@article {pmid41496864,
year = {2025},
author = {Shi, H and Zhang, X and Liu, L and Thompson, F and Li, X and Sun, H and Mi, H and Zhang, XH and Zhang, Y},
title = {Vertically stratified carbon fixation and coupling processes in deep-sea sediment.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf242},
pmid = {41496864},
issn = {2730-6151},
abstract = {Deep-sea sediments represent a vast yet underexplored reservoir of microbial carbon fixation, playing a critical role in global carbon cycling. However, the vertical distribution of carbon-fixing microorganisms, metabolic pathways, and the underlying energy sources and environmental drivers remain poorly understood. In this study, we investigated microbial carbon fixation and associated energy metabolism in South China Sea (SCS) sediment across 0-690 cm depth. Our findings revealed that dissolved inorganic carbon (DIC) and ammonium (NH4[+]) concentrations were key environmental drivers of carbon fixation and linked redox processes. Carbon fixation gene diversity increased with sediment depth, while the network complexity of functional genes and taxa involved in these processes declined. A distinct vertical succession of dominant microbial carbon-fixation pathways and their associated energy metabolisms was observed along the sediment depth: the Calvin-Benson-Bassham (CBB) and reductive glycine (rGLY) pathways dominated surface sediments, driven by nitrite oxidation, whereas the Wood-Ljungdahl (WL) pathway prevailed in deeper anoxic layers, supported by hydrogen and carbon monoxide oxidation. Taxonomically, Gammaproteobacteria and Methylomirabilia were abundant carbon-fixing groups in surface sediments, while Desulfobacterota, Chloroflexota, and Aerophobota became predominant at depth. Most carbon-fixing metagenome-assembled genomes (MAGs) exhibited mixotrophic lifestyles, and representative carbon fixation MAGs from Methylomirabilota, Dehalococcoidia (Chloroflexota) and Aerophobetes exhibited different metabolic features compared to their counterparts from other environments. These findings underscore the carbon fixation potential of deep-sea subsurface microbial communities and advance the understanding of carbon fluxes in deep biosphere.},
}

@article {pmid41496862,
year = {2025},
author = {Rojas-Vargas, J and Samperio-Ramos, G and Camacho-Ibar, VF and Pajares, S},
title = {Taxonomic and functional stability of sedimentary microbial communities in a pristine upwelling-influenced coastal lagoon.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf241},
pmid = {41496862},
issn = {2730-6151},
abstract = {Coastal lagoons are dynamic transitional ecosystems shaped by complex hydrodynamic and biogeochemical processes. Their sediments host diverse microbial communities essential for nutrient cycling, organic matter sequestration, and pollutant degradation. However, the taxonomic and functional profiles of these communities remain poorly understood, especially in pristine systems. Here, shotgun metagenomics was used to investigate microbial diversity and functional potential in a seagrass-dominated coastal lagoon on the Mexican Pacific coast, influenced by seasonal upwelling and with minimal anthropogenic impact. Despite pronounced physicochemical gradients and oceanographic variability, these sediments harbored a diverse and taxonomically conserved microbial community. 60% of genera and 38% of species (with relative abundance >0.1%) were consistently shared across sites and the two upwelling seasons, with Gammaproteobacteria, Deltaproteobacteria, Alphaproteobacteria, Flavobacteria, and Actinobacteria as dominant taxa. Genes associated with nitrogen and sulfur metabolic pathways were consistently detected, suggesting the presence of a conserved functional core supporting key biogeochemical processes. In contrast, genes related to antibiotic resistance and virulence factors exhibited more heterogeneous distributions. Among measured physicochemical variables, only nitrate and ferric iron significantly influenced microbial community structure and its functional repertoire, suggesting that additional factors likely contribute to the broader distribution of these communities. These findings reveal a high degree of taxonomic and functional stability of microbial communities in a minimally impacted lagoon, providing a valuable baseline for understanding microbial dynamics in coastal sediments primarily shaped by oceanographic processes.},
}

@article {pmid41496502,
year = {2026},
author = {Majzoub, ME and Santiago, FS and Raich, SS and Sirigeri, P and Simovic, I and Tedla, N and Kaakoush, NO},
title = {Immunoglobulin A protease from Sutterella wadsworthensis modifies outcome of infection with Campylobacter jejuni and is associated with microbiome diversity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611543},
doi = {10.1080/19490976.2025.2611543},
pmid = {41496502},
issn = {1949-0984},
mesh = {Humans ; *Immunoglobulin A/metabolism ; Animals ; Phylogeny ; *Campylobacter jejuni/physiology ; *Campylobacter Infections/microbiology/immunology ; *Gastrointestinal Microbiome ; Mice ; *Clostridiales/enzymology/genetics/classification ; Neutrophils/immunology/microbiology ; *Bacterial Proteins/genetics/metabolism ; China ; Phagocytosis ; Epithelial Cells/microbiology ; Serine Endopeptidases ; },
abstract = {Sutterella wadsworthensis is an enigmatic member of the microbiota, previously reported to be present in healthy humans yet also associated with certain gut diseases and their therapeutic outcomes. Here, we report on S. wadsworthensis classified to S. wadsworthensis_A that encodes an immunoglobulin A (IgA) protease that digests human IgA1 and IgA2 but not mouse IgA. The activity of this IgA protease could influence the trajectory of Campylobacter jejuni infection in human epithelial cells and phagocytosis in primary neutrophils. Comparative genomics and screening of metagenomic samples revealed that the protease shared sequence identity with an IgA protease from a bacterium that colonized other mammals and that S. wadsworthensis harboring IgA protease can be detected in individuals globally. Individuals positive for S. wadsworthensis IgA protease in China and Fiji (detection at >90% similarity) were found to have a different microbiome when compared to individuals where the protease was not detected. Phylogenetic analysis of pathogen IgA proteases along with IgA proteases from members of the microbiota suggested that there may be a unique subset of microbiota-derived IgA proteases. Our results highlight the importance of taxonomic resolution in microbiome studies and identify a subgroup of S. wadsworthensis that may be of potential clinical relevance.},
}

Humans
*Immunoglobulin A/metabolism
Animals
Phylogeny
*Campylobacter jejuni/physiology
*Campylobacter Infections/microbiology/immunology
*Gastrointestinal Microbiome
Mice
*Clostridiales/enzymology/genetics/classification
Neutrophils/immunology/microbiology
*Bacterial Proteins/genetics/metabolism
China
Phagocytosis
Epithelial Cells/microbiology
Serine Endopeptidases

@article {pmid41496335,
year = {2026},
author = {Li, G and Zhao, Z and Machitani, M and Ishikawa, R and Ishikawa, K and Yokota, N and Haba, R and Nakamura, K and Sun, Z and Kurahara, LH and Hirano, K},
title = {Elucidation of mechanisms underlying the therapeutic effects of cordycepin on pulmonary hypertension, with a focus on cell senescence and gut microbiota.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {194},
number = {},
pages = {118923},
doi = {10.1016/j.biopha.2025.118923},
pmid = {41496335},
issn = {1950-6007},
abstract = {INTRODUCTION: Pulmonary hypertension (PH) is a progressive cardiopulmonary disorder characterized by excessive pulmonary vascular remodeling and aberrant proliferation of pulmonary artery smooth muscle cells (PASMCs). Emerging evidence suggests that gut microbiota dysbiosis contributes to PH development. Cordycepin, a natural adenosine analogue derived from Cordyceps militaris, has demonstrated antiproliferative and microbiota-modulating properties; however, its mechanism of action in PH remains unclear.

OBJECTIVE: Elucidate the mechanisms underlying the therapeutic effects of cordycepin on PH, focusing on cellular senescence and gut microbiota.

METHODS: The effects of cordycepin on PH pathology were investigated by transcriptome analysis of PASMCs from patients, and metagenomic analysis of rodent PH models. Cellular senescence was analyzed in lung tissue from p16[Ink4a]-Cre[ERT2] reporter mice and in rat bone marrow-derived macrophages (BMDMs).

RESULTS: RNA sequencing analysis revealed activation of p53 signaling by cordycepin in PASMCs. Cordycepin suppressed CDK1 expression and TERT phosphorylation at threonine 249. It ameliorated vascular and cardiac remodeling in PH rat and mouse models. Cordycepin induced M1-like macrophage senescence in p16 [Ink4a] reporter mice lungs and rat BMDMs. Cordycepin significantly reshaped the gut microbiota, increasing beneficial genera (e.g. Alistipes and Acetatifactor) and reducing proinflammatory taxa (e.g., Ruminococcus), with modulating key metabolic pathways, including short-chain fatty acid, tryptophan, and vitamin K2 metabolism.

CONCLUSION: Cordycepin exerts multi-target therapeutic effects in PH by inhibiting PASMC proliferation via the p53-CDK1/pTERT axis, modulating gut microbiota-linked immunometabolism and induces proinflammatory macrophage senescence. These findings support cordycepin as a promising candidate for PH therapies targeting the vascular, immune, and gut-lung axes.},
}

@article {pmid41496236,
year = {2025},
author = {Huang, C and Huang, P and Zhang, Y and Bartlam, M and Wang, Y},
title = {Ecological filtering enhanced by smaller PBS biodegradable microplastics constrains ARG dynamics in the soil plastisphere.},
journal = {Environment international},
volume = {207},
number = {},
pages = {110030},
doi = {10.1016/j.envint.2025.110030},
pmid = {41496236},
issn = {1873-6750},
abstract = {Microplastics (MPs) are increasingly recognized as hotspots for antibiotic resistance genes (ARGs), yet the combined effects of polymer type and particle size on ARG dynamics in the soil plastisphere remain unclear. Here, we employed metagenomic assembly and binning to explore how MP polymer type and particle size jointly modulate ARG carrying frequencies (ACFs), mobility, and microbial hosts with polyethylene (PE), polystyrene (PS), and biodegradable polybutylene succinate (PBS) MPs across a size gradient (1000, 500, and 106 μm). PBS, PS, and PE plastispheres exhibited different size-related trends in ARG association, with PBS showing the strongest and most consistent decline in ACFs. Only PBS showed a corresponding reduction in ARG-MGE co-localization, suggesting size-dependent constraints on horizontal gene transfer. Distinct ARG combinations in ARG-Carrying Contigs (ACCs) also showed plastic-type selectivity, with complex resistance clusters absent in 106 μm PBS samples, potentially due to environmental constraints that limit the assembly or persistence of multigene resistance structures. Potential pathogens Enterobacter bugandensis and Stutzerimonas urumqiensis were markedly reduced in 106 μm PBS samples, a pattern not observed in PS or PE. Bacterial community analysis revealed that smaller PBS particles were associated with reduced richness, increased evenness, and more competitive interactions within co-occurrence networks. These features, together with the decline in ARG abundance and mobility, suggest that enhanced ecological filtering may occur in smaller biodegradable plastispheres, jointly limiting the persistence of resistance genes and their bacterial hosts. Together, our findings highlight the importance of considering both MP type and particle size in assessing plastisphere-associated ARG risks.},
}

@article {pmid41496069,
year = {2026},
author = {Zhao, Y and Wang, H and Lu, Y and Lou, D},
title = {Evolving landscapes in childhood asthma-gut microbiota research: A bibliometric analysis from 2000 to 2024.},
journal = {Medicine},
volume = {105},
number = {1},
pages = {e46594},
doi = {10.1097/MD.0000000000046594},
pmid = {41496069},
issn = {1536-5964},
support = {ZHGF2024-1//The Key Construction Discipline of Immunology and Pathogen biology in Zhuhai Campus of Zunyi Medical University/ ; NO. QKHRC-CXTDã€"2025〕046//The Program for High level Innovative Talents in the Guizhou Province/ ; },
mesh = {Humans ; *Asthma/microbiology/immunology ; *Bibliometrics ; *Gastrointestinal Microbiome ; Child ; Dysbiosis ; *Biomedical Research/trends ; },
abstract = {BACKGROUND: Pediatric asthma, a chronic inflammatory airway disorder, is increasingly recognized for its association with gut microbiota dysbiosis, mediated through immune dysregulation and systemic inflammation. Recent advancements in multi-omics technologies and the "gut-lung axis" hypothesis have propelled this field into a research frontier. This bibliometric study delineates global research trends, collaborative networks, and emerging directions in pediatric asthma-gut microbiota research.

METHODS: Publications from the Web of Science Core Collection (2000-2024) were systematically retrieved using keywords related to asthma, children, and gut microbiota. Data from 635 articles (392 original studies, 243 reviews) were analyzed via CiteSpace and VOSviewer to map country/institutional contributions, author networks, citation metrics, and keyword clusters. Non-English publications, patents, and conference abstracts were excluded.

RESULTS: Global output demonstrated exponential growth, with 62% of articles published between 2018 to 2022. The United States led in productivity (180 articles, 28.35%) and citations (10,851), while Canada achieved the highest citation impact (121.12 citations/article). Key contributors included Prof Stuart E. Turvey (19 articles, 2463 citations) and Prof B. Brett Finlay (140.07 citations/article). The University of British Columbia dominated institutional contributions (28 articles, 149.11 citations/article). The Journal of Allergy and Clinical Immunology emerged as the top journal (33 articles, 126.48 citations/article). Seminal works highlighted early-life gut dysbiosis (e.g., reduced Lachnospira and Faecalibacterium) and cesarean delivery's role in asthma risk. Keyword clustering revealed 6 themes: disease phenotypes (asthma-allergy comorbidity), microbiota dynamics (dysbiosis, short-chain fatty acids [SCFAs]), immune mechanisms (T helper 17 cells/Treg imbalance, gut-lung axis), developmental exposures (antibiotics, breastfeeding), methodologies (metagenomics), and therapeutic strategies.

CONCLUSION: This study underscores a paradigm shift from descriptive microbial profiling to mechanistic exploration of microbiota-derived metabolites (e.g., SCFAs) and early-life interventions. Future priorities include elucidating causal pathways via longitudinal cohorts, developing microbiota-targeted therapies, and leveraging multi-omics integration. Despite limitations in database scope, this analysis highlights accelerating translation from basic research to clinical applications through global collaboration. Researchers should prioritize interdisciplinary studies to unravel the "microbiome-immune-development" triad and optimize personalized asthma management.},
}

Humans
*Asthma/microbiology/immunology
*Bibliometrics
*Gastrointestinal Microbiome
Child
Dysbiosis
*Biomedical Research/trends

@article {pmid41495893,
year = {2026},
author = {Bouras, G and Grigson, SR and Mirdita, M and Heinzinger, M and Papudeshi, B and Mallawaarachchi, V and Green, R and Kim, RS and Mihalia, V and Psaltis, AJ and Wormald, PJ and Vreugde, S and Steinegger, M and Edwards, RA},
title = {Protein structure-informed bacteriophage genome annotation with Phold.},
journal = {Nucleic acids research},
volume = {54},
number = {1},
pages = {},
doi = {10.1093/nar/gkaf1448},
pmid = {41495893},
issn = {1362-4962},
mesh = {*Genome, Viral ; *Molecular Sequence Annotation/methods ; *Bacteriophages/genetics ; *Viral Proteins/chemistry/genetics ; *Software ; Protein Conformation ; },
abstract = {Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here, we introduce Phold, an annotation framework utilizing protein structural information that combines the ProstT5 protein language model and structural alignment tool Foldseek. Phold assigns annotations using a database of over 1.36 million predicted phage protein structures with high-quality functional labels. Benchmarking reveals that Phold outperforms existing sequence-based homology approaches in functional annotation sensitivity whilst maintaining speed, consistency, and scalability. Applying Phold to diverse cultured and metagenomic phage genomes shows it consistently annotates over 50% of genes on an average phage and 40% on an average archaeal virus. Comparisons of phage protein structures to other protein structures across the tree of life reveal that phage proteins commonly have structural homology to proteins shared across the tree of life, particularly those that have nucleic acid metabolism and enzymatic functions. Phold is available as free and open-source software at https://github.com/gbouras13/phold.},
}

*Genome, Viral
*Molecular Sequence Annotation/methods
*Bacteriophages/genetics
*Viral Proteins/chemistry/genetics
*Software
Protein Conformation

@article {pmid41495863,
year = {2026},
author = {Ali, H and Rafiq, M and Manzoor, M and Gillani, SW and Degen, A and Iqbal, A and Wang, W and Rafiq, MK and Shang, Z},
title = {Seasonal shifts in vegetation, soil properties, and microbial communities in Western Himalayan forests.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00842-y},
pmid = {41495863},
issn = {2524-6372},
support = {31961143012//Natural Science Foundation of China/ ; ANSO-SBA-2023-02//Science-based Advisory Program of The Alliance of National and International Science Organizations for the Belt and Road Regions/ ; },
abstract = {BACKGROUND: The western Himalayan forest ecosystem faces escalating pressures from climate change and anthropogenic activities, demanding improved conservation strategies. Effective management requires understanding the seasonal fluctuations in vegetation, soil properties and microbial communities, but they remain poorly characterized across high altitude forests. We assessed these variables in 10 forest sites during the winter of 2023 and summer of 2024, analysing vegetation diversity, soil parameters, and microbial metagenomics.

RESULTS: We found pronounced seasonal shifts in plant and microbial diversities, and in soil properties. Plant species richness, and Shannon and Simpson diversity indices were higher (p < 0.001) in summer than in winter while the community maturity index was higher (p < 0.02) in winter than in summer. Soil properties exhibited clear seasonal patterns: pH, available phosphorus (AP), microbial biomass carbon (MBC) and cation exchange capacity (CEC) were higher (p < 0.05) in summer, whereas soil moisture (SM) and soil organic carbon (SOC) were higher (p < 0.05) in winter. Microbial alpha diversity indices (Shannon, Chao, and Sobs) were elevated (p < 0.05) in summer, while the Simpson index was elevated in winter, indicating a shift in community dominance. Beta diversity analyses revealed a significant seasonal shift in overall metabolic potential (KEGG orthologs; ANOSIM R = 0.222, p = 0.016), but not in general protein functions (COG), carbohydrate-active enzymes (CAZy), or taxonomic composition (RefSeq). Therefore, despite taxonomic turnover, core metabolic functions were maintained, indicating strong functional redundancy. Structural equation models (SEM) confirmed distinct seasonal dynamics, revealing stronger plant-soil-microbe interactions and a greater proportion of variance explained by the model in summer (R[2]=0.64-0.72 for key paths) than in winter (R[2]=0.52-0.63).

CONCLUSIONS: The findings demonstrate that the western Himalayan ecosystem undergoes a fundamental seasonal reorganization. Summer is characterized by increased biodiversity, distinct soil conditions, and more dynamic microbial-ecosystem interactions, while winter exhibits greater community maturity and functional stability. The resilience of core ecosystem processes is underpinned by microbial functional redundancy, which ensures metabolic continuity despite taxonomic shifts. We recommend that forest management strategies account for these seasonal dynamics and focus on preserving the conditions that support this critical functional redundancy.},
}

@article {pmid41495321,
year = {2026},
author = {Sato, Y and Sato, Y and Deki, O and Tsuji, K and Tsurui-Sato, K},
title = {Estimated predator composition using environmental DNA analyses and color patterns of male guppies in introduced rivers.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-34186-x},
pmid = {41495321},
issn = {2045-2322},
support = {17K19298//Japan Society for the Promotion of Science/ ; 26249024//Japan Society for the Promotion of Science/ ; 19K12419//Japan Society for the Promotion of Science/ ; },
abstract = {Understanding the mechanisms underlying the successful invasion of the guppy, Poecilia reticulata, a globally invasive species, is important in the field of invasion biology. The body color pattern of male guppies is known to influence predation risk; however, the relationship between body color pattern and local predator guilds has been addressed in only a few studies. To investigate this relationship, we analyzed 32 water samples and 305 male guppies from eight introduced populations on the main island of Okinawa, Japan. The environmental DNA metabarcoding analysis of teleosts from the waters identified six potential guppy predator families, Anguillidae, Eleotridae, Gobiidae, Cichlidae, Mugilidae, and Cyprinidae; however, there was no detection of Characiformes, which are one of the major predators of guppies in their original habitat. Using imaging analysis of color spot areas of male guppies, we found that 16 of 18 potential predator × color combinations exhibited a statistically significant association between body color and the presence of predator families. For example, a negative association between orange spots and Anguillidae, and a positive association between blue-green spots and Cichlidae. These results suggest that the guppy in Okinawa was ecologically released from a major predator in its native habitat and adapted to the new environment through color pattern changes.},
}

@article {pmid41495312,
year = {2026},
author = {Kiran, R and Sharma, M and Subramanian, S and Patil, SA},
title = {Halophilic Anaerobic Cultures Enriched with CO2:H2 from Different Saline Environments Reveal Unknown Autotrophic Bacterial Diversity and Modular Carbon Fixation Pathways.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02654-6},
pmid = {41495312},
issn = {1432-184X},
abstract = {The subsurface sediments of saline-aquatic systems host diverse microbes, with unclear ecological roles and challenging lab cultivability. Chemolithotrophic anaerobes involved in CO2-fixation are one of the poorly studied groups. This study focused on understanding these bacteria from subsurface sediments of four representative saline environments, two marine (i.e., Coastal Arabian and Bay of Bengal seas) and two lake (Sambhar and Lonar) systems through enrichment and metagenomics. Enrichment cultures with bicarbonate/CO2 and hydrogen as the carbon and energy sources, respectively, showed CO2 fixation, producing acetic and formic acids as the major organic products. Enriched culture with Sambhar Lake sediment produced more formic acid (391 ± 8 mg/L) than acetic acid (92 ± 20 mg/L); however, other enriched cultures produced considerably higher acetic acid (up to 966 ± 24 mg/L) than formic acid (up to 367 ± 30 mg/L). The organics production was accompanied by unique thread-like (up to 500 μm long) aggregates, harbouring chains of rod and oval-shaped microbes in all cultures. Metagenome sequencing revealed dominance of Vibrio spp. (relative sequence abundance of 91% to 97%) across all cultures, while canonical CO2-fixing taxa were nearly absent (< 0.01%). KEGG analysis revealed partial genes for various CO2 fixation pathways, including Wood-Ljungdahl, reverse-TCA, dicarboxylate-hydroxybutyrate, hydroxypropionate bicycle, hydroxypropionate-hydroxybutyrate, and the reductive-glycine pathway. The presence of a near-complete serine variant of the reductive glycine pathway, which has been demonstrated in engineered systems, suggests that this pathway may play an operational role in natural systems. The consistent production of organic acids and incomplete pathway representation suggests modular CO2 fixation within the Vibrio-dominated enriched mixed cultures.},
}

@article {pmid41494802,
year = {2026},
author = {Mayorga, L and Noguera Segura, A and Campderros, L and Pons-Tarin, M and Soler, Z and Vega-Abellaneda, S and Serrano-Gomez, G and Herrera-deGuise, C and Robles-Alonso, V and Borruel, N and Manichanh, C},
title = {Distinct microbial mediators link diet to inflammation in Crohn's disease and ulcerative colitis.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337480},
pmid = {41494802},
issn = {1468-3288},
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) arises from complex interactions among diet, host and gut microbiome. Although diet influences intestinal inflammation, the microbial and metabolic pathways involved, and their differences between Crohn's disease (CD) and ulcerative colitis (UC), the two main subtypes of IBD remain unclear.

OBJECTIVE: To investigate how the gut microbiome mediates the effects of habitual diet on inflammatory activity in IBD.

DESIGN: This longitudinal study included 198 adults (100 healthy controls, 49 CD, 49 UC), participants completed a validated food frequency questionnaire. Dietary quality was evaluated using established indices (Alternative Mediterranean Diet, Healthy Eating Index-2015, Índice de Alimentación Saludable, Mean Adequacy Ratio, Plant-Based Dietary Indexes, Healthy Food Diversity). Participants also provided two stool samples (baseline and 6 months). Shotgun metagenomics (n=366) enabled taxonomic and functional profiling. Causal mediation analyses were used to identify microbial features mediating the effect of diet on inflammation.

RESULTS: IBD patients exhibited lower dietary diversity, fibre intake and nutritional adequacy compared with controls. Microbiome diversity was lowest in CD, intermediate in UC and correlated positively with higher intake of fibre, fruit, vegetables and nuts, and negative with processed foods and sugary beverages. Causal mediation analyses revealed that in CD, coffee, whole wheat bread and healthier diets lowered the Harvey-Bradshaw index through specific bacterial species and metabolites. In UC, Mediterranean-like diets, fruits and coffee reduced C reactive protein via greater microbial richness, reduced dysbiosis and short-chain fatty acid-related functions.

