@article {pmid41115830,
year = {2025},
author = {Yang, F and Xu, W and Zhu, L and Tian, X and Duan, Y and Xu, Y and Huang, Q and Zhao, F},
title = {Multiple Roles of Extracellular Vesicles in Promoting Microbial-Driven Manganese Reduction.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c05310},
pmid = {41115830},
issn = {1520-5851},
abstract = {Microbial-driven manganese (Mn) reduction influences the geochemical cycling of Mn and the environmental fate of various organic and inorganic substances. Extracellular vesicles (EVs) are known to impact microbial metabolic activities, but their specific role in Mn reduction remains arcane. Here, we explored the potential involvement of environmental EVs in this process through metagenomic analysis and validated their function using representative functional strains. There are 8.05 and 12.89% of EVs originating from electroactive microorganisms in soil and wastewater, respectively. The addition of EVs increases the birnessite reduction rate of Shewanella oneidensis MR-1 from 2.31 μmol/(L·h) to 20.86 μmol/(L·h). Microbial physiological assays and in situ electrochemical analyses revealed that EVs enhanced cellular metabolism, promoted biofilm formation, and facilitated extracellular electron transfer (EET). The presence of diverse redox enzymes and metabolites in EVs contributed to more efficient substrate utilization and energy conservation, which promoted biomass accumulation and increased substrate consumption by 45.33%. The inner and outer membrane c-type cytochromes, along with flavins contained in the EVs, are essential for promoting microbial EET. These findings highlight the multifaceted role of EVs in microbial-driven Mn reduction, which might also participate in other element cycles in the same way.},
}

@article {pmid41114585,
year = {2025},
author = {Aries Marchington, M and Gasvoda, H and Michelotti, M and Rodriguez-Caro, F and Gooman, A and Perez, A and Hensley-McBain, T},
title = {APOE genotype and sex drive microbiome divergence after microbiome standardization in APOE-humanized mice.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0042925},
doi = {10.1128/msphere.00429-25},
pmid = {41114585},
issn = {2379-5042},
abstract = {The APOE4 allele is the greatest known genetic factor for sporadic or late-onset Alzheimer's Disease (LOAD). Gut microbiome (GMB) dysbiosis can lead to poorer outcomes in disease. The intersection of sex, APOE genotype, inflammation, and gut microbiota is incompletely understood. Previous studies in humans and humanized APOE mice have demonstrated APOE-genotype-specific differences in the GMB. However, most of these studies were unable to resolve bacteria to the species level. It remains unclear how GMB changes with age and sex in the context of APOE genotype. In this study, humanized male mice with either APOE 2, 3, or 4 genotype were bred with the same two C57BL/6J sisters to standardize microbiomes across lines and monitor divergence based on APOE allele. Stool samples were collected at breeder set up and from the heterozygous (F1) and homozygous (F2) generations at wean and 6 months old. Stool was assessed via shallow shotgun sequencing to enable species and strain-level taxonomic resolution. The heterozygous pups' microbiome resembled each other at wean across all genotypes. However, the heterozygous pups and their homozygous offspring continued to diverge, particularly the APOE2 females. In homozygous mice, the GMB demonstrated significant divergence at 6 months of age based on sex and APOE genotype. In comparison to their APOE3 and APOE4 counterparts, APOE2 females and males demonstrated an increased quantity of bacteria associated with anti-inflammatory profiles, including in the Lachnospiraceae family (Lachnospiraceae bacterium UBA3401) and decreased quantities in the Turicibacteraceae family (higher levels are associated with LOAD).IMPORTANCEThe APOE4 allele is implicated as a significant risk factor for many diseases, including cardiovascular disease (responsible for more deaths than any other disease) and sporadic or late-onset Alzheimer's Disease (accounts for an estimated 60%-80% of all dementia cases). It is known that the gut microbiome (GMB) is affected by different genotypes and disease states. Mouse model studies have environmental and genetic controls, allowing a specific gene to be studied. This study aims at discovering key GMB species differences allowing for future therapeutic targets. The GMB of the experimental mice was standardized, and genotype and sex-specific divergence was observed with species and even strain level taxonomic resolution. Reported here are the first data demonstrating GMB divergence over time driven by APOE genotype from an inherited source and the first data to identify APOE genotype-specific bacteria species that may serve as therapeutic targets in APOE-driven disease.},
}

@article {pmid41114582,
year = {2025},
author = {Zhang, Z and Wang, Z and Teng, P and Yu, T and Zhang, Y},
title = {Oxygen-tolerant nitrogen fixation in a marine alga-colonizing Planctomycetota.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0131625},
doi = {10.1128/aem.01316-25},
pmid = {41114582},
issn = {1098-5336},
abstract = {UNLABELLED: The microbiomes colonizing macroalgal surfaces orchestrate nutrient fluxes and symbiotic interactions within the algal environment. Among these communities, Planctomycetota are often dominant taxa. Although nitrogenase (nif) gene clusters have been identified in Planctomycetota isolates and metagenome-assembled genomes, functional validation of nitrogen fixation in pure culture has remained elusive. Moreover, the mechanisms enabling these bacteria to overcome oxygen sensitivity and fix nitrogen in algal-associated oxic niches remain unexplored. Here, we isolated Crateriforma sp. HD03, a Planctomycetota strain from the surface of Saccharina japonica (kelp), and provided the first experimental evidence of nitrogen-fixing activity in pure-cultured Planctomycetota. Strain HD03 harbors a complete nifHDKBEN gene cluster and exhibits a remarkable nitrogen fixation rate of 14.2 ± 1.5 nmol C2H4/(10[7] cells)/h under aerobic conditions. Genomic and physiological analysis reveals a suite of adaptations that likely mitigate oxygen stress, including genes associated with biofilm formation, hopanoid lipid synthesis, FeSII protein, hydrogenase, and bacterial microcompartments. Notably, while strain HD03 demonstrates oxygen-tolerant nitrogen fixation in pure culture, co-culture experiments with kelp under a photoperiod revealed that nifH (nitrogenase reductase gene) expression peaks during the low-oxygen dark phase, indicating that HD03 utilizes diurnal rhythms to temporally separate nitrogen fixation from photosynthetic oxygen production. A genomic survey of 142 Planctomycetota strains from NCBI GenBank database and HD03 identified two distinct clades harboring complete nifHDK gene clusters, suggesting a nitrogen-fixing potential across the phylum. By bridging the gap between genomic potential and functional validation, this study establishes Planctomycetota as important but underappreciated contributors to marine nitrogen input.

IMPORTANCE: Planctomycetota are abundant colonizers of macroalgal surfaces, yet their role in nitrogen fixation has remained unresolved despite genomic evidence of nitrogenase (nif) genes. Until now, no functional validation of nitrogen fixation in pure-cultured Planctomycetota has been reported. Here, we isolated Crateriforma sp. HD03 from kelp and for the first time demonstrated its ability to fix nitrogen in pure culture, confirming this key metabolic potential in marine Planctomycetota. Strain HD03 overcomes oxygen stress through a combination of biofilm formation and diurnal regulation of nifH expression, allowing nitrogen fixation under aerobic conditions to cope with the algal environment's oxic nature. Furthermore, genomic surveys revealed nitrogen fixation gene clusters across multiple Planctomycetota clades, suggesting widespread nitrogen-fixing capability in this phylum. Collectively, these findings identify Planctomycetota as important nitrogen providers in the ocean.},
}

@article {pmid41114530,
year = {2025},
author = {Xiao, Y and Zhang, X and Shao, B and Wu, Z and Li, X and Yi, D and Li, T and Yang, T and Zhu, J and Huang, T and Deng, Y and Qiu, T and Yang, G and Sun, X and Wang, N},
title = {Hydroxytyrosol Improves Metabolic Dysfunction-Associated Fatty Liver Disease Dependent on the Modulation of Gut Microbiota.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c07003},
pmid = {41114530},
issn = {1520-5118},
abstract = {The global threat of metabolic dysfunction-associated fatty liver disease (MAFLD) is significant, but effective measures are still lacking. To explore the potential impact of hydroxytyrosol (HT), a plant polyphenol, in the metabolic outcomes of MAFLD and the mediating role of the gut microbiota, we performed an 8-week randomized placebo-controlled clinical trial in MAFLD patients and collected fecal bacteria for metagenomics analysis and targeted metabolomics. In this population-based trial, we have revealed that HT mitigates liver injury and steatosis in patients with MAFLD, as well as systemic glucolipid metabolism disorder. Through analysis of the differences in bacterial taxon and functional profiles, as well as correlation analysis between species and metabolic indicators, it was found that Fusicatenibacter saccharivorans (F. saccharivorans), the microbial species with the greatest difference after HT intervention, was also the most significantly correlated with metabolic parameters of MAFLD and showed a significant positive correlation with the content of fecal butanoic acid. Butanoic acid was further associated with MAFLD-related metabolic indexes. To confirm the potential causal relationship between alterations in gut microbiota induced by HT intervention and improved MAFLD metabolic phenotypes, fecal microbiota transplantation (FMT) was conducted using a model of pseudogerm-free mice. We have further demonstrated that the fecal microbiota from donors of MAFLD patients receiving HT supplementation can ameliorate liver and systemic phenotypes in western-diet-induced MAFLD mice, interpreting the robust action of gut microbiota remodeled by HT in improving MAFLD. Consequently, HT supplementation may represent a tactic for improving MAFLD by modulating the composition and functionality of the gut microbiota.},
}

@article {pmid41114048,
year = {2025},
author = {Andermann, TM and Zeng, K and Guirales-Medrano, S and Groth, A and Ramachandran, BC and Sun, S and Sorgen, AA and Hill, L and Bush, AT and Liu, H and Jones, C and Roach, J and Conlon, BP and Rao, G and Chao, NJ and Fodor, AA and Sung, AD},
title = {Duration of Hospitalization is Associated with the Gut Microbiome in Patients Undergoing Hematopoietic Stem Cell Transplantation: Early Results from a Randomized Trial of Home Versus Hospital Transplantation.},
journal = {OBM transplantation},
volume = {9},
number = {3},
pages = {},
pmid = {41114048},
issn = {2577-5820},
abstract = {Home-based hematopoietic stem cell transplantation (HCT) is an innovative care model with growing interest, but its impact on the gut microbiome remains unexplored in a randomized setting. We present interim results from the first randomized controlled trials (RCT) evaluating the effect of HCT location-home versus hospital-on gut microbial diversity and antimicrobial resistance (AMR) gene carriage. We hypothesize that patients randomized to undergo home HCT would have higher gut taxonomic diversity and lower AMR gene abundance compared to those undergoing standard hospital HCT. We analyzed stool samples from the first 28 patients enrolled in ongoing Phase II RCTs comparing home (n = 16) and hospital (n = 12) HCT at Duke University using shotgun metagenomic sequencing to compare taxa and AMR gene composition between groups. We also performed a secondary analysis comparing patients who received transplants at outpatient infusion clinics versus inpatient standard HCT to evaluate the influence of hospitalization duration. In the primary RCT analysis, taxonomic and AMR gene α- and β-diversity were comparable between home and hospital groups, reflecting similar durations of hospitalization despite group allocation. In contrast, secondary analyses demonstrated that patients transplanted in outpatient infusion clinics who experienced significantly reduced hospitalization had higher gut taxonomic α-diversity and differential β-diversity, although AMR gene diversity remained unchanged. In summary, randomization by transplant location did not impact the gut microbiota to the same extent as the duration of hospitalization, although secondary analyses were heavily confounded. Even when taxonomic differences were observed, AMR genes were similar between groups. This RCT represents a novel investigation into how care setting influences the gut microbiome during HCT. Our findings suggest that hospital duration, rather than randomization allocation alone, is the primary driver of microbial disruption. These results underscore the potential for reducing hospital duration to mitigate microbiome injury, thereby informing future interventions to reduce infection risk and improve patient outcomes.},
}

@article {pmid41114028,
year = {2025},
author = {Huang, H and Tong, Y and Hu, X and Liao, FK and Chen, R},
title = {The application value and challenges of metagenomic next-generation sequencing in the diagnosis of periprosthetic joint infection after arthroplasty.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1686503},
pmid = {41114028},
issn = {2296-858X},
abstract = {Metagenomic next-generation sequencing (mNGS) demonstrates high sensitivity, rapid diagnostic capabilities, and the potential to identify complex pathogens in periprosthetic joint infection (PJI) following arthroplasty, particularly when conventional culture methods are limited. mNGS enables the detection of polymicrobial infections and rare/fastidious pathogens, along with the ability to predict antimicrobial resistance (AMR) genes; however, the concordance between genotypic predictions and phenotypic resistance profiles requires further validation. In clinical practice, mNGS overcomes biofilm-related diagnostic barriers, facilitating early targeted antibiotic therapy and potentially reducing unnecessary revision surgeries, thereby lowering overall healthcare costs and improving patient outcomes. Nevertheless, its widespread adoption is hindered by high costs, lack of standardization, and risks of false-positive/false-negative results. Future research priorities include optimizing sample processing protocols, host DNA depletion, establishing diagnostic thresholds, and validating mNGS through integration with conventional methods. This review synthesizes recent advances in the diagnostic accuracy and clinical utility of mNGS for PJI, aiming to provide evidence-based insights for therapeutic decision-making and enhance the prevention and management of PJI.},
}

@article {pmid41114012,
year = {2025},
author = {Wang, H and Li, J and Huang, W},
title = {Case Report: Fever of unknown origin with hemophagocytic lymphohistiocytosis and intestinal hemorrhage-a successfully treated case of severe visceral leishmaniasis.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1663551},
pmid = {41114012},
issn = {2296-858X},
abstract = {In recent years, some cases of severe visceral leishmaniasis (VL) in immunocompetent adults have gradually been reported. Hemophagocytic lymphohistiocytosis (HLH) and intestinal hemorrhage are two rare complications in patients with VL. Without treatment, the mortality rate of such patients is extremely high. We report a case of a 31-year-old immunocompetent male who initially presented with fever of unknown origin (FUO), later developed HLH and experienced multiple episodes of life-threatening intestinal hemorrhage. The diagnosis of visceral leishmaniasis was confirmed through metagenomic next-generation sequencing (mNGS). The patient was successfully treated with amphotericin B deoxycholate (AmB-D) and supportive care. During the two-year follow-up period, no new complications were found. This case highlights the value of mNGS in the diagnosis of complex infectious diseases and emphasizes the clinical significance of the multidisciplinary collaborative model for patients with VL and complex complications. It can provide a reference for the early diagnosis and comprehensive treatment of severe VL.},
}

@article {pmid41114005,
year = {2025},
author = {Sun, R and Xu, W and Xu, Y and Xu, Z and Tan, Y and Li, J and Liu, H and Yung, CCM},
title = {Environmental gradients shape viral-host dynamics in the Pearl River estuary.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf164},
pmid = {41114005},
issn = {2730-6151},
abstract = {Marine viruses play critical roles in shaping microbial communities and driving biogeochemical cycles, yet their dynamics in estuarine systems are not well characterized. Here, we conducted a comprehensive metagenomic analysis of viral communities and virus-host interactions across the Pearl River estuary, a dynamic subtropical estuary in southern China. Using 24 metagenomic libraries from eight sampling sites, we identified 29,952 viral populations, with Uroviricota and potential Uroviricota accounted for 80.48% of taxa, underscoring their ecological importance. A key finding of our integrated analysis is the unexpectedly high abundance of nucleocytoplasmic large DNA viruses in offshore waters, which suggests a more significant role for eukaryotic viruses in coastal ecosystems than previously acknowledged and correlates with elevated levels of their eukaryotic hosts. Environmental variables, particularly salinity and nutrient availability, emerged as key drivers of viral and host distribution patterns. By linking environmental gradients to distinct community "envirotypes" and their underlying genomic features, we revealed novel virus-host interactions and highlighted the impact of environmental gradients on microbial ecology. Additionally, viral auxiliary metabolic genes linked to phosphorus and nitrogen metabolism suggest critical roles in modulating host metabolic pathways and influencing nutrient cycling. Our findings demonstrate how spatial heterogeneity and environmental gradients shape viral and microbial ecology in estuarine ecosystems. Our findings provide a holistic, multi-domain view of microbial and viral ecology, demonstrating how integrating prokaryotic, eukaryotic, and viral community analyses offers a more complete understanding of ecosystem function in these critical transition zones.},
}

@article {pmid41113669,
year = {2025},
author = {Onohuean, H and Naik Bukke, SP and Thalluri, C and Abass, KS and Choonara, YE},
title = {Exosome engineering for targeted therapy of brain-infecting pathogens: molecular tools, delivery platforms, and translational advances.},
journal = {Frontiers in medical technology},
volume = {7},
number = {},
pages = {1655471},
pmid = {41113669},
issn = {2673-3129},
abstract = {Central nervous system (CNS) infections caused by pathogens such as HIV, Herpes simplex virus, Cryptococcus neoformans, and Toxoplasma gondii remain among the most difficult to treat due to the physiological barrier posed by the blood-brain barrier (BBB), pathogen latency, and systemic toxicity associated with conventional therapies. Exosome-based delivery systems are becoming a game-changing platform that can solve these therapeutic problems using their natural biocompatibility, minimal immunogenicity, and capacity to cross the BBB. This review current developments in exosome engineering that aim to make brain-targeted therapy for neuroinfectious illnesses more selective and effective. Much focus is on new molecular methods like pathogen-specific ligand display, aptamer conjugation, lipid modification, and click-chemistry-based surface functionalisation. These methods make it possible to target diseased areas of the brain precisely. Exosomes can also carry therapeutic payloads, such as anti-viral and antifungal drugs, gene editing tools like CRISPR/Cas9 and siRNA, and more. This makes them helpful in changing pathogens' persistence and the host's immunological responses. The paper tackle problems with translation, such as biodistribution, immunogenicity, GMP production, and regulatory issues. Future possibilities like synthetic exosomes, combinatory medicines, and delivery design that uses AI. The combination of nanotechnology, molecular biology, and infectious disease therapies shows that exosome engineering offers a new way to meet the clinical needs that are not satisfied in treating CNS infections.},
}

@article {pmid41113648,
year = {2025},
author = {Dong, L and Du, Y and Qiu, F and Zhang, M and Wang, X and Zhu, X and Yao, Y and Li, J and Ji, X and Zhu, X},
title = {Metagenomic insights reveal the differences in the community composition and functional characteristics of the sea turtle microbiomes based on host species and tissue region.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1652229},
pmid = {41113648},
issn = {1664-302X},
abstract = {INTRODUCTION AND METHODS: Sea turtles have been proposed as health indicators of marine ecosystems for their characteristic of longevity and migratory, but they are facing serious threats due to various factors. The microbial communities within animals play an important role in health and disease. Our study aims to explore a thorough evaluation of the sea turtle microbiome by examining the oral, nasal, and cloacal microbial communities of three species: green turtles, hawksbills, and loggerheads, through metagenomic sequencing.

RESULTS: Utilizing approximately 705.81 GB of metagenomic sequencing data from 63 samples collected from different turtle species and tissue regions, we created a nonredundant sea turtle microbial gene catalog (STMGC) containing 10,733,232 unique genes through the de-redundancy of open reading frames (ORFs). Our findings revealed that the sea turtle microbiomes were primarily composed of Pseudomonadota (formerly Proteobacteria) and Bacteroidota (formerly Bacteroidetes). The tissue region was a key factor affecting the variability in the sea turtle microbiome, with green turtles showing notable differences among the three turtle species. Pseudomonadota was significantly more abundant in oral samples, while Bacteroidota was more prevalent in nasal samples. Campylobacterota was identified as significantly more abundant in cloacal samples. Importantly, we discovered 389 genera and 1,445 species of potential pathogens within the sea turtle microbiome, indicating potential pathogenic risks that warrant further investigation alongside culturomics. Additionally, our study highlighted significant functional differences among the three turtles and tissue regions. It is worth noting that among the three sea turtles, antibiotic resistance genes are more prevalent in hawksbills, while virulence genes are more abundant in loggerheads. Moreover, within the three tissue regions, antibiotic resistance genes are higher in oral samples, while virulence genes are more extensive in cloacal samples.

CONCLUSION: The findings in our study demonstrate that the microbial composition and function in these sea turtles exhibit both species-specific and region-specific variations. The implications of these associations and the underlying mechanisms not only provide valuable insights for future studies on the microbial communities of turtles, but also lay the foundation for further research on the health interrelationships among sea turtles, marine and terrestrial animals, humans and the environment, and for defining "One Health" factors.},
}

@article {pmid41113647,
year = {2025},
author = {Meng, Y and Xu, Y and Hu, D and Pan, Q and Weng, L and Huang, W and Zhao, J and Lan, W and Shi, Q and Yu, Y and Jiang, Y},
title = {Evaluating the effects of hospital wastewater treatment on bacterial composition and antimicrobial resistome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1620677},
pmid = {41113647},
issn = {1664-302X},
abstract = {Hospital wastewater treatment systems (HWTS) are crucial in reducing the spread of antimicrobial resistance genes (ARGs) and antibiotic-resistant bacterial pathogens in hospital wastewater. This study aims to evaluate the impact of HWTS on the changes of bacterial composition and the relative abundance of ARGs. We collected wastewater samples from influent and effluent in a university hospital, and performed metagenomic sequencing. The results showed that HWTS altered the bacterial composition, with a decrease in the proportion of Gammaproteobacteria. However, phylogenetic analysis of metagenome-assembled genomes showed that Mycobacterium and Zoogloea from influent and effluent had a close relationship. A total of 140 non-redundant ARGs were identified based on open reading fragments analysis, with beta-lactam and aminoglycoside resistance genes being the most prevalent. The relative abundance of ARGs generally decreased after wastewater treatment (p < 0.0001), with 70.0% of genes that conferring resistance to "last-resort" antibiotics being undetectable in the effluent. However, the relative abundance of quaternary ammonium compounds resistance genes increased in the effluent. We identified that 66.4% of ARGs were located on plasmids, and 17.9% of ARGs were adjacent to mobile gene elements (MGEs), suggesting their potential for mobility. Subsequent analysis showed that ARGs originating from plasmids and adjacent to MGEs were negatively associated with their relative abundance reduction. In conclusion, this study provides a comprehensive evaluation of the impact of HWTS on composition of bacteria and the relative abundance of ARGs, highlighting the importance of effective wastewater treatment in combating the spread of antimicrobial resistance.},
}

@article {pmid41113646,
year = {2025},
author = {Chen, X and Wu, J and Fan, D and Zhang, P and Li, Y and Cao, Y and Cao, M},
title = {Gut viral metagenomics identifies viral signatures and their role in depression.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1573851},
pmid = {41113646},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiome has been implicated in the onset and progression of depression. Yet, the role of the gut virome in depression remains unexplored, and a diagnostic model has not been satisfactorily constructed.

METHODS: Herein, we analysed the gut virome profiles of 29 patients with depression and 33 healthy controls using bulk metagenome sequencing.

RESULTS: A total of 45 differentially abundant viral taxa were identified, among which four, s_Stenotrophomonas_virus_Pokken, g_Pokkenvirus, s_Dickeya_virus_AD1, and g_Alexandravirus, demonstrated strong diagnostic potential (AUCs > 0.8). These four viruses also exhibited strong correlations, suggesting they may constitute a synergistic ecological cluster. Function annotation revealed seven metabolic pathways with significant differences, including alanine, aspartate, and glutamate metabolism, branched-chain amino acid (BCAA) biosynthesis, and energy metabolism in patients with depression.

CONCLUSION: This study identified four distinct viral signatures for depression and proposes novel viral biomarkers for the diagnosis of depression, offering a robust diagnostic approach and new insights into the pathological mechanisms of depression.},
}

@article {pmid41113645,
year = {2025},
author = {Durán-González, E and Ramírez-Tejero, JA and Pérez-Sánchez, M and Morales-Torres, C and Gómez-Morano, R and Díaz-López, C and Martínez-Lara, A and Cotán, D},
title = {Fibromyalgia diagnosis from a multi-omics approach: a gut feeling.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1641185},
pmid = {41113645},
issn = {1664-302X},
abstract = {BACKGROUND: Fibromyalgia is a complex disorder whose main symptoms are chronic widespread pain and fatigue and affects between 0.2 and 6.6% of the world population. Nowadays, there are no molecular biomarkers that could facilitate diagnosis. The latest efforts by researchers have focused on studying problems at the level of central nervous system sensitivity, inflammation, and oxidative disorders.

METHODS: A total of 892 women were initially enrolled in the study. For individuals who met the inclusion criteria, a plasma proteome analysis was conducted using blood samples. Briefly, blood was collected, centrifuged, and analyzed by liquid nano-chromatography coupled to tandem mass spectrometry. After the raw data analysis, proteins with statistically significant differential abundance and a fold change over 1.2 (20% increase in fibromyalgia compared with control samples) or under 0.8 (20% decrease in fibromyalgia compared with control samples) in fibromyalgia were selected. For fecal metagenome analysis, fecal samples were collected and processed for DNA extraction. Amplicon sequencing of V3-V4 regions from the 16S ribosomal RNA gene was performed using the Illumina MiSeq platform. The statistical analysis was conducted using R v4.3.2 base packages.

RESULTS: After applying exclusion criteria, 242 women (199 patients and 43 age- and environmentally paired controls) provided plasma and feces samples, as well as properly filled health questionnaires. A total of 30 proteins and 19 taxa were differentially expressed in fibromyalgia patients, and their integration into an algorithm allows for discrimination between cases and controls. The multi-omic approach for biomarker discovery in this study proposes a multifactorial connection between gut microbiota and mitochondria-derived oxidative stress and inflammation.

CONCLUSIONS: Plasma and fecal multi-omics analysis suggest an intricate and multifactorial connection between gut microbiota and mitochondria-derived oxidative stress and inflammation in FM patients, with glyceraldehyde-3-phosphate dehydrogenase and Streptococcus salivarius as leading actors.

