Linking gut microbiome to HIV-1 reservoir size in people living with HIV.}, journal = {Gut pathogens}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13099-026-00828-2}, pmid = {41913289}, issn = {1757-4749}, abstract = {The gut microbiome is altered during HIV-1 infection and contributes to immune dysfunction and inflammation in people living with HIV (PLWH), these changes may persist despite effective antiretroviral therapy (ART). We explored the associations between the fecal gut microbiome and blood HIV-1 reservoir size in PLWH (n = 30) on long-term ART. The intact proviral DNA assay (IPDA) and shotgun metagenomic sequencing were performed to identify microbial species and metabolic pathways associated with the size of the HIV-1 reservoir. PLWH with a smaller intact reservoir exhibited lower evenness compared to individuals with a larger intact reservoir. We found that Phocaeicola plebeius and Lachnospira sp000437735 were significantly enriched in individuals with a smaller intact reservoir and lower intact-to-total proviral ratio, respectively. We observed a negative association between Faecalibacterium prausnitzii and a positive association of Prevotella copri, with the intact proviral reservoir size. Additionally, the metabolic pathways of glycolysis and branched-chain amino acid biosynthesis were enriched in individuals with larger reservoir. HIV reservoir size in blood is associated with gut microbiome evenness, specific metabolic pathways and microbial signatures, including Lachnospira, Prevotella, and Faecalibacterium. Our findings underscore the potential role of the gut microbiome in viral persistence, raising the possibility that modulating microbial composition could influence the HIV reservoir.}, }
@article {pmid41913691, year = {2026}, author = {Erens, J and Heine, C and Lötters, S and Krehenwinkel, H and Crawford, AJ and Rueda-Solano, LA and Plewnia, A}, title = {A Field-Deployable eDNA Metabarcoding Workflow Including De Novo Reference Assembly for Characterising Understudied Biodiversity Hotspots.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70122}, doi = {10.1111/1755-0998.70122}, pmid = {41913691}, issn = {1755-0998}, support = {//Ministerium f&#xfc;r Wirtschaft, Verkehr, Landwirtschaft und Weinbau Rheinland-Pfalz/ ; //Deutsche Gesellschaft f&#xfc;r Herpetologie und Terrarienkunde/ ; //Forschungsfonds of Trier University/ ; //Forschungsinitiative Rheinland-Pfalz through Trier University/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Animals ; *Biodiversity ; *Amphibians/classification/genetics ; *DNA, Environmental/genetics ; Workflow ; *Metagenomics/methods ; }, abstract = {Field-deployable DNA metabarcoding offers a transformative approach to biodiversity research and monitoring, yet its application remains limited due to technical constraints and a lack of reference data in poorly studied ecosystems. Combining isothermal Recombinase Polymerase Amplification (RPA) and Oxford Nanopore sequencing, we introduce a two-step approach that uses non-invasive species barcoding to directly generate reference sequences for use in environmental DNA (eDNA) metabarcoding, and enables real-time, PCR-free and cost-effective molecular assessment of ecological communities in the field. Using an endemic and understudied tropical amphibian assemblage as a model, we demonstrate the functionality of this novel workflow. De novo generation of a reference sequence library from amphibian skin swab samples significantly improved the accuracy and taxonomic resolution of sequence assignments from eDNA samples, particularly on the species level, in turn allowing a characterisation of fine-scale patterns in community composition. Beyond generating new RPA-compatible amphibian metabarcoding primers, our results show that combining field-based eDNA metabarcoding with the offline assembly of a local reference database can directly bridge existing data gaps in molecular biodiversity monitoring, providing a scalable solution to accelerate biodiversity assessments in data-deficient ecosystems. This workflow paves the way for broader deployment of molecular tools in global biodiversity hotspots-particularly in remote and resource-limited tropical regions-to directly contribute critical baseline data, and support conservation efforts in regions where they are most urgently needed.}, }
@article {pmid41913730, year = {2026}, author = {Kwoji, ID and Edwards, W and Ruffell, A and Shaw, D and Denoyelle, C and Figuiredo, A and Guadano-Procesi, I and Makkimane, J and Pantzi, K and Godfrey, A and Gentekaki, E and Stensvold, CR and Kolisko, M and Tsaousis, A}, title = {BlastoDB: first release of a community-driven multi-omics and epidemiological resource for Blastocystis biology and subtyping.}, journal = {Open research Europe}, volume = {6}, number = {}, pages = {65}, pmid = {41913730}, issn = {2732-5121}, abstract = {BlastoDB (https://www.blastodb.com/) is developed as an open-access, community-driven resource dedicated to Blastocystis, one of the most common yet understudied intestinal protists. BlastoDB will offer the scientific community up-to-date, curated information on Blastocystis by integrating epidemiological data, microbiome profiles, multi-omics datasets (genomics, transcriptomics, proteomics, and metabolomics), reference sequences for subtypes, protocols, microscopy images, and related metadata. In this initial release, we describe the data model, database architecture, curation pipelines, and web interface, which together facilitate subtype classification, comparative and integrative analyses, and cross-study synthesis of epidemiological and experimental data. We outline submission and governance workflows designed to support community contributions, training activities, and sustainable curation under the " Blastocystis under One Health" COST Action (CA21105). Finally, we highlight planned extensions, including expanded metagenomic and metatranscriptomic content, automated genome quality assessments, metagenome-assembled genomes, and geospatial and analytical dashboards. BlastoDB provides a central, FAIR-aligned hub for Blastocystis data, images, and protocols, reducing technical barriers and fostering a collaborative ecosystem for studying this globally prevalent protist.}, }
@article {pmid41913758, year = {2026}, author = {Chin, D and Campbell, B and Petersen, J and Lim, SJ and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and ,  and ,  and ,  and ,  and , }, title = {The chromosomal genome sequence of the buttercup lucine, Anodontia alba Link, 1807 (Lucinida: Lucinidae) and its associated microbial metagenome sequences.}, journal = {Wellcome open research}, volume = {11}, number = {}, pages = {131}, pmid = {41913758}, issn = {2398-502X}, abstract = {We present a genome assembly from an individual Anodontia alba (buttercup lucine; Mollusca; Bivalvia; Lucinida; Lucinidae). The genome sequence has a total length of 1 862.85 megabases. Most of the assembly (99.28%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 18.48 kilobases. Gene annotation of this assembly by Ensembl identified 12 083 protein-coding genes. From the metagenome data, we recovered four bins, of which three were high-quality MAGs.}, }
@article {pmid41913906, year = {2026}, author = {Lu, P and Liu, M and Zhang, L and Fan, JJ and Han, G and Hou, B and Meng, Y and Wang, L and Sun, Y}, title = {Gut-Brain Axis Dysregulation in Inflammatory Bowel Disease: Implications for Coagulation Abnormalities and Extraintestinal Manifestations.}, journal = {International journal of general medicine}, volume = {19}, number = {}, pages = {590621}, pmid = {41913906}, issn = {1178-7074}, abstract = {Inflammatory bowel disease (IBD) involves chronic intestinal inflammation driven by gut-brain axis imbalance, fostering complications through an "inflammation-neuro-coagulation" triad. Current staging systems inadequately capture the dynamics of this multidimensional network. Therefore, integrated multi-omics analyses-including metagenomics, metabolomics, and single-cell transcriptomics-are essential to construct dynamic models that monitor coagulation, microbiome, and metabolism for precise assessment of disease activity and thrombotic or bleeding risks. Interventions targeting gut-brain axis nodes, such as eliminating tissue factor-positive (TF[+]) T cells or modulating vagal activity, show potential to disrupt the inflammation-coagulation cycle, although rigorous randomized trials are still needed. Artificial intelligence (AI)-assisted systems that integrate real-time biomarker monitoring with multi-omics predictions represent a novel paradigm for managing IBD-related coagulation dysfunction. Key challenges include elucidating gut-brain-liver axis regulation of coagulation and characterizing platelet functional heterogeneity. Future efforts must prioritize ethically compliant multi-omics platforms and racially stratified risk models to advance personalized coagulation management in IBD.}, }
@article {pmid41914171, year = {2026}, author = {Yildirim, EA and Laptev, GY and Tiurina, DG and Filippova, VA and Ilina, LA and Novikova, NI and Sokolova, KA and Ponomareva, ES and Brazhnik, EA and Zaikin, VA and Klyuchnikova, IA and Bolshakov, VN and Korochkina, EA and Vorobyov, NI and Griffin, DK and Romanov, MN}, title = {Compositional and Functional Metabolic Shifts in the Endometrial Microbiota of Cows (Bos taurus) During the Transition Period: A Metagenomic Next-Generation Sequencing Approach.}, journal = {Frontiers in bioscience (Elite edition)}, volume = {18}, number = {1}, pages = {39439}, doi = {10.31083/FBE39439}, pmid = {41914171}, issn = {1945-0508}, support = {24-16-00131//Russian Science Foundation/ ; }, mesh = {Animals ; Female ; Cattle/microbiology ; *Endometrium/microbiology/metabolism ; *Microbiota ; High-Throughput Nucleotide Sequencing ; *Metagenomics ; }, abstract = {BACKGROUND: Significant alterations in feeding, housing, and physiology are observed in dairy cows during the transition period (3 weeks pre- and post-calving), in addition to changes in the composition and abundance of the endometrial microbiota. Thus, this study aimed to evaluate any changes in the composition and predicted metabolic pathways in the cow uterine microbiome during this transition period.<br><br>METHODS: Scrapings were sampled from the endometrial surface of clinically healthy cows (n = 3) in dynamics as follows: in the 10 Days period before, and on Days 3, 5, and 20 after calving. Total DNA was isolated from the samples, and the composition of the microbial community was assessed using targeted next-generation sequencing (NGS) technology. Based on the subsequent NGS data, the dynamics of the predicted metabolic pathways of the microbiota were evaluated.<br><br>RESULTS: Seven superphyla and phyla of microorganisms were found in the endometrial microbiota of cows during the transition period. Among these, the phylum Firmicutes (with a dominant class of Clostridia) and the superphylum Fusobacteriota (represented by a single class of Fusobacteriia) can be considered the dominant bacteria in the endometrium, with representation noted from 25.2 to 68.2% and from 12.3 to 51.1%, respectively. The microbiome composition underwent significant changes (p < 0.05) during the transition period. In particular, the high abundance of the Fusobacteriaceae family (up to 68.2%) in the uterus of clinically healthy cows was unexpected, given the potential association of Fusobacteriaceae with the occurrence of metritis in cows. The numbers of microorganisms in two dominant classes, Fusobacteriia and Clostridia, showed generally opposite changes in their relative abundance during the transition period. The predicted functional potential level for 32 pathways in the endometrium changed (p < 0.05) in cows during the transition period. Indeed, the activity of the predicted pathways, such as pyridoxal 5'-phosphate biosynthesis I and teichoic acid (poly-glycerol) biosynthesis, was lowered on day 3 postpartum (p < 0.05).<br><br>CONCLUSIONS: Microbiota composition and the activity of the predicted metabolic pathways in the cow endometrium underwent significant changes at different critical stages in the transition period. Moreover, even clinically healthy cows exhibited signs of dysbiotic disorders.}, }
@article {pmid41914631, year = {2026}, author = {Arogundade, AA and Dumaguit, CDC and Melton, A and Buerki, S and Bittleston, LS}, title = {Exploring sagebrush leaf microbial metagenomes from deep, host-derived sequencing.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0219825}, doi = {10.1128/spectrum.02198-25}, pmid = {41914631}, issn = {2165-0497}, abstract = {Advanced sequencing technologies and improvements in bioinformatics have provided a new way to study plant-associated microbial communities, including the use of host genomic sequencing. Our study focuses on the leaf microbiome of basin big sagebrush (Artemisia tridentata subsp. tridentata), a foundational shrub of western North America. We analyzed Illumina shotgun sequences from sagebrush leaves to investigate the metagenomes of leaf-associated microbes that were sequenced alongside their plant hosts. We aimed to profile the leaf microbiome across different sample sources (magenta box, greenhouse, and field/wild), reconstruct metagenome-assembled genomes (MAGs) where possible, and investigate functional gene annotations of the resulting MAGs, specifically with regard to the potential metabolism of sagebrush chemicals. To achieve this, Illumina shotgun sequence reads (containing both host and associated microbial reads) were mapped to the reference genomes of Artemisia tridentata, Artemisia annua, and the human reference genome to remove plant host and human-associated sequences. Host-cleaned reads were then analyzed using microbial metagenomics techniques. Taxonomic profiling revealed that Phyllobacterium and Sphingomonas were the most abundant microbial genera in greenhouse-grown plants, with very little variation among the samples. Wild, field-collected samples were much more variable and were dominated by Klebsiella and Aureobasidium species. From the co-assembly of greenhouse samples, we reconstructed two high-quality MAGs (a Phyllobacterium species and a Sphingomonas species) with >98% completion and <1% contamination. Functional annotation of these MAGs uncovered genes associated with the degradation and metabolism of camphor and other essential oils such as pinene, geraniol, and limonene, which are part of sagebrush leaf chemistry.IMPORTANCEBig sagebrush (Artemisia tridentata), the foundation species of the sagebrush steppe, has broad ecological importance because its evergreen leaves offer nutrients and shade that facilitate the establishment of diverse understory plants in arid environments. Sagebrush leaves contain various secondary metabolites, including terpenoids, flavonoids, and phenolic compounds. These chemicals contribute to the plant's defense mechanisms against herbivores and pathogens. Despite this, sagebrush hosts diverse bacterial and fungal communities. We found that the microbial metagenome-assembled genomes (MAGs) we recovered contained genes that have the potential to degrade some of the chemical compounds in sagebrush leaves that could inhibit the growth of other microbes. This is the first study to mine plant genome data using host-derived sequences to generate microbial MAGs. Our results showed that MAGs can be recovered from plant host-derived sequence data, providing a new way to explore the identity and functional capabilities of difficult-to-culture microbes.}, }
@article {pmid41914733, year = {2026}, author = {Nandi, S and Stephens, TG and Garcia, R and Sánchez-García, M and Roberson, LM and Avalos, JL and Chundawat, SPS and Bhattacharya, D}, title = {Rafts of change: microbial and functional dynamics in simulated Sargassum strandings.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0235725}, doi = {10.1128/aem.02357-25}, pmid = {41914733}, issn = {1098-5336}, abstract = {Massive influxes of pelagic Sargassum spp. across the tropical Atlantic and Caribbean regions have created urgent ecological and economic challenges that need to be addressed to stabilize local ecosystems. Use of this abundant biomass feedstock resource for biorefining and bioproducts manufacturing is a promising avenue, but this goal requires elucidating the microbial processes that regulate Sargassum degradation, which are still poorly understood. Here, we investigated the microbial degradation of the benthic Sargassum filipendula by native microbiota using multi-omics approaches. Metagenomic and meta-transcriptomic analyses identified diverse carbohydrate-active enzymes (CAZymes), including alginate lyases, fucoidanases, and cellulases, that were differentially expressed over the course of the in vitro degradation timeline. Furthermore, we identified the need for arsenic detoxification pathways in microbes utilizing Sargassum-derived substrates. We observed a suite of factors influencing microbial dynamics, including prokaryotic competition, arsenic detoxification, viruses, and substrate availability. Lineages potentially capable of degrading recalcitrant polysaccharides such as fucoidan appeared to be rapidly outcompeted by other bacteria that utilized simpler substrates like mannitol. These results highlight the metabolic potential of native marine microbial communities to degrade complex Sargassum polysaccharides and the importance of the in vitro degradation experiment time scale to capture the activities of non-dominant specialists. Our findings elucidate microbial ecosystem dynamics during Sargassum degradation and provide novel insights that can be used to advance the development of biotechnological approaches that leverage renewable Sargassum biomass as a biorefinery feedstock of the future.IMPORTANCEThis work addresses a crisis in the tropical Atlantic and Caribbean regions, the massive population growth and stranding of the floating brown seaweed Sargassum, which is wreaking havoc on ecosystems and fouling beaches vital to local tourism. One solution to this problem is to utilize the seaweed as feedstock to generate useful bioproducts. This approach requires characterizing the microbiome of Sargassum that drives its degradation in nature. To this end, we devised an in-lab degradation assay using Sargassum and identified a variety of carbohydrate-active enzymes, including alginate lyases, fucoidanases, and cellulases which break down seaweed cell wall polysaccharides. We also find that microbes compete in the closed reactors, with diversity being reduced over time. These results highlight the metabolic potential of native marine microbial communities to degrade Sargassum and elucidate microbial ecosystem dynamics during this process. These insights allow the use of renewable Sargassum as a biorefinery feedstock of the future.}, }
@article {pmid41914849, year = {2026}, author = {Deng, T and Wang, H and Zhang, S-F and Wu, X-Y and Yang, Z-S and Wang, D-Z and Zheng, Y}, title = {Functional determinism amid taxonomic stochasticity: insights into rules governing the assembly of algal-microbial symbioses.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0035926}, doi = {10.1128/aem.00359-26}, pmid = {41914849}, issn = {1098-5336}, abstract = {Marine algal-microbial symbioses constitute essential functional units that drive ocean biogeochemical cycles and trigger harmful algal blooms. Yet, a long-standing controversy persists regarding the mechanisms of algal-microbial symbiose assembly, specifically whether phycosphere microbiota are predominantly shaped by deterministic algal-driven selection or by stochastic environmental processes, with no definitive resolution to date. Here, we examined phycosphere communities associated with a series of Skeletonema strains, tracking their taxonomic and functional dynamics across successive growth stages. Despite pronounced taxonomic diversity, reflected in distinct community compositions, successional trajectories, and microbial networks, shotgun metagenomic analyses revealed highly conserved functional repertoires across samples, with consistently abundant core pathways, including amino acid biosynthesis, secondary metabolite and antibiotic production, and ABC transport systems. Statistical analyses further revealed a marked decoupling of taxonomy and function, with functional redundancy enabling taxonomically distinct lineages to perform equivalent metabolic roles. Based on these findings, we propose a dual assembly model in which deterministic algal host-driven selection constrains functional composition, while stochastic processes govern species-level membership. This "function-first, taxonomy-stochastic" paradigm reconciles opposing assembly theories, underscores functional resilience in the face of taxonomic turnover, and provides a conceptual foundation for the rational design of synthetic algal-microbial consortia in marine biotechnological applications.IMPORTANCEMarine algae live in close association with diverse microorganisms that influence nutrient cycling and ecosystem stability. Yet, how these algal-microbial partnerships assemble and maintain functional integrity remains unresolved. Using Skeletonema as a model, this study demonstrates that while the microbial species surrounding different algal strains vary greatly, their metabolic functions remain remarkably consistent. This finding reveals that algal hosts deterministically shape the functional needs of their microbiome, whereas the specific bacterial members fulfilling those roles are interchangeable. Such a "function-first" organization explains how algal-microbial symbioses persist despite environmental fluctuations. Understanding these assembly rules not only advances our knowledge of marine microbial ecology but also provides a conceptual foundation for engineering stable and resilient algal-microbial consortia for sustainable ocean biotechnologies.}, }
@article {pmid41915015, year = {2026}, author = {Sun, Y and Wu, X and Zanina, OG and Rivkina, EM and Lloyd, KG and Löffler, FE and Vishnivetskaya, TA}, title = {Incomplete Denitrifying Bacteria Drive N2O Fluxes in Ancient Siberian Permafrost Microcosms.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag034}, pmid = {41915015}, issn = {1574-6941}, abstract = {Nitrous oxide (N2O) contributes to stratospheric ozone depletion and global warming. Knowledge about microbial formation and consumption of N2O in old permafrost remains limited. Permafrost samples collected on the East Siberian Sea coast of Russia from a single borehole at depths of 5.4 and 16.9 m, which showed presence of nitrogen substances and nitrogen cycling genes, were used to establish microcosms supplemented with NO3-- and N2O to assess denitrification and N2O consumption at 4 and 20°C. Rapid N2O formation was observed in NO3--supplemented microcosms, but N2O consumption was slow and incomplete over a 1-year incubation in all microcosms. Twenty-three qualified metagenome-assembled genomes (MAGs) harboring genes involved in NO3- and/or N2O reduction were recovered from both NO3-- and N2O-supplemented microcosms. Twenty MAGs represent novel taxa. Four MAGs, two of each from NO3-- and N2O-supplemented microcosms, contained nosZ genes indicating N2O consumption potential, however the complete denitrification (i.e., NO3-→N2) gene sets were not detected in these MAGs. Though, N2O production exceeded N2O consumption in NO3--supplemented microcosms at 4°C. Our microcosm experiments suggest N2O formation surpasses its consumption in newly-thawed ~120 kyr old permafrost, emphasizing the importance of using integrated approaches to assess and predict N turnover in response to permafrost degradation.}, }
@article {pmid41915265, year = {2026}, author = {Volk, A and Mills, M and Chae, S and Lee, J}, title = {Investigation of cyanobacteria-hosted antibiotic resistance genes in cyanoHAB-impacted drinking water sources.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {41915265}, issn = {1614-7499}, abstract = {Freshwater cyanobacterial blooms (cyanoHABs) are expanding across the world, and their frequency and severity are becoming more intense due to prevalent eutrophication and a changing climate. Traditionally, the concerns about cyanoHABs have mainly focused on cyanotoxins in water. CyanoHABs are also hypothesized to play a role in the antibiotic resistome, but whether cyanobacteria host clinically relevant antibiotic resistant genes (ARGs) in the environment is largely unknown. To investigate this emerging issue, we examined whether cyanobacteria host ARGs within the broader microbiome context. We looked for the presence of cyanobacteria-hosted ARGs using shotgun metagenomic sequencing of drinking water source samples collected during the bloom season (summer and fall) from Lake Erie and Grand Lake St. Marys (GLSM). ARGs were annotated using DeepARG and Resistance Gene Identifier (RGI). Cyanobacteria were annotated to host genes conferring putative antibiotic resistance, including efflux pumps qac/EmrE, vatB, van genes, and an OXA homolog. A maximum likelihood tree with cyanobacteria and OXA reference sequences showed OXA-like homology across multiple families of cyanobacteria. Most cyanobacteria sequences clustered in a large clade with ybxI, suggesting very limited or negligible class-D beta-lactamase activity, but a small subset formed a clade with OXA-2 and OXA-46. While those hits suggest potential resistance to clinical antibiotics, overall cyanobacteria were not found to host ARGs conferring resistance to drugs of last resort in these samples. Additionally, BLAST searches of the cyanobacteria ARG contigs and coding sequences resulted in top hits for cyanobacteria, further supporting that annotated genes are likely intrinsic rather than acquired. rpoB2 and arlR ARG annotations appear to be spurious hits on housekeeping genes, which demonstrates the need to verify automated ARG annotation tool results. Selected cyanotoxins, cyanobacteria, and ARGs were also chosen for quantification. We found high levels of Microcystis in Lake Erie as well as Planktothrix and microcystin concentrations in GLSM, supporting previous trends in these water bodies. This study takes a novel approach, pairing the issues of cyanoHABs and ARGs together in two drinking water sources. In a changing climate, drinking water treatment strategies should consider the treatment and public health implications of multiple contaminants.}, }
@article {pmid41915324, year = {2026}, author = {Varshney, A and Sarethy, IP}, title = {Metagenome-based insights into bacteriophage diversity of an urban river ecosystem.}, journal = {Molecular biology reports}, volume = {53}, number = {1}, pages = {}, pmid = {41915324}, issn = {1573-4978}, }
@article {pmid41905084, year = {2026}, author = {Xiang, H and Deng, Y and Xu, Y and Zhang, X and Zhang, C and Guo, B and Xu, Z and Wang, Y}, title = {Fe-S interactions and geological background shape phosphorus bioavailability in mangrove sediments.}, journal = {Marine pollution bulletin}, volume = {228}, number = {}, pages = {119655}, doi = {10.1016/j.marpolbul.2026.119655}, pmid = {41905084}, issn = {1879-3363}, abstract = {Mangrove sediments act as critical phosphorus (P) sinks and potential sources in coastal ecosystems, with P release risk dominated by bioavailable phosphorus (BAP), including exchangeable P, iron-bound P (Fe-P), and organic P (OP). While Fe-S cycles tightly regulate P speciation, how the geological background mediates Fe-S-P coupling across heterogeneous mangroves remains unclear. We integrated Fe-S-P fractionation, water-soluble organic matter (WSOM) fluorescence spectroscopy, and metagenomics to compare volcanic weathering (V) and Quaternary coastal (Q) sediments in Dongzhai Harbor. Key findings are as follows: Total P in shallow V sediments (8.89-30.90 μmol/g) is higher than in Q (6.95-17.09 μmol/g). OP dominates V's BAP (48.87%) linked to OP mineralization genes (e.g., appA), whereas Fe-P dominates Q's BAP (57.31%) and is stabilized by amorphous Fe oxides. In deep V sediments, Fe-P is positively correlated with acid-volatile sulfide (AVS; R[2] = 0.57) and Fe/S reduction genes (fsr, omcF), indicating Fe-S-coupled P mobilization and release. In deep Q sediments, Fe-P remains stabilized by Feox1, and P mobilization is driven by microbial iron reduction, with iron-reduction genes (e.g., mtrA) being significantly enriched. Two distinct P release pathways are identified: in volcanic weathering zone sediments, P release shifts from OP dominance to Fe-S-coupled regulation, while in Quaternary coastal zone sediments, Fe-P mobilization relies on microbial iron reduction. These findings clarify the geological controls on Fe-S-P interactions in mangrove sediments, providing a scientific basis for site-specific P risk assessment and the formulation of targeted strategies for mangrove ecosystem restoration and coastal eutrophication control.}, }
@article {pmid41905194, year = {2026}, author = {Li, J and Silvester, R and Williams, RC and Chan-Herur, V and Goldman, M and Fidler, D and Jones, DL}, title = {Metagenomics-based source attribution of antimicrobial resistance in wastewater for improved epidemiological risk assessment.}, journal = {Water research}, volume = {298}, number = {}, pages = {125810}, doi = {10.1016/j.watres.2026.125810}, pmid = {41905194}, issn = {1879-2448}, abstract = {Wastewater-based epidemiology (WBE) offers a powerful approach for monitoring antimicrobial resistance (AMR) at the population level. However, distinguishing between human gut-derived and sewer-derived AMR-carrying organisms remains a key challenge for accurate surveillance and risk assessment. In this study, we used genome-resolved metagenomics to distinguish human gut-derived organisms, and their associated antimicrobial resistance genes (ARGs), mobile genetic elements (MGEs) and virulence-associated determinants (VFs), from taxa endemic to the sewer network. We applied this approach to wastewater samples collected from three hospital outflows (near-source healthcare sites), as well as from untreated influent and final treated effluent at the corresponding municipal wastewater treatment plants serving the surrounding communities. Along the wastewater pathway, microbial communities progressively shifted from human gut-associated to sewer adapted taxa; consequently, the final treated effluent was dominated by sewer-adapted taxa. Human gut-derived taxa were further examined in detail: 84% carried ARGs and VFs, predominantly within Bacillota and Bacteroidota; all gut-associated Pseudomonadota also harboured multiple ARGs, VFs and MGEs. Opportunistic-pathogen taxa of gut origin (Escherichia coli, Klebsiella spp., E. faecium) accounted for a substantial fraction of ARGs in hospital wastewater. Combined sewer overflow (CSO) events may allow these carriers to bypass wastewater treatment and reach receiving waters, posing public health risks. This genome-resolved framework strengthens WBE by resolving human-derived contributions for surveillance and risk assessment.}, }
@article {pmid41905375, year = {2026}, author = {Wrønding, T and Vomstein, K and Lundgaard, AT and DeLong, K and Mollerup, S and Mortensen, B and Bosma, EF and Hellerung, AM and Engel, EV and Wiil, KD and Heintz, JE and Halkjær, SI and Hugerth, LW and Hartwig, TS and Petersen, AM and Thomsen, AB and Westergaard, D and la Cour Freiesleben, N and Westh, H and van Hylckama Vlieg, JET and Ensign, LM and Nielsen, HS}, title = {Vaginal microbiota transplantation for treatment of vaginal dysbiosis without the use of antibiotics: a double-blind, randomised controlled trial in women with vaginal dysbiosis.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101294}, doi = {10.1016/j.lanmic.2025.101294}, pmid = {41905375}, issn = {2666-5247}, abstract = {BACKGROUND: A vaginal microbiota dominated by Lactobacillus species is associated with reduced risk of infection and adverse reproductive outcomes. Effective interventions to restore healthy microbiota remain scarce. In this study, we aimed to assess the efficacy of vaginal microbiota transplants (VMTs) without antibiotic pretreatment in achieving conversion to a Lactobacillus-dominated vaginal microbiome.<br><br>METHODS: This single-centre, double-blind, randomised controlled trial was done at Copenhagen University Hospital (Hvidovre, Denmark) between June 1, 2021, and March 1, 2023. We enrolled women aged 18-40 years with asymptomatic or symptomatic molecular vaginal dysbiosis (<10% total relative abundance of Lactobacillus spp and >20% relative abundance of Gardnerella spp, Fannyhessea vaginae, and Prevotella spp) who were otherwise healthy premenopausal women and not pregnant as recipients; donors were healthy women aged 18-40 years with a Lactobacillus-dominated vaginal microbiota (>80%) and a low (<5%) abundance of Gardnerella spp, F vaginae, and Prevotella spp, and negative screening for sexually transmitted infections. Participants were randomly assigned (3:1) to the intervention or placebo through a computer-generated schedule with block randomisation and stratification by hormonal contraception. Participants and investigators were masked to the group. Up to three administrations of VMT or placebo were given across three menstrual cycles, with follow-up for six cycles. The primary endpoint was resolution of dysbiosis at any timepoint during follow-up, defined as at least 70% relative abundance of Lactobacillus spp and less than 10% combined abundance of Gardnerella spp, F vaginae, and Prevotella spp, as assessed by shotgun metagenomic sequencing of vaginal samples. This analysis was done in the intention-to-treat population, excluding any participants who withdrew consent. An extension study assessed the effect of antiseptic pretreatment before additional VMT in refractory participants. This study was registered with ClinicalTrials.gov (NCT04855006) and is completed.<br><br>FINDINGS: A total of 302 women were screened, of whom 49 were enrolled. 37 women were randomly assigned to the VMT group (mean age 26&#xb7;1 years [SD 3&#xb7;8]) and 12 to the placebo group (27&#xb7;3 years [4&#xb7;8]). The primary outcome showed no significant difference in dysbiosis resolution between active and placebo groups (HR 0&#xb7;65; 95% CI 0&#xb7;20-2&#xb7;16, p=0&#xb7;49). In an extension study of refractory participants, five (50%) of the ten women who received antiseptic pretreatment followed by VMT had a microbiome conversion. Adverse events occurred in 15 (42%) VMT participants and five (42%) placebo participants; none were serious or led to withdrawal. A single pregnancy and one new human papillomavirus infection occurred, both unrelated to treatment.<br><br>INTERPRETATION: VMT without antibiotics did not significantly improve microbiome conversion in this trial. However, findings from the extension study suggest that antiseptic pretreatment might enhance efficacy. Future trials should explore optimised dosing and use donor engraftment as a primary outcome.<br><br>FUNDING: Freya Biosciences.}, }
@article {pmid41905742, year = {2026}, author = {Wu, Z and Duan, A and Liu, Y and Chen, R and Md Din, MF and Sanjaya, EH and Ali, EAE and Saad, A and Liu, Z and Chen, H}, title = {Mechanistic insights into sulfate-driven performance adaptation and membrane fouling in a UASB-SBR-AXMBR system: metabolic network reconstruction and microbial community succession.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124374}, doi = {10.1016/j.envres.2026.124374}, pmid = {41905742}, issn = {1096-0953}, abstract = {Sulfate-rich wastewater poses considerable challenges to the operational stability of biological treatment systems. This study investigated the long-term (294 days) response of a combined UASB-SBR-AXMBR process to stepwise increases in sulfate concentration from 100 to 2000 mg/L. The system maintained stable carbon and nitrogen removal performance under sulfate stress, with COD removal exceeding 90.3% and total nitrogen removal stabilizing at 85.5% via a partial nitritation-anammox (PN/A) pathway. However, high sulfate loading significantly intensified membrane fouling, with the primary driving factor likely being the co-deposition of elemental sulfur (S[0]) and soluble extracellular polymeric substances (S-EPS). Microbial analysis revealed persistent enrichment of Bacteroidota and Proteobacteria in the SBR, alongside a marked increase in Anammoxoglobus (from 17.1% to 51.2%) in the Anaerobic Ammonia Oxidation Membrane Bioreactor (AXMBR), underpinning system resilience. Metagenomic profiling further indicated adaptive shifts in key nitrogen-cycling genes (hao, amoA) and sulfur metabolism pathways. Notably, sulfate-reducing bacteria (SRB) outcompeted methanogens, redirecting carbon flow from methanogenesis to sulfur reduction, while niche diversification in the AXMBR expanded nitrogen removal pathways. These findings provide new mechanistic insights into the adaptive responses of integrated bioprocesses under sulfate stress and provide practical guidance for the treatment of high-sulfate industrial wastewaters such as monosodium glutamate effluent.}, }
@article {pmid41905975, year = {2026}, author = {Barbe, V and de Toro-Martín, J and Garneau, V and Couture, P and Roy, D and Couillard, C and Marette, A and Vohl, MC}, title = {Functional gut microbiome signatures underlying interindividual variability in metabolic responses to red raspberry consumption.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-45955-7}, pmid = {41905975}, issn = {2045-2322}, }
@article {pmid41906088, year = {2026}, author = {Bai, D and Wang, Z}, title = {Neurosyphilis with simultaneous brain and spinal cord involvement mimicking intracranial tumors: a case report.}, journal = {BMC neurology}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12883-026-04836-2}, pmid = {41906088}, issn = {1471-2377}, }
@article {pmid41906342, year = {2026}, author = {Wu, J and Tian, J and Zhang, X and Kong, Z}, title = {Metagenomic Analysis of Soybean Rhizosphere Microbiome in Black Soil: Community Composition and Functional Insights.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70505}, pmid = {41906342}, issn = {1365-3040}, support = {XDA28030201//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 32241045//National Natural Science Foundation of China/ ; }, }
@article {pmid41907005, year = {2026}, author = {Jeunen, GJ and Mills, S and Bailie, M and Mauvisseau, Q and Lamare, M and Mariani, S and Pearman, W and Zavodna, M and Treece, J and Ferreira, S and Gemmell, NJ}, title = {Recovering Historical eDNA From Museum-Preserved Filter Feeders via Non-Destructive Metabarcoding.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70132}, doi = {10.1111/1755-0998.70132}, pmid = {41907005}, issn = {1755-0998}, support = {MFP-UOO2116//Royal Society of New Zealand Marsden Fast-Start Fund/ ; ANTA1801//Ministry of Business, Innovation, and Employment/ ; //University of Otago Research Grant (UORG)/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; Museums ; Animals ; *Metagenomics/methods ; *Specimen Handling/methods ; RNA, Ribosomal, 16S/genetics ; *Preservation, Biological/methods ; Fishes/genetics ; }, abstract = {Recent technical advances have significantly enhanced the value of museum specimens for molecular research, with metagenomic and metabarcoding approaches expanding further the utility of museum collections. However, given the finite number of specimens, there is a critical need to move past destructive DNA extraction approaches and to explore non-destructive techniques. In this proof-of-concept study, we evaluated the feasibility of extracting historical eDNA from the ethanol preservative used to store museum specimens. We compared a variety of extraction methods (centrifugation, evaporation, filtration, and precipitation) using ten replicate samples per treatment for statistical analyses. To assess potential differences in preservative-derived eDNA recovery across different filter-feeding taxonomic groups, we included a bryozoan, a demosponge, and a glass sponge. Comparative analyses with tissue biopsies revealed that 10 mL ethanol filtration performed equal to or, in some instances, outperformed tissue biopsies for all three specimens when examining the historical eDNA of Antarctic fish using a 16S rRNA metabarcoding approach, both for the number of species detected (α-diversity) and community characterisation (β-diversity). This initial study demonstrates the potential of ethanol preservative as a valuable, non-destructive source of historical eDNA from museum-stored filter-feeding specimens. These findings highlight the viability of non-destructive sampling for molecular research on museum collections, preserving specimen integrity while enabling biodiversity assessments. Further refinement of non-destructive eDNA extraction could expand its applicability across taxa, collection types, and preservation methods, ensuring the long-term sustainability of museum-based genomic, metagenomic, and metabarcoding research.}, }
@article {pmid41907295, year = {2026}, author = {Liu, J and Zhou, Y and Xu, F and Liu, W and Chen, H and Yan, Q and Guo, J and Lai, L}, title = {Case Report: Cavitary Legionella pneumophila pneumonia in a kidney transplant recipient: mNGS-guided diagnosis and prolonged combination therapy.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1697062}, pmid = {41907295}, issn = {2296-858X}, abstract = {Legionella pneumophila is an uncommon but potentially life-threatening cause of pneumonia in solid organ transplant (SOT) recipients. Diagnosis is challenging due to nonspecific features and the limited sensitivity of conventional assays. Metagenomic next-generation sequencing (mNGS) offers unbiased detection and may be particularly valuable in immunocompromised hosts with refractory pneumonia. We report the first documented case in Asia of cavitary Legionella pneumonia in a kidney transplant recipient. A 60-year-old man presented with fever and bilateral pulmonary nodules 5 months post-transplant. Despite empirical antifungal and antibacterial therapy, his condition progressed radiologically to cavitary disease. Bronchoalveolar lavage fluid mNGS identified abundant L. pneumophila reads, confirming the diagnosis. Initial azithromycin monotherapy achieved transient improvement but failed to prevent radiological progression. Escalation to prolonged dual therapy with azithromycin and levofloxacin resulted in rapid symptomatic relief, progressive cavity regression on serial computed tomography, and preserved allograft function. Sequential blood-based mNGS demonstrated declining pathogen reads paralleling recovery. This brief research report emphasizes three practice points for SOT recipients with refractory pneumonia: (1) early mNGS can shorten time-to-diagnosis when routine tests are inconclusive; (2) Legionella infection may manifest with atypical cavitary lesions in immunocompromised hosts, warranting scheduled imaging even when symptoms improve; and (3) prolonged macrolide-fluoroquinolone combination therapy may be required for severe or non-resolving cases. Together with our literature review, this case expands understanding of the radiological spectrum, diagnostic strategies, and therapeutic considerations of Legionella pneumonia in transplant populations.}, }
@article {pmid41907709, year = {2024}, author = {Nirmalkar, K and Patel, J and Kang, DW and Bellinghiere, A and Bowes, DA and Qureshi, F and Adams, JB and Krajmalnik-Brown, R}, title = {Bimodal distribution of intestinal Candida in children with autism and its potential link with worse ASD symptoms.}, journal = {Gut microbes reports}, volume = {1}, number = {1}, pages = {2358324}, pmid = {41907709}, issn = {2993-3935}, abstract = {The gastrointestinal (GI) tract harbors a complex and remarkably diverse microbial ecosystem that profoundly impacts various aspects of health and pathophysiology. While bacteria overwhelmingly represent most of the GI microbiota, it is imperative to consider the presence and function of fungal constituents (i.e. mycobiota) within the GI ecosystem. The substantial incidence of GI disorders and associated manifestations in children diagnosed with autism spectrum disorder (ASD) suggests a plausible contributory role of the gut mycobiota. This work aimed to elucidate the gut mycobiota in a cohort of 38 typically developing children (TD) and 40 children with ASD. Fecal samples were collected from all participants, autism severity and GI symptoms were assessed to unravel the potential implications of mycobiota alterations in the gut. We performed fungal internal transcribed spacer (ITS) gene amplicon sequencing to analyze the fungal composition and investigate their relationship with GI and autism symptoms. Among gut mycobiota, Saccharomyces cerevisiae was significantly lower (relative abundance) in the ASD fecal samples compared to TD children. Candida and C. albicans demonstrated a bimodal distribution among children with ASD. The small subset of children with elevated C. albicans or decreased S. cerevisiae had increased Autism Treatment Evaluation Checklist (ATEC) scores. Our findings suggest that a deficit of S. cerevisiae, and an overgrowth of C. albicans in a subset of children is associated with worse autism severity. Future work employing shotgun metagenomics with a larger cohort is encouraged to advance understanding of the functional role of fungi, and their possible interplay with GI symptoms and autism severity in children with ASD.}, }
@article {pmid41907719, year = {2024}, author = {Dixit, K and Ahmed, A and Singh, A and Inamdar, M and Chavan, S and Bodkhe, R and Mehtab, W and Chauhan, A and Saroj, SD and Ahuja, V and Shouche, Y and Dhotre, D and Makharia, G}, title = {Site-Specific Gut Microbial Signatures in Non-Celiac Gluten Sensitivity.}, journal = {Gut microbes reports}, volume = {1}, number = {1}, pages = {2438621}, pmid = {41907719}, issn = {2993-3935}, abstract = {Gut microbiota in non-celiac gluten sensitivity (NCGS) has been poorly studied for its involvement in the disorder and site specificity. We investigated small intestinal, large intestinal and stool microbiota profiles in patients with NCGS and highly overlapping disorder irritable bowel syndrome (IBS) as well as effect of gluten-free diet (GFD) on microbiota in patients with NCGS. True NCGS patients were recruited based on serological response for anti-gliadin antibodies, 6-week gluten free diet (GFD) and symptom recurrence with gluten-rechallenge. Analyses using 16S rRNA gene amplicon and shotgun sequencing revealed community differences in core microbiome and diversity measures across sample types indicating dysbiosis mainly in mucosa-associated small intestinal microbiome of NCGS patients. Genera Elusimicrobiaum, Succinivibrio, Bacillus and Alcaligenes appeared as signatures in small intestine and stool in NCGS patients. Presence of differential taxa co-occurring at sampling sites, enabled recognition of site-specific microbial signatures. GFD led to a shift in mucosa-associated small intestinal core microbiome. Metagenome analysis revealed subtle differences in pathways for amino acid biosynthesis including L-ornithine. Mucosa-associated small intestine microbial structure was quite distinct in patients with NCGS in comparison to that with IBS.}, }
@article {pmid41908157, year = {2024}, author = {Pfavayi, LT and Sibanda, EN and Baker, S and Woolhouse, M and Mduluza, T and Mutapi, F}, title = {Diversity and composition of gut protist in young rural Zimbabwean children.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1399160}, pmid = {41908157}, issn = {2813-4338}, abstract = {BACKGROUND: The human gut microbiome harbours diverse species of archaea, bacteria, fungi, protists and viruses. To date, most gut microbiome studies have focused on bacteria, neglecting other microbial communities. Consequently, less is known about the diversity and abundance of the latter. Here, we aimed to characterise the diversity and composition of protists in the gut of preschool-aged children (PSAC) in rural Zimbabwe relative to host age, sex, and schistosome infection status.<br><br>METHODS: The gut protist of 113 PSAC (1-5 years) was examined via shotgun metagenomic sequencing and analysed for diversity. Variation in protist abundance with host and environmental factors was analysed by permutational multivariate analysis of variance (PERMANOVA). To investigate how the composition of specific taxa varies across age, sex, nutritional measures and Schistosoma hematobium infection status, analysis of the composition of microbiomes (ANCOM) was used.<br><br>RESULTS: Eighty protist genera were identified, and the most abundant genera detected was Blastocystis. The prevalence of pathogenic protists was comparatively low, with 12.4% and 3.4% of the participants' gut colonised by E. histolytica and Cryptosporidium, respectively. Of all the independent variables only S. haematobium infection showed significant relationship with the structure of the gut protist, being associated with increases in Peronospora, Pseudoperonospora, Plasmopara and Blastocystis (FDR= 0.009).<br><br>SUMMARY: This study provides data on the prevalence and diversity of the gut protists in young Zimbabwean children with an emphasis on the host factors; age, sex and schistosome infection status. Our results showed no association between the host factors investigated, including anthropometric measures adjusted for age and the intestinal protist composition and structure, but S. haematobium infection status was associated with composition of specific taxa. There is a need for more studies determining how pathogenic protist interact with non-pathogenic protist in people exhibiting clinical symptoms to inform therapy and nutraceuticals.}, }
@article {pmid41908294, year = {2026}, author = {Schulz, S and Börner, S and Bitter, K and Gheit, H and Partsakhashvili, J and Ukkat, J and Misiak, D and Reichert, S}, title = {Possible association between the microbiota in subgingival and atherosclerotic plaque in a cohort of patients with carotid stenosis.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2648325}, pmid = {41908294}, issn = {2000-2297}, abstract = {BACKGROUND: Periodontal pathogens have been implicated in systemic diseases, including atherosclerosis. This study investigates the relationship between subgingival and microbial colonization of carotid plaque in patients undergoing carotid endarterectomy (DRKS00021598).<br><br>METHODS: Microbial samples from both subgingival and carotid plaques were collected from 25 hospitalized patients. Preoperative all patients underwent periodontal examination. The microbial composition was assessed using metagenomics sequencing of 16S rRNA gene (V3/V4 regions).<br><br>RESULTS: Bacterial DNA was detected in both subgingival and carotid plaque samples. The microbial composition differed between both communities. Alpha diversity was significantly higher in subgingival samples than in carotid plaques (p&#x2009;=&#x2009;0.039). Beta diversity analysis, (including unweighted UniFrac (p&#x2009;<&#x2009;0.001), linear discriminant analysis, principal component analysis) confirmed significant differences between subgingival and carotid plaque microbiota. The study revealed overlaps in a few individual cases.<br><br>CONCLUSIONS: These findings show that carotid plaque microbiota differ from subgingival communities and are not exclusively of oral origin, suggesting additional systemic sources.}, }
@article {pmid41908297, year = {2026}, author = {Shantha, JG and Chen, C and Hinterwirth, A and Gonzales, JA and Acharya, NR and Lietman, TM and Doan, T}, title = {Integrated metagenomic sequencing and phage display-based immunoprecipitation sequencing for presumptive viral infection: a case report.}, journal = {American journal of ophthalmology case reports}, volume = {42}, number = {}, pages = {102561}, pmid = {41908297}, issn = {2451-9936}, abstract = {PURPOSE: To report a case of uveitis in which unbiased metagenomic sequencing (MDS) and phage immunoprecipitation sequencing (PhIP-Seq) were performed on intraocular fluid.<br><br>OBSERVATIONS: A female patient with a past medical history of human immunodeficiency virus (HIV-1) who presented with chronic active anterior and intermediate uveitis with cystoid macular edema in the left eye. She had a previous ocular history of viral retinitis presumed to be secondary to cytomegalovirus (CMV). An anterior chamber tap was performed for viral polymerase chain reactions (PCRs), MDS, and pathogen PhIP-Seq. PCR testing and MDS were negative for pathogen genetic materials. PhIP-Seq detected antibody enrichment of CMV, as well as HIV-1 andSARS-CoV-2.<br><br>CONCLUSIONS: The combination of MDS and PhIP-Seq has the potential to provide additional insights into the pathogenesis and the ocular microenvironment of uveitis patients.}, }
@article {pmid41908958, year = {2026}, author = {Song, Y and Pu, X and Liu, Q and Hou, S and Zou, D and Xiang, Y and Gu, S and Chu, M}, title = {Dietary energy alters jejunal microbial function without changing its structure in small-tailed Han sheep.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1730873}, pmid = {41908958}, issn = {2297-1769}, abstract = {Dietary energy levels typically influence the structure and functional profile of the gastrointestinal microbial community. In this study, thirty 6-month-old Small-tailed Han (STH) sheep were randomly divided into three groups and fed corn-based diets with different energy levels for 150 days. Jejunal contents were then collected and analyzed using metagenomic sequencing to assess microbial alpha diversity and taxonomic composition. Functional annotation and enrichment analysis were performed using the KEGG database. Principal coordinate analysis (PCoA) and alpha diversity indices (Chao1, Shannon, Simpson and good coverage) revealed no significant changes in the overall structure or macro-ecological characteristics of the jejunal microbial community in response to dietary energy levels. At the phylum level, Bacillota was the absolutely dominant phylum, while at the genus level, Methanobrevibacter was the most abundant genus. The abundances of these core microbial taxa did not differ significantly among groups. However, KEGG functional enrichment analysis revealed significant differences in microbial functions between groups. The low-energy group exhibited enrichment in pathways related to energy deficiency and stress adaptation, whereas the high-energy group showed significant enrichment in pathways associated with active growth and anabolic metabolism. In conclusion, although dietary energy levels did not significantly alter the microbial community structure in the jejunum of STH sheep, they profoundly influenced its functional potential. These findings suggest that dietary energy may modulate host nutrient acquisition and health status by regulating the functional characteristics of the jejunal microbiota.}, }
@article {pmid41909054, year = {2025}, author = {Hanna, M and Huang, S and Ross, M and Reyes, A and Perera, D and Surathu, A and Cregeen, SJ and Hagan, J and Pammi, M}, title = {Microbiome Signatures and Inflammatory Biomarkers in Culture-Negative Neonatal Sepsis.}, journal = {Applied microbiology (Basel, Switzerland)}, volume = {5}, number = {3}, pages = {}, pmid = {41909054}, issn = {2673-8007}, abstract = {Overuse of antibiotics is a concern in 'culture-negative sepsis' but it is unclear whether this is due to infection with viruses, fungi or other microbes that are not easily cultured, or whether it results from inflammatory processes. In a prospective study, we enrolled 50 preterm neonates with culture-positive sepsis (CP), culture-negative sepsis (CN), and asymptomatic preterm controls (CO). The microbiome of stool, skin, and blood, including bacterial, viral and fungal components and serum cytokine profiles were evaluated. The microbiome alpha or beta diversity did not differ between CN and CO groups. A MaAsLin analysis revealed increased relative abundances of specific bacterial and fungal genera in stool and skin samples in the CN group compared to CO. The virome analysis identified 24 viruses from skin samples, but they were not statistically different among the three groups. The cytokine and chemokine biomarker profiles were elevated in the CP group but were not statistically different between the CN and CO groups. Although the CN group had a longer hospital stay and higher BPD rates than the controls in unadjusted analyses, these differences were not significant after adjusting for gestational age and birth weight. The CN infants demonstrated microbial shifts without systemic immune activation or significantly worse clinical outcomes, supporting the rationale for discontinuing antibiotics in the absence of positive cultures.}, }
@article {pmid41909251, year = {2026}, author = {Sun, F and Yuan, M and Liao, C and Sun, Y and Yu, L and Zhuo, Y and Peng, Y and Tang, X and Zeng, Q and Song, J and Tao, X and Li, Q and Chen, M and Zhang, Y}, title = {Optimizing flue-cured tobacco planting patterns: enhanced rhizosphere nutrient availability and microbial community dynamics.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1735540}, pmid = {41909251}, issn = {1664-302X}, abstract = {INTRODUCTION: Continuous monoculture of flue-cured tobacco causes soil degradation and microbial dysbiosis. While crop rotation can alleviate these obstacles, how different cropping patterns regulate soil carbon (C) and nitrogen (N) metabolic functions remains unclear.<br><br>METHODS: A four-year field experiment compared tobacco monoculture (CK), tobacco-maize rotation (TM), tobacco-rice rotation (TR), and tobacco-sweet potato intercropping (TP). Soil physicochemical properties, enzyme activities, metagenomic sequencing, and microbial network analysis were integrated.<br><br>RESULTS: TR significantly improved soil health: pH (+6.6%), organic matter (+22.1%), and urease activity (+12.5%). It enriched beneficial microbes (Pseudomonadota +16.4%, Mucoromycota +327%) and upregulated C-cycle (korA +42.3%) and N-assimilation genes (amoC +460%), while suppressing denitrification (nirK). TM increased available P/K but enriched oligotrophic taxa and reduced sucrase activity. TP triggered pathogenic fungi (Olpidium +160%), depleted beneficial microbes, and broadly suppressed C/N metabolic genes (cbbL -94.5%, nirS -21.8%).<br><br>DISCUSSION: Cropping patterns differentially reshape microbial communities and metabolic functions, determining their efficacy against continuous cropping obstacles. TR establishes efficient C/N cycling with "high assimilation, low denitrification," whereas TP induces pathogenic proliferation and metabolic suppression. This provides a functional framework for designing cropping systems to enhance soil health and tobacco productivity.}, }
@article {pmid41909254, year = {2026}, author = {Pan, K and Zhang, Z and Feng, L and Wu, X and Yang, X and He, X and Xiao, Y and Yang, D and Duan, C and Wang, Q}, title = {Biochar regulates putative keystone microbial taxa to drive phosphorus cycling and increase availability in urban greenspace soils.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1786258}, pmid = {41909254}, issn = {1664-302X}, abstract = {The quality of soil in urban green spaces often deteriorates due to poor design practices, insufficient maintenance, and environmental pressures associated with urbanization. Although biochar, as an effective soil additive, can significantly improve the soil quality in greenspace, it significantly influences the phosphorus (P) cycling processes through functional regulation of microbial community; however, further analysis is essential to validate this mechanism. Therefore, this study reported pot experiments using Euonymus kiautschovicus, a typical urban greenspace plant, followed by metagenomic analysis for investigating microbial-driven P cycle mechanisms. Four treatment groups were established according to the dosage of biochar, including 0% (CK), 4% (BC4), 8% (BC8), and 12% (BC12). Biochar application significantly increased soil available P (AP) and total P (TP) content, with BC12 demonstrating maximum AP and TP content of 21.79 mg kg[-1] and 0.62 g kg[-1], respectively. On the one hand, biochar serves as a direct source of P. On the other hand, it enhances AP by regulating P-cycling functional microorganisms. Random forest model identified phnP, phoA, relA, ppnK, pstA, phnD, and pstS as the putative keystone genes regulating soil P cycling. Microbial co-occurrence network analysis and partial least squares path modeling (PLS-PM) demonstrated that the biochar application improved soil AP by regulating putative keystone microbial taxa (Modules 1 and 2) involved in P cycling. This study elucidates the microbial mechanisms underlying biochar-mediated P cycling in greenspace soils, providing a scientific basis for biochar application for improved soil quality in urban greenspace.}, }
@article {pmid41909264, year = {2026}, author = {Li, L and Zhao, D and Du, R and Tang, K and Zhang, Y}, title = {Niche adaptation of particle-associated ammonia-oxidizing archaea sustains nitrification under marine deoxygenation.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1773718}, pmid = {41909264}, issn = {1664-302X}, abstract = {Marine deoxygenation is restructuring coastal microbial niches and metabolic networks, with cascading effects on biogeochemical cycles, a key component of which is the nitrogen cycle. Particles constitute a critical ecological interface that mediates microbial niche partitioning and oxygen-sensitive balance between nitrogen loss and retention in deoxygenating coastal waters. However, the niche-dependent metabolic partitioning of microbial communities and its influence on the nitrogen cycle under deoxygenation remains poorly constrained. We conducted a 22-day field investigation of the deoxygenated water column off the Zhoushan coast, China, combining temporal [15]N-tracer-based nitrification rate measurements with size-fractionated metagenomic sequencing during the day of the most severe bottom-water oxygen depletion. Our data revealed a nitrification hotspot in the low-oxygen waters below the pycnocline, with persistently elevated rates and an enriched abundance of ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria. Notably, particle-associated AOA exhibited significantly enriched genomic potential for coupled nitrogen cycling and carbon fixation, while the dominant groups adapted to low-oxygen particles via distinct metabolic strategies. Nitrosomarinus-like AOA exhibited higher gene counts (amoA-normalized) for ammonia (amt) and high-affinity phosphate (pst) transporters, whereas their Water column group A-like counterparts were enriched in low-affinity phosphate transporters (pit). Urease gene enrichment in both major AOA clades implicates urea as an ecologically relevant alternative nitrogen source for ammonia acquisition in coastal waters. Furthermore, particle-associated AOA may couple nitrite production and consumption via co-enriched ammonium monooxygenase (amoA) and nitrite reductase (nirK), potentially increasing nitrogen loss through local nitrite utilization. Collectively, our findings demonstrate that differential adaptation across clades underpins the pivotal role of AOA in nitrogen cycling under deoxygenation.}, }
@article {pmid41909265, year = {2026}, author = {Nagy, &#xc1; and Tóth, GE and Sály, P and Pereszlényi, CI and Babinszky, GC and Makrai, L and Somogyi, BA and Gyuranecz, M}, title = {Development of Nanopore amplicon sequencing method for culture-free genotyping of Bacillus anthracis strains directly from environmental samples.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1771578}, pmid = {41909265}, issn = {1664-302X}, abstract = {Fast and accurate genetic subtyping of pathogens is required to respond appropriately to biological events caused by natural outbreaks or bioattacks involving anthrax. In this study, we developed and validated a culture-free genotyping method that combines a multiplex PCR-based amplicon sequencing method on the Nanopore platform with in silico multiple-locus variable-number tandem repeat analysis (MLVA) of 31 loci to identify an unknown Bacillus anthracis strain directly from environmental samples. The novel method accurately identified repeat numbers for all loci in 12 different MLVA genotype Bacillus anthracis strains analyzed in the study, matching 100% with the reference capillary electrophoresis and Sanger sequencing results. The detection limit of the method, at which all 31 variable-number tandem repeat loci were successfully identified, was found to be 10[4] CFU spores/sample for pure spore samples and at 10[6] CFU spores/sample for spiked environmental samples from three matrices (soil, swab, and muddy water). Specificity tests yielded negative results for samples containing only non-Bacillus anthracis members of the Bacillus cereus group, which produced sequencing reads for 15 loci but were non-specific to Bacillus anthracis. To validate the method, we genotyped 11 Bacillus anthracis strains originating from a historical collection of Hungarian isolates. The MLVA31 typing scheme classified the strains into five groups, four of which fell into the A.Br.008/009 Trans-Eurasian (TEA) group within the clade A, and one into the B.Br.CNEVA group within the clade B. The largest group within clade A comprises six strains that are assumed to be members of the dominant Bacillus anthracis population in Hungary. Our results demonstrate that PCR-based amplicon sequencing using the portable MinION device is highly effective for on-site genotyping of pathogens directly from environmental samples. This establishes the NGS-based MLVA genotyping as a valuable tool for biodefense laboratories in preliminary forensic investigations of bioterrorism-related anthrax outbreaks. Furthermore, our results provide new insights into the genetic diversity of Bacillus anthracis in a region (Hungary, Central Europe) that is underrepresented in research and has limited scientific data.}, }
@article {pmid41909643, year = {2026}, author = {Yao, Y and Hu, X and Li, R and Tan, Z and Yu, H and Lin, Z and Zhang, T and Habimana, O}, title = {Probiotic yeast engineers a protective biofilm environment to enhance bioremediation and seahorse health in aquaculture.}, journal = {Biofilm}, volume = {11}, number = {}, pages = {100357}, pmid = {41909643}, issn = {2590-2075}, abstract = {Sustainable animal farming via intensive aquaculture relies on a balanced microbial ecosystem that promotes animal well-being. This research explored the use of the probiotic yeast Saccharomyces boulardii to influence tank biofilm microbiomes for improving the health of lined seahorses, Hippocampus erectus. Following a severe mortality event at week 6 that affected both groups, the control group demonstrated partial recovery to 71.4% survival, whereas the probiotic group achieved a higher survival, with a final rate of 88.9% after a disease challenge. This recovery led to a notable reduction in enteritis occurrences with a significant increase in average body weight and a 3.9-fold increase in activity compared to control conditions. Shotgun metagenomic analysis indicated that the enhancements were significantly supported by a marked reorganization of the tank's biofilm community. Probiotic supplementation significantly reduced microbial diversity and selected for a beneficial consortium enriched in taxa with recognized roles in nutrient cycling, including Rhodobacterales (involved in sulfur cycling and pathogen antagonism) and Pirellulaceae (key in polysaccharide breakdown). This engineered biofilm has greater genetic potential for energy generation, glucose degradation, and inorganic ion transfer. Crucially, virulence factor genes and pathogen-associated sequences were substantially suppressed in probiotic-treated biofilms. Our research shows that S. boulardii acts as a crucial modulator, creating a protective biofilm that boosts bioremediation while decreasing pathogenic threats. This ecological approach to the application of probiotics (targeting the environmental rather than host-associated microbiome) may offer a sustainable means to promote health and resilience within aquaculture systems.}, }
@article {pmid41909838, year = {2026}, author = {Zhang, B and Wang, L and Wang, J and Qi, D and Zhang, N}, title = {Comparative diagnostic performance of metagenomic next-generation sequencing and conventional microbial culture in spinal infections: a systematic review and meta-analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1689254}, pmid = {41909838}, issn = {2235-2988}, mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; *Spinal Diseases/diagnosis/microbiology ; *Microbiological Techniques/methods ; }, abstract = {BACKGROUND: Spinal infections are relatively uncommon but clinically serious conditions that require timely and accurate diagnosis to prevent severe complications. Traditional microbial culture methods remain the gold standard but suffer from low sensitivity and prolonged turnaround times. Metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic tool offering broad-spectrum pathogen detection. However, its diagnostic performance in spinal infections remains unclear.<br><br>OBJECTIVE: To systematically evaluate and compare the diagnostic accuracy of mNGS and conventional microbial culture in detecting pathogens in spinal infections.<br><br>METHODS: This systematic review and meta-analysis adhered to the 2020 PRISMA guidelines and was registered in PROSPERO. A comprehensive literature search of PubMed, Cochrane Library, Web of Science, and Scopus was performed up to July 2025. Studies involving suspected spinal infection patients tested by both conventional microbiological methods and metagenomic next-generation sequencing (mNGS) were included. Data extraction and quality assessment were independently conducted by two reviewers using standardized tools. Meta-analyses were performed to pool diagnostic accuracy metrics, and publication bias was assessed.<br><br>RESULTS: A total of 14 studies involving 1,353 patients were included after screening 4,132 records. All studies originated from China, with sample sizes ranging from 17 to 301. Quality assessment showed generally high methodological rigor with low risk of bias. Conventional meta-analysis demonstrated that mNGS had significantly better positive agreement (OR = 0.46, p < 0.00001), higher sensitivity (OR = 0.45, p < 0.00001), and superior negative predictive value (OR = 0.36, p < 0.00001) compared to traditional methods, while specificity and positive predictive value were comparable. Diagnostic meta-analysis revealed pooled sensitivity and specificity of 0.86 and 0.90, respectively, with an AUC of 0.90, indicating high diagnostic accuracy. Fagan nomogram analysis showed that with a 50% pre-test probability, positive and negative mNGS results corresponded to post-test probabilities of 89% and 13%, respectively. No significant publication bias was detected.<br><br>CONCLUSIONS: mNGS exhibits superior sensitivity and overall diagnostic accuracy compared to traditional microbial culture in spinal infections, supporting its use as a valuable complementary diagnostic tool. Further prospective, multicenter studies are warranted to validate these findings and promote standardized clinical implementation.<br><br>PROSPERO, identifier CRD420251114975.}, }
@article {pmid41909845, year = {2026}, author = {Wang, C and Min, M and Dai, Z and Wang, G and Wang, Y and Hu, T and Ma, Y and Zhang, S and Wu, C and Zhou, R}, title = {Diagnostic value of metagenomic next-generation sequencing in patients with febrile lung cancer with negative conventional microbiological tests and without neutropenia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1715563}, pmid = {41909845}, issn = {2235-2988}, mesh = {Humans ; *Lung Neoplasms/complications/microbiology/diagnosis ; Retrospective Studies ; Female ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; *Metagenomics/methods ; Aged ; *Fever/microbiology/diagnosis/etiology ; Aged, 80 and over ; }, abstract = {INTRODUCTION: Fever in nonneutropenic lung cancer often remains microbiologically unresolved because of the limitations of conventional microbiological tests (CMT). We assessed whether plasma metagenomic next-generation sequencing (mNGS) improves diagnostic yield and accelerates defervescence in these patients.<br><br>METHODS: We retrospectively analyzed 53 CMT-negative febrile lung cancer patients (August 2023-October 2024). Patients were classified into high-suspicion infectious fever (HSIF) or high-suspicion tumor fever (HSTF) groups based on mNGS results, and clinical management was adjusted accordingly.<br><br>RESULTS: mNGS identified pathogens in 69.8% (37/53) of patients, commonly including Epstein-Barr virus, Mycobacterium tuberculosis, and Candida albicans. Patients in the HSIF group showed significantly higher baseline inflammatory markers than those in the HSTF group. Importantly, following mNGS-guided antimicrobial therapy, the HSIF group achieved significantly higher defervescence rates at 48&#xa0;h (73.0% vs. 37.5%; p&#xa0;=&#xa0;0.029) and 96&#xa0;h (89.2% vs. 68.8%; p&#xa0;=&#xa0;0.027) compared to the HSTF group.<br><br>DISCUSSION: In conclusion, in CMT-negative, nonneutropenic febrile lung cancer, plasma mNGS significantly increases pathogen detection and informs antimicrobial decisions associated with earlier defervescence, although interpretation is limited by the retrospective design and lack of an independent gold standard.}, }
@article {pmid41909847, year = {2026}, author = {Huang, Y and Cai, Q and Chen, Y and Amutijiang, D and Lu, Y and Huang, W and Li, L}, title = {Phage characterization analysis in respiratory samples from infected patients based on metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1779296}, pmid = {41909847}, issn = {2235-2988}, mesh = {Humans ; *Metagenomics/methods ; *Bacteriophages/genetics/classification/isolation &amp; purification ; *High-Throughput Nucleotide Sequencing ; Sputum/virology/microbiology ; Bronchoalveolar Lavage Fluid/virology/microbiology ; *Respiratory Tract Infections/virology/microbiology ; Male ; Female ; Middle Aged ; Bacteria/virology/genetics ; Aged ; Computational Biology ; Adult ; Virome ; }, abstract = {BACKGROUND: Respiratory tract infections are common infectious diseases, with microbial dysbiosis closely linked to clinical outcomes in the host. As key regulators of bacteria, phages can influence the structure and stability of microbial communities by infecting host bacteria. Metagenomic next-generation sequencing (mNGS) enables comprehensive analysis of phage community characteristics in clinical samples.<br><br>METHODS: This study included 6,404 clinical samples, comprising 4,837 bronchoalveolar lavage fluids (BALF) and 1,567 sputum samples, for metagenomic next-generation sequencing (mNGS), while collecting patient demographics, sample types, mNGS results, and clinical outcomes. Host-derived sequences were removed post-sequencing and aligned against viral reference databases. Phage community structures across sample types were assessed using alpha and beta diversity metrics. Spearman correlation analysis explored associations between phages and bacteria. Further bioinformatics analysis was performed on 194 samples, including viral sequence assembly and identification using SPAdes, VirSorter2, and PhaMer; CD-HIT clustering and redundancy removal; CheckV quality assessment; PhaTYP lifestyle prediction; Prodigal protein gene annotation; and BLASTP alignment against the CARD database to screen for phage resistance genes.<br><br>RESULTS: The sputum and BALF groups exhibited comparable richness, diversity, and evenness, yet their community structures differed significantly. Intensive Care Unit (ICU) admission status was closely associated with reduced phage community diversity and significant alterations in community structure, and the abundance distribution of several phage families (Peduoviridae, Autoscriptoviridae, Casjensviridae, Demerecviridae) also changed significantly. Additionally, the phage community structure in sputum samples was significantly associated with patient clinical outcomes. Correlation analysis demonstrated that the Aliceevansviridae family in sputum samples had extensive positive associations with various bacteria. After assembly, 69.5% of pOTUs were predicted to be temperate phages, and 28.9% were predicted to be virulent phages; moreover, the vast majority (99.2%) of phage sequences showed low similarity to antibiotic resistance genes.<br><br>CONCLUSION: This study identifies distinct phage community characteristics across respiratory sample types and reveals that ICU patients exhibit reduced phage diversity and markedly altered community structures. Furthermore, the phage composition in upper respiratory tract samples shows a clear relationship with patient prognosis, providing new insights into respiratory infection microecology.}, }
@article {pmid41909891, year = {2025}, author = {Manzoor, H and Kayani, MUR}, title = {Insights into the gut microbiome-metabolite dynamics in breast cancer.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2483446}, pmid = {41909891}, issn = {2993-3935}, abstract = {In recent years, understanding the intricate connection between gut microbiome and cancer development has gained significant attention. The gut microbiome has a key role in maintaining overall human health and modulating the body's defense mechanism against various diseases. This review examines the multifaceted association between the gut microbiome and breast cancer, providing a comprehensive overview of studies from the last two decades that investigate both anti-cancer and pro-cancer properties of gut metabolites. Compounds such as nisin, inosine, acetate, propionate, and conjugated linoleic acids have demonstrated potential as therapeutic agents against breast cancer, while others, including butyrate, lactate, certain bile acids, and secondary metabolites, exhibit dual roles, showing both anti-cancer and pro-cancer properties under different conditions, with some implicated in tumor progression. Moreover, emerging research highlights the dual roles of these metabolites in influencing the efficacy of conventional breast cancer therapies. Despite promising evidence, the molecular mechanisms underlying these opposing actions remain unclear and require further investigation. To advance our understanding, future research should prioritize elucidating these mechanisms, establishing dose-response relationships, and conducting animal and clinical studies to validate in vitro findings. This review also identifies key gaps and highlights potential directions for future research in this field.}, }
@article {pmid41909892, year = {2025}, author = {Montenegro-Borbolla, E and Wakim El-Khoury, J and Bertelli, C and Schoepfer, A and Guery, B and Galperine, T}, title = {Resolution of long-term severe irritable bowel syndrome following fecal microbiota transplantation: A case report and microbiota analysis.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2487905}, pmid = {41909892}, issn = {2993-3935}, abstract = {The diagnosis and management of irritable bowel syndrome (IBS) is challenging due to its complex symptoms and inconsistent treatment responses. Given the important role of gut microbiota in gastrointestinal health, fecal microbiota transplantation (FMT) is a promising intervention. We describe the case of a 55-y-old woman without prior gastrointestinal issues who, following severe depression, developed multiple gastrointestinal symptoms, including abdominal pain, fluctuating bowel habits, and a persistent burning sensation in her mouth and upper gastrointestinal tract. At Lausanne University Hospital, she was diagnosed with IBS resistant to multiple lines of treatment and a multidisciplinary team proposed multiple oral FMTs. One-month post-FMT, her gastrointestinal symptoms significantly improved and remained better after a year, with only the burning sensation persisting. Analysis of pre- and post-FMT samples and donor material, using 16S rRNA amplicon metagenomics, revealed a 90% genus-level taxonomic overlap between the patient and the donor. The observed changes in the relative abundance of these genera, including the enrichment of beneficial gut commensals, as well as the elimination of IBS-associated genera likely supported her recovery. Overall, FMT led to substantial improvement in her long-standing gastrointestinal symptoms.}, }
@article {pmid41909896, year = {2025}, author = {Yasuda, T and Takagi, T and Naito, Y and Inoue, R and Mizushima, K and Asaeda, K and Hashimoto, H and Kitae, H and Uchiyama, K and Ouchi, N and Adachi, A and Kamitani, T and Matoba, S and Itoh, Y}, title = {Sarcopenia-related gut microbiota in the elderly: Insights from the longevity region of Kyotango and its nutritional associations.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2591561}, pmid = {41909896}, issn = {2993-3935}, abstract = {Sarcopenia is influenced by the gut microbiota and dietary habits; however, the underlying mechanisms remain elusive. This study investigated the gut microbiota composition of elderly individuals in a healthy longevity region and examined its association with sarcopenia and dietary habits. Fecal metagenomic analysis was used to identify gut microbiota taxonomy. Sarcopenia was diagnosed on the basis of grip strength, gait speed, and muscle volume. Japanese dietary habits were assessed using a brief-type self-administered diet history questionnaire. A total of 318 elderly individuals from Kyotango were recruited, 5.7% of whom were diagnosed with sarcopenia. Individuals with sarcopenia exhibited a lower abundance of a genus belonging to the family Lachnospiraceae, and a higher abundance of Megasphera. Several butyrate-producing bacteria, including Lachnospira and Coprococcus showed a positive correlation with sarcopenia related factors, whereas Dorea and Streptococcus were negatively correlated. Hierarchical cluster analysis revealed that these beneficial genera were also positively associated with the frequent intake of traditional Japanese dietary components. These findings suggest that the observed microbial and dietary associations may provide a mechanistic basis for potential protective effects against sarcopenia. Our findings suggest that butyrate-producing bacteria associated with Japanese dietary patterns play a protective role against sarcopenia.}, }
@article {pmid41909897, year = {2025}, author = {Gitton-Quent, O and Sola, M and Maziers, N and Hiol, A and Dechamp, N and Le Chatelier, E and Touvier, M and Galan, P and David, A and Morabito, C and Famechon, A and Quinquis, B and Mariadassou, M and Veiga, P and Dore, J and Berland, M and Deschasaux-Tanguy, M}, title = {Alterations in gut microbiota characteristics along a type 2 diabetes risk gradient linked with family history.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2527766}, pmid = {41909897}, issn = {2993-3935}, abstract = {Type 2 diabetes (T2D) is a major global health issue, with growing evidence linking it to gut microbiome changes. However, whether these alterations precede T2D onset and act as predictors, risk factors, or contributors remains unclear. This study analyzed the gut microbiota of 192 individuals from the French NutriNet-Santé cohort, divided into four groups: non-T2D adults with no (n = 47), one (n = 48), or two (n = 51) T2D-affected parents, and T2D-affected adults (n = 46). A progressive microbiota shift was observed in non-T2D groups based on parental history, converging toward the T2D profile. Changes included altered enterotype distribution, increased oral-associated species, disrupted ecological networks, and a shift in Gram-positive-to-negative ratios. Notably, Prevotella copri abundance increased, alongside bacteria potentially enhancing branched-chain amino acid (BCAA), lipopolysaccharide (LPS), and acetate production. Diet also influenced microbiota patterns, with sweet product intake, vitamin levels, and copper/zinc ratios playing roles. A gradual microbiome transition from non-diabetic to T2D participants underscores its association with family history-based risk. While these shifts may reflect or drive T2D progression, further studies are needed to confirm these findings and explore their potential for preventive strategies.}, }
@article {pmid41909909, year = {2025}, author = {Wang, H and Yu, S and Zhao, K and Hu, T and Wu, Z and Liang, H and Lin, X and Cui, L and Yao, J and Liu, X and Tong, X and He, N and Xiao, L and Kristiansen, K and Li, S and Zou, Y}, title = {Faecalibacterium longum alleviates high-fat diet-induced obesity and protects the intestinal epithelial barrier in mice.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2459599}, pmid = {41909909}, issn = {2993-3935}, abstract = {Numerous studies have indicated that depletion of Faecalibacterium is related to obesity. Here we show that Faecalibacterium longum CM04-06 out of 29 strains of the Faecalibacterium genus annotated in CGR2 exhibited the strongest inverse correlation with body mass index (BMI) in a cohort of 1120 han Chinese individuals. Administration of F. longum CM04-06 to mice prevented high-fat diet (HFD)-induced obesity, improved glucose tolerance, reduced adipose tissues mass, and liver steatosis. Supplementation with F. longum CM04-06 reduced the level of pro-inflammatory cytokines in liver, colon, and circulation. F. longum CM04-06 protected the intestinal epithelial barrier increasing the expression of tight junction proteins. Metagenomic sequencing indicated that F. longum supplementation did not change the overall composition of the gut microbiota in mice, but selectively increased the relative abundance of Staphylococcus xylosus and Staphylococcus nepalensis. In conclusion, our results point to a potential therapeutic potential of F. longum CM04-06.}, }
@article {pmid41909910, year = {2025}, author = {Batool, M and McMahon, S and Franklin, S and Ramont, C and Sahasrabhojane, P and Chang, CC and Hayase, T and Hayase, E and Blazier, JC and Jenq, R and Shelburne, S and Galloway-Peña, J}, title = {Gut microbiome features and resistome elements associated with colonization and infection with antibiotic-resistance threats.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2570502}, pmid = {41909910}, issn = {2993-3935}, abstract = {Infection with antimicrobial-resistant (AR) pathogens is a leading cause of morbidity and mortality among patients with hematological malignancies; however, little is known about the gut microbiome dynamics in acute myeloid leukemia patients and its impact on AR infections (ARI) and/or colonization with AR pathogens (ARC). Longitudinal stool samples collected from 154 patients undergoing induction chemotherapy were analyzed using 16S rRNA sequencing, selective and differential media culturing, MALDI-TOF, and VITEK2 to identify patients with ARC or ARI and to isolate AR infectious and colonizing bacterial strains. Shotgun metagenomic sequencing of baseline stool samples revealed taxa abundances, resistome features, and KEGG pathways associated with AR-events. Baseline observed species were lower in patients with AR-events (p = 0.01). Although several baseline taxa were more abundant in AR-event patients, they were not statistically significant when they were corrected for false discovery. Functional analysis revealed that penicillin and cephalosporin biosynthesis pathways were significantly enriched in patients with ARC. In summary, identifying the baseline microbiome, resistome, and functional pathway biomarkers may forecast an increased risk of ARI and/or ARC, thereby informing antimicrobial treatment strategies in AML patients.}, }
@article {pmid41909911, year = {2025}, author = {Shi, J and Nguyen, SM and Yu, D and Wang, L and Liu, L and Cai, H and Wu, J and Long, J and Cai, Q and Shrubsole, MJ and Zheng, W and Shu, XO}, title = {Association of physical activity with gut microbiome among low-income black American adults in the Southern Community Cohort Study.}, journal = {Gut microbes reports}, volume = {2}, number = {1}, pages = {2589861}, pmid = {41909911}, issn = {2993-3935}, abstract = {Physical activity (PA) has been suggested to influence the gut microbiome. We evaluated this association among low-income Black American adults. This study included 489 self-identified Black American participants from the Southern Community Cohort Study. PA data, including exercise/sport- and work/home-related moderate-vigorous PA (MVPA), was collected at cohort enrollment (2002-2009). Stool samples were collected between 2018 and 2021, and microbial composition was profiled using shotgun metagenomic sequencing. General linear regression models were employed to evaluate associations between PA and gut microbial α-diversity, abundance of individual species and metabolic pathways. Among all participants, MVPA measures were not associated with Shannon α-diversity (p > 0.05) and explained approximately 0.2-0.3% variation of Bray-Curtis dissimilarity. A total of 32 bacterial species, including seven Bacteroides species, two Streptococcus species, two Prevotella species, and nine microbial metabolic pathways, including D-fucofuranose biosynthesis, xyloglucan degradation, biosynthesis of L-citrulline, L-aspartate and L-asparagine biosynthesis, and urea cycle, were significantly associated with work/home-related and/or total MVPA (all false discovery rates < 0.10). In conclusion, MVPA, particularly from work and home activities, may modulate the composition and functionality of the gut microbiome among Black American adults.}, }
@article {pmid41910132, year = {2026}, author = {Sáenz, JS and Yergaliyev, T and Rios-Galicia, B and Seifert, J and Camarinha-Silva, A}, title = {The chicken gut virome: spatial structuring and extensive diversity of 19,778 viral populations.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0019126}, doi = {10.1128/msystems.00191-26}, pmid = {41910132}, issn = {2379-5077}, abstract = {UNLABELLED: Viral communities, especially phages, affect prokaryotic diversity and thus influence the host's metabolic processes. However, the makeup and role of the chicken gut virome remain poorly understood. To address this gap, we mined 1,458 chicken gut metagenomes and 56 viral-enriched samples to recover viral sequences and assemble a comprehensive collection of draft viral genomes. We identified 19,778 viral operational taxonomic units (vOTUs), of which 97% were dsDNA phages from the Caudoviricetes class, primarily targeting gut bacteria such as Lactobacillus, Limosilactobacillus, and Escherichia. Most protein-coding genes in these genomes were uncharacterized and lacked known biological functions. Additionally, the distribution of vOTUs across samples showed that the chicken virome is highly individual-specific. Yet, the viral community also exhibited strong spatial stratification along the gastrointestinal tract, with notable differences between proximal and distal regions, primarily driven by phages linked to the Lactobacillaceae family. Moreover, this study shows that the geographical region, breed, and diet drive the chicken gut viral diversity and composition. This underscores the significant novelty of the chicken gut virome and its largely unexplored functional potential, much of which would be missed if analyses were restricted to fecal samples.<br><br>IMPORTANCE: The chicken gut harbors a vast community of viruses that remain largely unexplored despite their potential to influence poultry health and productivity. By analyzing 1,514 samples from different gut regions across 15 countries, we discovered nearly 20,000 distinct viruses, most of which were previously unknown phages. The chicken virome showed strong spatial differences along the gastrointestinal tract, meaning each gut section harbors a unique viral community, underscoring that fecal samples alone miss much of the virome's diversity. We also uncovered that the geographical region, breed, and diet could drive the chicken gut viral diversity and composition. Overall, our findings greatly expand our understanding of gut virus diversity and microbiome ecology, offering a valuable foundation for developing strategies to monitor or manipulate the microbiome to improve poultry health.}, }
@article {pmid41910137, year = {2026}, author = {Li, X and Wang, H and Abdelrahman, HA and Kelly, AM and Roy, LA and Soto, E and Wang, L}, title = {Temperature modulates gut microbiome disruption and resistome enrichment in oxytetracycline-treated channel catfish (Ictalurus punctatus).}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0418725}, doi = {10.1128/spectrum.04187-25}, pmid = {41910137}, issn = {2165-0497}, abstract = {UNLABELLED: Oxytetracycline (OTC) is one of the few antibiotics approved by the U.S. Food and Drug Administration for catfish aquaculture. Unfortunately, OTC resistance has been frequently detected in production environments, with the fish gut identified as a potential hotspot for resistance selection. In aquaculture systems, water temperature is a critical factor influencing fish physiology, antibiotic pharmacokinetics, and water resistome development. However, its role in modulating OTC effects on the fish gut microbiome remains underexplored. This study examined temperature-dependent microbiome and resistome responses in channel catfish (Ictalurus punctatus) when treated with OTC at 20°C, 25°C, and 30°C. Gut contents collected at treatment completion and after withdrawal were analyzed via metagenomic sequencing. In untreated fish, temperature alone shaped microbial structure and function, with the Shannon diversity increasing with temperatures and the β-diversity differing significantly across temperature groups. After OTC exposure, microbial responses were markedly temperature dependent with few taxa affected at 20°C, whereas substantial shifts occurred at 25°C and 30°C, indicating reduced microbial resilience at higher temperatures. OTC elevated total antimicrobial resistance gene (ARG) abundance, enriching tetracycline and β-lactam resistant genes consistent with co-selection. ARG-host linkages were diffuse at 20°C but consolidated within Klebsiella, Enterococcus, Enterobacter, and Paraclostridium at 25°C and 30°C. Notably, OTC-induced dysbiosis persisted through the withdrawal period. These findings demonstrate that temperature modulates both the magnitude and persistence of OTC-driven microbiome disruption and resistome enrichment, underscoring the importance of temperature-aware antibiotic management to mitigate antimicrobial resistance risks and safeguard fish health and food safety in aquaculture.<br><br>IMPORTANCE: This study reveals that water temperature critically shapes how antibiotics affect the gut microbiome and antimicrobial resistance in channel catfish. Metagenomic sequencing results showed that oxytetracycline (OTC) treatment caused minimal disruption of the microbiome at 20&#xb0;C, but induced significant community shifts and enrichment of antimicrobial resistance genes (ARGs) at 25&#xb0;C and 30&#xb0;C. Higher temperatures reduced microbial resilience, consolidating ARGs within key bacterial genera such as Klebsiella and Enterococcus. Importantly, OTC-induced microbiome changes and resistance persisted through the withdrawal period. These findings highlight temperature as a major driver of antibiotic impact in aquaculture, emphasizing the prudent use of antibiotics at different disease breakout temperatures.}, }
@article {pmid41910214, year = {2026}, author = {Zhang, F and Xu, W and Zeng, R and Chen, J and Huang, J}, title = {Limosilactobacillus reuteri normalizes gut microbiota dysfunction and social deficits of rat offspring associated with prenatal exposure to stress.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2649440}, doi = {10.1080/19490976.2026.2649440}, pmid = {41910214}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Female ; Pregnancy ; *Limosilactobacillus reuteri/physiology ; Rats ; *Prenatal Exposure Delayed Effects/microbiology ; Male ; Social Behavior ; Oxytocin/metabolism ; Fecal Microbiota Transplantation ; *Stress, Psychological/microbiology ; Rats, Sprague-Dawley ; *Probiotics/administration &amp; dosage ; Paraventricular Hypothalamic Nucleus/metabolism ; Behavior, Animal ; }, abstract = {Prenatal stress (PS) is a potential risk factor for social behavior impairment in offspring. Here, we demonstrate that PS induces gut microbiota alterations that are associated with impaired sociability and social novelty preference in rat offspring. In addition, we found that these behavioral deficits could be partially rescued through either cohousing with normal offspring or fecal microbiota transplantation from control donors. Metagenomic analysis identified Limosilactobacillus reuteri (L. reuteri) as a key species based on the considerable difference in its abundance between the PS and control offspring. Subsequent investigations revealed that supplementing L. reuteri during critical neurodevelopmental windows restored oxytocin levels in the paraventricular nucleus (PVN) and rescued dopamine reward pathway function, thereby ameliorating PS-induced social deficits. Notably, these beneficial effects were completely abolished by either treatment with an oxytocin receptor antagonist or subdiaphragmatic vagotomy. Thus, both oxytocin signaling and vagal afferent pathways play essential roles in the observed benefits of L. reuteri. Our findings indicate that social behavior impairments in offspring exposed to prenatal maternal stress can be explained by a novel mechanism involving the gut microbiota-brain axis: whereby PS-induced depletion of specific commensal bacteria (particularly L. reuteri) disrupts vagus nerve-mediated oxytocinergic modulation of PVN-to-VTA dopaminergic circuits, ultimately leading to social behavior impairments in offspring.}, }
@article {pmid41910252, year = {2026}, author = {Yang, H and Liu, W and Niu, J and Geng, B and Qiu, P and Li, H and Bao, J and Pu, X and Li, Y and Jia, X and Sun, Y and Han, Y}, title = {Integrated metagenomic-metabolomic insights into plant-microbe interactions mediated by Bacillus volatile compounds.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0252325}, doi = {10.1128/aem.02523-25}, pmid = {41910252}, issn = {1098-5336}, abstract = {Modulation of plant-microbe interactions with signaling molecules offers a promising strategy to promote plant growth and stress adaptation. However, identifying effective signaling molecules and elucidating the mechanisms for regulating the rhizosphere microbiome remain major challenges. In this study, the roles and mechanisms of Bacillus volatile compounds as potential signaling molecules in plant-microbe interactions were investigated. First, the genome and metabolism of a novel Bacillus subtilis strain capable of producing acetoin and 2,3-butanediol were studied, and the titers of the two compounds were increased to 86.76 g/L by sequential metabolic engineering. Subsequently, the effects of volatile compounds on the growth of vegetables (Brassica rapa and Solanum lycopersicum var.) were studied. Plant growth, nutrient (nitrogen, phosphorus, and potassium) utilization efficiency, and salt stress resistance were improved significantly. Compared with water as a control, significant changes in the abundance of 109 microbial genera of B. rapa's rhizosphere microbiome were identified with volatile compound application. Notably increased microbes included nitrogen-fixing, phosphate- and potassium-solubilizing, stress-resistant, plant growth-promoting, and auxin-secreting microbes. Additionally, genes involved in nitrogen, phosphorus, and potassium utilization in the rhizosphere microbiome were significantly increased, and corresponding metabolism was found. Finally, metabolomic analyses of S. lycopersicum var.'s roots and leaves revealed 67 significantly upregulated compounds with the application of volatile compounds. These compounds were primarily involved in stress resistance, oxidative stress alleviation, free radical scavenging, and auxin-related plant growth promotion. This work demonstrates that Bacillus volatile compounds regulate rhizosphere microbiome and plant-microbe interactions and enhance plant nutrient utilization efficiency, stress tolerance, and growth.IMPORTANCEPlant productivity and stress resilience are strongly influenced by interactions between plants and the rhizosphere microbiome, yet practical strategies to rationally modulate native soil microbial communities remain limited. This study demonstrates that Bacillus volatile compounds, specifically acetoin and 2,3-butanediol, function as effective signaling molecules that coordinate plant-microbe interactions in the rhizosphere. By integrating plant physiology, metagenomics, and metabolomics, we show that these volatile compounds not only enhance plant growth and nutrient use efficiency but also reprogram rhizosphere microbial communities toward functions that benefit nitrogen, phosphorus, and potassium acquisition and stress adaptation. Notably, volatile application improved plant salt tolerance, highlighting their strong ecological and physiological impact. This work provides mechanistic evidence that Bacillus-derived volatiles act as signaling molecules to activate the rhizosphere microbiome and plant metabolic responses. The findings offer a scalable and environmentally friendly strategy for improving crop performance and soil health, with broad implications for sustainable agriculture.}, }