CONCLUSION: Diet quality influences inflammation in IBD through distinct microbiome pathways: specific taxa and metabolites mediate effects in CD, whereas microbial richness and global composition drive protection in UC.},
}

@article {pmid41494342,
year = {2026},
author = {Hu, P and Chen, S and Qian, Y and Hong, Y and Lin, JG and He, B and Gu, JD},
title = {Efficient nitrogen removal by coupling with methane metabolism in three landfill leachate wastewater treatment systems.},
journal = {Journal of hazardous materials},
volume = {502},
number = {},
pages = {141035},
doi = {10.1016/j.jhazmat.2026.141035},
pmid = {41494342},
issn = {1873-3336},
abstract = {High concentration of ammonium-nitrogen (NH4[+]-N) is a widley known characteristic of landfill leachate, and therefore, a thorough understanding of the active nitrogen-related microorganisms is essential for designing an efficient landfill leachate treatment system. Here, we analyze the microbial nitrogen cycling and metabolic interactions at three full-scale landfill leachate treatment plants. Specifically, using metagenomics and metatranscriptomics techniques, we elucidate the mechanisms underlying high NH4[+]-N removal rates achieved through distinct N removal strategies (nitrification-denitrification system at Jilong (JL), denitrification-ammonia oxidation-partial nitrification system at Xinfeng (XF), and simultaneous nitrification-denitrification-ammonia oxidation system at Wenshan (WS)), all three plants achieved efficient NH4[+]-N removal of 96 %, 97.96 % and 97.33 % for JL, XF, and WS, respectively. Highly active methane (CH4)-associated microorganisms, particularly CH4-catabolizing bacteria, exhibited strong interactions with denitrifying bacteria in all three treatment plants, promoting effective nitrogen removal in the landfill treatment systems. In addition, enhanced anammox activity in WS treatment plant in 2023 and 2015 was compared using nitrogen-15 isotope labeling and in situ transcriptome analysis. By comparing microbial metabolic activity, strong interactions were observed between anammox bacteria and other nitrogen-transforming microbes. Meanwhile, detailed physicochemical parameter analysis revealed that optimal Fe[3] [+] concentrations significantly promote the enrichment and enhanced activity of anammox bacteria. Collectively, this study highlights strategies for microbial-mediated high-efficiency ammonia nitrogen removal in full-scale landfill leachate and explains the underlying mechanisms that may lead to increased abundance and activity of anammox bacteria.},
}

@article {pmid41494287,
year = {2026},
author = {Feng, N and Fu, C and You, J and Wang, D and Feng, X and Su, Y},
title = {Controlled release of coated antioxidants inhibits Citrobacter rodentium colonization in the colon of rats by reducing gut redox potential.},
journal = {Redox biology},
volume = {89},
number = {},
pages = {104005},
doi = {10.1016/j.redox.2026.104005},
pmid = {41494287},
issn = {2213-2317},
abstract = {Intestinal redox potential serves as a critical parameter reflecting the dynamic characteristics of the gut microenvironment. To precisely modulate the intestinal redox potential and evaluate its inhibition of pathogenic colonization, this study built a controlled release system and further investigated its role in gut health under a lower redox potential. The results demonstrated that the controlled release formulation significantly reduced fecal redox potential more effectively than uncoated antioxidants. By optimizing the hydrodynamic size and zeta potential of ethoxyquin (EQ) and ferulic acid (FA), the coated FA formulation maintained high efficiency in reducing redox potential and reversed body weight loss induced by pathogenic infection. Both coated EQ (EQC) and FA (FAC) selectively enriched beneficial genera, such as Lactobacillus and Limosilactobacillus, while suppressing opportunistic pathogens like Klebsiella. Notably, coated FA demonstrated enhanced efficacy in alleviating Citrobacter rodentium (C. rodentium)-induced weight loss and reducing pathogens burden compared to uncoated FA. Mechanistically, coated FA promoted the enrichment of Lactobacillus reuteri (L. reuteri), suppressed the proliferation of Enterobacteriaceae, and enhanced intestinal Muc2 gene expression. Functional metagenomic analysis revealed that FAC significantly downregulated ABC transporter activity in Enterobacteriaceae, thereby impairing biofilm formation and synergizing with mucus secretion to inhibit pathogen colonization. Further in vitro co-culture trials confirmed that under a lower redox system, L. reuteri had a stronger inhibitory effect on C. rodentium as well as the expression of their virulence genes ((tir, ler). Collectively, these findings suggest that precise modulation of colonic redox potential through controlled release strategies represents a promising approach to enhance host defense against enteric pathogens via microbiota reprogramming.},
}

@article {pmid41494246,
year = {2026},
author = {Ding, J and Guo, T and Xia, H and Huang, K and Li, M and Li, F},
title = {Earthworm mediated microbial quorum sensing accelerates organic matter transformation during vermicomposting of dewatered sludge.},
journal = {Waste management (New York, N.Y.)},
volume = {212},
number = {},
pages = {115332},
doi = {10.1016/j.wasman.2026.115332},
pmid = {41494246},
issn = {1879-2456},
abstract = {Vermicomposting (VC) relies on the synergistic interaction between earthworms and microorganisms to drive the degradation of organic matter (OM). Quorum sensing (QS), which governs earthworm-microorganism interactions, may influence dissolved organic matter (DOM) transformation during VC. However, the presence of QS and the functional roles of signaling molecules during VC remain unclear. This study investigated earthworm mediated microbial QS in driving microbial community succession and accelerating DOM transformation during VC, by contrasting the process without earthworms. The results showed that VC exhibited a distinct decomposition pathway, achieving significantly faster DOM degradation and mineralization (P < 0.01), compared to the control. Additionally, earthworms markedly facilitated the transformation of protein-like compounds into humic-like substances over a shorter period. Their presence also modified acyl-homoserine lactone (AHL) synthesis patterns and suppressed AHLs hydrolysis, resulting in a 96.14 % increase (P < 0.01) in short-chain AHLs. Metagenomic analysis revealed that earthworm in VC significantly altered the bacterial diversity (P < 0.05), enriching modularity coefficient and deterministic processes by 18.75 % and 87.03 %, respectively. Finally, AHL-responsive microorganisms significantly influencing physicochemical and DOM transformation during the VC. This study suggests that earthworms enhance AHL-type QS regulation in microbial communities, improving their metabolic functions and accelerating DOM transformation.},
}

@article {pmid41493405,
year = {2025},
author = {Seidel, F and Nygren, TM and Opgen-Rhein, B and Hecht, T and Boehne, M and Weickmann, J and Anderheiden, F and Reineker, K and Böcker, D and Rentzsch, A and Wiegand, G and Fischer, M and Kiski, D and Frede, W and Ruf, B and Tarusinov, G and Papakostas, K and Logeswaran, T and Schiebel, A and Voges, I and Kaestner, M and Kramp, J and Kerst, G and Khedim, M and Gatzweiler, E and Wannenmacher, B and Knirsch, W and Meyer-Dobkowitz, L and Donner, B and Klingner, J and Rau, C and Haller, S and Brinkmann, A and Nitsche, A and Noldt, M and Schmoock, G and Herzmann, C and Degenhardt, U and Bühler, S and Enders, M and Hermes, J and Rolfs, N and Manuylova, T and Schwarzkopf, E and Beudt, J and Siffczyk, C and Schubert, S and Sandfort, M and Klingel, K},
title = {Severe Myocarditis Increase in Children Associated With Parvovirus B19 Infection: MYKKE Registry and German Surveillance Data.},
journal = {JACC. Heart failure},
volume = {},
number = {},
pages = {102854},
doi = {10.1016/j.jchf.2025.102854},
pmid = {41493405},
issn = {2213-1787},
abstract = {BACKGROUND: Following a surge in myocarditis in Germany since August 2023, many with parvovirus B19 (B19V) detection, concerns arose about causes and countermeasures.

OBJECTIVES: The authors aimed to verify the association among B19V, myocarditis increase, and severity.

METHODS: Data from the pediatric multicenter registry (MYKKE) from 27 centers were analyzed. B19V myocarditis cases were defined by polymerase chain reaction (PCR) positivity in blood or myocardium with clinical or histopathologic myocarditis evidence. Comprehensive clinical, histopathologic, and epidemiologic analyses were conducted. Past patients were hospitalized from 2013 to July 2023, current from August 2023 to November 2024. Registry data were compared with surveillance and consultant laboratory data. Specimens of current cases underwent metagenomic analysis and B19V sequencing.

RESULTS: Since 2013, 922 myocarditis patients including 126 (13.6%) with B19V myocarditis were enrolled. With 57 of 126 (45.2%) current cases, B19V myocarditis increased, compared with other myocarditis causes. Most current cases were patients who were <2 years of age (64.9%), 56.1% were female. The ratio of B19V myocarditis to incidence did not increase compared with the earlier period. Current cases presented with more reduced ejection fraction (29.0% vs 34.5%; P = 0.007), linked to severe cardiac T-cell infiltration and high numbers of B19V copies. Increased severity was associated with younger age. Phylogenetic analysis identified B19V genotype 1A, without sequence variants indicating increased virulence.

CONCLUSIONS: The increase in pediatric myocarditis since August 2023 was associated with B19V, more likely explained by disproportionately young current cases and young children's vulnerability than a virulent strain. Raising clinicians' awareness and proactive, interdisciplinary approaches are essential for improving prevention of B19V infection, management of myocarditis, and treatment strategies in this vulnerable cohort. (Myocarditis Registry for Children and Adolescents [MYKKE]; NCT02590341).},
}

@article {pmid41493389,
year = {2026},
author = {Buchheister, S and Bolsega, S and Rösel-Birk, S and Smoczek, A and Scheele, T and Bleich, A and Basic, M},
title = {Unraveling potential bacterial contamination in germ-free husbandry using bacterial viability staining.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag001},
pmid = {41493389},
issn = {1365-2672},
abstract = {AIMS: Hygienic monitoring (HM) of germ-free (GF) mouse colonies is exceptionally challenging. The test accuracy of the applied diagnostic methodology has to be outstanding to provide proof of absence of all living microorganisms confirming the GF status. In this context, microscopy of native intestinal content serves as a highly sensitive diagnostic tool for the detection of bacterial contaminants. However, with this method residual microorganisms may be detected. To overcome this risk of false-positive results, we complemented our analyses with a bacterial viability staining of the intestinal content of GF mice.

METHODS AND RESULTS: Intestinal contents of GF mice (n=13) from five isolators were analyzed by bacterial culture and phase-contrast microscopy. Additionally, 16S rRNA gene PCR analysis and metagenomic sequencing were performed. To distinguish between live and dead bacteria, intestinal content was stained by a Bacterial Viability Kit and analyzed by fluorescence microscopy.While culture medium proved sterility of a sample material, increased amounts of scattered bacterial structures were detected during microscopic analysis, indicating potential contamination. Molecular techniques pointed to a presence of environmental bacteria. However, viability staining revealed the presence of only dead (double-stained) bacteria in all samples. Likewise, non-viable bacteria have been identified in samples obtained from irradiated feed, probably being the source of bacterial structures found in GF mice.

CONCLUSIONS: Altogether, detected bacterial structures were proven to be non-viable and therefore should not be interpreted as isolator contaminants. Thus, in our hands, with the herein described report of suspected contamination we prove, that bacterial viability staining served as a highly valuable screening tool, enhancing diagnostic quality of the HM of GF colonies.},
}

@article {pmid41493379,
year = {2026},
author = {Forry, SP and Servetas, SL and Kralj, JG and Hunter, ME and Dootz, JN and Jackson, SA},
title = {A mathematical framework to correct for compositionality in microbiome data sets.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0112625},
doi = {10.1128/aem.01126-25},
pmid = {41493379},
issn = {1098-5336},
abstract = {The increasing use of metagenomic sequencing (MGS) for microbiome analysis has significantly advanced our understanding of microbial communities and their roles in various biological processes, including human health, environmental cycling, and disease. However, the inherent compositionality of MGS data, where the relative abundance of each taxon depends on the abundance of all other taxa, complicates the measurement of individual taxa and the interpretation of microbiome data. Here, we describe an experimental design that incorporates exogenous internal standards in routine MGS analyses to correct for compositional distortions. A mathematical framework was developed for using the observed internal standard relative abundance to calculate "Scaled Abundances" for native taxa that were (i) independent of sample composition and (ii) directly proportional to actual biological abundances. Through analysis of mock community and human gut microbiome samples, we demonstrate that Scaled Abundances outperformed traditional relative abundance measurements in both precision and accuracy and enabled reliable, quantitative comparisons of individual microbiome taxa across varied sample compositions and across a wide range of taxon abundances. By providing a pathway to accurate taxon quantification, this approach holds significant potential for advancing microbiome research, particularly in clinical and environmental health applications where precise microbial profiling is critical.IMPORTANCEMetagenomic sequencing (MGS) analysis has become central to modern characterizations of microbiome samples. However, the inherent compositionality of these analyses, where the relative abundance of each taxon depends on the abundance of all other taxa, often complicates interpretations of results. We present here an experimental design and corresponding mathematical framework that uses internal standards with routine MGS methods to correct for compositional distortions. We validate this approach for both amplicon and shotgun MGS analysis of mock communities and human gut microbiome (fecal) samples. By using internal standards to remove compositionality, we demonstrate significantly improved measurement accuracy and precision for quantification of taxon abundances. This approach is broadly applicable across a wide range of microbiome research applications.},
}

@article {pmid41493376,
year = {2026},
author = {Shklyar, AA and Mesentsev, YS and Smirnov, AV and Nassonova, ES},
title = {Nucleophaga amutiana, sp. nov.-a novel intranuclear parasite of amoebae from the Far East of Russia expands the diversity and biogeography of microsporidia-like organisms.},
journal = {Mycologia},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/00275514.2025.2586430},
pmid = {41493376},
issn = {1557-2536},
abstract = {The genus Nucleophaga comprises poorly studied intranuclear parasites that infect amoebae. Currently classified within the phylum Rozellomycota, this genus belongs among numerous lineages with unresolved taxonomic positions, primarily identified through metagenomic studies. Three species of Nucleophaga were described at the morphological and molecular levels-N. amoebae, N. terricolae, and N. striatae, all isolated in Europe. Here, we report the discovery of a fourth species of the genus, isolated from the Far East of Russia, infecting nuclei of Thecamoeba sp. A detailed light microscopic study revealed several remarkable morphological features of this organism. For the first time, the division of Nucleophaga plasmodium was illustrated. Experimental infections demonstrated that Thecamoeba quadrilineata and T. foliovenanda can support the development of the parasite, whereas Nucleophaga showed abnormal development in T. onigiri and was unable to survive in T. vumurta. Phylogenetic analysis, based on the nuc 18S rRNA gene sequences, placed the new isolate as a distinct lineage within the genus Nucleophaga. Based on its molecular characteristics, the studied isolate was described as a new species, Nucleophaga amutiana.},
}

@article {pmid41493186,
year = {2026},
author = {Queiroz, VF and Jivaji, AM and Aylward, FO},
title = {Tiny giants in a big ocean.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0299225},
doi = {10.1128/spectrum.02992-25},
pmid = {41493186},
issn = {2165-0497},
abstract = {Prasinoviruses infect some of the most abundant photosynthetic eukaryotes in the ocean, shaping microbial dynamics and playing a major role in nutrient cycling. Despite their ecological significance, they have only been explored in a few marine systems. In a recent study, A. B. de Silva, S. W. Polson, C. R. Schvarcz, G. F. Steward, and K. F. Edwards (Microbiol Spectr 13:e02583-24, 2025, https://doi.org/10.1128/spectrum.02583-24) describe four new prasinoviruses isolated from the tropical North Pacific. The comparative analyses highlighted the placement of these viruses within known prasinovirus lineages while also revealing novel genetic features. To assess their ecological reach, the authors mapped metagenomic reads from global data sets, demonstrating that these viruses are not confined to the Pacific but are globally distributed. These findings expand our understanding of prasinovirus diversity and evolution and highlight their widespread occurrence across oceanic regions.},
}

@article {pmid41492995,
year = {2026},
author = {Sathaye, SB and Sharma, N and Bhaumik, J and Sahoo, D and Rai, AK and Singh, SP},
title = {Novel Glutamate Decarboxylase from Ethnic Food Metagenome: A Potential Biocatalyst to Produce a Nonproteinaceous Amino Acid, γ-Aminobutyric Acid.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11421},
pmid = {41492995},
issn = {1520-5118},
abstract = {This study reports the biochemical characterization of a novel variant of glutamate decarboxylase (mtGAD), identified from an ethnic food, Kinema. The mtgad gene was cloned from the Kinema metagenome and expressed in a heterologous host, Escherichia coli. The enzyme mtGAD was extracted and purified for biochemical characterization. The enzyme showed optimal activity for γ-aminobutyric acid (GABA) synthesis at 50 °C and pH 4.5. The kinetic parameters of mtGAD were computed to be 29.2 mM Km, 561.8 s[-1] kcat, and 23.2 mM[-1] s[-1] kcat/Km. The in silico protein structure analysis, followed by molecular docking and molecular dynamics simulation, revealed that the binding with pyridoxal-5'-phosphate (PLP; a cofactor for mtGAD) reduces the fluctuations in the structure at high temperatures, contributing to the thermal stability of mtGAD. Furthermore, the conversion of about 60% monosodium glutamate (MSG) into GABA was achieved in approximately 3 h of catalytic reaction with 200 mM MSG, treated with 6.67 U mtGAD. A high turnover number with moderate thermal and pH stability makes mtGAD a potential biocatalyst for GABA production.},
}

@article {pmid41492410,
year = {2025},
author = {Wallau, GDL and Barbier, E and Machado, LC and da Silva, AF and Dias, YJM and Dezordi, FZ and Tomazatos, A and Horváth, B and Lins, RD and Bernard, E and Cadar, D},
title = {Ambecovirus, a novel Betacoronavirus subgenus circulating in neotropical bats, sheds new light on bat-borne coronaviruses evolution.},
journal = {Virus evolution},
volume = {11},
number = {1},
pages = {veaf094},
pmid = {41492410},
issn = {2057-1577},
abstract = {Understanding the viral diversity harboured by wildlife is essential for effective mapping and prevention of future zoonotic outbreaks. Bats, in particular, are recognized as natural reservoirs for several high-impact zoonotic viral pathogens, including coronaviruses responsible for Severe Acute Respiratory Syndrome (SARS), the rabies virus, diverse paramyxoviruses, Marburg, Ebola, Nipah, and Hendra viruses. However, a large extent of bat viruses remains unexplored, especially in highly biodiverse regions of the Neotropics such as Brazilian ecosystems. We used a meta-transcriptomic approach to characterize new virus genomes found in blood, oral, and anal samples collected from cave- and noncave bats from Northeast Brazil, Caatinga, and Atlantic Forest biomes. From a total of 19 coronavirus-positive bats, we have assembled two complete genomes of a new Betacoronavirus subgenus, named Ambecovirus (American betacoronavirus). The subgenus herein described is phylogenetically placed between the Sarbeco-/Hibeco-/Nobecovirus and the Merbeco-/Embecovirus clades, being basal to the former. While the conserved S2 region of the spike protein retained hallmark domains, including HR1 and HR2, the S1/S2 cleavage site and the furin cleavage site, the S1 region consistently displayed only the N-terminal domain. The receptor-binding domain from the C-terminal domai (CTD) region could not be identified due to high dissimilarity relative to known congeners. The detection of Ambercovirus in sympatric Pteronotus gymnonotus and Carollia perspicillata bats suggests potential interspecies transmission. Longitudinal sampling confirmed persistent Ambecovirus infection in P. gymnonotus over multiple years and virus dispersion at a minimum distance of 270 km between caves. The present study confirms that viral diversity in neotropical hosts remains largely unknown, not just in Brazil but likely in the other countries of the region, supporting the need for a systematic approach to virome exploration and analysis followed by in vitro experimentation to assess zoonotic potential.},
}

@article {pmid41492364,
year = {2025},
author = {Solly, EF and Jaeger, ACH and Barthel, M and Six, J and Mueller, RC and Hartmann, M},
title = {Soil water limitation intensity alters nitrogen cycling at the plant-soil interface in Scots pine mesocosms.},
journal = {Plant and soil},
volume = {516},
number = {1},
pages = {705-723},
pmid = {41492364},
issn = {0032-079X},
abstract = {BACKGROUND AND AIM: More intense episodes of drought are expected to affect terrestrial nitrogen (N) cycling by altering N transformation rates, the functioning of soil microorganisms, and plant N uptake. However, there is limited empirical evidence of how progressive water loss affects N cycling at the plant-soil interface.

METHODS: We adopted [15]N tracing techniques and metagenomic analyzes of microbial genes involved in N cycling to assess how different levels of soil water availability influenced the fate of N derived from decomposing litter in mesocosms with Scots pine saplings.

RESULTS: With increasing water limitation, the release of N from decomposing litter into the soil declined rapidly. However, moderate levels of water limitation barely affected the microbial metagenome associated with N cycling and the uptake of N by the saplings. Comparatively, severe levels of water limitation impaired plant N uptake, and increased the prevalence of microbial N-cycling genes potentially involved in mechanisms that protect against water stress. Genes associated with the uptake and release of N during mineralization and nitrification declined under low soil water contents.

CONCLUSIONS: When soil water becomes largely unavailable, the cycling of N at the plant-soil interface is slowed down, and microbial and plant tolerance mechanisms may prevail over N uptake and microbial decomposition.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-025-07758-z.},
}

@article {pmid41492358,
year = {2026},
author = {Pan, D and Jiang, M and Wang, Y and He, J and Tang, J and Liu, S and Li, M and Jiang, X and Xu, Q},
title = {Multi-omics reveals associations between the microbiota-gut-brain axis and antidepressant effects of vagus nerve stimulation.},
journal = {Neurobiology of stress},
volume = {40},
number = {},
pages = {100777},
pmid = {41492358},
issn = {2352-2895},
abstract = {BACKGROUND: Major depressive disorder is a severe mental health condition characterized by persistent depressed mood and loss of interest. Current first-line pharmacotherapies often exhibit limited therapeutic performance and adverse side effects. Transcutaneous auricular vagus nerve stimulation (taVNS) is a promising, safe, and noninvasive alternative intervention with demonstrated neuromodulatory efficacy. Nevertheless, its mechanisms remain unclear. This study investigated whether the antidepressant properties of taVNS are associated with the microbiota-gut-brain axis, focusing on the potential crosstalk between differentially expressed hippocampal proteins and the gut microbiota.

METHODS: A chronic unpredictable mild stress (CUMS) rat model of depression was established, and taVNS was administered for 14 days. Hippocampal proteomic profiling was performed using data-independent acquisition. Fecal metagenomic sequencing was conducted to characterize alterations in gut microbial communities. Key signaling pathways were validated using Western blot, qRT-PCR, HE staining, and transmission electron microscopy, all of which were employed to systematically assess behavioral, proteomic, microbial, and molecular changes.

RESULTS: Proteomics and molecular analyses revealed that taVNS upregulated hippocampal expression of glutamate ionotropic receptor N-methyl-D-aspartate type subunit 1 (GluN1) and brain-derived neurotrophic factor (BDNF), while simultaneously restoring mitogen-activated protein kinase (MAPK) signaling activity. Metagenomic profiling demonstrated that taVNS increased the abundance of Akkermansia muciniphila and reduced Ligilactobacillus reuteri. Ligilactobacillus levels were positively correlated with synaptogyrin-1 (Syngr1), indicating their potential association in enhancing the antidepressant effects mediated by the GluN1/MAPK/BDNF signaling cascade.

CONCLUSION: TaVNS significantly alleviated depression-like behaviors in CUMS-exposed rats. The underlying mechanism may involve the restoration of synaptic function of glutamatergic neurons by regulating the GluN1/MAPK/BDNF signaling pathway. In addition, taVNS reshaped the gut microbiota, markedly increasing the abundance of Akkermansia muciniphila and Ligilactobacillus murinus while reducing Limosilactobacillus reuteri and Lactobacillus johnsonii. The positive correlation between Syngr1 protein level and Ligilactobacillus abundance in the hippocampus suggests that the microbiota-gut-brain axis may play a key role in the antidepressant effects of taVNS.},
}

@article {pmid41492297,
year = {2025},
author = {Cordeiro, NF and Coppola, N and Ferreira, F and Vignoli, R and Bado, I},
title = {What are we eating?. Detection of antibiotic resistance mechanisms in frozen chicken nuggets imported from Brazil.},
journal = {One health (Amsterdam, Netherlands)},
volume = {21},
number = {},
pages = {101171},
pmid = {41492297},
issn = {2352-7714},
abstract = {The rise of antibiotic resistance is a growing challenge, affecting humans, the environment, and animals. Under the One Health framework, this study investigated resistance mechanisms to critically important antibiotics in frozen chicken nuggets imported from Brazil. Eighty nugget samples were cultured on selective media containing ceftriaxone, ciprofloxacin, or colistin. Isolates were identified using MALDI-TOF, and antibiotic susceptibility was assessed by disk diffusion. Eight samples were also analyzed using shotgun metagenomic sequencing processed through the SqueezeMeta pipeline. Nineteen Enterobacterales resistant mainly to β-lactams and to a lesser extent, to quinolones and aminoglycosides, were identified. Eight Pseudomonas spp. were recovered, including one P. fulva resistant to colistin. Metagenomics revealed predominant Firmicutes, (Bacillaceae, Lactobacillaceae, and Paenibacillaceae) with low γ-Proteobacteria levels. Additionally, we detected resistance genes against several antibiotics. This study highlights the role of imported food in spreading AMR and the value of combining metagenomics with conventional microbiology to strengthen One Health surveillance.},
}

@article {pmid41491791,
year = {2026},
author = {Seo, J and Araneta, RP and Lee, JH and Montecillo, JA and Yoo, HJ and Lee, YY and Park, CM and Cho, A and Lee, H and Yoon, HY and Kim, MJ and Kim, JM and Lee, YH and Lee, NY and Park, NJ and Han, HS and Seo, I and Chong, GO},
title = {Standardizing vaginal microbial profiling: evaluating swab materials, storage conditions, and host DNA depletion strategies.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {2},
pmid = {41491791},
issn = {1471-2180},
support = {RS-2023-KH135444//Ministry of Health and Welfare/ ; },
abstract = {BACKGROUND: Studies on understanding female health from a microbial perspective have proliferated in recent years; however, validated protocols for swab materials, storage conditions, and host DNA depletion remain limited for vaginal microbiome studies. This study investigates these critical aspects to enhance microbial profiling accuracy.