TRIAL REGISTRATION: NCT05921409.},
}

@article {pmid41113638,
year = {2025},
author = {Verma, D and Zhang, Z and Liu, J},
title = {Editorial: Tobacco disease and biological control.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1694523},
pmid = {41113638},
issn = {1664-302X},
}

@article {pmid41113400,
year = {2025},
author = {Ning, H and Feng, R and Wu, H and Sun, C},
title = {[Innovative Practices of Precision Nutrition in Obesity Intervention: From Theory to Application].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {56},
number = {4},
pages = {893-899},
pmid = {41113400},
issn = {1672-173X},
mesh = {Humans ; *Obesity/prevention & control ; *Precision Medicine/methods ; Metabolomics ; Genomics ; Diet ; },
abstract = {Obesity has emerged as a critical global public health challenge, with an urgent need for effective prevention and control strategies. Traditional nutritional intervention approaches often overlook individual variability and dietary complexity, which limits their effectiveness in achieving precision-based prevention and control. In this context, nutritional intervention strategies are gradually shifting from population-based models to individualized precision nutrition models, which integrate and analyze multidimensional data to open new pathways for obesity prevention and control. The theoretical framework of precision nutrition is based on the recognition that individual heterogeneity in biological mechanisms underlies individual variations in nutritional needs. The research approaches in precision nutrition include genomics, epigenetics, metagenomics, metabolomics, and integrated multi-omics analyses. In terms of application, precision nutrition combines advanced external dietary exposure assessment tools-such as Internet-based dietary assessment systems and AI-driven image recognition-with omics-derived internal biomarkers to enable accurate quantification of dietary intake. Principles such as holistic dietary integrity, full coverage of dietary restrictions, optimized cooking methods, and chrononutrition are emphasized in intervention strategies. Future efforts in precision nutrition should focus on overcoming technical challenges, including thorough integration of multi-omics data and the development of intelligent decision-making systems. The goal is to move beyond generalized, "one-size-fits-all" model toward tailored, precision-based intervention. Precision nutrition will provide essential scientific and technological support for the Healthy China 2030 initiative and help usher in a new era of scientific and individualized obesity prevention and control.},
}

Humans
*Obesity/prevention & control
*Precision Medicine/methods
Metabolomics
Genomics
Diet

@article {pmid41112778,
year = {2025},
author = {Dong, Y and Fan, S and He, S and Zhao, W and Lancuo, Z and Sharshov, K and Li, Y and Wang, W},
title = {Comparative analysis of fecal DNA viromes in Large-billed crows and Northern ravens reveals diverse viral profiles.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20170},
pmid = {41112778},
issn = {2167-8359},
mesh = {Animals ; *Crows/virology ; *Feces/virology ; *Virome/genetics ; *DNA, Viral/genetics ; *DNA Viruses/genetics/isolation & purification/classification ; Metagenomics ; },
abstract = {As facultative scavenger birds, crows carry various parasites, viruses, and bacteria, making them significant infection hosts and transmission vectors. In this study, we employed viral metagenomics to enrich viral particles from three fecal samples of the Northern ravens (Corvus corax) and four fecal samples of the Large-billed crows (Corvus macrorhynchos). Viral DNA was then extracted, and seven sequencing libraries were constructed. The composition and characteristics of the DNA viromes in the feces of these two facultative scavenging bird species were analyzed using the Illumina NovaSeq platform (PE150 mode). The results showed that the fecal DNA viruses carried by Northern ravens mainly belonged to Parvoviridae (31.49%), Caudoviricetes_Unclassified (21.91%), Microviridae (21.57%), and Genomoviridae (18.2%), while those carried by Large-billed crows were predominantly Genomoviridae (29.7%), Parvoviridae (26.15%), and Caudoviricetes_Unclassified (22.15%). Diversity analysis using Richness, Shannon, and Simpson indices showed no significant differences in viral composition between the two crow species. Additionally, principal coordinate analysis (PCoA) (F = 1.079, P = 0.155) and non-metric multidimensional scaling (NMDS) (F = 1.079, P = 0.154) analyses demonstrated no distinct separation between the two groups. Moreover, the KEGG-enriched pathways in both crow species were primarily associated with metabolic and genetic information processing functions. The selection of the Large-billed crows and Northern ravens in this study was based on their widespread distribution, close association with human settlements, and distinctive scavenging behavior. Comparative analysis of the diversity and composition of their DNA viral communities offers a basis for evaluating the zoonotic risks associated with these scavenger birds.},
}

Animals
*Crows/virology
*Feces/virology
*Virome/genetics
*DNA, Viral/genetics
*DNA Viruses/genetics/isolation & purification/classification
Metagenomics

@article {pmid41112578,
year = {2025},
author = {Chen, J and Xu, Q and Zhang, L and Zhang, D and Wu, X},
title = {Enrichment of prevotella melaninogenica in the lower respiratory tract links to checkpoint inhibitor pneumonitis and radiation pneumonitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1594460},
pmid = {41112578},
issn = {2235-2988},
mesh = {Humans ; Male ; Female ; Middle Aged ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; *Radiation Pneumonitis/microbiology ; *Prevotella/isolation & purification/genetics/classification ; Microbiota ; Lung Neoplasms/drug therapy ; *Immune Checkpoint Inhibitors/adverse effects ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Pneumonia/microbiology ; Lung/microbiology ; },
abstract = {BACKGROUND: Checkpoint inhibitor pneumonitis (CIP) and radiation pneumonitis (RP) lead to anti-cancer therapy discontinuation and poor diagnosis. The human microbiome is related to various respiratory diseases. However, the role of the lung microbiome in CIP and RP remains unknown. Our study aimed to explore the lower respiratory tract (LRT) microbiome in CIP/RP patients.

METHODS: The study enrolled 61 patients with pneumonitis or pneumonia, including 23 with CIP/RP, and 38 with lung cancer with pneumonia (LC-P). Metagenomic next-generation sequencing (mNGS) was performed to identify the microbiota in bronchoalveolar lavage fluid (BALF), and bioinformatics methods were used to compare the microbial differences between CIP/RP and LC-P groups. Correlation analysis was conducted to explore the relationship between LRT microbiota and clinical features.

RESULTS: The Prevotella was the dominant genus in both groups. The Prevotella melaninogenica, which belongs to the Prevotella genus, was the dominant species in the CIP/RP group and the second most abundant species in the LC-P group. Compared to the LC-P group, the CIP/RP group had significantly high levels of Prevotella melaninogenica species and lymphocyte percentage in BALF but significantly low levels of lymphocytes, eosinophils and albumin in peripheral blood. In addition, the Prevotella melaninogenica species had a negative correlation with peripheral blood lymphocytes.

CONCLUSION: The enrichment of Prevotella melaninogenica species in LRT and a decreased level of peripheral blood lymphocytes are associated with CIP/RP.},
}

Humans
Male
Female
Middle Aged
Aged
Bronchoalveolar Lavage Fluid/microbiology
*Radiation Pneumonitis/microbiology
*Prevotella/isolation & purification/genetics/classification
Microbiota
Lung Neoplasms/drug therapy
*Immune Checkpoint Inhibitors/adverse effects
High-Throughput Nucleotide Sequencing
Metagenomics
*Pneumonia/microbiology
Lung/microbiology

@article {pmid41112491,
year = {2025},
author = {Kumari V S, S and Potdar, V and Shinde, M and Parashar, D and Alagarasu, K and Cherian, S and Lavania, M},
title = {Dysbiosis of the oropharyngeal microbiota in COVID-19: distinct profiles in patients with severe respiratory symptoms.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2569523},
pmid = {41112491},
issn = {2000-2297},
abstract = {BACKGROUND: COVID-19 has been strongly associated with alterations in the oropharyngeal microbiota, yet the microbial features linked to disease severity remain unclear.

OBJECTIVE: This study aimed to elucidate the microbial signatures associated with COVID-19 disease severity.

DESIGN: 16S rRNA gene sequencing was employed to profile the oropharyngeal microbiota of patients with varying degrees of COVID-19 severity.

RESULTS: A significant reduction in alpha diversity suggests a major microbial dysbiosis in critically ill patients compared to less severe cases and healthy individuals, whereas beta diversity analysis revealed a broadly conserved community structure across different groups. Comparative analysis showed significant depletion of the phylum Fusobacteriota and enrichment of bacterial families, including Corynebacteriaceae, Methylobacteriaceae, Acetobacteraceae, Bradyrhizobiaceae, Lactobacillaceae, Staphylococcaceae, Propionibacteriaceae, and Moraxellaceae. Rothia mucilaginosa was notably enriched in patients with severe respiratory symptoms, and many of the enriched taxa are known opportunistic pathogens associated with respiratory infections.

CONCLUSION: The marked dysbiosis and enrichment of opportunistic pathogens in the oropharyngeal microbiota of critically ill patients indicate their possible role in respiratory complications. The identified microbial patterns highlight the potential of microbiome profiling as a tool for disease prognosis and guide further research into the role of microbes in COVID-19 pathogenesis and implications for treatment protocols.},
}

@article {pmid41112258,
year = {2025},
author = {Filippi Xavier, L and Gacesa, R and da Rocha, GHO and Broering, MF and Scharf, P and Lima, FDS and Faber, KN and Harmsen, H and Hoffmann, C and Farsky, SHP},
title = {Annexin A1 levels affect microbiota in health and DSS-induced colitis/inflammatory bowel disease development.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1679071},
pmid = {41112258},
issn = {1664-3224},
mesh = {Animals ; *Annexin A1/genetics/metabolism ; *Gastrointestinal Microbiome ; Humans ; Mice ; Mice, Knockout ; *Colitis/chemically induced/microbiology/metabolism ; Mice, Inbred C57BL ; Dextran Sulfate ; Male ; *Inflammatory Bowel Diseases/microbiology/metabolism ; Female ; Disease Models, Animal ; Dysbiosis ; Feces/microbiology ; Adult ; Middle Aged ; },
abstract = {BACKGROUND: Inflammatory Bowel Diseases (IBDs) are characterized by intestinal dysbiosis and immune dysregulation. Annexin A1 (AnxA1) promotes epithelial repair and inhibits immune responses during IBD. However, AnxA1's impact on gut microbiota during IBD remains unclear. Here, we experimentally investigated the microbiota profile during colitis in wild-type (WT) and AnxA1-deficient mice (AnxA1[-/-]), and evaluated an observational cohort in IBD patients with high or low AnxA1 expression.

METHODS: Colitis was induced in C57BL/6 WT and AnxA1 [[-]/[-]] mice via oral administration of 2% DSS for six days. Fecal samples were collected at baseline, peak inflammation (day 6), and during the recovery phase (day 10) for 16S rRNA sequencing. Human microbiota data from the Lifelines Dutch Microbiome Project cohort, including IBD and healthy subjects, were analyzed for AnxA1 expression using R software.

RESULTS: Healthy AnxA1[-/-] mice exhibited reduced microbial richness and a distinct gut microbiota composition, marked by increased Proteobacteria and Parasutterella, and reduced Deferribacterota, Campylobacterota, and Verrucomicrobiota. During DSS-induced colitis, AnxA1[-/-] mice showed greater weight loss and heightened inflammation, displaying earlier and more pronounced microbial shifts, including increased Proteobacteria, Cyanobacteria, Parabacteroides, Bacteroides, and Escherichia-Shigella. In contrast, WT mice exhibited delayed changes, with expansion of Alloprevotella, Akkermansia, and Faecalibaculum after day 6. In human IBD samples, Crohn's disease (CD) patients with low AnxA1 expression and active inflammation presented an altered microbiota enriched in Lachnoclostridium and Parabacteroides, while ulcerative colitis (UC) patients showed phylum-level shifts modulated by AnxA1 levels. Notably, non-inflamed CD and UC patients with low AnxA1 differed significantly in microbiota composition. Moreover, inflamed CD patients with high AnxA1 expression showed microbial profiles resembling those of healthy controls, while low AnxA1 expression was associated with a more pronounced dysbiotic state.

CONCLUSION: AnxA1 is implicated in microbiota control under healthy and IBD conditions. Accordingly, the microbiota of healthy AnxA1[-/-] mice, colitic AnxA1[-/-] mice, and IBD patients with low AnxA1 expression exhibit dysbiosis compared to their respective controls. Together, these unprecedented findings reveal AnxA1 as a potential regulatory protein in the immune-microbiota axis involved in IBD pathogenesis.},
}

Animals
*Annexin A1/genetics/metabolism
*Gastrointestinal Microbiome
Humans
Mice
Mice, Knockout
*Colitis/chemically induced/microbiology/metabolism
Mice, Inbred C57BL
Dextran Sulfate
Male
*Inflammatory Bowel Diseases/microbiology/metabolism
Female
Disease Models, Animal
Dysbiosis
Feces/microbiology
Adult
Middle Aged

@article {pmid41112053,
year = {2025},
author = {Li, P and Xie, L and Zheng, H and Feng, Y and Mai, F and Tang, W and Wang, J and Lan, Z and Lv, S and Jayawardana, T and Koentgen, S and Xu, S and Wan, Z and Chen, Y and Xu, H and Shen, S and Zhang, F and Yang, Y and Hold, G and He, F and El-Omar, EM and Yu, G and Chen, X},
title = {Gut microbial-derived 3,4-dihydroxyphenylacetic acid ameliorates reproductive phenotype of polycystic ovary syndrome.},
journal = {iMeta},
volume = {4},
number = {5},
pages = {e70065},
pmid = {41112053},
issn = {2770-596X},
abstract = {Polycystic ovary syndrome (PCOS) is a prevalent endocrine and reproductive disorder affecting women of reproductive age. While the gut microbiota has been implicated in PCOS pathophysiology, the role of microbial-derived metabolites as mediators of host-microbe interactions remains poorly defined. Here, we integrated untargeted gut metabolomics with metagenomic profiling in patients with PCOS and identified a marked depletion of 3,4-dihydroxyphenylacetic acid (DHPAA), a flavonoid-derived microbial catabolite. Oral administration of DHPAA ameliorated PCOS-like phenotypes in two mouse models by suppressing bone morphogenetic protein signaling and reducing anti-Müllerian hormone (AMH) levels. We found that DHPAA production depends on gut microbial degradation of dietary flavonoids. We further identified a bacterial species, Streptococcus thermophilus, consistently depleted in PCOS across two human cohorts and a mouse model, restored DHPAA levels and improved reproductive outcomes in mice. Conversely, a β-galactosidase-deficient mutant of S. thermophilus failed to confer these benefits, highlighting β-galactosidase as a critical enzyme in DHPAA biosynthesis. Our findings establish DHPAA as a key microbial metabolite linking diet, microbiota, and reproductive health, and propose its potential as a novel therapeutic candidate for PCOS.},
}

@article {pmid41112047,
year = {2025},
author = {Xu, M and Guan, S and Zhong, C and Ma, M and Tao, L and Huang, G},
title = {Characterizing the microbiome of "sterile" organs in experimental mice and evidence of translocation of bacteria from the gut to other internal organs.},
journal = {iMeta},
volume = {4},
number = {5},
pages = {e70081},
pmid = {41112047},
issn = {2770-596X},
abstract = {Using culturomics and metagenomics, we demonstrate the existence of non-pathogenic microbiota in the internal organs of healthy experimental mice, challenging the traditional dogma of organ sterility. Based on the analysis of 104 commercially sourced mice (C57BL/6J, BALB/c, ICR), the study reveals that over 20% of the analyzed mice harbored a high microbial burden in the internal organs and identified a total of 463 microbial species. Several species, including Ligilactobacillus murinus, Alcaligenes faecalis, Micrococcus luteus, Pseudochrobactrum asaccharolyticum, Escherichia coli, and Microbacterium sp., were frequently identified and were abundant in the mouse tissues. Further investigation implies that microorganisms in the "sterile" tissues could be associated with the gut microbiota. Given the wide use of experimental mice in medical and biological research, these findings of resident microorganisms in the animal's internal organs raise concerns about potential variability in experimental outcomes.},
}

@article {pmid41112045,
year = {2025},
author = {Zhang, Y and Gilbert, JA and Liu, X and Nie, L and Xu, X and Gao, G and Lyu, L and Ma, Y and Fan, K and Yang, T and Zhang, Y and Zhang, J and Chu, H},
title = {SynCom-mediated herbicide degradation activates microbial carbon metabolism in soils.},
journal = {iMeta},
volume = {4},
number = {5},
pages = {e70058},
pmid = {41112045},
issn = {2770-596X},
abstract = {Extensive herbicide residues in the black soil of northeastern China are considered a significant agricultural pollution threat, yet effective bioremediation of this complex and persistent mixture remains a challenge. We identified 16 bacterial species that associated with these herbicide residues in situ, nine of which were culturable and could degrade multiple herbicides. From these strains, we constructed a four-member synthetic microbial community (SynCom) that degrades multiple herbicides, stabilizes colonization, increases soil bacterial biodiversity, and alters soil enzyme activity. Under laboratory conditions, the SynCom degraded eight herbicides within 48 h with >60% efficiency, and accumulated carbon on the cell surface of the constituent species. In black soil microcosm trials, the SynCom achieved 60%-99% degradation efficiency of the endogenous herbicides over 35 days and was able to consistently maintain biomass above 10[4] cfu/g soil. Additionally, SynCom application resulted in an accumulation of carbohydrate-active enzymes and microbial necromass-associated carbon, which suggests activation of soil microbial carbon metabolism. In support of this, metagenomic analyses identified a significant increase in the abundance of genes involved in the tricarboxylic acid cycle, pyruvate metabolism, and glycolysis. This SynCom represents a compelling bioremediation solution that simultaneously improves soil microbial carbon metabolism activity in polluted soils.},
}

@article {pmid41112040,
year = {2025},
author = {Johansen, PL and Chatzigiannidou, I and Berzina, L and Kristiansen, K and Brix, S},
title = {Unveiling soil microbial diversity through ultra-deep short-read metagenomic sequencing and co-assembly.},
journal = {iMeta},
volume = {4},
number = {5},
pages = {e70075},
pmid = {41112040},
issn = {2770-596X},
abstract = {By combining ultra-deep short-read shotgun metagenomic sequencing with 5-sample co-assembly across 600 agricultural soil samples, we significantly enhanced the representation and recovery of microbial communities in both clay and sandy soils. Despite an average of 107 Gb clean reads per sample, projections indicated that 1-4 Tb per sample would be required to capture 95% of the microbial community. Co-assembly of five biological replicates markedly improved metagenomic recovery, yielding up to 3.7× more metagenome-assembled genomes, up to 95% more unique genes, and broader recovery of prokaryotic phyla compared to single-sample assemblies.},
}

@article {pmid41110780,
year = {2025},
author = {Sreekutti, S and Ndomondo, S and Sharma, P and Patel, R and Mevada, V},
title = {Forensic application of metagenomics: Methods and future directions.},
journal = {Journal of microbiological methods},
volume = {239},
number = {},
pages = {107300},
doi = {10.1016/j.mimet.2025.107300},
pmid = {41110780},
issn = {1872-8359},
abstract = {The microbial communities are found commonly in our environment, making it impossible to touch any surface without interfering with them. The human microbiome, primarily bacteria in the saliva, skin, and gut, can be used for forensic purposes. Human-associated and environmental samples, such as soil, water, etc., carry the microbiome, which can be used for geolocation inference. These microbiomes have considerable potential for use in forensic investigations, including many instances of sexual violence, post-mortem examinations, individual identification, and location identification. Recent developments in metagenomic sequencing have greatly contributed to microbial analysis. Yet, because of certain issues and challenges, the forensic application of microbiomes is still in its infancy. This article reviewed the use of metagenomics in forensic science and some of the main obstacles that are faced by experts in this area. The first and foremost issues noted were the lack of standardization protocols and a poor reference database for research studies. Some limitations, such as storage sensitivity and limited samples, are also indicated. Future research studies should concentrate on more standardized investigations to overcome these difficulties and explore the enormous potential of microbiomes for beneficial applications in forensic contexts.},
}

@article {pmid41110713,
year = {2025},
author = {Wang, T and Zhang, Q and Li, J and Dan, Q and Peng, Y},
title = {Unlocking the potential of anaerobic ammonia oxidation: Enhancing nitrogen removal in municipal wastewater through strategic nitrate introduction and microbial synergy.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133523},
doi = {10.1016/j.biortech.2025.133523},
pmid = {41110713},
issn = {1873-2976},
abstract = {Coordinating the utilization of raw carbon sources with anammox nitrogen removal is pivotal in mainstream wastewater treatment. A novel strategy was developed to enhance nitrogen removal and anammox performance by introducing nitrate into the anoxic stage of an anaerobic/aerobic/anoxic anammox process treating municipal wastewater. This strategy achieved a nitrogen removal efficiency of 97.6 ± 0.9 %, reducing effluent total inorganic nitrogen to 1.8 ± 0.9 mg/L at a high N loading rate (87.7 ± 1.4 g N/m[3]/d) and a low C/N (2.8). After nitrate introduction, anammox contribution increased to 58.9 % and the relative abundance of the anammox genus Candidatus Brocadia increased by 250 %. Metagenomic analysis revealed upregulation of key genes ackA and acs, supporting endogenous carbon storage and utilization by denitrifying glycogen-accumulating organisms (DGAOs). This cooperation between anammox bacteria and DGAOs provided potential for integrating anammox into the mainstream and nitrate wastewater treatment, paving the way for sustainable nutrient management.},
}

@article {pmid41110566,
year = {2025},
author = {Wu, Z and He, Z and Dou, P and Wang, K and Zhang, Y},
title = {Study on the intestinal metabolism and absorption of polysaccharides from Dendrobium officinale.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {148390},
doi = {10.1016/j.ijbiomac.2025.148390},
pmid = {41110566},
issn = {1879-0003},
abstract = {Dendrobium officinale polysaccharide (DOP) is widely recognized for its excellent pharmacological activities, however, the in-depth pharmacokinetic characteristic remains unrevealed, significantly hindering its further development. It was hypothesized that Bacteroides predominantly mediates the in vivo metabolism of DOP via polysaccharide utilization loci (PULs), and the resulting oligosaccharides can be directly absorbed by the intestine. To verify this hypothesis, metagenomic sequencing analysis was first employed, confirming that DOP stimulates an upregulation of PULs associated with carbohydrate metabolism within the gut microbiota dominated by Bacteroides. The metabolized oligosaccharides were correlated with highly expressed endo-β-1,4-mannanase from Bacteroides. Further utilizing fluorescent labeling techniques, it was demonstrated that oligosaccharides derived from DOP metabolism are directly absorbed by intestinal tissues. Unabsorbed metabolites subsequently undergo disordered metabolism by gut microbiota into small molecules such as short-chain fatty acids. Collectively, these findings provide novel evidence for elucidating the pharmacological activities of DOP and offer new insights into pharmacokinetic research for other polysaccharides.},
}

@article {pmid41110291,
year = {2025},
author = {Liu, C and Liu, Y and Li, Y and Liu, M and Lu, H and Liu, X and Lu, M},
title = {Host-dominated oxidative cascades and transgenerational Cu transfer drive population collapse in Spodoptera frugiperda under chronic CuO nanoparticle exposure: Implications for nano-pesticide environmental risk assessment.},
journal = {Environment international},
volume = {205},
number = {},
pages = {109874},
doi = {10.1016/j.envint.2025.109874},
pmid = {41110291},
issn = {1873-6750},
abstract = {The increasing use of CuO nanoparticles (NPs) in agriculture raises urgent concerns about their long-term ecological risks, particularly regarding transgenerational reproduction and gut microbiota in pest species. Here, we chronically exposed Spodoptera frugiperda to a sublethal concentration of CuO NPs (25 mg/kg). Population collapse occurred in the F4 generation (0 % survival), driven by pronounced oxidative stress (CAT and MDA activities increased up to 2.0-fold), substantial Cu accumulation in eggs (12 → 30 ng/mg) and gut tissue (25 → 750 ng/mg), and impaired reproductive output (33 % reduction in egg production with only 30 % hatching in F3). Although gut microbial diversity remained structurally stable (Shannon index, P > 0.05), metagenomic analysis revealed functional reprogramming, particularly in energy metabolism. Sterile larva inoculation assays confirmed that microbiota exacerbated toxicity, though direct NPs effects dominated. These findings highlight that current risk assessment frameworks, which are primarily focused on acute toxicity and microbial composition, severely underestimate the hazards of nanopesticides. We advocate for integrating multigenerational toxicity testing and metagenomic profiling into nano-pesticide risk evaluations to better capture population-level outcomes.},
}

@article {pmid41109936,
year = {2025},
author = {Ali, A and Khattak, AI and Chawla, D and Hasan, F and Khan, H and Ali, MA and Moeez, A and Tanveer, S and Ubaidullah, and Afridi, MJ and Ikram, J and Hayat, S and Shah, FZ and Nadeem, A and Nadeem, MA and Mushtaq, A and Haroon, W and Bharadwaj, HR and Dahiya, DS and Mansoor, E},
title = {Diagnostic Performance of Metagenomic Next-Generation Sequencing (mNGS) and Culture in Infected Pancreatic Necrosis: A Systematic Review and Meta-Analysis.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {41109936},
issn = {1573-2568},
abstract = {BACKGROUND: Infected pancreatic necrosis (IPN) is a severe complication of acute pancreatitis, requiring prompt diagnosis. Conventional microbial culture, the current gold standard, has limitations in sensitivity and turnaround time. Metagenomic next-generation sequencing (mNGS) offers rapid, comprehensive pathogen detection, but its diagnostic performance for IPN remains unclear.

METHODS: We conducted a systematic review and meta-analysis following PRISMA-DTA guidelines, prospectively registered in PROSPERO (CRD420251008574). PubMed, Embase, and Web of Science databases were searched from inception to March 2025. Seven studies (313 patients) evaluating mNGS for IPN diagnosis were included, with four providing direct comparisons to culture. Pooled sensitivity, specificity, and area under the curve (AUC) were calculated using a random-effects model. Heterogeneity was assessed using I[2] statistics.

RESULTS: In double-arm analysis, mNGS showed significantly higher sensitivity (0.87, 95% CI: 0.72-0.95) than culture (0.36, 95% CI: 0.23-0.51), with comparable specificity (0.83 for both). The AUC for mNGS (0.92, 95% CI: 0.79-0.94) surpassed that of culture (0.52, 95% CI: 0.27-0.86). Single-arm analysis confirmed mNGS as a reliable standalone test (sensitivity: 0.86; specificity: 0.85; AUC: 0.89). A threshold effect (r = - 0.991) indicated variability in diagnostic criteria across studies.

CONCLUSIONS: mNGS outperforms culture in diagnosing IPN, offering higher sensitivity and faster results. Its ability to detect diverse pathogens, including fastidious and polymicrobial infections, makes it a valuable tool for early intervention. However, challenges like cost, standardization, and interpretation persist. Future studies should focus on prospective validation and cost-effectiveness to integrate mNGS into routine clinical practice.},
}

@article {pmid41109511,
year = {2025},
author = {Wang, W and Wang, H and Zhang, Q and Li, L and Lian, X and Yin, C and Lin, Y and Li, Z and Wang, Y and Han, Z and Shen, F and Chen, X and Sun, R and Wang, T},
title = {Diagnosis of spinal infections caused by fastidious bacteria: a multicenter, retrospective observational study.},
journal = {The spine journal : official journal of the North American Spine Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.spinee.2025.10.019},
pmid = {41109511},
issn = {1878-1632},
abstract = {BACKGROUND CONTEXT: Identifying pathogens in pyogenic spinal infections is essential for guiding clinical treatment. However, the fastidious characteristics of certain bacteria often make traditional microbial culture methods ineffective, resulting in diagnostic delays and postponed intervention. In recent years, metagenomic next-generation sequencing (mNGS) has shown strong potential in analyzing complex microbial communities, offering a more advanced strategy for pathogen detection.