@article {pmid41910273, year = {2026}, author = {Tobias-Hünefeldt, SP and Woodhouse, JN and Ruscheweyh, H-J and Sunagawa, S and Russnak, V and Streit, WR and Grossart, H-P}, title = {Osmotolerance is a driver of microbial carbon processes in the Elbe estuary.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0179025}, doi = {10.1128/msystems.01790-25}, pmid = {41910273}, issn = {2379-5077}, abstract = {UNLABELLED: Estuaries are blue carbon loci, storing and exchanging carbon between aquatic, atmospheric, and terrestrial environments. Estuarine particles facilitate the transformation and transport of organic matter. The fate of particulate organic matter in estuaries is driven by structural changes in polymers that modify buoyancy, determining the proportions of sinking and suspended particles. In the open ocean and coastal ecosystems, the microbial composition and function of sinking and suspended particles differ, impacting carbon remineralization and sedimentation rates. We leverage 190 metagenomes and 73 metatranscriptomes to assess free-living, sinking, and suspended particle-associated microbial composition and function across the Elbe estuary. The salinity gradient in the Elbe estuary is the primary driver of microbiome composition and function. Transparent exopolymer particles (TEP) production was localized to freshwater, with seemingly no TEP-associated organisms detected above 20 practical salinity units (PSU). We observed differences in the function of free-living and particle-associated microbial communities, with diazotrophs enriched on particles. We observed that sinking particles may better support methanogenesis, and suspended particles showed signs of continued primary and secondary production. From this, we conclude that activities such as dredging, which resuspend sediment, will exacerbate carbon turnover and greenhouse gas emissions, and reduced dredging may lower greenhouse gas (GHG) emissions in the Elbe estuary. Many of these GHG linking processes are inhibited by salinity due to the osmosensitivity of methanogens and methanotrophs along the estuary. Changes in sea level and precipitation rates will likely directly interact with activities such as dredging, with as yet uncertain impacts on microbial carbon processing and storage.<br><br>IMPORTANCE: Estuaries, lower river areas that merge into oceans, play a large role in Earth's carbon cycle. Estuaries store carbon and manage greenhouse gases, exchanging carbon between land, water, and the air. As carbon travels down estuaries, it is processed by free-living and particle-associated microbes. We explore the relationship between environmental conditions and present and expressed genes. Based on gene profiles, methane concentrations in the water column may be related to the abundance of sinking particles, while suspended particles are linked to growth and energy acquisition. Therefore, the balance of suspended vs. sinking particles is important in highly turbid estuaries, like the Elbe estuary, where urban activities affect greenhouse gas emissions and salinity intrusions. Dredging often tips the balance toward sinking particles and therefore increased greenhouse gas emissions. Our study thereby informs future policy decisions and the impact these decisions will have on our future climate.}, }
@article {pmid41910342, year = {2026}, author = {Dixit, K and Busi, SB and Ahmed, A and Kshirsagar, A and Jäger, C and Singh, A and Shah, V and Saroj, SD and Ahuja, V and Wilmes, P and Shouche, Y and Makharia, G and Dhotre, D}, title = {Multi-meta-omics reveal distinct microbial genomic profiles and metabolic dysregulation in non-celiac gluten sensitivity.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0085625}, doi = {10.1128/msphere.00856-25}, pmid = {41910342}, issn = {2379-5042}, abstract = {UNLABELLED: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis, and its symptoms overlap with irritable bowel syndrome (IBS). The gut microbiome is likely to play a role in the pathogenesis of NCGS. We analyzed the gut microbiome in patients with NCGS and in patients with IBS, using shotgun metagenomics and metabolomics of fecal samples. Analyses of taxonomic and functional microbial diversity revealed a higher abundance of methanogenic archaea, such as Methanobrevibacter filiformis, Methanobrevibacter boviskoreani, Methanosphaera stadtmanae, and a higher fold change in urea, uridine 5-monophosphate, and adenosine monophosphate in patients with NCGS compared to patients with IBS, who showed higher fold changes in metabolites gamma-aminobutyric acid and lactic acid. Furthermore, pangenome and metabolome analyses revealed disease-specific gene clusters, as well as genomic and metabolic features differentiating NCGS from IBS. While patients with NCGS did not show lower potential for gluten degradation, a lower synthetic potential for fructan beta-fructosidase was found in them. The present study provides an extensive analysis of taxonomic, genomic, and metabolic features that may play a role in the pathogenesis and symptom development in patients with NCGS.<br><br>IMPORTANCE: Non-celiac gluten sensitivity (NCGS) is an emerging diagnosis with symptoms that overlap with irritable bowel syndrome (IBS). Using shotgun metagenomics and metabolomics, we report deeper insights into the microbiome profile, including viral and archaeal diversity, lower fructan degradation potential, the differential abundance of metabolites, and genomic features of gut bacteria in patients with NCGS. Understanding the microbiome associated with this disorder may shed light on the possible role of the microbiome in the pathophysiology of NCGS.}, }
@article {pmid41910375, year = {2026}, author = {Sprenger, GA and Gee, JE and Elrod, MG and Weiner, ZP and Gulvik, CA}, title = {Shotgun metagenome sequencing and informatics can accurately form a metagenome-assembled genome (MAG) of the bacterial tier 1 select agent Burkholderia pseudomallei for rapid public health response events.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0292625}, doi = {10.1128/spectrum.02926-25}, pmid = {41910375}, issn = {2165-0497}, abstract = {Shotgun metagenomics, when sufficient read depth exists for each taxon, enables capturing metagenome-assembled genomes (MAGs) directly from a microbial community. In 2021, an aromatherapy spray contaminated with Burkholderia pseudomallei caused an outbreak of melioidosis in the United States. Metagenome-assembled genome binning depends in part on different nucleotide compositions, and the contaminated aromatherapy spray contained other bacteria, including related species (e.g., Burkholderia cepacia, Burkholderia cenocepacia, Burkholderia multivorans, Burkholderia pseudomultivorans, Cupriavidus pauculus, and Pseudomonas aeruginosa with average nucleotide identity (ANI) to B. pseudomallei being 84.2%, 84.4%, 84.7%, 84.8%, 75.7%, and 72.3%, respectively, and AAI being 79.5%, 79.8%, 80.5%, 80.4%, 62.5%, and 52.9%, respectively). We performed metagenomic sequencing on the contaminated aromatherapy spray to determine if a public metagenomic pipeline (https://github.com/nf-core/mag) can form a MAG of B. pseudomallei. Upon completion of the pipeline, inter- and intracontig comparisons revealed few potential contaminants of related taxa. Conservative removal of those contigs was especially valuable, ultimately obtaining an ANI of 99.9% between the B. pseudomallei MAG and the genome of an isolate from the aromatherapy spray. This underscores the importance of quality checking recovered MAGs (e.g., for congeneric chimerism) for high-resolution objectives such as outbreak pathogenomics. Importantly, our analysis revealed that the identical conclusion was made possible with the B. pseudomallei MAG (as with its corresponding isolate genome), which was that the aromatherapy B. pseudomallei originated from South Asia (specifically India). Because rapid read-based (k-mer) taxonomic classification methods often report false positives, this operational framework could be valuable for rapid biothreat radar detection systems in public health surveillance.IMPORTANCEIn 2021, an imported aromatherapy spray caused a U.S. outbreak of melioidosis after contamination with Burkholderia pseudomallei. Using shotgun metagenomics, we reconstructed a near-complete genome of the pathogen directly from the product, despite the presence of other related microbes. The assembled genome showed 99.9% similarity to a cultured isolate. This work demonstrates that metagenomics can recover high-quality pathogen genomes from complex samples, supporting outbreak investigations and enhancing public health surveillance.}, }
@article {pmid41910449, year = {2026}, author = {Santos, JCE and Go, DJL and Unciano, RD and Yu, PK and Lao, AR and Enriquez, MLD and Espiritu, LM and Shrestha, AMS}, title = {Investigating the resistome, taxonomic composition, and mobilome of bacterial communities in hospital wastewaters of Metro Manila using a shotgun metagenomics approach.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0396325}, doi = {10.1128/spectrum.03963-25}, pmid = {41910449}, issn = {2165-0497}, abstract = {We profiled antibiotic resistance genes, bacterial communities, and mobile genetic elements in untreated hospital wastewater from three tertiary hospitals in Metro Manila using shotgun metagenomic sequencing. The resistome analysis revealed high abundances of genes known to confer resistance against sulfonamides (sul1, sul2), aminoglycosides (aadS), and macrolides/streptogramins (msrE, mphE). High-risk resistance genes were also detected, including those known to confer resistance to β-lactams (blaOXA, blaTEM, blaGES, blaNDM, blaKPC), colistins (mcr-5), and tetracyclines [tet(C), tet(A), tet(L), tet(M)]. Comparisons with hospital wastewater resistome profiles from regional neighbors and other lower-and-middle-income countries indicated broadly similar relative abundances of dominant resistance genes, with differences largely driven by low-abundance resistance genes. The bacterial community was dominated by the phylum Pseudomonadota, with high relative abundances of the genera Stenotrophomonas, Rhodococcus, and Pseudomonas, while ESKAPEE pathogens were detected at lower levels. A diverse array of mobile genetic elements-many known to be associated with resistance to multiple drug classes and disinfectants-was also observed. Overall, this study provides a valuable preliminary evidence base for future antimicrobial resistance and epidemiological surveillance efforts in the Philippines, particularly those employing wastewater-based approaches.IMPORTANCEAntimicrobial resistance (AMR) is a growing public health threat caused by pathogenic bacteria that are no longer controlled by commonly used treatments. Infections caused by these resistant bacteria may lead to prolonged illness, more severe symptoms, or even death. Hospitals are critical hotspots for the emergence and spread of AMR. Their wastewater, which contains antibiotics, medical and human waste, and diverse microbial communities, can support the persistence and dissemination of resistant bacteria. The significance of this research lies in identifying and characterizing these bacterial communities and the resistance genes they carry. Such information can provide an indication of the resistance burden faced by patients and serve as an early warning system to strengthen infection prevention and control measures, support national surveillance efforts, and inform the development of more effective treatment and management strategies in healthcare settings.}, }
@article {pmid41910593, year = {2026}, author = {Bartelli, TF and Baydogan, S and Sahin, I and Hoffman, KL and Petrosino, J and Blackburn, KW and Zhao, J and Wood, A and Ayvaz, T and Surathu, A and Cagigas, MN and Barcenas, EC and Mata, T and Nguyen, VK and Zulbaran-Rojas, A and Li, L and Faraoni, EY and White, JR and Ajami, N and Li, L and Yadav, D and Conwell, DL and Serrano, J and Pandol, SJ and Fogel, EL and Van Den Eden, SK and Vege, SS and Topazian, MD and Park, WG and Hart, PA and Forsmark, C and Bellin, MD and Maitra, A and Bhutani, M and Kim, M and Van Buren, G and Fisher, WE and McAllister, F and , }, title = {Whole Metagenomic Profiling Identifies a Gut Microbial Signature for Chronic Pancreatitis via Machine Learning.}, journal = {Pancreas}, volume = {}, number = {}, pages = {}, doi = {10.1097/MPA.0000000000002618}, pmid = {41910593}, issn = {1536-4828}, abstract = {BACKGROUND: Pancreatitis significantly alters the microbial composition of the oral and intestinal compartments, causing dysbiosis that may contribute to disease mechanisms and potentially serve as a basis for diagnosis or treatment.<br><br>OBJECTIVE: To determine whether the oral or gut microbial signature can classify chronic pancreatitis (CP).<br><br>METHODS: Stool samples (n=707) were collected from participants in the Prospective Evaluation of Chronic Pancreatitis for Epidemiologic and Translational Studies (PROCEED). Samples were distributed among 200 healthy (HC), 310 CP, 49 acute pancreatitis (AP) and 148 recurrent acute pancreatitis (RAP). Additionally, saliva samples were collected for a subset of participants (n=156). Whole genome sequencing was performed to assess microbiome composition. Machine learning algorithms were utilized to identify a signature with microbial features predictive of CP.<br><br>RESULTS: Gut alpha diversity was significantly decreased in AP, RAP, and CP compared to HC, with CP exhibiting the lowest diversity. In contrast, oral microbial diversity showed no significant variation across groups. Beta diversity analysis revealed distinct gut microbiome compositions between HC and pancreatitis subtypes, with CP showing the most pronounced differences. Random forest models using gut microbial species demonstrated robust predictive performance for CP using a minimum of 10 species (Area under the curve - AUC: 0.834; accuracy: 0.774). Despite similarities in gut microbiome composition across pancreatitis subtypes, a unique gut microbial signature for CP was identified highlighting the microbiome's potential in CP diagnosis.<br><br>CONCLUSION: Our study reveals a gut microbial signature predictive of CP using machine learning models in a large US multi-institutional cohort.}, }
@article {pmid41910796, year = {2026}, author = {Zahran, E and Elbahnaswy, S and Bruce, TJ and Hegab, YE and Palic, D}, title = {Preliminary microbiome characterization of shrimp gut and pond water in Egyptian aquaculture farms: Implications for pathogen dynamics and management practices.}, journal = {Veterinary research communications}, volume = {50}, number = {3}, pages = {}, pmid = {41910796}, issn = {1573-7446}, }
@article {pmid41910951, year = {2026}, author = {Dasgupta, S}, title = {Metagenomics in Obstructive Lung Diseases: Insights into Microbial Dysbiosis, Host-Microbe Interactions, and the Gut-Lung Axis.}, journal = {Omics : a journal of integrative biology}, volume = {}, number = {}, pages = {15578100261419483}, doi = {10.1177/15578100261419483}, pmid = {41910951}, issn = {1557-8100}, abstract = {Obstructive lung diseases (OLDs), including asthma and chronic obstructive pulmonary disease (COPD), arise from complex interactions among microbial ecosystems, host immunity, metabolic regulation, and environmental exposures. Metagenomic approaches have substantially advanced understanding of these interactions by enabling comprehensive profiling of respiratory and gut-associated microbiomes and their functional potential. Evidence indicates that asthma is frequently associated with early-life microbial perturbations, reduced community diversity, enrichment of Streptococcus, Moraxella, and allergen-associated fungi, and gut dysbiosis that influences immune maturation and tolerance. In contrast, COPD is characterized by adult-onset dysbiosis with Proteobacteria dominance, depletion of commensal anaerobes such as Prevotella and Veillonella, and functional signatures linked to chronic inflammation, xenobiotic metabolism, and exacerbation risk. Across both diseases, alterations in gut microbial composition and metabolite profiles, including short-chain fatty acids, highlight the gut-lung axis as a key regulatory interface shaping airway immune responses. Despite these advances, critical knowledge gaps remain, including limited longitudinal data, incomplete multi-kingdom analyses, and insufficient mechanistic and translational validation of disease-associated microbiome signatures. This review integrates current metagenomic evidence to delineate disease-specific and shared microbial patterns, examines host-microbe interaction pathways within molecular and clinical contexts, and critically evaluates the implications and limitations of microbiome-based interventions. By framing microbiome research within a systems biology and public health perspective, this article underscores the importance of context-dependent interpretation and identifies priorities for future longitudinal, mechanistic, and translational studies in OLDs.}, }
@article {pmid41911008, year = {2026}, author = {Hosen, ME and Horwood, PF and Sarker, S}, title = {Integrating metagenomics and metatranscriptomics into Orthoflavivirus diagnosis: a transformative approach for clinical virology.}, journal = {The Journal of general virology}, volume = {107}, number = {3}, pages = {}, doi = {10.1099/jgv.0.002247}, pmid = {41911008}, issn = {1465-2099}, mesh = {*Metagenomics/methods ; Humans ; *Flaviviridae Infections/diagnosis/virology ; *Flaviviridae/genetics/isolation &amp; purification ; Transcriptome ; *Gene Expression Profiling/methods ; Virology/methods ; }, abstract = {Diagnostic inaccuracies are a major yet often overlooked threat to global health, leading to delayed treatment, preventable harm and systemic gaps in disease control. Among the most affected domains are Orthoflavivirus infections, which pose ongoing diagnostic challenges due to antigenic cross-reactivity, overlapping clinical symptoms and the narrow temporal sensitivity of standard tools such as serology and reverse transcription polymerase chain reaction. These constraints have led to widespread misdiagnoses and underreporting, ultimately hampering both effective clinical management and public health response. Recent advances in metagenomic and metatranscriptomic sequencing offer a transformative solution by enabling unbiased, simultaneous pathogen detection and real-time profiling of viral and host transcriptomics. In this review, we assess the diagnostic performance and translational value of these approaches in resolving Orthoflavivirus infections, with case examples from clinical settings in countries like the USA, UK, China and Germany which have already implemented these approaches into routine diagnosis in some settings. We examine key methodological considerations, including optimal sample timing, sample types and processing, sequencing strategy selection and the diagnostic performance of various platforms. We highlight the growing use of metatranscriptomics for detecting active infections, profiling viral and host responses, identifying coinfections and supporting real-time surveillance. We also discuss the key challenges such as technical expertise, lack of standardization, cost, turnaround time and regulatory approval that currently limit global implementation. Finally, we highlight emerging international efforts to integrate sequencing-based diagnostics into routine hospital workflows. Together, these innovations mark a critical shift toward precision diagnostics for Orthoflavivirus infections, with broad implications for clinical settings.}, }
@article {pmid41911519, year = {2026}, author = {Zhang, H and Cao, Z and Zha, X and Wang, W and Jashenko, R and Hu, H and Ji, R}, title = {Host intestinal microbiota adaptive changes following Paranosema locustae infection and mechanism of chronic pathogenesis.}, journal = {Journal of insect science (Online)}, volume = {26}, number = {2}, pages = {}, doi = {10.1093/jisesa/ieag027}, pmid = {41911519}, issn = {1536-2442}, support = {2023D01D08//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; TSYCLJ0016//Tianshan Talent Training Program/ ; 32260254//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Female ; Male ; *Orthoptera/microbiology ; Bacteria/classification ; }, abstract = {Paranosema locustae infection reduces the abundance and diversity of the intestinal bacteria in locusts, although the microbial adaptive changes and the underlying mechanism of chronic pathogenesis remain unclear. In this study, the intestinal microbial changes in Calliptamus italicus (Linnaeus, 1758) (Orthoptera: Acrididae) were analyzed with metagenomic sequencing after P. locustae infection. Results showed that the diversity of intestinal microbial communities in C. italicus declined after P. locustae infection, while the abundance of infection-specific taxa in C. italicus in the experimental groups was significantly higher than those in the control groups, irrespective of sex (P<0.05). The populations of opportunistic pathogenic bacteria such as Klebsiella aerogenes and Enterococcus faecalis increased significantly (P < 0.05). Meanwhile, the abundances of probiotics such as Pediococcus acidilactici and Enterobacter hormaechei increased significantly (P <0.05), which could inhibit the pathogenicity of P. locustae. The results suggested that the interplay of changes in the species and quantities of probiotics and pathogenic bacteria in the intestine of C. italicus after P. locustae infection was an important factor contributing to the difficulty of P. locustae in quickly breaching the host defense system and to its chronic pathogenicity.}, }
@article {pmid41893914, year = {2026}, author = {Pistone, D and Bevivino, G and Dipaola, MG and Bandi, C and Lombardo, F}, title = {Current and emerging molecular diagnostic approaches in the detection of human parasites.}, journal = {Parasitology research}, volume = {125}, number = {1}, pages = {}, pmid = {41893914}, issn = {1432-1955}, abstract = {Microscopy and morphological identification remain the gold standard for diagnosing most parasitic infections, yet their limited sensitivity in asymptomatic or low-burden cases, along with technical constraints, has accelerated the adoption of molecular diagnostics. Over the past three decades, advances in nucleic acid amplification and sequencing technologies have transformed parasite detection by improving sensitivity, specificity, and reproducibility, enabling earlier intervention and stronger surveillance. PCR remains the foundation of molecular diagnostics, with real-time PCR and digital PCR improving analytical performance and quantification. Multiplex qPCR supports simultaneous detection of multiple pathogens, while dPCR enables absolute quantification and rare variant detection, although broader implementation is limited by instrument cost. Isothermal amplification methods such as tHDA, NASBA, LAMP, and RPA offer rapid, low-cost amplification at constant temperature and are well suited for field diagnostics in resource-limited settings. Next-Generation Sequencing has advanced genotyping and epidemiological surveillance by resolving cryptic species, resistance mutations, and mixed infections through targeted panels, whole-genome sequencing, and metagenomics. CRISPR/Cas-based assays provide rapid and sensitive nucleic acid detection with strong potential for point-of-care deployment due to their simplicity and adaptability. Emerging biomarkers, including circulating cell-free DNA, non-coding RNAs, and microRNAs in extracellular vesicles, offer promising non-invasive diagnostic strategies, though further validation is required. This review offers a concise overview of these molecular approaches, emphasizing recent innovations such as dPCR, NGS, CRISPR/Cas systems, and biomarker-based detection. For each method, core technical principles, representative applications, and comparative strengths and limitations are presented to illustrate their diagnostic potential.}, }
@article {pmid41900284, year = {2026}, author = {Kwon, H and Seo, JW and Jeong, M and Kim, Y and Chang, CL and Kim, JH and Choi, GE}, title = {Dietary Administration of a Soybean Fermented Preparation Reshapes Gut Microbial Community Structure and Colonic Mucosal Features in BALB/c Mice.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, pmid = {41900284}, issn = {2076-2607}, support = {NRF-2022R1F1A1074419//National Research Foundation of Korea/ ; NRF-2022S1A5C2A04093562//National Research Foundation of Korea/ ; //Busan Metropolitan City and Busan Techno Park/ ; //RESEARCH FUND offered from Catholic University of Pusan in 2024./ ; }, abstract = {BACKGROUND/AIM: Fermented soybean-based products are known to influence gut microbial composition; however, the long-term effects of multicomponent soybean fermented preparations on gut microbiota and colonic mucosal features remain insufficiently characterized. This study examined the effects of a commercially available soybean fermented preparation (SFP), containing additional fermented plant and marine derived components, on gut microbial community structure and colonic histological features in BALB/c mice.<br><br>METHODS: BALB/c mice received oral SFP (1000 mg/kg) for 30 and 60 days. Gut microbial communities were analyzed using full-length rRNA operon sequencing. Colonic mucosal architecture and goblet cell density were evaluated via histological analysis (H&amp;E).<br><br>RESULTS: SFP supplementation induced significant &#x3b2;-diversity separation at both 30 and 60 days (p < 0.05), indicating consistent restructuring of the gut microbial community. While alpha diversity (Observed OTUs) remained stable at 30 days, Shannon and Simpson indices were significantly reduced at 60 days (p = 0.001), indicating reduced community evenness driven by increased dominance of specific taxa, including Duncaniella. At the genus level, SFP administration was associated with increased relative abundances of Akkermansia, Lactobacillus, and Duncaniella, accompanied by reductions in several genera previously linked to dysbiosis. Histological analysis demonstrated a significant increase in goblet cell density (p < 0.01) in SFP-treated mice.<br><br>CONCLUSIONS: Long-term SFP supplementation was associated with sustained alterations in gut microbial composition and measurable histological changes in the colonic mucosa. While these findings indicate that SFP intake influences microbial structure and goblet cell abundance, further studies are required to determine the functional and physiological implications of these changes, particularly in relation to epithelial barrier function and host health.}, }
@article {pmid41901695, year = {2026}, author = {Philips, CA and Oommen, TT and Theruvath, AH and Sreemohan, A and Baby, A and Alex, AA and Thomas, S and John, SM and Ahamed, R and Tharakan, A and Augustine, P}, title = {Novel Insights on Clinical Outcomes Using Integrated Shotgun Metagenomic Profiling of the Gut Microbiome, Resistome, and Host Immune-Inflammatory Response in Hospitalized Patients with Decompensated Cirrhosis.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41901695}, issn = {2076-0817}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Liver Cirrhosis/microbiology/immunology/mortality ; Male ; *Metagenomics/methods ; Female ; Middle Aged ; Aged ; Hospitalization ; Adult ; India ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Background and Aims: Sepsis drives mortality in cirrhosis, yet the gut antimicrobial resistance (AMR) landscape remains unmapped in high-burden settings like India. This study aimed to integrate shotgun metagenomics with deep immunophenotyping to define the gut-immune-resistome axis and correlate specific microbial and genetic signatures with clinical outcomes in decompensated cirrhosis. Methods: We analysed 78 hospitalized patients with cirrhosis using stool shotgun metagenomics, multiplex cytokine arrays, and flow cytometry. The microbiome and resistome (AMR genes) were mapped and correlated with disease severity, immune function (monocyte HLA-DR, neutrophil CD64), and clinical endpoints including mortality. Results: Disease severity was characterized by a "Gram-negative bloom" (Klebsiella) alongside pathogenic Enterococcus expansion and novel markers: Clostridium sp. C5-48 (severe decompensation) and Sutterella (ascites). A specific, dense resistome predicted adverse outcomes; the quinolone-resistance gene QnrB4 correlated with mortality and immune paralysis, while the carbapenemase OXA-833 gene was linked to gastrointestinal bleeding. Notably, the commensal Ligilactobacillus salivarius was associated with systemic inflammatory cytokines. Conclusions: This study reveals a "pathogenic ecosystem" in Indian decompensated cirrhosis where the resistome is intrinsically linked to host immune failure. The identification of specific prognostic markers (QnrB4, OXA-833) and inflammatory associations with L. salivarius challenges generic probiotic use and underscores the urgent need for precision, resistome-targeted therapies.}, }
@article {pmid41901767, year = {2026}, author = {He, P and Wang, H and Li, P and Yan, Y and Gao, L and Chen, L}, title = {Pyogenic Spondylitis with Epidural Abscess Caused by Streptococcus suis Serotype 2 ST7: Tissue mNGS Confirmation and Whole-Genome Characterization of a Human Isolate.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41901767}, issn = {2076-0817}, support = {2026JKP-07//Disease Prevention and Control Innovation Team of Zhejiang Province/ ; }, mesh = {Humans ; *Spondylitis/microbiology/diagnosis ; *Streptococcus suis/genetics/isolation &amp; purification/classification/drug effects ; Aged ; *Epidural Abscess/microbiology/diagnosis ; *Streptococcal Infections/microbiology/diagnosis/drug therapy ; Male ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Serogroup ; Whole Genome Sequencing ; Animals ; Swine ; Magnetic Resonance Imaging ; Phylogeny ; }, abstract = {Streptococcus suis is an emerging zoonotic pathogen that typically causes bacteremia or meningitis in humans, whereas vertebral osteomyelitis with epidural abscess is exceedingly rare and may be missed. We describe a 65-year-old farmer with fever and severe low back pain after long-term bare-handed handling of raw pig lungs. Pre-treatment blood cultures yielded S. suis identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). After transient improvement on empirical therapy, fever recurred with worsening lumbar pain. Contrast-enhanced magnetic resonance imaging (MRI) demonstrated multilevel thoracolumbar pyogenic spondylitis with an epidural abscess and a sub-ligamentous abscess beneath the posterior longitudinal ligament (PLL) extending from L2 to L5. Computed tomography-guided lumbar biopsy followed by tissue metagenomic next-generation sequencing (mNGS) detected S. suis, providing concordant evidence supporting pathogen involvement at the vertebral focus. The bloodstream isolate (SS-JX2025-01) was serotype 2, sequence type 7 (ST7). It remained susceptible to β-lactams and glycopeptides but was resistant to macrolide-lincosamide and tetracycline classes, consistent with erm(B), tet(O), tet(40), and ant(6)-Ia detected by whole-genome sequencing (WGS). Virulence profiling revealed an epf[+]/sly[+]/mrp[-] pattern with multiple adhesins and immune-evasion factors, whereas canonical 89K pathogenicity island markers were absent. Core-genome phylogeny placed SS-JX2025-01 within the Chinese ST7 lineage associated with previous outbreaks. This biopsy-supported case expands the clinical spectrum of invasive S. suis infection, highlights the value of tissue mNGS as an adjunct for supporting deep-seated foci in zoonotic infections, and underscores the importance of occupational prevention in small-scale farming households.}, }
@article {pmid41901791, year = {2026}, author = {Alessandri, G and Beligni, G and Gori Savellini, G and Mistral De Pascali, A and Gobbo, F and Montarsi, F and Mileto, D and Rizzo, L and Cusi, MG}, title = {Molecular Epidemiology of Toscana Virus in Northern and Central Italy Using Metagenomic Next-Generation Sequencing.}, journal = {Pathogens (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, pmid = {41901791}, issn = {2076-0817}, support = {PE00000007//NextGeneration EU-MUR PNRR Extended Partnership Initiative on Emerging Infectious Diseases INF-ACT/ ; P2022WYNAH//Ministero dell'Universit&#xe0; e della Ricerca, Progetti di Rilevante Interesse Nazionale PRIN2022 PNRR/ ; }, mesh = {Italy/epidemiology ; *Sandfly fever Naples virus/genetics/classification/isolation &amp; purification ; Humans ; Phylogeny ; Molecular Epidemiology ; Animals ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Genome, Viral ; Genotype ; Phylogeography ; Psychodidae/virology ; }, abstract = {Toscana virus (TOSV) is an arthropod-borne virus, transmitted by sandflies, which represents a major cause of aseptic meningitis in Mediterranean countries during summer months. Despite its epidemiological importance, recent genomic data on circulating Italian strains remain limited. We performed comprehensive phylogenetic and genotypic characterization of 34 TOSV isolates (32 obtained from human biological samples and 2 from sandfly homogenates) collected between 2022 and 2025 from Northern/Central Italy. All the sequenced isolates clustered within Lineage A, with strains circulating in Tuscany showing significantly lower intra group genetic divergence (p < 0.05), indicative of compartmentalized local circulation. Both S and M segments exhibited negative selection and identified non-synonymous mutations deserving functional investigation. This study documents stable Lineage A predominance across Italian regions, with Tuscany showing distinct phylogeographic structuring. mNGS proves effective for TOSV genomic surveillance, supporting refined public health strategies, including targeted sandfly control in endemic foci.}, }
@article {pmid41902210, year = {2026}, author = {Zhang, Y and Ding, X and Tao, X and Tuohuti, N and Wang, X and Maimaiti, A and Su, Z and Ma, X}, title = {Viral Metagenomic Analysis Reveals High Prevalence of Dromedary Camel Bocavirus and Porcine Astrovirus in Bactrian Camel Intestinal Tissue.}, journal = {Viruses}, volume = {18}, number = {3}, pages = {}, pmid = {41902210}, issn = {1999-4915}, support = {2022KY025//Autonomous Region Science and Technology Commissioner Project of Xinjiang Uygur Autonomous Region, China/ ; }, mesh = {Animals ; *Camelus/virology ; *Bocavirus/genetics/isolation &amp; purification/classification ; Phylogeny ; Metagenomics ; *Parvoviridae Infections/veterinary/epidemiology/virology ; *Astroviridae Infections/veterinary/epidemiology/virology ; *Intestines/virology ; China/epidemiology ; Prevalence ; *Mamastrovirus/genetics/isolation &amp; purification/classification ; Swine ; Virome ; }, abstract = {Bactrian camels (Camelus bactrianus) are economically vital livestock in arid regions; however, their intestinal virome is poorly understood. We employed viral metagenomics to analyze intestinal tissue samples from deceased camels at a breeding facility in Urumqi, Xinjiang, China, and uncovered a diverse viral population dominated by dromedary camel bocavirus (DBoV1) and porcine astrovirus (PoAstV5). A molecular epidemiological survey of 261 anal swab samples collected across Xinjiang revealed prevalence rates of 36.40% (95/261) for DBoV1 and 26.44% (69/261) for PoAstV5, indicating their widespread circulation. Phylogenetic analyses of the DBoV1 NS1 and PoAstV5 ORF1a genes showed close relationships with known strains, with no evidence of recombination. This study expands the known viral spectrum of Bactrian camels, marking the first report of PoAstV5 in this species, a finding suggestive of cross-species transmission. These results enhance our understanding of camel viral diversity and provide critical data for managing enteric diseases in camel populations, with potential implications for livestock health and surveillance of zoonotic risks.}, }
@article {pmid41902228, year = {2026}, author = {Shankar, A and Zheng, H and Cowan, D and Jia, H and Osis, G and Burgin, A and Sheth, M and Hoff, NA and Halbrook, M and Rimoin, AW and Goldberg, TL and Chapman, CA and Ting, N and Switzer, WM}, title = {Molecular Characterization of Complete Simian Foamy Virus Genomes from Three Colobine Monkeys Reveals Highly Divergent Evolutionary Trajectories and Identifies Transmission to Humans.}, journal = {Viruses}, volume = {18}, number = {3}, pages = {}, pmid = {41902228}, issn = {1999-4915}, support = {TW009237//Canada Research Chairs Program ; NIH/ ; R01 AI084787/GF/NIH HHS/United States ; R01 AI077376-04A1/GF/NIH HHS/United States ; }, mesh = {Animals ; *Simian foamy virus/genetics/classification/isolation &amp; purification ; *Genome, Viral ; Phylogeny ; *Retroviridae Infections/transmission/virology/veterinary ; Humans ; *Evolution, Molecular ; *Monkey Diseases/virology/transmission ; Colobus/virology ; *Colobinae/virology ; }, abstract = {Simian foamy viruses (SFVs) are ancient retroviruses that co-evolve with nonhuman primates (NHPs), although genomic data from Asian and African monkeys are limited. We report the characterization of three new SFV colobine genomes from two Asian species (Trachypithecus francoisi (Tfr) and Pygathrix nemaeus (Pne)) and one African monkey (Colobus guereza, Cgu), obtained via metagenomics analysis of peripheral blood leukocyte tissue culture isolates. Genomic analyses found conserved structural, enzymatic, and auxiliary genes flanked by long terminal repeats, with all major transcriptional and structural motifs highly preserved. An in-frame Δtas mutation in tissue culture and ex vivo specimens was identified in the SFVpne genome, which may promote viral latency. Phylogenetic analyses revealed that these colobine SFVs have distinct evolutionary trajectories without clustering together, contradicting a strict virus-host co-evolution. We developed a new generic SFV PCR assay using these genomes with increased detection sensitivity for Colobinae SFVs and identified four new human infections with Cgu-derived SFV in the Democratic Republic of Congo. Our findings indicate that SFV evolution in colobine monkeys is shaped by host switching, cross-species transmission, and high viral diversity. Our study underscores the importance of broadening SFV genomic sampling to better understand viral evolution, zoonotic risk, and improved diagnostic capabilities.}, }
@article {pmid41902303, year = {2026}, author = {Munguti, FM and LaTourrette, K and Silva, G and Maina, S and Kilalo, DC and Macharia, I and Mwango'mbe, AW and Nyaboga, EN and Garcia-Ruiz, H}, title = {Metagenomics Analysis of Viruses Associated with Cassava Brown Streak Disease in Kenya.}, journal = {Viruses}, volume = {18}, number = {3}, pages = {}, pmid = {41902303}, issn = {1999-4915}, support = {Grant ID: RU/2018/CARP+/04//MasterCard Foundation/ ; }, mesh = {Kenya ; *Plant Diseases/virology ; *Manihot/virology ; *Potyviridae/genetics/classification/isolation &amp; purification ; Phylogeny ; Genome, Viral ; *Metagenomics ; Polymorphism, Single Nucleotide ; }, abstract = {Cassava brown streak disease (CBSD), caused by cassava brown streak virus (CBSV; Ipomovirus brunusmanihotis) and Ugandan cassava brown streak virus (UCBSV; Ipomovirus manihotis) (family Potyviridae, genus Ipomovirus), is increasingly becoming a threat to cassava production in several parts of Africa, especially in Eastern, Central and Southern Africa. In Kenya, the disease continues to wreak havoc on cassava production leading to a significant reduction in crop yields and economic losses of up to USD 1 billion. Variation in virus populations make the control of CBSD challenging as virus genomic variation can affect the accuracy of diagnostic tests, lead to resistance breaking isolates and jeopardize strategies of breeding for resistance. CBSV and UCBSV populations obtained from cassava fields in Kenya were characterized. In total, 44 new complete sequences of CBSV and UCBSV were assembled and 40 sequences successfully submitted to GenBank. Single Nucleotide Polymorphism (SNP) analysis revealed that the cylindrical inclusion protein (CI) is the most stable region across the genome of CBSV and UCBSV. In contrast, protein 1 (PI) and the coat protein (CP) were the most hypervariable regions. Phylogenetic analysis showed three major geographical groupings for both UCBSV and CBSV isolates, suggesting a continued spread of the viruses through human-mediated movement of infected planting materials. The data obtained in this study can support the development of disease management strategies through improved molecular diagnostic tests and targets for breeding for resistance against CBSD.}, }
@article {pmid41903008, year = {2026}, author = {Heyse, J and Props, R and Defoirdt, T and Boon, N}, title = {Life strategies of bacterial taxa in rearing water microbiomes of whiteleg shrimp (Litopenaeus vannamei) larviculture.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41903008}, issn = {1573-0972}, support = {1S80618N//Fonds Wetenschappelijk Onderzoek/ ; 1221020N//Fonds Wetenschappelijk Onderzoek/ ; }, }
@article {pmid41903026, year = {2026}, author = {Wolthuis, JC and Schultheiss, JPD and Magnúsdóttir, S and Stigter, E and Tang, YF and Jans, J and Oldenburg, B and de Ridder, J and van Mil, S}, title = {Univariate- and machine learning-based plasma metabolite signature differentiates PSC-IBD from IBD and is predicted to be driven by gut microbial changes.}, journal = {Metabolomics : Official journal of the Metabolomic Society}, volume = {22}, number = {2}, pages = {}, pmid = {41903026}, issn = {1573-3890}, mesh = {Humans ; *Machine Learning ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/diagnosis/blood/metabolism/microbiology ; *Cholangitis, Sclerosing/diagnosis/blood/metabolism ; *Metabolomics/methods ; Male ; Female ; Biomarkers/blood ; Adult ; Middle Aged ; Crohn Disease/diagnosis/blood ; Colitis, Ulcerative/diagnosis/blood/metabolism ; Metabolome ; Mass Spectrometry ; }, abstract = {INTRODUCTION: Inflammatory bowel disease (IBD) is a group of chronic inflammatory conditions of the gastrointestinal tract comprising two major phenotypes, Crohn's disease (CD) and ulcerative colitis (UC). Up to 8% of patients with IBD also develop primary sclerosing cholangitis (PSC), characterised by cholestasis and progressive destruction of the biliary tree, resulting in cirrhosis, end-stage liver disease and cholangiocarcinoma. Clinical outcome can currently not be improved through medication, denoting the importance of diagnosis prior to irreversible damage, which requires biomarkers of (early) disease.<br><br>OBJECTIVES: We employed direct infusion mass spectrometry (DI-MS)-based metabolomics on plasma to build predictive, potentially diagnostic models for PSC-IBC and other phenotypes including IBD subtype, stricture and fistula presence and more. We used this dataset to simultaneously investigate aetiology of these phenotypes.<br><br>METHODS: Samples of 348 IBD patients were included for analysis. The data was analysed using our previously reported tool, MetaboShiny. We built predictive models using Random Forest (RF), and subsequently combined with univariate statistics to rank m/z features connected to PSC-IBD. This ranking was used to perform mummichog enrichment analysis connected to metabolic and metagenomic changes.<br><br>RESULTS: The highest performing predictive model differentiated PSC-IBD from PSC. The metabolic signature was enriched in changes to amino acid and vitamin metabolism, alongside changes to the metagenome suggesting decreases in anti-inflammatory microbial species and increases in pro-inflammatory species.<br><br>CONCLUSION: These results demonstrate the potential of DI-MS-based metabolomics with machine learning to create diagnostic models and generate hypotheses on the metabolomic-metagenomic level. Sharing our dataset of patients will enrich future human IBD metabolomics research possibilities.}, }
@article {pmid41903099, year = {2026}, author = {Sumona, AA and Hossen, MB and Hadi, SB and Haque, MA and Haider, MN and Hossain, MT and Alam, MS}, title = {Host-derived Probiotics Enhance Immune Response and Gut Microbiome in the Freshwater Prawn Macrobrachium rosenbergii.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41903099}, issn = {1867-1314}, }
@article {pmid41903138, year = {2026}, author = {Zheng, W and Wu, C and Wang, Y and Yan, X and Han, W and Liu, X and He, C and Chen, X and Zhou, X and Zhang, L and Liu, C and Xu, J and Wang, J and Yuan, X and Song, W and Wang, X and Liang, S and Huang, J and Zhang, Y and Yang, R and Zhang, L and Qin, N and Ma, X and Xu, Q and Li, G}, title = {Mutation elevation and functional alterations in Escherichia coli are pertinent to the onset of gestational diabetes mellitus.}, journal = {Cell reports}, volume = {45}, number = {4}, pages = {117143}, doi = {10.1016/j.celrep.2026.117143}, pmid = {41903138}, issn = {2211-1247}, abstract = {In the gut microbiome, purifying selection clears deleterious mutations. However, it is unknown whether this selection pressure is modifiable or what its health implications are. Here, we studied metagenomic and metabolic changes linked to gestational diabetes mellitus (GDM), and observed an increase in Escherichia coli (E. coli) mutations during host pregnancy, linking these genetic changes to host physiology. Severe depletion of bacterial genes before GDM onset was mostly traced to E. coli despite its stable abundance-indicating that functional genetic signals outweigh taxonomic shifts. E. coli and related microbes displayed pregnancy-linked single nucleotide polymorphism elevation, enriched at GDM onset in loci encoding membrane and biofilm components. These pangenomic alterations correlated with handicapped intermicrobial interactions of E. coli and with host serum metabolic abnormalities. We propose that pregnancy relaxes purifying selection, permitting mutation elevation in certain gut bacteria. Resulting functional deficits, potentially through altered ecology and metabolism, may subsequently impact host glucose regulation.}, }
@article {pmid41903180, year = {2026}, author = {Xu, Y and Akinbi, H and Shen, Z and Zhu, J and Shi, L and Du, L and Haslam, DB}, title = {Clinical Care Practices Shape Microbiome-Associated Bloodstream Infection Risk in Geographically Distinct NICUs.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciag213}, pmid = {41903180}, issn = {1537-6591}, abstract = {BACKGROUND: Bloodstream infections (BSI) remain a major cause of morbidity and mortality in preterm infants. Although BSI pathogens vary geographically, the role of local microbial colonization patterns and clinical practices in driving these differences is not well understood.<br><br>METHODS: We conducted a prospective cohort study on 127 preterm infants from two geographically distinct NICUs: University of Cincinnati Medical Center (UCMC, USA) and Children's Hospital, Zhejiang University School of Medicine (ZCH, China). Six hundred and sixty-nine longitudinal stool and skin samples collected during the first three weeks of life underwent metagenomic sequencing. Associations between microbiome composition, clinical factors, and BSI epidemiology were evaluated using Generalized Linear Mixed Models and Random Forest.<br><br>RESULTS: Distinct gut and skin microbiome profiles were observed between NICUs and corresponded closely with local BSI patterns. Staphylococcus aureus predominated at UCMC, while Klebsiella pneumoniae and Enterococcus species were more common at ZCH. Skin microbiota showed strong association with BSI isolates, implicating the skin as an underrecognized potential reservoir for pathogen translocation. Linear mixed models and Random Forest machine learning approaches revealed that clinical practices, including intravenous catheter placement and antibiotic exposure had greater influence on microbiome composition than geographic location alone.<br><br>CONCLUSIONS: Our findings demonstrate that modifiable clinical care practices shape the developing microbiome of preterm infants and contribute to geographic differences in BSI epidemiology. The skin microbiome represents a potentially significant risk factor for invasive infection. Further work to clarify how specific clinical practices influence pathogen colonization may inform strategies to reduce BSI incidence in preterm infants.}, }
@article {pmid41903463, year = {2026}, author = {Rathnayake, M and Shaik, NA and Palkumbura, A and Ranaraja, A and Basnayake, Y and Basyouni, R and Taylor, A and Ambrose, N and Popowich, S and Ayalew, LE and Tikoo, S and Gomis, S}, title = {Effects of conventional and raised without antibiotic feeding systems and exposure to infectious bursal disease virus on microbial diversity of the jejunal microbiota in broiler chickens.}, journal = {Poultry science}, volume = {105}, number = {6}, pages = {106823}, doi = {10.1016/j.psj.2026.106823}, pmid = {41903463}, issn = {1525-3171}, abstract = {Preventative use of antimicrobials in the feed in broiler chicken production is decreasing due to consumer demand. Hence broiler chickens raised without antibiotics (RWA) receive increased attention. The objective of this study was to compare jejunal microbiota in RWA and conventional feeding systems in commercial broiler chickens. A total of 6 broiler chicken farms were selected for this study, in each farm raising both conventional and RWA chicken flocks. Jejunal contents were collected from Ross 308 (n=8/flock) at 25 d of age for metagenomics analysis for 16SrRNA amplicon sequencing. Serum samples from each flock were tested for infectious bursal disease virus (IBDV) and chicken anemia virus (CAV). The 16SrRNA microbial analysis revealed that there was no substantial impact of feeding systems on the diversity of the microbial community between RWA and conventional feeding systems. The condemnation rate was significantly higher in RWA flocks compared to conventional flocks (p = 0.037). Significantly high antibody titer against IBDV was detected in 9 (75%) of 12 flocks. The microbiota significantly differed in flocks exposed to IBDV compared to flocks not exposed to IBDV irrespective of the feeding system. Alpha diversity indices revealed that richness (p = 0.025), Chao1 (p = 0.031), and Shannon index (p = 0.04) were significantly lower in flocks exposed to IBDV indicating reduced species diversity. Flocks exposed to IBDV had increased Escherichia, Anaerotignum, Clostridium, Weissella andLiquorilactobacillus genera while Furfurilactobacillus, Helicobacter, Campylobacter, Fructilactobacillus and Terrisporobacter were decreased compared to flocks not exposed to IBDV. These results suggest that broiler chickens exposed to IBDV infection irrespective of the feeding system lead reduction in microbial diversity. This study highlights the importance of control strategies of IBDV in broiler flocks since IBDV infection not only causes immunosuppression but also affects intestinal microbiota.}, }
@article {pmid41903724, year = {2026}, author = {Ouyang, E and Liu, J and Zhou, Z and Yang, H and Wang, W and Qian, K and Zhu, M and Wei, Z and Sun, X and Chen, Z}, title = {Metagenomic Surveillance of Temperature-Drived Bacterial Threats to Drinking Water Safety.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124364}, doi = {10.1016/j.envres.2026.124364}, pmid = {41903724}, issn = {1096-0953}, abstract = {Climate warming may exacerbate the risk of pathogenic bacteria and antibiotic resistance genes (ARGs) in aquatic environments. However, research on the impact of climate warming on bacterial pathogenic risks and virulence factors (VFs) communities in drinking water sources remains scarce. This study combined field multi-season monitoring with controlled laboratory temperature simulation experiments. Using 16S rRNA and metagenomic sequencing, we investigated the effects of gradually increasing temperature on pathogenic bacteria and VF community in the Gan River source area. A significant positive correlation with temperature was observed in the seasonal shifts of Legionella, Mycobacterium, and Pseudomonas during field multi-season monitoring. Our laboratory temperature simulation experiments further illustrated the differential modulation of temperature on opportunistic pathogens and their VFs. The abundance of 9 specific VFs was significantly associated with temperature. Within the high-temperature range (35-40 °C), Legionella showed a synergistic increase in both its population and the abundance of its VF (Hsp60); Mycobacterium's VF (NuoG) abundance increased significantly with increasing temperature, while the population size remained stable. Furthermore, 3 key bacterial infectious disease pathways- Bacterial invasion of epithelial cells, Staphylococcus aureus infection, and Vibrio cholerae infection were significantly enriched with elevated temperature. Furthermore, high temperatures may also weaken the microbial inactivation efficiency of the conventional chlorine disinfection process, thereby posing a potential threat to drinking water safety. This study elucidates how elevated temperature is linked to the enhanced pathogenic potential of opportunistic pathogens, mediated through the differential regulation of VFs. This provides a scientific basis for assessing aquatic microbial risks under climate warming.}, }
@article {pmid41903868, year = {2026}, author = {Manfredonia, I and Chioso, L and Mateescu, I and Konu, M and Brons, JK and Deelman-Driessen, C and Viljakainen, L and Wertheim, B and Lequime, S}, title = {Prevalence and distribution of two polycipiviruses in wild black garden ants (Lasius niger L.) in the Netherlands.}, journal = {Journal of invertebrate pathology}, volume = {217}, number = {}, pages = {108611}, doi = {10.1016/j.jip.2026.108611}, pmid = {41903868}, issn = {1096-0805}, abstract = {Metagenomic studies have revealed diverse viruses in insects. Yet, our understanding of the ecology of insect viruses, especially in ants, remains limited, despite the insects' ecological importance. Viruses of the family Polycipiviridae are increasingly recognized as widespread yet poorly characterized components of ant viromes. In this study, we investigated the prevalence and genetic diversity of Lasius niger virus 1 (LniV-1) and Myrmica scabrinodis virus 1 (MsaV-1) in wild colonies of the black garden ant (Lasius niger L.) across the Netherlands. We surveyed 40 wild L. niger colonies, sampled at geographically distinct locations, using RT-PCR to assess viral prevalence and genetic diversity. Viral prevalence was estimated at both colony and individual levels. Amplicons were sequenced to explore potential correlations between geographic distribution and genetic diversity for both viruses. In addition, complete or almost complete viral genome sequences were obtained and assembled for one MsaV-1 genome from Groningen, The Netherlands, and one MsaV-1 and one LniV-1 from Vienna, Austria. In the Netherlands, LniV-1 was detected in 17.5% of colonies, whereas MsaV-1 was detected in 27.5%, including evidence of co-infection at the colony level. Neither the geographical distribution of infected colonies nor the inferred phylogenies for both viruses showed strong geographic structuring. The prevalence in workers within colonies was variable, ranging from 10 to 60%. These findings suggest that polycipiviruses are common in natural L. niger populations and may transmit via both horizontal and vertical routes. This study provides baseline data on ant-virus interactions in natural environments, advancing understanding of viral ecology in social insects and informing future research on virus transmission dynamics in natural ecosystems.}, }
@article {pmid41904207, year = {2026}, author = {Yan, Y and Zhen, W and Hongxia, S and Zhenhong, S and Xianghui, M and Na, W and Li, S and Defeng, W}, title = {Impact of Lactobacillus johnsonii on glycemic control and lipid metabolism in type 2 diabetes with circadian disruption.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-025-94359-6}, pmid = {41904207}, issn = {2045-2322}, support = {(BJK2024152)//Funded by Science and Technology Project of Hebei Education Department/ ; (20241988)//Hebei Province Medical Science Research Project Plan for 2024/ ; (No. [2020] No.23).//Project Fund of Clinical Medicine Excellent Talents funded by Hebei Provincial Department of Finance/ ; }, }
@article {pmid41904356, year = {2026}, author = {Vojtkuf, I and Čačković, A and Soares, AR and Probst, AJ and Orlić, S}, title = {Seasonal Dynamics of Freshwater Bacterial Communities in Continental and Mediterranean Lakes.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02743-0}, pmid = {41904356}, issn = {1432-184X}, support = {426547801//Deutsche Forschungsgemeinschaft/ ; IP-2020-02-9021//Hrvatska Zaklada za Znanost/ ; }, }
@article {pmid41904418, year = {2026}, author = {Kousar, R and Latif, S and Zahoor, M and Tabassum, S}, title = {A pilot study revealed the gut microbiota based on 16S rRNA metagenomics in gestational diabetes.}, journal = {BMC genomic data}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12863-026-01413-x}, pmid = {41904418}, issn = {2730-6844}, }
@article {pmid41904571, year = {2026}, author = {Kolenda, R and Hassan, MM and Arrieta-Gisasola, A and Kamara, A and Ansorge, R and Sidorczuk, K and Acton, L and Thilliez, G and Baker, DJ and Burdukiewicz, M and Stares, MD and Browne, HP and Le Gall, G and Torres, RC and Chavez-Arroyo, A and Garrett, J and Stevens, MP and Lawley, TD and Bäumler, AJ and La Ragione, R and Hildebrand, F and Kingsley, RA}, title = {Copper is an intestinal habitat filter affecting the gut microbiota interactions with Salmonella Typhimurium.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-025-02322-4}, pmid = {41904571}, issn = {2049-2618}, support = {BB/W003155/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {BACKGROUND: Foodborne pathogens, including Salmonella enterica serovar Typhimurium (S. Typhimurium), pose a significant threat to both human health and livestock productivity. The pandemic S. Typhimurium ST34 clone acquired a genomic island (SGI-4) conferring high copper resistance, an adaptation relevant in the context of the widespread use of copper sulphate at therapeutic levels in pig farming. We investigated how high dietary copper influences the piglet gut microbiota and Salmonella-microbiota interactions that may explain the global spread of S. Typhimurium ST34.<br><br>RESULTS: An on-farm study combined with faecal shotgun metagenomics revealed that several potential Salmonella competitor species, including Bifidobacterium, Escherichia, and Lactobacillus, were less abundant in piglets on high-copper diets. Anaerobic and aerobic culturing alongside whole genome sequencing of 131 species and copper sulphate susceptibility testing identified copper resistance gene acquisition in selected microbes, particularly within Escherichia. Niche competition assays demonstrated that copper resistance is critical for inter-species competition under high-copper conditions, with Salmonella's Type VI Secretion System providing a distinct advantage over Escherichia in the copper-modified niche.<br><br>CONCLUSIONS: Our findings suggest that copper supplementation alters the piglet gut environment, impacting competitive dynamics between pathogenic and commensal bacteria, likely to influence the zoonotic transmission of pathogens. Video Abstract.}, }
@article {pmid41904606, year = {2026}, author = {Birkeland, S and Rohde Mæhlum, I and Senneset, M and Wik Taxerås, I and Snipen, L and Markov Arnesen, H and Boysen, P and Carlsen, H}, title = {A naturalized gut microbiome interacts with dietary fibers to protect against colonic inflammation.}, journal = {Gut microbes}, volume = {18}, number = {1}, pages = {2649435}, doi = {10.1080/19490976.2026.2649435}, pmid = {41904606}, issn = {1949-0984}, mesh = {Animals ; *Dietary Fiber/metabolism/administration &amp; dosage ; *Gastrointestinal Microbiome ; Mice ; *Colitis/prevention &amp; control/microbiology/chemically induced ; Feces/microbiology ; Dextran Sulfate ; Colon/microbiology/pathology ; Mice, Inbred C57BL ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Male ; Disease Models, Animal ; Intestinal Mucosa/metabolism/microbiology ; }, abstract = {"Feralized" mice, housed in farmyard-type environments, show a matured immunophenotype, altered intestinal barrier, and a shifted gut microbiome compared to conventionally housed laboratory mice. Since dietary fibers support gut health in part by microbial fermentation into immunomodulatory short-chain fatty acids, we hypothesized that feralization influences the intestinal barrier by enhancing the fiber-degrading properties of the microbiome. We explored whether susceptibility to low-grade dextran sulfate sodium-induced colitis differed between feralized and clean laboratory mice fed diets high or low in fermentable fibers. Feralized mice were protected against colitis, displaying low disease scores and biomarkers of inflammation in feces, plasma, and liver; and altered colonic mucosal gene expression, compared to clean mice. This protection was strongest with a fiber-rich diet, which, in contrast, worsened colitis in clean mice. Transfer of fecal microbiota from feralized mice to clean recipients conferred colitis protection. Fecal metagenome-assembled genomes revealed that the fiber-rich diet enriched the microbiome with predicted genes encoding fiber-degrading enzymes, while the low-fiber diet promoted mucin-degrading enzyme genes. However, the dominant microbial species contributing to these functions differed between feralized and laboratory mice. Differential abundance of bacterial taxa in feralized and laboratory mice further identified potential microbial modulators of colitis that merit targeted investigation in future studies. Overall, these findings suggest that fibers affect intestinal inflammation in a microbiota-dependent manner, underscoring the complex interplay between diet and microbiota in disease development.}, }
@article {pmid41904875, year = {2026}, author = {Mu, H and Hu, Y and Zhang, S and Zhang, X and Wei, Q}, title = {Anaerobic digestion model reconstruction of red mud-Pretreated food waste based on the Metagenomics: Improvement of the high-solid ADM1 incorporating SAO and DIET metabolic pathways.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129357}, doi = {10.1016/j.jenvman.2026.129357}, pmid = {41904875}, issn = {1095-8630}, abstract = {Anaerobic Digestion Model No. 1 (ADM1) can accurately describe the biochemical processes in anaerobic digestion (AD) of wastewater, but it fails in the simulation of organic waste's AD due to the different biochemical reaction pathways. To address this limitation, this study proposed an ADM1 improved method based on metagenomics information. For the red mud pretreated food waste anaerobic digestion system, an anaerobic digestion model (RF-ADM1) was developed, focusing on integrating two functional pathways: syntrophic acetate oxidation (SAO) and direct interspecies electron transfer (DIET). Feature kinetic parameters for DIET (Y_pro_ac and Y_bu_ac) were extracted to enhance the model's ability to characterize metabolic processes within this system. The coefficient of determination (R[2]) of the batch experiment reaches 0.996, while Theil's inequality coefficient (TIC) of continuous testing reaches 0.05.}, }
@article {pmid41904906, year = {2026}, author = {Zheng, Y and Wu, Q and Xia, Y and Deng, H and Zhao, Y and Luo, J and Feng, D and Ge, C}, title = {Dark side of biodegradable microplastics in mangrove ecosystem: Plastisphere as an overlooked hotspot of sulfate-reducing metabolism.}, journal = {Water research}, volume = {298}, number = {}, pages = {125802}, doi = {10.1016/j.watres.2026.125802}, pmid = {41904906}, issn = {1879-2448}, abstract = {Microplastics (MPs) have increasingly accumulated in the sulfate-rich and anoxic mangrove sediment. However, it remains unclear whether MPs serve as hotspots for sulfate-reducing microbes (SRM) and what potential risks this activity poses to this ecosystem. To address this issue, polyethylene MPs (PE-MPs) and polylactic acid MPs (PLA-MPs) were in-situ exposed to bare mudflat, invasive S. apetala and native B. gymnorhiza sediment, respectively. After 150 days of exposure, microbially-driven sulfur metabolism patterns on plastisphere in three distinct habitats were compared using metagenomic sequencing. Results showed that PLA-MPs enriched more SRM than PE-MPs and non-MPs particles. Dissimilatory sulfate reduction was one of the most abundant sulfur-metabolic pathways on plastisphere, and the abundance of genes driving this process on MPs followed an order of mudflat (9.37 % ± 0.72 %) < S. apetala (22.31 % ± 5.29 %) < B. gymnorhiza (28.69 % ± 1.10 %), indicating that MPs in B. gymnorhiza sediment fostered more active sulfate reduction, primarily driven by sat/met3, apr and dsr gene clusters. Furthermore, CO2 release from plastisphere was greater on PLA-MPs than on PE-MPs in sediments. Given the tight coupling between sulfate reduction and organic carbon degradation, these findings highlighted the potential of biodegradable MPs to affect carbon-sulfur biogeochemical processes in mangrove ecosystems.}, }
@article {pmid41905022, year = {2026}, author = {Benschop, KSM and Zwagemaker, F and Andersson-Li, L and Andrés, C and Antón, A and Berengua, C and Berginc, N and Bessaud, M and Bisseux, M and Bujaki, E and Canning, B and Christiansen, CB and Couderé, K and Broberg, EK and Cassidy, H and Castilletti, C and Celma, C and Cinek, O and Deézsi-Magyar, N and Eis-Hübinger, AM and Flipse, J and Jiřincová, H and Gatej, R and Georgieva, I and Giardina, F and González-Sánchez, A and Hack, B and Helfferich, J and Hutchings, S and Hietanen, E and Hönemann, M and Virant, MJ and Kalogera, E and Johannesen, CK and Kenicer, J and Kleines, M and Lagarejos, E and Landaas, ET and Kandulu, CC and Xavier López Labrador, F and Lunar, MM and Maier, M and Majumdar, M and Martin, J and McClure, CP and Muñoz-Almagro, C and Ošep, A and Øverbø, J and Palminha, P and Papa, A and Pariani, E and Pellegrinelli, L and Pietsch, C and Piralla, A and Poljak, M and Pomari, E and Prats-Méndez, I and Rector, A and Reuter, G and Riess, M and Ruta, S and Schibler, M and Nilsen, HS and Simmonds, P and Sourvinos, G and Szomor, K and Susi, P and Tabain, I and Vallely, P and von Eije, KJ and Weil, M and Wieczorek, M and Wollants, E and Wolthers, KC and Zuckerman, NS and Fischer, TK and Harvala, H}, title = {Next generation sequencing approaches for the detection and characterization of enteroviruses in clinical, public health, and research settings: Expert view of the European non-polio enterovirus network (ENPEN).}, journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology}, volume = {184}, number = {}, pages = {105940}, doi = {10.1016/j.jcv.2026.105940}, pmid = {41905022}, issn = {1873-5967}, abstract = {Enteroviruses (EVs) are a common cause of a wide spectrum of infectious diseases, ranging from mild respiratory illnesses to severe neurological conditions, particularly affecting children. Current molecular methods, such as 5'UTR-based PCR for detection and (partial) VP1 gene sequencing for typing, are widely utilized. However, Next-Generation Sequencing (NGS), and bioinformatics offer a comprehensive alternative, enabling full-genome analyses for improved virus characterization, genomic epidemiological surveillance, and outbreak investigation. Despite its advantages, implementation of NGS poses challenges, particularly in standardizing and optimizing laboratory workflows (wet-lab) and bioinformatics analyses (dry-lab), methods that are not often readily accessible in many laboratories. Here, we discuss the potential of NGS as a tool for EV detection/characterization in clinical virology, public health, and research settings. We provide practical options for actions for implementing NGS to advance the understanding and management of enterovirus infections. These recommendations are based on expert discussions during the recent European non-polio enterovirus network (ENPEN) workshop held in Corfu, Greece, on 23-24 May 2024, aiming to guide harmonization of NGS practices across clinical, public health, and research settings.}, }
@article {pmid41905052, year = {2026}, author = {Liu, Z and Zhao, C and Chen, N and Zhu, K and Chen, Y and Feng, C}, title = {Synergistic and competitive interactions between solid carbon sources and current-driven sulfate reduction in a single-chamber microbial electrolysis cell.}, journal = {Journal of hazardous materials}, volume = {508}, number = {}, pages = {141881}, doi = {10.1016/j.jhazmat.2026.141881}, pmid = {41905052}, issn = {1873-3336}, abstract = {Conventional microbial sulfate reduction technologies for sulfate pollution control often suffer from low efficiency, insufficient sulfur immobilization, and poor stability under extreme carbon-to-sulfur (C/S) ratios, leading to secondary pollution. To overcome these limitations, this study combined electrical stimulation with a solid-phase carbon source (wheat straw) to construct a single-chamber microbial electrolysis cell for long-term operation. Under optimal conditions (hydraulic retention time = 2.0 d, C/S = 1.5, current density = 100 mA/m[2]), the sulfate removal efficiency and the accumulation rate of dissolved sulfide reached 92.45% and 26.30%, respectively. The system maintained stable performance over 293 days and during five shock events, demonstrating a pronounced synergistic effect between electrical input and the carbon source. The iron anode facilitated the directional conversion of sulfide into FeS and S[0], enabling efficient sulfur immobilization and significantly suppressing secondary pollution. During operation, microbial activity was sustained at a high level (electron transport system activity = 0.357 μL O2·g[-1]·min[-1], ATP = 0.024 μmol). Metagenomic analysis revealed that electrical stimulation markedly enhanced the abundance of sulfur metabolism-related genes and promoted direct extracellular electron transfer process, whereas the wheat straw facilitated mediated extracellular electron transfer through the slow release of exogenous electron shuttles. The synergistic interaction between these processes optimized the electron transfer network within the system. This study elucidates the mechanisms underlying directional sulfur transformation and electron transfer during long-term operation, providing critical insights for optimizing microbial ecosystems involved in sulfate reduction and supporting the practical application of this technology in water in situ remediation.}, }
@article {pmid41730992, year = {2026}, author = {Escalante, C and Reyes, AM and Zhao, C and Balkcom, KS and Jacobson, AL and Strayer-Scherer, A and Martin, KM and Koebernick, J and Huseth, A and Kozieł, E and Small, I and Greene, JK and Otulak-Kozieł, K and Mulvaney, MJ and Price, PP and Briseño, RIA and Bag, S and Conner, K}, title = {Metatranscriptomics analysis reveals the cotton virome in the southern United States.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41730992}, issn = {2045-2322}, mesh = {*Gossypium/virology/genetics ; *Virome/genetics ; *Plant Viruses/genetics/classification ; High-Throughput Nucleotide Sequencing ; Genome, Viral ; Phylogeny ; Plant Diseases/virology ; *Transcriptome ; United States ; Metagenomics ; Gene Expression Profiling ; }, abstract = {High-throughput sequencing (HTS) has expanded our perspective on the distribution and diversity of plant viruses. Furthermore, improvements in HTS and decreasing sample costs have enabled the discovery of novel plant viruses in field-collected samples. This study examined the putative virome of cotton samples collected from fields across the southern United States. Leaf samples were collected, and total RNA was extracted. Library preparation was performed from pooled samples within locations before sequencing on an Illumina platform. Sequenced libraries were mapped to the cotton reference genome, and the resulting sequences were de novo assembled. A metatranscriptomics analysis revealed complete genome contigs of cotton leafroll dwarf virus in all tested samples. Additionally, 29 putative families of RNA and DNA plant viruses co-infecting cotton were found. Seven families of RNA viruses were more prevalent across all locations. These families included Botourmiaviridae, Hypoviridae, Mitoviridae, Narnaviridae, Partitiviridae, Solemoviridae, and Totiviridae. The information obtained in this investigation will help develop a broader perspective on cotton virus diversity and whether co-infections of viruses can influence (negatively or positively) plant physiology, product quality, and yield.}, }
@article {pmid41761093, year = {2026}, author = {Qureshi, A and Wahid, A and Qazi, S and Shahzad, MK and Kiani, HM and Asif, MDA}, title = {DynaBiome: interpretable unsupervised learning of gut microbiome dysbiosis via temporal deep models.}, journal = {BMC bioinformatics}, volume = {27}, number = {1}, pages = {}, pmid = {41761093}, issn = {1471-2105}, abstract = {PURPOSE: Gut microbiome dysbiosis is a critical determinant for autologous fecal microbiota transplantation (Auto-FMT) eligibility, yet current classification approaches rely predominantly on supervised learning with manually annotated sequencing labels, which are often scarce. This study proposes DynaBiome, a framework designed to predict gut dysbiosis by leveraging unsupervised learning and clinical phenotypic proxies as a scalable alternative to ground-truth genomic labeling.<br><br>METHODS: Our framework employs an LSTM autoencoder architecture to capture temporal microbiome dynamics within 14-day windows. The model reconstructs normal microbiome patterns, where high reconstruction errors signal potential dysbiosis. To ensure rigorous evaluation and prevent data leakage, the dataset was partitioned via a strict patient-level split. Unsupervised anomaly signals were refined via phenotypic proxy labels (e.g., fever, neutropenia) via weak supervision, and ensemble learning methods were applied to optimize classification performance.<br><br>RESULTS: The initial LSTM autoencoder successfully flagged dysbiotic sequences but required refinement to reduce false positives. Ensemble learning significantly enhanced predictive accuracy. The stacked ensemble (with Logistic Regression meta-learner) demonstrated optimal performance with an ROC AUC of 0.8908 and a Weighted F1-score of 0.7909. This approach significantly outperformed the standard One-Class SVM baseline (ROC AUC 0.6033), confirming the superiority of deep temporal modeling over static anomaly detection. Critically, the model achieved performance levels comparable to fully supervised baselines, confirming the efficacy of the proxy-label framework.<br><br>CONCLUSION: Integrating unsupervised temporal feature extraction with stacked ensemble methods provides a viable framework for dysbiosis prediction. These results demonstrate that leveraging phenotypic via weak supervision can effectively approximate supervised baselines, thereby reducing the reliance on comprehensive metagenomic annotations for longitudinal patient monitoring.}, }
@article {pmid41895431, year = {2026}, author = {Ceruti, A and Bisia, M and Balatsos, G and Kobialka, RM and Zamil, MF and Hasan, A and Truyen, U and Lucati, F and Sanpera-Calbet, I and Palmer, JRB and Alam, MS and Michaelakis, A and Wahed, AAE}, title = {MosquitoID: Rapid metagenomic sequencing for offline mosquito surveillance.}, journal = {Acta tropica}, volume = {}, number = {}, pages = {108071}, doi = {10.1016/j.actatropica.2026.108071}, pmid = {41895431}, issn = {1873-6254}, abstract = {Mosquitoes transmit numerous infectious diseases, with climate change expanding their global distribution through warmer environments. Next-generation sequencing offers significant advantages for mosquito genomic surveillance and potential early warning systems. In this study, a portable metagenomic sequencing approach using Oxford Nanopore Technologies (ONT) for field-based mosquito analysis (MosquitoID protocol) was developed, enabling species and host feeding patterns identification, and pathogen detection all coming from a single amplification-free workflow. DNA was extracted from 62 mosquito samples (Aedes albopictus, Aedes cretinus, Culex pipiens, Culiseta longiareolata) from Greece and Spain, either single-species pools (1-19 specimens),mixed-species pools, wirth reverse purification method or archived samples. Additionally, 30 pooled Aedes aegypti samples from Bangladesh underwent cDNA reverse purification. All samples were sequenced using ONT rapid barcoding kits. Offline bioinformatics analysis via Geneious screened custom BLAST databases for species, host, and virus identification. MosquitoID accurately identified mosquito species in 89% of samples overall, with main discrepancies in Aedes cretinus. Virus screening detected Phasi Charoen-like virus in cDNA samples. Host DNA sequences identified multiple species including horses, cattle, and ducks. This study demonstrates metagenomic ONT sequencing's effectiveness for rapid host, species, and virus identification. After further benchmarking, the approach shows potential for real-time disease monitoring and enhanced surveillance systems. Integrating portable next-generation sequencing with offline bioinformatics tools could significantly strengthen mosquito-borne disease prevention strategies, particularly for non-bioinformaticians and in resource-limited settings.}, }
@article {pmid41895455, year = {2026}, author = {Yin, W and Li, Y and Pan, A and Wu, J and Su, X and Xiao, X and Dong, F and Xu, L and Chen, C and Fu, H and Sun, F}, title = {Synergistic inhibition and microbial adaptation in anammox systems under long-term salinity and fulvic acid stress.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134498}, doi = {10.1016/j.biortech.2026.134498}, pmid = {41895455}, issn = {1873-2976}, abstract = {Salinity and fulvic acid frequently coexist in high-strength wastewater, yet their combined effects on anaerobic ammonium oxidation (anammox) remain unclear. This study evaluated their impacts on reactor performance, microbial community structure, and functional genes. Moderate salinity (5-10 g L[-1] NaCl) slightly enhanced anammox activity, whereas higher salinity (15 g L[-1]) and fulvic acid (> 60 mg L[-1]) significantly inhibited nitrogen removal. Under such combined stress, specific anammox activity decreased by about 40%, indicating a synergistic inhibition. Extracellular polymeric substances increased by 198%, suggesting a microbial stress-response strategy. Microbial community analysis showed a decline in Planctomycetes by 11%, and enrichment of Proteobacteria by 7% and Chloroflexi by 4%. Metagenomic results revealed suppression of key anammox genes and enrichment of denitrification genes, with quorum sensing and polysaccharide biosynthesis genes increased, suggesting EPS-mediated adaptation under combined stress. These findings provide insights for improving anammox stability in saline and humic-rich wastewater treatment systems.}, }
@article {pmid41895928, year = {2026}, author = {Movsesijan, T and Alcañiz, AJ and Roch, FF and Chaughtai, MS and Dzieciol, M and Stessl, B and Thalguter, S and Strachan, CR and Raindl, M and Wagner, M and Selberherr, E and Quijada, NM}, title = {Biofilm capacity of the psychrophilic bacteria triggers their persistence in the equipment and their spread to beef products throughout processing.}, journal = {Food research international (Ottawa, Ont.)}, volume = {232}, number = {}, pages = {118808}, doi = {10.1016/j.foodres.2026.118808}, pmid = {41895928}, issn = {1873-7145}, mesh = {*Biofilms/growth &amp; development ; Animals ; Cattle ; *Red Meat/microbiology ; *Food Handling/instrumentation ; *Food Microbiology ; *Psychrobacter/genetics/isolation &amp; purification/physiology ; *Equipment Contamination ; Pseudomonas/genetics/isolation &amp; purification/physiology ; Abattoirs ; *Food Contamination/analysis ; *Meat Products/microbiology ; }, abstract = {Microbial contamination in food processing remains a persistent and complex challenge. Understanding the sources, contributing factors, and control measures is essential for effective mitigation. In this study we employed a combination of metagenomic sequencing, targeted culturomics, and whole-genome sequencing of key isolates to gain a comprehensive view of bacterial dynamics and functional capabilities throughout a working shift in a beef slaughter and cutting facility. This allowed us to identify which bacteria are i) most prevalent in the clean facility before the start of the work, ii) able to establish themselves over time, and iii) detectable in the final product. We further generated a functional profile of the microbial community within the facility, with a particular focus on antimicrobial resistance and biofilm formation genes, and the presence of specific pathogens and spoilage organisms. Both culture-based and sequencing data showed that Psychrobacter and Pseudomonas strains present in the final product were also detected on the membrane skinner, a machine used to remove all the excess tissues from meat, and in the drains even after cleaning. We found a high number of genes involved in biofilm formation in Psychrobacter immobilis, a characteristic that may explain their biofilm capacity and the survival of this species during the cleaning process and persistence throughout the facility. Taken together, our findings suggest potential sources of contamination and highlight the advantages of integrating culture-dependent methods with high-throughput sequencing technologies to enhance microbial monitoring and control strategies in food production environments.}, }
@article {pmid41895935, year = {2026}, author = {Li, H and Hu, H and Lu, W and Liu, J and Peng, Q and Wang, S and Dan, T}, title = {Metagenomic analysis of lactic acid bacteria communities in inner Mongolian fermented dairy products: influence of milk source and geography.}, journal = {Food research international (Ottawa, Ont.)}, volume = {232}, number = {}, pages = {118849}, doi = {10.1016/j.foodres.2026.118849}, pmid = {41895935}, issn = {1873-7145}, mesh = {Animals ; *Cultured Milk Products/microbiology ; China ; *Metagenomics/methods ; *Lactobacillales/genetics/classification/isolation &amp; purification ; Cattle ; *Milk/microbiology ; *Food Microbiology ; Fermentation ; Geography ; Horses ; }, abstract = {Inner Mongolia, a key grassland region in China, has a long-standing tradition of fermented dairy products. This study aimed to elucidate the influence of milk source and geographical origin on the community structure and functional characteristics of lactic acid bacteria (LAB) in fermented milk. Twenty-four fermented milk samples from four regions were subjected to metagenomic sequencing analysis including α/β-diversity assessment, taxonomic classification, and functional annotation. The milk source and geographical region jointly shaped the diversity of LAB. The LAB community structure in fermented mare milk displayed more pronounced geographical differentiation than that in fermented cow milk. The core dominant LAB species included Lactobacillus kefiranofaciens, Lactobacillus helveticus, and Lactococcus lactis, with L. helveticus being more abundant in fermented mare milk. The functional profiles of LAB varied depending on the milk source used. The data indicated that milk source was a primary factor associated with the core LAB composition, while geographical origin was associated with the modulation of community diversity and functional attributes. These findings provide region-specific insights into the microbial ecology of traditional Inner Mongolian fermented dairy products.}, }
@article {pmid41895941, year = {2026}, author = {Zhang, J and Li, Y and Zhao, X and Wang, Q and Li, J and Xia, Y and Jambal, T and Dorjgotov, D and Zha, M and Chen, Y}, title = {The cheese of Xilingol: A comparative study on microbial diversity and metabolic profiles across typical and meadow steppes.}, journal = {Food research international (Ottawa, Ont.)}, volume = {232}, number = {}, pages = {118860}, doi = {10.1016/j.foodres.2026.118860}, pmid = {41895941}, issn = {1873-7145}, mesh = {*Cheese/microbiology/analysis ; Milk/microbiology ; *Food Microbiology ; Animals ; Moraxella/isolation &amp; purification/metabolism ; Lactococcus lactis/isolation &amp; purification/metabolism ; *Microbiota ; *Metabolome ; Amino Acids/analysis ; China ; }, abstract = {Xilingol cheese (hurood), a traditional product of Inner Mongolia, acquires its superior flavor and quality from region-specific microbial communities. Understanding the microorganisms and metabolites of hurood across different grassland ecosystems is crucial. This study collected milk and hurood samples from typical and meadow steppes. A total of 179 species were identified, with Moraxella osloensis being more abundant in milk and Lactococcus lactis dominant in hurood. Additionally, 26 differential metabolites were screened from different grasslands, with 19 metabolites found in higher concentrations in hurood, such as N-lactoyl-phenylalanine and N-Acetyl-L-Histidine. These differential metabolites are mainly involved in lipid, carbohydrate, amino acid, and energy metabolism. Spearman correlation analysis revealed that L. lactis was significantly and positively correlated with differential metabolites such as O-phospho-l-serine and gluconic acid, which may affect hurood quality through carbohydrate and protein metabolism, especially amino acid metabolism. M. osloensis was positively correlated with metabolites such as 2-Methylhippuric acid and γ-Glu-Cys. Samples from typical steppe showed a richer microbial diversity, while samples from meadow steppe exhibited a higher enrichment of beneficial microorganisms and metabolites. Superior milk quality and the environmental conditions for lactic acid bacteria colonization may both promote the formation of superior flavor characteristics and functional components. This observational study offers valuable insights into the microbial and metabolic characteristics of hurood, thereby supporting efforts to improve hurood quality.}, }
@article {pmid41895971, year = {2026}, author = {Silva, FA and Cabral, L and de Assis, BBT and Ferreira, DP and Egea, MB and Pimentel, TC and Magnani, M}, title = {Microbiota of foods: a comprehensive review of diversity and potential implications.}, journal = {Food research international (Ottawa, Ont.)}, volume = {232}, number = {}, pages = {118899}, doi = {10.1016/j.foodres.2026.118899}, pmid = {41895971}, issn = {1873-7145}, mesh = {*Food Microbiology ; *Fermented Foods/microbiology ; *Microbiota ; Fermentation ; Metagenomics ; Humans ; Metabolomics ; Bacteria/classification/genetics ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; }, abstract = {Microbial communities play a central role in food ecosystems. Fermented foods, in particular, host complex and dynamic microbiomes that are shaped by raw materials, fermentation substrates, processing environments, and regional production practices. This review provides an in-depth analysis of microbial diversity in various spontaneously fermented food products, including beverages, dairy products, and ethnic and other traditional food products. It highlights how microbial composition evolves throughout fermentation and how specific microorganisms contribute to the safety and sensory profiles of the final products. The field has undergone a methodological transformation, moving from classical culture-based methods to advanced omics technologies. Culture-independent approaches such as metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metabolomics enable a more comprehensive characterization of microbial communities, providing insights not only into their taxonomic composition but also into their functional roles. Despite increasing interest in metagenomics and metatranscriptomics, metataxonomic high-throughput sequencing, particularly 16S rRNA and ITS gene analyses, remains the most widely used technique due to its lower cost and accessibility. However, it provides limited resolution at the species level and cannot distinguish between live and dead cells. Microbiome characterization using omics has practical implications for the food industry, including the identification of microbial signatures in artisanal foods and the improvement of understanding fermentation processes. Our manuscript emphasizes a broad comparative overview of microbial diversity across multiple categories of fermented foods and integrates this with a methodological perspective on omics approaches used to characterize these communities. Findings outline the main methodological approaches, sequencing platforms, primer sets, and bioinformatic tools used in studies, as well as the current limitations and future directions in the field. Integrative multi-omics strategies are expected to significantly enhance food safety, quality, traceability, and functionality across diverse food systems.}, }
@article {pmid41896456, year = {2026}, author = {Habot-Wilner, Z and Ostrovsky, M and Zur, D and Schwartz, S and Hagin, D and Gadoth, A and Ben-Ami, R and Paran, Y and Goldshmidt, H and Slutzkin, M and Adler, A and Levytskyi, K}, title = {Response to: 'Comment on 'Metagenomic next-generation sequencing: a game changer in the diagnosis of unique intraocular infections''.}, journal = {Eye (London, England)}, volume = {}, number = {}, pages = {}, pmid = {41896456}, issn = {1476-5454}, }
@article {pmid41896477, year = {2026}, author = {Shaw, J and Marin, MG and Li, H}, title = {High-resolution metagenome assembly for modern long reads with myloasm.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {41896477}, issn = {1546-1696}, support = {R01HG010040//U.S. Department of Health &amp; Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; PDF-587396//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; }, abstract = {Long-read metagenome assembly promises complete genomic recovery from microbiomes. However, the complexity of metagenomes poses challenges. Here we present myloasm, a metagenome assembler for modern long reads such as PacBio HiFi and Oxford Nanopore Technologies (ONT) R10.4 long reads. Myloasm uses polymorphic k-mers to construct a high-resolution string graph and then leverages differential abundance for graph simplification. On real-world ONT metagenomes, myloasm assembled three times more complete circular contigs than the next-best assembler. Myloasm can make ONT and HiFi assemblies comparable. For example, on a jointly sequenced gut metagenome, myloasm with ONT assembled more complete circular genomes than any assembler with HiFi. Myloasm also recovers previously inaccessible within-species diversity. Here, we recovered six complete Prevotella copri single-contig genomes from a gut metagenome and eight complete TM7 (Saccharibacteria) contigs with >93% similarity from an oral metagenome. Overall, we show that myloasm outperforms existing long-read metagenome assemblers across a range of environments and modern sequencing technologies.}, }
@article {pmid41896490, year = {2026}, author = {Zheng, M and Yang, X and Tian, R and Xia, X and Xu, Q and Hui, Y and Chen, S and Liu, Y and Wang, A}, title = {A Segatella Copri-centered Gut Microbiota-mediated Metabolic Dysregulation Associated with Transition from Asymptomatic to Symptomatic Intracranial Atherosclerosis.}, journal = {Translational stroke research}, volume = {17}, number = {2}, pages = {}, pmid = {41896490}, issn = {1868-601X}, support = {82504498//National Natural Science Foundation of China/ ; 82473699//National Natural Science Foundation of China/ ; 2022YFC3600600//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Middle Aged ; *Intracranial Arteriosclerosis/metabolism/microbiology ; Case-Control Studies ; Aged ; Biomarkers/blood ; Metabolomics ; *Ischemic Stroke/metabolism/microbiology ; }, abstract = {The mechanisms underlying the continuum from asymptomatic intracranial atherosclerotic stenosis (aICAS) to symptomatic intracranial large-artery atherosclerotic ischemic stroke (iLAA-IS) remain unclear. We investigated the gut microbiota-metabolite axis in this transition to identify predictive biomarkers and clarify key functional pathways. In a case-control study (63 iLAA-IS cases; 56 aICAS controls), fecal shotgun metagenomics and untargeted plasma metabolomics were profiled. Using machine learning with 10-fold nested cross-validation, we identified five robust biomarkers associated with the transition: Alistipes putredinis (risk-associated) and four protective features (Segatella copri, Gln-Gly, Methionine Sulfoxide, and N6-Acetyl-L-Lysine). Integrated models incorporating these markers significantly improved predictive performance relative to conventional risk factors (e.g., mean AUC of Gln-Gly: 0.9104 vs. 0.7188). Mechanistic analyses revealed a Segatella copri-centered metabolic dysregulation: its depletion coincided with a broad loss of anabolic pathways (BCAA biosynthesis, folate-SAM-methionine metabolism, and tRNA charging), which were positively linked to amino acid-related metabolites. In contrast, the pathways of Alistipes putredinis showed no such coupling. These findings suggest that the aICAS-to-iLAA-IS transition is characterized by chronic metabolic dysregulation, involving a Segatella copri-centered microbiota-metabolite axis. This multi-omic signature offers novel insights into stroke pathogenesis and potential targets for prevention.}, }
@article {pmid41896556, year = {2026}, author = {Walsh, LH and Soni, V and Ancla, J and Somerville, V and Segata, N and Joyce, S and Sinderen, DV and Mahony, J and Shkoporov, AN and Kenny, JG and Cotter, PD and O'Sullivan, O}, title = {Mining of food metagenomes reveals an unexplored diversity of dsDNA bacteriophages.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00941-9}, pmid = {41896556}, issn = {2055-5008}, support = {DOMINO-101060218//European Union's Horizon Europe programme/ ; }, abstract = {Bacteriophages are key drivers of microbial ecology, co-existing and co-evolving with bacteria across diverse environments. Limitations in culturing, alongside advances in sequencing and bioinformatics, have driven the use of metagenomics to explore viral diversity. Viral-specific analysis of >3000 food metagenomes from cFMD produced the FVGC, comprising ~3400 metagenome-assembled viruses, most of which belong to novel Caudoviricetes lineages (n = 91), with only ~15% represented in IMG/VR v4. Together, these findings reveal extensive uncharacterized viral diversity in food systems. Beyond serving as a reference, the FVGC facilitates detailed investigation of virus-host interactions. Viral sequences were pervasive across microbial genomes, with several bacterial families exhibiting near-universal associations with viral elements. Bacterial antiviral defence systems were abundant and taxonomically diverse, dominated by restriction-modification systems, while CRISPR-Cas systems showed pronounced lineage-specific distributions; in contrast, viral anti-defence genes were detected at low frequency (<10% of MAVs). Host prediction linked MAVs to clinically relevant taxa, including expanded ESKAPE pathogens such as Klebsiella pneumoniae, Acinetobacter baumannii, Staphylococcus aureus, and Enterobacter spp., highlighting the ecological connectivity between food-associated viruses and clinically important bacteria. Antimicrobial resistance signals were scarce, suggesting minimal phage-mediated AMR dissemination in food environments. This new publicly available viral database represents a valuable resource for further exploration of viral diversity.}, }
@article {pmid41896639, year = {2026}, author = {Puetz, LC and O Delmont, T and Mitchell, AL and Finn, RD and Zhang, G and Shepeleva, DV and Kharlamova, AV and Kukekova, AV and Trut, LN and Gilbert, MTP}, title = {Gut microbiome community structure correlates with different behavioral phenotypes in the Belyaev Farm-Fox Experiment.}, journal = {Communications biology}, volume = {9}, number = {1}, pages = {}, pmid = {41896639}, issn = {2399-3642}, support = {NIH R35 GM144276//U.S. Department of Health &amp; Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; RSF-21-44-04405//Russian Science Foundation (RSF)/ ; DNRF143 Center for Evolutionary Hologenomics//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Behavior, Animal ; *Foxes/microbiology/physiology ; Phenotype ; Domestication ; Male ; }, abstract = {Domestication represents one of the largest biological shifts of life on Earth, and for many animal species, behavioral selection is thought to facilitate early stages of the process. The gut microbiome of animals can respond to environmental changes and have diverse and powerful effects on host behavior. As such, we hypothesize that selection for tame behavior during early domestication, may have indirectly selected on certain gut microbiota that contribute to the behavioral plasticity necessary to adapt to the new social environment. Here, we explore the gut microbiome of foxes from the tame and aggressive strains of the "Russian-Farm-Fox-Experiment". Microbiota profiles reveal a significant depletion of bacteria in the tame fox population that have been associated with aggressive and fear-related behaviors in other mammals. Our metagenomic survey allows for the reconstruction of microbial pathways enriched in the gut of tame foxes, such as glutamate degradation, which converge with host genetic and physiological signals, revealing a potential role of functional host-microbiota interactions that could influence behaviors associated with domestication. Overall, by characterizing how compositional and functional potential of the gut microbiota and host behaviors co-vary during early animal domestication, we provide further insight into our mechanistic understanding of this adaptive, eco-evolutionary process.}, }
@article {pmid41896653, year = {2026}, author = {Zhao, Z and Yang, Y and Zhang, L and He, X and Ding, K and Chen, Y and Huo, Y and Li, P and Li, R and Ali, T and Zhao, D and Choe, H and Ma, J and Shang, D and Zhang, L}, title = {Multi-omics and network pharmacology reveal the mechanisms of Scutellaria barbata D.Don and Scleromitrion diffusum (Willd.) R.J.Wang against pancreatic cancer.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-45676-x}, pmid = {41896653}, issn = {2045-2322}, support = {2022-BS-244//Liaoning Provincial Doctoral Research Startup Fund Project/ ; XLYC1907113//Liaoning Revitalization Talents Program/ ; 2022RJ19//Distinguished Young Scholars in Dalian/ ; }, abstract = {Pancreatic cancer (PC) is a common gastrointestinal malignancy whose initiation and progression may be closely linked to the gut microbiota. Previous research indicates that Scutellaria barbata D. Don and Scleromitrion diffusum (Willd.) R.J. Wang (SB-SD) exhibit diverse biological activities, such as anti-inflammatory, antioxidant, and antitumor effects, though their precise regulatory mechanisms are not fully elucidated. Here, we treated PC cells with SB-SD to assess its impact on cell viability, apoptosis, migration, and cell cycle progression, while Western blotting analyzed the expression of HSP90AA1, MAPK3, p53, CDK1, and p21. We also established a pancreatic cancer xenograft model in nude mice to evaluate the in vivo inhibitory effect of SB-SD on tumor growth. Furthermore, we employed metagenomic sequencing, untargeted metabolomics, and quantitative proteomics to comprehensively profile changes in the gut microbiota, serum metabolites, and differentially expressed proteins, with Western blotting subsequently validating BCKDK, GATM and p53 expression. The results show that SB-SD significantly inhibited PC cell proliferation, promoted apoptosis, and induced S/G2 phase cell cycle arrest, potentially via modulation of the HSP90AA1/MAPK3 signaling pathway. Measurements of tumor volume and weight, complemented by histopathological analysis, confirmed that SB-SD effectively suppressed the growth of PANC-1 xenograft tumors. Integrated multi-omics analyses suggest that the antitumor effects of SB-SD may involve the modulation of key gut microbes like Bacteroides caccae and Lactobacillus, the promotion of choline metabolism, and the regulation of BCKDK and GATM. Together, these findings not only corroborate the direct antitumor activity of SB-SD against pancreatic cancer but also offer novel mechanistic insights by constructing a microbiota-metabolite-protein interaction network.}, }
@article {pmid41896698, year = {2026}, author = {Jung, S and Militsi, E and Huck, O}, title = {Oral Microbiome in Systemic Autoimmune Diseases: A Systematic Review.}, journal = {Oral diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/odi.70215}, pmid = {41896698}, issn = {1601-0825}, abstract = {OBJECTIVE: The oral cavity represents a key but underexplored interface between host immunity and microbial communities. The aim of this systematic review was to synthesize current literature on oral microbiota alterations in systemic autoimmune diseases.<br><br>METHODS: PubMed and Web of Science databases were searched for human studies published between January 2000 and April 2025. Eligible observational studies compared adults with diagnoses of systemic autoimmune diseases to controls and characterized oral microbiota diversity and/or composition using sequencing-based methods. Different oral habitats were analyzed (saliva, dental plaque, oral mucosa, gingival crevicular fluid).<br><br>RESULTS: 42 studies met inclusion criteria: 19 on rheumatoid arthritis, 18 on primary Sj&#xf6;gren's syndrome, 5 on systemic lupus erythematosus, and 1 on anti-neutrophil cytoplasmic autoantibody-associated vasculitis. 16S rRNA gene sequencing predominated and only 3 studies used shotgun metagenomics, among which one also profiled the oral virome. Across systemic autoimmune diseases, dysbiosis was characterized by enrichment of anaerobic genera (Prevotella, Veillonella) and depletion of commensals (Neisseria, Haemophilus), with distinct &#x3b2;-diversity separation from controls. Periodontal disease and reduced salivary secretion significantly modulated microbial communities but did not fully explain disease-associated alterations.<br><br>CONCLUSION: The oral microbiome exhibited shared dysbiotic signatures. However, methodological and clinical heterogeneity limited direct comparison between studies.}, }