RESULTS: Three swab materials were evaluated, with minimal variations in bacterial composition observed across different swab materials. The DNA yield and host DNA contamination remained comparable. Mock samples, used to assess the effects of storage conditions (without freezing, -20 °C, and -80 °C), revealed no significant impact on microbial composition. Additionally, the NEBNext® Microbiome DNA Enrichment Kit demonstrated effective performance in host DNA removal and bacterial community recovery, even with reduced reagent volumes.

CONCLUSIONS: These findings underscore the importance of optimizing swab selection and host DNA depletion strategies to enhance microbiome profiling in clinical samples.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04523-1.},
}

@article {pmid41491699,
year = {2026},
author = {Wang, R and Zhang, W and He, Z and Zhou, Y and Chen, C and Song, K and Shang, Q and Wu, Y and Gu, P and Shu, D and Zhao, L},
title = {Core microbiota recruited by healthy grapevines enhance resistance against root rot disease.},
journal = {Genome biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13059-025-03905-y},
pmid = {41491699},
issn = {1474-760X},
support = {2023BCF01026//Key Research and Development Program of Ningxia/ ; 2025NC-YBXM-068//Key Research and Development Projects of Shaanxi Province/ ; 32372501//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Root rot disease caused by fungal pathogens of wine grapevines poses a serious threat to their growth and results in a substantial economic impact on grape industry. The rhizosphere microbiome recruited to plants is critical for mitigating soil-borne pathogens. However, how beneficial microbes influence disease resistance remains unclear.

RESULTS: We investigate the composition and gene functions of microorganisms in wine grapevines with root rot disease and healthy controls by amplicon and metagenomic sequencing. We use culturomics and in vivo experiments to verify the pathogen and beneficial strains to improve plant health. We find that root rot disease in grapevines significantly affects rhizosphere microbiome diversity and composition. The microbial interkingdom network indicates that the disease destabilizes the bacteria-fungi co-occurrence network. We find that plants recruit the potentially beneficial bacteria Pseudomonas, Bacillus and Streptomyces in healthy rhizosphere soil. By culturomics, we confirm that Fusarium solani is the main pathogen causing root rot disease. We further observe that these three key beneficial bacteria from the co-occurrence networks enhance the resistance of grapevines to pathogens. Furthermore, metagenomic analysis reveals that beneficial bacterial strains suppress pathogens by enriching potential functional genes in pathways involved in disease resistance.

CONCLUSIONS: Our findings highlight the critical role of disease resistance pathways of potentially beneficial microorganisms in fighting disease and supporting plant health, offering new insight for the exploration of beneficial microbial resources and providing a basis for the development of biological control of grape root rot disease.},
}

@article {pmid41491676,
year = {2026},
author = {Long, Y and Guo, J and Dai, L and Jiang, J},
title = {Interactions between phytoplankton and bacterioplankton communities in Caohai plateau lake, revealed by environmental DNA metagenomics.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {4},
pmid = {41491676},
issn = {1471-2180},
support = {QKHJC-ZK[2023]YB233//Guizhou Provincial Science and Technology Projects, China/ ; 32360036//National Natural science Foundation of china/ ; QSS2024001//Talent Team Proiect of Guizhou lnstitute of Biology,china/ ; QKHPT[2025]015//Guizhou Provincial science and Technology Projects, China/ ; },
mesh = {*Phytoplankton/genetics/classification/physiology ; *Lakes/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; China ; *DNA, Environmental/genetics ; *Plankton/genetics/classification ; Ecosystem ; *Microbial Interactions ; },
abstract = {Phytoplankton-bacterioplankton interactions critically influence aquatic ecosystem stability, yet their dynamics remain poorly understood in eutrophic plateau lakes. This study employed environmental DNA (eDNA) metagenomics to investigate these cross-kingdom relationships in Caohai Plateau Lake, a vulnerable wetland undergoing macrophyte-to-algae regime shifts, integrating correlation analysis, niche overlap, redundancy analysis (RDA), co-occurrence networks, and neutral community model (NCM). A total of 331 phytoplankton species across 10 phyla were characterized in the phytoplankton community, dominated by Cyanophyta with Microcystis as the representative genus, while bacterioplankton communities were primarily structured by Proteobacteria and Sphingomonas. The assembly of phytoplankton community was primarily driven by stochastic processes (R[2]>0.90). Co-occurrence network analysis showed phytoplankton interactions were dominated by positive effects (84.25%), whereas bacterioplankton networks exhibited balanced positive and negative effects. Metabolic specialization emerged through LEfSe analysis: phytoplankton specialized in photosynthesis and carbon storage, while bacterioplankton dominated anaerobic respiration (propanoate metabolism). The positive interactions were more prevalent than negative ones; combined with the metabolic complementarity of phytoplankton and bacterioplankton, this suggests that mutualism is more dominant than competition in cross-kingdom interactions. High niche overlap under sufficient nutrients (TP) facilitated species coexistence of phytoplankton and bacterioplankton by minimizing resource competition, thereby promoting stochastic community assembly, while keystone taxa (Cyanothece, Sphingobium) mediated ecosystem stability. This work demonstrates that nutrient enrichment promote stochastic assembly in eutrophic plateau lakes.},
}

*Phytoplankton/genetics/classification/physiology
*Lakes/microbiology
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
China
*DNA, Environmental/genetics
*Plankton/genetics/classification
Ecosystem
*Microbial Interactions

@article {pmid41491168,
year = {2026},
author = {Zhao, Y and Dai, L and Wang, L and Wang, L},
title = {Case report: a case of neonatal Candida osteomyelitis with septic arthritis and literature review.},
journal = {BMC pediatrics},
volume = {26},
number = {1},
pages = {9},
pmid = {41491168},
issn = {1471-2431},
abstract = {A preterm infant who previously experienced Candida septicemia at 18 days of life and was treated with standard antifungal therapy presented one month later with signs of multifocal osteomyelitis and arthritis. Causative Candida albicans was detected by metagenomic next-generation sequencing (mNGS). Since the symptoms of neonatal candidal osteomyelitis are typically insidious, early diagnosis and appropriate treatment are crucial. Moreover, incision and drainage of the affected joint are essential for a favorable prognosis.},
}

@article {pmid41491581,
year = {2026},
author = {Chen, T and Yu, S and Li, K and Huang, K and Shi, W and Chen, H and Hong, Q and Zhang, Y and Wang, J and Yu, Z and Wang, J},
title = {Rumen microbiota inoculation indicates collaborative mechanisms enhancing propionate supply to alleviate weaning stress in lambs.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02283-8},
pmid = {41491581},
issn = {2049-2618},
support = {2023YFD1300901//the Ministry of Science and Technology of the People's Republic of China/ ; D21C170001//the Natural Science Foundation of Zhejiang Province/ ; 31622056//the National Natural Science Foundation of China/ ; 226-2025-00026//Fundamental Research Funds for the Central Universities/ ; },
abstract = {BACKGROUND: The transition from milk to solid feed during weaning often imposes metabolic stress on young ruminants due to energy deficits. Previous studies suggest that ruminal microbiota transplantation from adults to juveniles can alleviate weaning stress, but the underlying mechanisms remain poorly defined.

RESULTS: In this study, 48 Hu lambs were randomly assigned to two groups (n = 24 each): an inoculated group (Inoc) that received lyophilized ruminal microbiota and a control group (Ctrl) that received no inoculation. We evaluated rumen fermentation characteristics, blood metabolites, hepatic glycogen levels, expression of hepatic gluconeogenic genes, and shifts in the rumen microbiome at three key time points-the end of weaning, 1 and 2 weeks post-weaning. Oral inoculation significantly elevated rumen propionate concentration, upregulated the gene expression of hepatic pyruvate carboxylase (EC 6.4.1.1) and glucose-6-phosphatase (EC 3.1.3.9), and increased hepatic glucose production. Microbiome analysis revealed increased colonization by lactic acid-producing bacteria (e.g., Olsenella and Sharpea) and propionate producers, such as Megasphaera elsdenii, alongside enriched families associated with propionate production, including Prevotellaceae, Succinivibrionaceae, and Erysipelotrichaceae. Genome-resolved metagenomics further demonstrated an increased abundance of metagenome-assembled genomes (MAGs) carrying polysaccharide utilization loci (PULs) and genes involved in lactate-to-propionate conversion. Notably, the inoculation promoted co-occurrence of functionally complementary MAGs-such as s_Megasphaera elsdenii (MAG98), s_Bilifractor sp902797025 (MAG125), s_Prevotella sp002391185 (MAG342), and s_Prevotella sp900540375 (MAG298)-that carry a wide repertoire of genes involved in polysaccharide degradation and lactate-to-propionate fermentation. In vitro co-culture experiments with Megasphaera elsdenii and Bilifractor porci confirmed their synergistic role in promoting propionate production.

CONCLUSIONS: This study demonstrates that oral inoculation of pre-weaned lambs with starter feed-adapted adult rumen microbiota facilitates the establishment of a microbial consortium capable of enhanced lactate and propionate production, thereby enhancing hepatic gluconeogenesis and energy homeostasis, which ultimately mitigates weaning stress. This approach may offer a promising strategy to facilitate dietary transition and enhance metabolic resilience in young ruminants during weaning by modulating rumen microbial composition toward a propionate-producing community. Video Abstract.},
}

@article {pmid41491235,
year = {2026},
author = {Huang, J and Feng, Z and Fu, J and Zou, J and Xiang, Q and Liu, X and Li, L and Yu, R},
title = {Amelioration of acute lung injury by Salvia miltiorrhiza-derived extracellular vesicles: through repair of the vascular barrier and modulation of lung microbiota.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {6},
pmid = {41491235},
issn = {1749-8546},
support = {2025JJ80078//Natural Science Foundation of Hunan Province/ ; 23B0379//Education Department of Hunan Province/ ; A2024010//Health Commission of Hunan Province/ ; kq2402183//Science and Technology Bureau, Changsha/ ; 22JBZ002//Hunan University of Chinese Medicine/ ; 24YS003//Hunan University of Chinese Medicine/ ; },
abstract = {BACKGROUND: Acute lung injury (ALI) is a severe respiratory disease characterized by diffuse lung injury, vascular barrier dysfunction, and inflammatory responses. Its current treatments such as corticosteroids often involve adverse effects, highlighting the need for alternative therapies. Salvia miltiorrhiza-derived extracellular vesicles (SMEVs) have shown a potential therapeutic value for ALI due to their anti-inflammatory and barrier-protective properties, but the specific mechanisms remain unclear.

METHODS: SMEVs were extracted and purified through differential centrifugation coupled with sucrose density gradient centrifugation, and were analyzed by transmission electron microscopy (TEM) and nanoparticle tracking analysis (NTA). Biosafety assessment was then conducted in zebrafish embryos, mouse organs, and human umbilical vein endothelial cells (HUVEC). Subsequently, the treatment efficacy of SMEV on LPS-induced HUVEC inflammation was evaluated in vitro. LPS-induced ALI mice were then treated with SMEVs to further evaluate the posttreatment lung histopathology, vascular barrier markers, and microbial composition using metagenomics in vivo.

RESULTS: SMEVs exhibited a typical bilayer structure (average size: 177.7 nm) and excellent biosafety properties. In vitro, SMEVs effectively reduced LPS-induced inflammation (IL-1β, IL-6, TNF-α) and promoted wound healing in HUVEC, while in vivo, SMEVs ameliorated pulmonary edema and inflammation, and restored the VE-cadherin expression. Metagenomic analysis revealed that SMEVs were capable of regulating lung microbiota and reducing the pathogenic bacterial (e.g., g-Listeria, g-Streptococcus) and microbial diversity and richness after LPS stimulation.

CONCLUSION: SMEVs can ameliorate ALI by repairing the vascular barrier and modulating lung microbiota, offering a novel therapeutic strategy for this disease. Future research may focus on the SMEV-microbiota-immune interaction targeting ALI treatment.},
}

@article {pmid41491053,
year = {2026},
author = {Manirakiza, B and Zhang, S and Addo, FG and Ifon, BE and James, N and Kiribou, R and Nadine, NIA and Nyandwi, V and Sebaziga, JN and Mukasekuru, R and de Dieu Uwizelimana, J},
title = {Untapped Microbial Diversity, Assemblages, and Interactions in Rwandan Geothermal Spring Mats, Africa.},
journal = {Current microbiology},
volume = {83},
number = {2},
pages = {123},
pmid = {41491053},
issn = {1432-0991},
support = {E51879084//National Natural Science Foundation of China/ ; E51579075//National Natural Science Foundation of China/ ; },
mesh = {*Hot Springs/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Rwanda ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; RNA, Ribosomal, 18S/genetics ; *Eukaryota/classification/genetics/isolation & purification ; Phylogeny ; },
abstract = {Research on prokaryotes living in geothermal ecosystems have broadened our understanding of their compositions and response to extreme environmental stresses, especially for plankton bacterial communities in hot spring water. However, the comprehensive exploration of microbial diversity, assemblages, and interactions in geothermal spring mats in Africa, particularly in Rwanda, remain underexplored. This study explored the bacterial and eukaryotic communities' biodiversity, assemblages, and interactions within microbial mats from the Bugarama hot pool (BHP; 40-47 °C) and Gisenyi hot springs (GHS; 58-71.4 °C) in Rwanda, using high-throughput sequencing of the 16S rRNA gene and 18S rRNA gene, complemented by null and neutral community models and physicochemical analytical methods. Interestingly, the bacterial Shannon, Evenness, and Simpson indices were significantly different (P < 0.05) among geothermal spring mats. In BHP and GHS, the abundances of Chloroflexota, Proteobacteria, Firmicutes, and Acidobacteriota were significantly higher in BHP (P < 0.05) than in GHS, whereas Cyanobacteria, Bacteroidota, Planctomycetota, Verrucomicrobiota, and Spirochaetota were significantly more abundant in GHS (P < 0.01). Conversely, Chloroplastida, Mucoromycota, Arthropoda, and Cryptomycota were significantly more prevalent in BHP (P < 0.05), while the SAR supergroup, Ascomycota, Nematoda, and Amoebozoa dominated in GHS (P < 0.05). Through null and neutral modeling, stochastic processes exerted greater influence on bacterial and eukaryotic community assembly in fine-scale variations within geothermal spring mats. Despite this stochastic predominance, abiotic environmental factors (deterministic processes) such as temperature, pH, salinity (EC and TDS), and nitrate cannot be entirely ruled out. Moreover, Co-occurrence network analysis (|r|> 0.7, P < 0.05) revealed more complex and stable microbial interactions at higher temperatures (GHS). These findings highlight the rich underexplored microbial diversity and interactions in Rwandan geothermal spring mats through metagenomic analysis, shedding light on ecological processes and dynamics in extreme environments. Despite being ignored in metagenomic studies, eukaryotic communities highlight novel temperature-tolerant taxa: Echinamoeba and Tubulinea in phylum Amoebozoa, Monhysterida in phylum Nematoda, and Novel_Clade_Gran-5 in phylum Cercozoa, which are both pathogens and fierce predators thriving in geothermal habitats.},
}

*Hot Springs/microbiology
*Bacteria/classification/genetics/isolation & purification
Rwanda
*Biodiversity
RNA, Ribosomal, 16S/genetics
*Microbiota
RNA, Ribosomal, 18S/genetics
*Eukaryota/classification/genetics/isolation & purification
Phylogeny

@article {pmid41490675,
year = {2026},
author = {Li, Y and Cao, L and Li, W and Yan, Y and Zuo, W and Xi, B and Huang, C},
title = {Unveiling nitrogen and sulfur cycling mechanisms of odor reduction in kitchen waste composting driven by exogenous bacterial consortia.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133923},
doi = {10.1016/j.biortech.2026.133923},
pmid = {41490675},
issn = {1873-2976},
abstract = {Odor emissions, primarily ammonia (NH3) and hydrogen sulfide (H2S) restrict the application of kitchen waste (KW) composting. Microbial inoculation is a promising strategy, yet mechanisms underlying odor mitigation remain unclear. KW composting with and without an immobilized bacterial consortium (IBC) was compared by monitoring physicochemical conditions, odor emissions, and microbial and functional profiles. IBC extended the thermophilic phase, improved composting efficiency, and reduced cumulative H2S (-44 %) and NH3 (-18 %). IBC reshaped bacterial, fungal and archaeal communities and strengthened microbial network connectivity. Metagenomic analysis showed IBC enriched nitrogen-fixation genes and suppressed ammonification, nitrification, denitrification, and nitrate reduction. IBC also enhanced thiosulfate and sulfite oxidation while inhibited reductive pathways linked to H2S formation. Partial least squares path model confirmed odor mitigation resulting from coordinated shifts in environmental conditions, microbial structure, and metabolic pathways. Overall, microbial inoculation effectively reduces odor emissions and enhances composting performance by redirecting nitrogen and sulfur transformations.},
}

@article {pmid41490674,
year = {2026},
author = {Hao, X and Zeng, W and Gong, Q and Zhan, M and Miao, H and Yuan, C and Peng, Y},
title = {Biochar derived from waste iron-rich biosludge promotes iron-nitrogen coupled nitrogen removal in wastewater treatment.},
journal = {Bioresource technology},
volume = {444},
number = {},
pages = {133935},
doi = {10.1016/j.biortech.2026.133935},
pmid = {41490674},
issn = {1873-2976},
abstract = {Traditional biological nitrogen removal faces sustainability challenges due to high energy consumption and chemical demands. This study developed a novel autotrophic process leveraging the Fe-N cycle, enhanced by biochar derived from waste iron-rich biosludge (BC-Fe). During 150-day operation, adding 1 g/L BC-Fe (450 °C) achieved a total nitrogen removal efficiency of 94 ± 1 %, reducing aeration energy by 68 % and eliminating the need for external carbon sources compared to conventional nitrification-denitrification. BC-Fe served as a substrate and electron shuttle, facilitating Fe(III) reduction coupled with anaerobic ammonium oxidation (Feammox), nitrate-dependent Fe(II) oxidation, and denitrification, thereby supplying nitrite for Anammox. It enhanced iron bioavailability and established integrated carbon, nitrogen, and iron cycles, promoting microbial metabolism and system resilience. Metagenomics revealed Candidatus Brocadia fulgida performing Feammox via hao, compensating for hzs/hdh deficiency, while Saprospiraceae utilized biochar-derived organics for denitrification. This work provides a scalable solution to promote circular economy principles in wastewater treatment.},
}

@article {pmid41490614,
year = {2026},
author = {Campos-Silva, R and Rahimi, F and Joshi, J and Voiniciuc, C and Zhou, J and Hanson, AD},
title = {Mining bacterial (meta)genomes for enzymes active in aerobic, mesophilic conditions.},
journal = {Analytical biochemistry},
volume = {},
number = {},
pages = {116045},
doi = {10.1016/j.ab.2026.116045},
pmid = {41490614},
issn = {1096-0309},
abstract = {Enzyme biochemistry can now draw on hundreds of thousands of prokaryotic genomes and metagenomes to identify orthologous genes for research, biocatalysis, and metabolic engineering. In many applications, adaptation to O2 and mild temperatures are essential. But as organism lifestyle information can be poor or absent (especially for metagenomes), it is challenging to avoid orthologous genes from anaerobes and extremophiles. Taking bacterial sulfide-dependent THI4 thiazole synthases as test-cases, we built computational pipelines that use only DNA sequence inputs to explore (i) the average oxidation state of carbon (ZC) in orthologous enzymes and (ii) the presence of O2-metabolism genes in the corresponding (meta)genomes. ZC has been proposed to be highest (least negative) in proteins of organisms from O2-rich, mesophilic environments. We found that ZC values of 2,300 THI4s ranged from -0.107 (relatively oxidized) to -0.302 (strongly reduced). As predicted, genes specifying cytochrome c or o oxidases (supporting respiration at relatively high O2 levels) and, to a lesser extent, cytochrome bd oxidases (which can function to scavenge O2) were more frequent in genomes encoding THI4s with high ZC values. Eight THI4s with ZC values in the top 5% and from (meta)genomes having cytochrome oxidases were tested for ability to complement a THI4Δ yeast strain in aerobic conditions. Three THI4 genes from a metagenome with cytochrome c/o oxidase (but without cytochrome bd) were active. These results support the feasibility of combining ZC and cytochrome oxidase profiles to identify bacterial orthologous enzymes that work in aerobic, mild temperature conditions.},
}

@article {pmid41490375,
year = {2025},
author = {Hou, S and Xie, E and Si, B and Xiao, Y and Ding, J and Yan, Z and Zhou, H and Cheng, H and Shen, Y and Li, Y},
title = {Nanobubble aeration accelerates manure wastewater sanitisation and enhances nitrogen retention while reduces greenhouse gas emissions.},
journal = {Water research},
volume = {292},
number = {},
pages = {125267},
doi = {10.1016/j.watres.2025.125267},
pmid = {41490375},
issn = {1879-2448},
abstract = {Manure wastewater is an organic effluent rich in nitrogen and is often regarded as a valuable recycled nutrient source for crop production; however, it also contains high concentrations of organic pollutants and pathogenic microorganisms, and inadequate treatment can lead to serious environmental and public health risks. Nanobubbles (NBs) aeration is an emerging high-efficiency gas-liquid mass-transfer technology, but its role in nitrogen conservation and hygienic stabilisation of nutrient-rich manure wastewater remains unclear. Here, a 180-day experiment with piggery wastewater compared four NBs and conventional aeration regimes against natural storage. We quantified sanitisation performance, nitrogen transformation, greenhouse-gas emissions, microbial communities and virulence factors, and determined oxygen transfer rate (OTR), oxygen transfer efficiency (OTE) and volumetric mass-transfer coefficient (kLa) under identical airflow. NBs aeration markedly increased dissolved oxygen and ·OH generation, thereby enhancing COD, BOD5 and Escherichia coliremoval and shortening the time to reach hygienic standards by 60 and 150 days compared with conventional aeration and natural storage, respectively.Although TN decreased in all treatments, the shorter sanitisation period under NBs aeration led to higher residual TN at compliance. The TN loss rate was 13.96% and 15.39% lower than under CA and CK, and cumulative N2O emissions were 30.21% lower than under conventional aeration. Network and metagenomic analyses showed that NBs aeration reshaped bacterial, fungal and archaeal communities, weakened virulence-factor connectivity, and strengthened the coupling between nitrogen-cycling microbes and gaseous nitrogen pathways. Quantification of OTR, OTE and kLa demonstrated that these benefits arise from the intrinsic mass-transfer properties of nanobubbles rather than an increased oxygen supply rate. Overall, this work provides new mechanistic insight and engineering evidence that NBs aeration can simultaneously accelerate manure wastewater sanitisation and improve nitrogen management for subsequent fertiliser reuse.},
}

@article {pmid41489359,
year = {2026},
author = {Yancey, CE and Hart, LN and Dick, GJ},
title = {Secondary metabolism of Microcystis: current understanding and recent advances in unlocking genomic and chemical diversity.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0163425},
doi = {10.1128/aem.01634-25},
pmid = {41489359},
issn = {1098-5336},
abstract = {The cyanobacterial genus Microcystis is globally distributed and known for its ability to produce microcystins, a structurally diverse group of cyanotoxins. However, the biosynthetic capacity of Microcystis is vast; its diverse genomes contain a variety of biosynthetic gene clusters (BGCs) encoding the synthesis of metabolites that may be toxic, have important ecological function, or have applications for biotechnology or drug discovery. Recent studies illustrate that these BGCs vary significantly across Microcystis strains, can be highly expressed in environmental conditions, and may play key roles in cellular physiology, grazer deterrence, and microbial interactions. However, many of these BGCs and metabolites remain poorly characterized or completely uncharacterized, having been identified only through genome sequencing or mass spectrometry, respectively, leaving no knowledge of their structure, bioactivity, or physiological or ecological functions. Here, we synthesize the current body of knowledge regarding the secondary metabolism of Microcystis in terms of genetic and chemical diversity, potential drivers of synthesis, and physiological and ecological functions. This review highlights the need for further research to characterize the largely unexplored genetic and chemical diversity of Microcystis in communities in the environment and discusses the challenges and opportunities of integrating high-throughput multiomic approaches to link uncharacterized gene clusters with their corresponding metabolites. Microcystis will continue to be a rich source for secondary metabolite research as its genetic and chemical potential likely plays a critical role in the persistence and observed dynamics of harmful algal blooms and may harbor uncharacterized toxins and metabolites.},
}

@article {pmid41489358,
year = {2026},
author = {Surgenor, K and McCormick, C},
title = {Diving into the hidden viral world of marine protists.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0126225},
doi = {10.1128/jvi.01262-25},
pmid = {41489358},
issn = {1098-5514},
abstract = {As the most abundant biological entities in the ocean, viruses of microbes play important roles in regulating host population dynamics and influencing biogeochemical cycles. Metagenomic surveys have revealed an astounding reservoir of viral genetic diversity in single-celled marine eukaryotes known as protists, but the vast majority of these viruses have not been directly observed, and information about their protist hosts remains fragmentary. The 2023 discovery of mirusviruses provides a striking example, whereby metagenomic surveys of samples collected by the Tara Oceans expedition led to the discovery of a new phylum of viruses, the Mirusviricota, with remarkable chimeric genomes encoding structural proteins from herpesviruses and enzymes from giant eukaryotic viruses. However, because mirusviruses were detected indirectly by metagenomics, their host range remained unclear, and their biological properties unexplored. Here, we provide new insights into research approaches to identify bona fide protist hosts for marine viruses and characterize virus-host interactions. A greater understanding of these viruses and their natural hosts will unlock opportunities to understand the roles that they play in regulating biogeochemical processes in marine habitats.},
}

