@article {pmid40813715,
year = {2025},
author = {Fanfoni, E and Bellassi, P and Fontana, A and Sinisgalli, E and Rocchetti, G and Piccinini, S and Morelli, L and Cappa, F},
title = {Metagenomics and untargeted metabolomics reveal antibiotic resistance dynamics in an anaerobic digestion-composting system treating organic fraction of municipal solid waste.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {106},
pmid = {40813715},
issn = {2524-6372},
abstract = {BACKGROUND: The growing population and associated increase in municipal solid waste (MSW) have promoted the use of sustainable waste management strategies. Given its high organic content, MSW can be treated through anaerobic digestion (AD) and aerobic composting (AC) to recover value-added products such as bioenergy and soil amendments. However, MSW is also recognized as a relevant source of antibiotic resistance genes (ARGs), raising concerns about environmental and public health impacts. This study aimed to elucidate the dynamics of ARGs and antibiotic compounds during the treatment of the organic fraction of municipal solid waste (OFMSW) through an integrated AD–AC system. By combining metagenomics and untargeted metabolomics, a comprehensive characterization of shifts in the microbial community, ARGs, and antibiotic compounds throughout the treatment stages was achieved. Shotgun sequencing enabled an in-depth resistome analysis based on metagenome-assembled genomes (MAGs), while untargeted metabolomics revealed the occurrence and transformation of antibiotic compounds across the system.

RESULTS: The integrated process resulted in a significant differentiation of microbial communities, resistome, and antibiotic compounds profiles, at different stages of the waste treatment plant. AD samples were mostly dominated by aminoglycoside and lincosamide ARGs, whereas AC samples by macrolide and rifamycin ARGs. Despite differences in drug class dominance, the composting process significantly increased both the ARGs diversity (i.e., digestate: H = 2.6 ± 0.1; mature compost: H = 3.7 ± 0.1) and abundance (i.e., mature compost vs. digestate: log2(FC) = 3.7). Untargeted metabolomics revealed distinct distributions of antibiotics among the six matrices (i.e., pulp, digestate, solid fraction, liquid fraction, fresh compost, and mature compost) suggesting limited degradation or transformation of some classes during treatment. Digestate was enriched in phenazines and trimethoprim derivatives, whereas mature compost mainly included phenicols and sulfonamides.

CONCLUSIONS: This study provides valuable insights into the fate of antibiotic resistance genes and the persistence of antibiotic compounds in an integrated AD and AC system treating OFMSW. Moreover, it was shown how the integration of -omics techniques as metagenomics and metabolomics can be systematically utilized to detect emerging ARGs and antibiotic compounds dynamics and monitor their ongoing evolution in biological waste treatment plants.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40793-025-00769-4.},
}

@article {pmid40813371,
year = {2025},
author = {Kiu, R and Darby, EM and Alcon-Giner, C and Acuna-Gonzalez, A and Camargo, A and Lamberte, LE and Phillips, S and Sim, K and Shaw, AG and Clarke, P and van Schaik, W and Kroll, JS and Hall, LJ},
title = {Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7569},
pmid = {40813371},
issn = {2041-1723},
support = {100974/C/13/Z//Wellcome Trust (Wellcome)/ ; BB/R012490/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/X011054/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/S017941/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
abstract = {Preterm infants (<37 weeks' gestation) are commonly given broad-spectrum antibiotics due to their risk of severe conditions like necrotising enterocolitis and sepsis. However, antibiotics can disrupt early-life gut microbiota development, potentially impairing gut immunity and colonisation resistance. Probiotics (e.g., certain Bifidobacterium strains) may help restore a healthy gut microbiota. In this study, we investigated the effects of probiotics and antibiotics on the gut microbiome and resistome in two unique cohorts of 34 very-low-birth-weight, human-milk-fed preterm infants - one of which received probiotics. Within each group, some infants received antibiotics (benzylpenicillin and/or gentamicin), while others did not. Using shotgun metagenomic sequencing on 92 longitudinal faecal samples, we reconstructed >300 metagenome-assembled genomes and obtained ~90 isolate genomes via targeted culturomics, allowing strain-level analysis. We also assessed ex vivo horizontal gene transfer (HGT) capacity of multidrug-resistant (MDR) Enterococcus using neonatal gut models. Here we show that probiotic supplementation significantly reduced antibiotic resistance gene prevalence, MDR pathogen load, and restored typical early-life microbiota profile. However, persistent MDR pathogens like Enterococcus, with high HGT potential, underscore the need for continued surveillance. Our findings underscore the complex interplay between antibiotics, probiotics, and HGT in shaping the neonatal microbiome and support further research into probiotics for antimicrobial stewardship in preterm populations.},
}

@article {pmid40813370,
year = {2025},
author = {Rakoff-Nahoum, S and Debelius, J and Valles-Colomer, M and Noordzij, HT and Esteban-Torres, M and Zhernakova, A and Brusselaers, N and Pettersen, VK},
title = {A reconceptualized framework for human microbiome transmission in early life.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7546},
pmid = {40813370},
issn = {2041-1723},
abstract = {Human development and physiology are fundamentally linked with the microbiome. This is particularly true during early life, a critical period for microbiome assembly and its impact on the host. Understanding microbial acquisition in early life is thus central to both our basic understanding of the human microbiome and strategies for disease prevention and treatment. Here, we review the historical approaches to categorize microbial transmission originating from the fields of infectious disease epidemiology and evolutionary biology and discuss how this lexicon has influenced our approach to studying the early-life microbiome, often leading to confusion and misinterpretation. We then present a conceptual framework to capture the multifaceted nature of human microbiome acquisition based on four key components: what, where, who, and when. We present ways these parameters may be assigned, with a particular focus on the 'transmitted strain' through metagenomics to capture these elements. We end with a discussion of approaches for implementing this framework toward defining each component of microbiome acquisition.},
}

@article {pmid40813051,
year = {2025},
author = {An, FJ and Niu, ZR and Liu, TN and Su, YZ},
title = {[Structure and Metabolic Function Characteristics of Soil Bacterial Communities under Different Vegetation Types in Arid Region].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {8},
pages = {5360-5368},
doi = {10.13227/j.hjkx.202407230},
pmid = {40813051},
issn = {0250-3301},
abstract = {The aim of this study was to explore the effects of different vegetation types on soil bacterial community structure and metabolic function in an oasis-desert ecotone and provide scientific theoretical basis for species allocation and management of vegetation reconstruction in arid desert ecosystem. Nitraria sphaerocarpa Maxim and Calligonum mongolicum Turcz are the main natural vegetation, Haloxylon ammodendron Bunge, and Hedysarum scoparium Fisch are the primary artificial vegetation, and Ha-Cm are the main mixed community in an oasis-desert ecotone in northwest China. Understanding soil microbial community structure and function under typical vegetation types is crucial for accurate management and sustainable use of desert vegetation. We used high-throughput sequencing technology to explore the effects of different vegetation types on the structure, diversity, and metabolic pathways of soil bacteria and to investigate the key factors driving the change of soil bacterial community structure. The results showed that the growth of artificial vegetation and natural vegetation significantly increased the richness and diversity of the soil bacterial community, but no significant difference was observed. Metagenomic analysis showed that the same dominant bacterial phyla existed in all soils, but the proportions were different. Actinobacteriota, Proteobacteria, and Chloroflexi were the absolute dominant bacterial phyla, accounting for 65.12%-78.68% of the total bacteria. Principal co-ordinates analysis showed significant differences in soil bacterial community structure in the planted forest but similarities in the natural forest. The metabolic pathways of soil bacteria in different vegetation communities were similar. Soil organic carbon （SOC）, available phosphorus （AP）, and pH were important abiotic factors affecting the functional structure of bacteria. The findings are helpful for furthering the understanding of plant-soil interaction in ecologically fragile deserts.},
}

@article {pmid40812707,
year = {2025},
author = {Wu, J and Chen, Y and Zhao, J and O'Brien, JW and Coin, L and Hai, FI and Sanderson-Smith, M and Jiang, G},
title = {Impact of human lifestyle on the pathogenic potential of urban wastewater.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122591},
doi = {10.1016/j.envres.2025.122591},
pmid = {40812707},
issn = {1096-0953},
abstract = {Domestic wastewater has been known for its pathogenic potential including the presence of pathogenic bacteria, virulence factor genes (VFGs) and antibiotic resistance genes (ARGs). While previous studies have investigated regional differences in microbial communities, the influence of population lifestyle factors on the pathogenic potential of wastewater microbiomes remains poorly understood. In this study, we analyzed ten Australian wastewater treatment plants (WWTPs) using Nanopore metagenomic sequencing to profile pathogens, ARGs, and VFGs, and examined their associations with health-related behaviors such as smoking, alcohol consumption, and obesity. A total of 196 pathogenic species, 951 ARG subtypes, and 380 VFGs were detected. Staphylococcus aureus was the most abundant pathogen, macB the dominant ARG, and lipooligosaccharides (LOS) the most prevalent VFG. While pathogen and ARG profiles were relatively stable across sites and showed limited association with lifestyle variables, VFG profiles demonstrated significant correlations with smoking rates, alcohol consumption, and nicotine levels in wastewater. Co-occurrence network analysis revealed strong interconnectivity among VFGs and between VFGs and ARGs, suggesting potential co-selection. Principal component analysis and diversity metrics further confirmed distinct patterns in VFG distribution across sites. These findings suggest VFGs as potentially sensitive indicators of behavioral health risks in wastewater-based epidemiology.},
}