PURPOSE: Evaluating mNGS versus microbial culture for diagnosing fastidious bacteria in pyogenic spinal infections.

STUDY DESIGN: A multicenter, retrospective observational study.

PATIENT SAMPLE: We retrospectively reviewed clinical data from 553 patients diagnosed with spinal infections across four medical centers between December 2019 and December 2024.

OUTCOME MEASURES: Identification of fastidious bacteria in patients.

METHODS: All patients underwent imaging and standard laboratory testing. Specimens from infected sites obtained through puncture or surgery were analyzed using both microbial culture and mNGS. According to predefined diagnostic, inclusion, and exclusion criteria for fastidious bacteria, 49 patients (8.86%, 49/553) were identified with pyogenic spinal infections caused by fastidious organisms. We compared the diagnostic outcomes of mNGS with those of culture-based methods for detecting fastidious bacterial pathogens in spinal infections.

RESULTS: Among the 49 patients, mNGS yielded a positive detection rate of 87.76% (43/49), which was significantly higher than that of conventional culture methods at 16.33% (8/49) (χ²=12.683, p < 0.001). Among the 41 culture-negative cases, mNGS successfully identified fastidious bacteria in 37, corresponding to an effective supplementary detection rate of 90.24% (37/41). While culture identified 5 species of fastidious bacteria, mNGS detected 15, giving an effective pathogen supplementation rate of 66.7% (10/15). These 15 bacteria fell into two groups: the first included those that cannot be cultured using routine clinical media (26/43, 60.47%), and the second included those that may sporadically grow in standard cultures but tend to show low positivity (17/43, 39.53%). Out of the total 553 cases, 382 were culture-negative. Among these, 37 (37/382, 9.69%) were identified as fastidious bacteria via mNGS. mNGS yielded results within 48 hours, significantly faster than the 3-7 days typically required by culture methods.

CONCLUSIONS: In cases of pyogenic spinal infections caused by fastidious bacteria, mNGS demonstrated a higher detection rate, wider pathogen range, and significantly shorter turnaround compared to traditional microbial culture. The culture-independent approach of mNGS presents a distinct advantage in identifying fastidious pathogens.},
}

@article {pmid41109083,
year = {2025},
author = {Wu, W and Song, J and Wu, Q and Wu, X and Sun, N and Xia, X},
title = {Development and evaluation of CD45-conjugated magnetic particles-based host cell depletion for enhanced metagenomic next-generation sequencing in bloodstream infection.},
journal = {Journal of chromatography. B, Analytical technologies in the biomedical and life sciences},
volume = {1267},
number = {},
pages = {124823},
doi = {10.1016/j.jchromb.2025.124823},
pmid = {41109083},
issn = {1873-376X},
abstract = {Metagenomic next-generation sequencing (mNGS) enables unbiased detection of human pathogens without prior assumptions. However, the direct detection of bloodstream infection pathogens is limited by host DNA interference, leading to the clinical adoption of microbial cell-free DNA mNGS (plasma cfDNA mNGS). This study developed a host cell depletion method based on immunomagnetic separation using CD45-conjugated magnetic particles (CD45-MPs, termed the IP method) to reduce host DNA interference and enhance mNGS performance for bloodstream pathogen detection. In simulated samples, known concentrations of pathogens (intact Escherichia coli and Candida albicans cells, fragmented Staphylococcus aureus genomic DNA) were spiked into whole blood samples, serially diluted 10-fold, and divided into whole blood, plasma, and IP-treated groups. These groups were analyzed using hematological analysis, microscopic smear, DNA concentration measurement, relative quantification of GAPDH using qPCR, and mNGS. Results showed that CD45-conjugated magnetic particles effectively removed host cells from whole blood (reducing cell count by 99.9%). The results of nucleic acid measurement and qPCR indicated that the supernatant from IP-treated samples contained significantly lower host DNA compared to whole blood and plasma groups. mNGS detection of simulated samples demonstrated that the IP method enabled detection of pathogens at concentrations as low as 100 CFU/mL for E. coli and S. aureus, and 50 CFU/mL for C. albicans. In clinical testing of 77 samples from patients with suspected bloodstream infections, mNGS combined with the IP method showed significantly higher positivity rates than plasma cfDNA mNGS. In conclusion, CD45-conjugated magnetic particles effectively deplete human cells and enhance the clinical performance of mNGS on the detection of bloodstream infections.},
}

@article {pmid41108980,
year = {2025},
author = {Liu, C and Li, C and Guo, X and Wang, L and Wang, N},
title = {Swine farming emissions drive deterministic assembly of antibiotic resistance genes in receiving River: A new ecological perspective.},
journal = {Water research},
volume = {289},
number = {Pt A},
pages = {124803},
doi = {10.1016/j.watres.2025.124803},
pmid = {41108980},
issn = {1879-2448},
abstract = {Livestock farming constitutes a critical reservoir of antibiotic resistance genes (ARGs). Following the fertilization of manure, ARGs enter agricultural soils and subsequently migrate into riverine ecosystem via paddy water (PW), posing potential environmental and public health risks. Understanding the ecological processes behind the assembly of ARG profiles is crucial for predicting the dynamics of ARGs and guiding effective mitigation strategies, while research gaps persist regarding how exogenous inputs affect ARG assembly in receiving environments. This study integrated source fingerprinting via metagenomic sequencing with analytical frameworks from community ecology processes to determine the specific influence of livestock farming emissions on ARG assembly in receiving river. The research targeted intensive swine farming regions in the lower Yangtze River Basin in China, and systematically collected manure-impacted PW as pollution source, alongside receiving river water (RW) and sediment (RS) matrices. In the ecosystem, 946 ARGs belonging to 24 types were identified. Despite the elevated abundance of ARGs in RW relative to RS, the composition in RS closely resembled that in PW and was enriched in high-risk genes (e.g., acrE and acrF), resulting in a higher risk score for RS compared to RW (p < 0.01). Network topology analysis revealed characteristics indicative of exogenous-driven ARG transmission, including high modularity and intra-type clustering of ARGs within modules. Variance partitioning analysis (VPA) collectively revealed that ARGs in RW exhibited a greater potential for horizontal transfer, whereas host communities exerted a predominant influence on ARG distribution in RS. Neutral model yielded fits of R[2] = 0.197 and 0.175 for RW and RS, respectively. Meanwhile, a null model-based stochasticity ratio ranged 30.3 %∼42.7 %, jointly demonstrating that deterministic processes, particularly heterogeneous selection, dominated ARG assembly in the river ecosystem, with a more pronounced effect in sediments. Crucially, removal of PW-specific ARGs led to a marked increase in the contribution of neutral processes, confirming livestock emissions as the core driver shifting assembly towards determinism. Fast expectation-maximization microbial source tracking (FEAST) quantified the contribution of swine farming to ARGs in RW and RS at 12.35 % and 31.09 %, respectively. This study provided novel insights into the deterministic role of exogenous inputs in governing ARG assembly within receiving environments, thus offering theoretical support for developing targeted strategies to control ARG dissemination.},
}

@article {pmid41108960,
year = {2025},
author = {Han, C and Zhang, H and Guan, W and Li, L and Zhao, Y and Gao, C and Zhao, Z and Xing, Q and Yuan, A and Guo, D and Gao, Y and Qiao, J and Peng, Y and Zhong, C and He, J and Li, Z and Xiong, X},
title = {From flagellar assembly to DNA replication: CJSe's role in mitigating microbial antibiotic resistance genes.},
journal = {Ecotoxicology and environmental safety},
volume = {305},
number = {},
pages = {119205},
doi = {10.1016/j.ecoenv.2025.119205},
pmid = {41108960},
issn = {1090-2414},
abstract = {The emergence of Antibiotic Resistance Genes (ARGs) in Campylobacter jejuni (CJ) poses a severe threat to food safety and human health. However, the specific impact of CJ and its variants on ARGs and other related factors remains to be further elucidated. Herein, integrated metagenomic sequencing and co-occurrence network analysis approach were employed to investigate the impact of CJ and CJ incorporated with biogenic selenium (CJSe) on ARGs, flagellar assembly pathways, microbial communities, and DNA replication pathways in chicken manure. Compared to the Control (CON) and CJ groups, the CJSe group exhibited 2.4-fold increase selenium levels (P < 0.01) in chicken manure. Notable differences were also observed between the CJ and CJSe groups, with sequence results showing a CJ > CJSe > CON trend in total ARG copy numbers. Furthermore, the CJSe group showed 31.6 % fewer flagellar assembly genes compared to the CJ group. Additionally, compared to the CJ group, CJSe inhibited pathways such as basal body/hook (e.g., FliH, FliO, FliQ reduced by 25-52 %) and stator (MotB downregulated by 42.3 %), suppressing flagellar assembly. We also found that both CJ and CJSe influenced bacterial DNA replication pathways, with the former increasing ARG-carrying bacteria and the latter, under selenium-induced selective pressure, reducing ARG-carrying bacteria. Moreover, compared to the CJ group, the CJSe group showed a significantly lower 9.72 % copy number of total archaeal DNA replication genes. Furthermore, through intricate co-occurrence network analysis, we discovered the complex interplay between changes in ARGs and bacterial and archaeal DNA replication dynamics within the microbial community. These findings indicate that CJSe mitigates the threat posed by CJ and reduces ARG prevalence, while its dual functionality enables applications in biofortified crop production and soil remediation in selenium-deficient regions, thereby advancing circular economy systems. While the current study demonstrates CJSe's dual functionality under controlled conditions, future work will implement a dedicated ecological risk assessment framework encompassing Se speciation/leaching tests and non-target organism assays to confirm environmental safety under field-relevant scenarios. This approach aligns with sustainable strategies for food security and public health safeguarding.},
}

@article {pmid41108937,
year = {2025},
author = {Yang, MT and Xie, LH and Wang, L and Gao, YQ and Liu, R and Ma, H and Lei, CC and Jiang, J and Su, JW and Zhang, XX and Ni, HB and Nan, FL},
title = {Metagenomic analysis of bile acid biotransformation by gut microbiota in wild birds.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {105956},
doi = {10.1016/j.psj.2025.105956},
pmid = {41108937},
issn = {1525-3171},
abstract = {Although gut microbiota-mediated bile acid (BA) metabolism is well characterized in mammals, its mechanisms in wild birds remain largely unknown, hindering our understanding of their ecological adaptation and health. In this study, metagenomic analysis was performed on 10,455 metagenome-assembled genomes (MAGs) derived from 718 wild bird gut samples, from which 1,034 high-quality non-redundant MAGs were selected for further analysis. Functional annotation analysis identified 755 MAGs encoding genes associated with BA biotransformation pathways, primarily derived from the phyla Bacillota_A, Bacteroidota, and Bacillota, with dominant genera including Helicobacter_G and Ligilactobacillus. Subsequent genomic analysis identified 379 MAGs encoding bile salt hydrolase (BSH), with phylogenetic classification demonstrating predominant affiliation to the Bacteroidota and Bacillota_A phyla. Compared to the BSH-producing microbiota in the human and chicken gut, the phylum Bacillota exhibited a notably higher relative abundance in wild birds. Within the wild bird gut microbiome, Helicobacter_G was identified as the predominant BSH-encoding genus, whereas its relative abundance was substantially lower in both humans and chickens. Moreover, migratory birds (MB) displayed significantly higher diversity of BA biotransformation genes than resident birds (RB), with Helicobacter_G being notably enriched at the genus level in MB, potentially associated with their heightened energy and nutritional demands during migration. Notably, in addition to residency status, host species emerged as the most influential factor shaping the compositional variation of BA biotransformation genes, followed by environmental factors and dietary habits. In summary, this study systematically elucidates the potential functions of gut microbiota in BA metabolism and their close associations with host ecological traits in wild birds, not only advancing our understanding of host-microbe interactions and metabolic adaptation mechanisms but also providing a theoretical foundation for future interventions targeting gut microbiota to improve wildlife health.},
}

@article {pmid41108646,
year = {2025},
author = {Jeon, JY and Allen, NM and Black, AN and DeWoody, JA},
title = {Short-Read Pangenomes and Their Potential Utility in Population and Conservation Genomics.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70060},
doi = {10.1111/1755-0998.70060},
pmid = {41108646},
issn = {1755-0998},
abstract = {As a collection of all the genetic variants in the gene pool, the pangenome is a concept that will become fundamental to conservation genomic studies. Unfortunately, most pangenomic approaches developed for humans and model organisms are financially impractical for conservation genomic studies of threatened or endangered species due to the high costs associated with deep sequencing multiple individuals using long-read platforms. Here, by integrating metagenomic and iterative map-then-assemble approaches, we (1) propose novel workflows to construct graph pangenomes from multiple low-coverage short-read datasets; (2) benchmark these short-read pangenomes (both linear and graph) against a previously published long-read graph pangenome of the barn swallow; and (3) evaluate the utility of our workflows in population and conservation genomics. Our results indicate that economical short-read graph pangenomes can recover the vast majority of the variants identified through expensive long-read graph approaches, and that these variants accurately detect important biological signals (e.g., spatial structure and independent taxonomic delineations). These results mean that researchers can utilize their limited, conservation-oriented funding to more fully characterize all the variants in a particular gene pool for population-level analyses.},
}

@article {pmid41108124,
year = {2025},
author = {Manzoor, M and Putaala, J and Zaric, S and Leskelä, J and Dong, A and Könönen, E and Lahti, L and Paju, S and Pussinen, PJ},
title = {Oral Microbial Determinants of Saliva and Serum Lipopolysaccharide Activity.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345251370995},
doi = {10.1177/00220345251370995},
pmid = {41108124},
issn = {1544-0591},
abstract = {Lipopolysaccharide (LPS) is a virulence factor of gram-negative bacteria, and endotoxemia or translocation of LPS in serum plays a significant role in oral and systemic pathologies. The contribution of the oral microbiome composition to saliva LPS activity and endotoxemia remains unclear. We investigated whether salivary and serum LPS levels are associated with oral microbiome diversity, taxonomic profiles, and functional characteristics. The oral microbiome was analyzed using metagenomic sequencing of saliva from 298 individuals enrolled in a multicenter case-control study, SECRETO (NCT01934725). Serum and salivary LPS activities were measured, and multiple linear regression models were fitted to identify the microbial taxa that predicted LPS levels. MaAsLin2 (Microbiome Multivariable Associations with Linear Models) was used to determine the associations of microbial functional features and LPS levels. Salivary alpha diversity was positively associated with serum LPS but negatively associated with salivary LPS, smoking, and antibiotic use in the preceding 1 to 6 mo. Community composition (beta diversity) differed between the salivary LPS tertiles (P = 0.001) but not between serum LPS tertiles. In total, 10 oral taxa associated with serum LPS tertiles and 59 with salivary LPS tertiles were identified. Prevotella, Neisseria, Leptotrichia, and Porphyromonas had significant positive associations with salivary LPS, whereas Fusobacterium had a negative association. Among these genera, Prevotella sp. E13_17, P. gingivalis, L. wadei, and F. nucleatum were the species with the strongest associations. Among the 1,016 oral microbiome metabolic features, several were linked to the biosynthesis of LPS, lipid A, and O-antigen pathways. The oral microbiome composition was strongly associated with salivary LPS activity in addition to weaker links to serum LPS. Oral microbiota-derived LPS activity in saliva was associated with microbial metabolism characterized by the predominance of proliferation and biosynthesis pathways. Our study indicates that dysbiosis of the oral microbiome is a source of increased salivary and serum LPS activity.},
}

@article {pmid41107843,
year = {2025},
author = {Meki, IK and Ahn, KB and Dundon, WG and Settypalli, TBK and Leth, C and Steinrigl, A and Revilla-Fernández, S and Schmoll, F and Ceglie, L and Berete, K and Metlin, A and Dhingra, M and Nowotny, N and Cattoli, G and Lamien, CE},
title = {Novel multiplex family-wide PCR and Nanopore sequencing of amplicons (FP-NSA) approach for surveillance of influenza- and coronaviruses in humans and animals.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {123},
pmid = {41107843},
issn = {1756-994X},
mesh = {Humans ; Animals ; *Nanopore Sequencing/methods ; *Coronavirus/genetics/isolation & purification/classification ; *Multiplex Polymerase Chain Reaction/methods ; *Influenza, Human/virology/diagnosis/epidemiology ; SARS-CoV-2 ; *Coronavirus Infections/virology/diagnosis ; *Orthomyxoviridae/genetics/isolation & purification ; },
abstract = {BACKGROUND: Recent outbreaks of zoonotic diseases like Ebola, Mpox, dengue fever, and COVID-19 highlight gaps in surveillance and early detection at disease hotspots. Virus family-wide diagnostic assays offer a cost-effective and sensitive alternative to metagenomics for initial virus identification. This study introduces a multiplex family-wide PCR coupled with Nanopore sequencing of amplicons (FP-NSA) for surveillance of novel and known zoonotic respiratory viruses, including influenza A and D viruses (IAV and IDV), alpha (α-), beta (β-), and gamma (γ-) coronaviruses (CoVs).

METHODS: This assay utilized primers in conserved regions of each virus group for multiplex reverse transcription (RT)-PCR coupled with the portable MinION device for rapid Nanopore sequencing. The FP-NSA was optimized using seven IAV subtypes, IDVs, and α- and β-CoVs. The analytical sensitivity of the FP-NSA was assessed using positive controls of known concentrations from each targeted viral family and validated using clinical samples and cell culture isolates from various host species and geographical origins. Potential novel viruses detected in the clinical samples, based on the FP-NSA, were further analyzed using metagenomics sequencing with the Sequence-Independent Single Primer Amplification (SISPA) approach.

RESULTS: The optimized FP-NSA assay efficiently detected all the targeted viruses singly as well as in co-infection scenarios of multiple respiratory viruses. Evaluation of the assay on 78 selected clinical and cell culture samples (from 184 initially screened) successfully detected IAVs; α-CoVs: porcine epidemic diarrhea virus (PEDV), human coronavirus (HCoV) NL63, and HCoV-229E; β-CoVs: HCoV-OC43, severe acute respiratory syndrome (SARS)-CoV-(1), SARS-CoV-2, and MERS-CoV; and γ-CoV infectious bronchitis virus (γ-CoV_IBV) infections. Additionally, the FP-NSA assay discovered a novel γ-CoV_IBV from Guinea that is phylogenetically distant from known genotypes using a SISPA metagenomics approach.

CONCLUSIONS: The assay's short PCR amplicons enable screening of samples within 4 h, from PCR to sequencing and bioinformatics analysis, providing an adequate number of pathogens' reads. The portable MinION device makes the assay suitable for pathogen surveillance in disease hotspots and resource-limited regions such as low- and middle-income countries. Thus, the FP-NSA assay is a valuable tool for detecting potential novel and known zoonotic respiratory viruses in the targeted families across various host species.},
}

Humans
Animals
*Nanopore Sequencing/methods
*Coronavirus/genetics/isolation & purification/classification
*Multiplex Polymerase Chain Reaction/methods
*Influenza, Human/virology/diagnosis/epidemiology
SARS-CoV-2
*Coronavirus Infections/virology/diagnosis
*Orthomyxoviridae/genetics/isolation & purification

@article {pmid41106786,
year = {2025},
author = {Guo, M and Zhao, H and Song, N and Huang, P and Li, M and Han, L and Zeng, KW and Lu, Z},
title = {Shenmai injection attenuates sepsis-associated acute lung injury by remodeling gut microbiota and restoring steroid hormone biosynthesis.},
journal = {Fitoterapia},
volume = {187},
number = {},
pages = {106935},
doi = {10.1016/j.fitote.2025.106935},
pmid = {41106786},
issn = {1873-6971},
abstract = {Sepsis-associated acute lung injury (SA-ALI), a critical complication of sepsis, is characterized by immune dysregulation-induced pulmonary dysfunction. Shenmai Injection (SMI) is a standardized herbal preparation consisting of Panax ginseng C.A.Mey (Hongshen) and Ophiopogon japonicus (Thunb.) Ker Gawl (Maidong), traditionally used for qi-replenishing, collapse-stabilizing, and lung-moistening therapy. Although clinically utilized in the management of SA-ALI, the specific mechanisms by which it acts against SA-ALI necessitate further investigation. The present study endeavors to comprehensively determine the therapeutic efficacy of SMI against SA-ALI through an integrated approach combining network pharmacology, metabolomics, metagenomic sequencing, and experimental validation. In this study, murine SA-ALI was established using lipopolysaccharide (LPS) and Poly(I:C). Results indicated that SMI administration significantly attenuated pulmonary inflammation, restored blood-gas barrier integrity, reduced serum pro-inflammatory cytokines and suppressed NF-κB pathway activation in SA-ALI mice. Network pharmacology elucidated the multi-targeted mechanism of SMI in modulating steroid hormone biosynthesis. Integrated metabolomics and target analysis revealed that ophiopogonin A/B and luteolin in SMI alleviates metabolic dysregulation by targeting key enzymes, including AKR1C3, HSD17B1/2, and SULT1E1. Metagenomic profiling demonstrated SMI-mediated gut microbiota remodeling, marked by suppression of pathogenic Chlamydiaceae (particularly Chlamydia abortus) and enrichment of commensal Lactobacillaceae. Correlation analysis showed that intestinal androstenedione and androsterone levels during SMI treatment recovery were negatively correlated with Chlamydia abortus abundance. In conclusion, SMI enhances the recovery from sepsis-associated SA-ALI by dual modulation of gut microbial ecology and host metabolic homeostasis, thereby establishing its potential as a multi-mechanistic therapeutic candidate for sepsis-related organ injury.},
}

@article {pmid41106415,
year = {2025},
author = {Grimm, SL and Kaufman, JT and Rice, DP and Whittaker, C and Bradshaw, WJ and McLaren, MR},
title = {Inferring the sensitivity of wastewater metagenomic sequencing for early detection of viruses: a statistical modelling study.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101187},
doi = {10.1016/j.lanmic.2025.101187},
pmid = {41106415},
issn = {2666-5247},
abstract = {BACKGROUND: Metagenomic sequencing of wastewater (W-MGS) can in principle detect any known or novel pathogen in a population. We aimed to quantify the sensitivity and cost of W-MGS for viral pathogen detection by jointly analysing W-MGS and epidemiological data for a range of human-infecting viruses.

METHODS: In this statistical modelling study, we analysed sequencing data from four studies of untargeted W-MGS to estimate the relative abundance of 11 human-infecting viruses. Corresponding prevalence and incidence estimates were obtained or calculated from academic and public health reports. We combined these estimates using a hierarchical Bayesian model to predict relative abundance at set prevalence or incidence values, allowing comparison across studies and viruses. These predictions were then used to estimate the sequencing depth and concomitant cost required for pathogen detection using W-MGS with or without use of a hybridisation capture enrichment panel.

FINDINGS: After controlling for variation in local infection rates, relative abundance varied by orders of magnitude across studies for a given virus. For instance, a local SARS-CoV-2 weekly incidence of 1% corresponded to a predicted SARS-CoV-2 relative abundance ranging from 3·8 × 10[-10] to 2·4 × 10[-7] across studies, translating to orders-of-magnitude variation in the cost of operating a system able to detect a SARS-CoV-2-like pathogen at a given sensitivity. Use of a respiratory virus enrichment panel in two studies greatly increased predicted relative abundance of SARS-CoV-2, lowering yearly costs by 27-fold (from US$7·87 million to $287 000) and 29-fold (from $1·98 million to $69 100) for a system able to detect a SARS-CoV-2-like pathogen before reaching 0·01% cumulative incidence.

INTERPRETATION: The large variation in viral relative abundance after controlling for epidemiological factors indicates that other sources of inter-study variation, such as differences in sewershed hydrology and laboratory protocols, have a substantial impact on the sensitivity and cost of W-MGS. Well chosen hybridisation capture panels can greatly increase sensitivity and reduce cost for viruses in the panel, but might reduce sensitivity to unknown or unexpected pathogens.