@article {pmid41489025,
year = {2026},
author = {Pace, R and Monti, MM and Cuomo, S and Affinito, A and Ruocco, M},
title = {Machine Learning Approaches to Assess Soil Microbiome Dynamics and Bio-Sustainability.},
journal = {Physiologia plantarum},
volume = {178},
number = {1},
pages = {e70719},
pmid = {41489025},
issn = {1399-3054},
mesh = {*Soil Microbiology ; *Machine Learning ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Fungi/genetics ; Soil/chemistry ; Agriculture ; Principal Component Analysis ; },
abstract = {Understanding soil microbiota dynamics is essential for enhancing bio-sustainability in agriculture, yet the complexity of microbial communities hampers the prediction of their functional roles. Artificial intelligence (AI) and machine learning (ML) offer powerful tools to analyse high-dimensional microbiome data generated by high-throughput sequencing. Here, we apply unsupervised AI-based algorithms to uncover microbial patterns that are not immediately recognisable but are crucial for characterising the biological status of agricultural soils. Soil samples were collected from a site in Northern Italy managed under four strategies: conventional farming without organic matter (C), with organic matter (C + O), with beneficial microorganisms but without organic matter (M), and with both beneficial microorganisms and organic matter (M + O). Metagenomic amplicon sequencing of the 16S ribosomal RNA (rRNA) gene and the internal transcribed spacer (ITS) region was used to profile bacterial and fungal communities. Principal component analysis (PCA), k-means clustering, and t-distributed stochastic neighbour embedding (t-SNE) revealed coherent temporal trajectories in both datasets, with sampling time and crop presence emerging as dominant drivers of community assembly and only subtle compositional shifts attributable to treatments. Fungal communities exhibited higher plasticity and a stronger response to management than bacterial communities, which converged towards a stable oligotrophic core. Our findings highlight the complementary roles of fungal and bacterial guilds and show that unsupervised ML-based workflows provide an effective framework to disentangle temporal and treatment effects in complex microbiome datasets. This exploratory study lays the groundwork for future predictive models aimed at identifying microbial indicators of soil biological status and supporting bio-sustainable agronomic decisions.},
}

*Soil Microbiology
*Machine Learning
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
Bacteria/genetics
Fungi/genetics
Soil/chemistry
Agriculture
Principal Component Analysis

@article {pmid41488896,
year = {2025},
author = {Liu, J and Huang, L},
title = {Case Report: Simultaneous Paragonimus skrjabini infection in twin girls with spontaneous emergence of a juvenile worm from the eyelid of the elder sister.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1708963},
pmid = {41488896},
issn = {2296-2360},
abstract = {We reported a rare case of paragonimiasis occurring in twin sisters who had eaten raw crabs 7 months ago. The elder sister complained of eyelid swelling and migratory lumps, while the younger sister was asymptomatic. Laboratory tests showed eosinophilia and elevated levels of inflammatory indicators in the two sisters. The brain MRI of the elder twin showed hyperintensity in the frontal lobe, suggesting cerebral hemorrhage. The chest CT image of the twins showed pulmonary involvement. Enzyme-linked immunosorbent assay (ELISA) for serum antibody test and metagenomic next-generation sequencing (mNGS) of subcutaneous tissue from the eyelid-obtained via sterile puncture aspiration under local anesthesia-confirmed Paragonimus skrjabini infection. After praziquantel treatment, both of the sisters recovered. This study aims to enhance clinical awareness and highlight the application of advanced molecular diagnostic technologies for identifying rare parasitic infections.},
}

@article {pmid41488894,
year = {2025},
author = {Lin, B and Zhu, Z and Yang, X and Li, Z and Zhou, H and Luo, M and Guan, J and Zou, Y and Chen, H and Zhuang, Z and Meng, S and Li, W and Yang, Q and Dai, D},
title = {Protocol for the efficacy and safety of fecal microbiota transplantation in children with autism spectrum disorder: a prospective single-center, single-arm interventional study.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1660773},
pmid = {41488894},
issn = {2296-2360},
abstract = {BACKGROUND: Autism spectrum disorder (ASD) is a neurodevelopmental condition affecting 0.7% of children globally, with 90% experiencing comorbid gastrointestinal (GI) symptoms. Fecal microbiota transplantation (FMT) may modulate ASD symptoms via the microbiota-gut-brain axis (MGBA).

METHODS: This open-label single-arm trial enrolls 30 children (2-12 years) with moderate-to-severe ASD, defined as a Childhood Autism Rating Scale (CARS) score of ≥36. Participants receive 3 nasojejunal FMTs (5 mL/kg) over 5 days. The primary outcomes are GI symptom improvement, assessed using the Gastrointestinal Symptom Rating Scale (GSRS), and ASD severity, assessed using the CARS. Secondary outcomes include social responsiveness (Social Responsiveness Scale, SRS), aberrant behaviors (Aberrant Behavior Checklist, ABC), and gut microbiota changes assessed by metagenomic next-generation sequencing (mNGS).

ETHICS AND DISSEMINATION: Ethical approval obtained from Shenzhen Children's Hospital Ethics Committee. Results will be disseminated via peer-reviewed publications and conference presentations.Clinical Trial Registration: https://www.chictr.org.cn/showproj.html?proj=229136, identifier ChiCTR2400083998. Registered on 2024-05-08. Registered title: "Efficacy and safety of fecal microbiota transplantation in treatment of autism spectrum disorder: a prospective single-center intervention study".},
}

@article {pmid41488762,
year = {2025},
author = {Zhao, Y and Hu, X and Li, C and Huang, J and Guo, K and Pan, Q and Yu, Z},
title = {Comprehensive Analysis of Vaginal and Gut Microbiome Alterations in Endometriosis Patients.},
journal = {International journal of women's health},
volume = {17},
number = {},
pages = {5775-5786},
pmid = {41488762},
issn = {1179-1411},
abstract = {PURPOSE: Endometriosis (EMS) is a chronic gynecological disorder with unclear pathogenesis. While the vaginal and gut microbiomes are known to influence EMS, few studies have analyzed both microbiomes integrally. This study aims to characterize the vaginal and gut microbiome profiles in EMS patients and evaluate their diagnostic potential.

PATIENTS AND METHODS: We conducted metagenomic sequencing on 22 paired vaginal and fecal samples from EMS patients and controls. Microbial composition, diversity, and metabolic pathways were analyzed. Machine learning models were employed to assess the predictive performance of microbiome features in EMS diagnosis.

RESULTS: EMS patients exhibited pronounced shifts in the vaginal microbiome, characterized by reduced Lactobacillus and increased Bifidobacterium and Gardnerella, which correlated with elevated luteinizing hormone (LH) and follicle-stimulating hormone (FSH) levels. The gut microbiome displayed decreased diversity, with a depletion of beneficial taxa such as Ruminococcus and Prevotella, alongside an enrichment of Dialister. Metabolic pathways in both microbial communities were significantly altered. Machine learning analyses demonstrated that gut microbiome features outperformed both vaginal microbiome and hormonal indices in predicting EMS, highlighting their strong diagnostic potential.

CONCLUSION: This study underscores the pivotal role of the gut microbiota in EMS and elucidates the complex interplay between microbial dysbiosis and disease pathogenesis. Our findings indicate that gut microbiome signatures may serve as superior diagnostic biomarkers for EMS, thereby paving the way for microbiome-based diagnostic and therapeutic strategies.},
}

@article {pmid41488684,
year = {2026},
author = {Zeng, A and Yang, M and Yang, T and Yang, W and Zhang, J},
title = {Effects of hot water treatment, silver hydroxide ion solution and carboxymethyl chitosan on Lanxangia tsao-ko quality.},
journal = {Food chemistry. Molecular sciences},
volume = {12},
number = {},
pages = {100326},
pmid = {41488684},
issn = {2666-5662},
abstract = {The fruit of Lanxangia tsao - ko (LT), a widely used spice, is highly perishable during storage and transportation making it essential to develop effective preservation methods. This study employed multi-omics techniques to evaluate the effects of three different treatments on the quality of LT during short-term storage. Results demonstrated that, compared to the tap water control group (TW), the hot water treatment group (HW), carboxymethyl chitosan treatment group (CMC), and hydrogen peroxide‑silver ion solution treatment group (SP) significantly suppressed the increase in color change intensity (ΔE), browning index (BI), weight loss rate (W%), and rot rate (R%) of LT. Furthermore, these treatments promoted the accumulation of beneficial flavor substances, while reducing the level of unfavorable ones. Both CMC and SP were effective in inhibiting the increase of LT's respiration intensity and the relative abundance of pathogenic microorganisms like Rhizopus microsporus and Rhizopus arrhizus. However, HW led to an abnormal decrease in respiration intensity and increases the relative abundance of certain pathogenic microorganisms. In summary, although the temperature setting in the hot water treatment group was not ideal, hot water treatment still significantly inhibited the spoilage and discoloration phenomenon. Both CMC and SP can effectively extend the storage and transportation period of LT in all aspects. This study provides a new idea for the preservation of LT.},
}

@article {pmid41488305,
year = {2025},
author = {Liu, Y and Wang, J and Wei, W and Xia, M and Ji, D and Wang, F and Zhang, X and Wang, W},
title = {Depth differentiation of microbial communities and nutrient cycling functional genes in semi-arid riparian soil.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1717707},
pmid = {41488305},
issn = {1664-302X},
abstract = {INTRODUCTION: Microbial communities and their associated carbon, nitrogen, and phosphorus metabolic processes play a role in maintaining ecological functions and nutrient cycling in riparian zones. However, systematic research on the coupling mechanisms of carbon, nitrogen, and phosphorus biogeochemical processes in soil profiles of semi-arid riparian soil is still limited.

METHODS: This study focused on the riparian zone of the Tuwei River, a typical semi-arid river. Metagenomic sequencing was used to analyze the composition of microbial communities and their carbon, nitrogen, and phosphorus metabolic functions across different soil depths along the river.

RESULTS: The dominant taxa across all depths and river sections were Proteobacteria (average relative abundance 49.85%) and Serratia (11.23%). Results from ANOVA and Tukey-Kramer post-hoc multiple comparison tests showed that microbial diversity significantly decreased with increasing soil depth (p < 0.05). Gene families associated with carbon fixation (accC, pccB), denitrification (nosZ, nirK), and phosphorus metabolism (purC, guaB, pyrG) were significantly enriched in surface soils and showed clear depth-dependent declines (p < 0.05). Partial Mantel tests revealed that microbial metabolic functions were significantly correlated with porosity (p < 0.05), soil organic carbon, total nitrogen, and total phosphorus, confirming that nutrient availability and soil structure are key regulators of microbial biogeochemical functions.

CONCLUSION: Our findings reveal that nutrient availability and soil structure jointly regulate the vertical distribution of microbial metabolic functions. These insights provide a scientific basis for ecological restoration and soil management in semi-arid riparian zones, where optimizing surface structure and nutrient inputs can stimulate microbial-driven biogeochemical cycling. Key functional taxa and genes may also serve as sensitive indicators for evaluating restoration effectiveness under climate-induced stress.},
}

@article {pmid41488304,
year = {2025},
author = {Duan, Y and Li, X and Chai, Y and Chen, H and Hou, H},
title = {Adlercreutzia-modulated polyunsaturated fatty acid metabolism underlies nicotine's anti-obesity effects.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1682370},
pmid = {41488304},
issn = {1664-302X},
abstract = {BACKGROUND: The regulatory effects of nicotine on energy balance through central and peripheral mechanisms have been reported. However, its impact on obesity and gut microbiota at safe doses remains unclear.

RESULTS: In this study, it was found that chronic oral nicotine administration daily at relative low dose (0.5 mg/kg) significantly alleviated high-fat diet (HFD)-induced obesity phenotypes in mice, including body weight gain, fat deposits, hepatic steatosis, inflammation and metabolic dysfunction. Gut microbiota depletion and fecal microbiota transplantation (FMT) confirmed that these beneficial effects were microbiota-dependent. Metagenomic sequencing confirmed that nicotine administration reshaped gut microbiota composition, and specifically enriched the commensal genus Adlercreutzia, whose increased abundance correlated with improved biochemical indicators related to obesity. Furthermore, transplantation of Adlercreutzia reproduced anti-obesogenic effects, suggesting it was a key factor for nicotine reducing HFD-induced obesity. Untargeted metabolomics analysis combined association analysis further demonstrated that nicotine modulated host metabolic profiles via gut microbiota-metabolite axis, particularly enhancing Adlercreutzia-linked lipid metabolites involved in polyunsaturated fatty acid (PUFA) metabolism.

CONCLUSION: Collectively, our study elucidates the critical involvement of gut microbiota in nicotine-induced obesity amelioration, uncovers a novel Adlercreutzia-PUFA metabolic axis mediating nicotine's anti-obesity effects, and highlight Adlercreutzia potentiation as a promising microbiota-directed invention strategy for obesity and metabolic syndrome.},
}

@article {pmid41488077,
year = {2025},
author = {Sun, X and Jiao, Q and Fu, X and Xie, T and Xie, W and Cheng, H and Chen, S},
title = {Case Report: Severe psittacosis in an elderly patient without avian exposure: diagnosis via metagenomic next-generation sequencing and rapid response to doxycycline.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1689333},
pmid = {41488077},
issn = {2296-858X},
abstract = {Chlamydia psittaci causes psittacosis in both birds and humans, typically following avian exposure. We present a case of severe psittacosis in a 73-year-old woman with no documented bird contact. The diagnosis was ultimately achieved through metagenomic next-generation sequencing (mNGS) after initial conventional serologic tests failed to identify a pathogen. The patient presented with fever and pneumonia that were unresponsive to broad-spectrum antibiotics. mNGS performed on a whole-blood sample collected on hospital day 5 detected C. psittaci, albeit with a low number of specific sequence reads (only 14 reads mapping to the C. psittaci genome). Oral doxycycline (100 mg q12h) was initiated promptly, resulting in defervescence within 24 h and resolution of inflammatory markers. Although community pet parrots were identified as a potential source, the patient denied any direct contact. This case highlights the risk of environmental aerosol transmission in the absence of direct avian exposure, demonstrates the critical role of mNGS in diagnosing culture-negative pneumonia, and underscores the efficacy of early doxycycline therapy. Strengthened public health surveillance of avian reservoirs is imperative to mitigate unrecognized transmission.},
}

@article {pmid41487523,
year = {2025},
author = {Gómez-Cebrián, N and Trull, MC and Gras-Colomer, E and Edo Solsona, MD and Poveda Andrés, JL and Puchades-Carrasco, L},
title = {Systemic metabolic reprogramming and microbial dysbiosis in Fabry disease: Multi-omics mechanisms and implications for drug development.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1702682},
pmid = {41487523},
issn = {1663-9812},
abstract = {Current treatments, including enzyme replacement and pharmacological chaperones, have improved disease outcomes but often fail to fully prevent progression or alleviate persistent symptoms, underscoring the need for novel therapeutic strategies. Recent systems biology and multi-omics approaches have revealed consistent and previously underappreciated alterations in systemic metabolism and the gut microbiota in FD. Here, we synthesize evidence from metabolomic, lipidomic, transcriptomic, and metagenomic studies in patients and experimental models, highlighting disturbances in redox balance, mitochondrial function, energy metabolism, and microbiota-derived metabolites such as short-chain fatty acids and tryptophan catabolites. These findings point to new mechanisms underlying gastrointestinal, inflammatory, and metabolic complications in FD, with direct implications for biomarker discovery and drug development. We further discuss the challenges of integrating multi-omics data into clinical research, the value of mechanistic studies in disease models, and the potential for translating omics-derived insights into precision diagnostics and targeted therapies. By framing FD as a systemic disorder of metabolic and microbial dysregulation, this review outlines a roadmap for mechanism-based interventions that extend beyond canonical glycosphingolipid targets.},
}

@article {pmid41487461,
year = {2026},
author = {Huang, MY and Li, Z and Zhang, W and Chen, HY and Liu, J and Li, CX},
title = {EBV+ and Kaposi's Sarcoma Herpesvirus-Associated Multicentric Castleman Disease in a Patient With HIV Infection: A Case Report.},
journal = {Case reports in infectious diseases},
volume = {2026},
number = {},
pages = {5567369},
pmid = {41487461},
issn = {2090-6625},
abstract = {Multicentric Castleman disease is a rare proliferative disease of lymphoid tissue. It has rarely been reported in Asian countries, particularly in HIV-positive patients. Here, we report a case of Kaposi's sarcoma herpesvirus-associated Multicentric Castleman disease (KSHV-MCD). A 44-year-old male HIV patient with a good response to antiretroviral therapy presented with recurrent fever and bilateral axillary masses. He was hospitalized for recurrent exacerbations, and it took 7 years from onset to definitive diagnosis. Lymph node biopsy suggested Castleman disease. Metagenomic next-generation sequencing (mNGS) of the blood showed that the patient was infected with KSHV (8327 sequence reads) and EBV (283 sequence reads). The patient was administered rituximab, thalidomide, sodium phosphonates, and ganciclovir. The patient's symptoms were completely relieved, and all indicators returned to normal, with no recurrence during follow-up. This case underlines that it is necessary to perform multiple lymph node biopsies or repeat the biopsies multiple times for the diagnosis of KSHV-MCD.},
}

@article {pmid41487438,
year = {2025},
author = {Chen, W and Liu, R and Qi, Q and Xu, L and Sun, G},
title = {Comparative Evaluation of mNGS and Traditional Culture Methods in Pathogen Detection for Pulmonary Infections.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {6991-6998},
pmid = {41487438},
issn = {1178-6973},
abstract = {PURPOSE: This study aimed to evaluate the diagnostic accuracy and clinical applicability of metagenomic next-generation sequencing (mNGS) in pulmonary infections by comparing it with traditional culture methods in a Traditional Chinese Medicine (TCM) hospital setting.

METHODS: This retrospective cohort study enrolled 67 consecutively admitted patients with radiologically and clinically confirmed pulmonary infections from the Department of Respiratory Infectious Diseases at Xinchang Hospital of Traditional Chinese Medicine between December 2022 and September 2024. Clinical specimens included blood, bronchoalveolar lavage fluid (BALF), sputum, hydrothorax and cerebrospinal fluid (CSF). mNGS and conventional culture were performed to compare detection rates and microbial community profiles.

RESULTS: Among 67 cases, mNGS identified pathogens in 89.55% (60/67), compared to 20.90% (14/67) by traditional culture. Of 14 dual-positive cases, only 1 (1/14, 7.14%) showed complete concordance, while most exhibited discordance or partial genus-level overlap. mNGS further detected viral co-infections in 44.78% (30/67) and identified fastidious/non-culturable pathogens such as enterovirus, human herpesvirus type 1, and Mycobacterium tuberculosis. Patients with chronic diseases were more susceptible to EB virus infections.

CONCLUSION: mNGS significantly enhances pathogen detection in pulmonary infections, supports targeted antimicrobial therapy, and holds potential for contributing to clinical outcomes and reducing antibiotic resistance.},
}

@article {pmid41487392,
year = {2026},
author = {Guzmán-Fierro, V and Quiroz, M and Moscoso, K and Arriagada, C and Espinoza, C and Mansilla, J and Contreras, D and Campos, V and Gallardo-Rodríguez, JJ and Riveros, G and Roeckel, M},
title = {Aerobic granular sludge as a regenerative system for nutrient removal and metal recovery from landfill leachate.},
journal = {RSC advances},
volume = {16},
number = {2},
pages = {1121-1133},
pmid = {41487392},
issn = {2046-2069},
abstract = {Landfill leachate is a complex and variable wastewater rich in organic matter, ammonium, salts, and metals, with low biodegradability and highly fluctuating composition. Its management still largely relies on energy- and chemical-intensive treatment schemes, making the treatment of raw, undiluted landfill leachate particularly challenging. This study evaluates, at lab scale, the potential of aerobic granular sludge (AGS) for achieving simultaneous pollutant removal and metal recovery in a 2-L column sequencing batch reactor fed with raw, undiluted landfill leachate collected from an active municipal landfill site. The reactor was operated for 198 days without dilution or addition of co-substrates. This operation resulted in stable granulation and high removal efficiencies, 94% for chemical oxygen demand (COD) and 97% for total nitrogen. Cation analysis shows that assimilation reached 600.47 µmol g[-1] TS, with calcium and magnesium being the predominant cations. Quantitative analyses revealed near-equal contributions from biosorption (53%) and bioaccumulation (47%), with magnesium dominating biosorption and calcium prevailing in bioaccumulation. Then, a partial metal recovery was achieved by desorption with 0.1 M NaCl, without compromising the granule structure, as verified by FTIR and scanning electron microscopy (SEM). However, the desorption process reduced nitrification and denitrification activities by factors of 3.7 and 1.8, respectively, while heterotrophic activity increased by 2.4-fold. Metagenomic analysis revealed microbial shifts following desorption, favouring genera such as Paracoccus and Burkholderia, which are associated with heterotrophic metabolism. These results demonstrate the potential of AGS as a regenerative biosorbent for treating landfill leachate and recovering metals. This approach supports sustainable and circular strategies for managing landfill leachate and similar complex effluents.},
}

@article {pmid41486240,
year = {2026},
author = {Aghajani, S and Kerdraon, M and Wilson, J and Galinat, S and André-Miral, C and Cregut, M and Jouanneau, S and Thouand, G},
title = {Screening of exoenzymes for guar gum biodegradation in activated sludge and soil.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {41486240},
issn = {1614-7499},
abstract = {Originally standardized biodegradation tests, designed for small molecules, are often considered inadequate for evaluating polymers, as they do not account for the crucial fragmentation step catalyzed by exoenzymes, which is essential for initiating the microbial degradation of polymers. In this study, the presence of EEs in the environment and their role in the biodegradation of guar gum, a WSP, were evaluated. A metagenomic shotgun approach assessed the abundance of genes encoding α-galactosidase and β-mannosidase in the Waste Water Treatment Plant (WWTP) and soil. Secondly, we employed sonication to release EEs, measured their activity, and evaluated the impact of their release on guar degradation using biodegradation tests. These findings indicated that genes encoding α-galactosidase and β-mannosidase were more abundant in the WWTP than in soil. A sonication protocol with a power density of 1 W/mL and a frequency of 20 kHz for 1 min (WWTP) and 2 min (soil) released EEs without significant cell lysis and significantly reduced the lag phase of guar-grafted acrylamide biodegradation from 8 to 5 days and decreased variability in native guar biodegradation by 10%. Our findings highlight the potential of WWTP and soil microbial communities to degrade guar gum by screening EEs and propose a new method for preparing the inoculum for WSPs biodegradation tests.},
}

@article {pmid41485666,
year = {2026},
author = {He, H and Han, L and Ni, W and Yu, J and Liu, K and Li, W and Li, C and Hu, S and Li, C and Li, X},
title = {The horse gut microbiota genome represents a vast novel reservoir of CAZymes.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {150042},
doi = {10.1016/j.ijbiomac.2025.150042},
pmid = {41485666},
issn = {1879-0003},
abstract = {Herbivores represent crucial subjects for mining highly efficient carbohydrate-active enzymes (CAZymes) from gut microbiomes. Here, we analyzed 12,763 metagenome-assembled genomes (MAGs) from the horse gut, revealing that its microbial community as a rich reservoir of CAZymes diversity, with 5,204,848 glycoside hydrolases (GHs) and 4,596,191 glycosyl transferases (GTs) identified. Our findings demonstrate that Bacteroidota (5,479,287 CAZymes) and Bacillota_A (2,987,684 CAZymes) serve as the primary functional phyla for plant polysaccharide degradation. A total of 17,250 polysaccharide utilization loci (PULs) discovered in Bacteroides species. Through comparative genomic screening, a total of 12,976 hypothetical genes were predicted in PULs. These genes represent a putative novel reservoir of CAZymes. We selected and identified a putative CAZyme, which encodes 452 amino acids and is designated H113. Our research has confirmed that H113 is a metal enzyme (Zn[2+] significantly enhancing its catalytic efficiency) capable of degrading α-1,4 glycosidic bonds in maltotriose and also exhibiting activity toward mannan, demonstrating optimal activity at pH 4.8 and 35 °C (specific activity: maltotriose: 82.2 U/mg, mannan: 2.3 U/mg). Phylogenetic analysis revealed H113 belongs to a conserved enzyme family with 1866 identified homologues. This study not only provides a reference for efficient discovery of novel CAZymes but also offers valuable resources for developing novel biocatalysts.},
}

@article {pmid41485494,
year = {2026},
author = {Miyachi, H and Shibata, R and Javornik Cregeen, SJ and Surathu, A and Sijaric, M and Espinola, JA and Sullivan, AF and Mansbach, JM and Camargo, CA and Zhu, Z},
title = {Interactions between host genetics and gut microbiome influence susceptibility to childhood asthma and lung function.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2025.12.1005},
pmid = {41485494},
issn = {1097-6825},
abstract = {BACKGROUND: The gut microbiome is thought to influence risk of childhood allergic diseases; however, data on species-level links to childhood asthma and lung function are limited, and the role of host genetics in the gut-lung axis remains unclear.

METHODS: In a multicenter cross-sectional study of children with a history of bronchiolitis, from the 35[th] Multicenter Airway Research Collaboration, we performed shotgun metagenomic profiling of stool samples at age 6 years and examined associations of gut microbiome with prevalent asthma and lung function. We also calculated polygenic risk scores (PRS) of asthma and lung function to investigate the interaction between host genetics and gut microbiome on these traits.