@article {pmid41897379, year = {2026}, author = {Zhang, Y and Zhao, B and Li, J and Yuan, T and Liu, Y and Sun, Z}, title = {Effects and Adaptive Responses of Sulfate-Reducing Biochemical System to Acid Stress.}, journal = {Biomolecules}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/biom16030444}, pmid = {41897379}, issn = {2218-273X}, support = {41772266//State Key Laboratory of Nuclear Resources and Environment, the National Natural Science Foundation of China/ ; }, mesh = {*Sulfates/metabolism ; Hydrogen-Ion Concentration ; *Desulfovibrio/metabolism/genetics ; Oxidation-Reduction ; *Adaptation, Physiological ; *Stress, Physiological ; Acids ; }, abstract = {A decrease in pH can affect the biochemical properties of a sulfate reduction system, but the stress responses to such pH fluctuations and acid-adaptive mechanisms of the microorganisms remain incompletely understood. Here, we compared the sulfate (SO4[2-]) reduction performance of a sulfate-reducing consortium (SRB system) and a pure Desulfovibrio sp. system (Des. system, control) under pH 7.0, 5.5, and 5.0 via batch experiments. A key novelty is the integration of microbial physiology and metagenomics to reveal adaptive mechanisms: the Des. system showed significant inhibition of growth and sulfate reduction with decreasing pH, while the SRB system maintained superior SO4[2-] removal efficiency through three synergistic adjustments: (1) physiological regulation (enhanced H[+]-ATPase activity, stress protein production, and cell membrane cyclopropane fatty acid content); (2) microbial community restructuring (enrichment of acid-resistant Bacillus and Clostridium); and (3) functional gene upregulation (sulfate import, dissimilar sulfate reduction, sulfide oxidation, and SOx system-related genes, p < 0.05). This study links physiological responses to metagenomic functional shifts under acid stress, providing critical theoretical support for applying sulfate-reducing consortia in acidic sulfate-containing wastewater remediation.}, }
@article {pmid41897502, year = {2026}, author = {Khan, A and Xiong, Z and Khan, IA and Cheng, X and Luo, Q and Jia, L and Liu, W and Huang, C and Chen, Z}, title = {Dimercaprol Reprograms Intestinal Redox Homeostasis and Organelle Crosstalk to Combat Iron-Induced Gut Dysbiosis Through NRF2/HO-1 Signaling.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/antiox15030356}, pmid = {41897502}, issn = {2076-3921}, support = {2024YFHZ0325//Zhengli Chen/ ; 32071161//Chao Huang/ ; 2023NSFC1929//Chao Huang/ ; }, abstract = {Gut disorders are largely caused by iron-induced microbial dysbiosis. Excess iron disrupts barrier integrity by inducing oxidative stress, leading to impaired cellular processes. The determination of therapeutic compounds that can reduce iron-induced damage and maintain gut cellular integrity is still a top objective. Dimercaprol (DP) represents a novel iron-chelating strategy for the treatment of iron-induced gut disorders. A chronic iron-overload model was established in mice via intragastric gavage of ferric citrate (FC) (286 mg/kg BW) for 16 weeks. Similarly, IPEC-J2 cells were exposed to FC (50 µmol/L) for 24 h. DP was used as a mechanistic probe to elucidate the pathways involved in iron-induced toxicity. Cells were transfected with or without NRF2 siRNA and exposed to DP post-FC. Colonic contents were assessed via metagenomics and metabolomics. Both in vivo and in vitro experiments were analyzed through a multifaceted analysis, Western blot, RT-qPCR, ELISA, transmission electron microscopy and immunofluorescence assays. Thiols in DP protect gut cells from damage by boosting their natural antioxidant defenses via the NRF2/HO-1 pathway. The DP mechanism of action is multifaceted, including enhancement of barrier integrity, protecting mitochondrial structure and function, suppression of inflammation and endoplasmic reticulum (ER) stress and restoration of gut microbial and metabolic homeostasis. These protective effects are mainly caused by the activation of the NRF2/HO-1 pathway, which makes DP a potential therapeutic agent for disorders caused by chronic gut injury induced by FC. DP provides strong protection against iron-induced gut damage by restoring organelle crosstalk, redox homeostasis and microbial-metabolic balance through NRF2/HO-1 signaling.}, }
@article {pmid41897791, year = {2026}, author = {Xie, M and Xue, F and Sun, M and Zhuang, Q and Tang, S and Huang, Y and Zhang, Y and Hu, J and Zhou, Y}, title = {Determination of the Modulatory Effects of Selenium-Enriched Egg Powder on the Physiological Immune Response and Cecal Microbiota of Kunming Mice.}, journal = {Foods (Basel, Switzerland)}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/foods15061069}, pmid = {41897791}, issn = {2304-8158}, support = {20252BAC240155//Natural Science Foundation Project of Jiangxi Province/ ; JX-202401//the Open research projects of key laboratories of the Jiangxi Province "Mechanism Research of the Regulation on Immune System by Selenium-enriched Eggs"/ ; }, abstract = {Se-enriched functional eggs are prevalent nowadays, which may help improve body health and anti-oxidant capacities. However, the modulatory effects on cecal microbiota are still limited. This study aims to investigate the underlying mechanism of Se-enriched egg powder in modulating the cecal microbiota of Kunming mice. A total of 72 mice were randomly assigned to a control treatment (CON), a conventional egg powder treatment (EP), and four gradient Se-enriched egg powder treatments (EPS1-EPS4, with the Se content ranging from 0.01 to 0.04% of total dietary content) for a 35-day feeding procedure. Parameters included growth performance, tissue Se content distribution, serum anti-oxidant capacities (GSH-Px, SOD, MDA), and immune cytokines (IgG, TNF-α), and cecal microbiota composition was further measured. Results showed dietary 0.02% (EPS2) significantly improved growth performance, physiological anti-oxidant defenses, and cytokine TNF-α (p < 0.05), while significantly reducing feed conversion ratio and malondialdehyde (MDA) compared with CON (p < 0.05). Metagenomic results revealed that Se-enriched egg powder significantly increased bacterial α-diversity and the abundance of Akkermansia, Bacteroides, and Bifidobacterium (p < 0.05), while significantly decreasing Desulfovibrio and Escherichia-Shigella (p < 0.05). In conclusion, dietary supplementation with Se-enriched egg powder effectively enhances growth performance, anti-oxidant capacity, and immunity, mainly through the promotion of beneficial bacteria diversity and suppression of pathogens.}, }
@article {pmid41897857, year = {2026}, author = {Yang, Y and Wang, J and Wang, Z and Li, C and Hu, X and Liao, S and Wang, L}, title = {Airborne Microbiome of Tropical Ostrich Farms: Diversity, Antibiotic Resistance, and Biogeochemical Cycling Potential.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/ani16060880}, pmid = {41897857}, issn = {2076-2615}, support = {42367014//The National Natural Science Foundation of China/ ; }, abstract = {The expansion of tropical specialty livestock farming raises urgent concerns about airborne pathogen and antibiotic resistance dissemination. Ostrich farming, characterized by high-density stocking and feed exposure, yet their microbial ecology remain poorly characterized. This study analyzed 48 bioaerosols samples from an ostrich farm in Hainan, China, across dry and rainy seasons using 16S rRNA sequencing and metagenomics. The bacterial community were dominated by Firmicutes, Proteobacteria, and Actinobacteria, followed by Staphylococcus, Bacillus, and Acinetobacter as predominant genera, with particle size significantly shaping their structure. Large particles (>7.0 μm) carried higher species richness, while medium particles (2.1-3.3 μm) exhibited the highest diversity and evenness. Notably, small particles (0.65-1.1 μm), which can penetrate deep into the lungs, were enriched with Brevibacillus and Corynebacterium. Metagenomic analysis identified 638 antibiotic resistance genes (ARGs), dominated by efflux pump-associated determinants. The detection of clinically relevant ARGs (e.g., mcr-1 and blaTEM) reflects the genetic potential of the airborne resistome, rather than confirmed resistance phenotypes or active horizontal gene transfer. Functional analysis revealed a strong potential for organic matter degradation, driven by abundant carbohydrate-active enzymes (CAZymes) and their corresponding CAZyme genes, as well as a nitrogen cycle dominated by assimilation and reduction pathways, while genes for nitrogen fixation and nitrification were absent. Our findings demonstrate that ostrich farming enhanced airborne microbial diversity and functional potential, facilitating the ARG dissemination and nitrogen transformation. This study provides critical insights into the ecological and health risks of bioaerosols in tropical livestock farms, informing environmental monitoring and risk management strategies.}, }
@article {pmid41897913, year = {2026}, author = {An, Q and Chen, S and Ma, S and Bai, R and Lu, Z and Liu, Y and Wang, F and Wang, Q and Song, Y and Zhang, G and Lyu, Y and Wang, L and Wang, Y and Xia, Z}, title = {Shotgun Metagenomics Reveals Gut Microbiome Remodeling with Altered Taxonomic Composition and Functional Potential in Diabetic Dogs.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/ani16060936}, pmid = {41897913}, issn = {2076-2615}, support = {1051-2225006//General Program of the 2025 Talent Fund, Veterinary Teaching Hospital, China Agricultural University/ ; }, abstract = {Gut microbiota dysbiosis is implicated in metabolic disorders, yet taxonomic and functional alterations in canine diabetes remain incompletely defined. Here, we performed shotgun metagenomic sequencing of fecal samples from 38 diabetic dogs and 37 healthy controls under controlled conditions (no recent antibiotic/probiotic exposure and stable commercial diets). Alpha-diversity indices did not differ between groups, whereas beta-diversity revealed significant separation of community structure at both genus and species levels (p < 0.05). Linear discriminant analysis effect size (LEfSe) identified enrichment of opportunistic-associated taxa in diabetic dogs, including Enterobacterales/Enterobacteriaceae (e.g., Escherichia coli, Klebsiella pneumoniae, Salmonella enterica) and Enterococcus faecalis. In contrast, healthy dogs were enriched for putatively beneficial taxa linked to bile acid and short-chain fatty acid (SCFA) metabolism, including Turicibacter spp. and Romboutsia spp. Functional profiling showed higher abundances of pathways related to carbohydrate/energy metabolism, membrane transport, and virulence/colonization in diabetic dogs; 17 KEGG level-3 pathways and 320 KOs differed at FDR < 0.05, with enriched modules including bacterial secretion systems, lipopolysaccharide biosynthesis, chemotaxis/flagellar assembly, and biofilm formation. Collectively, canine diabetes is associated with a remodeled gut microbiome characterized by expansion of opportunistic pathogens and elevated virulence and metabolic potential, supporting exploration of microbiota-targeted strategies as a complement to conventional management.}, }
@article {pmid41897927, year = {2026}, author = {Fukuda, EP and Lu, Y and Fowler, E and Jessup, RW and Drewery, ML}, title = {Metagenomic Insights into the Effects of Dietary Thymol on the Structure and Function of the Rumen Microbial Community in Beef Steers Consuming Forage.}, journal = {Animals : an open access journal from MDPI}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/ani16060950}, pmid = {41897927}, issn = {2076-2615}, support = {2021-77040-34881//National Institute of Food and Agriculture/ ; 2020-38422-32250//National Institute of Food and Agriculture/ ; N/a//Translational Health Research Center/ ; }, abstract = {While essential oils are gaining momentum as a strategy to modulate rumen function and potentially reduce enteric methane in cattle, little is known about how their bioactive components, terpenes, affect rumen microbes. Our objective was to evaluate how in vivo doses of thymol affect the structure and function of the rumen microbial community via whole genome shotgun sequencing (WGS). Four beef steers were used in a 4 × 4 Latin square with four 28 d periods. Steers consumed ad libitum forage and received one of four thymol doses (0 [CON], 120 [120-T], 240 [240-T], and 480 [480-T] mg/kg forage intake). Rumen contents were separated into liquid and solid fractions, DNA was extracted, analyzed via WGS, and assessed with orthogonal contrasts. After FDR correction, no taxa were affected by thymol; however, raw p-values demonstrated responses to thymol supplementation for solid-associated uncultured Lachnospiraceae bacterium (p = 0.04), uncultured Methanobrevibacter (p = 0.05), and uncultured Coriobacteriaceae bacterium (p = 0.02). Liquid-associated uncultured Prevotellaceae bacterium (p = 0.03), Prevotella sp. (p = 0.04), and Bacteroides sp. (p = 0.02) also responded to thymol, with the highest abundances observed at various thymol doses. Genes involved in energy production and amino acid metabolism transport were observed at the highest abundances at 240-T, while genes associated with cell cycle control, cell division, and chromosome partitioning were present in the highest abundances at 120-T. The findings suggest that thymol exerts dose-dependent effects on rumen microbial abundances and functional pathways, with 240 mg/kg forage intake appearing to be the most effective dose to downregulate methanogenic enzymes while also enhancing the enzymes associated with metabolism without negatively impacting microbial diversity.}, }
@article {pmid41898277, year = {2026}, author = {Qiu, D and Suo, L and Wei, T and Lu, Z and Weng, Q and Xiao, J and Wang, X and Xu, Q and Wu, J}, title = {Mediation Role of Gut Microbiota in the Causal Relationship Between m6A Regulatory Genes and Metabolic Dysfunction-Associated Steatotic Liver Disease: A Mendelian Randomization Study.}, journal = {Biomedicines}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/biomedicines14030630}, pmid = {41898277}, issn = {2227-9059}, support = {3502Z20227102//Qinyu Xu/ ; }, abstract = {Background: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a globally prevalent condition with a complex pathogenesis. While both m6A RNA methylation regulators and gut microbiota have been independently implicated in MASLD, their potential causal interplay remains unexplored. This study aimed to investigate the causal relationships among m6A regulatory genes, gut microbiota, and MASLD, and to assess the mediating role of gut microbiota. Methods: We performed a two-sample Mendelian randomization (MR) analysis using publicly available genome-wide association study (GWAS) data. Genetic instruments for m6A regulators were derived from blood expression quantitative trait loci (eQTL) data. Gut microbiota and MASLD data were obtained from large-scale metagenomic and disease GWAS, respectively. The inverse-variance weighted method was the primary analysis, supplemented by sensitivity and mediation analyses to evaluate potential mediating pathways. Results: Genetically predicted levels of four m6A regulators showed significant causal associations with MASLD risk: ALKBH3 increased risk (OR = 1.17), whereas ALKBH5 (OR = 0.89), CBLL1 (OR = 0.76), and RBM15B (OR = 0.83) were protective. Nineteen gut microbial taxa were causally linked to MASLD. Among these, seven taxa were influenced by the four identified m6A genes. Although no mediation effects reached strict statistical significance, the pathway from ALKBH5 to MASLD via Parabacteroides abundance showed a suggestive indirect effect accounting for 21.9% of the total effect (p = 0.068). Given the limited statistical power of mediation analyses in MR settings, this observation should be interpreted with caution and requires validation in larger, well-powered studies. Conclusions: This MR study provides genetic evidence supporting causal roles of specific m6A regulators in MASLD and suggests that gut microbiota may partially mediate these relationships. The findings highlight a potential "m6A-gut microbiota-liver" axis in MASLD pathogenesis.}, }
@article {pmid41898335, year = {2026}, author = {Schultheiss, HP and Escher, F and Aleshcheva, G and Wiegleb, G and Baumeier, C}, title = {Diagnostic and Therapeutic Options in Myocarditis and Inflammatory Cardiomyopathy.}, journal = {Biomedicines}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/biomedicines14030691}, pmid = {41898335}, issn = {2227-9059}, support = {KK5175802AP2, KK5463501AP2, KK5463901AP2//Federal Ministry of Economic Affairs, Germany/ ; 10169096, 10169098, 10169028//ProFIT grant of the Investitionsbank Berlin/co-funded by EFRE/ ; }, abstract = {Myocarditis and inflammatory cardiomyopathy are inflammatory diseases of the heart muscle that can have both infectious and non-infectious causes. They can be caused by an unresolved viral infection or other infection, or they can be autoimmune, toxic, or allergic in nature. The specific identification of the pathogen and/or confirmation of inflammation can only be achieved through direct tissue analysis using endomyocardial biopsy (EMB), as neither detection of the virus nor assessment of the quality and intensity of the inflammation is possible using non-invasive methods. Accordingly, the removal and analysis of an EMB is considered the diagnostic gold standard in international guidelines and statements. The sudden onset of atypical angina pectoris and initially exertion-dependent dyspnea, as well as arrhythmias, pericardial effusion, and progressive symptoms of heart failure, indicate an acute inflammatory process of the myocardium. In addition, nonspecific symptoms such as fatigue and reduced physical performance may also occur. Diagnostic evaluation includes an electrocardiogram (ECG), cardiac imaging, and laboratory tests. The analysis of the EMB is crucial for a definitive diagnosis and thus for the initiation of an etiology-based, specific and personalized therapy. This includes histological and immunohistochemical inflammation diagnostics as well as molecular virological diagnostics. These enable both the detection of viruses and the assessment of transcriptional virus activity. New analyses using metagenomic next generation sequencing (NGS) techniques provide insights of enormous diagnostic and therapeutic relevance. This applies both to the spectrum of detectable pathogens and to the possibility of confirming transcriptional viral activity. In addition, gene expression profiling enables the differentiation of specific forms of myocardial inflammation (e.g., giant cell myocarditis, cardiac sarcoidosis, and eosinophilic myocarditis) and reduces the influence of "sampling errors" in focal inflammatory processes. The treatment of heart failure or ventricular arrhythmias is always symptomatic according to general evidence-based guidelines. In severe cases, mechanical circulatory support or even a heart transplant may be necessary. Patients with histologically confirmed myocardial inflammation or intramyocardial viral infection can be offered specific, causal, and personalized therapy. These patients can be successfully treated with immunosuppressive or antiviral therapy, which significantly improves the prognosis of the disease.}, }
@article {pmid41898386, year = {2026}, author = {Tahtouh Zaatar, M and Othman, R and Abushawish, M and Akl, M and Alachkar, MT and Almatboona, G and Alriyami, F and Alshaibani, A and Ashkanani, D and Basharova, M and Imam, M and Khassay, N and Mikhael, MS and Naderi Far, R and Shaqra, S and Verwey, K and Suleimanova, A and Yousafzada, M and Burmagina, Y}, title = {The Women's Microbiome: Molecular Insights, Clinical Gaps, and Future Frontiers in Precision Health with Implications for Gulf Cooperation Council Populations.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, doi = {10.3390/ijms27062521}, pmid = {41898386}, issn = {1422-0067}, mesh = {Humans ; Female ; *Microbiota ; *Women's Health ; *Precision Medicine ; Probiotics ; Pregnancy ; Vagina/microbiology ; Gastrointestinal Microbiome ; }, abstract = {The human microbiome has emerged as a central regulator of health and disease; however, women-specific microbiome research has only recently gained focused scientific attention. Accumulating evidence demonstrates that microbial ecosystems across the gut, vagina, skin, breast tissue, and reproductive tract are dynamically shaped by female hormones, life-stage transitions, and environmental exposures. These interactions influence immune regulation, metabolic homeostasis, reproductive outcomes, mental health, and cancer risk, in part through microbiome-mediated endocrine pathways such as the estrobolome. Advances in high-resolution molecular technologies-including metagenomics, metabolomics, spatial and single-cell profiling, and artificial intelligence-driven modeling-have shifted microbiome research from descriptive taxonomy toward functional, mechanistic, and predictive science. These approaches highlight microbial function and metabolite production as stronger determinants of health outcomes than taxonomic composition alone. Nonetheless, major gaps persist, including limited causal evidence, methodological heterogeneity, underrepresentation of non-Western populations, and barriers to clinical translation. Microbiome-targeted interventions, including probiotics, prebiotics, postbiotics, and emerging microbiota-based therapies, have garnered increasing interest in women's health. Select Lactobacillus and Bifidobacterium strains show potential in modulating vaginal and gastrointestinal health, pregnancy outcomes, and immune function; however, clinical effects remain highly strain-specific and context-dependent. Discrepancies between experimental findings, commercial claims, and validated clinical use underscore the need for rigorous, women-centered trials and standardized outcome measures. This narrative review synthesizes current molecular insights into the women's microbiome across endocrine interactions, pregnancy, reproductive and metabolic health, lifestyle influences, and microbiome-based therapeutic strategies. We integrate clinical perspectives to identify diagnostic and translational challenges and propose future directions emphasizing precision microbiome medicine, validated biomarkers, careful evaluation of microbiome-targeted interventions, and inclusive research frameworks, including populations from the Gulf Cooperation Council (GCC). Collectively, this review positions the microbiome as a critical yet underutilized axis in women's health and outlines a roadmap toward personalized, evidence-based care across the female lifespan.}, }
@article {pmid41898595, year = {2026}, author = {Makiel, K}, title = {Anti-Inflammatory Diets in Metabolic Syndrome and Obesity: Multi-Omics Perspectives on the Interplay Between Gut Microbiota, DNA Methylation, and Adipokine Regulation-A Narrative Review.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, doi = {10.3390/ijms27062734}, pmid = {41898595}, issn = {1422-0067}, support = {//University of Physical Education, 31-571 Cracow, Poland/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolic Syndrome/diet therapy/metabolism/genetics/microbiology ; *Obesity/diet therapy/metabolism/genetics/microbiology ; *Adipokines/metabolism/genetics ; *DNA Methylation ; *Diet ; Animals ; Inflammation ; Nutrigenomics ; Multiomics ; }, abstract = {An anti-inflammatory dietary pattern represents a key component of non-pharmacological management in obesity and metabolic syndrome (MetS), as it targets chronic low-grade inflammation, adipose tissue dysfunction, insulin resistance, and disturbances of the gut-metabolic axis. In the present work, we outline a framework for an "omics-based" approach that integrates data on gut microbiota composition and function (metagenomics), adipokine profiles, nutrigenomics, epigenetics, and related transcriptomic and metabolomic layers in order to enable more precise characterization of the metabolic phenotype and to support precision nutrition strategies. The proposed dietary model emphasizes the quality rather than merely the quantity of macronutrients, with particular focus on lipid profile optimization. Specifically, total fat intake is recommended to remain below 30% of total energy through the reduction in saturated fatty acids (SFA), trans fats, and excessive omega-6 fatty acids, alongside increased consumption of omega-3 PUFA (EPA/DHA) and plant-based sources of α-linolenic acid (ALA). Concurrently, greater intake of lean protein sources and low-glycemic-index carbohydrates rich in dietary fibre-particularly fermentable fractions-is recommended. The model also highlights the importance of polyphenols with antioxidant and immunomodulatory properties. To enhance feasibility and long-term adherence, recommendations are structured as flexible food substitutions rather than rigid prescriptions. Further well-designed interventional studies are required to confirm the impact of a multi-omics-based anti-inflammatory diet on both molecular and clinical endpoints.}, }
@article {pmid41898625, year = {2026}, author = {Chaplin, AV and Podoprigora, IV and Shcherbakova, VA and Zakharzhevskaya, NB and Evseev, PV and Vasilyeva, AA and Koshkin, FA and Kardonsky, DA and Vorobyeva, EA and Kashatnikova, DA and Kazakova, VD and Efimov, BA}, title = {Parabacteroides vesiculifaciens sp. nov., a Novel Immunomodulatory, Vesicle-Producing Gut Commensal Isolated from the Human Gut.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, doi = {10.3390/ijms27062763}, pmid = {41898625}, issn = {1422-0067}, support = {24-75-10100//Russian Science Foundation/ ; }, mesh = {Humans ; Phylogeny ; *Gastrointestinal Microbiome ; *Bacteroidetes/genetics/classification/isolation &amp; purification ; Feces/microbiology ; Genome, Bacterial ; Animals ; HT29 Cells ; Extracellular Vesicles/metabolism ; Mice ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The genus Parabacteroides comprises widespread gastrointestinal commensals, known to produce immunomodulatory molecules and extracellular vesicles, yet its full diversity is incompletely cataloged. This study describes strain ASD2025[T], isolated from healthy child feces, using a polyphasic taxonomic approach including phenotypic profiling, chemotaxonomy, and comparative genomics. Cells were non-motile, polymorphic rods that produced extracellular vesicles. Phylogenomic analysis placed ASD2025[T] within the genus Parabacteroides within a species complex consisting of P. acidifaciens, P. hominis, "P. massiliensis", P. merdae, and P. johnsonii, with average nucleotide identities to the type strains of 85.5-89.9%. The large genome (5.16 Mbp, 46.2% GC content) contained integrative conjugative elements harboring antibiotic resistance genes and hankyphage-related prophage. The strain produced succinate as the major metabolic end product, and its major fatty acids were anteiso-C15:0, iso-C17:0 3-OH, and C15:0. Conditioned medium from ASD2025[T] antagonized the interleukin-8 response caused by E. coli lipopolysaccharide in HT29 cells. The majority of related metagenome-assembled genomes originate from mouse microbiomes. Based on these distinct characteristics, strain ASD2025[T] (=VKM B-3926[T] = JCM 37967[T]) represents a novel species of the genus Parabacteroides, for which the name Parabacteroides vesiculifaciens sp. nov. is proposed.}, }
@article {pmid41898646, year = {2026}, author = {Dang, X and Hanson, BA and Lopez, M and Miller, J and Jimenez, M and Koralnik, IJ}, title = {Predictive Utility of ViroFind Detection of Blood and CSF Virome for Viral Presence in Human Brain Tissue.}, journal = {International journal of molecular sciences}, volume = {27}, number = {6}, pages = {}, doi = {10.3390/ijms27062789}, pmid = {41898646}, issn = {1422-0067}, support = {DA048493/DA/NIDA NIH HHS/United States ; }, mesh = {Humans ; *Brain/virology ; *Virome ; HIV Infections/virology/blood/cerebrospinal fluid ; Male ; Female ; Herpesvirus 4, Human/isolation &amp; purification/genetics ; Adult ; High-Throughput Nucleotide Sequencing ; Middle Aged ; Torque teno virus/genetics/isolation &amp; purification ; Viral Load ; Viruses/genetics/isolation &amp; purification ; }, abstract = {Viral presence in the brain may contribute to chronic neurologic diseases. However, investigating these associations is limited by the difficulty of directly sampling brain tissue in living individuals. Here, we evaluated whether peripheral viral detection using unbiased target-enrichment next-generation sequencing could inform viral presence in the brain across a diverse set of viral taxa. We applied ViroFind to matched brain, blood (peripheral blood mononuclear cells, spleen, and/or lymph node), and cerebrospinal fluid (CSF) to assess the predictive utility of viral detection in blood and CSF for identifying viral presence in brain samples obtained from the National NeuroAIDS Tissue Consortium, including both HIV-infected (HIV[+]) and HIV-uninfected (HIV[-]) individuals without known active viral infection of the brain. Blood negativity was generally more informative for predicting the absence of viruses in the brain than blood positivity for predicting viral presence. CSF viral detection demonstrated limited predictive utility for brain presence across most viral taxa examined. Among blood[+] individuals, viral burden differed significantly between brain[+] and brain[-] cases for Epstein-Barr virus (EBV), parvovirus, and torque teno virus (TTV). Blood viral burden showed moderate ability to distinguish brain[+] from brain[-] cases for EBV and parvovirus, and strong discriminatory ability for TTV, with similar decision thresholds across HIV[+] and HIV[-] individuals.}, }
@article {pmid41898837, year = {2026}, author = {Li, S and Chiodi, C and Maucieri, C and Della Lucia, MC and Zardinoni, G and Ravi, S and Squartini, A and Concheri, G and Geng, G and Wang, Y and Stevanato, P}, title = {Profiling Soil-Plant-Microbial Communities: DNA and Multi-Omics Techniques.}, journal = {Genes}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/genes17030303}, pmid = {41898837}, issn = {2073-4425}, mesh = {*Soil Microbiology ; Rhizosphere ; Metagenomics/methods ; *Microbiota/genetics ; *Plants/microbiology/genetics ; Genomics/methods ; Metabolomics/methods ; Plant Roots/microbiology/genetics ; Crops, Agricultural/microbiology/genetics ; Multiomics ; }, abstract = {Interactions among plant roots, soil, and microorganisms in the rhizosphere regulate nutrient cycling, plant health, and ecosystem resilience. Recent advances in DNA sequencing and multi-omics are contributing to a shift from primarily descriptive surveys toward more mechanistic and predictive frameworks. This review synthesizes methodological developments and conceptual insights spanning microbial ecology, functional genomics, and agricultural applications. We first summarize DNA-based approaches-marker-gene sequencing, shotgun metagenomics, and quantitative nucleic acid assays-and then complementary omics layers, including metatranscriptomics, metaproteomics, metabolomics, epigenomics, ionomics, and phenomics. We next outline computational advances in data integration, network modeling, and visualization that help represent complex multi-layered datasets as biologically interpretable systems. Applications relevant to climate resilience and sustainable agriculture are discussed, including the design of synthetic microbial communities, the identification of biomarkers for soil health and stress tolerance, and case studies in which rhizosphere multi-omics informs crop breeding and soil management strategies. Overall, these developments underscore the potential of treating microbes as functional and, to some extent, manageable components of the plant holobiont. Looking ahead, we identify key research gaps involving standardized workflows, cross-scale causal inference, and real-time monitoring pipelines that integrate molecular diagnostics with remote sensing and edge-cloud analytics. By linking ecological mechanisms with translational practice, multi-omics frameworks may support the development of more sustainable, data-driven agriculture that better aligns productivity with environmental stewardship.}, }
@article {pmid41898993, year = {2026}, author = {Tanachaiwiwat, P and Sanscrainte, ND and Okech, BA and Estep, AS}, title = {Insecticide Resistance Mutations, Enzymatic Activity, and Pathogen Infection in Culex quinquefasciatus from Haiti.}, journal = {Insects}, volume = {17}, number = {3}, pages = {}, doi = {10.3390/insects17030331}, pmid = {41898993}, issn = {2075-4450}, support = {P0138_22_HS//Armed Forces Health Surveillance Directorate, Global Emerging Infection Surveillance Program/ ; 6036-10400-002-000-D//United States Department of Agriculture/ ; }, abstract = {Haiti is a Caribbean country of about 11 million people with a high burden of mosquito-transmitted disease and limited vector control, thereby making effective operational mosquito control of high importance. Previous studies have examined vector-borne disease burden and insecticide resistance markers in Haitian Aedes and Anopheles mosquitoes, but not Culex species. In this study, we examined collections of Culex quinquefasciatus from 12 locations in northern and southern Haiti for the presence of markers of insecticide resistance (using a variety of target-site mutations and biochemical assays) and pathogens (using a deep-sequencing microbiome workflow). The metagenomic analysis identified Wolbachia, Rhabdoviridae, and Plasmodium infections in all sample pools at relatively high levels, along with less frequent detections of other potential pathogens. Insecticide resistance marker examination identified variable frequencies of knockdown resistance and acetylcholinesterase resistance mutations, as well as variation in resistance-associated enzymatic activities in these populations. These findings indicate that insecticide resistance to pyrethroid and organophosphate insecticides is likely. Although there was variation among Culex mosquito populations and no clear activity pattern, enzymatic activity was significantly higher at the southern sites than at the northern sites. Similar findings in Cx. quinquefasciatus populations in other locations in the Americas strongly suggest that vector control with pyrethroid and organophosphate adulticides may be of limited efficacy.}, }
@article {pmid41900279, year = {2026}, author = {De Luca, L and Menna, F and Lupo, S and Vingolo, EM and Carlà, MM and Mancini, M and Oliverio, GW and Minutoli, L and Baldascino, A and Mazzotta, C and Aragona, P and Meduri, A}, title = {The Ocular Surface Bacterial Microbiome and the Impact of Contact Lens Use: A Literature Review.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/microorganisms14030518}, pmid = {41900279}, issn = {2076-2607}, abstract = {The ocular surface microbiome plays a critical role in maintaining ocular health, preventing infections, and regulating immune responses. Contact lens (CL) wear has been linked to alterations in microbial composition, potentially leading to dysbiosis and increased susceptibility to ocular infections. This review aims to summarize current evidence on the effects of CL use on the ocular microbiome and to discuss strategies to preserve microbial homeostasis. A literature search was conducted in PubMed, Scopus, Web of Science, and Google Scholar for English-language human studies published between January 2005 and January 2025. We included original studies and systematic reviews evaluating the ocular surface bacterial community in contact lens (CL) wearers using either sequencing-based approaches (microbiome; e.g., 16S rRNA gene sequencing/metagenomics) or culture-based methods (microbiota). Two authors screened titles/abstracts and full texts. Overall, 12 studies met the inclusion criteria and were qualitatively synthesized. Across included studies, CL wear was associated with reproducible changes in the ocular surface bacterial community, most commonly a shift toward a skin-like profile and increased detection/relative abundance of opportunistic taxa (e.g., Pseudomonas, Acinetobacter, and Staphylococcus aureus) together with reduced representation of typical ocular commensals in several sequencing-based datasets. Culture-based studies reported increased recovery of opportunistic bacteria from lenses and storage cases, supporting contamination/biofilm-related mechanisms. Lens care solutions and preservatives were reported to modulate bacterial profiles and may contribute to dysbiosis, although evidence remains heterogeneous across study designs and analytic pipelines. CL use is associated with significant alterations in the ocular microbiome, increasing the risk of microbial keratitis and corneal inflammatory events. Strategies to maintain microbial balance, including careful selection of lens care products and development of antimicrobial lenses, may improve ocular surface health in CL wearers. Future longitudinal studies with standardized sampling and analytic workflows are needed to clarify causal links between CL-associated microbial changes and clinical outcomes.}, }
@article {pmid41900290, year = {2026}, author = {Singh, K and Mitra, S}, title = {Operationalising Genomic Surveillance for Antimicrobial Resistance in Low- and Middle-Income Countries: A One Health Perspective from Bangladesh.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/microorganisms14030527}, pmid = {41900290}, issn = {2076-2607}, abstract = {Antimicrobial resistance (AMR) represents a critical global health challenge, with low- and middle-income countries (LMICs) disproportionately affected due to limited surveillance capacity. Advances in microbial genomics offer powerful tools for AMR detection and monitoring; however, translating these technologies into sustainable, policy-relevant surveillance systems in resource-constrained settings remains challenging. This review synthesises current approaches to genomic surveillance of AMR in LMICs and presents Bangladesh as a case study to illustrate how genomic, environmental, and clinical data can be integrated within a One Health framework. We examine key barriers to implementation, including laboratory infrastructure, bioinformatics capacity, data governance, and cross-sector coordination, alongside emerging opportunities for capacity building and regional collaboration. Using Bangladesh as a case study, we highlight practical pathways for embedding genomic surveillance into national AMR strategies, integrating human, animal, and environmental reservoirs of antibiotic resistance. We argue that genomic surveillance can move beyond data generation to inform infection prevention, antibiotic stewardship, and public health decision making when supported by context-appropriate infrastructure and interdisciplinary engagement. By focusing on operational and translational considerations rather than technology alone, this review provides actionable insights for microbiologists, public health practitioners, and policymakers seeking to strengthen AMR surveillance systems in LMICs through a One Health approach.}, }
@article {pmid41900318, year = {2026}, author = {Liu, X and Xiao, N and Yu, J and Geng, X and Zhang, M and Zhang, Y and Xu, H and Nie, C and Wang, M and Li, L}, title = {Divergent Microbial Community and Pathogenicity at a University-Urban Interface: A Comparative Analysis.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/microorganisms14030557}, pmid = {41900318}, issn = {2076-2607}, support = {grant number 2022YFE0199800//National Key Research and Development Program of China/ ; grant number 24-1-8-smjk-13-nsh//Qingdao Science and Technology Wellness Promotion Demonstration Program/ ; grant number 82271658//the National Natural Science Foundation of China/ ; grant number SKLMTFCP-2023-01//SKLMT Frontiers and Challenges Project/ ; grant numbers ZR2024QD228 and ZR2024QC311//Shandong Provincial Natural Science Foundation/ ; grant number 24-4-4-zrjj-40-jch//Qingdao Natural Science Foundation/ ; grant number FDLAP24008//Opening Project of Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP)/ ; }, abstract = {Environmental metagenomics and microbial taxonomy provide essential frameworks to evaluate how population structures shape the evolution of antimicrobial resistance and microbial community dynamics within densely populated environments. To evaluate microbial community composition and pathogenic potential, high-touch surfaces at high-traffic sites on and off campus were analyzed using metagenomics and characterization of 188 bacterial isolates, including antibiotic susceptibility testing, hemolytic assays, and whole-genome sequencing. Off-campus sites showed significantly higher bacterial richness and more complex communities enriched with diverse potential pathogens. Notably, high-risk carbapenemase genes were predominantly identified in these off-campus urban environments. In contrast, on-campus environments harbored less diverse communities dominated by opportunistic, antibiotic-resistant Staphylococcus species, with metagenomic analysis confirming a concentrated enrichment of β-lactam resistance determinants associated with methicillin-resistant staphylococci. Phenotypic profiling revealed extensive antimicrobial resistance, with 84.7% of isolates exhibiting resistance to at least one antibiotic and 35.1% of Staphylococcus showing hemolytic activity. Whole-genome sequencing further revealed that these resistance and pathogenic traits are predominantly localized on mobile plasmids, highlighting a high potential for horizontal gene transfer. These findings indicate that population activities shape distinct microbial communities in closely adjacent environments and highlight the importance of monitoring high-risk resistance determinants in densely populated university settings.}, }
@article {pmid41900320, year = {2026}, author = {Cheng, H and Han, J and Liu, K and Wang, L and Meng, Q and Liu, C and Liu, X and Wang, M and Yang, F and Li, X}, title = {Integrated Metagenomic and Metabolomic Profiling of Boar Semen During Ambient-Temperature Storage.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/microorganisms14030560}, pmid = {41900320}, issn = {2076-2607}, support = {2022020101//Agricultural Breeds Research Project of Henan Province/ ; HAAS2023RCQD01//the Key Technology Research and Development Program for Precision and Efficient Breeding of Local Pigs in Hainan Province/ ; }, abstract = {The reproductive efficiency of breeding boars substantially influences swine industry productivity. Sperm viability during ambient-temperature storage is critically affected by environmental factors, including microbial activity. This study aimed to elucidate the dynamics and interactions between the seminal microbiome and metabolome during boar semen storage at 17 °C. Using integrated 16S rRNA sequencing and untargeted metabolomics, we analyzed semen samples from six healthy boars (31-33 months old) collected at day 0 (control), 2, 4, and 6 of storage. Our results demonstrate that storage leads to a marked decline in microbial diversity, progressive enrichment of the opportunistic genus Proteus, depletion of key antioxidant and cofactor metabolites such as vitamin B6, and extensive metabolic reprogramming-including alterations in short-chain fatty acid, purine, and lipid oxidation pathways. Multi-omics correlation analysis further revealed strong associations between microbial succession and metabolic shifts, highlighting their combined role in driving sperm functional decline. These findings provide a mechanistic basis for improving semen preservation strategies through microbiome and metabolite-targeted interventions.}, }
@article {pmid41900339, year = {2026}, author = {Malik, PK and Mohapatra, A and Trivedi, S and Kolte, AP and Sahoo, A and Bhatta, R}, title = {In Vitro Degradation of Chlorpyrifos by the Ruminal Microbes: Insights from the Rumen Metagenome.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/microorganisms14030581}, pmid = {41900339}, issn = {2076-2607}, abstract = {In vitro studies were conducted in a series to investigate if the ruminal microbes are capable of degrading chlorpyrifos. This in vitro study presents the results from three experiments: Exp. I was conducted without feed, while Exp II and III were conducted with feed, either with or without methanol for dissolving chlorpyrifos, respectively. A basal diet comprising finger millet straw and concentrate was prepared. Incubation medium with feed but without chlorpyrifos served as the control. A total of six replicates each of control and chlorpyrifos spiked were used for the incubation. The pesticide concentration in the incubation medium before and after 24 h of incubation was analyzed using GC-MS/MS. The genomic DNA was isolated from the incubation fluid of the individual samples, and the shotgun metagenomic sequencing was performed. The clean reads were taxonomically classified using the Kraken2 database, and microbial classification at different taxonomic ranks was separated using Pavian v1.0. The microbial genes in the metagenome data were predicted and assigned functional roles using the MetaErg v1.2.3 pipeline. The assigned KEGG Orthology (KO), EC numbers (Enzyme Commission number), Gene Ontology (GO), and corresponding NCBI taxonomy information relevant to chlorpyrifos metabolism/degradation were retrieved. Results from the study revealed that the chlorpyrifos concentration was decreased from 5.78 to 1.64 ppm over 24 h of in vitro incubation with feed. Similar alpha and beta diversity indices between control and chlorpyrifos treatments revealed that the richness and the evenness of the microbial population were not affected by the presence of chlorpyrifos in the rumen fluid. There was no difference in the microbiota affiliated to the major phyla such as Bacteroidota, Fibrobacterota, Bacillota, and Pseudomonadota. The EC 3.1.8.1, EC 3.1.3.1, EC 1.14.13.-, and EC 1.1.1.- reported for chlorpyrifos degradation were not detected in the metagenome, and only EC 3.1.1.1 was identified, which demonstrated that degradation of chlorpyrifos was carried out by the affiliated enzyme carboxylesterase. The presence of GO:0004035, GO:0004364, GO:0019637, GO:0016791, and GO:0042178 in the metagenome strengthens that the chlorpyrifos degradation in the present study was primarily assigned to the rumen microbiota. This in vitro study provided insights into the rumen microbiota involved in the chlorpyrifos degradation and the initial clue that the rumen microbes are capable of degrading chlorpyrifos. Further, the animal studies in different species with the variable levels of chlorpyrifos are also warranted to confirm the efficacy of rumen microbes in mixed syntrophy and determine the threshold capabilities of the ruminal microbes.}, }
@article {pmid41900342, year = {2026}, author = {Ntzouvaras, A and Koletti, A and Zografaki, ME and Marka, S and Skliros, D and Vasilakis, G and Karavidas, I and Koukouvinis, AK and Efrose, RC and Kalloniati, C and Tzovenis, I and Flemetakis, E}, title = {Isolation and Characterization of Microalgae Isolates from Hydroponic Effluent Water: Metagenomics and Biotechnological Insights.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/microorganisms14030582}, pmid = {41900342}, issn = {2076-2607}, support = {PRIMA2019-04//European Union research and innovation Horizon 2020/ ; }, abstract = {Hydroponic systems are gaining prominence in sustainable agriculture, yet their nutrient-rich effluents remain an underexplored source of microbial biodiversity with potential biotechnological interest. In this study, shotgun metagenomic sequencing was employed to profile, with a high taxonomic resolution, the photosynthetic microbial community in hydroponic effluent before and after a natural algal bloom, revealing pronounced shifts in microbial composition. Notably, relative abundance increased sixfold for Chlamydomonas reinhardtii and tenfold for Bigelowiella natans. Four dominant microalgal strains (PR1-PR4) were subsequently isolated and characterized through integrative morphological and molecular taxonomy, with phylogenetic analyses based on four genetic markers (18S rRNA, ITS, rbcL and tufA) confirming that each isolate represents a distinct lineage within Chlorophyceae families, including Chlorella sp., Chlamydomonas sp., and Scenedesmus sp. Growth kinetics under three temperature regimes, typical of Greek environmental conditions from spring to autumn (15 °C, 23 °C, 32 °C), demonstrated broad ecological plasticity and rapid biomass production, highlighting strains with strong adaptive resilience. Biochemical profiling of the isolates revealed significant inter-strain differences in primary and secondary metabolite content, including proteins (up to 43% DW), lipids (up to 31% DW), carbohydrates (up to 44% DW), photosynthetic pigments, phenolics, flavonoids, and antioxidant activity. The observed metabolic diversity of autochthonous microalgal strains from hydroponic environments, combined with their high growth rates, underscores their potential for applications in bioremediation, bioenergy, and the development of value-added products within a circular bioeconomy framework.}, }
@article {pmid41900399, year = {2026}, author = {Yi, X and Lin, Y and Peng, Y and Liu, Y and Ning, C and Lei, J and Wang, L and Chen, C and Wu, L and Liao, J}, title = {Urbanization-Induced Shifts in Microbial Functional Genes of Wetland Nitrogen Cycling Promote Nitrous Oxide (N2O) Emissions.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/microorganisms14030640}, pmid = {41900399}, issn = {2076-2607}, support = {32401392//National Natural Science Foundation of China/ ; OT-S-KTA4//Hunan Forest Quality Improvement and Efficiency Enhancement Demonstration Project Funded by the European Investment Bank Loan/ ; XLKY202216//Forestry Science and Technology Innovation Project of Hunan Province/ ; XLKY202319//Forestry Science and Technology Innovation Project of Hunan Province/ ; 2024JJ5235//Hunan Provincial Natural Science Foundation of China/ ; }, abstract = {Urban wetlands are assumed to contribute to nitrous oxide (N2O) emissions; however, the microbial mechanisms underlying enhanced N2O fluxes in urban wetlands and differences in microbial responses between aquatic and soil compartments have not been clearly identified. Here, we characterized the nitrogen (N) cycling microbial communities and their functional metabolic pathways in urban and rural wetlands using metagenomics and N2O flux measurements. Results showed that urbanization drove a 6~8-fold increase in N2O fluxes from urban wetlands compared to rural wetlands. Structural equation modeling (SEM) confirmed that urbanization intensity was a primary driver (standardized coefficients: 0.72 for soil and 0.92 for water). In wetland water, N2O emissions were negatively correlated with inorganic nutrient concentrations (coefficient = -0.62). Aquatic microbial communities exhibited substantial taxonomic shifts but preserved network connectivity, indicating adaptive strategies for surviving urban perturbations at the cost of reduced functional redundancy. In wetland soil, microbial communities maintained stability under urbanization, which was attributed to environmental buffering from heterogeneous microenvironments. Soil N2O emissions were positively linked to microbial alpha diversity (coefficient = 0.79). Furthermore, urban wetlands enriched genes mediating nitrification and denitrification while depleting genes associated with N fixation and organic N metabolism. This functional shift reflects microbial specialization in processing elevated reactive N (Nr) inputs from urban sources, trapping urban wetlands in an "N loss loop" that reinforces high N2O fluxes. This study elucidates the microbial mechanisms governing wetland N2O emissions under urbanization, thereby enhancing understanding of microbially mediated N cycling in the urban wetland ecosystem.}, }
@article {pmid41900403, year = {2026}, author = {Zhang, W and Fan, C and Yang, L and Sun, Y and Tang, L}, title = {Integrated Metagenomic and Metabolomic Analyses Reveal Rhizosphere Soil Microecological Changes in Thlaspi arvense L. Lines with Different Alkaloid Contents.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/microorganisms14030643}, pmid = {41900403}, issn = {2076-2607}, support = {CARS-16-S3//The China Agriculture Research System of MOF and MARA/ ; }, abstract = {Pennycress (Thlaspi arvense L.), a representative and economically valuable cover crop, supports and enhances key ecological processes throughout its life cycle via its root system. It is hypothesized that pennycress selectively modulates its rhizosphere microbial community through root-derived metabolites, which may influence both the crop's growth and the subsequent crops in rotation. However, systematic investigations comparing the rhizosphere microbiomes and metabolomes among different pennycress lines remain limited. This study employed metagenomic and metabolomic approaches to examine the dynamic changes in the rhizosphere microbial community and metabolite profiles of three pennycress lines with significantly different total alkaloid contents. The goal was to elucidate the interactions between microbes and metabolites. Results indicated significant differences in microbial community structure across the cultivars. JiL67 maintained stable community diversity, while LiN54 (with the lowest alkaloid content) showed reduced diversity. HeL43 (with the highest alkaloid content) exhibited increased diversity but also potential community homogenization, accompanied by the significant enrichment of microbial taxa capable of alkaloid tolerance. Metabolomic analysis identified metabolites such as Portulacaxanthin II, Oleanolic acid, and Soraphen A as significantly enriched in the rhizosphere soil of pennycress. This study reveals the shifts in rhizosphere microbial communities and metabolites linked to different pennycress lines and uncovers their interactive mechanisms, providing a scientific foundation for developing more economically efficient pennycress cultivation strategies.}, }
@article {pmid41900432, year = {2026}, author = {Guerrero-Torres, LE and García-Galindo, JJ and Gómez-Galindo, MF and Delgado, DIR and Retolaza Carlos, CE and Suárez-Rico, DO and Beltrán-Ramírez, A and Balleza Alejandri, LR}, title = {The Gut Microbiota in Parkinson's Disease: Mechanistic Insights into Microbial-Host Interactions.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/microorganisms14030673}, pmid = {41900432}, issn = {2076-2607}, abstract = {Parkinson's disease (PD) is a multifactorial neurodegenerative disorder characterized by progressive motor and non-motor manifestations, including early gastrointestinal dysfunction. Growing evidence implicates the gut microbiota as an active modulator of host immune tone and neurodegenerative vulnerability, extending beyond descriptive taxonomic associations toward functional and metabolic mechanisms. PD-associated dysbiosis is consistently characterized by altered microbial functional capacity, including reduced short-chain fatty acid (SCFA) production, enrichment of pro-inflammatory metabolic traits, and sustained immune stimulation at the intestinal interface. These shifts promote chronic low-grade inflammation and intestinal barrier perturbations, creating conditions that may facilitate abnormal α-synuclein aggregation within the enteric nervous system. Current management predominantly relies on dopaminergic replacement and related symptomatic strategies, such as levodopa combinations, dopamine agonists, monoamine oxidase-B and catechol-O-methyltransferase (COMT) inhibitors, and device-aided therapies, which alleviate symptoms but do not halt underlying neurodegeneration or modify long-term disease course. These therapeutic limitations have intensified interest in upstream mechanisms that might be amenable to disease-modifying interventions, particularly those arising at the level of the gut microbiota and gut-immune-brain axis. This narrative review integrates clinical, metagenomic, metabolomic, and mechanistic evidence to propose a unified model in which microbiota-driven immune and metabolic perturbations may act as upstream drivers converging on α-synuclein pathology, neuroinflammation, and neurovascular dysfunction.}, }
@article {pmid41900479, year = {2026}, author = {Park, H and Kim, JS and Kim, DJ and Suk, KT}, title = {Strain Diversity in the Human Microbiome: Personal Variation, Pathobionts, Therapeutics, and Methodological Challenges.}, journal = {Microorganisms}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/microorganisms14030720}, pmid = {41900479}, issn = {2076-2607}, support = {NRF-2020R1I1A3073530//National Research Foundation of Korea/ ; NRF-2020R1A6A1A03043026//National Research Foundation of Korea/ ; }, abstract = {Advances in sequencing technologies have transformed human microbiome research, yet most analyses still rely on species-level profiles. However, strains rather than species represent the true ecological and functional units of the microbiome. Individual strains can vary substantially in gene content, metabolic capacity, virulence factors, antimicrobial resistance, and host-interaction properties. These differences critically influence immune responses, epithelial barrier integrity, disease susceptibility, and therapeutic outcomes. Here, we synthesize recent human microbiome studies that provide robust strain-resolved evidence, focusing on three major themes: (i) the emergence and long-term persistence of personalized strain repertoires, (ii) strain-specific pathobiont traits that drive host pathology, and (iii) the implications of strain-level ecology for the development of next-generation microbiome therapeutics. We also highlight key methodological innovations including high-resolution amplicon profiling, advanced metagenomic and single-cell genomics, and culture-based functional approaches that collectively enable strain-level resolution and are reshaping the field.}, }
@article {pmid41901034, year = {2026}, author = {Lee, YK and Kim, HY and Shim, D}, title = {A Triple-Hit Multi-Omics Framework for Psoriasis: Microbial Metabolic Remodeling and Immune Cell Methylome Signature Associated with an AMP-Dominant Lesional Program.}, journal = {Life (Basel, Switzerland)}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/life16030516}, pmid = {41901034}, issn = {2075-1729}, support = {RS-2023-00263429//Ministry of Science and ICT (MSIT), South Korea/ ; }, abstract = {The gut-skin axis is increasingly implicated in psoriasis pathogenesis, yet the cross-compartment convergence of molecular programs remains incompletely defined. We constructed a conceptual "Triple-Hit" multi-omics framework by integrating five independent public datasets spanning gut microbial functional remodeling (shotgun metagenomics), systemic immune cell methylomes (PBMC and CD8+ T-cell EPIC 850K), and lesional skin regulatory layers (miRNA and bulk RNA-seq). In the gut compartment, functional profiles exhibited a selective reduction in microbial lipid catabolic potential, including decreased fatty acid degradation and a lowered composite lipid degradation score, alongside heterogeneous shifts across SCFA-associated metabolic pathways. Systemically, PBMC methylomes revealed widespread regional remodeling (45,396 DMRs) enriched for membrane-proximal signaling and cytoskeletal programs, while CD8+ T cells showed specific epigenetic alterations in lipid- and glycosphingolipid-associated loci, suggesting a systemic metabolic-epigenetic alignment. In the skin, we identified a compact miRNA signature (168 DE-miRNAs) and a mechanistically interpretable, directionality-constrained miRNA-mRNA bridge that aligns with an AMP-dominant inflammatory transcriptome, consistent with reduced post-transcriptional restraint. Collectively, these findings support a convergent multi-omics framework linking putative microbial metabolic remodeling, systemic immune priming, and cutaneous effector programs. This study provides a systems-level perspective on psoriasis pathogenesis, highlighting the metabolic-epigenetic-transcriptional convergence as a potential avenue for therapeutic intervention.}, }
@article {pmid41901100, year = {2026}, author = {Kim, HJ and Park, J and Oh, S and Kim, D and Kim, HJ and Jo, C and Kim, EB and Jang, A}, title = {Effect of Alpha-Lipoic Acid, Betaine, and L-Carnitine Supplementation on Gut Microbiota and Obesity Biomarkers in Mice.}, journal = {Nutrients}, volume = {18}, number = {6}, pages = {}, doi = {10.3390/nu18060925}, pmid = {41901100}, issn = {2072-6643}, support = {2022R1A2C1005235//National Research Foundation of Korea/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Carnitine/pharmacology/administration &amp; dosage ; *Obesity/microbiology/metabolism ; *Betaine/pharmacology/administration &amp; dosage ; Male ; *Thioctic Acid/pharmacology/administration &amp; dosage ; Mice, Inbred C57BL ; *Dietary Supplements ; Diet, High-Fat/adverse effects ; Biomarkers/blood ; Mice ; Disease Models, Animal ; Leptin/blood ; }, abstract = {Background/Objectives: This exploratory study (n = 6 per group) investigated the associations between supplementation with α-lipoic acid (AL), betaine (BT), and L-carnitine (LC) and gut microbiota composition in a high-fat diet (HFD)-induced obesity mouse model. Methods: Four-week-old male C57BL/6J mice were fed a control diet (10% fat), HFD (60% fat), or HFD supplemented with AL, BT, or LC (300 mg/kg BW/day) for nine weeks. Results: All three compounds were associated with shifts in microbial composition compared to the HFD-only group. While AL and BT supplementation moderately modulated specific Firmicutes and Bacteroidetes taxa, LC supplementation was linked to a more pronounced reduction in the Firmicutes/Bacteroidetes ratio and a decreased abundance of genera such as Christensenellaceae, Lachnospiraceae, and Coprococcus 3. These microbial changes were correlated with obesity-related metabolic and adiposity markers, including leptin and lipid parameters. Furthermore, functional profiling via PICRUSt suggested potential alterations in amino acid metabolism; however, these findings represent inferred metabolic potential rather than direct metagenomic measurements. Conclusions: Collectively, these results indicate differential associations between dietary supplementation and gut microbiota composition in HFD-fed mice. Although this study was conducted within an exploratory framework and utilized a modest sample size, the observed microbial shifts consistently paralleled metabolic alterations, supporting biologically plausible associations that warrant further mechanistic investigation.}, }
@article {pmid41901112, year = {2026}, author = {Solano-Aguilar, G and Lakshman, S and Chen, C and Beshah, E and Molokin, A and Vinyard, B and Dawson, HD and Santin-Duran, M and Bruna, G and Smith, A and Urban, JF}, title = {Fruit and Vegetable Supplemented-Diet Ameliorates Dextran Sodium Sulfate (DSS)-Induced Colitis by Modulating Host Transcriptome and Gut Metagenome Response.}, journal = {Nutrients}, volume = {18}, number = {6}, pages = {}, doi = {10.3390/nu18060937}, pmid = {41901112}, issn = {2072-6643}, support = {Cris 8040-51000-058-00D//United States Department of Agriculture/ ; }, mesh = {Animals ; Dextran Sulfate ; *Fruit ; *Colitis/chemically induced/prevention &amp; control/microbiology/diet therapy ; *Transcriptome ; *Gastrointestinal Microbiome ; *Dietary Supplements ; *Vegetables ; Swine ; *Metagenome ; Disease Models, Animal ; *Diet ; Colon/pathology ; }, abstract = {Background/Objectives: Dietary intake of fruits and vegetables (FVs) has been inversely associated with a lower risk of ulcerative colitis. Using a pig model, we evaluated the effect of FV supplementation on dextran sulfate sodium (DSS)-induced colitis. Methods: Six-week-old pigs were fed a grower diet (negative control), grower diet + 4% DSS (positive control), half-FV diet + DSS, or full-FV diet + DSS. FV levels matched half or full daily recommendations from the Dietary Guidelines for Americans (DGA). Clinical signs were monitored; proximal colon contents (PCs) and mucosa (PCM) were analyzed for metagenome, transcriptome and histopathology. Results: Full-FV pigs showed no diarrhea, less fecal occult blood (FOB), crypt hyperplasia, but no changes in gene expression or microbiome diversity (p < 0.05). Half-FV pigs had increased FOB, differentially expressed genes (DEGs) linked to tissue remodeling, crypt/goblet cell hyperplasia and two cases of diarrhea (p < 0.05). DSS controls showed reduced immune-related DEGs, altered microbiome, PCM erosion, FOB, and persistent diarrhea in one pig (p < 0.05). Conclusions: A three-week full-FV diet conferred protection against DSS-induced colitis, with a dose-dependent protection of intestinal tissue and gut metagenome under inflammatory challenge.}, }
@article {pmid41901564, year = {2026}, author = {Gonzalez, A and Argotsinger, J and Oram, RJ and Miller, JL}, title = {Impact of Metagenomic Next-Generation Sequencing on Antibiotic Management in Pediatric Patients.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {62}, number = {3}, pages = {}, doi = {10.3390/medicina62030482}, pmid = {41901564}, issn = {1648-9144}, mesh = {Humans ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods/statistics &amp; numerical data ; Child ; Male ; Female ; Child, Preschool ; *Metagenomics/methods ; Infant ; *Anti-Bacterial Agents/therapeutic use ; Adolescent ; Pediatrics/methods ; }, abstract = {Background and Objectives: Metagenomic next-generation sequencing (mNGS) is an emerging diagnostic tool used to guide the management of infectious diseases. However, clinical criteria in which there is a clear benefit have not been identified, and more real-world clinical experience is needed to identify patient populations in which mNGS testing may have the most benefit. The aim of this article is to evaluate the utilization of mNGS to determine the impact on clinical practice for pediatric patients. Materials and Methods: This retrospective analysis included pediatric patients that had a mNGS test performed between January 2020 and September 2024. The primary outcome was the clinical impact of the mNGS test on patient management defined as either a positive impact or no impact. Secondary outcomes included test turnaround time, agreement or discordance between conventional testing and mNGS, and hospital length of stay. Results: Forty-six mNGS tests in 42 patients were evaluated. Of 60 organisms identified from the 46 tests, 27 organisms (45%) were considered clinically significant. mNGS had a positive clinical impact in 18 (39.1%) patients, primarily due to antimicrobial modifications (16, 34.8%) and new diagnoses (6, 13.0%). The majority of patients with a positive clinical impact were immunosuppressed (15/18, 83.3%). Conclusions: mNGS demonstrated utility in a subset of pediatric patients, particularly those considered immunosuppressed. Its ability to confirm or exclude infections, particularly fungal infections in this patient population, contributed to its impact. However, its limited benefit in immunocompetent patients underscores the importance of careful patient selection to optimize diagnostic and antimicrobial stewardship.}, }
@article {pmid41887505, year = {2026}, author = {Wang, Q and Zhang, J and Xia, Y and Zha, M and Li, J and Jambal, T and Dorjgotov, D and Tseveen, S and Chen, Y}, title = {Traditional fermented goat milk products in Mongolia: Analysis from the perspective of metagenomics to metabolomics.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-27796}, pmid = {41887505}, issn = {1525-3198}, abstract = {Mongolia is known for its rich dairy traditions, with goat milk representing a distinctive and valuable dairy resource. Fermentation improves the quality and nutritional value of goat milk, which is closely associated with microbial activity. As traditional Mongolian fermented dairy products primarily depend on natural fermentation, investigating the microbial and metabolic changes during this process is essential for understanding product quality. In this observational study, raw goat milk (RGM) and fermented goat milk (FGM) samples were collected from Mongolia, and a total of 102 microbial species were identified using shotgun metagenomic sequencing. The RGM contained a higher proportion of viruses and nonlactic acid bacteria (non-LAB), including Macrococcus caseolyticus. Following fermentation, the microbial community composition shifted, becoming dominated by LAB species such as Lactobacillus helveticus and Lactobacillus delbrueckii, with beneficial microorganisms attaining predominant abundance. A total of 22 differential metabolites were identified between RGM and FGM. Approximately half of these metabolites were related to AA metabolism, while the remainder were involved in energy metabolism, antioxidant processes, and lipid metabolism. Spearman correlation analysis suggested that LAB, primarily Lactobacillus species, were positively associated with the abundance of metabolites such as organic acids and AA in the fermented products. In contrast, the presence of pathogenic microorganisms such as viruses showed a negative correlation with fermentation efficiency markers. It was hypothesized as a potential factor affecting product quality, possibly through disrupting host microbial metabolism. Overall, this observational study identifies understanding of the factors governing FGM quality and provides a scientific foundation for improving the goat milk industry and harnessing microbial resources in traditional fermented dairy products.}, }
@article {pmid41887507, year = {2026}, author = {Scott, J and Brouard, JS and Drouin, G and Ouellet, DR and Ster, C and Petri, RM}, title = {Microbiota Changes in Rumen and Milk Corresponding to Dietary Protein Intake in Transition Dairy Cows.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2025-27576}, pmid = {41887507}, issn = {1525-3198}, abstract = {During the transition period in dairy cows, the incidence of disease increases due to a negative energy balance affecting both the metabolic and immune health status. Limiting milk production at the beginning of lactation improves the metabolic status of cows. However, past strategies tested to achieve this reduction either negatively impacted milk yield for the rest of the lactation or were difficult to implement on large-scale dairy farms. This study evaluated the impact of a temporary reduction in metabolizable protein (MP) supply during the transition period on the rumen and milk microbiota and their metabolic composition. Treatment cows (n = 5) were fed 80% of their MP needs (80MP) from 14 d before calving to 14 d after calving, before being switched to a 100% MP diet (100MP) for an additional 14 d. Control cows (n = 6) were fed 100MP for the entire experiment. Samples of rumen content and milk were taken in the immediate Postpartum phase (PP) on d 2 and 7, as well as after dietary change in the experimental Recovery phase (RP) on d 21 and 28 postpartum. All samples were extracted for DNA and analyzed using shotgun metagenomic sequencing (Illumina NovaSeq). Milk samples were additionally analyzed for composition, and rumen fluid was analyzed for short-chain fatty acids and ammonia-N. Significant changes to the microbial composition were almost exclusively associated to effect of day of sampling, with the exception being the family Micrococcaceae, which was found to be differentially abundant in the 100MP compared with the 80% group in PP milk samples. This study used a metagenomics approach to understanding the impact of altered protein supply on rumen and milk microbiota, to better understand impacts on these separate ecosystems.}, }
@article {pmid41887601, year = {2026}, author = {Wei, Y and Liu, Q and Gong, Z and Han, GZ}, title = {Unveiling the cryptic diversity and distribution of elements related to virophage mavirus through deep mining of pPolB proteins.}, journal = {Virologica Sinica}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.virs.2026.03.009}, pmid = {41887601}, issn = {1995-820X}, abstract = {Virophages are unique double-stranded DNA (dsDNA) viruses that parasitize viruses of Nucleocytoviricota (NCVs). While conventionally viewed as a viral group, growing evidence suggests that "virophage" is better understood as a parasitic lifestyle, rather than a natural group. Despite this conceptual shift, their diversity and evolution remain largely obscure and contentious. Through deep mining of protein-primed type B DNA polymerase (pPolB) in 7,041 eukaryotic genomes and 12,053 metagenomes sampled globally, we expand the diversity of pPolB-carrying mavirus virophage-related elements (pMVREs), which include virophages, transpovirons, and Polinton-like viruses (PLVs). Our phylogenomic and metagenomic mining reveals the widespread distribution of pMVREs in eukaryotic genomes (97/7,041, 1.38%) and global environments (2,450/12,053, 20.33%). pMVREs possess genome architectures of high plasticity and promiscuity. The presence of pMVREs and NCVs is statistically correlated in both eukaryotic genomes and global metagenomes, supporting a specific co-occurrence association between pMVREs and NCVs. Moreover, pMVRE diversity and composition exhibit strong heterogeneity across global ecosystems. Together, this study unveils a vast diversity of virophage-related elements and provides insights into the intricate relationship among virophages, transpovirons, PLVs, pMVREs, and NCVs.}, }
@article {pmid41887858, year = {2026}, author = {Zheng, D and Li, D and Wang, J}, title = {Beyond ammonia-oxidizing bacteria-centric paradigms: Geobacter-assisted anodic anaerobic ammonia oxidation.}, journal = {Journal of environmental sciences (China)}, volume = {163}, number = {}, pages = {399-408}, doi = {10.1016/j.jes.2025.07.035}, pmid = {41887858}, issn = {1001-0742}, mesh = {*Geobacter/metabolism/physiology ; *Ammonia/metabolism ; Oxidation-Reduction ; Electrodes ; Anaerobiosis ; Biofilms ; Bacteria/metabolism ; *Anaerobic Ammonia Oxidation ; }, abstract = {Anodic anaerobic ammonium oxidation (anodic anammox) presents a sustainable approach for nitrogen removal, yet its bioelectrochemical mechanisms remain unclear due to biofilm complexity and undefined roles of electroactive microorganisms (EAMs). This study reveals that nitrite (NO2[-]) is the direct product of ammonia-oxidizing bacteria (AOB)-driven anodic anammox, with extracellular electron transfer (EET) mediated by indirect mechanisms via redox shuttles. Metagenomic analysis identified two ammonia oxidation pathways: (1) a novel short-range nitrification pathway (NH4[+] → NO2[-]) governed by ncd2 genes, and (2) a traditional ammonia oxidation pathway (NH4[+] → NH2OH) facilitated by amoABC. Intriguingly, Geobacter exhibited potential NH2OH oxidation capability, bridging AOB activity and electrode respiration. Functional inhibition experiments demonstrated that EAMs-derived electron shuttles and reactive oxygen species (ROS) are critical for enhancing EET efficiency, with ROS serving as a key electron acceptor for AOB under anaerobic conditions. Spatial and metabolic synergy between EAMs and AOB-via substrate cross-feeding, cofactor provision, and electron transfer-was essential for maintaining biofilm stability. These findings challenge the conventional view of AOB-driven anodic anaerobic anammox mechanisms and provide new insights into sustainable nitrogen removal in engineered bioelectrochemical systems.}, }
@article {pmid41887859, year = {2026}, author = {Chen, J and Li, G and Liu, J and Yuan, X and Zhao, G and Yang, X and Huang, S and Zheng, Z}, title = {Comparative assessment of novel nematicide trifluenfuronate and fosthiazate on soil ecosystem: From microbial community structure to KEGG functional pathways.}, journal = {Journal of environmental sciences (China)}, volume = {163}, number = {}, pages = {409-419}, doi = {10.1016/j.jes.2025.05.033}, pmid = {41887859}, issn = {1001-0742}, mesh = {*Soil Microbiology ; *Soil Pollutants/toxicity ; Soil/chemistry ; *Antinematodal Agents/toxicity ; Ecosystem ; *Microbiota/drug effects ; RNA, Ribosomal, 16S ; Bacteria ; Organophosphorus Compounds ; Thiazolidines ; }, abstract = {In recent years, the increasing demand for environmentally friendly pesticides in agricultural production has driven the development of novel pesticides characterized by high efficiency, low toxicity, and improved environmental compatibility. Simultaneously, greater emphasis is being placed on evaluating their impact on the soil ecosystem to ensure sustainable pesticide use and the stability of agroecosystems. In this study, we employed 16S rRNA gene high-throughput sequencing and metagenomic analysis to compare the effects of the novel nematicide trifluenfuronate and the commonly used nematicide fosthiazate on soil physicochemical properties, bacterial community structure, and metabolic functions in cucumber cultivation soils. Results showed that soil enzyme activity, microbial community structure and diversity exhibited the most significant differences on day 7 following nematicide application but stabilized by day 100. Both nematicide type and concentration were key factors influencing bacterial community structure. Compared to fosthiazate, trifluenfuronate more significantly enhanced soil bacterial community abundance while exerting fewer negative impacts on related enzyme activities and KEGG pathways. In addition, fosthiazate preferentially regulated membrane-associated efflux genes, whereas trifluenfuronate primarily interfered with the transcriptional regulation of target genes to mitigate antibiotic stress. These alterations in microbial community structure and function led to changes in soil nutrient bioavailability. This made the trifluenfuronate treatment group have higher available nitrogen and phosphorus content to supply to cucumber. This research contributes to understanding their ecological effects and paves the way for future sustainable pesticide research.}, }
@article {pmid41887904, year = {2026}, author = {Jin, R and Chen, C and Zhang, J and Li, Y and Wu, Y and Wang, F and Chen, Z and Huang, T and Cheng, Q and Yu, X and Jia, P}, title = {Solid waste dumping differentially impacts soil prokaryotic, fungal, and viral communities: Insights from metagenomics.}, journal = {Journal of environmental sciences (China)}, volume = {163}, number = {}, pages = {867-879}, doi = {10.1016/j.jes.2025.10.021}, pmid = {41887904}, issn = {1001-0742}, mesh = {*Soil Microbiology ; Metagenomics ; *Microbiota ; Fungi ; *Solid Waste ; Soil/chemistry ; Soil Pollutants/analysis ; *Refuse Disposal ; Environmental Monitoring ; }, abstract = {Rapid urbanization and industrialization have dramatically increased global solid waste generation, placing immense pressure on waste management systems. In many developing countries, illegal and uncontrolled dumping remains widespread, yet its ecological impacts, particularly on soil microbial communities, are still poorly understood. To address this knowledge gap, we applied high-throughput amplicon sequencing and metagenomic profiling to analyze soil microbiomes across three categories of solid waste dumping. Our results show that solid waste dumping significantly altered both biotic and abiotic components of soil ecosystems. Soil properties shifted abruptly, with elevated pH and increased concentrations of pollutants such as petroleum hydrocarbons and fluorides. Microbial communities were extensively restructured, exhibiting both taxonomic turnover and functional adaptations. Viral communities displayed greater sensitivity to dumping-induced disturbances than prokaryotic or fungal communities. These findings provide new insights into soil microbiome responses to anthropogenic pollution and highlight taxon-specific adaptation strategies. To our knowledge, this is among the first comparative studies integrating prokaryotic, fungal, and viral responses to solid waste dumping using high-throughput molecular approaches. Our findings present a novel perspective that may guide future monitoring efforts and enhance approaches to environmental damage identification and assessment.}, }
@article {pmid41888119, year = {2026}, author = {Rodríguez-Varela, R and Pochon, Z and Mas-Sandoval, A and Yaka, R and Fortes-Lima, CA and García Rubio, A and Márquez-Grant, N and Marí, J and Graziani, G and Ferrer Abárzuza, A and Vicente, M and Lorca-Francisco, L and Linderholm, A and Lagerholm, VK and Arauna, LR and Pérez-Ramallo, P and Krzewińska, M and Schlebusch, CM and Götherström, A}, title = {Analysis of medieval burials from Ibiza reveals genetic and pathogenic diversity during the Islamic period.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41888119}, issn = {2041-1723}, support = {2019-00849_VR//Vetenskapsr&#xe5;det (Swedish Research Council)/ ; }, mesh = {Humans ; History, Medieval ; *Islam/history ; Spain ; *Burial/history ; *Genetic Variation ; Metagenomics ; Gene Flow ; *Leprosy/microbiology/history/genetics ; DNA, Ancient/analysis ; Male ; Cemeteries ; }, abstract = {Ibiza, an island in present-day Spain, was conquered in 902 CE by the Umayyad Emirate of Córdoba. The island remained under Islamic rule until 1235. Here, we analyse the genetic and metagenomic profiles of 13 individuals from an Islamic cemetery in Ibiza, dated to 950-1150 CE. Genome-wide analyses reveal heterogeneity, with ancestry components from Europe, North Africa, and Sub-Saharan Africa. Our analyses estimate that North African gene flow occurred two to seven generations before these individuals lived, suggesting admixture following the Islamic conquest of Iberia and potentially on Ibiza itself. Notably, two individuals trace their Sub-Saharan origins to distinct regions, Senegambia and present-day southern Chad, providing direct evidence of trans-Saharan connections via military and slave networks documented in contemporary Arabic sources. Metagenomic analyses detect several pathogens in this community, with one individual carrying Mycobacterium leprae, offering insight into the presence of leprosy in Ibiza. Our findings align with the historically documented two-pulse demographic model, indicating an initial settlement following the early tenth-century conquest and a second influx associated with Almoravid movements in the twelfth century. These securely dated genomes offer insights into medieval population dynamics and health in the Balearics.}, }
@article {pmid41888125, year = {2026}, author = {Fu, J and Zhang, J and He, R and Dong, Q and Mao, H and Shen, W and Wu, W and Chen, X and Ma, W and Zhai, Q and Chen, L and Zhou, H and Hu, S and He, Y and Qi, C}, title = {A global metagenomic atlas of aging identifies a microbiota phase transition associated with disease risk.}, journal = {NPJ biofilms and microbiomes}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41522-026-00970-4}, pmid = {41888125}, issn = {2055-5008}, support = {2023A1515012538//Basic and Applied Basic Research Foundation of Guangdong Province/ ; NSFC82300623//National Natural Science Foundation of China/ ; NSFC82272391//National Natural Science Foundation of China/ ; NSFC82302610//National Natural Science Foundation of China/ ; 2019YFA0802300//National Key Research and Development Program of China/ ; }, abstract = {Biological aging has been associated with altered risk of aging-related diseases, but the contribution of the gut microbiota to this process remains poorly understood. Here, we constructed an interpretable gut microbiota age clock using metagenomic data from 8115 fecal samples across five continents. We discovered a key microbial perturbation occurring at 56-60 years of chronological age, which was validated in an independent cohort of 2263 metagenomes. This perturbation was associated with a decline in ecological stability and substantial changes in the abundance of core species. Notably, the association between gut microbiota age and diseases was identified to be significantly altered before and after this inflection time. Moreover, within-species analyses uncovered phylogenetic divergence for seven age-related species, such as Escherichia coli, alongside functional alterations in older individuals, including enhanced cell motility, carbohydrate metabolism and horizontal gene transfer. Overall, our global gut microbiome atlas uncovers a critical age transition phase, highlighting opportunities for microbiota-based therapies and offering novel insights into evolutionary dynamics during aging.}, }
@article {pmid41888178, year = {2026}, author = {Ariaeenejad, S and Abedanzadeh, S}, title = {Enhanced stability and reusability of metagenomic laccase via immobilization on functionalized mesoporous silica for antibiotic contaminant removal.}, journal = {Scientific reports}, volume = {16}, number = {1}, pages = {}, pmid = {41888178}, issn = {2045-2322}, mesh = {*Laccase/chemistry/metabolism/genetics ; *Silicon Dioxide/chemistry ; *Enzymes, Immobilized/chemistry/metabolism ; *Anti-Bacterial Agents/chemistry/isolation &amp; purification/metabolism ; Enzyme Stability ; Porosity ; *Metagenome ; Water Pollutants, Chemical/chemistry ; Biodegradation, Environmental ; Metagenomics ; Doxycycline/chemistry ; Imidazoles/chemistry ; }, abstract = {The extensive application of tetracycline antibiotics in agriculture and medicine has led to persistent contamination of aquatic and terrestrial ecosystems, disrupting microbial communities and contributing to the spread of antibiotic resistance. Conventional treatment methods often suffer from poor efficiency, limited stability, and high environmental costs, underscoring the need for robust and sustainable alternatives. Here, we present a biocatalytic platform in which a metagenome-derived laccase (PersiLac1) is covalently immobilized onto imidazole-functionalized SBA-15 mesoporous silica to overcome the limitations of free laccase, including low stability and high leaching. Immobilization markedly enhanced thermal stability, reusability, and catalytic efficiency toward the degradation of doxycycline (DC) and tetracycline (TC). The optimized system exhibited minimal enzyme leaching (9.6% at 25 °C; 22.0% at 80 °C) and achieved removal efficiencies of 76.7 ± 2.8% for DC and 53.7 ± 2.1% for TC within 24 h. High removal performance was maintained even at elevated antibiotic concentrations (200 mg L[-1]), with 43.9% and 42.8% removal for DC and TC, respectively. The immobilized laccase retained over 83% (DC) and 73% (TC) of its initial activity after 10 consecutive reuse cycles. To the best of our knowledge, this is the first report of integrating a metagenomic laccase with an imidazole-functionalized SBA-15 support for antibiotic degradation, offering a unique combination of enhanced stability, high reusability, and environmentally relevant performance. These findings highlight the potential of this immobilization strategy as a sustainable and high-performance solution for the remediation of antibiotic contaminants in water systems.}, }
@article {pmid41888223, year = {2026}, author = {Afshar Jahanshahi, D and Ariaeenejad, A and Hasannejad, A and Zabihi, MR and Ghaffari, MR and Ariaeenejad, S and Kavousi, K}, title = {MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-44250-9}, pmid = {41888223}, issn = {2045-2322}, support = {4020052//Center for International Scientific Studies &amp; Collaborations (CISSC)/ ; }, abstract = {Antimicrobial agents play a vital role in human and environmental health, with applications spanning medicine, food preservation, agriculture, and biotechnology. Among them, enzybiotics enzyme-based antimicrobials have emerged as powerful alternatives to conventional antibiotics due to their targeted mechanisms and lower propensity for resistance. Beyond their medical relevance, enzybiotics have emerging applications in food preservation, animal health, and agriculture, thereby broadening their industrial and environmental value. To support the discovery and characterization of these versatile biomolecules, we present the first genome-resolved metagenomic gene and protein targeted enzybiotic catalog focused on enzybiotics, derived from diverse environmental microbiomes. The Microbial Enzybiotic Gene and Protein Catalog (MiGPC), integrates 15 whole-metagenome datasets from oceans, soils, fecal samples, vegetation, and plastic-contaminated environments, capturing a wide ecological spectrum. Enzybiotic sequences were compiled through a hybrid strategy combining public database mining and manual literature curation, yielding over 136,000 enzybiotic sequences, 7654 metagenome-assembled genomes (MAGs), and ~ 100 million unique genes and proteins. MiGPC integrates taxonomic and enzybiotic gene profiles, offering a robust platform for the discovery, annotation, and ecological mapping of antimicrobial enzymes. Functional analyses using KEGG and eggNOG revealed that approximately 62% of the genes remained uncharacterized, highlighting a rich source of potentially novel functions. Glycoside hydrolases and glycosyl transferases were the most prevalent CAZyme families, while the dominant enzybiotic-producing taxa belonged primarily to the Pseudomonadota and Bacillota phyla. Statistical modeling uncovered two major ecological clusters that distinguished polluted from relatively pristine environments. MiGPC enables high-throughput screening of previously unexplored metagenomes, facilitating the identification of novel antimicrobial agents from under characterized ecosystems. Overall, MiGPC represents a landmark resource that will support multi-omics research, microbial ecology, and the development of next-generation biotechnological solutions based on enzybiotics.}, }
@article {pmid41888360, year = {2026}, author = {Belay, G and Suarez, C and Simachew, A and Paul, CJ}, title = {Microorganisms and functional genes in an aerobic-anoxic integrated gold mine wastewater treatment system.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41888360}, issn = {1573-0972}, }
@article {pmid41888867, year = {2026}, author = {Tao, M and Fan, Y and Qian, L and Liu, H and Ming, Y and Yu, X and Wu, K and Niu, M and Yan, Q and Huang, X and He, Z}, title = {Microbially driven methane and sulfur cycling processes and coupling mechanisms in mangrove sediments.}, journal = {Environmental microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40793-026-00877-9}, pmid = {41888867}, issn = {2524-6372}, support = {2021M703751//China Postdoctoral Science Foundation/ ; SML2023SP205, SML2024SP002, SML2024SP022//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 42430707, 52070196, 32370113 and 92251306//National Natural Science Foundation of China/ ; 2024A1515010931//Guangdong Basic and Applied Basic Research Foundation/ ; }, abstract = {BACKGROUND: Methane (CH4) as a powerful greenhouse gas is the second largest contributor to global climate warming. Mangrove sediments are an important natural source of biogenic CH4 with rich organic carbon (C) and diverse sulfur (S) compounds, ideally for studying CH4 and S cycling processes and coupling mechanisms. Here we sampled mangrove sediment cores and analyzed their key microbial groups, key environmental factors and possible coupling mechanisms for CH4 and S cycling by metagenome sequencing approaches.<br><br>RESULTS: Our results showed that Methanomicrobiales and Methanophagales were predominant methanogens, Methanospirareceae was a representative of anaerobic methanotrophic archaea (ANME), and Desulfobacteraceae and Desulfobulbaceae were abundant sulfate-reducing bacteria (SRB), while Ectothiorhodospiraceae, Chromatiaceae and Comamonadaceae were dominant S-oxidizers. Correlation network analysis revealed positive interactions among methanogens, ANME and SRB. Also, metagenome-assembled genome (MAG) analysis indicated interspecies hydrogen transfer and extracellular electron exchange via conductive pili, flagella, and cytochromes were potential coupling mechanisms between methanogens and SRB. ANME could form consortia with SRB by intermediate metabolites (e.g., acetate) and/or direct interspecies electron transfer (e.g., flagella, pili, cytochromes). Furthermore, methanogen MAGs encoded thiosulfate oxidation and partial sulfate reduction pathways, while the ANME MAGs possessed potentials for S disproportionation and incomplete sulfate reduction. Additionally, SO4[2-], total sulfur, moisture content and salinity were important environmental factors affecting the microbial community structure and gene families involved in CH4 and S cycling.<br><br>CONCLUSION: This study provides novel insights into coupling mechanisms of CH4 and S cycling processes in mangrove sediments, having important implications for mitigating global warming.}, }
@article {pmid41888912, year = {2026}, author = {Krull, J and Sidhu, C and Solanki, V and Bligh, M and Rößler, L and Singh, RK and Huang, G and Robb, CS and Teeling, H and Seeberger, PH and Schweder, T and Crawford, CJ and Hehemann, JH}, title = {Sulfated mannan of diatoms selects host-specific microbiota in the sunlit ocean.}, journal = {Microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s40168-026-02379-9}, pmid = {41888912}, issn = {2049-2618}, support = {101029842//MSCA/ ; Project number 570219261//Deutsche Forschungsgemeinschaft/ ; HE 7217/5-1//DFG/ ; 101044738//ERC/ ; }, abstract = {BACKGROUND: Diatoms, a keystone phylum in Earth's ecosystems, are responsible for substantial oxygen production and the fixation of carbon dioxide in the form of carbohydrates that fuel global food webs. They host diverse prokaryotes, yet how diatoms preferentially recruit those with complementary metabolic traits remains unknown.<br><br>RESULTS: We discovered that diatoms exude a C6-sulfated &#x3b1;-1,3-mannan that serves as a selective carbon source for adapted Polaribacter. Its structure was resolved using NMR spectroscopy, chromatography, chemical synthesis, and enzymatic dissection. Biochemical, physiological, and structural analyses demonstrated, that specialized Bacteroidota employ a four-enzyme pathway to metabolize this glycan. Metagenomic and transcriptomic data revealed that sulfated mannan utilization loci are globally abundant and actively expressed in surface ocean bacterioplankton. Because this mannan provides only carbon, oxygen, sulfur, and hydrogen, bacteria must obtain other essential elements elsewhere, reinforcing metabolic interdependence.<br><br>CONCLUSIONS: Together, these results define a chemically specific interaction between diatoms and specialized bacteria that is mediated by a single sulfated polysaccharide and a dedicated four-enzyme degradation pathway. Presence of this pathway in marine metagenomes and transcriptomes indicates that a sulfated mannan from diatoms exerts selection pressure in the sunlit ocean microbiome.}, }
@article {pmid41889037, year = {2026}, author = {Muddiman, KJ and Doble, A and Stephen, AS and Bescos, R and Illsley, CS and Nicholas, TL and Hanks, S and Toit, LD and Brookes, ZLS}, title = {A Pilot Study Assessing the Oral Microbiome in Women of Menopausal Age: Do Oral Nitrate-Reducing Bacteria Play a Role?.}, journal = {International dental journal}, volume = {76}, number = {3}, pages = {109518}, doi = {10.1016/j.identj.2026.109518}, pmid = {41889037}, issn = {1875-595X}, abstract = {INTRODUCTION: The links between oral health and female ageing are poorly understood, but many changes occur in the oral cavity of menopausal women that affect quality of life, and few current oral health interventions consider gender as part of their approach. The aim of this pilot study was to test the hypothesis that the oral microbiome and microenvironment change during female ageing and are thus worthy of further consideration both experimentally and clinically.<br><br>METHODS: This observational pilot study retrospectively assessed women aged 18 to 89 years (n = 60) attending a UK primary care dental school facility for blood pressure screening, further analysing the salivary oral microbiome using metagenomics and the biochemical microenvironment using high-performance liquid chromatography. Periodontal health screening (Basic Periodontal Examination [BPE]) was then conducted as part of routine clinical care.<br><br>RESULTS: The cross-sectional design classified women into <32 years (n = 18), 40 to 49 years (n = 10), 50 to 59 years (n = 20), and 60+ years (n = 12), but the differences in salivary oestradiol levels between groups were inconclusive. Small numbers were not enough to detect differences in oral microbiome abundance, but nitrate-reducing species (P < .05), nitrate-nitrite-reducing activity (P < .05), and buffering capacity all increased as women aged 60+ years (P < .01), warranting increased numbers. Ageing women also had higher blood pressure (P > .05), were more likely to have periodontal pockets >5.5 mm (BPE4), and had an increased abundance of Porphyromonas (P < .05), but a full periodontal assessment is needed.<br><br>CONCLUSIONS: These observations suggest that the composition of the oral microbiome changes as women age, and thus, prospective and longitudinal oral microbiome studies with larger numbers are needed, including concurrent full periodontal assessment, plasma hormonal levels, and salivary flow. However, this study suggests that the oral microbiome in older women may require special consideration, with an increased focus on tailored oral hygiene interventions for this group.}, }
@article {pmid41889316, year = {2026}, author = {Niyazi, HA and Niyazi, HA and AbdulMajed, H and Juma, N and Helmi, N and Alqarni, M and Saleh, BH and Zubair, M and Alfadil, A and Alhazmi, W and Alharbi, OS and Halabi, WS and Altalhi, R and Moglad, E and Alharbi, MT and Gazzaz, M and Alharthi, TM and Altayb, HN and Ibrahem, K}, title = {Pan-genome analysis and phylogenetic characterization of Klebsiella pneumoniae from global isolates.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/17460913.2026.2617118}, pmid = {41889316}, issn = {1746-0921}, abstract = {AIMS: This study aimed to investigate the global genetic diversity, evolutionary relationships, and antimicrobial resistance (AMR) profiles of Klebsiella pneumoniae by performing a comprehensive pan-genome and phylogenetic analysis across worldwide isolates.<br><br>MATERIALS AND METHODS: A total of 72,057 K. pneumoniae genomes were retrieved from the NCBI database, from which 91&#xa0;high-quality representative genomes each from a unique country were selected based on completeness, metadata availability, and sequence quality. Genomic assemblies were assessed using QUAST, annotated with PROKKA, and analyzed for pan-genomic composition and phylogenetic relatedness using standard bioinformatics pipelines.<br><br>RESULTS: The pan-genome revealed a large accessory component, reflecting extensive genomic plasticity and adaptability. QUAST analysis indicated significant variability in genome size and contig number, while PROKKA annotation identified diverse coding sequences, tRNA, rRNA, and AMR genes. Phylogenetic clustering demonstrated both geographically localized and globally disseminated lineages, suggesting regional adaptation and intercontinental transmission.<br><br>CONCLUSIONS: This study provides a global perspective on the genomic diversity and evolutionary patterns of K. pneumoniae. The widespread presence of AMR determinants underscores the urgent need for continuous genomic surveillance and integration of metagenomic approaches to improve monitoring, infection control, and therapeutic strategies against multidrug-resistant strains.}, }
@article {pmid41889516, year = {2026}, author = {Mao, J and Jin, Q and Ye, D and Yang, Y}, title = {Case Report: A rare presentation of pulmonary tuberculosis with extensive ground-glass opacities in an immunocompetent patient: lessons from metagenomic next-generation sequencing.}, journal = {Frontiers in medicine}, volume = {13}, number = {}, pages = {1696371}, pmid = {41889516}, issn = {2296-858X}, abstract = {Pulmonary tuberculosis (PTB) is typically diagnosed through sputum smear microscopy and culture. However, diagnosis is challenging in patients with atypical radiological features and negative conventional tests. Ground-glass opacities (GGOs) are common but non-specific computed tomography (CT) findings and are rarely observed in immunocompetent PTB patients. We report the first case of an immunocompetent 53-year-old female presenting with extensive bilateral GGOs without classic clinical symptoms. Conventional microbiological cultures, acid-fast staining, and serological assays were all negative. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified Mycobacterium tuberculosis, further supported by a positive T-spot TB assay. Standard anti-tuberculosis therapy led to complete resolution of GGOs over nine months, confirmed by follow-up CT imaging. This case underscores the diagnostic challenge of atypical PTB presenting with non-classical CT manifestations in an immunocompetent host. It highlights the decisive role of mNGS as a complementary tool in cases where conventional methods fail, enabling timely diagnosis, precise treatment, and improved patient outcomes.}, }
@article {pmid41889550, year = {2026}, author = {Xiu, Q and He, H and Liu, Z and Ou, X and Meng, Y and Zhao, K and Yang, Q and Zhang, X and Hou, Y and Yao, S and Gao, P and Xia, W}, title = {Biosurfactant-driven desorption and remediation of heavy oil contaminated soils underpinned by molecular simulations and microbial dynamics.}, journal = {RSC advances}, volume = {16}, number = {18}, pages = {16316-16328}, pmid = {41889550}, issn = {2046-2069}, abstract = {This study integrates molecular dynamics simulations and bench-scale experiments to investigate the adsorption and desorption behaviors of heavy oil on five mineral substrates: SiO2, kaolinite, muscovite, and Ca[2+]-/Na[+]-montmorillonite. Adsorption followed Langmuir isotherms, with montmorillonite exhibiting the highest capacities (0.061-0.062 molecules per Å[2] for aromatics in simulations; 0.086-0.091 g g[-1] in bench-scale tests) and SiO2 the lowest (0.027 pcs per Å[2]; 0.013 g g[-1]). Among four biosurfactants evaluated-rhamnolipid, sophorolipid, trehalose lipid, and mannosylerythritol lipid-sophorolipid consistently achieved the greatest desorption efficiency, removing up to 99.63% of adsorbed oil from Na[+]-montmorillonite and 96.04% from field-contaminated soil. 16S rRNA and metagenomic sequencing revealed an increased abundance of hydrocarbon-degrading bacteria within the soil microbial community, highlighting a synergistic effect between biosurfactant-induced desorption and biodegradation. These findings underscore the critical roles of mineralogical properties, oil fraction characteristics, and biosurfactant selection in soil washing treatment. This work presents a viable and eco-friendly strategy for remediating crude oil-contaminated soils, with important implications for optimizing large-scale environmental restoration efforts.}, }