@article {pmid40812705,
year = {2025},
author = {Gao, H and Guo, Z and Huang, F and Li, S and He, X and Fernio, JU and Lv, W and Zhou, L and Du, S and Shen, M and Xu, R},
title = {Core Microbiota with Antimonite Oxidation Coupled Nitrogen Fixation Traits Persist in the Rhizosphere of Pioneer Plants in Antimony Tailings.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122586},
doi = {10.1016/j.envres.2025.122586},
pmid = {40812705},
issn = {1096-0953},
abstract = {Antimony (Sb) tailings pose a dual challenge to plant colonization, combining high metal(loid) toxicity with nitrogen (N) limitation, both of which constrain pioneer plant establishment and hinder ecological restoration. Rhizosphere microbiota, particularly Sb(III) oxidation coupled with nitrogen fixation (SbNF) taxa, are critical in mitigating such stresses. However, the composition and persistence of these functional microbes may vary across plant species, leading to untargeted selection. Here, we investigated the rhizosphere microbiomes of two pioneer species-Miscanthus sinensis (herbaceous) and Boehmeria nivea (shrubby)-in Sb tailings. A shared core microbiota (>20% of the genera) was identified, within which certain taxa exhibited SbNF capabilities with plant growth-promoting (PGP) potential. Through integrated metagenomic binning, culture-based isolation, and functional validation, we identified core genera, such as Pseudomonas and Streptomyces, that were consistently enriched across plant types and exhibited robust SbNF capacities, versatile PGP traits, and community assembly interactions. These findings reveal a conserved assembly mechanism of functional rhizobacteria in Sb-stressed environments and offer promising microbial candidates for the development of bioinoculants to support phytoremediation in metalloid-contaminated ecosystems.},
}

@article {pmid40812586,
year = {2025},
author = {Zhu, C and Zhang, D and Wang, Y and Zhang, C and Wang, S and Xue, J and Lan, Z and Xun, Z and Zhang, L and Chao, J and Liang, Y and Xue, W and Pu, Z and Zhu, T and Ning, C and Sang, X and Wang, H and Jiang, X and Yang, X and Zhao, H},
title = {Gut microbiota and metabolite signatures predict severe immune-related adverse events in advanced hepatobiliary cancers.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.08.016},
pmid = {40812586},
issn = {2090-1224},
abstract = {INTRODUCTION: Immune checkpoint inhibition (ICI) has proven to be a major breakthrough in hepatobiliary cancers treatment. However, immune-related adverse events (irAEs) remain a major concern. The gut microbiome has been implicated in ICI efficacy; however, specific alterations in the multi-kingdom gut microbiota associated with severe irAEs are not well understood.

OBJECTIVES: We aimed to identify the signatures of gut microbiota, fungi, and metabolites in patients with advanced hepatobiliary cancers with severe irAEs compared to those in patients experiencing mild or no irAEs.

METHODS: We enrolled 168 patients with advanced hepatobiliary cancers between June 2018 and June 2022 (72 in the train set, 31 in test set 1, and 65 in test set 2). Multi-kingdom microbiota profiles were investigated using metagenomic, ITS2, and metabolomic datasets.

RESULTS: The presence of severe irAEs was associated with significantly longer overall survival compared with the irAE-Mild and irAE-No groups. Patients with severe irAEs showed significant differences in the composition of bacteria and metabolites, but relatively few differences in fungi, and had more complex network associations of multi-kingdom gut microbiota compared with the irAE-Mild and irAE-No groups. A predictive model based on four bacteria and six metabolites simultaneously discriminated irAE-Severe from irAE-Mild and irAE-No with high accuracy.

CONCLUSION: Patients with severe irAEs exhibited unique changes in microbiota-fungi-metabolite interactions. Gut microbiota- and/or metabolite-based algorithms could be used as additional tools for predicting severe irAEs and as potential prognostic markers in advanced hepatobiliary cancers.},
}

@article {pmid40812483,
year = {2025},
author = {Han, Q and Xia, S and Huang, X and He, J and Yin, Y and Yin, J},
title = {Age-related differences in the gut microbiota of pigs influence fat deposition in the mouse.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.07.022},
pmid = {40812483},
issn = {1541-6100},
abstract = {BACKGROUND: The gut microbiota significantly influences lipid metabolism, but the impact of its developmental patterns at different growth stages on fat deposition remains unclear.

OBJECTIVES: This study aimed to explore the dynamic changes in microbial diversity and composition during the growth of pig models and assess their involvement in fat deposition.

METHODS: Forty-five Duroc-Landrace-Yorkshire (DLY) crossbred pigs were euthanized at five ages: 90, 120, 150, 180, and 210 days of age (n=9). Fecal samples were collected 1 day and 15 days before each euthanasia, and the fecal microbiota were detected by 16S rRNA sequencing. The backfat thickness, serum lipid levels, intramuscular fat, and fatty acid content in the longissimus dorsi muscle of pigs were measured to assess lipid metabolism. Fecal microbiota transplantation (FMT) from DLY pigs of different ages to antibiotics-challenged mice (n=8) was used to confirm the effects of microbial development on fat deposition. Metagenomic sequencing was conducted on feces from pigs aged 150 and 180 days and their corresponding transplanted mice to identify key strains involved in fat deposition.

RESULTS: We observed marked alterations and an increase in intestinal microbial α-diversity with age, peaking at 150 days of age in DLY pigs (P<0.05). Spearman correlation analyses indicated that 20 genera significantly correlated with the muscle fatty acid contents (P<0.05). FMT further confirmed that the developmental patterns of the gut microbiota affected host fat deposition, with notable differences observed between the fecal microbiota at day 150 and 180 of age in pigs. Schaalia canis was identified as a potential key microbial strain involved in the developmental patterns of the gut microbiota-governed fat deposition, and its colonization in mice reduced fat deposition by downregulating of LXRα/β gene expressions (P<0.05).

CONCLUSIONS: This study indicated that gut microbiota development impacted fat deposition in pigs, with Schaalia canis capable of inhibiting fat deposition.},
}

@article {pmid40812337,
year = {2025},
author = {Liu, C and Rosen, EA and Stohs, EJ and Imlay, H and Nigo, M and Gottesdiener, LS and So, M and Tverdek, F and Dadwal, S and Gudiol, C and Satlin, MJ and Seo, SK and Trubiano, JA and Banerjee, R and Hanson, KE and Abbo, LM},
title = {Tackling antimicrobial resistance in people who are immunocompromised: leveraging diagnostic and antimicrobial stewardship.},
journal = {The Lancet. Infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/S1473-3099(25)00311-1},
pmid = {40812337},
issn = {1474-4457},
abstract = {Antimicrobial resistance (AMR) disproportionately affects people who are immunocompromised due to their frequent encounters with the health-care system and repeated, prolonged exposure to antibiotics. AMR threatens to undermine continued advances in cancer care, haematopoietic cell transplantation, and solid organ transplantation by severely restricting therapeutic options. The convergence of several factors in the diagnostic evaluation of infection among individuals with immunocompromising conditions contributes to excess and inappropriate antibiotic use. Diagnostic and antimicrobial stewardship are key complementary strategies to address these challenges with shared goals of improving patient outcomes, reducing harm, and mitigating the risk of AMR. In this Series paper, we discuss opportunities to enhance use of existing diagnostic tools (eg, culture-based diagnostics, molecular diagnostics, and other tools such as antibiotic allergy delabelling), emerging diagnostic tools (eg, metagenomic sequencing and host response profiling), and digital innovation, to optimise antibiotic use, and the potential for precision medicine approaches to combat AMR in people who are immunocompromised.},
}