RESULTS: In the 300 children included for this study, three bacterial species (e.g., Bacteroides vulgatus, Eisenbergiella massiliensis, Butyricimonas virosa) were differentially associated with FEV1, and four bacterial species were differentially associated with FEV1/FVC (e.g., Bifidobacterium longum) (MaAsLin: FDR<0.25). Furthermore, host genetics-gut microbiome interaction analysis showed association of B.vulgatus (FDR=0.037) and Bacteroides uniformis (FDR=0.037) with FEV1/FVC among children with high FEV1/FVC PRS. Additionally, Ruminococcus bromii (FDR=0.067) and Alistipes indistinctus (FDR=0.13) were suggested to have protective associations with asthma, specifically in children with high asthma PRS, indicating that host genetics can modulate the effect of gut microbiome on these respiratory outcomes.

CONCLUSION: By applying the metagenomic approach to a multicenter cohort of children with a history of bronchiolitis during infancy, this study suggests potential interplay of host genetics with gut microbiome, and their integrated relationship with childhood asthma and lung function.},
}

@article {pmid41485293,
year = {2025},
author = {Meng, Y and Hou, Y and Zhang, R and Guo, Z and Zhang, Z and Li, J and Yan, Y and Chang, Y and Li, D and Chang, L and Li, M and Gao, H},
title = {Jinlida ameliorates diabetic kidney disease via gut microbiota-dependent production of pyridoxamine targeting renal AGEs/RAGE and TGF-β pathways.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {150},
number = {},
pages = {157744},
doi = {10.1016/j.phymed.2025.157744},
pmid = {41485293},
issn = {1618-095X},
abstract = {BACKGROUND: Diabetic kidney disease (DKD) is the leading cause of chronic kidney disease and end-stage renal disease (ESRD), necessitating novel therapies beyond conventional approaches. Emerging evidence indicates that gut microbiota dysbiosis promotes DKD progression through metabolite-mediated renal injury. Jinlida (JLD) is a clinically validated traditional Chinese medicine with antidiabetic activity, but its microbiota-mediated renoprotective mechanism remains unclear.

PURPOSE: This study investigates whether JLD alleviates DKD by modulating gut microbiota and vitamin B6 metabolism, and elucidates the renoprotective mechanism of its key metabolite, pyridoxamine (PM).

METHODS: To assess JLD's microbiota-dependent effects, we employed antibiotic-induced pseudo-germ-free mice and fecal microbiota transplantation (FMT). Metagenomics and untargeted metabolomics delineated gut microbiota and metabolite compositional changes. Renal PM levels were quantified by LC-MS/MS. The renoprotective effects and mechanisms of direct PM supplementation against DKD were further evaluated in vivo and in vitro.

RESULTS: JLD's therapeutic effects on proteinuria and glomerulosclerosis were shown to partially depend on microbiota homeostasis. Metabolomic analysis demonstrated that JLD significantly upregulated the vitamin B6 metabolic pathway and increased levels of related metabolites, including PM and pyridoxine (PN). Metagenomic analyses indicated that JLD remodeled the gut microbiota composition and enriched pathways related to cofactor biosynthesis, and markedly increased the relative abundance of key enzyme genes involved in the de novo (DXP-dependent) vitamin B6 biosynthesis pathway - namely pdxJ, pdxB, dxs and dxr. Genes related to vitamin B6 activation and conversion (pdxH, aldH) showed no significant changes, suggesting that JLD may promote PM accumulation by enhancing the microbiota's capacity for vitamin B6 biosynthesis rather than its subsequent activation/conversion. Source-tracking pinpointed Paramuribaculum intestinale as the core functional species. In vitro culture experiments showed that JLD markedly promoted the growth of this strain and elevated PM production, and that the strain's conditioned culture medium effectively inhibited formation of advanced glycation end-products (AGEs). Notably, direct supplementation with PM recapitulated the renoprotective effects of JLD in vivo. Mechanistically, PM inhibited the AGEs-RAGE-NF-κB-AP-1 axis and TGF-β receptor signaling, thereby suppressing NF-κB-driven inflammation and Smad2-mediated fibrosis.

CONCLUSION: JLD remodels the gut microbiota and enhances its de novo vitamin B6 biosynthetic capacity, leading to accumulation of PM. Gut-derived PM enters the circulation and functions as an effector molecule targeting the kidney; through PM's direct carbonyl-trapping activity it scavenges AGEs and suppresses the AGEs-RAGE axis as well as downstream inflammatory and profibrotic signaling, thereby exerting renoprotective effects. This study reveals PM as a microbially derived metabolite with therapeutic potential in DKD and offers a new metabolism-directed strategy for DKD treatment.},
}

@article {pmid41485252,
year = {2026},
author = {Xu, Y and Zhao, B and Li, F and Song, S and Liu, J and Liu, Z and Wang, Y and Ji, J and Liu, Z and Zhou, W and Wang, X and Zhou, M},
title = {Tucidinostat ameliorates DSS-induced ulcerative colitis by inhibiting cellular senescence, modulating the p53 signaling pathway and cell cycle, and restoring the gut microbiota-metabolite Axis.},
journal = {International immunopharmacology},
volume = {171},
number = {},
pages = {116155},
doi = {10.1016/j.intimp.2025.116155},
pmid = {41485252},
issn = {1878-1705},
abstract = {Ulcerative colitis (UC) is a chronic inflammatory bowel disease with a complex etiology, and its pathological process is closely associated with cellular senescence. Based on an anti-senescence drug screening system, this study identified Tucidinostat (TUC) as an agent with anti-senescence properties and investigated its therapeutic potential and mechanisms of action in a DSS-induced ulcerative colitis model. Using an in vitro model of colonic epithelial cells and an in vivo C57BL/6 mouse model, both induced by DSS treatment, we systematically evaluated changes in body weight, colon length, histopathological scores, levels of inflammatory cytokines, and senescence-associated markers. Our results demonstrated that TUC significantly inhibited cellular senescence and effectively alleviated colitis-related symptoms. Transcriptomic analysis and Western blotting further revealed that TUC exerts its effects by modulating the p53 signaling pathway and cell cycle progression. Furthermore, integrated metagenomic and untargeted metabolomic analyses revealed that TUC reshapes the gut microbiota-metabolite axis by promoting the proliferation of beneficial bacteria (e.g., s__Eubacterium plexicaudatum and s__Ligilactobacillus murinus) and increasing the levels of beneficial metabolites, such as alpha-muricholic acid and kynurenic acid. In summary, this study provides the first evidence that Tucidinostat can ameliorate ulcerative colitis by targeting cellular senescence, regulating the p53/cell cycle signaling network, and restoring gut microbiota-metabolite homeostasis, offering a novel potential therapeutic strategy for this disease.},
}

@article {pmid41484966,
year = {2026},
author = {Fu, R and Liang, XJ and Yang, WM and Li, R and Shi, YR and Guo, L and Yu, H and Chen, YH and Wang, HN},
title = {Gut microbial signatures in schizophrenia: exploring archaea, fungi, and bacteria.},
journal = {BMC psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12888-025-07721-3},
pmid = {41484966},
issn = {1471-244X},
support = {LHJJ24YF06//Interdisciplinary Integration Project of Xijing hospital/ ; 82201679//National Natural Science Foundation of China/ ; 82330043//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Gut microbial, mainly bacterial dysbiosis, has been demonstrated in patients with schizophrenia (SCH). However, the signatures and differences of minority gut microbiota in SCH, such as archaea and fungi, have been poorly addressed.

METHODS: We obtained stool samples from 61 SCH patients and 69 healthy controls (HC), and analyzed the compositional and functional alterations of gut archaea, fungi, and bacteria using metagenomic shotgun sequencing (MSS). Additionally, we developed potential biomarkers to distinguish SCH from HC.

RESULTS: SCH patients showed significantly lower archaeal α-diversity compared with that of HC. Whereas there were significant differences between SCH and HC in β-diversity at the species level of archaea, fungi and bacteria. Meanwhile, the functional differences between the two groups were concentrated in glucose, lipid and amino acid metabolic pathways. Furthermore, we established potential diagnostic archaeal (9 species, AUC = 0.73), fungal (8 species, AUC = 0.69), and bacterial (22 species, AUC = 0.74) microbiomes for differentiating SCH patients from HC.

CONCLUSIONS: This study describes a more comprehensive understanding of abnormal gut microbiome in SCH and might provide candidate targets for the development of a microbe-based diagnosis for SCH.

TRIAL REGISTRATION: Chinese Clinical Trial Registry: ChiCTR2000032118, registration date: 2020/04/20.},
}

@article {pmid41484564,
year = {2026},
author = {Tang, LX and Yang, ZF and Yang, YS and Li, LH and Phurbu, D and Zheng, YY and Zhu, JY and Zhu, D and Lv, ZH and Xie, KQ and Hu, W and Yin, YR},
title = {[Not Available].},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-025-02000-6},
pmid = {41484564},
issn = {2191-0855},
support = {No. 202101AU070138 and 202501AT070411//Yunnan Applied Basic Research Projects/ ; NSFC, Nos. 32560004 and 32570003//National Natural Science Foundation of China/ ; No. 230212528080//Xingdian Talent Support Program of Yunnan Province/ ; Nos. 2024YNLCYXZX0081 and YWLCYXZX2023300075//Yunnan Provincial Clinical Medical Center for Emergency Traumatic Dis-eases/ ; No. XZ202501ZY0019//Science and Technology Projects of the Xizang Autonomous Region, China/ ; },
abstract = {Uricase, a key enzyme in purine metabolism, is widely used for uric acid detection and for treating gout and hyperuricemia. To obtain a uricase with both high activity and thermal stability, we cloned and heterologously expressed a novel uricase gene (tc1-uox2) from the Tengchong hot spring metagenome and combined enzymatic characterization with molecular dynamics simulations. TC1-Uox2 exhibited optimal catalytic activity at 35 °C and pH 8.0. It showed remarkable thermal stability, retaining over 40% residual activity after 16 h at 40 °C and maintaining over 80% activity for 14 h at physiological temperature (37 °C). In vitro uric acid-lowering assays demonstrated that 1 µg/mL TC1-Uox2 reduced serum uric acid to below 360 µM within 20 min in whole-blood samples from six hyperuricemic patients. Comparative molecular dynamics simulations with rasburicase indicated that, based on RMSF, radius of gyration (Rg), and hydrogen-bond counts, TC1-Uox2 adopts a more compact overall structure. Free energy landscape (FEL) analysis further revealed that TC1-Uox2 occupies deeper and narrower energy basins, consistent with greater conformational rigidity and thermodynamic stability. These findings elucidate the structural basis of its enhanced thermostability. In summary, TC1-Uox2 is a high-activity, high-stability uricase candidate that represents a promising enzyme target for biotherapeutic intervention in hyperuricemia and illustrates the translational potential of extreme-environment metagenomics for metabolic disease applications.},
}

@article {pmid41484024,
year = {2025},
author = {Abuqwider, J and Pasolli, E and Scidà, G and Corrado, A and Vitale, M and De Filippis, F and Ercolini, D and Annuzzi, G and Rivellese, AA and Bozzetto, L},
title = {Gut microbiome profiles and associated functional pathways are linked to Mediterranean diet adherence and blood glucose control in adults with type 1 diabetes mellitus.},
journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD},
volume = {},
number = {},
pages = {104487},
doi = {10.1016/j.numecd.2025.104487},
pmid = {41484024},
issn = {1590-3729},
abstract = {BACKGROUND AND AIMS: The Mediterranean diet (MD) has been associated with better glycaemic control in children with type 1 diabetes mellitus (T1DM) and favourable microbiome profiles in healthy individuals. However, it remains unclear whether MD adherence is associated with glycaemic control via microbiome. This study examined the relationships among MD adherence, gut microbiome, and glycaemic control in adults with T1DM and assessed the microbiome's ability to predict clinical and dietary outcomes.

METHODS AND RESULTS: In a cross-sectional study of 253 adults with T1DM, dietary intake was assessed using the EPIC food frequency questionnaire, and MD adherence was measured using the rMED score. Participants were stratified by adherence level (low, medium, high). Glycaemic control was evaluated using HbA1c and CGM metrics. Shotgun metagenomic sequencing of stool samples (n = 103) assessed the gut microbiome. Statistical analyses included ANOVA, PERMANOVA, LEfSe, and machine learning modeling. Higher MD adherence was associated with lower HbA1c levels (7.1 % vs 7.7 %; p < 0.001), greater time in range (67.0 % vs 59.4 %; p-trend = 0.03), and higher HDL cholesterol (1.62 vs 1.39 mmol/L; p = 0.01). High MD adherence was linked to a greater abundance of bacterial species such as Faecalibacterium prausnitzii. Both high MD adherence and lower HbA1c were associated with distinct microbiome functional pathways. Microbiome-based machine learning models predicted dietary patterns and clinical metrics.

CONCLUSIONS: In adults with T1DM, greater MD adherence is associated with better glycaemic control and a favourable gut microbiome. Specific microbial pathways may underlie these associations. Integrating diet and microbiome data supports personalized care. The study was registered at ClinicalTrials.gov with the identifier NCT05936242.},
}

@article {pmid41483288,
year = {2026},
author = {Lema, NK and Gemeda, MT and Woldesemayat, AA},
title = {Uncovering resistomes in hospital and pharmaceutical industry wastes: insights from shotgun metagenomic profiling.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41483288},
issn = {1618-1905},
}

@article {pmid41482808,
year = {2026},
author = {Ip, YCA and Allan, EA and Hirsch, SL and Kelly, RP},
title = {Fast, Flexible, Feasible: A Transparent Framework for Evaluating eDNA Workflow Trade-Offs in Resource-Limited Settings.},
journal = {Molecular ecology resources},
volume = {26},
number = {1},
pages = {e70091},
pmid = {41482808},
issn = {1755-0998},
support = {GR042390//OceanKind/ ; GR016745//David and Lucile Packard Foundation/ ; },
mesh = {*Workflow ; Animals ; *DNA, Environmental/isolation & purification/genetics ; *Fishes/genetics/classification ; *Metagenomics/methods/economics ; Time Factors ; Sensitivity and Specificity ; Computational Biology/methods ; Biodiversity ; Resource-Limited Settings ; },
abstract = {Environmental DNA (eDNA) analysis enables biodiversity monitoring by detecting organisms from trace genetic material, but high reagent costs, cold-chain logistics and computational demands limit its broader use, particularly in resource-limited settings. To address these challenges and improve accessibility, we directly compared multiple workflow components, including four DNA extraction methods, two primer sets, three Nanopore basecalling models, and two demultiplexing pipelines. Across 48 workflow combinations tested in an aquarium with 15 fish species, we mapped trade-offs between cost, sensitivity, and processing speed to assess where time and resource savings are possible without compromising detection. Workflows using the Qiagen Blood and Tissue (BT) extraction kit and amplification using the MiFish-U primer set provided the highest sensitivity, detecting ≥ 12 of 15 species by ~3-5 h and reaching the 15-OTU plateau at ~8-10 h with Oxford Nanopore's high accuracy (HAC) basecalling model. Chelex, an alternative lower-cost extraction method, showed partial recovery only (≤ 9 OTUs by 61 h) even with extended sequencing, and did not recover all 15 OTUs. DirectPCR and QuickExtract offered field-friendly extraction alternatives that achieved comparable recovery in ~10-12 h, though their cost-effectiveness varied. While the MarVer1 primer was designed to broaden vertebrate detection, it recovered the same fish species as MiFish-U, though with fewer total reads. Real-time sequencing trials (0-61 h) revealed that high-efficiency workflows (BT + HAC) reached detection plateaus rapidly, indicating sequencing time can be reduced without sacrificing accuracy. The OBITools4 bioinformatics pipeline enabled automated demultiplexing but discarded more reads than an alternative, ONTbarcoder2.3, which retained low-abundance taxa at the cost of manual curation. Rather than identifying a single 'best' workflow, this study provides a transparent decision framework for prioritising cost, speed, and sensitivity in eDNA applications, supporting scalable, cost-effective eDNA monitoring in resource-limited settings.},
}

*Workflow
Animals
*DNA, Environmental/isolation & purification/genetics
*Fishes/genetics/classification
*Metagenomics/methods/economics
Time Factors
Sensitivity and Specificity
Computational Biology/methods
Biodiversity
Resource-Limited Settings

@article {pmid41482538,
year = {2026},
author = {Trigodet, F and Sachdeva, R and Banfield, JF and Eren, AM},
title = {Troubleshooting common errors in assemblies of long-read metagenomes.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41482538},
issn = {1546-1696},
abstract = {Assessing the accuracy of long-read assemblies, especially from complex environmental metagenomes that include underrepresented organisms, is challenging. Here we benchmark four state-of-the-art long-read assembly software programs, HiCanu, hifiasm-meta, metaFlye and metaMDBG, on 21 PacBio HiFi metagenomes spanning mock communities, gut microbiomes and ocean samples. By quantifying read clipping events, in which long reads are systematically split during mapping to maximize the agreement with assembled contigs, we identify where assemblies diverge from their source reads. Our analyses reveal that long-read metagenome assemblies can include >40 errors per 100 million base pairs of assembled contigs, including multi-domain chimeras, prematurely circularized sequences, haplotyping errors, excessive repeats and phantom sequences. We provide an open-source tool and a reproducible workflow for rigorous evaluation of assembly errors, charting a path toward more reliable genome recovery from long-read metagenomes.},
}

@article {pmid41482458,
year = {2026},
author = {Zhou, CB and Zhao, LC and Qin, Y and Yu, J and Li, W and Feng, Q and Tong, X and Abuduaini, R and Lu, SY and Tang, H and Zhang, YX and Cui, Y and Xiao, L and Song, LH and Ni, LK and Wu, K and Zhong, H and Jiang, YC and Zou, Y and Leng, XX and Wang, M and Zhao, WY and Wang, CJ and Liu, Q and Zhang, JQ and Hu, C and Chen, YX and Yao, YF and Zhu, S and Fang, JY},
title = {Streptococcus anginosus-derived methionine promotes gastric cancer progression.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336966},
pmid = {41482458},
issn = {1468-3288},
abstract = {BACKGROUND: Streptococcus anginosus has been linked with an increasing risk of gastric cancer (GC) and recognised as a signature for GC screening.

OBJECTIVE: To investigate the promotional effect of S. anginosus in terms of its metabolic interactions with the host.

DESIGN: We used the functional profiles of shotgun metagenomic sequencing from stools to detect bioactive molecules relevant to S. anginosus. In vivo and in vitro experiments were used to validate the facilitation of S. anginosus to GC progression. S. anginosus clinical strains were isolated and cultivated from cancerous tissues to verify its promotion of GC via methionine production. S. anginosus ΔmetE mutant strains were constructed to confirm the critical role of metE in methionine biosynthesis.

RESULTS: We verified S. anginosus facilitated GC progression in vivo and in vitro. Our functional analysis of metagenomes revealed a significant enrichment of bacterial methionine biosynthesis pathways in GC patients with high S. anginosus abundance. Methionine, identified here as one of the primary microbial metabolites derived from S. anginosus, contributed to GC progression in humans and mice. S. anginosus strains from cancerous tissues were found to promote GC via methionine production. We further observed a higher abundance and prevalence of metE gene in cancer stool metagenomes. By constructing an S. anginosus ΔmetE mutant strain, we confirmed the critical role of metE in methionine biosynthesis.

CONCLUSION: Our results elucidate the role of S. anginosus-derived methionine in GC progression, shedding light on intricate metabolic interplay between S. anginosus and host.},
}

@article {pmid41482085,
year = {2025},
author = {Yang, B and Xia, Q and Ji, X and Su, K and Yu, T and Xiao, Z and Shi, C and Luo, Z and Wang, X and Xu, W and Gao, Y and Hua, H and Shan, J},
title = {Ganjie Decoction protects against respiratory syncytial virus infection by activating PI3K/AKT-apoptosis axis and regulating gut microbiota metabolism.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121142},
doi = {10.1016/j.jep.2025.121142},
pmid = {41482085},
issn = {1872-7573},
abstract = {Ganjie Decoction (GJD), a traditional Chinese medicine (TCM) formula commonly used for respiratory diseases, has shown therapeutic potential against RSV pneumonia. However, its pharmacological mechanisms against respiratory syncytial virus (RSV) pneumonia are not fully understood.

AIM OF STUDY: This study aimd to characterize the active components of GJD and systematically investigate its therapeutic effects and underlying mechanisms in RSV-induced pneumonia.

MATERIALS AND METHODS: To evaluate the therapeutic efficacy of GJD in RSV-infected mice, we monitored body weight, performed qPCR, and conducted histopathological examination of lung tissues. The chemical constituents of GJD were characterized using UPLC-MS. Key bioactive compounds and their potential targets were predicted using network pharmacology and molecular docking. The underlying mechanisms were further elucidated using immunohistochemistry and western blotting. The interactions between GJD and the gut microbiota were explored using antibiotic depletion, fecal microbiota transplantation (FMT), metagenomic sequencing, and in vitro co-culture assays. Untargeted metabolomics was employed to assess GJD-induced metabolic alterations. Finally, the role of 4-hydroxyphenylacetic acid (4-HPA) was investigated through cell viability assays, immunofluorescence staining, and western blot analysis in vitro.

RESULTS: GJD significantly mitigated weight loss, attenuated pulmonary viral load, and suppressed inflammation in RSV-infected mice. Network pharmacology and molecular docking revealed that specific compounds in GJD target the PI3K/AKT signaling pathway. This finding was validated by western blotting and immunohistochemistry, which demonstrated that GJD suppresses PI3K/AKT pathway activation, thereby attenuating apoptosis and ameliorating RSV-induced pneumonia. Notably, these protective effects were markedly attenuated in mice with depleted gut microbiota. Furthermore, the therapeutic effects of GJD against RSV pneumonia were transferable via gut microbiota transplantation. GJD restored RSV-induced dysbiosis of the gut microbiota, with Lactobacillus reuteri emerging as one of the most enriched microbes following treatment. Metabolomics analysis identified 4-HPA as a microbiota-dependent metabolite significantly upregulated by GJD. Remarkably, administration of 4-HPA reproduced GJD's therapeutic effects in RSV-infected mice and activated the KEAP1/NRF2 antioxidant pathway, suggesting that 4-HPA functions as a key mediator of GJD's anti-RSV activity.

CONCLUSIONS: These findings suggest that GJD alleviates RSV pneumonia through a synergistic mechanism that modulates the PI3K/AKT-apoptosis pathway, restores gut microbial balance, and normalizes metabolic disturbances. This study systematically elucidates the mechanistic basis underlying the therapeutic effects of GJD against RSV pneumonia.},
}

@article {pmid41481471,
year = {2026},
author = {Regan, MD and Chiang, E and Grahn, M and Tonelli, M and Assadi-Porter, FM and Suen, G and Carey, HV},
title = {Host-microbiome mutualism drives urea carbon salvage and acetogenesis during hibernation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {1},
pages = {e2518978123},
doi = {10.1073/pnas.2518978123},
pmid = {41481471},
issn = {1091-6490},
support = {IOS-1558044//NSF (NSF)/ ; P41GM136463//HHS | NIH (NIH)/ ; DGE-1747503//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; RGPIN-2021-03109//Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; 21HLSRM06//Canadian Space Agency (CSA)/ ; },
mesh = {Animals ; *Hibernation/physiology ; *Urea/metabolism ; *Sciuridae/microbiology/physiology/metabolism ; *Carbon/metabolism ; *Acetates/metabolism ; *Gastrointestinal Microbiome/physiology ; *Symbiosis/physiology ; Acetic Acid/metabolism ; Fatty Acids, Volatile/metabolism ; *Host Microbial Interactions/physiology ; },
abstract = {Hibernation is a seasonal survival strategy employed by certain mammals that, through torpor use, reduces overall energy expenditure and permits long-term fasting. Although fasting solves the challenge of winter food scarcity, it also removes dietary carbon, a critical biomolecular building block. Here, we demonstrate a process of urea carbon salvage (UCS) in hibernating 13-lined ground squirrels, whereby urea carbon is reclaimed through gut microbial ureolysis and used in reductive acetogenesis to produce acetate, a short-chain fatty acid (SCFA) of major value to the host and its gut microbiota. We find that urea carbon incorporation into acetate is more efficient during hibernation than the summer active season and that while both host and gut microbes oxidize acetate for energy supply throughout the year, the host's ability to absorb and oxidize acetate is highest during hibernation. Metagenomic analysis of the gut microbiome indicates that genes involved in the degradation of gut mucins, an abundant endogenous nutrient, are retained during hibernation. The hydrogen disposal associated with reductive acetogenesis from urea carbon helps facilitate this mucin degradation by providing a luminal environment that sustains fermentation, thereby generating SCFAs and other metabolites usable by both the host and its gut microbes. Our findings introduce UCS as a mechanism that enables hibernating squirrels and their gut microbes to exploit two key endogenous nutrient sources-urea and mucins-in the resource-limited hibernation season.},
}

Animals
*Hibernation/physiology
*Urea/metabolism
*Sciuridae/microbiology/physiology/metabolism
*Carbon/metabolism
*Acetates/metabolism
*Gastrointestinal Microbiome/physiology
*Symbiosis/physiology
Acetic Acid/metabolism
Fatty Acids, Volatile/metabolism
*Host Microbial Interactions/physiology

@article {pmid41481285,
year = {2026},
author = {Zhu, J and Huang, Z and Lin, Y and Zhu, J and Min, R and Wan, Z and Chen, Y and Zhu, J and Xing, L and Li, S and Olovo, CV and Wang, X and Li, G and Zhang, P},
title = {The potential immunological mechanisms of gut microbiota dysbiosis caused by antibiotics exacerbate the lethality of influenza viruses.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2609451},
doi = {10.1080/19490976.2025.2609451},
pmid = {41481285},
issn = {1949-0984},
mesh = {Animals ; *Dysbiosis/immunology/chemically induced/microbiology ; *Gastrointestinal Microbiome/drug effects/immunology ; *Anti-Bacterial Agents/adverse effects ; Mice ; *Orthomyxoviridae Infections/immunology/drug therapy/mortality/virology/microbiology ; Antiviral Agents/therapeutic use/pharmacology ; *Influenza A virus/drug effects/pathogenicity/immunology ; Lung/immunology/virology/pathology/drug effects ; Humans ; Mice, Inbred C57BL ; },
abstract = {BACKGROUND: Antibiotics are not recommended to treat influenza A virus (IAV). However, antibiotic misuse for IAV persists worldwide. How to scientifically use antibiotics for IAV-infected patients remains a considerable challenge.