FUNDING: The Wellcome Trust, Open Philanthropy, and Musk Foundation.},
}

@article {pmid41106267,
year = {2025},
author = {Cai, F and Wang, Y and Xie, M and Li, G and Wang, S and Daygon, VD and Tian, D and Ni, G and Liu, X and Zhang, R and Lei, L and Yuan, Z and Guo, J and Zhang, X and Hu, S},
title = {Pyrogenic carbon-stimulated nitrate-dependent anaerobic methane oxidation: insights into redox activity and conductivity in anaerobic methanotrophic archaea metabolism and microbial dynamics.},
journal = {Water research},
volume = {289},
number = {Pt A},
pages = {124798},
doi = {10.1016/j.watres.2025.124798},
pmid = {41106267},
issn = {1879-2448},
abstract = {Pyrogenic carbon (PC) plays a critical role in regulating greenhouse gas emissions by influencing methanogenesis and methane oxidation in aquatic environments. However, its impact on nitrate-dependent anaerobic oxidation of methane (AOM), associated methane emissions, and the underlying mechanisms remain poorly understood. Here, we demonstrated that in nitrate-dependent AOM consortia amended with HNO3-treated biochar and graphite (representing redox-active and conductive forms of PC, respectively), AOM rates were significantly elevated by 2.7- and 4.4-fold, respectively, compared to unamended biotic controls. This enhancement was accompanied by a pronounced proliferation of anaerobic methanotrophic archaea, specifically "Candidatus Methanoperedens nitroreducens", along with elevated metabolic activity driven by enhanced electron transport and energy conservation, as indicated by significantly increased electron transfer system activity, total adenine nucleotide levels, and concentrations of key redox carrier F420. Metagenomic analysis revealed that PC addition reshaped microbial interactions. Notably, graphite facilitated the potential establishment of direct interspecies electron transfer between "Ca. M. nitroreducens" and coexisting denitrifying populations (Bacteroidota sp. and Ignavibacteriaceae sp.), while also fostering the formation of new interspecies networks that enabled division of labor within the denitrification pathway. These findings not only advance the mechanistic understanding of PC-facilitated methane mitigation in aquatic ecosystems but also suggest strategies for engineering AOM-based systems to optimize methane removal and nitrogen cycling in environmental applications.},
}

@article {pmid41105996,
year = {2025},
author = {Chen, ZY and Gao, FZ and Bai, H and He, LY and Liu, YS and Ying, GG},
title = {Airborne free DNA in chicken farms: The overlooked traits in microbial diversity, viral composition, and antimicrobial resistance risk.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140144},
doi = {10.1016/j.jhazmat.2025.140144},
pmid = {41105996},
issn = {1873-3336},
abstract = {The enrichment of DNA from total suspended particulates (TSP) onto 0.22 µm pore size filters (intracellular DNA, iDNA) is a critical step in characterizing the airborne microbiome. However, free DNA (< 0.22 µm, fDNA) may harbor unrecognized microbial and genetic components. In this study, metagenomic analysis was employed to compare airborne fDNA and iDNA from eight chicken houses. Overall, the average concentration of fDNA was 5.6-fold higher than that of iDNA. A total of 587 genera spanning 28 phyla were identified in fDNA, including 162 genera absent from iDNA. Notably, 39.7 % of open reading frames were unique to fDNA, involving key metabolic and regulatory pathways. A total of 50.2 % viral contigs were only detected in fDNA, carrying mobile genetic elements, virulence factor genes, and resistance genes against antibiotics, biocides, and metals. The total absolute abundance of the antibiotic resistome was higher in fDNA, with 79.2 % of significantly varied genes enriched therein, including 16 high-risk genes. Metagenomic binning further supported that fDNA harbors broader microbial diversity and functional traits. These findings underscore airborne fDNA as an underexplored reservoir of microbial and genetic diversity, meriting further investigation for its ecological and public health implications.},
}

@article {pmid41104935,
year = {2025},
author = {Feijão, E and Duarte, IA and Pereira, M and Pascoal, P and Nunes, M and Tanner, SE and Dias, R and Duarte, B and Matos, AR and Figueiredo, A and Fonseca, VF},
title = {Gilthead sea bream gut bacteriome as a valuable tool for seafood provenance analysis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0150825},
doi = {10.1128/aem.01508-25},
pmid = {41104935},
issn = {1098-5336},
abstract = {The increasing demand for high-quality seafood underscores the significant challenges posed by rampant seafood fraud. This study aimed to identify regional capture biomarkers by using the gut bacteriome of Sparus aurata specimens through state-of-the-art long-read sequencing allied to machine learning tools. The gut bacteriomes of animals from four different fishing areas on the Portuguese coast were sequenced. The alpha and beta diversity analyses were shown to enable Center-South gut bacteriome differentiation from other fishing areas due to higher abundance of species of the phyla Pseudomonadota, Bacteroidota, and Bacillota and classes such as Alphaproteobacteria, Betaproteobacteria, and Bacilli. The gradient boosting machine (GBM) model selected by the H2O automatic machine learning pipeline presented a high global accuracy during training and validation phases, identifying Center-South and South sample provenance with 100% and 71.1% accuracy, respectively. By integrating the most important OTUs to the GBM model with the regional biomarkers identified through point biserial correlation analysis (indicspecies packages), a reduced set of five provenance biomarkers was identified, belonging to Gammaproteobacteria, Betaproteobacteria, and Bacilli classes, possibly highlighting the anthropogenic activities surrounding the fishing areas and local environmental abiotic factors. This study highlights the extensive and valuable information obtained by long-read sequencing and couples it with the potential of machine learning algorithms to ultimately demonstrate its efficiency in providing efficient and highly accurate seafood provenance biomarkers. This study also reports the likely influence of industrial and recreational activities, population density, and water management facilities on the gut bacteriome of S. aurata.IMPORTANCEThis study significantly contributes to a topic of utmost importance-seafood provenance analysis and seafood fraud-by leveraging gut bacteriome profiling. Through the application of long-read sequencing and machine learning, it identifies reliable biomarkers that distinguish gilthead sea bream from different fishing areas. These findings enhance traceability methods by providing a robust tool to combat seafood fraud and ensure food authenticity, thereby protecting the supply chain, the consumer, and the environment. Additionally, this study explores the possible interactions between the gut bacteriome and the industrial, recreational, and environmental factors that could influence the identified biomarkers of regional provenance while also offering insights into the composition of the marine ecosystems surrounding the fishing areas. This approach has broader implications for fishery management, sustainable sourcing, and regulatory enforcement.},
}

@article {pmid41104113,
year = {2025},
author = {Kulaš, A and Lemonnier, C and Alric, B and Kahlert, M and Trobajo, R and Udovič, MG and Rimet, F},
title = {Can genetic diversity in microalgae species be explained by climate: an overview of metabarcoding with diatoms.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf171},
pmid = {41104113},
issn = {2730-6151},
abstract = {Diatoms, a diverse and abundant group of microalgae, play a crucial role in the functioning of rivers, and are widely used as indicators of ecological quality. This microalgae group has an intraspecific genetic diversity that is poorly understood on a global scale. We examined their genetic diversity using metabarcoding data from Nordic to Equatorial rivers (n = 1103 samples). Notably, 61% of genetic variants were endemic to a single climate zone, including 33% from the Equatorial zone. Looking at the genetic diversity within species, one third of the species showed geographic pattern between climate zones and the phylogenetic structure of their communities indicated that they were shaped by environmental filtering. Another third showed no geographic pattern, and their communities were in majority shaped by neutral processes. A final group was between these two situations. Interestingly, no geographic pattern was observed within the same climate zones, even in regions over 10 000 km apart. We conclude that the numerous species showing allopatric diversification between climate zones, would deserve to be separated into new species to improve diatom-based biomonitoring tools. For future studies, expanding geographical sampling coverage, together with using multi-markers or metagenomes approaches would enable to go beyond these results.},
}

@article {pmid41104112,
year = {2025},
author = {Hayes, A and Zhang, L and Snape, J and Feil, E and Kasprzyk-Hordern, B and Gaze, WH and Murray, AK},
title = {Common non-antibiotic drugs enhance selection for antimicrobial resistance in mixture with ciprofloxacin.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf169},
pmid = {41104112},
issn = {2730-6151},
abstract = {Antimicrobial resistance (AMR) is a major health concern, and a range of antibiotic and non-antibiotic agents can select for AMR across a range of concentrations. Selection for AMR is often investigated using single compounds, however, in the natural environment and the human body, pharmaceuticals will be present as mixtures, including both non-antibiotic drugs (NADs), and antibiotics. Here, we assessed the effects of one of three NADs in combination with ciprofloxacin, a commonly used antibiotic that is often found at concentrations in global freshwaters sufficiently high to select for AMR. We used a combination of growth assays and qPCR to determine selective concentrations of mixtures and used metagenome sequencing to identify changes to the resistome and community composition. The addition of the three NADs to ciprofloxacin altered the selection dynamics for intI1 compared to the ciprofloxacin alone treatments, and sequencing indicated that mixtures showed a stronger selection for some AMR genes such as qnrB. The communities exposed to the mixtures also showed changed community compositions. These results demonstrate that NADs and ciprofloxacin are more selective than ciprofloxacin alone, and these mixtures can cause distinct changes to the community composition. This indicates that future work should consider combinations of antibiotics and NADs as drivers of AMR when considering its maintenance and acquisition.},
}

@article {pmid41103765,
year = {2025},
author = {Li, M and Bi, J and Wang, X and Li, H},
title = {The hidden nitrogen nexus: stochastic assembly and linear gene synergies drive urban park microbial networks.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1652652},
pmid = {41103765},
issn = {1664-302X},
abstract = {Urban parks play a significant role in environmental greening, cultural heritage, and recreational activities. The diversity and distribution of park environmental microbiota have become a hot focus of microbial ecology. However, there has been limited attention on the functional attributes of microbial communities, highlighting the importance of studying the distribution and diversity of functional genes in urban parks. Here, we employed metagenomic sequencing and binning to explore the diversity, assembly, and functional synergy of nitrogen cycling genes from the grassland soil and water in urban parks. Our results showed that glutamate metabolism and assimilatory nitrate reduction are the predominant nitrogen cycling pathways in both the soil and water. The diversity of nitrogen cycling genes in water was more abundant than in soil. The assembly of nitrogen cycling genes in both the soil and water was primarily driven by stochastic processes. Nutrient factors (such as total sulfur) were the most significant influencers of nitrogen cycling genes in park soil, while bacterial communities were the most critical determinants in water. The gene narH, involved in multiple nitrogen cycling metabolic pathways, was identified as an important marker of nitrogen storage in both soil and water. Through metagenomic binning, we discovered linear arrangements of multiple nitrogen cycling genes, such as narG-narH-narJ-narI, which collectively participate in the reduction of nitrate to nitrite, demonstrating the synergy, functional redundancy, and complementarity among nitrogen cycling genes. Our study holds significant implications for the biochemical cycling and the management of nitrogen pollution in urban parks.},
}

@article {pmid41103762,
year = {2025},
author = {Sheng, X and Zhu, J and Li, W and Wan, J and Wu, K and Yang, P and Duan, R and Yang, Z and Bai, J and Zheng, Y},
title = {Antimony-resistant PGPR mitigates Sb toxicity and accumulation in peppers by restructuring rhizosphere microorganisms.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1658223},
pmid = {41103762},
issn = {1664-302X},
abstract = {Plant growth-promoting rhizobacteria (PGPR) provide a sustainable biofertilizer strategy for remediating heavy metal-contaminated soils by enhancing plant stress resistance through rhizosphere microbiota interactions. However, the mechanisms by which PGPR modulate rhizosphere communities and plant growth under antimony (Sb) stress remain poorly understood. This study investigated the effects of inoculating Sb-tolerant Cupriavidus sp. S-8-2 in pepper (Capsicum annuum L.) cultivated under varying levels of Sb contamination (0, 500, 1,000 mg/kg), employing a combination of metagenomic profiling and physicochemical analyses. Pot experiments demonstrated that inoculation significantly enhanced plant growth and nutrient acquisition while alleviating oxidative stress in Sb-stressed plants. Crucially, it reduced Sb translocation, resulting in a 54.75% decrease in shoot Sb content, along with a 33.33% increase in leaf biomass and a 38.98% increase in root biomass under 1,000 mg/kg Sb treatment. In parallel, rhizosphere properties such as total nitrogen (TN), total phosphorus (TP), and soil organic matter (SOM) were improved, as evidenced by an 81.35% increase in acid phosphatase activity under the same Sb concentration. Microbiota analysis revealed that inoculation enriched stress-responsive bacterial phyla, such as Proteobacteria and Actinobacteria, as well as key functional genera associated with Sb tolerance (e.g., Ramlibacter) and nutrient cycling (e.g., Nitrospira), despite a decrease in alpha-diversity. Co-occurrence networks analysis indicated that inoculation significantly enhance node connectivity and mean degree in rhizosphere bacterial networks, reflecting an increase in structural complexity, especially under severe Sb stress (1,000 mg/kg). These findings demonstrate that Cupriavidus sp. S-8-2 enhances plant resistance to Sb by restructuring the rhizobacterial community and improving soil health, with reducing Sb accumulation in edible parts, thereby highlighting its potential as a biofertilizer for safe crop production in Sb-contaminated soils. For the first time, our study explored the potential of Sb-tolerant PGPR to alleviate Sb stress in pepper plants cultivated in Sb-polluted soils.},
}

@article {pmid41103722,
year = {2025},
author = {Menozzi, E and Geiger, M and Meslier, V and Fierli, F and Gilles, M and Chau, KY and David, A and Shahar Golan, R and Famechon, A and Koletsi, S and Morabito, C and Quinquis, B and Pons, N and Ehrlich, SD and Macnaughtan, J and Almeida, M and Schapira, AH},
title = {Exploring the relationship between GBA1 host genotype and gut microbiome in the GBA1 [L444P/WT] mouse model: implications for Parkinson's disease pathogenesis.},
journal = {Frontiers in neuroscience},
volume = {19},
number = {},
pages = {1546203},
pmid = {41103722},
issn = {1662-4548},
abstract = {BACKGROUND: Heterozygous variants in GBA1 are the commonest genetic risk factor for Parkinson's disease (PD), but penetrance is incomplete. GBA1 dysfunction can cause gastrointestinal disturbances and microbiome changes in preclinical models. Mounting evidence suggests that the microbiota-gut-brain axis is potentially implicated in PD pathogenesis. Whether the gut microbiome composition is influenced by host GBA1 genetics in heterozygosis has never been explored.

OBJECTIVES: This study aimed to evaluate whether heterozygosity for the GBA1 pathogenic L444P variant can cause perturbations in gut microbiome composition.

METHODS: Faecal samples collected from GBA1 [L444P/WT] and GBA1 [WT/WT] mice at 3 and 6 months of age were analysed through shotgun metagenomic sequencing.

RESULTS: No differences in α- and β-diversities were detected between genotyped groups, at either time point. Overall, we found a little variation in the gut microbiome composition and functional potential between GBA1 [L444P/WT] and GBA1 [WT/WT] mice over time.

CONCLUSION: Host GBA1 genotype does not impact gut microbiome structure and composition in the presented GBA1 [L444P/WT] mouse model. Studies investigating the effect of a second hit on gut physiology and microbiome composition could explain the partial penetrance of GBA1 variants in PD.},
}

@article {pmid41103389,
year = {2025},
author = {Shi, G and Yan, P and Shen, S and Tang, P and Chen, P and Sun, L and Xing, S and Fang, C and Li, C and Lin, L and Zhang, C},
title = {The insight into instability mechanism of Jiangxiangxing Baijiu fermentation and the key functional regulation of Schizosaccharomyces pombe.},
journal = {Food chemistry: X},
volume = {31},
number = {},
pages = {103085},
pmid = {41103389},
issn = {2590-1575},
abstract = {Jiangxiangxing Baijiu (JXXB) suffers from quality instability due to its complex spontaneous fermentation. This study compared fermented grains from excellent (Group-E) and normal (Group-N) workshops, identifying 28 volatiles as distinguished substances for quality. The core functional species were revealed by integrated meta-genomic and meta-transcriptomic sequencing analysis. Moreover, Schizosaccharomyces pombe and Acetilactobacillus jinshanensis were demonstrated as key functional contributors, while only Schi. pombe was highlighted active participation in both heap fermentation and pit fermentation. Notably, the proportions and doses of the functional yeasts, particularly Schi. pombe, were higher in Group-E, resulting in the higher quality. Furthermore, the industrial-scale bioaugmentation with Schi. pombe enhanced substrate utilization, elevated the production of flavor substances by 13.61 %, and improved the yield and excellent-quality proportion of base Baijiu by 32.18 % and 37.16 %, respectively. This study provided insights into the quality instability mechanism of JXXB, and fostered a foundation for ensuring consistent quality in solid-state fermentation.},
}

@article {pmid41102833,
year = {2025},
author = {Rodriguez, K and Ricci, F and Ni, G and Iram, N and Palfreyman, R and Gonzalez-Garcia, RA and Heffernan, J and Greening, C and Adame, MF and Marcellin, E},
title = {Abundant and active acetogens enhance the carbon dioxide sink of Blue Carbon ecosystems.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {207},
pmid = {41102833},
issn = {2049-2618},
support = {CE 200100029//Australian Research Council Centre of Excellence in Synthetic Biology/ ; },
mesh = {*Carbon Dioxide/metabolism ; Wetlands ; Soil Microbiology ; Carbon Cycle ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Metagenomics/methods ; Hydrogen/metabolism ; *Carbon Sequestration ; Bioreactors/microbiology ; *Archaea/metabolism/genetics/classification/isolation & purification ; Photosynthesis ; Carbon/metabolism ; Ecosystem ; },
abstract = {BACKGROUND: Blue Carbon ecosystems, which include all tidal wetlands, mitigate climate change by capturing and storing carbon dioxide (CO2) from the atmosphere. Most carbon fixation in these systems is thought to be driven by plant and microbial photosynthesis, whereas chemosynthetic processes are assumed to play a minor role. However, these ecosystems often contain anoxic environments ideal for chemosynthetic microbes such as acetogens.

RESULTS: In this study, we show that acetogens are abundant and active mediators of carbon sequestration in tidal wetland soils. We combined metagenomic analysis of CO2 fixation genes and reconstruction of microbial genomes with enrichment and analysis of gas-fermenting acetogens in bioreactors. Genome-resolved metagenomics revealed that diverse microbes can mediate carbon fixation, primarily through the Calvin-Benson-Bassham (CBB) cycle and Wood-Ljungdahl pathway (WLP). These include various bacteria and archaea capable of reductive acetogenesis. Based on these findings, we established bacterial enrichment cultures from tidal wetland soils using hydrogen (H2) and CO2 as the sole energy and carbon sources. Bioreactor analysis revealed that these enrichments are dominated by clostridial acetogens that grow rapidly by converting CO2 into acetate and other products.

CONCLUSIONS: Collectively, these results reveal Blue Carbon ecosystems harbor microbial communities that can exclusively subsist by using CO2 as their sole electron acceptor and carbon source. This provides evidence for a novel carbon sink pathway within these ecosystems beyond the well-known mechanisms of photosynthetic carbon fixation and soil sequestration. Additionally, the discovery and enrichment of these chemosynthetic communities provide opportunities for developing further mechanisms of CO2 removal through industrial gas fermentation. Video Abstract.},
}

*Carbon Dioxide/metabolism
Wetlands
Soil Microbiology
Carbon Cycle
*Bacteria/metabolism/genetics/classification/isolation & purification
Metagenomics/methods
Hydrogen/metabolism
*Carbon Sequestration
Bioreactors/microbiology
*Archaea/metabolism/genetics/classification/isolation & purification
Photosynthesis
Carbon/metabolism
Ecosystem

@article {pmid41102734,
year = {2025},
author = {Lv, Y and Zhang, L and Zhang, Y},
title = {Clear niche partitioning of nitrite-oxidizing bacteria from the bottom and the slope of Mariana Trench.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {208},
pmid = {41102734},
issn = {2049-2618},
support = {42306104//National Natural Science Foundation of China/ ; 42122043//National Natural Science Foundation of China/ ; 2023M742237//China Postdoctoral Science Foundation/ ; HRSJ-ZSZX-008//Project of Hainan Research Institute/ ; 21TQ1400201//Shanghai Jiao Tong University, Shanghai Pilot Program for Basic Research-Shanghai Jiao Tong University/ ; 2023YFC2812800//National Key Research and Development Program of China/ ; },
mesh = {*Nitrites/metabolism ; Oxidation-Reduction ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Geologic Sediments/microbiology ; Metagenome ; Ecosystem ; Microbiota ; Metagenomics/methods ; Phylogeny ; Nitrogen Cycle ; },
abstract = {BACKGROUND: The hadal zone, characterized by extreme hydrostatic pressure and geographic isolation, hosts microbial communities uniquely adapted to these harsh conditions. While niche partitioning has been observed in other deep-sea environments, its existence within hadal trench ecosystems remains controversial. Focusing on the Mariana Trench, we investigated whether nitrite-oxidizing bacteria (NOB) exhibit depth-stratified ecological specialization between slope (6000-10,000 m) and bottom (> 10,000 m) sediments. By analysing the genomic features and ecological interactions of NOB, we aimed to resolve their functional roles in nitrogen cycling under distinct hadal microniches.

RESULTS: We reconstructed 8 high-quality NOB metagenome-assembled genomes (MAGs) from 58 sediment metagenomes, revealing stark niche differentiation between depth zones. Slope-dominant NOB harboured expanded genetic arsenals for antioxidation (e.g. superoxide dismutase) and osmoprotection (compatible solute transporters), Suggesting enhanced adaptive capacity to pressure-adjacent stresses. Metatranscriptomics revealed 1.48 × (nxrA) and 1.28 × (aclA) greater expression of nitrite oxidation and carbon fixation genes in slope communities than in their bottom counterparts. Network analysis identified slope NOB as keystone taxa with elevated among-module connectivity and intramodule linkages, in contrast with bottom NOB, which exhibited localized nitrate-production gene networks. Functional profiling revealed complementary biogeochemical roles: slope NOB primarily consumed nitrite, whereas bottom populations dominated nitrate synthesis.

CONCLUSION: Our multiomics analysis revealed depth-dependent niche partitioning among hadal NOB, with transcriptional and network evidence supporting distinct pressure adaptation strategies and biogeochemical functions. The slope-bottom differentiation in stress response systems and nitrogen transformation pathways highlights how micron-scale environmental gradients drive microbial specialization in Earth's deepest ecosystems. These findings establish NOB as critical mediators of hadal biogeochemical cycles and provide a framework for understanding microbial resilience in extreme biospheres. Video Abstract.},
}

*Nitrites/metabolism
Oxidation-Reduction
*Bacteria/metabolism/genetics/classification/isolation & purification
*Geologic Sediments/microbiology
Metagenome
Ecosystem
Microbiota
Metagenomics/methods
Phylogeny
Nitrogen Cycle

@article {pmid41102233,
year = {2025},
author = {Kwak, MJ and Park, J and Park, H and Yoon, J and Lee, J and Hahnke, RL and Lee, SW and Kwon, SK and Song, JY and Kim, JF},
title = {Polyphasic and comparative genomic characterization of a novel Mariniflexile species in the rhizosphere microbiome of tomato resistant to bacterial wilt.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36158},
pmid = {41102233},
issn = {2045-2322},
support = {918011-4//Ministry of Agriculture, Food and Rural Affairs/ ; NRF-2023R1A2C3004496//Ministry of Science and ICT, South Korea/ ; NRF-2018R1A6A1A03025607//Ministry of Education, South Korea/ ; },
mesh = {*Solanum lycopersicum/microbiology ; *Rhizosphere ; Phylogeny ; *Plant Diseases/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Genome, Bacterial ; Ralstonia solanacearum ; Soil Microbiology ; Genomics ; Disease Resistance ; },
abstract = {A plethora of microbes resides in the plant rhizosphere, and some play roles in host health and disease. We previously isolated a Gram-negative, aerobic, rod-shaped rhizobacterium, TRM1-10, that contributes to bacterial wilt resistance of tomato caused by Ralstonia solanacearum. In this study, we characterized TRM1-10 through physiological and biochemical analyses, complemented by whole genome sequencing and comparative genomic analyses. Phylogenetic analysis using the 16S rRNA gene and genome sequences revealed that TRM1-10 belongs to the genus Mariniflexile and represents a new lineage. TRM1-10 also exhibits noticeable differences in physiological and biochemical characteristics compared to other Mariniflexile species. Thus, based on phylogenetic affiliation and chemotaxonomic characteristics, we propose this bacterium as a novel species in the genus, Mariniflexile rhizosphaerae sp. nov. (type strain TRM1-10[T] = KCTC 18646P[T] = DSM 33122[T]). Comparative genome analyses revealed that TRM1-10 harbors more genes linked to soil adaptation compared to other phylogenetically related Mariniflexile species, most of which are associated with marine habitats. The genomic features of TRM1-10 and other strains in the species may allow the taxon to adapt to the soil and rhizosphere, compete effectively with the resident soil microbiota, and contribute to plant health.},
}

*Solanum lycopersicum/microbiology
*Rhizosphere
Phylogeny
*Plant Diseases/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Genome, Bacterial
Ralstonia solanacearum
Soil Microbiology
Genomics
Disease Resistance

@article {pmid41102171,
year = {2025},
author = {Leu, AO and Woodcroft, BJ and McIlroy, SJ and Tyson, GW},
title = {Potential for aerobic hydrocarbon oxidation in archaea.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9188},
pmid = {41102171},
issn = {2041-1723},
mesh = {Oxidation-Reduction ; *Hydrocarbons/metabolism ; *Archaea/metabolism/genetics/classification ; Aerobiosis ; Phylogeny ; Genome, Archaeal ; Metagenome ; Gene Transfer, Horizontal ; Mixed Function Oxygenases/genetics/metabolism ; },
abstract = {Over the last decade, there have been significant advances in our understanding of anaerobic hydrocarbon oxidation in archaea. However, the ability to oxidise hydrocarbons aerobically has been described in bacteria but not yet in archaea. Here, we provide evidence supporting potential aerobic hydrocarbon oxidation ability in archaea belonging to a novel order within the class Syntropharchaeia, which we propose to name Candidatus 'Aerarchaeales'. This order is represented by six metagenome-assembled genomes (MAGs) spanning three genera that are found in terrestrial and marine ecosystems. In particular, MAGs belonging to a newly defined genus, Ca. 'Aerovita', encode a copper monooxygenase complex with homology to bacterial hydrocarbon monooxygenases. The presence of genes encoding other oxygen-dependent enzymes, such as haem-copper oxygen reductase, indicates that Ca. 'Aerovita' may be capable of aerobic respiration. Our findings suggest that horizontal gene transfer between archaeal and bacterial domains facilitated the evolution of aerobic hydrocarbon-oxidizing archaea.},
}

Oxidation-Reduction
*Hydrocarbons/metabolism
*Archaea/metabolism/genetics/classification
Aerobiosis
Phylogeny
Genome, Archaeal
Metagenome
Gene Transfer, Horizontal
Mixed Function Oxygenases/genetics/metabolism

@article {pmid41101270,
year = {2025},
author = {Wang, H and Wu, Y and Zhang, Q and Li, X and Weng, H and Zhang, L and Peng, Y},
title = {Dynamic redox regimes drive metabolic versatility of a Candidatus Brocadia in municipal wastewater treatment.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124781},
doi = {10.1016/j.watres.2025.124781},
pmid = {41101270},
issn = {1879-2448},
abstract = {Deciphering the adaptive mechanisms of anaerobic ammonium-oxidizing (anammox) bacteria to redox dynamics is pivotal for overcoming critical bottlenecks in achieving carbon-neutral wastewater treatment. This study uncovers the survival strategy and response mechanisms of a Candidatus Brocadia strain (B. SW5) thriving in municipal wastewater treatment system with continuous anaerobic-aerobic-anoxic cycling. Isotopic labeling and metagenomic analyses confirmed that the B. SW5 adapts to fluctuating environmental stresses. Comparative genomic and transcriptomic analyses demonstrated that B. SW5 exhibits more comprehensive metabolic pathways than conspecific strains in single environments. Beyond fatty acid metabolism/transport, B. SW5 alleviates organics inhibition by upregulating enzymes for aromatic compound and antibiotic efflux/catabolism in anaerobic stage. In addition to the classical superoxide dismutase-catalase antioxidant system, B. SW5 employs a complete aerobic respiratory chain containing cbb3-type cytochrome c oxidase to directly scavenge intracellular oxygen during aerobic stage. Furthermore, B. SW5 encodes and expresses multiple functionally redundant nitrate reductase genes. These phylogenetically distinct duplicate genes enable survival in substrate-deprived anoxic conditions by constructing complete assimilatory/dissimitative nitrate reduction pathways. These findings elucidate the molecular mechanisms underlying B. SW5 adaptability to redox-fluctuating systems through metabolic versatility, providing a theoretical foundation and novel paradigm for developing energy-efficient wastewater treatment technologies.},
}