@article {pmid40812303,
year = {2025},
author = {Huang, Y and Zhang, X and Yu, C and Liu, Y and Kang, H and Liu, Y and Ni, Y and Xia, Y and Jiang, Z and Chen, J and Zhao, K and Han, L and Zou, X and Wang, J and Lei, T and Gan, C and Zhang, H},
title = {Lactobacillus acidophilus promotes cognitive function recovery via regulating microglial peroxisomal function in cerebral ischemia.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.07.018},
pmid = {40812303},
issn = {1934-6069},
abstract = {Cerebral ischemia causes significant mortality and is accompanied by inflammatory reactions that exacerbate damage. While the gut microbiota is linked to clinical outcomes, specific treatments and mechanisms remain unclear. Our metagenomics linked low Lactobacillus abundance to cognitive decline in patients with cerebral ischemia. L. acidophilus supplementation alleviated post-ischemic deficits in murine middle cerebral artery occlusion and bilateral carotid artery stenosis models. The neuroprotective effects of L. acidophilus were driven by enhanced gut absorption of linoleic acid (LinA). L. acidophilus-induced LinA activates peroxisomes in microglia, triggering microglial reprogramming to an anti-inflammatory state via reactive oxygen species (ROS) scavenging and β-oxidation-mediated epigenetic changes. These L. acidophilus-driven effects are lost upon dietary deficits in LinA, microglia depletion, or peroxisome disruption. A randomized clinical trial showed that L. acidophilus improved cognition and cerebral blood flow in ischemic patients. This study was registered at ClinicalTrials.gov (NCT05845983). Collectively, these findings reveal a therapeutic axis whereby L. acidophilus drives microglial reprogramming, providing a basis for microbiome-targeted neurotherapies.},
}

@article {pmid40812187,
year = {2025},
author = {Tričković, M and Kieser, S and Zdobnov, EM and Trajkovski, M},
title = {Subspecies of the human gut microbiota carry implicit information for in-depth microbiome research.},
journal = {Cell host & microbe},
volume = {33},
number = {8},
pages = {1446-1458.e4},
doi = {10.1016/j.chom.2025.07.015},
pmid = {40812187},
issn = {1934-6069},
abstract = {Microbial strains within a single species can exhibit distinct functional characteristics due to variations in gene content and often show individual specificity, which can obscure unbiased associations and hinder deductive research. Here, we comprehensively define the human gut microbiota at a consistently annotated operational subspecies unit (OSU) resolution in an unbiased, cohort-independent manner, demonstrating that this approach can generalize across diverse global populations while maintaining specificity and improving interstudy reproducibility. We develop panhashome-a sketching-based method for rapid subspecies and species quantification and identification of genes that drive intraspecies variations-and show that subspecies carry implicit information undetectable at the species level. We identify subspecies associated with colorectal cancer (CRC) whose sibling subspecies or species are not, while a machine-learning CRC diagnostic algorithm based on subspecies outperformed species-level methods. This subspecies catalog allows identification of genes that drive functional differences between subspecies as a fundamental step in mechanistically understanding microbiome-phenotype interactions.},
}

@article {pmid40811873,
year = {2025},
author = {Simpson, AM and Chase, AB and Rodríguez-Verdugo, A and Martiny, JB},
title = {Investigating bacterial evolution in nature with metagenomics.},
journal = {Current opinion in microbiology},
volume = {87},
number = {},
pages = {102654},
doi = {10.1016/j.mib.2025.102654},
pmid = {40811873},
issn = {1879-0364},
abstract = {Metagenomic sequencing has revolutionized our ability to capture the vast genetic diversity of microbiomes. The technique provides an especially detailed characterization of intraspecific diversity, and a growing number of studies are using that information to investigate bacterial evolution in nature. Here, we review how these studies operationally define evolution, the sampling approaches and metrics used, and the interpretation of the observed evolutionary signatures. Current studies address three main themes: (1) the mechanisms that generate genetic diversity, (2) the spatiotemporal structure of that diversity, and (3) the evolutionary processes that determine its fate. While metagenomics provides enormous potential to investigate in situ evolution, the approach also introduces new questions, including whether populations defined by read mapping are meaningful proxies for biological units of evolution. Addressing these questions will facilitate investigation of the role of evolution relative to ecological shifts in shaping a microbiome's response to environmental change.},
}

@article {pmid40811403,
year = {2025},
author = {Alanko, JN and Biagi, E and Puglisi, SJ},
title = {Finimizers: Variable-Length Bounded-Frequency Minimizers for $k$-mer Sets.},
journal = {IEEE transactions on computational biology and bioinformatics},
volume = {22},
number = {2},
pages = {899-910},
doi = {10.1109/TCBBIO.2025.3545285},
pmid = {40811403},
issn = {2998-4165},
abstract = {The minimizer of a $k$-mer is the smallest $m$-mer inside the $k$-mer according to some total order $< $ of the $m$-mers. Minimizers are often used as keys in hash tables in indexing tasks in metagenomics and pangenomics. The main weakness of minimizer-based indexing is the possibility of very frequently occurring minimizers, which can slow query times down significantly. Popular minimizer alignment tools employ various and often wild heuristics as workarounds, typically by ignoring frequent minimizers or blacklisting commonly occurring patterns, to the detriment of other metrics (e.g., alignment recall, space usage, or code complexity). In this paper, we introduce frequency-bounded minimizers, which we call finimizers, for indexing sets of $k$-mers. The idea is to use an order relation $< $ for minimizer comparison that depends on the frequency of the minimizers within the indexed $k$-mers. With finimizers, the length $m$ of the $m$-mers is not fixed, but is allowed to vary depending on the context, so that the length can increase to bring the frequency down below a user-specified threshold $t$. Setting a maximum frequency solves the issue of very frequent minimizers and gives us a worst-case guarantee for the query time. We show how to implement a particular finimizer scheme efficiently using the Spectral Burrows-Wheeler transform ($SBWT$) (Alanko et al. Proc. SIAM ACDA, 2023) augmented with longest common suffix information. In experiments, we explore in detail the special case in which we set $t = 1$. This choice simplifies the index structure and makes the scheme completely parameter-free apart from the choice of $k$. A prototype implementation of this scheme exhibits $k$-mer localization times close to, and often faster than, state-of-the-art minimizer-based schemes.},
}

@article {pmid40811323,
year = {2025},
author = {Alamin, M and Liu, KJ},
title = {Phylogenetic Placement of Aligned Genomes and Metagenomes With Non-Tree-Like Evolutionary Histories.},
journal = {IEEE transactions on computational biology and bioinformatics},
volume = {22},
number = {4},
pages = {1323-1334},
doi = {10.1109/TCBBIO.2024.3519311},
pmid = {40811323},
issn = {2998-4165},
abstract = {Phylogenetic placement is the computational task that places a query taxon into a reference phylogeny by analyzing biomolecular sequences or other evolutionary characters. A chief advantage of phylogenetic placement over traditional phylogenetic reconstruction is computational scalability, and the former has many applications in phylogenetics and beyond. Existing phylogenetic placement methods share the common simplifying assumption that a phylogenetic tree suffices for modeling evolutionary history. However, a growing body of research indicates that non-tree-like evolution is prevalent throughout the Tree of Life - the evolutionary history of all life on Earth - which in fact may not be a tree at all. More general graph representations such as phylogenetic networks have therefore been proposed, and a new generation of phylogenetic network reconstruction methods are under active development. But the simplifying assumption made by phylogenetic tree placement methods is fundamentally at odds with the non-tree-like evolutionary histories of many microbes and other organisms. The consequences of this conflict are poorly understood. In this study, we conduct a comprehensive performance study to directly assess the impact of non-tree-like evolution on phylogenetic tree placement of genomes and metagenomes. Our study includes in silico simulation experiments as well as empirical data analyses. We find that the topological accuracy of phylogenetic tree placement degrades quickly as genomic sequence evolution becomes increasingly non-tree-like. We then introduce NetPlacer, a new statistical method for phylogenetic network placement of genomes and metagenomes. Initial experiments with NetPlacer provide a proof-of-concept, but also point to the need for greater computational scalability.},
}

@article {pmid40811208,
year = {2025},
author = {Alonso-Reyes, DG and Albarracin, VH},
title = {Arche: An Advanced Flexible Tool for High-Throughput Annotation of Functions on Microbial Contigs.},
journal = {IEEE transactions on computational biology and bioinformatics},
volume = {22},
number = {4},
pages = {1924-1934},
doi = {10.1109/TCBBIO.2025.3576198},
pmid = {40811208},
issn = {2998-4165},
abstract = {The growing volume of microbial genomic data has increased the need for annotation tools that are both comprehensive and accessible. However, existing pipelines often present substantial limitations: some are constrained to a single database or search algorithm, others require complex installations, or high computational resources. Arche is a command-line annotation pipeline designed to overcome these challenges by integrating a flexible and hierarchical workflow that combines multiple search strategies (BLAST, DIAMOND, HMMER3) and databases (UniProtKB, KOfam, TIGRFAMs, NCBIFAMs, and Pfam). Arche supports the annotation of prokaryotic genomes and metagenomes, and it produces detailed functional tables including enzyme commission (E.C.) numbers, KEGG and eggNOG orthologous identifiers, gene names, and protein descriptions. Benchmarking against widely used tools such as Prokka, Bakta, RAST, MicrobeAnnotator, and eggNOG-mapper shows that Arche retrieves a higher number of functional identifiers per gene in many cases. By offering modularity, compatibility with standard desktop systems, and more manageable database requirements than other high-throughput tools, Arche provides a practical and robust solution for functional annotation in genomic and metagenomic studies.},
}

