@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 & 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 & 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 & 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 & 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 & 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 {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.

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 × 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.

RESULTS: ASP supplementation reduced CH₄ yield by 54% (g CH₄/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 CH₄ 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 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 : 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.

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.

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 & 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.},
}

Animals
*Cytokinins/blood/metabolism
Humans
Mice
*Diet
*Gastrointestinal Microbiome
*Mammals/metabolism
Metabolomics
Metagenomics
Feces/chemistry
Swine
Bacteria/classification/genetics/metabolism/isolation & purification
*Microbiota

@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 & biotechnology},
volume = {42},
number = {7},
pages = {},
pmid = {42287489},
issn = {1573-0972},
mesh = {*Fungi/classification/genetics/isolation & purification ; *DNA Barcoding, Taxonomic ; *Biodiversity ; *Wetlands ; *Mycobiome ; Basidiomycota/genetics/classification ; Geologic Sediments/microbiology ; *Rhizophoraceae/microbiology ; Ecosystem ; Ascomycota/genetics/classification/isolation & 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.},
}

*Fungi/classification/genetics/isolation & purification
*DNA Barcoding, Taxonomic
*Biodiversity
*Wetlands
*Mycobiome
Basidiomycota/genetics/classification
Geologic Sediments/microbiology
*Rhizophoraceae/microbiology
Ecosystem
Ascomycota/genetics/classification/isolation & purification
Phylogeny

@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.

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.

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.

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&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.

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 < 0.05), whereas methanogens enrichment exhibited heterogeneity, with the dominant methanogen Methanobrevibacter exhibiting negative correlations with the other 11 methanogens (P < 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 < 0.05). Random forest model analysis screened 34 microbial genera as biomarkers for CH4 production.

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 & 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.

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).

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 < 0.01). Candida albicans (p = 0.032) and Abiotrophia defectiva (p=0.011) were enriched in AE, whereas Haemophilus parainfluenzae (p = 0.038) and Prevotella pallens (p = 0.022) were more abundant in Stable. Correlation analyses showed that Candida albicans was positively associated with exacerbation frequency (p < 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.

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.},
}

Humans
*High-Throughput Nucleotide Sequencing
*Lung Diseases, Interstitial/microbiology/diagnosis
Female
*Metagenomics/methods
*Microbiota/genetics
Retrospective Studies
Male
Bacteria/classification/genetics/isolation & purification
Aged
Phenotype
Middle Aged
Sensitivity and Specificity
Metagenome

@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 & 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.

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.

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.

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.},
}

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 & purification
Adult
Antifungal Agents/therapeutic use

@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.

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.

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%, χ[2]=0.045, P = 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.

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.},
}

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

@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.

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 δ 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.

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.},
}

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

@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.

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.

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.

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.

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.

METHODS: Metagenomic profiling, molecular diagnostics, phylogenetic analyses, and multilocus genotyping were used to investigate microbial communities associated with symptomatic cassava plants.

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.

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.

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).

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.

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.},
}

Humans
*Gastrointestinal Microbiome/physiology
Multiomics
Animals
*Homeostasis
*Circadian Rhythm
*Bone and Bones/metabolism/physiology
Bone Remodeling
Metabolomics
Fatty Acids, Volatile/metabolism
Osteogenesis

@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.

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) ≥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.

RESULTS: This is a study protocol; no results are available.

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.

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.

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 < 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 = 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.

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.

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.

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 β-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.

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.

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.

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.

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.

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.

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.

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 × 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 £120-£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.

