@article {pmid41062543,
year = {2025},
author = {Prast-Nielsen, S and Granström, AL and Kiasat, A and Ahlström, G and Edfeldt, G and Rautiainen, S and Boulund, F and Andersson, FO and Lindberg, J and Schuppe-Koistinen, I and Gustafsson, UO and Engstrand, L},
title = {Associations of the intestinal microbiota with plasma bile acids and inflammation markers in Crohn's disease and ulcerative colitis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {35039},
pmid = {41062543},
issn = {2045-2322},
mesh = {Humans ; *Bile Acids and Salts/blood ; *Gastrointestinal Microbiome ; *Crohn Disease/blood/microbiology ; *Colitis, Ulcerative/blood/microbiology ; Female ; Male ; Adult ; Biomarkers/blood ; Middle Aged ; *Inflammation/blood ; Case-Control Studies ; Feces/microbiology ; },
abstract = {Our study explores signatures for Crohn's disease (CD) and Ulcerative Colitis (UC) reflecting an interplay between the intestinal microbiota, systemic inflammation, and plasma bile acid homeostasis. For this, 1,257 individuals scheduled for colonoscopy were included and completed a comprehensive questionnaire. Individuals with IBD ('CD' n = 64 and 'UC' n = 55), were age- and gender-matched to controls without findings during colonoscopy. Shotgun metagenomic profiles of the fecal microbiota and plasma profiles of inflammatory proteins and bile acids were used to build disease classifiers. Omics integration identified associations across datasets. B. hydrogenotrophica was associated with CD and C. eutactus, C. sp. CAG167, B. cellulosilyticus, C. mitsuokai with controls. Ten inflammation markers were increased in CD, and eleven bile acids and derivatives were decreased in CD, while 7a-Hydroxy-3-oxo-4-cholestenoate (7-HOCA) and chenodeoxycholic acid (CDCA) were increased compared to controls.In UC, commensals such as F. prausnitzii and A. muciniphila were depleted. CCL11, IL-17A, and TNF were increased in UC and associated to gut microbial changes. Correlations between taxa and bile acids were all positive. For both CD and UC, taxonomic differences were primarily characterized by a reduction in commensal gut microbes which exhibited positive correlations with secondary bile acids and negative correlations with inflammation markers.},
}

Humans
*Bile Acids and Salts/blood
*Gastrointestinal Microbiome
*Crohn Disease/blood/microbiology
*Colitis, Ulcerative/blood/microbiology
Female
Male
Adult
Biomarkers/blood
Middle Aged
*Inflammation/blood
Case-Control Studies
Feces/microbiology

@article {pmid41062510,
year = {2025},
author = {Feng, S and Zhang, B and Wang, H and Xiong, Y and Tian, A and Yuan, X and Pan, C and Guo, X},
title = {Enhancing peptide identification in metaproteomics through curriculum learning in deep learning.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8934},
pmid = {41062510},
issn = {2041-1723},
support = {R15LM013460//U.S. Department of Health & Human Services | NIH | U.S. National Library of Medicine (NLM)/ ; R01AT011618//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; R01AT011618//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; },
mesh = {*Deep Learning ; *Proteomics/methods ; *Peptides/analysis ; Humans ; Gastrointestinal Microbiome ; Neural Networks, Computer ; Databases, Protein ; Metagenome ; },
abstract = {Metaproteomics offers a powerful window into the active functions of microbial communities, but accurately identifying peptides remains challenging due to the size and incompleteness of protein databases derived from metagenomes. These databases often contain vastly more sequences than those from single organisms, creating a computational bottleneck in peptide-spectrum match (PSM) filtering. Here we present WinnowNet, a deep learning-based method for PSM filtering, available in two versions: one using transformers and the other convolutional neural networks. Both variants are designed to handle the unordered nature of PSM data and are trained using a curriculum learning strategy that moves from simple to complex examples. WinnowNet consistently achieves more true identifications at equivalent false discovery rates compared to leading tools, including Percolator, MS[2]Rescore, and DeepFilter, and outperforms filters integrated into popular analysis pipelines. It also uncovers more gut microbiome biomarkers related to diet and health, highlighting its potential to support advances in personalized medicine.},
}

*Deep Learning
*Proteomics/methods
*Peptides/analysis
Humans
Gastrointestinal Microbiome
Neural Networks, Computer
Databases, Protein
Metagenome

@article {pmid41062486,
year = {2025},
author = {Tu, Z and Sun, H and Wang, T and Liu, Y and Xu, Y and Peng, P and Qin, S and Tu, C and He, B},
title = {Node role of wild boars in virus circulation among wildlife and domestic animals.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {8938},
pmid = {41062486},
issn = {2041-1723},
mesh = {Animals ; *Sus scrofa/virology ; *Animals, Wild/virology ; Swine/virology ; *Animals, Domestic/virology ; China/epidemiology ; Disease Reservoirs/virology ; Virome/genetics ; Humans ; *Viruses/genetics/classification/isolation & purification ; *Swine Diseases/virology ; Zoonoses/virology ; Phylogeny ; },
abstract = {Wild boars are considered pest animals in most of their distribution ranges, but their role as virus reservoirs has long been overlooked, with the circulation dynamics of their viruses rarely investigated. Here we prepared a data set, that is, BrCN-Virome, of 9281 viral metagenomes by pan-viromic analyses of 2535 organ and 274 blood samples from 466 healthy and 50 dead wild boars across 127 locations in 26 provincial regions of China. Compared to domestic pigs, BrCN-Virome shows different viromic composition, with a great expansion in the DNA virus diversity. Some wild boar viruses are traced to humans, domestic animals, wildlife, and arthropods, with several evidently or potentially related to epizootics or zoonoses. Pig pathogens spread widely in wild boars and are responsible for a substantial portion of wild boar mortality, with occurrences of co-infection with multiple African swine fever viruses. These results indicate that wild boars are a node animal connecting different animal taxa in the virus circulation network, and that their viruses not only pose a major threat to the pig industry but also challenge wildlife conservation and public health, highlighting the need for routine surveillance of wild boar viruses and active control of the wild boar population.},
}

Animals
*Sus scrofa/virology
*Animals, Wild/virology
Swine/virology
*Animals, Domestic/virology
China/epidemiology
Disease Reservoirs/virology
Virome/genetics
Humans
*Viruses/genetics/classification/isolation & purification
*Swine Diseases/virology
Zoonoses/virology
Phylogeny

@article {pmid41062001,
year = {2025},
author = {Ghaffar, T and Valeriani, F and Romano Spica, V},
title = {The Sex Related Differences in Health and Disease: A Systematic Review of Sex-Specific Gut Microbiota and Possible Implications for Microbial Pathogenesis.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108094},
doi = {10.1016/j.micpath.2025.108094},
pmid = {41062001},
issn = {1096-1208},
abstract = {BACKGROUND: The gut microbiota, a complex ecosystem influenced by various physiological and environmental factors, has been increasingly recognized for its role in health and disease. Emerging evidence suggests that sex differences, particularly mediated by sex hormones and physiological variations, significantly influence the composition and diversity of the gut microbiome. This systematic review aimed to evaluate and synthesize the current knowledge on sex-related variations in gut microbiota across human and animal studies.

METHODS: We conducted a systematic review of 24 eligible studies, selected from an initial 13,205 articles, focusing on healthy populations and next-generation sequencing-based microbiota profiling in both humans and animal models.

RESULTS: The results reveal sex-specific differences in microbial diversity and taxa abundance; however, the consistency and significance of these findings vary across studies, with females generally exhibiting higher levels of Akkermansia and Bifidobacterium, while males showed increased levels of Prevotella and Escherichia. These findings suggest that sex may be a contributing, but not necessarily dominant, biological variable shaping microbiome architecture across various species, including mice, pigs, deer, and humans, and highlight the influence of hormonal fluctuations, body composition, and lifestyle factors on gut microbial ecosystems.

CONCLUSION: Our findings underscore the importance of considering sex as a key biological variable in microbiome research and its potential implications for disease susceptibility, therapeutic interventions, and microbiome-targeted strategies in microbial pathogenesis. Moreover, evidence from human studies remains limited, especially those using 16S rRNA gene sequencing, which may lack the resolution to detect strain-level or functional differences. Incorporating multi-omics approaches such as metagenomics, metatranscriptomics, and metabolomics may offer deeper insights into sex-dependent microbial dynamics.However, these implications remain largely associative and require mechanistic validation in future studies.},
}

@article {pmid41061960,
year = {2025},
author = {Wang, H and Sheng, J and Zhang, Y and Lan, H and Lu, X and Li, X and Zhao, X},
title = {Detection of zoonotic Coxiella burnetii causing chronic Q fever endocarditis in a Chinese geriatric patient by mNGS.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2025.09.015},
pmid = {41061960},
issn = {2213-7173},
abstract = {OBJECTIVES: Q (query) fever, caused by Coxiella burnetii, is often linked to negative bacterial cultures. Infective endocarditis with negative cultures is difficult to diagnose and treat. Our case demonstrates that metagenomic next-generation sequencing (mNGS) can provide a rapid and accurate method for pathogenetic diagnosis in infectious diseases.

CASE PRESENTATION: We reported a case of infective endocarditis with negative blood cultures in a male patient with a history of sheep farming and previous aortic valve replacement (AVT) and atrial septal defect atrial septal defect (ASD) repair. Blood tests showed positive serum immunofluorescent antibodies to rickettsia, while mNGS of perivalvular abscess tissue suggested C. burnetii. Doxycycline 0.1 g q12h and hydroxychloroquine 0.2 g q12h were used for postoperative antibiotic treatment. The genome of the C. burnetii C2245173Z was assembled on the Illumina platform, and no known antibiotic resistance genes were detected. Phylogenetic analysis of C. burnetii genomes shows a genetic relationship between animal-derived strains and human-derived strains.

CONCLUSIONS: The application of mNGS could provide a rapid and accurate assay in clinical diagnosis and play a decisive role in the pathogenetic diagnosis of some infectious diseases. Doxycycline plus hydroxychloroquine remains an effective treatment for chronic Q fever endocarditis. In addition, phylogenetic tree analysis indicates that C. burnetii infection may pose a potential risk to humans working with livestock.},
}

@article {pmid41061540,
year = {2025},
author = {Zhang, L and Gao, X and Li, G and Xu, Z and Luo, W},
title = {Metagenomic insights to effective elimination of resistomes in food waste composting by lime addition.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140065},
doi = {10.1016/j.jhazmat.2025.140065},
pmid = {41061540},
issn = {1873-3336},
abstract = {Food waste contains abundant resistomes, including antibiotic and heavy metal resistance genes (ARGs and MRGs), which pose risks to the environment and human health. Composting can be used for food waste treatment, but it fails to effectively eliminate these resistomes. Thus, this study investigated the performance of lime to regulate the dynamics and mobility of ARGs and MRGs in food waste composting by metagenomics. Genome-resolved analysis was further conducted to identify the ARGs and MRGs hosts and their horizontal gene transfer (HGT) events. Results showed that lime addition at 1 % (wet weight) could significantly promote temperature and pH increase to sterilize hosts, particularly pathogen bacteria (e.g. Acinetobacter johnsonii and Enterobacter cloacae), thus reducing the abundance of resistomes by more than 57.1 %. This sterilization notably reduced the number of mobile ARGs and MRGs driven by mobile genetic elements (MGEs). The contribution of MGEs located on chromosomal sequences to horizontally transfer ARGs and MRGs was significantly higher than that on mobilizable plasmids. Further analysis indicated that the reduced resistomes by lime was mainly attributed to effective sterilization of hosts rather than decreased HGT diversity. Thus, this study provides valuable insights into use lime as a low-cost control of resistomes in waste recycling.},
}

@article {pmid41061488,
year = {2025},
author = {Yang, M and Huang, Y and Liu, J and Wang, G and Mei, Y and Ge, L and Du, Q and Li, H and Zhao, N},
title = {Characterisation of microbial succession and exploration of the stability maintenance strategy of phage community on microbes in radish paocai.},
journal = {International journal of food microbiology},
volume = {444},
number = {},
pages = {111479},
doi = {10.1016/j.ijfoodmicro.2025.111479},
pmid = {41061488},
issn = {1879-3460},
abstract = {Previous research focused on the safety control of phages in food. In recent years, numerous phages have been extensively characterised in fermented foods, where they change along with fermentation process but do not compromise product quality. However, the potential roles of phages in fermented foods remain unclear. Microbial steady state is critical for maintaining normal radish paocai fermentation. To explore stability maintenance strategies for phages, their structure and interactions with microbes were investigated across two microbial structural systems during fermentation. Microbial counts showed the absence of fungi in the non-steady-state environment (NE), whereas high fungal levels (6.78 ± 0.09 log colony-forming units/mL) were detected in the steady-state environment (SE). Metagenomic analysis revealed that microbial structure remained stable in SE but changed markedly in NE. Pediococcus ethanolidurans and Lactococcus lactis were the species that differed significantly between SE and NE. Microbial succession exhibited a significant association with physicochemical environments in NE (P < 0.05), whereas microbial abundance fluctuations were unaffected by physicochemical stress in SE. Caudoviricetes was identified as the dominant viral class. Cluster analysis showed that NE systems displayed high variability with dramatic shifts across multiple viral genera (Clusters 3-6). In NE, 25 lytic and 226 lysogenic phages were identified, while 3 lytic and 29 lysogenic phages were found in SE. Phage host prediction indicated preferential targeting of harmful bacteria (e.g., Escherichia) in NE, contrasted with phage predation on fermentation-associated lactic acid bacteria in SE. Genomic analysis indicated that Lactiplantibacillus abundance and its corresponding phages remained stable in SE but increased sharply in NE on day 3. Lactiplantibacillus phages isolated from NE and SE displayed strict host specificity at the strain level and exhibited potent lytic activity across different fermented food matrices. This study advances our understanding of steady-state maintenance mechanisms in vegetable fermentation systems and offers new insight for cross-system phage applications.},
}

@article {pmid41060906,
year = {2025},
author = {Sawyer, FM and Stossi, F and Nachman, E and Britton, RA and Bolt, MJ and Mancini, MA and Estes, MK and Blutt, SE},
title = {A pipeline for rapid, high-throughput imaging and quantitative analysis of human intestinal organoids.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0332418},
doi = {10.1371/journal.pone.0332418},
pmid = {41060906},
issn = {1932-6203},
mesh = {Humans ; *Organoids/cytology/metabolism ; *Intestinal Mucosa/cytology ; *High-Throughput Screening Assays/methods ; Microscopy, Confocal/methods ; Image Processing, Computer-Assisted/methods ; *Intestines/cytology ; Cell Proliferation ; },
abstract = {Human intestinal organoids (HIOs) are a model system for studying human intestinal epithelium. Utilizing HIOs for high-throughput studies remains inefficient, as analyzing their cellular composition and responses to varying experimental conditions requires extensive time and labor. We describe a 96-well plate-based automated pipeline for rapidly imaging and quantifying fluorescent labeling in HIOs using a high-throughput confocal microscope and image analysis software. The pipeline was leveraged to quantify varying levels of cell proliferation among donor HIO lines in response to microbial products. Cytoplasmic fluorescence via antibody labeling was also quantified with the pipeline, enabling measurement of the prevalence of specific cell types in HIOs. This platform offers a novel approach to efficiently and rapidly image and quantify fluorescent staining and immunolabeling in HIOs and has many potential applications, including drug screening, toxicity testing, intestinal barrier integrity and transport studies, microbiome and host-pathogen interaction studies, and lineage tracking.},
}

Humans
*Organoids/cytology/metabolism
*Intestinal Mucosa/cytology
*High-Throughput Screening Assays/methods
Microscopy, Confocal/methods
Image Processing, Computer-Assisted/methods
*Intestines/cytology
Cell Proliferation

@article {pmid41060725,
year = {2025},
author = {Liu, Y and Tang, J and Wang, Y and Cui, F and Yang, Y},
title = {Intracranial infection caused by Mycoplasma hominis after neurosurgical operation: an easily overlooked but serious condition.},
journal = {Journal of infection in developing countries},
volume = {19},
number = {9},
pages = {1425-1431},
doi = {10.3855/jidc.20729},
pmid = {41060725},
issn = {1972-2680},
mesh = {Humans ; Male ; *Mycoplasma hominis/isolation & purification/genetics ; *Mycoplasma Infections/diagnosis/drug therapy/microbiology ; Aged ; Anti-Bacterial Agents/therapeutic use ; *Neurosurgical Procedures/adverse effects ; *Postoperative Complications/microbiology/diagnosis/drug therapy ; },
abstract = {INTRODUCTION: Mycoplasma hominis (M. hominis) is a commensal that mainly colonizes in the microflora of the genitourinary tracts and is associated with urogenital tract infections. There are reports of central nervous system (CNS) infections in neonates caused by M. hominis. Nevertheless, M. hominis CNS infections in non-neonatal patients are extremely rare. Herein, we have reported a case of a man who suffered from intracranial infection secondary to M. hominis after neurosurgical operation. Additionally, we reviewed the relevant published literature to raise awareness on such infections and highlight the importance of proper treatments.

CASE PRESENTATION: A 68-year-old man underwent emergence craniotomy for intracerebellar hemorrhage. He presented with a moderate fever unresponsive to piperacillin-tazobactam on the seventh day after the surgery. His body temperature continued to increase, and he presented with signs of CNS infection. The antimicrobial therapy was switched to meropenem and vancomycin. No obvious reduction in the body temperature was observed. The cerebrospinal fluid (CSF) obtained previously revealed tiny point colonies which were morphologically consistent with M. hominis and subsequently confirmed by metagenomic next-generation sequencing (mNGS). Thus, M. hominis induced intracranial infection was diagnosed, and a combination therapy with moxifloxacin and minocycline was implemented. Fortunately, the patient's body temperature decreased to normal range after effective antibiotic therapy.

CONCLUSIONS: Based on the lesson of our case and a thorough review of published literature, the possibility of M. hominis induced CNS infections after neurosurgical intervention should not be ignored, especially when there is no response to standard antimicrobial therapy.},
}

Humans
Male
*Mycoplasma hominis/isolation & purification/genetics
*Mycoplasma Infections/diagnosis/drug therapy/microbiology
Aged
Anti-Bacterial Agents/therapeutic use
*Neurosurgical Procedures/adverse effects
*Postoperative Complications/microbiology/diagnosis/drug therapy

@article {pmid41060484,
year = {2025},
author = {Khan, MF},
title = {Enhancing stability of enzymes for industrial applications: molecular insights and emerging approaches.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {10},
pages = {362},
pmid = {41060484},
issn = {1573-0972},
support = {82930-NP//University College Dublin/ ; },
mesh = {Enzyme Stability ; *Enzymes/chemistry/metabolism/genetics ; Protein Engineering/methods ; Hydrogen-Ion Concentration ; Biocatalysis ; Biotechnology ; },
abstract = {The growing demand for robust biocatalysts in industrial bioprocesses has intensified the pursuit of enzymes capable of functioning under extreme physicochemical conditions. This work critically examines the molecular determinants of enzyme stability, including thermostability, pH tolerance, halotolerance, resistance to solvents and oxidative stress, mechanical resilience to shear and pressure, and storage stability. These traits are essential for sustained catalytic performance in sectors such as bioenergy, pharmaceuticals, food, textiles, and environmental remediation. Recent advances in structure-guided engineering, molecular dynamics, and mutational profiling have enabled rational strategies to enhance enzyme resilience. By adopting a multi-parametric lens, this study bridges specific molecular adaptations with industrial challenges, offering a systems-level framework often lacking in single-condition analyses. It also explores emerging frontiers, including AI-assisted enzyme design, metagenomic discovery from extremophiles, and synthetic reconstruction of adaptive pathways, paving the way for next-generation biocatalysts optimised for scalability, performance, and sustainability. The novelty of this work lies in its integrative approach combining molecular insight, environmental origin, and computational tools to guide the development of industrially robust enzymes.},
}

Enzyme Stability
*Enzymes/chemistry/metabolism/genetics
Protein Engineering/methods
Hydrogen-Ion Concentration
Biocatalysis
Biotechnology

@article {pmid41060313,
year = {2025},
author = {Hays, MD and Fuchsman, CA},
title = {SAR11 ecotypes across ocean basins change with depth due to changes in light and oxygen.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf221},
pmid = {41060313},
issn = {1751-7370},
abstract = {SAR11 bacteria are ubiquitous and abundant heterotrophs that are important mediators of marine biogeochemical cycles. Within the SAR11 clade smaller ecotypes inhabit different ecological niches. Using metagenomic read placement onto a phylogenetic tree of RNA polymerase (rpoB), we were able to determine the distribution of different ecotypes both geographically and by depth. Our method avoids biases from the absence of quality sequenced genomes for deep SAR11 ecotypes. Depth profiles that range from the surface to the bathypelagic were analyzed at 30 stations in 6 ocean basins. In the euphotic zone, changes in the dominant primary producer from eukaryotic algae to cyanobacteria, did not cause the abundance of SAR11 to shift between stations. However, specific SAR11 ecotypes did correlate with eukaryotic phytoplankton (1a.3 and 1a.4) or picocyanobacteria (1b.2, 1b.4, and IIaB). In the lower euphotic and mesopelagic zones, group IIb.x was overwhelmingly the dominant species but group 1c was also present, and we found several new deep sub-ecotypes of 1b. The shift between the surface SAR11 community, dominated by 1a and surface 1b sub-ecotypes, and the mesopelagic ecotype groups, corresponded to the maximum decrease in the light-dependent proteorhodopsin/rpoB ratio, indicating that many deep ecotypes did not possess proteorhodopsin. This ecotype switch repeatedly corresponded to the maximum in Low Light I Prochlorococcus, leading to the hypothesis that changes in light motivates the ecotype switch. Environmentally abiotic factors like light and temperature appear to be determining factors in the SAR11 ecotype distribution throughout the global oceans.},
}

@article {pmid41060304,
year = {2025},
author = {Bueno de Mesquita, CP and Olm, MR and Bissett, A and Fierer, N},
title = {High strain-level diversity of Bradyrhizobium across Australian soils.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf222},
pmid = {41060304},
issn = {1751-7370},
abstract = {Global surveys of soil bacteria have identified several taxa that are nearly ubiquitous and often the most abundant members of soil bacterial communities. However, it remains unclear why these taxa are so abundant and prevalent across a wide range of soil types and environmental conditions. Here we use genome-resolved metagenomics to test the hypothesis that strain-level differences exist in these taxa that are not adequately captured with standard marker gene sequencing, and that distinct strains harbor unique traits that reflect adaptations to different soil environments. We analyzed data from 331 natural soils spanning Australia to assess strain differentiation in Bradyrhizobium, a dominant soil bacterial genus of ecological importance. We developed a workflow for strain-level bacterial analyses of complex soil metagenomes, combining genomes from pre-existing databases with new genomes generated via targeted assembly from metagenomes to detect 181 Bradyrhizobium strains across the soil collection. In addition to a high degree of phylogenetic variation, we observed substantial variation in pangenome content and inferred traits, highlighting the breadth of diversity within this widespread genus. Although members of the genus Bradyrhizobium were detected in >80% of samples, most individual strains were restricted in their distributions. The overall strain-level community composition of Bradyrhizobium varied significantly across geographic space and environmental gradients, and was particularly associated with differences in temperature, soil pH, and soil nitrate and metal concentrations. Our work provides a general framework for studying the strain-level ecology of soil bacteria and highlights the ecological and pangenomic diversity within this dominant soil bacterial genus.},
}

@article {pmid41059692,
year = {2025},
author = {Bedi de Silva, A and Polson, SW and Schvarcz, CR and Steward, GF and Edwards, KF},
title = {Genomic diversity and global distribution of four new prasinoviruses from the tropical north Pacific.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0258324},
doi = {10.1128/spectrum.02583-24},
pmid = {41059692},
issn = {2165-0497},
abstract = {Viruses that infect phytoplankton are an integral part of marine ecosystems, but the vast majority of viral diversity remains uncultivated. Here, we introduce four near-complete genomic assemblies of viruses that infect the widespread marine picoeukaryote Micromonas commoda, doubling the number of reported genomes of Micromonas dsDNA viruses. All host and virus isolates were obtained from tropical waters of the North Pacific, a first for viruses infecting green algae in the order Mamiellales. Genome length of the new isolates ranges from 205 to 212 kb, and phylogenetic analysis shows that all four are members of the genus Prasinovirus. Three of the viruses form a clade that is adjacent to previously sequenced Micromonas viruses, while the fourth virus is relatively divergent from previously sequenced prasinoviruses. We identified 61 putative genes not previously found in prasinovirus isolates, including a phosphate transporter and a potential apoptosis inhibitor novel to marine viruses. Forty-eight genes in the new viruses are also found in host genome(s) and may have been acquired through horizontal gene transfer. By analyzing the coding sequences of all published prasinoviruses, we found that ~25% of prasinovirus gene content is significantly correlated with host genus identity (i.e., Micromonas, Ostreococcus, or Bathycoccus), and the functions of these genes suggest that much of the viral life cycle is differentially adapted to the three host genera. Mapping of metagenomic reads from global survey data indicates that one of the new isolates, McV-SA1, is relatively common in multiple ocean basins.IMPORTANCEThe genomes analyzed here represent the first viruses from the tropical North Pacific that infect the abundant phytoplankton order Mamiellales. Comparing isolates from the same location demonstrates high genomic diversity among viruses that co-occur and presumably compete for hosts. Comparing all published prasinovirus genomes highlights gene functions that are likely associated with adaptation to different host genera. Metagenomic data indicate these viruses are globally distributed, and one of the novel isolates may be among the most abundant marine viruses.},
}

@article {pmid41059690,
year = {2025},
author = {Venkatachalam, S and Granskog, MA and Gonçalves-Araujo, R and Divine, DV and Vipindas, PV and Jabir, T and Shereef, A and Jain, A},
title = {Distinct bacterial community structures with abundant carbon degradation and sulfur metabolisms found in different sea-ice types from the Central Arctic Ocean.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0129125},
doi = {10.1128/spectrum.01291-25},
pmid = {41059690},
issn = {2165-0497},
abstract = {The rapid decline of sea ice in the relatively understudied Central Arctic Ocean has a significant impact on bacterial biodiversity and the ecological functions they support. We investigated the bacterial community composition and the associated metabolic functions from three geographically distinct sea-ice floes: first-year ice (FYI) at the North Pole and western Nansen Basin and second-year or multi-year ice (SYI/MYI) in the western Amundsen Basin. We resolved the sea-ice bacterial community diversity at species-level precision using a long-read amplicon (n = 18) and metagenomic (n = 3) sequencing approach. The amplicon sequencing highlighted marked differences in bacterial community structure driven by ice age, floe origin, and environmental factors, demonstrating pronounced vertical structuring among ice horizons. Bacterial taxa like Paraglaciecola psychrophila, Hydrogenophaga crassostreae, Octadecabacter arcticus, and Polaribacter irgensii mainly dominated the bottom layers of SYI/MYI, whereas species Actimicrobium antarcticum, Polaromonas cryoconiti, O. antarcticus, and Rhodoferax sp. dominated the FYI. Similarly, notable taxonomic differences were observed in bacterial taxa inhabiting the surface and interior layers of FYI and SYI/MYI (e.g., F. frigoris and Hydrogenophaga sp.). The metagenomic analysis showed the prevalence of sulfur cycling-associated (assimilatory and dissimilatory sulfur metabolism) and complex carbon degradation processes in sea ice. We also elucidated the potential ecological role of novel metagenome-assembled genomes belonging to the genus Aquiluna through phylogenomic and pangenomic analyses. Overall, our findings revealed novel insights on the distinct bacterial communities that inhabit ice horizons and their associated ecological functions correlating with sea-ice type, origin, and habitat characteristics in the Central Arctic Ocean.IMPORTANCEThe Arctic region is warming nearly four times faster than the global average, leading to the continuous replacement of its thick multi-year sea ice with thinner first-year ice. The reduction in Arctic sea-ice cover was previously shown to have cascading effects on sea-ice-associated microbial communities and their role in the functioning of the ecosystem. This study provides the first high-resolution, species-level insight into the bacterial community composition and metabolic potential across different sea-ice types in the Central Arctic Ocean-an understudied yet rapidly changing environment. By combining long-read amplicon and metagenomic sequencing, we uncover distinct bacterial assemblages and functional metabolic roles that were shaped by the ice age and other physicochemical properties. Our findings highlight the ecological importance of sea-ice associated bacterial communities and the prevalence of sulfur metabolism and carbon degradation processes in different sea-ice types found in the central Arctic Ocean through genome-resolved metagenomics.},
}

@article {pmid41059063,
year = {2025},
author = {Hu, J and Cyle, KT and Yuan, W and Shi, W},
title = {Metagenomic evidence clarifies the texture-dependent cascading effects of organic degradation on soil hypoxia and N2O emission.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1670657},
pmid = {41059063},
issn = {1664-302X},
abstract = {INTRODUCTION: Soil pore-scale aeration is a crucial yet often overlooked factor influencing the effectiveness of nitrous oxide (N2O) emission mitigation strategies. Our previous work revealed a hundred-fold variation in N2O emissions among soils under apparently aerobic conditions and texture-dependent mitigation effects of biochar-manure co-compost (BM) compared to manure compost (M).