@article {pmid41101029,
year = {2025},
author = {Ma, L and Liu, F and Zhou, M and Zhang, M and Zheng, J and Wang, Z and He, Z and Yan, Q and Wu, B and Wang, C and Shu, L},
title = {Amoebae contribute to the diversity and fate of antibiotic resistance genes in drinking water system.},
journal = {Environment international},
volume = {204},
number = {},
pages = {109867},
doi = {10.1016/j.envint.2025.109867},
pmid = {41101029},
issn = {1873-6750},
abstract = {Free-living amoebae represent a significant eukaryotic group that thrives in drinking water systems, posing considerable risks to water quality due to their inherent pathogenicity and associations with various microorganisms. However, the symbiotic microbial profiles of different amoeba species and the impact of amoeba-bacteria interactions on the antibiotic resistome within drinking water systems remain poorly understood. In this study, we obtained 24 amoeba isolates from tap water, encompassing diverse phyla within the amoeba lineage. Through metagenome sequencing, we uncovered variations in symbiotic microbiome composition across different amoeba species and strains. Notably, amoebae acted as vectors for human pathogens, including bacteria and viruses. The majority of symbionts carried multiple antibiotic-resistance genes and virulence factors. Furthermore, dominant symbiotic species could be cultured independently, underscoring the critical role of amoebae in preserving and transmitting antibiotic-resistant opportunistic pathogens in drinking water systems. Disinfection experiments demonstrated highly diverse viability of amoebae and their protective capabilities for symbionts against chlorine disinfection. Our findings expand the germplasm bank for amoebae and symbiotic bacteria derived from tap water and emphasize the necessity for further research on amoeba-bacteria symbiosis to ensure drinking water quality and public health safety.},
}

@article {pmid41100443,
year = {2025},
author = {Shi, F and Zou, D and Zhang, L and Guo, N and Yu, J and Degen, AA and Tang, X and Ren, S and Ru, Y and Zheng, S and Zhang, Y and Wang, D},
title = {Increased urea nitrogen salvaging by a remodeled gut microbiota helps nonhibernating pikas maintain protein homeostasis during winter.},
journal = {PLoS biology},
volume = {23},
number = {10},
pages = {e3003436},
doi = {10.1371/journal.pbio.3003436},
pmid = {41100443},
issn = {1545-7885},
mesh = {*Gastrointestinal Microbiome/physiology ; Animals ; *Nitrogen/metabolism ; *Urea/metabolism ; Seasons ; *Lagomorpha/metabolism/microbiology/physiology ; Homeostasis ; *Proteostasis/physiology ; Feces/microbiology ; Diet, Protein-Restricted ; Male ; Liver/metabolism ; Herbivory ; Fecal Microbiota Transplantation ; },
abstract = {Nitrogen balance is a major challenge for herbivores when consuming a low-nitrogen diet. Gut microbiota-mediated urea nitrogen recycling facilitates protein homeostasis during times of nitrogen deficiency, yet its relevance to wild nonhibernating small mammals remains unclear. Here, through a combination of isotope tracing, metagenomics, targeted short-chain fatty acid analysis, and fecal microbiota transplantation, we investigated the effects of protein restriction in winter on urea nitrogen recycling in plateau pikas (Ochotona curzoniae) of the Qinghai-Tibetan Plateau. Hepatic urea-cycle metabolism was downregulated during winter protein restriction, accompanied by increases in beneficial bacteria with ureolytic capacity (such as the genus Alistipes), gut urease activity, and urea transporters, and acetate production, with a consequent increase in nitrogen reincorporation into the pika's protein pool. Critically, supplementing a low-protein diet with yak fecal microbiota enhanced the ureolytic capacity by increasing Alistipes abundance, revealing a critical mechanism whereby interspecies horizontal microbial transfer between sympatric species enhances host protein homeostasis. Our results reveal a functional role for the gut microbiota in urea nitrogen recycling to maintain protein balance in winter-active herbivorous small mammals and contribute to our understanding of species coexistence and mammalian adaptation to high-altitude environments. Our findings establish that microbiota-driven urea nitrogen recycling is a key adaptive strategy for protein homeostasis in winter-active herbivores. This work provides new insights into the mechanisms of mammalian adaptation to high-altitude environments and the dynamics of interspecies coexistence.},
}

*Gastrointestinal Microbiome/physiology
Animals
*Nitrogen/metabolism
*Urea/metabolism
Seasons
*Lagomorpha/metabolism/microbiology/physiology
Homeostasis
*Proteostasis/physiology
Feces/microbiology
Diet, Protein-Restricted
Male
Liver/metabolism
Herbivory
Fecal Microbiota Transplantation

@article {pmid41099560,
year = {2025},
author = {Patel, RR and Triplett, LR and Taerum, SJ and Nason, SL and Wilson, CO and Steven, B},
title = {Diverse soil protists show auxin regulated growth in partnership with auxin-producing bacteria.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf234},
pmid = {41099560},
issn = {1751-7370},
abstract = {Predatory protists are single-cell eukaryotic organisms capable of hunting and ingesting bacteria and other microorganisms, which are thought to enrich populations of beneficial bacteria in the rhizosphere, potentially influencing plant health. However, the mechanisms underpinning protist interactions with plant growth promoting bacteria are not well understood. We examined the conservation of plant beneficial traits in bacteria associated with ten protists of diverse lineages that were isolated from the maize rhizosphere. Metagenomics, whole-genome sequence analysis, and functional assays of 61 groups of protist-associated bacteria identified tryptophan-dependent biosynthesis of the auxin hormone indole-3-acetic acid (IAA) as the most prevalent predicted trait. Mass spectrometry confirmed that all the protist cultures accumulated IAA after tryptophan supplementation, and that IAA production was bacterial-dependent. Hypothesizing that IAA affects protist function, we observed that exogenous IAA significantly increased the culture density and cell size of all ten protists. Examination of four partial protist genome assemblies identified 13 candidate auxin metabolic gene homologs conserved across plants and protists, and transcriptomic analysis of a Colpoda sp. protist revealed differential expression of thousands of genes in the presence of IAA, further supporting auxin regulation of protist function. These findings demonstrate that soil microeukaryotes can widely host auxin-producing bacteria and that much broader range of eukaryotic lineages perceive and respond to auxin signals than previously recognized. This significantly expands the known breadth of auxin perception as an interkingdom signal, with important implications for soil nutrient cycling and rhizosphere ecology.},
}

@article {pmid41099535,
year = {2025},
author = {Rusanova, A and Mamontov, V and Ri, M and Meleshko, D and Trofimova, A and Fedorchuk, V and Ezhova, M and Finoshin, A and Lyupina, Y and Isaev, A and Sutormin, D},
title = {Taxonomically different symbiotic communities of sympatric Arctic sponge species show functional similarity with specialization at species level.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0114725},
doi = {10.1128/msystems.01147-25},
pmid = {41099535},
issn = {2379-5077},
abstract = {UNLABELLED: Marine sponges harbor diverse communities of associated organisms, including eukaryotes, viruses, and bacteria. Sponge-associated microbiomes contribute to the health of host organisms by defending them against invading bacteria and providing them with essential metabolites. Here, we describe the microbiomes of three sympatric species of cold-water marine sponges-Halichondria panicea, Halichondria sitiens, and Isodictya palmata-sampled at three time points over a period of 6 years in the White Sea. We identified the sponges as low microbial abundance species and detected stably associated bacteria that represent new taxa of sponge symbionts within Alpha- and Gammaproteobacteria. The sponges carried unique sets of unrelated species of symbiotic bacteria, illustrating the varying complexity of their microbiomes. At the community level, sponge-associated microbiomes shared common symbiotic features: they encoded multiple eukaryotic-like proteins, biosynthetic pathways and transporters of amino acids and vitamins essential for sponges. At the species level, however, different classes of eukaryotic-like proteins and pathways were distributed between dominant and minor symbionts, indicating specialization within microbiomes. Particularly, the taurine and sulfoacetate import and degradation pathways were associated exclusively with dominant symbionts in all three sponge species, suggesting that these pathways may represent symbiotic features. Our study indicates convergent evolution in the microbiomes of sympatric cold-water sponge species, as reflected by strong functional similarity despite the presence of distinct, taxonomically unrelated symbiotic communities.

IMPORTANCE: Sponges are regarded among the earliest multicellular organisms and the most ancient examples of animal-bacterial symbiosis. The study of host-microbe interactions in sponges has advanced rapidly due to the application of next-generation sequencing (NGS) technologies that help overcome the challenges of investigating their communities. However, many sponge species, particularly those from polar ecosystems, remain poorly characterized. Here, we demonstrate that three sympatric cold-water sponge species, including two analyzed for the first time, harbor distinct sets of bacterial symbionts, stably associated over 6 years. Using CORe contigs ITerative Expansion and Scaffolding, an algorithm developed in this study, we reconstructed high-quality symbiont genomes and revealed shared features indicative of convergent evolution toward symbiosis. Notably, we identified a potentially novel symbiotic feature-a gene cluster likely involved in sulfoacetate uptake and dissimilation. We also observed shifts in microbiome composition, associated with increasing water temperatures, raising concerns about the impact of global warming on cold-water ecosystems.},
}

@article {pmid41099512,
year = {2025},
author = {Elkassas, SM and Fortunato, CS and Grim, SL and Butterfield, DA and Holden, JF and Vallino, JJ and Algar, CK and Zeigler Allen, L and Larson, BT and Proskurowski, G and Reddington, E and Stewart, LC and Topçuoğlu, B and Huber, JA},
title = {Metabolic and population profiles of active subseafloor autotrophs in young oceanic crust at deep-sea hydrothermal vents.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0186825},
doi = {10.1128/aem.01868-25},
pmid = {41099512},
issn = {1098-5336},
abstract = {UNLABELLED: At deep-sea hydrothermal vents, magmatically driven rock-water reactions in the crust generate gases and other reduced compounds that subseafloor microorganisms use for chemolithoautotrophy. In this study, microbial autotrophs from three diffuse flow hydrothermal vents at Axial Seamount in 2013 and 2014 were isotopically labeled using RNA stable isotope probing, targeting subseafloor autotrophic mesophiles (30°C), thermophiles (55°C), and hyperthermophiles (80°C). We constructed taxonomic and functional profiles of active chemolithoautotrophs, examined population distributions across sites, and linked primary producers to their specific metabolic strategies within the subseafloor community. Dominant autotrophs exhibited hydrogen-dependent dissimilatory metabolisms, such as sulfur and nitrate reduction and methanogenesis, as well as microaerophilic sulfide oxidation even at 80°C, consistent with fluid chemistries at each site. While hydrogenotrophic methanogenic archaea (Methanothermococcus) were restricted in their distribution and activity, hydrogenotrophic sulfur and nitrate reducers from the Aquificota (Thermovibrio) and Campylobacterota (Nautiliaceae, Hydrogenimonas, and Desulfurobacteriaceae) were consistently active and present at all sites and years at both the population and community levels. Hydrogenase transcripts were significantly differentially expressed, and diverse hydrogenases were found in metagenome-assembled genomes of Aquificota members, highlighting the importance and versatility of their hydrogen utilization strategies, which likely contribute to their cosmopolitan distribution across geochemically disparate subseafloor sites. Together, this study provides new insights into the functional dynamics and distribution of key subseafloor autotrophic microbial communities in young oceanic crust at deep-sea hydrothermal vents.

IMPORTANCE: Deep-sea hydrothermal vents are hotspots for life in the dark ocean, where rich animal ecosystems are supported by microbial primary producers utilizing the abundant chemical energy supplied by high-temperature water-rock reactions. Despite increasing knowledge about the geochemistry and microbiology of deep-sea hydrothermal vents, there is still a gap in our understanding of the key microbial players who fix much of the carbon at these sites, especially in the productive subseafloor. In this study, stable isotope probing was used to label active microbial autotrophs in diffuse flow venting fluids from three sites over 2 years and was combined with metatranscriptomic sequencing to identify their specific metabolic strategies. This research highlights the microbial community composition, function, gene regulation, and population dynamics that enable hydrothermal ecosystems to persist.},
}

@article {pmid41099510,
year = {2025},
author = {Wallace, BA and Varona, NS and Stiffler, AK and Vermeij, MJA and Silveira, C},
title = {High microbial diversity, functional redundancy, and prophage enrichment support the success of the yellow pencil coral, Madracis mirabilis, in Curaçao's coral reefs.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0120825},
doi = {10.1128/msystems.01208-25},
pmid = {41099510},
issn = {2379-5077},
abstract = {UNLABELLED: Coral reefs have undergone extensive coral loss and shifts in community composition worldwide. Despite this, some coral species appear naturally more resistant, such as Madracis mirabilis (herein Madracis). Madracis has emerged as the dominant hard coral in Curaçao, comprising 26% of coral cover in reefs that declined by 78% between 1973 and 2015. Although life history traits and competitive mechanisms contribute to Madracis's success, these factors alone may not fully explain it, as other species with similar traits have not shown comparable success. Here, we investigated the potential role of microbial communities in the success of Madracis on Curaçao reefs by leveraging a low-bias bacterial and viral enrichment method for metagenomic sequencing of coral samples, resulting in 77 unique bacterial metagenome-assembled genomes and 2,820 viral genomic sequences. Our analyses showed that Madracis-associated bacterial and viral communities are 12% and 20% richer than the communities of five sympatric coral species combined. The Madracis-associated bacterial community was dominated by Ruegeria and Sphingomonas, genera that have previously been associated with coral health, defense against pathogens, and bioremediation. These communities also displayed higher functional redundancy, which is often associated with ecological resilience. The viral community exhibited a 50% enrichment of proviruses relative to other corals. These proviruses had the genomic capacity to laterally transfer genes involved in antibiotic resistance, central metabolism, and oxidative stress responses, potentially enhancing the adaptive capacity of the Madracis microbiome and contributing to Madracis's success on Curaçao's reefs.

IMPORTANCE: Understanding why some coral species persist and thrive while most are in fast decline is critical. Madracis mirabilis is increasingly dominant on degraded reefs in Curaçao, yet the role of microbial communities in its success remains underexplored. This study highlights the potential role of Madracis-associated bacterial and viral communities in supporting coral resilience and competitive success. By identifying key microbial partners and viral genes that may enhance host stress tolerance and defense against pathogens, we broaden the understanding of how the coral holobiont contributes to species persistence under environmental stress. These insights are valuable for predicting key microbial community players in reef interactions and may inform microbiome-based strategies to support coral conservation and restoration.},
}

@article {pmid41099501,
year = {2025},
author = {Feeser, K and Longley, R and Gallegos-Graves, LV and Albright, M and Shakya, M},
title = {Recovering new viruses from New Mexico soils.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0090825},
doi = {10.1128/mra.00908-25},
pmid = {41099501},
issn = {2576-098X},
abstract = {Here, we utilized metagenomic and size-filtered virome sequencing to recover 4,157 medium, high, or complete quality viral genomes from soils taken from three high elevation sites in New Mexico, USA. Among recovered viral genomes, 90% were from size-filtered samples, indicating the importance of this enrichment in assessments of complex viromes.},
}

@article {pmid41098988,
year = {2025},
author = {Bautista, J and Fuentes-Yépez, MP and Adatty-Molina, J and López-Cortés, A},
title = {Microbial signatures in metastatic cancer.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1654792},
pmid = {41098988},
issn = {2296-858X},
abstract = {Metastasis remains the leading cause of cancer-related death, yet the biological determinants that enable tumor cells to disseminate and colonize distant organs are incompletely understood. Emerging evidence identifies the microbiome, not merely as a bystander, but as an active architect of the metastatic cascade. Microbial communities residing in the gut, mucosal barriers, and within tumors shape metastatic progression by modulating immune surveillance, stromal remodeling, oncogenic signaling, and therapy response. Intratumoral and even intracellular microbes regulate epithelial-mesenchymal transition, angiogenesis, and immune escape, while gut-derived metabolites condition pre-metastatic niches and alter systemic immunity. Technological advances in spatial transcriptomics, single-cell multi-omics, and metagenomics have revealed a spatially organized, functionally integrated microbial ecosystem within tumors, challenging long-held assumptions of sterility in cancer biology. This review synthesizes five converging dimensions of this paradigm: microbial interactions in the metastatic tumor microenvironment; microbiome-mediated immunoediting and metastatic escape; the role of intratumoral and intracellular bacteria in dissemination; spatial-multi-omic approaches to map microbial niches; and microbial biomarkers predictive of metastasis and therapy outcomes. Collectively, these findings recast the microbiome as a critical and targetable determinant of metastasis. Deciphering the tumor-microbe-host triad holds transformative potential for biomarker development, therapeutic innovation, and precision oncology.},
}

@article {pmid41098928,
year = {2025},
author = {Kimbell, LK and Ali, N and Adelgren, M and Kohls, S and Folvarska, V and Marshall, CW and Newton, RJ and Wang, Y and McNamara, P},
title = {Antibiotic Resistome Changes Associated with Different Types of Corrosion Inhibitors When Chlorine is Used as a Disinfectant.},
journal = {ACS ES&T engineering},
volume = {5},
number = {10},
pages = {2474-2485},
pmid = {41098928},
issn = {2690-0645},
abstract = {Drinking water distribution systems contain chlorine and metals that can promote antibiotic resistance. Corrosion inhibitors are required to prevent the leaching of metals into drinking water. While utilities have a choice of which corrosion inhibitor they employ, the impact of corrosion inhibitor type when combined with chlorine on antibiotic resistance is unknown. The objective of this research was to understand the impacts of zinc orthophosphate, sodium orthophosphate, and sodium silicate, three commonly used corrosion inhibitors, on antibiotic resistance when mixed with chlorine. Culture-based plating was paired with metagenomics analysis on lab-scale microcosms. The addition of all three corrosion inhibitors resulted in a significantly higher absolute abundance of antibiotic resistant bacteria with resistance to rifampicin, sulfamethoxazole, and vancomycin, while the addition of phosphate-based inhibitors (sodium orthophosphate and zinc orthophosphate) at 1 mg/L also resulted in significantly higher absolute abundance of ampicillin-resistant bacteria. Exposure to all three types of corrosion inhibitors and free chlorine led to significantly higher abundances of ARGs conferring resistance to the target antibiotics used in the phenotypic assessment. Observed changes in the resistomes compared to the controls were influenced by an enrichment in ARGs responsible for multidrug resistance and resistance to peptide antibiotics. In general, most of the ARGs were associated with chromosomes, but a significant increase in the number of ARGs colocated with plasmid and integron sequences was observed. In contrast, the abundance of viral-associated ARGs decreased in the treatments compared to the controls. These results highlight the importance of corrosion inhibitor selection and the potential impacts on antibiotic resistance in potable water systems.},
}

@article {pmid41098901,
year = {2025},
author = {Gong, W and Ma, X and Wang, G and Guo, Y and Zhuo, Z and Han, C and Wu, Y},
title = {Analysis of co-infection in severe and critical patients with influenza A (H1N1) pneumonia using metagenomic next-generation sequencing on bronchoalveolar lavage samples.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1669328},
pmid = {41098901},
issn = {2235-2988},
mesh = {Humans ; *Coinfection/microbiology/epidemiology/virology ; Male ; Female ; *Influenza, Human/virology/complications/epidemiology ; Middle Aged ; *Influenza A Virus, H1N1 Subtype/genetics/isolation & purification ; Retrospective Studies ; High-Throughput Nucleotide Sequencing ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; Adult ; Metagenomics/methods ; Aged ; Bacteria/classification/genetics/isolation & purification ; Critical Illness ; *Pneumonia, Viral/virology ; Prevalence ; },
abstract = {OBJECTIVES: The study aimed to clarify the co-infection patterns in adult patients with severe influenza A (H1N1) pneumonia using Metagenomic Next-Generation Sequencing (mNGS) and to examine their impact on clinical outcomes, particularly focusing on the differences between severe and critical patient groups.

METHODS: This retrospective analysis evaluated bronchoalveolar lavage fluid (BALF) from 53 adult patients diagnosed with severe influenza A (H1N1) pneumonia. Patients were categorized into severe and critical groups depending on the need for invasive ventilation. mNGS was utilized to detect and analyze co-infections, which included fungal, bacterial and viral pathogens. Statistical analysis was conducted to assess the prevalence of these co-infections and their association with clinical outcomes, such as 28-day mortality.

RESULTS: In the cohort, 48 patients (90.6%) experienced co-infections. In the severe group, fungal infections were noted in 14 patients (66.7%), bacterial in 4 patients (19.0%), and viral in 11 patients (52.4%). Among the critical group, 22 patients (68.8%) had fungal, 23 patients (71.9%) had bacterial, and 10 patients (31.3%) had viral co-infections. There was a significantly higher incidence of co-infections in critical patients (P = 0.0002), with notable differences in Acinetobacter baumannii prevalence between the groups (P = 0.0339). Aspergillus emerged as the predominant fungal genus across the study. Septic shock (odds ratio [OR] 33.63[4.29-538.3]; P = 0.003) and fungal co-infection (OR 24.42[1.98-810.6]; P = 0.029) were identified as independent risk factors for 28-day mortality.

CONCLUSION: The study revealed a high rate of co-infections in both severe and critical patients suffering from influenza A (H1N1) pneumonia, with a higher frequency of bacterial infections in critical patients. Importantly, septic shock and fungal co-infections were independently associated with increased 28-day mortality, highlighting the need for monitoring and management of co-infections in these patients.},
}

Humans
*Coinfection/microbiology/epidemiology/virology
Male
Female
*Influenza, Human/virology/complications/epidemiology
Middle Aged
*Influenza A Virus, H1N1 Subtype/genetics/isolation & purification
Retrospective Studies
High-Throughput Nucleotide Sequencing
*Bronchoalveolar Lavage Fluid/microbiology/virology
Adult
Metagenomics/methods
Aged
Bacteria/classification/genetics/isolation & purification
Critical Illness
*Pneumonia, Viral/virology
Prevalence

@article {pmid41098899,
year = {2025},
author = {Li, W and Di, X and Lv, X and Zhang, L and Yu, J},
title = {Characteristics of adults with influenza A virus pneumonia and co-infections identified by mNGS in Jilin, China during 2024-2025.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1662422},
pmid = {41098899},
issn = {2235-2988},
mesh = {Humans ; *Coinfection/epidemiology/virology/microbiology/diagnosis ; Male ; China/epidemiology ; Female ; *Influenza, Human/epidemiology/virology/diagnosis ; Middle Aged ; Retrospective Studies ; Adult ; Aged ; High-Throughput Nucleotide Sequencing ; *Influenza A virus/genetics/isolation & purification/classification ; *Pneumonia, Viral/epidemiology/virology/diagnosis ; Metagenomics/methods ; Severity of Illness Index ; Influenza A Virus, H3N2 Subtype/genetics/isolation & purification ; Bronchoalveolar Lavage Fluid/virology ; Influenza A Virus, H1N1 Subtype/genetics/isolation & purification ; },
abstract = {INTRODUCTION: Influenza A virus (IAV) was included in the World Health Organization priority pathogen list for 2024 owing to its pandemic potential. We aimed to investigate the characteristics of IAV pneumonia and co-infection identified using metagenomic next-generation sequencing (mNGS) in hospitalized patients in Jilin, China, during 2024-2025.

METHODS: This retrospective study included patients hospitalized for IAV pneumonia. All patients underwent mNGS testing using sputum or bronchoalveolar lavage fluid. Patients were categorized into mild-to-moderate (MM) and severe-to-critical (SC) groups, depending on their disease severity. We analyzed demographic data, clinical manifestations, laboratory findings, and imaging results, and compared the two groups.

RESULTS: Of the 73 patients included, 45 were in the MM group and 28 were in the SC group. Compared with nucleic acid tests of throat swabs, mNGS has higher sensitivity for detecting IAV (60% vs 100%). H1N1 and H3N2 were the predominant IAV subtypes. Underlying conditions, especially asthma and chronic obstructive pulmonary disease, were associated with an increased risk of severe illness. The D-dimer levels were higher, and lymphocyte counts were lower in patients in the SC group than in those in the MM group. Of the 73 patients, 63 (86.3%) had secondary infections, with bacterial infections being more prevalent (mild/moderate: 26 [58%] and severe/critical: 24 [86%]) than fungal infections (23 [51%] and 23 [82%], respectively).

CONCLUSIONS: mNGS is a sensitive method for detecting IAV co-infections, effectively identifying co-infection with pathogenic bacterial strains. Hospitalized patients with IAV pneumonia, especially those with H3N2 infection and chronic airway disease, showed a high prevalence of severe and critical illness [total: 8 [11%], severe/critical: 7 [25%]). Fungal infections were frequent regardless of the presence of underlying comorbidities, and patients with SC disease were more likely to develop gram-negative bacterial and fungal infections. These findings may assist clinicians in the early identification of critically ill patients and the provision of appropriate empirical treatment.},
}

Humans
*Coinfection/epidemiology/virology/microbiology/diagnosis
Male
China/epidemiology
Female
*Influenza, Human/epidemiology/virology/diagnosis
Middle Aged
Retrospective Studies
Adult
Aged
High-Throughput Nucleotide Sequencing
*Influenza A virus/genetics/isolation & purification/classification
*Pneumonia, Viral/epidemiology/virology/diagnosis
Metagenomics/methods
Severity of Illness Index
Influenza A Virus, H3N2 Subtype/genetics/isolation & purification
Bronchoalveolar Lavage Fluid/virology
Influenza A Virus, H1N1 Subtype/genetics/isolation & purification

@article {pmid41098770,
year = {2025},
author = {Zhou, F and Wu, Y and Ren, B and Liu, Y and Luo, K and Li, Q and Huang, F and Peng, X and Li, Y and Su, Z and Li, J},
title = {Meta-omics reveals subgingival plaque reconstruction dynamics.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2569528},
pmid = {41098770},
issn = {2000-2297},
abstract = {BACKGROUND: The homeostasis of the subgingival microbiome is crucial for periodontal health, although the dynamics governing its community variation remain insufficiently studied. This study aims to investigate the dynamics of subgingival microbiota reassembly after disruption, focusing on core taxa, functions, and driving forces.

METHODS: 339 subgingival plaques in periodontally healthy states were collected before and after ultrasonic cleaning across 12 timepoints for 1 year. All samples underwent full-length 16S rRNA sequencing; 30 were selected for metagenomic sequencing.

RESULTS: Our findings revealed that disturbed subgingival microbiota underwent short-term disruptions but subsequently reverted to baseline, maintaining stability within a year. Homogeneous selection dominated assembly, driving convergent structure under consistent pressure. Such a recovery process was accompanied by key taxa increased sequentially: Pseudomonas fluorescens early, Haemophilus parainfluenzae mid-stage, and Capnocytophaga spp. late. Functionally, reconstruction began with energy metabolism, expanded via biofilm formation and LPS biosynthesis mid-stage, and involved late apoptosis and complex amino acid metabolism. Microbial interactions, including positive regulation from Veillonella HMT 780 to Fusobacterium HMT 248, internally drove community assembly.