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.},
}

*DNA, Fungal/chemistry/genetics
Genome, Fungal
*Fungi/genetics
Nucleic Acid Conformation
*Sequence Analysis, DNA/methods

@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.},
}

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

@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.},
}

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

@article {pmid42295988,
year = {2026},
author = {Soge, OO and Fifer, H and Alexander, S and Buss, SN},
title = {Diagnostics and novel laboratory approaches to combat Neisseria gonorrhoeae antimicrobial resistance.},
journal = {Expert review of molecular diagnostics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14737159.2026.2689689},
pmid = {42295988},
issn = {1744-8352},
abstract = {INTRODUCTION: Neisseria gonorrhoeae (gonococcus, GC) has developed resistance to all antimicrobials recommended for gonorrhea treatment, owing to its genetic plasticity and capacity to acquire antimicrobial resistance (AMR). This review examines the crucial role of diagnostics and novel laboratory approaches in mitigating the spread of GC-AMR and in preserving the long-term effectiveness of current and future antimicrobials for gonorrhea.

AREAS COVERED: Recent advances in diagnostics and novel laboratory approaches for detection of GC-AMR, enhancing GC-AMR surveillance and clinical management of gonorrhea.

EXPERT OPINION: The rapid emergence and global dissemination of multidrug-resistant GC including ceftriaxone-resistant strains poses a grave challenge to current gonorrhea control and prevention strategies. The implementation of rapid diagnostics and novel laboratory approaches can, when used appropriately, support the rapid detection of GC-AMR, ensure timely treatment, reduce transmission, and preserve last-line antibiotics by enabling resistance-guided therapy. These diagnostics and novel laboratory approaches are also crucial for the early detection of emerging resistance to antimicrobials recently approved by the FDA, and other antimicrobials currently under development and anticipated for future clinical use. Integrating culture-based GC-AMR surveillance with rapid molecular assays targeting genetic determinants of AMR offers a comprehensive approach for robust monitoring and timely response to the ever-evolving GC-AMR.},
}

@article {pmid42296170,
year = {2026},
author = {Diale-Makhongela, MO and Mpai, T and Bopape, FL and Mtsweni, P and Salawu-Rotimi, A and Shargie, NG and Gerrano, AS and Morey, L and Kubheka, B and Hassen, AI},
title = {16S rRNA-based metagenomics insights into the microbial diversity and functional attributes of soils from the rhizosphere of selected C4 crops of farms in Mpumalanga and Limpopo provinces, South Africa.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0347776},
doi = {10.1371/journal.pone.0347776},
pmid = {42296170},
issn = {1932-6203},
mesh = {*Rhizosphere ; *RNA, Ribosomal, 16S/genetics ; South Africa ; *Soil Microbiology ; *Metagenomics/methods ; *Crops, Agricultural/microbiology ; Pennisetum/microbiology/growth & development ; Sorghum/microbiology/growth & development ; Soil/chemistry ; Bacteria/genetics/classification ; Phylogeny ; Farms ; Biodiversity ; Carbon/metabolism ; },
abstract = {The rhizosphere serves as a hub for a variety of microorganisms that are highly beneficial to crop production and improvement of soil health. However, intensive farming practices including utilization of agrochemicals can cause a decline in microbial diversity that could severely compromise soil health and crop productivity. Here we investigated the taxonomic abundance and functional diversity of the microbial communities of sorghum and pearl millet rhizosphere soil samples from sixteen farms in Mpumalanga and Limpopo Provinces of South Africa. Soil samples were collected at the rhizosphere of sorghum and pearl millet crops and pooled into 34 samples. The soil samples were used for 16S rRNA amplicon sequencing analysis, soil physicochemical properties, and community-level physiological profiles. The results indicated that carbon utilization was highest in the majority of soil samples from Jane Furse, which also demonstrated greater microbial richness. The 16S rRNA amplicon sequencing analysis provides insight into the relative abundance of soil microbial communities, where at phylum level Planctomycetes, Proteobacteria, and Actinobacteria were the most predominant in all farms, but their relative abundances varied. Our results revealed that physicochemical properties could affect microbial abundance and diversity. The distance-based redundancy analysis (dbRDA) explained 46.8% of the variation in the soil bacterial community structure, with Mn, Fe, NO3[-]-N, and Ca identified as the key soil physicochemical variables shaping community composition. Thus, this study may contribute to advancing sustainable agricultural practices by providing baseline data that may inform future bioinoculant development.},
}