METHODS: We analyzed soils of three textures-clay loam (CL), silt loam (SL), and sand (SA)-amended with BM or M. Metagenomic sequencing was used to profile microbial community composition and functional genes, with a focus on aeration-sensitive taxa and pathways.

RESULTS: We demonstrate that these changes of N2O emissions are aligned with variations in aeration-sensitive microbes and genes. SA, with the highest N2O emissions, was most abundant in obligate and facultative anaerobes and denitrification-related genes, while CL, with the lowest emissions, had more genes related to fermentation and dissimilatory nitrate reduction. Compared to M, BM in CL favored genes for microbial processes requiring a more reducing environment, likely because biochar-induced finer pores, exacerbating oxygen diffusion limitations. This severe oxygen restriction in CL after BM addition was substantiated by greater reductions in CO2 efflux and C-cycling genes than in the other soils.

DISCUSSION: Our findings suggest that hypoxic pore abundance and the severity of pore anaerobiosis imparted by degradation of organic amendments varied with soil texture and are the overriding factors of soil greenhouse gas (GHG) emissions. Metagenomic traits provide a sensitive tool for detecting pore-scale environmental shifts, improving our mechanistic understanding of soil-dependent GHG emissions following organic amendments.},
}

@article {pmid41059058,
year = {2025},
author = {Wang, Y and Bai, Z and Liu, Y and Wang, Y and Xu, J and Lai, Z},
title = {Influence of the gut microbiota on the pharmacokinetics of tacrolimus in liver transplant recipients: insights from microbiome analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1616985},
pmid = {41059058},
issn = {1664-302X},
abstract = {INTRODUCTION: Tacrolimus is crucial for immunosuppression after liver transplantation, but its pharmacokinetics vary markedly among individuals. Emerging evidence suggests that the gut microbiota may influence its metabolism, although the underlying mechanisms remain unclear.

METHODS: This study analyzed the fecal microbiota from 38 postliver transplant patients and 31 healthy controls via 16S rDNA amplicon and shotgun metagenomic sequencing. Patients were stratified into three groups on the basis of oral tacrolimus dosage and blood concentration: LDLBC (low dose, low blood concentration), LDHBC (low dose, high blood concentration), and SDLBC (standard dose, low blood concentration).

RESULTS: Posttransplant patients presented significantly reduced gut microbial diversity. Specific bacterial taxa, including Enterococcus raffinosus, Intestinibacter bartlettii, and Bacteroides fragilis, were enriched in patients with lower tacrolimus blood concentrations. In contrast, Phascolarctobacterium faecium and Streptococcus salivarius were associated with increased drug levels. Functional analysis revealed differences between patient subgroups in ATP-binding cassette (ABC) transporters and drug efflux pumps, suggesting a potential microbial influence on tacrolimus absorption and metabolism. Additionally, antibiotic resistance genes were more abundant in patients with lower tacrolimus blood concentrations, particularly in the Escherichia coli-enriched groups.

DISCUSSION: These findings underscore the influence of the gut microbiota on tacrolimus pharmacokinetics and support the potential of microbial composition as a biomarker for optimizing immunosuppressive therapy.},
}

@article {pmid41059040,
year = {2025},
author = {Zhu, N and Gao, J and Wu, R and Jia, S and Guo, X and Sun, D and Guan, Q},
title = {Metagenomic insights into respiratory viral signatures in lower respiratory tract infections with and without respiratory failure.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1637352},
pmid = {41059040},
issn = {2235-2988},
mesh = {Humans ; *Respiratory Tract Infections/virology/microbiology/complications ; *Metagenomics ; Male ; Middle Aged ; Female ; Bacteria/classification/genetics/isolation & purification ; *Viruses/classification/genetics/isolation & purification ; *Virome ; Bronchoalveolar Lavage Fluid/virology/microbiology ; Microbiota ; Aged ; *Respiratory Insufficiency/virology/microbiology ; Adult ; },
abstract = {OBJECTIVE: Lower respiratory tract infections (LRTIs) are a significant cause of morbidity and mortality worldwide, with the respiratory microbiome playing a pivotal role in disease pathogenesis. Comprehensive profiling of the lower respiratory tract virome allows investigation of potential differences between LRTIs and non-LRTIs, helps identify virus-associated taxa linked to pulmonary disease, and provides insights into virome-host interactions involved in respiratory health.

METHODS: In this study, we compared viral and bacterial microbiome characteristics of LRTI patients with non-LRTI controls by α-diversity, β-diversity (PCoA, NMDS, ANOSIM), and differential abundance (LEfSe) analyses using metagenomic sequencing of bronchoalveolar lavage fluids, and further performed these comparisons similarly in respiratory failure (RF) patients and non-RF patients in the LRTI group. In addition, virus-bacteria co-occurrence patterns, the correlations between viral and bacterial abundance profiles, and the associations between microbial features and host clinical indicators were assessed using Spearman correlation analysis.

RESULTS: Overall, no significant differences in viral and bacterial α- or β-diversity were detected between LRTI (n=39) and non-LRTI (n=9) groups. However, among LRTI patients with RF (n=5), distinct viral taxonomic signatures were observed, including enrichment of Phixviricota, Malgrandaviricetes, Petitvirales, and Microviridae lineages. Despite taxonomic shifts, overall viral diversity remained similar between RF and non-RF subgroups. Bacterial communities showed no notable stratification across clinical categories. Correlation analyses revealed that uncultured human fecal viruses were negatively associated with lymphocyte counts, while Streptococcus-related bacteriophages correlated positively with C-reactive protein (CRP) levels.

CONCLUSION: The overall composition and diversity of the respiratory microbiome were insufficient to distinguish LRTI from non-LRTI conditions. However, within the LRTI cohort, patients with RF exhibited distinct viral taxonomic profiles compared to non-RF individuals. Additionally, several viral taxa were correlated with host clinical indicators irrespective of clinical subgroup. These findings highlight virome compositional differences associated with RF within LRTI patients, but do not imply causal effects, and warrant further investigation.},
}

Humans
*Respiratory Tract Infections/virology/microbiology/complications
*Metagenomics
Male
Middle Aged
Female
Bacteria/classification/genetics/isolation & purification
*Viruses/classification/genetics/isolation & purification
*Virome
Bronchoalveolar Lavage Fluid/virology/microbiology
Microbiota
Aged
*Respiratory Insufficiency/virology/microbiology
Adult

@article {pmid41059035,
year = {2025},
author = {Huang, Y and Zhang, M and Tian, Y and Lan, X and Jin, W and Bai, Y and Zang, Q and Chen, M and Su, Z and Zhang, W and Aishan, G and Geng, M and Xie, J and Tong, P},
title = {A novel broad-spectrum lytic phage vB_EcoM_P3322: isolation, characterization, and therapeutic potential against avian pathogenic Escherichia coli.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1645263},
pmid = {41059035},
issn = {2235-2988},
mesh = {Animals ; *Escherichia coli/virology/pathogenicity ; *Escherichia coli Infections/therapy/veterinary/microbiology ; *Myoviridae/isolation & purification/classification/ultrastructure/genetics/physiology ; Host Specificity ; *Phage Therapy/methods ; Wastewater/virology ; *Coliphages/isolation & purification/classification/ultrastructure/physiology/genetics ; Columbidae/microbiology ; Genome, Viral ; Phylogeny ; Poultry Diseases/therapy/microbiology ; Hydrogen-Ion Concentration ; },
abstract = {INTRODUCTION: The widespread misuse of antibiotics has accelerated the emergence of multidrug-resistant bacterial strains, presenting a major threat to global public health. Bacteriophages (phages), owing to their host-specific lytic activity and self-replicating nature, have emerged as promising alternatives or adjuncts to conventional antibiotic therapies.

METHODS: In this study, a lytic phage targeting avian pathogenic Escherichia coli (APEC) was isolated from farm wastewater. The phage's morphological characteristics, host range, optimal multiplicity of infection (MOI), one-step growth curve, pH stability, thermal stability, chloroform sensitivity, and in vitro antibacterial activity were determined. Subsequently, the therapeutic efficacy of the phage was evaluated in a pigeon model.

RESULTS: In this study, we isolated and characterized a lytic phage, designated vB_EcoM_P3322, from farm wastewater targeting APEC. Transmission electron microscopy classified vB_EcoM_P3322 within the Myoviridae family. The phage exhibited broad lytic activity against five Escherichia coliserotypes (O8:H10, O15:H18, O51:H20, O149:H20, and O166:H6). Optimal biological parameters included a multiplicity of infection (MOI) of 1, a latent period of 10 minutes, an 80-minute burst period, and a burst size of 252 PFUs/cell. vB_EcoM_P3322 maintained stable lytic activity across a pH range of 5-9 and temperatures from 4°C to 50°C, although it was sensitive to chloroform. In vitro, the phage effectively suppressed bacterial growth within 6 hours at MOIs of 0.1, 1, and 10. Whole-genome sequencing revealed a 151,674 bp double-stranded DNA genome encoding 279 predicted open reading frames. No virulence factors, toxin genes, antibiotic resistance genes, or lysogeny-related elements were identified, affirming its safety for therapeutic application. Phylogenetic analysis indicated 98.44% nucleotide identity (97% coverage) with phage vB_EcoM_Ro121c4YLVW (GenBank: NC_052654), suggesting a close evolutionary relationship. In a pigeon infection model, vB_EcoM_P3322 treatment significantly improved survival and reduced histopathological damage in the liver and spleen. Metagenomic analysis of duodenal contents revealed a marked reduction (P < 0.01) in E. coli abundance in the treatment group, indicating selective pathogen clearance and modulation of gut microbiota.

DISCUSSION: In summary, vB_EcoM_P3322 displays broad-spectrum lytic activity, robust environmental stability, potent antibacterial efficacy both in vitro and in vivo, and a safe genomic profile. These attributes support its potential as a novel biocontrol agent for managing APEC infections in poultry farming.},
}

Animals
*Escherichia coli/virology/pathogenicity
*Escherichia coli Infections/therapy/veterinary/microbiology
*Myoviridae/isolation & purification/classification/ultrastructure/genetics/physiology
Host Specificity
*Phage Therapy/methods
Wastewater/virology
*Coliphages/isolation & purification/classification/ultrastructure/physiology/genetics
Columbidae/microbiology
Genome, Viral
Phylogeny
Poultry Diseases/therapy/microbiology
Hydrogen-Ion Concentration

@article {pmid41058886,
year = {2025},
author = {Liu, Y and Li, L and Yang, L and Yang, Y and An, H and Li, D and Wang, X},
title = {Clinical Features and Treatment Strategies of Q Fever Spinal Infection: A Pooled Analysis of 39 Cases and Narrative Review of the Literature.},
journal = {Open forum infectious diseases},
volume = {12},
number = {10},
pages = {ofaf584},
pmid = {41058886},
issn = {2328-8957},
abstract = {BACKGROUND: The incidence of spinal infections is increasing; However, pathogen identification remains challenging. Although Q fever spinal infection is reported infrequently, its accrual incidence is likely underestimated. The causative agent, Coxiella burnetii, cannot be routinely cultured. Consequently, physicians often misdiagnose Q fever spinal infection as spinal tuberculosis, leading to severe patient harm. Thus, improving clinicians' awareness of the clinical characteristics of Q fever spinal infection is urgently needed.

METHODS: We present a case of Q fever spinal infection and conducted literature searches in PubMed and the Chinese core journals of the Wanfang Database using keywords including "Q fever," "Coxiella burnetii," "spinal infection," "osteomyelitis," "spondylodiscitis," and "psoas abscess." Additional reports were identified through cross-referencing, with a cutoff date of 6 November 2024. Cases were included if patient age, sex, and baseline medical history were documented. Clinical data were retrospectively analyzed, and clinical features were compared between the aneurysm-associated group and the isolated spinal infection group. Fisher's exact probability test was used to evaluate the incidence difference.

RESULTS: A total of 39 adult patients were enrolled (mean age: 67.82 ± 10.51 years, male: 34,87.2%), Eleven cases reported potential pathogen exposure. Thirty-three cases presented with early-onset of lower back pain, and 13 developed fever during the disease course. Thirty-four cases involved the lumbar spine, exhibiting continuous lesions of 1-3 vertebral bodies, with imaging features of vertebral osteomyelitis, discitis, paravertebral soft-tissue swelling, and/or adjacent aneurysmal changes. Among 21 cases with routine blood tests, 2 showed elevated leukocyte counts, 5 had mild anemia, and the remainder were normal. Serological testing was performed in 34 cases, with 29 testing positive on the first time; PCR testing was conducted in 25 cases, with 23 cases detecting positive specimens; and rapid diagnosis confirmed in all 3 cases via metagenomic next-generation sequencing (mNGS). Inflammatory reactions were identified in all 21 biopsied cases, with inflammatory granulomas reported in 7 and explicitly excluded in 4. There were 24 cases complicated with aneurysm and 15 cases with isolated spinal infection. A significant difference in CRP elevation rate was observed between the two groups (14/15, 93.33% vs 4/8, 50.00%, P = .033). Early local lesion debridement combined with doxycycline-based multidrug therapy showed favorable outcomes. Serological monitoring demonstrated low sensitivity for assessing therapeutic efficacy.

CONCLUSIONS: This study systematically summarizes the clinical characteristics of Q fever spinal infection and, for the first time, reports features associated with its distinct clinical subtypes. Q fever should be considered in case of chronic spinal infections-especially those complicated with vascular lesions. Based on clinical history evaluation, rapid diagnosis may be achieved through mNGS of specimens from local lesions. Combined with early initiation of doxycycline-based regimens, timely debridement of necrotic tissues and purulent material may improve treatment outcomes. Further investigations are needed to identify reliable biomarkers for monitoring therapeutic efficacy and to establish optimal treatment strategies for subtypes of Q fever spinal infection.},
}

@article {pmid41058622,
year = {2025},
author = {Cai, ZZ and Zeng, DM and Lei, LW and Xiao, S},
title = {Rotavirus gastroenteritis complicating meningitis caused by Bacteroides uniformis detected using mNGS: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1601953},
pmid = {41058622},
issn = {2296-858X},
abstract = {This case report describes a rare instance of pediatric meningitis caused by Bacteroides uniformis (B. uniformis) following rotavirus gastroenteritis in a 1-year-4-month-old boy, diagnosed using metagenomics next-generation sequencing (mNGS). Bacterial meningitis (BM) is a life-threatening disease in children, particularly those under 5 years old, and early identification of the pathogen is crucial for reducing mortality and improving prognosis. B. uniformis, a Gram-negative, non-spore-forming, obligate anaerobic bacillus and common gut commensal, is rarely implicated in human infections, particularly pediatric meningitis. The child presented with vomiting, diarrhea, convulsions, and syncope, and was initially treated for meningitis and rotavirus gastroenteritis. Despite negative bacterial cultures, mNGS identified B. uniformis in the cerebrospinal fluid (CSF). Treatment was switched from ceftriaxone to meropenem (0.45 g, IV every 8 h) based on its good blood-brain barrier penetration and likely susceptibility of B. uniformis. The child's condition improved significantly, with follow-up lumbar puncture showing normal CSF parameters and no detectable pathogens. The case suggests that rare anaerobic meningitis may occur against the backdrop of rotavirus gastroenteritis and underscores the importance of using mNGS for accurate pathogen detection in bacterial meningitis, as well as the need for early initiation of appropriate antimicrobial therapy.},
}

@article {pmid41058503,
year = {2025},
author = {Castro, M and Vida, R and Galeano, J and Cuesta, JA},
title = {Scarce data, noisy inferences and overfitting: the hidden flaws in ecological dynamics modelling.},
journal = {Journal of the Royal Society, Interface},
volume = {22},
number = {231},
pages = {20250183},
doi = {10.1098/rsif.2025.0183},
pmid = {41058503},
issn = {1742-5662},
support = {//Agencia Estatal de Investigación/ ; },
mesh = {*Models, Biological ; *Ecosystem ; Bayes Theorem ; *Microbiota ; Humans ; },
abstract = {Metagenomic data has significantly advanced microbiome research by employing ecological models, particularly in personalized medicine. The generalized Lotka-Volterra (gLV) model is commonly used to understand microbial interactions and predict ecosystem dynamics. However, gLV models often fail to capture complex interactions, especially when data are limited or noisy. This study critically assesses the effectiveness of gLV and similar models using Bayesian inference and a model reduction method based on information theory. We found that ecological data often leads to non-interpretability and overfitting due to limited information, noisy data and parameter sloppiness. Our results highlight the need for simpler models that align with the available data and propose a distribution-based approach to better capture ecosystem diversity, stability and competition. These findings challenge current bottom-up ecological modelling practices and aim to shift the focus towards a statistical mechanics view of ecology based on distributions of parameters.},
}

*Models, Biological
*Ecosystem
Bayes Theorem
*Microbiota
Humans

@article {pmid41058431,
year = {2025},
author = {Jiménez-Arroyo, C and Molinero, N and Del Campo, R and Delgado, S and Moreno-Arribas, MV},
title = {Human gut microbiome study through metagenomics: Recent advances and challenges for clinical implementation.},
journal = {Enfermedades infecciosas y microbiologia clinica (English ed.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.eimce.2025.09.011},
pmid = {41058431},
issn = {2529-993X},
abstract = {Metagenomics has decisively advanced the study of the gut microbiome, enabling a better understanding of its importance for human health. Metataxonomics, based on the sequencing of the 16S rRNA gene, provides taxonomic profiles of prokaryotes, while shotgun metagenomics allows a comprehensive characterization of all DNA present in a sample. With adequate sequencing depth, the latter increases taxonomic resolution to the strain level and provides detailed information on the functional potential of the microbiota. However, the lack of standardization in sample collection and processing, sequencing technologies, and data management limits the comparability of results and their implementation in clinical laboratories. This review offers a practical and updated framework on metagenomic methodologies, data analysis, and the application of artificial intelligence tools, highlighting advances and best practices to facilitate the integration of functional microbiome analysis into clinical practice and to overcome current challenges.},
}

@article {pmid41057946,
year = {2025},
author = {Ren, Y and Wu, YH and Chen, J and Luo, ZH and Xu, XW},
title = {New insights into the evolution and metabolism of the bacterial phylum Candidatus Acidulodesulfobacteriota through metagenomics.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {127},
pmid = {41057946},
issn = {2524-6372},
support = {42376133//National Natural Science Foundation of China/ ; 2021YFF0501303//National Key R&D Program of China/ ; },
abstract = {Candidatus Acidulodesulfobacterales, a formerly proposed bacterial order within the Deltaproteobacteria lineage, represents an ecologically significant group in sulfur-rich environments. Their diversity and functional potential in artificial acid mine drainage (AMD) ecosystems have been well studied; however, their distribution and ecological role in marine hydrothermal sulfides remain poorly understood. Here we integrated publicly available metagenome-assembled genomes (MAGs) with a newly reconstructed MAG from hydrothermal sulfides to perform comprehensive phylogenetic, metabolic, and host-virus interaction analyses. Phylogenomic and 16S rRNA gene analyses indicated that this lineage represents a distinct phylum-level clade, leading us to propose the designation Ca. Acidulodesulfobacteriota. Metabolic reconstructions indicated a versatile lifestyle, encompassing pathways for carbon fixation, nitrogen fixation, sulfur metabolism, iron oxidation, and hydrogen oxidation. Notably, the concatenated DsrAB protein phylogeny and the mixed enzyme types involved in Dsr-dependent dissimilatory sulfur metabolism suggest that Ca. Acidulodesulfobacteriota may represent a transitional lineage in the evolutionary shift from reductive to oxidative Dsr metabolism. Viral auxiliary metabolic genes (AMGs) associated with this phylum were predicted to modulate host metabolic pathways, including folate biosynthesis and sulfur metabolism, highlighting intricate host-virus interactions. These findings advance our understanding of the evolution, metabolic potential, and ecological roles of Ca. Acidulodesulfobacteriota in biogeochemical cycling.},
}

@article {pmid41057624,
year = {2025},
author = {Han, D and Liu, C and Yang, B and Yu, F and Liu, H and Lou, B and Shen, Y and Tang, H and Zhou, H and Zheng, S and Chen, Y},
title = {Metagenomic fingerprints in bronchoalveolar lavage differentiate pulmonary diseases.},
journal = {NPJ digital medicine},
volume = {8},
number = {1},
pages = {599},
pmid = {41057624},
issn = {2398-6352},
support = {2023YFC2308300//Key Technologies Research and Development Program/ ; 82472371//National Natural Science Foundation of China/ ; },
abstract = {Recent advances in unbiased metagenomic next-generation sequencing (mNGS) enable simultaneous examination of microbial and host genetic material. We developed a multimodal machine learning-based diagnostic approach to differentiate lung cancer and pulmonary infections by analyzing 402 bronchoalveolar lavage fluid (BALF) mNGS datasets, including lung cancer (n = 123), bacterial infections (n = 114), fungal infections (n = 79), and pulmonary tuberculosis (n = 86). The training cohort revealed differences in microbial profiles, bacteriophage abundance, host gene and transposable element expression, immune cell composition, and tumor fraction derived from copy number variation (CNV). The integrated model (Model VI) achieved an AUC of 0.937 (95% CI, 0.910-0.964) in the training cohort and 0.847 (95% CI, 0.776-0.918) in the test cohort. A rule-in/rule-out strategy further improved accuracy in differentiating lung cancer from tuberculosis (accuracy = 0.896), fungal (accuracy = 0.915), and bacterial (accuracy = 0.907) infections. These findings highlight the potential of mNGS-based multimodal analysis as a cost-effective tool for early and accurate differential diagnosis.},
}

@article {pmid40631202,
year = {2025},
author = {Palmer, SN and Mishra, A and Gan, S and Liu, D and Koh, AY and Zhan, X},
title = {Identifying Optimal Machine Learning Approaches for Human Gut Microbiome (Shotgun Metagenomics) and Metabolomics Integration with Stable Feature Selection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.06.21.660858},
pmid = {40631202},
issn = {2692-8205},
support = {U01 AI169298/AI/NIAID NIH HHS/United States ; T32 AI005284/AI/NIAID NIH HHS/United States ; R01 GM126479/GM/NIGMS NIH HHS/United States ; R56 HG011035/HG/NHGRI NIH HHS/United States ; P01 AI179406/AI/NIAID NIH HHS/United States ; R01 HG011035/HG/NHGRI NIH HHS/United States ; },
abstract = {UNLABELLED: Microbiome research has been limited by methodological inconsistencies. Taxonomy-based profiling presents challenges such as data sparsity, variable taxonomic resolution, and the reliance on DNA-based profiling, which provides limited functional insight. Multi-omics integration has emerged as a promising approach to link microbiome composition with function. However, the lack of standardized methodologies and inconsistencies in machine learning strategies has hindered reproducibility. Additionally, while machine learning can be used to identify key microbial and metabolic features, the stability of feature selection across models and data types remains underexplored, despite its importance for downstream experimental validation and biomarker discovery. Here, we systematically compare Elastic Net, Random Forest, and XGBoost across five multi-omics integration strategies: Concatenation, Averaged Stacking, Weighted Non-negative Least Squares (NNLS), Lasso Stacking, and Partial Least Squares (PLS), as well as individual omics models. We evaluate performance across 588 binary and 735 continuous models using human gut microbiome-derived metabolomics and taxonomic data derived from metagenomics shotgun sequencing data. Additionally, we assess the impact of feature reduction on model performance and feature selection stability. Among the approaches tested, Random Forest combined with NNLS yielded the highest overall performance across diverse datasets. Tree-based methods also demonstrated consistent feature selection across data types and dimensionalities. These results demonstrate how integration strategies, algorithm selection, data dimensionality, and response type impact both predictive performance and the stability of selected features in multi-omics microbiome modeling.