CONCLUSION: Our study clarifies species and functional dynamics during subgingival microbiota reconstruction and maps time-directed networks among stage-specific bacteria, offering a theoretical basis for targeted microbiome regulation.},
}

@article {pmid41098739,
year = {2025},
author = {Fan, Y and Tan, Z and Wang, Z and Pan, H and Zhou, J and Yang, J and Zhang, G},
title = {Evaluation of non-invasive diagnostic tests for Mycoplasma pneumoniae pneumonia.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1656192},
pmid = {41098739},
issn = {1664-3224},
mesh = {Humans ; *Pneumonia, Mycoplasma/diagnosis/microbiology/immunology/blood ; Male ; Female ; *Mycoplasma pneumoniae/immunology/genetics ; Middle Aged ; Immunoglobulin M/blood ; Retrospective Studies ; Adult ; Aged ; Sensitivity and Specificity ; Antibodies, Bacterial/blood ; Community-Acquired Infections/diagnosis/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; *Diagnostic Tests, Routine/methods ; High-Throughput Nucleotide Sequencing ; Young Adult ; },
abstract = {BACKGROUND: Accurate and timely identification of Mycoplasma pneumoniae pneumonia (MPP) remains a clinical challenge. Although nasopharyngeal swab nucleic acid testing (NAAT) and serum IgM antibody assays are widely used, their diagnostic performance varies across studies. This study aimed to retrospectively evaluate the sensitivity and specificity of the two non-invasive methods (NAAT and serum IgM antibody assays) for MPP in real-world clinical settings.

METHODS: We conducted a retrospective study of adult patients hospitalized for community-acquired pneumonia (CAP) from January 2024 to October 2024. All enrolled patients underwent bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF-mNGS) and had received at least one of two non-invasive tests (NAAT or serum IgM antibody assays). The sensitivity and specificity of NAAT and serum IgM antibody assays were calculated against the final diagnosis. A non-inferiority test was used to determine whether the sensitivity of NAAT or serum IgM antibody assays was not inferior to that of mNGS.

RESULTS: Among 594 patients included in the analysis, 60 were diagnosed with MPP based on a composite reference standard that included laboratory testing results and adjudication by two senior clinicians in accordance with clinical and radiological findings. The sensitivity and specificity of NAAT were 74.1% and 99.3%, respectively, while those of serum IgM antibody assays were 23.6% and 98.0%. McNemar's test revealed a statistically significant difference in sensitivity between mNGS and the two non-invasive tests (NAAT and serum IgM antibody assays) (P<0.05). The non-inferiority analysis revealed that both NAAT (sensitivity difference: -24.2%, 95% CI: -36.1 to -12.1%; P<0.01) and serum IgM antibody assays (-76.5%, 95% CI: -96.6 to -56.3%; P<0.01) failed to meet the 10% non-inferiority margin compared to mNGS.

CONCLUSION: In clinical practice, a positive result from either NAAT or serum IgM antibody assays can serve as reliable adjunct evidence for diagnosing MPP. However, in cases with a high clinical suspicion of MPP, negative results from both methods are not sufficient to rule out the diagnosis. For MPP, mNGS remains the most effective diagnostic method compared to non-invasive testing alternatives.},
}

Humans
*Pneumonia, Mycoplasma/diagnosis/microbiology/immunology/blood
Male
Female
*Mycoplasma pneumoniae/immunology/genetics
Middle Aged
Immunoglobulin M/blood
Retrospective Studies
Adult
Aged
Sensitivity and Specificity
Antibodies, Bacterial/blood
Community-Acquired Infections/diagnosis/microbiology
Bronchoalveolar Lavage Fluid/microbiology
*Diagnostic Tests, Routine/methods
High-Throughput Nucleotide Sequencing
Young Adult

@article {pmid41098538,
year = {2025},
author = {He, X and Zhao, Q and Zhang, J and Shi, J and Wan, N and Tang, B and Tian, B and Li, P},
title = {Potential and application of Fusobacterium nucleatum in the diagnosis and treatment of colorectal cancer.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1652702},
pmid = {41098538},
issn = {1664-302X},
abstract = {Colorectal cancer (CRC), as a globally prevalent malignant tumor, relies on in-depth analysis of tumor microenvironment regulation mechanisms for precision diagnosis and treatment. Fusobacterium nucleatum (F. nucleatum), a key carcinogenic bacterium, has been revealed in recent studies to play multidimensional roles in CRC initiation, progression, and metastasis. This review systematically summarizes the progress of Fn applications in CRC full-cycle management: (1) In the diagnostic field, Fn detection technology based on fecal samples has developed into a new non-invasive screening strategy. Cohort studies show its diagnostic performance (AUC 0.82-0.89), with significant correlations to tumor stage (III/IV stage OR = 2.87), lymph node metastasis (HR = 1.94), and reduced 5-year survival rate (35% vs. 62%); (2) For therapeutic monitoring, dynamic Fn load changes can predict chemotherapy (OR = 0.63) and immunotherapy responses (PFS extended by 2.1 months); (3) In prognostic evaluation, metagenomic analysis shows that high Fn abundance is closely related to TNM staging (C-index 0.81 vs. 0.69) and recurrence risk (AUC = 0.88). Notably, a nomogram model integrating Fn biomarkers can improve the predictive accuracy of the traditional TNM staging system by 17.3%. Although existing evidence supports the clinical translational value of Fn, its standardized detection protocols, threshold setting, and targeted intervention strategies (such as antibiotic therapy and phage therapy) still require validation through multi-center prospective studies. This review provides evidence-based medical evidence for the application of Fn in CRC precision medicine by integrating multi-omics data.},
}

@article {pmid41098531,
year = {2025},
author = {Juárez-Aragón, MC and Pantoja-Irys, JR and de la Rosa-Manzano, E and Garrido-Olvera, L and Mujica-Sánchez, H and Trejo-De León, CR and Vázquez-Lobo, A},
title = {Microbiome diversity across physicochemical gradient in low-medium enthalpy springs at the Sierra Madre Oriental eastern flank, northeastern Mexico.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1663000},
pmid = {41098531},
issn = {1664-302X},
abstract = {INTRODUCTION: Bacterial communities are fundamental to the functionality of thermal springs where they engage in essential processes such as the oxidation of sulfur, reduction of nitrates, carbon fixation, production of unique metabolites, and stabilization of microbial trophic networks. Northeastern Mexico presents a diverse array of thermal springs located within tropical karst systems situated among folded mountains and ancient inactive karstic regions. The geological complexity of these environments indicates a substantial potential for microbiome diversity; however, the composition and functional dynamics of microbial communities in these springs have not been thoroughly investigated.

METHODS: This study involved the collection of water samples from six hot springs, to characterize the planktonic microbiome using advanced metagenomic sequencing techniques. Additionally, we examined the relationship between microbial composition and physicochemical parameters.

RESULTS: Our analysis identified a total of 425 microbial species, which included 409 bacterial species, 13 eukaryotic organisms, and 3 archaeal taxa. The Ojo Caliente and Mainero Azufroso springs displayed the highest microbial diversity, whereas the Balneario El Bañito and Taninul springs exhibited the lowest. The Phyum Pseudomonadota was the predominant across the majority of springs, while Campylobacterota and Chlorobiota were specifically identified in the less diverse Balneario El Bañito and Taninul springs, respectively. A total of 30 indicator species were identified, predominantly in El Bañito and Potrero Prieto springs, emphasizing the distinctiveness of their microbial environments. Moreover, we found that electrical conductivity and bicarbonate concentration had a significant impact on the structure of this microbial communities.

DISCUSSION: This study highlights the ecological importance of these unique ecosystems in northeastern Mexico, with the Mainero Azufroso and Ojo Caliente springs identified as reservoirs of high microbial diversity.},
}

@article {pmid41098344,
year = {2025},
author = {Li, H and Wei, J and Zhou, S and Zhan, Z and Tang, J and Wang, W and Tang, H},
title = {Metagenomic Next-Generation Sequencing Unmasks Atypical Rabies - Guangxi Zhuang Autonomous Region, China, 2024.},
journal = {China CDC weekly},
volume = {7},
number = {39},
pages = {1251-1257},
pmid = {41098344},
issn = {2096-7071},
abstract = {Human rabies remains nearly universally fatal despite medical advances. Diagnosis is frequently delayed when patients present with atypical symptoms, and the failure to receive postexposure prophylaxis (PEP) continues to be a major contributor to mortality worldwide.

WHAT IS ADDED BY THIS REPORT?: This represents the first confirmed human rabies case in Guangxi caused by the JSTZ190314 strain, successfully identified through metagenomic next-generation sequencing (mNGS). The patient initially presented with urinary symptoms that led to a misdiagnosis before characteristic neurological manifestations developed, ultimately progressing to brain death 28 days after neurological onset (34 days from initial urinary symptoms).

This case demonstrates the critical importance of mNGS in diagnosing atypical rabies presentations and emphasizes the urgent need for enhanced early clinical recognition, standardized PEP administration protocols, and strengthened regional viral surveillance systems.},
}

@article {pmid41098206,
year = {2025},
author = {Chen, Y and Li, M and Gan, X and Wang, Y and Tang, X and Zhou, Y and Niu, T},
title = {Metagenomic Next-Generation Sequencing Unveils Prognostic Microbial Synergism and Guides Precision Therapy in Candidemia: A Retrospective Cohort Study.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5263-5275},
pmid = {41098206},
issn = {1178-6973},
abstract = {PURPOSE: Candidemia remains a life-threatening infection, compounded by diagnostic delays and limited prognostic tools. While metagenomic next-generation sequencing (mNGS) offers rapid pathogen detection, its prognostic utility and therapeutic impact in candidemia remain unestablished.

PATIENTS AND METHODS: This retrospective cohort study analyzed 97 candidemia patients with positive blood mNGS at West China Hospital (2020-2024). Multivariable logistic regression and survival analyses identified mortality predictors, while therapeutic impacts were assessed through antifungal regimen modifications.

RESULTS: The 28-day mortality was 44.3% (43/97). Blood mNGS outperformed cultures in species identification (5 vs 4 species) and co-infection detection. Bacterial co-detections (HR=2.00, 95% CI:1.15-3.48; p<0.05) doubled mortality risk. SOFA score was the strongest mortality predictor (adjusted OR=1.29 per point; p<0.001). mNGS-guided antifungal initiation reduced mortality by 52.4% in treatment-naïve patients (22.6% vs 75.0%; p<0.05), though regimen adjustments in pretreated cases showed no benefit (p>0.05). Notably, Candida species exhibited equivalent virulence (log-rank p>0.05), and mNGS read counts lacked prognostic value (p>0.05).

CONCLUSION: mNGS transforms candidemia management by enabling early risk stratification (via SOFA scores and co-infection profiles) and precision therapy initiation. Its capacity to unmask high-risk bacterial synergists and guide time-sensitive interventions supports integration into diagnostic algorithms, particularly for culture-negative cases. Further validation of standardized mNGS protocols is warranted to maximize clinical impact.},
}

@article {pmid41097911,
year = {2025},
author = {Verhoeven, JTP and Malwe, AS and Roussel, N and Nielsen, IB and Mak, SST and Nielsen, TK and Barnes, CJ},
title = {Adaptive sampling with Oxford Nanopore offers a simple way to improve the efficiency of plant metagenomic studies.},
journal = {The New phytologist},
volume = {248},
number = {4},
pages = {1620-1624},
doi = {10.1111/nph.70450},
pmid = {41097911},
issn = {1469-8137},
support = {60770//Villum Fonden/ ; AUFF-E-2024-9-14//Aarhus Universitets Forskningsfond/ ; },
}

@article {pmid41097662,
year = {2025},
author = {He, J and Shu, X and Pan, H and Wang, M and Song, Y and Zhou, F and Lian, L and Chen, L and Ma, G and Zhao, Y and Li, R and Liu, L},
title = {Ginseng Polysaccharides Inhibit Aspergillus sydowii-Driven Lung Adenocarcinoma via Modulating Gut Microbiota-Bile Acid Metabolism Axis.},
journal = {Cancers},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/cancers17193134},
pmid = {41097662},
issn = {2072-6694},
support = {(82204677, 82474267//National Natural Science Foundation of China/ ; 2024ZD0521405//National Science and Technology Major Project of China/ ; GZNL2023A02009//Major Project of Guangzhou National Laboratory/ ; 20241112//Traditional Chinese Medicine Bureau of Guangdong Province Project/ ; QZ2023ZZ11//State Key Laboratory of Traditional Chinese Medicine Syndrome/ ; HQL2024PZ005//Chinese Medicine Guangdong Laboratory/ ; 2025M773868//China Postdoctoral Science Foundation/ ; },
abstract = {BACKGROUND: Lung cancer is the leading cause of cancer-related mortality globally, with lung adenocarcinoma (LUAD) as the most common subtype. Dysbiotic intratumoral mycobiomes drive LUAD pathogenesis, and Aspergillus sydowii (A. sydowii) acts as a key oncogenic fungal species. Ginseng polysaccharides (GPs), bioactive phytochemicals with immunomodulatory and oncostatic properties, counteract fungal infections and restore immunosurveillance in LUAD.

METHODS: Subcutaneous and orthotopic LUAD murine models were established by implanting Lewis lung carcinoma (LLC) cells. Subcutaneous tumors were infected intratumorally and orthotopic models via nasal inoculation. GPs (200 mg/kg/day) were orally administered to evaluate tumor growth. Metagenomic and targeted bile acid metabolomic profiling of fecal and tumor tissues was performed, with Spearman correlations analyzed using R packages.

RESULTS: GPs significantly inhibited A. sydowii-induced tumor growth in both models. In subcutaneous tumors; GPs reduced volume (p < 0.05) and weight vs. infected controls. In orthotopic models, GPs decreased pathological nodules and lung weight, with micro-CT/H&E confirming attenuated hyperplasia. Metagenomics showed GPs restored gut homeostasis by enriching Lactobacillus/Muribaculum intestinale and suppressing pro-inflammatory Alistipes. Targeted metabolomics revealed reduced β-Hyodeoxycholic Acid (3β-HDCA), Chenodeoxycholic acid 24-acyl-b-D-glucuronide (CDCA-24G) and 3β-hydroxychol-5-en-24-oic acid (5-isoLCA) after GP treatment. Network analysis confirmed significant microbe-bile acid interactions.

CONCLUSIONS: GPs exert antitumor effects against A. sydowii-induced LUAD by modulating gut microbiota and bile acid metabolism. This identifies GPs as a promising therapy for mycobiome-influenced cancers, with dual targeting of fungal infection and metabolic reprogramming.},
}

@article {pmid41097145,
year = {2025},
author = {Tuigunov, D and Sinyavskiy, Y and Nurgozhin, T and Zholdassova, Z and Smagul, G and Omarov, Y and Dolmatova, O and Yeshmanova, A and Omarova, I},
title = {Precision Nutrition and Gut-Brain Axis Modulation in the Prevention of Neurodegenerative Diseases.},
journal = {Nutrients},
volume = {17},
number = {19},
pages = {},
doi = {10.3390/nu17193068},
pmid = {41097145},
issn = {2072-6643},
support = {Grant No. AP23489983//This research is funded by the Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {Humans ; *Neurodegenerative Diseases/prevention & control/microbiology ; *Gastrointestinal Microbiome/physiology ; *Brain ; *Precision Medicine/methods ; *Brain-Gut Axis/physiology ; Prebiotics/administration & dosage ; Probiotics/administration & dosage ; },
abstract = {In the recent years, the accelerating global demographic shift toward population aging has been accompanied by a marked increase in the prevalence of neurodegenerative disorders, notably Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and multiple sclerosis. Among emerging approaches, dietary interventions targeting the gut-brain axis have garnered considerable attention, owing to their potential to modulate key pathogenic pathways underlying neurodegenerative processes. This review synthesizes current concepts in precision nutrition and elucidates neurohumoral, immune, and metabolic regulatory mechanisms mediated by the gut microbiota, including the roles of the vagus nerve, cytokines, short-chain fatty acids, vitamins, polyphenols, and microbial metabolites. Emerging evidence underscores that dysbiotic alterations contribute to compromised barrier integrity, the initiation and perpetuation of neuroinflammatory responses, pathological protein aggregations, and the progressive course of neurodegenerative diseases. Collectively, these insights highlight the gut microbiota as a pivotal target for the development of precision-based dietary strategies in the prevention and mitigation of neurodegenerative disorders. Particular attention is devoted to key bioactive components such as prebiotics, probiotics, psychobiotics, dietary fiber, omega-3 fatty acids, and polyphenols that critically participate in regulating the gut-brain axis. Contemporary evidence on the contribution of the gut microbiota to the pathogenesis of Alzheimer's disease, Parkinson's disease, and multiple sclerosis is systematically summarized. The review further discusses the prospects of applying nutrigenomics, chrononutrition, and metagenomic analysis to the development of personalized dietary strategies. The presented findings underscore the potential of integrating precision nutrition with targeted modulation of the gut-brain axis as a multifaceted approach to reducing the risk of neurodegenerative diseases and preserving cognitive health.},
}

Humans
*Neurodegenerative Diseases/prevention & control/microbiology
*Gastrointestinal Microbiome/physiology
*Brain
*Precision Medicine/methods
*Brain-Gut Axis/physiology
Prebiotics/administration & dosage
Probiotics/administration & dosage

@article {pmid41097095,
year = {2025},
author = {Russell, T and Formiconi, E and Casey, M and McElroy, M and Mallon, PWG and Gautier, VW},
title = {Viral Metagenomic Next-Generation Sequencing for One Health Discovery and Surveillance of (Re)Emerging Viruses: A Deep Review.},
journal = {International journal of molecular sciences},
volume = {26},
number = {19},
pages = {},
doi = {10.3390/ijms26199831},
pmid = {41097095},
issn = {1422-0067},
support = {101132970//European Commission/ ; },
mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Animals ; One Health ; *Communicable Diseases, Emerging/virology/epidemiology ; *Viruses/genetics ; SARS-CoV-2/genetics ; Genome, Viral ; Zoonoses/virology ; },
abstract = {Viral metagenomic next-generation sequencing (vmNGS) has transformed our capacity for the untargeted detection and characterisation of (re)emerging zoonotic viruses, surpassing the limitations of traditional targeted diagnostics. In this review, we critically evaluate the current landscape of vmNGS, highlighting its integration within the One Health paradigm and its application to the surveillance and discovery of (re)emerging viruses at the human-animal-environment interface. We provide a detailed overview of vmNGS workflows including sample selection, nucleic acid extraction, host depletion, virus enrichment, sequencing platforms, and bioinformatic pipelines, all tailored to maximise sensitivity and specificity for diverse sample types. Through selected case studies, including SARS-CoV-2, mpox, Zika virus, and a novel henipavirus, we illustrate the impact of vmNGS in outbreak detection, genomic surveillance, molecular epidemiology, and the development of diagnostics and vaccines. The review further examines the relative strengths and limitations of vmNGS in both passive and active surveillance, addressing barriers such as cost, infrastructure requirements, and the need for interdisciplinary collaboration. By integrating molecular, ecological, and public health perspectives, vmNGS stands as a central tool for early warning, comprehensive monitoring, and informed intervention against (re)emerging viral threats, underscoring its critical role in global pandemic preparedness and zoonotic disease control.},
}

Humans
*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
Animals
One Health
*Communicable Diseases, Emerging/virology/epidemiology
*Viruses/genetics
SARS-CoV-2/genetics
Genome, Viral
Zoonoses/virology

@article {pmid41095773,
year = {2025},
author = {Suárez-Cortés, M and Juan-Pérez, A and Molina-Rodríguez, A and Araújo de Castro, J and Castaño-Molina, MÁ and Fernández-Ruiz, VE and Jiménez-Méndez, A and Martínez Pérez-Munar, P and Rico-Chazarra, S and Ramos-Molina, B and Sánchez-Solís, M and Blanco-Carnero, JE and Ruiz-Alcaraz, AJ and Núñez-Sánchez, MÁ},
title = {Dynamics of the Epigenome, Microbiome, and Metabolome in Relation to Early Adiposity in the Maternal-Infant Axis: Protocol for a Prospective, Observational Pilot Study in the Spanish NEMO Cohort.},
journal = {Journal of clinical medicine},
volume = {14},
number = {19},
pages = {},
doi = {10.3390/jcm14196694},
pmid = {41095773},
issn = {2077-0383},
support = {22080/JLI/22//Fundación Séneca - Agencia de Ciencia y Tecnología de la Región de Murcia/ ; CP23/00051//Instituto de Salud Carlos III/ ; },
abstract = {Background: Childhood obesity has reached epidemic levels in developed countries and is an emerging concern in developing regions. Children with excess weight are more likely to maintain this condition over time into adulthood and face a higher risk of developing metabolic disorders such as type 2 diabetes, hypertension, metabolic dysfunction-associated liver disease, and dyslipidemia. Early identification of obesity risk is, therefore, a key public health challenge. Methods: This is an observational, prospective, single-center cohort pilot study in 66 mother-infant dyads recruited at the Gynecology and Obstetrics Service of the Virgen de la Arrixaca University Hospital (Murcia, Spain). The primary objective is to identify early-life, non-invasive biomarkers associated with increased adiposity by integrating multi-omics approaches and analyzing maternal-infant interactions. Pregnant women will be enrolled during the third trimester and will undergo a baseline visit at 38 weeks of gestation for clinical and anthropometric assessment. Buccal swabs and fecal samples will be collected at baseline and in the peripartum period for epigenetic (DNA methylation), metagenomic, and metabolomic analyses. Infants will be evaluated at birth and followed at 6 months, 1 year, 2 years, and 3 years. Each visit will include detailed anthropometric measurements, along with collection of buccal swabs and fecal samples for multi-omics profiling. Conclusions: This multidisciplinary study aims to assess how maternal factors influence infant epigenetic and microbial patterns, and their relation to adiposity development. Early identification of such biomarkers may guide personalized prevention strategies and reduce the long-term burden of obesity-related comorbidities.},
}

@article {pmid41095699,
year = {2025},
author = {Ziad, GA and Jalal, D and Hashem, M and Sayed, AA and Mahfouz, S and Bayoumi, A and Lotfi, M and Hassanain, O and Tolba, M and Madney, Y and Shalaby, L and Elanany, M},
title = {Rapid Identification of Carbapenemase Genes Directly from Blood Culture Samples.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/diagnostics15192480},
pmid = {41095699},
issn = {2075-4418},
support = {#54699605//Pfizer Global Medical Grants/ ; },
abstract = {Background/Objectives: The rapid identification of carbapenemase genes directly from positive blood culture (BC) samples shortens the time needed to initiate optimal antimicrobial therapy for Carbapenemase-Producing Enterobacterales (CPE) infections. Several commercial automated PCR systems are available for detecting CPE resistance genes but are expensive. The Xpert[®] Carba-R assay (Cepheid GeneXpert System) has high sensitivity and specificity for the detection of carbapenamase genes from bacterial colonies or rectal swabs, with an affordable price. This assay was not used for positive BC testing of CPE resistance genes. Whole-Genome Sequencing (WGS) for resistance genes can be used as the gold standard at a research level. In this study, we evaluated the performance of the Xpert[®] Carba-R assay for the early detection of carbapenamase genes directly from positive BCs, using WGS as the gold standard. Methods: A prospective observational study was conducted at Children's Cancer Hospital-Egypt (CCHE-57357). All positive BCs underwent direct gram staining and conventional cultures. A total of 590 positive BCs containing Gram-negative rods (GNRs) were identified. The Xpert[®] Carba-R assay was used to detect carbapenemase genes directly from the positive BC bottle compared with WGS results. Results: Among the 590 GNR specimens, 178 were found to carry carbapenemase genes using the Xpert[®] Carba-R assay, with results obtained in approximately one hour. The main genotypes detected were blaNDM, blaOXA-48-like, and dual blaNDM/blaOXA-48-like at 27%, 29%, and 33%, respectively. The agreement between Xpert[®] Carba-R assay and WGS results was almost perfect for the genotype resistance pattern of isolates and individual gene detection. Conclusions: The use of the Xpert[®] Carba-R assay directly from BC bottles was an easy-to-use, time-saving, affordable tool with high accuracy in identifying carbapenemase genes and, thus, shortens the time needed to initiate optimal antimicrobial therapy for CPE infections.},
}

@article {pmid41094699,
year = {2025},
author = {Serrana, JM and Dessirier, B and Nascimento, FJA and Broman, E and Posselt, M},
title = {Microbial hydrocarbon degradation potential of the Baltic Sea ecosystem.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {204},
pmid = {41094699},
issn = {2049-2618},
support = {Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; Project No. 30002687//Stockholm University Center for Circular and Sustainable Systems (SUCCeSS) Postdoc Funding/ ; },
mesh = {*Hydrocarbons/metabolism ; Biodegradation, Environmental ; *Seawater/microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Ecosystem ; Metagenome ; Petroleum/metabolism ; Microbiota ; Metagenomics/methods ; *Water Pollutants, Chemical/metabolism ; Oceans and Seas ; },
abstract = {BACKGROUND: The Baltic Sea receives petroleum hydrocarbons from various point sources. The degradation of these contaminants in the environment is typically facilitated by a variety of microorganisms that possess a range of genes and metabolic functions related to the degradation of various hydrocarbon substrates. However, our understanding of natural attenuation and the microbial capacity to degrade these contaminants within the Baltic Sea ecosystem remains limited. In this study, we compiled metagenomes from the benthic and pelagic ecosystems across the Baltic Sea to identify microorganisms and characterize their genes and metabolic functions involved in the degradation of hydrocarbon compounds.

RESULTS: Known hydrocarbon-degrading phyla, i.e., Pseudomonadota, Myxococcota A, Actinomycetota, and Desulfobacterota, were identified within the Baltic Sea metagenome-assembled genomes (MAGs). Notably, 80% of the MAGs exhibited multiple hydrocarbon degradation gene annotations (> 10 reads per kilobase million). Aerobic degradation was the predominant pathway for hydrocarbon degradation across environmental samples. Hydrocarbon degradation gene abundances varied among samples and Baltic Sea subbasins, with long-chain alkanes and dibenzothiophene compounds being the preferred substrates. Species richness and diversity of both benthic and pelagic microorganisms positively correlated with hydrocarbon degradation gene diversity, with the pelagic ecosystem exhibiting significantly higher richness and diversity compared to the benthic ecosystem. Additionally, the composition of the hydrocarbon degradation genes across the Baltic Sea subbasins was influenced by oil spill history, with areas that experienced higher spill volumes showing lower microbial diversity, suggesting potential enrichment of specific hydrocarbon degraders. Among the environmental factors assessed, depth played a significant role in shaping the composition of genes involved in hydrocarbon degradation within the Baltic Sea.