@article {pmid41889698, year = {2026}, author = {Almatrafi, R and Alasiri, A and Almuneef, G and Al-Hazzani, AA and Alghoribi, MF and Hakami, M and Arafah, AM and Alotibi, RS and Alrabiah, S and Alqurainy, N and Ajina, R and Aldriwesh, MG}, title = {First metagenomic analysis of age-associated changes in the gut microbiome among healthy Saudi adults: SAMS pilot study.}, journal = {Frontiers in aging}, volume = {7}, number = {}, pages = {1733638}, pmid = {41889698}, issn = {2673-6217}, abstract = {INTRODUCTION: The gut microbiome undergoes dynamic changes with aging across diverse healthy populations. However, data from Saudi Arabia remain limited. This pilot study investigated age-related variations in the gut microbiome among healthy Saudi adults to characterize region-specific microbial signatures and identify taxa potentially associated with aging in a healthy population.<br><br>METHODS: We established the Saudi Aging and Microbiome Study (SAMS) to investigate age-related changes in fecal microbiome of Saudi adults. In this pilot phase, 145 healthy participants aged 19-69&#xa0;years were enrolled. Shotgun metagenomic sequencing was performed to profile fecal microbiome at the species level. Microbial diversity and taxonomic composition were compared across five age groups. Spearman and confounder-adjusted partial Spearman correlation were applied to identify taxa significantly associated with chronological age.<br><br>RESULTS: We analyzed fecal microbiome of 145 healthy adults distributed among five age groups: G1 (19-29&#xa0;years, n = 33; 22.7%), G2 (30-39&#xa0;years, n = 30; 20.7%), G3 (40-49&#xa0;years, n = 27; 18.6%), G4 (50-59&#xa0;years, n = 31; 21.4%), and G5 (60-69&#xa0;years, n = 24; 16.6%). Of these, 75 (51.7%) were male, and 70 (48.3%) were female. Alpha diversity increased from young to older adulthood for observed richness and Shannon indexes (all q < 0.05). Beta diversity also varied significantly with age (PERMANOVA R [2] = 0.13, q = 0.023), indicating distinct microbial community structures in healthy older adults. At the phylum level, Firmicutes significantly increased with age (FC = 1.35; q = 0.026), whereas Bacteroidota decreased (FC = 0.59; q = 0.01). Consistent with these trends, Blautia obeum showed positive correlations, while Bacteroides thetaiotaomicron and Phocaeicola vulgatus showed negative correlations with chronological age.<br><br>CONCLUSION: In healthy Saudi adults, increasing age was associated with higher microbial diversity and compositional shifts at phylum and species levels. These age-associated microbial taxa might represent biomarkers of healthy aging and suggest an enhanced community capacity for short-chain fatty acids (SCFAs) production, a hypothesis warranting validation through future functional analyses.}, }
@article {pmid41889866, year = {2026}, author = {Van Camp, AG and Park, J and Ozcelik, E and Eskiocak, O and Ozler, KA and Papciak, K and Subhash, S and Alwaseem, H and Ergin, I and Chung, C and Shah, V and Yueh, B and Fein, MR and Durmaz, C and Mozsary, C and Kilic, E and Garipcan, A and Damle, N and Najjar, D and Nelson, TM and Ryon, KA and Butler, DJ and Patel, CJ and Thaiss, CA and Birsoy, K and Mason, CE and Meydan, C and Tierney, BT and Beyaz, S}, title = {Diverse high-fat diets drive multi-omic reprogramming that persists after dietary reversal.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.17.708620}, pmid = {41889866}, issn = {2692-8205}, abstract = {Dietary fat composition modulates host physiology and the gut microbiome, but the long-term effects of specific fat sources and the extent to which these changes resolve after dietary reversal remain incompletely defined. Here, we present a longitudinal multi-omic resource of mice maintained for one year on a purified control diet, seven high-fat diets differing in predominant fat source, or reversal regimens in which animals were switched from high-fat to control diet after 4 or 9 months. We further incorporated two cohorts with distinct pre-existing microbiome configurations to determine how baseline community structure shapes diet-induced remodeling of the gut microbiome ecosystem. By integrating longitudinal phenotyping, fecal metagenomics, fecal metabolomics, plasma metabolomics and lipidomics, and intestinal single-cell RNA sequencing, we defined the shared and dietary fat-specific responses across host and microbiome compartments. Baseline microbiome composition strongly influenced microbial responses to diet, indicating that pre-existing community structure is a major determinant of dietary ecosystem remodeling. Although many altered features shifted toward baseline after dietary reversal, only approximately half of diet-associated microbial changes recovered within the study window. A subset of taxa exhibited persistent alterations, including sustained depletion of Lactobacillus johnsonii and Bifidobacterium pseudolongum and sustained enrichment of Alistipes finegoldii , consistent with a "microbiome memory" of prior high-fat diet exposure. This memory effect is mirrored in the host, by sustained suppression of major histocompatibility complex class II (MHC-II) gene expression in intestinal epithelial cells after dietary reversal. These findings indicate that dietary fats leave a lasting imprint on the host-microbiome interactome that survives dietary intervention. Together, these data establish a resource for defining how dietary fat source, baseline microbiome composition, and dietary history shape host-microbiome states. The entire resource is available online as an RShiny app.}, }
@article {pmid41890171, year = {2026}, author = {Zhao, S and Sai, Y and Jia, M and Qiao, Y and Guo, W and Ding, W and Shao, X and Zheng, Y}, title = {Comprehensive insights into the mechanism of flavor formation in Cheonggukjang: Integration of metagenomics, volatomics, and metabolomics.}, journal = {Food chemistry: X}, volume = {35}, number = {}, pages = {103756}, pmid = {41890171}, issn = {2590-1575}, abstract = {Microbial metabolism shapes the unique flavor profile of Cheonggukjang; however, the formation pathways of characteristic flavor compounds mediated by microbiota remain unclear, hindering precise quality control. To fill this gap, this study innovatively integrated metagenoics, volatilomics, and metabolomics to systematically decode the flavor formation mechanism during Cheonggukjang fermentation. Volatile compound analysis defined three fermentation stages for Cheonggukjang (0-18, 18-60, and 60-72 h), identifying the 60-72 h period as the most critical for flavor formation. A total of 15 key flavor compounds were identified, with 10 designated stage-specific flavor markers. LefSe analysis revealed that Bacillus subtilis, Bacillus velezensis, Caldibacillus thermoamylovorans, and Bacillus licheniformis were the key biomarkers across different fermentation stages, while redundancy analysis (RDA) indicated that total sugar as the key driver of microbial succession. Additionally, this study reconstructed the metabolic network responsible for characteristic flavor formation and identified C. thermoamylovorans, B. licheniformis, B. velezensis, B. subtilis, Bacillus paralicheniformis, and Caldibacillus hisashii as core functional microbiota modulating amino acid metabolic to drive flavor development. This study lays a theoretical framework for standardizing Cheonggukjang production and targeted regulating its flavor quality.}, }
@article {pmid41890980, year = {2026}, author = {Shi, Y and Sanderson, H and Chuan, J and Khan, IUH and Sunohara, M and Craiovan, E and Lapen, DR and Diarra, M and Chen, W}, title = {Dual-platform metagenomic surveillance distinguishes pathogen and resistome hotspots across agricultural and mixed-use watersheds.}, journal = {One health (Amsterdam, Netherlands)}, volume = {22}, number = {}, pages = {101384}, pmid = {41890980}, issn = {2352-7714}, abstract = {Freshwater systems embedded in agricultural landscapes serve as dynamic reservoirs and conduits for fecal-associated microbes, zoonotic pathogens, and antimicrobial resistance (ARG) and virulence factor (VF) genes. Yet factors that govern their densities and diversity remain a research challenge. From 2016 to 2021, we conducted a longitudinal water surveillance in an agriculturally dominated river basin in eastern Ontario, Canada; characterizing fecal-associated bacterial communities using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Agricultural drainage ditches consistently harbored higher fecal-associated bacterial diversity with pronounced seasonal shifts; i.e., higher levels during larger flow periods in spring and fall. Elevated discharge was associated with enrichment of genera containing zoonotic or opportunistic pathogens, such as those in Pseudomonas, Sphingomonas, and Massilia. Conditionally rare taxa (CRTs), although typically low in abundance, accounted for ∼12.6% of all pathogen-associated genera and disproportionately contributed to community turnover, highlighting their role as transient reservoirs of microbial risk. Shotgun metagenomics detected 27 ARGs, primarily at mixed-use sites, and 14 VFs, mainly in agricultural ditches. Clinically relevant β-lactamase genes (e.g., oxa, imp, sme) co-occurred with metal-resistance operons, a pattern suggestive of possible co-selection, although selective agents were not directly measured. Although the prevalence of ARG and VF was low (<5% of samples), their ecological context indicates potential transmission pathways. Limited overlap in ARGs between short-read and metagenome-assembled genome (MAG)-based profiling reflects their complementary strength: gene-level sensitivity versus host-resolved analysis. Together, these findings demonstrate the utility of integrated amplicon and shotgun metagenomic surveillance for proactive One Health risk assessment in agricultural watersheds.}, }
@article {pmid41891006, year = {2026}, author = {Mills, EG and Evans, KM and Dorazio, AJ and Squires, KM and Sundermann, AJ and Stellfox, ME and Culyba, MJ and Shields, RK and Van Tyne, D}, title = {Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistant Enterococcus faecium.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.11.26348025}, pmid = {41891006}, abstract = {UNLABELLED: Colonization of the gastrointestinal (GI) tract by vancomycin-resistant Enterococcus faecium (VREfm) often precedes bloodstream infection and serves as a reservoir for onward patient transmission in healthcare settings. Routine clonal isolate-based sequencing often underestimates within-patient diversity, and can miss transmission involving low-abundance and co-colonizing strains. Here we applied culture-enriched metagenomic sequencing to matched GI tract and blood VREfm populations collected ≤14 days apart from 35 patients with positive VREfm blood cultures collected between 2020 and 2025 at a single hospital. GI populations exhibited greater within-patient diversity than bloodstream populations, including multi-strain colonization in five patients. Among single-strain populations, variant analysis suggested distinct environment-specific pressures between the GI tract and bloodstream environments. To assess transmission using culture-enriched metagenomic sequencing, we compared all 70 VREfm populations against 470 contemporary clinical VREfm isolate genomes collected from the same hospital and identified 19 putative transmission clusters, including six clusters involving multi-strain populations. Together, these results demonstrate how culture-enriched metagenomic sequencing improves resolution for assessing within-patient VREfm diversity and enhances the detection of transmission events that could be missed by clonal isolate-based surveillance.<br><br>IMPACT STATEMENT: VREfm bloodstream infection is often seeded from bacteria colonizing the gut. The genetic diversity within gut and blood VREfm populations, and the role of this diversity in bacterial transmission, has been difficult to resolve as genomic surveillance typically relies on sequencing a clonal clinical isolate from each patient. Using culture-enriched metagenomic sequencing of matched GI tract and bloodstream VREfm populations from 35 patients at a single hospital, we found that the GI tract reservoir contained VREfm populations with greater strain and variant diversity than populations collected from the bloodstream. By integrating population sequencing with a large collection of VREfm clinical isolate genomes, we further demonstrate that different strains co-colonizing the GI tract of the same patient can reside in multiple putative transmission clusters, revealing potential transmission links that clone-based approaches are likely to miss. These findings demonstrate the potential utility of culture-enriched metagenomic sequencing for higher-resolution hospital surveillance of bacterial transmission. Applying this approach to other bacterial pathogens could improve our ability to detect and interpret transmission involving heterogeneous microbial populations that colonize and infect hospitalized patients.<br><br>DATA SUMMARY: Patient demographic data and clinical characteristics can be found in Table S1 (online Supplementary Material). All sequencing data generated in this study has been deposited in the National Center for Biotechnology Information (NCBI) under BioProject PRJNA901969, with sample accession numbers listed in Table S2 . Sequences used to construct the local reference strain database are available at NCBI BioProject PRJNA475751, with accession numbers listed in Table S3 . Variants identified in single-strain blood and GI populations are listed in Table S4 . Accession numbers for clinical isolate genomes included in transmission analyses are listed in Table S5 .<br><br>REPOSITORIES: Sequencing data generated in this study is deposited in the National Center for Biotechnology Information (NCBI) under BioProject PRJNA901969.}, }
@article {pmid41891018, year = {2026}, author = {Basso, M and Hildebrand, F and Winder, C and Baker, DJ and Manders, R and Barberis, M and Gibbons, SM and Cohen Kadosh, K}, title = {Anxiety associated with dietary intake and gut microbiome features in a cross-sectional cohort of sub-clinically anxious young women.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.18.26348688}, pmid = {41891018}, abstract = {Background Emerging evidence highlights the gut-brain axis as a key pathway linking diet and anxiety, yet the key determinants remain unclear. Most studies have focused on single components of diet and rarely integrate long- and short-term intake. Furthermore, prior gut-brain work has focused on microbiome composition, while functional features remain underexplored. In this study, we investigated associations between long- and short-term dietary intake, gut microbiome composition and functions, and anxiety in a subclinical cohort of 46 females (18-24 years) from the United Kingdom. Results Long-term diet quality was assessed using the Healthy Eating Index (HEI-2020) derived from a food frequency questionnaire, stratifying participants into lower and higher diet quality clusters. Short-term dietary intake was assessed via 24-hour recalls. Shotgun metagenomics of stool samples was used to assess differences in alpha and beta diversity indices, species abundances, and bacterial pathways putatively metabolizing gut-brain-axis-relevant molecules. Anxiety was measured using the State-Trait Anxiety Inventory (state subscale STAI-s). Regression models identified diet quality (HEI cluster) as the primary dietary feature of anxiety variation. The presence of Ruminococcus gnavus and Flavonifractor plautii and the abundances of Bilophila wadsworthia and Bacteroides thetaiotaomicron were positively associated with anxiety. The presence of Feacalibacterium prausnitzii and greater abundances of butyrate, propionate, and GABA synthesis pathways were inversely associated with anxiety. Non-linear models revealed a U-shaped relationship between inositol synthesis and STAI-s. Finally, we found that habitual diet quality may modulate anxiety-related responses to short-term dietary variation. Conclusions These findings reveal widespread links between long-term diet quality, microbiota composition and function, and anxiety symptoms. These results point towards several promising targets for prebiotic, probiotic, postbiotic, and dietary interventions aimed at reducing anxiety.}, }
@article {pmid41891399, year = {2026}, author = {Elsheikh, M and Ibrahim, MA and Fares, S and Bhongade, M and Adhem, K and Ramirez-Morales, XI and Kaseb, AO and Petrosino, J and Hassan, MM and Jalal, PK}, title = {Influence of Gut Microbiota on Response to Immune Check Point Inhibitors in MASLD Patients With HCC: Unraveling the Connection.}, journal = {Cancer medicine}, volume = {15}, number = {4}, pages = {e71738}, doi = {10.1002/cam4.71738}, pmid = {41891399}, issn = {2045-7634}, support = {R21CA293626/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Liver Neoplasms/drug therapy/immunology/microbiology/complications ; *Carcinoma, Hepatocellular/drug therapy/immunology/microbiology/complications ; Dysbiosis/microbiology ; Drug Resistance, Neoplasm ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; }, abstract = {Immune checkpoint inhibitors (ICIs) have emerged as a promising treatment for various cancers, including advanced hepatocellular carcinoma (HCC). However, a significant proportion of patients with HCC, particularly those with metabolic dysfunction-associated liver disease (MASLD), exhibit resistance to ICI therapy. Studies have revealed that the presence of specific gut bacteria, such as Akkermansia, Bifidobacterium, and Lachnoclostridium, is associated with improved outcomes with ICI-treated HCC patients. Conversely, the overgrowth of bacteria like Enterobacteriaceae is linked to resistance to therapy. This review investigates the role of gut microbiota in shaping immune checkpoint inhibitor responses in MASLD-related hepatocellular carcinoma, focusing on how dysbiosis may contribute to ICI resistance and exploring microbiome modulation strategies, such as fecal microbiota transplantation and probiotics, aiming to optimize therapeutic outcomes.}, }
@article {pmid41891696, year = {2026}, author = {Toth, CRA and Molenda, O and Nesbø, CL and Luo, F and Devine, CE and Chen, X and Wu, K and Xiao, JZ and Puri, R and Guo, S and Bawa, N and Wang, P-H and Wei, Y and Flick, R and Edwards, EA}, title = {Identification of a highly expressed gene cluster likely coding for benzene activation enzymes in a methanogenic enrichment culture.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0208325}, doi = {10.1128/aem.02083-25}, pmid = {41891696}, issn = {1098-5336}, abstract = {UNLABELLED: The oil refinery (OR) consortium is a model methanogenic enrichment culture used to study anaerobic benzene degradation. Over half of the culture's bacterial community consists of two closely related Desulfobacterota strains, designated ORM2a and ORM2b, whose mechanisms of benzene activation are unknown. Three proteomics data sets were integrated and analyzed using high-quality OR metagenomes and metagenome-assembled genomes (MAGs), including a complete circularized ORM2a MAG, to identify active metabolic pathways and proteins expressed during methanogenic benzene degradation. Among the proteins identified were Bam-like subunits of an ATP-independent benzoyl-CoA degradation pathway, as well as downstream β-oxidation proteins yielding acetate. The most abundant proteins identified mapped to two ORM2a gene clusters of unknown function. Homologous and syntenic gene clusters were identified in the MAGs of ORM2b and a sulfate-reducing Pelotomaculum that also degrades benzene, as well as in nine contigs assembled from hydrothermal vent metagenomes. Extensive homology and structural predictions suggest that the first cluster-termed the "Magic" gene cluster-encodes for enzymes catalyzing the chemically challenging activation of benzene and subsequent transformation steps yielding benzoyl-CoA. The second ("Nanopod") gene cluster encodes a transmembrane complex that may facilitate benzene transport across the cell membrane. Phylogenomic analyses place ORM2a and ORM2b within a novel genus of strict anaerobes specialized for benzene degradation, which we propose naming "Candidatus Anaerobenzenivorax."<br><br>IMPORTANCE: Benzene is a widespread, persistent, and toxic pollutant that can accumulate in anoxic environments such as groundwater and sediments. Benzene can be metabolized in the absence of oxygen; however, despite decades of research, the biochemical mechanisms for benzene activation under anaerobic conditions remain unproven. This study provides strong genetic and proteomic evidence for a new suite of enzymes that initiate anaerobic benzene activation. These findings lay a foundation for future biochemical studies and expand our understanding of how microbes carry out difficult chemical reactions in the absence of oxygen.}, }
@article {pmid41891698, year = {2026}, author = {Li, Y and Ji, M and Tu, Q}, title = {Patterns and drivers of macro- and micro-diversity of mudflat intertidal archaeomes along the Chinese coasts.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0143425}, doi = {10.1128/msystems.01434-25}, pmid = {41891698}, issn = {2379-5077}, abstract = {Archaea are widespread in Earth's ecosystems, contributing to ecosystem multifunctioning and stability. Compared to bacteria, our understanding of the biodiversity and underlying drivers of archaeal communities in representative ecosystems remains much less tapped. In this study, the macro- and micro-diversity of mudflat intertidal archaeomes were comprehensively analyzed at a large geographic scale, aiming to resolve the ecological drivers determining the variations in archaeal biodiversity. The compositions of mudflat intertidal archaeal taxa highly varied, especially the dominant Thaumarcheota and Euryarchaeota, but maintained relatively stable functional potential across space, demonstrating that functional traits were selected by the ecosystem in priority. While archaeal communities carried important functional traits mediating various biogeochemical cycling processes, horizontal gene transfer played critical roles in endowing functional genes for many archaeal lineages, such as the citric acid cycle in Methanosarcinia and various amino acid metabolism genes in Thermoplasmata. Spatial scaling, including latitudinal diversity gradient and distance-decay patterns (DDR), was clearly observed for archaeal taxonomic groups, but only DDR was weakly observed for functional traits. Intra-population genetic variations were significantly and positively associated with community macro-diversity, demonstrating covariations between nucleotide-level micro- and community-level macro-diversity. The compositions of intertidal archaeomes were mainly structured by homogeneous selection, with different phylogenetic bins being shaped by distinct ecological processes and remarkable variations across different sites. The study contributes to a comprehensive insight into the mechanisms shaping archaeal diversity and ecological characteristics within a fluctuating ecosystem.IMPORTANCEThe dynamic intertidal mudflat ecosystems host intense biogeochemical activities mediated by microbial communities, among which archaea contribute as an essential component but remain much less understood compared to bacteria. To gain better insights into the diversity, functional potential, and ecological drivers of archaeal communities in intertidal mudflats, archaeal phylogenetic signatures and genomic sequences were recovered via amplicon sequencing of 16S rRNA genes and shotgun metagenomes, targeting both macro- and micro-diversity. The results showed that archaeal taxonomic composition highly varied across space, whereas the functional potential remained relatively stable. Horizontal gene transfer served as an important source of archaeal metabolic diversity, obtaining additional genes linked to key biochemical pathways. The dominance of environmental selection further demonstrated the ecological forces governing archaeal communities in highly variable coastal habitats. This study established a large-scale framework for understanding the microbial ecology of intertidal archaeomes in dynamic coastal ecosystems.}, }
@article {pmid41892210, year = {2026}, author = {Liang, X and Li, X and Mi, N and Wu, Y and Wu, J and Chen, H and Liu, D}, title = {Early-Life Diarrhea Disrupts Antioxidant-Immune Homeostasis and Gut Microbiota in Suckling Calves.}, journal = {Biology}, volume = {15}, number = {6}, pages = {}, doi = {10.3390/biology15060450}, pmid = {41892210}, issn = {2079-7737}, support = {YLXKZX-NND-012//First-class Disciplines of Inner Mongolia Scientific Research Special Program/ ; 2023-JSGG-5//National Center of Technology Innovation for Dairy/ ; BR22-11-17//Basic Scientific Research Business Project of Universities directly under the Inner Mongolia Au-tonomous Region/ ; 2024LHMS03054//nner Mongolia Natural Science Foundation Project/ ; }, abstract = {Calf diarrhea is a common early-life disorder that adversely affects growth, oxidative balance, immune function, and intestinal microbiota, thereby compromising health and production performance. This study systematically investigates the effects of naturally occurring diarrhea in 7-day-old suckling calves on oxidative stress, immune responses, intestinal barrier integrity, and gut microbiota structure and function. Fecal scores, serum antioxidant and immune indices, and intestinal permeability markers were measured, and fecal samples were subjected to metagenomic sequencing. Diarrhea-affected calves exhibited higher fecal scores, increased oxidative stress indicated by reduced total antioxidant capacity, elevated lipid peroxidation, and altered antioxidant enzyme activities. Humoral immunity was impaired, inflammatory responses were dysregulated, and intestinal barrier function was disrupted. Gut microbial diversity declined, showing a depletion in health-associated taxa and the enrichment of opportunistic pathogens. Correlation analyses revealed that pathogenic bacteria abundance positively associated with diarrhea severity, oxidative stress, inflammation, and barrier disruption, while beneficial genera correlated with antioxidant and immune function. Functional profiling indicated a microbial shift from amino acid metabolism and antioxidant homeostasis toward carbohydrate and energy metabolism under diarrheic conditions. These findings highlight the pivotal role of gut microbiota dysbiosis in diarrhea pathogenesis and provide a foundation for developing microbiome-targeted interventions to improve calf health.}, }
@article {pmid41892424, year = {2026}, author = {Gomes, E and Mesquita, TG and Serra, P and Araújo, D and Almeida, C and Machado, A and Oliveira, R and Castro, J}, title = {Antimicrobial Resistance in the Food Chain: Bridging Knowledge Gaps for Effective Detection and Control.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/antibiotics15030262}, pmid = {41892424}, issn = {2079-6382}, support = {https://doi.org/10.54499/2024.13640.PEX//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; https://doi.org/10.54499/2022.07654.PTDC//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; APTA4shiga (number 14840)//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e Tecnologia/ ; }, abstract = {Antimicrobial resistance (AMR) poses a critical global public health threat, with the food chain serving as a significant transmission route connecting animals, environment, and humans. This review adopts a One Health perspective to analyze the key drivers of AMR dissemination across animal agriculture, aquaculture and food processing. We evaluate detection methodologies, contrasting the regulatory gold standard of culture-based phenotypic testing with rapid molecular advancements, including Whole Genome Sequencing (WGS), metagenomics, and emerging CRISPR-Cas diagnostics. While molecular tools offer unprecedented speed and resolution, challenges such as matrix interference, the viable but non-culturable (VBNC) state, and the genotype-phenotype disconnect remain. Finally, integrated mitigation strategies are also described, ranging from on-farm antimicrobial stewardship and innovative biofilm control to consumer hygiene practices. It is essential to bridge the technical and regulatory gaps in AMR surveillance in order to develop effective interventions and ensure a safer food system.}, }
@article {pmid41892439, year = {2026}, author = {Gomes-Gonçalves, S and Bento, JT and Moreira, G and Mourão, J and Cruz, R and Esteves, F and Baptista, AL and Pereira, MA and Caseiro, P and Carreira, P and Figueira, L and Mesquita, JR}, title = {Comprehensive Shotgun Metagenomic Profiling of Antibiotic Resistance Genes in Sheep and Goat Farming Environments.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/antibiotics15030277}, pmid = {41892439}, issn = {2079-6382}, support = {PRR-C05-i03-I-000190//RumiRes project-"Vigil&#xe2;ncia epidemiol&#xf3;gica de resist&#xea;ncias antimicrobianas e res&#xed;duos medicamentosos em Pequenos ruminantes da Regi&#xe3;o Centro"/ ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a growing global health concern, driven in part by antibiotic use in animal production systems. Despite its relevance, the microbiome and resistome of small ruminant farm environments remain largely underexplored.<br><br>METHODS: In this study, shotgun metagenomics was applied to environmental samples from 46 sheep, goat and mixed-species farms across 14 municipalities in central Portugal.<br><br>RESULTS: Microbial profiling revealed a well-preserved microbiome with Pseudomonadota, Actinomycetota, Bacteroidota and Bacillota (syn. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes respectively) as the most dominant phylum across different farm types. Regarding AMR, a total of 706 unique antimicrobial resistance genes (ARGs), covering 15 antibiotic classes, were detected. Tetracycline, aminoglycoside and macrolide resistance genes dominated across all samples, forming a conserved core resistome. While overall resistome profiles were broadly similar among farm types, significant differences were observed in specific ARG classes, such as pleuromutilin and fosfomycin.<br><br>CONCLUSIONS: These findings highlight small ruminant farm environments as potential reservoirs of clinically relevant ARGs, including WHO highest priority critically important antimicrobial (HPCIA) resistance genes for macrolides (mph(c), erm(f), erm(b)) and fluoroquinolones (qnrD1), as well as critically important antimicrobial (CIA) resistance genes for glycopeptides (vanR-SC, vanR-O) and aminoglycosides (str, aadA), supporting the need to incorporate these environments into surveillance strategies.}, }
@article {pmid41892455, year = {2026}, author = {Dashti, AA and Vali, L and Walsh, F}, title = {Metagenomic Profiling of Soil Microbiomes and Resistomes in Arid Ecosystems of Kuwait.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/antibiotics15030294}, pmid = {41892455}, issn = {2079-6382}, support = {(RN01/15))//Kuwait University/ ; (code EASREF).//University of Gloucestershire/ ; }, abstract = {Background/Objective: This study addresses a significant knowledge gap in the literature concerning antibiotic resistance genes (ARGs) in arid soils by employing metagenomic approaches to characterise their diversity, using Kuwait as a model environment. Methods: Soil samples were collected from two agriculturally managed sites (K1 and K3) and one coastal unmanaged site (K2), representing distinct ecological conditions. Results: Taxonomic profiling revealed notable variation in microbial communities at both the phylum and genus levels. Alpha diversity analyses based on the Chao1 and Shannon indices indicated that agricultural soils exhibited greater microbial richness and diversity than the coastal soil. Beta diversity analysis further demonstrated substantial differences in microbial community composition among the sites. Consistent with previous soil microbiome studies, ARGs such as tetA, aac(3)-Ib, sul1, qep, muxB, mexW, mexB, and macB were detected across the sites. However, the identification of distinct clinically relevant resistance genes, including ugd, blaOXA-18, blaCMY-19, blaMOX-7, blaFOX-7, blaLRA-12, and novA, suggests the influence of site-specific or extreme selective pressures. Conclusions: Several of the detected ARGs appear to be rare or previously unreported in soil environments. Although the sample size is too small to support broad generalisations, the detection of ugd in soil is particularly noteworthy, suggesting that soils may serve as reservoirs of polymyxin resistance, potentially undermining the effectiveness of polymyxin antibiotics.}, }
@article {pmid41892478, year = {2026}, author = {Scarlata, GGM and Belančić, A and Štimac, D and Fajkić, A and Meštrović, T and Abenavoli, L}, title = {Bacteriophage Therapy Against Shigella spp.: A Precision Antimicrobial Strategy.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {15}, number = {3}, pages = {}, doi = {10.3390/antibiotics15030317}, pmid = {41892478}, issn = {2079-6382}, abstract = {Shigellosis remains a significant global cause of infectious colitis, increasingly complicated by multidrug-resistant strains and the microbiota-disrupting effects of broad-spectrum antibiotics. Although conventional antimicrobial therapy can reduce symptom duration and bacterial shedding, it also contributes to gut dysbiosis, loss of colonization resistance, and further selection for antimicrobial resistance. These challenges have renewed interest in precision antimicrobial strategies, particularly bacteriophage therapy, which provides strain-level specificity and preserves the gut microbiota. This narrative review evaluates the biological rationale, preclinical and early clinical evidence, safety considerations, and translational challenges associated with bacteriophage therapy targeting Shigella spp. The historical development and mechanistic basis of phage therapy are summarized, with emphasis on the advantages of obligately lytic phages, receptor-specific targeting, self-amplification at infection sites, and activity against both planktonic and biofilm-associated bacteria. Recent microbiota research indicates that shigellosis is closely associated with early and persistent disruption of gut ecology, including depletion of short-chain fatty acids-producing taxa and reduced microbial resilience. Phage-based approaches may reduce pathogen burden while preserving beneficial microbial communities. Evidence from in vitro systems, animal models, human intestinal organoids, and a Phase 1 clinical trial demonstrates targeted efficacy and favorable safety profiles for Shigella-specific phages and phage cocktails. Major barriers to clinical adoption include immune interactions, phage resistance dynamics, genomic safety screening, regulatory classification, and the need for standardized susceptibility testing. Future directions emphasize the development of personalized phage therapy platforms that integrate rapid diagnostics, phage libraries, metagenomics, and artificial intelligence-assisted matching to enable scalable, precision treatment.}, }
@article {pmid41892488, year = {2026}, author = {Mise, K and Wasai-Hara, S and Itoh, H}, title = {Global terrestrial distribution of N2O-reducing Acidobacteriota members.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag073}, pmid = {41892488}, issn = {1751-7370}, abstract = {Nitrous oxide (N2O) is a potent greenhouse gas, and soil is its largest terrestrial source. Microbial N2O reductase (NosZ) is the only known enzyme capable of reducing N2O to N2, making nosZ-harboring prokaryotes important sinks in terrestrial ecosystems. Despite being among the most abundant and ubiquitous bacterial phyla in soil, the potential role of Acidobacteriota in N2O reduction remains largely unexplored. In this study, we addressed this gap using genomic, metagenomic, and physiological analyses. We first analyzed 199,602 prokaryotic genomes, including genomes from both isolated strains and metagenome-assembled genomes. We found that 491 Acidobacteriota genomes harbored nosZ, predominantly the Sec-dependent NosZ gene (nosZII). Global metagenomic analysis of 321 soil samples revealed that Acidobacteriota nosZII is one of the most abundant groups of nosZ and distributed across different continents. Among Acidobacteriota, nosZII from the class Vicinamibacteria was the most prevalent in the soils. Finally, we provide the physiological evidence of N2O-reducing activity in Acidobacteriota by demonstrating that the Vicinamibacteria type strain, Luteitalea pratensis KCTC52215T, can reduce N2O. Taken together, these findings highlight the previously overlooked potential role of Acidobacteriota as a global N2O sink and underscore the need to include them in future studies on soil N2O dynamics.}, }
@article {pmid41892593, year = {2026}, author = {Krasenbrink, J and Chen, SC and Tanabe, TS and Sarikeçe, H and Meurs, P and Borusak, S and Samrat, R and Guan, G and Priemer, C and Osvatic, J and Séneca, J and Hausmann, B and Speth, DR and Selberherr, E and Wanek, W and Schleheck, D and Mussmann, M and Loy, A}, title = {Sulfoquinovose degradation by cow rumen microbiota.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag069}, pmid = {41892593}, issn = {1751-7370}, abstract = {Sulfoquinovose, a sulfonated sugar derived from the thylakoid membrane lipid sulfoquinovosyl diacylglycerol, is abundant in photosynthetic organisms and plays a key role in global sulfur cycling. Its degradation in nature is mediated by specialized bacteria, many of which rely on the enzyme sulfoquinovosidase (YihQ) to release sulfoquinovose from sulfoquinovosyl (diacyl)glycerol. Despite its ecological importance, the diversity and functional roles of sulfoquinovose-degrading microorganisms remain poorly characterized in natural environments. Here, we developed a yihQ-targeted amplicon sequencing approach to investigate the richness and distribution of SQ-degrading bacteria across selected environments. We revealed high richness of yihQ-containing microorganisms in the analyzed cow rumen samples, far exceeding that observed in human and mouse gut microbiomes, suggesting an important role of sulfoquinovose metabolism in ruminant digestion. Anoxic microcosm experiments with sulfoquinovose-amended rumen fluid revealed cooperative microbial degradation of sulfoquinovose to sulfide via isethionate cross-feeding. Amplicon sequencing and genome-resolved metagenomics and metatranscriptomics identified yet undescribed and uncultured sulfoquinovose-degrading taxa. Members of Caproiciproducens (Acutalibacteraceae), Candidatus Limivicinus (Oscillospiraceae), and Sphaerochaetaceae transcribed the isethionate-producing sulfo-transketolase pathway, whereas isethionate was likely respired by a Candidatus Mailhella bacterium (Desulfovibrionaceae). This study presents a functional gene-based assay for tracking environmental yihQ richness, highlights sulfoquinovose degradation as a central metabolic process in the cow rumen, describes previously unknown sulfoquinovose-metabolizing bacteria, and advances understanding of sulfur physiology in complex microbial communities.}, }
@article {pmid41892682, year = {2026}, author = {Murgina, O and Stafeeva, K and Karaulova, S and Vostrikova, A and Kononova, S and Chursina, D and Pozdeeva, S and Makogonova, A and Burakova, I and Pogorelova, S and Morozova, P and Smirnova, Y and Syromyatnikov, M and Shutikov, V and Mikhailov, E and Gureev, A}, title = {Probiotic Bacillus subtilis, but Not a Lactobacillus spp., Ameliorates Cognitive Impairment in a Mouse Model of LPS and Zidovudine-Induced Neuroinflammation.}, journal = {Brain sciences}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/brainsci16030340}, pmid = {41892682}, issn = {2076-3425}, support = {FZGW-2024-0003//Mikhail Syromyatnikov/ ; }, abstract = {Background/Objectives: The gut-brain axis is increasingly recognized as a critical modulator of cognitive function. This study investigated the neurotoxic effects of combined exposure to bacterial lipopolysaccharide (LPS) and the antiretroviral drug zidovudine (ZDV) in a mouse model, and evaluated the protective potential of two probiotic interventions: Bacillus subtilis and a mixture of lactobacilli. Methods: Cognitive function was assessed using the Morris water maze (MWM). Gut microbiota composition was analyzed by 16S rRNA sequencing, and intestinal morphology was examined histologically. Gene expression of neuroinflammatory markers and mitophagy-related genes in brain tissue was quantified by RT-PCR. Plasma levels of cell-free mitochondrial DNA (cf-mtDNA) were measured as a marker of mitochondrial damage. Results: Combined LPS + ZDV exposure induced systemic inflammation, impaired spatial memory, damaged the intestinal mucosa, and caused dysbiosis characterized by an increase in pro-inflammatory Muribaculaceae. In the brain, LPS + ZDV significantly upregulated Tnfa expression, confirming neuroinflammation. Bacillus subtilis administration prevented cognitive deficits, maintained Tnfa at control levels, and significantly reduced Il1b and Il6 expression compared to the LPS + ZDV group. This was accompanied by activation of the PINK1/PTEN-dependent mitophagy pathway, prevention of cf-mtDNA release, and restoration of gut microbial diversity. In contrast, the Lactobacilli mixture not only failed to improve outcomes but was associated with exacerbated intestinal damage, more pronounced cognitive dysfunction, and no reduction in neuroinflammatory markers. Conclusions: Combined exposure to LPS and ZDV induces gut-brain axis dysfunction characterized by neuroinflammation, cognitive impairment, intestinal damage, and dysbiosis. Bacillus subtilis effectively preserves cognitive function through activation of PINK1/PTEN-dependent mitophagy and suppression of neuroinflammation, highlighting its potential as a therapeutic candidate for cognitive impairments associated with gut-brain axis dysfunction. The contrasting effects of the lactobacilli mixture underscore the critical importance of strain-specificity in probiotic interventions.}, }
@article {pmid41893096, year = {2026}, author = {Fan, J and Liu, S and Zhang, H and Jin, C and Wu, N}, title = {Dysbiosis of the Gut-Lung Axis and Its Immune Correlates During Pulmonary Cryptococcus neoformans Infection.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/jof12030163}, pmid = {41893096}, issn = {2309-608X}, support = {Grant No. 2023YFC2506004//National Key Research and Development Program of China/ ; }, abstract = {Cryptococcus neoformans is a major fungal pathogen responsible for life-threatening meningitis, especially in immunocompromised individuals. Although the gut-lung axis is known to regulate immune responses in respiratory infections, its role in cryptococcosis remains unclear. This study aimed to define the dynamic changes in the gut and lung microbiota and their relationship with host immunity during C. neoformans infection. Using a mouse model, we found that pulmonary infection induced significant dysbiosis in both the lung and gut microbiota, marked by decreased beneficial commensals and increased opportunistic pathogens. Integrated analysis showed these microbial shifts were closely associated with distinct immune responses: lung dysbiosis correlated with a strong IL-17-mediated pulmonary inflammatory response, while gut dysbiosis was linked to systemic immune activation in the spleen. Functional metagenomic prediction further revealed widespread disruption in microbial metabolic pathways, including energy metabolism and biosynthesis, in both sites. Importantly, a positive correlation was observed between lung and gut dysbiosis, indicating an interconnected gut-lung axis during cryptococcosis. These findings demonstrate that C. neoformans infection causes coordinated disruptions in microbiota and immunity across the gut-lung axis, underscoring the microbiome as a critical modulator of host response and suggesting potential avenues for microbiome-targeted therapies.}, }
@article {pmid41893137, year = {2026}, author = {Francis, DV and Kishorkumar, M and Ahmed, ZFR and Neumann, EG and Kurup, SS}, title = {Molecular Advances and Sustainable Strategies in Mushroom Production for Food Security: A Review.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/jof12030205}, pmid = {41893137}, issn = {2309-608X}, support = {21R097//ARIFSID/ ; }, abstract = {Mushrooms offer a promising solution for sustainable food production due to their nutritional value, low resource requirements, and ability to grow in diverse environments. As interest in mushrooms grows, it is important to understand where current research is focused and where key gaps remain. A bibliometric analysis of 776 research articles indexed in Web of Science revealed a strong emphasis on yield, substrate reuse, and enzymatic degradation, but limited attention to molecular approaches, climate adaptation, and studies from arid regions such as the Middle East. Building on these findings, this review explores the ecological diversity of mushrooms and their adaptations across tropical, temperate, boreal, and arid ecosystems. It discusses the role of mycorrhizal and microbial interactions in nutrient cycling and environmental resilience, including desert truffle symbioses. Key pathways and genetic regulation involved in lignin degradation are outlined, along with recent advancements in transcriptomics, proteomics, genomics, metabolomics, and metagenomics that support improved cultivation and bioactive compound production. The review also addresses sustainable practices, such as microbiome integration and resource recycling, to enhance mushroom farming. The aim is to bring together ecological insights and molecular strategies to support sustainable mushroom production, particularly in regions facing resource and climate challenges.}, }
@article {pmid41893308, year = {2026}, author = {Yeerjiang, B and Manaer, T and Liu, X and Bieerdimulati, R and Nabi, X}, title = {Mechanistic Insights into Lactobacillus harbinensis and Other Probiotics Regulating Lipid Metabolism in T2DM Mice via the PPARγ-LXRα-NPC1L1 Signaling Pathway Based on Multi-Omics Analysis.}, journal = {Metabolites}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/metabo16030157}, pmid = {41893308}, issn = {2218-1989}, support = {No. 82260640//National Natural Science Foundation of China/ ; }, abstract = {Background/Objectives: Intestinal dysbiosis is a pivotal trigger of type 2 diabetes mellitus (T2DM). Our previous studies confirmed that composite probiotics derived from fermented camel milk (CPCM), containing Lactobacillus harbinensis and 13 other strains, can ameliorate glucose and lipid metabolism in T2DM mice by reshaping bile acid profiles, and its effect may be associated with the PPARγ-LXRα-NPC1L1 signaling pathway. Methods: Metagenomic analysis characterized alterations in intestinal microbiota structure and functional genes post-CPCM intervention, proteomic analysis detected changes in protein expression profiles related to glucose and lipid metabolism in mice, and Caco-2 cells were used for in vitro validation to clarify the regulatory effect of exopolysaccharides (EPS) (the active component of CPCM) on the PPARγ-LXRα-NPC1L1 signaling pathway. Results: The results showed that CPCM significantly improved glucose and lipid metabolism and remodeled the intestinal flora structure in mice, markedly enriching beneficial bacteria such as Lactobacillus and Akkermansia and enhancing the expression of functional genes related to the peroxisome proliferator-activated receptor (PPAR) signaling pathway and short-chain fatty acid synthesis in the microbiota. Proteomic analysis revealed that CPCM reversed the expression of key proteins involved in fatty acid oxidation and transport, thereby restoring the function of the PPAR signaling pathway. In vitro experiments validated that extracellular polysaccharides, the active component of CPCM, significantly upregulated the expression of PPARγ and liver X receptor α (LXRα) and inhibited the expression of Niemann-Pick C1-Like 1 (NPC1L1), a cholesterol absorption transporter, in Caco-2 cells. Conclusions: In conclusion, CPCM ameliorates glucose and lipid metabolic disorders in T2DM through multiple mechanisms: reshaping the intestinal probiotic community, enhancing its beneficial metabolic functions, restoring the activity of the PPARγ-LXRα signaling pathway, and subsequently downregulating NPC1L1.}, }
@article {pmid41893658, year = {2026}, author = {Lisjak, A and Correa Lopes, B and Pilla, R and Nemec, A and Lampreht Tratar, U and Suchodolski, JS and Tozon, N}, title = {Assessment of Fecal Microbiota in Healthy Dogs and Dogs with Cutaneous Mast Cell Tumors Treated with Electrochemotherapy Combined with Gene Electrotransfer of IL-12.}, journal = {Veterinary sciences}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/vetsci13030241}, pmid = {41893658}, issn = {2306-7381}, support = {P3-0428, P4-0053, P3-0003, and J4-2546//The Slovenian Research and Innovation Agency/ ; The microbiome research at the Gastrointestinal Laboratory at Texas A&amp;M University is in part funded through Purina PetCare Research Excellence Fund//Purina PetCare Research Excellence Fund/ ; }, abstract = {Cancer is a major health concern, with its incidence rate continuing to increase. There is growing interest in the microbiota and its role in carcinogenesis, as it significantly influences physiological and pathological processes. Various aspects of the microbiome have been shown to have both anti-tumor and pro-tumor effects. Advances in techniques such as high-throughput DNA sequencing have greatly improved our understanding of microbial populations in the human and canine gut. We aimed to (1) characterize the intestinal microbiota of healthy dogs and dogs with cutaneous mast cell tumors (MCTs), (2) assess changes in the intestinal microbiota of dogs undergoing electrochemotherapy (ECT) combined with gene electrotransfer (GET) of the IL-12 plasmid (IL-12), and (3) explore possible associations with the expression of immune markers Programmed cell death protein 1 (PD-1), Programmed death-ligand 1 (PD-L1), and Granzyme B (GZMB) in MCT tissue. Stool samples were collected from healthy dogs (n = 24) and dogs with MCTs (n = 24) before and after ECT and IL-12 GET. DNA was extracted from the samples, and shallow shotgun sequencing was performed. Immunohistochemistry was performed on the tumors to assess the expression of PD-1, PD-L1, and GZMB. The dysbiosis index, alpha diversity, and beta diversity did not differ between groups. Regarding microbial composition, Bifidobacterium animalis, Corynebacterium variabile, Lactobacillus johnsonii, Pediococcus pentosaceus, Streptococcus anginosus, Streptococcus equinus, Streptococcus intermedius, Clostridium thermobutyricum, Megasphaera elsdenii, and Anaerobiospirillum sp. were found in lower relative abundance in feces of dogs with MCTs, while Bacteroides togonis, Lactobacillus amylolyticus, Prevotella sp. CAG:279, and Megamonas hypermegale were more abundant compared to healthy dogs. Our study provides further insight into the composition of the gut microbiota in dogs with MCTs, where ECT and IL-12 GET did not lead to major shifts. We were unable to establish any association between the expression of immune markers and the microbiota.}, }
@article {pmid41893667, year = {2026}, author = {Karakaya, E and Satıcıoğlu, &#x130;B and Yarım, D and Güran, &#xd6; and Güran, C and Alpman, U and Atalan, G and Abay, S and Aydın, F}, title = {Culture and Metagenomic Insights into the Ear Microbiota in Dogs with Healthy Ears and Otitis Externa.}, journal = {Veterinary sciences}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/vetsci13030250}, pmid = {41893667}, issn = {2306-7381}, support = {TSA-2022-12342 and THD-2024-13751//Erciyes University/ ; }, abstract = {The canine ear microbiota plays an important role in ear health, and dysbiosis is associated with otitis externa (OE) and antimicrobial resistance (AMR). This study aims to investigate the ear microbiota of dogs with healthy ears and OE using bacterial culture-based methods and shotgun metagenomic sequencing, and to screen for AMR and virulence-associated genetic signatures. Ear swab specimens from 100 healthy and 100 OE-affected dogs were analyzed. The isolates obtained via bacterial culture were identified by MALDI-TOF MS and 16S rRNA sequencing. Metagenomic analysis was performed via Illumina shotgun sequencing. The most commonly defined species in healthy dogs in culture were Staphylococcus pseudintermedius (24.5%) and Staphylococcus epidermidis (5.7%); in dogs with OE, the most commonly defined species were S. pseudintermedius (30.5%), and Clostridium perfringens (4.5%). In healthy samples, metagenomic analysis revealed higher relative abundances of Bacteroides fragilis (15.8%) and Ezakiella coagulans (8.2%), while S. pseudintermedius (38.7%) dominated in OE. AMR profiling demonstrated diverse resistance determinants, including efflux pump systems and methicillin resistance-associated genes. In conclusion, the present study shows that S. pseudintermedius is a predominant member of canine ear microbiota, with higher presence in OE highlighting microbial shifts, and demonstrates that combining culture and metagenomic analyses provides a concise view of microbial communities and clinical relevance.}, }
@article {pmid41893692, year = {2026}, author = {Shehla, S and Obaid, MK and Niaz, S and Khan, MA and Ahmad, AA and Abdel-Maksoud, MA and Alamri, A and Alrokayan, S and Shoaib, M and Shams, S and Ren, Q}, title = {Shotgun Metagenomics Reveals Microbial Diversity, Resistome, and Plasmidome in Dairy Cattle Feces.}, journal = {Veterinary sciences}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/vetsci13030275}, pmid = {41893692}, issn = {2306-7381}, support = {ORF-RC-2026-2600//King Saud University/ ; }, abstract = {Fecal microbiota are shaped by upstream digestive processes and reflect the outcome of host-microbe interactions, including the resistant microbial fraction that survives to be excreted. This is particularly crucial for assessing zoonotic risks and environmental contamination, as feces are the primary source of dissemination, which is considered an emerging One Health threat. Therefore, we conducted a pilot study to obtain the exploratory findings regarding the cattle GIT microbial composition, potential resistome, and their transmission drivers, such as plasmids, using metagenomic analysis from different districts in Khyber Pakhtunkhwa (KP) province, Pakistan. For this purpose, a total of 150 fecal samples (50 from each district) of healthy cattle were collected from various farms in Mardan (FC1), Peshawar (FC2), and Dera Ismail Khan (FC3) districts. Total DNA from each sample was extracted, pooled (FC1, FC2, and FC3), and sequenced via the Illumina platform. Bacteria were the highly abundant kingdom, while Pseudomonadota and Bacillota were dominant phyla in all samples. Caryophanon latum and Escherichia coli were highly abundant at the species level. A large resistome (40-49 genes), including critical genes, such as tet(X), blaOXA-427, and plasmidomes (16-22), such as IncF, was detected in the samples. The prominence of certain commensal or opportunistic pathogens in the fecal microbiota may indicate the presence of sub-clinical gastrointestinal disruptions or disease that may affect cattle herds. The fecal resistome is extensive, identifying dairy cattle in these regions as important reservoirs for AMR genes capable of spreading via HGT. This pilot study establishes that the fecal microbiota of dairy cattle in this region are not merely a waste product but a complex ecosystem, rich in microbiota of One Health significance.}, }
@article {pmid41893724, year = {2026}, author = {Qiu, Q and Gong, T and Du, L and Li, W and Hu, Y and Li, D and Zhou, C and Liu, W}, title = {Comparative Analysis of Microbial Community Structure and Function in the Gut of South China Tigers Under Different Dietary Treatments.}, journal = {Veterinary sciences}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/vetsci13030307}, pmid = {41893724}, issn = {2306-7381}, support = {2110499//Diagnosis and Treatment of Genetic Diseases and Training for Stereotypic Behaviors in South China Tigers at Changsha Ecological Zoo/ ; 2110499//Artificial breeding of Reeves's pheasant (Syrmaticus reevesii) at Changsha Ecological Zoo/ ; }, abstract = {The gut microbiota is a crucial component of a tiger's health and plays a significant role in adapting to changes in food and the environment. Although extensive studies have been carried out on the gut microbiota of tigers, investigating the responses of gut microbial composition and function to preadaptation to wild predation patterns under captive conditions is particularly significant for South China tigers, given that it is the only tiger subspecies existing solely in captive settings at present. Here, we performed shotgun metagenomic sequencing for a comprehensive analysis of the gut microbiota of South China tigers assigned to two dietary groups (live prey group, LP group; frozen meat group, FM group), thereby generating abundant valuable data for this endangered subspecies. The results indicated that the core intestinal microbial composition was similar between the two dietary groups. Differential analysis revealed associations between dietary treatments and microbial abundance in the intestines of South China tigers. Functional gene analysis revealed that the LP group exhibited upregulation of genes and pathways related to antimicrobial resistance, bacterial infection-related disease, cell motility and proliferation, while the FM group displayed efficient energy metabolism. A total of 1251 antibiotic resistance genes (ARGs) were identified in the gut microbiome of South China tigers. The core resistome mainly included resistance to peptides, glycopeptides, tetracyclines, fluoroquinolones, and macrolides. In addition, the differences in ARGs between the LP group and FM group may be related to a broader range of animal tissues of live prey and the processing conditions of frozen meat. In summary, although feeding live prey did not change the core framework of the gut microbiota in South China tigers, it was associated with differences in microbial abundance, metabolic pathways, and antibiotic resistance gene profiles.}, }
@article {pmid41894043, year = {2026}, author = {Tian, X and Feng, Y and Wang, C and Zhao, W and Xue, L and Zhu, L and Ji, X and Wang, H and Gu, Y and Jiang, Q and Zhang, J}, title = {Analysis of the characteristics of rumen microorganisms and their metabolites and plasma metabolites in crossbred beef cattle at different stages.}, journal = {Veterinary research communications}, volume = {50}, number = {3}, pages = {}, pmid = {41894043}, issn = {1573-7446}, support = {2021BEF01002//Major Project of Science and Technology ofNingxia Autonomous Region/ ; 2023AAC03050//Natural Science Foundation of Ningxia Hui Autonomous Region/ ; }, }
@article {pmid41894133, year = {2026}, author = {Zhang, X and Chen, L and Wang, F and Xu, X and Wu, Y and Xu, J and Xu, Y and He, X}, title = {Torque teno virus in the lower respiratory tract: association with immunosuppression but not mortality in severe pneumonia-a multicenter retrospective cohort study.}, journal = {European journal of clinical microbiology &amp; infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41894133}, issn = {1435-4373}, support = {2024C3186//Key Research and Development Program of Zhejiang Province/ ; GZY-ZJ-KJ-24030//Major Project of National-Zhejiang Provincial Administration of Traditional Chinese Medicine/ ; }, }
@article {pmid41894264, year = {2026}, author = {Yu, Y and Hong, S and Wang, Z and Li, S and Zhang, S}, title = {Leptospirosis-induced diffuse alveolar hemorrhage: A rare case report from a non-epidemic area and literature review.}, journal = {Medicine}, volume = {105}, number = {13}, pages = {e48131}, doi = {10.1097/MD.0000000000048131}, pmid = {41894264}, issn = {1536-5964}, support = {No. LY21H100002//Zhejiang Natural Science Foundation Project/ ; No.2024C31025//Science and Technology Plan Project of zhoushan/ ; }, mesh = {Humans ; Female ; *Leptospirosis/complications/diagnosis/drug therapy ; Aged ; *Hemorrhage/etiology/diagnosis/microbiology ; *Pulmonary Alveoli/pathology ; *Lung Diseases/etiology/diagnosis/microbiology ; Shock, Septic/etiology ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {RATIONALE: Leptospirosis is an uncommon cause of severe pneumonia and diffuse alveolar hemorrhage (DAH), particularly in non-endemic areas, posing a significant diagnostic challenge. This case highlights the critical role of advanced molecular diagnostics in identifying this rare and life-threatening presentation.<br><br>PATIENT CONCERNS: A 65-year-old woman presented with an acute onset of high fever, chest tightness, and rapidly progressive shortness of breath.<br><br>DIAGNOSES: The patient was initially misdiagnosed with severe community-acquired pneumonia. She subsequently developed septic shock and multiple organ dysfunction syndrome. A definitive diagnosis of leptospirosis-induced DAH was confirmed through metagenomic next-generation sequencing, reverse transcription quantitative PCR, and subsequent seroconversion shown by immunoglobulin M enzyme-linked immunosorbent assay.<br><br>INTERVENTIONS: Upon diagnosis, targeted antimicrobial therapy with intravenous penicillin was initiated. Supportive care included management of septic shock and lung-protective ventilation for concomitant acute respiratory distress syndrome.<br><br>OUTCOMES: Following the confirmation of leptospirosis and initiation of targeted treatment, the patient's condition gradually stabilized. After a course of intensive care, she made a full recovery and was successfully discharged.<br><br>LESSONS: This case underscores that leptospirosis can present as fulminant DAH even in non-endemic regions. A high index of suspicion, aided by epidemiological clues and the rapid application of metagenomic next-generation sequencing/reverse transcription quantitative PCR, is crucial for timely diagnosis. Prompt targeted antimicrobial therapy combined with intensive organ support is essential for a favorable outcome in severe cases.}, }
@article {pmid41894564, year = {2026}, author = {McCartin, LJ and Vohsen, SA and Wood, AL and Horowitz, J and Orozco-Juarbe, JJ and Pittoors, N and Morrissey, D and Vaga, CF and Hansel, CM and Collins, AG and Quattrini, AM and Herrera, S}, title = {Accounting for Intra- and Intergenomic Sequence Variation in Reference Barcodes Improves eDNA Metabarcoding Biodiversity Assessment.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70130}, doi = {10.1111/1755-0998.70130}, pmid = {41894564}, issn = {1755-0998}, support = {NA18OAR0110289//NOAA Ocean Exploration/ ; NA21OAR0110202//NOAA Ocean Exploration/ ; NA18NOS4780166//National Centers for Coastal Ocean Science/ ; //Smithsonian Institution/ ; //Smithsonian Women's Committee/ ; //Bureau of Ocean Energy Management/ ; 2000013668//National Academies of Sciences, Engineering, and Medicine/ ; //NOAA Fisheries Office of Science and Technology/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Animals ; *DNA, Environmental/genetics ; Puerto Rico ; *Anthozoa/genetics/classification ; *Genetic Variation ; *Metagenomics/methods ; RNA, Ribosomal, 28S/genetics ; }, abstract = {Environmental DNA (eDNA) metabarcoding can rapidly characterise biodiversity, yet its accuracy and effectiveness are limited by incomplete DNA barcode reference databases. We evaluated how comprehensive reference databases that include sequence variation within genomes (intragenomic) and across individuals and species (intergenomic) improve eDNA-based biodiversity assessments. We collected coral tissue and water samples at deep sites offshore Puerto Rico for reference barcoding and eDNA metabarcoding. Genome skimming coral specimens yielded 28S barcodes for 314 of 346 samples (90.8%) and revealed divergent intragenomic 28S lineages in multiple octocoral families. Incorporating local reference barcodes substantially changed ASV taxonomic classifications: 22 ASVs (8.9%) gained genus-level resolution, 19 ASVs (7.7%) were reassigned to different genera, and 14 ASVs (5.7%) lost incorrect genus-level classifications. Thus, incomplete reference databases produce not only unclassified ASVs but also false positive detections and ecologically meaningful misclassifications. When intragenomic 28S lineages were excluded from the reference database, 18 ASVs (7.4%) could not be classified to family or genus, demonstrating that unrecognised intragenomic variation can be mistaken for unsampled taxa. Integrating reference genome skimming and eDNA metabarcoding expanded known coral family richness by 36% at depths shallower than 1000 m and by 181% at depths greater than 1000 m. eDNA also detected two coral families previously unknown off Puerto Rico and nearby islands, underscoring its potential for biodiversity discovery.}, }
@article {pmid41894872, year = {2026}, author = {Chen, H and Chai, Z and Chen, J and Song, C and Zheng, M}, title = {Anthraquinone-2-sulfonate enhances endogenous denitrification and phosphorus removal: Electron shuttle-mediated syntrophic partnerships.}, journal = {Water research}, volume = {298}, number = {}, pages = {125783}, doi = {10.1016/j.watres.2026.125783}, pmid = {41894872}, issn = {1879-2448}, abstract = {Endogenous denitrification (EnD) and denitrifying phosphorus removal (DPR) offer distinct advantages for low-carbon wastewater treatment, yet the nutrient removal performance is often constrained by inefficient electron transfer and nitrite/free nitrous acid (FNA) inhibition. Here, we demonstrate that anthraquinone-2-sulfonate (AQS) acts as an effective redox mediator to overcome these bottlenecks. With nitrate (NO3[-]-N) as the electron acceptor, the addition of 0.05 mmol/L AQS significantly amplified the electron transfer system activity (ETSA) by 3.66-fold. Consequently, this enhancement promoted the NO3[-]-N removal rate to 25.90 mg/(g VSS·h) (12.65-fold increase) and increased the phosphorus uptake rate to 3.69 mg/(g VSS·h) (1.95-fold improvement), achieving removal efficiencies of 96.22±1.00 % and 96.03±2.98 % for phosphorus and nitrogen, respectively. Moreover, when nitrite (NO2[-]-N) served as the electron acceptor, AQS enhanced the phosphorus uptake rate and nitrogen removal rate by 1.69-fold and 1.54-fold, respectively. Microbial analysis revealed a robust syntrophic partnership wherein Thauera, Candidatus Competibacter and Defluviicoccus (functioning as denitrifying glycogen-accumulating organisms) efficiently reduced NO3[-]-N to NO2[-]-N, which was subsequently scavenged by Dechloromonas and Candidatus Accumulibacter clade Ⅱ (functioning as denitrifying polyphosphate-accumulating organisms) for coupled phosphorus uptake. Metagenomic analysis further indicated that AQS facilitated electron transfer from Complexes I/Ⅱ to nitrate reductase and Complex Ⅲ, accelerating NO2[-]-N generation while alleviating FNA toxicity via coupled electron transfer from Cyt c to nitrite reductase. Crucially, this accelerated electron flux potentially intensified the proton motive force, suggesting an enhanced capacity for ATP generation to fuel the upregulation of phosphate transport (pit/pst) and polyphosphate synthesis (ppk) genes. These findings highlight AQS as a promising strategy to regulate electron transfer kinetics and metabolic coupling for advanced nutrient removal.}, }
@article {pmid41894881, year = {2026}, author = {Zhao, Y and Li, Y and Zheng, Y and Yan, P and Lai, Y and Wang, X and Zhuang, LL and Zhang, J}, title = {Enhanced co-removal of nutrients and glyphosate from rural sewage in siphon-driven constructed wetlands: Optimization and mechanisms.}, journal = {Water research}, volume = {298}, number = {}, pages = {125812}, doi = {10.1016/j.watres.2026.125812}, pmid = {41894881}, issn = {1879-2448}, abstract = {Constructed wetlands (CWs) often suffer from limited carbon/oxygen availability and poorly controlled redox conditions, constraining pollutant removal from rural sewage. Hence, siphon-driven CWs (S-CWs) were optimized for the co-removal of the typical rural pollutant glyphosate (N-(phosphonomethyl)glycine, PMG) and typical wastewater pollutants (carbon (C), nitrogen (N), phosphorus (P)). S-CWs exhibited strong PMG resilience, tolerating up to 8 mg/L, and achieved 50.91-92.14%, 50.93-56.82% and 96.19-97.18% for PMG, N and P removal, respectively. These results indicated superior performance compared with unaerated and aerated CWs. Mechanistic analysis showed that PMG removal was dominated by biodegradation in the aerobic, carbon-enriched inlet area of S-CWs. This process was driven by genera such as Alcaligenes and Geobacillus, and enzymes like PhnI, PhnJ via aminomethylphosphonic acid (AMPA) and C-P lyase pathways, as confirmed by metagenomics and AlphaFold 3 predictions. PMG transiently inhibited N removal by suppressing denitrification but not nitrification. However, microbial adaptation over 135 days restored N removal along the first 50% pathway, even under high PMG stress (10 mg/L). In contrast, P removal was more persistently inhibited throughout the system, as the additional PMG-derived P increased total P load and accelerated substrate adsorption saturation. Long-term operation confirmed the robustness of S-CWs, including reduced effluent toxicity, healthier plant growth, lower oxidative stress, and minimal clogging (only 1.40-13.53% porosity decline). These observations highlight the hydraulic stability and long-term suitability of S-CWs for treating PMG-laden rural wastewater.}, }
@article {pmid41881444, year = {2026}, author = {Kringeland, GD and Tangedal, S and Julian, D and Paytuví-Gallart, A and Sanseverino, W and Bertelsen, RJ and Husebø, GR and Knudsen, KS and Lehmann, S and Nielsen, R and Eagan, TML}, title = {Antimicrobial resistance genes and antibiotic use in chronic lung disease: a bronchoscopy study of the lower airways microbiome.}, journal = {BMJ open respiratory research}, volume = {13}, number = {1}, pages = {}, doi = {10.1136/bmjresp-2025-003864}, pmid = {41881444}, issn = {2052-4439}, mesh = {Humans ; Male ; Female ; Cross-Sectional Studies ; Bronchoscopy ; Middle Aged ; Aged ; *Anti-Bacterial Agents/therapeutic use ; *Microbiota/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; Pulmonary Disease, Chronic Obstructive/microbiology/drug therapy ; Case-Control Studies ; *Lung Diseases/microbiology/drug therapy ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Chronic Disease ; }, abstract = {BACKGROUND: Antimicrobial resistance genes (ARGs) in the respiratory microbiome are poorly characterised. We compared the presence of ARGs in healthy controls with patients with chronic lung disease in a cross-sectional study, adjusted for time since antibiotic use.<br><br>METHODS: Bronchoalveolar lavage was collected from 100 controls, and 93 patients with chronic obstructive pulmonary disease (COPD), 13 with asthma, 34 with sarcoidosis, 12 with idiopathic pulmonary fibrosis (IPF) and 11 patients with unclassifiable interstitial lung disease (uILD). Participants had not used antibiotics 14 days prior to sampling. Shotgun metagenomic sequencing was performed with Illumina NovaSeq. ARGs were identified using the National Database of Antibiotic-Resistant Organisms. Sample reads were normalised to counts per million.<br><br>RESULTS: In total, 38% of controls had at least one ARG, compared with 51%, 39%, 65% and 83% of patients with COPD, asthma, sarcoidosis and IPF, respectively (p=0.01). ARGs against tetracycline (33%) were the most common ARG class, followed by beta-lactam and macrolide resistance (both 26%). In a logistic regression analysis adjusted for sex, age, body composition, smoking and antibiotic use, the OR (95%&#x2009;CI) for having ARGs in the lower airways was 1.30 (0.70 to 2.41) in COPD, 1.00 (0.29 to 3.52) in asthma, 3.52 (1.40 to 8.83) in sarcoidosis, 6.40 (1.25 to 32.73) in IPF and 3.27 (0.76 to 14.16) in uILD compared with controls. Overall mean (SD) ARG counts per million were 403.8 (537.7) in the 35 subjects who had used antibiotics &#x2264;3 months before bronchoscopy, compared with 197.6 (355.9) in the 228 subjects without (p=0.02).<br><br>CONCLUSION: The presence of ARGs in the lower airways microbiome was significantly higher in patients with sarcoidosis and IPF than in controls. The counts per million for ARGs were significantly associated with recent antibiotic use.}, }
@article {pmid41881804, year = {2026}, author = {Gutiérrez, J and Vergara-Amado, J and Martorell, C and Navedo, JG and Wille, M and Guajardo-Leiva, S and Castro-Nallar, E and Verdugo, C}, title = {Functional Shifts in the Gut DNA Virome in a Long-Distance Migratory Shorebird During the Pre-Migratory Fattening.}, journal = {Molecular ecology}, volume = {35}, number = {6}, pages = {e70315}, doi = {10.1111/mec.70315}, pmid = {41881804}, issn = {1365-294X}, support = {FONDECYT N&#xb0;1191769//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; ANILLO ATE220062//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Doctoral scholarship N&#xb0;21201700//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; //The Pathogen Watchtower Program (Biotia Inc. &amp; The Rockefeller Foundation)/ ; //Universidad Austral de Chile/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Charadriiformes/virology/physiology ; *Animal Migration ; *Virome/genetics ; Feces/virology ; Metagenomics ; Metagenome ; }, abstract = {Migration represents one of the most energetically demanding phases in the life cycle of long-distance migratory birds. Pre-migratory fattening is a critical preparatory stage characterized by hyperphagia, rapid fat accumulation, organ remodelling, and immune modulation. Although the gut microbiome has been recognized as a key contributor to these physiological adaptations, the role of the gut virome remains poorly understood. In this study, the diversity, functional potential, and temporal dynamics of the gut DNA virome in a trans-hemispheric migratory shorebird, the Hudsonian godwit (Limosa haemastica), were assessed during pre-migratory fattening. Adult individuals were maintained under controlled aviary conditions for 15 weeks during the preparation for northbound migration, and faecal samples were collected at two distinct physiological time points: at the beginning and the end of pre-migratory fattening. Shotgun metagenomic sequencing revealed 798 high-quality viral operational taxonomic units (vOTUs), the majority of which were bacteriophages (92%). Potential functional annotation identified auxiliary metabolic genes (AMGs) associated with nucleotide metabolism, redox balance, and host adaptation. Although overall gut virome diversity did not differ between stages, significant changes in potential functional profiles of phages were observed, especially during the final stage of fattening when energy demands are at their highest. In addition to bacteriophages, we report two divergent adenoviruses potentially associated with the Siadenovirus and Aviadenovirus genera. These findings suggest that dynamic viral communities may play underrecognized roles in supporting host physiology during energetically costly life stages.}, }
@article {pmid41881873, year = {2026}, author = {Zhao, C and Yao, R and Xiong, M and Liu, X and Yu, J and Jumpponen, A and Romantschuk, M and Ur Rahman, S and Hui, N}, title = {Microbial exposure and antibiotic resistance gene dynamics shift between indoor and outdoor school activities.}, journal = {Ecotoxicology and environmental safety}, volume = {314}, number = {}, pages = {120044}, doi = {10.1016/j.ecoenv.2026.120044}, pmid = {41881873}, issn = {1090-2414}, abstract = {School curricular and extracurricular activities, including indoor study and sports like basketball, significantly impact adolescent physical and mental health. However, their effects on hand and nasal microbiomes, particularly regarding antibiotic resistance genes (ARGs), are underexplored. Here, we recruited 42 junior middle school students in Shanghai to investigate microbial composition and ARGs, collecting 336 hand and nasal samples after handwashing, indoor study, indoor basketball, and outdoor basketball. Our results showed that playing basketball either indoors or outdoors increased microbial diversity in nasal cavities and on hands, compared to post-handwashing. Notably, nasal microbiomes were predominantly derived from hand microbiomes, regardless of the activity performed. Among ARGs, macB genes were more abundant after outdoor basketball than indoor basketball, with this difference more pronounced in nasal cavities than on hands. Metagenomic sequencing identified Aureimonas phyllosphaerae as the primary macB gene host. Although this bacterium harbors ARGs, it is non-pathogenic and lacks mobile genetic elements, indicating a low potential for horizontal gene transfer or interspecies ARG transmission. Collectively, even though students may be exposed to more ARGs during outdoor activities, the health risks are likely minimal because the observed ARG bacteria are non-pathogenic and the likelihood of interspecies ARG transmission is low.}, }
@article {pmid41881888, year = {2026}, author = {Tuveng, TR and Hagen, LH and Rese, M and Eijsink, VGH and Arntzen, M&#xd8;}, title = {Meta-omics profiling of denitrifying bacterial communities with lignin as carbon source.}, journal = {Microbiological research}, volume = {308}, number = {}, pages = {128503}, doi = {10.1016/j.micres.2026.128503}, pmid = {41881888}, issn = {1618-0623}, abstract = {Lignin is the most abundant renewable source of aromatic carbon and its microbial depolymerization and metabolism under aerobic conditions is well studied. However, lignin breakdown in the absence of oxygen remains poorly understood. In this study, we established long-term bacterial enrichment cultures supplied with diverse lignin preparations as the sole carbon source under denitrifying conditions. Denitrification dynamics were followed by monitoring nitrogenous gases. Metagenomics analysis of eight enrichments involving five lignins recovered 62 metagenome-assembled genomes (MAGs), several of which encoded enzymes for both denitrification and anaerobic metabolism of aromatic compounds. Quantitative metaproteomics confirmed expression of such enzymes and additionally showed that several MAGs expressed multiple oxidoreductases and uncharacterised proteins that are potential candidates for involvement in lignin modification. The detection of several oxygen-dependent oxidoreductases despite anaerobic conditions prompts intriguing discussion of potential mechanistic explanations. This systems-level study expands our understanding of bacterial processing of lignin-associated carbon in anaerobic environments and suggests enzymatic targets for further exploration of lignin depolymerization under oxygen-limited conditions.}, }
@article {pmid41882035, year = {2026}, author = {Kumar, M and Ansari, WA and Singh, A and Kumar, SC and Zeyad, MT and Chakdar, H and Farooqi, MS and Sharma, A and Srivastava, S and Jha, GK and Srivastava, AK}, title = {Impact of genotype and soil fertility on wheat rhizosphere microbiota under the trans-gangetic plain.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-36646-4}, pmid = {41882035}, issn = {2045-2322}, support = {2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; }, abstract = {The effects of genotypes (HD3086 and PBW343) and soil physicochemical properties on the wheat rhizospheric bacterial communities along the trans Indo-Gangetic plains were studied. The trans-Indo-Gangetic Plains of India are one of the areas in the country where wheat is grown the most. Despite the agricultural significance of this region, extensive studies on the rhizosphere microbial abundance and community structure related to wheat cultivation in this area are still lacking. To address this knowledge gap, the present study was undertaken to characterize the rhizosphere microbiome using full-length 16 S rRNA-based metagenomic profiling, implementing universal primers, tailed with PacBio Sequel II barcode sequences, providing new insights into microbial dynamics across this major wheat-producing landscape. Statistical analysis revealed significant differences in both abundance and diversity among the different soil samples and wheat genotypes. Four phyla exhibited significant differences in relative abundance between the genotypes (p < 0.05): Proteobacteria (p = 0.002), Planctomycetes (p = 0.000), Verrucomicrobia (p = 0.000), and Firmicutes (p = 0.030). The number of genera identified in genotype HD3086 across all locations was 421, while it was 322 for genotype PBW343. There were 251 genera found common, with 170 genera exclusively present in HD3086 and 71 in PBW343. Significant differences were observed in the relative abundance of eighteen genera (p < 0.05) between the genotypes; some of them include Luteolibacter, Gemmata, Pseudomonas, Stenotrophobacter, Pseudarthrobacter, Devosia, Lacibacter, Gaiella, Luteimonas, and Nitrosospira. Correlation analysis indicated significant associations between microbial diversity and soil parameters like pH, total and available nitrogen, potassium, phosphorus, iron, and organic carbon for both varieties. Core taxa analysis revealed 27 core taxa across both genotypes. The study highlights significant genotype effects on rhizosphere microbiomes, with implications for soil health and crop management strategies.}, }
@article {pmid41882344, year = {2026}, author = {Muammar, A and Retnaningrum, E and Daryono, BS and Prijambada, ID and Yashima, Y and Peterbauer, C}, title = {A fast workflow to explore active enzymes from environmental samples through functional metagenomics.}, journal = {Applied microbiology and biotechnology}, volume = {110}, number = {1}, pages = {}, pmid = {41882344}, issn = {1432-0614}, mesh = {*Metagenomics/methods ; Feces/microbiology ; Workflow ; Animals ; *Cellulases/genetics/metabolism ; Indonesia ; Multiplex Polymerase Chain Reaction ; Gene Library ; Metagenome ; }, abstract = {Functional metagenomics has emerged as an effective tool for discovering novel enzymes directly from environmental samples, overcoming the limitations of traditional culture-based methods. In this study, we used a functional metagenomic approach on stool samples from Axis kuhlii, an endemic deer species from Indonesia, to identify active cellulases. We created an efficient workflow for expression of metagenomic sequences directly in Komagatella phaffii by combining metagenomic sequencing to investigate enzyme diversity, multiplex PCR to build a genes library, and rolling circle amplification (RCA) to streamline the cloning process, eliminating the need for intermediate Escherichia coli transformation and propagation steps. Furthermore, a semi-high-throughput screening method was used to evaluate multiple samples at once, allowing for the rapid identification of active enzymes. Using this approach, we discovered five endoglucanases and three β-glucosidases with confirmed enzyme activity. This study shows that functional metagenomics can bridge the gap between computational predictions and experimental validation, providing a reliable platform for enzyme discovery and characterization from complex environmental microbiomes. KEY POINTS: • We established K. phaffii expression of metagenomic sequences via multiplex PCR and RCA. • This approach links metagenomic and activity screening to enable enzyme discovery. • Eight active cellulases were obtained from environmental samples through this approach.}, }
@article {pmid41882399, year = {2026}, author = {Çilkiz, M}, title = {Microbial Biotechnology in Agriculture.}, journal = {Progress in molecular and subcellular biology}, volume = {62}, number = {}, pages = {251-306}, pmid = {41882399}, issn = {0079-6484}, mesh = {*Agriculture/methods ; *Biotechnology/methods ; Soil Microbiology ; Metagenomics/methods ; Crops, Agricultural/growth &amp; development/microbiology ; Metabolomics/methods ; Fertilizers ; }, abstract = {Global food security has become one of the greatest challenges of the twenty-first century due to the rapidly growing world population's food demands and environmental threats such as climate change, soil erosion, and the depletion of freshwater resources. The extensive use of chemical fertilizers and pesticides throughout conventional agriculture has increased productivity significantly, but it has additionally resulted in major ecological and socioeconomic problems, such as soil acidity, groundwater resource pollution, and decreased biodiversity. In this regard, microbial biotechnology is a particularly noteworthy technique that improves agricultural production while promoting environmental sustainability, maintaining ecological balance, and making effective use of resources. This application makes use of microorganisms to enhance soil health and structure, promote plant growth, and minimize both abiotic and biotic stresses. Microbial applications include nitrogen fixation, as well as biofertilizers that reduce the dependency on synthetic materials and biopesticides. Microbial consortia and biostimulants that improve plant physiology by producing phytohormones produce more dependable and durable consequences in the field. Metagenomics and metabolomics are the two types of omic technologies used in these areas of study that provide a thorough description of the variety and roles of microorganisms. Furthermore, the intentional production of microbes targeted at specific organisms has been made practical via synthetic biology and gene editing techniques. In-depth case studies performed in several countries reveal that microbial technologies significantly reduced expenses and improved soil production, advancing the sustainable development goals. Nevertheless, there are several barriers to the widespread use of microbial biotechnology in agriculture. These include unpredictable conditions in the fields, strict regulations, especially related to genetically modified organisms' problems with product quality, and farmers' insufficient understanding. Microbial biotechnology aims to accomplish its full potential as an advancement in technology and as an essential aspect of resource-efficient and environmentally friendly agricultural systems via responsible innovation, adaptable regulations, and worldwide cooperation.}, }
@article {pmid41882401, year = {2026}, author = {Erözden, AA and Tavşanlı, N and Çalışkan, M and Arıkan, M}, title = {Microbial Omics.}, journal = {Progress in molecular and subcellular biology}, volume = {62}, number = {}, pages = {333-366}, pmid = {41882401}, issn = {0079-6484}, mesh = {*Metabolomics/methods ; *Proteomics/methods ; *Genomics/methods ; Metagenomics/methods ; *Computational Biology/methods ; Transcriptome ; Microbiota ; *Bacteria/genetics/metabolism ; }, abstract = {Omics technologies have revolutionized research across diverse fields, and their increasing use in microbiology has provided new opportunities for understanding microbial life. These methods enable detailed investigation of the molecular biology of individual organisms as well as the complex interactions within microbial communities. In this chapter, we describe key single-organism omics approaches, including genomics, transcriptomics, proteomics, and metabolomics, as well as meta-omics techniques such as metagenomics, metatranscriptomics, metaproteomics, and meta-metabolomics. We also discuss integrative multi-omics strategies for studying microbial ecosystems. For each omics method, we outline its main features, experimental and bioinformatic workflows, major applications, and commonly used computational tools, thereby providing a practical guide for researchers aiming to explore microbial structure, function and interactions at multiple molecular levels.}, }
@article {pmid41882608, year = {2026}, author = {Chen, M and Wu, Z and Du, Y and Jiang, J and Feng, J}, title = {Construction of caries risk assessment scale and oral microecology analysis of adolescents with fixed orthodontic treatment.}, journal = {BMC oral health}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12903-026-08114-y}, pmid = {41882608}, issn = {1472-6831}, }
@article {pmid41882673, year = {2026}, author = {Deng, J and Qiu, Q and Ye, S and Yu, J and Yao, D and Deng, H and Wang, C and Han, L and Deng, Y and Chen, Y and Liu, Y and Liu, C and Shang, X and Fang, X and Lu, C}, title = {Disentangling environmental and disease-specific signatures in the gut microbiome of psoriasis: discovery of Fimenecus sp. as a novel biomarker and characterization of the gut virome.}, journal = {Journal of translational medicine}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12967-026-08013-4}, pmid = {41882673}, issn = {1479-5876}, abstract = {BACKGROUND: The contribution of the gut microbiome to the pathogenesis of psoriasis remains a subject of debate, with inconsistent findings across studies likely confounded by environmental factors. This study aimed to statistically disentangle the effects of a shared household environment from disease-specific microbial signatures in psoriasis. Our objective was to identify novel, multi-kingdom biomarkers, encompassing bacteria and viruses, that hold significant diagnostic and therapeutic potential.<br><br>METHODS: We conducted a nested case-control study, performing shotgun metagenomic sequencing on stool samples from 143 participants. The cohort comprised 98 psoriasis patients, 28 healthy cohabiting relatives, and 17 unrelated healthy controls. A comprehensive multi-kingdom analysis of bacteria, viruses, and their associated metabolic pathways was implemented. To ensure the robustness of our findings, a two-stage discovery-validation strategy was employed to identify distinct microbial features associated with psoriasis.<br><br>RESULTS: Our analysis revealed that the shared household environment was the predominant factor shaping the overall gut microbiome structure. Despite this strong confounding effect, we successfully identified a novel bacterial species, Fimenecus sp000432435, as a robust biomarker for psoriasis, achieving an area under the curve (AUC) of 0.84. Genomic functional prediction indicated that this species encodes pathways with the potential for B-vitamin and secondary bile acid biosynthesis. Furthermore, characterization of the gut virome identified five disease-associated bacteriophages. Among these, vBin_422 exhibited a significant negative correlation with the abundance of Fimenecus sp000432435, suggesting a potential ecological interaction. Notably, the biotin biosynthesis pathway was negatively correlated with disease severity, whereas specific viral taxa showed a positive correlation with systemic inflammatory markers within the patient cohort.<br><br>CONCLUSIONS: Controlling for environmental confounders reveals that psoriasis is associated with sparse but distinctmicrobial signatures rather than broad dysbiosis. Fimenecus sp000432435 is a promising candidate for non-invasive diagnostics, while the characterized virome opens new therapeutic avenues targeting bacteriophage-bacteria interactions in psoriasis management.<br><br>TRIAL REGISTRATION: ChiCTR-IOR-17011075. Registered 6 April 2017, http://www.chictr.org.cn/showproj.aspx?proj=17334.}, }
@article {pmid41882801, year = {2026}, author = {Langlois, A and Duplessis, M and Ronholm, J and Vincent, AT and Poulin-Laprade, D and Petri, RM}, title = {Impact of differential dietary concentrations of cobalt, manganese and zinc on gastrointestinal microbiome and resistome of lactating dairy cattle.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00554-9}, pmid = {41882801}, issn = {2524-4671}, }
@article {pmid41883029, year = {2026}, author = {Dip, SA and Mallick, D and Acharjee Shuvo, U and Barua Soumma, S and Rafsani, F and Kumar Paul, B and Ahmed Moumi, N and Ahmed, S and Zhang, L}, title = {Large language model agents for biological intelligence across genomics, proteomics, spatial biology, and biomedicine.}, journal = {Briefings in bioinformatics}, volume = {27}, number = {2}, pages = {}, doi = {10.1093/bib/bbag110}, pmid = {41883029}, issn = {1477-4054}, support = {2125798//Virginia Tech, the Department of Computer Science, and the U.S. National Science Foundation (NSF)/ ; 2344169//Virginia Tech, the Department of Computer Science, and the U.S. National Science Foundation (NSF)/ ; 2319522//Virginia Tech, the Department of Computer Science, and the U.S. National Science Foundation (NSF)/ ; }, mesh = {*Genomics/methods ; *Proteomics/methods ; Humans ; *Computational Biology/methods ; *Artificial Intelligence ; Large Language Models ; }, abstract = {Large language models (LLMs) are evolving from passive predictors into agentic systems capable of planning, tool-use, and multimodal reasoning. This shift is especially consequential for biology, where complex, noisy, and multi-scale data require adaptive and integrative computational strategies. In this review, we provide the first systematic synthesis of LLM-based agents across genomics, molecular biology, imaging, biomedical analysis, and automated bioinformatics workflows. We analyze >60 emerging systems and organize them within a unifying framework that characterizes agentic traits, such as autonomous decision-making, external tool invocation, memory, and self-correction. Across domains, agentic LLMs show early promise in enabling multi-step analysis, linking heterogeneous evidence, and supporting exploratory scientific tasks. At the same time, our comparative assessment highlights consistent challenges, including unstable reasoning, limited biological grounding, retrieval misalignment, and barriers to reproducibility and biosafety. We conclude by outlining opportunities for trustworthy and collaborative biological agents, including multimodal integration, closed-loop experimental design, and robust evaluation practices. This survey aims to clarify the emerging landscape and chart a path toward reliable agentic systems for biological discovery.}, }
@article {pmid41883089, year = {2026}, author = {Duchêne, C and Jaubert, M and Falciatore, A}, title = {Beyond red/far-red sensing: phytochrome perception of the marine light field by microalgae.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71128}, pmid = {41883089}, issn = {1469-8137}, support = {ANR-25-CE20-4776//Agence Nationale de la Recherche/ ; ANR-20-CE20-0024//Agence Nationale de la Recherche/ ; ANR-25-CE20-1717//Agence Nationale de la Recherche/ ; ANR-11-LABX-0011-01//Agence Nationale de la Recherche/ ; 101082304//Fourth Framework Programme/ ; }, abstract = {Phytochromes (PHYs) are a major group of photoreceptors, described as red and far-red light sensors in land plants. Recent genomic and metagenomic explorations have revealed the presence of PHYs also in various eukaryotic microalgae originating from distinct endosymbiotic events. Growing evidence indicates that these PHYs are spectrally and functionally tuned to shorter wavelengths, which are prevalent in the aquatic environments as depth increases. Investigations using emerging phytoplankton model species, along with environmental surveys, are uncovering new PHY-mediated responses that likely influence their growth and distribution in marine environments. This Tansley Insight explores the implications of these discoveries for understanding the evolution and functional significance of this major photoreceptor class in the upper ocean, where light drives both energy and information flow.}, }
@article {pmid41883376, year = {2026}, author = {Mao, C and Wang, Y and Li, X and Kong, Q and Al-Farraj, SA and Xu, EG and Grossart, HP and Huang, J and Song, W}, title = {Resistance Gene Dynamics, Biogeochemical Coupling, and Ecological Risks in Sediments of Anthropogenically Impacted Lake Wetlands in China.}, journal = {Environment &amp; health (Washington, D.C.)}, volume = {4}, number = {3}, pages = {420-433}, pmid = {41883376}, issn = {2833-8278}, abstract = {Antibiotic resistance is a growing global threat to both public health and ecosystem stability. While the "One Health" framework emphasizes the need to monitor antibiotic resistance genes (ARGs) across diverse environments worldwide, the risks posed by ARGs in lakes affected by human activities, particularly in lake sediments that serve as natural reservoirs of ARGs, remain poorly understood. Metagenomics enables culture-independent analysis of microbial communities and resistance genes, providing essential insights into ARG dynamics. This study investigates microbial communities, ARGs, metal resistance genes (MRGs), and mobile genetic elements (MGEs) in sediments from Lake Donghu and Lake Weishan in China, two contrasting lake ecosystems subject to urbanization and agricultural activities for over four decades, using high-throughput metagenomic sequencing and assembly. ARGs and MRGs were more strongly influenced by deterministic environmental factors, particularly heavy metals (Cd, Pb, Cu), whereas microbial community structures were predominantly shaped by stochastic processes. Metagenomic binning yielded 293 metagenome-assembled genomes (MAGs), 125 of which were identified as potential ARG hosts, with Proteobacteria and Desulfobacterota being the most common. These hosts frequently cocarried MGEs, virulence factor genes (VFGs), and MRGs and exhibited metabolic pathways linked to carbon, nitrogen, and greenhouse gas (CO2 and N2O) cycling. Dissolved organic carbon (DOC) was determined as a key factor influencing microbial metabolism and promoting resistance gene dissemination. Our findings highlight a tight coupling between ARG dissemination, microbial ecological functions, and biogeochemical processes, underscoring ecosystem-level risks associated with resistance proliferation in human-impacted wetlands of China and elsewhere.}, }
@article {pmid41883694, year = {2026}, author = {Feigl, V and Röhberg, MZ and Masa, K and Hegedűs, H and Janek, Z and Deák, V and Fehér, C and Buda, K and Medgyes-Horváth, A}, title = {Extremophilic microbial isolates and metagenomic analysis of Greek and Hungarian bauxite residues.}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {50}, number = {}, pages = {e00956}, pmid = {41883694}, issn = {2215-017X}, abstract = {Bauxite residue (BR) is an extreme environment for microorganisms. The aim of the work was to isolate extremophilic microorganisms for further biotechnological applications, such as bioleaching or waste rehabilitation. At the same time, metagenomic analysis was performed to monitor short-term changes in deposited BR. We isolated and identified alkaliphilic and extreme halotolerant strains of Nesterenkonia massiliensis, N. natronophila, Micrococcus luteus, Aspergillus iizukae, Gibellulopsis serrae, and G. nigrescens from Greek and Hungarian BRs. Most strains were siderophore producers, cellulose degraders and produced oxalic and acetic acids. Metagenomic analysis revealed a shift in the most abundant bacterial classes from the freshly produced BR during 1 month and 3 months of storage: from Gammaproteobacteria (29% relative abundance), to Actinomycetes (31%) and Gammaproteobacteria (39%), respectively. Metagenomic analysis showed the presence of Nesterenkonia species. These results highlight the diverse microbiome of BR and underscore its potential as a valuable reservoir of extremophilic microorganisms.}, }
@article {pmid41883790, year = {2026}, author = {Way, J and Sherman, T and Leleika, S and Crippen, K and Wilson, R and Fida, TT}, title = {Enrichment and comparative metagenomics of microbes involved in biocorrosion of gas transport or storage steel infrastructure.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1771929}, pmid = {41883790}, issn = {1664-302X}, abstract = {Biocorrosion, also known as microbiologically influenced corrosion (MIC), is the deterioration of metals caused by microbial activities that compromise the structural integrity, reliability, and safety of steel infrastructure. To identify the genetic determinants that MIC-causing microorganisms may use to attack steel infrastructure, field samples from natural gas infrastructure with a potential history of MIC were collected, enriched for different MIC categories, and subjected to whole-genome shotgun sequencing for metagenomic analysis. Biofilms were grown on carbon steel coupons or glass slides as attachment substrates to assess differences in microbial community composition and metabolic activities. The highest corrosion activities were observed in enrichments dominated by acid-producing bacteria (APB) and hydrogen-utilizing bacteria. APB enrichments resulted in the highest accumulation of organic acids and a severe decrease in culture fluid pH. A total of 57 metagenome-assembled genomes were recovered from the biofilms, some of which differed between carbon steel coupons and glass slide substrates. The metagenomes contained most of the known genes implicated in MIC and sulfide production, with substantial variation in estimated gene copy numbers among metagenomes and attachment substrates. Overall, comparative analysis of these biofilm metagenomes enriched from natural gas production and processing infrastructure highlights similarities to microbial communities commonly observed in oil production and processing systems and provides an overview of candidate genes that may be used as molecular probes for MIC.}, }