@article {pmid40811063,
year = {2025},
author = {Qu, EB and Baker, JS and Markey, L and Khadka, V and Mancuso, C and Tripp, AD and Lieberman, TD},
title = {Intraspecies associations from strain-rich metagenome samples.},
journal = {Cell reports},
volume = {44},
number = {8},
pages = {116134},
doi = {10.1016/j.celrep.2025.116134},
pmid = {40811063},
issn = {2211-1247},
abstract = {Genetically distinct strains of a species can vary widely in phenotype, reducing the utility of species-resolved microbiome measurements for detecting associations with health or disease. While metagenomics theoretically provides information on all strains in a sample, current strain-resolved analysis methods face a tradeoff: de novo genotyping approaches can detect novel strains but struggle when applied to strain-rich or low-coverage samples, while reference database methods work robustly across sample types but are insensitive to novel diversity. We present PHLAME, a method that bridges this divide by combining the advantages of reference database approaches with novelty awareness. PHLAME explicitly defines clades at multiple phylogenetic levels and introduces a probabilistic, mutation-based framework to quantify novelty from the nearest reference. By applying PHLAME to publicly available human skin and vaginal metagenomes, we find clade associations with coexisting species, geography, and host age. The ability to characterize intraspecies associations and dynamics in previously inaccessible environments will enable strain-level insights from accumulating metagenomic data.},
}

@article {pmid40810759,
year = {2025},
author = {Frere Martiniuc, C and de Assis Leite, DC and Seldin, L and Jurelevicius, D},
title = {Viral Diversity in Polar Hydrocarbon-Contaminated Soils: A Transect Study from King George Island, Antarctica.},
journal = {Food and environmental virology},
volume = {17},
number = {3},
pages = {43},
pmid = {40810759},
issn = {1867-0342},
abstract = {Viruses are key components of soils, influencing microbial dynamics and biogeochemical cycles. Here, we used shotgun metagenomics to analyze the virome of hydrocarbon-contaminated and uncontaminated soils from King George Island, Antarctica. Viral sequences were obtained from metagenomes of all soils; however, the relative abundance of viruses was higher in hydrocarbon-contaminated soils compared to uncontaminated soils. Our results indicate that viral distribution correlates with polycyclic aromatic hydrocarbons (PAHs) in King George Island soil (p = 0.05). Taxonomic analysis of viral contigs revealed viruses from realms Duplodnaviria, Varidnaviria, Monodnaviria, and Riboviria. While Caudoviricetes (realm Duplodnaviria) represented more than 90% of the relative abundance of viruses found in hydrocarbon-contaminated soils, this class represented less than 62% of the viruses of uncontaminated soils. Most viral hosts detected in King George Island soils belonged to hydrocarbon-degrading bacterial genera from the phyla Pseudomonadota and Actinomycetota. Hydrocarbon contamination resulted in the enrichment of well-characterized viruses at the expense of previously uncharacterized viral taxa, which were predominantly detected in non-contaminated soils. Among them, Gordonia-related Stormageddonvirus was the most abundant viral entity identified in King George Island soil. Viral auxiliary metabolic genes (AMGs) associated with nitrogen and phosphate cycles were found in different Caudoviricetes-related contigs. Our results further indicate that Caudoviricetes abundance is correlated with the carbon: phosphate (C:P) ratio in King George Island soils. We propose the Caudoviricetes may actively contribute to microbial competition for phosphorus in hydrocarbon-contaminated soils. These findings shed light on the intricate interplay between viruses, microbial hosts, and environmental contamination in Antarctic soils.},
}

@article {pmid40810220,
year = {2025},
author = {Ni, Z and Yanxi, C and Lianqun, J and Xinya, LI and Yixin, MA},
title = {Huayu Qutan formula can improve platelet aggregation in acute coronary syndrome rats by regulating gut microbes to drive trimethylamine/flavin containing monooxygenase 3/trimethylamine N-oxide pathway.},
journal = {Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan},
volume = {45},
number = {4},
pages = {747-758},
pmid = {40810220},
issn = {2589-451X},
support = {82104841//National Natural Science Foundation of China Project: based on the Theory of "the Heart is in Harmony with the Small Intestine" to Explore the Influence and Mechanism of Gut Microbes on High Platelet Reactivity of Acute Coronary Syndrome with Phlegm and Blood Stasis Syndrome/ ; L202039//Education Department of Liaoning Province Young Science and Technology Talents "Seedling" Project: to Explore the Effect and Mechanism of Huayu Qutan Formula on Platelet Function in Acute Coronary Syndrome Patients with Phlegm and Blood Stasis Syndrome after Percutaneous Coronary Intervention based on Intestinal Microbiome/ ; },
abstract = {OBJECTIVE: To investigate the effects of gut microbes regulation of the trimethylamine (TMA)/flavin containing monooxygenase 3 (FMO3)/trimethylamine N-oxide (TMAO) pathway on platelet aggregation in acute coronary syndrome (ACS) rats and the intervention of Huayu Qutan formula.

METHODS: The ACS rats with syndrome of phlegm and blood stasis rats were established. Platelet, platelet aggregation, platelet activation markers and TMA/FMO3/ TMAO pathway were detected. Metagenomics technology was employed to analyze the characteristics of the gut microbiota.

RESULTS: Huayu Qutan formula and gut microbes could inhibit high platelet reactivity and regulate the TMA/ FMO3/TMAO pathway. The dominant bacteria in ACS rats including but not limited to the major phyla, Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria, also including some low abundance phyla, Fusobacteria, Verrucomicrobia, Spirochaetes, and Deferribacteres. The dominant bacteria in the Huayu Qutan formula group were Synergistetes, Deferribacteres, Deferribacteraceae, Faecalibacterium and Mucispirillum. In the Huayu Qutan formula combined with fecal bacteria enema group, the dominant bacteria were Verrucomicrobia, Verrucomicrobiae, Akkermansia and Verrucomicrobium. These gut microbiota were correlated with pathways such as Riboflavin metabolism and Arachidonic acid metabolism.

CONCLUSION: Huayu Qutan formula may prevent ACS by modulating gut microbes Synergistetes, Faecalibacterium and Allobaculum, regulating the iron metabolism of Deferribacteres, and driving the TMA/FMO3/TMAO pathway to regulate gut microbiota function, and improving platelet aggregation. Akkermansia may serve as a promising probiotic, which could drive TMA/FMO3/ TMAO pathway to regulate Arachidonic acid metabolism to improve platelet aggregation. The findings of this study provide a theoretical basis for the theory of "the heart is connected with the small intestine".},
}

@article {pmid40810199,
year = {2025},
author = {Lin, YT and Sayols-Baixeras, S and Graells, T and Dekkers, KF and Baldanzi, G and Nguyen, D and Larsson, A and Feldreich, TR and Nielsen, N and Eklund, AC and Holm, JB and Nielsen, HB and Bergström, G and Smith, JG and Malinovschi, A and Engström, G and Orho-Melander, M and Fall, T and Ärnlöv, J},
title = {Identification of gut microbiome signatures and metabolites associated with albuminuria in type 2 diabetes.},
journal = {The Journal of clinical endocrinology and metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1210/clinem/dgaf453},
pmid = {40810199},
issn = {1945-7197},
abstract = {CONTEXT: Type 2 diabetes is a growing global concern with serious complications, including kidney damage and cardiovascular morbidity and mortality. Monitoring albuminuria, which is associated with these complications, is crucial in optimal diabetes management. Gut microbiota composition has been suggested to impact albuminuria, but large studies with granular data are lacking.

METHODS: We investigated the relationship between 1002 gut microbial species, 1308 plasma metabolites and albuminuria in 752 participants with type 2 diabetes from the Swedish CArdioPulmonary BioImage Study. To determine the relative abundance of species, we employed deep shotgun metagenomic sequencing of fecal samples. Plasma metabolites were analyzed using mass spectrometry-based methods.

RESULTS: We identified three species that were associated with albuminuria, including Sellimonas intestinalis, Eggerthellales sp., Ellagibacter isourolithinifaciens. Two of these species were replicated in an independent pre-diabetic population (n=3,423) in SCAPIS. In total, 36 annotated metabolites were associated with the three albuminuria-signature species. Functional mapping of the signature species suggests a role in the regulation of the metabolites of imidazole propionate and trigonelline, which have previously been reported to play roles in the progression of albuminuria.