KEY POINTS: A total of 1,323 models were developed to comprehensively evaluate prediction performance and the robustness of feature selection for human gut microbiome (metabolomics and taxonomy from metagenomics shotgun sequencing) datasets. These models included three widely used machine learning algorithms - Elastic Net, Random Forest and XGBoost - applied across five integration strategies and single-omics approaches on datasets with binary and continuous outcomes.For continuous outcomes, Random Forest combined with NNLS integration achieved the highest performance and maintained strong predictive performance across full-dimensional and feature-reduced datasets.For binary outcomes, Random Forest consistently performed well regardless of the integration strategy. Notably, single-omics models, especially those using metabolomics data, outperformed integrative approaches.Tree-based models demonstrated greater consistency in feature selection across different dimensionalities and integration strategies.},
}

@article {pmid39764050,
year = {2025},
author = {Nasr, E and Pechlivanis, N and Strepis, N and Amato, P and Bernt, M and Bhardwaj, A and Blankenberg, D and Brites, D and Cumbo, F and Do, K and Ferrari, E and Griffin, TJ and Gruening, B and Hiltemann, S and Hyde, CJ and Jagtap, P and Mehta, S and Métris, KL and Momin, S and Nelson, TM and Oba, A and Pavloudi, C and Péguilhan, R and Price, GR and Psomopoulos, F and Rosic, N and Schatz, MC and Schiml, VC and Siguret, C and Soranzo, N and Stubbs, A and Van Heusden, P and Vohra, M and , and Zierep, P and Batut, B},
title = {Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.23.629682},
pmid = {39764050},
issn = {2692-8205},
support = {U24 AI183870/AI/NIAID NIH HHS/United States ; U41 HG006620/HG/NHGRI NIH HHS/United States ; },
abstract = {The explosion of microbial omics data has outpaced the ability of many researchers to analyze it, with complex tools and limited computational resources creating barriers to discovery. To address this gap, we present the Microbiology Galaxy Lab: a free, globally accessible, community-supported platform that combines state-of-the-art analytical power with user-friendly accessibility. Supported by the Galaxy and global microbiology communities, this platform integrates over 315 tool suites and 115 curated workflows, enabling comprehensive metabarcoding, (meta)genomic, (meta)transcriptomic, and (meta)proteomic data analysis within a FAIR-aligned environment. It also supports research in the health and infectious disease sectors, as well as in environmental microbiology. The platform's utility is exemplified through various use cases, including antimicrobial resistance tracking, biomarker prediction, microbiome classification, and functional annotation of key microbes. Built on reproducibility and community engagement, it supports creation, sharing, and updating of best-practice workflows. Over 35 tutorials and learning paths empower scientists, fostering an ecosystem that keeps resources at the forefront of microbial science. The Microbiology Galaxy Lab enables collective analysis, democratising research, thereby accelerating discovery across the global microbiology community (microbiology.usegalaxy.org, .eu, .org.au, .fr).},
}

@article {pmid41059288,
year = {2023},
author = {Cameron, ES and Blaxter, ML and Finn, RD},
title = {plastiC: A pipeline for recovery and characterization of plastid genomes from metagenomic datasets.},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {475},
pmid = {41059288},
issn = {2398-502X},
abstract = {The use of culture independent molecular methods, often referred to as metagenomics, have revolutionized the ability to explore and characterize microbial communities from diverse environmental sources. Most metagenomic workflows have been developed for identification of prokaryotic and eukaryotic community constituents, but tools for identification of plastid genomes are lacking. The endosymbiotic origin of plastids also poses challenges where plastid metagenomic assembled genomes (MAGs) may be misidentified as low-quality bacterial MAGs. Current tools are limited to classification of contigs as plastid and do not provide further assessment or characterization of plastid MAGs. plastiC is a workflow that allows users to identify plastid genomes in metagenome assemblies, assess completeness, and predict taxonomic association from diverse environmental sources. plastiC is a Snakemake workflow available at https://github.com/Finn-Lab/plastiC. We demonstrate the utility of this workflow with the successful recover of algal plastid MAGs from publicly available lichen metagenomes.},
}

@article {pmid41056780,
year = {2025},
author = {Chang, X and Ma, Y and Zhang, J and Wang, T and Li, H and Wang, L},
title = {Size-specific effects of polyethylene microplastics (100-10,000 nm) on the soil resistome and pathogens revealed via metagenomics and machine learning.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127517},
doi = {10.1016/j.jenvman.2025.127517},
pmid = {41056780},
issn = {1095-8630},
abstract = {Microplastics (MPs) and antibiotic resistance genes (ARGs) are widespread, persistent environmental contaminants. However, the influence of MP particle size on ARGs dissemination and soil ecosystem health remains unclear. Herein, polyethylene MPs of three sizes (100, 1,000, and 10,000 nm) were incubated in ARG-contaminated soils for 45 days to evaluate their effects on soil physicochemical properties, microbial communities, ARGs, mobile genetic elements (MGEs), and pathogen abundance. MP exposure significantly increased soil water (up to 4.07-fold), total nitrogen (up to 50.34 %), and ammonium nitrogen (up to 38.54 %) contents. Conversely, soil organic carbon content decreased with increasing MP size. MPs markedly reduced the activities of key enzymes, including alkaline phosphatase (by 87.65 %), sucrase (by 10.96 %), and urease (by 54.17 %). Microbial α-diversity increased; however, the abundance of potentially pathogenic Pseudomonadota increased by up to 41.88 %, whereas that of beneficial Actinobacteria and Chloroflexi declined. MPs promoted the expression of 44 ARGs and 15 MGEs, with smaller MPs exhibiting stronger enrichment. They also increased the expression of virulence factors and the abundance of human- and plant-associated pathogens. Random forest modeling revealed that smaller MPs primarily drove these changes by altering soil physicochemical properties and microbial dynamics. Collectively, these findings demonstrate that MPs, especially smaller particles, simultaneously alter soil chemistry, suppress enzyme activities, reshape microbial communities, and enhance ARGs expression and pathogen proliferation, underscoring their significant ecological and human health risks in agricultural soils.},
}

@article {pmid41056245,
year = {2025},
author = {Roongpiboonsopit, D and Wairit, S and Nithisathienchai, C and Pakdee, A and Cheibchalard, T and Sayasathid, J and Wilantho, A and Tongsima, S and Somboonna, N},
title = {Oral microbiome dysbiosis in acute ischemic stroke and transient ischemic attack patients.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0333676},
doi = {10.1371/journal.pone.0333676},
pmid = {41056245},
issn = {1932-6203},
mesh = {Humans ; Male ; Female ; *Dysbiosis/microbiology ; *Ischemic Attack, Transient/microbiology ; *Microbiota/genetics ; Middle Aged ; Case-Control Studies ; Aged ; *Ischemic Stroke/microbiology ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Saliva/microbiology ; Bacteria/genetics/classification ; *Mouth/microbiology ; },
abstract = {Oral microbiome (bacterial community) may influence systemic inflammation and vascular health, which both are critical factors in a pathogenesis of ischemic stroke. This study aimed to evaluate differences in the saliva microbiome of acute ischemic stroke (AIS) and transient ischemic attack (TIA) patients compared with matched healthy controls, hypothesizing that AIS and TIA patients are associated with oral microbiome shift. A prospective case-control study was conducted in Naresuan University Hospital, Thailand, to compare the saliva microbiome of AIS and TIA stroke patients of Thai ethnic with matched healthy controls. Microbial profiles were analyzed by metagenomics combined 16S rRNA gene sequencing to assess microbial alpha diversity, taxonomic composition, beta diversity, and microbial functional pathways.Forty-one patients (31 AIS and 10 TIA) and 20 age- and sex-matched stroke-free healthy controls were included in this study. Baseline characteristics were comparable between groups, apart from higher rates of hypertension, diabetes, and smoking in the patient group. Patients exhibited significantly higher alpha-diversity genus richness by OTUs and Chao1 index than controls (p < 0.001), highlighting an altered microbial community structure. Phylum-level analysis revealed an increased abundance of Bacillota (p = 0.0285) in the patient group, with a statistically decreasing trend for Bacteroidota, Actinomycetota and Pseudomonadota (p < 0.05). At the genus level, Streptococcus was more significantly abundant in the patients (p = 0.0171), while Prevotella was reduced. The patient and control groups were statistically separated in beta-diversity analysis (PERMANOVA, p < 0.001), with species biomarker analysis by LEfSe (Linear discriminant analysis effect size) could suggest species markers for each group. Functional pathway analysis showed the patient group the significantly higher in functional categories of, for examples, xenobiotics biodegradation and metabolism, cardiovascular diseases, signal transduction, and membrane transport (Welch's t-test, p < 0.05). In conclusion, this study demonstrated the statistical alterations in the saliva microbiome of AIS and TIA patients, characterized by increased genus richness diversity and relatively distinct microbial shifts that may be associated with stroke-related inflammation. The findings suggest the saliva microbiome analysis as potential as a non-invasive biomarker for stroke risk and its role in stroke pathophysiology.},
}

Humans
Male
Female
*Dysbiosis/microbiology
*Ischemic Attack, Transient/microbiology
*Microbiota/genetics
Middle Aged
Case-Control Studies
Aged
*Ischemic Stroke/microbiology
RNA, Ribosomal, 16S/genetics
Prospective Studies
Saliva/microbiology
Bacteria/genetics/classification
*Mouth/microbiology

@article {pmid41056240,
year = {2025},
author = {Brenner, LN and Huang, CY and Kim, M and Bringhurst, L and Richards, CJ and Sicilian, L and Neuringer, I and Putman, MS and Lai, PS},
title = {Dysglycemia and the airway microbiome in cystic fibrosis.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0331847},
doi = {10.1371/journal.pone.0331847},
pmid = {41056240},
issn = {1932-6203},
mesh = {Humans ; *Cystic Fibrosis/microbiology/complications ; *Microbiota ; Male ; Female ; Adult ; Sputum/microbiology ; *Diabetes Mellitus/microbiology/etiology ; Glucose Tolerance Test ; Young Adult ; Lung/microbiology ; Respiratory Function Tests ; Pseudomonas aeruginosa ; },
abstract = {BACKGROUND: Cystic fibrosis-related diabetes (CFRD) is one of the most common non-pulmonary complications in people living with cystic fibrosis (pwCF), seen in up to 50% of adults. Even when correcting for severity of CFTR mutations, those with CFRD have more pulmonary exacerbations, lower lung function, and increased mortality than those with normal glucose tolerance (NGT).

METHODS: Expectorated sputum samples were collected from 63 pwCF during routine outpatient visits (29 with CFRD, 12 with IGT and 22 with NGT). Oral glucose tolerance test results, A1c levels, and pulmonary function tests closest to the time of sputum collection were obtained from the medical record. Samples underwent metagenomics sequencing and raw reads were processed through the bioBakery workflow for taxonomic profiling at the species level as well as predicted functional profiling and antibiotic resistance profiling. Viral profiling was performed with Marker-MAGu. Differences in alpha diversity, beta diversity, and differential abundance were assessed. Microbiome and phage signatures of CFRD were generated using sparse partial least squares models which were subsequently used as a primary predictor of lung function using multivariate linear regression.

RESULTS: In linear models, CFRD status compared to NGT was associated with a lower alpha diversity (reciprocal Simpson -1.98 [-3.80,-0.16], p = 0.033) and differences in microbial community composition (Bray Curtis dissimilarity PERMANOVA R2 0.17, p = 0.011). Pseudomonas aeruginosa and Streptococcus gordonii had higher relative abundance in CRFD vs NGT participants (2.43 [0.027, 4.82], unadjusted p = 0.056 and 1.11 [0.58, 1.64] unadjusted p= < .001 respectively). There were global differences between CFRD vs NGT in both functional pathways and antibiotic resistance genes. In multivariate models adjusting for age, sex, antibiotic use, and modulator therapies, virome but not microbiome signatures of CFRD were associated with lower FEV1 percent predicted (-6.4 [95% CI -10.2, -2.6]%, p = 0.001 for each 10% increase in virome score).

CONCLUSION: Differences in the airway microbiome in those with dysglycemia in CF are associated with poorer lung function.},
}

Humans
*Cystic Fibrosis/microbiology/complications
*Microbiota
Male
Female
Adult
Sputum/microbiology
*Diabetes Mellitus/microbiology/etiology
Glucose Tolerance Test
Young Adult
Lung/microbiology
Respiratory Function Tests
Pseudomonas aeruginosa

@article {pmid41055380,
year = {2025},
author = {Du, J-Y and Zhang, Z-J and Tan, L and Yang, J-Y and Yang, R-N and Chen, Y-L and Tan, G-F and Li, J and Li, W-J and Yang, L and Cai, J and Shen, D-L and Zhu, H-R and Fan, Z-X and Yuan, M-L and Zhang, W},
title = {Gut microbiota dysbiosis and metabolic perturbations of bile/glyceric acids in major depressive disorder with IBS comorbidity.},
journal = {mBio},
volume = {},
number = {},
pages = {e0244725},
doi = {10.1128/mbio.02447-25},
pmid = {41055380},
issn = {2150-7511},
abstract = {Major depressive disorder (MDD) and irritable bowel syndrome (IBS) exhibit high comorbidity, yet their shared pathophysiology remains unclear. Previous studies have primarily focused on the psychological health in the IBS population, without considering psychiatric diagnoses or stratifying different psychological states, potentially leading to biased findings. This study employed multi-omics approaches to characterize gut microbiota and serum metabolites in 120 MDD patients (47 with IBS and 73 without IBS) and 70 healthy controls (HCs). MDD with IBS patients showed significantly higher depression (Hamilton depression scale [HAMD-17]) and anxiety (Hamilton anxiety scale [HAMA-14]) scores than MDD-only patients (P < 0.05). Metagenomic sequencing of fecal samples revealed increased alpha diversity (Chao1/Shannon indices) and Firmicutes dominance in both MDD groups vs HC, while Actinobacteria enrichment specifically marked MDD with IBS. Functionally, MDD with IBS uniquely activated D-amino acid/glycerolipid metabolism pathways (Kyoto Encyclopedia of Genes and Genomes). Serum metabolomics identified comorbid-specific perturbations: downregulation of bile acids (CDCA, GCDCA, GCDCA-3S) and upregulation of glyceric acid/glutaconic acid. Our study also found that Eggerthella lenta and Clostridium scindens are differentially abundant bacteria that are involved in bile acid metabolism, and that microbial genes (e.g., K03738) are associated with glyceric acid production. These findings implicate gut microbiota-driven bile acid/glyceric acid dysregulation in MDD with IBS comorbidity, supporting the gut-brain axis as a therapeutic target for probiotics or microbiota transplantation.IMPORTANCEMajor depressive disorder (MDD) exhibits a high comorbidity rate with irritable bowel syndrome (IBS). Our study, conducted on 120 MDD patients (47 of whom were comorbid with IBS) and a control group of 70 individuals, revealed that MDD-IBS comorbid patients demonstrated significantly higher depression/anxiety scores. Multi-omics analysis indicated substantial alterations in the gut microbiota (e.g., Firmicutes, Actinobacteria) and serum metabolites (e.g., bile acids, glyceric acid) among MDD-IBS patients, which were associated with specific metabolic pathways. Therefore, the new aspect of this study was the inclusion of patients with MDD but without IBS symptoms, which provided a deeper understanding of the intestinal microbiota dysregulation associated with comorbid IBS and MDD. These findings suggest that there may be involvement of the gut-brain axis, providing new research directions for potential therapeutic targets.CLINICAL TRIALSThis study is registered with the Chinese Clinial Trial Registry as ChiCTR2100041598.},
}

@article {pmid41055333,
year = {2025},
author = {Sharma, S and Narahari, HP and Raman, K},
title = {Harnessing machine learning for metagenomic data analysis: trends and applications.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0164224},
doi = {10.1128/msystems.01642-24},
pmid = {41055333},
issn = {2379-5077},
abstract = {Metagenomic sequencing has revolutionized our understanding of microbial ecosystems by enabling high-resolution profiling of microbes across diverse environments. However, the resulting data are high-dimensional, sparse, and noisy, posing challenges for downstream data analysis. Machine learning (ML) has provided an arsenal of tools to extract meaningful insights from such large and complex data sets. This review surveys the existing state of ML applications in metagenomic data analysis, from traditional supervised and unsupervised learning to time-series modeling, transfer learning, and newer directions such as causal ML and generative models. We highlight certain key challenges and delve into important issues like model interpretability, emphasizing the importance of explainable AI (XAI). We also compare ML with mechanistic models, commenting on their relative advantages, disadvantages, and prospects for synergy. Finally, we preview future directions, such as the incorporation of multi-omics data, synthetic data generation, and Agentic AI systems, highlighting the increasingly prominent role that AI and ML will play in the future of microbiome science.},
}

@article {pmid41054501,
year = {2025},
author = {Wang, W and Mo, Q and Ding, X and Pan, J},
title = {Metagenomic Next-Generation Sequencing Reveals Tannerella forsythia in Lung Abscesses: A Retrospective Case Series Linking Smoking, Oral Health, and Diagnostic Challenges.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5193-5205},
pmid = {41054501},
issn = {1178-6973},
abstract = {PURPOSE: Tannerella forsythia (T. forsythia) is a Gram-negative anaerobic bacterium commonly found in the oral cavity of patients with periodontitis, but lung abscesses caused by this pathogen are extremely rare in the literature. This study aimed to characterize the clinical features, diagnostic challenges, and treatment outcomes of T. forsythia-associated lung abscesses through four case analyses.

PATIENTS AND METHODS: We retrospectively reviewed four patients treated between April 2023 and May 2024 with lung abscesses confirmed by chest computed tomography (CT) and T. forsythia detection via metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF). Conventional cultures were performed but yielded negative results. Clinical data, including demographics, symptoms, imaging findings, and treatment regimens, were analyzed.

RESULTS: All patients had oral diseases, and 75% were long-term smokers. The primary clinical manifestations were nonspecific respiratory symptoms, including cough, fever, chest pain, and hemoptysis. Chest CT revealed consolidation and cavitation in the upper lobes of the lungs. T. forsythia was successfully detected by mNGS of BALF, while conventional cultures failed to identify pathogens in all cases. All patients received combination antibiotic therapy based on metronidazole and piperacillin-tazobactam, with some cases requiring additional antibiotics. Following treatment, significant clinical improvement was observed, and follow-up imaging demonstrated gradual resolution of the lesions.

CONCLUSION: This study is limited by its small sample size and the lack of confirmatory tests, which warrant validation in larger prospective cohorts. Our findings highlight the advantages of mNGS in detecting fastidious pathogens (such as the anaerobic bacterium T. forsythia), providing new insights for the diagnosis of similar infections in the future. Additionally, the results identify smoking and poor oral health as common features that may be associated with the development of T. forsythia-associated lung abscesses.},
}

@article {pmid41053880,
year = {2025},
author = {Shittu, OE and Enagbonma, BJ and Babalola, OO},
title = {Deciphering the influence of fertilization systems on the Allium ampeloprasum rhizosphere microbial diversity and community structure through a shotgun metagenomics profiling approach.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {126},
pmid = {41053880},
issn = {2524-6372},
support = {CRP/ZAF22-03)//ICGEB, Italy/ ; NRF//South African National Research Foundation/ ; },
abstract = {BACKGROUND: Chemical fertilizer application in agriculture over the years has been a vital instrument to boost agricultural yields and soil fertility, but has threatened the diversity of the rhizosphere microbiomes in the soil. However, knowledge about the impacts of biofertilizers (BF) as well as chemical fertilizers (CF) on Allium ampeloprasum rhizosphere's microbiomes is still limited. Hence, this study investigated the metagenomic profiling of A. ampeloprasum rhizosphere under different fertilization systems and in bulk soils, to obtain a depiction of their associated microbial diversity and community structure, which will inform best agricultural practices.

METHOD: The entire DNA sample was mined from soil samples taken from an independent uncultivated bulk soil and the rhizosphere of A. ampeloprasum treated with chemical and biofertilizer and subjected to shotgun metagenomics sequencing.

RESULTS: The taxonomic analysis of our metagenome unveiled that while all soil samples exhibited similar core microbial phyla, Bacteroidota and Verrucomicrobiota were exclusive to the biofertilizer (G2) plot. Actinobacteria and Pseudomonadota (Proteobacteria) were predominant in the biofertilizer plot (G2), chemical fertilizer (G1), and bulk soil (G3) plots, respectively. Genera such as Dyadobacter, Verrucomicrobium, Streptomyces, and Haliangium were exclusively detected in the biofertilizer plot (G2). Alpha diversity analysis showed that G2 harboured the most diverse microbial community, followed by G3, with the lowest diversity found in the G1 plot, highlighting the importance of biofertilizer in increasing microbial diversity. The observed differences in the microbial diversity and community structure are highly linked to the nature of fertilizer applied and the distinct physicochemical parameters of the three plots. However, redundancy analysis subsequently highlighted total nitrogen and carbon as the key environmental influencers impacting the microbial community structure and composition.

CONCLUSION: This study underscores the potential of biofertilizers in boosting the rhizosphere microbial diversity, improving soil health, and offer a sustainable alternative to chemical fertilizers, thereby supporting long-term agricultural sustainability and resilience in food production systems.},
}

@article {pmid41053318,
year = {2025},
author = {Vitry, G and Angdisen, J and Sawant, MA and Arriaga, P and Irgen-Gioro, S and Peshette, P and Vuong, DC and Ilhardt, P and Fehr, J and Cwikla, B and Ponnaiya, B and Inman, JL and Snijders, AM and Hamid, S and Caballero-Lima, D and Garty, G and Apfeldorf, K and Laiakis, EC},
title = {Using a full thickness bioengineered human skin equivalent as a model for radiation biology research.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34702},
pmid = {41053318},
issn = {2045-2322},
support = {W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; W911NF-22-C-0064//Intelligence Advanced Research Projects Activity/ ; },
mesh = {Humans ; *Skin/radiation effects/microbiology/metabolism ; Animals ; Mice ; Microbiota/radiation effects ; Bioengineering ; Cell Proliferation/radiation effects ; Dose-Response Relationship, Radiation ; },
abstract = {Radiation exposure from radiological or nuclear events, medical treatments, or spaceflight poses significant health risks, yet human-specific models to investigate radiation effects on skin remain limited. This study establishes a novel in vitro platform using a full-thickness bioengineered human skin equivalent colonized with natural mixed human microbiota (coHSEs) to assess radiation-induced biological responses. We exposed coHSEs to acute doses of up to 4 Gy with x-rays and evaluated their viability, structural integrity, and molecular responses over 25 days. The coHSE model demonstrated sustained viability without dose-dependent opportunistic microbial overgrowth when procedural optimizations were applied. Radiation-induced epidermal remodeling did not compromise tissue architecture or swabbing-based sample collection. Cell proliferation analyses revealed dose- and time-dependent dynamics, with consistent dermal cell density maintained across radiation doses. Comparative multi-omic analyses, including untargeted metabolomics, targeted lipidomics, and 16 S metagenomics, revealed conserved metabolic and microbial responses to radiation in both coHSEs and skin from irradiated mice. Enriched pathways such as arachidonic acid and fatty acid metabolism, along with shifts in microbial taxa including Lachnospiraceae, support the translational relevance of the coHSE model. This system offers a scalable, ethical, and physiologically relevant platform for radiation biology, biodosimetry, and therapeutic development, advancing terrestrial health research with promising application for space research.},
}

Humans
*Skin/radiation effects/microbiology/metabolism
Animals
Mice
Microbiota/radiation effects
Bioengineering
Cell Proliferation/radiation effects
Dose-Response Relationship, Radiation

@article {pmid41052982,
year = {2025},
author = {Cao, Y and Fan, X and Zang, T and Qiu, T and Fang, Q and Bai, J and Liu, Y},
title = {Prenatal depression-associated gut microbiota induces depressive-like behaviors and hippocampal neuroinflammation in germ-free mice.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {383},
pmid = {41052982},
issn = {2158-3188},
support = {2023AFB710//Natural Science Foundation of Hebei Province (Hebei Provincial Natural Science Foundation)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Female ; *Hippocampus/metabolism/pathology/immunology ; Mice ; Pregnancy ; Fecal Microbiota Transplantation ; *Depression/microbiology/metabolism ; *Dysbiosis/microbiology/complications ; Humans ; Lipopolysaccharides/blood ; Germ-Free Life ; *Neuroinflammatory Diseases/metabolism/microbiology ; Microglia ; *Pregnancy Complications/microbiology ; Disease Models, Animal ; Behavior, Animal ; Interleukin-6/metabolism ; Tumor Necrosis Factor-alpha/metabolism ; },
abstract = {Numerous studies have described the role of the microbiome-gut-brain axis in depression. However, the molecular mechanisms underlying the involvement of gut microbiota in the development of prenatal depression are limited. In this study, fecal microbiota from women with prenatal depression was transplanted into germ-free mice to investigate the potential causal relationships between the gut microbiota and depressive phenotypes. Shotgun metagenomic sequencing and untargeted metabolomics approaches were used to investigate the characteristics of gut microbiota and microbial metabolites. The levels of neuroinflammation in the brain were detected using immunofluorescence and real-time quantitative PCR. We found significant changes in gut microbiota composition and metabolites in mice with fecal microbiota transplantation (FMT) from women with prenatal depression, including decreased Ligilactobacillus, increased Akkermansia, and abnormal glycerophospholipid metabolism. Besides, significant increase in plasma lipopolysaccharide (LPS) levels and significant proliferation of microglia in the hippocampus were observed in mice receiving FMT from women with prenatal depression, accompanied by a significant increase in the expression of nuclear factor-κB (NF-κB) p65, tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) mRNA. The gut microbiota and its metabolites were strongly associated with depressive-like behaviors, plasma LPS and neuroinflammation. Our study collectively demonstrates that dysbiosis of the gut microbiota may play a causal relationship in the development of prenatal depression. This process potentially involves the activation of neuroinflammation through the LPS-NF-κB signaling pathway.},
}

Animals
*Gastrointestinal Microbiome/physiology
Female
*Hippocampus/metabolism/pathology/immunology
Mice
Pregnancy
Fecal Microbiota Transplantation
*Depression/microbiology/metabolism
*Dysbiosis/microbiology/complications
Humans
Lipopolysaccharides/blood
Germ-Free Life
*Neuroinflammatory Diseases/metabolism/microbiology
Microglia
*Pregnancy Complications/microbiology
Disease Models, Animal
Behavior, Animal
Interleukin-6/metabolism
Tumor Necrosis Factor-alpha/metabolism