@article {pmid41883806, year = {2026}, author = {Peng, L and Zhang, Y and Li, X and Hu, Z}, title = {Integrated multi-omics analysis reveals gut microbiota and metabolic characteristics in coronary heart disease.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1743914}, pmid = {41883806}, issn = {1664-302X}, abstract = {BACKGROUND: Coronary heart disease (CHD) is a leading cause of morbidity and mortality worldwide. Increasing evidence indicates that gut microbiota dysbiosis contributes to CHD pathogenesis through metabolic, inflammatory, and coagulation-related mechanisms. However, comprehensive multi-omics investigations of individuals with CHD remain limited. In this study, we aimed to characterize the multi-omics features of CHD and to identify potential diagnostic biomarkers.<br><br>METHODS: The study included 10 patients with clinically diagnosed CHD and 10 healthy controls. Blood and fecal samples were collected for further analysis. The gut microbiota composition was assessed using 16S ribosomal RNA high-throughput sequencing, and shotgun metagenomic sequencing was further performed to evaluate microbial functional potential through the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation and differential pathway analysis. Non-targeted metabolomic profiling was performed using ultra-high-performance liquid chromatography coupled with Orbitrap mass spectrometry, and quantitative proteomic analysis was conducted using liquid chromatography-tandem mass spectrometry. Functional interaction networks between differentially expressed metabolites and proteins were constructed using Spearman correlation analysis, and the diagnostic potential of candidate biomarkers was evaluated using receiver operating characteristic (ROC) curve analysis.<br><br>RESULTS: At the phylum level, the CHD group exhibited an increased abundance of Pseudomonadota and a decreased abundance of Bacillota and Actinomycetota. At the genus level, Escherichia-Shigella, Bacteroides, and Klebsiella were significantly enriched, whereas Bifidobacterium and Faecalibacterium were decreased in abundance. Shotgun metagenomic analysis revealed functional remodeling of gut microbiota in CHD, with upregulation of KEGG pathways related to energy metabolism, inflammatory signaling, and host-microbe interactions. Serum metabolomics and proteomic analyses identified 32 differentially expressed metabolites and 38 differentially expressed proteins, respectively. Correlation analysis revealed significant associations between phospholipid metabolites and apolipoproteins, inflammatory mediators and the complement system, asymmetric dimethylarginine and endothelial function-related proteins, and oxidative stress metabolites and antioxidant proteins. ROC analysis identified several potential biomarkers with high diagnostic value.<br><br>CONCLUSION: We demonstrate that individuals with CHD exhibit significant gut microbiota dysbiosis, distinct metabolic pathway alterations, and aberrant expression of coagulation- and inflammatory-related proteins. These findings provide novel insights into potential targets for CHD prevention and treatment strategies.}, }
@article {pmid41884347, year = {2026}, author = {Liu, H and Li, J and Yang, K and Li, H and Cao, S and Bao, Y and Feng, L and Zhang, L and Niu, J and Tian, T}, title = {Oral microbiome alterations and their association with long-term heavy metal exposure and early health effects.}, journal = {Journal of oral microbiology}, volume = {18}, number = {1}, pages = {2647511}, pmid = {41884347}, issn = {2000-2297}, abstract = {BACKGROUND: Long-term heavy metal exposure poses health risks, and non-invasive biomarkers for early detection are needed.<br><br>OBJECTIVE: This study investigated whether oral microbiome alterations can serve as a non-invasive indicator of long-term HMs exposure and associated early biological effects.<br><br>DESIGN: Soil, buccal mucosa, blood, and urine samples were collected from contaminated (CA) and uncontaminated (UA) areas. Soil contamination was assessed, and internal biomarkers were measured. Oral bacterial diversity was analyzed using metagenomic sequencing.<br><br>RESULTS: Severe Cd and Pb contamination was found in CA soil. Participants in CA had elevated internal Cd levels, renal impairment, and immune alterations. Oral microbiome analysis revealed decreased alpha diversity, reduced network complexity, and a shift from beneficial to pathogenic keystone taxa in CA. Functional analysis showed enrichment of stress-response pathways, suppression of metabolic pathways, and increased pathways linked to human diseases. Specific bacterial taxa correlated with internal biomarker levels.<br><br>CONCLUSIONS: There is a close association between long-term HMs exposure and reproducible, multi-faceted shifts in the oral microbiome. The oral microbiome may represent a promising, non-invasive biomarker for assessing environmental exposure and its early biological impacts.}, }
@article {pmid41885442, year = {2026}, author = {Rysava, M and Stredanska, K and Schwarzerova, J and Jakubickova, M and Cejkova, D and Aytan-Aktug, D and Otani, S and Dolejska, M and Palkovicova, J}, title = {Dynamic changes in the plasmidome and resistome in the gastrointestinal tract of chickens.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0407425}, doi = {10.1128/spectrum.04074-25}, pmid = {41885442}, issn = {2165-0497}, abstract = {The expansion of intensive poultry farming has led to a substantial increase in antibiotic use, which, in turn, has promoted the accumulation of antibiotic resistance genes (ARGs). The chicken gut serves as a reservoir for these genes and provides favorable conditions for their horizontal transfer via mobile genetic elements, such as plasmids. Through this process, commensal bacteria can transfer ARGs to pathogens, facilitating their spread and increasing the risk of transmission to humans. In this study, long-read sequencing was used to characterize the plasmidome and resistome in 12 fecal samples from 3 houses of a commercial broiler chicken farm. All chickens received enrofloxacin in the first days of life, with one house additionally treated with sulfamethoxazole/trimethoprim combination. For comparison, metagenomic analysis using short-read sequencing was performed on the same samples. This study revealed the presence of various ARGs associated with resistance to 25 antibiotic classes. A strong genetic association between MOBP-type plasmids and fluoroquinolone resistance was observed within broiler chicken farms. Temporal trends indicated progressive mobilization of these ARGs, suggesting an increasing potential for horizontal gene transfer. While fluoroquinolone resistance expanded over time, diaminopyrimidine resistance remained stable despite the antibiotic treatment. Most ARGs were carried on small plasmids, and complete plasmid reconstructions ranged from 2.6 to 47.6 kb. Our findings demonstrate that plasmidome sequencing enables high-resolution detection of resistance-associated plasmids that may be overlooked by conventional metagenomic approaches. The observed patterns are consistent with an association between fluoroquinolone use in poultry farms and the presence of plasmid-mediated resistance genes with potential for horizontal dissemination.IMPORTANCEDespite the crucial role of plasmids in antimicrobial resistance (AMR) dissemination, studies focusing on plasmidomes, defined as the complete set of plasmids, remain limited. This study is the evidence that chicken farms, where fluoroquinolone treatment is a standard practice, act as an important reservoir of plasmid-mediated antibiotic resistance which may not be revealed by commonly used approaches. Combining a metagenomic approach with a focus on plasmids enhances our ability to understand the genetic context and mechanisms underlying AMR transmission. The findings emphasize the importance of targeted plasmid analysis to improve surveillance and risk assessment of AMR transmission in microbial ecosystems.}, }
@article {pmid41885716, year = {2026}, author = {Xu, H and Yang, H and Shi, Y and Hu, X and Zhang, L and Li, P and Ma, Y and Yang, T and Xu, Y and Dong, C and Shen, Q}, title = {Genotype-Dependent Rhizosphere Microbiome Assembly Improves Potassium Use Efficiency in Pear Rootstocks Under Low Potassium Stress.}, journal = {Plant, cell &amp; environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.70499}, pmid = {41885716}, issn = {1365-3040}, support = {32272802//National Science Foundation of China/ ; CARS-28-10//China Agriculture Research System/ ; }, abstract = {Potassium (K) is a vital nutrient for fruit quality in pears (Pyrus spp.), and rhizosphere microbes play a critical role in enhancing plant K uptake and utilization. To investigate the genotype-dependent influences of the rhizosphere microbiome on potassium use efficiency (KUE) in pears, we compared two rootstocks with contrasting KUE (Pyrus betulaefolia and Pyrus ussuriensis) using integrated pot and long-term field experiments, 16S rRNA amplicon sequencing, and metagenomic analyses. Synthetic community (SynCom) inoculation and transcriptome profiling were employed to elucidate the mechanisms underlying enhanced K acquisition. Under low-K conditions, P. betulaefolia recruited distinct microbial communities, which significantly improved K accumulation by upregulating genes (e.g., ATP1A, kdPB, and COG3158) associated with K transport and homoeostasis. Field trials further confirmed that P. betulaefolia-grafted trees sustained higher Bacillaceae abundance, superior fruit quality, and elevated K content than P. ussuriensis under K-deficient conditions. SynComs constructed from five Bacillaceae strains enhanced low-K tolerance by promoting root metabolic activity, stimulating root hair development, modulating K[+] transporter (e.g., NRT2.4) expression, and activating calcium-dependent signalling pathways. Inoculation with SynComs led to substantial improvements under K limitation, including a 105.86% increase in plant biomass, a 164.99% increase in K accumulation, and a 125.91% enhancement in the aboveground K utilisation index. These findings reveal that genotype-driven enrichment of Bacillaceae-dominated microbiomes significantly enhances pear KUE, offering mechanistic insights to guide the development of microbiome-based bioinoculants and breeding of "microbiome-responsive" rootstocks for sustainable fruit production under K-limiting conditions.}, }
@article {pmid41885787, year = {2026}, author = {Ayed, M and Cadavez, V and Gonzales-Barron, U}, title = {Current research trends towards the control of protozoans in foods.}, journal = {Italian journal of food safety}, volume = {}, number = {}, pages = {}, doi = {10.4081/ijfs.2026.15114}, pmid = {41885787}, issn = {2239-7132}, abstract = {Protozoan parasites such as Cryptosporidium spp., Giardia duodenalis, Toxoplasma gondii and Cyclospora cayetanensis remain difficult-to-control hazards in food due to environmental persistence, low infectious doses, and the interpretability gap between nucleic acid detection and infectivity. This review synthesizes 4-year research trends shaping protozoan control in food systems, focusing on three critical pillars: matrix-adapted front-end processing (concentration, lysis, inhibitor management); inhibitor-resilient quantification; and sequencing-based attribution for outbreak investigation and source tracking. Recent benchmarking across wastewater, the water-soil-produce nexus, and food-relevant matrices repeatedly indicates - depending on matrix and study design - that upstream workflow steps often dominate analytical sensitivity and reproducibility. Accordingly, tiered analytical strategies are emerging in which the quantitative polymerase chain reaction (PCR) technique supports scalable screening, droplet digital PCR is used for decision-grade confirmation/quantification under inhibition and low-template conditions, and targeted sequencing or metagenomics is deployed selectively for traceback and contextual investigation. We integrate these developments into an actionable control framework that links prevention at the water-soil-plant interface with tiered analytics and viability-aware interpretation of post-intervention results. Research priorities ahead include harmonized performance reporting (recovery, inhibition controls, limit of detection/quantification), transparent endpoint hierarchy for intervention claims (detectability versus viability/infectivity), and interoperable sequence databases to enable cross-laboratory attribution and program-level learning. The field is moving from "can we detect?" towards "can we decide? - requiring reproducible front-end processing, inhibitor-resilient quantification, interoperable attribution resources, and endpoint discipline for intervention efficacy claims.}, }
@article {pmid41886617, year = {2026}, author = {Qiao, Z and Chen, Z and Gong, H and Guo, X and Yu, H and Chen, L}, title = {Exogenous Elemental Sulfur Promoting Methane Production and Simultaneous Ammonia Nitrogen Removal in Anaerobic Digestion of Food Waste: Experimental Verification and Mechanism Analysis.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c18148}, pmid = {41886617}, issn = {1520-5851}, abstract = {The treatment of food waste (FW) via anaerobic digestion (AD) is frequently plagued by a low methane yield and ammonia (NH4[+]) inhibition. This study demonstrates that the addition of elemental sulfur (S[0]) effectively mitigates both of these issues. Through batch and continuous experiments, it was found that the specific methane yield was enhanced by up to 48.1% and the NH4[+] concentration decreased by 26.9% at the optimal S[0] dosages of 20 mg/L. Metagenomic analysis revealed a dual mechanism underlying this enhancement: at low dosages, S[0] provides a sulfur-containing functional group for the biosynthesis of methyl-coenzyme M, thereby accelerating the rate-limiting "methyl-transfer" step in methanogenesis; at high dosages, it promotes the biosynthesis of coenzyme A, which markedly enhances acidogenesis. Furthermore, S[0] alleviates NH4[+] inhibition by fostering a synergistic interaction between sulfate-reducing bacteria and anammox bacteria, which convert NH4[+] to N2. Continuous operation over 140 days confirmed the long-term stability and effectiveness of this S[0] addition strategy. This study provides mechanistic insights into S[0]-driven methanogenesis in complex organic waste (FW) and offers a cost-effective, sustainable approach to enhancing AD efficiency and stability.}, }
@article {pmid41886785, year = {2026}, author = {Tian, M and Li, J and Dai, S and Ma, L}, title = {Clinical Characteristics and Management of Four Cases of Visceral Leishmaniasis-Associated Hemophagocytic Lymphohistiocytosis.}, journal = {The American journal of tropical medicine and hygiene}, volume = {}, number = {}, pages = {}, doi = {10.4269/ajtmh.25-0530}, pmid = {41886785}, issn = {1476-1645}, abstract = {The aim for the present study was to analyze clinical features, diagnostic approaches, and therapeutic strategies for visceral leishmaniasis (VL)-associated hemophagocytic lymphohistiocytosis (HLH) in pediatric patients. The clinical characteristics and test results of the children were summarized. Among the four patients, three resided in VL-endemic regions, and one had traveled to a VL-endemic region. All patients presented with recurrent fever (>38.5°C), hepatosplenomegaly, and decreased hemoglobin (HGB) levels ([78.75 ± 8.50] g/L) and platelet (PLT) counts ([59.50 ± 17.48] × 109/L). Before a definitive diagnosis could be made, patients exhibited progressive declines in white blood cell counts, HGB levels, and PLT counts, along with elevated triglyceride, serum cytokine (interleukin [IL]-6, IL-10, IL-2R, and tumor necrosis factor α) levels. Bone marrow aspirate smears revealed hemophagocytosis and Leishmania donovani (LD) bodies in all cases: two were diagnosed via direct identification of LD bodies, one was diagnosed through re-examination of bone marrow smears after confirming a travel history, and one was diagnosed via re-examination prompted by metagenomic next-generation sequencing, which revealed leishmaniasis. All the patients were initially diagnosed with HLH and received HLH-directed immunochemotherapy before VL diagnosis, with suboptimal response. After confirmation of VL, sodium stibogluconate therapy was initiated, resulting in a partial response in all cases. Etiological investigation is critical for HLH diagnosis. For VL-associated HLH, sodium stibogluconate as targeted therapy rapidly controls HLH, facilitates immunosuppression withdrawal, and significantly improves patient outcomes. White blood cell count, HGB level, PLT count, and lactate dehydrogenase level may serve as critical prognostic biomarkers for VL-associated HLH.}, }
@article {pmid41886955, year = {2026}, author = {Ling, GC and Chen, SJ and Li, ZL and Yang, S and Xiao, YY and Xiao, M and Zhang, YY and Zhong, HJ and Zhang, JY and Li, Y and Xie, JJ}, title = {A microbiota-tryptophol-AhR axis mediates the gut-kidney protective effects of Hushen Tongfengtai Granules in hyperuricemic nephropathy.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {155}, number = {}, pages = {158089}, doi = {10.1016/j.phymed.2026.158089}, pmid = {41886955}, issn = {1618-095X}, abstract = {BACKGROUND: Hyperuricemia (HUA) may result in hyperuricemic nephropathy (HN), and gut dysbiosis with barrier dysfunction can worsen disease progression. Hushen Tongfengtai granules (HSTFT), a traditional Chinese herbal prescription, have been used clinically to mitigate HUA and related renal injury. However, the mechanisms behind their effects remain to be explored.<br><br>OBJECTIVE: To find HSTFT to mitigate HN through mechanisms dependent on gut microbiota.<br><br>METHODS: Fecal metagenomics and UPLC-ESI-MS/MS metabolomics were employed to identify key microbial taxa and metabolites modulated by HSTFT. Antibiotic-treated mice were used to investigate the gut microbiota-dependent mechanisms of HSTFT. In vivo and in vitro experiments were further conducted to validate the ameliorative effects of HSTFT on gut dysbiosis and barrier dysfunction in HUA mice.<br><br>RESULTS: HSTFT could improve renal injury and intestinal barrier dysfunction in HUA. Fecal metagenomic analysis revealed enrichment of Bifidobacterium breve. Antibiotic depletion could abolish the therapeutic efficacy of HSTFT, while Bifidobacterium breve (B.breve) recolonization could restore intestinal and renal protection. Metabolomic analysis identified tryptophol as a key HSTFT-associated metabolite. Exogenous tryptophol (TOL) recapitulated the protective effects and may activate the aryl hydrocarbon receptor (AhR) pathway. The AhR antagonist CH223191 could inhibit the TOL/HSTFT-mediated protective effects on intestinal barrier integrity and renal function.<br><br>CONCLUSION: HSTFT could ameliorate HN by enhancing intestinal barrier integrity and renal protection, with the underlying mechanism involving upregulation of intestinal B.breve and its metabolite TOL via AhR pathway activation.}, }
@article {pmid41887041, year = {2026}, author = {Huang, J and Fu, Z and Zhou, S and Hu, J and Yu, G and Qin, C and Ma, Z}, title = {Metagenomic insights into sex-specific taxonomic and functional differentiation of epidermal mucus microbiota in the humphead wrasse (Cheilinus undulatus).}, journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics}, volume = {59}, number = {}, pages = {101810}, doi = {10.1016/j.cbd.2026.101810}, pmid = {41887041}, issn = {1878-0407}, abstract = {The humphead wrasse (Cheilinus undulatus) is a large coral reef fish of high ecological and economic importance, whose epidermal mucus microbiota plays a critical role in host defense, immune regulation, and environmental adaptation. However, the influence of host sex on the structure and functional potential of epidermal mucus microbiota remains poorly understood. In this study, epidermal mucus samples were collected from sexually mature female and male humphead wrasse, and shotgun metagenomic sequencing was performed to systematically compare microbial community composition, diversity, and functional gene profiles between sexes. The results showed no significant differences in alpha diversity (ACE and Shannon indices) between female (FM) and male (M) groups. In contrast, beta diversity analyses and hierarchical clustering revealed clear sex-related separation of microbial community structures at both phylum and genus levels. Although both groups were dominated by Pseudomonadota, Bacillota, Bacteroidota, and Verrucomicrobiota, their relative abundances and sex-specific taxa differed markedly. Functional annotation based on KEGG indicated that female-specific taxa harbored a greater number and broader range of functional genes, mainly associated with carbohydrate, amino acid, energy, and cofactor metabolism, as well as disease-related pathways. Furthermore, Comprehensive Antibiotic Resistance Database (CARD) and the Virulence Factor Database (VFDB) analyses revealed that female-specific taxa exhibited higher diversity of antibiotic resistance genes and virulence factors, whereas male-specific taxa showed a more limited functional repertoire, primarily related to basic metabolism and biofilm formation. Overall, this study demonstrates pronounced sex-associated differences in both the taxonomic composition and functional potential of epidermal mucus microbiota in humphead wrasse, highlighting the importance of host sex in shaping host-microbiome interactions and providing new insights for health management and conservation of coral reef fishes.}, }
@article {pmid41887065, year = {2026}, author = {Song, J and Hou, YN and Li, R and Feng, Z and Wang, AJ and Ren, N and Wei, W and Ni, BJ and Huang, C}, title = {Ectoine modulates mixotrophic denitrification pathway partitioning to sustain stable nitrogen and phenol removal under hypersaline stress.}, journal = {Water research}, volume = {298}, number = {}, pages = {125764}, doi = {10.1016/j.watres.2026.125764}, pmid = {41887065}, issn = {1879-2448}, abstract = {Hypersaline wastewater containing phenolic compounds imposes coupled osmotic and cytotoxic stresses that severely disrupts biological treatment processes. While compatible solutes are known to enhance cellular osmoprotection, their capacity to regulate microbial metabolic, particularly the balance between autotrophic and heterotrophic denitrification pathways under combined salinity stress remain poorly understood. This study reveals that the compatible solute ectoine modulates pathway partitioning in mixotrophic denitrification systems, enabling efficient nitrogen and phenol removal under 4% salinity. The ectoine amended reactor maintained nitrogen removal above 95% and phenol degradation above 80%, whereas the unprotected control collapsed to 34% and 33% respectively. Multi-scale mechanistic investigations revealed a coordinated protection cascade. First, ectoine enhanced cellular resilience by suppressing reactive oxygen species (ROS) by 88.2%, maintaining ATP level and electron transport activity, thereby preserving bioenergetic integrity. Second, structural fortification was achieved through intensified extracellular polymeric substance (EPS) production. The protein-to-polysaccharide ratio increased from 0.70 to 1.51 creating a protective matrix that stabilized membrane permeability and preserved catalytic enzymes, with nitrate reductase and nitrite reductase activities increasing 2.16- and 2.93-fold. Third, metagenomic profiling revealed community reconfiguration, with selective enrichment of halotolerant heterotrophs (Halomonas, Marinobacter) to 49% relative abundance. Aromatic‑degradation genes (catA, benB) rose by 7‑ and 48‑fold, while nitrogen‑metabolism genes (nasA, norC) remained high representation. This restructuring reversed pathway contributions from 81% sulfur-autotrophic dominance to 82% heterotrophic dominance. Ectoine thus functions as a metabolic modulator that links cellular stress alleviation and community-level functional potential to pathway repartitioning, offering a feasible strategy for the biotreatment of saline phenolic wastewater.}, }
@article {pmid41887066, year = {2026}, author = {Wang, H and Wu, Y and Weng, H and Zhang, L and Peng, Y}, title = {Denitrification mode management selects resource-conserving consortia for low-carbon municipal wastewater treatment.}, journal = {Water research}, volume = {298}, number = {}, pages = {125775}, doi = {10.1016/j.watres.2026.125775}, pmid = {41887066}, issn = {1879-2448}, abstract = {Low-carbon municipal wastewater treatment increasingly relies on carbon-limited denitrification, yet how carbon limitation reorganizes denitrifying communities and their greenhouse-gas footprint remains poorly resolved. We implemented denitrification mode management in a municipal wastewater sequencing batch reactor by switching from anaerobic-aerobic (AO) to anaerobic-aerobic-anoxic (AOA) operation. This shift moved denitrification from an pre-anaerobic stage with higher carbon availability to a post-anoxic stage where readily available carbon was limited. We combined metagenomics and metatranscriptomics to link process performance with microbial traits and gene expression. The mode switch improved nitrogen removal from 67.1 ± 1.8% to 88.5 ± 3.9% and reduced carbon requirement from 4.9 ± 0.5 to 3.3 ± 0.4 mg COD per mg N removed, while decreasing the N2O emission factor from 0.024 to 0.005 mg N2O-N per mg NO3[-]-N and lowering CO2 and CH4 emissions by 20-30%. Carbon-limited post-denitrification selected taxa with smaller genomes, reduced metabolic redundancy and a pronounced shift from broad extracellular carbon catabolism and complete denitrification towards intracellular carbon storage and truncated denitrification. Intracellular carbon pools insulated organics at the single-cell level and buffered electron delivery across denitrification steps, enabling a division-of-labour network that prevents electron imbalance and suppresses N2O build-up. Together, these findings link denitrification mode management to trait-based community restructuring and offer a process-level framework for understanding low-carbon, low-emission nitrogen removal under carbon-limited conditions.}, }
@article {pmid41887069, year = {2026}, author = {Qiang, H and Xu, X and Liu, Z and Heo, S and Yue, X and Zhou, A and Makinia, J}, title = {New insights into the interplay between chain elongation and homoacetogenesis in microbial electrosynthesis: Chloroform-enhanced medium-chain carboxylate production.}, journal = {Water research}, volume = {298}, number = {}, pages = {125790}, doi = {10.1016/j.watres.2026.125790}, pmid = {41887069}, issn = {1879-2448}, abstract = {Microbial electrosynthesis (MES)-assisted chain elongation (CE) is a promising strategy for sustainable medium-chain carboxylic acid (MCCA) production from waste streams. However, MES induces inevitable H2 evolution, and the understudied interaction between H2-driven homoacetogenesis and CE creates a critical knowledge gap. To resolve this metabolic conflict, chloroform (CHCl3) at 0.0075%-0.045% was used to inhibit homoacetogenesis, with systematic investigations on carbon flux distribution, functional microbial communities, and key metabolic pathways. Results showed 0.03% CHCl3 optimized MCCA production to 2902.8 ± 116.1 mg COD/L (103.0% increase), with electron efficiency (40.8%) and acetate utilization efficiency (94.3%) significantly higher than the Control (21.8% and 43.5%, respectively). Homoacetogenesis inhibition conserved reducing power (moderated H2, lowered NAD[+]/NADH) and redirected acetyl-CoA to drive CE. Microbial community analysis revealed enriched chain-elongating bacteria with more modular, cooperative interaction networks. Metagenomic analysis confirmed elevated abundances of reverse β-oxidation genes (e.g., ACAT, crt) and reduced homoacetogenesis genes (e.g., cooF, cooS) after treatment. Taxon-function contribution analysis identified Clostridium_kluyveri as the dominant functional agent for CE-related key genes. Economic and life-cycle assessments demonstrated a net economic gain of $1.61-4.22/m[3] and mitigated key environmental impacts due to improved product yield. This study elucidates how regulating the competition between homo-acetogens and chain-elongating bacteria directionally enhances CE, providing a novel ecological perspective and strategy for optimizing electricity-driven biomanufacturing processes.}, }
@article {pmid41887245, year = {2026}, author = {Reddy, K and Sinha, P and Antcliffe, DB and McDowell, C and Bradley, PA and Black, L and Murphy, L and Barbaras, J and Conlon, J and Camporota, L and Ostermann, M and Hopkins, P and Szakmany, T and Cherian, S and Welters, I and Brealey, D and Parekh, D and Rostron, AJ and Bos, LDJ and Nichol, A and Shankar-Hari, M and Gordon, AC and Delucchi, K and O'Kane, CM and Matthay, MA and Calfee, CS and McAuley, DF and , }, title = {Bedside identification of subphenotypes in acute respiratory failure (PHIND): a multicentre, observational cohort study.}, journal = {The Lancet. Respiratory medicine}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2213-2600(26)00040-8}, pmid = {41887245}, issn = {2213-2619}, abstract = {BACKGROUND: Acute respiratory distress syndrome (ARDS) is a clinically defined, biologically heterogeneous condition with no proven disease-modifying therapies. Retrospective analyses have identified two biologically distinct subphenotypes (hyperinflammatory and hypoinflammatory) of ARDS, with differing outcomes and responses to therapy. Rapid identification of these subphenotypes in an actionable timeframe has previously not been possible. The PHIND study aimed to prospectively identify these subphenotypes and to demonstrate differing 60-day mortality.<br><br>METHODS: The PHIND study was a prospective, multicentre, observational cohort study conducted in intensive care units (ICUs) within the National Health Service in the UK and the Health Service Executive in Ireland. Adult patients aged 18 years and older with ARDS or acute hypoxaemic respiratory failure (AHRF) were enrolled within 72 h of onset of the syndrome. Eligible patients were required to be receiving invasive mechanical ventilation, non-invasive ventilation, or high-flow nasal oxygen. Plasma interleukin (IL-6) and soluble TNF receptor-1 (TNFR1) were quantified at enrolment using a near-patient benchtop immunoanalyser (Randox multiSTAT) with a run time of approximately 1 h. Together with plasma bicarbonate measured from an arterial blood sample, these values were used to prospectively determine subphenotypes on an individual patient basis using a validated parsimonious logistic regression model. The primary outcome was 60-day mortality. The study was registered on ClinicalTrials.gov, NCT04009330.<br><br>FINDINGS: Between Nov 22, 2019, and Sept 28, 2023, 1853 patients from 30 centres were screened for eligibility. Of these, 1328 were excluded and 525 were recruited into the study, with 512 individuals included. 308 (60%) patients were male, 204 (40%) were female, and mean age was 57&#xb7;0 years (SD 15&#xb7;1). 443 (87%) patients were white, 18 (4%) were Black, and 16 (3%) were Asian. 490 were subphenotyped using the near-patient assay: 89 (18%) were classified as hyperinflammatory and 401 (82%) as hypoinflammatory. The primary outcome of 60-day mortality was measured in 486 patients after four patients withdrew consent for confirmation of vital status. 60-day mortality was significantly higher in the hyperinflammatory group (45 [51%] of 88) than in the hypoinflammatory group (111 [28%] of 398; risk ratio 1&#xb7;8 [95% CI 1&#xb7;4-2&#xb7;4], p<0&#xb7;0001). After adjustment, hyperinflammatory patients had increased odds of 60-day mortality (adjusted odds ratio 2&#xb7;7 [95% CI 1&#xb7;6-4&#xb7;4], p=0&#xb7;0002).<br><br>INTERPRETATION: Rapid identification of ARDS inflammatory subphenotypes using a near-patient assay was feasible and associated with many clinical characteristics and outcomes consistent with those described in earlier retrospective studies, including mortality, prevalence of sepsis, and incidence of metabolic acidosis. These findings support the implementation of precision medicine approaches in ARDS and the urgent need for prospective, subphenotype-stratified interventional trials.<br><br>FUNDING: Innovate UK, Randox Laboratories, and Belfast Health &amp; Social Care Trust.}, }
@article {pmid41887297, year = {2026}, author = {Lin, X and Yang, J and Kong, H and Pu, L and Ma, P and Mu, W and Sheng, H and He, J and Zou, Y and Wang, Y and Guo, X and Zhang, S and Wang, S}, title = {Metagenomic analysis of the gut microbiota in Cryptosporidium-infected Tibetan sheep.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {108461}, doi = {10.1016/j.micpath.2026.108461}, pmid = {41887297}, issn = {1096-1208}, abstract = {Cryptosporidium are important causative parasitic protozoa that cause gastrointestinal discomfort and diarrhea in humans and animals, posing a huge threat to public health. Ruminants serve as the main source of Cryptosporidium infection. However, the relationship between this intestinal parasite and host gut microbiota in Tibetan sheep remains almost unknown. In the present study, using nested PCR targeting the SSU rRNA gene, we detected Cryptosporidium in 9% (38/420) of fecal samples. The positive rate was significantly higher in 4-7 month-old lambs than in adult sheep. Infection of Cryptosporidium spp. was associated with limited overall structural and functional alterations of the host gut microbiota, characterized by increased the relative abundance of Escherichia and reduced functional pathways related to amino acid biosynthesis and nucleotide/nucleoside biosynthesis. Additionally, the data indicates that age served as a primary determinant of the gut microbiota, whereas Cryptosporidium load showed no significant association with microbial variation. Machine learning model analysis revealed that these differential microbial features could effectively discriminate between infected and uninfected animals. These findings elucidate that Cryptosporidium infection is associated with specific and limited gut microbiota alterations in sheep.}, }
@article {pmid41887416, year = {2026}, author = {Zhang, L and Xie, J and Lu, Y and Kong, L and Zhou, L and Wu, S and Wang, W and Huang, J and Li, J and Cheng, S}, title = {Enhanced nitrogen removal and mitigated greenhouse gas emissions in bioelectrochemical system-modular moving bed wetland at low temperature: Functional zonation and multi-pathway electron transfer.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134493}, doi = {10.1016/j.biortech.2026.134493}, pmid = {41887416}, issn = {1873-2976}, abstract = {This study integrated bioelectrochemical systems (BESs) into modular moving bed constructed wetlands (MMBCWs) to mitigate low temperature constraints on nitrogen removal and greenhouse gas emissions. Conventional MMBCW, microbial fuel cell-MMBCW (MFC-MMBCW), and microbial electrolysis cell-MMBCW (MEC-MMBCW) were constructed to assess feasibility. Results showed that MEC-MMBCW achieved superior nitrogen removal and the lowest global warming potential under cold conditions. Biofilm characteristics and metagenomic analyses revealed that MEC-MMBCW established spatially stratified functional zones. Specifically, the anode promoted organic matter and ammonia oxidation, while enhanced denitrification outcompeted compensatory anammox in the cathode. Furthermore, a multi-pathway extracellular electron transfer (EET) network mediated by extracellular polymeric substances (EPS), cytochrome c, and conductive pili accelerated electron transfer rates. These mechanisms synergistically boosted metabolic potential and activated latent degradation pathways, enhancing treatment resilience. Consequently, MEC-MMBCW represents a viable strategy for sustainable wastewater treatment in cold regions.}, }
@article {pmid41887490, year = {2026}, author = {Li, Z and Fu, J and Hu, J and Li, T and Xu, Y}, title = {Sediment-water interface reoxygenation by NO3-LDH promotes tetracycline degradation in sediments and modulates antibiotic resistance gene dynamics.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124357}, doi = {10.1016/j.envres.2026.124357}, pmid = {41887490}, issn = {1096-0953}, abstract = {The widespread presence of antibiotics in aquatic sediments, together with hypoxic conditions, constrains oxygen-driven natural degradation, thereby prolonging their environmental persistence. In this work, nitrate-intercalated layered double hydroxide (NO3-LDH) was employed as a controlled-release nitrate amendment to alleviate interfacial oxygen limitation while minimizing the secondary environmental risks associated with the high release peaks of conventional nitrate reagents. As a result, NO3-LDH increased dissolved oxygen (DO) from 1.05 to 3.39 mg/L, enhanced TC removal from 64.5% to 89.8% within 15 d, and reduced the combined abundance of tetracycline resistance genes (tetA, tetQ, and tetS) by 53.0%. Mechanistically, DO enrichment increased •OH generation 1.94-fold and upregulated cytochrome P450-related genes, supporting coupled enhancement of abiotic oxidation and oxygen-dependent microbial transformation. The improved oxidative microenvironment also favored the enrichment of aerobic aromatic-degrading taxa, further promoting TC attenuation. Although overall antibiotic resistance genes (ARGs) levels declined, fluoroquinolone- and macrolide-associated ARGs exhibited a transient early increase, likely triggered by an abrupt redox perturbation upon oxygen recovery that imposed oxidative stress on anaerobic microorganisms, intensified ATP-demanding stress responses, and increased membrane permeability. As interfacial redox conditions stabilized and TC concentrations decreased, these stress responses subsided and ARGs abundances declined at later stages. Overall, restoring interfacial DO strengthens oxygen-driven natural antibiotic degradation and inhibits the long-term accumulation of ARGs, providing a mechanistically grounded strategy for in situ remediation of antibiotic-contaminated sediments.}, }
@article {pmid41876075, year = {2026}, author = {Wu, H and Wang, H and Man, S and Yan, Q}, title = {Biogenic FeS Reshapes microbial interactions to regulate acetogenesis in CO2-Fed microbial electrosynthesis.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134480}, doi = {10.1016/j.biortech.2026.134480}, pmid = {41876075}, issn = {1873-2976}, abstract = {Inefficient electron transfer and poorly coordinated microbial communities often limit stable CO2-to-acetate conversion in microbial electrosynthesis (MES). Herein, Shewanella oneidensis MR-1 was introduced to induce in situ biogenic FeS formation at the cathode to regulate microbial interactions and enhance acetogenesis. Under the acetogenesis dominant condition (RAT: sludge to MR-1 ratio of 2:1, Fe/S = 5/10 mM, initial MR-1 inoculation), acetate production reached 1330.6 mg L[-1] with the carbon recovery efficiency of 62.9%. Community and metagenomic analyses showed that FeS selectively enriched acetogens and Fe/S transforming microorganisms while restructuring functional pathways related to redox metabolism and energy conservation. Co-occurrence network analysis further revealed that FeS promoted coordinated, function oriented microbial interactions rather than competitive associations. This study highlights the role of biogenic FeS in linking electron transfer with microbial cooperation, providing a mechanistic basis for improving MES performance through community level regulation.}, }
@article {pmid41876513, year = {2026}, author = {Jovicic, D and Anestis, K and Fiutowski, J and Jørgensen, BB and Kjeldsen, KU and Rotaru, AE}, title = {Genome-centric metagenomics reveals electroactive syntrophs in a conductive particle-dependent consortium from coastal sediments.}, journal = {Nature communications}, volume = {17}, number = {1}, pages = {}, pmid = {41876513}, issn = {2041-1723}, support = {1026-00159B//Natur og Univers, Det Frie Forskningsr&#xe5;d (Natural Sciences, Danish Council for Independent Research)/ ; 101045149//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {*Geologic Sediments/microbiology ; *Metagenomics/methods ; Acetates/metabolism ; Oxidation-Reduction ; Electron Transport ; Phylogeny ; *Microbial Consortia/genetics ; Methane/metabolism ; Methanosarcina/metabolism/genetics ; Charcoal ; Cytochromes/metabolism/genetics ; Genome, Bacterial ; }, abstract = {Conductive particles are common in coastal sediments, yet their role in shaping methane-producing communities and pathways remains unclear. We applied genome-resolved metagenomics to a sediment-derived consortium serially transferred for a decade and obligately dependent on granular activated carbon (GAC). We discovered a particle-obligate food web composed of electrogenic syntrophic acetate oxidizers (SAO), an electrotrophic methanogen, and necromass recyclers. The primary SAO electrogen, Candidatus Geosyntrophus acetoxidans, represents a new genus and possesses a complete acetate oxidation pathway and extracellular electron-transfer (EET) machinery, including two porin-cytochrome conduits, 43 additional multiheme cytochromes and conductive pili. A secondary SAO, a Lentimicrobium sp. with a giant PCC-cluster, supplies an alternative EET-linked acetate-oxidation route. Electrons from electrogens transfer via GAC to a Methanosarcina equipped with the heptaheme cytochrome MmcA and flagellin for electron uptake. These results provide a genomic blueprint of this particle-obligate environmental consortium and suggest an overlooked acetate-to-methane electron-transfer route in geoconductor-rich anoxic sediments.}, }
@article {pmid41876637, year = {2026}, author = {Wang, R and Ma, R and Cai, Y and Zhang, L and Lu, W and Zheng, W and Kong, J and Miao, Q and Li, X and Guan, L and Gao, Y and Chen, K and Kwan, ATH and McIntyre, RS and Xu, G and Yu, CK and Lam, BY and So, KF and Lin, K}, title = {Exploratory characterization of gut microbiota and cognitive profiles in adolescents with subthreshold depression: a shotgun metagenomics sequencing study.}, journal = {Npj mental health research}, volume = {5}, number = {1}, pages = {}, pmid = {41876637}, issn = {2731-4251}, support = {No. 2021A1515011361//Natural Science Foundation of Guangdong Province/ ; No. 202102020735//Science and Technology Program of Guangzhou/ ; No. 2024SRP208//Guangzhou Medical University Research Capacity Enhancement Program/ ; No. 202007030012//Science and Technology Program of Guangzhou, China/ ; No. 202007030012//Science and Technology Program of Guangzhou, China/ ; No. 82171531//National Natural Science Foundation of China/ ; No. PX-66221557//Guangzhou Medical University student innovation ability enhancement Program/ ; STG STG1/M-501/23-N//the Hong Kong RGC theme-based Strategic Target Grant Scheme/ ; }, abstract = {Subthreshold depression (SD) in adolescents is a prevalent condition associated with significant functional impairment and an increased risk of developing major depressive disorder. Currently, the lack of reliable objective markers complicates its accurate identification. Investigating the gut microbiome may offer novel insights into its underlying mechanisms. This study aimed to investigate the association between gut microbiome and cognitive function in adolescents with subthreshold Depression (SD). Thirty-eight adolescents with SD and 139 clinically-well (CW) adolescents were recruited. Gut microbiome and cognitive function were assessed by metagenomic sequencing and the MATRICS Consensus Cognitive Battery (MCCB), respectively. Compared with the CW adolescents, the SD group showed higher relative abundance of Spirochaetes, Synergistetes, Spirochaetia, Synergistia, Spirochaetales, Rhizobiales, Synergistales, Thermoanaerobacterales, Rhodospirillales, Synergistaceae, and Oxalobacteraceae at four levels. The Spatial Span scores were higher in the SD group compared to the CW group. Moreover, EggNOG analyses showed a significant negative correlation of the intracellular trafficking secretion, and vesicular transport with the Spatial Span scores. The KEGG pathway of the neurodegenerative diseases and translation was depleted in the microbiome of adolescents with SD. The higher abundance of Spirochaetes, Spirochaetia, and Spirochaetales was the best predictor of SD in adolescents. Our findings suggest that gut microbiome abnormalities, depressive symptoms, and cognitive influences co-occur in adolescents with SD, which may play a crucial role in the pathogenesis of SD and cognitive function in adolescent. Gut microbiome may serve as a potential biomarker for the identification and treatment of adolescents with SD.}, }
@article {pmid41876857, year = {2026}, author = {Peñuelas, J and Zheng, B and Tariq, A and Sardans, J}, title = {Microbial phosphorus cycling in terrestrial ecosystems.}, journal = {Nature reviews. Microbiology}, volume = {}, number = {}, pages = {}, pmid = {41876857}, issn = {1740-1534}, abstract = {Phosphorus is an essential yet often limiting macronutrient that shapes primary productivity and microbial activity in terrestrial ecosystems. Unlike carbon and nitrogen cycles, which have gaseous phases, the terrestrial phosphorus cycle is primarily governed by soil biogeochemistry, wherein microorganisms orchestrate key transformations. This Review synthesizes current knowledge of the microbial phosphorus cycle, emphasizing the diverse mechanisms used by bacteria, fungi and archaea to mobilize phosphorus (for example, via phosphatases such as PhoA and PhoD and organic acids such as citrate) and to directly enhance plant phosphorus uptake. We explore the ecological significance of these processes in maintaining soil health, supporting ecosystem productivity and influencing carbon sequestration. We propose the Microbial Phosphorus Adaptive Evolution Theory (MPAET): chronic phosphorus scarcity drives evolutionary and ecological shifts in microbial communities towards higher scavenging investment, polyphosphate handling and lipid remodelling. Furthermore, we examine how environmental factors, land use and climate modulate these shifts (for example, phoD expression increases under phosphorus stress), with cascading effects on ecosystem function and global phosphorus availability. New technologies such as metagenomics, [18]O-phosphate tracing and nanoscale secondary ion mass spectrometry are now revolutionizing our understanding of these dynamics. This Review underscores the critical need to integrate microbial phosphorus cycling into ecosystem models and to develop sustainable strategies for phosphorus smart management. Such approaches are essential for addressing global challenges related to soil degradation, food security and environmental change.}, }
@article {pmid41877267, year = {2026}, author = {Peirson, LE and McKenney, EA and Patterson, JR and Beasley, JC and Périquet-Pearce, S and Cloete, C and Melton, MH and PetersonWood, B and Portas, R and Aschenborn, O and Lafferty, DJR}, title = {African carnivore gut bacterial diversity and composition are associated with sample condition but not storage technique.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00553-w}, pmid = {41877267}, issn = {2524-4671}, support = {Financial Assistance Award no. DE-EM0005228//U.S. Department of Energy/ ; Peter White Scholar Award//Northern Michigan University/ ; }, abstract = {Non-invasive fecal sampling is essential for molecular wildlife studies such as gut microbiome (GMB) research, yet field conditions often limit preservation options. To test the effects of preservation methods on the results of GMB community composition, we compared gut bacterial communities in paired fecal samples preserved in stabilization tubes and air-dried in paper bags collected from anesthetized African lions (Panthera leo) and spotted hyenas (Crocuta crocuta) in Etosha National Park, Namibia. Additional opportunistic samples from the ground around carnivore feeding sites that varied in moisture content were also analyzed. No differences in alpha or beta diversity were detected between preserved and dried samples, although bacterial beta diversity differed between preserved and opportunistic samples, supported by NMDS ordinations and PERMANOVA results. Core bacterial communities remained consistent across opportunistic sample conditions, indicating that host-associated taxa persist despite environmental exposure supporting the use of opportunistic samples for GMB studies in remote arid settings. However, consistent sampling protocols and future field-based desiccation studies remain critical for comparative analyses. These findings highlight that rapid air-drying offers a reliable, low-cost preservation option that maintains core microbiome patterns, expanding the feasibility of GMB research in remote or resource-limited field contexts where refrigeration and preservatives may be unavailable.}, }
@article {pmid41877288, year = {2026}, author = {Wei, G and Liu, M and Huang, L and Chen, C}, title = {Metagenomic sequencing reveals the dynamic changes of pig gut fungal composition following the ages and identifies fungal species associated with diarrhea in piglets.}, journal = {Animal microbiome}, volume = {}, number = {}, pages = {}, doi = {10.1186/s42523-026-00551-y}, pmid = {41877288}, issn = {2524-4671}, support = {32272831//National Natural Science Foundation of China/ ; }, }
@article {pmid41877461, year = {2026}, author = {Tagliabue, A and Furfaro, G and Pallavicini, A and Martino, F and Zane, L and Sattin, E and Valle, G and Piraino, S and Turon, X}, title = {Comparative Multi-Marker Environmental DNA Metabarcoding of Marine Metazoan Communities: Water vs. Sediment.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70126}, doi = {10.1111/1755-0998.70126}, pmid = {41877461}, issn = {1755-0998}, support = {MCIU/AEI/10.13039/501100011033//BlueDNA PID2023-146307OB/ ; CCI 2014IT16M2OP005//Programma Operativo Nazionale Ricerca e Innovazione 2014-2020/ ; ECS00000043//Interconnected Nord-Est Innovation Ecosystem/ ; //European Regional Development Fund/ ; 2020J3W3WC//Italian Ministry of Education, Universities and Research/ ; D33C22000960007//National Recovery and Resilience Plan/ ; C93C22002810006//National Recovery and Resilience Plan/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *DNA, Environmental/genetics ; Animals ; *Geologic Sediments ; *Biodiversity ; *Aquatic Organisms/classification/genetics ; RNA, Ribosomal, 18S/genetics ; Electron Transport Complex IV/genetics ; *Metagenomics/methods ; *Seawater ; }, abstract = {This study investigates the metazoan biodiversity in the Southern Adriatic Sea using environmental DNA (eDNA) metabarcoding. Sediment and adjacent water samples were collected from three sites (one pristine, two impacted by human activities) at three distances from the coast across two seasons. The complex four-factor experimental design (576 samples) addresses key sources of eDNA variability and provides a valuable comparison of markers (COI and 18S) and sample types, which remain rare in the literature. Results showed differences in the number and type of taxa identified, taxonomic resolution, and number of amplicon sequence variants (ASV) per operational taxonomic unit (OTU) across markers. The obtained overall community structure (beta-diversity) was similar for both markers. Sediment samples had higher OTU richness, but lower diversity than water samples. The two sample types provided distinct and only partially overlapping views of biodiversity. Sediment samples were rich in benthic species, whereas water samples featured mostly planktonic and nektonic species. Biodiversity varied by site and season, with sediment samples showing less seasonal variability. The pristine site did not host higher biodiversity than impacted sites, likely because of the latter's habitat heterogeneity. This study confirms the effectiveness of eDNA metabarcoding for biodiversity assessment in coastal ecosystems and provides a foundational dataset for future monitoring. By highlighting the complementary nature of COI and 18S markers and the role of sample type, this research supports integrating eDNA metabarcoding into routine environmental monitoring programs while emphasising the need for further standardisation and improved reference databases.}, }
@article {pmid41877907, year = {2026}, author = {Xie, S and Zhang, H and Xie, Y and Liu, F and Ye, S and Liu, X and Lai, Z}, title = {Analysis of the Clinical Features of HSV-2 Encephalitis Confirmed by the mNGS Technique: Insights Derived from Seven Patient Studies.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {567731}, pmid = {41877907}, issn = {1178-6973}, abstract = {BACKGROUND: Herpes simplex virus type 2 (HSV-2) encephalitis is rare in immunocompetent adults. Diagnosis typically depends on cerebrospinal fluid (CSF) polymerase chain reaction (PCR), which has limited sensitivity and potential for false negatives. Metagenomic next-generation sequencing (mNGS) provides unbiased pathogen detection, facilitating rapid HSV-2 identification in CSF and minimizing misdiagnosis risks, especially in atypical cases or immunocompetent individuals. This study examines the diagnostic value of mNGS in a cohort of patients with HSV-2 encephalitis presenting atypically.<br><br>METHODS: A retrospective analysis was performed on patients diagnosed with HSV-2 encephalitis using mNGS at our institution between January 2022 and January 2025. Clinical characteristics, ancillary test results, and patient outcomes were analyzed to evaluate the diagnostic value of mNGS.<br><br>RESULTS: Seven patients (2 males, 28.57%; 5 females, 71.43%) with a mean age of 33.57 years were included; one had pre-existing immunodeficiency (14.28%). Most presented atypical symptoms; six treated within three days fully recovered, while one with delayed treatment died. Mean follow-up was 14.71 &#xb1; 5.82 months. Higher viral sequence counts correlated with worse outcomes. Initial CSF analysis showed normal cell counts in one patient; all exhibited lymphocytic pleocytosis and elevated protein levels.<br><br>CONCLUSION: This study contributes to the limited clinical data on adult HSV-2 encephalitis by summarizing clinical manifestations and treatment outcomes, thereby informing improved diagnostic and management strategies. It also highlights the prognostic importance of early diagnosis and immune status assessment through the application of mNGS.}, }
@article {pmid41877920, year = {2026}, author = {Zeng, F and Zhu, T and Chen, X and Huang, K and Liu, L and Wang, G and Mai, J and Zhang, S}, title = {Gut microbiota and metabolic status during pregnancy in captive Asian elephants.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1749490}, pmid = {41877920}, issn = {2297-1769}, abstract = {BACKGROUND: The gut microbiota is regarded as one of the key factors regulating host health. The gut microbiota and its connection to fecal metabolites are crucial for supporting fetal development and ensuring maternal health during reproductive stages. Although studies have examined Asian elephants, the composition and function of the gut microbiota in pregnant and non-pregnant captive Asian elephants have not been reported.<br><br>METHODS: We compared the fecal microbiota and fecal metabolites of pregnant (G1), non-pregnant (never gotten pregnant after reaching sexual maturity, G2), and subadult (G3) captive Asian elephants using metagenomic sequencing and untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics.<br><br>RESULTS: We found significant differences in the gut microbiota among the G1, G2, and G3 groups. The phylum Bacteroidetes showed notable differences between G1 and G2. The analysis of fecal metabolomics revealed significant differences in 49 metabolites between G1 and G2, of which 25 were upregulated and 24 were downregulated. These results suggested significant differences in the composition of gut microbiota and fecal metabolites during reproductive stages, while gut microbial diversity remained stable. These findings inform our ongoing research on the potential health conditions of captive Asian elephants, with the aim of better understanding the role of the gut microbiota in reproductive regulation.}, }
@article {pmid41877937, year = {2025}, author = {Zhang, M and Pak, H and King, SD and Zuniga, AA and Hassan, YA and King, MD}, title = {Mitigating airborne pathogen risks in a full-scale meat processing facility.}, journal = {Total environment microbiology}, volume = {1}, number = {3}, pages = {}, pmid = {41877937}, issn = {3050-6417}, abstract = {Foodborne illnesses caused by Shiga toxin-producing Escherichia coli (STEC) and Salmonella represent a major public health concern, particularly in meat processing facilities where bioaerosols generated during processes like carcass spraying and dehiding can lead to contamination. In this study, we assessed airborne concentrations of STEC and Salmonella at multiple locations within a full-scale meat processing facility using quantitative polymerase chain reaction (qPCR) and Illumina MiSeq sequencing. Additionally, we utilized computational fluid dynamics (CFD) simulations to model airflow within the facility and evaluated the effectiveness of air curtains in mitigating the transfer of bioaerosols between high-risk (dehiding and tripe) and low-risk (chiller and fabrication) areas. qPCR results showed that pathogen concentrations in the dehiding rooms were 126 GCN/m[3] for STEC and 105 GCN/m[3] for Salmonella during spring, with levels rising significantly in summer (2198 GCN/m[3] for STEC and 1799 GCN/m[3] for Salmonella). Simulated airflow patterns revealed that entrained bioaerosols could be transported from unclean to clean areas, increasing the risk of cross-contamination. The use of air curtains effectively reduced this spread by creating barriers between high- and low-risk areas. Our findings suggest that bacterial survivability and aerosolization was enhanced in summer, highlighting the critical role of environmental factors and airflow management in controlling contamination risks. This study demonstrates the value of integrating experimental data with CFD simulations to assess pathogen spread and identify effective mitigation strategies in meat processing facilities.}, }
@article {pmid41878086, year = {2026}, author = {Luo, D and Jia, S and He, W and Fan, Z and Yin, W}, title = {Periplaneta americana Powder Alleviates Neuropathic Pain and is Associated with Gut Microbiota Changes in Rats.}, journal = {Journal of pain research}, volume = {19}, number = {}, pages = {564911}, pmid = {41878086}, issn = {1178-7090}, abstract = {BACKGROUND: This study aims to evaluate the therapeutic potential of Periplaneta americana powder (PAP) in alleviating neuropathic pain in a rat model of sciatic nerve injury induced by chronic constriction injury (CCI), and to systematically analyze its effects on the composition and structure of the gut microbiota during the intervention process, with the goal of elucidating the mechanisms underlying the analgesic effects of PAP.<br><br>METHODS: A rat model of CCI was established (n = 12 per group), and PAP was administered for intervention. The analgesic effects were evaluated using mechanical withdrawal threshold (MWT) and thermal withdrawal latency (TWL). Pathological changes in the spinal cord and colon tissues were examined via hematoxylin-eosin (HE) staining, and the expression of the astrocyte marker glial fibrillary acidic protein (GFAP) in the spinal cord was detected by immunohistochemistry. The expression levels of pro-inflammatory cytokines TNF-&#x3b1; and IL-1&#x3b2; in spinal cord tissues were measured using enzyme-linked immunosorbent assay (ELISA). Fecal samples were collected at the endpoint of treatment for metagenomic sequencing and analysis.<br><br>RESULTS: After PAP treatment, behavioral tests in CCI rats showed a significant increase in MWT and TWL (P < 0.05). Histological analysis revealed marked alleviation of spinal cord and colon tissue damage as well as reduced inflammatory cell infiltration (P < 0.05). Immunohistochemistry further demonstrated a significant decrease in GFAP expression in the spinal cord (P < 0.05). ELISA results showed that the expression levels of TNF-&#x3b1; and IL-1&#x3b2; in spinal cord tissues were significantly decreased (P < 0.05).Metagenomic analysis indicated that PAP reshaped the gut microbiota structure, increased the abundance of SCFA-producing bacteria, and was associated with the butyrate metabolism pathway.<br><br>CONCLUSION: This study indicates that PAP can significantly alleviate neuropathic pain in a rat model of sciatic nerve chronic constriction injury (CCI) and suppress the central inflammatory response.Notably, this effect is accompanied by changes in the gut microbiota, particularly characterized by a significant alteration in the abundance of short-chain fatty acid-producing bacteria. These results suggest that PAP not only possesses substantial analgesic effects but may also mediate the intervention of CCI-induced neuropathic pain by regulating the structure of the gut microbiota.}, }
@article {pmid41878266, year = {2026}, author = {Huang, J and Yan, X and Su, Q and Tu, H and Yu, Z and Liu, D and Wu, B}, title = {Temporal dynamics of gut microbiota and virome in preterm infants: insights from longitudinal metagenomic analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1598786}, pmid = {41878266}, issn = {2235-2988}, mesh = {Humans ; *Infant, Premature ; *Gastrointestinal Microbiome/genetics ; Infant, Newborn ; *Metagenomics ; *Virome ; *Bacteriophages/genetics/isolation &amp; purification/classification ; Longitudinal Studies ; *Bacteria/classification/genetics/isolation &amp; purification ; Female ; Male ; Feces/microbiology/virology ; Enterococcus faecalis ; Gastrointestinal Tract/microbiology ; }, abstract = {INTRODUCTION: Preterm infants exhibit heightened vulnerability to morbidity and mortality due to their underdeveloped immune systems and immature gastrointestinal tract. The gut microbiota plays a pivotal role in neonatal health, yet its establishment is influenced by multiple factors, including prematurity, antibiotic exposure, and feeding modalities. This study aimed to examine the interactions among gut bacteriophages, bacterial communities, and clinical variables in preterm infants to identify potential microbial biomarkers associated with health outcomes.<br><br>METHODS: We employed metagenomic shotgun sequencing and co-occurrence network analysis to characterize the virome and bacterial communities in 12 preterm neonates at 14 and 28 days post-birth. This approach enabled the identification of dynamic microbial colonization patterns and key bacterial species and bacteriophages associated with clinical parameters.<br><br>RESULTS: Staphylococcus epidermidis exhibited a significant decline over time, whereas Enterococcus faecalis and its associated bacteriophages showed progressive enrichment, becoming predominant by day 28. In contrast, the relative abundances of Clostridioides difficile and Klebsiella pneumoniae remained statistically stable between the two time points (14 vs. 28 days).<br><br>DISCUSSION: These findings suggest that microbial changes during the first month of life may reflect a combination of host developmental processes and external influences, such as antibiotic exposure or delivery mode. The observed microbial signatures provide preliminary insights into early gut microbiota and virome development in preterm infants. However, their functional relevance and long-term stability require confirmation in larger, well-powered longitudinal studies with denser temporal sampling. The enrichment of Enterococcus faecalis may indicate its opportunistic colonization potential in the preterm gut and warrants further investigation regarding its role in gut homeostasis and immune system maturation.}, }
@article {pmid41878461, year = {2026}, author = {Li, Z and Zhang, Y and Xu, D and Huang, B}, title = {Diagnostic and therapeutic journey of infantile endobronchial tuberculosis: a case report.}, journal = {Frontiers in pediatrics}, volume = {14}, number = {}, pages = {1778717}, pmid = {41878461}, issn = {2296-2360}, abstract = {BACKGROUND: Endobronchial tuberculosis (EBTB) in infants is rare and is often overlooked because of nonspecific clinical manifestations. Coexisting primary immunodeficiency and opportunistic infections further increased diagnostic and therapeutic complexity.<br><br>CASE PRESENTATION: We reported a male infant aged 40 days who presented with fever and mild cough. Chest imaging showed progressive bilateral nodular and granulomatous lesions despite broad-spectrum antibacterial therapy. Microbiological evaluation revealed positive T-SPOT.TB and GeneXpert MTB/RIF results from bronchoalveolar lavage fluid (BALF), while metagenomic next-generation sequencing identified Pneumocystis jirovecii. Genetic testing demonstrated a heterozygous IKZF1 mutation, consistent with underlying immunodeficiency. Serial bronchoscopies confirmed necrotizing endobronchial tuberculosis with airway stenosis. The patient received standard anti-tuberculosis therapy, systemic corticosteroids, trimethoprim-sulfamethoxazole, intravenous immunoglobulin, and repeated bronchoscopic intraluminal drug delivery. Clinical and radiological remission was achieved, with no airway sequelae during 18-month follow-up.<br><br>CONCLUSIONS: This case highlighted the unique coexistence of infantile EBTB, IKZF1-related immunodeficiency, and P. jirovecii coinfection. Early bronchoscopy played a pivotal diagnostic and therapeutic role. Repeated intraluminal bronchoscopic therapy combined with systemic treatment might prevent irreversible airway damage in severe pediatric EBTB.}, }
@article {pmid41878469, year = {2026}, author = {de Azevedo, PS and Vedovatto, MM and de Freitas, PCG and Luz, RBS and Streit, RSA and Persinoti, GF}, title = {parsomics: a data-driven framework for metagenomics data integration powered by a local relational database.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbag049}, pmid = {41878469}, issn = {2635-0041}, abstract = {MOTIVATION: Metagenomics enables the analysis of complex microbial communities directly from environmental samples, resulting in massive datasets that are processed using multiple tools and workflows. Data integration is key for metagenomics research, however, challenges in data organization and management locally remain open in existing workflows.<br><br>RESULTS: We present parsomics, a lightweight and extensible data management tool designed for efficient local storage, organization, and integration of metagenomic analysis results. Built upon PostgreSQL and implemented in Python, parsomics leverages a user-defined configuration file to automatically construct a relational database tailored to metagenomics-based data. It is user-friendly, easy to deploy, and implements modular plugin-based extensions to support diverse data types and outputs. parsomics can be installed in every major GNU/Linux environment and currently focuses on prokaryotic metagenomics analysis.<br><br>parsomics is an open-source project and its source code is available at https://gitlab.com/parsomics under the GPLv3 license. Comprehensive documentation can be found at https://parsomics.org and https://api.parsomics.org.}, }
@article {pmid41878742, year = {2026}, author = {Armijo-Godoy, G and Cottet, L and Rupayan, A and Carrasco, M and Levicoy, D and Salvo-Garrido, H}, title = {Functional and ecological characterization of Labrys methylaminiphilus subsp. lupini subsp. nov., associated with Lupinus luteus nodules in acidic soils of southern Chile.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1759558}, pmid = {41878742}, issn = {1664-302X}, abstract = {BACKGROUND: Members of the genus Labrys are widely distributed in soil and plant-associated environments, yet their ecological roles and functional contributions within plant-associated microbiomes remain poorly understood. Labrys methylaminiphilus strain La1 was isolated from nodules of Lupinus luteus growing in acidic soils of southern Chile, providing an opportunity to investigate strain-level traits relevant to plant-microbe interactions under environmental stress.<br><br>METHODS: Strain La1 was characterized using physiological and biochemical, chemotaxonomic, and genomic approaches, including whole-genome sequencing and comparative genomics. Functional traits related to plant interaction were assessed through in vitro assays for indole-3-acetic acid (IAA) production, antifungal activity against lupine pathogens, and in planta experiments evaluating plant growth under salinity and osmotic stress. The ecological distribution of closely related taxa was inferred from screening of publicly available environmental microbiomes using protologger pipeline.<br><br>RESULTS: Although strain La1 showed high genomic similarity to L. methylaminiphilus JLW10[T], it exhibited distinct phenotypic, metabolic, and ecological features. These included tolerance to acidic and moderately saline conditions, utilization of rhizosphere-associated carbon sources, and a fatty acid profile consistent with adaptation to terrestrial environments. Genomic analyses revealed genes related to stress tolerance, exopolysaccharide biosynthesis, carbohydrate-active enzymes, siderophore production, IAA synthesis, and non-ribosomal peptide synthetases. Consistent with these traits, La1 inhibited the growth of Colletotrichum lupini and Pleiochaeta setosa and significantly enhanced L. luteus biomass under osmotic and salinity stress. Metagenomic screening indicated that sequences closely related to La1 are predominantly associated with soil, rhizosphere, and plant-associated habitats.<br><br>CONCLUSION: This study demonstrates that strain La1 represents a functionally versatile and ecologically specialized lineage within L. methylaminiphilus, contributing traits relevant to plant-associated microbiomes in acidic soils. This integrated functional and ecological evidence supports the designation of Labrys methylaminiphilus subsp. lupini subsp. nov. and highlights the relevance of strain-level analyses for understanding plant-microbe interactions.}, }
@article {pmid41878750, year = {2026}, author = {Du, Z and Li, L and Liu, J and Wang, H and Li, J and Xu, Y and Cui, L and Yin, J}, title = {Wheat-Dependent Exercise-Induced Anaphylaxis Patients on a Wheat-Free Diet Exhibit a Gut Microbiota Composition More Similar to Healthy Individuals.}, journal = {Journal of asthma and allergy}, volume = {19}, number = {}, pages = {464532}, pmid = {41878750}, issn = {1178-6965}, abstract = {PURPOSE: There are limited studies on the intestinal microbiome in patients with wheat-dependent exercise-induced anaphylaxis (WDEIA), and changes in the gut microbiome in WDEIA patients after wheat-free diet have not been studied.<br><br>METHODS: This is a cross-sectional analysis. Fecal samples and clinical data were collected from 26 non-wheat-free patients with WDEIA, 11 wheat-free patients with WDEIA, and 24&#xa0;healthy controls (HCs). The gut microbiota was evaluated through metagenomic sequencing.<br><br>RESULTS: The sequencing revealed differences in the gut microbiome between patients with WDEIA on a non-wheat-free diet and HCs; more specifically, the non-wheat-free group exhibited a downregulation of two families (Rikenellaceae and Odoribacteraceae), three genera (Alistipes, Odoribacter, and Catenibacterium), and four species (Bacteroides_stercoris, Alistipes_putredinis, Bacteroides_intestinalis, and Bacteroides_cellulosilyticus). A wheat-free diet is associated with intestinal flora more similar to the structure of healthy individuals. The species Bacteroides_stercoris was negatively correlated with T-IgE, and the genus Catenibacterium was negatively correlated with T-IgE, as well as wheat, gluten, or gliadin-specific IgE. The genus Catenibacterium was positively correlated with the healthy control-enriched "Apoptosis (ko04210)" pathway and negatively correlated with the non-wheat-free WDEIA group-enriched "Thyroid hormone signaling pathway (ko04919)" pathway.<br><br>CONCLUSION: Patients with WDEIA exhibit a specific gut microbiota signature and function, which demonstrated the potential association between the gut microbiome and WDEIA development. WDEIA patients on a wheat-free diet exhibit a gut microbiome composition more similar to healthy individuals.}, }
@article {pmid41878990, year = {2026}, author = {Sun, Y and Li, Y and Temur, B and Lin, Y and Liu, Y and Yi, L and Sun, Z and Zhang, G and Li, J and Guo, Y and Li, L and Cai, J and Tian, W and Meng, G and Jiang, L and Fang, M and Ding, F and Zhou, X and Tu, C and He, B}, title = {Diversity Patterns of Domestic Herbivore Viruses in China Reveal Transmission Dynamics with Disease Management Implications.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e17444}, doi = {10.1002/advs.202517444}, pmid = {41878990}, issn = {2198-3844}, support = {32130104//National Natural Science Foundation of China/ ; 2025-NK-112//Qinghai Science and Technology Achievement Transformation Special Project/ ; }, abstract = {Domestic herbivores have complex interactions with humans and wildlife, playing important roles in zoonotic and epizootic disease emergence and transmission. Yet their viral diversity and cross-species transmission dynamics remain understudied. Through pan-viromic profiling of 10,225 swabs and 4,304 serum samples from 5,710 adult individuals across China's five major herbivore-rearing provinces, we prepare the domestic herbivore viromic catalog of China (DhCN-Virome) comprising 1,085,360 viral metagenomes, nearly capturing their family-level viral diversity while expanding by 2.3-fold global subgenus-level viral diversity. Distinct viromic signatures emerge across herbivore species and sample types. Viral communities generally follow a "higher openness, greater stability" pattern, with animals raised in confined settings being more susceptible to external influences. Viral circulations, particularly involving viruses of health concern, occur primarily within herbivore species but also extensively between herbivores and other species, including potential human-herbivore and avian-horse viral transmission. Bacteriophages constitute the most abundant viral entities, characterized by lytic replication strategies with some targeting pathogenic bacterial hosts. These findings expand our knowledge of herbivore viral diversity patterns and ecological transmission dynamics, underscoring the need for unified disease management strategies across all herbivore species. Particularly, the risk viruses represent potential triggers for future outbreaks, necessitating urgent epidemiological surveillance and vaccination programs.}, }
@article {pmid41879294, year = {2026}, author = {Liu, Y and Zhao, X and Gao, J and Xu, K}, title = {Therapeutic Evolution and Outcomes in EGPA Complicated by Diffuse Alveolar Hemorrhage: case-based review.}, journal = {Modern rheumatology case reports}, volume = {}, number = {}, pages = {}, doi = {10.1093/mrcr/rxag028}, pmid = {41879294}, issn = {2472-5625}, abstract = {BACKGROUND: Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare systemic vasculitis characterized by asthma, eosinophilia, and multi-organ involvement. Diffuse alveolar hemorrhage (DAH) is an uncommon but life-threatening pulmonary complication in EGPA.<br><br>CASE PRESENTATION: We report a 49-year-old previously healthy woman who presented initially with asthma-like symptoms and later developed fever, hemoptysis, cutaneous purpura, and periorbital edema. Laboratory evaluation revealed marked eosinophilia, anemia, elevated inflammatory markers, and strongly positive MPO-ANCA. Bronchoalveolar lavage fluid (BALF) was hemorrhagic and contained hemosiderin-laden macrophages, indicating DAH. Broad-spectrum antibiotics were empirically initiated but discontinued after metagenomic next-generation sequencing (mNGS) of BALF excluded infection. Bone marrow biopsy showed eosinophilic hyperplasia without clonal mutations. A diagnosis of MPO-ANCA positive EGPA with DAH was established. The patient received pulse methylprednisolone, prednisone, intravenous immunoglobulin, mepolizumab, and rituximab. Clinical symptoms improved rapidly, and radiological signs of alveolar hemorrhage nearly resolved within days.<br><br>CONCLUSION: Our case illustrates that integration of rituximab and mepolizumab with corticosteroids can achieve rapid remission and steroid sparing in EGPA-DAH. While evidence remains limited to case reports and small series, targeted biologics may fundamentally improve outcomes in this high-risk subset. Prospective studies are warranted to define optimal treatment strategies.}, }
@article {pmid41879323, year = {2026}, author = {Mortensen, GA and Schmidt, H and Radivojac, P and Ye, Y and Haas, DM}, title = {Metagenomic profiling and predictive modeling of the gut microbiome reveal signatures of gestational disease.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0315525}, doi = {10.1128/spectrum.03155-25}, pmid = {41879323}, issn = {2165-0497}, abstract = {The gut microbiome plays a vital role in maternal health and pregnancy outcomes, yet its impact on conditions like gestational hypertension (GH) and gestational diabetes mellitus (GDM) remains poorly understood. This study explores how the gut microbiome differs between pregnant women with these conditions and healthy controls, using metagenomic sequencing to analyze microbial composition and function. Our findings reveal that women with GH and GDM exhibit greater microbiome variability and distinct shifts in bacterial communities compared to healthy pregnancies. Key beneficial bacteria, such as Bacteroides fragilis and Roseburia intestinalis, were reduced in cases, suggesting potential disruptions in gut-related metabolic and immune functions. In addition to multiple differentially abundant species of Sphingobacterium in cases versus controls, functional analysis indicated changes in carbohydrate and lipid metabolism, reinforcing the microbiome's connection to metabolic health. Furthermore, machine learning models demonstrated promising results in predicting disease status based on microbiome data, underscoring the potential for gut bacteria as potential predictive biomarkers for pregnancy-related conditions. These insights highlight the gut microbiome's role in pregnancy health and suggest it may be a promising target for future interventions aimed at reducing complications and improving maternal-fetal outcomes.IMPORTANCEGut microbial dysbiosis has been implicated in pregnancy complications, yet most studies rely on 16S rRNA sequencing, which limits resolution and functional insight. Here, using shotgun metagenomic sequencing and machine learning, we identified robust microbial taxonomic and functional signatures that distinguish gestational hypertension and gestational diabetes from healthy pregnancies. A combined feature set enabled accurate classification of disease status, with overlapping features between statistical and predictive frameworks underscoring biological relevance. Altogether, our study defines high-resolution microbiome signatures with translational potential as predictive biomarkers for maternal health, while also providing an open, reproducible analysis pipeline to support future investigations.}, }
@article {pmid41879886, year = {2026}, author = {Chen, W and Li, X and Zhao, X and Zuo, Z and Wang, D and Zhao, F}, title = {GMW: a hybrid graph-based approach for post-assembly metagenome analysis and decontamination.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {41879886}, issn = {1869-1889}, abstract = {Accurate genome assembly from metagenomic sequencing data remains challenging, particularly in mixed infections involving multiple pathogens, due to data complexity and contaminant sequences. Here, we present GMW (Genomic Microbe-Wise), a novel computational tool that improves pathogen genome assembly accuracy and enhances contaminant removal capabilities by simplifying the post-assembly graph. GMW leverages community detection algorithms, sequence similarity analysis, and coverage patterns to resolve strain mixtures and improve assembly accuracy. Using datasets of influenza A virus subtypes, we demonstrate GMW's ability to disentangle mixed infections and reconstruct complete viral genomes with high precision. Additionally, GMW outperforms traditional sequence similarity methods in classifying target contigs from contaminants. This tool also provides interactive visualization modules to streamline the inspection of assembly outputs, including simplified representations of complex assembly graphs. By enhancing assembly quality and contamination filtering, GMW emerges as a versatile solution for applications in clinical diagnostics, microbial ecology, and pathogen surveillance.}, }
@article {pmid41880538, year = {2026}, author = {Consuegra-Asprilla, JM and Cuesta-Astroz, Y and González, &#xc1;}, title = {Characterization of the vaginal microbiome and its metabolic potential in Colombian patients with recurrent vulvovaginal candidiasis.}, journal = {Medical mycology}, volume = {}, number = {}, pages = {}, doi = {10.1093/mmy/myag026}, pmid = {41880538}, issn = {1460-2709}, abstract = {Recurrent vulvovaginal candidiasis (RVVC) is a multifactorial condition in which vaginal microbiota dysbiosis plays a key role. This study aimed to characterize the vaginal microbiome of patients with RVVC using metagenomic sequencing. Vaginal scraping samples were collected from 34 women aged 20-47 years and classified into three groups: (1) 14 women with RVVC who had experienced 3-7 episodes of VVC in the previous year; (2) 9 women with severe RVVC, defined as ≥8 episodes in the last year; and (3) 11 healthy women as controls. The results revealed an increased relative abundance of bacteria associated with bacterial vaginosis-including Gardnerella vaginalis, Gardnerella swidsinskii, and Prevotella bivia-as well as higher levels of Lactobacillus iners in both RVVC groups. In contrast, healthy women showed greater abundance of Lactobacillus crispatus and Lactobacillus gasseri. Diversity analyses indicated lower α-diversity in the healthy group compared to RVVC patients. Metabolic potential profiling showed a differential increase in sequences related to the phosphotransferase system (PTS), fructose/mannose metabolism, pentose phosphate pathway, and cysteine/methionine and purine metabolism in RVVC groups relative to controls; no significant differences were observed between RVVC groups, indicating that microbial profiles alone do not correlate with the degree of disease severity. These findings provide relevant insights into the taxonomic and functional characteristics of the vaginal microbiome in women with RVVC and may support the development of targeted therapeutic strategies.}, }
@article {pmid41880703, year = {2026}, author = {Liang, H and Liu, J and Huang, Y and Wang, Z and Wang, J and Liu, H and Zhang, L and Peng, Y}, title = {Engineering the anammox pathway in a full-scale AOA process for industrial wastewater treatment.}, journal = {Water research}, volume = {298}, number = {}, pages = {125793}, doi = {10.1016/j.watres.2026.125793}, pmid = {41880703}, issn = {1879-2448}, abstract = {The anammox process holds significant potential for municipal wastewater treatment, yet its full-scale application in industrial wastewater treatment plants (IWTP), particularly within endogenous denitrification-based processes, remains challenging. This study demonstrates the successful establishment of the anammox pathway in a full-scale (16,000 m[3]/d) anaerobic-aerobic-anoxic (AOA) process IWTP by implementing a synergistic control strategy that integrates low dissolved oxygen (DO: 0.5 - 1.4 mg/L) with residual ammonia (1.6 - 2.9 mg/L) at the aerobic outlet. During 450 days of operation, the system achieved stable and advanced nitrogen removal, with effluent NH4[+]-N and total nitrogen (TN) averaging only 0.2 mg/L and 5.7 mg/L, respectively. Metagenomic and isotope tracing analyses identified that the anoxic zone biofilm as a functional hotspot for anammox, where the relative abundance of anammox bacteria (AnAOB), predominantly Candidatus Brocadia, was significantly enriched to 0.074%. This community contributed to 36.7% of the TN removal via dual pathways coupling anammox with endogenous and exogenous partial denitrification. Economically, the incorporation of anammox reduced aerobic zone aeration energy consumption by 18.2% and decreased external carbon dosage by 44.4%. This work provides a pioneering demonstration of anammox under complex water quality conditions and offers a viable technological route toward low-carbon wastewater treatment.}, }
@article {pmid41881056, year = {2026}, author = {Chetruengchai, W and Sriwattanapong, K and Manaspon, C and Fakhruddin, KS and Samaranayake, L and Shotelersuk, V and Porntaveetus, T}, title = {Metagenome and Metabolic Pathways in Plaque Biofilms of Thai ELANE-Associated Neutropenic Patients: An Original Study and Scoping Review.}, journal = {European journal of dentistry}, volume = {}, number = {}, pages = {}, doi = {10.1055/s-0046-1818559}, pmid = {41881056}, issn = {1305-7456}, abstract = {Congenital neutropenia, particularly ELANE-associated forms, is associated with recurrent oral infections and aggressive periodontitis. While ELANE deficiency compromises oral health, its relationship to plaque biofilm ecology and metabolic function remains unclear. The oral microbiome-metabolome interplay in this condition remains largely uncharacterized globally. Here, we address this gap by characterizing the dental plaque metagenome and inferred metabolic pathways in a defined cohort of Thai neutropenia patients.In this exploratory study, we sequenced dental plaque samples from a defined cohort of nine individuals: three patients with severe congenital neutropenia or cyclic neutropenia (CyN) with confirmed ELANE variants, and six from age- and gender-matched healthy controls. Shotgun metagenomics was used for genomic analysis, followed by comprehensive microbiota examination. Subsequently, MetaCyc, a curated database, was used for in silico analysis and comparisons of the predicted functional pathways between the test and control plaque biofilms.The principal coordinate analysis plot and heat map revealed distinct segregation of microbial profiles between the patients and control groups. A significant variation in the proportions of the five core phyla was noted in patients and controls. Two commensal species, Aggregatibacter sp oral taxon 458 and Leptotrichia sp oral taxon 212, were enriched in the controls. Conversely, four species were significantly enriched in the patients, Selenomonas flueggei, Streptococcus milleri, Kingella oralis, and Actinobaculum sp oral taxon 183; the latter being notably elevated across all patients. The MetaCyc in silico analyses suggested predicted enrichment of functional pathways associated with inflammation and oxidative stress in patients, including L-methionine biosynthesis IV, formaldehyde assimilation III, L-rhamnose degradation, and the superpathway of (R,R)-butanediol biosynthesis pathways.Our study advances the understanding of ELANE-associated periodontitis by moving beyond descriptive microbiota analysis to suggest potential associations between host immune deficiency, microbial dysbiosis, and the microbiota-associated metabolic pathway alterations. These findings provide preliminary insights into targeted periodontal care in neutropenic patients, though further validation in larger cohorts is required.}, }
@article {pmid41881128, year = {2026}, author = {Song, Z and Yang, J and Zhang, L and Peng, Y}, title = {Photocatalytic Fe3O4@CDs Drives Nitrite-Independent extracellular respiration of anammox via efficient bidirectional electron transfer.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134489}, doi = {10.1016/j.biortech.2026.134489}, pmid = {41881128}, issn = {1873-2976}, abstract = {Anaerobic ammonium oxidation (Anammox) process relying on extracellular electron transfer (EET) overcomes nitrite scarcity in practical wastewater, but inefficient EET rate constrains nitrogen removal. Herein, Fe3O4 with carbon dot shell (Fe3O4@CDs) was self-assembled with anammox bacterial as a photocatalytic hybrid. Building on bacteria inward uptake of photogenerated electrons from CDs and outward transfer of respiratory electrons to Fe3O4, a bidirectional electron pathway was established firstly. This novel route achieved efficient nitrite-independent Anammox, enabling direct and rapid removal of 80 mg/L NH4[+]-N. To elucidate efficient nitrogen removal essence, metagenomics was employed to reveal photogenerated electrons fate and their mediated nitrogen metabolism mechanism. Results showed that, following assembly via -P-O bonds, bacteria internalized CDs photogenerated electrons (0.82 µA/cm) into menaquinone (MQ) pool. This influx activated energy-generation route constructed by bc1 and Rnf enzymes, increasing intracellular ATP level by 3.36---6.51-fold. Consequently, energy drove electrons pumping from MQ pool to cytochrome c, followed by transport outward via CDs, pili and flavin, amplifying electrons eflux by 1.77-fold. Such efflux generated MQ pool electron vacancies, which were efficiently replenished by electrons from hydrazine synthase- and hydrazine dehydrogenase-catalyzed NH4[+]-N oxidation to N2 without nitrite. Underpinned by the photogenerated electron-driven EET process, Anammox bacteria was enriched from 25.26% to 48.02%, thus sustaining a total nitrogen removal efficiency of > 97% for over 80 days-far exceeding the performance of existing system. This technology provides an efficient and sustainable theoretical framework for the application of anammox in practical wastewater treatment.}, }
@article {pmid41881328, year = {2026}, author = {Zhang, N and Wang, J and Yang, S and Liu, F}, title = {Biogeochemical and genomic drivers of groundwater DNRA: predictability of ammonium accumulation risk.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {128006}, doi = {10.1016/j.envpol.2026.128006}, pmid = {41881328}, issn = {1873-6424}, abstract = {Widespread ammonium (NH4[+]-N) contamination in groundwater, with local concentrations exceeding 20 mg/L, challenges traditional nitrogen removal, which is dominated by denitrification. Dissimilatory nitrate reduction to ammonium (DNRA), a nitrogen-retaining pathway, competes with denitrification. However, the environmental conditions that promote DNRA in aquifers and its quantitative contribution to NH4[+]-N loading remain critical knowledge gaps in groundwater nitrogen cycling research. We investigated how C/N ratios, Fe[2+] concentrations, initial NO3[-]-N, hydrochemical types, total dissolved solids (TDS), and pH influenced DNRA efficiency and its competition with denitrification. We found that DNRA efficiency peaked in organic-rich aquifers (15.70-26.69%) and was minimum in industrially and agriculturally contaminated groundwater (0.71%). High Fe[2], high initial NO3[-]-N, and HCO3[-]-type environments markedly promoted DNRA, whereas Cl[-]-type water inhibited it. Competition analysis revealed that elevated C/N ratios, Fe[2+], and TDS increased the relative contribution of DNRA to nitrate reduction. Metagenomic analysis further demonstrated that high C/N ratios and Fe[2+]-rich conditions promoted DNRA dominance via selective enrichment of Enterobacteriaceae carrying the abundant nrfA gene. Conversely, high mineralization and Na-Cl water types drastically reduced DNRA efficiency by suppressing the expression of key functional genes. Furthermore, under intermittent nitrate input, NH4[+]-N accumulated even with low DNRA efficiency, posing long-term water quality risks. We developed a DNRA efficiency prediction model using the Extreme Gradient Boosting algorithm (R[2] = 0.92), thereby enabling accurate assessment across diverse groundwater conditions. This work advances mechanistic understanding and provides an innovative predictive methodology for assessing DNRA-driven NH4[+]-N enrichment risks in groundwater.}, }
@article {pmid41871945, year = {2026}, author = {Vázquez-Castellanos, JF and Yoon, SJ and Won, SM and Raes, J and Kwon, HC and Si, J and Suk, KT}, title = {Stage-dependent gut microbiome and functional signatures across the liver disease spectrum: an integrative multicohort study.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-337436}, pmid = {41871945}, issn = {1468-3288}, abstract = {BACKGROUND: The gut-liver axis plays a critical role in liver disease progression; however, how gut microbial ecology and function vary across disease stages remains unclear.<br><br>OBJECTIVE: To define stage-specific microbial and functional signatures and evaluate their diagnostic potential.<br><br>DESIGN: We analysed faecal samples from 1168 individuals spanning healthy controls, fatty liver, hepatitis, cirrhosis and hepatocellular carcinoma by 16S rRNA sequencing, with a subset (n=141) profiled by shotgun metagenomics. To increase statistical power and enable external validation, 2376 publicly available metagenomic datasets, including 734 liver-related, were integrated. Machine learning-based multicohort analysis was used to identify microbial biomarkers, assess risk factors and classify disease stages.<br><br>RESULTS: Microbial diversity declined and a low-richness enterotype expanded with disease severity. Machine learning revealed a discordance in hepatitis, which lacked taxonomic markers but was defined by a conserved functional signature of biosynthetic upregulation. In contrast, advanced stages featured consistent markers like Ligilactobacillus and Veillonella, with strain-level evidence confirming oral-gut transmission. Functional profiling delineated a metabolic continuum from anabolic precursor synthesis in hepatitis to virulence factor production in cirrhosis and putrefactive metabolism in carcinoma. Comparative analysis confirmed that these signatures were distinct from those in non-liver metabolic and oncologic disorders. Importantly, the expansion of oral-derived Veillonella spp and the low-richness enterotype were significantly associated with increased mortality.<br><br>CONCLUSION: This large-scale study delineates stage-dependent ecological and functional remodelling of the gut microbiome across liver diseases. These findings highlight the potential of microbiome-based markers for non-invasive diagnosis and prognostic risk stratification in liver diseases.}, }
@article {pmid41872229, year = {2026}, author = {Ji, M and Li, Y and Wang, M and Liu, X and Gong, X and Tu, Q}, title = {Unveiling the biodiversity of large DNA viruses in intertidal mudflats via metagenomics.}, journal = {Nature communications}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41467-026-71095-7}, pmid = {41872229}, issn = {2041-1723}, abstract = {Large DNA viruses (LDVs) are unique members of the Earth's virosphere, remarkable for their extra-large genome sizes and broad metabolic potential. However, our knowledge of this viral group remains very limited, particularly in complex dynamic habitats. In this study, 237 metagenome-assembled LDV genomes are comprehensively recovered from intertidal mudflats using multiple sampling and sequencing strategies totaling 5.3 TB data. A phylogenetically distinct subgroup within Imitervirales is identified, showing broad associations with multiple eukaryotic lineages. Certain LDV populations can persist locally and exhibit significant genomic variations potentially driven by dynamic intertides. Ecological patterns are observed at both community and genetic levels, with giant viruses showing steeper community turnover but weaker nucleotide diversity variations than large phages. Moreover, LDVs exhibit similar macroecological patterns to their potential hosts, which substantially shape LDV community assembly. The intertidal LDVs encode diverse functional genes, most of which remain uncharacterized, with a 27.32% improvement for unknown phage genes using a protein language model. Although giant viruses and large phages share comparable functional gene composition, they exhibit distinct preferences for specific metabolic pathways, especially those associated with carbon and nitrogen cycling. This study broadens our understanding of the biodiversity and ecology of LDVs in the understudied intertidal ecosystems.}, }
@article {pmid41872577, year = {2026}, author = {Shan, X and Cao, K and Jeckel, H and Alcalde, RE and Trindade, IB and Kwiecinski, JV and Newman, DK}, title = {Drought drives elevated antibiotic resistance across soils.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41872577}, issn = {2058-5276}, support = {2R01AI127850-06A1//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health &amp; Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2209379//National Science Foundation (NSF)/ ; ALTF 191-2023//European Molecular Biology Organization (EMBO)/ ; }, abstract = {Antibiotic resistance is a growing threat to human health and is often attributed to excessive clinical usage that selects for resistance. Although many antibiotics are derived from soil microorganisms, how environmental changes to soil ecosystems might promote resistance is poorly understood. Here we establish drought as a driving force of antibiotic resistance in the soil, with potentially far-reaching public health consequences. Across various geographic regions and soil types, we consistently observe metagenomic signatures of enrichment for antibiotic producers under drought conditions. Experimentally, we demonstrate that drought-induced lowering of water content concentrates natural antibiotics, thereby intensifying selection against sensitive strains and favouring antibiotic-resistant bacteria. Using clinical surveillance data from 116 countries, we show that the average frequency of hospital antibiotic resistance is strongly correlated with the local aridity index, even after controlling for regional income differences. Together, our findings reveal an underrecognized link between climate factors and antibiotic resistance.}, }
@article {pmid41872600, year = {2026}, author = {Segev, T and Barak, D and Zahavi, L and Godneva, A and Rein, M and Krongauz, D and Samocha-Bonet, D and Rossman, H and Weinberger, A and Segal, E}, title = {Diet-microbiome associations in 10,068 individuals from the Human Phenotype Project to guide personalized nutrition.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {41872600}, issn = {1546-170X}, abstract = {Diet is a major environmental factor influencing the human gut microbiome. However, the effects of specific foods and dietary patterns on microbial composition, diversity and function is not fully understood, limiting progress toward personalized dietary strategies. Here, leveraging 10,068 participants from the Human Phenotype Project with app-based diet logs and shotgun metagenomics, we predicted diet-microbiome associations at species-level resolution. Diet significantly predicted microbial diversity (richness r = 0.26, Shannon Index r = 0.24), the relative abundance of 669 of 724 species tested (92.4%, false discovery rate <0.05), and 313 of 320 pathways (97.8%, false discovery rate <0.05). Feature attribution identified distinct food-microbe links, including coffee with Lawsonibacter asaccharolyticus (r = 0.43), yogurt with Streptococcus thermophilus (r = 0.42) and milk with Bifidobacterium species (r = 0.31-0.36). In parallel, broader dietary patterns, especially the degree of food processing, emerged as predictors of microbial diversity and composition. We also show that diet-microbiome associations persist over four years, with 82.5% of species exhibiting significant longitudinal tracking between predicted and observed abundances. Finally, we developed an exploratory analysis for simulating personalized dietary interventions with predicted microbiome shift effects that are associated with improvements in cardiometabolic health. Our findings demonstrate that diet is strongly associated with microbiome composition, diversity and function, and highlight its potential for guiding personalized interventions.}, }
@article {pmid41872963, year = {2026}, author = {Kim, B and Kim, HN and Cheong, HS and Jeong, S and Kim, J and Park, DI and Joo, EJ}, title = {Fecal microbiota from hepatitis B-infected individuals alters triglyceride metabolism and microbial pathways in mice.}, journal = {Gut pathogens}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13099-026-00825-5}, pmid = {41872963}, issn = {1757-4749}, support = {RS-2023-KH135855//Korea Health Industry Development Institute/Republic of Korea ; NRF-2021R1A2C4002454//National Research Foundation of Korea/ ; }, }
@article {pmid41874180, year = {2026}, author = {Garzon, A and Miramontes, C and Weimer, BC and Profeta, R and Hoyos-Jaramillo, A and Fritz, HM and Pereira, RV}, title = {Characterizing the nasopharyngeal microbiome and resistome of dairy cattle with and without bovine respiratory disease.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0264825}, doi = {10.1128/spectrum.02648-25}, pmid = {41874180}, issn = {2165-0497}, abstract = {Bovine respiratory disease (BRD) remains a significant economic challenge in dairy cattle despite extensive vaccination programs that have been developed and implemented during the last few decades. This study investigated the nasopharyngeal microbiome and resistome of dairy cattle across various life stages to understand the roles of microbial communities associated with BRD. A case-control study was conducted on three commercial dairy farms in Northern California, collecting nasopharyngeal swabs from 69 animals, including preweaned calves, weaned heifers, and lactating cows with and without BRD. Shotgun metagenomic sequencing was used to characterize both microbiome and resistome profiles observed at the time of BRD diagnosis. Results revealed that BRD is associated with distinct microbial community patterns, rather than the increased abundance of a specific pathogen. Age was a critical factor influencing microbial diversity, with adult cows showing the highest diversity and weaned heifers with BRD showing the lowest. A total of 1,164 bacterial species were identified, with BRD cases harboring 14 unique species compared to control animals. BRD cases were characterized by the co-occurrence of multiple respiratory pathogens, including Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mesomycoplasma species, which showed positive correlation with BRD cases but negative correlations in BRD controls, while BRD control animals showed significantly higher abundance of commensal Staphylococcus species. Resistome analysis identified 65 antimicrobial resistance genes, with BRD cases harboring more unique resistance genes than BRD controls. These findings challenge traditional single-pathogen models and demonstrate that BRD is likely the result of complex microbial community interactions and changes in community abundance, providing new potential targets to explore when considering prevention strategies toward promoting microbial communities that prevent or reduce the risk of BRD.IMPORTANCEBovine respiratory disease (BRD) represents one of the most economically challenging conditions in cattle production, with an estimated direct cost that exceeds $165 million annually in the United States alone. Despite decades of vaccination efforts targeting known pathogens, BRD prevalence remains unchanged, indicating an incomplete understanding of disease pathogenesis. This study provides critical insights by shifting focus from individual pathogens to entire microbial communities, revealing that BRD involves complex bacterial interactions, as well as the role of the understudied nasal commensal microbiome in healthy animals. The identification of distinct "pathobiomes" associated with disease and protective commensal communities in healthy animals fundamentally changes approaches to BRD prevention and treatment. The discovery that age significantly influences microbiome stability highlights critical intervention periods. Furthermore, the association between BRD and increased antimicrobial resistance genes raises concerns about current treatment and overall management practices, selecting for drug-resistant communities. This research provides a foundation for developing microbiome-based diagnostic tools and interventions supporting healthy microbial ecosystem development.}, }