*Rhizosphere
*RNA, Ribosomal, 16S/genetics
South Africa
*Soil Microbiology
*Metagenomics/methods
*Crops, Agricultural/microbiology
Pennisetum/microbiology/growth & development
Sorghum/microbiology/growth & development
Soil/chemistry
Bacteria/genetics/classification
Phylogeny
Farms
Biodiversity
Carbon/metabolism

@article {pmid42296229,
year = {2026},
author = {Yu, Q and Liu, F and Xu, R and Jie, J and Tang, M and Li, D and Gu, Y and Song, L},
title = {Bronchoscopic Cytology and Metagenomic Sequencing to Differentiate Cancer Treatment-related and Infectious Lung Injury.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {231},
pages = {},
doi = {10.3791/70725},
pmid = {42296229},
issn = {1940-087X},
mesh = {Humans ; *Bronchoscopy/methods ; Bronchoalveolar Lavage Fluid/cytology/microbiology ; *Metagenomics/methods ; *Lung Injury/diagnosis/microbiology/etiology/pathology/genetics ; *High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Patients with cancer treatment-related lung injury (CTLI) frequently present with non-specific respiratory symptoms and radiological changes that closely mimic infectious pneumonia or tumor progression, presenting a significant challenge for a definitive diagnosis. Traditional diagnostic processes, mainly evaluated through blood biomarkers and standard microbial cultures, usually cannot make a clear diagnosis and take too much time. Here, we present a comprehensive protocol to diagnose CTLI by combining bronchoalveolar lavage fluid (BALF) cytological analysis with metagenomic next-generation sequencing (mNGS). The procedural workflow consists of three primary stages. First, standardized bronchoscopy is performed to obtain high-quality BALF samples. Second, conducting cytological analysis of the obtained BALF samples provides a snapshot of the lung microenvironment. This allows identification of inflammatory features and screening for malignant cells to exclude tumor progression. Finally, mNGS is utilized to identify or exclude active infectious etiologies. This advanced genomic technique achieves rapid, highly sensitive, and unbiased pathogen detection, successfully overcoming the limitations of traditional cultures. Representative results using this method demonstrate that this approach can effectively distinguish immune-related pneumonitis from active pulmonary infections or tumor progression. Compared with traditional diagnostic methods, this protocol has the advantage of quickly and accurately distinguishing CTLI from infectious etiologies and occult malignancies. Ultimately, this standardized workflow clarifies clinical diagnoses, guides critical treatment decisions, and improves patient outcomes.},
}

Humans
*Bronchoscopy/methods
Bronchoalveolar Lavage Fluid/cytology/microbiology
*Metagenomics/methods
*Lung Injury/diagnosis/microbiology/etiology/pathology/genetics
*High-Throughput Nucleotide Sequencing/methods

@article {pmid42296622,
year = {2026},
author = {Pravara, R and Praveen, R and Seema, B},
title = {Microbial allies in a cotton pest: A descriptive account of associated microbiota dynamics in Dysdercus cingulatus across development.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {60},
number = {},
pages = {101902},
doi = {10.1016/j.cbd.2026.101902},
pmid = {42296622},
issn = {1878-0407},
abstract = {BACKGROUND: Hemipteran insects harbour several symbiotic partners, mainly bacteria, which play pivotal roles for hosts like dietary provision, support overall physiology, xenobiotic degradation and manipulate/regulate behaviour. Most of these symbionts usually reside and operate from the digestive tracts of the animals. Cotton is one of the major cash crops in India and Dysdercus cingulatus (D. cingulatus) though a secondary pest, is causing significant destruction of cotton bolls, poor lint quality and reduce oil content of seeds. Premature opening of cotton bolls often leads to bacterial and fungal infections, thus resulting in extensive economic loss worldwide. D. cingulatus is a hemimetabolous insect that comprises of developmental stages like egg, nymph (5 instar stages), and adult. The present work explored the ontogeny specific diversity in the associated microbiota and predicted their probable functional inputs in D. cingulatus.