CONCLUSIONS: These findings provide additional evidence of the potential impact of microbial species and contribute to our understanding of the complex relationship between the gut microbiome, plasma metabolites, and albuminuria in individuals with diabetes.},
}

@article {pmid40809522,
year = {2025},
author = {Yu, H and Liang, D and Ding, X and Gao, H and Fan, G and Song, Y and Sun, S and Huang, Q and Liu, S and Zhang, Z},
title = {Comparison of microbial culture, metagenomic next-generation sequencing and droplet digital polymerase chain reaction methods for pathogen detection in patients with neurosurgical central nervous system infection.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1606283},
pmid = {40809522},
issn = {2235-2988},
abstract = {BACKGROUND: Neurosurgical central nervous system infections (NCNSIs) are one of the most common complications in neurosurgical patients, followed by neurosurgery itself, trauma, implants or infection need to be treated by surgery. However, the diagnosis of NCNSIs continues to pose a significant challenge. The primary objective of this study was to comprehensively assess the diagnostic performance of metagenomic next-generation sequencing (mNGS) and Multiplex Droplet Digital PCR (ddPCR) in elucidating the microbiological etiologies underlying NCNSIs in affected patients.

METHODS: Data on 127 enrolled NCNSIs patients were collected from Emergency Neurosurgical Intensive Care Unit at Qilu Hospital of Shandong University from June 2022 to October 2024. The clinical record, cerebrospinal fluid or pus routine, biochemical tests, microbial smear and culture, mNGS and ddPCR results, time to positive culture(TTPC), time from sample harvesting to final positive results (THTR) obtained by the physician, turn-around time for mNGS and ddPCR, and follow-up data were collected and analyzed.

RESULTS: A total of 127 patients were enrolled in this study. In comparison to the positive rate achieved by traditional culture method (59.1%) in diagnosing NCNSIs, the overall pathogen detection rates of mNGS and ddPCR were markedly elevated (86.6%, p<0.01 and 78.7%, p<0.01, respectively). Notably, the administration of empiric antibiotics did not significantly influence the positive detection rates of either mNGS or ddPCR. When stratified by infection type, mNGS and ddPCR demonstrated notably higher positive detection rates in three specific categories of NCNSIs-ventriculitis, intracranial abscess, and implant-associated infections-compared to meningitis. Among the 127 patients, 37 (29.1%) tested positive via mNGS but negative via microbial culture, whereas 11 patients were positive via mNGS but negative via ddPCR. The mean TTPC for microbial culture was 15.1 ± 10.4 hours. Furthermore, the mean THTR for microbial culture, mNGS and ddPCR were 22.6 ± 9.4 hours, 16.8 ± 2.4 hours and 12.4 ± 3.8 hours, respectively. Importantly, ddPCR exhibited a significantly shorter THTR compared to mNGS (p<0.01).

CONCLUSION: mNGS and ddPCR hold the potential to substantially augment the diagnostic efficacy for NCNSIs patients. It is advisable that, in future clinical practice, mNGS and ddPCR be more extensively employed for the early and precise identification of pathogens in NCNSIs patients.},
}

@article {pmid40809278,
year = {2025},
author = {Zhang, T and Zhang, L and He, Y and Hou, J and Tao, H},
title = {Exploring the metabolomics and metagenomics of chronic obstructive pulmonary disease (COPD) and lung cancer: unraveling the complex interplay.},
journal = {Journal of thoracic disease},
volume = {17},
number = {7},
pages = {5268-5281},
pmid = {40809278},
issn = {2072-1439},
abstract = {Chronic obstructive pulmonary disease (COPD) and lung cancer are two leading respiratory disorders that impose substantial morbidity, mortality, and healthcare burdens worldwide. Epidemiological evidence indicates that patients with COPD have a significantly increased risk of developing lung cancer, suggesting potential shared pathophysiological mechanisms between these two conditions. Understanding the underlying molecular mechanisms of these diseases is crucial for the improvement of early detection, diagnosis, and treatment. In recent years, advances in high-throughput technologies have enabled the emergence of metabolomics and metagenomics as powerful tools in biomedical research. Metabolomics allows for the comprehensive profiling of small-molecule metabolites, providing a global snapshot of metabolic dysregulation associated with disease onset and progression. Concurrently, metagenomics facilitates an in-depth analysis of the microbial communities residing in the respiratory and gastrointestinal tracts, shedding light on the crucial roles of the microbiota in modulating host immunity, inflammation, and carcinogenesis. Metabolomics and metagenomics, cutting-edge fields in biomedical research, provide valuable insights into the intricate interplay between host genetics, environmental factors, and microbial communities. These two omics disciplines offer unique but complementary perspectives on the complex biological processes linking COPD and lung cancer. In this review, we delve into the recent research findings on altered metabolomics and metagenomics in COPD and lung cancer, while also exploring the possible associations between these two areas of study.},
}

@article {pmid40809226,
year = {2025},
author = {Bae, J and Woo, W and Gardner, SE},
title = {The wound microbiome associated with deep sternal wound infection: a scoping review.},
journal = {Journal of thoracic disease},
volume = {17},
number = {7},
pages = {5330-5346},
pmid = {40809226},
issn = {2072-1439},
abstract = {BACKGROUND: Deep sternal wound infection (DSWI) is a serious complication following cardiovascular surgery, increasing patient mortality and healthcare burden. Understanding the wound microbiome, including microbial load, microbial diversity, presence/abundance of common wound microorganisms, and biofilm formation, is crucial for improving infection prevention, diagnosis, and management. This scoping review aims to: (I) summarize DSWI definitions, specimen acquisition methods, and microbial identification techniques; (II) synthesize current DSWI literature regarding microbial load, microbial diversity, presence/abundance of common wound microorganisms, and biofilm formation.

METHODS: A scoping review was conducted using PubMed and EMBASE to identify studies on the wound microbiome in DSWI. Studies were included if they were in English, focused on adults, and published in journals. Exclusion included secondary sources, case reports, transplant populations, and other nosocomial infections. Data extraction followed a standardized approach, and findings were synthesized narratively, with a table summarizing study details. Seventy-one studies were included in this scoping review.

RESULTS: The Centers for Disease Control and Prevention (CDC) criteria were most commonly used for DSWI. Specimen location was unspecified in 60.6% of studies, while 14.1% specified the mediastinum. Methods of specimen acquisition were reported in only 25.3% of studies. Culture techniques were predominant (91.5%), while molecular or imaging methods were used in only 8.5%. Among studies using culture, Staphylococcus aureus was the most common microorganism, and 22.5% investigated polymicrobial infections. Molecular studies identified resistance genes such as blaZ in Staphylococci and blaKPC in carbapenem-resistant Enterobacteriaceae (CRE). Biofilm formation was examined in only 2.8% of studies, with findings linking staphylococci to biofilm presence in DSWI.

CONCLUSIONS: This review revealed critical gaps in DSWI research, including poor reporting of specimen acquisition, a narrow focus on common wound microorganisms, and an overreliance on culture-based methods. The lack of standardized specimen collection reporting reduces data reliability and comparability. Limited use of molecular techniques restricts insights into microbial complexity. Advanced molecular techniques, including polymerase chain reaction, 16S ribosomal RNA (rRNA) sequencing, and metagenomic sequencing, are needed to improve microbiome characterization. Addressing these gaps will improve infection prevention and management for DSWI.},
}

@article {pmid40809220,
year = {2025},
author = {Liu, Z and Yao, Y and Wang, L and Yu, Y and Zhou, H},
title = {Diagnostic performance of metagenomics sequencing for pulmonary fungal infections: a clinical evaluation using the Nanopore platform.},
journal = {Journal of thoracic disease},
volume = {17},
number = {7},
pages = {5238-5249},
pmid = {40809220},
issn = {2072-1439},
abstract = {BACKGROUND: Pulmonary fungal infections are becoming increasingly prevalent, particularly among immunocompromised patients. Traditional culture-based and serological diagnostic methods exhibit low sensitivity and prolonged turnaround times (TATs), highlighting the need for more efficient diagnostic approaches. This study aims to evaluate the diagnostic performance of metagenomic third-generation sequencing (mTGS) using the Oxford Nanopore platform (Oxford Nanopore Technologies) for the detection of fungal pathogens in lower respiratory tract infections, and to compare its effectiveness with conventional diagnostic methods.

METHODS: This study evaluated the clinical utility of mTGS with the Nanopore platform for diagnosing lower respiratory tract fungal infections (LRTFIs). Between January and August 2022, bronchoalveolar lavage fluid (BALF) samples were collected from 253 patients with suspected fungal infections across four medical centers in Hangzhou, China. Fungal detection was performed through both mTGS and conventional culture, and diagnostic performance was assessed via bioinformatics analysis and clinical adjudication.