@article {pmid41874256, year = {2026}, author = {Lam, WKJ and Chan, KKP and Wang, G and Lai, CKC and Kang, G and Chan, C and Leung, ACY and Wong, NHL and Tso, CSN and Chow, KM and Ramakrishnan, S and Wong, KT and Lau, CHY and Ng, JKC and Lo, RLP and Yip, WH and Ngai, JCL and To, KW and Tse, IOL and Cheng, SH and Shang, H and Chan, KW and Lai, A and Chan, CML and Lee, VCT and Malki, Y and Choy, LYL and Ma, ML and Zhou, Q and Yu, SCY and Jiang, P and Ko, FWS and Chan, KCA and Hui, DSC and Lee, YCG and Lo, YMD}, title = {Sequencing of Pleural Fluid and Plasma for Tuberculous Pleuritis.}, journal = {NEJM evidence}, volume = {5}, number = {4}, pages = {EVIDoa2500237}, doi = {10.1056/EVIDoa2500237}, pmid = {41874256}, issn = {2766-5526}, mesh = {Humans ; *Tuberculosis, Pleural/diagnosis/microbiology/blood ; Male ; Female ; Middle Aged ; *Mycobacterium tuberculosis/genetics/isolation &amp; purification ; *Pleural Effusion/microbiology ; *DNA, Bacterial/analysis ; Prospective Studies ; Sensitivity and Specificity ; Aged ; Adult ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: The laboratory diagnosis of tuberculous pleuritis (TBP) is hindered by the paucibacillary nature of Mycobacterium tuberculosis in the pleural space, resulting in low sensitivity of microbiological culture and polymerase chain reaction-based analyses on pleural fluid. The use of metagenomic next-generation sequencing for diagnosing TBP may be limited by the background noise of DNA from nontuberculous mycobacteria.<br><br>METHODS: We performed targeted sequencing to analyze M. tuberculosis DNA in paired pleural fluid and plasma from prospectively enrolled consecutive patients with new-onset pleural effusion. We used a bioinformatics alignment algorithm to the M. tuberculosis genome that was masked for regions with high sequence similarity to nontuberculous mycobacteria. Our primary outcome was a comparison of diagnostic sensitivity between M. tuberculosis sequencing as described above and culture using McNemar's test.<br><br>RESULTS: Among the included 329 patients with pleural effusion, 34 patients with TBP were identified. Targeted sequencing detected M. tuberculosis DNA fragments in the pleural fluid of all TBP cases (median, 267.6 reads per 10 million [RP10M]; interquartile range [IQR], 30.8-2644.3) but absent in 288 out of 295 (97.6%) non-TBP samples (median, 0 RP10M; IQR, 0-0). Targeted sequencing of pleural fluid achieved a sensitivity of 97.1% for TBP detection at a cutoff of 2 RP10M, in contrast to 47.1% by M. tuberculosis culture (P<0.001, McNemar's test). Sequencing yielded an area-under-the-curve value of 0.9996 (95% confidence interval, 0.9988-1.0000) for differentiating TBP and non-TBP. Plasma analysis by targeted sequencing with the same alignment algorithm reported an area-under-the-curve value of 0.9475 (95% confidence interval, 0.8929-1.0000).<br><br>CONCLUSIONS: Targeted sequencing of pleural fluid with selectively masked M. tuberculosis genomic alignment accurately diagnosed TBP and outperformed conventional diagnostic tests. (Supported by InnoHK and the Hong Kong Tuberculosis, Chest and Heart Diseases Association; ClinicalTrials.gov number, NCT05397730.).}, }
@article {pmid41874416, year = {2026}, author = {Koseli, E and Tyc, KM and Buzzi, B and Akbarali, HI and Damaj, MI}, title = {The Role of the Gut Microbiome in Nicotine Withdrawal and Dependence.}, journal = {Nicotine &amp; tobacco research : official journal of the Society for Research on Nicotine and Tobacco}, volume = {}, number = {}, pages = {}, doi = {10.1093/ntr/ntag057}, pmid = {41874416}, issn = {1469-994X}, abstract = {INTRODUCTION: Smoking is considered a global pandemic with more than 1.3 billion people being active smokers. Increasing evidence suggests that nicotine exposure can lead to changes in the gut microbiome, increases in permeability, and impaired mucosal immune responses in the gastrointestinal tract. However, the literature on behavioral aspects of nicotine-microbiome interaction, such as dependence and withdrawal, is limited. In this study, we used homologous fecal material transplants (FMT) to modify the gut microbiome and its impact on the intensity of nicotine withdrawal in mice.<br><br>METHODS: We used osmotic minipumps as an application of chronic nicotine for 15&#xa0;days and orally gavaged FMT 2x a day to the mice. We assessed the nicotine withdrawal by measuring the number of somatic signs and anxiety-like behaviors at 24&#xa0;h and 1&#xa0;week after the mini pump removal. Fecal samples were also collected points to identify the gut microbiome changes.<br><br>RESULTS: Fecal transplants reduced the number of somatic signs and anxiety-like behaviors in nicotine-treated mice up to a week after the removal of minipumps. The shotgun metagenomic results of the fecal samples from 24&#xa0;h after minipumps removal time point show altered gut microbiome with a significant shift in the species composition between the nicotine treated and its homologous FMT treatment.<br><br>CONCLUSIONS: Our results indicate that under our experimental conditions fecal transplant can reduce the severity of nicotine withdrawal. This suggests that interactions along the gut-brain axis are important for the development of nicotine dependence and might help lower the risk of cancer and other serious health problems in humans.}, }
@article {pmid41874421, year = {2026}, author = {Wang, J and Lu, L and Sun, Y and Messer, LF and Wu, M and Duan, Z and Shi, J and Yang, Y and Li, C and Mao, Y and Zhu, D and Rillig, MC and Wang, X}, title = {AHL-mediated quorum sensing drives plastisphere formation and elevates pathogenic potential.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrag066}, pmid = {41874421}, issn = {1751-7370}, abstract = {The biofilm colonizing plastic debris, termed 'the plastisphere', is of growing global concern due to escalating plastic pollution. However, the biological mechanisms underpinning plastisphere formation remain poorly understood. Here, we analyzed public global metagenomes, revealing a significant enrichment of genes associated with quorum sensing (QS) and biofilm formation, with a pronounced signal for acyl-homoserine lactone (AHL) QS. Using controlled microfluidic and tubular column experiments, we further demonstrate that exogenous AHL actively promotes plastisphere formation, biomass accumulation, and extracellular polymeric substance production on microplastics, whereas a quorum quenching agent (AHL acylase) effectively inhibits these processes. Multi-omics analyses revealed that AHLs can transcriptionally activate genes involved in adhesion, motility, chemotaxis, and matrix production, fundamentally reshaping community structure, restructuring inferred microbial interaction networks, and driving community assembly toward stronger deterministic selection. AHL stimulation also increased the relative abundance and expression of pathogen-associated and virulence-related functions, suggesting an elevated virulence potential within the plastisphere under QS-promoting conditions. Together, our findings establish AHL-mediated QS as a central driver of plastisphere assembly and a key determinant of risk profile, highlighting its critical role in understanding and potentially mitigating the growing environmental and health hazards associated with microplastic pollution.}, }
@article {pmid41874457, year = {2026}, author = {Mohr, AE and Berryman, CE and Harris, MN and Lawrence, AB and Chakraborty, N and Campbell, R and Dimitrov, GI and Gautam, A and Hammamieh, R and Lieberman, HR and Rood, JC and Pasiakos, SM and Karl, JP}, title = {Testosterone administration partially modulates gut microbiota responses to severe energy deficit.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpendo.00291.2025}, pmid = {41874457}, issn = {1522-1555}, support = {W81XWH-14-1-0335//DOD | OSD | Defense Technical Information Center (ADD)/ ; W81XWH-17-2-0026//DOD | OSD | Defense Technical Information Center (ADD)/ ; Joint Program Committee-5//Military Operational Medicine Research Program (MOMRP)/ ; //DOE | Oak Ridge Institute for Science and Education (ORISE)/ ; T32DK137525//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; }, abstract = {Severe diet- and exercise-induced energy deficit (SED) suppresses androgen production in healthy men, altering metabolism and driving muscle loss. The gut microbiota modulates host metabolism, yet the community's response to SED and any role of androgen hormones are unclear. Herein, healthy, physically-active men were randomized to receive 200mg/wk testosterone enanthate (n = 24) or placebo (n = 26) during a 28-day residential intervention that restricted energy intake and increased energy expenditure inducing a ~2000 kcal/d SED. Multi-omic analyses revealed altered gut microbiota composition, reduced fecal short-chain fatty acids (SCFA), and shifts in bacterial metabolic pathways toward lipid utilization and mucin degradation during SED, suggesting adverse effects of SED on gut microbiota metabolic functions. Testosterone administration preserved certain SCFA-producing taxa and bioenergetic pathways without fully counteracting effects of SED indicating a limited but potentially important interplay between androgen status and the gut microbiota under conditions of SED.}, }
@article {pmid41874663, year = {2026}, author = {Hu, C and Lin, M and Hu, T and Zeng, Y and Zeng, R and Wang, C}, title = {Linking Bacterial r/k Ecological Shifts to Spatiotemporal Nitrogen Removal Dynamics in Recirculating Aquaculture Systems.}, journal = {Microbial ecology}, volume = {}, number = {}, pages = {}, doi = {10.1007/s00248-026-02742-1}, pmid = {41874663}, issn = {1432-184X}, support = {NO.2024SJRC4//the Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.LTO2326//State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences/ ; NO.2023A04J0897//Guangzhou Science and Technology Program Project/ ; NO.SL2023E04J00185//Demonstration and Promotion of Key Technologies for Land-based Factory Farming of Hybrid Eleotris oxycephala/ ; }, }
@article {pmid41874734, year = {2026}, author = {de Medeiros Azevedo, T and Aburjaile, FF and Pandolfi, V and Ferreira-Neto, JRC and Fracetto, GGM and de Oliveira Silva, RL and Gonçalves-Oliveira, RC and de Carvalho Azevedo, VA and Brenig, B and Benko-Iseppon, AM}, title = {Unlocking the microbiome of an extremophile plant: metagenomic insights into Calotropis procera's endo-rhizosphere communities.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41874734}, issn = {1573-0972}, }
@article {pmid41874898, year = {2026}, author = {Son, JS and Lee, SY and Sang, MK and Spinelli, F and Ryu, CM}, title = {Protective holobiome promotes strawberry tolerance of biotic stresses.}, journal = {Stress biology}, volume = {6}, number = {1}, pages = {}, pmid = {41874898}, issn = {2731-0450}, support = {. RS-2022-RD010288//RDA/ ; CN00000022//Italian Academy for Advanced Studies in America, Columbia University/ ; KRIBB202434//Korea Research Institute of Bioscience and Biotechnology/ ; }, abstract = {The commercial cultivation of strawberry (Fragaria × ananassa) is increasingly challenged by biotic stresses such as plant pathogens and insect pests, while climate change exacerbates abiotic stresses. Reliance on chemical fumigants and broad-spectrum pesticides presents risks to human health, environmental quality, and microbial diversity. The strawberry holobiome, defined as the integrated community of plant-associated microorganisms that inhabit the rhizosphere, phyllosphere, endosphere, and fruit surface, is emerging as a key determinant of plant health and productivity. Recent metagenomic and metabolomic studies have identified cultivar-specific microbial consortia that suppress plant disease, enhance stress tolerance via induced systemic resistance, and modulate fruit quality. The engineering of synthetic microbial communities (SynComs) offers a targeted approach to microbiome augmentation, but the lack of high-resolution functional data hinders the development of effective SynComs, especially in hydroponic and substrate culture systems. This review synthesizes recent advances in holobiome profiling, evaluates microbial biocontrol strategies against major pathogens, and outlines future directions, including AI (artificial intelligence)-driven community design, integrated multi-omics analysis, and microbiome-assisted breeding. Addressing these gaps will enable precision management of the strawberry microbiome to sustain yield, quality, and resilience under dynamic environmental conditions.}, }
@article {pmid41874931, year = {2026}, author = {Gong, K and Xie, Z and Zhang, P and Xu, J and Huang, J and Li, X and Huang, L}, title = {Limosilactobacillus reuteri LR-99 Modulates Gut Microbiota and Core Symptoms in Children with Autism Spectrum Disorder: A Single-arm Pilot Study.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {41874931}, issn = {1867-1314}, support = {3502Z202372073//Xiamen Natural Science Foundation of China/ ; }, }
@article {pmid41875072, year = {2026}, author = {van der Heyde, M and Curran, M and Floeckner, S and Nevill, P and White, NE and Austin, AD and Guzik, MT}, title = {Validating COI eDNA Metabarcoding Primers for Detection of Subterranean Fauna.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70127}, doi = {10.1111/1755-0998.70127}, pmid = {41875072}, issn = {1755-0998}, support = {LP190100555//Australia Research Council Linkage Project/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *DNA Primers/genetics ; *DNA, Environmental/genetics ; *Electron Transport Complex IV/genetics ; Animals ; Biodiversity ; *Metagenomics/methods ; }, abstract = {Subterranean ecosystems host a diverse range of ancient fauna, but studying these ecosystems is challenging due to significant sampling difficulties. Environmental DNA (eDNA) metabarcoding offers a promising approach for monitoring subterranean biodiversity, yet issues such as primer bias and non-target amplification can complicate its effectiveness. Thus, thorough validation of metabarcoding primers is crucial for accurate and comprehensive assessments of subterranean faunal diversity. This study aimed to address the need for robust primer validation through in silico, in vitro and in situ analyses, shedding light on primer performance across various subterranean taxa. The primary objective was to evaluate the effectiveness of COI metabarcoding primers for assessing subterranean faunal diversity. In silico analyses involved curating COI sequences from the Barcode of Life Database (BOLD) and selecting 14 primer combinations for in vitro testing using mock communities. Results revealed varying primer performance in terms of PCR efficiency and detection limits across different taxa. One primer combination (BF1/jgHCO2198) detected 82% of taxa in the mock community, but only at high DNA concentrations of the target taxa. The highest proportion of subterranean taxa detected in a diluted mock community was 68% using the fwhF2/fwhR2n primer combination. For in situ field validation, this same primer set detected 13 out of 16 subterranean taxa identified in haul net samples, along with an additional four taxa not identified by haul net. These findings highlight the potential of COI metabarcoding and the critical importance of primer selection for eDNA studies aimed at conserving subterranean biodiversity.}, }
@article {pmid41875156, year = {2026}, author = {Shen, LQ and Wang, L and Yao, Z and Lin, D and Ye, YQ and Zhang, WR and Ye, M and Sun, MM and Du, S and Wu, D and O'Connor, P and Zhu, D}, title = {Phages drive the dissemination of antibiotic resistance genes by facilitating host adaptation to heavy metal stress.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {123}, number = {13}, pages = {e2535653123}, doi = {10.1073/pnas.2535653123}, pmid = {41875156}, issn = {1091-6490}, support = {22193062//MOST | National Natural Science Foundation of China (NSFC)/ ; 2024YFE0106300//MOST | National Key Research and Development Program of China (NKPs)/ ; 2023321//Youth Innovation Promotion Association of the Chinese Academy of Sciences (CAS YIPA)/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; }, mesh = {*Metals, Heavy/toxicity/metabolism ; *Bacteriophages/genetics/physiology ; Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Adaptation, Physiological/genetics ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/virology/drug effects ; Stress, Physiological ; Genes, Bacterial ; China ; Gene Transfer, Horizontal ; }, abstract = {Heavy metals are increasingly recognized as major drivers of antibiotic resistance gene (ARG) dissemination in soil ecosystems. However, the role of phages in heavy metal-driven ARG dissemination and the underlying mechanisms remain poorly understood. Here, through integrative metagenomic, viromics, and metabolomic analyses of paddy soils across China, we reveal that soil phages promote ARG dissemination under heavy metal stress, likely through two potential mechanisms. First, phage-encoded auxiliary metabolic genes (AMGs) reprogram host metabolism to enhance bacterial survival and adaptation, thereby facilitating the cotransfer of adjacent ARGs and indirectly promoting horizontal dissemination. Second, phage-encoded heavy metal detoxification genes (HDGs) directly mediate metal detoxification, driving the cotransfer of neighboring ARG fragments and inducing lipid peroxidation-associated increases in membrane permeability, which collectively enhance ARG mobilization. We further identify a significant enrichment of lysogenic phages coharboring ARGs with AMGs or HDGs (AMG-ARG and HDG-ARG fragments), underscoring their contribution to ARG dissemination. Phage transplantation experiments confirm that elevated heavy metal stress triggers lysogenic phage-mediated ARG transduction to bacterial hosts. Cumulatively, our experiments highlight the pivotal role of phages in mediating ARG transfer under heavy metal pressure and underscore the necessity of incorporating phage dynamics into ARG risk assessments.}, }
@article {pmid41875508, year = {2026}, author = {Estrada, CSD and de Oliveira, OA and Lopes, TAC and Maria, CRC and Avelino-Alves, D and Lima, M and Vidal, LM and de Siqueira Campos, L and Dias, GM and Thompson, C and Tschoeke, D and Thompson, F}, title = {Rhodolith metagenome diversity shifts across the Great Amazon System.}, journal = {The Science of the total environment}, volume = {1027}, number = {}, pages = {181652}, doi = {10.1016/j.scitotenv.2026.181652}, pmid = {41875508}, issn = {1879-1026}, abstract = {Rhodolith-forming coralline algae in the Great Amazon Reef System (GARS) occur under strong light and redox gradients imposed by the Amazon River plume. We tested whether a conserved microbial and metabolic core persists across sectors while functions reorganize with local conditions. We conducted shotgun metagenomics on rhodolith holobionts collected in the South, Central, and North sectors and profiled taxonomic composition and pathway markers (KEGG/SEED; METABOLIC). Bacteria dominated the holobiont, with Proteobacteria, Chloroflexi, and Bacteroidetes prevailing, and Thaumarchaeota as the main archaeal lineage. Functional profiles showed structured not random variation among sectors. In the South, high water transparency supported oxygenic phototrophy (psa/psb, rbcL/S; phycobiliproteins) and stronger coupling between carbon fixation and respiration. The Central sector displayed a transitional configuration combining oxygenic and anoxygenic phototrophy (pufL/M; bch genes) with co-occurring nitrification-denitrification (amoA, nxrAB, nirK, nosZ), indicating tight NS cycling. The North was enriched in sulfur redox pathways linked to suboxic microzones, with sulfate-reducing and sulfur-oxidizing lineages and contributions from methanogenic archaea. Across sectors, high diversity and functional redundancy likely underpin holobiont persistence in mesophotic settings. Our results indicate a resilient, sector-specific reorganization of rhodolith-associated microbiomes along plume-driven gradients, with implications for biogenic calcification and biogeochemical stability under climate change and ocean acidification scenarios.}, }
@article {pmid41875555, year = {2026}, author = {Lu, L and Li, M and Kang, G and Wu, P and Wang, N and Tan, Y and Su, G and Ruan, J and Zhang, S}, title = {Fate of per- and polyfluoroalkyl substances (PFAS) and microbial communities in wastewater treatment: Disinfection-driven changes in microbial dynamics and PFAS profiles.}, journal = {Ecotoxicology and environmental safety}, volume = {314}, number = {}, pages = {120059}, doi = {10.1016/j.ecoenv.2026.120059}, pmid = {41875555}, issn = {1090-2414}, abstract = {Municipal wastewater treatment plants (MWWTPs) are both sinks and sources of per- and polyfluoroalkyl substances (PFAS) due to limited removal efficiency in current treatment systems. However, the role of treatment processes, especially disinfection, in altering PFAS and microbial communities remains underexplored. In this study, we investigated the occurrence of 17 PFAS in two MWWTPs in Northwest China and characterized microbial communities through metagenomic sequencing. Results showed that total PFAS concentrations increased from 56.8 to 60.3 ng/L in MWWTPA and from 5.1 to 19.1 ng/L in MWWTPB, indicating ineffective removal. Perfluoropentanoic acid (PFPeA) and perfluorononanoic acid (PFNA) dominated the influent, accounting for 86.6% and 33.3% in MWWTPA and MWWTPB, respectively. In contrast, perfluorooctanesulfonic acid (PFOS, 46.8-52.4%) and perfluorooctanoic acid (PFOA, 5.1-8.9%) concentrations increased markedly in the effluent, becoming the predominant PFAS. Meanwhile, disinfection also altered microbial diversity and homogenized community structures between the two MWWTPs. Further analysis revealed strong associations (p < 0.01) between elevated PFAS levels and specific microbial taxa, including Actinomycetia and Thermoprotei, alongside increased relative abundance of genes annotated as haloacid dehalogenases, monooxygenases, and cytochrome P450. These associations may reflect potential influences on PFAS precursor dynamics. Overall, these findings highlight the importance of considering both chemical and microbial shifts when evaluating PFAS behavior during wastewater treatment.}, }
@article {pmid41875615, year = {2026}, author = {Kesavan, D and Meenatchi, R and Mohanakrishna, R and Tripathi, A and B S, Y and Narayanane, S and Gupta, S and Yadav, P and Pasupuleti, M and Mani, G and Balachandran, KRS and Rangamaran, VR and Verma, P and Kumar, AG and Vinithkumar, NV and Gopal, D and Pazhani, GP and Arockiaraj, J}, title = {Metagenomic mining of microbial communication genes from Indian deep-sea sediments using a quorum sensing- and quenching-related protein database.}, journal = {Marine genomics}, volume = {86}, number = {}, pages = {101245}, doi = {10.1016/j.margen.2026.101245}, pmid = {41875615}, issn = {1876-7478}, abstract = {Cell-to-cell communication among microbes plays a key role in environmental adaptation and highly contributes to global biogeochemical cycling. However, microbial communication systems in deep-sea sediments, where diverse microbial communities employ quorum sensing (QS) and quorum quenching (QQ) mechanisms to regulate ecological interactions, remain largely understudied. Their distribution patterns and functional dynamics in deep-sea ecosystems are poorly understood. This study investigated QS and QQ communication systems alongside microbial community distribution in Arabian Sea sediments collected from depths of 334, 492, 550, and 992 m across the northern and southern Arabian Sea. Shotgun metagenomic sequencing was performed in conjunction with a curated QS- and QQ-related protein (QSP) database. Both individual assemblies and metagenome-assembled genomes (MAGs) were analyzed to comprehensively identify communication-associated proteins. In total, around 359 QSPs were detected across four sediment samples. Shallow sediments (334 and 492 m) exhibited greater abundance and diversity of QS and QQ elements, particularly acyl-homoserine lactone (AHL)-driven QS systems and acylase/lactonase-based QQ systems, indicating active microbial interactions. In contrast, deeper sediments (550 and 992 m) displayed reduced diversity of canonical QS elements with enrichment of autoinducer-2 (AI-2), diffusible signal factor (DSF), and cyclic-di-GMP signalling pathways, suggesting adaptive mechanisms conducive to oligotrophic and high-pressure conditions of deep-sea. Correlation analyses revealed potential intra- and inter-system associations among QS regulators and QQ enzymes, indicating complex regulatory networks. MAG-derived protein analyses detected conserved catalytic motifs, and molecular docking supported functional interactions with signal molecules. Overall, these findings provide a preliminary overview of QS and QQ related genes in deep sea sediments of the Arabian Sea and suggest potential variability in microbial communication systems within these environments.}, }
@article {pmid41875710, year = {2026}, author = {Gadoin, E and Massot, M and Callens, M and Arnout, P and Bedhomme, S and Rajkovic, A}, title = {Shotgun metagenomic profiling reveals a high diversity of taxa and genes within biofilms formed on microplastics incubated in urbanised aquatic ecosystems.}, journal = {Marine pollution bulletin}, volume = {228}, number = {}, pages = {119569}, doi = {10.1016/j.marpolbul.2026.119569}, pmid = {41875710}, issn = {1879-3363}, abstract = {Microplastics (MPs) are ubiquitous in aquatic ecosystems, where they are colonized by microbial communities, called the plastisphere. Of great concern is the detection of potential pathogens and antimicrobial resistance genes (ARG) in the plastisphere, which might be transported across ecosystems through MPs drifting. We used shotgun metagenomic profiling to assess taxa diversity, ARG and virulence genes (VG), within biofilm formed on polypropylene (PP) particles incubated in situ in five locations, following an anthropic gradient around Ostend (Belgium). Our results demonstrated significant variability of the plastisphere across incubation sites, but not between PP and control glass beads. Potential pathogenic bacteria (PPB) represented about 7% of bacterial reads within biofilms and VG were mainly involved in nutrition and adherence. Using dqPCR results to normalize metagenomic reads, we demonstrated a selective enrichment of ARG and VG in biofilms, while these were less abundant but more diverse in surrounding water. These findings highlight the presence of PPB, ARG and VG across all sites, likely driven by anthropogenic pressures. Although no substrate-specific effect was detected, the ability of PP particles to act as microbial reservoirs, coupled with their high mobility, reinforces concerns about their potential role in the transport and dissemination of microbial hazards.}, }
@article {pmid41875745, year = {2026}, author = {Zhang, H and Li, B and Ni, R and Ye, L and Bai, G and Zhao, J}, title = {Stable functional consortium assembly via uncoupled SAD/anammox inoculation drives synergistic nitrogen‑sulfur removal in sediment.}, journal = {Water research}, volume = {297}, number = {}, pages = {125768}, doi = {10.1016/j.watres.2026.125768}, pmid = {41875745}, issn = {1879-2448}, abstract = {The remediation of black‑odorous sediments remains challenging due to the intricate sediment matrix, the co-occurrence of multiple pollutants, and the difficulty in maintaining stable functional microbial consortia under fluctuating redox conditions. Although calcium nitrate (CN) is a used chemical oxidant, its sole application often results in incomplete nitrogen removal and risks of secondary pollution. While the integration of CN with sulfur-autotrophic denitrification (SAD) and anaerobic ammonia oxidation (anammox) presents a promising alternative, the microbial, especially concerning the assembly and efficacy of different microbial inoculation strategies, are poorly understood. This study systematically compared two distinct bioaugmentation approaches: the pre-coupled addition of a SAD and anammox consortium versus an uncoupled strategy involving separate additions of SAD and anammox consortium, both in combination with CN. Results demonstrated that the CN+S+A (uncoupled) treatment achieved optimal performance, enhancing the removal of NH4[+], NO3[-], and total nitrogen by 42%, 40%, and 35%, respectively, compared to CN alone, while also effective oxidizing acid‑volatile sulfide. Mechanistic analysis revealed that CN first optimized the sediment microenvironment. The uncoupled inoculation uniquely fostered a stable, dual-core microbial consortium dominated by Thiobacillus (3.00%) and Candidatus Brocadia (0.83%), which established a sustainable "sulfur-driven nitrogen removal" cycle. Metagenomic and isotopic tracing confirmed the enrichment of key functional genes and elevated process rates underpinning this synergy. These findings highlight that CN combined with uncoupled bioaugmentation is a novel and effective strategy for rebuilding stable nitrogen-sulfur cycles in black-odorous sediments.}, }
@article {pmid41875962, year = {2026}, author = {Rector, A and Karatas, M and Bloemen, M and De Coninck, L and Swinnen, J and Close, L and Thijssen, M and Pourkarim, MR and Matthijnssens, J and Desmet, S and Van Ranst, M and Johnson, MC and Wollants, E}, title = {Airplane wastewater as a gateway for pathogen surveillance wastewater surveillance in airplane.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105930}, doi = {10.1016/j.meegid.2026.105930}, pmid = {41875962}, issn = {1567-7257}, abstract = {BACKGROUND: Air travel plays a key role in the global spread of many diseases, including COVID-19. Surveillance of international travelers is useful for the detection of emerging viruses and variants of concern, especially in a context of global relaxations in testing policy. We aimed to assess the feasibility of using wastewater surveillance from airplanes as a method for monitoring SARS-CoV-2 variants and other pathogens entering Belgium.<br><br>METHODS: From January to March 2023, in the wake of the COVID pandemic, 32 wastewater samples were collected at Brussels Airport from direct flights originating in Beijing, China. We applied various qPCR panels and sequencing methods, including hybrid-capture metagenomic sequencing (Twist Bioscience) targeting more than fifteen thousand strains of known human and animal viruses.<br><br>RESULTS: Nineteen out of 32 samples tested positive for SARS-CoV-2. Various other pathogens, including enterovirus/rhinovirus, adenovirus, norovirus, adenovirus 40/41, and multiple clinically relevant bacteria, were identified using respiratory and gastrointestinal qPCR panels. In 7 samples, SARS-CoV-2 variants could be determined, belonging to known lineages BA4/BA5, BA4.6/BF7, and XBB. Moreover, hybrid-capture approach allowed us to recover complete genomes of viruses from families Polyomaviridae, Papillomaviridae, Herpesviridae as well as Aichivirus A and Hepatitis B virus.<br><br>CONCLUSION: This pilot project demonstrates the feasibility of detecting SARS-CoV-2 and its variants in wastewater of commercial airplanes. This method offers a valuable means of obtaining information from regions with limited SARS-CoV-2 genomic surveillance data. Moreover, using a hybrid-capture approach, a broad range of viruses of concern can be detected. The implementation of this novel screening approach is promising for enhancing traveler-based surveillance.}, }
@article {pmid41876072, year = {2026}, author = {Shen, Q and Xiong, JQ and Wang, Q and Yang, L and Shen, Z and Lei, Z and Ru, S}, title = {Cyanobacteria-driven morphology and adaptive microbial succession: Resilience mechanisms in algal-bacterial granular sludge under tripartite stress.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134481}, doi = {10.1016/j.biortech.2026.134481}, pmid = {41876072}, issn = {1873-2976}, abstract = {Algal-bacterial granular sludge (ABGS) is a promising wastewater treatment technology, yet its practical application is constrained by its unknown stability under realistic multi-stressor conditions. This work demonstrated that ABGS could withstand combined low temperature (< 15°C), carbon scarcity, and sulfamethoxazole (SMX) exposure (0-100-1000 μg/L) through the defense strategy that integrated morphological, microbial and metabolic adaptations. Metagenomics revealed a metabolic trade-off, characterized by the downregulation of energy-intensive pathways (e.g., oxidative phosphorylation and TCA cycle), and the upregulation of biosynthetic and stress-responsive pathways (e.g., glyoxylate shunt and amino sugar metabolism), redirecting carbon towards extracellular polymeric substances (EPS) production. This was synergized by the protective cyanobacterial surface barrier and reconfigured protein-rich EPS for SMX sequestration. Microbial community restructuring enhanced functional resilience, as exemplified by the shift from Nitrospira to Candidatus Nitrotoga, which sustained stable nitrification. This coordinated adaptation not only enabled the robust removal of COD (> 90%) and NH4[+]-N (> 97%), but also suppressed the proliferation of antibiotic resistance genes (ARGs) under 100 μg/L SMX stress. These findings position ABGS as self-engineering ecosystems that actively modulate microbial community assembly and metabolic networks to remove nutrients and mitigate the dissemination of ARGs.}, }
@article {pmid41876074, year = {2026}, author = {Zhang, Y and Wu, J and Yue, C and Wang, X and Qu, Y and Zhang, X and Sun, Y and Liu, Z and Qu, J and Xu, X}, title = {Enhancing anaerobic digestion of agricultural waste via a stable Fe-Emodin-Biochar composite: Kinetic performance, energy recovery, and metabolic insights.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134463}, doi = {10.1016/j.biortech.2026.134463}, pmid = {41876074}, issn = {1873-2976}, abstract = {Anaerobic digestion (AD) efficiency is often constrained by energy transfer in interspecies electron transfer. To address this, a cost-effective electron mediator was engineered by immobilizing industrial-grade Emodin onto an Fe-biochar matrix via one-step hydrothermal synthesis. The optimal composite (Fe/Emodin molar ratio 1.5:1) achieved a 43.3 % increase in cumulative methane yield and shortened the lag phase by 38.1 %. According to biochemical tests, the composite reduced energy barriers on the breakdown of volatile fatty acids, as shown by a 2.2-fold rise in ATP levels and increased expression of Coenzyme F420. A community shift marked by the co-enrichment of Methanothrix and syntrophic bacteria was revealed by metagenomic analysis. A change from energetically constrained hydrogen transfer to pathways mediated by the composite was suggested by the abundance of Type IV pili genes and Cytochrome c genes, which suggested the possible activation of direct interspecies electron transfer (DIET). By utilizing low-cost precursors and overcoming the instability of free mediators, this study offers a scalable biotechnological method for agricultural residue valorization. Furthermore, this approach demonstrates economic viability and potential life-cycle sustainability.}, }
@article {pmid41865966, year = {2026}, author = {Zhou, L and Zhu, S and Wu, J and Wang, W and Zhao, Z and Hao, X and Wang, J and Yu, W and Li, Y and Liang, J}, title = {Co-inoculation of arbuscular mycorrhizal fungi and rhizobia reshapes microbial ecology and nutrient metabolism to rehabilitate iron ore tailings.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124325}, doi = {10.1016/j.envres.2026.124325}, pmid = {41865966}, issn = {1096-0953}, abstract = {Arbuscular mycorrhizal fungi (AMF) and rhizobia play crucial roles in soil-plant systems for ecological restoration. However, their specific remediation characteristics and synergistic effects on tailings remain poorly understood. In this study, we investigated the remediation characteristics of tailings inoculated with AMF and rhizobia, focusing specifically on synergy mechanism for iron tailings improvement under the co-inoculation. The results demonstrated that microbial inoculation significantly enhanced overall remediation performance. The co-inoculation led to a 6.25-fold increase in alfalfa biomass, substantial improvements in nutrient availability (N/C/P), and enhanced soil structure through aggregate formation. Concurrently, the cadmium bioavailability was effectively reduced by 35.56%. Functional metabolic analysis revealed that the upregulation of phosphate-related genes (phoB, phoR) enhanced microbial phosphate solubilization and plant phosphate uptake efficiency. Furthermore, the primary pathways for nitrogen uptake shifted from reliance on biological nitrogen fixation to prioritizing internal nitrogen cycling, while activation of the GABA shunt reduced dependence on the TCA cycle. Notably, the restructured microbial community preferentially stimulated organic carbon-nitrogen (C/N) metabolism, and these metabolic shifts were key to enhanced plant nutrients acquisition efficiency. These findings indicate that AMF and rhizobia could stimulate microbial community restructuring and drive the remodeling of nutrient metabolism in tailings, representing a pivotal process in promoting soil formation from tailings.}, }
@article {pmid41866421, year = {2026}, author = {Mathur, S and Prasad, M and Kumar, S and Chaurasia, A and Ranjan, R}, title = {A metagenomic survey of the rhizosphere bacterial community of P. longum from the herbal garden, Dayalbagh Educational Institute (D.E.I), Agra, India.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {42}, number = {4}, pages = {}, pmid = {41866421}, issn = {1573-0972}, }
@article {pmid41866581, year = {2026}, author = {Halo, BA and Aljabri, YAS and Glick, BR and Yaish, MW}, title = {Metagenomic and functional insights into root endophytic bacteria associated with drought stress in cowpea.}, journal = {Scientific reports}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41598-026-45459-4}, pmid = {41866581}, issn = {2045-2322}, support = {IG/SCI/BIOL/24/03//Sultan Qaboos University, College of Science, Oman/ ; }, }
@article {pmid41867450, year = {2026}, author = {Jia, C and Liu, X and Liu, W and Yao, X and Chen, X and Zhao, J and Wang, P and Ge, W and Han, Y}, title = {Multi-Omics Reveal the Potential Associations of Streptococcus, 13'-Hydroxy-Alpha-Tocopherol and Glutathione Metabolism in Children with Chronic Rhinosinusitis with Nasal Polyps.}, journal = {Journal of inflammation research}, volume = {19}, number = {}, pages = {567582}, pmid = {41867450}, issn = {1178-7031}, abstract = {BACKGROUND: Chronic rhinosinusitis with nasal polyps (CRSwNP) in children is a clinically significant inflammatory disorder characterized by persistent symptoms and complex underlying mechanisms. This study used multi-omics approaches to investigate potential microbial and metabolic associations in pediatric CRSwNP.<br><br>METHODS: Nasal secretions from 20 children with CRSwNP and 19&#xa0;healthy controls were analyzed using metagenomics, untargeted metabolomics, and proteomics.<br><br>RESULTS: CRSwNP patients showed higher microbial diversity and altered microbial communities, with increased Streptococcus abundance. Metabolomic sequencing revealed that 13'-Hydroxy-alpha-tocopherol was significantly upregulated in the CRSwNP group and exhibited a positive correlation with the abundance of Streptococcus. Proteomic sequencing revealed that proteins involved in glutathione metabolism were significantly downregulated in the CRSwNP group, with GCLM and GGCT showing a significant negative correlation with 13'-Hydroxy-alpha-tocopherol.<br><br>CONCLUSION: These associative findings suggest potential links among Streptococcus, 13'-Hydroxy-&#x3b1;-tocopherol, and glutathione metabolism, indicating that oxidative stress-related imbalance may contribute to pediatric CRSwNP. These results provide preliminary evidence that 13'-Hydroxy-&#x3b1;-tocopherol may serve as a potential biomarker for pediatric CRSwNP.}, }
@article {pmid41867493, year = {2025}, author = {Alali, M and Imani, M}, title = {Bayesian Topology Inference of Regulatory Networks under Partial Observability.}, journal = {Results in control and optimization}, volume = {19}, number = {}, pages = {}, pmid = {41867493}, issn = {2666-7207}, abstract = {Biological systems, such as microbial communities in metagenomics and gene regulatory networks (GRNs) in genomics, are composed of a vast number of interacting components observed through inherently noisy data. These systems play a critical role in understanding fundamental biological processes, including gene regulation, microbial interactions, and cellular dynamics. For example, microbial communities involve complex interactions between microbes, bacteria, genes, and small molecules observed through omics data, while GRNs consist of numerous interacting genes observed via various gene-expression technologies. However, reconstructing the topology of such networks poses significant challenges due to their large scale, high dimensionality, and the presence of noise. Existing inference techniques often struggle with scalability, interpretability, and overfitting, making them unsuitable for analyzing large and complex biological systems. To overcome these challenges, this paper proposes a Bayesian topology optimization framework for efficient and scalable inference of regulatory networks modeled as partially-observed Boolean dynamical systems (POBDS). The method combines the Boolean Kalman Filter (BKF) as an optimal estimator for POBDS, with Bayesian optimization, which employs Gaussian Process regression and a topology-inspired kernel function to model the log-likelihood function. Numerical experiments demonstrate the superior performance of our framework. In the p53-MDM2 network, our method accurately infers topology with 8 and 16 unknown regulations, achieving higher log-likelihood with 100 and 200 evaluations, respectively. For the mammalian cell cycle network with 10 unknown regulations, proposed method identifies the correct topology among 59,049 possibilities with lower error and faster convergence.}, }
@article {pmid41867523, year = {2026}, author = {Kanno, N and Ohtani, T and Oda, N and Kato, S and Ohkuma, M and Shigeto, S}, title = {Domain-Level Classification of Archaea and Bacteria Using AI-Assisted Single-Cell Raman Spectroscopy.}, journal = {ACS omega}, volume = {11}, number = {10}, pages = {16913-16921}, pmid = {41867523}, issn = {2470-1343}, abstract = {Archaea and Bacteria are two fundamentally distinct domains of life that share prokaryotic traits, yet differ markedly in molecular and cellular architecture. While many archaeal species identified thus far have been found in extreme environments, recent metagenomic studies have revealed their widespread presence in moderate habitats, including soils, oceans, and even the human microbiome. However, archaea remain less well characterized than bacteria, largely due to the technical challenges associated with culturing and identifying these microorganisms. In this study, we present a culture-independent method for discriminating archaea from bacteria at the single-cell level using Raman spectroscopy combined with machine learning. We constructed a Raman spectral data set comprising 22 prokaryotic species (11 archaea and 11 bacteria) and developed a domain-level Archaea-Bacteria (AB) classifier using the LightGBM tree-based machine learning algorithm. Our AB classification model achieved an average classification accuracy of 89.1% and a sensitivity of 98.1% on eight representative species (including two independent held-out test species) with minimal data size and preprocessing. We also compared its performance to convolutional neural networks with transfer learning, a widely used deep learning approach. Our method provides a robust analytical framework for archaeal detection and represents a valuable addition to the microbiological toolkit, particularly for studying unculturable or low-abundance archaeal populations in complex microbial communities.}, }
@article {pmid41867691, year = {2026}, author = {Jiang, D and Wang, Y and Ling, Y and Eremin, SA and Mukhametova, LI and Du, J and Hu, H}, title = {Impacts of high-temperature and humidity transportation on rice quality: an integrated analysis of microbial community succession and flavor compound alterations.}, journal = {Frontiers in nutrition}, volume = {13}, number = {}, pages = {1792369}, pmid = {41867691}, issn = {2296-861X}, abstract = {This study investigated the dynamic changes in rice quality, microbial communities, and volatile compound profiles during simulated summer transportation (35 °C, 70% RH, 15 days). Indica rice samples were systematically collected every 3 days and analyzed using HS-SPME-GC-MS/MS, HS-GC-IMS, and metagenomic sequencing. Prolonged transportation significantly altered the physicochemical properties of the rice. Moisture content plateaued on day 12, while germination rates declined significantly starting from day 6. Furthermore, fatty acid values increased continuously due to accelerated lipid hydrolysis and oxidation. Visible mold growth became evident on day 12, marking a critical tipping point for quality deterioration. The odor activity value (OAV) and relative odor activity value (ROAV) analyses revealed that the decline in unsaturated fatty aldehydes such as (E)-2-nonenal and the significant accumulation of alcohols, ketones, and short-chain esters, including 1-octen-3-ol and ethyl acetate, drove the transition from a "fresh and fatty" aroma to one characterized by moldy, fermented, and pungent notes. Metagenomic analysis demonstrated a profound ecosystem shift from bacterial dominance (Proteobacteria, Actinobacteria) to fungal dominance. Notably, Lichtheimia surged from <0.01% to 23.95%, becoming the dominant genus, while Aspergillus increased from 0.03% to 4.57%. Correlation analysis indicated that while Pseudomonas was associated with elevated fatty acid levels, the flavor shift was primarily linked to microbial succession. These findings provide insights into the synergistic mechanisms of rice spoilage and suggest that specific volatile markers could serve as early warning indicators for quality control in real-world grain logistics.}, }
@article {pmid41867766, year = {2026}, author = {Schmitt, MS and Lee, KK and Bunbury, F and Landsittel, JA and Vitelli, V and Kuehn, S}, title = {Learning functional groups in complex microbiomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.03.709366}, pmid = {41867766}, issn = {2692-8205}, abstract = {From soil to the gut, communities composed of thousands of microbes perform functions such as carbon sequestration and immune system regulation. Here, we introduce a data-driven approach that explains how community function can be traced to just a few groups of microbes or genes. In gut communities, our neural-network based clustering algorithm correctly recovers known functional groups. In the ocean metagenome, it distills ~500 gene modules down to three sparse groups highlighting survival strategies at different depths. In soils, it distills ~ 4400 bacterial species into two groups that enter a mathematical model of nitrate metabolism. By combining interpretable ML with strain isolation and sequencing experiments, we connect the metabolic specialization of each group to community-wide responses to perturbations. This integrated approach yields simple structure-function maps of microbiomes, allowing the discovery of molecular mechanisms underlying human and environmental health. More broadly, we illustrate how to do function-informed dimensionality reduction in biology.}, }
@article {pmid41867767, year = {2026}, author = {Nguyen, MH and Schatz, MC}, title = {Perseus: Lineage-Aware Refinement of Kraken2 Taxonomic Classification for Long Read Metagenomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.64898/2026.03.06.710148}, pmid = {41867767}, issn = {2692-8205}, abstract = {MOTIVATION: Long-read metagenomic sequencing improves assembly contiguity and enables genome-resolved analysis of complex microbial communities, but accurate taxonomic classification of long reads and assembled contigs remains challenging. Highly scalable k-mer-based classifiers such as Kraken2 frequently over-assign fine-rank taxonomic labels when applied to long-read data, producing high false positive classification rates driven by sparse or localized k-mer matches, particularly in microbiomes with extensive taxonomic novelty.<br><br>RESULTS: We present Perseus , a lineage-aware confidence estimation framework for taxonomic classification that models the spatial distribution and hierarchical consistency of k-mer evidence along sequences. This formulation reframes taxonomic classification as a hierarchical confidence estimation problem rather than a single-rank prediction task. Perseus refines k-mer-level taxonomic signals from Kraken2 using a multi-headed convolutional neural network that estimates calibrated confidence scores for taxonomic correctness at each canonical rank. Using these estimates, Perseus confirms assignments, backs off to higher taxonomic ranks, or abstains when evidence is insufficient, prioritizing correctness and lineage consistency over overly specific assignments. Across simulations of taxonomic novelty and real-world metagenomic datasets, Perseus consistently and substantially reduces the false assignment rate while improving precision and lineage-consistent accuracy. These improvements are most pronounced for long reads and assembled contigs, where spatial context enables reliable discrimination between consistent taxonomic signal and spurious matches.<br><br>Perseus integrates with existing Kraken2 workflows and is available at https://github.com/matnguyen/perseus .<br><br>CONTACT: mnguye99@jh.edu , mschatz@cs.jhu.edu.<br><br>SUPPLEMENTARY INFORMATION: Supplementary data are available online.}, }
@article {pmid41868021, year = {2026}, author = {Zhan, M and Tu, S and Yang, S and Yin, Y and Wang, Z and Zhang, F and Zhang, Y and Wang, Q and Zhao, C and Wang, X and Wang, H and Chen, H}, title = {Clinical Utility of Metagenomic Next-Generation Sequencing in Diagnosing Central Nervous System Infections in Hematopoietic Stem Cell Transplant Recipients: A Retrospective and Prospective Cohort Study.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {554425}, pmid = {41868021}, issn = {1178-6973}, abstract = {BACKGROUND: Diagnosing central nervous system infections (CNSI) in hematopoietic stem cell transplant (HSCT) recipients remains challenging due to nonspecific presentations and low sensitivity of conventional microbiological methods.<br><br>METHODS: This study evaluated the clinical utility of cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) in 127 HSCT recipients (87 retrospective, 40 prospective) from Peking University People's Hospital. Pathogens detected by mNGS and conventional methods were validated via Sanger sequencing.<br><br>RESULTS: mNGS identified 20 pathogen-positive samples (19 confirmed by sequencing), while conventional methods detected none. mNGS demonstrated 82.6% sensitivity and 99.0% specificity for CNSI diagnosis, with sensitivity rising to 100.0% when combined with conventional approaches. Notably, mNGS excelled in detecting viral pathogens, particularly in allogeneic HSCT recipients.<br><br>CONCLUSION: Our findings advocate for the integration of mNGS into the diagnostic algorithm for CNSI, especially in immunocompromised hosts. This approach enables earlier and more precise pathogen identification, which has the potential to streamline antimicrobial therapy and improve clinical management. To maximize its benefit and ensure reliable interpretation, mNGS results should be correlated with comprehensive clinical and paraclinical data. Further prospective studies are warranted to validate its impact on therapeutic decision-making and patient prognosis.}, }
@article {pmid41868024, year = {2026}, author = {Wang, QL and Teng, SN and Zhang, XJ and Guo, YX and Kong, Y and Tian, XH and Zhang, Y}, title = {Fatal Primary Amoebic Meningoencephalitis in Coastal Areas of North China in an Immunocompetent Patient: A Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {559408}, pmid = {41868024}, issn = {1178-6973}, abstract = {PURPOSE: Primary amoebic meningoencephalitis (PAM) is a rapidly fatal infection caused by Naegleria fowleri (N. fowleri) with a mortality rate exceeding 95%. This study presented the clinical course, diagnosis, treatment, and outcome of a confirmed PAM case in an adult female. Additionally, we analyzed the epidemiology of PAM in China and review the therapeutic regimens of surviving cases worldwide, aiming to enhance disease awareness and improve clinical outcomes.<br><br>CASE PRESENTATION: The patient was a 50-year-old immunocompetent woman with a history of hot spring bathing before symptom onset, which was not initially disclosed. Moreover, her early infectious symptoms, particularly fever following a tick bite in an orchard, directed clinical suspicion toward tick-borne disease. Four days later, she was hospitalized with generalized convulsions and coma. Clinical examination suggested a bacterial intracranial infection, and treatment with meropenem and vancomycin was initiated. However, her condition deteriorated rapidly. The presence of N. fowleri was identified by cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) and smear. The etiology was clarified only after retrospective confirmation of hot spring contact, which was later confirmed by blood mNGS. Despite intensive therapy with amphotericin B (AmB), the patient unfortunately died. To provide insights into PAM management in China, we also conducted a systematic analysis of 15 domestic cases and 18 global survivors.<br><br>CONCLUSION: PAM is characterized by rapid progression, underscoring the importance of early diagnosis. In cases of rapidly advancing meningoencephalitis, clinicians should maintain a high index of suspicion for rare pathogens such as N. fowleri, with thorough and repeated assessment of recent environmental exposures such as hot spring immersion or freshwater swimming. Early application of mNGS is essential for timely pathogen identification. While AmB remains the first-line therapy, its dosing and duration should be tailored to individual patient factors, and combination therapy should be considered to enhance efficacy. Overall, improved clinical vigilance, advanced pathogen diagnostics, and standardized anti-amoebic therapy form the cornerstone of enhancing outcomes in PAM. As the first documented PAM case in Shandong Province, China, this report highlights the need for heightened awareness in coastal regions while contributing valuable epidemiological insights into this devastating disease.}, }
@article {pmid41868028, year = {2026}, author = {Wang, Z and Ma, R and Ding, Z and Ma, L and Liu, X and Wang, Y}, title = {Brucellosis Complicated by Thyroid Abscess and Life-Threatening Hemophagocytic Syndrome: A Case Report.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {583365}, pmid = {41868028}, issn = {1178-6973}, abstract = {INTRODUCTION: Brucella infections can affect various systems in the body, such as the osteoarticular and genitourinary systems; however, cases involving the thyroid gland are rare. This case report describes the clinical management of a thyroid abscess associated with brucellosis in a farmer.<br><br>CASE PRESENTATION: A 67-year-old male farmer presented to Shanxi Bethune Hospital on 17 March 2024 with a chief complaint of "intermittent fever with fatigue for over 3 months and neck swelling and pain for 2 months". Upon admission, his serum Brucella tube agglutination test titre was 1:200, Rose Bengal plate agglutination test was positive, and blood culture was negative for Brucella. Neck computed tomography revealed a low-density nodular shadow in the right thyroid lobe measuring approximately 4.79&#xd7;4.45 cm. Coffee-coloured pus was aspirated during thyroid puncture. Pathogenic metagenomic next-generation sequencing and pus culture confirmed Brucella infection as the cause of the thyroid abscess. During treatment, the patient developed hemophagocytic syndrome. The patient's condition was controlled with aggressive anti-infective therapy and glucocorticoid treatment. However, because of symptom recurrence, the patient ultimately underwent surgical intervention, comprising partial thyroidectomy, abscess incision and drainage, and thyroid injection, following which he recovered fully.<br><br>CONCLUSION: This article reports an extremely rare case of brucellosis leading to a thyroid abscess. Physicians should consider the possibility of brucellosis when encountering patients with thyroid abscesses and be vigilant of other potential complications.}, }
@article {pmid41868358, year = {2026}, author = {Ribeiro-Junior, MR and Cardwell, KF and Nascimento, D and Espindola, AS and Ramachandran, A and Gupta, SK and Tyungu, D}, title = {Rapid detection of human and animal respiratory viruses using Microbe Finder (MiFi[®]).}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1743643}, pmid = {41868358}, issn = {1664-302X}, abstract = {Rapid and accurate detection of respiratory pathogens is essential for timely diagnosis, effective treatment, and outbreak monitoring in both human and veterinary medicine. We evaluated the Microbe Finder (MiFi[®]) software for detection of nine RNA viruses of human and veterinary clinical importance. Species specific signature sequences in the different pathogen genomes were identified, and specific electronic probe sets were curated using the MiFi[®] software. Analytical specificity and sensitivity were evaluated through simulated metagenomes and public sequence databases, respectively. Host-specific internal control probes were designed to ensure diagnostic reliability and quality control. Diagnostic performance was assessed using Oxford Nanopore sequence data from clinical nasal swab samples. In silico validation showed 100% specificity across 83 datasets and limits of detection as low as 0.0010% of total reads (10 reads per 10[6]) for some targets. Internal controls generated stable background signals without interfering with pathogen detection. In vivo testing of 44 clinical samples matched PCR performance for Human respiratory syncytial virus (HRSV), Influenza B virus (IBV), Influenza A virus (IAV), Bovine respiratory syncytial virus (BRSV), and Canine distemper virus (CDV). These findings demonstrate that the MiFi[®] software enables rapid, multiplex, and strain-specific detection of respiratory viruses in metagenomic sequence data without the need for advanced bioinformatics expertise. The approach supports scalable use in clinical laboratories, veterinary diagnostics for surveillance and triage, offering a valuable tool for improving respiratory pathogen detection across diverse settings.}, }
@article {pmid41869352, year = {2026}, author = {Zhou, YM and Cui, XQ and Zhao, P and Peng, ZG and Guo, N and Sun, HB and Liu, SL}, title = {The species, distribution, resistance of donor-derived pathogens and their impact on solid organ transplant recipients.}, journal = {Frontiers in immunology}, volume = {17}, number = {}, pages = {1777244}, pmid = {41869352}, issn = {1664-3224}, mesh = {Humans ; Middle Aged ; Male ; Female ; Retrospective Studies ; *Tissue Donors ; Adult ; *Transplant Recipients ; *Liver Transplantation/adverse effects ; *Kidney Transplantation/adverse effects ; Aged ; *Organ Transplantation/adverse effects ; Drug Resistance, Multiple, Bacterial ; Incidence ; Bacteria/isolation &amp; purification/drug effects ; }, abstract = {BACKGROUND: Donor-derived infections (DDIs) have become a significant cause of infection in organ transplant recipients. Elaborating on the species, distribution, and resistance of donor-derived pathogens (DDPs) holds important implications.<br><br>METHODS: A retrospective cohort study included 302 deceased donors and their corresponding 464 kidney transplant recipients and 175 liver transplant recipients. We detected DDPs in preservation fluid (PF) using both conventional culture and mNGS, and subsequently analyzed the incidence of DDIs after transplantation.<br><br>RESULTS: 89.4% (270/302) of donors had positive cultures. Predominant multidrug-resistant organism included HLAR-Enterococcus, CRAB, CRKP, CRPA, MRS and ESBL-Escherichia coli. Compared with conventional culture, mNGS exhibited superior sensitivity for detecting bacteria and fungus in PF, with shorter turnaround time (p < 0.001). The incidences of DDIs in kidney and liver transplant recipients were 16.6% (77/464) and 19.4% (34/175) respectively. The recipients with DDIs were associated with elevated serum creatinine or total bilirubin levels, increased infection events, higher risks of graft loss, elevated mortality, and longer length of hospital stay (p < 0.05).<br><br>CONCLUSIONS: Multidrug-resistant organism are prevalent in deceased donors, with PF contamination primarily originating from donors. Integration of mNGS into donor screening protocols enables timely antimicrobial intervention, potentially improving transplant outcomes.}, }
@article {pmid41869502, year = {2026}, author = {Wang, D and Xu, X and Liu, L and Wang, C and Deng, Y and Polz, MF and Zhang, T}, title = {Hi-C sequencing deciphers phage and plasmid host networks in wastewater biofilms.}, journal = {Environmental science and ecotechnology}, volume = {30}, number = {}, pages = {100683}, pmid = {41869502}, issn = {2666-4984}, abstract = {Mobile genetic elements (MGEs) such as bacteriophages and plasmids profoundly shape microbial community structure and drive horizontal gene transfer across ecosystems. Wastewater treatment systems, with their high cell densities, steep physicochemical gradients and close cell-to-cell contact, act as hotspots for MGE proliferation and exchange, yet the in situ assembly dynamics and host interaction networks of these elements have remained largely unresolved because conventional methods fail to establish direct MGE-host linkages in complex matrices. Here we show that an integrated framework combining metagenomics, metatranscriptomics, metaviromics, and Hi-C proximity ligation sequencing enables the efficient elucidation of DNA phage and plasmid assembly dynamics alongside their host interaction networks in biofilms. We reconstructed 17,672 viral operational taxonomic units and 11,454 high-confidence non-redundant plasmids, and established 529 phage-host and 5739 plasmid-host associations that link up to 52 % of phages to 56 % of prokaryotes and 70 % of plasmids to 91 % of prokaryotes, respectively. Hi-C substantially expanded and refined these networks, revealing taxon-specific and multi-host patterns. Host community composition and biofilm architecture emerge as primary drivers of MGE occurrence and abundance along the reactor flow path. Expression of auxiliary metabolic genes, antibiotic resistance genes and virulence factors carried by these MGEs demonstrates their active roles in modulating biogeochemical cycles and maintaining ecosystem stability. These findings establish a scalable, cultivation-independent framework for deciphering MGE-host networks in complex microbial ecosystems, and underscore the power of Hi-C sequencing to transform our mechanistic understanding of gene flow, resistome dissemination, and ecological resilience in engineered and natural microbiomes.}, }
@article {pmid41869518, year = {2026}, author = {Liu, J and Wu, R}, title = {Intraoperative sampling for postoperative metagenomic next-generation sequencing to guide biofilm-targeted therapy for Cutibacterium acnes infective endocarditis complicated by ruptured sinus of Valsalva aneurysm: a case report.}, journal = {Frontiers in cardiovascular medicine}, volume = {13}, number = {}, pages = {1707117}, pmid = {41869518}, issn = {2297-055X}, abstract = {BACKGROUND: Cutibacterium acnes is an easily overlooked pathogen in infective endocarditis (IE) due to its slow growth, propensity for biofilm formation, and high rate of culture-negative results. When complicated by structural heart disease such as a ruptured sinus of Valsalva aneurysm (RSVA), its indolent course can lead to severe hemodynamic compromise.<br><br>CASE SUMMARY: A 35-year-old male with a known ventricular septal defect (VSD) and unruptured aortic sinus aneurysm presented with persistent fever and progressive heart failure (NYHA class IV). Echocardiography revealed a ruptured right coronary sinus of Valsalva aneurysm (RCSVA) into the right ventricular outflow tract (RVOT) with a large vegetation. Blood cultures were negative. After 6 days of ineffective empirical antibiotic therapy, emergency surgery was performed to resect the aneurysm and vegetation and repair the cardiac structures. Intraoperatively, a vegetation sample was collected for metagenomic next-generation sequencing (mNGS). Postoperatively, mNGS identified Cutibacterium acnes with high sequence reads (1,284) and coverage (47.62%), enabling a definitive diagnosis. Pathology confirmed microcolonies and necrotic inflammation. The antibiotic regimen was switched to a regimen with potential activity against biofilms with oral doxycycline and intravenous clindamycin for 6 weeks. The patient's inflammatory markers normalized, and cardiac function recovered to NYHA class I, with no recurrence at 12-month follow-up.<br><br>CONCLUSION: This case highlights the diagnostic synergy of intraoperative histopathology and mNGS for pathogen identification, underscores the rationale for biofilm-conscious adjuvant therapy, and reaffirms the crucial role of early surgical debridement and repair in achieving cure.}, }
@article {pmid41869816, year = {2026}, author = {Tumeo, A and Miliotis, G and O'Connor, A and Vijayakumar, V and Sengupta, P and McDonagh, F and Kovarova, A and Clarke, C and Hooban, B and Kumar Singh, N and Rosado, AS and Raman, K and Venkateswaran, K}, title = {Plasmidome, resistome, and virulence-associated gene characterization of Acinetobacter johnsonii in NASA cleanrooms and a clinical setting.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0250325}, doi = {10.1128/spectrum.02503-25}, pmid = {41869816}, issn = {2165-0497}, abstract = {Evidence suggests the persistence of non-spore-forming Acinetobacter johnsonii in high-stakes controlled and nutrient-limited environments. Here, we investigated the mechanisms underlying this adaptability through a comprehensive genomic analysis of 22 isolates of A. johnsonii from NASA's Payload Hazardous Servicing Facility (PHSF) and one carbapenem-resistant strain (E154408A) from patient colonization in Ireland. Core-genome phylogeny revealed clustering of PHSF-originating isolates in a monophyletic clade divergent from the main species lineage. Species-wide virulence-associated genes and metabolic reconstruction indicated the exclusive presence in PHSF-originating isolates of two complete efflux pumps and a conserved allantoin racemase, suggesting adaptability for multiple environmental stresses. The ubiquity of blaOXA in genomes analyzed (n = 112) and the phenotypically validated multidrug-resistant profile of the E154408A strain highlight A. johnsonii's potential as an antimicrobial resistance (AMR) reservoir. Plasmidome analysis suggested gain/loss events across the monophyletic population and potential AMR acquisition pathways. Genome-to-metagenome mapping identified genomic signatures of A. johnsonii in PHSF >10 years post-initial isolation.IMPORTANCEAcinetobacter johnsonii is increasingly recognized as an emerging human pathogen, with growing evidence of its ability to persist in controlled, high-stakes environments, posing risks as both a persistent environmental contaminant and an antimicrobial resistance (AMR) reservoir. Yet, gaps remain in our understanding of its AMR profile and the mechanisms that enable its enhanced environmental adaptability. This knowledge is necessary in contexts where biological cleanliness is a priority, such as clinical settings and spacecraft assembly facilities' cleanrooms, where contamination of hardware with terrestrial microorganisms is concerning. In this study, we aim to address some of the key knowledge gaps by providing genomic insights into a rare multidrug-resistant clinical isolate and 22 NASA cleanroom isolates that persisted for over a decade in extremely clean conditions. Our findings will help assess the contamination risk of A. johnsonii in high-stakes environments and ultimately strengthen our ability to manage this microbial contaminant across terrestrial and extraterrestrial settings.Cleanroom-derived A. johnsonii genomes show traits consistent with increased adaptability.Genomic signatures of A. johnsonii persisted in the cleanrooms for over 10 years.blaOXA is ubiquitously found in all 112 A. johnsonii genomes analyzed.Isolate E154408A is the first reported patient colonization case by carbapenem-resistant A. johnsonii in Europe.}, }
@article {pmid41869825, year = {2026}, author = {Mehta, A and Stebliankin, V and Mathee, K and Narasimhan, G}, title = {MEditome: Computational Detection of RNA Edit Sites Using de Novo Assembly in Microbiomes.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {}, number = {}, pages = {15578666261428562}, doi = {10.1177/15578666261428562}, pmid = {41869825}, issn = {1557-8666}, abstract = {RNA editing is a post-transcriptional modification that alters single-nucleotide sites within RNA strands, thus diversifying transcriptomes and proteomes and modulating gene expression. While better characterized in eukaryotes and in a few microbes, the study of RNA editing in entire microbiomes remains unexplored. Recent studies have demonstrated that A-to-I RNA editing contributes to bacterial adaptation and pathogenicity. Previously, we developed MetaEdit, a reference-based computational pipeline to detect RNA edit sites in microbiomes. While MetaEdit successfully identified RNA edit sites in Escherichia coli within the context of the human gut microbiome, including previously reported loci, it relied primarily on aligning reads to reference genomes of target bacteria. This dependence on reference genomes introduced potential biases, as editing can only be identified in reference genomes, while editing in novel microbial strains missing from the reference databases could be overlooked. Even for reference genomes, the search for edit sites is inefficient since it would have to be conducted one reference genome at a time.Here, we introduce MEditome, employing de novo assembly to overcome these limitations. This crucial change enables the detection of RNA edit sites across all microbial organisms in the microbiome, including novel bacterial strains for which comprehensive reference genomes are unavailable. Using sequencing data from the Integrative Human Microbiome Project, MEditome identified 2,295 unique RNA editing sites across diverse bacterial taxa. Several of these overlaps with previously identified edits in E. coli detected by MetaEdit in hok/gef gene family and arginine-associated genes, providing in silico validation of accuracy. We observed taxon-specific editing patterns and gene-level differential editing associated with inflammatory bowel disease, highlighting RNA editing as a potential regulatory mechanism influencing microbial adaptation and host-microbe interactions.}, }
@article {pmid41869887, year = {2026}, author = {Wang, Z and Guo, S and Li, J and Huang, Q and Ning, J and Xia, B and Lv, X and Liu, X and Gao, Z and Li, J and Liu, L and Song, M and Wang, J}, title = {Identifying Cytokine Motif-Containing, Immunomodulatory Bacterial Proteins in Human Gut Microbiome.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e20332}, doi = {10.1002/advs.202520332}, pmid = {41869887}, issn = {2198-3844}, support = {2025YFA1309200//National Key Research and Development Program of China/ ; 2023KF-05//Open funding project of State Key Laboratory of Pharmaceutical preparation/ ; }, abstract = {Accumulating evidence emphasizes the importance of microbiota-immune interactions in health and disease development, and identified bacteria-derived small-molecule metabolites as well as macromolecules such as peptides and proteins as promising therapeutic approaches. Here, we identify cytokine motif-containing, immunomodulatory bacterial proteins (CMCPs) as a special category of bacterial proteins in both bacterial genomes and gut metagenomes using Hidden Markov Models (HMMs). We further find eight colorectal cancer‑associated CMCPs differentially enriched in patients or healthy controls. Engineered E. coli Nissle 1917 (EcN) expressing selected CMCPs administered to Apc[min/+] mice selectively colonize intestinal tumors, deliver functional CMCPs in situ, and elicit significant antitumor immune responses while reducing tumor burden. In vitro, purified CMCPs modulate mouse splenic T cells, bone marrow‑derived macrophages and dendritic cells. Our findings indicate that bacterially encoded CMCPs can directly modulate tumor immunity and serve as microbiota‑derived proteins as candidate immunomodulators, which can further be applied in microbiome-mediated immune therapies for CRC.}, }
@article {pmid41870053, year = {2026}, author = {Pasaribu, B and Vincent Mishael Dilens, C and Wahyudin Lewaru, M and Ayuningrum, D and Patria, MP and Juliandri Prihadi, D and Purba, NP and Untung Kurnia Agung, M and Maqbul, I and Sulistiowati, S}, title = {Shotgun metagenomic dataset of seawater bacterial communities from Pari Islands, Indonesia.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0147625}, doi = {10.1128/mra.01476-25}, pmid = {41870053}, issn = {2576-098X}, abstract = {Pari Island is located in Seribu Islands, Indonesia, and is well-known for its marine biodiversity. Shotgun metagenomic sequencing was performed using the DNaseq-G400 platform, and bioinformatics approaches were applied to analyze the sequence data.}, }
@article {pmid41870088, year = {2026}, author = {Park, J-Y and Yoon, CK and Lee, J-J and Shin, YJ and Kim, B-S}, title = {Potential role of the ocular surface microbiome in dry eye: microbial interactions and symptom alleviation.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0010426}, doi = {10.1128/msystems.00104-26}, pmid = {41870088}, issn = {2379-5077}, abstract = {Dry eye is a prevalent ocular disorder characterized by tear film instability, inflammation, and ocular discomfort. Although the ocular surface (OS) microbiome contributes to immune regulation and pathogen defense, its role in dry eye pathophysiology remains unclear. Therefore, the present study aimed to characterize alterations in the OS microbiome of patients with dry eye undergoing cyclosporin A or NewHyalUni treatment and to identify their potential roles related to clinical improvement. Patients with dry eye were treated with either cyclosporin A and NewHyalUni drop combination or NewHyalUni alone. OS samples were collected before and after treatment, and the microbiome was analyzed by whole metagenome sequencing. Potential contaminants were removed before downstream analysis to account for the low-biomass nature of OS samples. Clinical evaluations included symptom scores and the assessment of meibomian gland dysfunction (MGD). No significant differences in the overall microbial composition were observed between the treatment groups. Nevertheless, both groups demonstrated symptomatic improvement. OS microbiome alterations were strongly correlated with improvements in MGD scores. Moreover, microbial interactions were found to shift following treatment. Key species (Staphylococcus epidermidis, Staphylococcus pseudintermedius, Streptomyces lividans, and Edwardsiella tarda) were identified as potential mediators of MGD score improvement by modulating microbiome functions and suppressing inflammation-associated species. Although distinct treatment regimens did not lead to divergent microbiome profiles, symptomatic improvement was associated with alterations in a specific microbiome. These findings highlight the OS microbiome's potential role in dry eye and support the development of microbiome-based therapeutic strategies.IMPORTANCEDry eye is a common ocular disorder with complex pathophysiology that extends beyond tear deficiency and inflammation. Despite growing evidence of host-microbiome interactions at mucosal surfaces, the contribution of the ocular surface (OS) microbiome to dry eye remains poorly understood. Our findings in this study reveal that shifts in specific taxa and ecological interactions correlate with improvements in meibomian gland function and dry eye symptoms, even in the absence of major changes in overall microbiota. By identifying microbial signatures potentially linked to clinical improvement, we provide systems-level insight into the role of low-biomass microbiomes in ocular health. This work expands the current understanding of microbiome-host dynamics in non-gut environments and supports future development of microbiome-informed therapeutic strategies.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT06936462.}, }
@article {pmid41870133, year = {2026}, author = {Ni, B and Chen, XP and Lin, D and Yao, Z and Xia, J and Zhang, TL and Zheng, J and Cai, TG and Wang, X and Vollertsen, J and Zhu, D and Zhu, DZ}, title = {Potential Viral Regulation of Sulfur Cycling in Urban Sewer Sediments.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c15040}, pmid = {41870133}, issn = {1520-5851}, abstract = {Sewer sediments are microbial hotspots for sulfur cycling and sulfide generation, which is the leading cause of sewer corrosion and poses significant economic losses and public safety concerns. However, viruses in sewer sediments remain inadequately explored regarding their characteristics, interactions with their hosts, and ecological regulatory potential for sulfur cycling. In this study, we explored viral characteristics and virus-host interactions in sewer sediments from three distinct types of urban functional areas through metagenomics and viromics. Compared with single-function (commercial and residential) areas, sewer sediments in multifunctional areas contain higher nutrients and nutrient-induced acidification, which can promote host density and drive a shift from lytic to lysogenic infection. This shift may potentially enhance sulfide formation through the insertion of more auxiliary metabolic genes related to sulfate reduction into host genomes. Conversely, a higher viral lytic tendency in single-function area can lyse sulfate-reducing microorganisms, thereby mitigating sulfide formation. Phage transplantation experiments and the high prevalence of key viral hosts across global sewers (76 cities across six countries) demonstrated the high potential of viruses in alleviating sewer corrosion. Our findings reveal the dual role of viruses as metabolic "tuners" in sewer sulfur dynamics, suggesting that comprehensive urban sewer management requires consideration of exploiting viral lysis.}, }
@article {pmid41870192, year = {2026}, author = {Ranga, A and Malhotra, AG and Singh, J and Pandey, KM}, title = {Genomic Sequencing from Sanger to Next-Generation Sequencing: Historical Context, Comparative Advances, and Prospects for Next-Generation Phenomics.}, journal = {Omics : a journal of integrative biology}, volume = {}, number = {}, pages = {15578100261433762}, doi = {10.1177/15578100261433762}, pmid = {41870192}, issn = {1557-8100}, abstract = {DNA sequencing has revolutionized biological and biomedical research, offering profound insights into genome organization, function, and variability. From the pioneering Sanger capillary electrophoresis method to the advent of next-generation sequencing, the field has evolved toward unprecedented speed, scalability, and cost decreases over the years. These advancements have enabled diverse applications across genomics, transcriptomics, metagenomics, epigenomics, and precision medicine, powering global initiatives such as the Human Genome Project, the Human Microbiome Project, and the 1000 Genomes Project. Bioinformatics has also advanced in data processing, variant detection, and functional annotation, helping transform raw sequencing data into biologically meaningful insights and knowledge. Although highly advanced, sequencing technologies still encounter challenges, including accuracy trade-offs and the need for efficient management of rapidly increasing volumes of data. Leveraging the genomic revolution, this review explores the shifts toward next-generation phenomics (NGP), an archetype that uses artificial intelligence that integrates multi-omics data with digital phenotyping, the Internet of Things, and real-time analytics. The goal of NGP is to integrate genotypic and phenotypic data to support predictive modeling of health, disease, and environmental interactions. By tracing history, advances in sequencing technologies, and future perspectives on NGP, this article offers a comprehensive overview for researchers and clinicians, highlighting how the integration of omics and digital data will drive the generation of personalized and systems-level biology.}, }
@article {pmid41870201, year = {2026}, author = {Li, N-P and Gupta, S and Kollipara, SK and Hung, T-H and Rao, GP and Kuo, C-H}, title = {Draft genome sequence of "Candidatus Phytoplasma australasiaticum" strain TBB-AP associated with tomato big bud disease in India.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0003326}, doi = {10.1128/mra.00033-26}, pmid = {41870201}, issn = {2576-098X}, abstract = {We report the draft metagenome-assembled genome (MAG) of "Candidatus Phytoplasma australasiaticum" strain TBB-AP, obtained from a symptomatic tomato plant collected in Andhra Pradesh, India. This assembly provides a genomic resource for functional and evolutionary studies of phytoplasmas associated with tomato big bud disease.}, }
@article {pmid41870280, year = {2026}, author = {Werbowy, O and Håkansson, M and Dorawa, S and Stefańska-Kaźmierczak, A and Svensson, LA and Al-Karadaghi, S and Jurczak-Kurek, A and Kwiatkowska-Semrau, K and Plotka, M and Fridjonsson, OH and Hreggvidsson, GO and Aevarsson, A and Dąbrowski, S and Kaczorowska, AK and Kaczorowski, T}, title = {Structural and functional characterization of a hyperthermostable single-stranded DNA-binding protein from a hot spring metagenome.}, journal = {Protein science : a publication of the Protein Society}, volume = {35}, number = {4}, pages = {e70538}, doi = {10.1002/pro.70538}, pmid = {41870280}, issn = {1469-896X}, support = {UMO-2019/34/H/NZ2/00584//National Science Centre (Poland)/ ; 685778//European Union Horizon 2020/ ; }, mesh = {*Hot Springs/microbiology ; *DNA-Binding Proteins/chemistry/genetics/metabolism ; *Metagenome ; Crystallography, X-Ray ; *DNA, Single-Stranded/metabolism/chemistry ; Models, Molecular ; Escherichia coli/genetics/metabolism ; *Bacterial Proteins/chemistry/genetics/metabolism ; Amino Acid Sequence ; Protein Multimerization ; }, abstract = {We present the structural and functional characterization of a single-stranded DNA-binding protein (SSB-M5) identified from a hot spring metagenome in Vatnajökull National Park, Iceland. This small protein (136 aa; 15,695 Da) shares 100% amino acid sequence identity with two previously uncharacterized SSBs from hyperthermophilic Fervidobacterium species. Functional complementation assay demonstrated that SSB-M5 can substitute for Escherichia coli SSB in an ssb[-] mutant strain, confirming its biological activity. A recombinant C-terminally His-tagged SSB-M5 was overproduced, purified to homogeneity, and subjected to structural, biochemical, and biophysical analysis. The crystal structure revealed that SSB-M5 forms a dimer through a crystallographic twofold axis, with each monomer contributing to a large antiparallel β-sheet. The flat surfaces of the β-sheets from the two dimers are packed together via a second crystallographic twofold axis, forming a tetramer that serves as the functional unit of the SSB-M5. Electrophoretic mobility shift assays showed that SSB-M5, after heat treatment up to 100°C, forms stable DNA-protein complexes with the (dT)40 oligo. Quantitative analyses revealed that SSB-M5 binds (dT)70 oligonucleotide with very high affinity (KD = 72 ± 6 pM). Hill analysis indicated cooperative binding, yielding an EC50 of 141 pM and a Hill coefficient of 2. Moreover, inclusion of SSB-M5 in PCR reactions significantly enhanced amplification by eliminating non-specific products. Together, these findings identify SSB-M5 as a hyperthermostable, high-affinity single-stranded DNA-binding protein with potential applications in molecular biology and biotechnology.}, }
@article {pmid41871361, year = {2026}, author = {Lipovac, J and Šikić, M and Vicedomini, R and Križanović, K}, title = {MADRe: Strain-level Metagenomic Classification Through Assembly-Driven Database Reduction.}, journal = {GigaScience}, volume = {}, number = {}, pages = {}, doi = {10.1093/gigascience/giag030}, pmid = {41871361}, issn = {2047-217X}, abstract = {Strain-level metagenomic classification is essential for understanding microbial diversity and functional potential, yet remains challenging, particularly when sample composition is unknown and reference databases are large and redundant. Here we present MADRe, a modular and scalable pipeline for long-read strain-level metagenomic classification based on Metagenome Assembly-Driven Database Reduction. Beyond system-level integration, MADRe introduces statistical strategies that leverage assembly-derived genomic context to guide database reduction and probabilistic read reassignment. Specifically, it combines long-read metagenome assembly, contig-to-reference reassignment using an expectation-maximization framework for reference reduction, and probabilistic read mapping reassignment on a reduced database to achieve sensitive and precise strain-level classification. We extensively evaluated MADRe on simulated datasets, mock communities, and a real anaerobic digester sludge metagenome. Across diverse similarity and coverage conditions, MADRe consistently improves precision by reducing false-positive strain detections. MADRe's design allows users to apply either the database reduction or read classification step individually. Using only the read classification step shows results on par with other tested tools. MADRe is open source and publicly available at https://github.com/lbcb-sci/MADRe.}, }
@article {pmid41871943, year = {2026}, author = {Awoniyi, M and El Hag, M and Hernandez, J and Yang, Q and Evans, N and Nemet, I and Ngo, B and Coskuner, D and Zhou, J and Farmer, M and Su, L and Zhou, H and Roach, J and Stappenbeck, T and Sartor, RB}, title = {Dysbiotic microbiota trigger colitis-associated colorectal cancer and imprint a distinctive bile acid profile in a PSC-IBD model.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2025-336675}, pmid = {41871943}, issn = {1468-3288}, abstract = {BACKGROUND: Primary sclerosing cholangitis-associated UC (PSC-UC) carries excess colorectal neoplasia despite often mild-appearing endoscopy, implicating persistent microscopic inflammation and microbiota-bile acid (BA) dysfunction.<br><br>OBJECTIVE: To test whether PSC-UC neoplasia is driven by transferable microbiota-mediated inflammation linked to secondary BA loss.<br><br>DESIGN: Surveillance colonoscopies (2012-2022) from PSC-UC (n=251) and UC-only (n=8839) were compared for segmental endoscopic/histological activity and dysplasia. We generated multidrug resistance protein 2 (MDR2)[-/-] &#xd7; interleukin (IL)-10[-/-] double-knockout (DKO) mice and used germ-free (GF) derivation, faecal microbiota transplantation (FMT), antibiotic conditioning and cohousing with shotgun metagenomics and liquid chromatography-tandem mass spectrometry BA profiling.<br><br>RESULTS: PSC-UC showed greater inflammatory activity and a right-shifted dysplasia burden versus UC-only. Under specific-pathogen-free conditions, DKO mice developed early right-predominant colitis and multifocal dysplasia progressing with age. DKO communities were depleted of 7&#x3b1;-dehydroxylation capacity with near absence of deoxycholic and lithocholic acids and no enrichment of canonical bacterial genotoxins. GF DKO mice were protected, whereas live DKO donor FMT reinstated severe colitis and dysplasia; sterile-filtered stool supernatant was inactive. IL-10[-/-] donor FMT or cohousing attenuated colitis and increased recipient secondary BA, whereas wild-type/MDR2[-/-] donor transfers were non-colitogenic. In GF DKO mice, direct deoxycholic acid repletion caused hepatotoxicity.<br><br>CONCLUSION: PSC-UC neoplasia associates with transmissible microbiota-dependent inflammation and secondary BA deficiency. Controlled restoration of BA-transforming microbial functions, rather than indiscriminate secondary BA replacement, is a rational translational direction.}, }
@article {pmid41680704, year = {2026}, author = {Huang, Y and Huang, X and Wei, X and Yang, X and Su, T and Duan, Q and Wan, J and Sun, Y and Xu, Y}, title = {Characterization of multiple herpes viremia via next-generation sequencing in patients with lower respiratory tract infections: a retrospective cohort study.}, journal = {BMC infectious diseases}, volume = {26}, number = {1}, pages = {}, pmid = {41680704}, issn = {1471-2334}, support = {H-2024060//the Yunnan health training project of high level talents/ ; XDYC-QNRC-2024-448//the Yunnan revitalization talent support program/ ; 202302AA310044-01//Key Projects of Yunnan Province Science and Technology Department/ ; }, abstract = {BACKGROUND: Lower respiratory tract infections (LRTIs) are a leading cause of the substantial morbidity and mortality associated with severe pneumonia. Herpesviruses (HHVs) frequently reactivate during critical illness, but their bronchoalveolar lavage fluid (BALF) coinfection patterns and clinical correlates remain incompletely defined.<br><br>METHODS: A retrospective cohort study was conducted among hospitalized adults with suspected LRTIs who underwent BALF next-generation sequencing (NGS) at the Yunnan First People&#x2019;s Hospital between November 2024 and May 2025. Two analytical workflows were evaluated, namely metagenomic DNA sequencing (mNGS-DNA) and a targeted NGS (tNGS) panel, including 289 and 675 patients, respectively. Participants were subsequently classified into a herpesvirus-detected (HD) group and a non-herpesvirus-detected group (non-HD).<br><br>RESULTS: In mNGS-DNA, detection frequencies were EBV 17.30%, CMV 14.88%, HHV-7 9.00%, HSV-1 8.30%, HHV-6 4.15%, and VZV 0.34%, single- and multi-virus positivity were 22.84% and 11.76%. In tNGS, the corresponding values were 17.93%, 12.00%, 7.11%, 10.07%, 2.96%, and 0.30%, single- and multi-virus positivity were 24.44% and 15.11%. HD patients were older and more likely to have severe pneumonia in both cohorts (P&#x2009;<&#x2009;0.0001). Bacteria were the predominant pathogens in the patients with suspected LRTIs, followed by viruses and fungi. In matched BALF subsets, sequencing outperformed culture for bacterial detection (mNGS-DNA 37.90% vs. 20.56%; tNGS 87.45% vs. 13.45%; all P&#x2009;<&#x2009;0.001), underscoring the complementary yield over conventional culture methods. HHVs exhibited the highest co-infection rates with pathogens such as Stenotrophomonas maltophilia, Klebsiella pneumoniae, and Candida albicans.<br><br>CONCLUSIONS: In BALF from hospitalized LRTI patients, EBV and CMV predominate among herpesviruses, with HHV-7 a frequent coinfection partner. These findings underscore the need for prospective studies to define the prognostic impact of HHV coinfections.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-026-12866-x.}, }
@article {pmid41860726, year = {2026}, author = {Stevens, KA and de Souza, JO and Li, H and Ouro-Djobo, A and Alabi, OJ and Al Rwahnih, M}, title = {Agave associated crinivirus A: a novel monopartite crinivirus homolog isolated from agave.}, journal = {Archives of virology}, volume = {171}, number = {4}, pages = {}, pmid = {41860726}, issn = {1432-8798}, abstract = {UNLABELLED: We describe the complete genome of the first monopartite and putative member of the genus Crinivirus which we propose naming agave associated crinivirus A (AaCA). AaCA was identified by high-throughput sequencing in an Agave tequilana leaf sample during a routine metagenomic screening of Agave plants from California. The 16,161 bp genome contains the protein hallmarks of the family Closteroviridae, the HSP70h and the three coat protein homologs (CPh, CP, CPm), along with the open reading frames (ORFs) unique to criniviruses. Two ORFs downstream of the CPm are unique to AaCA. The monopartite nature of the genome was verified by PCR and Sanger sequencing. Phylogenetic analysis of the HSP70h gene clusters AaCA basally with existing criniviruses.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00705-026-06580-x.}, }
@article {pmid41862850, year = {2026}, author = {Li, Z and Wu, C and Huang, D and Liang, Y and Zhai, Y and Mai, C and Han, Y and Tang, LA and Wang, W and Ning, C and Tan, W}, title = {Metagenomics reveals pathogenic diversity and temporal dynamics in severe pneumonia among patients in adult intensive care unit.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13107-x}, pmid = {41862850}, issn = {1471-2334}, support = {2021YFC2300101//the National Key Research and Development Program of China/ ; }, }
@article {pmid41863347, year = {2026}, author = {Lutfi, A and Holstein, T and Andreotti, S and Muth, T}, title = {MegaPX: fast and space-efficient peptide assignment method using IBF-based multi-indexing.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btag134}, pmid = {41863347}, issn = {1367-4811}, abstract = {MOTIVATION: A central problem for metaproteomic analysis is the often-unknown taxonomic composition of the analyzed microbiomes. Using a database search, the standard approach requires prior knowledge of which proteins and taxa to include in the protein reference database or to use tailored metagenome-derived databases, which are expensive and error-prone in their generation. A possible strategy to circumvent this database search issue is de novo sequencing, where peptide sequences are directly identified from mass spectra. However, these sequences must still be mapped back to potentially extensive databases. Here, alignment-based approaches enable robust and precise results, with the potential drawback of high memory usage and long run times.<br><br>RESULTS: We present MegaPX, a software for rapidly classifying de novo peptide sequences against large protein databases. MegaPX implemented as a C&#x2009;++-based tool, uses an alignment-free, k-mer approach as a taxonomic classification method with the possibility of generating mutated reference databases for error-tolerant searching. It uses various algorithms, including interleaved Bloom filters, to efficiently compute approximate membership queries, ensuring fast processing times while querying and indexing large databases in a multi-indexing fashion. We demonstrate the potential of MegaPX by analyzing different samples, including metaproteomics, against extensive reference databases, highlighting its use as a fast screening tool.}, }
@article {pmid41863618, year = {2026}, author = {Majumder, D and Dash, S and Bhattacharya, D and Gill, HS and Raja, V and Dewi, JR and Roy, A and Rajeev, M and Pandit, S and Sharma, S and Dwivedi, SP and Nag, M and Lahiri, D}, title = {Genetically engineered lipases: advances in expression and upscaling for industrial applications.}, journal = {Archives of microbiology}, volume = {208}, number = {6}, pages = {}, pmid = {41863618}, issn = {1432-072X}, }
@article {pmid41863619, year = {2026}, author = {Jonathan, AR and Balasubramanian, VK and Ho, ST and Chen, YP and Khunnamwong, P and Chou, JY}, title = {Next-generation strategies for PLA degradation: microbial consortia, metagenomics, enzyme engineering and AI-guided approaches.}, journal = {Archives of microbiology}, volume = {208}, number = {6}, pages = {}, pmid = {41863619}, issn = {1432-072X}, support = {MOST 111-2621-B-018-001 to Jui-Yu Chou//Ministry of Science and Technology, Taiwan/ ; }, mesh = {*Metagenomics/methods ; *Microbial Consortia ; Biodegradation, Environmental ; *Polyesters/metabolism ; Artificial Intelligence ; Fungi/metabolism/genetics ; Bacteria/metabolism/genetics ; }, abstract = {Polylactic acid (PLA) is one of the most widely used biodegradable bioplastics; however, its slow degradation under natural conditions limits its environmental sustainability. This review summarizes recent advances in microbial and biotechnological strategies that enhance PLA biodegradation across diverse ecosystems. Emerging approaches include screening insect gut microbiota, isolating fungal species with strong adsorption or enzymatic capacities, and exploring soil, compost, and aquatic microbiomes using metagenomics and environmental DNA (eDNA) tools. Microbial consortia, thermophilic degraders, and co-culture systems are highlighted as effective solutions to overcome the intrinsic crystallinity and hydrolysis-dependent breakdown of PLA. Beyond natural systems, this review emphasizes the increasing role of synthetic biology, directed evolution, and artificial intelligence (AI) in engineering high-performance PLA-degrading enzymes. AI-driven structural prediction and machine-learning platforms offer new possibilities for designing robust depolymerases with improved specificity, thermostability, and catalytic efficiency. Collectively, these multidisciplinary strategies provide a roadmap for accelerating PLA degradation in industrial composting, wastewater treatment, and bioremediation. Future integration of ecological screening with computational enzyme engineering is expected to advance scalable and sustainable PLA waste management.}, }
@article {pmid41863708, year = {2026}, author = {Mishra, AK and Verma, S and Mishra, A and Khan, G and Singh, H}, title = {Unlocking the role of microbiome through gut-skin axis to alleviate aging: current perspectives and future scope.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {41863708}, issn = {2509-2723}, abstract = {The microbiota of intestinal origin has a significant impact on the aging process, affecting skin health and overall cell longevity. Aging is marked by physiological alterations, such as enhanced oxidative stress, which is intensified by external factors like UV radiation and environmental pollution. The gut microbiota profoundly influences immune functions and results in reduced inflammation, which contributes to the anti-aging process. The present review is an attempt to showcase the current studies on the gut-skin axis, investigating the impact of gut-derived metabolites, particularly short-chain fatty acids, postbiotics, synbiotics, and psychobiotics, on the function of skin barriers and the aging process. Dietary supplements, including prebiotics along with probiotics, have demonstrated significant potential in altering gut microbiota composition and, in turn, improving skin health. Future studies must focus on investigating the connection between gut microbiota and cellular senescence, the effectiveness of microbiota-targeted therapeutics, and the incorporation of targeted therapy to delay the aging process. Comprehending these processes may facilitate the development of novel ways to enhance healthy aging and alleviate age-related diseases through the gut-skin axis via microbiome regulation.}, }
@article {pmid41863933, year = {2026}, author = {Dong, X and Zhu, L and He, Y and Li, C and Wu, R and Li, D}, title = {Microbial degradation of plastics in the environment: Mechanisms, enzymatic pathways, and constraints from laboratory studies to environmental reality.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129422}, doi = {10.1016/j.jenvman.2026.129422}, pmid = {41863933}, issn = {1095-8630}, abstract = {Microplastic (MP) pollution has become a persistent environmental challenge, raising increasing concern due to its global distribution and potential risks to human health. Biological degradation, including microbial and insect mediated processes, represents a promising and environmentally sustainable strategy for mitigating plastic and MP pollution; however, its effectiveness remains highly variable and strongly context dependent. This review systematically summarizes recent advances in microbial degradation of plastic, as well as emerging research on insect mediated plastic biodegradation, focusing on degrading microorganisms, key enzymes, metagenomic discovery, and enzyme engineering strategies. A wide range of bacterial and fungal taxa capable of degrading major plastic polymers, including polyethylene (PE), polypropylene (PP), polyethylene terephthalate (PET), polystyrene (PS), polyvinyl chloride (PVC), polyurethane (PU), and polylactic acid (PLA), has been reported. In addition, several insect species capable of ingesting and transforming plastics have been identified as model systems for studying plastic degradation, where mechanical fragmentation, host digestive processes, and gut microbial metabolism jointly contribute to polymer transformation. Among these, PET degrading enzymes, particularly PETase, are the most extensively characterized, benefiting from detailed structural insights and intensive protein engineering efforts that have markedly enhanced catalytic efficiency and thermostability. In contrast, enzymatic mechanisms involved in the biodegradation of polyolefins such as PE and PP remain poorly understood, representing a major knowledge gap. Recent metagenomic approaches have substantially expanded the repertoire of candidate plastic degrading enzymes by accessing uncultured MP associated microbial communities and insect gut microbiomes. Nevertheless, functional validation and evaluation under environmentally relevant conditions remain critical bottlenecks. Moreover, most reported degradation efficiencies are derived from optimized laboratory settings and may substantially overestimate microbial performance under natural environmental constraints, including low temperature, high salinity, nutrient limitation, and mixed polymer substrates. Overall, this review highlights the gap between laboratory based biodegradation studies and real world applications and emphasizes the need for integrated strategies to advance scalable plastic and MP remediation solutions.}, }