RESULTS: Here, we investigated the impact of antibiotics on viral pathogenicity, pulmonary-intestinal antiviral immunity, and antiviral drug efficacy. Our findings indicated that antibiotic intervention exacerbated IAV-caused mortality and lung injury in mice, manifested as increased mortality rates, shortened survival time, aggravated pulmonary injury, and excessive inflammatory responses. Furthermore, antibiotic pretreatment significantly diminished the efficacy of antivirals. Metagenomic sequencing revealed that antibiotics reduced the diversity and abundance of beneficial gut microbiota, including Lactobacillus and Bifidobacterium, while promoting the proliferation of pathogenic bacteria such as Klebsiella pneumoniae and Escherichia coli. Mechanistically, antibiotic intervention exacerbated IAV-caused excessive inflammatory responses by the blockage of pulmonary-intestinal antiviral immune pathways, which were caused by the upregulation of PKR, RIG-I, ISG15, and TRIM25 levels while downregulating IPS-1 mRNA levels. However, it is noteworthy that the combination of antibiotics and antiviral drugs effectively offset the adverse effects of antibiotic pretreatment on influenza mortality by upregulating IPS-1 levels and partially restoring pulmonary-intestinal immune homeostasis.

CONCLUSIONS: Pulmonary-intestinal immune homeostasis imbalance caused by antibiotic misuse can not only markedly exacerbate the lethality of IAV, but also significantly attenuate the efficacy of antiviral drugs. A mechanistic study confirmed that gut microbes dysbiosis caused by antibiotic pretreatment exacerbates the homeostasis imbalance of host antiviral immunity by blocking the RIG/MDA5/IPS-1 antiviral signaling pathway. However, combination therapy with antibiotics and antivirals effectively reversed the fatal outcome exacerbated by antibiotic pretreatment. Collectively, our findings not only provide a scientific explanation from the perspective of antiviral immunity as to why antibiotics should not be arbitrarily used to treat viral infections but also lay the scientific foundation for the rational clinical use of antivirals and antibiotics for treating influenza.},
}

Animals
*Dysbiosis/immunology/chemically induced/microbiology
*Gastrointestinal Microbiome/drug effects/immunology
*Anti-Bacterial Agents/adverse effects
Mice
*Orthomyxoviridae Infections/immunology/drug therapy/mortality/virology/microbiology
Antiviral Agents/therapeutic use/pharmacology
*Influenza A virus/drug effects/pathogenicity/immunology
Lung/immunology/virology/pathology/drug effects
Humans
Mice, Inbred C57BL

@article {pmid41481221,
year = {2026},
author = {Sun, S and Ning, Z and Xu, H and Peng, S and Gao, C and Hu, X},
title = {Diagnostic value of plasma cell-free DNA metagenomic next-generation sequencing in patients with suspected infections and exploration of clinical scenarios-a retrospective study from a single center.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2608531},
doi = {10.1080/07853890.2025.2608531},
pmid = {41481221},
issn = {1365-2060},
mesh = {Humans ; Retrospective Studies ; Female ; Male ; *High-Throughput Nucleotide Sequencing/methods ; *Cell-Free Nucleic Acids/blood/genetics ; Middle Aged ; *Metagenomics/methods ; Aged ; Adult ; Sensitivity and Specificity ; Blood Culture ; *Communicable Diseases/diagnosis/blood ; Coinfection/diagnosis/blood/microbiology ; },
abstract = {BACKGROUND: Plasma cell-free DNA metagenomic next-generation sequencing (mNGS) is a non-invasive comprehensive method for the etiological diagnosis of various infectious diseases. However, research on the early diagnosis and real-world clinical impact of plasma mNGS in patients with suspected infection are still limited.

MATERIALS AND METHODS: This study retrospectively included 140 patients with suspected infections who underwent early plasma mNGS and conventional culture testing. Referring to the clinical diagnosis of infectious diseases, the diagnostic performance of plasma mNGS and culture tests was compared, and the application scenarios and clinical effects of plasma mNGS were evaluated.

RESULTS: The positive rate of plasma mNGS was significantly higher than that of culture methods (55.71% vs 25.10%, p < 0.001) and blood cultures (55.71% vs 12.86%, p < 0.001). Regarding clinical diagnosis, the sensitivity of plasma mNGS was significantly higher than that of culture (58.27% vs 37.80%, p = 0.002). The combination of mNGS and culture achieved a higher detection sensitivity (69.29%), especially in patients with multi-site co-infections (73.68%) and blood infections (73.17%). Plasma mNGS demonstrated higher sensitivity in patients with procalcitonin (PCT) index > 5 ng/ml or human neutrophil lipocalin (HNL) index > 200 ng/ml. In terms of treatment, a total of 69 patients (54.33%) benefited from plasma mNGS.

CONCLUSION: This study highlights the significant improvement in pathogen detection performance by combining conventional culture with plasma mNGS detection, especially in patients with multi-site co-infections and blood infections. Early use of plasma mNGS as an adjunct to culture can better guide clinicians to initiate appropriate anti-infective therapy.},
}

Humans
Retrospective Studies
Female
Male
*High-Throughput Nucleotide Sequencing/methods
*Cell-Free Nucleic Acids/blood/genetics
Middle Aged
*Metagenomics/methods
Aged
Adult
Sensitivity and Specificity
Blood Culture
*Communicable Diseases/diagnosis/blood
Coinfection/diagnosis/blood/microbiology

@article {pmid41480976,
year = {2026},
author = {Rao, C and Su, X and Xia, Y and Li, N and Wan, Y and Lyu, H and Song, T and Dong, W and Shen, X},
title = {From Physical Architecture to Ecosystem Function: Tillage Exerts Indirect Control on Nitrogen Transformation by Restructuring Preferential Flow Paths.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c12351},
pmid = {41480976},
issn = {1520-5851},
abstract = {How long-term tillage drives nitrogen (N) function succession by degrading vadose zone preferential flow paths remains unclear. This study investigated croplands across multiple tillage chronosequences by integrating dye tracing, [15]N isotope tracing, and metagenomic techniques. The study shows that tillage-induced degradation of preferential flow structures homogenizes the vadose zone and reshapes N-cycling communities, shifting denitrifiers from nirK- to nirS-dominated assemblages. Consistent with this community turnover, gross nitrification rates in shallow preferential paths are 30.8% higher than in the adjacent matrix in short-term tillage, whereas in deep layers matrix denitrification and DNRA rates exceed those in preferential paths by 37.9 and 76.1%, and anammox appears only in the matrix at medium- and long-term tillage, indicating a concentration of reductive N processes in the matrix. Path analysis further shows that tillage-driven alterations in hydraulic properties (path coefficient = -0.91, p < 0.01), together with these community and process-rate shifts, redirect the dominant N pathway from hotspot-driven nitrification in preferential channels to matrix-driven reductive N loss, converting a nitrate-leaching-prone system into one with higher gaseous emission potential. This establishes a mechanistic link linking soil hydraulic degradation to N functional succession and supports targeted, stage-dependent farmland nitrogen management.},
}

@article {pmid41480659,
year = {2026},
author = {Balbino, KP and Kravchychyn, ACP and Cândido, FG and Dias, MME and Mendes, TAO and Oliveira, LL and Castro, LCV and Bressan, J and de la Garza, AL and Milagro, FI and Zulet, MA and Hermsdorff, HHM},
title = {Precision nutrition in weight loss and neuroendocrine control of people with obesity: The study protocol of a factorial randomised controlled trial (GenON Programme).},
journal = {Diabetes, obesity & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1111/dom.70414},
pmid = {41480659},
issn = {1463-1326},
support = {444037/2023-3//National Council for Scientific and Technological Development - CNPq/ Brazilian Ministry of Health - MoH, Brazilian National Program of Genomics and Precision Health - Genomas Brasil/ ; Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {AIMS: Precision nutrition, guided by genetic testing, has emerged as a promising approach for managing obesity. However, robust clinical trials testing its effectiveness in real-world dietary interventions remain scarce. The GenOn Programme aims to evaluate whether tailoring nutritional care based on genetic risk for obesity enhances weight loss, satiety control, and metabolic outcomes in adults with overweight and obesity.

MATERIALS AND METHODS: The GenOn Programme is an 18-week, 2 × 2 factorial, randomised controlled trial including 120 adults classified as high or low genetic risk for obesity (variants: FTO rs9939609 and rs1121980; MC4R rs1782313; LEP rs7799039). Participants are randomised to standard or satiety-focused dietary counselling. Both groups receive five calorie-restricted (-500 kcal/day), nutritionally balanced meal plans. The satiety arm additionally includes a high-protein breakfast, daily granola supplementation and behavioural strategies. Assessments at baseline, Week 12, and Week 18 include weight loss, body composition, satiety perception, quality of life, cardiometabolic markers, (epi)genetics, inflammation, neuroendocrine regulation, and metagenomics.

RESULTS AND CONCLUSIONS: The GenOn Programme is a randomised controlled trial to test a precision nutrition approach for overweight and obesity, integrating genetics, dietary strategies, and behavioural support. Findings may inform dietitians and healthcare systems on the clinical value of genetically guided nutritional care to improve outcomes in the treatment of overweight and obesity.},
}

@article {pmid41480317,
year = {2025},
author = {Zakharzhevskaya, NB and Erdes, SI and Belousova, EA and Samolygo, IS and Manina, MA and Kondrashova, PV and Lomakina, EY and Kardonsky, DA and Vorobyeva, EA and Shagaleeva, OY and Silantyev, AA and Kazakova, VD and Kashatnikova, DA and Kalachnuk, TN and Kolesnikova, IV and Chaplin, AV and Markelova, MI and Grigoryeva, TV and Olekhnovich, EI and Veselovsky, VA and Morozov, MD and Zoruk, PY and Boldyreva, DI and Vanyushkina, AA and Efimov, BA},
title = {Combined metabolomic and metagenomic analysis reveals inflammatory bowel disease diversity in pediatric and adult patients.},
journal = {World journal of gastroenterology},
volume = {31},
number = {48},
pages = {112653},
pmid = {41480317},
issn = {2219-2840},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metabolomics/methods ; *Colitis, Ulcerative/microbiology/diagnosis/metabolism ; *Crohn Disease/microbiology/diagnosis/metabolism ; Feces/microbiology ; Child ; Middle Aged ; Male ; Female ; *Metagenomics/methods ; Adolescent ; Child, Preschool ; Aged ; Biomarkers/metabolism/analysis ; Age Factors ; Adult ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; },
abstract = {BACKGROUND: The gut microbiota displays pronounced compositional differences between pediatric and adult populations, both under normal conditions and during the development of inflammatory bowel disease (IBD). These structural variations are accompanied by substantial changes in microbial metabolic activity.

AIM: To identify novel early diagnostic biomarkers of IBD, we performed an integrated multi-omics analysis that included assessing microbial community structure and profiling microbial metabolic activity in pediatric and adult cohorts with ulcerative colitis (UC) and Crohn's disease (CD).

METHODS: The study cohort consisted of two distinct age groups with confirmed IBD diagnoses: Adult patients (aged 45 to 70) and pediatric patients (aged 5 to 15), each diagnosed with either CD or UC. 16S rRNA gene sequencing was performed using the MinION™ Mk1B platform, with data acquisition carried out via MinKNOW software version 22.12.7 (Oxford Nanopore Technologies). Stool samples were analyzed using a Shimadzu QP2010 Ultra GC/MS system equipped with a Shimadzu HS-20 headspace extractor.

RESULTS: Comparative analysis revealed significant age-related differences in the abundance of Bacteroidota, with pediatric IBD patients showing a lower prevalence compared to adults. Microbial profiling identified Streptococcus salivarius and Escherichia coli as potential biomarkers for assessing IBD risk in children. Furthermore, metagenomic analysis uncovered five microbial signatures with diagnostic potential for CD: Ralstonia insidiosa, Stenotrophomonas maltophilia, Erysipelatoclostridium ramosum, Blautia spp., and Coprococcus comes. Using comprehensive metabolomic profiling, we developed and validated novel risk prediction algorithms for pediatric IBD. The CD risk stratification model identifies high-risk patients based on two key biomarkers: An elevated IBD risk coefficient score and reduced levels of 1H-indole-3-methyl. The UC risk prediction model incorporates three metabolic biomarkers indicative of increased disease risk: An elevated risk coefficient score, increased acetate levels, decreased pentanoic acid, and altered excretion of p-cresol (4-methylphenol).

CONCLUSION: Functional metabolomics holds transformative potential for IBD diagnostics across all age groups, with especially significant implications for pediatric patients. The distinct metabolic and metagenetic profiles observed in the pediatric cohort may represent primary alterations in IBD, providing valuable insights for exploring novel mechanisms underlying disease pathogenesis.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metabolomics/methods
*Colitis, Ulcerative/microbiology/diagnosis/metabolism
*Crohn Disease/microbiology/diagnosis/metabolism
Feces/microbiology
Child
Middle Aged
Male
Female
*Metagenomics/methods
Adolescent
Child, Preschool
Aged
Biomarkers/metabolism/analysis
Age Factors
Adult
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/metabolism/classification/isolation & purification

@article {pmid41480270,
year = {2025},
author = {Bustos-Caparros, E and Viver, T and Gago, JF and Venter, SN and Bosch, R and Konstantinidis, KT and Rodriguez-R, LM and Rossello-Mora, R},
title = {Uneven sequencing (coverage) depth can bias microbial intraspecies diversity estimates and how to account for it.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf228},
pmid = {41480270},
issn = {2730-6151},
abstract = {An unbiased and accurate estimation of intraspecies diversity, i.e. the extent of genetic diversity within species (or microdiversity), is crucial for clinical and environmental microbiome studies. Although it is well appreciated that sequencing depth (or coverage depth) below 10X can provide biased estimates of microdiversity, typically underestimating diversity due to the random sampling of alleles, there is a widely accepted convention that microdiversity estimates tend to be relatively stable at sequencing depth exceeding 10X. Therefore, discarding species with <10X or rarefying to 10-20X sequencing depth are generally used to compare microdiversity among taxa and samples. Our findings showed that these biases may persist even at depth levels above 50-200X for all popular sequencing platforms, including Illumina, PacBio, and Oxford Nanopore. The biases mostly, but not always, represent an underestimation of diversity and were attributable to the incomplete recovery of Single Nucleotide Variants (SNVs) at lower sequencing depth levels. To address this issue, we recommend using rarefaction-based approaches to standardize data at least 50X, and ideally at 200X sequencing depth, which reduces differences between observed and expected microdiversity values to <0.5%. Furthermore, the Average Nucleotide Identity of reads (ANIr) metric is significantly less sensitive to sequencing depth variability than nucleotide diversity (π), making it a robust alternative for estimating microdiversity at sequencing depth close or exceeding 10X, without a need to rarefying data. Therefore, the sequencing depth thresholds proposed herein provide a more standardized framework for direct comparisons of microdiversity across samples and studies.},
}

@article {pmid41480265,
year = {2025},
author = {Ren, G and Gubry-Rangin, C and Wang, W and Liu, R and Liu, J and Liu, J and Zhang, XH and Liu, J},
title = {Purifying selection and low recombination facilitated sequential colonization of benthic and pelagic coastal ocean by ammonia-oxidizing archaea.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf234},
pmid = {41480265},
issn = {2730-6151},
abstract = {The evolutionary adaptation of archaea to ecologically diverse habitats remains poorly understood. Ammonia-oxidizing archaea (AOA) exhibit significant diversification across various environmental conditions; however, their ecological dynamics, diversification, and associated evolutionary processes are still largely unexplored in coastal environments, which contain extensive ecosystem heterogeneity. Combining newly assembled metagenomic data from Chinese marginal seas (2059 km coverage) with global datasets (spanning over 16 000 km), these knowledge gaps were explored across a continental-scale latitudinal gradient. It revealed that coastal AOA genomic diversity is latitude-dependent, with predicted optimum growth temperatures and substrate metabolic pathways explaining the geographical distribution. The two dominant genus-level clades exhibited significantly distinct benthic-pelagic niches, associated with specific genes involved in nutrient uptake and stress resistance. Phylogenomic reconstructions suggest that AOA initially colonized the coastal ocean sediments around 718 million years ago (Mya), and subsequent purifying selection and low recombination facilitated the AOA niche expansion into marine coastal environments. By revealing the evolutionary trajectories of Nitrososphaeria and their differential colonization patterns, our findings offer a novel perspective on the mechanisms of AOA diversification in the coastal ocean. This work advances our understanding of microbial diversification and niche differentiation of AOA in coastal ecosystems as well as the evolutionary forces shaping their global biogeography.},
}

@article {pmid41480263,
year = {2025},
author = {Ma, M and Wang, M and Liang, Y and Guo, Y and Zhang, H and Cao, L and Fu, L and Hu, G and Li, C and Mock, T and Li, C},
title = {Microbial communities and metabolic functions vary with spatial heterogeneity in cold-seep carbonates.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf232},
pmid = {41480263},
issn = {2730-6151},
abstract = {Cold-seep carbonates, formed through interactions among methane, fluid chemistry, and microbial chemosynthesis, represent biodiversity hotspots in the deep sea. Spatial heterogeneity within these carbonates arises from variations in methane flux, yet the microbial contributions to this heterogeneity remain underexplored. Here we combined remotely operated vehicle-based in situ measurements, X-ray imaging, metagenomics, qPCR, and [13]C-CH4 stable-isotope labeling to investigate microbial communities across carbonate habitats in the South China Sea. We found that methane flux linked to carbonate structural properties, shapes microbial metabolic interactions, notably anaerobic methane oxidation coupled with aragonite and FeS precipitation. These processes may contribute to self-sealing carbonate features, potentially reducing methane permeability and influencing geochemical gradients and geomorphology. Our findings reveal that microbiomes and their feedbacks play a significant role in shaping habitat-scale spatial heterogeneity of cold-seep carbonates, improving our understanding of methane cycling and carbonate ecosystem dynamics.},
}

@article {pmid41480114,
year = {2025},
author = {Robayo-Cuevas, C and Junca, H and Uribe, S and Gómez-Palacio, A},
title = {Detection of endosymbiotic, environmental, and potential bacterial pathogens in diverse mosquito taxa from Colombian tropical forests using RNAseq.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1727830},
pmid = {41480114},
issn = {1664-302X},
abstract = {INTRODUCTION: Mosquitoes of the subfamily Culicinae transmit pathogens of major medical and veterinary importance, particularly in tropical regions where urbanization and ecological change promote arbovirus circulation. In Colombia, rural Culicinae species are diverse and harbor microbiomes that may influence vector competence, yet their bacterial communities remain poorly characterized.

METHODS: We characterized the bacterial microbiota of multiple Culicinae species and morphotypes collected from two rural localities in Antioquia, Colombia, using an integrated metagenomic approach. Ribosomal 16S rRNA sequences were extracted from total RNA-seq datasets to infer bacterial community composition and assess α- and β-diversity. Diversity metrics (Chao1 and Shannon indices), Discriminant Analysis of Principal Components (DAPC), and Bray-Curtis ordination were used to evaluate community structure. In parallel, de novo assembled contigs were taxonomically annotated against the NCBI NR bacterial database to obtain complementary taxonomic and functional insights.

RESULTS: Culex morphotypes exhibited the highest richness and evenness, whereas Aedes and Trichoprosopon showed lower diversity. Ordination and DAPC analyses revealed partial clustering by species and tribe. Both the 16S and assembly-based analyses showed complex bacterial assemblages dominated by Wolbachia (up to 60% of reads in several Aedes and Culex morphotypes), followed by environmental genera such as Pseudomonas and Acinetobacter (10-20%). Lower-abundance taxa of medical and veterinary importance-including Salmonella, Borrelia, and Clostridium (<5%)-were also detected. Bacterial community structure differed among mosquito species; Aedes albopictus was enriched in lactic acid bacteria, while Culex morphotypes exhibited broader environmental and endosymbiotic profiles.

DISCUSSION: This study provides the first comprehensive metagenomic description of bacterial communities associated with rural Culicinae mosquitoes in Colombia. The predominance of symbionts such as Wolbachia and Spiroplasma, coupled with distinct bacterial signatures among host species, highlights the ecological complexity of these microbiomes and their potential relevance for microbiome-based strategies in sustainable arboviral disease management.},
}

@article {pmid41480112,
year = {2025},
author = {Fu, J and Bu, G and Aimaier, S and Yang, Y and Bao, Z and Wulasihan, M},
title = {Sex-specific association between gut Faecalibacterium prausnitzii and hypertension in male individuals.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1683587},
pmid = {41480112},
issn = {1664-302X},
abstract = {OBJECTIVE: While gut microbiota (GM) dysbiosis has been implicated in hypertension, the sexassociated microbial signatures and their underlying mechanisms remain poorly understood, particularly in populations living in unique geographical and climatic conditions.

DESIGN: Through an integrated approach combining 16S rRNA sequencing, shotgun metagenomics, and serum metabolomics, we systematically investigated the sex-associated characteristics of the gut microbiota in hypertension among a cohort of 200 participants from Xinjiang.

METHODS: An initial cohort analysis identified Faecalibacterium as a male-associated biomarker for hypertension. Subsequent species-level characterization revealed that Faecalibacterium prausnitzii (F. prausnitzii) showed significant negative correlations with systolic blood pressure (SBP). This male-specific association was consistently observed across both 16S rRNA sequencing and shotgun metagenomic datasets. Then, our integrated analysis suggested a potential pathway through which F. prausnitzii may be linked to systolic blood pressure in male individuals, with N-phenylacetylglutamine (PAGln) identified as a potential mediating metabolite.