CONCLUSIONS: Using metagenomics, we profiled the native microorganisms associated with hydrocarbon degradation in the Baltic Sea. This knowledge will aid in understanding the natural capacities of microbial communities, potentially linked to the natural attenuation of hydrocarbon pollutants in the area. Insights into microbial degradation potential can enhance predictions of petroleum pollutant persistence and accumulation, support mitigation strategies for marine pollution, and reveal the ecological resilience of native microbial communities in marine ecosystems. Video Abstract.},
}

*Hydrocarbons/metabolism
Biodegradation, Environmental
*Seawater/microbiology
*Bacteria/metabolism/classification/genetics/isolation & purification
Ecosystem
Metagenome
Petroleum/metabolism
Microbiota
Metagenomics/methods
*Water Pollutants, Chemical/metabolism
Oceans and Seas

@article {pmid41094674,
year = {2025},
author = {Yuan, M and Lv, X and Yuan, Y and Kang, M and He, F},
title = {Disseminated Listeria monocytogenes and human pegivirus-1 coinfection.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1335},
pmid = {41094674},
issn = {1471-2334},
mesh = {Humans ; Middle Aged ; *Listeria monocytogenes/isolation & purification/genetics ; *Coinfection/virology/microbiology/diagnosis ; Male ; *Listeriosis/complications/drug therapy ; *Flaviviridae Infections/complications/virology/diagnosis ; *Flaviviridae/isolation & purification/genetics ; Anti-Bacterial Agents/therapeutic use ; *Meningitis, Listeria/drug therapy/diagnosis/complications/microbiology ; },
abstract = {BACKGROUND: Listeria monocytogenes is one of the major bacteria responsible for meningitis. Controversy exists regarding the neuropathological effect of human pegivirus-1 (HPgV-1). Whether HPgV-1 interacts with L. monocytogenes is unknown. Herein, we describe a multiple myeloma patient with disseminated L. monocytogenes and HPgV-1 coinfection.

CASE PRESENTATION: The case of a 57-year-old patient with fever accompanied by headache, dizziness, nausea, vomiting of stomach contents, and urinary and faecal incontinence is presented. Through metagenomic next-generation sequencing and the detection of L. monocytogenes and HPgV-1 in cerebrospinal fluid, along with blood culture of L. monocytogenes and PCR of HPgV-1 in the blood, a diagnosis of HPgV-1 and L. monocytogenes meningitis, HPgV-1 viremia, and L. monocytogenes sepsis was made, enabling timely and proper treatment with meropenem. After treatment, the patient recovered and was discharged from the hospital.

CONCLUSIONS: To our knowledge, this is the first reported case of disseminated L. monocytogenes and HPgV-1 coinfection. Determining whether HPgV-1 was responsible for meningitis will require further research, including histopathological analysis.},
}

Humans
Middle Aged
*Listeria monocytogenes/isolation & purification/genetics
*Coinfection/virology/microbiology/diagnosis
Male
*Listeriosis/complications/drug therapy
*Flaviviridae Infections/complications/virology/diagnosis
*Flaviviridae/isolation & purification/genetics
Anti-Bacterial Agents/therapeutic use
*Meningitis, Listeria/drug therapy/diagnosis/complications/microbiology

@article {pmid41094150,
year = {2025},
author = {Zhang, Y and Bhosle, A and Bae, S and Eckenrode, K and Huang, X and Tang, J and Lavrentovich, D and Awad, L and Hua, J and Wang, Y and Morgan, XC and Li, B and Krueger, A and Garrett, WS and Franzosa, EA and Huttenhower, C},
title = {Predicting functions of uncharacterized gene products from microbial communities.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41094150},
issn = {1546-1696},
support = {R24DK110499//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; U19AI110820//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; },
abstract = {The majority of genes in microbial communities remain uncharacterized. Here we develop a method to infer putative function for microbial proteins at scale by assessing community-wide multiomics data. We predict high-confidence functions for >443,000 protein families (~82.3% previously uncharacterized), including >27,000 protein families with weak homology to known proteins and >6,000 protein families without homology. These were drawn from 1,595 gut metagenomes and 800 metatranscriptomes from the Integrative Human Microbiome Project (HMP2/iHMP). Integrating additional information such as sequence similarity, genomic proximity and domain-domain interactions improves performance of the method. Our method's implementation, FUGAsseM, is generalizable and predicts protein function in both well-studied and undercharacterized communities. FUGAsseM achieves similar levels of accuracy in the context of microbial communities when compared to state-of-the-art approaches designed for application to single organisms while simultaneously providing much greater breadth of coverage. This initial study expands the functional landscape of the human gut microbiome and allows for exploration of microbial proteins in undercharacterized communities.},
}

@article {pmid41094135,
year = {2025},
author = {Dahlman, S and Avellaneda-Franco, L and Rutten, EL and Gulliver, EL and Solari, S and Chonwerawong, M and Kett, C and Subedi, D and Young, RB and Campbell, N and Gould, JA and Bell, JD and Docherty, CAH and Turkington, CJR and Nezam-Abadi, N and Grasis, JA and Lyras, D and Edwards, RA and Forster, SC and Barr, JJ},
title = {Isolation, engineering and ecology of temperate phages from the human gut.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41094135},
issn = {1476-4687},
abstract = {Large-scale metagenomic and data-mining efforts have revealed an expansive diversity of bacteriophages (phages) within the human gut[1-3]. However, functional understanding of phage-host interactions within this complex environment is limited, largely due to a lack of cultured isolates available for experimental validation. Here we characterize 134 inducible prophages originating from 252 human gut bacterial isolates using 10 different induction conditions to expand the experimentally validated temperate phage-host pairs originating from the human gut. Importantly, only 18% of computationally predicted prophages could be induced in pure cultures. Moreover, we construct a 78-member synthetic microbiome that, when co-cultured in the presence of human colonic cells (Caco2), led to the induction of 35% phage species. Using cultured isolates, we demonstrate that human host-associated cellular products may act as induction agents, providing a possible link between gastrointestinal cell lysis and temperate phage populations[4,5]. We provide key insights into prophage diversity and genetics, including a genetic pathway for domestication, finding that polylysogeny was common and resulted in coordinated prophage induction, and that differential induction can be influenced by divergent prophage integration sites. More broadly, our study highlights the importance of culture-based techniques, alongside experimental validation, genomics and computational prediction, to understand the biology and function of temperate phages in the human gut microbiome. These culture-based approaches will enable applications across synthetic biology, biotechnology and microbiome fields.},
}

@article {pmid41093983,
year = {2025},
author = {Zhang, J and Sekela, JJ and Hutchinson, LE and Yang, J and Sellers, RS and Bhatt, AP and Redinbo, MR},
title = {Sex-dependent responses in mice to indomethacin-induced organ injury and gut microbiome-targeted alleviation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {36025},
pmid = {41093983},
issn = {2045-2322},
support = {NIH R35 award GM152079/NH/NIH HHS/United States ; },
mesh = {Animals ; *Indomethacin/adverse effects/toxicity ; Female ; Male ; *Gastrointestinal Microbiome/drug effects ; Mice ; Mice, Inbred C57BL ; *Anti-Inflammatory Agents, Non-Steroidal/adverse effects/toxicity ; Sex Factors ; Spleen/drug effects/pathology ; Liver/drug effects/pathology ; Colon/drug effects/pathology ; RNA, Ribosomal, 16S/genetics ; Glucuronidase/antagonists & inhibitors/metabolism ; Sex Characteristics ; },
abstract = {Nonsteroidal anti-inflammatory drugs (NSAIDs) are used widely but produce gastrointestinal (GI) toxicities in both short- and long-term users. Previous studies have shown that the intestinal microbiota play an important role in gut damage and that gut microbial β-glucuronidase (GUS) inhibitors can alleviate NSAID-induced injury in male mice by blocking the GI reactivation of NSAID-glucuronides. Here, in both male and female C57BL/6 mice, we examine the effects of indomethacin alone and with the GUS inhibitor UNC10201652. Oral delivery of 5 mg/kg body weight indomethacin over 5 days decreased body weight, induced colonic and hepatic inflammatory cytokine gene expression, and enlarged the spleens of both male and female mice. However, sex-specific inflammatory responses to indomethacin were observed, with males demonstrating more colonic injury while females presented greater splenic and hepatic toxic responses. Females also showed a unique indomethacin-induced bloom of fecal Verrucomicrobia as measured by 16S rRNA metagenomic sequencing. UNC10201652 alleviated aspects of these indomethacin-induced toxicities, including features of the male-specific colonic damage and the female-specific compositional changes and spleen and liver toxicities. Thus, GI and non-GI tissues in male and female mice respond distinctly to indomethacin-induced damage. These findings advance our understanding of how sex impacts systemic responses to xenobiotic exposure and may lead to improved therapeutic outcomes with these widely used drugs.},
}

Animals
*Indomethacin/adverse effects/toxicity
Female
Male
*Gastrointestinal Microbiome/drug effects
Mice
Mice, Inbred C57BL
*Anti-Inflammatory Agents, Non-Steroidal/adverse effects/toxicity
Sex Factors
Spleen/drug effects/pathology
Liver/drug effects/pathology
Colon/drug effects/pathology
RNA, Ribosomal, 16S/genetics
Glucuronidase/antagonists & inhibitors/metabolism
Sex Characteristics

@article {pmid41093555,
year = {2025},
author = {Suto, Y and Horiba, K and Masuda, Y and Tanaka, K and Hashino, M and Kuroda, M and Fukuda, H},
title = {Candida tropicalis Brain Abscess Diagnosed by Metagenomic Next-Generation Sequencing: A Case Report.},
journal = {Internal medicine (Tokyo, Japan)},
volume = {},
number = {},
pages = {},
doi = {10.2169/internalmedicine.5937-25},
pmid = {41093555},
issn = {1349-7235},
abstract = {We report the case of a 59-year-old HIV-negative male diagnosed with a brain abscess following vasculitis-associated stroke. The causative pathogen remains unidentified using conventional methods including culture and rapid multiplex PCR. Craniotomy and biopsy were performed to establish a definitive diagnosis, and metagenomic next-generation sequencing (mNGS) of the abscess tissue identified Candida tropicalis as the causative pathogen. This case highlights the utility of mNGS in identifying pathogens in culture-negative CNS infections, even when conventional methods fail to detect the causative agent, particularly when evaluating abscess pus.},
}

@article {pmid41093108,
year = {2025},
author = {Chandel, N and Patel, P and Somvanshi, PR and Verma, AK and Thakur, V},
title = {Inverse association between serum vitamin B12 level and abundance of potential B12-producing gut microbes in Indian children.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.10.021},
pmid = {41093108},
issn = {1541-6100},
abstract = {BACKGROUND: The human gut microbiome is a natural source of essential micronutrients like B-vitamins, which are utilized by both the host and other community members. The prevalence and abundance of known B-vitamin producers and B-vitamin biosynthesis pathways have already been reported in gut microbiome cohorts of a few countries including India.

OBJECTIVE: To test whether the presence of B-vitamin producers/biosynthetic pathways associates with serum B-vitamin levels, taking B12 as a case example.

METHODS: Fecal samples were collected from non-deficient (serum B12 level > 210 pg/mL, n=29) and B12 deficient (serum B12 level < 210 pg/mL, n=30) children from a tribal region of central India. Whole metagenomic DNA was extracted, sequenced, and analyzed for taxonomic profiling and diversity comparisons. Differentially abundant taxa between two groups were identified. The prevalence and abundance of potential B12 producers were compared, and their association with serum B12 level was established.

RESULTS: A comparison of within-sample diversity between the two groups didn't show any difference; however, between-sample diversity was significantly less in the B12 deficient group. Differential abundance testing also showed different microbiome structure in the B12 deficient group, where a higher abundance of B12 transporter-carrying Bacteroides thetaiotaomicron, a few pathogenic species, and ten known B12 producers was observed. Potential B12 producers were also significantly prevalent and abundant in the deficient group. Their cumulative abundance was also significantly higher in the deficient group and showed a negative association with serum B12 levels.

CONCLUSION: A higher abundance of potential B12 producers in the deficient group suggested an adaptive mechanism by the gut microbiome to meet the community's B12 requirements, by selectively promoting the growth of B12 producers, but causality remains to be proved.},
}

@article {pmid41093042,
year = {2025},
author = {Noordzij, HT and Wortel, MT and Heintz-Buschart, A and Petrikonyte, P and de Muinck, EJ and Trosvik, P},
title = {Assembly-based analysis of the infant gut microbiome reveals novel ubiquitous plasmids.},
journal = {Plasmid},
volume = {134},
number = {},
pages = {102761},
doi = {10.1016/j.plasmid.2025.102761},
pmid = {41093042},
issn = {1095-9890},
abstract = {Little is known about the role of mobile genetic elements in natural ecosystems such as the infant gut microbiome. Here, we conduct the most comprehensive longitudinal study of the infant plasmidome to date by analyzing monthly fecal samples from 12 infants from birth to one year of age. We employ an assembly-based bioinformatic pipeline for the reconstruction and identification of full-length plasmids, including a novel approach for assigning putative plasmid hosts. We then investigated plasmid content and dynamics in the infant gut microbiome. After assembly and identification, we identified 620 unique circular plasmids in the infant cohort, including a number of novel sequences. Independent assembly of the same plasmids in several samples and infants helped corroborate the authenticity of the plasmids. Among the observed plasmids was the recently described ubiquitous and abundant Bacteroides plasmid pBI143. Overall, the genus Bacteroides had the highest plasmid carriage, while the highest plasmid diversity was observed in Clostridium, including 5 previously unknown widespread plasmids. Lastly, we leveraged the longitudinal nature of our dataset to investigate contemporaneous correlations between temporal variations in plasmid abundances and species dynamics. This enabled us to link co-residing plasmids and tightly linked plasmid-taxon pairs within each infant. These insights into plasmid ecology help us understand determinants driving plasmid distribution in complex microbial communities.},
}

@article {pmid41093027,
year = {2025},
author = {Li, KY and Zhou, JL and Tian, ZH and Gao, F},
title = {N-acyl-homoserine lactone regulation of nutrient removal, microbial community assembly, and process efficacy in dialysis membrane-algal-bacterial photobioreactors.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133502},
doi = {10.1016/j.biortech.2025.133502},
pmid = {41093027},
issn = {1873-2976},
abstract = {Quorum sensing is a central mechanism by which signal bacteria sense and integrate signaling molecules to coordinate gene expression and physiological activities at the community level. To investigate how exogenous signal molecules regulate the maintenance of algal-bacterial symbiosis, this study constructed a dialysis membrane-coupled algal-bacterial photobioreactor and separately amended it with N-butyryl-l-homoserine lactone (C4-HSL), N-hexanoyl-l-homoserine lactone (C6-HSL), and N-(3-oxodecanoyl)-l-homoserine lactone (3-oxo-C10-HSL), systematically investigated their effects on nutrient removal, microbial community composition, and functional characteristics within the system. Compared with the control, all three N-acyl-homoserine lactones (AHLs) enhanced total nitrogen and total phosphorus removal and stimulated biomass (sludge) growth, while redirecting microalgal carbon allocation toward lipid accumulation; notably, the C6-HSL treatment achieved the highest nitrogen (80.39 %) and phosphorus (53.01 %) removal efficiencies. Metagenomic analyses revealed that exogenous AHLs exerted selective effects on the microbial assemblage, enriching dominant signal-responsive bacteria whose relative abundance was positively correlated with nitrogen and phosphorus removal performance. Furthermore, genes associated with nitrogen metabolism, the tricarboxylic acid cycle, and glycolysis were more abundant in the 3-oxo-C10-HSL and C6-HSL groups, indicating that strengthened metabolic coupling likely underpins the observed biomass increase and enhanced nutrient removal. Collectively, these findings demonstrate that AHL-mediated signaling is a key driver shaping algal-bacterial interactions, community assembly, and functional expression.},
}

@article {pmid41092906,
year = {2025},
author = {Wu, L and Li, Y and Wang, W and Deng, L and Ge, H and Cui, M and Bi, N},
title = {Gut microbiota predictive of the efficacy of consolidation immunotherapy and chemoradiotherapy toxicity in lung cancer.},
journal = {Med (New York, N.Y.)},
volume = {},
number = {},
pages = {100877},
doi = {10.1016/j.medj.2025.100877},
pmid = {41092906},
issn = {2666-6340},
abstract = {BACKGROUND: Gut microbiota (GM) predict responses to immune checkpoint inhibitors (ICIs) in patients with advanced lung cancer. However, its role in patients with locally advanced lung cancer undergoing chemoradiotherapy (CRT) combined with consolidation ICIs remains unclear.

METHODS: A total of 177 fecal samples were collected pre- and post-CRT. Using 16S ribosomal RNA (16S rRNA) sequencing and metagenomic data from an internal cohort and published studies, the kinetics of microbiota were analyzed using the Wilcoxon signed-rank test, while prognostic factors for progression-free survival (PFS) were identified using Cox regression modeling and machine learning algorithms.

FINDINGS: The GM configuration was unaffected by traditional CRT. However, in cases of CRT with consolidation ICIs, patients with long-PFS showed a higher alpha diversity at baseline, followed by a reduction during treatment, contrasting with the stable diversity observed in the short-PFS group. Enrichment of the symbiotic microbe Akkermansia muciniphila (Akk) after CRT was observed, with its increased abundance correlating with extended distant metastasis-free survival in patients undergoing CRT with consolidation ICIs. Notably, the trend in Akk variation was a prognostic indicator of survival outcomes in patients undergoing CRT combined with ICIs. GM was also involved in the development of treatment-related pneumonia and was a promising predictive marker for severe pneumonia.

CONCLUSIONS: CRT with consolidation ICIs has more pronounced effects on the GM than CRT alone in patients with locally advanced lung cancer. The dynamic variation in Akk has predictive potential for patient survival in this context.

FUNDING: This study was supported by the National Science and Technology Major Project.},
}

@article {pmid41092847,
year = {2025},
author = {Zhang, Y and Su, K and Munir, F and Wang, W and Liang, X and Wang, J and Hua, J and Ma, W},
title = {Gut microbiome metagenomics in diarrheic and healthy Simmental cattle from Ningxia Province, China.},
journal = {Research in veterinary science},
volume = {197},
number = {},
pages = {105922},
doi = {10.1016/j.rvsc.2025.105922},
pmid = {41092847},
issn = {1532-2661},
abstract = {INTRODUCTION: The gut microbiome plays a crucial role in health and disease. This study aims to investigate the composition, characteristics, and functional diversity of the intestinal microbiome by performing metagenomic sequencing on fecal samples from diarrheic and healthy Simmental cattle.

RESULTS: This study compared the gut microbiome differences between two groups of Simmental cattle (5 diarrheic and 20 healthy) in Ningxia province, China. Metagenomic analysis revealed higher microbial heterogeneity in the diarrheic group, likely reflecting pathogen-driven ecological disruption, whereas the healthy group was dominated by butyrate-producing and fiber-degrading bacteria, maintaining intestinal homeostasis. Antibiotic resistance gene analysis detected glycopeptide resistance genes in both groups, but the healthy group also carried aminoglycoside/tetracycline resistance genes and poxtA. KEGG pathway analysis showed that the diarrheic group was enriched in purine synthesis-related pathways, while the healthy group exhibited dominant metabolic pathways such as glutamine synthase. Virulence factor analysis indicated that the diarrheic group had higher abundances of capsular polysaccharides and type IV secretion systems, potentially promoting bacterial colonization and immune evasion. In summary, diarrheic cattle harbored a gut microbiome dominated by opportunistic pathogens, accompanied by metabolic dysregulation and antimicrobial resistance risks, whereas healthy cattle maintained a microbial community rich in short-chain fatty acid producers. This study provides a theoretical foundation for gut microbiome modulation and antimicrobial resistance control in ruminants.

CONCLUSION: This study revealed distinct gut microbiome composition and function between diarrheic and healthy cattle through sequencing analysis. The findings offer insights for ruminant diarrhea management and provide a basis for developing more scientific antibiotic management strategies in animal husbandry.},
}

@article {pmid41092755,
year = {2025},
author = {Hu, X and Gu, H and Wang, Y and Xu, Y and Li, Y and Yu, Z and Liu, J and Jin, J and Liu, X and Wang, G},
title = {Biodegradable microplastics show greater potential than conventional types in facilitating antibiotic resistance gene enrichment and transfer through viral communities.},
journal = {Environment international},
volume = {204},
number = {},
pages = {109855},
doi = {10.1016/j.envint.2025.109855},
pmid = {41092755},
issn = {1873-6750},
abstract = {Whether and how conventional (CP) and biodegradable microplastics (BP) affect viral communities and virus-carried antibiotic resistance genes (ARGs) in agricultural soils remains largely unknown. Here, we established a soil microcosm incubation with addition of 1 % (w/w) microplastics (MPs) in maize-cultivated soil that had been treated with different fertilizers for over 10 years, and the dynamic variations of viral communities and ARG profiles were investigated using a combination of metagenomic and metatranscriptomic methods. Our results revealed that BP, but not CP, significantly decreased viral α-diversity, changed viral community structure, community resistance and taxonomic turnover in all fertilized treatments. Caudoviricetes was the most dominate viral class and BP significantly increased the abundances of viral families (i.e. Phycodnaviridae) in all fertilized treatments, while CP altered the viral family abundance mainly observed in manure-amended soils. Also, BP was associated with increased ARG α-diversity, altered ARG community structure and community resistance, especially at the transcriptional level. Particularly, BP significantly enriched high-risk ARGs and mobile genetic elements (MGEs) in soils regardless of fertilization regimes. Correlation analysis revealed the important role of lytic viruses in shaping the abundance of high-risk ARGs and MGEs. Furthermore, BP induced more variations in reconstructed metagenome-assembled genome (MAGs), and significantly enriched high-risk ARGs carried by phage genomes. Co-occurrence patterns revealed three Actinobacteriota MAGs as primary viral hosts sharing high-risk ARGs with phages and containing multiple MGEs. Notably, we identified four viral genomes carrying ARG transcripts identical to their hosts. Both CP and BP differentially stimulated ARG expression in these virus-host systems, withmarkedlystronger effects observed in manure-amended soils. In conclusion, this study revealed a high risk of ARG dissemination induced by biodegradable MP residues regardless of fertilization regimes, while conventional MPs strengthen the ARG health risks mainly in manure-amended soils.},
}

@article {pmid41092742,
year = {2025},
author = {Norgan, AP and Sadiq, Q and Fedyshyn, B and Wolf, MJ and Enninga, EAL},
title = {Pan-viral metagenomic sequencing demonstrates that cryptic viral infection is rarely observed in villitis of unknown etiology.},
journal = {Placenta},
volume = {171},
number = {},
pages = {205-209},
doi = {10.1016/j.placenta.2025.10.009},
pmid = {41092742},
issn = {1532-3102},
abstract = {INTRODUCTION: Aberrant maternal immune responses are implicated in villitis of unknown etiology (VUE), but the underlying cause of this loss of tolerance, including cryptic causative or precipitating infections, has been difficult to define. Herein, we performed pan-viral metagenomic sequencing of placentas with VUE to investigate the possibility of cryptic viral infection as a contributing factor in this inflammatory pathology.

METHODS: Placentas evaluated at a single tertiary medical center between 2010 and 2024 were included in this study. Overall, the cohort included infectious villitis due to cytomegalovirus (CMV; n = 4), VUE (n = 25), and a reference group composed of pathologically unremarkable placentas (n = 17). Total nucleic acid was extracted from formalin-fixed paraffin embedded (FFPE) placental tissues and subjected to pan-viral metagenomic sequencing (PVMS) to identify viral-associated reads.

RESULTS: PVMS detected reads mapping to CMV in 4 (of 4) of CMV cases. For VUE cases, 22 (of 25) had no identifiable viral reads, while 1 case demonstrated CMV reads and two had papillomavirus reads. The control samples demonstrated no identifiable reads in 13 (of 17) samples, while 3 cases had reads mapping to human papillomavirus 16 and one case had reads mapping to human Herpesvirus 6.