@article {pmid41052966,
year = {2025},
author = {Tang, W and Hexter, C and Dai, R and Fortin, SG and Tracey, JC and Intrator, N and Kunes, MA and Wan, XS and Jayakumar, A and Shi, D and Ward, BB},
title = {Substrate Effect on the Contribution of Ammonium and Urea to Marine Nitrification and Nitrous Oxide Production.},
journal = {Environmental microbiology},
volume = {27},
number = {10},
pages = {e70187},
doi = {10.1111/1462-2920.70187},
pmid = {41052966},
issn = {1462-2920},
support = {OCE-1946516//National Science Foundation/ ; 675459//Simons Foundation/ ; //University of South Florida/ ; },
mesh = {*Nitrification ; *Nitrous Oxide/metabolism ; *Urea/metabolism ; *Archaea/metabolism/genetics ; *Ammonium Compounds/metabolism ; Oxidation-Reduction ; *Seawater/microbiology/chemistry ; Ammonia/metabolism ; Nitrites/metabolism ; },
abstract = {Nitrification (microbial oxidation of ammonia to nitrite and nitrate) controls nitrogen speciation and is the main source of nitrous oxide (N2O) in the ocean. It was recently shown that the most abundant marine ammonia oxidizers, the ammonia-oxidising archaea (AOA), are also capable of oxidising urea, providing a previously ignored source of nitrite. Here, we show that the relative magnitude of urea and ammonia oxidation rates, and the relative rates of N2O production from the two substrates, is correlated with the ratio of the substrate concentrations. By examining all reported measurements of urea and ammonium concentrations and the paired urea and ammonia oxidation rates, we show that this relationship likely holds across the global ocean. Examination of newly acquired and previously published metagenomic data shows that the fraction of AOA with the genetic capability for urea oxidation increases with the urea:ammonium ratio, rather than depending on the urea or ammonium concentration alone. These results corroborate the correlation between substrate ratios and oxidation rate ratios, and extend it to N2O production. This may help explain the distribution of nitrification rates and N2O production in the ocean.},
}

*Nitrification
*Nitrous Oxide/metabolism
*Urea/metabolism
*Archaea/metabolism/genetics
*Ammonium Compounds/metabolism
Oxidation-Reduction
*Seawater/microbiology/chemistry
Ammonia/metabolism
Nitrites/metabolism

@article {pmid41052412,
year = {2025},
author = {Dias, ME and Breyer, GM and Torres, MC and Wuaden, CR and Rebelatto, R and Kich, JD and Dorn, M and Siqueira, FM},
title = {Overview of the microbiome and resistome of swine manure in commercial piglet farms and its application in grazing soils.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/09593330.2025.2566429},
pmid = {41052412},
issn = {1479-487X},
abstract = {The environmental spread of antimicrobial resistance genes (ARGs) through the use of animal manure in agriculture has become a significant concern. This study investigated the impact of applying swine manure treated through biodigestion on the spread of ARGs in agricultural soils in the Midwest region of Brazil. Samples of untreated and treated manure, fertilized soil, and unfertilized soil were collected from three piglet production units. Bacterial communities and ARGs were characterized through metagenomic sequencing and bioinformatics. Bacterial profiles in fertilized and unfertilized soils were highly similar across all farms. In contrast, biodigestion reduced the total number of ARGs in treated manure. Of the 399 ARGs detected in fertilized soils, 67% were also found in unfertilized soils, and 12% were shared exclusively with treated manure. The presence of numerous ARGs in unfertilized soils highlights the role of environmental dissemination routes, such as runoff, dust, or wildlife, in shaping soil resistomes even in areas without manure application. These findings suggest a stable bacterial and resistome profile in soils, regardless of manure application. Although antimicrobial residues were not evaluated, the results reinforce the need for responsible antibiotic use and effective manure management to minimize environmental ARG dissemination.},
}

@article {pmid41052332,
year = {2025},
author = {Ni, G and Wang, M and Walker, N and Muetzel, S and Schmidt, O and Fischer, A and Stemmler, RT and Leung, PM and Zhang, X and Li, Q and Jain, S and Jespersen, M and Grinter, R and Archer, SDJ and Pacheco, D and Lowe, K and Pope, PB and Müller, V and Pitta, DW and Janssen, PH and Watson, M and Attwood, GT and Ver Loren van Themaat, E and Kindermann, M and Greening, C},
title = {Methanogenesis inhibition remodels microbial fermentation and stimulates acetogenesis in ruminants.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {41},
pages = {e2514823122},
doi = {10.1073/pnas.2514823122},
pmid = {41052332},
issn = {1091-6490},
support = {APP1178715//Federal Government | DHAC | National Health and Medical Research Council (NHMRC)/ ; FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; },
mesh = {Animals ; *Methane/metabolism/biosynthesis ; *Fermentation/drug effects ; *Rumen/microbiology/metabolism ; Cattle ; *Gastrointestinal Microbiome/drug effects ; *Propanols/pharmacology ; Animal Feed ; *Ruminants/microbiology/metabolism ; Microbiota/drug effects ; Fatty Acids, Volatile/metabolism ; },
abstract = {Rumen microbiota enable ruminants to grow on fibrous plant materials, but also produce methane, driving 5% of global greenhouse gas emissions and leading to a loss of gross energy content. Methanogenesis inhibitors such as 3-nitrooxypropanol (3-NOP) decrease methane emissions in ruminants when supplemented in feed. Yet we lack a system-wide, species-resolved understanding of how the rumen microbiota remodels following inhibition and how this influences animal production. Here, we conducted a large-scale trial with 51 dairy calves to analyze microbiota responses to 3-NOP, pairing host performance, emissions, and nutritional profiles with genome-resolved metagenomic and metatranscriptomic data. 3-NOP supplementation decreased methane emissions by 62%, modulated short-chain fatty acid and H2 levels, and did not affect dietary intake or animal performance. We created a rumen microbial genome catalogue (27,884 genomes) that mapped to the meta-omic data at high rates. There was a strong reduction of methanogens and stimulation of reductive acetogens, primarily uncultivated lineages such as "Candidatus Faecousia." However, there was a shift in major fermentative communities away from acetate production in response to hydrogen gas accumulation. In vitro incubations recapitulated these results and showed an enrichment of acetate from reductive acetogenesis. Altogether, the divergent responses of the fermentative and hydrogenotrophic communities lead to net hydrogen build-up and limit potential productivity gains from methane reduction. By linking ruminant greenhouse gas emissions and productivity to specific microbial species, this study emphasizes the importance of microbiota-wide analysis for optimizing methane mitigation strategies and identifies promising strategies to simultaneously reduce emissions while increasing animal production.},
}

Animals
*Methane/metabolism/biosynthesis
*Fermentation/drug effects
*Rumen/microbiology/metabolism
Cattle
*Gastrointestinal Microbiome/drug effects
*Propanols/pharmacology
Animal Feed
*Ruminants/microbiology/metabolism
Microbiota/drug effects
Fatty Acids, Volatile/metabolism

@article {pmid41052251,
year = {2025},
author = {Qin, Z and Yang, Z and Zhang, Y and Qi, L and Peng, Y and Deng, S and Wang, Y},
title = {Biotin Limitation Attenuates Streptococcus mutans Cariogenicity by Disrupting Metabolic Flux and Virulence Pathways.},
journal = {Caries research},
volume = {},
number = {},
pages = {1-24},
doi = {10.1159/000548822},
pmid = {41052251},
issn = {1421-976X},
abstract = {INTRODUCTION: Our previous metagenomic analysis revealed higher frequencies of biotin-related genes (i.e., bioY, bioM, bccP) in caries-active children, indicating a potential role of biotin in caries pathogenesis. This study investigated a biotin limitation strategy against the primary cariogenic bacterium Streptococcus mutans (S. mutans), including its effects on cariogenic phenotypes, gene expression, and metabolomics.

METHODS: S. mutans UA159 was cultured in biotin-free medium supplemented with different biotin concentrations. The cariogenic phenotypes of the strain, including growth kinetics, biofilm formation, exopolysaccharide (EPS) production, lactate synthesis, acid/oxidative tolerance, and membrane fluidity, were measured and compared across biotin concentrations. Biofilm architecture was visualized via confocal laser-scanning microscopy (CLSM) and scanning electron microscopy (SEM). Quantitative real-time polymerase chain reaction (RT-qPCR) was employed to analyze the expression of genes associated with virulence and biotin metabolism. Metabolomic analysis was performed to characterize metabolic perturbations induced by biotin limitation in S. mutans.

RESULTS: Under biotin limitation, S. mutans exhibited significantly reduced cariogenic phenotypes, accompanied by cell elongation and reduced membrane fluidity. At the molecular level, biotin limitation suppressed the expression of key virulence-associated genes and induced a compensatory upregulation of genes involved in biotin uptake and biotin-dependent carboxylases. Metabolomic analysis under biotin-limited conditions in S. mutans revealed perturbed pathways in central carbon metabolism and nucleotide metabolism.

CONCLUSION: Biotin limitation significantly reduced the cariogenic potential of S. mutans by disrupting metabolic flux and virulence gene expression, highlighting biotin uptake and metabolism as potential targets for anti-caries therapies.},
}

@article {pmid41051042,
year = {2025},
author = {Nancy, and Lakhawat, SS and Kumar, R and Sharma, PK},
title = {Cloning, Expression, Purification, and Characterization of Superoxide Dismutase from the Soil Metagenome.},
journal = {Protein and peptide letters},
volume = {},
number = {},
pages = {},
doi = {10.2174/0109298665415743250926072254},
pmid = {41051042},
issn = {1875-5305},
abstract = {INTRODUCTION: Superoxide Dismutases (SODs) are enzymes that catalyze the conversion of toxic free radicals generated during stress conditions into nontoxic forms. Thus, the enzyme superoxide dismutase contributes to the adaptation and survival of microorganisms across a variety of environmental conditions, making it an indispensable enzyme during the response to stress. In this study, we embarked upon investigating and characterizing a Superoxide Dismutase (SOD) from DNA extracted directly from garden soil, where the average temperature ranges from 4°C- 45°C.

MATERIALS AND METHODS: Metagenomic DNA was extracted by employing a kit. The gene was amplified using PCR. The amplified PCR product was gel eluted and ligated into the pGEMT-easy vector and subcloned into an expression vector. The protein was purified using Ni-NTA chromatography and characterized using biophysical, biochemical, and computational approaches.

RESULTS: The recombinant SOD was expressed and purified; the purified protein exhibited activity and stability over a broad pH and temperature range, with optimal activity observed at 40°C and pH 8, respectively. The enzyme remains completely stable at 40°C for 3 h. However, in contrast, it loses 50% of its activity when incubated at 50°C and 60°C for 3 h. The biophysical investigation revealed stable confirmation of the secondary structure of the protein, as evident from circular dichroism and intrinsic Tryptophan (Trp) fluorescence studies. In silico sequence and structural analysis revealed a close similarity of the SOD reported in this study to the Mn SOD of multi- Bacillus species. Molecular simulation dynamics experiments revealed the all-over conformational stability of protein structures at varying pH, indicating broad pH functioning of the enzyme.

DISCUSSION: The study provides a comprehensive analysis of the structure and function of a superoxide dismutase enzyme derived from a soil metagenome. A Mn2+ binding site identified in the study offers an opportunity to further facilitate engineering and design of mutant SOD.

CONCLUSION: The enzyme exhibits distinct attributes that hold significant industrial relevance. Owing to the wide functionality of SOD at different pH and temperature, it can be tailored for its potential industrial applications, which include its therapeutic potential, thus opening new avenues for enhanced antioxidant therapies and novel biocatalyst designing.},
}

@article {pmid41050906,
year = {2025},
author = {Wiese, M and Klaassens, ES and Hatt, V and Kreikamp, A and Baak, ML and Heerikhuisen, M and Van Der Vossen, JMBM},
title = {Demonstration of phage inhibitory action against Clostridium perfringens LMG 11264 within a complex chicken cecal microbiota in vitro.},
journal = {Frontiers in antibiotics},
volume = {4},
number = {},
pages = {1599939},
pmid = {41050906},
issn = {2813-2467},
abstract = {INTRODUCTION: Clostridium perfringens strains may cause foodborne illness, and 95% of human infections are linked to the consumption of contaminated meat, including chicken products. In poultry, C. perfringens infection may cause necrotic enteritis, and infections are associated with high mortality rates partially due to antibiotic resistance, which hampers efficient treatment. In-vitro screening approaches of alternative treatment options, for instance, specific phages, represent a promising strategy for the selection of novel interventions to combat infections.

MATERIAL AND METHODS: In this study, we explored the application of a C. perfringens strain LMG 11264-specific phage #7 introduced at 10[4] pfu/mL to inhibit the growth of C. perfringens at 10[6] cfu/mL compared to two antibiotics (amoxicillin at 10 µg/mL and clindamycin at 10 µg/mL) within complex chicken cecal microbiota in vitro. Samples for gDNA isolation, qPCR, and metagenome sequencing were taken at the beginning and after 24 and 48 h of incubation.

RESULTS: The C. perfringens strain LMG 11264 proliferated within the untreated complex microbiota and reached levels of approximately 10[8] and 10[9] genome equivalents per mL after 24 and 48 h of incubation, respectively. The phage intervention with phage #7 inhibited the growth of C. perfringens LMG 11264 significantly; the inhibitory effects were similar to those exerted by the antibiotic intervention with amoxicillin and stronger than the inhibitory effects with clindamycin. In the absence of the C. perfringens challenge, we found a significant effect of amoxicillin (p = 0.040) or clindamycin (p = 0.000017) compared to the untreated control after 24 h of incubation, and the phage addition did not affect the alpha diversity expressed as Chao index significantly (p = 1). In addition, the endogenous C. perfringens in the chicken microbiota appeared insensitive to phage #7. The phage titer of phage #7 only increased in the presence of the inoculated C. perfringens strain LMG 11264. In conclusion, the i-screen model can be implemented to test the efficacy and specificity of phage therapy in vitro.},
}

@article {pmid41050878,
year = {2025},
author = {Chetty, C and Mafunda, N and Happel, AU and Khan, A and Cooley Demidkina, B and Yende-Zuma, N and Saidi, Y and Mahabeer Polliah, A and Lewis, L and Osman, F and Radebe, P and Passmore, JS and Kwon, D and Ravel, J and Ngcapu, S and Liebenberg, L and Symul, L and Holmes, S and Mitchell, CM and Potloane, D},
title = {Randomized trial of multi-strain Lactobacillus crispatus vaginal live biotherapeutic products after antibiotic therapy for bacterial vaginosis: study protocol for VIBRANT (vaginal lIve biotherapeutic RANdomized trial).},
journal = {Contemporary clinical trials communications},
volume = {48},
number = {},
pages = {101554},
pmid = {41050878},
issn = {2451-8654},
abstract = {BACKGROUND: Globally, approximately 30 % of women have bacterial vaginosis (BV). Antibiotic treatment is frequently followed by recurrence, likely due to lack of colonization with beneficial lactobacilli.

METHODS: This is a Phase 1, randomized, placebo-controlled trial of vaginal live biotherapeutic products (LBP) after antibiotic treatment for BV to establish Lactobacillus colonization. The LBP are vaginal tablets containing 6 L. crispatus strains (LC106) or 15 L. crispatus strains (LC115), at 2 x 10[9] colony forming units (CFU) per dose. Participants with BV in the United States and South Africa will receive seven days of oral metronidazole twice daily and will be randomized 1:1:1:1:1 to: seven days placebo; seven days LC106; three days LC106/four days placebo; seven days LC106 starting day 3 of the metronidazole course; or seven days LC115. Safety will be assessed by the number and percentage of ≥ Grade 2 related adverse events during or after product use. The primary outcome is LBP colonization defined as relative abundance ≥5 % of any LBP strain or ≥10 % of a combination of LBP strains by metagenomic sequencing any time in the 5 weeks after randomization. A generalized linear model will measure the association between treatment group and colonization, adjusting for site.

CONCLUSIONS: This study seeks to establish proof of concept for a multi-strain LBP to promote vaginal L. crispatus colonization in two geographically distinct populations.

TRIAL REGISTRATION: South African National Clinical Trials Registry (SANCTR DOH-27-102023-8342; October 27, 2023) and ClinicalTrials.gov (NCT06135974; November 11, 2023).

PROTOCOL VERSION: 2.0 dated October 03, 2023.},
}

@article {pmid41050761,
year = {2025},
author = {Zhou, X and Yang, C and Liu, X and Wang, J and Li, Y and Pan, L and Peng, S and Yu, H and Deng, X},
title = {Clinical performance of metagenomic next-generation sequencing for distinction and diagnosis of Mucorales infection and colonization.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1631960},
pmid = {41050761},
issn = {2235-2988},
mesh = {Humans ; *Mucormycosis/diagnosis/microbiology/drug therapy ; *Mucorales/genetics/isolation & purification/classification ; Male ; Female ; Middle Aged ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Aged ; Adult ; ROC Curve ; Antifungal Agents/therapeutic use ; Microbiota ; },
abstract = {Mucormycosis is a lethal fungal infection disease with high mortality rate. However, investigations assessing the value of metagenomic next-generation sequencing (mNGS) for distinguishing Mucorales infection from colonization are currently insufficient. A retrospective analysis of clinical date from 71 patients at Sichuan Provincial People's Hospital from September 2021 to September 2024 was conducted. The performance of mNGS in distinguishing Mucorales infection from colonization, along with the differences in patients' characteristics, imaging characteristics, antimicrobial adjustment, and microbiota, were examined. Among the 71 patients, 51 were identified as Mucorales infection group (3 proven and 48 probable cases), and 20 were colonization group (possible cases). Receiver operating characteristic (ROC) curve for mNGS indicated an area under the curve of 0.7662 (95%CI: 0.6564-0.8759), with an optimal threshold value of 51 for discriminating Mucorales infection from colonization. The infection group exhibited a higher proportion of antimicrobial adjustments compared to the colonization group (64.71% vs. 35.00%, P < 0.05), with antifungal agent changed being more dominant (43.14% vs. 10.00%, P < 0.01). Mucorales RPTM value, length of hospital stays, hsCRP, immunocompromised, malignant blood tumor, and antifungal changed were significantly positively correlated with Mucorales infection. Rhizomucor pusillus showed significant differences between the two groups. The abundance of Torque teno virus significantly increased in the infection group, whereas the colonization group exhibited higher abundance of Rhizomucor delemar. mNGS is a valuable tool for differentiating colonization from infection of Mucorales. Malignant blood tumor, immunocompromised, length of hospital stays and hsCRP were significant different indicators between patients with Mucorales infection from colonization.},
}

Humans
*Mucormycosis/diagnosis/microbiology/drug therapy
*Mucorales/genetics/isolation & purification/classification
Male
Female
Middle Aged
Retrospective Studies
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Aged
Adult
ROC Curve
Antifungal Agents/therapeutic use
Microbiota

@article {pmid41050671,
year = {2025},
author = {Duan, H and Xu, B and Luo, P and Chen, T and Zou, J},
title = {Microbial metabolites and their influence on the tumor microenvironment.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1675677},
pmid = {41050671},
issn = {1664-3224},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Neoplasms/immunology/metabolism/therapy/microbiology ; Animals ; Immunotherapy ; *Microbiota/immunology ; Fatty Acids, Volatile/metabolism ; },
abstract = {While tumor immunotherapy has achieved remarkable progress in many hematological malignancies, its efficacy remains limited by key challenges, including the immunosuppressive microenvironment of solid tumors, metabolic abnormalities, and drug resistance. As a central mechanism underlying impaired immune function, metabolic reprogramming of immune cells has emerged as a pivotal focus for unraveling tumor immune evasion and therapeutic resistance. Advances in metagenomics have highlighted the significance of the human commensal microbiome as a 'second genome.' Microbial metabolites, whether circulating systemically or accumulating locally, serve as key messengers linking the microbiota to tumor immunometabolism. This review comprehensively examines the regulatory roles and metabolic mechanisms through which microbial metabolites-including short-chain fatty acids (SCFAs), bile acids, tryptophan metabolites, and lipopolysaccharides (LPS)-modulate tumor immunity and immunotherapeutic responses via immune cell metabolism. These metabolites shape the tumor immune microenvironment and influence immunotherapeutic efficacy by reprogramming immune cell metabolic and biosynthetic pathways. This review underscores the central regulatory role of microbial metabolites as the 'second genome' in tumor immunometabolism, offering a theoretical foundation and potential targets to elucidate mechanisms of immunotherapeutic resistance and advance microbiota metabolism-based precision interventions.},
}

Humans
*Tumor Microenvironment/immunology
*Neoplasms/immunology/metabolism/therapy/microbiology
Animals
Immunotherapy
*Microbiota/immunology
Fatty Acids, Volatile/metabolism

@article {pmid41050203,
year = {2026},
author = {Wang, Q and Shan, S and Sun, Q and Zhao, X and Yuan, C and Mou, Y and Wang, J and Yan, C and Wang, Q and Rui, Q and Li, C},
title = {The coupling effect of Penicillium baileys W2 in the Aspergillus flavus inhibition and peanut growth promotion.},
journal = {Synthetic and systems biotechnology},
volume = {11},
number = {},
pages = {127-140},
pmid = {41050203},
issn = {2405-805X},
abstract = {Aspergillus flavus is a significant plant pathogen, and peanut crops are particularly vulnerable to aflatoxin contamination. This vulnerability underscores the need for more effective control methods. In this study, the strain Penicillium baileys W2 was isolated from the rhizosphere soils of healthy peanut seedlings. The fermentation extract exhibited concentration-dependent inhibition of pathogenic A. flavus growth, with a minimum inhibitory concentration (MIC) of 55 % and a minimum fungicidal concentration (MFC) of 60 %. Physiological data and transcriptome analysis demonstrated that the W2 fermentation supernatant inhibited A. flavus growth by disrupting membrane permeability. Metabolomics analysis identified active compounds, including propylparaben, taxifolin, and phloretin, which exhibited significant antagonistic effects against A. flavus. Additionally, we evaluated the impact of the W2 fermentation broth on peanut growth promotion and on rhizosphere microbial community structure using metagenomic sequencing. The reduction of harmful soil microorganisms contributed to the maintenance of soil health, whereas the increased abundance of beneficial microorganisms enhanced peanut seedling growth by facilitating soil nutrient cycling. These findings indicate that the development and application of P. baileys strain W2 or its fermentation extract aligns with sustainable agricultural principles and offers a promising biological control approach.},
}

@article {pmid41049781,
year = {2025},
author = {Wang, B and He, T and Cheng, Y and Chen, H and Hu, Y and Liu, Y and Wang, F and Chen, L},
title = {Targeted enhancement strategies for Sojae Semen Praeparatum: Impact of Aspergillus oryzae and Bacillus subtilis on microbial communities, flavor substances, and functional components.},
journal = {Food chemistry: X},
volume = {30},
number = {},
pages = {102931},
pmid = {41049781},
issn = {2590-1575},
abstract = {Sojae Semen Praeparatum (SSP), a traditional Chinese fermented soybean product, was optimized through novel single/double enhancement fermentation using Aspergillus oryzae and Bacillus subtilis. Enhanced fermentation significantly increases the production of flavor amino acids. Using headspace solid-phase extraction microextraction gas chromatography-mass spectrometry (HS-SPEM-GC-MS) technology, 51 critical flavor substances were identified, confirming that enhanced fermentation improves the flavor profile of SSP. Isoflavone quantification revealed that enhancement strategies promoted isoflavone conversion. Enzyme inhibition and antioxidant activities were superior in the double enhancement fermentation group. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis demonstrated a significant increase in SSP's enrichment in the flavone and flavonol biosynthesis pathway. Screening identified 19 key flavonoid components strongly correlated with bioactivity, and enhancement fermentation notably enhancing their accumulation. Metagenomic sequencing revealed 14 key differential microorganisms, essential to flavor development and activity enhancement in SSP. This study offers valuable insights for optimizing fermentation processes to enhance product quality.},
}

@article {pmid41049190,
year = {2025},
author = {Liu, C and Li, B and Wu, Q and Chen, D and Zhou, W and Ao, J},
title = {The effects and mechanism of urease inhibitor and its combination with nitrification inhibitor on nitrous oxide emission across four soil types.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1663261},
pmid = {41049190},
issn = {1664-462X},
abstract = {Nitrogen (N) fertilization is essential for ensuring crop productivity, while excessive N application significantly increases greenhouse gases (GHGs) emissions, particularly nitrous oxide (N2O). Urease inhibitors (UI) and combined urease and nitrification inhibitors (UN) have demonstrated potential in mitigating GHGs emission, though their efficiency with great variation across different soils types. In this study, controlled incubation experiments were conducted using four types of agricultural soils to evaluate the mitigation potential of UI and UN application and to investigate their underlying mechanisms. N fertilization significantly increased N2O emissions by 5.1~99.9-fold and elevated CO2 emissions by 13.6~65.4% across all soil types. The UI treatment decreased the peak of NO2 [-] concentrations in two alkaline soils, while the UN treatment decreased both NO2 [-] and NO3 [-] concentrations in all four soils. In terms of GHG mitigation, UI treatment reduced N2O emissions by 16.5~57.4% in alkaline soils and reduced CO2 emissions by 6.5~49.3% across four soil types. The UN treatment demonstrated superior efficacy, reducing N2O emissions by 52.5~92.4% and CO2 emissions by 4.2~87.2% across all soils. Metagenomic sequencing revealed that both UI and UN significantly inhibited the relative abundances of key functional genes associated with nitrification (hao and nxrAB), dissimilatory nitrate reduction (narGHI/napAB), nitrite reduction (nirS/nirK), and nitric oxide reduction (norBC). Random forest identified key factors influencing the N2O mitigation efficiency of UI and UN. These included soil properties such as soil pH, total nitrogen, organic matter, available potassium, water-filled pore space, texture. Additionally, partial functional genes related to nitrification, denitrification, carbon and methane metabolism, sulfur and phosphorus cycling were also identified as key contributors. Overall, these findings provide valuable insights for the region-specific application of UI and UN to effectively mitigate GHGs emissions. The identification of key soil abiotic and biotic factors offers a theoretical foundation for optimizing inhibitors application and enhancing their mitigation efficiency.},
}

@article {pmid41049022,
year = {2025},
author = {Cohodes, M and Fernandez, A and Ashkin, D and Reed, C and Park, S and Banaei, N and Fung, M and Jacobson, K and Goswami, ND},
title = {Curated cases from the TB expert network: Unplugged! Series: Use of plasma microbial cell-free DNA metagenomic sequencing to diagnose Mycobacterium tuberculosis.},
journal = {Journal of clinical tuberculosis and other mycobacterial diseases},
volume = {41},
number = {},
pages = {100563},
pmid = {41049022},
issn = {2405-5794},
abstract = {A 52-year-old U.S.-born man with diabetes and a kidney transplant 3 months prior presented with fever of unknown origin and left-sided weakness. On admission, he was found to have right internal carotid artery thrombus and cerebral infarct. He developed respiratory failure and underwent treatment for Pseudomonas bacteremia. Fevers continued through hospital day 30 and computed tomography (CT) scans demonstrated an esophageal mass, hepatic lesions, and pulmonary nodules, which were new compared to pre-transplant imaging 2 years prior. While awaiting results from acid-fast bacilli (AFB) cultures from sputum and tissue, plasma microbial cell-free DNA (mcfDNA) metagenomic sequencing was ordered on day 29 and was positive for Mycobacterium Tuberculosis (Mtb). Based on the results of mcfDNA sequencing, clinical presentation, and radiographic findings, a diagnosis of tuberculosis disease was made, and anti-tuberculosis treatment was initiated. While awaiting results from acid-fast bacilli (AFB) cultures and molecular studies from sputum and tissue, plasma microbial cell-free DNA (mcfDNA) metagenomic sequencing was ordered on day 29 and was positive for Mycobacterium Tuberculosis (Mtb). The patient was discharged on hospital day 60; 27 days after discharge, 58 days after the Mtb PCR resulted positive from tissue biopsy, and 60 days after the positive mcfDNA, sputum cultures returned positive for Mycobacterium tuberculosis.},
}

@article {pmid41048510,
year = {2025},
author = {Mieremet, A and van der Wurff, M and Pagan, L and Ferrer-González, E and Seo, J and Schuren, FHJ},
title = {Taxonomic and functional profiling of the vulvar microbiome indicates variations related to ecological signatures, aging, and health status.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1633147},
pmid = {41048510},
issn = {1664-302X},
abstract = {INTRODUCTION: The vulvar microbiome is adjacent to that of the skin and the vagina and connects microbiomes present on a stratified epithelial barrier to that of a mucosal barrier. Yet, the characterization of the microbiome in the vulvar region of the body is understudied, although dysbiosis in the microbiome of the skin or vagina have been linked to impairments in women's health.