RESULTS: The data obtained using 16S rRNA gene sequencing (NovaSeq 6000) revealed presence of members of Proteobacteria (65.83%), Firmicutes (24%), Actinobacteria (10%) phyla throughout the ontogeny of D. cingulatus. Highest alpha diversity of these symbiotic bacteria was recorded in the third instar nymphs in contrast to rest of the developmental stages. Among all the observed genera, Stenotrophomonas, Hungatella and Glutamicibacter were predominant from egg to adult stages. MicFunPred, a tool used for predicting the probable functional inputs of these symbionts, hinted at their probable stage specific contribution in crucial biochemical pathways such as polyketide biosynthesis, ascorbate/aldarate metabolism, pentose phosphate and glyoxylate cycles, steroid hormone and peptidoglycan biosynthesis, and glycolysis/pyruvate metabolism.

CONCLUSIONS: The primary investigations on the ontogenetic composition and diversity of associated microbiota, suggest dynamic shifts in D. cingulatus, concurrent with their probable functions/roles in the host development and metabolism. To the best of our knowledge, this is the first report on symbiotic microbiota variation across the developmental stages of D. cingulatus that provides preliminary descriptive observations that may guide future functional and experimental investigations into microbiota-based pest management.},
}

@article {pmid42296787,
year = {2026},
author = {Lu, HB and Kong, LY and Chen, L and Chen, GJ},
title = {Janthinobacterium foliorum sp. nov., isolated from the decayed leaves of wild alpine rhododendron.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {4},
pages = {126736},
doi = {10.1016/j.syapm.2026.126736},
pmid = {42296787},
issn = {1618-0984},
abstract = {Janthinobacterium strains, which belong to the family Oxalobacteraceae, have attracted considerable attention due to their ability to synthesize violacein and degrade polyphenols. Wild alpine rhododendrons dominate the mountainous vegetation in southwestern China, and their leaf litter decomposition contributes to humification in alpine lakes. The Janthinobacterium strains may play a key role in the decomposition of these leaf litters. In 2025, metagenomic approaches combined with isolation and cultivation methods were applied to investigate microbial resources in stacked decayed leaves from these alpine lakes. The predominant phyla are Pseudomonadota and Actinomycetota with the relative abundances of 47.9% and 39.9%, respectively. The relative abundance of genus Janthinobacterium is only 0.1% in the community, but 11 Janthinobacterium strains were isolated. Based on the ANI and phylogenomic analyses, strains Du111 and Du118 should represent a novel species, for which the name Janthinobacterium foliorum sp. nov. is proposed. The ANI and AAI values between Janthinobacterium aestuarii and Janthinobacterium violaceum are 95.5% and 97.1%, respectively, implying that the recent proposed J. violaceum is the synonym of J. aestuarii. Comparative genomic analyses further reveal that not each of Janthinobacterium strains could produce violacein and prodigiosin, but most Janthinobacterium strains have the potential for participating in the decomposition of lignin and cellulose. This study clarifies the novel role of Janthinobacterium strains, showing that the isolated strains do not represent a novel taxonomic species but have adapted to the alpine microenvironment associated with Rhododendron leaf litter.},
}

@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},
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 Warmińsko-Mazurski w Olsztynie/ ; No. 12.610.002-110//Uniwersytet Warmińsko-Mazurski w Olsztynie/ ; No. 12.610.002-110//Uniwersytet Warmińsko-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 {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.},
}

*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

@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.

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.

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.

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 & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; P30AI161943//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01DA059394//U.S. Department of Health & 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 .},
}