@article {pmid41863937, year = {2026}, author = {Liu, X and Liu, X and Zhu, D and Wang, J and Wang, Z and Liu, W and Zhou, X and Zhou, H and Wu, L}, title = {Harvesting reshapes greenhouse gas exchange in reservoir drawdown soils via soil state control and context-dependent microbial functions.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129375}, doi = {10.1016/j.jenvman.2026.129375}, pmid = {41863937}, issn = {1095-8630}, abstract = {Reservoir drawdown zones, the seasonally exposed and re-flooded margins of reservoirs, are extensive pulsed wetlands that can act as hotspots of greenhouse gas (GHG) exchange. Vegetation harvesting is common in these zones, yet its net climate effect across CO2, CH4, and N2O, and the controls behind it, remain unclear. We compared harvested and unharvested plots across longitudinal river reaches and elevation bands in the drawdown zone of the Three Gorges Reservoir (China). We measured soil-atmosphere fluxes of CO2, CH4, and N2O, together with soil physicochemical properties and metagenome-derived functional markers. Harvesting increased CO2 flux and decreased CH4 flux, while N2O showed no detectable net treatment effect. Across analyses, soil hydrothermal and nutrient conditions were the dominant predictors of flux variation; microbial functional signals added information mainly through soil-dependent interactions. In CO2-equivalent terms, lower CH4 emissions only partly compensated for higher CO2, leaving a net positive effect under both 20- and 100-year horizons. These results underscore that harvest impacts in drawdown soils should be assessed as multi-gas trade-offs and interpreted through soil moisture-redox dynamics.}, }
@article {pmid41863981, year = {2026}, author = {Fu, Z and Fu, J and Wang, Y and Zhan, K and Liang, Y and Ao, N and Shen, Q and Liu, C}, title = {Effects of tea polyphenols on intestinal barrier, antioxidant capacity, and cecal microbiota in lion-head geese.}, journal = {Poultry science}, volume = {105}, number = {6}, pages = {106706}, doi = {10.1016/j.psj.2026.106706}, pmid = {41863981}, issn = {1525-3171}, abstract = {Tea polyphenols are natural bioactive compounds associated with enhanced antioxidant capacity and improved gut health in poultry. This study evaluated the effects of dietary supplementation with tea polyphenols on intestinal morphology, barrier integrity, antioxidant status, and cecal microbiota in lion-head geese. A total of 240 one-day-old male lion-head geese were randomly allocated to 2 treatments: a basal diet (control) or the same diet supplemented with 1,000 mg/kg tea polyphenols (catechin purity, 50.4%) for 18 wk (6 replicates/treatment; 20 birds/replicate). Compared with the control, dietary supplementation with tea polyphenols significantly increased villus height and villus-to-crypt ratio (V/C) in the jejunum and ileum (P < 0.05) and reduced serum lipopolysaccharide (LPS) concentration (P < 0.05), whereas serum diamine oxidase (DAO) activity did not differ (P > 0.05). In the jejunum, mRNA expression of ZO-1, Claudin-5, and Occludin was significantly upregulated (P < 0.05); in the ileum, mRNA expression of ZO-1, Claudin-5, Occludin, and E-cadherin was significantly upregulated (P < 0.05). Tea polyphenols increased jejunal total antioxidant capacity (T-AOC) and upregulated GPX1, GPX2, HO-1, and Nrf2 mRNA expression (P < 0.05). In the ileum, tea polyphenols significantly increased glutathione peroxidase (GSH-Px) and total superoxide dismutase (T-SOD) activities, decreased malondialdehyde (MDA) content, and upregulated SOD1, GPX1, GPX2, HO-1, and Nrf2 mRNA expression (P < 0.05). Metagenomic sequencing showed lower relative abundances of Firmicutes and Verrucomicrobia at the phylum level (P < 0.05). At the genus level, tea polyphenols increased Prevotella and Subdoligranulum and decreased Oscillibacter and Desulfovibrio (P < 0.05). Functional annotation (KEGG, eggNOG, and CAZy) indicated enrichment of carbohydrate transport and metabolism, glycosyltransferases (GT), and polysaccharide lyases (PL) in the tea polyphenol group. Spearman correlation analysis indicated positive associations of Prevotella with KEGG thermogenesis and the two-component system, and of Desulfovibrio with biotin metabolism (P < 0.05). Overall, tea polyphenols promoted intestinal development, enhanced barrier- and antioxidant-related responses, and altered the composition and functional potential of the cecal microbiota, supporting improved gut health in lion-head geese.}, }
@article {pmid41864025, year = {2026}, author = {Yu, H and Zhang, X and Liang, Y and Mu, Q and Shi, X and Deng, Z and Chen, J and Cao, J and Deng, Y and Han, Z and Chen, H and Zhang, C}, title = {Deciphering the environmental fate of halogenated organic compounds in cold seep sediments: Insights from non-targeted analysis and metagenomics across vertical redox gradients.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141804}, doi = {10.1016/j.jhazmat.2026.141804}, pmid = {41864025}, issn = {1873-3336}, abstract = {Halogenated organic compounds (HOCs) are pervasive in marine environments, yet their molecular diversity, vertical distribution, and fate in deep-sea ecosystems remain largely uncharted. Here, we integrated non-targeted analysis, geochemical profiling, and metagenomics to systematically analyze a 500-cm sediment core from the Haima deep-sea cold seep, deciphering these key aspects and their controlling factors. Non-targeted analysis identified 669 HOCs (at molecular formula level), predominantly of marine origin with saturated structures. The highest HOC diversity was found in the oxic/suboxic (OS) zone, where 73.4% of the frequently detected HOCs reached their peak abundance. Concurrently, a marked decrease in organochlorines was observed at the OS-suboxic/anoxic (SA) interface, followed by level stabilization below this transition, suggesting regulation by abrupt redox shifts. Correlation analyses revealed co-regulation of HOC distribution by geochemical (e.g., depth, pH, and SO4[2-]) and microbial (e.g., reductive and hydrolytic dehalogenases) factors. Metagenomics combined with redundancy analysis further demonstrated significant interactions between HOCs and dehalogenating microbial community along the vertical profile. In summary, this study provided an integrated perspective on the biogeochemical cycling of HOCs in the deep-sea cold seep, linking their removal at redox boundaries, long-term burial, and spatial organization to underlying microbial and geochemical drivers.}, }
@article {pmid41864266, year = {2026}, author = {Wang, X and Wang, Y and Yan, G and Chu, N and Huang, H and Nie, W}, title = {The Clinical Diagnostic Value of Metagenomic Next-Generation Sequencing for Patients with Suspected Nontuberculous Mycobacterial Osteoarticular Infection: A National Multicenter Clinical Cohort.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {108578}, doi = {10.1016/j.ijid.2026.108578}, pmid = {41864266}, issn = {1878-3511}, abstract = {OBJECTIVE: This study aimed to determine the accuracy of metagenomic next-generation sequencing (mNGS) in diagnosing non-tuberculous mycobacteria (NTM) osteoarticular infection (OAI) and compare it with mycobacteria growth indicator tube (MGIT) culture.<br><br>METHODS: This study was conducted on 193 patients with suspected NTM OAI treated from January 2019 to July 2022 at the Beijing Chest Hospital, Capital Medical University, Yantai Qishan Hospital or The Fourth People's Hospital of Nanning who had mNGS assay and MGIT culture results. Clinical comprehensive diagnosis was taken as the "gold standard". We investigated the diagnostic sensitivity, specificity, predictive value, and likelihood ratio of these tests.<br><br>RESULTS: Of the 193 patients, 26 (13.47%) were diagnosed with NTM OAI, and 167 (86.53%) had non-NTM OAI. Compared to the MGIT culture results, mNGS showed higher sensitivity (100.0% vs. 7.7%), specificity (99.4% vs. 80.2%), positive predictive value (96.3% vs. 5.7%), negative predictive value (100.0% vs. 84.8%), positive likelihood ratio (167.000 vs. 0.389) and negative likelihood ratio (0.000 vs. 1.150). The area under the curve of the mNGS assay was 0.997 (95% confidence interval, 0.990-1.000).<br><br>CONCLUSIONS: The mNGS assay had greater diagnostic accuracy than the MGIT culture in patients with suspected NTM OAI.}, }
@article {pmid41864408, year = {2026}, author = {Wang, Z and Chen, Z and Zhu, L and Liu, Y and Wen, Q}, title = {Substrate type determines the interplay between metabolic efficiency and microbial stress response in mixed culture PHA production under high salinity.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124330}, doi = {10.1016/j.envres.2026.124330}, pmid = {41864408}, issn = {1096-0953}, abstract = {Polyhydroxyalkanoates (PHAs) from mixed cultures offer a sustainable alternative to plastics, and high salinity presents a promising selective pressure for PHA producers. However, the osmotic stress imposed by high salinity perturbs carbon and energy metabolism, yet how different volatile fatty acid (VFA) substrates influence PHA synthesis efficiency under sustained saline conditions remains poorly understood, particularly regarding carbon flux partitioning and energy trade-offs. This study investigated the effects of single VFA (acetate, propionate, butyrate, and valerate) on the enrichment, PHA accumulation, and metabolic flux of PHA-producing mixed cultures under 1.8% salinity. Butyrate and valerate-fed systems achieved superior PHA accumulation (0.636 ± 0.015 and 0.698 ± 0.005 g PHA/g VSS, respectively) compared to acetate (0.541 ± 0.006 g PHA/g VSS) and propionate (0.382 ± 0.021 g PHA/g VSS). This was due to more direct precursor supply and lower energy demands. Carbon flux analysis confirmed butyrate and valerate directed over 85% of utilized carbon to PHA, whereas propionate diverted more to cell maintenance. Metagenomics revealed that Paracoccus was a versatile salt-tolerant PHA producer across all substrates. Cultures fed with butyrate and valerate also exhibited enhanced respiratory chain activity and higher ATP/NAD(P)H, enabling better salt stress while maximizing PHA synthesis. These findings highlight the critical interplay between VFA type, salt stress, and metabolic trade-offs, providing crucial insights for optimizing high-salinity waste to PHA bioprocesses.}, }
@article {pmid41864933, year = {2026}, author = {Dai, QB and Lai, LM and Zhu, Q and Yuan, L}, title = {Clinical efficacy of plasma cell-free dna metagenomic next-generation sequencing in diagnosing bloodstream infections.}, journal = {BMC infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1186/s12879-026-13134-8}, pmid = {41864933}, issn = {1471-2334}, support = {20242BAB20430//the Natural Science Foundation of Jiangxi Province/ ; 202510284//the Science and Technology Plan of Jiangxi Provincial Health Commissio/ ; }, }
@article {pmid41865546, year = {2026}, author = {Fan, X and Wang, Y and Liang, W and Ma, X and Zhang, W and Yu, C}, title = {Organic fertilizers reduce N2O and NH3 emissions by regulation soil nitrogen pool and microbiome.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129432}, doi = {10.1016/j.jenvman.2026.129432}, pmid = {41865546}, issn = {1095-8630}, abstract = {Organic fertilizers are generally considered beneficial towards maintaining long term soil health, yet they could elevate N2O and NH3 emissions which raise concerns regarding air pollution and climate change. In this study, four types of organic fertilizers (raw sheep manure, RSM; composted sheep-manure organic fertilizer, OF; biochar-amended organic fertilizer, CharOF; sterilized OF, SOF) were applied onto three kinds of soils in microcosm cultivation to explore their effects on N2O and NH3 emissions and the underlining mechanisms. The results showed that traditional organic fertilizers (RSM and OF) significantly increased N2O and NH3 emissions from the soils, whereas CharOF reduced by as much as 23.0% in N2O and 18.4% in NH3 from that of RSM/OF peaks. Both OF and SOF significantly increased soil total nitrogen (TN) and organic nitrogen (Org-N), while CharOF significantly improved soil NO3[-]-N, NH4[+]-N and microbial biomass nitrogen (MBN). Metagenomic sequencing showed that RSM and OF significantly increased denitrification genes norB and narI, dissimilatory nitrate reduction genes nasA, napA and nirB, and mineralization gene ureC, while CharOF slightly suppressed denitrification genes nirS and narI, dissimilatory nitrate reduction genes nasA/B, napA, nirB and NR, and mineralization gene ureC. RDA analysis revealed that NO3[-]-N, NH4[+]-N, MBN and pH were the environmental factors affecting NC relevant genes and gas emissions. PLS-PM model revealed that soil nitrogen pool correlated stronger to the NH3 and N2O emissions than that of nitrogen cycle (NC) relevant genes. This study provides a theoretical foundation for the promotion of low-pollution fertilization practices in green agriculture, and contributes to the advancement of agricultural sustainability. Additionally, it offers fresh perspectives on organic fertilizer production and its role in enhancing socio-economic systems for public benefits.}, }
@article {pmid41865575, year = {2026}, author = {Xie, H and Zhou, J and Shi, Y}, title = {Bioaugmentation of weathered petroleum-contaminated soil with a yeast-based consortium: Degradation performance and mechanism insights.}, journal = {Journal of hazardous materials}, volume = {507}, number = {}, pages = {141830}, doi = {10.1016/j.jhazmat.2026.141830}, pmid = {41865575}, issn = {1873-3336}, abstract = {Bioremediation of total petroleum hydrocarbons (TPHs) in weathered soil is often constrained by the inefficiency of indigenous microbial synergistic networks. The mechanisms governing these network responses remain poorly understood, frequently overlooking the system-level functional dynamics. This 7-week study contrasted biostimulation (NZ) with yeast-based bioaugmentation (NS), linking microbial succession and functional network reconstruction to TPHs degradation. The NS group showed a clear advantage in TPHs removal (83.1%) and, crucially, in degrading the heavy C22-C40 fraction (76.3%). The NZ community, despite possessing degradation genes, was trapped in a "functional lock", lacking a cohesive synergistic network. The TPHs and heavy C22-C40 fraction removal efficiencies of the NZ community are only 75.3% and 39.3%, respectively. In contrast, the introduced Saccharomyces cerevisiae in the NS group acted as a pioneer species. It initiated a system-wide reconstruction by (1) altering the soil microenvironment through intense metabolic stress responses (e.g., upregulation of protein quality control systems and high-affinity MFS transporters) and (2) activating a novel, synergistic indigenous consortium, including Altererythrobacter and Cellulosimicrobium. It is indicated that effective bioaugmentation is not the mere addition of strains but a deliberate ecological network reconstruction. The pioneer species alleviates the functional stagnation of the native community, driving the emergence of a novel, highly effective synergistic degradation system. This provides a key theoretical basis for developing bioremediation technologies centered on ecological network regulation.}, }
@article {pmid41865593, year = {2026}, author = {Asokan, S and Banerjee, N and Saleem, M and Atiyah, HM and Pandey, RK and Abbas, RK and Yousif, SIA and Radhamanalan, G and Parashar, A and Gowtham, B and Balaji, VK and Jacob, T and Vijayan, S and Rajeswary, D and Atiyah, MM}, title = {Healthcare associated infections (HAI): Insights into epidemiology, microbiology, and diagnostics.}, journal = {Diagnostic microbiology and infectious disease}, volume = {115}, number = {3}, pages = {117376}, doi = {10.1016/j.diagmicrobio.2026.117376}, pmid = {41865593}, issn = {1879-0070}, abstract = {Healthcare associated infections remain a major global health concern because they increase illness, mortality, hospital stay, and healthcare costs. This review provides an updated synthesis of recent evidence on the epidemiology, microbiology, diagnostics, and prevention of healthcare associated infections. These infections arise from patient susceptibility, invasive procedures, antibiotic overuse, contaminated equipment, and poor infection control practices. Device associated infections such as catheter associated urinary tract infection, central line associated bloodstream infection, ventilator associated pneumonia, and surgical site infection are common and often involve multidrug resistant pathogens. Biofilm formation on devices and hospital surfaces creates persistent reservoirs that promote resistance spread. Advances in automated culture systems, rapid molecular assays, metagenomics, and whole genome sequencing improve detection and surveillance. This article integrates evidence from 2020 to 2025 to provide a multidisciplinary framework for understanding and controlling HAIs.}, }
@article {pmid41865818, year = {2026}, author = {Wang, J and Sun, Y and Zhang, Y and Guo, Y and Liu, J and Wang, X and Yang, Y and Shi, L}, title = {Mechanisms underlying differences in nitrogen removal characteristics of anammox granular sludge immobilization filler with varying particle sizes: Performance, structure, and nitrogen removal pathways.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134471}, doi = {10.1016/j.biortech.2026.134471}, pmid = {41865818}, issn = {1873-2976}, abstract = {The anaerobic ammonium oxidation (anammox) process serves as a green, low-carbon, and sustainable wastewater nitrogen removal technology. However, anammox processes based on granular sludge systems face structural instability issues, resulting in the loss of anammox bacteria (AnAOB). In this study, an immobilized filler system for AnAOB based on hydrogel encapsulation was constructed using anammox granular sludge (AnGS) of varying particle sizes (G1: < 0.10 cm, G2: 0.10-0.20 cm, G3: 0.20-0.32 cm, and G4: > 0.32 cm). The differences in nitrogen removal characteristics, microstructures, and pathways of these AnGS immobilized fillers were thoroughly investigated. The large particles (G3 and G4) immobilized fillers showed the best nitrogen removal performance, with total nitrogen removal rates reaching 0.591 kgN·m[-3]·d[-1] and 0.615 kgN·m[-3]·d[-1], respectively. The G2 immobilized filler was more conducive to the self-growth and enrichment of AnAOB, and the absolute abundance and relative abundance of Candidatus Brocadia increased by 23-fold and 9.20-fold, respectively. Conversely, the G1 immobilized filler displayed the poorest nitrogen removal rate due to insufficient microbial growth. The G1-G3 immobilized fillers possessed uniform and dense small pores, whereas the G4 filler featured uniform large pores. Metagenomic analysis confirmed that the abundance of denitrification-related genes in G3 and G4 immobilized fillers was highest, indicating that anammox and denitrification synergistically achieve nitrogen removal, whereas G2 immobilized fillers mainly relied on anammox. This study provides a crucial theoretical basis and technical guidance for optimizing the application of anammox immobilized filler systems.}, }
@article {pmid41865820, year = {2026}, author = {Luo, Z and Li, W and Zhang, N and Lei, M and Chen, B and Li, Y and Liu, Q and Zhang, M and Lv, S and Cheng, F and Li, J}, title = {A novel continuous-flow three-stage tandem system based on partial nitrification/Anammox granular sludge and partial denitrification-Anammox biofilm (PN/A-PD-A) for advanced nitrogen removal from mature landfill leachate.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134474}, doi = {10.1016/j.biortech.2026.134474}, pmid = {41865820}, issn = {1873-2976}, abstract = {A novel continuous-flow system coupling partial nitrification/Anammox (PN/A), partial denitrification (PD), and Anammox (Amx) biofilm reactors was developed (PN/A-PD-A) to treat mature landfill leachate (MLL). To maximize synergy, the NH4[+]-N removal in the PN/A reactor was regulated based on the NO2[-]-N accumulation ratio (NAR) in the PD stage, ensuring optimal substrate stoichiometry for the final Amx polishing step. Over 174 days of operation, the system achieved a superior total nitrogen removal efficiency (TNRE) of 98.30 ± 0.14% (effluent TN: 21.80 ± 1.71 mg/L). The PN/A granular sludge, enriched with Candidatus_Kuenenia (5.87%) and Nitrosomonas (9.73%), demonstrated high adaptability to MLL characteristics and contributed to 83.51% of the TN removal. In the PD stage, the dominant genus Thauera (43.91%) facilitated efficient NAR (82.86 ± 1.61%) at a limited COD/NO3[-]-N ratio of 2.32 ± 0.02. The Anammox biofilm (Candidatus_Kuenenia, 27.80%) in the Amx reactor contributed to 13.10% of TN removal, ensuring to meet the MLL discharge standard. Kinetic and metagenomic analyses confirmed that distinct shifts from complete to partial nitrification (and denitrification) in enzymes activity and gene abundance under chronic MLL stress underpinned the robust NO2[-]-N accumulation in both PN/A and PD reactors. Notably, compared to conventional nitrification-denitrification process, the PN/A-PD-A system significantly reduced oxygen demand (60.18%), exogenous organic carbon consumption (91.61%), sludge yield (83.72%), and CO2 emission (94.66%), demonstrating a sustainable pathway for low-carbon nitrogen removal from high-strength wastewater.}, }
@article {pmid41865821, year = {2026}, author = {Wang, X and Liang, BJ and Wu, DN and Zhang, XM and Zhao, HP and Lai, CY}, title = {Efficient anaerobic metformin biodegradation driven by a Cross-Feeding Consortium: Novel Pathways, Enzymes, and toxicity dynamics.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {134473}, doi = {10.1016/j.biortech.2026.134473}, pmid = {41865821}, issn = {1873-2976}, abstract = {Metformin is one of the most widely prescribed antidiabetic drugs worldwide and is now ubiquitously detected in aquatic environments, yet its anaerobic biodegradation remains largely unexplored and mechanistically unresolved. Here, an anaerobic membrane bioreactor (AnMBR) was operated and near-complete metformin removal (∼98%) at influent concentrations up to 5.3 mg/L was achieved, corresponding to a maximum degradation rate of 7.2 mg/L/d, approximately sixfold higher than previously reported anaerobic systems degrading metformin. High-resolution mass spectrometry identified three concurrent anaerobic metformin transformation pathways. Notably, a previously unreported biological C-N bond cleavage route yielding dimethylguanidine was discovered, expanding the known anaerobic metabolic repertoire of metformin. In silico toxicity prediction revealed a non-monotonic toxicity trajectory during metformin transformation, with transiently elevated toxicity at intermediates (particularly 2,4-AMT) followed by an overall attenuation at the terminal product guanidine. Metagenomic and metatranscriptomic analyses uncovered a cooperative, cross-feeding microbial network dominated by Ignavibacterium album and Denitrolinea symbiosum, and identified HypAB (metformin-to-guanylurea), YafV and AmiA/B/C/E (guanylurea-to-guanidine), and, critically, SpeB as the key enzyme initiating the newly proposed C-N bond cleavage pathway. Molecular dynamics simulations further suggested stable binding of metformin to SpeB with strong affinity, providing mechanistic support for SpeB-mediated initiation of the novel pathway. Overall, this study establishes the first mechanistic framework for anaerobic metformin biodegradation, reveals an unprecedented C-N scission pathway, and demonstrates that high-rate, low-carbon pharmaceutical removal can be achieved through intrinsic microbial metabolism, offering new conceptual and practical foundations for energy-efficient treatment of emerging pharmaceutical contaminants.}, }
@article {pmid41865866, year = {2026}, author = {Wang, Y and Wang, D and Wang, H}, title = {Comparative analysis of the gut microbiome and bile acid profiles in sympatric Rana chensinensis and Fejervarya multistriata tadpoles.}, journal = {Comparative biochemistry and physiology. Part A, Molecular &amp; integrative physiology}, volume = {}, number = {}, pages = {111996}, doi = {10.1016/j.cbpa.2026.111996}, pmid = {41865866}, issn = {1531-4332}, abstract = {Environmental temperature is an essential exogenous factor influencing the gut microbiota of amphibians, which exerts profound physiological impacts on the host by modifying bile acids (BAs). Even sympatric amphibians often have considerably different optimal breeding temperatures. However, the effect of different developmental temperatures on gut microbiota and BA profiles in sympatric amphibians remains unclear. To address this deficiency, morphological, histological, metagenomics and metabolomics information were compared between Rana chensinensis (R. chensinensis) and Fejervarya multistriata (F. multistriata) tadpoles. Morphological and histological results showed that body mass index (BMI), intestinal mass to body mass ratio (IM/BM), and enterocyte height (EH) were higher in F. multistriata, whereas body mass (BM), total length (TL), and intestine mass (IM) were higher in R. chensinensis. Metagenomics analysis revealed the relative abundance of microorganisms (Bacteroides, Clostridium, and Enterococcus) producing bile salt hydrolase (BSH) is higher in F. multistriata, whereas the relative abundance of microorganisms (Dorea spp, Extibacter muris, Clostridium leptum, and Proteocatella sphenisci) possessing the BAI operon is higher in R. chensinensis. Comparative metabolomic analysis identified that F. multistriata has a higher ratio of unconjugated to conjugated BAs (CA/TCA, CDCA/TCDCA, and DCA/TDCA), which may suppress the abundance of pathogen (e.g., Clostridioides difficile). Additionally, the lower TDCA content in F. multistriata may be potentially linked to its stronger absorptive capacity. In contrast, R. chensinensis exhibits a higher ratio of DCA to CA, which probabaly enhance their cold tolerance. Overall, this study elucidated the potential impacts of developmental temperature-driven differences in gut microbiota and BAs on sympatric amphibians' physiological metabolism.}, }
@article {pmid41784805, year = {2026}, author = {Shen, J and Gao, J and Gao, L and Yan, D and Wang, Y and Meng, J and Li, H and Chen, D and Wu, J}, title = {Melatonin ameliorates autistic-like behaviors by restoring gut microbiota-derived tryptophan metabolites.}, journal = {Cellular and molecular life sciences : CMLS}, volume = {83}, number = {1}, pages = {}, pmid = {41784805}, issn = {1420-9071}, support = {2023-MS-310, 2019-BS-098//Natural Science Foundation of Liaoning Province/ ; LJKQZ2021149//Scientific Research Fund of Liaoning Provincial Education Department/ ; }, abstract = {UNLABELLED: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social deficits and repetitive stereotyped behavior. Disrupted microbiota‒gut‒brain axis (MGBA) signaling contributes to the pathology of ASD and cognitive disability. Melatonin (MT), a naturally occurring compound, has shown potential in ameliorating core symptoms of ASD and mitigating gut microbiota dysbiosis, yet the underlying mechanism is poorly understood. This study aimed to investigate whether exogenous melatonin improves behavioral deficits in valproic acid (VPA)-exposed male offspring rats, and the modulation of gut microbiota-derived tryptophan metabolites. In prenatal VPA-induced model rats, microbial diversity and construction was analyzed through metagenomic sequencing, targeted-metabolomics and transcriptomics were conducted to explore related metabolic pathways and molecular profiles. We identified 7 gut bacterial genus causally associated to ASD: Faecali-bacterium, Lachnospiraceae, Ruminococcaceae, Butyricimonas, and Bacteroides exhibited protection, whereas Erysipelotrichaceae and Clostridia enhanced risk. The exacerbation of Erysipelotrichaceae and Clostridia by VPA versus restoration of Faecalibacterium, Butyricimonas, Bacteroides and Bifidobacterium by melatonin, which are known to participate in tryptophan metabolism. Correspondingly, systemic metabolomics pointed to melatonin’s restoration of tryptophan metabolic disorders (IDO1-kynurenine, TPH1/2-serotonin-melatonin, and Indole-3-propionic acid (IPA)) induced by VPA, paralleled the rectification of microglial reactivity, synaptic proteins, dendritic morphology, and hippocampal neurogenesis. These molecular profiles were further integrated by transcriptomics, highlighted tryptophan-derived neurotransmitters and neuroactive ligand-receptor interaction, contributing to enhanced social and cognitive behaviors under melatonin intervention. Based on multi-omic analysis, our findings underscore key bacteria and metabolites contributing to neurological and immune dysfunction in VPA-exposed rats, providing novel targets for possible therapeutics of melatonin.<br><br>GRAPHICAL ABSTRACT: [Image: see text]<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00018-026-06163-8.}, }
@article {pmid41862052, year = {2026}, author = {Rajalakshmi, SG and Ramesh Babu, K and Viswanathan, P}, title = {Investigating gut microbiome dysbiosis in adults with chronic kidney disease: Diabetes-induced alterations via metagenomics and qPCR.}, journal = {Life sciences}, volume = {}, number = {}, pages = {124336}, doi = {10.1016/j.lfs.2026.124336}, pmid = {41862052}, issn = {1879-0631}, abstract = {BACKGROUND: Type 2 diabetes (T2D) is a major contributor to diabetic nephropathy, the leading cause of chronic kidney disease (CKD). This study investigated gut microbial dysbiosis and composition shift among healthy individuals and diabetic patients with or without CKD using a 16S rRNA metagenomic approach, validated by qRT-PCR and clinical data integration to identify the significant key genera associated with disease progression.<br><br>METHODS: Stool samples from 22 individuals were analysed using 16S rRNA amplicon sequencing to assess gut microbiota composition. Differential abundance analysis, LEfSe, and network-based methods were employed to identify key taxa. Significant features were validated by qRT-PCR. Integrated approaches, including Pearson correlation, WGCNA, random forest, and propensity score matching, were used to associate microbial features with clinical markers. Functional enrichment of microbial pathways was predicted using PICRUSt2.<br><br>KEY FINDINGS: A total of 1409 amplicon sequence variants (ASVs) were identified. Bray-Curtis dissimilarity showed significant microbial diversity differences between disease and healthy subjects (p&#x202f;<&#x202f;0.031). Key taxa associated with eGFR and serum creatinine (sCr) included Bacteroidetes uniformis (LFC +9), Ruminococcus (LFC +8.1), and Dialister succinatiphilus (LFC +6.7), linked to disease progression and metabolic regulation. In contrast, protective taxa such as Bifidobacterium adolescentis (LFC -9.5), Faecalibacterium prausnitzii (LFC -6.39), Collinsella, and Megasphaera elsdenii were reduced. Integration of Pearson correlation, WGCNA, propensity score matching, and random forest classification revealed microbial features associated with clinical covariates.<br><br>SIGNIFICANCE: Our findings show the gut microbiome shifts begin in diabetics without CKD conditions but become more pronounced in diabetics with CKD, with a lower ratio of beneficial bacteria, reflecting a gradual microbial imbalance along disease progression.}, }
@article {pmid41856866, year = {2026}, author = {Jelen, BI and Baker, BJ}, title = {Mapping environmental microbiomes across an entire country.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2026.02.013}, pmid = {41856866}, issn = {1878-4380}, abstract = {Microbial diversity underpins ecosystem function and resilience, yet large-scale spatial baselines remain rare. Singleton et al. present a Danish atlas of environmental microbiomes, revealing nationwide patterns of diversity. By emphasizing gamma diversity, they show how nitrifying communities differ in scale and composition between natural and disturbed habitats.}, }
@article {pmid41857415, year = {2026}, author = {}, title = {Metagenomic surveillance of zoonotic yellow fever and spillover dynamics at a forest-urban interface.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {41857415}, issn = {2058-5276}, }
@article {pmid41857851, year = {2026}, author = {Yu, X and Wen, Z and Zhou, W and Zheng, Y and Chen, J and Xiao, WJ and Lin, S and Liang, H and Duan, X and Wang, W and Wu, H and Chen, X}, title = {Respiratory syndromic disease study in Shanghai community population.}, journal = {BMJ open}, volume = {16}, number = {3}, pages = {e103001}, doi = {10.1136/bmjopen-2025-103001}, pmid = {41857851}, issn = {2044-6055}, mesh = {Humans ; China/epidemiology ; Male ; Female ; *Respiratory Tract Infections/epidemiology/microbiology ; Adult ; Prospective Studies ; Middle Aged ; Adolescent ; Aged ; Child ; Young Adult ; Child, Preschool ; Incidence ; Coinfection/epidemiology ; Urban Population ; Seasons ; }, abstract = {PURPOSE: This prospective community-based cohort study (Acute Respiratory Infection Epidemiological Characteristics Assessment Study (ARI-ECAS)) aims to systematically monitor acute respiratory infection (ARI) incidence, characterise multiple pathogen coinfection patterns and explore microbial landscape dynamics in Shanghai's general population. By integrating syndromic surveillance, molecular diagnostics and metagenomic sequencing, the study seeks to enhance understanding of ARI epidemiology, seasonal variation and host-pathogen interactions to inform predictive modelling and optimise public health interventions in high-density urban environments.<br><br>PARTICIPANTS: The study enrolled 15&#x2009;199 permanent residents from all 16 districts of Shanghai, with baseline oropharyngeal swab samples across five representative districts (Xuhui, Jing'an, Jiading, Songjiang and Fengxian). Inclusion criteria required residency &#x2265;6 months and consent for weekly follow-ups. Exclusion criteria addressed mobility limitations (planned relocation >6 months) and recent ARI history. Participants provided demographic, behavioural and clinical data via the Shanghai Health Cloud platform, with baseline and symptomatic-phase biological samples collected for analysis.<br><br>FINDINGS TO DATE: During the initial 8-month surveillance period (May 2024-January 2025), the ARI-ECAS cohort demonstrated critical insights into the epidemiology of acute respiratory infections in Shanghai's urban communities. Among 15&#x2009;199 participants, 10.96% reported symptomatic episodes, of whom 21.43% experienced recurrent infections. Pathogen detection using targeted next-generation sequencing (tNGS) identified microbial aetiologies in 53.52% of symptomatic cases, revealing a high prevalence of coinfections: 27.96% involved dual pathogens, while 33.01% showed polymicrobial interactions (&#x2265;3 pathogens). Notably, 85.09% of symptomatic episodes were self-managed, underscoring a low healthcare-seeking rate (14.91%) consistent with patterns observed in urban China during postpandemic transitions.<br><br>FUTURE PLANS: The current phase of data collection will conclude in June 2025; however, syndromic surveillance and tNGS protocols will be sustained to capture multiyear seasonal transmission patterns. To enhance comparative rigour, future protocols will aim to collect samples from participants during asymptomatic periods in the subsequent year to serve as seasonal baseline controls. Building on this foundation, the study will integrate contact behaviour and mobility surveys to quantify parameters critical for understanding pathogen transmission dynamics (eg, household contacts and public transportation usage). Furthermore, pathogen detection and metagenomic data will be combined with transcriptomic and metabolomic profiling in selected cases to model multipathogen interaction networks and delineate host immune response pathways, thereby advancing mechanistic insights into polymicrobial cocirculation.}, }
@article {pmid41857857, year = {2026}, author = {Ngoumou, GB and Ngandeu Schepanski, S and Blakeslee, SB and Diedering, A and Twal, E and Raue, SL and Schroeder, M and Wicaksono, WA and Stritter, W and Berg, G and Seifert, G}, title = {Effects of fermented versus unfermented red cabbage on symptoms, immune response, inflammatory markers and the gut microbiome in young adults with allergic rhinoconjunctivitis: a randomised controlled trial protocol.}, journal = {BMJ open}, volume = {16}, number = {3}, pages = {e115290}, doi = {10.1136/bmjopen-2025-115290}, pmid = {41857857}, issn = {2044-6055}, mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Adult ; Young Adult ; *Brassica ; Quality of Life ; *Fermented Foods ; Adolescent ; Randomized Controlled Trials as Topic ; *Conjunctivitis, Allergic/immunology/diet therapy ; *Rhinitis, Allergic/immunology/diet therapy ; Female ; Male ; Biomarkers ; }, abstract = {INTRODUCTION: Allergic rhinoconjunctivitis (ARC) is a highly prevalent immune-mediated condition associated with substantial symptom burden, impaired quality of life and increased healthcare use. Emerging evidence highlights the role of the gut microbiome in immune regulation and allergic disease. Fermented foods may contain live microbes (when unpasteurised or uncooked) and bioactive postbiotic metabolites that can modulate immune responses. Despite growing interest in dietary strategies targeting the microbiome, no randomised controlled trial has compared fermented versus unfermented red cabbage for ARC.<br><br>METHODS AND ANALYSES: This single-centre, randomised, controlled trial with a sensory-matched, unfermented cabbage comparator investigates the effects of daily consumption of fermented red cabbage for 8 weeks compared with an unfermented red cabbage control in young adults (18-35 years) with ARC. A total of 158 participants will be randomly assigned (1:1). The primary outcome is change in Total Nose and Eye Symptom Score from baseline to week 8. Secondary outcomes include daily symptoms and medication use captured via mobile ecological momentary assessments, quality of life, psychological well-being, gastrointestinal symptoms, systemic inflammatory markers, total IgE, immune cell profile and metagenomic characterisation of stool samples. A nested qualitative component explores participants' experiences and acceptability of the intervention. Analyses will include mixed-effects models, time-series analyses incorporating daily pollen counts and comprehensive microbiome statistics. Safety outcomes and adverse events will also be assessed.<br><br>ETHICS AND DISSEMINATION: This study was approved by the Ethics Committee of Charit&#xe9;-Universit&#xe4;tsmedizin Berlin (EA4/043/25) and is conducted in accordance with the Declaration of Helsinki and Good Clinical Practice. Results will be disseminated through peer-reviewed publications, conference presentations and a lay summary provided to participants. Anonymised datasets and analysis scripts will be made available in public repositories, and metagenomic sequencing data will be deposited in an international sequence archive to ensure transparency and reproducibility.<br><br>TRIAL REGISTRATION NUMBER: DRKS00036475.}, }
@article {pmid41858204, year = {2026}, author = {Chen, X and Ji, M and Yan, D and Liu, Y and Chen, Y and Dong, R and Shen, L and Takeuchi, N and Kong, W}, title = {Metabolic capacities and potential microbial interactions in red and green snow of the Antarctic Peninsula.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.71089}, pmid = {41858204}, issn = {1469-8137}, support = {32161123004//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 72574092//National Natural Science Foundation of China/ ; }, abstract = {Colored (red and green) snow is widespread in Antarctica due to climate warming. This phenomenon reduces snow albedo, accelerates snowmelt, alters microbial functions, and impacts regional geochemical cycles. Diverse microorganisms are associated with this phenomenon, yet their functions remain poorly understood. We employed metagenomic sequencing to reveal the metabolic interactions and functional specialization within microbial communities of colored snow, focusing on carbon, nitrogen, phosphorus, and sulfur metabolism. While broad metabolic profiles were similar between red and green snow, targeted analysis of specific pathways revealed significant enrichment of denitrification and organic-phosphorus mineralization genes in green snow and labile carbon degradation genes in red snow. Betaproteobacteria were dominant drivers of nitrogen, sulfur, and phosphorus transformation, while diverse eukaryotic algae and bacteria were responsible for carbon fixation. Additionally, we recovered 2257 bacteriophages, 529 algal viruses, and 2302 secondary metabolite gene clusters. Specifically, viruses encoded 126 auxiliary metabolic genes that may influence the elemental cycling of hosts, while secondary metabolites, such as pyoverdine, may assist algal iron acquisition. Our findings offer new insights into the metabolic potentials and interactions of microbial communities in Antarctic colored snow, highlighting their potential relevance to snow biogeochemical processes.}, }
@article {pmid41858247, year = {2026}, author = {Groninga, J and Wittig, L and Bouderka, F and Bornemann, TLV and Lipp, JS and Schubotz, F and Keden, S and Probst, AJ and Hinrichs, KU}, title = {Novel Extended Tetraether Lipids Found in a High-CO2 Geyser.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70286}, doi = {10.1111/1462-2920.70286}, pmid = {41858247}, issn = {1462-2920}, support = {101118631/ERC_/European Research Council/International ; }, mesh = {*Carbon Dioxide/metabolism/analysis ; *Archaea/genetics/metabolism/chemistry ; Germany ; *Groundwater/microbiology ; *Lipids/chemistry ; *Ethers/chemistry ; Metagenome ; *Glyceryl Ethers/chemistry ; }, abstract = {The growing research into the archaeal lipidome has uncovered a remarkable structural diversity in isoprenoidal glycerol dialkyl glycerol tetraethers (iGDGTs) and revealed complex membrane adaptations, especially in extreme environments. We performed a comprehensive analysis of the lipidome from the subsurface aquifer of the CO2-rich, cold-water Geyser Andernach (Germany), using ultra-high-resolution mass spectrometry. We detected iGDGT-0, presumably derived from the dominant community member Candidatus Altiarchaeum, providing supporting evidence for its ability to synthesise tetraethers, as previously predicted from metagenomic data. Beyond the typical iGDGT-0 and acyclic glycerol trialkyl glycerol tetraether (iGTGT-0), we discovered novel structural derivatives, here referred to as extended iGDGTs and iGTGTs, characterised by the asymmetrical addition of up to two isoprenoid units to only one of their hydrocarbon side chains, analogous to those found in extended archaeols. The apparent absence of GDGT ring synthase A and B genes in the corresponding metagenome-assembled genome raises the possibility that the producing archaea may utilise extended iGDGTs as a membrane adaptation to cope with the nutrient-depleted conditions of the geyser environment, highlighting the adaptive flexibility of archaea to extreme physicochemical conditions.}, }
@article {pmid41858251, year = {2026}, author = {Morissette, O and Côté, G and Couillard, MA and Pouliot, R and Bernatchez, L}, title = {Trait-Based Biomonitoring Using eDNA Metabarcoding to Assess Anthropogenic Disturbances on Freshwater Fish Communities.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70131}, doi = {10.1111/1755-0998.70131}, pmid = {41858251}, issn = {1755-0998}, mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/classification/genetics ; *DNA, Environmental/genetics ; Quebec ; Ecosystem ; Fresh Water ; Rivers ; *Biological Monitoring/methods ; Biodiversity ; *Environmental Monitoring/methods ; *Metagenomics/methods ; *Biota ; }, abstract = {Various anthropogenic disturbances affect the succession of aquatic habitats along dendritic river networks. Bioindicator taxa, such as fish, can be used to assess the effects of these disturbances on habitat quality. Environmental DNA (eDNA) metabarcoding offers a novel approach to complement traditional sampling and analysis of bioindicator taxa. Here, we apply a trait-based biomonitoring framework, focusing on fish tolerance to pollution, to assess habitat quality and fragmentation within two watersheds in southern Québec (Canada). We sampled 193 sites within the dendritic networks of the Châteauguay and St. François watersheds and estimated fish community tolerance indices on the basis of 12S metabarcoding. We found a significant correlation between the fish community tolerance index and environmental factors such as subwatershed land use, precipitation and elevation. We also found that river fragmentation caused by dams affected fish assemblages and native fish movement but also prevented the spread of the non-native common carp. Finally, we applied random-forest modelling to predict the tolerance of fish communities to disturbances in unsampled areas, providing a broader understanding of habitat quality within catchments. Our research highlights how eDNA metabarcoding for large-scale biomonitoring and river fragmentation studies provides a cost-effective and non-invasive method for assessing fish biodiversity and riverine ecosystem health.}, }
@article {pmid41858257, year = {2026}, author = {Geerts, MM and Curto, M and Alverson, AJ and Stone, J and Gante, HF}, title = {Disentangled Assembly Graphs Reveal Hidden Eukaryotic Diversity in eDNA Metagenomic Data.}, journal = {Molecular ecology resources}, volume = {26}, number = {3}, pages = {e70128}, doi = {10.1111/1755-0998.70128}, pmid = {41858257}, issn = {1755-0998}, support = {STG/21/044//KU Leuven Research Fund/ ; 11Q4724N//Fonds Wetenschappelijk Onderzoek/ ; UIDP/50027/2020//InBIO Program&#xe1;tico FUI 2020-2023/ ; DEB-2331644//Division of Environmental Biology/ ; }, mesh = {*Metagenomics/methods ; *Diatoms/genetics/classification ; Phylogeny ; *Computational Biology/methods ; *DNA, Environmental/genetics ; *Eukaryota/genetics/classification ; Metagenome ; *Biodiversity ; Czech Republic ; Fresh Water/microbiology ; }, abstract = {Genome assembly graphs contain valuable yet frequently overlooked information that can enhance assembly completeness by revealing contig connectivity. Here, we demonstrate how leveraging these information-rich structures enables the discovery of hidden microeukaryotic diversity in environmental DNA shotgun metagenomic datasets. While GetOrganelle has previously been used for organellar genome assembly from isolated tissues, we present its first application to water eDNA metagenomic data, using diatoms as an example. We tested the efficiency of this organellar genome assembly tool on three freshwater eDNA metagenomic datasets with varying diatom abundances, finding that GetOrganelle alone yields fragmented scaffolds due to mixed-species complexity. By implementing manual disentanglement of assembly graphs, we successfully recovered complete organellar genomes from these assemblies. From high-abundance bloom samples, we recovered complete plastomes of Stephanodiscus hantzschii with 99.9% pairwise identity across distant geographical locations (USA and Czech Republic). From a lower abundance non-bloom sample, we reconstructed a potentially novel Cyclotella plastome with only 94.0% identity to its closest available reference, Cyclotella atomus. Our assembly quality assessment confirmed effective manual disentanglement even at low diatom abundances. By integrating sequence similarity, gene order conservation and phylogenetic analysis, we achieved robust species-level resolution and resolved previous taxonomic uncertainties. Our findings demonstrate that mining eDNA metagenomic data with GetOrganelle reveals previously hidden microeukaryotic diversity and provides higher taxonomic resolution than traditional binning methods. This approach proves especially valuable for microeukaryotes, where reference organellar genomes remain underrepresented in existing databases.}, }
@article {pmid41858380, year = {2026}, author = {Beran, P and Rost, M and Beranová, K and Kváč, M and Stehlíková, D and Udoh, OE and Jozová, E and Čurn, V}, title = {genCRC32: collision-free CRC32-based hashing of DNA sequences.}, journal = {Bioinformatics advances}, volume = {6}, number = {1}, pages = {vbaf315}, pmid = {41858380}, issn = {2635-0041}, abstract = {MOTIVATION: Efficient and collision-free hashing of DNA sequences is essential for accuracy and performance in bioinformatics applications such as genome assembly, sequence alignment, and metagenomic classification. Traditional hashing methods often result in collisions, impacting the precision and/or performance of downstream analyses. Thus, it is highly advantageous to have hashing functions that guarantee collision-free mappings for DNA sequences, particularly for k-mers up to length 16, where practical limits for 32-bit hashing are reached. In this study, we evaluate genCRC32 as a hashing primitive, reporting collision behavior, bucket balance, sensitivity to single-base changes, and speed to inform its potential use in downstream tools. Evaluation within specific software tools is outside the scope of this paper and is planned as future work.<br><br>RESULTS: We present genCRC32, an innovative hashing method that integrates a straightforward preprocessing step (gen32) with CRC32 hashing, specifically identifying eight CRC32 polynomials that ensure collision-free hashing for all DNA k-mers up to 16 nucleotides in length. Through extensive empirical evaluations, genCRC32 demonstrated zero collisions for these k-mers, achieving a one-to-one mapping without auxiliary data structures. Benchmark tests confirmed minimal computational overhead introduced by preprocessing, maintaining hashing performance comparable to established methods such as MurmurHash3 and xxHash32.<br><br>The source code for genCRC32 is publicly available at: https://github.com/berybox/genCRC32. The implementation is provided in Go (version 1.24) and leverages only standard libraries, ensuring portability and ease of integration into existing bioinformatics workflows.}, }
@article {pmid41858392, year = {2026}, author = {Tu, W and Zeng, P and Wu, Z and Li, Z and Yu, T and Zhang, W and Chen, R and Liang, L}, title = {A case report of brain abscess caused by Nocardia cyriacigeorgica identified by metagenomic next-generation sequencing.}, journal = {World journal of emergency medicine}, volume = {17}, number = {2}, pages = {199-201}, pmid = {41858392}, issn = {1920-8642}, }
@article {pmid41858535, year = {2026}, author = {Zhang, L and Chen, S and Li, H and Li, L and Liu, H}, title = {Molecular epidemiology and genomic analysis of bulbul coronavirus in Guangdong, China.}, journal = {Frontiers in veterinary science}, volume = {13}, number = {}, pages = {1659863}, pmid = {41858535}, issn = {2297-1769}, abstract = {INTRODUCTION: Bulbul coronavirus (BuCoV), a delta coronavirus recently identified in passerine birds, remains poorly characterized regarding its ecology and evolutionary dynamics. This study aimed to determine the prevalence of BuCoV in wild avifauna, clarify its evolutionary relationship with other delta coronaviruses, and identify genetic signatures potentially relevant to host adaptation and cross-species transmission in southern China.<br><br>METHODS: From 2023 to 2024, we conducted molecular surveillance across 12 regions in Guangdong Province, China. A total of 2,145 avian fecal samples were collected and screened for BuCoV using real-time quantitative PCR. The complete genomes of representative strains were obtained using next-generation sequencing. Subsequent analyses included phylogenetic reconstruction using maximum likelihood methods, recombination detection using RDP4 and SimPlot, and comparative amino acid analysis.<br><br>RESULTS: BuCoV was detected exclusively in Shenzhen (3/168, 1.78%), with all positive samples originating from bulbuls (Pycnonotus spp.). The Shenzhen strain GD2411 exhibited the highest nucleotide identity with BuCoV strains HKU11-796 (97.26%) and HKU11-934 (96.79%), but far lower similarity (78.9%-82.4%) to other delta coronaviruses. Phylogenetic analysis placed GD2411 in a monophyletic clade with HKU11 strains. Recombination analyses revealed mosaic structures within the spike (S) gene, involving multiple coronavirus lineages. Thirty-one amino acid substitutions were detected in the S protein, together with mutations in RdRp, 3CLpro, and nucleocapsid.<br><br>DISCUSSION: These findings suggest that BuCoV GD2411 emerged through inter-lineage recombination and is undergoing adaptive evolution, particularly in the spike protein. The detection of BuCoV exclusively in Shenzhen, a critical node in the East Asian-Australasian Flyway, suggests that migratory birds may facilitate viral dissemination. The identified mutations may affect viral replication, host adaptation, or immune evasion. These findings provide essential baseline genomic and epidemiological data critical for understanding BuCoV diversity and assessing potential zoonotic risks in southern China.}, }
@article {pmid41858674, year = {2026}, author = {Zholdasbek, A and Tekebayeva, Z and Kulzhanova, K and Abzhalelov, A and Bekshin, Z and Yevneyeva, D and Saylau, M and Li, X and Tan, Z and Wang, Z and Temirkhanov, A and Nurbekova, Z}, title = {Microbiome and plant relationship: a symbiosis against phytopathogens.}, journal = {Frontiers in plant science}, volume = {17}, number = {}, pages = {1722279}, pmid = {41858674}, issn = {1664-462X}, abstract = {Phytopathogens are among the major biotic stressors limiting global crop productivity. Conventional control methods, including chemical pesticides and fungicides, have contributed to pathogen resistance, environmental pollution, and soil degradation, highlighting the need for sustainable alternatives. This review highlights innovative, eco-friendly strategies that exploit plant-microbe interactions to enhance plant health and resilience across diverse agroecosystems. Rhizosphere-, phyllosphere-, and endosphere-associated microbial assemblages contribute to plant immune enhancement through induced systemic resistance, competitive nutrient exclusion, antimicrobial metabolite production, and mycoparasitism. The review emphasizes the functional roles of beneficial microbial communities and the emerging applications of synthetic consortia and bio-organic fertilizers to improving disease suppression, nutrient use efficiency, and soil fertility. In addition, recent progress in omics-based tools and microbial formulation technologies is discussed as a key driver for translating laboratory findings into practical field applications. However, large-scale implementation remains challenged by high research costs, limited metagenomic infrastructure, and the lack of standardized microbial formulations across environments. Strengthening institutional capacity, integrating omics-based tools, and improving technology transfer will be essential to unlock the full potential of microbiome-based pathogen control. Overall, this review highlights microbiome-based interventions as a sustainable alternative to chemical-intensive plant protection strategies under changing environmental conditions.}, }
@article {pmid41859061, year = {2026}, author = {Wang, Z and Yang, R and Xiao, Y and Huang, B and Yang, Z and Yang, L}, title = {Primary Cutaneous Aspergillosis Due to Aspergillus flavus in an Immunocompetent Patient.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {565781}, pmid = {41859061}, issn = {1178-6973}, abstract = {Invasive aspergillosis is a life-threatening infection caused by Aspergillus species, affecting the lungs, central nervous system, nasal and orbital regions, and skin. Primary cutaneous aspergillosis (PCA) occurs through direct skin inoculation via trauma, burns, or surgical wounds, with Aspergillus fumigatus, Aspergillus flavus, and Aspergillus niger as common causative species, and is rare in immunocompetent individuals. We report a case of PCA in a 56-year-old immunocompetent patient with facial and right ankle ulcers, persisting for two years. The patient had no history of diabetes, corticosteroid use, or immunodeficiency. Fungal culture and metagenomic next-generation sequencing (mNGS) confirmed A. flavus infection. Voriconazole therapy, surgical debridement, and specialized wound care led to the gradual healing of the ulcers. This case highlights the importance of early diagnosis and intervention to prevent infection spread and progression to systemic aspergillosis or septic shock.}, }
@article {pmid41859064, year = {2026}, author = {Gu, P and An, X and Wei, Y and Xu, W and Han, Y and Gao, Q and Liu, S and Bi, Y}, title = {Elusive Diagnosis of Recurrent Subcutaneous Emphysema: Nocardia farcinica Infection in an Immunocompetent Female Patient.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {556094}, pmid = {41859064}, issn = {1178-6973}, abstract = {This case report describes an immunocompetent female with recurrent subcutaneous emphysema and refractory soft tissue infections involving multiple non-contiguous sites-bilateral breasts, chest wall, and upper limb-over seven years, consistent with disseminated nocardiosis. Initial presentations mimicked bacterial mastitis, with localized swelling, erythema, crepitus, and elevated inflammatory markers. Despite repeated incision and drainage procedures, antibiotic therapies, and bilateral mastectomies, symptoms recurred persistently. Conventional microbial cultures repeatedly failed to identify a pathogen, while metagenomic next-generation sequencing (mNGS) of a late-stage chest wall lesion ultimately revealed Nocardia farcinica, an opportunistic actinomycete with a known propensity for systemic dissemination even in immunocompetent hosts. The patient's atypical clinical course-marked by multifocal gas-forming soft tissue necrosis, chronic recurrence, and resistance to empiric treatments-underscores the diagnostic challenges posed by fastidious pathogens like Nocardia. Key lessons include the utility of mNGS in identifying culture-elusive organisms, the importance of considering nocardiosis in refractory subcutaneous infections regardless of immune status, and the necessity of prolonged, targeted antimicrobial regimens (eg, sulfonamides) combined with surgical intervention. This case highlights evolving paradigms in managing complex disseminated infections through advanced genomic diagnostics and multidisciplinary approaches.}, }
@article {pmid41859067, year = {2026}, author = {Jiang, X and Wu, L and Duan, S and Bian, J and Lv, T and Zheng, L and Zhao, Y and Shen, P and He, J and Chen, Y}, title = {Long-Term Antibiotic-Driven Gut Microbiota Disruption Promotes Toxigenic Clostridioides difficile Proliferation: A Four-Year Retrospective Study of a Single ICU Patient.}, journal = {Infection and drug resistance}, volume = {19}, number = {}, pages = {562973}, pmid = {41859067}, issn = {1178-6973}, abstract = {OBJECTIVE: This four-year longitudinal study of a single critically ill patient leverages deep temporal profiling to unravel the dynamic interplay between antibiotic pressure, gut microbiota, and Clostridioides difficile (C. difficile) colonization, providing temporal insights unattainable through cross-sectional designs.<br><br>METHODS: We performed a retrospective analysis of one critically ill patient (2015-2019). Sixty-four fecal samples were subjected to toxigenic C. difficile culture and metagenomic sequencing. To isolate short-term effects, we implemented a 7-day retrospective window, categorizing each sample based on antibiotic exposure in the preceding week: no antibiotics, monotherapy, or polypharmacy.<br><br>RESULTS: Antibiotic exposure significantly reduced microbial diversity and promoted dysbiosis. Crucially, we identified a transitional C. difficile colonization state (Tcd&#xb1;) that potentially determines progression to toxigenic (Tcd+) or non-toxigenic (Tcd-) outcomes. Analysis using the 7-day window revealed that intensive antibiotic pressure was strongly associated with successional progression towards toxigenic dominance. Conversely, brief antibiotic-free intervals were linked to partial restoration of microbial network complexity and a competitive landscape favoring non-toxigenic strains.<br><br>CONCLUSION: This deep temporal profiling of a single case provides novel, hypothesis-generating insights. The identification of a transitional colonization state and the association between short-term antibiotic pressure and colonization outcomes define critical dynamics for future validation. These findings highlight the potential of longitudinal data to inform precise antibiotic stewardship strategies in high-risk, critically ill populations.}, }
@article {pmid41859237, year = {2026}, author = {Xiao, Y and Zhao, R and Zhao, W and Wang, P and Xiao, X and Peng, X and Jing, H}, title = {Genomics-based insights into the expanded diversity and adaptation strategies of hadal trench anammox bacteria.}, journal = {ISME communications}, volume = {6}, number = {1}, pages = {ycag011}, pmid = {41859237}, issn = {2730-6151}, abstract = {Anaerobic ammonium oxidation (anammox) bacteria are an important functional guild in the nitrogen cycle and contribute up to 50% of nitrogen loss in the global ocean. Hadal trenches have been recognized as a hotspot of marine biogeochemical cycles; however, the metabolic traits, ecological adaptations, and potential origins of anammox bacteria in this critical habitat remain largely unexplored. Here, we reconstructed eight anammox metagenome-assembled genomes from sediments of four hadal trenches (Diamantina, Kermadec, Mariana, and Yap), which represent four out of the five distinct anammox bacterial families (i.e. Candidatus Scalinduaceae, Ca. Anammoxibacteraceae, Ca. Subterrananammoxibiaceae, and Ca. Bathyanammoxibiaceae). The dominant trench anammox bacteria, affiliated with Ca. Scalindua, were similar to those found in shallow coastal sediments and oxygen-deficient seawaters. Beyond the core anammox metabolism, the hadal Ca. Scalindua genomes contain genes encoding cyanase and urease, indicating that they can utilize cyanate and urea besides ammonium to thrive in the hadal trenches. Compared to trench-derived Ca. Subterrananammoxibiaceae and Ca. Bathyanammoxibiaceae, ABC-type Fe[3+] transporter and sulfate transporter CysZ could help trench-derived Ca. Anammoxibacteraceae genomes to uptake Fe[3+] and synthesize sulfur-containing amino acids. Molecular clock analysis suggests that the ancestors of the hadal anammox bacterial lineages appeared on Earth 1.46-0.07 billion years ago, significantly earlier than the geological formation of the trenches. The first hadal anammox bacteria were likely derived from shallower sediments and were transported into the trenches via sediment wasting. Overall, our study reveals a remarkable diversity of hadal anammox bacteria and their origin as well as survival strategies in hadal sediments.}, }
@article {pmid41859321, year = {2026}, author = {Salama, RA and Abdel Kader, RG and Wadid, NA}, title = {Artificial intelligence in combating challenges in antimicrobial resistance: a narrative review.}, journal = {Infection prevention in practice}, volume = {8}, number = {2}, pages = {100522}, pmid = {41859321}, issn = {2590-0889}, abstract = {Antimicrobial resistance (AMR) is a major global health challenge that threatens the effective prevention and treatment of infections. It arises from increasing resistance rates, limited diagnostic capacity, inappropriate antimicrobial use, and a declining pipeline of new antibiotics. These challenges highlight the need for innovative approaches to complement existing AMR control strategies. Artificial intelligence (AI) has emerged as a valuable tool to address the complexity and scale of AMR. This narrative review examines how AI can be more effectively integrated into key components of AMR management. By analysing large clinical and laboratory datasets, AI-based surveillance and predictive models enable near real-time monitoring of resistance patterns and early outbreak detection. AI-powered diagnostic tools, including image analysis and genomic methods, improve rapid pathogen identification and prediction of antimicrobial susceptibility. In clinical practice, AI-driven decision support systems strengthen antimicrobial stewardship by optimizing prescribing and monitoring antibiotic use. In addition, deep learning approaches accelerate antimicrobial drug discovery and repurposing, reducing development timelines. AI also enhances the detection and surveillance of resistance genes through genomic and metagenomic analyses across human, animal, and environmental settings. Despite its potential, AI applications in AMR face challenges related to data quality, bias, interoperability, privacy, and clinician adoption. Therefore, AI should be seen as a tool that supports, rather than replaces, existing AMR strategies. When regulated well and integrated within One Health frameworks, AI can strengthen surveillance, improve treatment decisions, and support evidence-based interventions to curb AMR.}, }
@article {pmid41859442, year = {2026}, author = {Wang, Y and Zhang, L and Huang, W and Wang, N and Sun, M and Wu, L and Wang, W and Shi, C}, title = {Metagenomic analysis of the community structure and functional potential of Tamarix rhizosphere microbiomes along a soil salinity gradient.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1756020}, pmid = {41859442}, issn = {1664-302X}, abstract = {INTRODUCTION: Soil salinization strongly shapes rhizosphere microbial communities and their functional potential in arid ecosystems. Tamarix is a key halophytic shrub in desert saline-alkali environments, yet how its rhizosphere microbiomes respond to natural salinity gradients remains insufficiently understood. Here, we compared community structure, functional potential, and potential salt-adaptation strategies across a soil salinity gradient.<br><br>METHODS: Rhizosphere soils of Tamarix were collected from four sites (S1-S4) in Xinjiang, China spanning increasing salinity. Soil physicochemical properties were measured, followed by shotgun metagenomic sequencing. Taxonomic profiles and functional annotations were generated from metagenomic data and compared among salinity groups.<br><br>RESULTS: Salinity was associated with clear shifts in community composition. Bacteria dominated at low-to-moderate salinity, whereas archaeal relative abundance increased at higher salinity, with Euryarchaeota becoming dominant in the high-salinity group. Functional profiling indicated that core metabolic pathways remained prevalent along the gradient, suggesting relative stability in overall metabolic capacity. However, higher salinity was accompanied by enrichment of functions linked to genetic information processing (e.g., translation and replication/repair) and ion transport, while lipid metabolism, cell motility, and signal transduction were reduced.<br><br>DISCUSSION: Together, these results support a salinity-driven transition in microbial functional strategy from "growth expansion" toward "homeostasis maintenance." Under high salinity, microbes appear to allocate more resources to maintaining cellular integrity and coping with stress, consistent with the observed enrichment of genetic information processing and repair-related functions. Mechanistically, the increased representation of Na[+]/H[+] antiporter systems and V/A-type ATPases in the very high salinity group suggests that energy-dependent ion homeostasis is a prominent adaptation, helping regulate intracellular ion balance and mitigate salt toxicity. In contrast, pathways for compatible solute synthesis (e.g., betaine and ectoine biosynthesis) were relatively reduced, indicating that osmoprotection may rely less on de novo solute production and more on ion regulation and maintenance processes along this gradient. Overall, the metagenomic evidence clarifies how Tamarix rhizosphere microbiomes restructure taxonomically and functionally with increasing salinity and highlights key candidate mechanisms underpinning salt-stress adaptation. These insights provide a microbial basis for understanding plant-microbe interactions in desert saline-alkali soils and may inform ecological restoration and management in salinized regions.}, }
@article {pmid41859445, year = {2026}, author = {Huang, Y and Liang, Q and Shen, Y and Chen, J and Xu, W}, title = {Oral microbiome dysbiosis in autism spectrum disorder: the oral-gut-brain axis and future perspectives: a narrative review.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1783810}, pmid = {41859445}, issn = {1664-302X}, abstract = {Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a steadily increasing global prevalence, yet its etiology remains largely unclear. Emerging evidence suggests that oral microbiome dysbiosis may contribute to the pathogenesis of ASD, potentially through the oral-gut-brain axis, although the exact role and causality remain to be fully established. In this narrative review, we synthesize recent clinical and metagenomic evidence on oral microbiome alterations in ASD and critically evaluate the potential pathways through which these microbial imbalances may impact neurodevelopmental outcomes. We summarize the key host-microbe interactions, including inflammatory signaling, epithelial barrier disruption, and immune-neural crosstalk, while emphasizing that direct causal evidence is still limited. Dysbiosis in individuals with ASD is characterized by altered microbial communities, including increased Streptococcus and decreased Prevotella, which correlate with clinical symptom severity. Moreover, metagenomic profiling has indicated the presence of potential biomarkers in the oral microbiome, which may serve as promising noninvasive diagnostic tools for ASD. While the clinical applications of oral microbiome diagnostics are still in the early stages, we explore the challenges and opportunities for developing these biomarkers for risk stratification. Finally, we outline future research directions that could enhance the understanding of the oral microbiome's role in ASD and facilitate the development of personalized intervention strategies.}, }
@article {pmid41859451, year = {2026}, author = {Cristofolini, M and Ronsivalle, M and Pramazzoni, M and Zaccarini, G and Pizzamiglio, V and Solieri, L}, title = {Role of microbial interactions in the impaired cultivability of thermophilic lactic acid bacteria in natural whey starter for Parmigiano Reggiano PDO cheese production.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1755652}, pmid = {41859451}, issn = {1664-302X}, abstract = {Natural whey starter (NWS) cultures play a pivotal role in the production of Parmigiano Reggiano (PR) Protected Designation of Origin (PDO) cheese; however, their microbial ecology and functional dynamics remain only partially understood. In particular, Lactobacillus delbrueckii subsp. lactis, a dominant species in type-D NWS communities, exhibits impaired cultivability that limits its isolation and characterization. Consequently, most studies have focused on strain variability within Lactobacillus helveticus, which is predominant in type-H NWS communities. In this study, we evaluated the effects of 14 different medium supplementations on the recovery and maintenance of L. delbrueckii subsp. lactis isolates from two PR NWS samples representatives of type-D and type-H communities. Although most supplementations increased lactobacilli plate counts compared with the control MRS medium, they failed to sustain cell viability during the purification for culture collection establishment. Moreover, these media altered species ratios in favor of L. helveticus, even when L. delbrueckii dominated the community according to metagenomic profiling (type-D NWS). Supplementation of MRS medium with cysteine and formic acid enabled the recovery of viable L. delbrueckii subsp. lactis isolates, accounting for 35% of the strains obtained from type-D NWS. Cross-feeding experiments further revealed that co-culturing L. delbrueckii with the formate-producing Streptococcus thermophilus significantly enhanced milk acidification compared with monocultures, indicating a beneficial metabolic interaction. In contrast, no such improvement was observed in the presence of L. helveticus, likely due to negative interactions with L. delbrueckii subsp. lactis. Accordingly, the impaired cultivability of L. delbrueckii subsp. lactis could thus be partially alleviated either in co-culture with S. thermophilus or under axenic conditions mimicking natural metabolite exchange between these species.}, }
@article {pmid41860433, year = {2026}, author = {Boers, D and Chapleur, O and Andersson, AF and Schnürer, A}, title = {Comparing the performance of functional versus taxonomic metagenomics for detecting ammonia disturbances in the biogas system.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiag029}, pmid = {41860433}, issn = {1574-6941}, abstract = {Biogas is a renewable energy source with great potential, but its production is frequently hindered by process disturbances, of which a high ammonia concentration is one common cause. It is desirable that such disturbances are found as early as possible; metagenomics data has the potential to improve this detection. This study compares functional and taxonomic aspects of metagenomics data, hypothesising that functional data will perform better for detecting ammonia disturbances. The hypothesis was tested by metagenomic sequencing of samples from three independent studies, which followed lab-scale reactors during ammonia disturbances. The resulting sequences were used to predict genes, which were functionally and taxonomically annotated. The read counts of these features were fitted to disturbance states and ammonia concentrations of reactor samples using regularised regression, which allowed filtering out irrelevant features even with limited sample sizes. Within studies, taxonomic data had similar or better performance in detecting ammonia disturbances and in fitting ammonia concentrations. When applying trained models to other studies however, while performance was generally poor, functional models more often performed better compared to taxonomic models than the other way around. All in all, our hypothesis that functional metagenomics would outperform taxonomic metagenomics only found limited support.}, }
@article {pmid41860453, year = {2026}, author = {Shen, S and Zhao, S and He, Z and An, X and Dong, J and Wang, L and Ji, W and Li, A}, title = {The Efflux-Two-Component System (TCS)-Virulence Axis Drives Resistance-Virulence Convergence in Aquatic "Superhost Precursors" under Pollution Stress.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.5c09604}, pmid = {41860453}, issn = {1520-5851}, abstract = {The coexpression of antibiotic resistance and virulence traits in aquatic bacteria represents an emerging ecological and public health threat, yet the mechanisms underlying their coordinated regulation under complex environmental pressures remain unclear. In this work, we integrated metagenomic, proteomic, and metabolomic data sets from surface water samples across the Yangtze River Basin in Jiangsu Province to elucidate the drivers of resistance-virulence convergence under multipollutant stress. Among 392 multidrug-resistant (MDR; resistant to ≥3 antibiotic classes) isolates, approximately 5% were identified as "culturable superhost precursors" exhibiting pandrug-resistant (PDR; resistant to ≥10 antibiotic classes) phenotypes. Multiomics analyses indicated frequent colocalization and synchronous activation of antibiotic resistance genes (ARGs) and virulence factors (VFs) in these environmental reservoirs. Functional assays under subinhibitory antibiotic exposure demonstrated enhanced cytotoxicity and efflux activity, accompanied by the upregulation of tolC and two-component regulators evgA/evgS. Together, these results characterize a putative redox-coupled efflux-two-component system (TCS)-virulence functional axis that synchronizes adaptive gene expression under pollution stress. Crucially, our findings challenge traditional antimicrobial resistance (AMR) surveillance approaches, which rely primarily on static gene abundance metrics, by demonstrating that the dynamic regulatory activation of this axis provides a more sensitive indicator of environmental health risks. Furthermore, tolC and evgA were identified as potential transcript-level biomarkers, providing a proof of concept for environmental antimicrobial resistance early warning tools within the One Health framework.}, }
@article {pmid41860568, year = {2026}, author = {Zhang, Y and Wu, Y and Li, X and Ren, T and Zhang, H and Chen, J}, title = {Klebsiella Enrichment Is Associated with Disease Severity in Ulcerative Colitis.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxag079}, pmid = {41860568}, issn = {1365-2672}, abstract = {BACKGROUND AND OBJECTIVE: Ulcerative colitis (UC), a chronic inflammatory bowel disease. This study uniquely undertook a parallel, severity-stratified comparison of both fecal and mucosal microbiota and metabolites in UC patients. Our objective was to identify niche-specific (fecal vs. mucosal) and severity-associated microbial and metabolic signatures, clarifying its potential clinical utility.<br><br>METHODS: A prospective cohort study (ChiCTR2300071816) enrolled 83 UC patients (&#x2265;18 years) from First Affiliated Hospital of Nanjing Medical University and Northern Jiangsu People's Hospital (Jan 2022-Dec 2024) and 30 healthy controls. Clinical data, stool, and rectal mucosal samples were collected. Metagenomic sequencing and metabolomics were performed. Disease severity was stratified by modified Mayo score to analyze microbiota diversity, differential genera, metabolites, and enriched metabolic pathways.<br><br>RESULTS: Fecal microbiota &#x3b1;-diversity was significantly lower in UC vs. controls (Shannon index 4.15 vs. 5.44, p=0.005); mucosal diversity showed no difference (p=0.63). Beta diversity did not differ. Severe UC exhibited a non-significant decrease in &#x3b1;-diversity (fecal: 3.99 vs. 4.37, p=0.14; mucosal: 3.40 vs. 3.72, p=0.92), significantly higher fecal/mucosal Klebsiella abundance, and lower Erysipelatoclostridium and Blautia abundance vs. mild-to-moderate UC. Metabolomics identified 363 fecal differential metabolites (e.g., allopurinol, histidine), enriching tyrosine and alanine/aspartate/glutamate metabolism pathways. Mucosal analysis revealed 127 differential metabolites (e.g., quinic acid, sphingosine), implicating sphingolipid metabolism and lysine synthesis.<br><br>CONCLUSION: UC demonstrates gut dysbiosis and metabolic disruption correlating with severity. Elevated Klebsiella abundance suggests a pathogenic role in progression. Distinct fecal and mucosal metabolic pathway alterations provide novel insights for disease classification and therapeutic targeting.}, }
@article {pmid41860897, year = {2026}, author = {Olaleye, M and O'Ferrall, AM and Goodman, RN and Kabila, DW and Peters, M and Falq, G and Samuel, J and Doyle, D and Gomez, D and Oloruntuyi, G and Isah, S and Adetunji, AS and Farley, E and Evans, NJ and Sherlock, M and Roberts, AP and Amirtharajah, M and Ainsworth, S}, title = {Shotgun metagenomic analysis of the oral microbiomes of children with noma.}, journal = {PLoS neglected tropical diseases}, volume = {20}, number = {3}, pages = {e0014118}, doi = {10.1371/journal.pntd.0014118}, pmid = {41860897}, issn = {1935-2735}, abstract = {Noma is a rapidly progressive orofacial gangrene that predominantly affects children living in extreme poverty. Despite its documentation since antiquity and its designation as a World Health Organisation Neglected Tropical Disease in 2023, the microbiological cause of noma remains poorly understood, with no specific organisms confidently identified as definitive aetiological agents. Here, we present the first deep shotgun metagenomic profiling of oral saliva microbiomes from 19 Nigerian children with acute noma. Our analyses of this preliminary study reveal marked microbial dysbiosis in noma microbiomes, with machine learning and multivariate statistical analyses indicating significant enrichment of Treponema, Porphyromonas, and Bacteroides, alongside depletion of Streptococcus and Rothia, as key microbial signatures of noma disease. From the dataset we recovered 40 high-quality Treponema metagenome assembled genomes (MAGs) spanning 19 species, 14 of which were novel. Notably, a novel species designated Treponema sp. A was detected in 15 of the 19 noma participants and was entirely absent from an internationally representative set of healthy saliva metagenomes. Re-analysis of previously published 16S rRNA datasets from children with noma in Niger also revealed Treponema sp. A to be highly prevalent in noma cases but extremely rare in controls. While these findings highlight Treponema, particularly Treponema sp. A, as an organism of interest and a potential contributor to noma pathogenesis, further comprehensive studies will be required to confirm this association and to clarify whether it reflects a causal role and/or is a genuine marker of noma dysbiosis. Additionally, analysis of antimicrobial resistance determinants detected in noma metagenomes revealed concerning levels of resistance to antibiotics commonly used in noma treatment, particularly β-lactams and metronidazole, especially among Prevotella spp. These findings provide the first high-resolution microbial framework for noma and offer a foundation for future research into its pathogenesis and the development of novel diagnostics, therapeutics, and preventive strategies in endemic settings.}, }
@article {pmid41861238, year = {2026}, author = {Yao, ML and Dai, Y and Zhang, W}, title = {Natural Products from the Oral Microbiome.}, journal = {Annual review of biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-biochem-051024-050248}, pmid = {41861238}, issn = {1545-4509}, abstract = {The human oral microbiome is a densely populated and chemically dynamic ecosystem where interspecies competition and cooperation shape community structure and influence host health. Metagenomic analyses reveal the immense biosynthetic potential of oral microbes to encode biosynthetic gene clusters (BGCs) and produce natural products. These metabolites are increasingly recognized as key mediators of microbial interactions, with many oral BGCs linked to health and disease. This review focuses on natural products in the oral microbiome derived from nonribosomal peptide synthetases and polyketide synthases, which are notable for their large size, modular machinery, and ecological relevance. We review the biosynthetic origins and bioactivities of these specialized metabolites in oral bacteria and discuss their biosynthetic regulation within the broader microbial community. Continued investment in whole-genome sequencing, integrative omics, and natural product discovery pipelines is essential for elucidating the microbial biochemical drivers of disease and advancing strategies to promote oral health.}, }
@article {pmid41861543, year = {2026}, author = {Mohapatra, RK and Choi, Y}, title = {Exploring multi-omics approaches in anammox-based wastewater treatment processes: A review of recent applications and technological advances.}, journal = {Journal of environmental management}, volume = {404}, number = {}, pages = {129342}, doi = {10.1016/j.jenvman.2026.129342}, pmid = {41861543}, issn = {1095-8630}, abstract = {Anaerobic ammonium oxidation (anammox) has arisen as a sustainable and energy-efficient approach for nitrogen removal in wastewater treatment. Recently, the utilization of multi-omics approaches, mainly metagenomics, metatranscriptomics, metaproteomics, and metabolomics has risen to reveal the complexity and functionality of anammox-based systems. These integrated approaches offer a comprehensive investigation of microbial community structure, gene expression, protein function, and metabolite dynamics across diverse operating contexts. Progress in high-throughput sequencing, mass spectrometry, and bioinformatics has facilitated the discovery of novel anammox bacteria, functional genes, and metabolic pathways, resulting in vital processes such as nitrogen cycling, microbial interactions, and system resilience. Metagenomics has shown the taxonomic and functional diversity within anammox consortia, whereas metatranscriptomics and metaproteomics have elucidated active metabolic pathways and functional responses to environmental alterations. Metabolomics has furnished direct evidence of metabolic states and biomarkers for enhancing reactor health and efficacy. Researchers have begun to elucidate the intricate physiological and biochemical mechanisms that govern the stability, recovery, and effectiveness of the anammox process through the integration of multi-omics datasets. This review explores recent technological breakthroughs and cutting-edge applications of multi-omics methods in anammox-based wastewater treatment. The article summarizes the principal research findings presented by numerous researchers, providing significant insights for the strategic design and management of robust and efficient water treatment systems aimed at future environmental sustainability.}, }
@article {pmid41861844, year = {2026}, author = {Tam, KK and Suster, CJE and Fong, W and Golubchik, T and Sivalingam, V and Jeoffreys, N and Tay, E and Ko, D and Wehrhahn, MC and Ginn, AN and Robson, J and Gardner, I and Papanicolas, LE and Kennedy, K and Graham, M and Tran, T and Speers, D and Cooley, L and Baird, RW and Meumann, EM and Harbidge, J and Campbell, S and Basile, K and Chen, SC and Sintchenko, V and Kok, J and Rockett, RJ}, title = {Genomic Surveillance Reveals Emergence and Spread of Macrolide-Resistant Mycoplasma pneumoniae in Australia During the 2023-2024 Epidemic.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiag163}, pmid = {41861844}, issn = {1537-6613}, abstract = {BACKGROUND: The resurgence of Mycoplasma pneumoniae (MP), first reported in China in 2023 was attributed to waning post-pandemic immunity with notable increases in macrolide-resistant MP (MRMP) (>80%). In Australia, infections peaked in early 2024, particularly among children under 15. While MRMP remains low in Europe, North America, and Australia (<5%), limited routine testing and surveillance restricts understanding of resistance dynamics. As macrolides are first-line therapy in many health settings, MRMP surveillance is essential for guiding empirical treatment and stewardship.<br><br>METHODS: We applied a novel capture-based targeted metagenomic sequencing (tNGS) to PCR-positive MP specimens (n=356) from across Australia. This approach enabled whole-genome recovery and MRMP detection directly from clinical specimens, without culture. MRMP detections were benchmarked against RT-PCR and clinical data were analysed to assess associations between resistance and healthcare utilisation.<br><br>RESULTS: This is the first genomics-informed national study of MP in Australia. We recovered 124 high-quality genomes, revealing a genetically diverse population with co-circulation of P1 Type 1 (69%) and Type 2 (31%). MRMP was identified in 13% of genomes, all belonging to clades prior to 2024 had only been reported in Asia (ST3 and ST14). MRMP cases were geographically widespread, suggesting importation and local transmission. Unlike reports from China, macrolide-susceptible clades (ST3, ST7, ST17 and ST20) predominated (87%) and were associated to significant lower healthcare utilisation compared to MRMP cases.<br><br>CONCLUSION: Our findings demonstrate the utility of tNGS for genomic epidemiology and highlight the need for MRMP surveillance. Although macrolides remain effective in Australia, emerging MRMP strains require close monitoring to inform treatment guidelines and antimicrobial stewardship.}, }
@article {pmid41861946, year = {2026}, author = {Wang, ST and Li, L and Yang, Q and Zhang, GF}, title = {Artificial reef age reshapes benthic microbial communities and modulates the genetic potential for nitrogen and sulfur cycling.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124314}, doi = {10.1016/j.envres.2026.124314}, pmid = {41861946}, issn = {1096-0953}, abstract = {Artificial reefs (ARs) are widely used to restore coastal ecosystems; however, the impact of reef age on microbial communities and their biogeochemical functions remains unknown. This study integrated metagenomic sequencing with physicochemical analysis to examine successional changes in benthic nitrogen and sulfur cycling along a chronosequence spanning from non-artificial reefs (0 years) to 14-year-old ARs in the coastal waters of the Bohai Sea, China. Our analysis revealed a systematic, time-dependent reorganization of the benthic microbiome, characterized by significant enrichment of ammonia-oxidizing archaea (Nitrososphaerota) and bacteria (Nitrospirota) in reefs older than 6 years. Conversely, taxa involved in coupled nitrate reduction and sulfur oxidation (Sulfurovum) declined significantly. Functionally, this led to a shift in genetic potential: the abundance of nitrification genes (amoB and amoC) increased, while genes associated with dissimilatory nitrate reduction (nirB and nrfA), denitrification (nosZ and napB), thiosulfate reduction (phsC and ttrB), and sulfur oxidation (sqr and sox) decreased. Genome-resolved analysis further demonstrated that these functional shifts were driven by the proliferation of nitrifiers and concurrent decline of versatile bacterial lineages. Importantly, this genomic shift was corroborated by geochemical observations of decreased ammonium and increased nitrate concentrations in both bottom seawater and sediments of ARs compared to non-artificial reefs. These results indicate that reef age reshapes benthic microbial communities and functions, favoring aerobic nitrification over anaerobic or microaerophilic nitrate reduction and sulfur metabolism. This study provides a scientific basis for AR adaptive management, underscoring the necessity of integrating microbial functional metrics into the long-term impact assessment of marine infrastructures.}, }
@article {pmid41861947, year = {2026}, author = {Guo, J and Liang, X and Lei, W and Zhang, Z and Shen, Y and Han, S and Wang, H and Qian, Y and Nie, B and Wang, L and He, S}, title = {Contrasting microbial sources of soil N2O emissions revealed by metagenomics in natural and agricultural soils along the Yellow River.}, journal = {Environmental research}, volume = {}, number = {}, pages = {124311}, doi = {10.1016/j.envres.2026.124311}, pmid = {41861947}, issn = {1096-0953}, abstract = {Soil nitrous oxide (N2O) emission is a potent greenhouse gas source, yet the dominant production pathway (nitrification vs. denitrification) and its microbial mechanisms in regions like the Yellow River Basin remain unclear, particularly under different land uses. In this study, we integrated qPCR quantification, metagenomic sequencing and binning, as well as microbial network analysis to investigate the dominant microbial processes and regulatory mechanisms underlying potential soil N2O production. Results showed that denitrification dominated regional potential N2O production (N2ODen, 56.71±102.94 nmol/(kg·h)), significantly exceeding nitrification (N2ONif, 4.34±4.27 nmol/(kg·h)). On average, both N2ODen (115.34±143.60 nmol/(kg·h)) and N2ONif (5.29±4.42 nmol/(kg·h)) in natural soils were higher than in cultivated soils (28.56±62.52 and 3.88±4.22 nmol/(kg·h), respectively). Mechanistically, natural soils were enriched with ammonia-oxidizing archaea (AOA) and incomplete denitrifiers (e.g., Acidobacteriota), which, along with a higher norB/nosZ and more stable co-occurrence network, favored N2O accumulation. In cultivated soils, microbial community stability was reduced; however, they were enriched with strong N2O reducers (e.g., Pseudomonadota, Gemmatimonadota), resulting in lower potential N2O production. Altitude, total nitrogen, and pH collectively influenced the potential N2O emission patterns by regulating functional genes and microbial metabolism. This study provides a scientific basis for regional greenhouse gas mitigation from a microbial ecology perspective.}, }
@article {pmid41418935, year = {2026}, author = {Chen, S and Li, W and Fan, L and Xu, C and Liu, S and Li, H and Liu, P and Zhu, W and Wu, X and Qin, P and Li, J and Ma, X and Wei, Y}, title = {Metatranscriptomics profiling reveals rodent- and shrew-borne viral diversity and evolutionary relationships in Guangzhou, China.}, journal = {Virologica Sinica}, volume = {41}, number = {1}, pages = {35-47}, doi = {10.1016/j.virs.2025.12.009}, pmid = {41418935}, issn = {1995-820X}, mesh = {Animals ; China/epidemiology ; *Shrews/virology ; *Rodentia/virology ; *Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; *Virome ; Rats ; Genetic Variation ; Evolution, Molecular ; Metagenomics ; Gene Expression Profiling ; }, abstract = {Emerging zoonotic infectious diseases, predominantly caused by viruses, pose increasing public health threats globally. Rodents and shrews are natural hosts for a variety of zoonotic viruses. Guangzhou is one of China's most densely populated cities and experiences frequent international and domestic population movements, making it a hotspot for infectious diseases. This study reports the metatranscriptomics virome of 208 rodents and shrews collected between June 2023 and December 2024 from four main urban areas (Tianhe, Baiyun, Liwan, Yuexiu) and five non-main urban areas (Zengcheng, Huadu, Conghua, Panyu, Nansha) in Guangzhou. Individual libraries were constructed from mixed tissue samples (liver, spleen, lung, and kidney) of each animal. Metatranscriptomics sequencing revealed diverse viral communities, identifying 24 viral strains across eight mammalian-associated viral families. Notably, we identified 17 known viruses and seven potentially novel viruses, including Seoul virus (5.2% prevalence in Rattus norvegicus from Panyu), Wenzhou mammarenavirus (13.2% in Rattus norvegicus from Conghua and Huadu), Jeilongvirus (29.4% in Rattus andamanensis from Panyu), and a divergent lineage of arteriviruses that may represent a new genus (maximum positivity rates of 2.9% in Rattus norvegicus and 5.7% in Rattus tanezumi). Phylogenetic analysis elucidated evolutionary relationships within key families such as Hantaviridae, Arenaviridae, Flaviviridae, and Parvoviridae, revealing distinct viral carriage patterns in Guangzhou City that are shaped by host species and geographical location. This is the first macro-level study of rodent and shrew viromes in Guangzhou and provides a scientific basis for strengthening surveillance of mammalian-associated viruses and preventing emerging zoonotic infectious diseases in the region.}, }
@article {pmid41850962, year = {2026}, author = {Zhao, Y and Zheng, J and Liu, Q}, title = {The diversity of emerging tick-borne viruses globally.}, journal = {Trends in parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pt.2026.03.001}, pmid = {41850962}, issn = {1471-5007}, abstract = {Zhang et al. provide the first global synthesis of 230 emerging tick-borne viruses, introducing a genomic model that predicts zoonotic risk. Their approach identifies 25 very-high-risk viruses and clinically validates three novel human pathogens, shifting the paradigm from reactive discovery to proactive risk assessment for global health security.}, }
@article {pmid41851124, year = {2026}, author = {Luzmore, A and Grauer, J and Barber, D and Lau, P and Jorgensen, G and Jain, S and Perron, GG}, title = {Seasonal frost improves probiotic and nutrient availability in fermented vegetables.}, journal = {NPJ science of food}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41538-026-00776-w}, pmid = {41851124}, issn = {2396-8370}, abstract = {Climate-driven shifts in seasonal frost patterns raise important questions about their impact on food quality and resilience. Here, we show that a single 12-h frost event at harvest can enhance both the microbial and nutritional properties of fermented cabbage and carrots, two cold-tolerant crops widely grown in the U.S. Northeast. Using microbial amplicon and metagenomic sequencing, we found that frost exposure led to subtle but consistent changes in microbial composition, including greater abundance of cold-adapted taxa such as Leuconostoc and Debaryomyces. These changes corresponded to increased abundance of genes involved in vitamin biosynthesis, particularly menaquinone (K2), cobalamin (B12), and threonine pathways. Nutritional assays confirmed higher concentrations of vitamins A and E in frost-conditioned carrot ferments and increased vitamin K1 in cabbage. Our findings suggest that exposure to seasonal frost can enhance the health-promoting and sensory qualities of fermented vegetables, offering a novel strategy for value-added, climate-resilient food production in temperate regions.}, }
@article {pmid41851530, year = {2026}, author = {Cohen, Y and Jansen, T and Onwuka, S and Elinav, E}, title = {Advances and opportunities in measuring dietary intake: from omics to AI.}, journal = {Nature metabolism}, volume = {}, number = {}, pages = {}, pmid = {41851530}, issn = {2522-5812}, abstract = {Accurate measurement of dietary intake remains a cornerstone challenge in optimizing the efficacy of nutritional interventions in human disease. Traditional self-reporting methods, although scalable and widely used, are prone to major bias and measurement error, thereby limiting their precision and clinical utility. In this Review, we highlight recent advances in technology-assisted food intake measurement, including image-based logging, wearable sensors and artificial intelligence (AI)-based dietary estimation, which may reduce reliance on recall and improve intake estimation. We review the emergence of non-invasive biological methodologies, such as metagenome-informed metaproteomics, in accurately enabling objective measurement of food intake and nutrient digestion and absorption in molecular resolution. We explore the possible interactions and effects of the gut microbiome in modulating such person-specific digestive and absorptive patterns and discuss challenges and prospects in the convergence of omics-based, measurement-based and AI-based dietary assessment tools into precision nutrition, in fulfilling its immense potential towards optimization of patient care.}, }
@article {pmid41851880, year = {2026}, author = {Sharma, AA and Martinou, AF and Cadar, D and Omirou, M and Neira, M and Christophides, GK}, title = {Integrated vector and arbovirus surveillance in Cyprus: first reports of Usutu virus and Culex pipiens bioform diversity highlight potential for zoonotic arbovirus transmission.}, journal = {Parasites &amp; vectors}, volume = {}, number = {}, pages = {}, doi = {10.1186/s13071-026-07350-z}, pmid = {41851880}, issn = {1756-3305}, support = {856612//Horizon 2020/ ; }, abstract = {BACKGROUND: Anthropogenic pressures, including urbanisation, globalisation and climate change, have facilitated an increased risk for emergence or re-emergence of mosquito-borne diseases into regions such as the Eastern Mediterranean and Middle East. Cyprus is a major stop-over site for migratory birds and has previously experienced outbreaks of West Nile virus (WNV). The island has native mosquito vector populations; however, it has also seen the recent establishment of invasive Aedes albopictus and Ae. aegypti mosquitoes. Given the dynamic climatic conditions and the shifting ecological and epidemiological landscapes in the region, the need for routine vector and pathogen surveillance has never been more critical.<br><br>METHODS: Herein, we present the results from localised adult mosquito surveillance that were conducted in two cities of Cyprus between 2019 and 2022. Mosquito taxa were identified through morphological analysis, and molecular techniques were used to further characterise the Culex pipiens bioforms. Engorged mosquito midguts were analysed to determine host blood meals. Metagenomic next-generation sequencing was employed to screen mosquito pools for arboviruses.<br><br>RESULTS: Our results provide the first report of Usutu virus in Cx. pipiens mosquitoes in Cyprus. Blood meal analysis identified multiple vertebrate hosts, including Cetti's warbler, a bird species previously reported to be seropositive for WNV on the island. Additionally, we report the presence of both Cx. pipiens pipiens and Cx. pipiens molestus, an ornithophilic and a mammophilic bioform, respectively, as well as their hybrids.<br><br>CONCLUSIONS: Our findings highlight the urgent need for enhanced mosquito surveillance strategies where mosquito populations will be regularly screened for pathogens to mitigate emerging risks of arbovirus transmission in Cyprus.}, }