METHODS: To better understand the role of the vulvar microbiome during healthy aging or during presentation of vulvar diseases, we analyzed the vulvar microbiome by shotgun metagenomic sequencing on composition at species level and for functional capacity. This was performed in a large population enrolled in the Vulvar Microbiome Leiden Cohort (VMLC), including a total of 58 healthy women in a broad age range (22-82 years). Moreover, we analyzed vulvar microbiome derived from 9 participants presenting a vulvar disease, including vulvar lichen sclerosus (LS; N = 6), or high-grade squamous intraepithelial lesion (HSIL; N = 3).

RESULTS: Compositional analyses showed a skin-, vagina-, or multispecies mixture- dominant bacterial signature, which revealed differences in the alpha diversity and functional capacity of the microbiome. Upon aging the presence of Lactobacillus iners, L. crispatus, and L. gasseri in the vulvar microbiome shifted toward reduction. In the microbiome of individuals with a vulvar disease, higher abundance of Staphylococcus hominis, Micrococcus luteus, Corynebacterium amycolatum, and Corynebacterium simulans was detected, and an altered functional capacity for the L-histidine pathway.

DISCUSSION: In conclusion, we identified variations in microbial taxa and functional capacities in the vulvar microbiome that are associated with age and disease (LS and HSIL), which can be targeted to develop microbiome-based vulvar therapies promoting women's health.},
}

@article {pmid41048504,
year = {2025},
author = {Ai, X and Huang, C and Liu, Q and Duan, R and Ma, X and Li, L and Shu, Z and Miao, Y and Shen, H and Lv, Y and Jiang, Z and Luo, H and Long, Z},
title = {Gut microbiome dynamics and functional shifts in healthy aging: insights from a metagenomic study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1629811},
pmid = {41048504},
issn = {1664-302X},
abstract = {INTRODUCTION: Population aging represents a significant challenge in contemporary society. The gut microbiome plays a critical role in maintaining host health and physiological functions, and its alterations with advancing age are closely associated with the process of healthy aging.

METHODS: This study conducted a comprehensive analysis of the gut microbiome in hundred healthy elderly individuals (aged ≥60) residing in Changshou Town, Zhongxiang City, Hubei Province, utilizing metagenomic sequencing technology. The primary objective was to investigate the changes in the gut microbiome and its potential functions during the latter stages of life. Participants were categorized into three distinct age groups: the Young-Old group (YO, ages 60-74), the Middle-Old group (MO, ages 75-89), and the Long-Lived Old group (LO, ages 90-99).

RESULTS: The findings indicate that the diversity of the gut microbiome tends to diminish with age. However, a significant reversal was observed among healthy longevity elderly individuals. Our analysis specifically focused on the trends in the alterations of gut microbiome species and their potential functions as age increases, revealing that the changes in major differential functions closely align with the trends in major differential species, demonstrating a strong positive correlation. The YO group exhibited a more diverse array of differential microbial characteristics and functional traits. Notably, there was a significant enrichment of Bacteroides stercoris in the YO group, which displayed a continuous decline with age, alongside a marked enrichment of pathways associated with xenobiotic biodegradation and metabolism. Furthermore, species significantly linked to aging-related pathways, such as oxidative phosphorylation, were identified through species functional correlation analysis. Specifically, Collinsella bouchesdurhonensis and Prevotella stercorea were enriched in the LO and YO groups, respectively. In total, we successfully obtained two hundred and thirty eight high-quality bins through metagenomic assembly, which included the identification of four species with 100% completeness, as well as the genomic information of the Methanobrevibacter smithii A across all groups.

DISCUSSION: This study characterizes the age-associated trends in gut microbiome composition and function during later-life healthy aging, providing exploratory insights that may inform future microecological intervention strategies, pending validation in longitudinal studies.},
}

@article {pmid41048502,
year = {2025},
author = {Peng, X and Wei, Y and Zhou, X},
title = {Enhancing pathogen identification through AI-assisted metagenomic sequencing.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1634194},
pmid = {41048502},
issn = {1664-302X},
abstract = {INTRODUCTION: To address the limitations of current metagenomic identification approaches, we proposed a principled AI-assisted architecture that enhances accuracy, scalability, and biological interpretability through three core innovations.

METHODS: Firstly, we developed a structured probabilistic model that formulates pathogen detection as a hierarchical and compositional inference task under taxonomic and ecological constraints. This framework enables the integration of phylogenetic priors and sparsity-aware mechanisms, reducing noise and ambiguity. By modeling taxonomic structure and ecological dependencies, the approach ensures more accurate identification, especially in complex or low-abundance microbial communities. Secondly, we introduced the Taxon-aware Compositional Inference Network (TCINet), a deep learning model that processes sequencing reads to produce taxonomic embeddings. TCINet estimates abundance distributions via masked neural activations that enforce sparsity and interpretability, while also propagating uncertainty through log-normal variance modeling. Designed to respect microbial phylogeny and co-occurrence patterns, TCINet enables scalable, biologically plausible inference across diverse clinical and environmental datasets. Thirdly, we presented the Hierarchical Taxonomic Reasoning Strategy (HTRS), a post-inference module that refines predictions by enforcing compositional constraints, propagating evidence across taxonomic hierarchies, and calibrating confidence using entropy and variance-based metrics. HTRS includes context-aware thresholding and co-occurrence priors to adaptively optimize performance based on dataset characteristics.

RESULTS: Together, these innovations create a unified framework for metagenomic identification that combines probabilistic modeling, deep learning, and structured reasoning.

DISCUSSION: The architecture delivers robust and interpretable results, making it suitable for applications in clinical diagnostics, environmental monitoring, and ecological research.},
}

@article {pmid41048492,
year = {2025},
author = {Chen, X and Yu, D and Yan, Y and Yuan, C and He, J},
title = {Soil viruses drive carbon turnover during subtropical secondary forest succession.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1633379},
pmid = {41048492},
issn = {1664-302X},
abstract = {INTRODUCTION: Soil viruses are increasingly recognized as key regulators of microbial ecology and ecosystem function, yet their roles in forest ecosystems, particularly during natural secondary succession, remain largely unexplored.

METHODS: We examined soil viral communities across five successional stages of secondary forests to investigate their taxonomic dynamics and functional potential. Using high-throughput viral metagenomics, we characterized viral community structure, abundance, and auxiliary metabolic gene content.

RESULTS: Our results demonstrate that soil viral abundance and community composition shift significantly with forest stand age. Viral richness increased during succession, with compositional transitions observed across stages; however, tailed bacteriophages consistently dominated. Structural equation modeling and linear mixed-effects analysis identified soil pH and bacterial diversity as primary environmental determinants of viral diversity. Functionally, soil viruses harbored auxiliary metabolic genes related to carbohydrate metabolism, indicating their potential involvement in modulating host metabolic processes. Successional trends in viral functional profiles revealed a transition from carbon assimilation to carbon release pathways, suggesting viral mediation of carbon turnover. Notably, the enrichment of glycoside hydrolase and glycosyl transferase genes across forest ages implies a role for viruses in shaping microbial carbon processing capacities through carbohydrate-active enzyme contributions.

DISCUSSION: These findings provide novel evidence that soil viruses actively participate in ecosystem succession by influencing microbial functional potential and biogeochemical cycling. This study underscores the ecological importance of soil viral communities in regulating carbon dynamics during secondary forest development.},
}

@article {pmid41048389,
year = {2025},
author = {Kong, S and Abrams, E and Binik, Y and Cappelli, C and Chu, M and Cornett, T and Culbertson, I and Garcia, E and Henry, J and Lam, K and Lampman, DB and Morenko, G and Rivera, I and Swift, T and Torres, I and Velez, R and Waxman, E and Wessely, S and Yuen, A and Lardner, CK and Weissman, JL},
title = {Metagenomes and metagenome-assembled genomes from tidal lagoons at a New York City waterfront park.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20081},
pmid = {41048389},
issn = {2167-8359},
mesh = {New York City ; *Metagenome ; *Parks, Recreational ; Metagenomics ; Humans ; *Seawater/microbiology ; Microbiota/genetics ; *Water Microbiology ; },
abstract = {New York City parks serve as potential sites of both social and physical climate resilience, but relatively little is known about how microbial organisms and processes contribute to the functioning of these deeply human-impacted ecosystems. We report the sequencing and analysis of 15 shotgun metagenomes, including the reconstruction of 129 high-quality metagenome-assembled genomes, from tidal lagoons and bay water at Bush Terminal Piers Park in Brooklyn, NY sampled from July to September 2024. Our metagenomic database for this site provides an important baseline for ongoing studies of the microbial communities of public parks and waterfront areas in NYC. In particular, we provide rich functional and taxonomic annotations that enable the use of these metagenomes and metagenome-assembled genomes for a wide variety of downstream applications.},
}

New York City
*Metagenome
*Parks, Recreational
Metagenomics
Humans
*Seawater/microbiology
Microbiota/genetics
*Water Microbiology

@article {pmid41048206,
year = {2025},
author = {Tao, H and Zheng, W},
title = {Non-Tuberculous Mycobacterial Infections of the Skin and Soft Tissue in a Chinese Population: A Retrospective Analysis of 15 Cases.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5139-5147},
pmid = {41048206},
issn = {1178-6973},
abstract = {BACKGROUND: Non-tuberculous mycobacteria (NTM) skin and soft tissue infections (SSTIs) are increasingly recognized but underdiagnosed in China.

METHODS: This retrospective study analyzed 15 confirmed cases of NTM SSTIs treated at a southern Chinese hospital from 2012 to 2022. Clinical data, including demographics, clinical presentations, comorbidities, diagnostic methods, treatment regimens, and outcomes, were collected and analyzed. Diagnostic efficacy of conventional culture and metagenomic next-generation sequencing (mNGS) was compared.

RESULTS: The median age of patients was 57 years, and 66.7% were farmers. Pathogens identified included Mycobacterium abscessus (20.0%), M. marinum (13.3%), and rapidly growing mycobacteria (13.3%). Immunocompromised states, such as anti-interferon-gamma autoantibody positivity, were present in 40.0%. mNGS demonstrated superior diagnostic performance, achieving a detection rate of 86.7% (13/15 cases), compared to 26.7% for culture. Treatment regimens, including clarithromycin, rifampin, ethambutol, and moxifloxacin, lasted 1-24 months. Outcomes showed cure in 8 patients (53.3%), improvement in 6 (40.0%), and 1 lost to follow-up.

CONCLUSION: NTM SSTIs present significant diagnostic and therapeutic challenges, with clinical variability and frequent association with immunocompromised states. M. abscessus, M. marinum, and M. avium were the predominant pathogens. mNGS improves detection but still should complement culture. Precise pathogen identification and tailored therapy are essential for achieving optimal outcomes, and further studies are needed to refine diagnostics and treatment strategies.},
}

@article {pmid41048034,
year = {2025},
author = {Wright, SL and Abdul-Aziz, M and Blaha, GN and Ta, CK and Gancz, A and Ademola-Popoola, IJ and Szécsényi-Nagy, A and Sereno, PC and Weyrich, LS},
title = {Wet Lab Protocols Matter: Choice of DNA Extraction and Library Preparation Protocols Bias Ancient Oral Microbiome Recovery.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70054},
doi = {10.1111/1755-0998.70054},
pmid = {41048034},
issn = {1755-0998},
abstract = {Ancient DNA (aDNA) analysis of archaeological dental calculus has provided a wealth of insights into ancient health, demography and lifestyles. However, the workflow for ancient metagenomics is still evolving, raising concerns about reproducibility. Few systematic investigations have examined how DNA extraction methods and library preparation protocols influence ancient oral microbiome recovery, despite evidence from modern populations suggesting that they do. This leaves a gap in our understanding of how wet-lab protocols impact aDNA recovery from dental calculus. In this study, we apply two DNA extraction and two library preparation methods in the aDNA field on dental calculus samples from Hungary and Niger. Samples from each context have similar chronological ages, but differences in their levels of aDNA preservation are notable, providing additional insights into how the efficacy of wet-lab protocols is impacted by sample preservation. Several metrics were employed to assess intra- and inter-sample variability, such as DNA fragment length recovery, GC content, clonality, endogenous content, DNA deamination and microbial composition. Our findings indicate that both DNA extraction and library preparation protocols can considerably impact ancient DNA recovery from archaeological dental calculus. Furthermore, no single protocol consistently outperformed the others across all assessments, and the effectiveness of specific protocol combinations depended on the preservation of the sample. These findings highlight the challenges of meta-analyses and underscore the need to account for technical variability. Lastly, our study raises the question of whether the field should strive to standardise methods for comparability or optimise protocols based on sample preservation and specific research objectives.},
}

@article {pmid41046791,
year = {2025},
author = {Wang, H and Chen, H and Ruan, C and Liao, J and Schwarz, C and Shi, B and Alvarez, PJJ and Yu, P},
title = {Nanoplastics induce prophage activation and quorum sensing to enhance biofilm mechanical and chemical resilience.},
journal = {Water research},
volume = {288},
number = {Pt B},
pages = {124712},
doi = {10.1016/j.watres.2025.124712},
pmid = {41046791},
issn = {1879-2448},
abstract = {Despite the prevalence of nanoplastics (NPs) in natural and engineered water systems and their association with microbial risks, bacterium-phage interactions have been largely overlooked in the context of biofilm formation. Here, we investigated the effects of positively (PS-NH2) and negatively (PS-COOH) charged polystyrene nanoplastics (PS-NPs) on dual-species biofilms composed of Escherichia coli (λ+) and Pseudomonas aeruginosa. PS-NPs promoted biofilm formation and stability at environmentally relevant concentrations (e.g., 100-1000 ng/L), with PS-NH2 exhibiting higher influence. The cellular internalization of PS-NPs increased the reactive oxygen species (ROS) levels by 2.18-2.25 folds, triggered prophage λ activation followed by lysis of E. coli (λ+) after exposure to PS-NPs. Transcriptomic analyses revealed that PS-NPs, especially PS-NH2, activated the SOS response (2.35-2.63-fold), λ phage replication (2.68-3.97-fold), and interspecies quorum sensing (2.24-5.13-fold), which was verified by the proteomic analyses. Therefore, PS-NPs stimulated protective extracellular polymeric substances (EPS) secretion with eDNA content increased to 325.8-433.8 μg/cm[2]. Enhanced EPS production contributed to improved biofilm mechanical properties (1.46-1.57-fold as measured by atomic force microscopy) and increased resistance to chlorine disinfection. Metagenomic analysis of pipeline biofilm demonstrated that PS-NPs promoted bacterium-phage interactions and enhanced bacterial antiviral defense systems, which stimulated multi-species biofilm formation and enhanced environmental resilience. Overall, our findings provide novel insights into the interplay between nanoplastics and bacterium-phage dynamics, highlighting increased microbial risks associated with waterborne nanoplastics.},
}

@article {pmid41046720,
year = {2025},
author = {Yang, J and Wang, S and Heal, KV and Chen, L and Zhou, C},
title = {Microbial functional groups activate insoluble rhizosphere phosphorus to mitigate P limitation of Chinese fir plantations.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127503},
doi = {10.1016/j.jenvman.2025.127503},
pmid = {41046720},
issn = {1095-8630},
abstract = {The decline in soil phosphorus (P) reserves and its low solubility pose significant challenges in long-term plantation cultivation. In P-limited subtropical environments, the rhizosphere microbial community and associated genes play a crucial role in driving P cycling and availability during the long-term development of forest plantations. Using the space-for-time substitution method, we investigated rhizosphere P cycling in Chinese fir (Cunninghamia lanceolata) plantations at different growth stages in Fujian Province, southern China. We utilized the modified Hedley fractionation method and metagenomic sequencing for rhizosphere soil samples from stand ages of 6, 26, 45, and 102 years. The results revealed that, with stand development, rhizospheric concentrations of total, stable and moderately labile P decreased significantly, whereas labile P became progressively enriched (P < 0.05). Genes involved in organic P mineralization and P transport were positively correlated with labile P concentrations in the rhizosphere (P < 0.05), whereas P metabolism regulatory genes were negatively correlated with moderately labile P (P < 0.05). Additionally, the dominant P-solubilizing bacteria-Bacteroidetes and Rudaea-exerted significant positive effects on labile P and negative effects on stable P, respectively (P < 0.05). Overall, rhizospheric P reserves were significantly depleted in the Chinese fir plantations during their developmental progression. However, this unsustainable trend in P reserves was mitigated through synergistic interactions between P-solubilizing bacteria and P metabolism genes, which catalyzed the conversion of insoluble P into labile P, while enhancing plant P uptake efficiency. Consequently, we propose science-informed management practices-such as optimizing P fertilization management, inoculating P-solubilizing microbial agents, utilizing organic fertilizers, and introducing native broadleaf species-to sustain functional stability and long-term productivity of subtropical plantation ecosystems.},
}

@article {pmid41000811,
year = {2025},
author = {Konnaris, MA and Saxena, M and Lazar, N and Silverman, JD},
title = {Uncertainty Modeling Outperforms Machine Learning for Microbiome Data Analysis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41000811},
issn = {2692-8205},
abstract = {Microbiome sequencing measures relative rather than absolute abundances, providing no direct information about total microbial load. Normalization methods attempt to compensate, but rely on strong, often untestable assumptions that can bias inference. Experimental measurements of load (e.g., qPCR, flow cytometry) offer a solution, but remain costly and uncommon. A recent high-profile study proposed that machine learning could bypass this limitation by predicting microbial load from sequencing data alone. To evaluate this claim, we assembled mutt, the largest public database of paired sequencing and load measurements, spanning 35 studies and over 15,000 samples. Using mutt, we show that published machine learning models fail to generalize: on average they perform worse than a naive baseline that always predicted the training set mean. These failures stem from covariate shift-limited shared taxa between studies, differences in community composition, and differences in preprocessing pipelines-that silently derail model inputs. In contrast, Bayesian partially identified models do not attempt to impute microbial load, but instead propagate scale uncertainty through downstream analyses. Across 30 benchmark datasets, Bayesian partially identified models consistently outperformed normalization and machine learning approaches, providing a principled and reproducible foundation for microbiome inference.},
}

@article {pmid41046693,
year = {2025},
author = {Theysgeur, S and Dugardin, C and Louvel, B and Lemière, S and Muchembled, J and Taminiau, B and Daube, G and Siah, A and Ravallec, R and Hilbert, JL and Lucau-Danila, A},
title = {Assessment of health effects of potato crop phytopharmaceuticals and storage products in a murine model.},
journal = {The Science of the total environment},
volume = {1002},
number = {},
pages = {180630},
doi = {10.1016/j.scitotenv.2025.180630},
pmid = {41046693},
issn = {1879-1026},
abstract = {Potatoes are among the most widely consumed staple foods worldwide, but their cultivation and storage frequently involve multiple phytopharmaceutical products (PPPs), raising concerns about the health risks of dietary pesticide residues. The health effects of multi-residue PPPs used in potato cultivation were assessed in an in vivo murine model, involving 36 mice, and evaluated through omics analyses. Two field cultivation methods (conventional and organic) and two post-harvest storage conditions (using 1,4-dimethylnaphthalene and mint essential oil as sprout inhibitor treatments) were considered. Potato tubers were processed into flour and administered to the animals at a moderate daily dose for 20 consecutive days. Nutrigenomic analyses revealed significant gene deregulations, with 70 genes affected in the liver, 56 in the jejunum, and 52 in the brain, suggesting disturbances in cellular proliferation, nervous system functions, lipid and carbohydrate metabolism, reproductive health, and immune responses. Metagenomic analyses indicated microbiota imbalances, including a shift in the Firmicutes/Bacteroidota ratio and changes in 2 bacterial genera with potentially adverse effects. The main residues suspected of producing these effects include propamocarb, carfentrazone, 1,4-dimethylnaphthalene, copper derivatives, and peppermint essential oil. These findings highlight the importance of large-scale omics approaches in uncovering potential biological disruptions, underscore the health risks associated with chronic dietary exposure to pesticide residues, particularly in mixtures, and emphasize the need to reassess regulatory standards to promote agricultural practices that minimize pesticide residues to better protect the environment and human health.},
}

@article {pmid41046691,
year = {2025},
author = {Zhang, N and Li, W and Wang, H and Lv, G},
title = {Metabolomic insights into rhizosphere microbial dynamics in desert plants under drought stress.},
journal = {The Science of the total environment},
volume = {1002},
number = {},
pages = {180653},
doi = {10.1016/j.scitotenv.2025.180653},
pmid = {41046691},
issn = {1879-1026},
abstract = {Drought hinders plant growth and development. However, studies on rhizospheric metabolism and microbial composition of desert plants under drought stress are limited. This study used untargeted metabolomics to detect that the differential metabolites included mainly alkaloids and their derivatives, benzenoids, lipids, and lipid molecules under drought stress. A Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the differences between drought stress in the rhizosphere environment were usually reflected in microbial metabolism, plant hormone biosynthesis, and secondary metabolite biosynthesis in different environments. Metagenomic analysis showed that the relative abundances of Chloroflexi, Firmicutes, and Gemmatimonadetes in the mild drought rhizosphere group (MiR) were significantly higher than those in the severe drought rhizospheric soil group (SR) in the phylum of the microorganisms; the relative abundance of Proteobacteria in the SR group was also significantly higher. Through the analysis of the correlation network, it is found that there is a significant correlation between microorganisms and differential metabolites. During drought stress, plants can indirectly influence the support of soil microbes by modifying the structure and concentration of metabolites, which helps to enhance drought tolerance. This study provides a theoretical basis for exploring new stress adaptation strategies and protecting soil microecology.},
}

@article {pmid41046678,
year = {2025},
author = {Alhaboub, A and Deschenes, NM and Li, XX and Williams, VR and Katz, KC and Park, SY and Aftanas, P and Wong, H and Sjaarda, C and Tozer, K and Maguire, F and Leis, J and Sheth, P and Kozak, R},
title = {Some assembly required: Comparison of bioinformatic pipelines for analysis of viral metagenomic sequencing from nosocomial respiratory virus outbreaks.},
journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology},
volume = {181},
number = {},
pages = {105877},
doi = {10.1016/j.jcv.2025.105877},
pmid = {41046678},
issn = {1873-5967},
abstract = {INTRODUCTION: Metagenomic sequencing (mGS) is a useful tool for identifying pathogens in patient samples. During nosocomial outbreaks of respiratory viruses, mGS allows for the identification of viral strains and provides insight into their genetic relatedness. Multiple bioinformatics analysis assembler are available for processing data, but a comprehensive comparison of their performance in for respiratory virus outbreaks has not been conducted.

METHODS: This study sequenced samples from five separate nosocomial outbreaks of RNA respiratory viruses. RNA was extracted from the samples, and cDNA was synthesized using random hexamers, and then sequenced on an Illumina Miniseq following Nextera DNA Flex library preparation. The data from each outbreak were analyzed using four different assemblers: MEGAHIT, rnaSPAdes, rnaviralSPAdes, and coronaSPAdes, to evaluate their analytical performance.

RESULTS: The mGS confirmed the viral identification and provided accurate strain identification for both coronavirus and parainfluenza virus samples. However, differences were observed between the assemblers in terms of the largest contigs produced and the proportion of the viral genome aligned with reference genomes. Notably, coronaSpades outperformed the other pipelines for analyzing seasonal coronaviruses, generating more complete data and covering a higher percentage of the viral genome.

CONCLUSION: Achieving a higher percentage of the viral genome sequence is crucial for a more detailed characterization, which is especially valuable for outbreak analysis where viral strains may only differ by a few genetic changes. Comparison of assemblers will allow for clinical laboratories to determine the bioinformatic pipeline that is optimal for helping clinicians better manage outbreaks.},
}

@article {pmid41046586,
year = {2025},
author = {Kwiatkowska, AM and Guzmán, JA and Lafaurie, GI and Castillo, DM and Cardona, AF},
title = {Exploring the role of the oral microbiome in saliva, sputum, bronchoalveolar fluid, and lung cancer tumor tissue: A systematic review.},
journal = {Translational oncology},
volume = {62},
number = {},
pages = {102557},
doi = {10.1016/j.tranon.2025.102557},
pmid = {41046586},
issn = {1936-5233},
abstract = {OBJECTIVE: To explore the association between the oral microbiome and the presence or progression of lung cancer (LC) using metagenomic sequencing techniques.

METHODS: Databases, including PubMed and EMBASE, were reviewed. Eligible studies included the study of oral microorganisms via genomic sequencing and molecular mechanisms associated with LC in saliva, sputum, bronchoalveolar lavage fluid (BALF), or tumor tissue from LC patients. A quality analysis of the studies was carried out, and a qualitative synthesis was performed according to the localization and sample type. Meta-analysis was performed on alpha diversity indexes.

RESULTS: Of the 1880 scrutinized articles, 50 studies were selected, comprising 29 cross-sectional, 7 case-control, and 14 cohort studies. The quality analysis sheds light on potential biases. The findings revealed a conspicuous overgrowth of specific microbial taxa in LC patients' saliva BALF samples of Veillonella and Streptococcus. Conversely, the Bacteroides genus, related to periodontal disease, exhibited no significant correlation with LC. Microorganisms in tumoral tissue were associated with poor prognosis. Veillonella was associated with a better response to ICIs therapy. Oral microorganisms were related to metabolic reprogramming with xenobiotic biodegradation, amino acid, sugar, sucrose, and lipidic metabolism, immune modulation, and proinflammatory responses.