RESULTS: Fungal infections were detected in 65 samples (29.3%), with 11 fungal species identified by mTGS, including Pneumocystis jirovecii, Cryptococcus neoformans, and Aspergillus fumigatus. Conventional culture identified only six species, missing key pathogens such as Pneumocystis jirovecii and Talaromyces marneffei. mTGS demonstrated a sensitivity of 78.1% [95% confidence interval (CI): 66.0-87.5%], a specificity of 90.5% (95% CI: 84.8-94.7%), a positive predictive value (PPV) of 76.9% (95% CI: 64.8-86.5%), and a negative predictive value (NPV) of 91.1% (95% CI: 85.4-95.0%). It showed high sensitivity for Pneumocystis jirovecii (76.5%) and Cryptococcus neoformans (82.4%) but lower sensitivity for Aspergillus spp. (66.7%). mTGS also co-detected viral and bacterial pathogens, offering comprehensive pathogen profiling, and significantly shortened the TATs to 7 hours as compared to 2-7 days for culture.

CONCLUSIONS: mTGS on the nanopore platform offers a rapid, sensitive, and comprehensive approach for diagnosing LRTFIs, particularly in immunocompromised patients. It serves as a valuable complementary tool for detecting mixed infections or culture-negative pneumonia. However, careful interpretation is needed regarding the clinical relevance of colonizing fungi such as Candida albicans.},
}

@article {pmid40809051,
year = {2025},
author = {Yin, Y and Lin, YT and Hu, GR and Yu, RL and Sun, XH and Yan, Y},
title = {Distinct bacterial community structures and arsenic biotransformation gene profiles in dust.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1607082},
pmid = {40809051},
issn = {1664-302X},
abstract = {INTRODUCTION: Microorganisms, which are ubiquitous in the environment, have evolved a diverse array of arsenic biotransformation genes (ABGs). Dust harbors a wide range of microorganisms. However, the distinct characteristics of bacterial community structures and ABG profiles in dust, compared with those in other environments such as soil and water, remain poorly understood.

METHODS: In this study, dust samples were simultaneously collected alongside surrounding soil and seawater samples in Xiamen, a coastal city of China, to investigate the distinct profiles and potential sources of bacterial communities and ABGs in dust using 16S rRNA gene amplicon sequencing and metagenomic sequencing.

RESULTS AND DISCUSSION: Abundant and diverse bacterial communities and ABGs were detected in dust, revealing significant differences in community structures and ABG profiles compared with those in soil and seawater. Soil was identified as the primary source for both bacterial communities and ABGs in dust through fast expectation-maximization microbial source tracking (FEAST). Acetobacteraceae, which showed significantly greater relative abundance (p < 0.001) in dust than in soil and seawater, was also identified as a keystone taxon in the dust bacterial co-occurrence network. Furthermore, metagenome-assembled genomes (MAGs) affiliated with Acetobacteraceae were effectively recovered from dust via metagenomic binning, and these MAGs harbored an array of ABGs, indicating that Acetobacteraceae could be important hosts for ABGs in dust. Overall, our findings offer new insights into bacterial communities and ABGs in dust, thereby improving our understanding of arsenic biogeochemical cycling.},
}

@article {pmid40809048,
year = {2025},
author = {Yu, Y and Wang, J and Shi, L and Sun, H and Cheng, B and Sun, Y},
title = {Adaptive characteristics of the gut microbiota of the scaly-sided merganser (Mergus squamatus) in energy compensation at different developmental stages.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1614319},
pmid = {40809048},
issn = {1664-302X},
abstract = {The gut microbiota is crucial for maintaining health, enhancing digestive efficiency, and promoting the development of the immune system of the host. However, for the endangered waterfowl, the scaly-sided merganser (Mergus squamatus), the physiological role of the composition and structure of its gut microbiota during its growth and development remains unclear. Herein, we conducted fecal metagenomic analyses on adult and subadult populations to assess differences in the gut microbiota composition and function within the same habitat. The results revealed that this species harbors a diverse gut microbiota assemblage, with Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes being the dominant phyla in adults and subadults. Notably, the abundance of the Firmicutes phylum is higher in adult, while the Actinobacteria phylum is more abundant in subadult individuals. There are significant differences in the diversity of the gut microbiota between the two age groups of the scaly-sided merganser. The alpha diversity index shows that the species richness and evenness of gut microbiota in adult scaly-sided merganser are higher than those in subadult individuals. Functional gene enrichment analysis further indicated that the adult gut microbiota had a higher ability to synthesize acetyl-CoA and pyruvate, along with enhanced conversion of acetyl-CoA to acetate. These findings suggest that the gut microbiota of the scaly-sided merganser can play a crucial role in concert with the host during the energy metabolism process in the growth and development stage. This study provides foundational data on the gut microbiota structure and function of this species and enhances our understanding of microbial dynamics during waterfowl development.},
}

@article {pmid40809047,
year = {2025},
author = {Zhang, P and Ren, M and Xu, Y and Wang, J},
title = {Metagenomic insights into surface sediment microbial community and functional composition along a water-depth gradient in a subtropic deep lake.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1614055},
pmid = {40809047},
issn = {1664-302X},
abstract = {Deep lakes play a critical role in global elemental cycling and serve as habitats for diverse microbial communities. However, studies on the effects of lake stratification on microbial composition and functional potential in surface sediments remain limited. Here, we investigated microbial community structure and functional composition using metagenomics of 38 surface sediments across a depth gradient of 0-90 m in Lugu Lake, China. Our results showed that Shannon diversity peaked at the thermocline for microbial communities, while a U-shaped pattern for functional genes. Microbial communities and functional genes in the surface sediments showed higher spatial heterogeneity at the shallow layer, whereas those at deeper layers tended toward more homogenized. Although water depth was the most important driver in explaining 29.9 and 26.5% of variance in microbial and functional gene composition, stochastic processes primarily governed the community assemblages, particularly dispersal limitation with the contribution of 43.7%. We further found the surface layer was enriched in genes mainly involved in aerobic metabolism and methanogenesis. In contrast, genes related to reduction reactions, including dissimilatory nitrate and sulfate reduction were more abundant in the thermocline and deep layer, reflecting lower redox potential in a deeper layer. Overall, our results provide evidence for microbial community stratification and functional partitioning in deep lakes.},
}

@article {pmid40808973,
year = {2025},
author = {Rao, J and Cui, X and Gao, Y and Hu, Y and Shen, Y},
title = {Molecular identification of the potential fifth species within genus Hydatigera (Cestoda: Taeniidae) in rodents of Guangdong province, China.},
journal = {International journal for parasitology. Parasites and wildlife},
volume = {28},
number = {},
pages = {101126},
pmid = {40808973},
issn = {2213-2244},
abstract = {Hydatigera (Cestoda: Taeniidae) is a recently resurrected genus based on molecular data, comprising only four valid species: Hydatigera taeniaeformis, Hydatigera krepkogorski, Hydatigera parva, and Hydatigera kamiyai. In this study, a total of 479 rodents were collected. In total, 46 livers with visible cysts were observed from five species of rodents collected in three locations of Guangdong province, China, in 2023. Molecular analysis utilizing 18S rRNA sequences indicated that 38 of the 46 liver cysts were infected by Hydatigera, suggesting that this genus represents the predominant tapeworm responsible for the visible liver cysts in rodents. Metagenomic next-generation sequencing (mNGS) was further used to obtain the mitochondrial genomes of these tapeworms. Phylogenetic analyses based on the 12 protein-coding genes (PCGs) and 18S rRNA both demonstrated the formation of two distinct clades: one comprising H. taeniaeformis, and the other representing a novel clade that is positioned as the sister clade to H. kamiyai, exhibiting genetic distance of 11.91 %-12.38 % for the 12 PCGs and 3.22 %-5.25 % for the 18S rRNA. Given the deep inter-species genetic distance, the novel clade identified in this study may be the fifth species within the genus Hydatigera, designated as Hydatigera sp. Both H. taeniaeformis and Hydatigera sp. were found to utilize not only wild rodents (N. huang, N. niviventer and R. andamanensis) but also house rats (R. norvegicus and R. tanezumi) as intermediate hosts. This finding indicates that they may have both sylvatic and synanthropic transmission cycles, raising concerns regarding their potential threat to humans and domestic animals.},
}