CONCLUSION: Our study establishes a microbe-metabolite-clinical trait axis in the pathophysiology of sex-associated hypertension and significantly advances our understanding of sex-driven host-microbe interactions.},
}

@article {pmid41479870,
year = {2025},
author = {Ghosh, N and Sinha, K},
title = {Guardians within: Cross-talk between the gut microbiome and host immune system.},
journal = {World journal of gastrointestinal pathophysiology},
volume = {16},
number = {4},
pages = {111245},
pmid = {41479870},
issn = {2150-5330},
abstract = {The gut microbiome, a complex ecosystem of trillions of microorganisms, plays a crucial role in immune system regulation and overall health. This review explores the intricate cross-talk between the gut microbiota and the host immune system, emphasizing how microbial communities shape immune cell differentiation, modulate inflammatory responses, and contribute to immune homeostasis. Key interactions between innate and adaptive immune cells - including macrophages, dendritic cells, natural killer cells, innate Lymphoid cells, T cells, and B cells - and gut microbiota-derived metabolites such as short-chain fatty acids are discussed. The role of commensal bacteria in neonatal immune system development, mucosal barrier integrity, and systemic immunity is highlighted, along with implications for autoimmune diseases, inflammatory conditions, and cancer immunotherapy. Recent advances in metagenomics, metabolomics, and single-cell sequencing have provided deeper insights into the microbiota-immune axis, opening new avenues for microbiome-based therapeutic strategies. Understanding these interactions paves the way for novel interventions targeting immune-mediated diseases and optimizing health through microbiome modulation.},
}

@article {pmid41479581,
year = {2025},
author = {Komatsu, H},
title = {Comparison of three pediatric studies investigating acute hepatitis of unknown etiology.},
journal = {World journal of virology},
volume = {14},
number = {4},
pages = {110435},
pmid = {41479581},
issn = {2220-3249},
abstract = {Between 2021 and 2023, approximately 400 pediatric cases of acute hepatitis of unknown etiology (AHUE) were reported in European countries and the United States. In 2023, three pediatric studies revealed that adeno-associated virus serotype 2 (AAV-2) infection was associated with AHUE. This article presents a summary and comparison of the results of metagenomic sequencing, viral whole-genome sequencing, virus-specific real-time polymerase chain reaction (PCR) and histological analysis of the liver, all of which were among the common investigative methods used in the three pediatric studies. All three pediatric studies revealed 80% or greater rates of positivity for AAV-2 in cases of AHUE according to metagenomic sequencing. Moreover, on the basis of PCR results, two studies revealed high AAV-2 positivity rates (96.4% and 81.2%) among cases of AHUE. These findings suggest that AAV-2 is a pathogen in AHUE. Coinfection with AAV-2 and one or more helper viruses (human adenovirus, human herpesvirus 6B, Epstein-Barr virus, etc.), high viral loads of AAV-2 in blood, anti-AAV-2 IgM and human leukocyte antigen typing could be candidate diagnostic criteria for AHUE. AAV-2 infection should be incorporated into clinical guidelines for the management of acute liver failure. Cidofovir can be administered if coinfection with AAV-2 and HAdV is detected.},
}

@article {pmid41478956,
year = {2026},
author = {Halford, C and Moragues-Solanas, L and Weller, SA and Gilmour, M},
title = {Whole Genome Amplification of Microbial DNA from Host-Depleted Clinical Samples.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3003},
number = {},
pages = {175-186},
pmid = {41478956},
issn = {1940-6029},
mesh = {Humans ; *Metagenomics/methods ; *Nucleic Acid Amplification Techniques/methods ; *DNA, Bacterial/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Clinical metagenomics (CMg) involves the untargeted sequencing of the genetic content of samples collected from patients and is a highly promising method for the diagnosis of infectious disease. Depending on the sample type, CMg can be reliant on the removal of the host genetic material from the sample to support detection of microbial pathogens, and this selective process (or an otherwise low abundance of microbial cells in the sample) may result in concentrations of DNA too low for productive sequencing. Whole genome amplification (WGA), the nonselective amplification of the total DNA of a sample, can be applied to significantly increase the concentration of DNA and enable CMg sequencing. This chapter describes the methods for the amplification of microbial DNA extracted from host-depleted wound swab samples using the GenomiPhi[™] V3 Ready-To-Go[™] (Cytiva) DNA WGA kit and host-depleted whole blood samples using the REPLI-g[®] Single-Cell WGA kit (Qiagen). This is followed by the de-branching and bead-based clean-up of the amplified DNA, resulting in highly concentrated DNA ready for CMg DNA sequencing.},
}

Humans
*Metagenomics/methods
*Nucleic Acid Amplification Techniques/methods
*DNA, Bacterial/genetics/isolation & purification
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods

@article {pmid41478955,
year = {2026},
author = {Cruz-Flores, R and Cáceres-Martínez, J and Dhar, AK},
title = {Laser Microdissection and Near Single-Cell Whole Genome Amplification.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3003},
number = {},
pages = {165-173},
pmid = {41478955},
issn = {1940-6029},
mesh = {*Single-Cell Analysis/methods ; *Laser Capture Microdissection/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; *Nucleic Acid Amplification Techniques/methods ; *Genome, Viral ; Paraffin Embedding ; Tissue Fixation ; Genomics/methods ; DNA, Viral/genetics/isolation & purification ; },
abstract = {Laser microdissection (LMD) and whole genome amplification (WGA) are powerful techniques that integrate molecular and histological approaches to enable the precise selection of a minimal number of virus-infected cells-down to near single-cell resolution-and the subsequent generation of whole viral genomes with minimal host DNA interference. This chapter presents a detailed protocol for LMD and near single-cell WGA, specifically optimized for the recovery and sequencing of viral genomes from formalin-fixed paraffin-embedded (FFPE) tissues. The method allows for the targeted isolation of infected cells, thereby reducing host genomic background and enhancing the detection of pathogen-specific signals for downstream next-generation sequencing (NGS). The protocol includes steps for tissue section preparation, cell isolation via LMD, DNA extraction using the PicoPure DNA Extraction Kit, and unbiased genome amplification using the SeqPlex DNA Amplification Kit-ensuring high-quality nucleic acid recovery suitable for NGS workflows.},
}

*Single-Cell Analysis/methods
*Laser Capture Microdissection/methods
Humans
High-Throughput Nucleotide Sequencing/methods
*Nucleic Acid Amplification Techniques/methods
*Genome, Viral
Paraffin Embedding
Tissue Fixation
Genomics/methods
DNA, Viral/genetics/isolation & purification

@article {pmid41318438,
year = {2025},
author = {Liu, J and Wu, J and Zhang, W and Huang, H and Liao, D},
title = {Disseminated Talaromyces marneffei infection mimicking tuberculosis in an HIV-negative adult with anti-IFN-γ autoantibodies: a case report.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {1},
pmid = {41318438},
issn = {1471-2334},
support = {2024J0112//the Nature Science Foundation of Fujian Province of China/ ; },
abstract = {BACKGROUND: Talaromyces marneffei (TM) is an opportunistic fungus causing life-threatening disseminated infections in immunocompromised individuals. While classically associated with HIV, TM is increasingly reported in HIV-negative patients, often misdiagnosed due to nonspecific manifestations.

CASE PRESENTATION: A 38-year-old HIV-negative Chinese woman with a history of thyroid cancer presented with a three-month history of fever, cough, weight loss, and subcutaneous masses. Imaging revealed diffuse pulmonary nodules and osteolytic bone destruction. She was initially misdiagnosed with tuberculosis and received anti-TB therapy without improvement. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified TM, which was later confirmed by fungal culture. Anti–interferon-gamma autoantibodies (anti–IFN-γ auto-Abs) were markedly elevated (111.72 ng/mL). She was treated with liposomal amphotericin B(L-AmB) followed by itraconazole, achieving temporary remission. One month post-discharge, TM recurred with new Sweet syndrome–like skin lesions. Immunomodulatory therapy combined with antifungals led to disease control.

CONCLUSION: This case highlights three key clinical insights: (1) TM can closely mimic tuberculosis, especially in HIV-negative individuals; (2) mNGS is a valuable diagnostic tool when conventional tests fail; and (3) Anti–IFN-γ auto-Abs may underlie recurrent or refractory TM infections. Clinicians in endemic regions should consider TM and evaluate immune status early in atypical or treatment-resistant cases.},
}

@article {pmid41316171,
year = {2025},
author = {Meldrum, OW and Tiew, PY and Xu, H and Low, DY and Ivan, FX and Narayana, JK and Jaggi, TK and Ching, J and Chotirmall, SH},
title = {Integrated multi-omics profiling for risk stratification in Asians with COPD.},
journal = {Respiratory research},
volume = {27},
number = {1},
pages = {2},
pmid = {41316171},
issn = {1465-993X},
support = {(#020458-00001//LKCMedicine-ICL Fellowship/ ; MOH-001636//National Research Foundation Singapore under its Open Fund-Large Collaborative Grant and administered by the Singapore Ministry of Health's National Medical Research Council/ ; MOH-001356//Singapore Ministry of Health's National Medical Research Council under its Clinician-Scientist Individual Research Grant/ ; MOH-001855//Singapore Ministry of Health's National Medical Research Council under its Clinician-Scientist Award (CSA) Investigator (INV) category/ ; RT1/22//Singapore Ministry of Education under its AcRF Tier 1 Grant/ ; },
abstract = {BACKGROUND: Comorbidity-based risk stratification in Chronic Obstructive Pulmonary Disease (COPD) incompletely captures inherent biological heterogeneity, particularly in Asian populations that demonstrate high-risk clinical phenotypes including prior pulmonary tuberculosis. We investigated whether integrated sputum multi-omics could improve risk stratification in an Asian COPD cohort.

METHODS: We conducted a prospective, multicenter assessment of N = 56 Asians with established COPD, classified as high- (N = 25; cardiovascular or ex-tuberculosis) or low-risk (N = 31; diabetic or low-comorbidity) based on established co-morbidity phenotyping. Sputum was subjected to mucus analysis (MUC5AC, MUC5B, mucus solids, rheology), metabo-lipidomics (LC-MS/MS) and microbiome assessment (shotgun metagenomics). Multivariate statistics was employed to integrate datasets.

RESULTS: High-risk Asian COPD demonstrates abnormal mucus biochemistry characterized by elevated MUC5AC; extensive metabo-lipidomic alterations characterized by dysregulated tryptophan-kynurenine metabolism and lipid remodeling with enrichment of lysophosphatidylcholines and triacylglycerols. Microbial networks are disrupted in high-risk patients, typified by antagonistic interactions driven by K. pneumoniae, H. influenzae and Neisseria spp. Integrative assessment combining all datasets partitioned the cohort into two clusters: SNF 1 (N = 34) and SNF 2 (N = 22), the former representing an unfavorable group characterized by exacerbations, hospitalizations, mucus dysfunction, microbial pathogens and dysregulated metabo-lipidomic pathways. Remarkably, 42% (N = 13 of 31) of the originally classified low risk COPD exhibited the unfavorable SNF 1 endotype, distinguished by more severe exacerbations (hospitalizations), K. pneumoniae and elevated hypoxanthine, creatine, spermine and phosphatidylcholines.

CONCLUSION: Integrative multi-omics profiling of Asian COPD significantly refines clinical risk stratification identifying a novel ‘high-risk’ biological endotype. Substantial proportions of clinically low-risk COPD exhibit this endotype, suggesting that clinical and co-morbidity profiling in Asians with COPD should be supplemented by molecular assessment to ensure accurate risk stratification.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12931-025-03440-1.},
}

@article {pmid41478953,
year = {2026},
author = {Lozano-Escobar, ED and Mateo-Cáceres, V and Mayoral-Campos, C and Redrejo-Rodríguez, M},
title = {Assessing Amplification Quality and Bias in MDA Methods Through Comparative Analysis of Short-Read Sequencing.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3003},
number = {},
pages = {131-148},
pmid = {41478953},
issn = {1940-6029},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; Humans ; DNA Copy Number Variations ; *Nucleic Acid Amplification Techniques/methods/standards ; *Sequence Analysis, DNA/methods ; Genomics/methods ; Metagenome ; },
abstract = {Although high-throughput sequencing methods have greatly improved over the last few years, direct sequencing remains unfeasible when DNA quantity or quality is limited. In such instances, various whole genome or metagenome amplification (WGA) techniques can generate sufficient DNA for multiple analyses, albeit with some amplification bias. Competent WGA analysis is typically evaluated by sequence coverage, assessed through two key parameters: depth, referring to the number of reads containing each nucleotide, and breadth, indicating the proportion of nucleotides in the consensus sequence relative to the original sequence length at the obtained depth. Adequate coverage is essential for detailed genomic analysis and the detection of population variants, copy number variations (CNVs), and structural variants (SVs). This chapter outlines a pipeline for analyzing Illumina sequencing data of amplified samples compared to non-amplified samples to assess the performance of various WGA methods, starting from raw sequences.},
}

*High-Throughput Nucleotide Sequencing/methods
Humans
DNA Copy Number Variations
*Nucleic Acid Amplification Techniques/methods/standards
*Sequence Analysis, DNA/methods
Genomics/methods
Metagenome

@article {pmid41478678,
year = {2026},
author = {Wang, Y and He, L and Hu, X and Guan, Y and Chen, X and Du, J and Chen, J and Ma, C and Ye, L},
title = {Metagenomic and culture-based genomics reveal virulence and resistance risks in Manila clam microbiomes.},
journal = {Food microbiology},
volume = {136},
number = {},
pages = {105001},
doi = {10.1016/j.fm.2025.105001},
pmid = {41478678},
issn = {1095-9998},
mesh = {Animals ; *Bivalvia/microbiology ; Metagenomics ; *Bacteria/genetics/isolation & purification/pathogenicity/drug effects/classification ; *Microbiota ; Virulence Factors/genetics ; Anti-Bacterial Agents/pharmacology ; Virulence ; Genomics ; *Drug Resistance, Bacterial ; Vibrio/genetics/pathogenicity/isolation & purification/drug effects ; Shellfish/microbiology ; Phylogeny ; },
abstract = {Bivalves are important aquaculture products whose safety is shaped by their microbiomes. Here, we present the first comprehensive characterization of Manila clam (Ruditapes philippinarum) microbiomes using both shotgun metagenomics (6 clams) and culture-based genomics (169 isolates, 40 draft genomes), integrating community, functional, and antimicrobial resistance profiling. Communities were dominated by Proteobacteria (99.3-99.9 %), with Pseudoalteromonas and Vibrio collectively accounting for 74.9-99.7 % and showing strong inverse correlations, defining Pseudoalteromonas-dominated, Vibrio-dominated, and mixed states. Species richness ranged from 22 to 180 per sample. Recognized human pathogens occurred at low abundance (<0.3 %), including Vibrio parahaemolyticus, Vibrio alginolyticus, and Photobacterium damselae, while opportunistic vibrios expanded in some clams (e.g., Vibrio cyclitrophicus 57.9 %). We reconstructed 34 high-quality MAGs, seven resolved to species (Pseudoalteromonas tetraodonis, V. cyclitrophicus, Shewanella aquimarina), alongside unclassified lineages. Metagenomes encoded 14 virulence-factor categories with 2281 subtypes, and isolate genomes added 93 further subtypes, including high-virulence loci in Escherichia coli and type III secretion genes in V. parahaemolyticus. Resistomes spanned 18 antibiotic classes with 511 subtypes; isolates contributed 22 additional antibiotic resistance genes(ARGs), including extended-spectrum β-lactamases (blaCTX-M-102) and blaNDM-1. Four carbapenemase-producing isolates (three Shewanella algae, one V. parahaemolyticus) carried blaNDM-1 on IncC plasmids, with the V. parahaemolyticus plasmid transferable to E. coli. Two P. tetraodonis MAGs encoded RiPP-like and terpene biosynthetic clusters plus phage-defense systems, consistent with Vibrio suppression. These findings demonstrate that clam microbiomes fluctuate between protective (Pseudoalteromonas) and pathogenic (Vibrio-Shewanella) states, providing a first integrated framework for assessing microbial risk, antimicrobial resistance, and food safety interventions in bivalve aquaculture.},
}

Animals
*Bivalvia/microbiology
Metagenomics
*Bacteria/genetics/isolation & purification/pathogenicity/drug effects/classification
*Microbiota
Virulence Factors/genetics
Anti-Bacterial Agents/pharmacology
Virulence
Genomics
*Drug Resistance, Bacterial
Vibrio/genetics/pathogenicity/isolation & purification/drug effects
Shellfish/microbiology
Phylogeny

@article {pmid41478427,
year = {2025},
author = {Zhou, Z and Xu, M and Gao, C and Zheng, C and Bao, K and Ma, J},
title = {Metagenomic insights into N2O emission pathways shaped by arsenic and hydrological regimes in mangrove soils: An incubation study.},
journal = {Environmental research},
volume = {292},
number = {},
pages = {123658},
doi = {10.1016/j.envres.2025.123658},
pmid = {41478427},
issn = {1096-0953},
abstract = {Mangrove wetlands are characterized by an abundant and complex nitrogen cycling (N-cycling) process during periodic tidal flooding, and increasing arsenic (As) concentration profoundly influences microbial ecosystems and nitrogen (N) transformation. However, the combined impacts of As and hydrology on nitrous oxide (N2O) emissions remain unclear. Here, a soil microcosm experiment was conducted under two hydrological regimes (non-flooded and flooded) and with three As addition levels (50, 100, and 200 mg kg[-1]) to examine their effects on N2O fluxes and N transformation. The results demonstrated that As addition significantly enhanced N2O uptake, reducing fluxes by 1.29-26.47 % and 3.18-10.04 % relative to the control (CK) under non-flooded and flooded conditions, respectively. Notably, the N2O uptake flux under flooded conditions was 3.01 times that of non-flooded conditions on average. Furthermore, influencing mechanisms on N2O emission differ significantly between hydrological regimes. In non-flooded treatments, As primarily decreased NO3[-]-N availability and increased NH4[+]-N retention via upregulating nirBD and nrfAH genes to enhance the DNRA pathway, which reduced the production of N2O. Meanwhile, As promoted N2O reduction mainly through the upregulation of the nosZ gene, resulting in more N2O uptake. However, As predominantly existed as As(III) in flooded treatments, which stimulated the expression of As-resistance genes. This response helped alleviate As toxicity on microorganisms. Additionally, the enhanced decomposition of SOC served as the major energy source for microorganisms, maintaining and even increasing the abundance of partial N-cycling functional genes. Meanwhile, under nitrate-limited conditions, one possible explanation for the observed N2O uptake is that its reduction was stimulated because N2O could serve as an alternative terminal electron acceptor. The altered C and N availability under As contamination also shifted the microbial nitrogen transformation pathways toward processes that produce less N2O. These findings provided valuable insights about N-cycling and adaptations of N functional microorganisms in heavy metal-stressed mangrove wetland ecosystems.},
}

@article {pmid41478169,
year = {2025},
author = {Wang, W and Zhang, S and Wang, Y and Ge, J and Li, L},
title = {Metagenomic and cytotoxicity insights into the migration behavior and pathogenic potential of multi-medium microorganisms in a wastewater treatment plant.},
journal = {Water research},
volume = {292},
number = {},
pages = {125285},
doi = {10.1016/j.watres.2025.125285},
pmid = {41478169},
issn = {1879-2448},
abstract = {As important interphases between the human society and natural water environments, wastewater treatment plants (WWTPs) accumulate a variety of human activity-related microorganisms. The characteristics of potential pathogenic microorganisms associated with WWTPs have gradually become a research hotspot. In this study, the distribution characteristics and migration patterns of potential pathogenic genera in different processes, media and seasons were investigated via the metagenomic analysis of samples regularly collected at a typical WWTP in North China. The results obtained 112 pathogenic bacteria and 33 pathogenic fungi in the wastewater, sludge, and bioaerosol samples. Resistance mechanisms were dominated by antibiotic efflux with proportion of 62.63-63.53%. Functional genes encoding offensive virulence factors (VFs) including adherence, secretion system, toxin, invasion, and actin-based motility were the most common category in all the WWTP samples. Network analysis revealed the presence of core antibiotic resistance genes (including mtrA, bcrA, oleC, MexB, PmrE) and core VFs (including Type IV pili (VF0082), HIS-I (VF0334), LOS (CFV494), and Alginate (VF0091)) on multiple microbes, which increased the survival rate of microorganisms even under adverse conditions and enhanced the invasion potential to cause diseases. Additionally, cell exposure experiments confirmed the ability of Pseudomonas aeruginosa to induce inflammatory responses in Beas-2B cells. Based on these findings, which offer the insight of a comprehensive understanding of the potential pathogenicity of microorganisms in WWTPs, it is recommended to improve regulation of effluents from WWTPs a nd the implementation of measures to reduce the risk posed by airborne pathogenic microorganisms.},
}

@article {pmid41478124,
year = {2025},
author = {Xing, W and Gai, X and Cheng, X and Fang, Z and Chen, G},
title = {Rhizosphere microbiome drives Betula luminifera adaptation to antimony mining sites through functional traits and transcriptional reprogramming.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140972},
doi = {10.1016/j.jhazmat.2025.140972},
pmid = {41478124},
issn = {1873-3336},
abstract = {Rhizosphere microbiome are pivotal for plant adaptation to extreme environments. However, the regulatory mechanisms underlying their control of the ecological adaptation of native woody plants in mining areas remain unclear. Here, we integrated metagenomic and transcriptomic analyses to elucidate how the rhizosphere microbiome facilitates Betula luminifera adaptation to antimony (Sb) mining sites. Under sterile conditions, B. luminifera from mining sites prioritized shoot growth, whereas control-origin seedlings favored root development. Microbial inoculation mitigated this growth dichotomy, balancing above- and belowground biomass allocation. Notably, B. luminifera from control sites upregulated antioxidant biosynthesis genes (α- and β-tocopherol pathways), while B. luminifera from mining sites enhanced lignin synthesis under Sb stress. After inoculation with rhizosphere microbiome from the mining-site, genes related to Sb/As resistance (ACR3, arsB/C) and soil nutrient cycle (narG, phnM) were significantly enriched in the rhizosphere of B. luminifera, which were contributed by Proteobacteria and Actinobacteria. Transcriptional profiling revealed that microbial inoculation triggered systemic upregulation of phytohormone-related genes (auxin, cytokinin, abscisic acid), enhancing stress resilience and growth. These findings unveil a synergistic plant-microbe adaptation mechanism in Sb polluted soils in mining sites, highlighting microbial-mediated trait trade-offs and transcriptional plasticity as drivers of ecological success in extreme environments.},
}

@article {pmid41478064,
year = {2025},
author = {Zhang, H and Zhang, S and Li, X and Wang, W and Kuang, H},
title = {Bupleurum polysaccharide improves CUMS-induced depressive behavior in rats by regulating the "microbiota-gut-brain Axis": a mechanism study based on metabolomics and metagenomics.},
journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences},
volume = {1270},
number = {},
pages = {124905},
doi = {10.1016/j.jchromb.2025.124905},
pmid = {41478064},
issn = {1873-376X},
abstract = {This study aimed to comprehensively investigate the antidepressant mechanisms of Bupleurum polysaccharide (BP) through the microbiota-gut-brain axis, employing an integrated multi-omics approach. Using a chronic unpredictable mild stress (CUMS) rat model of depression, we evaluated BP's effects on depressive-like behaviors and analyzed its regulatory mechanisms on metabolites and gut microbiota through combined metabolomics and metagenomics. Structural characterization revealed that Bupleurum polysaccharide SPAP-1 is an acidic homogeneous polysaccharide with a molecular weight of approximately 100 kDa, primarily composed of glucose, mannose, rhamnose, and other monosaccharides. Pharmacodynamic assessments demonstrated that BP significantly ameliorated CUMS-induced depressive behaviors, including weight loss, reduced food intake, anhedonia, and behavioral despair (P < 0.05). Metabolomic analysis identified 19 differential metabolites, with BP reversing 11 of them, primarily involved in phenylalanine and tryptophan metabolism pathways. Western blot analysis confirmed BP's regulatory effects on key enzymes Got1 and Lta4h. Metagenomic results showed that BP remarkably reshaped gut microbiota structure, restored microbial diversity, optimized the Firmicutes/Bacteroidetes ratio, enriched beneficial genera (Agathobacter, Phocaeicola), and inhibited pathogenic genera (Ruminococcus). Crucially, integrated multi-omics analysis revealed significant microbiota-metabolite correlations, demonstrating that BP-promoted beneficial bacteria positively correlated with neurotransmitter precursors, while BP-inhibited pathogenic bacteria associated with pro-inflammatory mediators. Mediation analysis further established the "microbiota → metabolite → behavior" causal chain, with Ruminococcus → LTB4 → despair behavior accounting for 42.3 % of the mediation effect. In conclusion, Bupleurum polysaccharide ameliorates depressive-like behaviors through multi-target regulation of the metabolite-microbiota interaction network, highlighting its potential as an antidepressant agent or functional food and providing a novel research paradigm for understanding the multi-target characteristics of traditional Chinese medicine polysaccharides.},
}

@article {pmid41477534,
year = {2026},
author = {Vallejos, G and Kim, C and Holroyd, KB and Thakur, KT},
title = {Evaluating the Clinical Impact of Metagenomic Next-Generation Sequencing in CNS Infections: A Diagnostic Pathway and Resource Utilization Modeling Study.},
journal = {Open forum infectious diseases},
volume = {13},
number = {1},
pages = {ofaf743},
pmid = {41477534},
issn = {2328-8957},
abstract = {BACKGROUND: Diagnosing meningitis and encephalitis remains challenging due to nonspecific clinical presentations and the limitations of traditional microbiological methods. Metagenomic next-generation sequencing (mNGS) offers a broad approach to detect pathogens, but its real-world impact on clinical decision-making remains undefined.

METHODS: We used a cohort of patients with confirmed central nervous system infections and autoimmune encephalitis (AE) who underwent traditional microbiological cerebrospinal fluid testing at Columbia University Irving Medical Center. Using published sensitivity and specificity data for mNGS, we applied Bayes' theorem to calculate different etiology-specific pretest probabilities and model the potential impact in the diagnostic workflows including the number of lumbar punctures (LPs), additional etiologic tests potentially avoided, and time to diagnosis.

RESULTS: The cohort includes 54 patients in the infectious cohort and 29 patients with confirmed autoimmune encephalitis. In a modeled scenario, utilizing an mNGS test, such as Delve Detect, in patients with DNA viral infections (n = 23) could lead to a reduction of up to 88 microbiological tests, 145 days to diagnosis, and 2 LPs in total. For bacterial infections (n = 16), estimated impact included a reduction of 30 microbiological tests, 144 days to diagnosis, and 12 LPs (Table 1). Although fungal, RNA viral and parasitic infections were less common, with adjusted positive predictive values of 92.8%, 89.5%, and 84.6%, respectively. In the autoimmune cohort, a total of 2 LPs, 126 microbiological tests, and 297 days to diagnosis could have been avoided through the use of mNGS.

CONCLUSIONS: Our analysis suggests that an mNGS test, such as Delve Detect, could potentially streamline diagnostic and treatment pathways in meningitis and encephalitis of infectious or autoimmune origin.},
}

@article {pmid41477211,
year = {2025},
author = {Mankiewicz-Boczek, J and Font-Nájera, A and Gin, KY and Graham, JL and Strapagiel, D and Gorney, RM and Kok, JWK and Te, SH and Kluska, M and Skóra, M and Seweryn, M and López-Hun, F},
title = {Bacterial community diversity and potential eco-physiological roles in toxigenic blooms composed of Microcystis, Aphanizomenon or Planktothrix.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1655370},
pmid = {41477211},
issn = {1664-302X},
abstract = {Cyanobacterial toxicity, cyanotoxins, and their impact on aquatic ecosystems and human health are well documented. In comparison, less is known about bloom-associated bacterial communities. Co-occurring bacteria can influence bloom development, physiology and collapse, and may also provide a niche for pathogenic bacteria. Existing research focuses on the cyanosphere of Microcystis-dominated blooms, despite the increasing prevalence of filamentous genera (Aphanizomenon and Planktothrix). This pilot study aimed to broaden our understanding of the bacterial consortia attached to morphologically distinct cyanobacteria (coccoid and filamentous) dominating phytoplankton communities and to explore their potential roles in amplifying the impacts of cyanobacterial blooms. We investigated four shallow freshwater bodies across three continents and two climate zones: an urban pond in the USA, a dammed reservoir and a natural lake in Poland, and an urban water body in Singapore. Amplicon sequencing (16S rRNA gene) was used to characterize bacterial communities, while shotgun metagenomics identified nitrogen- and phosphorus-cycling genes to infer potential eco-physiological functions. Cyanobacteria dominated bacterioplankton assemblages at all sites (>35.6%), with bloom composition influencing toxigenic profiles. A mixed bloom of Microcystis, Snowella, and Aphanizomenon had the broadest range of cyanotoxin synthetase genes (mcyE, cyrJ, anaF and sxtA). Microcystis blooms correlated with increased Roseomonas, while Planktothrix co-occurred with Flavobacterium - both bacteria likely contribute to nutrient-cycling within blooms and represent potential opportunistic pathogens for aquatic organisms and humans. The Microcystis cyanosphere exhibited the highest number of significant positive correlations with bacteria (19 relations), compared to Planktothrix and Aphanizomenon (11 and 2 relations, respectively). Non-diazotrophic blooms of Microcystis and Planktothrix showed greater abundances of nitrogen - (ureB, glnA, narB, and narHZ) and phosphorus-cycling genes (phoBHPR and ppk1), indicating a strong dependence on associated bacteria for nutrient acquisition compared to diazotrophic Aphanizomenon. These findings suggest that Aphanizomenon-dominated blooms may be sustained by simpler microbiomes. Our results provide preliminary evidence of cyanosphere heterogeneity potentially shaped by the dominance or coexistence of three morphologically and eco-physiologically distinct genera of cyanobacteria. A comprehensive knowledge of the taxonomy and functional roles of bloom-associated microbiomes is therefore essential to understand bloom activity, evaluate the environmental threat, and develop effective strategies for prevention and mitigation.},
}

@article {pmid41477025,
year = {2025},
author = {Miao, H and Wang, Z and Chen, S and Wang, J and Ma, H and Liu, Y and Yang, H and Guo, Z and Wang, J and Cui, P},
title = {Application of machine learning in the discovery of antimicrobial peptides: exploring their potential for ulcerative colitis therapy.},
journal = {eGastroenterology},
volume = {3},
number = {4},
pages = {e100253},
pmid = {41477025},
issn = {2976-7296},
abstract = {BACKGROUND: Ulcerative colitis (UC) is a chronic, relapsing inflammatory bowel disease with complex aetiology and limited treatment options. Antimicrobial peptides (AMPs), as endogenous immune effectors, have recently emerged as promising therapeutic agents in UC. However, systematic identification and functional evaluation of AMPs remain underexplored. We aimed to discover novel AMPs with potential therapeutic efficacy in UC by leveraging machine learning-based prediction and validating their impact in an experimental colitis model.