CONCLUSION: Overgrowth of specific oral microorganisms in the saliva and BALF is associated with diagnosis, poor prognosis, and low response to immunotherapy. Veillonella could be a marker for response to ICIs therapy. Further well-designed studies should evaluate the impact of the oral microbiome on the response to ICIs.},
}

@article {pmid41045990,
year = {2025},
author = {Liu, Y and Zheng, Y and Wang, L and Guo, Y and Huang, G and Yuan, Z and Wang, F and Gai, W and Xing, J},
title = {Bacteriophage combined with mNGS enhances the specificity of bacterial infection diagnosis.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106618},
doi = {10.1016/j.jinf.2025.106618},
pmid = {41045990},
issn = {1532-2742},
abstract = {INTRODUCTION: Metagenomic next-generation sequencing (mNGS) is an important tool for enhancing pathogen detection in infected patients. However, distinguishing between specimens that are infected or colonized is still a major challenge.

OBJECTIVES: To explore the composition of bacteriophages in the blood and respiratory tract of the human body, the association between bacteriophage detection and bacterial infections, and whether bacteriophages can assist in differentiating infectious pathogens according to mNGS results.

METHODS: Clinical samples from hospitalized patients were collected between January 2023 and February 2024. DNA and cell-free DNA were extracted from BALF and plasma retrospectively to identify the pathogens present, and bacteriophage annotations were conducted.

RESULTS: A total of 299 samples, comprising 136 blood samples and 163 BALF samples, were obtained from 218 patients. Compared with the samples negative for bacteria, both blood and bronchoalveolar lavage fluid (BALF) samples infected with Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and S. aureus showed a corresponding increase in the proportions of phages related to these pathogens. In BALF samples with Acinetobacter baumannii infection, the proportions of Autographiviridae, Siphoviridae, and Myoviridae were significantly greater than those in the Acinetobacter baumannii colonization group. The sensitivity of Myoviridae for differentiating between infection and colonization was 86.36%, and the specificity was 52.94%.

CONCLUSION: In sepsis, compared with conventional mNGS methods alone, the use of bacteriophages combined with mNGS was more effective in identifying causative pathogens and had higher specificity. These findings may provide new ideas and tools for improving clinical infection diagnosis.},
}

@article {pmid41045972,
year = {2025},
author = {Song, X and Meng, H and Yang, T and Li, Y and Zheng, F and Yan, X},
title = {Female accessory reproductive glands of Paederus fuscipes serve as a reservoir of symbiotic pederin-producing bacteria.},
journal = {Insect biochemistry and molecular biology},
volume = {},
number = {},
pages = {104408},
doi = {10.1016/j.ibmb.2025.104408},
pmid = {41045972},
issn = {1879-0240},
abstract = {Paederus fuscipes, an ecologically and medically important species, is known for its blistering toxin pederin in hemolymph. Evidence demonstrates that the toxin is synthesized by the uncultured symbiotic pederin-producing bacteria (PPB) in P. fuscipes, but the biological characteristics of PPB within the beetle host remain poorly characterized. Here, we investigated PPB abundance variations in P. fuscipes across different factors (sexes, life stages, habitats, and organs), along with their colonization sites and metabolic potentials. The findings revealed that the PPB abundance in female P. fuscipes at the level of individuals and tissues exhibited stable colonization patterns, independent of habitat and time changes. Notably, PPB dominated the bacterial community in females (relative abundance ≥ 66.08%) and nearly occupied reproductive organs (relative abundance ≥ 96.31%). Moreover, our results indicated that PPB were predominantly enriched in the accessory glands of female reproductive organs, which could serve as a reservoir for PPB proliferation. Although PPB were not cultured in this study, metagenomic binning yielded the draft genome of PPB (CheckM completeness = 85.14%, contamination = 0), in which genes related to pederin biosynthesis were identified. Phylogenetic analyses revealed that PPB formed a sister clade to Pseudomonas aeruginosa rather than nesting within the P. aeruginosa lineage. Metabolic module prediction analysis revealed specific deficiencies in PPB's energy metabolism and amino acid biosynthesis pathways, suggesting limited free-living potential for PPB. Collectively, this study provides insights into PPB biological characteristics within their beetle host and paves the way for biotechnological exploitation related to pederin production.},
}

@article {pmid41045941,
year = {2025},
author = {Alcolea-Medina, A and Snell, LB and Humayun, G and Al-Yaakoubi, N and Ward, D and Alder, C and Patel, V and Vivian, F and Meadows, CIS and Wyncoll, D and Paul, R and Barratt, N and Batra, R and Edgeworth, J and Nebbia, G and Whitehorn, J},
title = {Rapid pan-microbial metagenomics for pathogen detection and personalised therapy in the intensive care unit: a single-centre prospective observational study.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101174},
doi = {10.1016/j.lanmic.2025.101174},
pmid = {41045941},
issn = {2666-5247},
abstract = {BACKGROUND: Most clinical metagenomic studies do not provide rapid results, detect pathogens from all microbial kingdoms, or measure clinical impacts. We aimed to evaluate the feasibility, performance, and clinical impacts of a rapid pan-microbial respiratory metagenomic service for patients admitted to intensive care units (ICUs).

METHODS: This was a single-centre observational study of a rapid metagenomics service that tests respiratory samples from ICU patients at Guy's and St Thomas' hospitals, London, UK, between Dec 5, 2023, and April 12, 2024. Testing used a previously published pan-microbial metagenomics workflow, which simultaneously detects bacteria, fungi, and DNA and RNA viruses; provides same-day preliminary results after 2 h; and provides final results after 24 h. Patients were included if they were aged 18 years or older, admitted to the ICU, had confirmed respiratory failure requiring supplemental oxygen or advanced airway support, and had at least one of the following: (1) clinical suspicion of lower respiratory tract infection based on clinical, biochemical, or radiological findings, (2) sepsis of unknown origin, and (3) concern from an intensive care physician regarding inflammatory pathology. Patients with a suspected or confirmed containment level three organism were excluded. The outcome was performance characteristics of the metagenomic test compared with routine diagnostic testing, detection of additional pathogens by metagenomics, change in antimicrobial prescribing within 24 h of testing, and initiation of immunomodulation.

FINDINGS: We processed 114 samples (1-5 per day) from 74 patients (39 [53%] female and 35 [47%] male). 107 (94%) of 114 samples passed quality control, of which 101 (94%) provided same-day preliminary results. Bacteria were detected in 45 (43%) of 104 tested specimens, fungal organisms in 17 (16%) of 104 tested specimens, and viruses in 28 (34%) of 83 tested specimens. Sensitivity in lower respiratory tract samples after 24 h was 97% (95% CI 87-100) for bacteria, 89% (65-99) for fungi, and 89% (71-98) for viruses, with only one false positive for bacteria. Metagenomics identified 42 pathogens not detected by other tests in 32 (30%) of 107 samples. Antimicrobial therapy was changed after metagenomic results from 30 (28%) of 107 samples: 22 (21%) were de-escalated and eight (7%) were escalated. Metagenomics contributed to the initiation of immunomodulation in 15 (20%) of 74 patients for a range of inflammatory conditions. Pathogens with clinical significance to local infection control or national public health were found in ten (14%) of 74 patients, including three invasive Group A streptococci, two parvovirus B19, and one each of HIV-1, measles virus, Mycobacterium tuberculosis, Neisseria meningitidis, and Mycoplasma pneumoniae.

INTERPRETATION: Respiratory metagenomics for ICU patients showed good performance and turnaround time, and diverse clinical and public health benefits. This ability to inform both personalised patient therapy and infectious disease surveillance needs evaluation in multicentre studies.

FUNDING: None.},
}

@article {pmid41045876,
year = {2025},
author = {Gebert, J and Böhnke-Brandt, S and Zander, F and Indenbirken, D and Bergmann, L and Krohn, I and Perner, M},
title = {Linking microbial community composition, microbial biomass and extracellular polymeric substances to organic matter lability gradients in sediments of the tidal Elbe River.},
journal = {The Science of the total environment},
volume = {1002},
number = {},
pages = {180614},
doi = {10.1016/j.scitotenv.2025.180614},
pmid = {41045876},
issn = {1879-1026},
abstract = {The port of Hamburg represents a transition zone between upstream, shallow regions of high net primary production and downstream deep and more turbulent waters in the tidal Elbe River in northwestern Germany. Correspondingly, strong gradients of degradable organic matter (OM) on a distance of a few river kilometers had been identified. This study links microbial community composition using 16S metagenomic amplicons and extracellular polymeric substances (EPS) composition to the observed gradients of sediment OM lability. It was hypothesized that lability gradients caused by higher concentrations of biogenic, autochthonous OM upstream and greater share of already stabilized OM downstream reflect in gradients of microbial community composition, diversity and EPS characteristics. Indeed, available OM was found to act as key driver regulating syntrophic microbial community composition and associated metabolic features, with location-specific overriding the effect of seasonal variations. Upstream sites with high available OM featuring lower bacterial but increased archaeal diversity and elevated methane and carbon dioxide fluxes, whereas lower OM lability downstream fostered a more diverse bacterial but decreased archaeal diversity. The ratio between microbial taxon richness and biomass correlated inversely with OM transformation rates. These patterns also reflected in increased EPS concentration produced in response to metabolic needs (i.e. polysaccharides and proteins), whereas structural components such as lipids, which can be more resistant under the prevailing anoxic conditions, remained more evenly distributed along the transect. Although bacterial relative abundances exceeded archaeal abundances (<1 %) by far, archaeal functional significance remained pivotal for the final release of carbon as methane and carbon dioxide under the mostly reducing conditions in the deposited sediment.},
}

@article {pmid41045656,
year = {2025},
author = {Tuffou, R and Windal, L and Delmotte, S and Skorski, G and Metton, I and Voisin, SN and Surribas, A and Beytur, S and Leborgne, M and Blanquart, H and Salducci, X and Feugier, A},
title = {Combining fermentation and vermicomposting for sustainable pet food waste management: Effects of waste profile and inoculum source.},
journal = {Waste management (New York, N.Y.)},
volume = {208},
number = {},
pages = {115176},
doi = {10.1016/j.wasman.2025.115176},
pmid = {41045656},
issn = {1879-2456},
abstract = {Ingredient production is the main driver of pet-food GHGs and land use. Indeed, the pet food industry uses nearly 495,000 km[2] of land annually. Yet, waste streams from production and declassified products remain underexplored as resources to produce high quality soil amendment. This study proposes an integrated approach to valorise such organic wastes through microbial fermentation prior to vermicomposting. Two experiments were conducted. (1) the effects of kibble incorporation ratio (15 % vs. 30 %), fibre source (spruce flakes, SF vs. beech sawdust, BS), and container size (50 L vs. 500 L) on fermentation dynamics, worm preference, and vermicompost properties were assessed. (2) the functional equivalence of commercial inoculum (EM®) and locally sourced indigenous microorganisms (IMO) was evaluated. Results showed that fibre type significantly influenced fermentation outcomes at low kibble incorporation, with BS lowering pH (from 9 in SF30% to 5.2 in BS15%, P < 0.001) and increasing redox potential (+213 %, P < 0.001). Electroconductivity was strongly affected by both kibble ratio (+110 %, P < 0.001) and fibre source (+130 %, P < 0.001). Worms displayed strong preference for BS-based substrates (+493 % density in 7 days, P < 0.001). Vermicompost derived from SF exhibited slower nitrogen and carbon mineralisation than BS. Container size had no effect on fermentation. EM® and IMO performed equivalently in fermentation efficiency, worm attraction, and functional microbial activity (metagenomic/metaproteomic analyses). This work demonstrates that combining microbial pre-digestion with vermicomposting can upcycle pet food waste into valuable soil amendments, while supporting local circular bioeconomy and sustainable waste management.},
}

@article {pmid41044998,
year = {2025},
author = {Modin, O and Zheng, D and Schnürer, A and Lundwall, T and Bolanos, SE and Olsson, J},
title = {From Low-Loaded Mesophilic to High-Loaded Thermophilic Anaerobic Digestion: Changes in Reactor Performance and Microbiome.},
journal = {Microbial biotechnology},
volume = {18},
number = {10},
pages = {e70238},
doi = {10.1111/1751-7915.70238},
pmid = {41044998},
issn = {1751-7915},
support = {//Käppalaförbundet/ ; //The Swedish Research Council (VR)/ ; },
mesh = {*Bioreactors/microbiology ; Anaerobiosis ; *Sewage/microbiology ; Methane/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Temperature ; *Microbiota ; *Archaea/classification/genetics/metabolism ; Metagenomics ; },
abstract = {This study investigated temporal dynamics in reactor performance and microbial community structure during anaerobic digestion of sewage sludge when the temperature was changed from 37°C to 55°C, followed by an increase in organic loading rate (OLR). Performance instability was observed immediately following the temperature increase and in the end of the study when the OLR was 11.1 ± 0.3 kgVS m[-3]d[-1]. The specific methane production peaked at 0.31 ± 0.06 Nm[3] kg[-1] volatile solids (VS) during thermophilic operation and when the OLR was 3.5 ± 0.9 kgVS m[-3]d[-1]. Using metagenomic sequencing, 304 species-representative genome bins (SGB) were assembled. Network analysis revealed that 186 SGB were associated with thermophilic conditions and several new species putatively involved in key reactor functions were identified. When reactor function initially stabilised, two hydrogenotrophic and one aceticlastic methanogen (Methanothermobacter spp. and Methanosarcina thermophila), the hydrolytic Coprothermobacter proteolyticus, and putative syntrophic propionate oxidisers (e.g., Pelotomaculaceae) had high relative abundance. During the peak in specific gas production, the community was dominated by one hydrogenotrophic Methanothermobacter species coexisting with syntrophic acetate oxidising bacteria (Thermacetogenium phaeum and other species). Finally, when the reaction function deteriorated due to high OLR, new hydrolytic taxa emerged and the same aceticlastic methanogen as seen during the initial acclimatisation phase returned.},
}

*Bioreactors/microbiology
Anaerobiosis
*Sewage/microbiology
Methane/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
Temperature
*Microbiota
*Archaea/classification/genetics/metabolism
Metagenomics

@article {pmid41044758,
year = {2025},
author = {Pérez-Pérez, L and Galisteo, C and Sanjuán, JMO and Cobo-Díaz, JF and Puente, H and Rubio, P and Carvajal, A and Arguello, H},
title = {Severity of Brachyspira hyodysenteriae colitis correlates to the changes observed in the microbiota composition and its associated functionality in the large intestine.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {105},
pmid = {41044758},
issn = {2524-4671},
support = {PRE2020-093762//Ministerio de Ciencia, Innovación y Universidades/ ; JDC2023-051122-I//Ministerio de Ciencia, Innovación y Universidades/ ; LE088P23//Junta de Castilla y León/ ; },
abstract = {BACKGROUND: The gut microbiota is essential for maintaining nutritional, physiological and immunological processes, but colonic infections such as swine dysentery, caused by Brachyspira hyodysenteriae (B. hyo) disrupt this homeostasis. This study uses shotgun and full-length 16S rRNA sequencing in faeces, colonic contents and mucosa from pigs challenged with B. hyo to provide a high-resolution characterisation of the taxa, functions and metagenome-assembled genomes (MAGs) of interest, disclose their association with the primary pathogen and how they are affected by the pathological changes of the infection.

RESULTS: Changes in the microbiota were associated with disease severity. In early infection, no major findings were observed in diversity or abundance analyses, whereas in acute infection, B. hyo load, mucosal neutrophil infiltration, epithelial ulceration and mucosal thickness were clearly associated with changes in microbiota ordination, which were also associated with a decrease in species richness. Changes included a significant increase in Acetivibrio ethanolgignens, Campylobacter hyointestinalis and Roseburia inulinivorans, which, with the exception of C. hyointestinalis, established themselves as part of the core microbiota and shifted the colonic enterotype in acutely infected animals. MAGs analyses revealed that no major virulence genes were detected in the genomes of the species co-interacting with B. hyo in acute infection. Similarly, functional changes were observed only after the onset of clinical signs, with an increase in functions related to inflammation and toxic effects on the colonic epithelium.

CONCLUSIONS: Our study shows that in colitis caused by B. hyo, changes in the microbiota are mainly a consequence of the lesions that occur in the intestine, with no differences observed in early infection. Similarly, the bacterial species that are increased at the onset of clinical signs may promote intestinal inflammation caused by B. hyo infection, but the analysis of their genomes rule out their participation in the primary infection.},
}

@article {pmid41044750,
year = {2025},
author = {Kang, L and Li, Y and Wang, J and Fu, J and Li, Q and Jiang, Q and Zhou, H and Xiao, H and Zhang, Z and Hong, M},
title = {Seasonal dynamics, dietary patterns, and bamboo leaf nutrition shape the phyllosphere-associated gut microbiota of red pandas.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {104},
pmid = {41044750},
issn = {2524-4671},
support = {grant no. 32470516//National Natural Science Foundation of China/ ; grant no. KCXTD2022-7//Innovation Team Funds of China West Normal University/ ; grant no. 2024NSFSC2082//Sichuan Natural Science Foundation/ ; },
abstract = {BACKGROUND: The gut microbiota of bamboo-eating red pandas (Ailurus fulgens) comprises a intricate and multifaceted ecosystem influenced by numerous factors. Despite considerable research dedicated to captive red pandas, the microbial dynamics observed in wild populations are still not well understood. To address this research gap, our study employed advanced techniques such as high-throughput sequencing and metagenomic analysis to characterize the microbial communities and their functional profiles in fresh fecal samples from wild red pandas and in samples of their primary food source. Our objective was to conduct a thorough examination of how seasonality, diet, bamboo leaf nutrition, and phyllosphere-associated microorganisms affect the gut microbiota of red pandas.

RESULTS: Our findings reveal that seasonal variations have a notable impact on the composition, structure, and functionalities of red pandas' gut microbiota. Specifically, autumn and winter exhibit heightened microbial diversity and richness. Moreover, during different feeding phases (leaf-feeding, shoot-feeding, and mixed-feeding), the gut microbiota displays varied cellulose-digesting abilities, marked by increased expression of key enzymes during high-fiber dietary phases. Our analysis reveals robust correlations between bamboo nutrients and microbial communities in both bamboo and red panda guts. Notably, bamboo's crude protein and phosphorus content are pivotal in shaping the phyllosphere and gut microbial communities, while crude fat, crude protein, and phosphorus emerge as key drivers of microbial structure. Seasonal fluctuations in microbial populations of both bamboo and red panda guts with shared genera, underscore their tight linkage and interconnected seasonal adaptations.

CONCLUSIONS: In conclusion, our study provides a comprehensive understanding of how seasonality, diet, and bamboo leaf nutrition shape the gut microbiota of red panda connected to bamboo microbiome. It underscores the gut microbes' indispensable role in facilitating red pandas' adaptation to their bamboo-based diet, crucial for their survival in natural habitats.},
}

@article {pmid41044404,
year = {2025},
author = {Rodríguez-Gijón, A and Pacheco-Valenciana, A and Milke, F and Dharamshi, JE and Hampel, JJ and Damashek, J and Wienhausen, G and Rodriguez-R, LM and Garcia, SL},
title = {Widely-distributed freshwater microorganisms with streamlined genomes co-occur in cohorts with high abundance.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34482},
pmid = {41044404},
issn = {2045-2322},
mesh = {*Fresh Water/microbiology ; Metagenome ; *Genome, Bacterial ; Genome Size ; Ecosystem ; *Bacteria/genetics/classification ; },
abstract = {Genome size is known to reflect the eco-evolutionary history of prokaryotic species, including their lifestyle, environmental preferences, and habitat breadth. However, it remains uncertain how strongly genome size is linked to prokaryotic prevalence, relative abundance and co-occurrence. To address this gap, we present a systematic and global-scale evaluation of the relationship between genome size, relative abundance and prevalence in freshwater ecosystems. Our study includes 80,561 medium-to-high quality genomes, from which we identified 9,028 species (ANI > 95%) present in a manually curated dataset of 636 freshwater metagenomes. Our results show that prokaryotes with reduced genomes exhibited higher prevalence and relative abundance, suggesting that genome streamlining may promote cosmopolitanism. Furthermore, network analyses revealed that the most prevalent prokaryotes have streamlined genomes that are found in co-occurrent cohorts potentially sustained by metabolic dependencies. Overall, species in these groups possess a diminished capacity for synthesizing different essential metabolites such as vitamins, amino acids and nucleotides, potentially fostering metabolic complementarities within the community. Moreover, we found the presence of the essential biosynthetic functions to be usage-dependent: nucleotide and amino acids biosynthesis are the most complete, whereas vitamin biosynthesis is most incomplete. Our results underscore genome streamlining as a central eco-evolutionary strategy that both shapes and is shaped by community dynamics, ultimately fostering interdependences among prokaryotes.},
}

*Fresh Water/microbiology
Metagenome
*Genome, Bacterial
Genome Size
Ecosystem
*Bacteria/genetics/classification

@article {pmid41044010,
year = {2025},
author = {Bleidorn, C and Sandberg, F and Martin, S and Vogler, AP and Podsiadlowski, L},
title = {The untapped potential of short-read sequencing in biodiversity research.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2025.09.001},
pmid = {41044010},
issn = {0168-9525},
abstract = {The power of short-read DNA sequencing in biodiversity research and evolutionary genomics is rapidly growing due to advances in technology and bioinformatics. Short-read sequencing offers powerful solutions for taxonomic identification, biomass estimation, and phylogenetic reconstruction. Moreover, short-read data enable robust estimation of genome size and repeat content, offering valuable insights into genome evolution. Though growing in popularity, long-read genome assemblies are often not feasible with material from museum collections or raw biodiversity samples. With the growing demand for DNA-based approaches in biodiversity research, short-read genomics provides an easily generated universal data source spanning all levels from individual genomes to ecosystems, and including all species on Earth, to achieve the objectives of the Global Biodiversity Framework (GBF) for the preservation of biodiversity.},
}

@article {pmid41043962,
year = {2025},
author = {Sessions, AL and Magnabosco, C and Barton, HA and Burkhardt, C and Dworkin, JP and Freissinet, C and French, KL and Glavin, DP and Leys, N and Maixner, F and Olsson-Francis, K and Probst, AJ and Quitté, G and Rampe, E and Steele, A and Carrier, BL and Hays, LE and Thiessen, F and Paardekooper, D and Hutzler, A and Harrington, AD and Teece, BL},
title = {Planning Considerations Related to Contamination Control for the Return and Analysis of Martian Samples.},
journal = {Astrobiology},
volume = {},
number = {},
pages = {},
doi = {10.1177/15311074251382157},
pmid = {41043962},
issn = {1557-8070},
abstract = {The joint National Aeronautics and Space Administration and European Space Agency Mars Sample Return (MSR) Campaign is a proposed multi-mission effort to bring selected geological samples from Mars to Earth for the purpose of scientific investigation. Significant parts of these investigations could be affected by Earth-sourced contamination that is either misinterpreted as having a martian origin or that masks a martian signal. The Mars 2020 Perseverance rover implemented strict contamination control requirements to limit contamination of the samples during sample collection. Contamination control and contamination knowledge requirements have not yet been established for the samples after they arrive on Earth. The MSR Sample Receiving Facility (SRF) Contamination Panel (SCP) was tasked with defining the terrestrial biological, organic, and inorganic contamination limits for martian samples during their residence inside the SRF. To reach our recommendations, the SCP studied (i) the previously proposed limits and rationale of the Organic Contamination Panel, (ii) cleanliness levels achieved for sampling hardware by the M2020 mission, (iii) recent improvements in analytical technology and detection limits, (iv) updated information regarding the organic content of martian samples (e.g., from the Sample Analysis at Mars instrument on the Curiosity rover and laboratory analyses of martian meteorites), and (v) information about the composition and geologic context of samples being collected by the Perseverance rover for return to Earth.},
}

@article {pmid41039216,
year = {2025},
author = {Ma, Y and Wang, D and Yu, X and Fan, Y and Yang, Z and Gao, X and Huang, X and Meng, J and Cheng, P and Liu, X and Liu, Z and Li, X},
title = {Moderate altitude exposure induced gut microbiota enterotype shifts impacting host serum metabolome and phenome.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {591},
pmid = {41039216},
issn = {1471-2180},
support = {2023YFE0114300//National key research and development program intergovernmental key projects/ ; No.2024A1515012697//Guangdong Provincial Basic and Applied Basic Research Fund Project/ ; No. 202206010044//Science and Technology Program of Guangzhou, China/ ; No. U24A20652//The Joint Funds of the Natural Science Foundation of China/ ; No. 82272246//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Consistent patterns of gut microbiota variations, particularly in relative abundance, have been identified in the adult human gut. Enterotype, another general measure of the gut microbiota, is a valuable approach for categorizing the human gut microbiota into distinct clusters. The impact of different enterotypes on human health varies, and the changes induced by moderate altitude exposure remain unclear. This study aimed to conduct a comprehensive investigation of the cascade effects triggered by enterotype shifts following moderate altitude exposure.

RESULTS: Using shotgun metagenome sequencing, participants before and after moderate-altitude exposure were classified into cluster BL (dominated by Blautia) and cluster BA (dominated by Bacteroides). Relative to cluster BL, cluster BA consisted predominantly of individuals exposed to moderate altitude. Compared to cluster BL, Cluster BA exhibited rewired metabolism of serum metabolites (i.e., amino acids, fatty acids and bile acids) and gut microbiota, lower inflammatory factor levels (i.e., tumor necrosis factor-α (TNF-α)), and sparser correlations among these parameters. Individuals with baseline BL enterotype who transitioned to the BA enterotype following moderate-altitude exposure showed prominent improvement in fasting blood glucose (FBG) levels, with higher abundance of Bacteroidetes species (e.g., Bacteroides thetaiotaomicron, and Bacteroides uniformis), but lower Proteobacteria species abundance (e.g., Escherichia coli) and decreased L-Glutamic acid levels. Furthermore, fecal microbiota transplantation (FMT) from moderate-altitude exposed individuals to high-fat diet (HFD) fed mice confirmed increased Bacteroides abundance shifts associated with improvements in glucose homeostasis regulation and rewired amino acid metabolism. In addition, significant increases in alanine aminotransferase (ALT) levels but decreased serum creatinine (Scr), arterial oxygen saturation (SaO2), 4-Hydroxyproline, L-Glutamic acid, L-Asparagine, L-Threonine, L-Citrulline, L-Lysine and Isovaleric acid levels were identified as potentially important signals for individuals upon moderate altitude exposure, regardless of the gut microbiota enterotype.