@article {pmid41851941, year = {2026}, author = {Shrestha, E and Katuwal, N and Sitaula, RK and Gurung, H and Shrestha, A and Karki, P and Shrestha, R}, title = {Identification of the Causative Pathogen in the 2023 Conjunctivitis Outbreak of Nepal Using Unbiased Metagenomic Next Generation Sequencing.}, journal = {Journal of Nepal Health Research Council}, volume = {23}, number = {3}, pages = {527-532}, doi = {10.33314/jnhrc.v23i03.4749}, pmid = {41851941}, issn = {1999-6217}, mesh = {Humans ; Nepal/epidemiology ; *Disease Outbreaks ; Female ; *High-Throughput Nucleotide Sequencing ; Male ; Child ; *Metagenomics/methods ; *Conjunctivitis/epidemiology/virology ; Adult ; Child, Preschool ; *Enterovirus C, Human/isolation &amp; purification/genetics ; Adolescent ; Young Adult ; Middle Aged ; Infant ; }, abstract = {BACKGROUND: In mid-2023, Nepal experienced a significant outbreak of conjunctivitis, affecting over 60% of outpatients in eye hospitals and prompting school closures. The outbreak, peaking in August, predominantly impacted children and individuals with compromised immunity. Clinical manifestations included sudden-onset redness, foreign body sensation, watery discharge, and occasional lid swelling. Most cases exhibited acute haemorrhagic conjunctivitis, with management involving ocular lubricants, personal hygiene, and topical antibiotics. This case series from Himalaya Eye Hospital in Pokhara details the genomic epidemiology and clinical characteristics of conjunctivitis cases during the outbreak.<br><br>METHODS: To understand the causative agents, conjunctival swabs from patients were subjected to unbiased metagenomic next-generation sequencing (mNGS) in Illumina iSeq100 at Dhulikhel Hospital Kathmandu University Hospital Results: This case series revealed the presence of Enterovirus C (coxsackievirus strain A24) as the major pathogen responsible for the outbreak.<br><br>CONCLUSIONS: This case series contributes valuable insights into the genomic diversity of conjunctivitis-associated viruses, highlighting the potential of mNGS in enhancing diagnostic capabilities and guiding public health responses.}, }
@article {pmid41852102, year = {2026}, author = {Qu, X and Liao, Y and Muthuri, CW and Winowiecki, LA and Zi, H and Zhang, Y and Li, X}, title = {Soil Functionality Undermined by Symbiotic Fungal Decline Following Forest Conversion.}, journal = {Environmental microbiology}, volume = {28}, number = {3}, pages = {e70268}, doi = {10.1111/1462-2920.70268}, pmid = {41852102}, issn = {1462-2920}, support = {W2412011//National Natural Science Foundation of China/ ; 32430069//National Natural Science Foundation of China/ ; jxsq2023102214//Double Thousand Plan of Jiangxi Province/ ; }, mesh = {*Soil Microbiology ; *Forests ; *Symbiosis ; *Soil/chemistry ; *Fungi/genetics/classification/physiology ; China ; Phosphorus/metabolism ; Carbon/metabolism ; Nitrogen/metabolism ; Biodiversity ; Bacteria/genetics/classification ; Ecosystem ; }, abstract = {The conversion of native forests to other terrestrial ecosystems represents a profound form of land-use change, threatening aboveground biodiversity and biomass. However, its impact on soil ecological functions remains uncertain, particularly the regulatory role of soil microbial communities. To address this, we evaluated soil functionality related to carbon, nitrogen and phosphorus cycling by measuring nine enzyme activities in soils from native forests, plantations and croplands in subtropical China. Our results demonstrated a significant decline in soil functionality following the conversion of native forests, with the most pronounced reductions observed in croplands. This decline in soil functionality was strongly associated with a decrease in fungal richness but was independent of bacterial alpha-diversity. Specifically, the reduction in the abundance of symbiotic fungi, including key taxa such as Lactifluus and Tomentella, was identified as a primary driver of the functional impairment. Metagenomic analyses further confirmed that the loss of microbial functional genes was linked to the observed decline in soil functionality. Our findings underscore the critical role of key fungal taxa in maintaining soil processes and highlight the importance of their conservation and restoration to ensure ecosystem functionality in managed landscapes.}, }
@article {pmid41852114, year = {2026}, author = {Kaneko, Y and Hino, T and Taminishi, S and Matoba, Y and Motooka, D and Hoshino, A and Matoba, S}, title = {Inhibition of N-Terminal Acetyltransferase C Mitigates Endoplasmic Reticulum Stress-Mediated Muscle Atrophy in Cancer Cachexia.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {17}, number = {2}, pages = {e70249}, doi = {10.1002/jcsm.70249}, pmid = {41852114}, issn = {2190-6009}, support = {22H03071//JSPS Grant-in-Aid Scientific Research/ ; 25K02651//JSPS Grant-in-Aid Scientific Research/ ; //Nakatomi Foundation/ ; }, mesh = {Animals ; *Cachexia/etiology/pathology ; *Endoplasmic Reticulum Stress ; *Muscular Atrophy/etiology/pathology/metabolism ; Mice ; Male ; *Neoplasms/complications ; Humans ; Unfolded Protein Response ; }, abstract = {BACKGROUND: Cancer cachexia is a complex syndrome marked by weight loss and muscle wasting, significantly impacting patient quality of life and survival. Mechanistically, it is characterized by suppressed protein synthesis and enhanced muscle catabolism, with the role of endoplasmic reticulum (ER) stress and unfolded protein response (UPR) becoming increasingly evident. This study aimed to explore ER stress-tolerant factors in muscle wasting and evaluate their potential to prevent muscle loss in cancer cachexia.<br><br>METHODS: A genome-wide CRISPR screening was conducted in the context of ER stress-mediated growth inhibition of C2C12 myoblasts. The candidate genes resistant to ER stress were further evaluated in C2C12 myotubes treated with conditioned medium of Lewis lung adenocarcinoma (LLC) cells. Twelve-week-old male mice were administered LLC cells and shRNA against Naa35 via adeno-associated virus. Four weeks later, tibialis anterior (TA) muscles were analysed for muscle mass, grip strength and molecular changes with quantitative polymerase chain reaction, western blotting and histological analysis.<br><br>RESULTS: CRISPR screening identified Naa35, Naa38 and Naa30, all three components of N-terminal acetyltransferase C, as key molecules for resistance to ER stress. The atrophic muscles of mice bearing LLC demonstrated an elevation of UPR, as well as 1.64-fold upregulation of Naa35 protein (p&#x2009;=&#x2009;0.0072). Among the three branches of the UPR, an ATF6 inhibitor, AEBSF, abolished upregulation of Naa35, Naa38 and Naa30, and an ATF6 activator, AA147, induced Naa35 expression in a dose-dependent manner (p&#x2009;<&#x2009;0.001). In cells treated with LLC conditioned medium, Naa35 knockdown reduced the amount of cathepsin K (CTSK) protein, which subsequently resulted in the CTSK-mediated proteolysis of insulin receptor substrate 1. In LLC-bearing mice, Naa35 knockdown led to a 65.4% reduction in CTSK protein expression (p&#x2009;<&#x2009;0.001) and preservation of the phosphorylation levels of protein kinase B (p&#x2009;<&#x2009;0.0324) and anabolic-related S6 kinase (p&#x2009;<&#x2009;0.0375). Concurrently, the expression of catabolism-related genes was repressed (MuRF1, p&#x2009;<&#x2009;0.0015; MAFbx1, p&#x2009;<&#x2009;0.0265). These alterations were associated with the restoration of TA muscle mass (2.52&#x2009;&#xb1;&#x2009;0.19 vs. 3.72&#x2009;&#xb1;&#x2009;0.45&#x2009;mg/g, p&#x2009;=&#x2009;0.0004), fibre area (1741&#x2009;&#xb1;&#x2009;992 vs. 2099&#x2009;&#xb1;&#x2009;1264&#x2009;mm[2], p&#x2009;<&#x2009;0.0001), grip strength in all four limbs (0.0328&#x2009;&#xb1;&#x2009;0.0076 vs. 0.0506&#x2009;&#xb1;&#x2009;0.0130&#x2009;N/g, p&#x2009;=&#x2009;0.0295) and wire mesh hanging time (496&#x2009;&#xb1;&#x2009;331 vs. 1038&#x2009;&#xb1;&#x2009;370&#x2009;s, p&#x2009;=&#x2009;0.0406).<br><br>CONCLUSIONS: Inhibition of N-terminal acetyltransferase C prevents ER stress-induced muscle wasting via the downregulation of CTSK and subsequent activation of the anabolic pathway. This suggests that N-terminal acetyltransferase C is a potential therapeutic target for combating muscle wasting in cancer cachexia.}, }
@article {pmid41852383, year = {2025}, author = {Urrutia-Angulo, L and Lavín, JL and Oporto, B and Aduriz, G and Hurtado, A and Ocejo, M}, title = {Resistome and microbiome profiling of bovine milk following antimicrobial dry cow therapy: insights from short- and long-read metagenomic sequencing.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1672438}, pmid = {41852383}, issn = {2813-4338}, abstract = {Selective antimicrobial dry cow therapy (DCT) is implemented as part of mastitis control programs, particularly in dairy cows with recent clinical episodes or elevated somatic cell counts. In this study, we investigated the effects of the use of antimicrobials at drying-off on the milk microbiota and resistome by comparing treated (T, n=18) and untreated (NT, n=13) cows. Milk samples from all animals were analyzed using short-read Illumina shotgun sequencing and a subset of 10 samples were also subjected to long-read Oxford Nanopore Technologies (ONT) sequencing. No significant differences in microbial composition or diversity were observed between treated and untreated groups with either technique, indicating that antimicrobial DCT may not induce long-term shifts in the milk microbiota. However, cows receiving antibiotic treatment showed a higher diversity and abundance of genetic determinants of resistance (GDRs) in their milk resistome. Findings from the two sequencing platforms revealed limited concordance in antimicrobial resistance gene content, highlighting that sequencing platform and bioinformatic pipeline choices substantially influence resistome profiling outcomes. Furthermore, the high proportion of host DNA limited sequencing depth and sensitivity, underscoring the need for improved host DNA depletion or targeted enrichment strategies. This study provides insights into the biological and methodological challenges of milk resistome characterization, particularly in low-biomass, host-DNA-rich samples and demonstrates the lack of standardized analytical approaches in resistome studies. Overall, our findings support the prudent use of antibiotics and highlight the need for further longitudinal studies to clarify the temporal dynamics of antimicrobial DCT effects on the milk resistome and microbiota.}, }
@article {pmid41852393, year = {2025}, author = {Wadop, YN and Muhammad, J and Bernal, R and Satizabal, CL and Beiser, A and Vasan, RS and Xavier, R and Kautz, T and Seshadri, S and Himali, JJ and Fongang, B}, title = {Adherence to Life's Essential 8 enhances gut microbiota diversity and cognitive performance.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1592023}, pmid = {41852393}, issn = {2813-4338}, abstract = {INTRODUCTION: Emerging evidence suggests a complex interplay among cardiovascular health, gut microbiome composition, and cognitive function. Life's Essential 8 (LE8), developed by the American Heart Association, includes vital metrics of cardiovascular health, such as diet, physical activity, nicotine exposure, sleep health, body mass index (BMI), blood glucose, blood lipids, and blood pressure.<br><br>METHODS: In this study, we analyzed data from 781 participants in the Framingham Heart Study (FHS) to explore the relationship between LE8 adherence, gut microbiota, and cognitive performance. Multivariable linear regression models and mediation analysis were used to investigate this relationship.<br><br>RESULTS: Participants with greater adherence to LE8 demonstrated significantly increased gut microbial diversity (&#x3b1;-diversity: Chao1, p = 0.0014; Shannon, p = 0.0071) and distinct microbial compositions (&#x3b2;-diversity: PERMANOVA p = 1e-4). Higher adherence to LE8 was related to an increased abundance of genera Barnesiella and Ruminococcus, while a reduced abundance of Clostridium was associated with higher LE8 adherence. Greater gut microbial diversity (&#x3b1;-diversity: Chao1, p = 0.0012; Shannon, p = 0.0066), and beneficial genera like Oscillospira correlated with better global cognitive scores (GCS). Taxonomic overlap analyses revealed microbial taxa that simultaneously influence both LE8 adherence and cognitive outcomes. Mediation analyses indicated that specific taxa, including Barnesiella and Lentisphaerae, mediated the link between LE8 adherence and cognitive performance. These taxa may serve as key modulators in the gut-brain axis, connecting cardiovascular and brain health. Conversely, higher Clostridium abundance was associated with poorer cognitive performance.<br><br>DISCUSSION: This study highlights the significance of comprehensive cardiovascular health metrics in shaping gut microbiota and enhancing cognitive resilience. Our findings underscore the therapeutic potential of targeting gut microbiota to mitigate cognitive decline, warranting further exploration through longitudinal and metagenomic studies.}, }
@article {pmid41852395, year = {2025}, author = {Ortega-Reyes, D and Takeuchi, T and Ogata, Y and Iwami, T and Suda, W and Kubota, T and Kubota, N and Kadowaki, T and Tomizuka, K and Ohno, H and Horikoshi, M and Terao, C}, title = {Interplay between host genetics and gut microbiome composition in the Japanese population.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1635907}, pmid = {41852395}, issn = {2813-4338}, abstract = {BACKGROUND: Host genetics significantly influence the composition of the gut microbiota, but this relationship remains poorly understood, especially in non-European populations. This study aims to investigate the associations between host genetic variation and gut microbiome composition in the Japanese population and to assess methodological factors affecting reproducibility in microbiome research.<br><br>METHODS: We performed whole-genome sequencing on 306 Japanese individuals and obtained their gut microbiome profiles using shotgun metagenomic sequencing. Genome-wide association studies (GWAS) were conducted to identify associations between host genetic variants and the relative abundance of microbial taxa and bacterial pathways. Phenome-wide association studies (PheWAS) were performed on predicted high-impact variants. Additionally, we compared methodological approaches to assess their impact on microbiome composition and reproducibility.<br><br>RESULTS: We identified significant associations between host genetic variants and the relative abundance of one bacterial family, one genus, one species and eight bacterial pathways (p &#x2264; 5&#xd7;10[-8]). However, none of these associations surpassed the stringent significance threshold of p &#x2264; 2.75&#xd7;10[-11]. Notably, we were unable to replicate associations reported in prior studies, including those conducted in Japanese populations, even regarding the direction of effects. Our PheWAS analysis uncovered a frameshift variant in the OR6C1 gene (rs5798345-CA) that was significantly associated with an increased abundance of Bacteroides uniformis. Furthermore, comparative analyses highlighted that methodological differences, particularly in sample processing and DNA extraction protocols, substantially influence the observed gut microbiome composition. This variability may be a key factor contributing to the lack of reproducibility across studies.<br><br>CONCLUSION: Our findings enhance the understanding of how host genetics shape the gut microbiota in the Japanese population and underscore the importance of methodological standardization in microbiome research. The identified associations between host genetic variants and specific microbial taxa provide insights into the complex interplay between genetics and the gut microbiome. Addressing methodological discrepancies is crucial for improving reproducibility and advancing knowledge of host-microbiome interactions.}, }
@article {pmid41852396, year = {2025}, author = {Zoruk, P and Morozov, M and Veselovsky, V and Strokach, A and Babenko, V and Klimina, K}, title = {Impact of DNA extraction techniques and sequencing approaches on microbial community profiling accuracy.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1688681}, pmid = {41852396}, issn = {2813-4338}, abstract = {BACKGROUND: Quality control in metagenomic data analysis is crucial for ensuring the accuracy and reliability of research results. Among the key steps in microbiome research, DNA extraction plays a critical role, as it directly determines DNA yield, integrity, and representation of microbial taxa.<br><br>RESULTS: We compared three commercial DNA extraction kits and our protocol specifically developed for the recovery of high molecular weight (HMW) DNA from complex microbial communities, using the ZymoBIOMICS Gut Microbiome Standard. The PureLin[&#x2122;] Microbiome DNA Purification Kit and our custom protocol provided superior recovery of DNA from Gram-positive bacteria, while the Wizard[&#xae;] kit and our protocol yielded HMW DNA suitable for long-read Oxford Nanopore sequencing. Among sequencing approaches, metagenomic sequencing on the Illumina platform provided the most accurate representation of the reference composition. However, all methods showed limited ability to detect taxa below 0.5% of relative abundance. Additionally, taxonomic classification based on 16S rRNA gene amplicon sequencing data misclassified closely related species due to high gene homology, a limitation not observed with metagenomic approaches.<br><br>CONCLUSIONS: Our study establishes that a customized DNA extraction protocol is optimal for comprehensive microbiome studies utilizing long-read sequencing technologies. We show that metagenomic sequencing outperforms 16S rRNA gene amplicon sequencing for species-level accuracy, providing a validated benchmark for future gut microbiome research.}, }
@article {pmid41852403, year = {2025}, author = {Helal, M and Bari, VK}, title = {Insights into human respiratory microbiome under dysbiosis and its analysis tool.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1549166}, pmid = {41852403}, issn = {2813-4338}, abstract = {The human respiratory tract microbiome is a multi-kingdom microbial ecology that inhabits several habitats along the respiratory tract. The respiratory tract microbiome promotes host health by strengthening the immune system and avoiding pathogen infection. The lung microbiome mostly originates in the upper respiratory tract. The balance between microbial immigration and removal determines the nature of the lung microbiome. Identification and characterization of microbial communities from airways have been made much easier by recent developments in amplicon and shotgun metagenomic sequencing and data analysis techniques. In pulmonary medicine, there is a growing interest in the respiratory microbiome, which has been linked to human health and illness. However, the primary causes of bacterial co-occurrence seem to be interactions with fungi and bacteria as well as host and environmental factors. This study focused on identifying techniques and the current understanding of the relationship between the microbiota and various lung diseases.}, }
@article {pmid41852404, year = {2025}, author = {Xuan, L and Sun, X and Wang, B and Chen, F and Yi, Y and Mao, H and Wang, Y and Zhao, G and Wang, J and Zhang, Y}, title = {Cold-water immersion alleviates intestinal damage induced by exertional heat stroke via modulation of gut microbiota in rats.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1531991}, pmid = {41852404}, issn = {2813-4338}, abstract = {OBJECTIVE: The pathogenesis of exertional heatstroke (EHS) involves substantial contributions from gut microbiota and their metabolites. In this study, we assessed whether cold water immersion (CWI) mitigates EHS-induced intestinal damage via alterations in the microbiome.<br><br>METHODS: An EHS model was created with 18 Wistar rats divided into three groups, that is, the EHS group comprising rats with exertional heat stroke, the CWI group with rats with heatstroke treated with cold water immersion, and the control (CTRL) group (rats with normothermia control). Pathological changes, core temperature (Tcore), and lactic acid (Lac) and endotoxin lipopolysaccharide (LPS) levels were evaluated. Fecal samples were subjected to metagenomic shotgun sequencing and liquid chromatography-mass spectrometry for microbiota and metabolomic profiling.<br><br>RESULTS: Hematoxylin and eosin staining showed that CWI treatment significantly reduced EHS-induced intestinal congestion, edema, and necrosis compared to the EHS group. The EHS group had the highest Tcore, while the CWI group had significantly lower Tcore than the EHS group. The CWI group had significantly reduced LPS and Lac levels, similar to those observed in the CTRL group. Microbiome analysis indicated that EHS disrupted gut bacteria, with an increase in the proportion of pathogens such as Desulfovibrio fairfieldensis, Desulfamplus magnetovallimortis, and Desulfococcus oleovorans (P<0.05). CWI treatment resolved these disturbances and restored the gut microbiota to a level similar to that of the CTRL group. Metagenomic analysis showed that CWI restored gut microbiota diversity (Shannon index, P<0.05), significantly reducing the proportion of pathogenic Desulfovibrio. Metabolomic profiling identified key metabolites, such as inosine, hypoxanthine, guanosine, and taurine (Variable importance in projection>1, P<0.05 with P-values adjusted for multiple comparisons using the Benjamini-Hochberg method, FDR<0.05), differentiating between the CWI and EHS groups.<br><br>CONCLUSION: The metabolites inosine, taurine, hypoxanthine, and guanosine correlated with restored gut microbiota, reduced proportion of Desulfovibrio, and attenuated inflammation (lower LPS/Lac), suggesting that their dual role in mitigating intestinal damage. These findings underscore the therapeutic potential of CWI by modulating microbial-derived metabolites, highlighting its impact on the intestinal health of patients with EHS.}, }
@article {pmid41852413, year = {2025}, author = {Guerrero-Toledo, FM and Espinosa-Solares, T and Hernández-Eugenio, G and Huber, DH}, title = {Community assembly following disturbance in batch anaerobic digesters displays highly reproducible secondary succession and a shifting stochastic-deterministic balance.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1707779}, pmid = {41852413}, issn = {2813-4338}, abstract = {The great diversity of anaerobic digestion (AD) microbiomes indicates high redundancy and flexibility in the assembly of the community. Moreover, AD microbiomes are frequently subjected to disturbances during start-up and operation that require (re)assembly. We tested the reproducibility of secondary succession and AD community assembly mechanisms using a pre-assembled microbiome that was subjected to intense disturbances. Microbiome diversity and functions were followed in replicate mesophilic batch digesters initiated with multiple stressors, including high feed-to-inoculum ratio and many foreign species. Three 10 L batch digesters were derived from a single long-term CSTR digester pre-adapted to poultry litter feedstock and operated in parallel. Physicochemical parameters (methane, acetate, propionate, butyrate, pH, N-NH3, COD) were measured. Metagenome samples were used to assess diversity and functions. Three performance phases were found along the successional gradient: (1) methane inhibition, (2) high methane production, and (3) low methane plateau. The inventory of species (>1600) remained nearly the same, however the relative abundance of species, families, and functions changed during each successional stage. Syntrophic bacteria peaked in abundance during the mid-succession, high methane stage. Succession of overall KEGG functions was highly similar although species and carbohydrate functions diverged during late succession, suggesting diversity of niche partitioning during degradation of recalcitrant organic matter. We estimated the relative contributions of stochastic and deterministic processes and found a shift in the balance during succession. Early succession was not dominated by either dispersal or selection while late succession was dominated by variable selection. In conclusion, methane production recovered following severe (non-lethal) disturbance in a pre-adapted digester microbiome through a reproducible community assembly pathway that shifted toward deterministic, variable selection over time.}, }
@article {pmid41852418, year = {2025}, author = {Berdy, BM and Williams, CE and Sizova, M and Jung, D and Tandogan, N and Goluch, ED and Epstein, S}, title = {Diverse cultivation strategies are necessary to capture microbial diversity in High Arctic lake sediment.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1619859}, pmid = {41852418}, issn = {2813-4338}, abstract = {While metagenomics has revolutionized our understanding of microbial diversity and function, the cultivation of microorganisms remains indispensable for elucidating their physiological characteristics and potential biotechnological applications. Cultivation provides context to the vast metagenomic datasets and helps verify metagenome-based hypotheses on microbial interactions. The majority of microorganisms remain uncultivated, and this is particularly prominent from extreme environments such as the Arctic. Here we aimed to contribute to the growing body of work investigating microbial ecology in extreme environments by assessing the efficacy of a variety of cultivation approaches in lake sediment in the High Arctic. To try and capture the full breadth of organisms present, we used standard, in situ, and anoxic cultivation methods. We cultured a total of 1,109 microorganisms which clustered into 155 OTUs (97% rRNA gene sequence similarity), representing organisms from Proteobacteria, Actinobacteria, Bacteroidota, and Firmicutes. Importantly, no single method of cultivation proved to be sufficient to represent the cultivable organisms within the environment. Rather, each method resulted in many unique OTUs. Therefore, multiple approaches should be used in conjunction to access the bulk of microbial taxa in a given environment.}, }
@article {pmid41852432, year = {2025}, author = {Mhuireach, G&#xc1; and Collins, S and Dietz, L and Horve, PF and Laguerre, A and Northcutt, D and Stenson, J and Wymelenberg, KVD and Gall, E and Fretz, M}, title = {Effects of wetting events on mass timber surface microbial communities and VOC emissions: implications for building operation and occupant well-being.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1395519}, pmid = {41852432}, issn = {2813-4338}, abstract = {INTRODUCTION: Humans have used wood as a construction material throughout history. Currently, mass timber products, such as cross-laminated timber (CLT), are becoming more popular as a structural material, since they are renewable and have a lower carbon footprint than concrete or steel. Nonetheless, some building types, such as healthcare, veterinary, and food manufacturing, avoid using structural mass timber due to concerns about microbial growth in the event of wetting. One solution is to use protective coatings on mass timber products to increase moisture resistance, although the coatings themselves may generate concerns about volatile organic compound (VOC) emissions. Natural uncoated wood also produces VOCs, some of which may have intrinsic antimicrobial effects.<br><br>METHODS: In this study, we inoculated coated and uncoated cross- laminated timber (CLT) blocks with a mock microbial community and isolated each block within individual sealed microcosms. We characterized VOCs and surface microbial communities from the CLT blocks before, during, and after wetting periods of varying durations. VOC concentration and emission rate were analyzed with chromatography-mass spectrometry (GC-MS), while microbial community abundance, diversity, and composition were analyzed through qPCR and shotgun metagenomics.<br><br>RESULTS: VOC emissions were elevated immediately after inoculation, then decreased through the remainder of the experiment, except for a plateau during the wetting period. VOCs from uncoated CLT blocks were primarily terpenes, while coated blocks emitted VOCs associated with coatings, plastics, and industrial solvents, as well as terpenes. One VOC-acetoin (3-hydroxy, 2-butanone)-was present at high levels across all samples immediately after microbial inoculation. Bacteria comprised 99.54% of the identified microbial sequences. The plastic control microcosm (not containing a CLT block) had higher abundance of viable bacteria for the majority of the study, but there was no difference in abundance between coated and uncoated blocks. Prior to wetting periods, microbial composition was driven primarily by sampling day, whereas surface type played a larger role during and after wetting periods.}, }
@article {pmid41852435, year = {2025}, author = {Trubl, G and Malard, L and Rahlff, J}, title = {Editorial: Ecology, evolution, and biodiversity of microbiomes and viromes from extreme environments.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1604002}, doi = {10.3389/frmbi.2025.1604002}, pmid = {41852435}, issn = {2813-4338}, }
@article {pmid41852443, year = {2025}, author = {Palazzi, CM and Ciampaglia, G and Binato, B and Ragazzini, M and Bertuccioli, A and Cavecchia, I and Matera, M and Cazzaniga, M and Zonzini, GB and Zerbinati, N and Tanda, ML and Di Pierro, F}, title = {Position statement of the Microbiota International Clinical Society.}, journal = {Frontiers in microbiomes}, volume = {4}, number = {}, pages = {1657750}, pmid = {41852443}, issn = {2813-4338}, }
@article {pmid41852664, year = {2026}, author = {Shibata, N and Yoshifuji, A and Oyama, E and Komatsu, M and Azegami, T and Hayashi, K and Ishii, Y and Hasegawa, N and Namkoong, H}, title = {Urinary microbiota and bacterial membrane vesicles in chronic kidney disease: contribution to antimicrobial-resistant urinary tract infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1748638}, pmid = {41852664}, issn = {2235-2988}, mesh = {Humans ; Male ; *Urinary Tract Infections/microbiology ; *Renal Insufficiency, Chronic/complications/microbiology ; Middle Aged ; *Microbiota ; *Drug Resistance, Bacterial ; RNA, Ribosomal, 16S/genetics ; Aged ; *Urine/microbiology ; Metagenomics ; *Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Adult ; Microscopy, Electron, Transmission ; Sequence Analysis, DNA ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/chemistry/genetics ; *Extracellular Vesicles/ultrastructure ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Chronic kidney disease (CKD) is associated with an increased risk of severe urinary tract infections (UTIs), particularly those caused by antimicrobial-resistant bacteria. Although urinary microbiota and bacterial membrane vesicles (BMVs) are thought to contribute to UTI pathogenesis, their roles in CKD remain insufficiently understood. In this exploratory study, urine samples were collected from 10 male patients with CKD (eGFR <45 mL/min/1.73 m[2]) and 10 male non-CKD controls (eGFR ≥60 mL/min/1.73 m[2]). Urinary microbiota and BMV fractions were isolated and analyzed to compare microbial composition and antimicrobial resistance gene (ARG) profiles, and to evaluate their potential involvement in UTI development and the emergence of antimicrobial resistance in CKD. Both fractions were subjected to shotgun metagenomic sequencing; metagenomic analysis of BMVs was performed using pooled samples within each group. In addition, BMV fractions were characterized by transmission electron microscopy and 16S rRNA gene PCR. Urinary microbiota α-diversity was significantly lower in patients with CKD than in controls (ACE index, p = 0.04). Vesicle-like structures consistent with BMVs, with diameters of 20-200 nm, were detected in urine samples from both controls and patients with CKD. Principal coordinate analysis demonstrated that BMV fractions clustered within the corresponding urinary microbiota profiles. Furthermore, multiple antimicrobial resistance genes (ARGs), including ftsI and adeF, were identified in both urinary microbiota and BMV fractions. This study provides exploratory evidence of reduced urinary microbiota α-diversity in patients with CKD and the presence of ARGs in both urinary microbiota and BMV fractions from controls and patients with CKD. These findings suggest microbiological factors that may contribute to the high incidence of antimicrobial-resistant UTIs in this population. Future validation in larger cohorts with individual-level BMV profiling will be required to determine whether analyses focusing on urinary microbiota and BMVs can contribute to a better understanding of antimicrobial-resistant UTIs and to improved infection risk assessment in patients with CKD.}, }
@article {pmid41852665, year = {2026}, author = {Zhang, Y and Wang, H and Yan, R and Wang, K and Man, J and Yang, L}, title = {Research advances on the urinary microbiome in non-infectious urinary tract diseases: from community composition to clinical prospects.}, journal = {Frontiers in cellular and infection microbiology}, volume = {16}, number = {}, pages = {1728182}, pmid = {41852665}, issn = {2235-2988}, mesh = {Humans ; *Microbiota ; Dysbiosis/microbiology ; *Urologic Diseases/microbiology/diagnosis ; *Urinary Tract/microbiology ; *Urine/microbiology ; Prostatic Neoplasms/microbiology ; }, abstract = {INTRODUCTION: With the rapid development of 16S rRNA sequencing and metagenomic technologies, the traditional concept of sterile urine has been completely overturned, and a diverse urinary microbiome has been identified even in healthy individuals. Increasing evidence indicates that dysbiosis of the urinary microbiome is closely associated with the onset and progression of various non-infectious urological diseases.<br><br>METHODS: This review systematically summarizes recent advances in the role of the urinary microbiome in non-infectious urological diseases, including bladder cancer, benign prostatic hyperplasia, prostate cancer, nephrolithiasis, interstitial cystitis/bladder pain syndrome, and urinary incontinence, with a focus on microbial dysbiosis, pathogenic mechanisms, and clinical applications.<br><br>RESULTS: Studies have shown that alterations in the composition and diversity of the urinary microbiome are closely related to chronic inflammation, immune dysregulation, metabolic disturbances, and changes in the local microenvironment. These alterations may contribute to disease pathogenesis through mechanisms such as persistent low-grade inflammation, abnormal metabolic activity, and biofilm formation. In recent years, non-invasive detection based on urinary microbial profiles has shown promising potential in the early diagnosis of bladder and prostate cancers, with some machine learning models achieving diagnostic accuracies above 80 percent. Furthermore, the urinary microbiome may influence the efficacy of immunotherapy, offering new insights for personalized precision medicine.<br><br>CONCLUSIONS: This review summarizes the mechanisms, research status, and clinical prospects of the urinary microbiome in non-infectious urological diseases, emphasizing the importance of methodological standardization and highlighting its potential applications in early screening, diagnostic stratification, and microbiome-targeted interventions.}, }
@article {pmid41852689, year = {2026}, author = {Anandan, S and Ali, A and Selvarajoo, A and Supramaniam, CV}, title = {Trichoderma combined with palm kernel shell biochar promotes root health and rhizosphere biodiversity in young oil palm seedlings infected with Ganoderma boninense.}, journal = {Frontiers in microbiomes}, volume = {5}, number = {}, pages = {1742803}, pmid = {41852689}, issn = {2813-4338}, abstract = {Oil palm (Elaeis guineensis) contributes up to 3% of gross domestic product (GDP) in Malaysia. Long-term monoculture production reduced natural biodiversity and increased severe threat by Ganoderma boninense, a causal agent of basal stem rot (BSR) disease. BSR recorded projections of 860,610 hectares of plantations to be devastated by BSR by 2040. While disease management has prioritised good sanitation practices, Trichoderma spp. is a potential solution to combatting G. boninense. In this study, we determined the efficacy of Trichoderma spp. isolate 4A added to palm kernel shell (PKS) biochar (T-mix) to improve oil palm root health. Three-month-old seedlings were observed in control treatments, T1 to T4 and Trichoderma sp. treatments, T5 to 12 with Ganoderma added in T7,8, 11 and 12. Root development parameters such as root architecture, length, diameter, and surface area were observed every two months for six months. Root length of T5 (3.3 m) and T9 (4.4 m) was higher than no-treatment control, T1 (2.5 m) indicating Trichoderma sp. support of root health. T9 (T-mix) has significantly improved root architecture in root scan with denser and multiple root branches as while all other diseased oil palms exhibit stunted roots. The diameter of roots shows similar trend to root length of T9 roots with the highest reading at 5.4 mm. T11 showed the overall improved fungal biodiversity at 6 months post inoculation with potential disease suppressive effects against other common pathogens such as Fusarium sp. This study highlights a new perspective of Trichoderma spp. treatment with biochar to provide protection to growing young oil palm root health, beyond disease control, indicating a beneficial role for early application at seedling stage. For long term application, Trichoderma spp. combined with biochar support healthy fungal dynamics without over-dominating indigenous fungal inhabitants. This is the first study to highlight the role of combined Trichoderma spp. and biochar in influencing the root architecture and rhizosphere dynamics of a perennial oil palm at the seedling stage. Overall, this study presents an exciting opportunity to use a new Trichoderma sp.-biochar solution in the battle against G. boninense.}, }
@article {pmid41852814, year = {2022}, author = {Jagadeeshwari, U and Sasikala, C and Rai, A and Indu, B and Ipsita, S and Ramana, CV}, title = {Characterization of metagenome-assembled genomes of two endo-archaea of Candida tropicalis.}, journal = {Frontiers in microbiomes}, volume = {1}, number = {}, pages = {1020341}, pmid = {41852814}, issn = {2813-4338}, abstract = {INTRODUCTION: Host-microbe interactions are pivotal in host biology, ecology, and evolution. Recent developments in sequencing technologies have provided newer insights into the same through the hologenome concept.<br><br>METHODS: We report here the study on metagenome-assembled genomes (MAGs) associated with Candida tropicalis (studied through shotgun metagenome sequencing), adding to the knowledge about endomicrobiomes of yeast. De novo assembly and binning recovered two partial archaeal genomes, taxonomically belonging to the phylum Asgardarchaeota.<br><br>RESULTS AND DISCUSSION: The phylogenomic analysis based on the core genes revealed that both the binned genomes cladded separately with the less studied and uncultivated 'Candidatus' superphylum, designated as Asgard archaea (the nearest known relative of eukaryotes). Between the two binned genomes, the average nucleotide index (ANI) was 71.2%. The average nucleotide identities (ANI) of the two binned genomes with 'Candidatus Heimdallarchaeota' were 60.4-61.2%. The metabolic pathways of both the binned genomes predicted genes belonging to sulfur reduction, Kreb's pathway, glycolysis, and C1 carbon metabolism. Further, both the binned genomes were predicted to support autotrophic as well as the heterotrophic mode of growth, which might probably help the host in its nutritional requirements also. Further, the genomes showed few eukaryotic signature proteins (ESPs) and SNARE proteins indicating that members of Asgardarchaeota are the closest relatives of eukaryotes. The gaps present in the metabolic potential of the MAGs obtained and the absence of a few essential pathways shows that they are probably in a symbiotic relationship with the host. The present study, reports for the first-time endosymbiosis of Asgard archaea with yeast. It also provides insights into the metabolic potential, ecology, evolutionary history, and endosymbiotic nature of the important but 160 poorly studied Asgard archaea.}, }
@article {pmid41852815, year = {2022}, author = {van Belkum, A and Lisotto, P and Pirovano, W and Mongiat, S and Zorgani, A and Gempeler, M and Bongoni, R and Klaassens, E}, title = {Being friendly to the skin microbiome: Experimental assessment.}, journal = {Frontiers in microbiomes}, volume = {1}, number = {}, pages = {1077151}, pmid = {41852815}, issn = {2813-4338}, abstract = {Both academia and dermatological and cosmetic industries have acknowledged that healthy skin microbiota contribute to overall skin integrity and well-being. This implies that formulations developed for personal care (skin, scalp, hair etc) or (medical and cosmetic) treatment need to be compatible with microbiota conservation or possibly even improvement. The various chemical and biological components and mixtures thereof intended for direct application to the skin should not extensively affect the qualitative and quantitative composition of the skin microbiota. A compound should promote beneficial microbes and inhibit pathogens. Compounds but also final products could be considered at least theoretically "microbiome friendly" while in some cases changes to the microbiota may even be considered beneficial. An important hurdle lies in the practical and methodological approaches to be used for defining microbiota inertia of compounds and formulations. Clear guidelines for assessing microbiome friendliness are lacking. We propose three testing concepts that may help to define microbiome friendliness based on the assessment of minimal microbiota perturbation and possibly elimination of potential pathogens. Methods to prove microbiome friendliness should ultimately be based upon (metagenomic rather than amplicon-based) next generation sequencing of naive versus compound- or final product-exposed skin microbiota in vivo, but preferably also including in vitro and ex vivo pre-screening methodologies to build an understanding of their consequences. As in many domains of microbiome research, the development of experimental process controls and internal standards, which are essentially lacking to date, should be taken as a future prerequisite. There is also a requirement from regulatory agencies to define and harmonize acceptance criteria.}, }
@article {pmid41852816, year = {2022}, author = {Tadmor, AD and Mahmoudabadi, G and Foley, HB and Phillips, R}, title = {Identification and spatio-temporal tracking of ubiquitous phage families in the human microbiome.}, journal = {Frontiers in microbiomes}, volume = {1}, number = {}, pages = {1097124}, pmid = {41852816}, issn = {2813-4338}, abstract = {Viruses are a major component of the human microbiome, yet their diversity, lifestyles, spatiotemporal dynamics, and functional impact are not well understood. Elucidating the ecology of human associated phages may have a major impact on human health due to the potential ability of phages to modulate the abundance and phenotype of commensal bacteria. Analyzing 690 Human Microbiome Project metagenomes from 103 subjects sampled across up to 18 habitats, we found that despite the great interpersonal diversity observed among human viromes, humans harbor distinct phage families characterized by their shared conserved hallmark genes known as large terminase subunit (TerL) genes. Phylogenetic analysis of these phage families revealed that different habitats in the oral cavity and gut have unique phage community structures. Over a ~7-month timescale most of these phage families persisted in the oral cavity and gut, however, presence in certain oral habitats appeared to be transitory, possibly due to host migration within the oral cavity. Interestingly, certain phage families were found to be highly correlated with pathogenic, carriage and disease-related isolates, and may potentially serve as novel biomarkers for disease. Our findings shed new light on the core human virome and offer a metagenomic-independent way to probe the core virome using widely shared conserved phage markers.}, }
@article {pmid41852852, year = {2026}, author = {Gusareva, ES and Vettath, VK and Gaultier, NE and Sadovoy, AV and Dacanay, JGA and Schuster, SC}, title = {Dermatophagoides pteronyssinus in ambient air bioaerosols.}, journal = {The journal of allergy and clinical immunology. Global}, volume = {5}, number = {3}, pages = {100667}, pmid = {41852852}, issn = {2772-8293}, abstract = {BACKGROUND: House dust mite (HDM) sensitization is a leading cause of allergic rhinitis and asthma worldwide, with Dermatophagoides pteronyssinus, Dermatophagoides farinae, and Blomia tropicalis being the primary allergenic species typically associated with indoor environments. Even effective multicomponent interventions creating an HDM-free indoor environment are often insufficient to prevent allergy, as HDM exposure may also occur outdoors.<br><br>OBJECTIVE: To assess the potential for outdoor HDM exposure, we applied air biomass sequencing and metagenomic techniques to detect HDM DNA in both indoor and outdoor bioaerosols, offering an alternative to conventional dust sampling methods.<br><br>METHODS: We used 2 data sets in this study: (1) a global data set comprising 1,171 outdoor air samples collected across 33 countries in open air environments and (2) a data set of indoor (n = 161) and outdoor (n = 156) air samples collected across 156 apartments from 106 locations in Singapore. All air samples were collected by drawing 24,000 to 36,000 L of air using SASS3100 air samplers; all samples were processed identically. Species-level taxonomic classification was performed using Kaiju software aligned to the National Center for Biotechnology Information nonredundant database, with a minimum threshold of 40 reads per taxon.<br><br>RESULTS: Analysis of 1,171 global outdoor air samples revealed D pteronyssinus as the most prevalent HDM species; it was detected in 208 samples, with abundance increasing from temperate toward equatorial regions. In Singaporean households, D pteronyssinus was found in 58.4% of indoor samples and 21.2% of nearby outdoor samples, with high median DNA read counts outdoors suggesting that exposure to HDM is not limited to domestic environments. B tropicalis and D farinae were also detected in Singapore, albeit at lower frequencies.<br><br>CONCLUSION: Our findings highlight the need to expand environmental allergen surveillance beyond household dust to include ambient and outdoor air, particularly in tropical climates.}, }
@article {pmid41853108, year = {2026}, author = {Khan, A}, title = {Disseminated Mycobacterium intracellulare subsp. chimaera infection, undiagnosed for years, highlights the enduring clinical utility of "old school" microbiological testing and a robust differential.}, journal = {ASM case reports}, volume = {2}, number = {2}, pages = {}, pmid = {41853108}, issn = {2996-2684}, abstract = {Disseminated Mycobacterium intracellulare subsp. chimaera (MC) infections are rare, slow-progressing, and easily overlooked, particularly when a patient's history of prior cardiac surgery is not incorporated into the diagnostic evaluation. In a recent ASM Case Reports article (1:e00003-25, 2025, https://doi.org/10.1128/asmcr.00003-25), Ladines-Lim et al. describe a disseminated MC infection in a patient with prior aortic and mitral valve replacement that remained undiagnosed for over 4 years. Conventional microbiological testing was not pursued early in the course of illness because the history of cardiopulmonary bypass was not linked with the constellation of unexplained symptoms. This case urges clinicians to remain vigilant and suspect MC in patients with prior open-chest cardiac surgery who present with gradually worsening, systemic symptoms. Since 2013, global outbreaks of delayed-onset MC infections have been traced to contaminated heater cooler devices, yet many centers continue to face barriers to replacing or monitoring such equipment. A delayed diagnosis in this case was eventually established by cell-free metagenomic next-generation sequencing (cfmNGS). However, the result was not acted upon until weeks later, after central nervous system involvement. A more timely, cost-effective diagnosis might have been achieved using traditional, widely available, culture-based testing guided by a robust exposure-driven differential. Clinicians should suspect MC in patients with prior cardiac surgery-even years earlier-who develop unexplained, progressive systemic symptoms. Early suspicion and appropriate testing are critical to improved outcomes. This case shows that next-generation sequencing assays are only as useful as the clinical reasoning guiding their use. Traditional microbiological testing-when leveraged early and thoughtfully-remains an accessible cornerstone of diagnosing complex MC infections.}, }
@article {pmid41853337, year = {2023}, author = {Peter, H and Michoud, G and Busi, SB and Battin, TJ}, title = {The role of phages for microdiverse bacterial communities in proglacial stream biofilms.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1279550}, pmid = {41853337}, issn = {2813-4338}, abstract = {Viruses modulate the diversity and activity of microbial communities. However, little is known about their role for the structure of stream bacterial biofilm communities. Here, we present insights into the diversity and composition of viral communities in various streams draining three proglacial floodplains in Switzerland. Proglacial streams are characterized by extreme environmental conditions, including near-freezing temperatures and ultra-oligotrophy. These conditions select for few but well-adapted bacterial clades, which dominate biofilm communities and occupy niches via microdiversification. We used metagenomic sequencing to reveal a diverse biofilm viral assemblage in these streams. Across the different floodplains and streams, viral community composition was tightly coupled to that of the bacterial hosts, which was underscored by generally high host specificity. Combining predictions of phage-host interactions with auxiliary metabolic genes (AMGs), we identify specific AMGs shared by phages infecting microdiverse clade members. Our work provides a step towards a better understanding of the complex interactions among bacteria and phages in stream biofilm communities in general and streams influenced by glacier meltwaters and characterized by microdiversity in particular.}, }
@article {pmid41853339, year = {2023}, author = {Wong, MT and Nesbø, CL and Wang, W and Couturier, M and Lombard, V and Lapebie, P and Terrapon, N and Henrissat, B and Edwards, EA and Master, ER}, title = {Taxonomic composition and carbohydrate-active enzyme content in microbial enrichments from pulp mill anaerobic granules after cultivation on lignocellulosic substrates.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1094865}, pmid = {41853339}, issn = {2813-4338}, abstract = {Metagenomes of lignocellulose-degrading microbial communities are reservoirs of carbohydrate-active enzymes relevant to biomass processing. Whereas several metagenomes of natural digestive systems have been sequenced, the current study analyses metagenomes originating from an industrial anaerobic digester that processes effluent from a cellulose pulp mill. Both 16S ribosomal DNA and metagenome sequences were obtained following anaerobic cultivation of the digester inoculum on cellulose and pretreated (steam exploded) poplar wood chips. The community composition and profile of predicted carbohydrate-active enzymes were then analyzed in detail. Recognized lignocellulose degraders were abundant in the resulting cultures, including populations belonging to Clostridiales and Bacteroidales orders. Poorly defined taxonomic lineages previously identified in other lignocellulose-degrading communities were also detected, including the uncultivated Firmicutes lineage OPB54 which represented nearly 10% of the cellulose-fed enrichment even though it was not detected in the bioreactor inoculum. In total, 3580 genes encoding carbohydrate-active enzymes were identified through metagenome sequencing. Similar to earlier enrichments of animal digestive systems, the profile encoded by the bioreactor inoculum following enrichment on pretreated wood was distinguished from the cellulose counterpart by a higher occurrence of enzymes predicted to act on pectin. The majority (> 93%) of carbohydrate-active enzymes predicted to act on plant polysaccharides were identified in the metagenome assembled genomes, permitting taxonomic assignment. The taxonomic assignment revealed that only a small selection of organisms directly participates in plant polysaccharide deconstruction and supports the rest of the community.}, }
@article {pmid41853340, year = {2023}, author = {Yang, Q and Wang, J and Zhang, D and Feng, H and Bozorov, TA and Yang, H and Zhang, D}, title = {Effects of multi-resistant ScALDH21 transgenic cotton on soil microbial communities.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1248384}, pmid = {41853340}, issn = {2813-4338}, abstract = {Transgenic crops are increasingly prevalent worldwide, and evaluating their impact on soil microbial communities is a critical aspect of upholding environmental safety. Our previous research demonstrated that overexpression of ScALDH21 from desiccant-tolerant moss, Syntrichia caninervis, in cotton revealed multi-resistance to drought, salt, and biotic stresses. We conducted metabarcoding using high-throughput sequencing to evaluate the effect of ScALDH21 transgenic cotton on soil microbial communities. We further conducted soil tests to analyze the chemical properties of transgenic and non-transgenic cotton, including the total content and availability of chemical elements (K, P, and N), organic matter, and pH value. Both transgenic and non-transgenic cotton fields exhibited soil pH values higher than 8. The presence of transgenic cotton significantly enhanced the availability of available K and the total content of total P in the soil. Alpha and beta diversity indices of soil microbiota showed no difference between two transgenic and non-transgenic cotton groups. Dominant clades of fungal and bacterial genera were equivalent at the phylum and genus levels in all three groups. The correlation analysis of microbial communities and soil environmental factors revealed the absence of significant differences between transgenic and non-transgenic cotton genotypes. Functional predictions of soil microbial communities indicated that microbial community function did not show significant differences between transgenic and non-transgenic cotton samples. These findings are essential for evaluating the environmental effects of transgenic crops and supporting the secure implementation of transgenic cotton.}, }
@article {pmid41853343, year = {2023}, author = {Ionescu, D and Zoccarato, L and Cabello-Yeves, PJ and Tikochinski, Y}, title = {Extreme fluctuations in ambient salinity select for bacteria with a hybrid "salt-in"/"salt-out" osmoregulation strategy.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1329925}, pmid = {41853343}, issn = {2813-4338}, abstract = {Abundant microbial biofilms inhabit underwater freshwater springs of the Dead Sea. Unlike the harsh (i.e., over 35% total dissolved salts) yet stable environment of the basin, the flow rate of the springs changes with random amplitude and duration, resulting in drastic shifts in salinity, pH, and oxygen concentrations. This requires the organisms to continuously adapt to new environmental conditions. Osmotic regulation is energetically expensive; therefore, the response of the biofilm organisms to rapid and drastic changes in salinity is interesting. For this purpose, we studied the metagenome of an enrichment culture obtained from a green biofilm-covered rock positioned in a spring. We obtained metagenome-assembled genomes (MAGs) of Prosthecochloris sp. (Chlorobiales), Flexistipes sp. (Deferribacterales), Izemoplasma (Izemoplasmatales), Halomonas sp. (Oceanospirillales), and Halanaerobium (Halanaerobiales). The MAGs contain genes for both the energetically cheaper "salt-in" and more expensive "salt-out" strategies. We suggest that the dynamic response of these bacteria utilizes both osmoregulation strategies, similar to halophilic archaea. We hypothesize that the frequent, abrupt, and variable-in-intensity shifts in salinity, typical of the Dead Sea spring system, select for microorganisms with scalable adaptation strategies.}, }
@article {pmid41853350, year = {2023}, author = {Oliveira, RS and Pinto, OHB and Quirino, BF and de Freitas, MAM and Thompson, FL and Thompson, C and Kruger, RH}, title = {Genome-resolved metagenomic analysis of Great Amazon Reef System sponge-associated Latescibacterota bacteria and their potential contributions to the host sponge and reef.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1206961}, pmid = {41853350}, issn = {2813-4338}, abstract = {The Great Amazon Reef System (GARS) is an extensive biogenic reef influenced by a plume layer of sediments. This creates an extreme environment where light is reduced, thus affecting physicochemical properties as well as living organisms such as sponges and their microbiomes. The sponge's microbiome has numerous ecological roles, like participation in biogeochemical cycles and host nutrition, helping the sponge thrive and contributing to the ecosystem. Also, sponges and sponge-associated microorganisms are rich sources of bioactive compounds, and their products are applied in different areas, including textile, pharmaceutical, and food industries. In this context, metagenome-assembled genomes (MAG), obtained from GARS sponges microbiota, were analyzed to predict their ecological function and were prospected for biotechnological features. Thus, in this work, tissues of GARS sponges were collected, their metagenomes were sequenced and assembled, and 1,054 MAGs were recovered. Ten of those MAGs were selected based on their taxonomic classification in the candidate phylum Latescibacterota and this group's abundance in GARS sponges. The workflow consisted of MAG's quality definition, taxonomic classification, metabolic reconstruction, and search for bioactive compounds. Metabolic reconstruction from medium to high-quality MAGs revealed genes related to degradation and synthesis pathways, indicating functions that may be performed by GARS sponge-associated Latescibacterota. Heterotrophy, a recurring attribute in Latescibacterota that might be crucial for GARS sponge holobiont nutrition, was verified by the presence of genes related to respiration and fermentation. Also, the analyzed bacteria may contribute to the host's survival in multiple ways, including host protection via defense systems; aid in nutrient consumption by breaking complex substrates and producing essential nutrients like vitamins and certain amino acids; and detoxification of mercury, arsenic, ammonia, and hydrogen sulfide. Additionally, genes linked to persistent organic pollutant degradation, including glyphosate, and biogeochemical cycles reactions, such as ammonification, sulfate reduction, thiosulfate disproportionation, phosphorus remineralization, and complex organic matter degradation, were identified, suggesting the participation of these Latescibacterota in bioremediation and nutrient cycling. Finally, the investigated MAGs contain genes for numerous bioactive compounds, including industrial enzymes, secondary metabolites, and biologically active peptides, which may have biotechnological value.}, }
@article {pmid41853380, year = {2023}, author = {Galeeva, JS and Starikova, EV and Fedorov, DE and Manolov, AI and Pavlenko, AV and Konanov, DN and Krivonos, DV and Babenko, VV and Klimina, KM and Veselovsky, VA and Morozov, MD and Gafurov, IR and Gaifullina, RF and Govorun, VM and Ilina, EN}, title = {Microbial communities of the upper respiratory tract in mild and severe COVID-19 patients: a possible link with the disease course.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1067019}, pmid = {41853380}, issn = {2813-4338}, abstract = {The microbiota of the respiratory tract remains a relatively poorly studied subject. At the same time, it is involved in modulating the immune response to infectious agents in the host organism, just like the intestinal microbiota. A relationship between the composition of the respiratory microbiota and the likelihood of development and the severity of COVID-19 may be assumed. In this study, we applied the 16S rRNA metagenomic sequencing to analyze the oropharyngeal swabs from 120 COVID-19 patients collected during the first and the second waves of the COVID-19 epidemic in Russia. Differential abundance analysis with respect to comorbidities suggested association of Neisseria oralis, Neisseria mucosa, unidentified Veillonella spp., Lautropia mirabilis species with more severe lung damage, and Streptococcus salivarius, Capnocytophaga sputigena and Haemophilus parahaemolyticus with a milder course of the disease. We hypothesize that the latter bacteria (or some of them) might be beneficial for the respiratory tract and might be able to alleviate the course of the COVID-19 disease.}, }
@article {pmid41853383, year = {2023}, author = {Ramirez Garcia, A and Greppi, A and Constancias, F and Ruscheweyh, HJ and Gasser, J and Hurley, K and Sturla, SJ and Schwab, C and Lacroix, C}, title = {Anaerobutyricum hallii promotes the functional depletion of a food carcinogen in diverse healthy fecal microbiota.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1194516}, pmid = {41853383}, issn = {2813-4338}, abstract = {INTRODUCTION: Anaerobutyricum hallii is a human gut commensal that transforms the heterocyclic amine 2-amino-1-methyl-6-phenylimidazo [4,5-b] pyridine (PhIP), a carcinogen from cooked meat. The transformation mechanism involves the microbial production of acrolein from glycerol, and its conjugation with PhIP, thus blocking its mutagenic potential. A potential cancer prevention strategy could therefore involve supplementing complex human microbial communities with metabolically competent bacteria such as A. hallii that can deplete PhIP. However, it has not been established how the proportion of A. hallii in diverse healthy human gut microbial communities relates to functional capacity for PhIP transformation and, moreover, how supplementing microbiomes with A. hallii affects this function.<br><br>METHODS: In this study, shotgun metagenomics was used to study taxonomic profiling, the abundance of glycerol/diol dehydratase (gdh)-harboring taxa, the proportion of resident A. hallii, and the reconstruction of A. hallii population genomes in the fecal samples of 20 healthy young adult donors. Furthermore, the influence of supplementing 10[6] cells/mL of A. hallii DSM 3353 with diluted fecal microbiota was characterized.<br><br>RESULTS AND DISCUSSION: Six microbiota were assigned to Bacteroides, nine to Prevotella, and five to Ruminococcus by enterotype-associated clustering. The total number of gdh copies in the 20 fecal microbiota expressed per 10[10] bacterial cells ranged between 1.32 &#xd7; 10[8] and 1.15 &#xd7; 10[9]. Eighteen out of the 20 donors were dominated by A. hallii, representing between 33% and 94% of the total gdh relative abundance of the samples. The microbiota with low A. hallii abundance (i.e., with a relative abundance < 1%) transformed less PhIP than the microbiota with high A. hallii abundance (i.e., with a relative abundance > 1%). Furthermore, supplementing the low-A. hallii-abundant microbiota with glycerol significantly increased the PhIP transformation capacity after 6 h while reducing total short-chain fatty acid (SCFA) levels, which is most likely due to acrolein production. Although acetate decreased in all microbiota with glycerol and with the combination of glycerol and A. hallii, for most of the microbiomes, butyrate production increased over time. Thus, for a significant number of diverse healthy human fecal microbiomes, and especially when they have little of the taxa to start with, supplementing A. hallii increases PhIP transformation. These findings suggest the need to test in vivo whether supplementing microbiomes with A. hallii reduces PhIP exposure.}, }
@article {pmid41853385, year = {2023}, author = {Leo, S and Cetiner, OF and Pittet, LF and Messina, NL and Jakob, W and Falquet, L and Curtis, N and Zimmermann, P}, title = {The association between the composition of the early-life intestinal microbiome and eczema in the first year of life.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1147082}, pmid = {41853385}, issn = {2813-4338}, abstract = {INTRODUCTION: The early-life intestinal microbiome plays a crucial role in the development and regulation of the immune system. Perturbations in its composition during this critical period have been linked to the development of allergic diseases.<br><br>OBJECTIVE: This study aimed to investigate the association between the composition of the early-life intestinal microbiome and the presence of eczema in the first year of life using shotgun metagenomic sequencing and functional analyses (metabolic pathways).<br><br>METHODS: Stool samples from 393 healthy term infants collected at 1 week of age were analyzed with shotgun metagenomic sequencing. Environmental and clinical data were prospectively collected using 3-monthly validated questionnaires. Participants were clinically assessed during study visits at 12 months of age. Eczema was diagnosed by the UK diagnostic tool and by a research nurse. Data analysis was stratified by delivery mode.<br><br>RESULTS: Eczema was diagnosed in 16.4% (60/366) of participants by nurse diagnosis. Infants born by cesarean section (CS) with nurse-diagnosed eczema had a higher relative abundance of Escherichia, Shigella, Enterobacter, and Citrobacter and a lower relative abundance of Veillonella than CS-born infants without eczema. In addition, CS-born infants without eczema had a higher abundance of genes involved in lactic fermentation. Vaginally born infants with eczema had a higher relative abundance of Bacteroides and a lower abundance of Streptococcus.<br><br>CONCLUSION: There is an association between the bacterial composition of the intestinal microbiome at 1 week of age and the presence of eczema in the first 12 months of life.}, }
@article {pmid41853387, year = {2023}, author = {Rodríguez-Ramos, J and Oliverio, A and Borton, MA and Danczak, R and Mueller, BM and Schulz, H and Ellenbogen, J and Flynn, RM and Daly, RA and Schopflin, L and Shaffer, M and Goldman, A and Lewandowski, J and Stegen, JC and Wrighton, KC}, title = {Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream.}, journal = {Frontiers in microbiomes}, volume = {2}, number = {}, pages = {1199766}, pmid = {41853387}, issn = {2813-4338}, abstract = {Although river ecosystems constitute a small fraction of Earth's total area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. To address this gap, we assessed how viral and microbial communities change over a 48-hour period by sampling surface water and pore water compartments of the wastewater-impacted River Erpe in Germany. We sampled every 3 hours resulting in 32 samples for which we obtained metagenomes along with geochemical and metabolite measurements. From our metagenomes, we identified 6,500 viral and 1,033 microbial metagenome assembled genomes (MAGs) and found distinct community membership and abundance associated with each river compartment (e.g., Competibacteraceae in surfacewater and Sulfurimonadaceae in pore water). We show that 17% of our viral MAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae, which we suggest are potential contributors to river carbon and nitrogen cycling via denitrification and nitrogen fixation. Together, these findings demonstrate that members of the surface water microbiome from this urban river are stable over multiple diurnal cycles. These temporal insights raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles.}, }
@article {pmid41853501, year = {2024}, author = {Faber, Q and Davis, C and Christner, B}, title = {Metagenomic inference of microbial community composition and function in the weathering crust aquifer of a temperate glacier.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1488744}, pmid = {41853501}, issn = {2813-4338}, abstract = {Bacterial, fungal, and algal communities that colonize aquatic systems on glacial ice surfaces mediate biogeochemical reactions that alter meltwater composition and affect meltwater production and storage. In this study, we sought to improve understanding of microbial communities inhabiting the shallow aquifer that forms seasonally within the ice surface of a glacier's ablation zone (i.e., the weathering crust aquifer). Using a metagenomic approach, we compared gene contents of microbial assemblages in the weathering crust aquifer (WCA) of the Matanuska Glacier (Alaska, USA) to those recovered from supraglacial features and englacial ice. High abundances of Pseudomonadota, Cyanobacteriota, Actinomycetota, and Bacteroidota were observed across all samples, while taxa in class Gammaproteobacteria were found at significantly higher abundances in the weathering crust aquifer. The weathering crust aquifer samples also contained higher abundances of Dothideomycetes and Microbotryomyetes; fungal classes commonly observed in snow and other icy ecosystems. Phylogenetic analysis of 18S rRNA and rbcL gene sequences indicated high abundances of algae in the WCA that are closely related (> 98% and > 93% identity, respectively) to taxa of Ancylonema (Streptophyta) and Ochromonas (Ochrophyta) reported from glacial ice surfaces in Svalbard and Antarctic sea ice. Many functional gene categories (e.g., homeostasis, cellular regulation, and stress responses) were enriched in samples from the weathering crust aquifer compared to those from proximal englacial and supraglacial habitats, providing evidence for ecological specialization in the communities. The identification of phagotrophic phytoflagellate taxa and genes involved in mixotrophy implies that combined phototrophic and heterotrophic production may assist with persistence in the low light, low energy, and ephemeral conditions of the weathering crust environment. The compositional and functional differences we have documented indicate distinct microbial distributions and functional processes occur in the weathering crust aquifer environment, and we discuss how deciphering these nuances is essential for developing a more complete understanding of ecosystem biogeochemistry in supraglacial hydrological systems.}, }
@article {pmid41853503, year = {2024}, author = {Greenman, N and Abdelli, LS and Hassouneh, SA and Ali, S and Johnston, C and Naser, SA and Azarian, T}, title = {Impact of propionic acid-rich diets on microbial composition of the murine gut microbiome.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1451735}, pmid = {41853503}, issn = {2813-4338}, abstract = {Propionic acid (PPA), an anti-fungal agent and common food additive, has been shown to induce atypical neurodevelopment in mice, accompanied by gastrointestinal dysfunction potentially resulting from gut dysbiosis. A putative association between dietary PPA exposure and gut dysbiosis is suggested but has not been explored directly. Here, we investigated PPA-associated alteration in gut microbial composition that may result in dysbiosis. Using long-read metagenomic sequencing, gut microbiomes of mice fed an untreated (n=9) or PPA-rich (n=13) diet were sequenced to assess differences in microbial composition and bacterial metabolic pathways. Dietary PPA was associated with an increased abundance of notable taxa, including several species of Bacteroides, Prevotella, and Ruminococcus, whose member species have previously been associated with PPA production. Microbiomes of PPA exposed mice also possessed a greater abundance of pathways related to lipid metabolism and steroid hormone biosynthesis. Our findings demonstrate PPA's effect in altering the gut microbiota and associated metabolic pathways. These observed changes highlight how preservatives listed as safe for consumption may affect gut microbiome composition with implications for one's health.}, }
@article {pmid41853504, year = {2024}, author = {Muwonge, A and Gerber, PF and Wee, BA and Thomson, J and Wang, J and Halbur, PG and Opriessnig, T}, title = {Exploring the utility of bioaerosol metagenomics compared to PCRs for swine pathogen surveillance.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1439108}, pmid = {41853504}, issn = {2813-4338}, abstract = {INTRODUCTION: Pathogen introduction and transmission at the farm, regional, or national level are associated with reduced animal welfare and negative impacts on herd economics. Ongoing infectious disease surveillance, active or passive, is therefore of high importance. For optimal resolution, each pig is sampled individually, for example by collecting blood or nasal swabs. In recent years, oral fluids have become very useful for population surveillance at the pen level. Another alternative is sampling the air to capture pathogens circulating across the entire barn via bioaerosols.<br><br>OBJECTIVE: This study aimed to examine the potential utility of bioaerosol metagenomics for pathogen detection on pig farms.<br><br>METHODS: Bioaerosols via automated air sampler, and oral fluid via pen-based ropes, were collected from each of two Scottish indoor pig farms. All samples were subjected to conventional routine bacterial isolation. Total genomic nucleic acids were extracted for PCR screening for three pig DNA viruses, three bacterial Mycoplasma species and an RNA virus. Illumina shotgun metagenomic sequencing was also conducted.<br><br>RESULTS: Oral fluids contained more DNA compared to bioaerosol samples. DNA integrity exhibited limited impact on PCR or sequence yield. While Streptococcus suis could be cultured from a single oral fluid sample, reads mapped to S. suis were detectable in all metagenomic samples. Other bacterial pig pathogens, including Mycoplasma hyorhinis, M. hyopneumoniae and M. hyosynoviae, were detected in oral fluid and aerosols by PCR and metagenomics. One of the two farms was PRRSV positive, and the virus was detectable via PCR in oral fluids but not in bioaerosols. Antimicrobial resistance (AMR) gene profiles had less variation between bioaerosols and oral fluids. Some identified AMR genes had strikingly similar abundance overall.<br><br>CONCLUSION: Overall, these findings indicate that there is potential utility of bioaerosol metagenomics for pathogen surveillance on pig farms; however, more research is needed for technical and cost optimization to allow for routine pathogen detection on livestock farms.}, }
@article {pmid41853506, year = {2024}, author = {John, D and Michael, D and Dabcheva, M and Hulme, E and Illanes, J and Webberley, T and Wang, D and Plummer, S}, title = {Corrigendum: A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on antibiotic induced changes in the gut microbiome.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1484878}, doi = {10.3389/frmbi.2024.1484878}, pmid = {41853506}, issn = {2813-4338}, abstract = {[This corrects the article DOI: 10.3389/frmbi.2024.1359580.].}, }
@article {pmid41853507, year = {2024}, author = {John, D and Michael, D and Dabcheva, M and Hulme, E and Illanes, J and Webberley, T and Wang, D and Plummer, S}, title = {A double-blind, randomized, placebo-controlled study assessing the impact of probiotic supplementation on antibiotic induced changes in the gut microbiome.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1359580}, pmid = {41853507}, issn = {2813-4338}, abstract = {The human gut microbiome, crucial for health, can be disrupted by antibiotic treatment, leading to various health issues and the rise of antimicrobial resistance (AMR). This study investigates the impact of a probiotic on the gut microbiome's composition and antimicrobial resistance genes (ARGs) content following antibiotic treatment. Conducted as a single-centre, double-blind, randomized, placebo-controlled trial, adults taking oral antibiotics were allocated into a probiotic or placebo group. Evaluations included viable cell enumeration and shotgun metagenomic sequencing for microbiome analysis, along with ARG assessment. The probiotic maintained the numbers of lactobacilli, significantly increased the Bacteroides population and decreased numbers of enterobacteria. The lactobacilli and enterococci numbers decreased in the placebo. The alpha diversity remained stable in the probiotic group throughout the study, but significant reductions were observed in the placebo group post antibiotic treatment. There was significant spatial separation in beta diversities between groups at the end of the study. Compared to baseline levels, there was a significant reduction in the abundance of ARGs in the probiotic group at the end of the study, while ARG abundance in the placebo group was comparable with baseline levels at the end of the study. Co-occurrence network analysis observed consistent betweenness centrality and node degree within group in the probiotic group whereas scores decreased in the placebo group. This study suggests that the probiotic may minimize the disruption of antibiotic treatment on the gut microbiome by preserving microbial diversity and reducing ARG abundance.}, }
@article {pmid41853508, year = {2024}, author = {Molotzu, MR and Cabras, PA and Di Marcantonio, L and Atzeni, R and Macciotta, NPP and Canu, A}, title = {Metagenomic analysis of goat feces from Ogliastra (Sardinia, Italy).}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1474497}, pmid = {41853508}, issn = {2813-4338}, abstract = {With its constitutive and functional characteristics, the intestinal microbiota plays a crucial role in the health condition of the animals. Variations in the composition and gene expression of the intestinal microbiota are associated with the risk of the onset of various pathologies of the gastrointestinal tract and chronic inflammatory intestinal diseases. The objectives of this study were to evaluate the variability in the composition of the intestinal microbiota of goats of different breeds (Sarda, Maltese, and Alpine) farmed in different flocks of the region of Ogliastra (Sardegna, Italy) and to assess whether the type of feeding (natural pasture grazing-based versus intensive) could affect the intestinal bacterial composition. We also evaluated possible differences in the composition of the intestinal microbiota between healthy and Caprine arthritis encephalitis (CAE)-affected goats. The economic damage caused by this pathology is due to the reduction in milk production, with infected animals having greater susceptibility to contract diseases. The results of our study highlighted a statistically significant difference (P = 0.001-0.005) in the intestinal bacterial composition between the intensively managed flock and the other natural pasture-based flock.g In particular, a significantly greater abundance of Acidoaminococcaceae in the intensive flock was obgserved. Furthermore, a significantly greater abundance of Prevotellaceae was found in two localities in which, out of a total of 29 animals, only four tested negative for CAE. From these data, we deduced that the presence of Prevotellaceae can be an indication of the disease. This difference could be attributed to the farming system, the Cardedu farm being the only intensive one, and to the geographical distance of this location from the other sampling sites. Therefore, the results of the present study suggest that extensive or intensive farm management may affect the intestinal microbiota of goats.}, }
@article {pmid41853526, year = {2024}, author = {Liu, S and Zhao, J and Feng, WL and Zhang, ZJ and Gu, YF and Wang, YP}, title = {Microbial community succession of cow manure and tobacco straw composting.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1301156}, pmid = {41853526}, issn = {2813-4338}, abstract = {Composting livestock manure using microorganisms is a safe and resourceful practice. The continual fluctuations in physicochemical parameters during composting are intricately linked to the composition of microbial communities. This study investigated the dynamics of microbial communities during the composting of cow manure and tobacco straw using amplicon sequencing and shotgun metagenomics. The sequencing results revealed major genera such as Sphaerobacter, Actinomadura, Thermomonospora, Flavobacterium, Bacillus, Hydrogenophaga, Pseudomonas, Lysinibacillus, Aneurinibacillus, and Azotobacter. Metagenomic analysis highlighted that the phylum Proteobacteria constituted the largest proportion. Furthermore, the presence of the genus Rhodococcus, known to cause human and animal diseases, gradually decreased over time. These findings offer initial insights into the microbial community composition and function during cow manure and tobacco straw composting.}, }
@article {pmid41853529, year = {2024}, author = {Huttelmaier, S and Shuai, W and Sumner, JT and Hartmann, EM}, title = {Phage communities in household-related biofilms correlate with bacterial hosts.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1396560}, pmid = {41853529}, issn = {2813-4338}, abstract = {The average American spends 93% of their time in built environments, almost 70% of that is in their place of residence. Human health and well-being are intrinsically tied to the quality of our personal environments and the microbiomes that populate them. Conversely, the built environment microbiome is seeded, formed, and re-shaped by occupant behavior, cleaning, personal hygiene and food choices, as well as geographic location and variability in infrastructure. Here, we focus on the presence of viruses in household biofilms, specifically in showerheads and on toothbrushes. Bacteriophage, viruses that infect bacteria with high host specificity, have been shown to drive microbial community structure and function through host infection and horizontal gene transfer in environmental systems. Due to the dynamic environment, with extreme temperature changes, periods of wetting/drying and exposure to hygiene/cleaning products, in addition to low biomass and transient nature of indoor microbiomes, we hypothesize that phage host infection in these unique built environments are different from environmental biofilm interactions. We approach the hypothesis using metagenomics, querying 34 toothbrush and 92 showerhead metagenomes. Representative of biofilms in the built environment, these interfaces demonstrate distinct levels of occupant interaction. We identified 22 complete, 232 high quality, and 362 medium quality viral OTUs. Viral community richness correlated with bacterial richness but not Shannon or Simpson indices. Of quality viral OTUs with sufficient coverage (614), 532 were connected with 32 bacterial families, of which only Sphingomonadaceae, Burkholderiaceae, and Caulobacteraceae are found in both toothbrushes and showerheads. Low average nucleotide identity to reference sequences and a high proportion of open reading frames annotated as hypothetical or unknown indicate that these environments harbor many novel and uncharacterized phage. The results of this study reveal the paucity of information available on bacteriophage in indoor environments and indicate a need for more virus-focused methods for DNA extraction and specific sequencing aimed at understanding viral impact on the microbiome in the built environment.}, }
@article {pmid41853533, year = {2024}, author = {Liu, Z and Shen, Y and Fu, Y and Sun, D and Li, L and Lv, Z}, title = {Association of resistome abundance with hyperuricaemia in elderly individuals: a metagenomics study.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1384703}, pmid = {41853533}, issn = {2813-4338}, abstract = {INTRODUCTION: Hyperuricaemia (HUA), one of chronic diseases, has an increased prevalence and is related to diseases such as gout, arthritis, infectious diseases, etc. Antimicrobial resistance (AMR) in the gut is considered as an atypical chronic disease, and poses risk to human health. The gut microbiome has been proved to be a reservoir for AMR and play an important role in HUA patients. The microbial characteristics of the gut in individuals with HUA have been previously explored, however, the characteristics of the resistome in individuals with HUA have remained largely unexplored.<br><br>METHODS: Thus, we investigated the landscape of the AMR in individuals with HUA and without HUA, and the potentially influential factors in a case-control study using metagenomics-based approaches.<br><br>RESULTS: We found that drinking juice and abnormal stool were risk factors associated with HUA. The taxonomic diversity of gut microbiota in individuals with HUA was lower than that in non-HUA individuals. Notably, a higher abundance and diversity of the resistome (entire antimicrobial resistance genes) was observed in individuals with HUA (median: 1.10 vs. 0.76, P = 0.039, U-test), especially in tetracycline resistance genes (median: 0.46 vs. 0.20, P < 0.001, U-test), which are associated with more complex mobile genetic elements (MGEs) in individuals with HUA. Furthermore, we found that a higher abundance of the resistome was positively correlated with uric acid (UA) levels and affected by several host-associated factors (mainly dietary habits). Specifically, pork consumption and the consumption of root and tuber vegetables were identified as contributing factors. We also found a higher abundance of virulence genes (VGs), mostly related to adherence, antimicrobial activity, competitive advantage, and exoenzymes, in the gut microbial community of individuals with HUA.<br><br>DISCUSSION: All findings revealed higher activity of the resistome and pathogenicity of the microbiota in individuals with HUA, indicating a higher health risk in the elderly HUA population.}, }
@article {pmid41853535, year = {2024}, author = {Alian, OM and Brazelton, WJ and Aquino, KA and Twing, KI and Pendleton, HL and Früh-Green, G and Lang, SQ and Schrenk, MO}, title = {Microbial community differentiation in vent chimneys of the Lost City Hydrothermal Field reflects habitat heterogeneity.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1401831}, pmid = {41853535}, issn = {2813-4338}, abstract = {Oceanic hydrothermal vent systems represent some of the oldest habitats on Earth and serve as analogs for extraterrestrial environments. The Lost City Hydrothermal Field (LCHF) near the Mid-Atlantic Ridge is one such environment, and its large chimneys are unique in hosting actively venting hydrothermal fluids that are primarily controlled by serpentinization reactions in the subseafloor. Microbial communities within LCHF have been studied for insights into their functional adaptations to the warm, alkaline, and dissolved inorganic carbon-limited environment. Metagenomic and mineralogical data collected during a recent expedition to Lost City were analyzed to delineate associations between microbial populations and physical, chemical and biological characteristics of the chimneys. Bacterial 16S rRNA gene sequences show a high degree of putative microdiversity within the relatively dominant genera Desulfotomaculum, Sulfurovum, Thiomicrorhabdus, and Serpentinicella, which represent a large core of the overall LCHF vent bacterial community. This microdiversity relates to the compositional fraction of aragonite, brucite, and calcite minerals within chimney samples rather than just the composition of nearby vent fluids. Although many species are found in both chimneys and venting fluids, the overall microbial community structures in chimney biofilms remain distinct from the hydrothermal fluids that flow through them. Shotgun metagenomic analyses reveal differences among genes predicted to be involved in carbon, methane, nitrogen and sulfur cycling with respect to their correlations to the abundances of specific minerals. These data hint at microenvironmental complexity lost within standard bulk analyses. The findings of this study underscore the need to more closely examine microbe-mineral interactions in natural environments, critically informing not just population-level distributions, but also the functional underpinnings of these extremophile microbial communities.}, }
@article {pmid41853539, year = {2024}, author = {Chandel, N and Gorremuchu, JP and Thakur, V}, title = {Antimicrobial resistance burden, and mechanisms of its emergence in gut microbiomes of Indian population.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1432646}, pmid = {41853539}, issn = {2813-4338}, abstract = {INTRODUCTION: The human gut microbiome harbors millions of bacterial species, including opportunistic pathogens, and this microbial community is exposed to antimicrobial agents present in food, the external environment, or drugs. Thus, it increases the risk of commensals being enriched with resistant genes, which may get even transmitted to opportunistic pathogens often with the help of mobile genetic elements. There is limited information about the current burden of resistant genes in the healthy gut microbiome of the Indian population, the latter is not only the largest in the world but is also periodically monitored for the prevalence of antibiotic resistance in clinical samples.<br><br>METHODS: We analyzed publicly available fecal whole-metagenome shotgun sequencing data from 141 samples from three healthy Indian cohorts for antimicrobial-resistance burden, and their likely transmission modes.<br><br>RESULTS: The overall resistance profile showed a higher number of resistance genes against tetracycline, glycopeptide, and aminoglycoside. Out of a total of 188 antimicrobial resistance genes identified in all cohorts, moderately to highly prevalent ones could potentially target seven of the 'reserve' group antibiotics (colistin, fosfomycin, Polymyxin). We also observed that geographical location affected the prevalence/abundance of some of the resistance genes. The higher abundance of several tetracycline and vancomycin resistance genes in tribal cohorts compared to the other two urban locations was intriguing. Species E. coli had the highest number of resistant genes, and given its relatively modest abundance in gut microbiomes can pose a risk of becoming a hub for the horizontal transfer of resistance genes to others. Lastly, a subset of the resistance genes showed association with several types of mobile genetic elements, which potentially could facilitate their transmission within the gut community.<br><br>DISCUSSION: This is a first systematic report on AMR genes in healthy gut microbiome samples from multiple locations of India. While trends for several of the prevalent AMR genes showed similarity with global data, but a few population specific trends need further attention by policy-makers. The association of AMR genes with mobile elements may pose a risk for transmission to other gut bacteria.}, }
@article {pmid41853546, year = {2024}, author = {Bailey, A and Hogue, S and Pierce, CM and Paul, S and La Fuente, N and Thapa, R and Kim, Y and Robinson, LA}, title = {Metagenomic characterization of the tracheobronchial microbiome in lung cancer.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1457537}, pmid = {41853546}, issn = {2813-4338}, abstract = {BACKGROUND: The tracheobronchial and oral microbiome may be associated with lung cancer, potentially acting as predictive biomarkers. Therefore, we studied the lung and oral bacteriome and virome in non-small cell lung cancer (NSCLC) patients compared to melanoma controls to discover distinguishable features that may suggest lung cancer microbial biomarkers.<br><br>METHODS: In this pilot case-control study, we recruited ten patients with early-stage NSCLC (cases) and ten age-matched melanoma patients (controls) who both underwent tumor resection. Preoperative oral gargles were collected from both groups, who then underwent transbronchoscopic tracheal lavage after intubation. Lung tumor and adjacent non-neoplastic lung were sterilely collected after resection. Microbial DNA from all lung specimens underwent 16S rRNA gene sequencing. Lavage and gargle specimens underwent whole-genome shotgun sequencing. Microbiome metrics were calculated to compare both cohorts. T-tests and Wilcoxon rank sum tests were used to test for significant differences in alpha diversity between cohorts. PERMANOVA was used to compare beta diversity.<br><br>RESULTS: No clear differences were found in the microbial community structure of case and control gargles, but beta diversity of case and control lavages significantly differed. Two species, Granulicatella adiacens and Neisseria subflava, which are both common oral commensal organisms, appeared in much higher abundance in case versus control lavages. Case lavages also maintained higher relative abundances of other oral commensals compared to controls.<br><br>CONCLUSIONS: Lung lavages demonstrated oral microbiota enrichment in cases compared to controls, suggesting microaspiration and resultant inflammation. The oral commensals Granulicatella adiacens and Neisseria subflava were more abundant in the tracheobronchial lavages of lung cancer versus melanoma patients, implicating these microorganisms as potential lung cancer biomarkers, warranting further validation studies.}, }
@article {pmid41853549, year = {2024}, author = {Mahmoudabadi, G and Homyk, K and Catching, AB and Mahmoudabadi, A and Foley, HB and Tadmor, AD and Phillips, R}, title = {Machine learning models can identify individuals based on a resident oral bacteriophage family.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1408203}, pmid = {41853549}, issn = {2813-4338}, abstract = {Metagenomic studies have revolutionized the study of novel phages. However these studies trade depth of coverage for breadth. We show that the targeted sequencing of a small region of a phage terminase family can provide sufficient sequence diversity to serve as an individual-specific barcode or a "phageprint'', defined as the relative abundance profile of the variants within a terminase family. By collecting ~700 oral samples from ~100 individuals living on multiple continents, we found a consistent trend wherein each individual harbors one or two dominant variants that coexist with numerous low-abundance variants. By tracking phageprints over the span of a month across ten individuals, we observed that phageprints were generally stable, and found instances of concordant temporal fluctuations of variants shared between partners. To quantify these patterns further, we built machine learning models that, with high precision and recall, distinguished individuals even when we eliminated the most abundant variants and further downsampled phageprints to 2% of the remaining variants. Except between partners, phageprints are dissimilar between individuals, and neither country-of-residence, genetics, diet nor cohabitation seem to play a role in the relatedness of phageprints across individuals. By sampling from six different oral sites, we were able to study the impact of millimeters to a few centimeters of separation on an individual's phageprint and found that such limited spatial separation results in site-specific phageprints.}, }
@article {pmid41853558, year = {2024}, author = {Pannoni, SB and Holben, WE}, title = {Wildlife fecal microbiota exhibit community stability across a longitudinal semi-controlled non-invasive sampling experiment.}, journal = {Frontiers in microbiomes}, volume = {3}, number = {}, pages = {1274277}, pmid = {41853558}, issn = {2813-4338}, abstract = {Wildlife microbiome studies are being used to assess microbial links with animal health and habitat. The gold standard of sampling microbiomes directly from captured animals is ideal for limiting potential abiotic influences on microbiome composition, yet fails to leverage the many benefits of non-invasive sampling. Application of microbiome-based monitoring for rare, endangered, or elusive species creates a need to non-invasively collect scat samples shed into the environment. Since controlling sample age is not always possible, the potential influence of time-associated abiotic factors was assessed. To accomplish this, we analyzed partial 16S rRNA genes of fecal metagenomic DNA sampled non-invasively from Rocky Mountain elk (Cervus canadensis) near Yellowstone National Park. We sampled pellet piles from four different elk, then aged them in a natural forest plot for 1, 3, 7, and 14 days, with triplicate samples at each time point (i.e., a blocked, repeat measures (longitudinal) study design). We compared fecal microbiota of each elk through time with point estimates of diversity, bootstrapped hierarchical clustering of samples, and a version of ANOVA-simultaneous components analysis (ASCA) with PCA (LiMM-PCA) to assess the variance contributions of time, individual and sample replication. Our results showed community stability through days 0, 1, 3 and 7, with a modest but detectable change in abundance in only 2 genera (Bacteroides and Sporobacter) at day 14. The total variance explained by time in our LiMM-PCA model across the entire 2-week period was not statistically significant (p>0.195) and the overall effect size was small (<10% variance) compared to the variance explained by the individual animal (p<0.0005; 21% var.). We conclude that non-invasive sampling of elk scat collected within one week during winter/early spring provides a reliable approach to characterize fecal microbiota composition in a 16S rDNA survey and that sampled individuals can be directly compared across unknown time points with minimal bias. Further, point estimates of microbiota diversity were not mechanistically affected by sample age. Our assessment of samples using bootstrap hierarchical clustering produced clustering by animal (branches) but not by sample age (nodes). These results support greater use of non-invasive microbiome sampling to assess ecological patterns in animal systems.}, }
@article {pmid41853664, year = {2026}, author = {Donbraye, E and McLeod, L and Chai, Z and Lacoste, SR and McCarthy, EL and Links, MG and Waldner, CL}, title = {Comparison of short nasal swab and deep nasopharyngeal swab sampling methods to describe BRD-associated viruses and bacteria detected using a metagenomics approach optimized for virus recovery in fall-placed beef calves shortly after feedlot arrival.}, journal = {Veterinary and animal science}, volume = {32}, number = {}, pages = {100609}, pmid = {41853664}, issn = {2451-943X}, abstract = {Short nasal swabs (SNS) have potential advantages of lower costs, collection time and training of personnel than deep nasopharyngeal swabs (DNPS) for detecting bovine respiratory disease (BRD) pathogens. This study examined differences between DNPS and SNS in BRD-associated pathogens detected using a nanopore metagenomic sequencing protocol, optimized for respiratory RNA viruses, collected from 150 calves in six feedlot pens. Short nasal swabs yielded higher viral read counts and prevalence than DNPS for BCoV (mean reads 75 versus 17; OR = 21.4, P = 0.001) and IDV (mean reads: 560 versus 192; OR = 2.60, P = 0.02). Agreement varied among viruses: IDV (κ=0.57), BRSV (κ=0.43), and BCoV at both ≥1 read (κ=0.35) and ≥30 reads (κ=0.10). No BoHV-1 and BAdV3 were detected. Mannheimia haemolytica was detected (≥14 reads) more frequently in SNS than DNPS (mean reads: 169 versus 57; OR = 5.73, P = 0.001), as was Pasteurella multocida (≥ 1 read) (mean reads: 4.0 versus 1.2; OR = 2.02, P = 0.02). Mesomycoplasma dispar was less prevalent in SNS (mean reads: 5.2 versus 29; OR = 0.27, P = 0.001). Detection of Histophilus somni, Bibersteinia trehalosi, and Mycoplasmopsis bovis did not differ between swab types. Agreement for detection of M. haemolytica (≥14 reads) was moderate (κ = 0.46, P = 0.001). For all other bacteria examined in this analysis, kappa values were very low. Short nasal swabs were a sensitive and practical alternative for BRD pathogen surveillance providing evidence of which viruses and bacteria are circulating, potentially informing vaccination and disease management.}, }
@article {pmid41853712, year = {2026}, author = {Yao, J and Wang, F and Li, H and Zhang, R and Ji, G and Liu, D}, title = {Comparative analysis of microbial diversity and clinical outcomes in critically ill patients with and without malignancies: a single-center retrospective cohort study.}, journal = {Frontiers in microbiology}, volume = {17}, number = {}, pages = {1777861}, pmid = {41853712}, issn = {1664-302X}, abstract = {BACKGROUND: Sepsis and septic shock are severe complications for surgical malignancy patients. Conventional diagnostics often fail to capture the complex infectome in these populations. This study aimed to characterize the distinct microbial and resistome landscapes in cancer versus non-cancer patients using multi-site metagenomic next-generation sequencing (mNGS) to support specific antimicrobial strategies.<br><br>METHODS: We conducted a single-center retrospective cohort study at the General Surgery ICU of Xuanwu Hospital, including 107 septic shock patients (52 cancer; 55 non-cancer). mNGS was performed on blood, bile, ascitic fluid, and bronchoalveolar lavage samples to identify pathogens and antibiotic resistance genes (ARGs). Findings were analyzed for their association with ICU length of stay and mortality.<br><br>RESULTS: Cancer patients were significantly older (median 68 vs. 51&#x202f;years, p&#x202f;<&#x202f;0.0001) with higher comorbidity scores (CCI: 7.0 vs. 4.0, p&#x202f;=&#x202f;0.006). However, mNGS revealed a lower pathogen detection rate in cancer patients (53.85% vs. 85.45%, p&#x202f;=&#x202f;0.0006) and a lower incidence of bacteremia (25.0% vs. 45.45%, p&#x202f;=&#x202f;0.0426). Cancer patients had shorter ICU LOS (9 vs. 13&#x202f;days, p&#x202f;=&#x202f;0.0369) and antibiotic durations (7 vs. 11&#x202f;days, p&#x202f;=&#x202f;0.0368). Dominant pathogens included Klebsiella pneumoniae and Enterococcus faecium, harboring diverse ARGs across beta-lactam and aminoglycoside categories. Multivariate Cox regression identified IL-6 (p&#x202f;=&#x202f;0.018) was significant prognostic indicators for cancer patients. We also examined the distribution of virulence factors, despite their low detection rates.<br><br>CONCLUSION: Septic shock in cancer patients exhibits a unique resistome signature and distinct prognostic drivers. The identification of microbial targets via mNGS was associated with the implementation of targeted antimicrobial strategies and inflammation monitoring. These findings suggest that mNGS provides valuable molecular insights that may support clinical management and prognostic stratification for cancer patients in the surgical ICU.}, }
@article {pmid41853717, year = {2026}, author = {Matturro, B and Tucci, M and Firrincieli, A and Niccolini, L and Peña-Álvarez, V and Resitano, M and Trinchillo, M and Peláez, AI and Rossetti, S and Petruccioli, M and Viggi, CC and Aulenta, F}, title = {Multi-guild microbial cooperation sustains long-term