METHODS: We established a machine learning-driven pipeline to predict candidate AMPs based on their structural and functional features. Top-ranked peptides were synthesised and subjected to in vitro antibacterial assays and proteolytic stability tests. Their therapeutic potential was evaluated using a dextran sulfate sodium (DSS)-induced colitis mouse model, assessing clinical indicators, histopathology, inflammatory markers and gut microbiota alterations. Metagenomic and metabolomic analyses provided insights into microbial community dynamics and metabolic pathways. To probe the role of gut microbes in AMP-mediated gut homeostasis, we conducted Akkermansia (A.) muciniphila replenishment experiments.

RESULTS: Several AMPs identified by machine learning exhibited potent antimicrobial activity and resistance to proteolytic degradation. In vivo, AMP administration ameliorated DSS-induced colitis symptoms, including body weight loss, Disease Activity Index and histological damage. Treatment also modulated the gut microbiome, increasing the abundance of A. muciniphila and restoring microbial balance. Functional metagenomic profiling revealed enrichment of genes involved in mucosal barrier protection and immunoregulation. These findings were supported by improved inflammatory cytokine profiles and enhanced epithelial integrity.

CONCLUSIONS: Our findings demonstrate that machine learning-guided discovery of AMPs is a viable approach to identify promising therapeutic agents for UC. By integrating multi-omics analyses, we reveal potential microbiota-mediated mechanisms underlying AMP efficacy. These insights provide a strong foundation for advancing AMP-based strategies in UC management.},
}

@article {pmid41476341,
year = {2025},
author = {Njage, PMK and Becsei, Á and Marques, ARP and Muchiri, BW and Pedersen, JLM and Otani, S and Avot, BJP and Pruden, A and Calarco, J and Harwood, V and Meschke, JS and Gonzalez, R and Sozzi, E and Sobsey, M and McNamara, P and Beck, N and Clark, K and Ballash, G and Mollenkopf, D and Wittum, T and Smith, B and Maile-Moskowitz, A and Kang, S and Capone, D and Aarestrup, FM},
title = {Sociodemographic and Health Factors Are Associated with Antimicrobial Resistance across Eight States in the United States.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c07425},
pmid = {41476341},
issn = {1520-5851},
abstract = {Recent studies suggest that country-level socioeconomic factors may explain antimicrobial resistance (AMR) patterns better than antimicrobial usage (AMU), but it remains unclear whether this holds for sociodemographic and health variation within countries. We used metagenomic analysis of untreated sewage to cross-sectionally characterize the bacterial resistome as a proxy for AMR at 44 wastewater treatment plants across eight USA states between 2019 and 2020. We examined associations between AMR with site-specific sociodemographic and health indicators and AMU. Spatial autocorrelation analyses were used to identify clusters of AMR. Gradient-boosted multivariate regression trees were applied to evaluate individual and joint predictor effects on AMR. Outpatient AMU explained negligible variation in AMR, whereas predictors related to economy, income, preventive health care, access to health care, social welfare, housing, and racial/ethnic composition showed the strongest associations. These relationships were observed across individual resistance classes and their combinations and predicted AMR nonlinearly, with thresholds where AMR shows sharp increases (risk factors) or decreases (protective factors). Significant interannual differences in resistome and bacteriome composition were observed between 2019 and 2020. Although causal inference is limited, the findings suggest that local-level indicators of health, economic conditions, well-being, and development may play an important role in shaping AMR within countries.},
}

@article {pmid41476181,
year = {2025},
author = {Fedi, S and Ghezzi, D and Firrincieli, A and Lopo, E and Romeo, A and Sauro, F and Cappelletti, M},
title = {Taxonomy and functional profile of microbial communities across the depths of the Alpine Cenote Abyss ice cave.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-29105-z},
pmid = {41476181},
issn = {2045-2322},
}

@article {pmid41476057,
year = {2025},
author = {Wu, Y and Wong, O and Chen, S and Wang, Y and Lu, W and Cheung, CP and Ching, JYL and Cheong, PK and Chan, S and Leung, P and Chan, FKL and Su, Q and Ng, SC},
title = {Distinct diet-microbiome associations in autism spectrum disorder.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67711-7},
pmid = {41476057},
issn = {2041-1723},
abstract = {Autism spectrum disorder (ASD) is linked to both altered gut microbiota and unhealthy diets; however, the mechanistic connections remain elusive. In this study, we conducted a systematic analysis of fecal microbiome metagenomic data, paired with granular dietary assessments and phenotypic profiles, across a cohort of 818 children (462 with ASD, 356 without ASD; mean age = 8.4 years; 27.3% female). By integrating dietary indices, nutrient intake, and food additive exposures, we uncovered ASD-specific linkages to the microbiome. Poor dietary quality correlated with aggregated core autistic symptoms, gastrointestinal complications, and atypical eating behaviors. Notably, children with ASD exhibited a more pronounced diet-microbiome interaction network compared to neurotypical peers, suggesting heightened microbial sensitivity to nutritional inputs. Furthermore, synthetic emulsifiers-specifically polysorbate-80 and carrageenan-were associated with disrupted microbial connectivity in ASD, a phenomenon attenuated in neurotypical children. Our findings elucidate the mechanistic links between dietary factors-particularly synthetic food additives-and microbiome dysregulation in ASD, urging a re-evaluation of dietary guidelines for ASD populations and laying the groundwork for personalized nutritional strategies.},
}

@article {pmid41475602,
year = {2025},
author = {Zhou, L and Zhang, M and Qiu, Y and Zhao, B and Li, H and Zhuang, WQ},
title = {'Protector' DNRA bacteria, shielding anammox systems from perfluorooctanoic acid by mitigating nitrite accumulation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133898},
doi = {10.1016/j.biortech.2025.133898},
pmid = {41475602},
issn = {1873-2976},
abstract = {The anaerobic ammonium oxidation (anammox) process is integral to nitrogen removal in wastewater treatment, but its effectiveness can be compromised by contaminants such as perfluorooctanoic acid (PFOA). This study revealed the protective mechanism of dissimilatory nitrate reduction to ammonium (DNRA) in protecting anammox bacteria from PFOA-induced toxicity in a lab-scale anaerobic membrane bioreactor (anammox-AnMBR), which operated for over 100 days. The system was exposed to stepwise PFOA increases (0.25, 0.5, and 0.75 mg/L). Nitrogen removal efficiency and extracellular polymeric substance (EPS) production were monitored. Microbial community dynamics were analyzed by metagenomic sequencing. Notably, increasing PFOA concentrations corresponded to stable NO2[-] levels and fluctuating NH4[+], suggesting a biphasic response to PFOA toxicity by the DNRA and anammox communities. Results indicate that DNRA bacteria were more tolerant to PFOA, even at high concentrations, than anammox bacteria. Metagenomic analysis further demonstrated the acute toxicity of high PFOA concentrations to anammox. The abundances of anammox functional genes (hzs, encoding hydrazine synthase; hdh, encoding hydrazine dehydrogenase) showed initial increases followed by declines at elevated PFOA concentrations. Concurrently, the increase in EPS (polysaccharides: 33.3 to 111.1 mg/g VSS; proteins: 3.0 to 247.6 mg/g VSS) indicated defense responses.},
}

@article {pmid41475601,
year = {2025},
author = {Tang, J and Liu, Y and Zhang, Q and Zhang, H and Ni, BJ and Lv, W},
title = {Multi-omics dissection of yeast-centric fungal-bacterial synergies in food-processing wastewater: insights from four full-scale treatment plants.},
journal = {Bioresource technology},
volume = {443},
number = {},
pages = {133911},
doi = {10.1016/j.biortech.2025.133911},
pmid = {41475601},
issn = {1873-2976},
abstract = {Fungal presence and ecological roles in activated sludge at municipal wastewater treatment plants are increasingly recognized, yet their diversity and functional contributions-especially of yeasts-in treating food-processing wastewater remain underexplored. High-throughput ITS and 16S rRNA sequencing and shotgun metagenomics, together with FUNGuild, were used to analyze microbial community structure, functional microorganisms, co-occurrence patterns, interkingdom interactions, functional pathways, and the distributions of degradation enzymes and functional genes for characteristic pollutants among four full-scale food-processing plants (seafood, pastry, orange-canning, and vegetable-oil refining). Community diversity and structural differences shaped by wastewater types, associated with metabolic traits and enzyme-secretion. Saccharomycetes emerged as the dominant fungal class; bacteria displayed more even class-level and genus-level distributions than fungi across plants, combining LEfSe (LDA > 4, p < 0.05) to reveal plant-specific environmental-driven taxa, mainly included members of Saccharomycetales among fungi. Module-based co-occurrence networks indicated symbiotic interactions among yeasts; predominant cooperation of fungal-bacterial interaction network, in which yeasts exhibited the highest degree among fungi; strong correlations between Saccharomycetales and functional genes. Metabolism was the most abundant functional pathway. "Undefined Saprotroph" was the most widespread fungal functional guild. We annotated 86 degradation enzymes and 150 functional genes targeting eight pollutant categories (proteins, lipids, starch, pectin, lignin, cellulose, hemicellulose, chitosan), elucidating plant-specific distributions and enzymatic synergies. These multi-plant comparisons disentangle conserved from plant-specific features of catabolism. Overall, this study elucidates microbial diversity, interactions, and functional potential in food-processing wastewater treatment, reveals yeasts as keystone microbes for pollutant degradation, and provides actionable insights for treatment strategies and process optimization.},
}

@article {pmid41475238,
year = {2025},
author = {Xin, H and Chen, S and Li, X and Chen, Z and Fan, Q and Luo, H and Liu, G and Mai, W},
title = {High-level chloramphenicol degradation in mariculture wastewater via cathodic nitro-reduction in a single-chamber bioelectrochemical system.},
journal = {Water research},
volume = {291},
number = {},
pages = {125174},
doi = {10.1016/j.watres.2025.125174},
pmid = {41475238},
issn = {1879-2448},
abstract = {The aim of this study was to investigate the mechanism of high-level chloramphenicol (CAP) degradation in mariculture wastewater using a single chamber bioelectrochemical system (BES). The reactor was assembled with carbon-brush electrodes and operated with sea mud as inoculum. Nearly complete removal of 200 mg/L CAP was achieved within 36 h when 2 g/L glucose was supplied as a co-substrate. With 200 mg/L CAP as the sole carbon source, BES at the close circuit achieved 28 ± 3% higher CAP removal than that at the open circuit within 72 h. CAP removal declined from 100 ± 5% to 45 ± 4% as the initial concentration increased from 200 to 600 mg/L within 36 h. High CAP concentration markedly inhibited sulfate-reducing bacteria (SRB), reducing the relative abundance of Desulfobulbus from 28.7% to < 0.5%, and decreasing sulfate removal from 90 ± 5% to < 56 ± 3% compared with the control. Nitro-reduction of CAP at the cathodic biofilm was determined as the predominant pathway among the three degradation routes in the BES. Metagenomic analysis revealed that 200 mg/L CAP significantly inhibited both multidrug efflux pump genes and key operons involved in dissimilatory sulfate reduction in the cathodic biofilm. Our results could be useful for eliminating high concentrations of antibiotic contaminants from seawater.},
}

@article {pmid41475234,
year = {2025},
author = {Wang, N and Lv, K and Guo, S and Peng, D},
title = {Functional imbalance between Thauera and anammox governs PD/A pathway stability under contrasting reactor modes.},
journal = {Water research},
volume = {291},
number = {},
pages = {125201},
doi = {10.1016/j.watres.2025.125201},
pmid = {41475234},
issn = {1879-2448},
abstract = {Partial denitrification coupled with anammox (PD/A) is a promising energy-efficient alternative for mainstream nitrogen removal, yet its stability under different reactor modes remains unclear. This study systematically compared sequencing batch (RS) and continuous-flow (RC) PD/A systems using performance monitoring, activity assays, and metagenomic analyses. RC maintained superior long-term stability, achieving >80% nitrogen removal with anammox contributing above 90%, whereas RS remained less stable (∼65% NRE, ∼75% anammox contribution) and relied more on complete denitrification. Activity assays revealed that PD activity in RS was 5.03 times that of anammox, favoring complete denitrification. In contrast, RC maintained balanced activities, with PD activity being 0.89 times that of anammox, supporting cooperative PD/A interactions. Metagenomic analysis further revealed that Thauera-associated Nir/Nor/Nos genes were markedly enriched in RS, indicating a stronger potential for complete denitrification. These findings demonstrate that reactor mode regulates PD/A interactions through distinct stabilization mechanisms, with continuous-flow operation enhancing microbial cooperation and system resilience. This study provides mechanistic insights and practical guidance for the stable implementation of mainstream PD/A processes.},
}

@article {pmid41475142,
year = {2025},
author = {Gallego-Cartagena, E and Morillas, H and Maguregui, M},
title = {Biodeterioration of built heritage in the context of climate change and atmospheric pollution: Toward transdisciplinary conservation strategies.},
journal = {The Science of the total environment},
volume = {1013},
number = {},
pages = {181313},
doi = {10.1016/j.scitotenv.2025.181313},
pmid = {41475142},
issn = {1879-1026},
abstract = {The built heritage -encompassing monuments, historic buildings and sculptural ensembles- is increasingly threatened by the synergistic impacts of climate change, atmospheric pollution and biological activity. This review critically analyses current understanding of the mechanisms driving the biodeterioration of built heritage, focusing on calcareous materials (e.g., limestone, marble and lime-based mortars), which are both widespread in built heritage and highly susceptible to degradation. We examine how environmental drivers -such as elevated humidity, temperature fluctuations, and pollutant deposition (SOₓ, NOₓ, particulate matter)-trigger complex physicochemical and biochemical reactions that compromise structural stability and aesthetic integrity. The review explores the metabolic strategies of biodeteriative organisms (fungi, algae, cyanobacteria), the interactions of pollutants and mineral substrates, and the consequent formation of salts, black crusts and corrosion products. We highlight the role of biomonitoring as a methodological and interpretive bridge linking atmospheric pollution to biodeterioration processes. In addition, we discuss emerging interdisciplinary methodologies - including functional metagenomics, microbial network analysis, and metabolomic profiling -and introduce the Function-Based Biodegradation Risk Assessment model, extended into a Multi-Level Risk Assessment Framework that connects microbial functionality, material diagnostics, and climate modeling. We contend that safeguarding built heritage in a changing climate requires transitioning from static, material-centred diagnostics to integrated, predictive frameworks that link microbial ecology, materials science, and climate dynamics, providing the basis for adaptive and anticipatory conservation strategies.},
}

@article {pmid41474788,
year = {2025},
author = {Wong, KX and Chen, ST and Ong, JJ and Gan, WY and Abdul Murad, NA and Chong, CW and Ramzi, NH},
title = {Exploring gut microbiome and nutritional status among children with Autism Spectrum Disorder (MY-ASD Microbiome): A study protocol.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0338801},
pmid = {41474788},
issn = {1932-6203},
mesh = {Humans ; *Autism Spectrum Disorder/microbiology ; *Gastrointestinal Microbiome ; Child ; Male ; Child, Preschool ; *Nutritional Status ; Case-Control Studies ; Feces/microbiology ; Saliva/microbiology ; Malaysia ; Female ; },
abstract = {BACKGROUND: Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterised by persistent deficits in social communication and the presence of restricted, repetitive behaviours or interests. Previous literature has identified a link between the gut and ASD; however, the underlying mechanisms remain unclear. Gut microbiota dysbiosis has been extensively reported in cohort studies of ASD, and specific microbial metabolites or by-products may serve as potential biomarkers for ASD. Additionally, children with ASD often exhibit food refusal, have a limited food repertoire and display a tendency to consume the same foods frequently; thus, these behaviours increase their risk of malnutrition (over-nutrition or under-nutrition) compared to typically developing (TD) healthy children. This study primarily aims to identify oral and gut microbiota among children with ASD and TD healthy children. The secondary aim is to determine the associations between oral and gut microbiota with nutritional status among children with ASD. The findings will enhance understanding of the aetiology of ASD and inform early intervention strategies to mitigate disease severity and early identification of malnutrition in genetically at-risk children.

METHODS AND ANALYSIS: This observational, age-matched, case-control study is conducted in Malaysia among 40 male children with ASD and age-matched with 40 TD healthy controls aged 4-10 years. The dependent variables include the microbiota profile, identified through metagenomic sequencing analysis of saliva and faecal samples, and autism severity, assessed through validated questionnaires. Independent variables include nutritional status, determined through Subjective Global Nutrition Assessment (SGNA), anthropometry and dietary measurements, gastrointestinal symptoms, eating behaviour, behavioural profile, and sleep quality. Data collection is expected to be completed by June 2026. The study nature may limit causality establishment. Analyses will use chi-square/ANOVA for group comparisons, SparCC for microbiota correlations, and mixed-effects logistic regression to model associations.

CONCLUSION: This study advances understanding of ASD-related microbiota, guiding personalised nutrition and precision healthcare in Malaysia.},
}

Humans
*Autism Spectrum Disorder/microbiology
*Gastrointestinal Microbiome
Child
Male
Child, Preschool
*Nutritional Status
Case-Control Studies
Feces/microbiology
Saliva/microbiology
Malaysia
Female

@article {pmid41474524,
year = {2025},
author = {Luo, S and Li, Z and Peng, Y and Xie, X and Zeng, Y and Dai, L and Zhang, X},
title = {Comparative metagenomics reveals the differential gut microbiota involved in bile acid metabolism in patients with crohn's disease.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {1},
pages = {21},
pmid = {41474524},
issn = {1573-0972},
support = {32101368//National Natural Science Foundation of China/ ; 2022YFE0119600//National Key Research and Development Program of China/ ; 2025JJ50123//Hunan Provincial Natural Science Foundation of China/ ; },
mesh = {Humans ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome/genetics ; *Crohn Disease/microbiology/metabolism ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Male ; Female ; Adult ; Feces/microbiology ; Middle Aged ; },
abstract = {Gut microbiota plays a critical role in bile acid (BA) metabolism within healthy populations, yet the differential species involved in BA metabolism in patients with Crohn's disease (CD) remains poorly characterized. To address this knowledge gap, we conducted a comparative metagenomics for nine CD patients and nine healthy controls. Integrated metagenomic species profiling and functional annotation, accompanied with species-function network analysis, reduced abundance in metabolism-associated genes and lower species-function correlation were predicted, suggesting a possible imbalance of microbial communities in CD group. Focused on functional genes involved in BA metabolism and their associated bacterial taxa, our results revealed that Anaerostipes hadrus-like (P = 0.001317), Roseburia intestinalis-like (P = 0.03542), and Coprococcus catus-like (P = 0.0005787), the microbial species related to bile salt hydrolase-coding gene, showed significantly lower abundance in CD patients. Conversely, Ruminococcus gnavus-like, related to 3α-hydroxysteroid dehydrogenase (3α-HSDH)- and 3β-HSDH-coding genes, demonstrated relatively higher abundance (P = 0.0257). Escherichia coli-like, the species for 7α-HSDH-coding genes, also exhibited higher abundance in CD group (P = 0.01044). Further network correlation analysis indicated that there was a potential association between these differential species with other co-occurring gut microbiota. Collectively, the findings identify and characterize the differential gut microbiota involved in BA metabolism in CD patients, which may provide the possible target microorganisms for future therapeutic interventions.},
}

Humans
*Bile Acids and Salts/metabolism
*Gastrointestinal Microbiome/genetics
*Crohn Disease/microbiology/metabolism
*Metagenomics/methods
*Bacteria/genetics/classification/metabolism/isolation & purification
Male
Female
Adult
Feces/microbiology
Middle Aged

@article {pmid41474055,
year = {2025},
author = {Mehar, K and K, KP and Sen, AP and Paliwal, RK and M, BK and Kalidhas, AM and Mohapatra, TK and Samrat, A and Jayabal, R},
title = {Next-Generation Eco-Omics: Integrating Microbial Function Into Predictive Ecosystem Models.},
journal = {Biotechnology and applied biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1002/bab.70121},
pmid = {41474055},
issn = {1470-8744},
abstract = {Microorganisms drive essential ecosystem functions by mediating carbon, nitrogen, sulfur, and phosphorus transformations that regulate productivity and shape climate feedbacks. Rapid methodological advances now allow precise linkage of microbial identity, in situ activity, and ecosystem processes across spatial and temporal scales. High-resolution approaches-including long-read metagenomics and Hi-C-generate near-complete metagenome-assembled genomes (MAGs) from diverse environments, enabling reconstruction of microbial and viral-host interaction networks. Activity-resolved tools such as quantitative stable isotope probing (qSIP) and bioorthogonal non-canonical amino acid tagging (BONCAT), combined with fluorescence-activated cell sorting (FACS), yield taxon-specific growth and substrate assimilation rates within hours. Single-cell isotope techniques, including Raman-SIP and nanoSIMS, deliver nanometer-scale metabolic insights. Spatial meta-omics platforms, such as MetaFISH and MALDI-MSI, map metabolites alongside microbial identities with micrometer-level precision. Meanwhile, autonomous sequencing systems, including environmental sample processors and nanopore adaptive sampling, enable real-time (<24 h) ecological surveillance. Integrating these multimodal datasets into trait-based frameworks has reduced uncertainty in carbon flux predictions by nearly 20%. This review synthesizes these innovations, outlines optimized analytical pipelines, and proposes a framework for embedding eco-omics into predictive ecosystem and climate models, supporting evidence-driven management aligned with Climate Action and Life on Land.},
}

@article {pmid41473771,
year = {2025},
author = {Mao, X and Hu, X and Fang, J},
title = {Gut microbiota-metabolite interactions in drug-induced liver injury: mechanisms, biomarkers, and therapeutic perspectives.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1737234},
pmid = {41473771},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Chemical and Drug Induced Liver Injury/microbiology/metabolism/therapy ; Biomarkers/metabolism ; Dysbiosis ; Animals ; Liver/metabolism ; },
abstract = {Drug-induced liver injury (DILI) remains a major obstacle in clinical pharmacotherapy and a leading cause of acute liver failure and drug withdrawal worldwide. Conventional mechanistic models centered on hepatic xenobiotic metabolism, oxidative stress, and immune injury cannot fully account for the substantial interindividual variability and the unpredictable nature of idiosyncratic DILI. Increasing evidence shows that the gut microbiota and its metabolites critically shape hepatic susceptibility through modulation of drug metabolism, inflammatory signaling, and intestinal barrier integrity. This review summarizes current understanding of the gut-liver axis in DILI pathogenesis, with a focus on microbial enzymes such as β-glucuronidase that reactivate detoxified drug conjugates, microbial dysbiosis that disrupts bile acid homeostasis, and depletion of short chain fatty acids and indole derivatives that normally support epithelial defenses and immunologic tolerance. Drug-specific microbial patterns are discussed, including acetaminophen, amoxicillin-clavulanate, anti-tuberculosis regimens, and immune checkpoint inhibitors. We introduce the concept of metabotype-dependent hepatotoxicity, which emphasizes that individual microbial metabolic profiles influence DILI risk. Advances in metagenomics, metabolomics, and integrative multi-omics enable the identification of microbial biomarkers and functional pathways associated with DILI susceptibility. Emerging therapeutic strategies include restoration of microbial homeostasis, selective inhibition of microbial enzymes, and supplementation of hepatoprotective metabolites. Finally, we outline key challenges and future directions toward translating microbiome-based insights into clinical prediction and precision prevention of DILI. Importantly, this review integrates microbial metabolic functions with precision hepatology concepts, highlighting how metabotype-driven variability can be leveraged for individualized DILI risk assessment.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Chemical and Drug Induced Liver Injury/microbiology/metabolism/therapy
Biomarkers/metabolism
Dysbiosis
Animals
Liver/metabolism