CONCLUSIONS: Moderate altitude exposure could induce enterotype switching, and a Bacteroides-dominant enterotype may be a beneficial pattern of the gut microbiome related to host metabolism. Moderate-altitude exposure has potential implications for glycemic control, suggesting new avenues for managing FBG levels in future.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04245-4.},
}

@article {pmid41043636,
year = {2025},
author = {Ba, XQ and Wang, MF and Huang, WL and Ye, XF and Xu, YY and Li, MM and Jiang, RF and Chen, CN},
title = {Talaromyces Marneffei Infection Involving the Central Nervous System in a Patient with Acquired Immunodeficiency Syndrome: A Case Report and Literature Review.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108096},
doi = {10.1016/j.ijid.2025.108096},
pmid = {41043636},
issn = {1878-3511},
abstract = {BACKGROUND: Talaromycosis, an opportunistic deep invasive mycosis, is caused by the fungus Talaromyces marneffei and is predominantly observed in individuals with acquired immunodeficiency syndrome (AIDS). Involvement of the central nervous system (CNS) is exceedingly rare and presents significant diagnostic challenges, often associated with high mortality rates.

CASE PRESENTATION: This report details a case of CNS Talaromyces marneffei infection in an AIDS patient who initially presented with epileptic seizures. Neuroimaging identified a ring-enhancing lesion within the right frontal lobe, concurrent with a marked elevation in serum β-D-glucan levels. The diagnosis was confirmed through a multimodal approach, including histopathological examination and metagenomic next-generation sequencing (mNGS). Postoperative management involved a sequential regimen of amphotericin B followed by voriconazole, leading to a favorable recovery. The patient is currently on a maintenance elvitegravir-based antiretroviral therapy regimen.

CONCLUSIONS: CNS Talaromyces marneffei infection in AIDS patients often lacks specific clinical manifestations, which complicates diagnosis and treatment. This case report contributes to the existing body of knowledge by presenting a successfully managed case, thereby enhancing the understanding of diagnostic and therapeutic strategies for similar future presentations.},
}

@article {pmid41043345,
year = {2025},
author = {Yu, C and Zhu, H and He, Y and Weng, R},
title = {Comparison of sulfur cyclings coupled with anaerobic ammonium oxidation in response to different river remediations.},
journal = {Journal of environmental management},
volume = {394},
number = {},
pages = {127523},
doi = {10.1016/j.jenvman.2025.127523},
pmid = {41043345},
issn = {1095-8630},
abstract = {The evolution from 'malodor' to 'algae bloom' in remediated urban rivers has received an ever-increasing attention due to relatively high nitrogen (N) loadings. As pivotal autotrophic processes, anaerobic ammonium oxidation (anammox) and sulfur-driven denitrification (SDD) represent promising candidates for N removal in remediated rivers with low C/N ratios. However, how and to what extent SDD is coupled with anammox remained largely unknown. Our investigations of four remediated urban rivers revealed that SDD was more prevalent than anammox, with Thiobacillus (0.13 %-2.51 %) dominating over Candidatus_Brocadia (0-0.02 %). The injection of Ca(NO3)2 greatly enhanced the coupling of SDD and anammox (SDDA) in anaerobic environments, achieving a maximum total nitrogen (TN) removal of 93.89 %. Metagenomic and metatranscriptomic analyses identified Thiobacillus, Thermomonas, and Candidatus_Brocadia as key microbial players, with their activities increased by 0.060 %, 0.015 %, and 0.498 %, respectively. Differently, Sulfurisoma, Dechloromonas, and Candidatus_Scalindua emerged as key players in Na2S2O3-group, while Sulfurisoma, Sulfurimonas, and Candidatus_Scalindua played pivotal roles in FeS2-group. Additionally, river simulations revealed that Na2S2O3-group showed the strongest SDDA coupling, supported by the highest abundances of soxB (0.14 %), narG (0.05 %), nirS (5.92 %), and hzsB (6.14 %). The FeS2-group demonstrated moderate coupling, whereas the Ca(NO3)2-group displayed the weakest performance. Moreover, Na2S2O3-group also exhibited excellent TN removal (87.58 %) in real river scenarios, indicating its potential as one promising N removal strategy for practical application. This study contributes to the understanding of S-N cyclings in river ecosystems and provides insights into manipulating N-reduction for possible application in remediated urban rivers.},
}

@article {pmid41043307,
year = {2025},
author = {Ji, Z and Liu, S and Tian, Z and Guo, N and Wei, W and Jiang, Q},
title = {Tooth Loss-Induced Gut Dysbiosis Promotes Neuroinflammation via L-Asparagine-Mediated Neuronal Toxicity.},
journal = {International dental journal},
volume = {75},
number = {6},
pages = {103929},
doi = {10.1016/j.identj.2025.103929},
pmid = {41043307},
issn = {1875-595X},
abstract = {INTRODUCTION AND AIMS: Tooth loss is not only a dental issue but also affects gut microbial composition and downstream physiological responses. This study investigates how tooth loss-induced alterations in the gut microbiota influence metabolic and neural function. This study aimed to elucidate the mechanistic links between microbiota dysbiosis, metabolic imbalance, and neuroinflammation following tooth loss.

METHODS: Using a murine model, the first molars of C57BL/6 mice were extracted, followed by the collection of fecal samples, serum, and brain tissue for subsequent metagenomic sequencing, metabolomics, and transcriptomics. Pro-inflammatory markers (IL-6, TNF-α) and PSD95 expression were assessed. The neurotoxic effects of key metabolite L-Asparagine were validated using HT22 neuronal cell models.

RESULTS: Tooth loss induced gut microbiota dysbiosis, which subsequently mediated pathological alterations in brain tissue, characterised by a reduction in beneficial Butyribacter and an increase in pathogenic taxa. Corresponding shifts in systemic metabolism were observed, along with changes in brain gene expression, particularly in genes related to neuroinflammation. In vitro experiments further demonstrated that L-Asparagine directly induced neurotoxicity in HT22 hippocampal neurons through ROS overproduction, apoptosis, and inflammatory activation.

CONCLUSION: Tooth loss induced gut microbiota dysbiosis, systemic metabolic disruptions, and neuroinflammatory responses. Our findings demonstrated that tooth loss exacerbated neuroinflammation via gut-derived L-Asparagine, providing a mechanistic link in the oral-gut-brain axis.

CLINICAL RELEVANCE: This study demonstrated that molar extraction in mice disrupted gut microbiota and promoted neuroinflammation via L-Asparagine, suggesting that maintaining oral integrity might help preserve neurological health. This could open new avenues for microbiota-targeted interventions in neurodegenerative disease prevention.},
}

@article {pmid41043233,
year = {2025},
author = {Sun, C and Liu, X and Wang, M and Zhang, Q and Geng, H and Ji, X and Wang, H and Li, S and Jin, E and Zhang, F},
title = {Metagenome-metabolome responses to linarin alleviate hepatic inflammatory response, oxidative damage, and apoptosis in an ETEC-challenged weaned piglet model.},
journal = {Ecotoxicology and environmental safety},
volume = {304},
number = {},
pages = {119145},
doi = {10.1016/j.ecoenv.2025.119145},
pmid = {41043233},
issn = {1090-2414},
abstract = {Enterotoxigenic Escherichia coli (ETEC), present in contaminated food, water, and environments, can induce hepatic injury via the gut-liver axis, posing a serious threat to ecological systems and public health. Linarin, a flavonoid extracted from Chrysanthemum indicum, exhibits anti-inflammatory and antioxidant properties, but its protective effects against ETEC-induced hepatic injury remain unclear. In this study, 24 weaned piglets were randomly assigned to four groups: BD+NB (basal diet + nutrient broth), LN+NB (basal diet + 150 mg/kg linarin + nutrient broth), BD+ETEC (basal diet + ETEC challenge), and LN+ETEC (basal diet + 150 mg/kg linarin + ETEC challenge). Dietary linarin significantly increased ADFI and the genes related to oxidative damage and bile acid metabolism, while decreasing F:G ratio, liver index, serum liver function-related parameters, and the genes related to inflammatory response and apoptosis. It also significantly altered the relative abundances of gut microbiota, which were closely associated with key hepatic metabolic pathways, including nicotinate and nicotinamide metabolism and fatty acid biosynthesis. Our study suggests that linarin alleviated ETEC-induced hepatic inflammation and apoptosis, enhanced antioxidant capacity, and regulated bile acid metabolism. The potential mechanism involves linarin modulating gut microbiota-mediated key hepatic metabolic pathways to exert protective effects. In contrast to previous flavonoid-ETEC studies that primarily focused on the gut, this study, based on the gut-liver axis, investigates the potential mechanisms by which linarin is associated with the alleviation of ETEC-induced hepatic injury through integrated analysis of gut microbiome metagenomics and liver metabolomics.},
}

@article {pmid41042849,
year = {2025},
author = {Shen, LQ and Lin, D and Ye, YQ and Liu, Y and Ni, B and Wu, D and Wang, L and Zhu, D},
title = {Combined pesticide pollution enhances the dissemination of the phage-encoded antibiotic resistome in the soil under nitrogen deposition.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {40},
pages = {e2516722122},
doi = {10.1073/pnas.2516722122},
pmid = {41042849},
issn = {1091-6490},
support = {2024YFE0106300//MOST | National Key Research and Development Program of China (NKPs)/ ; 22193062//MOST | National Natural Science Foundation of China (NSFC)/ ; 42207013//MOST | National Natural Science Foundation of China (NSFC)/ ; 42222701//MOST | National Natural Science Foundation of China (NSFC)/ ; 2023321//Youth Innovation Promotion Association of the Chinese Academy of Sciences (CAS YIPA)/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; },
mesh = {*Bacteriophages/genetics ; *Nitrogen ; *Soil Microbiology ; *Pesticides/toxicity ; Soil/chemistry ; Bacteria/genetics/virology/drug effects ; *Drug Resistance, Microbial/genetics ; *Soil Pollutants ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Phage-mediated dissemination of antibiotic resistance genes (ARGs) intensifies health threat in the environment. Increasing amounts of pesticides are entering the soil ecosystem, yet their potential influence on phage-mediated ARG spread, particularly under conditions of global change, remains poorly understood. In this study, we performed a long-term field experiment simulating pesticide contamination under nitrogen deposition and examined the role of soil phages in ARG spread and host adaptation using metagenomic and viromic sequencing. Combined pesticide markedly elevated the abundance of phage-encoded ARGs under nitrogen deposition. By enhancing phage-host interactions and increasing the co-occurrence of auxiliary metabolic genes with ARGs, phages may further facilitate the transfer of ARGs to bacterial hosts, conferring hosts a competitive edge in intensified microbial competition driven by combined pesticide exposure under nitrogen deposition. The phage-driven mechanism was supported by in vitro cultivation experiments, demonstrating that phages harboring ARGs, shaped by long-term combined pesticide exposure under nitrogen deposition, can infect bacterial hosts and confer resistance. Collectively, our findings underscore the pivotal role of phages in ARG mobilization under environmental stressors, reinforcing the importance of accounting for phage activity in ARG risk assessments under global change.},
}

*Bacteriophages/genetics
*Nitrogen
*Soil Microbiology
*Pesticides/toxicity
Soil/chemistry
Bacteria/genetics/virology/drug effects
*Drug Resistance, Microbial/genetics
*Soil Pollutants
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics

@article {pmid41042593,
year = {2025},
author = {Varliero, G and Bauder, A and Stierli, B and Qi, W and Frey, B},
title = {Host-virome associations in the weathering crust of a rapidly retreating temperate Alpine glacier.},
journal = {Microbial genomics},
volume = {11},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001524},
pmid = {41042593},
issn = {2057-5858},
mesh = {*Ice Cover/microbiology/virology ; *Bacteria/genetics/virology/classification ; *Microbiota/genetics ; *Viruses/genetics/classification/isolation & purification ; Switzerland ; Metagenomics/methods ; Ecosystem ; Host Specificity ; },
abstract = {Glaciers are retreating rapidly, altering ecosystem dynamics and increasing meltwater outflow into populated areas. Understanding microbial-virome interactions is crucial for predicting the consequences of this release. We sampled ice from four shallow pits in the weathering crust of the Rhonegletscher, Swiss Alps, and found a microbiome dominated by bacteria and microeukaryotes, alongside a metavirome infecting both groups. Viruses exhibited variable host specificity, with some targeting particular taxa and others showing a broader infectivity range. Variable genomic regions, including metagenomic and metaviromic islands, were enriched in genes related to replication, recombination, repair and transposable elements. Detected auxiliary metabolic genes were primarily involved in host coenzyme biosynthesis, uptake or utilization and in altering bacterial methylation patterns to evade detection. These findings underscore the major role of viruses in regulating microbial dynamics in glaciers and their potential downstream environmental impacts.},
}

*Ice Cover/microbiology/virology
*Bacteria/genetics/virology/classification
*Microbiota/genetics
*Viruses/genetics/classification/isolation & purification
Switzerland
Metagenomics/methods
Ecosystem
Host Specificity

@article {pmid41042396,
year = {2025},
author = {Wu, J and Zhou, J and Zhao, Q and Yang, C and Bai, Y},
title = {Metagenomic analysis of microbial community dynamics in konjac rhizosphere during soft rot disease progression.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {212},
pmid = {41042396},
issn = {1432-0614},
support = {32072558//the Nature Science Foundation of China/ ; 2024-620-000-001-007//Hubei Agricultural Science and Technology Innovation Center Innovation Team Project/ ; },
mesh = {*Rhizosphere ; *Plant Diseases/microbiology ; *Soil Microbiology ; Metagenomics ; *Amorphophallus/microbiology ; *Microbiota/genetics ; Bacteria/classification/genetics/isolation & purification ; Fungi/genetics/classification ; },
abstract = {Amorphophallus konjac, the sole glucomannan-rich species in the Araceae family, faces significant yield and quality losses due to soft rot disease. Understanding the relationship between soil microbial communities and soft rot incidence is critical for sustainable konjac production. Metagenomic profiling was employed to systematically characterize the spatiotemporal dynamics of rhizosphere microbiomes during disease progression. Microbial alpha diversity (Chao1 index) exhibited a significant peak in the rhizosphere of diseased plants at the mature stage, contrasting with stable diversity patterns in healthy and latently infected groups, indicating dysbiosis-associated richness inflation during disease progression. Principal coordinate analysis (PCoA) revealed significant divergence in rhizosphere microbial structures between diseased and healthy/latently infected groups, with higher compositional variability observed in diseased samples. At the phylum level, Chloroflexi and Acidobacteria abundances in healthy mature plants exceeded those in diseased plants by 11.54% and 4.6%, respectively, while pathogenic Rhizopus arrhizus and Rhizopus microsporus were significantly enriched in diseased mature plants. Correlation analyses demonstrated predominantly negative associations between bacterial species and soil factors, contrasting with positive fungal correlations. KEGG pathway annotation identified carbohydrate metabolism and amino acid synthesis as core microbial functions in the konjac rhizosphere. Collectively, Chloroflexi and Acidobacteria were validated as putative biocontrol agents, while Rhizopus spp. emerged as key drivers of soft rot development. These findings provide mechanistic insights for designing microbiome-based biocontrol strategies to mitigate konjac soft rot, offering a sustainable alternative to conventional agrochemical reliance. KEY POINTS: • Diseased konjac microbial richness peaks; healthy plants enrich Chloroflexi/Acidobacteria. • Rhizopus pathogens drive soft rot; bacteria and fungi show opposing soil factor links. • Lays groundwork for microbiome approaches to cut agrochemicals in konjac rot control.},
}

*Rhizosphere
*Plant Diseases/microbiology
*Soil Microbiology
Metagenomics
*Amorphophallus/microbiology
*Microbiota/genetics
Bacteria/classification/genetics/isolation & purification
Fungi/genetics/classification

@article {pmid41041976,
year = {2025},
author = {Breusing, C and Hauer, MA and Hughes, IV and Becker, JS and Casagrande, D and Phillips, BT and Girguis, PR and Beinart, RA},
title = {Contrasting Genomic Responses of Hydrothermal Vent Animals and Their Symbionts to Population Decline After the Hunga Volcanic Eruption.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70126},
doi = {10.1111/mec.70126},
pmid = {41041976},
issn = {1365-294X},
support = {//Schmidt Ocean Institute/ ; EPSCoR Cooperative Agreement OIA-#1655221//National Science Foundation/ ; OCE-0732369//Division of Ocean Sciences/ ; OCE-1536331//Division of Ocean Sciences/ ; OCE-1736932//Division of Ocean Sciences/ ; 1747454//National Science Foundation Graduate Research Fellowship Program/ ; //Argonne National Laboratory/ ; },
abstract = {Genetic bottlenecks are evolutionary events that reduce the effective size and diversity of natural populations, often limiting a population's ability to adapt to environmental change. Given the accelerating human impact on ecosystems worldwide, understanding how populations evolve after a genetic bottleneck is becoming increasingly important for species conservation. Ash deposits from the 2022 Hunga volcanic eruption in the Southwest Pacific led to a drastic decline of animal symbioses associated with hydrothermal vents in this region, allowing insights into the effects of population bottlenecks in the deep sea. Here, we applied metagenomic sequencing to pre- and post-eruption samples of mollusc-microbial symbioses from the Lau Basin to investigate patterns of genetic variation and effective population size. Our data indicate that animal host populations currently show only small changes in genome-wide diversity but in most cases experienced a long-term decline in effective size that was likely intensified by the volcanic impact. By contrast, host-associated symbiont populations exhibited a notable decrease in genomic variation, including potential loss of certain habitat-specific strains. However, detection of environmental sequences resembling mollusc symbionts suggests that lost host-associated symbiont diversity might be recovered from the free-living symbiont pool. The differences between host and symbiont populations might be related to their contrasting genetic structures and pre-existing levels of connectivity, although the full extent of population bottlenecks in the host animals might only be recognisable after a few generations. These results add to our understanding of the evolutionary dynamics of animal-microbe populations following a natural disturbance and help assess their resilience to both natural and anthropogenic impacts.},
}

@article {pmid41041810,
year = {2025},
author = {Oskolkov, N and Jin, C and Clinton, SL and Guinet, B and Wijnands, F and Johnson, E and Kutschera, VE and Kinsella, CM and Heintzman, PD and van der Valk, T},
title = {Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf108},
pmid = {41041810},
issn = {2047-217X},
support = {KAW 2021.0048 [P.D.H., F.W.]//Knut and Alice Wallenberg Foundation/ ; KAW 2022.0033 [P.D.H.]//Knut and Alice Wallenberg Foundation/ ; //National Bioinformatics Infrastructure Sweden at SciLifeLab/ ; VR 2020-04808//Swedish Research Council/ ; KAW 2020.0239//SciLifeLab and Wallenberg Data Driven Life Science Program/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *DNA, Ancient/analysis ; Animals ; Phylogeny ; Archaea/genetics/classification ; },
abstract = {Ancient environmental DNA is increasingly vital for reconstructing past ecosystems, particularly when paleontological and archaeological tissue remains are absent. Detecting ancient plant and animal DNA in environmental samples relies on using extensive eukaryotic reference genome databases for profiling metagenomics data. However, many eukaryotic genomes contain regions with high sequence similarity to microbial DNA, which can lead to the misclassification of bacterial and archaeal reads as eukaryotic. This issue is especially problematic in ancient eDNA datasets, where plant and animal DNA is typically present at very low abundance. In this study, we present a method for identifying bacterial- and archaeal-like sequences in eukaryotic genomes and apply it to nearly 3,000 reference genomes from NCBI RefSeq and GenBank (vertebrates, invertebrates, plants) as well as the 1,323 PhyloNorway plant genome assemblies from herbarium material from northern high-latitude regions. We find that microbial-like regions are widespread across eukaryotic genomes and provide a comprehensive resource of their genomic coordinates and taxonomic annotations. This resource enables the masking of microbial-like regions during profiling analyses, thereby improving the reliability of ancient environmental metagenomic datasets for downstream analyses.},
}

*Metagenome
*Metagenomics/methods
*DNA, Ancient/analysis
Animals
Phylogeny
Archaea/genetics/classification

@article {pmid41041613,
year = {2025},
author = {Ma, R and Xu, B and Chen, X and Sun, Q and Li, Y and Zheng, Q and Jiao, N and Zhang, R},
title = {Prophages in marine Citromicrobium: diversity, activity, and interaction with the host.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf148},
pmid = {41041613},
issn = {2730-6151},
abstract = {Lysogeny was frequently detected in marine ecosystems, while how temperate phage genomes (prophages) impact marine microbial population or individual dynamics remained poorly understood. Using marine Citromicrobium strain collection as a model system, we revealed that 58% (22/38) were lysogens harboring 31 prophages that can be grouped into five novel genera (φA-φE). Prophage-encoded genes constituted 9% of host accessory genome, significantly expanding the microdiversity among citromicrobial clonal strains. Metagenomic abundance correlations indirectly supported the "Piggyback-the-Winner" dynamics for φA/φE, evidenced by their sublinear growth pattern with increasing host abundance. Most prophages were capable of spontaneous induction and exhibited high lytic activity when triggered by mitomycin C. Importantly, host-range profiling revealed these prophages deployed a dual "Kill-the-Relatives" and "Colonize-the-Relatives" strategy, and meanwhile, they protected parental host strains through superinfection immunity and enhanced phage resistance with greater prophage carriage. Sequencing data showed the dominance of Mu-like phages over non-Mu-like partners upon induced from the double lysogens. Our analysis further hinted at a unique Mu-type within-host competitive strategy: selectively targeting genes of co-resident prophages and host hypothetical genes, while avoiding self-damage and host metabolic genes potentially essential for phage lytic growth or progeny release. Collectively, this work establishes prophages as key architects of bacterial adaptation and provides new perspectives for prophage-driven evolution in marine bacterial hosts.},
}

@article {pmid41041524,
year = {2025},
author = {Happi, A and Sijuwola, A and Omah, IF and Ogunsanya, O and Saibu, F and Ayinla, A and Adedokun, O and Fadele, J and Nwofoke, C and Adelabu, A and Ogundana, E and Lawal, O and Elias, O and Okokoh, E and Colquhoun, R and Achonduh-Atijegbe, O and Nta, H and Onimajesin, A and Momoh, F and Mari-Saez, A and Redding, D and Murray, K and Hanefeld, J and Sesay, AK and Rambaut, A and Happi, C},
title = {Metagenomics reveals cryptic circulation of zoonotic viruses in Nigeria.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7630852/v1},
pmid = {41041524},
issn = {2693-5015},
abstract = {Zoonotic spillover events pose an ongoing threat to global health, with historic and recent viral diseases of international concern emerging from animal reservoirs 1-6. In Nigeria, limited surveillance of animal hosts at the human and animal interface continues to hinder our understanding of viruses that are cryptically circulating in animals near human dwellings with potential for consequential spillover events. We performed unbiased metagenomic next‑generation sequencing (mNGS) on tissue and swab samples collected from 240 individual animals across 11 taxa (rodents, shrews, bats, goats, sheep, pigs, dogs, cats, chickens, cattle egrets, and lizards) in two Lassa‑affected Nigerian states (Ondo and Ebonyi). Host‑depleted sequencing reads were assembled into contigs, taxonomically classified, and subjected to phylogenetic analyses to characterize viral diversity, host associations, and evidence of cross‑species transmission. Across all samples, we identified 214 distinct viral taxa spanning 33 families, of which 41% (n = 83) represent novel species by ICTV criteria. Positive‑sense RNA viruses dominated (Coronaviridae, Picornaviridae, Astroviridae), followed by negative‑sense RNA, single‑ and double‑stranded DNA, and double‑stranded RNA viruses. Notably, human‑associated enteroviruses-including Hepatitis A virus (genotype 1b), echoviruses, coxsackieviruses, and noroviruses-were detected in goats, pigs, dogs, and chickens, indicating cryptic circulation of human pathogens in peridomestic and domesticated animals. Phylogenetic reconstructions revealed multiple cross‑species viral sharing events, particularly among rodents, goats, sheep, and pigs, and extensive recombination within Nigerian Betacoronavirus 1 lineages. Interestingly we found a putative novel avian like coronavirus in rodents, goats and sheep. Ecological modelling demonstrated that host species identity, sample type, and sampling effort were primary drivers of viral richness and abundance, and that higher overall viral diversity strongly predicted cross‑species transmission potential. Our integrated mNGS approach uncovered a rich and dynamic virome within animals inhabiting human‑dominated environments in Nigeria, including undetected circulation of human enteric viruses. These findings underscore the importance of broad‑taxonomic, real‑time surveillance at human-animal interfaces to inform early‑warning systems and pandemic preparedness, particularly in low‑resource settings.},
}

@article {pmid41041139,
year = {2025},
author = {Berlanga, M and Martín-García, A and Guerrero, R and Riu-Aumatell, M and López-Tamames, E},
title = {Changes in healthy Wistar rat gut microbiome by short-term dietary cava lees intervention.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1641612},
pmid = {41041139},
issn = {2296-861X},
abstract = {INTRODUCTION: The gut microbiome plays a crucial role in host health through complex host-microbe interactions. Beta-glucans, structural polysaccharides found in yeast cell walls, have emerged as promising modulators of immune function and microbial ecology. Cava lees, a by-product of sparkling wine production composed of Saccharomyces cerevisiae cell walls, represent a rich source of beta-glucans that could be upcycled for nutritional and therapeutic applications.

METHODS: Twenty-four Wistar rats (12 males, 12 females) were randomly divided into control and treatment groups. The treatment group received daily doses of 2,000 mg lees/kg body weight for 14 days. Shotgun metagenomic analysis was performed to assess microbial composition and functional changes.

RESULTS: A 14-day cava lees supplementation study revealed significant shifts in gut microbiota composition and function. Baseline microbiota was dominated by Bacillota (64-72%) and Bacteroidota (23-32%) with sex-specific differences at the family level. Post-supplementation analysis showed increased Shannon diversity across both sexes, with beneficial enrichment of Bifidobacteriaceae and Rikenellaceae families and reduction of Eubacteriaceae. While global metabolic profiles remained stable, targeted functional pathways were significantly changed, including butyrate production genes. Females exhibited particularly elevated secondary bile acid modification genes (Mann-Whitney-Wilcoxon test p = 0.032), and male oxidative stress response pathways (Mann-Whitney-Wilcoxon test p = 0.016) showing both a potentially sex-dependent responses to dietary intervention.