@article {pmid40808764,
year = {2025},
author = {Abdallah, RZ and Elbehery, AHA and Ouf, A and Siam, R},
title = {Microbial dark matter spearheading the biogeochemical cycle in the Solar Lake of Taba, Egypt.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100433},
pmid = {40808764},
issn = {2666-5174},
abstract = {Microbial dark matter (MDM) represents a vast, uncultured fraction of microbial life with largely unknown ecological roles, particularly in extreme environments. This study investigates MDM in the hypersaline microbial mats of Solar Lake, Taba, Egypt, using shotgun metagenomics (∼70 M reads/sample; triplicate sampling across four sites). A total of 364 metagenome-assembled genomes (MAGs) were recovered, of which 116 (∼30 %) were classified as MDM, comprising 55 % archaeal and 45 % bacterial lineages. Functional annotation revealed that ∼14 % of the MDM MAGs had the genetic potential to fix carbon. The genetic makeup of Ca. Lokiarchaeota (5 MAGs, 4.3 %) and Heimdallarchaeota (1 MAG, 0.86 %) suggest a mixotrophic lifestyle. Some non-methanogenic MAGs had the genetic capacity to utilize methanol and glycine-betaine as carbon sources. In addition, Ca. Marinisomatota MAGs had the genetic potential to degrade polysaccharides, while KSB1 MAGs harbored genes for carbohydrate degradation, denitrification, and nitrogen fixation. The high relative abundance of the SOX gene complex, in Ca. Asgardarchaeota and Ca. Coatesbacteria (RBG-13-66-14), highlights MDM community involvment in thiosulfate oxidation. Additionally, a novel Myxococcota MAG encoded a complete photosynthetic gene cluster, including photosystem II, suggesting phototrophic activity along with Cyanobacteria. Collectively, the genetic makeup of the Solar Lake MDM community underpins key processes such as carbon cycling, sulfur reduction, thiosulfate oxidation, nitrogen fixation, and denitrification, driving the biogeochemical dynamics of this unique hypersaline ecosystem.},
}

@article {pmid40808715,
year = {2025},
author = {Pozdniakova, S and Uchida, A and Fontal, A and Cañas, L and Santamaria, S and Hui, LY and Luhung, I and Schuster, SC and Rodó, X and Borràs, S},
title = {Integrating air microbiome for comprehensive air quality analysis.},
journal = {iScience},
volume = {28},
number = {7},
pages = {113015},
pmid = {40808715},
issn = {2589-0042},
abstract = {Air quality monitoring typically overlooks the biological composition of airborne particles, despite its relevance to human health. This study evaluated the feasibility of using filters from high-volume air samplers, widely employed in air quality networks, to analyze bioaerosol content through shotgun metagenomic sequencing. We developed a DNA extraction method for ultra-low biomass samples and assessed the impact of sampling duration, particle size selection, and filter material on microbial diversity. Our findings show that prolonged continuous sampling reduces species detection, while larger particle size selectors capture a broader range of microbial content, particularly fungi. Comparisons with a dedicated bioaerosol sampler confirmed that these filters can yield comparable results. This work demonstrates that existing air quality infrastructure can be leveraged for airborne microbiome monitoring, offering a practical and cost-effective approach to integrate biological data into routine assessments and support a more comprehensive understanding of air quality and its implications for public health.},
}

@article {pmid40808637,
year = {2025},
author = {Ferhaoui, N and Sebaihia, M and Sekizuka, T and Kuroda, M},
title = {Shotgun Metagenomic Investigation of the Microbiome in Diabetic Foot Infections Compared to Healthy Skin.},
journal = {Wound repair and regeneration : official publication of the Wound Healing Society [and] the European Tissue Repair Society},
volume = {33},
number = {4},
pages = {e70074},
doi = {10.1111/wrr.70074},
pmid = {40808637},
issn = {1524-475X},
support = {//Algerian Ministry of Higher Education and Scientific Research (DGRSDT/MESRS)/ ; JP23fk0108666j0401//Research Program on Emerging and Reemerging Infectious Diseases of the Japan Agency for Medical Research and Development/ ; },
abstract = {Diabetic foot infection (DFI) is a major complication of diabetes, causing significant morbidity and mortality. Host factors and microorganisms in DFI can disrupt healing processes, leading to chronic, non-healing wounds. The aim of this study was to characterise the microbiome of DFIs and contralateral healthy foot skin (CHFS). Thirty-two diabetic patients were enrolled in this study. Samples were obtained from DFIs and CHFS from the same patient. The microbiome was profiled using metagenomic shotgun sequencing. All the samples were polymicrobial, with a predominance of the obligate anaerobes belonging to Bacteroidetes in PEDIS 4. While PEDIS 3 and 2 were dominated by Proteobacteria. CHFS showed similar bacterial composition across all grades of severity, and the most abundant genera detected were Corynebacterium, Staphylococcus, Pseudomonas, and Cutibacterium. The CHFS was more diverse than DFIs in PEDIS 3 and 4. However, DFIs and CHFS in PEDIS 2 present similar diversity. In addition, DFIs of this grade exhibited a high proportion of Corynebacterium as well as CHFS. PCoA analysis demonstrated that the community structure of DFIs was different from that of CHFS, with Prevotella, Bacteroides, and Porphyromonas the main contributors to the clustering. Neighbour-Net analyses revealed that DFIs exhibited lower diversity compared to CHFS and harboured a more homogeneous dominant bacterial community. Our study revealed a high abundance of obligate anaerobes, including Bacteroides, Prevotella, Morganella, and Porphyromonas, in more severe infections; along with a decrease in microbial diversity. Additionally, there was a decrease in the abundance of key bacteria from the normal skin microbiota.},
}

@article {pmid40808601,
year = {2025},
author = {Qian, Y and Xiao, L and Zhou, Y and Deng, L},
title = {Metagenomic sequence classification based on local sensitive hashing and Bi-LSTM.},
journal = {Journal of bioinformatics and computational biology},
volume = {23},
number = {4},
pages = {2550012},
doi = {10.1142/S021972002550012X},
pmid = {40808601},
issn = {1757-6334},
abstract = {Current metagenomic classification methods are limited by short k-mer lengths and database dependency, resulting in insufficient taxonomic resolution at the species and genus level. This study proposes the first method integrating Locality-Sensitive Hashing (LSH) and Bidirectional Long-Short Term Memory (Bi-LSTM) networks for metagenomic sequence classification. The approach reduces runtime reliance on reference databases by learning discriminative features directly from sequences, while supporting long k-mers. The method consists of three key steps: (1) k-mer representation via locality-sensitive hashing, (2) k-mer embedding implementation using the skip-gram model, (3) label assignment to embedded vectors, followed by training in a Bi-LSTM network. Experimental results demonstrate superior classification performance at the genus level compared to existing models. Future work will explore the application of this method in the rapid detection of clinical pathogens.},
}

@article {pmid40808234,
year = {2025},
author = {},
title = {Correction to 'Metagenomic Exploration Uncovers Several Novel "Candidatus" Species Involved in Acetate Metabolism in High-Ammonia Thermophilic Biogas Processes'.},
journal = {Microbial biotechnology},
volume = {18},
number = {8},
pages = {e70217},
doi = {10.1111/1751-7915.70217},
pmid = {40808234},
issn = {1751-7915},
}

@article {pmid40807507,
year = {2025},
author = {Pei, Y and Chen, M and Chen, Q},
title = {Microbial Dynamics in a Musalais Wine Fermentation: A Metagenomic Study.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {15},
pages = {},
doi = {10.3390/foods14152570},
pmid = {40807507},
issn = {2304-8158},
support = {32302049//National Natural Science Foundation of China Youth Science Fund Project/ ; 2023B02029//Key Research and Development Program of the Xinjiang Uygur Autonomous Region/ ; },
abstract = {This study provides a comprehensive analysis of the microbial dynamics involved in the fermentation process of traditional Musalais wine, an intangible cultural heritage of Xinjiang. Utilizing metagenomic sequencing, we identified 2894 microbial species, of which 494 persisted throughout the fermentation process. Saccharomyces cerevisiae was the dominant species, with its prevalence increasing from 97.35% in the early phase to 99.38% in the mid phase, before slightly decreasing to 98.79% in the late phase. Additionally, 24 non-Saccharomyces yeast species, including Hanseniaspora uvarum, Lachancea thermotolerans, and Torulaspora delbrueckii, were detected. Common species associated with other fermented foods, including Wickerhamomyces anomalus, Kluyveromyces marxianus, Saccharomyces eubayanus, and Zygosaccharomyces parabailii, were also identified. Notably, species not previously used in food fermentation, such as Saccharomyces jurei, Sodiomyces alkalinus, Vanrija pseudolonga, and Moesziomyces antarcticus, were also identified in this study. Furthermore, the Kyoto Encyclopedia of Genes and Genomes (KO) and Gene Ontology (GO) revealed notable variations in metabolic pathways and enriched functional genes. In addition, a total of 82 volatile compounds were detected in the final product, with higher alcohols (60.12%), esters (37.80%), and organic acids (1.80%) being the most prevalent. These results offer important insights into microbial interactions and their influence on Musalais wine quality, laying the groundwork for optimizing the fermentation process.},
}