DISCUSSION: Utilizing PVMS, we did not identify cryptic viral sequences in 88 % of morphologic VUE cases. In one clinical VUE case, CMV sequences were identified, suggesting a misclassification of infectious villitis. Both papillomavirus and herpesvirus sequences have previously been identified in the placenta, with unknown clinical significance. Overall, these findings exclude active viral infection as a potential etiology of VUE.},
}

@article {pmid41092730,
year = {2025},
author = {Wang, Y and Wen, S and Yu, Q and Huang, H and Tang, Y and Miao, C and Xia, Y and Guan, F},
title = {Microbiologically influenced corrosion of oil-water pipeline steel from local field failure case to specific Shewanella & Desulfovibrio corrosion highlights the significance of hydrocarbon-degrading bacteria.},
journal = {Bioelectrochemistry (Amsterdam, Netherlands)},
volume = {168},
number = {},
pages = {109129},
doi = {10.1016/j.bioelechem.2025.109129},
pmid = {41092730},
issn = {1878-562X},
abstract = {Unconventional natural gas pipeline corrosion is associated with microbes, especially sulfate-reducing bacteria (SRB), though it is uncertain if SRB's role is overemphasized. Using metagenomics, corrosion immersion, and microbial cultivation, diverse hydrocarbon-degrading microorganisms, such as Shewanella, in corroded pipeline rust layers, oil-water mixtures, and produced water from unconventional natural gas fields are identified. These bacteria use crude oil as a carbon source, accelerating pitting corrosion of carbon steel and forming corrosion product films (Pitmax = 28.96 μm). The 16S rRNA sequencing results show that Shewanella, prevalent in various steel service environments, is a potential key microorganism in pipeline corrosion. X70 steel exhibits lower electron transfer resistance than Desulfovibrio in the Shewanella medium. Shewanella's aerobic respiration degrades crude oil and oxidizes iron, speeding up iron oxide formation and magnesium phosphate precipitation. Microbial acidification of the oil-water medium also contributes to severe pitting corrosion beneath the oil film. Crude oil accelerates microbial growth. Thus, studying carbon steel corrosion in oil-water environments must consider the impact of hydrocarbon-degrading microorganisms.},
}

@article {pmid41092706,
year = {2025},
author = {Zhang, X and Yang, B and Zhang, H and Guo, X and Zhang, Y},
title = {Nicosulfuron-driven antibiotic resistance in corn silage: Effect and its mitigation by zinc oxide nanoparticles.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140119},
doi = {10.1016/j.jhazmat.2025.140119},
pmid = {41092706},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs) present in animal feed represent a significant threat to human health via the food chain, and pesticide application in crop production may further accelerate the ARGs dissemination. Corn silage, a primary forage for herbivorous livestock, has been shown to harbor diverse ARGs; however, the impact of pesticide-induced stress and potential mitigation strategies on ARG proliferation remains poorly understood. This study investigated the mechanistic link between nicosulfuron exposure and ARG dynamics in corn silage, as well as the mitigating effects of zinc oxide nanoparticles (ZnO NPs) on ARG under nicosulfuron exposure using metagenomic sequencing and high-throughput quantitative PCR. Nicosulfuron exposure increased (P < 0.05) ARG diversity and abundance, enriched (P < 0.05) ARG-hosting genera such as Pantoea, Escherichia, and Klebsiella, and intensified (P < 0.05) the correlation between ARGs and mobile genetic elements (MGEs). Additionally, it disrupted microbial metabolic pathways and elevated (P < 0.05) the ARG-associated risk index in corn silage. Conversely, ZnO NPs alleviated (P < 0.05) these effects by reducing the abundance of key ARGs-bacA, tetM, and ermB, enhancing microbial diversity, promoting beneficial genera such as Levilactobacillus and Companilactobacillus, and decreasing the complexity of ARG-MGE-microbe co-occurrence networks in corn silage under nicosulfuron exposure. Structural equation modeling indicated that there was a significant association between bacterial community and ARGs proliferation, and it had the strongest explanatory power for the variation in ARGs abundance, followed by MGEs. These findings underscore the ecological risks associated with nicosulfuron and demonstrate that ZnO NPs have the potential to mitigate ARGs dissemination in pesticide-contaminated silage. However, this potential does not qualify ZnO NPs as an effective strategy, and their role in promoting safer forage production still requires further evaluation.},
}

@article {pmid41092232,
year = {2025},
author = {Meneguzzi, M and Bravo, J and Gaire, TN and Ferm, PM and Torremorell, M and Boucher, C and Noyes, NR},
title = {Enriched Long-Read Sequencing of Co-circulating Viruses in Complex Samples.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf261},
pmid = {41092232},
issn = {1537-1719},
abstract = {At present, no single workflow is available for quick and accurate identification and analysis of genomes of various viruses present together in a field or clinical sample, particularly when followed by long-read sequencing. Our work addressed this limitation by combining targeted enrichment with long-read, real-time sequencing. Using a panel of probes targeting 16,069 complete viral genomes, we validated this workflow (termed TELSVirus) on complex sample matrices collected from pigs, and compared its performance to traditional methods including rRT-PCR and shotgun metagenomics. Using serial dilutions of samples with known viral status, we observed that TELSVirus generated viral reads for dilutions up to 10-9. TELSVirus was able to detect viral targets when shotgun metagenomic long- and short-read datasets did not, and when rRT-PCR results were undetermined. Finally, we performed TELSVirus on 144 oral fluid samples collected in the field, which are highly complex and diverse samples used for viral surveillance in swine. We identified a high prevalence of relatively understudied viruses, often found co-circulating with better-characterized viruses. In many cases, TELSVirus generated ultra-deep genome coverage, allowing for further genomic epidemiological investigations, although bioinformatic methods need further development to work robustly with TELSVirus data. Our results support using TELSVirus for rapid detection and genomic characterization of multiple low-abundance viruses from single samples using long-read sequencing.},
}

@article {pmid41091222,
year = {2025},
author = {Tajdozian, H and Seo, H and Kim, S and Rahim, MA and Park, HA and Sarafraz, F and Yoon, Y and Kim, H and Barman, I and Park, CE and Ghorbanian, F and Lee, S and Jeong, HR and Song, HY},
title = {Microbiome therapeutic PMC101 inhibits the translocation of carbapenem-resistant Klebsiella while enhancing eubiosis in antibiotic-induced dysbiosis mice.},
journal = {Medical microbiology and immunology},
volume = {214},
number = {1},
pages = {49},
pmid = {41091222},
issn = {1432-1831},
support = {No. RS-2023-00219563//Ministry of Science and ICT, South Korea/ ; P248400003//Korea Institute for Advancement of Technology/ ; },
mesh = {Animals ; *Dysbiosis/chemically induced/microbiology/therapy ; *Carbapenem-Resistant Enterobacteriaceae/drug effects/physiology ; *Anti-Bacterial Agents/adverse effects/pharmacology ; Mice ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; *Klebsiella Infections/microbiology/therapy ; *Bacterial Translocation/drug effects ; Carbapenems/pharmacology ; Humans ; Mice, Inbred C57BL ; Feces/microbiology ; },
abstract = {Carbapenem-resistant Enterobacteriaceae (CRE), known for their extensive antibiotic resistance, pose a severe global medical threat. Therefore, developing novel therapeutics beyond conventional antibiotics is urgently needed, and the importance of microbiome therapeutics is increasingly being recognized. This study explores the expanded systemic efficacy of PMC101, a microbiome therapeutic, beyond intestinal CRE infections and investigates its mechanism of action from a microbiome perspective. First, the genetic characteristics of the novel strain were identified through whole-genome analysis, and a scalable cultivation process was established as part of the overall development of this microbiome therapeutic. PMC101 increased the survival rate to 100%, significantly reduced disease severity scores, and prevented weight loss in CRE-infected mice treated with antibiotics. These effects are attributed to the inhibition of CRE growth in stool and the reduced detection of CRE in the lungs and kidneys, indicating suppression of systemic translocation. Metagenomic analysis revealed that PMC101 prevented the reduction in microbial population caused by antibiotics and CRE infection, restored species diversity indices, and mitigated dysbiosis while promoting eubiosis. This CRE translocation suppression was closely associated with increased CRE translocation-microbiome index, defined as the ratio of Bacteroidetes to Proteobacteria. This relationship was further confirmed through simulations using a human intestinal microbial ecosystem model. Additionally, increases in short-chain fatty acids, reductions in excessive inflammatory responses, and decreases in tissue damage were observed, all of which contribute to preventing CRE translocation. Finally, pathogen inhibition effects and safety tests were conducted, confirming the prophylactic potential of PMC101 as a microbiome therapeutic. These findings strongly support PMC101 as a promising candidate for future microbiome-based therapies against CRE infections.},
}

Animals
*Dysbiosis/chemically induced/microbiology/therapy
*Carbapenem-Resistant Enterobacteriaceae/drug effects/physiology
*Anti-Bacterial Agents/adverse effects/pharmacology
Mice
*Gastrointestinal Microbiome/drug effects
Disease Models, Animal
*Klebsiella Infections/microbiology/therapy
*Bacterial Translocation/drug effects
Carbapenems/pharmacology
Humans
Mice, Inbred C57BL
Feces/microbiology

@article {pmid41089932,
year = {2025},
author = {Zhang, W and Guo, H and Xu, W and Chen, W and Hu, Y and Wang, Z},
title = {Di-(2-ethylhexyl) phthalate-degrading functional microorganisms were identified in black soil based on high throughput analysis.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100479},
pmid = {41089932},
issn = {2666-5174},
abstract = {Di-(2-ethylhexyl) phthalate (DEHP) has become an increasingly serious pollutant in soils. Microbial degradation represents a highly promising approach for its remediation. In this study, four black soils were used to simulate the natural degradation of DEHP over a 75-day microenvironmental experiment. High-throughput analysis was conducted to investigate the distribution and abundance of functional genes in soil microorganisms, aiming to explore functional microbial information. The degradation efficiency of DEHP in black soils was 76.37 %, 74.16 %, 92.21 %, and 75.35 %. The α-diversity of microbial community was positively correlated with the degradation rate. Actinobacteria and Proteobacteria exhibited sensitivity to DEHP contamination. Xanthomonaceae, Sphingomonadaceae, Hypomicrobiaceae, and Comamonadaceae contributed to the upstream metabolism of DEHP. The abundances of Rhodococcus, Sphingomonas, Nocardioides, and Arthrobacter were positively correlated with the abundance of functional genes enriched in the black soil for benzoate degradation. Concurrently, 10 DEHP-degrading bacterial communities were identified, and the taxonomic and functional profiles of certain members within these communities were consistent with the metagenomic data. Bacterial communities JQ104, JQ52, and JQ129 degraded >98 % of DEHP (400 mg/L) in 48 h, demonstrating remarkable degradation efficiency. This study demonstrated the dynamic impact of the indigenous microbiome on DEHP contamination and verified the degradation capabilities of key functional microorganisms.},
}

@article {pmid41089718,
year = {2025},
author = {Takahashi, Y and Fujitani, H and Taniguchi, I and Gotoh, Y and Shimada, Y and Ikeda, S and Hayashi, T and Tago, K and Hayatsu, M and Tsuneda, S},
title = {Acid tolerance and metabolic potential of comammox and nitrite-oxidizing Nitrospira enriched from soil.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf167},
pmid = {41089718},
issn = {2730-6151},
abstract = {Nitrification is the two-step microbial oxidation of ammonia to nitrate via nitrite, and it can contribute to environmental problems in soils. Some nitrifiers have been cultivated from acidic soils at pH <5.5, allowing their metabolic potential and phylogeny to be investigated through genomic analyses. However, the genomic features of the genus Nitrospira remain poorly understood in the context of acid tolerance, despite its wide distribution in acidic environments. This study aimed to characterize the physiology and genomics of acid-tolerant Nitrospira enriched from an acidic soil. Using a metagenomic approach, two closed genomes of Nitrospira were reconstructed: a complete ammonia-oxidizing (comammox) bacterium and a nitrite-oxidizing bacterium (NOB). Both enriched Nitrospira survived at pH <5.5 in physiological tests, and the enriched comammox Nitrospira was phylogenetically close to clones derived from acidic soils. The active-site residues of hydroxylamine oxidase, a key nitrification enzyme, were conserved between the comammox Nitrospira characterized in this study and the previously reported betaproteobacterial ammonia oxidizers. This conservation suggests that existing nitrification inhibitors targeting this enzyme may also inhibit ammonia oxidation by comammox Nitrospira in acidic soils. Although the comammox and NOB Nitrospira in this study shared nearly all key metabolic pathways with Nitrospira species identified from neutral pH environments, both possessed passive urea transporters homologous to those found in acid-tolerant bacteria. These results revealed the acid tolerance of the enriched Nitrospira at pH <5.5, as well as their genomic features shared with acid-tolerant bacteria, rather than with previously reported Nitrospira species.},
}

@article {pmid41089454,
year = {2025},
author = {Hu, X and He, Z and Liu, C and Zhang, Y and Mu, D and Guskov, VY and Wang, K and Yao, Y and Jin, D and Lu, J and Ning, Y and Jiang, G},
title = {Revealing Amur tiger family pedigrees based on age identification using fecal microbiome and kinship analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1666201},
pmid = {41089454},
issn = {1664-302X},
abstract = {INTRODUCTION: The construction of a species' family pedigree is crucial for understanding population structure, assessing genetic diversity, and conserving the genetic resources of endangered species. However, developing non-invasive and reliable methods for age identification in wild individuals remains a significant challenge in family pedigree establishments.

METHODS: In this study, we employed 16S rRNA sequencing and metagenomic analysis to examine 30 fecal samples collected from captive Amur tigers across three distinct age groups, aiming to identify the age-specific biomarker, which could subsequently facilitate age determination of wild individuals and support the construction of species pedigree.

RESULTS: Our results demonstrate that, through 16S rRNA high-throughput sequencing, 16 potential microbial age biomarkers were identified in fecal samples from captive Amur tigers, and the ages of 17 captive individuals were distinguished. Notably, f_Erysipelotrichaceae_Unclassified and Paraclostridium, identified as potential age-associated bacterial markers in captive Amur tigers, were also detected in fecal samples from wild individuals of this species. To explore their potential application in age inference for Amur tigers, we integrated genetic relationship analysis with these potential age-specific biomarkers to construct a comprehensive pedigree of wild Amur tigers.

DISCUSSION: This study established a comprehensive scientific framework for pedigree reconstruction based on age determination in Amur tigers and developed a scalable, non-invasive methodology offering opportunities for population structure and promoting the precision of conservation for wild tigers.},
}

@article {pmid41089363,
year = {2025},
author = {Park, T and Praisler, G and Wenner, BA},
title = {Treatment of dual-flow continuous culture fermenters with an organic essential oil product minimally influenced prokaryotic microbiome.},
journal = {Journal of animal science and technology},
volume = {67},
number = {5},
pages = {1018-1032},
pmid = {41089363},
issn = {2055-0391},
abstract = {Previous research reported an essential oil (EO) product decreasing methane (CH4) production by dual-flow continuous culture (DFCC); this product could assist organic dairy producers in decreasing emissions. Our objective was to assess the effect of this EO product on the microbial populations within DFCC. Here, we hypothesized that the EO either decreased protozoal population or induced shifts in the bacterial relative abundance to decrease CH4 production. Metagenomic DNA was extracted from previous effluent samples taken from a DFCC system (n = 2) across four experimental periods, after which samples were sequenced the 16S rRNA gene and microbial taxonomy was assigned using the SILVA v138 database. The treatments included a control (CON) diet (60:40 concentrate:orchardgrass pellet mix, 17.1% crude protein, 33.0% neutral detergent fiber, 20.1% acid detergent fiber, and 27.1% starch) fed twice daily for a total of 80 g/d dry matter, or the same CON diet with the addition of EO at 3 mg/d. Protozoa were also quantified in both fermenter contents and unpooled daily effluent samples. The statistical model included fixed effects of treatment and fermenter, and random effect of period, using either MaAsLin2 or the adonis2 function in the vegan package of R for microbial features, or SAS mixed model for protozoal counts. The results were deemed significant at Q < 0.05 and p < 0.05 for the MaAsLin2 and adonis2/SAS analyses, respectively. For the protozoal populations, the treatments had no significant effect (p > 0.10) on the total counts, differentiated groups, or cell outflow. The addition of EO increased the relative abundance of Methanobrevibacter and decreased that of uncultured Methanomethylophilaceae (Q < 0.05). In contrast, EO addition had no significant effect on archaeal α- or β-diversity (p > 0.05). Despite not having a significant effect on the β-diversity of archaeal and bacterial communities, EO decreased (p < 0.05) α-diversity indices in prokaryotic communities. Moreover, EO decreased (Q < 0.01) the relative abundance of Clostridia UCG-014, Rikenellaceae RC9 gut group, and Christenellaceae R7 group, and increased (Q < 0.01) others including Treponema, Succinivibrionaceae UCG-002, and Ruminococcus. Offsetting shifts in the relative abundance of fiber-degrading bacteria and detailed methanogen communities deserves further investigation including predicted metabolic pathways impacted by population shifts induced by this EO combination.},
}

@article {pmid41089014,
year = {2025},
author = {Li, B and Xu, F and Xia, M and Li, X and Hou, X and Lyu, X and Guo, X},
title = {[Retrospective clinical analysis of 31 cases of necrotizing fasciitis of the neck with or without descending necrotizing mediastinitis].},
journal = {Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology head and neck surgery},
volume = {39},
number = {10},
pages = {971-975},
doi = {10.13201/j.issn.2096-7993.2025.10.014},
pmid = {41089014},
issn = {2096-7993},
mesh = {Humans ; Retrospective Studies ; *Fasciitis, Necrotizing/complications/therapy ; *Mediastinitis/complications ; *Neck/pathology ; Male ; Female ; Middle Aged ; Adult ; Aged ; Prognosis ; },
abstract = {Objective:To summarize the clinical characteristics and management experience of complications in patients with cervical necrotizing fasciitis （CNF） with or without descending necrotizing mediastinitis （DNM）, in order to provide a basis for optimizing diagnosis and treatment strategies. Methods:A retrospective analysis was conducted on the clinical data of 31 patients diagnosed with CNF and DNM at Shandong Provincial Hospital Affiliated to Shandong First Medical University between October 2019 and March 2024. A comprehensive evaluation was performed based on the patients' clinical characteristics, metagenomic next-generation sequencing （mNGS） pathogen detection results, imaging assessments, surgical interventions, management approaches for specific complications, and prognostic outcomes. Results:Among the 31 patients, 10 had severe diabetes mellitus. Etiological analysis was summarized as follows: 5 cases were odontogenic, 3 were of tonsillar origin, 3 were due to endogenous esophageal injury, 2 were due to exogenous cervical trauma, 2 originated from a congenital branchial cleft fistula, and 16 cases had an unknown etiology. Among them, 29 patients underwent surgery via an external cervical approach, 1 patient underwent surgery via an intraoral approach, and 1 patient received ultrasound-guided puncture and drainage therapy. Ultimately, 29 patients were cured and discharged （including 1 patient who experienced two instances of major neck vessel rupture and successfully underwent two interventional embolization procedures for hemostasis）; 2 patients died after failed rescue efforts due to concurrent sepsis and multiple organ dysfunction. The treatment success rate was 93%, and the mortality rate was 7%. In this cohort of CNF and DNM cases, only a minority had a clearly identified odontogenic cause; although the etiology was unknown in most cases, imaging consistently showed oropharyngeal lymph node necrosis, suggesting a possible pharyngeal origin of infection in adults. The mNGS pathogen profile was predominantly Gram-positive bacteria, accompanied by anaerobic bacilli and fungi. Conclusion:CNF and DNM are severe and rapidly progressive conditions that can lead to life-threatening complications within hours. Timely recognition can reduce unnecessary examinations and expedite treatment.},
}

Humans
Retrospective Studies
*Fasciitis, Necrotizing/complications/therapy
*Mediastinitis/complications
*Neck/pathology
Male
Female
Middle Aged
Adult
Aged
Prognosis

@article {pmid41088813,
year = {2025},
author = {Guo, YN and De, R and Wang, FM and Han, ZZ and Liu, LY and Sun, Y and Yao, Y and Ma, XL and Liu, S and Zhu, C and Qu, D and Zhao, LQ},
title = {Molecular Characterization of New Recombinant Human Adenoviruses Detected in Children with Acute Respiratory Tract Infections in Beijing, China, 2022-2023.},
journal = {Biomedical and environmental sciences : BES},
volume = {38},
number = {9},
pages = {1071-1081},
doi = {10.3967/bes2025.105},
pmid = {41088813},
issn = {2214-0190},
mesh = {Humans ; *Adenoviruses, Human/genetics/classification/isolation & purification ; *Respiratory Tract Infections/virology/epidemiology ; Child, Preschool ; Child ; *Recombination, Genetic ; Male ; Beijing/epidemiology ; Infant ; Female ; Phylogeny ; *Adenovirus Infections, Human/virology/epidemiology ; Acute Disease ; Genome, Viral ; },
abstract = {OBJECTIVE: Recombination events are common and serve as the primary driving force of diverse human adenovirus (HAdV), particularly in children with acute respiratory tract infections (ARIs). Therefore, continual monitoring of these events is essential for effective viral surveillance and control.

METHODS: Respiratory specimens were collected from children with ARIs between January 2022 and December 2023. The penton base, hexon, and fiber genes were amplified from HAdV-positive specimens and sequenced to determine the virus type. In cases with inconsistent typing results, genes were cloned into the pGEM-T vector to detect recombination events. Metagenomic next-generation sequencing (mNGS) was performed to characterize the recombinant HAdV genomes.

RESULTS: Among 6,771 specimens, 277 (4.09%, 277/6,771) were positvie for HAdV, of which 157 (56.68%, 157/277) were successfully typed, with HAdV-B3 being the dominant type (91.08%, 143/157), and 14 (5.05%, 14/277) exhibited inconsistent typing results, six of which belonged to species B. The penton base genes of these six specimens were classified as HAdV-B7, whereas their hexon and fiber genes were classified as HAdV-B3, resulting in a recombinant genotype designated P7H3F3, which closely resembled HAdV-B114. Additionally, a partial gene encoding L1 52/55 kD was identified, which originated from HAdV-B16.

CONCLUSION: A novel recombinant, P7H3F3, was identified, containing sequences derived from HAdV-B3 and HAdV-B7, which is similar to HAdV-B114, along with additional sequences from HAdV-B16.},
}

Humans
*Adenoviruses, Human/genetics/classification/isolation & purification
*Respiratory Tract Infections/virology/epidemiology
Child, Preschool
Child
*Recombination, Genetic
Male
Beijing/epidemiology
Infant
Female
Phylogeny
*Adenovirus Infections, Human/virology/epidemiology
Acute Disease
Genome, Viral

@article {pmid41088467,
year = {2025},
author = {Osburn, ED and Weissman, JL and Strickland, MS and Bahram, M and Stone, BW and McBride, SG},
title = {Relative abundances of bacterial phyla are strong indicators of community-scale microbial growth rates in soil.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {131},
pmid = {41088467},
issn = {2524-6372},
support = {2131837//National Science Foundation/ ; 2020-67034-41310//National Institute of Food and Agriculture/ ; },
abstract = {BACKGROUND: To improve our understanding of microbial systems, it is essential to refine the conceptual frameworks that connect microorganisms to their ecological functions. While trait-based approaches can provide nuanced perspectives on how microorganisms influence ecosystem processes, there is ongoing debate over the link between microbial taxonomic classifications and life history traits. Here, we integrate genomic, metagenomic, amplicon sequencing, and experimental (stable isotope probing) data to investigate the scaling of bacterial growth traits from individual taxa to complex assemblages and to identify specific taxonomic groups of soil bacteria that can be used as indicators of community-scale microbial growth.

RESULTS: Our results revealed broadly different distributions of growth rates among bacterial phyla, including significantly different mean and median rates. This, in turn, manifested in strong relationships between relative abundances of some phyla and community-scale growth rates in soil. Specifically, we calculated community weighted mean growth rates using measured growth rates of constituent taxa and found that the fast-growing taxa that had sufficient abundance and ubiquity across samples to contribute to variation in community-average growth were mostly lineages of Proteobacteria (e.g., Sphingomonas). As a result, the relative abundance of phylum Proteobacteria was the single strongest taxonomic predictor of community-average growth, explaining up to ~ 60% of the variation in growth rates across communities. In contrast, Verrucomicrobia were consistent indicators of slower community-average growth. These patterns were especially strong when using taxon-level growth rates measured following carbon and nitrogen additions to soil.

CONCLUSIONS: Our results demonstrate that phylum relative abundances can be strong indicators of community-level bacterial growth despite the wide variation in growth rates observed within phyla. The stronger phylum-growth relationships for whole assemblages than are apparent for individual taxa are due to relative abundance-weighted trait averaging in complex assemblages, i.e., at the community scale, broad differences in growth traits among phyla become more important than variation within phyla. Overall, our results provide clarity regarding the use of bacterial taxonomic information for inferring traits, demonstrating that high taxonomic ranks can be valid indicators of microbial traits in soil provided that inferences are drawn at the appropriate scale.},
}

@article {pmid41088378,
year = {2025},
author = {Chen, Z and Jia, Y and Li, H and Fan, R and Cao, Y and Ni, L and Yang, L and Yuan, Z and Zhu, K and Gao, Y and Lin, Y},
title = {Effects of zacopride and multidimensional impacts of cross-kingdom symbiosis: gut microbiota modulates coronary microvascular dysfunction via the chlorophyll/heme-tryptophan metabolic axis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1097},
pmid = {41088378},
issn = {1479-5876},
support = {20210302123485//Fundamental Research Program of Shanxi Province/ ; BYJL065//Shanxi Province Higher Education "Billion Project" Science and Technology Guidance Project/ ; NSFC-82102104//National Natural Science Foundation of China/ ; 2021M702054//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats, Sprague-Dawley ; *Tryptophan/metabolism ; Male ; *Symbiosis/drug effects ; *Benzamides/pharmacology/therapeutic use ; *Coronary Vessels/drug effects/physiopathology ; *Microvessels/drug effects/physiopathology ; Rats ; *Microcirculation/drug effects ; },
abstract = {BACKGROUND: Coronary Microvascular Dysfunction (CMD) represents a critical pathological substrate for ischemic heart disease and is strongly associated with major adverse cardiovascular events. Zacopride, known for its dual cardiovascular regulatory properties targeting the 5-HT4 receptor and Kir2.1 channel, lacks evidence regarding its systemic impact on the gut microbiota-metabolism axis. Therefore, this study aims to elucidate the structural and metabolic characteristics of gut bacteria and fungi in CMD, and to explore the multidimensional therapeutic mechanisms of Zacopride through "microbial remodeling-metabolic regulation-microcirculation repair."

METHODS: Sixty Sprague-Dawley rats were randomized into three groups: coronary microvascular dysfunction (CMD), healthy control (NC), and Zacopride intervention (ZAC). CMD and ZAC groups received high-fat diet plus streptozotocin (STZ, 35 mg/kg) for modeling. ZAC rats were orally administered 5 mg/kg Zacopride daily for 7 days. Transthoracic Doppler echocardiography measured left anterior descending coronary artery resting/stress peak flow velocity and coronary flow reserve (CFR). Ileocecal contents underwent bacterial-fungal metagenomic sequencing to identify differential metabolic pathways. Spearman's correlation assessed cross-kingdom ecological interactions. Nine machine learning algorithms constructed classification models, with Random Forest (RF) and an optimal model identifying key genera. Linear Discriminant Analysis Effect Size validated microbial biomarkers.

RESULTS: Zacopride partially restored the CFR in CMD rats, demonstrating a therapeutic effect, and exerted a beneficial influence on the structure and diversity of the gut microbiota. The CMD state significantly reduced the expression levels of the Chlorophyll a and tryptophan metabolic pathways in the gut microbiota. Zacopride specifically restored the Chlorophyll a pathway but did not significantly recover the tryptophan metabolic pathway. RF and Elastic Net (ENET) identified JC017, Chromelosporium, and Barnesiella as biomarker microbiota for CMD. Notably, JC017 primarily mediate the therapeutic effects of Zacopride via direct or indirect modulation of the Chlorophyll a metabolic pathway. Chromelosporium, acting as an interactive hub between fungi and bacteria, formed a cross-kingdom symbiotic relationship with Bradyrhizobium. Additionally, the reduction in Barnesiella abundance constitutes a distinctive feature of gut microbial dysbiosis in CMD.

CONCLUSION: This study provides the first evidence that the gut microbiota modulates the pathogenesis of CMD through the "chlorophyll/heme-tryptophan metabolic axis." Furthermore, we demonstrate that Zacopride exerts therapeutic effects by remodeling microbiota-host interactions and regulating this metabolic axis, revealing a novel mechanistic link between microbial metabolism and CMD progression.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Rats, Sprague-Dawley
*Tryptophan/metabolism
Male
*Symbiosis/drug effects
*Benzamides/pharmacology/therapeutic use
*Coronary Vessels/drug effects/physiopathology
*Microvessels/drug effects/physiopathology
Rats
*Microcirculation/drug effects