CONCLUSION: Working with healthy individuals provides a clear understanding of the normal, baseline microbiota composition and function before any intervention. These findings suggest a degree of plasticity of the gut microbiome and its responsiveness to dietary modifications. Beta-glucans from cava lees appear to create a favorable environment for beneficial bacteria, with sex-specific changes of certain bacterial families and functions. These findings provide a foundation for future translational research in humans. Nonetheless, to establish their true impact on human health, these observations in rodent models must be validated through appropriately designed human clinical studies.},
}

@article {pmid41040987,
year = {2025},
author = {Li, Y and Zhang, L and Ma, G and Li, C and Hu, W and Ren, R and Zang, Y and Ying, D and Qiu, S and Jin, S and Qiu, C and Cao, X},
title = {Optimization of decision thresholds for Mycobacterium tuberculosis can effectively improve the performance of mNGS in tuberculosis diagnosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1646194},
pmid = {41040987},
issn = {2235-2988},
mesh = {Humans ; *Mycobacterium tuberculosis/genetics/isolation & purification ; Female ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Male ; Middle Aged ; Adult ; *High-Throughput Nucleotide Sequencing/methods ; ROC Curve ; Bronchoalveolar Lavage Fluid/microbiology ; Sensitivity and Specificity ; *Metagenomics/methods ; Aged ; Young Adult ; },
abstract = {BACKGROUND: Pulmonary tuberculosis (TB) diagnosis remains challenging due to limitations in traditional methods. This study aimed to optimize the metagenomic next-generation sequencing (mNGS) threshold for Mycobacterium tuberculosis complex (MTBC) detection and evaluate its efficacy compared to standard diagnostic approaches.

METHODS: A total of 264 bronchoalveolar lavage fluid (BALF) samples were collected from patients with suspected pulmonary TB at Yongkang First People's Hospital between January 2022 and June 2023. After excluding patients with incomplete data, 59 clinically confirmed TB patients and 111 with non-tuberculous conditions were enrolled. mNGS data were analyzed to calculate reads per million (RPM) for MTBC, and thresholds of 0.02, 0.05, and 0.10 RPM were evaluated for diagnostic efficacy using clinical diagnosis as the gold standard.

RESULTS: The area under the receiver operating characteristic (ROC) curve (AUC) for mNGS in diagnosing TB at RPM thresholds of ≥0.02, ≥0.05, and ≥0.10 were 0.881, 0.873, and 0.814, respectively. The optimal detection threshold was found at RPM ≥ 0.05. Comparative analysis showed mNGS (AUC = 0.873) outperformed routine culture (0.718), PCR (0.741), and Xpert (0.763). Combining mNGS with these methods improved AUC values to 0.837, 0.868, and 0.873, respectively.

CONCLUSION: Optimizing the mNGS threshold to ≥0.05 significantly enhances MTBC detection in pulmonary TB. Combining mNGS with traditional methods further improves diagnostic efficacy, suggesting a potential role for mNGS in clinical TB management.},
}

Humans
*Mycobacterium tuberculosis/genetics/isolation & purification
Female
*Tuberculosis, Pulmonary/diagnosis/microbiology
Male
Middle Aged
Adult
*High-Throughput Nucleotide Sequencing/methods
ROC Curve
Bronchoalveolar Lavage Fluid/microbiology
Sensitivity and Specificity
*Metagenomics/methods
Aged
Young Adult

@article {pmid41040929,
year = {2025},
author = {Cho, HY and Park, HJ and Choi, JS and Kim, SH and Ryu, MO and Seo, KW},
title = {Delineating the fecal microbiome of healthy domestic short-hair cats in South Korea.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1571107},
pmid = {41040929},
issn = {2297-1769},
abstract = {BACKGROUND: The gut microbiome is a vital component of an organism's health, influencing metabolism, immune function, and overall homeostasis. In this study, we aimed to characterize the gut microbiota of healthy domestic short-hair cats in South Korea and evaluate the effects of age, body condition score (BCS), sex, and diet on microbial composition.

METHODS: From August to December 2023, 40 healthy cats aged 1-14 years with a body condition score (BCS) of 5-9 were selected. Cats were excluded if they had taken probiotics or antibiotics, exhibited gastrointestinal symptoms within the last 6 months, or had blood work abnormalities. DNA quantification was performed, and libraries targeting the V3 and V4 regions were prepared according to the Illumina 16S metagenomic sequencing protocol with a read length of 2 × 300 bp. The relative abundance of bacteria at the phylum, genus, and species levels was assessed according to the age, sex, diet, and BCS of the cats, with major bacterial groups selected for chart analysis.

RESULTS: Examination of the fecal samples from 40 healthy cats (aged 0.5-14 years) using 16S rRNA gene sequencing revealed 2,721 bacterial amplicon sequence variants. The predominant phyla were Bacillota, Bacteroidota, and Actinomycetota. Although age did not significantly affect alpha diversity, a trend toward increased diversity was observed in cats aged 7-14 years. Phocaeicola was more abundant in older cats, suggesting a possible association with age-related conditions. Furthermore, Verrucomicrobiota was enriched in cats with a BCS of 8-9, and Ruminococcus torque was positively correlated with higher BCS. Sex-based differences indicated increased levels of Pseudomonadota, Finegoldia magna, and Sutterella massiliensis in neutered males, potentially linked to inflammatory pathways. Dietary analysis revealed an increased abundance of Blautia and Lachnoclostridium following a combination of dry and wet food.

CONCLUSION: Our findings provide critical insights into the core microbiota of domestic short-hair cats in South Korea, emphasizing the influence of geographic, physiological, and environmental factors on gut microbial diversity. The results offer a valuable foundation for advancing feline gut health research and enhancing health management strategies for felines, particularly in South Korea.},
}

@article {pmid41040912,
year = {2025},
author = {Matsumura, M and Mitsui, H and Woo, T and Suzuki, T and Arai, H and Koike, C and Kataoka, T and Motooka, D and Fukushima, K and Okudela, K},
title = {Identification of key molecules in micropapillary progression of lung adenocarcinoma: A comprehensive gene expression analysis study using the spatial gene expression solution methodology.},
journal = {Oncology letters},
volume = {30},
number = {5},
pages = {533},
pmid = {41040912},
issn = {1792-1082},
abstract = {The micropapillary histological subtype is a high-grade element and a poor prognostic marker in lung adenocarcinoma (LUAD). This subtype develops through the lepidic-filigree micropapillary (filigree)-conventional/overt micropapillary (mPAP) pathway. The present study aimed to identify key molecules that promote this progression. To this end, gene expression profiles specific to lepidic, filigree and mPAP elements were investigated in histological sections obtained from 4 different LUAD cases. The 10× Genomics Visium Spatial Gene Expression Solution was used due to its superior resolution compared with conventional microdissection techniques. Cellular retinoic acid binding protein 2 (CRABP2), carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) and mucin 21 (MUC21) were identified as common molecules with significantly elevated levels along the lepidic-filigree-mPAP pathway. Furthermore, the present findings indicated that CRABP2 may serve an important role in the early stage of this process, as its level significantly increases during the transition from the lepidic to the filigree substage. Immunohistochemical analysis of the expression of CRABP2, CEACAM5 and MUC21 proteins in 207 surgically resected LUAD samples (expanded sample size) was performed. The present study revealed an increase in the expression levels of CRABP2 between the lepidic and filigree elements, and between filigree and mPAP for CEACAM5 and MUC21. Thus, these three proteins were demonstrated to serve roles in the lepidic-filigree-mPAP pathway at different stages. Notably, these molecules were associated with poor prognosis, characterized by an elevated recurrence rate and poor survival rate. In conclusion, crucial molecules that promote the lepidic-filigree-mPAP pathway, and exhibit potential clinical utility as prognostic markers and molecular therapeutic targets, were identified.},
}

@article {pmid41040880,
year = {2025},
author = {Wang, J and Gu, H and Gao, H and Zhang, T and Li, B and Zhang, M and Jiang, F and Song, P and Liang, C and Fan, Q and Xu, Y and Zhang, R},
title = {Developmental dynamics and functional adaptation of gut microbiota in Mongolian wild asses (Equus hemionus hemionus) across ontogenetic stages in arid desert ecosystems.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1659661},
pmid = {41040880},
issn = {1664-302X},
abstract = {Understanding the composition and function of gut microbiota is essential for elucidating how wild animals adapt to arid environments. The Mongolian wild ass (Equus hemionus hemionus), which inhabits harsh desert ecosystems, offers an ideal model for such investigations. This study employed metagenomic sequencing of fecal samples to characterize the composition and structure of the gut microbiota in adult, subadult, and juvenile Mongolian wild asses, with functional annotation based on the KEGG, CARD, and CAZy databases. Our study revealed that Bacillota and Bacteroidota were the dominant phyla, together accounting for over 85% of relative abundance, with their ratio (B/B value) showing clear age-dependent shifts. Juveniles were dominated by Bacillota (high B/B value), consistent with adaptation to a milk-based, protein- and lactose-rich diet, whereas adults shifted toward Bacteroidota dominance (low B/B value), with relative abundance increasing from 39.53% to 64.92%, reflecting enhanced polysaccharide and fiber degradation, thereby providing microecological support for adaptation to low-energy, high-fiber desert vegetation resources. Alongside this transition, α-diversity significantly increased with age, while β-diversity patterns shifted from dispersed to clustered, indicating a more complex, stable, and mature gut community. Over 58% of predicted genes were assigned to metabolic pathways, highlighting the essential contribution of gut microbes to herbivore digestion. Polysaccharide lyases, enriched in adults and subadults, were positively correlated with Bacteroidota abundance, highlighting their central role in fiber degradation and stable energy supply, thereby supporting adaptation to arid desert habitats. In contrast, juveniles were characterized by enrichment of the galactose metabolism pathway, high abundance of Pseudomonadota (LEfSe LDA > 4), and the largest number of antibiotic resistance genes (AROs), including 17 potential key AROs, reflecting greater microbial plasticity and higher environmental exposure risks during early development. This study provides the first systematic characterization of age-related gut microbiome dynamics and functional adaptations in the endangered Mongolian wild ass, offering novel insights into microbial contributions to host energy optimization and resilience in arid ecosystems, with implications for conservation strategies.},
}

@article {pmid41040879,
year = {2025},
author = {Hoepfner, C and Guzmán, D and Vidal-Veuthey, B and Foronda, V and Beggs, A and Cárdenas, JP and Vargas, VA and Alfaro, FD},
title = {Functional stratification and enzymatic arrangement in microbial communities across a hypersaline depth gradient.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1624058},
pmid = {41040879},
issn = {1664-302X},
abstract = {Extreme environments comprise a significant portion of Earth's terrestrial surface, posing challenges, such as extreme temperatures, pressure, pH extremes, oxygen and nutrient scarcity, and high salinity. Hypersaline ecosystems, such as those in the Andean Cold Deserts, exemplify extreme environments where microbial life has evolved specialized survival mechanisms. The Central Andean Mountains host extensive salt flats exposed to extreme temperature fluctuations, intense ultraviolet radiation, and high soil salinity. While most studies focus on surface layers, the impact of soil depth on functional diversity remains poorly understood. This study utilized shotgun metagenomics and functional annotation to explore enzymatic diversity across a 8-meter depth gradient in the Uyuni Salt Flat aiming to understand microbial adaptations to depth and abiotic stress. Our findings revealed a complex, stratified microbial ecosystem. Surface layers showed high abundance of amylases, enzymes that degrade accessible carbohydrates, likely derived from photosynthetic communities or surface-imported organic matter. These patterns suggest a dominance of strategies for rapid carbon decomposition. Intermediate depths exhibited elevated lipase and peroxidase activity, reflecting the presence of complex lipids and oxidative stress management, essential for survival in oxygen-limited, high-salinity zones. Lipase support lipid utilization as a carbon source, while peroxidase activity points to redox adaptations for microbial resilience under fluctuating oxidative conditions. Deeper sediment layers showed a shift toward protease and peptidase activity, indicating organic nitrogen recycling in nutrient-deprived environments and suggesting an efficient protein degradation system among halophilic archaea. Peroxidases remained abundant even at these depths, supporting sustained redox regulation and biogeochemical cycling thus enabling microbes to manage redox imbalances in high-salinity, low-oxygen settings. The enzymatic diversity across the depth gradient demonstrates functional stratification and remarkable microbial adaptability to hypersaline conditions. This functional resilience underpins nutrient cycling and organic matter decomposition deep in the salt flats. Notably, the identified halophilic enzymes, stable and active under high-salinity conditions, hold significant potential for biotechnological applications. This study contributes to our understanding of microbial life's complexity in hypersaline environments, enhancing our ability to harness extremophilic enzymes for biotechnological applications while underscoring the ecological value of these unique habitats.},
}

@article {pmid41040656,
year = {2025},
author = {Wilkins, L and Yuen, B and Petersen, J and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the mollusc, Ctena decussata (O.G.Costa, 1829) and its bacterial endosymbiont Candidatus Thiodiazotropha sp. CDECU1 (Chromatiales).},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {435},
pmid = {41040656},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Ctena decussata (Mollusca; Bivalvia; Lucinida; Lucinidae). The genome sequence has a total length of 1,658.05 megabases. Most of the assembly (97.83%) is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 53.28 kilobases in length. The genome of Candidatus Thiodiazotropha sp. CDECU1, a bacterium associated with C. decussata was also assembled.},
}

@article {pmid41040369,
year = {2025},
author = {Rehman, Y and Kim, Y and Tong, M and Blaby, IK and Blaby-Haas, CE and Beatty, JT},
title = {Mining thermophile photosynthesis genes: a synthetic operon expressing Chloroflexota species reaction center genes in Rhodobacter sphaeroides.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.22.677880},
pmid = {41040369},
issn = {2692-8205},
abstract = {Photosynthesis is the foundation of the vast majority of life systems, and therefore the most important bioenergetic process on earth, and the greatest diversity in photosynthetic systems are found in microorganisms. However, understanding of the biophysical and biochemical processes that transduce light to chemical energy has derived from the relatively small subset of proteins from microbes that are amenable to cultivation, in contrast to the huge number of microbial DNA sequences encoding proteins that catalyze the initial photochemical reactions that has been deposited in databases, such as from metagenomics. We describe the use of a Rhodobacter sphaeroides laboratory strain for expression of heterologous photosynthesis genes to demonstrate the feasibility of mining this resource, focusing on hot spring Chloroflexota gene sequences. Using a synthetic operon of genes, we produced a photochemically active complex of reaction center proteins in our biological system. We also present bioinformatic analyses of anoxygenic type II reaction center sequences from metagenomic samples collected from hot (42-90° C) springs available through the JGI IMG database, to generate a resource of diverse sequences that potentially are adapted to photosynthesis at such temperatures. These data provide a view into the natural diversity of anoxygenic photosynthesis, through a lens focused on high-temperature environments. The approach we took to express such genes can be applied for potential biotechnology purposes as well as for studies of fundamental catalytic properties of these heretofore inaccessible protein complexes.},
}

@article {pmid41040146,
year = {2025},
author = {He, W and Bobanga, T and Piantadosi, A and Popkin-Hall, ZR and Vulu, F and Collins, MH and Kashamuka, MM and Tshefu, AK and Juliano, JJ and Parr, JB},
title = {Evidence of dengue virus transmission and a diverse Aedes mosquito virome on the Democratic Republic of Congo-Angola border.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.16.633031},
pmid = {41040146},
issn = {2692-8205},
abstract = {Aedes mosquitoes are widely distributed across the Democratic Republic of Congo (DRC), and are major vectors of dengue (DENV), Zika, chikungunya (CHIKV), and yellow fever (YFV) viruses. While the high burden of malaria in the DRC receives considerable attention, arboviruses remain understudied. In the setting of recent CHIKV and YFV outbreaks in southwestern DRC, we collected Aedes mosquitoes in three areas of Kimpese, DRC, near the Angola border, to investigate their virome. Metagenomic and targeted sequencing of eight randomly selected field mosquito pools, comprising 155 mosquitoes from three collection sites, confirmed high-confidence DENV reads and human blood meals in six (75%) and eight (100%) pools, respectively. We find diverse mosquito viromes including other known and putative human and animal viruses. Our findings provide strong evidence of endemic DENV transmission along the DRC-Angola border and illustrate the potential of wild-caught mosquitoes for xenosurveillance of emerging pathogens.},
}

@article {pmid41039672,
year = {2025},
author = {Silvester, R and Webster, G and Perry, WB and Farkas, K and Rushton, L and Craine, N and Cross, G and Kille, P and Weightman, AJ and Jones, DL},
title = {Genome-resolved metagenomics uncovers antimicrobial resistance gene carriers in hospital and municipal wastewater environments.},
journal = {The Science of the total environment},
volume = {1002},
number = {},
pages = {180607},
doi = {10.1016/j.scitotenv.2025.180607},
pmid = {41039672},
issn = {1879-1026},
abstract = {Wastewater-based epidemiology (WBE) is a powerful approach to study antimicrobial resistance (AMR) dynamics at the population level. Using genome-resolved metagenomics, we recovered 3978 metagenome-assembled genomes (MAGs) from archived metagenome sequences generated under the national wastewater surveillance programme across Wales, UK. Taxonomic profiling of MAGs revealed a diverse bacterial community, with significant compositional shifts observed across seasons and sample sources. Approximately 13.6 % of the MAGs carried one or more antimicrobial resistance genes (ARGs), with genes conferring resistance to tetracycline and oxacillin being the most prevalent within the wastewater microbiomes. We also recovered yet-uncultivated microbial genomes- often referred to as "microbial dark matter" harbouring clinically relevant ARGs, offering insights into previously uncharacterised resistance reservoirs in wastewater. ARG-host associations shifted between untreated influent and treated effluent, with effluent profiles also varying significantly between secondary and tertiary treatments, revealing the impact of treatment type on ARG host composition. This study represents the first comprehensive genome-resolved metagenomic characterisation of ARG carriers across both hospital and municipal wastewater in Wales, effectively bridging clinical and environmental compartments. Our findings highlight the need to integrate high-resolution genome-resolved metagenomic surveillance into national AMR monitoring frameworks to track emerging threats, characterise ARG reservoirs and inform targeted public health interventions.},
}

@article {pmid41039256,
year = {2025},
author = {Jin, W and Zhang, Y and Su, X and Xie, Z and Wang, R and Wang, Y and Qiu, Y and He, Y},
title = {Effects of different land use on functional genes of soil microbial carbon and phosphorus cycles in the desert steppe zone of the Loess Plateau.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {607},
pmid = {41039256},
issn = {1471-2180},
support = {32072394//National Natural Science Foundation of China/ ; 23ZSCQ030//Gansu Province Intellectual Property Project/ ; 2022-01//Chinese Academy of Sciences regional development projects for young scholars/ ; },
mesh = {*Soil Microbiology ; *Phosphorus/metabolism ; China ; Soil/chemistry ; Grassland ; *Carbon/metabolism ; Desert Climate ; *Carbon Cycle/genetics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Microbiota ; Metagenomics ; },
abstract = {Desert grassland ecosystems on China's Loess Plateau are characterized by diverse land use types and varying human disturbances. We aimed to evaluate how land use influences soil microbial communities and functional genes related to carbon (C) and phosphorus (P) cycling. To do this, we selected five representative land use types: natural grassland, 20-year abandoned farmland, 12-year alfalfa grassland, 5-year Lanzhou lily farmland, and 17-year Platycladus orientalis forest. High-throughput metagenomic sequencing and soil physicochemical analyses were conducted. Proteobacteria dominated the nutrient-rich lily soil, while Actinobacteria were more abundant in the other soils. Available phosphorus (AP) had the strongest influence on microbial community structure and gene composition (p < 0.01). The relative abundance of ppdK, rpiB, glpX, and epi (C fixation genes), and purS (purine metabolism) was significantly higher in forest soil than in abandoned farmland (p < 0.05). Similarly, forest soil showed elevated levels of mttB and acs (methanogenesis), sdhA (TCA cycle), pstS (P transport), and pps (pyruvate metabolism) compared to alfalfa soil. Lily soil exhibited significantly higher abundance of acr genes (involved in the hydroxypropionate-hydroxybutylate cycle) and phnE (an ATP-binding cassette transporter) than natural grassland and alfalfa soils (p < 0.05). Microbial networks involved in C and P cycling were simpler but more functionally specialized in forest soil. Positive microbial interactions related to C and P cycling were strongest in lily soil. These findings provide important insights into soil microbial functional adaptation and offer a foundation for sustainable land use management on the Loess Plateau.},
}

*Soil Microbiology
*Phosphorus/metabolism
China
Soil/chemistry
Grassland
*Carbon/metabolism
Desert Climate
*Carbon Cycle/genetics
*Bacteria/genetics/metabolism/classification/isolation & purification
Microbiota
Metagenomics

@article {pmid41039213,
year = {2025},
author = {IJdema, F and Arias-Giraldo, LM and Vervoort, E and Struyf, T and Van den Ende, W and Raaijmakers, JM and Lievens, B and De Smet, J},
title = {Metagenome-based identification of functional traits of the black soldier fly gut microbiome associated with larval performance.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {612},
pmid = {41039213},
issn = {1471-2180},
support = {S008519N//ENTOBIOTA/ ; IMP20028//KU Leuven Impuls grant/ ; C3/22/041//KU Leuven CHITINERY grant/ ; G0C4622N//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Animals ; Larva/microbiology/growth & development ; *Gastrointestinal Microbiome/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Metagenome ; *Diptera/microbiology/growth & development ; Animal Feed/analysis ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Diet ; Phylogeny ; Chickens ; },
abstract = {BACKGROUND: The relationship between microbiomes and their hosts has been the subject of intensive study in recent years. For black soldier fly larvae (BSFL) (Hermetia illucens L., Diptera: Stratiomyidae), correlations between shifts in its microbial gut community composition and its health and performance suggest that the BSFL gut microbiome encodes important functions that complement the insect's own immune system and metabolism. To date, most BSFL microbiome studies have been based on 16S rRNA sequencing data. Because this approach derives a lot of information from very short sequencing reads, it was hypothesized that more insight into bacterial functionality could be generated using more extensive sequencing technologies. Here, whole genome shotgun (WGS) metagenomic sequencing was employed to investigate which microbiome-associated taxa and functions were associated with increased performance of larvae reared on a chicken feed (CF) or artificial supermarket food waste (SFW) based diet.

RESULTS: Taxonomic and functional profiling of the BSFL gut microbiome revealed a significant shift in response to diet, where bacterial genes encoding specific metabolic functions, such as the metabolism of sorbitol, were significantly enriched in the microbiome of larvae reared on SFW-diet. This indicates that the nutritional composition of the substrate alters the gut bacterial composition by providing competitive benefits or new niches for specific bacteria that can utilise these compounds. Moreover, specific microbial functions, such as cobalamin synthesis, appear to be correlated with larval performance. Aside from metabolic functions, biosynthetic gene cluster analysis revealed potential antimicrobial competition and protective functions among bacterial species. Improved taxonomic resolution provided by WGS led to the identification of several metagenome assembled genomes (MAGs), including a potentially novel BSFL-associated Scrofimicrobium species. Furthermore, there were differences in larval performance between rearing diets, and larval growth was correlated with high abundance of several MAGs.

CONCLUSIONS: Variation in the nutritional and bacterial load of a diet can result in functional shifts in the gut microbiome of the larvae. Analysis of the BSFL metagenome identified several bacteria that are positively correlated with larval performance, which could potentially provide beneficial metabolic functions for the host that should be further explored.},
}

Animals
Larva/microbiology/growth & development
*Gastrointestinal Microbiome/genetics
*Bacteria/genetics/classification/isolation & purification/metabolism
*Metagenome
*Diptera/microbiology/growth & development
Animal Feed/analysis
RNA, Ribosomal, 16S/genetics
Metagenomics
Diet
Phylogeny
Chickens

@article {pmid41039197,
year = {2025},
author = {Mpai, T and Diale, MO and Shargie, N and Gerrano, AS and Mtsweni, PN and Bopape, FL and Bairu, M and Hassen, AI},
title = {Functional and taxonomic profiles of soil microbial communities of tropical legume soils from smallholder farmers' fields in Tzaneen, Limpopo province, South Africa.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {601},
pmid = {41039197},
issn = {1471-2180},
support = {PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; PHP012403000067//Department of Agriculture (DoA), South Africa/ ; },
abstract = {BACKGROUND: Soil microorganisms play a vital role as the major indicators of soil health in sustainable agricultural farming systems. However, intensive cultivation and unrecommended farmers' soil management practices negatively affect the soil microbial communities, and hence that of the soil health. Here, we investigated the functional and taxonomic diversity of soil microorganisms on six selected smallholder farmers that grow Bambara groundnut (Vigna subterranea) and dry bean (Phaseolus vulgaris) in Limpopo Province, South Africa using metagenomics and phenotypic profiles studies. Five soil samples, randomly collected per farm and pooled into a single representative sample were used. Metagenomics raw read quality control, genome assembly and annotation were performed on the KBase platform while the community level physiological profile analysis was done using Biolog Ecoplates™.

RESULTS: The results indicated that the soil microbial communities in Chosen Generation farm had higher rates of carbon source utilization. Likewise, it showed greater microbial abundance of varying taxonomy in which Actinobacteria, Firmicutes and Proteobacteria were the predominant phyla while Bacillus, Streptomyces, Microvirga and Bradyrhizobium were the most represented genera.

CONCLUSIONS: This study reports that soils from the six farms studied are enriched with genetically and physiologically diverse microorganisms that are responsible for crop growth. While soil physico-chemical properties can be associated with microbial diversity in this study, further studies on farming practices such as fertilizer and irrigation are recommended to further explore their possible effects on soil microbes.},
}

@article {pmid41039183,
year = {2025},
author = {Al-Shaibani, MM and Zin, NM and Remali, J and Sidik, NM and Al-Mekhlafi, NA and Mariappan, V and Sukri, A},
title = {Anticancer compounds from Streptomyces: insights from metagenomics and mechanistic perspective.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {41039183},
issn = {1874-9356},
support = {FRGS/1/2016/STG05/UKM/02/5//Ministry of Higher Education/ ; },
abstract = {Cancer continues to be a leading cause of death globally, driving the ongoing search for novel bioactive compounds with therapeutic potential. Metagenomic sequencing has revolutionized this pursuit by enabling the direct detection and genomic assembly of previously uncultured Streptomyces species from environmental DNA, circumventing traditional cultivation limitations. This review explores recent advances in metagenomics-driven discovery of anticancer compounds derived from Streptomyces, with a focus on identifying biosynthetic gene clusters (BGCs) responsible for producing bioactive secondary metabolites. Over the past decade, metagenomic approaches have been adopted to uncover new species of Streptomyces and anticancer compounds. Although metagenomics has been adopted in research and discovery of new Streptomyces, its application in the discovery of Streptomyces-related pathways pertaining to anticancer compounds remains limited. Furthermore, clinical translation remains limited, highlighting the need for further research. By examining metagenomic methodologies and the mechanisms of action of these compounds, this review provides an updated and focused perspective on Streptomyces-derived anticancer agents and their potential for future drug development.},
}