@article {pmid40807496,
year = {2025},
author = {Du, Q and Fu, R and Zhao, M and Xu, M},
title = {Comparing a Whole Grain Blend with Polished White Rice for Starch Digestibility and Gut Microbiota Fermentation in Diabetic Patients: An In Vitro Study.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {15},
pages = {},
doi = {10.3390/foods14152557},
pmid = {40807496},
issn = {2304-8158},
support = {No. 24CA008-02//the Financial Program of Beijing Academy of Science and Technology (BJAST)/ ; },
abstract = {The high glycemic index (GI) of polished white rice (WR) presents challenges for blood glucose control in diabetes. This study investigated the in vitro digestibility of a whole grain blend (WGB, composed of black, red, and brown rice) and its effects on the gut microbiota in elderly diabetic individuals. WGB exhibited lower starch digestibility (69.76 ± 5.71% vs. 73.02 ± 6.16%) and a reduced estimated glycemic index (eGI, 73.43 ± 4.49 vs. 77.55 ± 2.64) than WR, likely due to its higher amylose content. WGB fermentation increased Bifidobacterium and Lactobacillaceae, reduced pro-inflammatory Bacteroides fragilis and Enterocloster bolteae, and released more arabinose and xylose. Additionally, WGB yielded higher isobutyrate, while WR contained more glucose and fructose in its structure, leading to increased acetate production and a more acidic environment. Functional analysis revealed that WGB upregulated pathways related to fatty acid elongation and fiber fermentation. These findings suggest WGB as a viable staple food alternative for diabetic patients, offering dual benefits in glycemic control and gut microbiota.},
}

@article {pmid40804876,
year = {2025},
author = {Kiselev, VV and Koshechkin, SI and Kurenkov, AV and Odintsova, VE and Zhigalova, MS and Tyakht, AV and Petrikov, SS and Yartsev, PA and Dmitriev, IV},
title = {Microbiome of the Proximal Small Intestine in Patients with Acute Pancreatitis.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {15},
pages = {},
doi = {10.3390/diagnostics15151911},
pmid = {40804876},
issn = {2075-4418},
support = {//The study was sponsored by the Moscow Center for Innovative Technologies in Healthcare/ ; },
abstract = {Currently, due to the complexity of obtaining samples, specific features of laboratory processing and analysis of the results, there is a lack of data on the microbial signature of the small intestine in healthy and diseased states of the upper gastrointestinal tract. Objective: To investigate the characteristics of the small intestinal microbiome in acute pancreatitis of varying severity and to identify correlations with clinical factors. Methods: This study included 30 patients with acute pancreatitis of varying severity treated between 1 January 2019 and 31 December 2021. The composition of the microbiota was analyzed by metagenomic sequencing of the 16S rRNA gene from jejunal samples. Results: The mortality rate in the study group was 23.3%. The small intestinal microbiome was dominated by Streptococcus (median relative abundance 19.2%, interquartile range 6.4-35.1%), Veillonella (3.4%; 0.6-7%), Granulicatella (2.7%; 0.6-5%), Fusobacterium (2.2%; 0.3-5.9%), Prevotella (1.5%; 0.3-8%), Haemophilus (0.9%; 0.2-10%), Gemella (0.8%; 0.2-4.3%), and Lactobacillus (0.2%; 0.1-0.9%). More severe disease was associated with decreased abundance of Neisseria mucosa, Parvimonas micra, and Megasphaera micronuciformis. In contrast, the relative abundance of the genera Streptococcus (species S. rubneri/parasanguinis/australis), Actinomyces, and several genera within the family Enterobacteriaceae was higher in these patients. Conclusions: The state of the microbiota has important prognostic value and correlates with the duration from the onset of the pain syndrome to the time of receiving qualified care in the hospital.},
}

@article {pmid40804538,
year = {2025},
author = {Torres Montaguth, OE and Buddle, S and Morfopoulou, S and Breuer, J},
title = {Clinical metagenomics for diagnosis and surveillance of viral pathogens.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40804538},
issn = {1740-1534},
abstract = {Metagenomics is becoming more widely used for diagnosis of viral infections and surveillance of viruses. Its pathogen-agnostic approach makes metagenomics useful for unknown and novel infection diagnosis, outbreak investigation, and new and emerging pathogen surveillance. New metagenomics methods, such as the use of rapid sequencing technologies and approaches that can selectively enrich for a wide range of viruses, are expanding the range of clinical and public health scenarios in which metagenomics can be used. Following the COVID-19 pandemic, there is increasing interest in viral surveillance worldwide, using clinical samples, potential zoonotic reservoirs and environmental sources, such as wastewater. Validation and accreditation of metagenomics protocols to ensure quality, together with further innovation in methods, will be necessary to bring metagenomics into routine service in clinical and public health laboratories.},
}

@article {pmid40803594,
year = {2025},
author = {Wenderlein, J and Burkhardt, W and Dietrich, S and Trefflich, I and Penczynski, K and Thomas, K and Salzinger, C and Abraham, K and Malorny, B and Weikert, C and Ansorge, R and Grützke, J},
title = {Beyond the plate: A pilot study exploring the microbial landscape of omnivores and vegans through amplicon sequencing and metagenomics.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clnesp.2025.08.008},
pmid = {40803594},
issn = {2405-4577},
abstract = {BACKGROUND & AIMS: Previous studies have described benefits and risks on human health associated with a vegan diet. Although it is recognized that diet affects the gut microbiota, there is no consensus on the effects of a vegan diet compared to omnivorous diet on the gut microbiota. We have conducted a pilot study to assess the differences between the gut microbiome of vegans and omnivores in 2017 and 2021.

METHODS: Fecal samples of 23 vegans and 23 omnivores (n = 46) were collected in 2017 and 2021 together with more than 300 dietary, lifestyle, and health related characteristics. The fecal microbiome was assessed comparing both amplicon sequencing and metagenome sequencing, to determine robust signals agnostic of sequencing approaches.

RESULTS: Dietary grouping itself explained a small (∼4%) but significant proportion of the individual variation between microbiota. Natural clustering of microbiomes explained an even larger proportion. We found Ruminococcus torques to be relatively enriched in omnivores compared to vegans across methods and years. Interestingly, this species has been previously associated with unfavorable health outcomes. Despite a low sample size, we found some consistent differences between microbiota of individuals consuming either a vegan or omnivorous diet.

CONCLUSIONS: These results were consistent with recently published gut microbiome signatures of vegans and omnivores across three different countries. Therefore, this small dataset allows a first insight into the gut microbiota of another county's omnivores and vegans whereby detailed and relevant dietary, lifestyle and health related characteristics collected in this study aid in understanding of the connection between respective diets and the microbiome.},
}

@article {pmid40803134,
year = {2025},
author = {Wu, F and Campbell, BC and Greenfield, P and Hose, GC and Midgley, DJ and George, SC},
title = {There and back again: Genomic insights into microbial life in a recirculating petroleum refinery wastewater biotreatment system.},
journal = {Microbiological research},
volume = {301},
number = {},
pages = {128299},
doi = {10.1016/j.micres.2025.128299},
pmid = {40803134},
issn = {1618-0623},
abstract = {Petroleum refinery wastewater biotreatment relies on microbes to remediate carbon, nitrogen, and sulfur compounds, yet their life strategies and ecological roles remain unclear. This study characterises the ecological functions of 20 metagenome-assembled genomes (MAGs) from a full-scale petroleum refinery wastewater treatment plant in southern China. The taxonomic identity, nutrient metabolism genes (including C/N/S cycling), carbohydrate-active enzymes, and CRISPR-Cas systems of these MAGs were analysed. The recovered MAGs represented bacteria primarily from the Pseudomonadota and Bacteroidota phyla. The major carbon sources for the represented organisms are likely aromatic and aliphatic compounds, as well as carbohydrates including peptidoglycan, chitin, and starch. Almost all MAGs contained genes for nitrate or nitrite reduction, while metabolic pathways for sulfur metabolism were generally less prevalent. Meiothermus sp. bin.89 was the most metabolically versatile MAG. This organism possessed genes that allowed it to recycle biomass, break down aliphatic and monoaromatic compounds, and perform anaerobic respiration using nitrate. However, it was likely the most susceptible to viral predation, as indicated by the high abundance of CRISPR spacers. Overall, the results revealed that stress-tolerant ecological traits were common among organisms in this microbiome, showcasing the ability of the microbes to obtain carbon from aromatic and aliphatic compounds. This study provides a substantial contribution towards future efforts in optimising microbiome stability for pollutant removal in petroleum refinery wastewater biotreatment systems.},
}

@article {pmid40802757,
year = {2025},
author = {Romanowicz, KJ and Resnick, C and Hinton, SR and Plesa, C},
title = {Exploring antibiotic resistance in diverse homologs of the dihydrofolate reductase protein family through broad mutational scanning.},
journal = {Science advances},
volume = {11},
number = {33},
pages = {eadw9178},
pmid = {40802757},
issn = {2375-2548},
abstract = {Antimicrobial resistance studies often focus on individual protein variants, neglecting broader protein family dynamics. Dihydrofolate reductase (DHFR), a key antibiotic target, has been extensively studied using deep mutational scanning, yet resistance mechanisms across this diverse protein family remain poorly understood. Here, we developed a synthetic metagenomics approach using DropSynth, a scalable gene synthesis platform, to construct a phylogenetically diverse library of 1536 DHFR homologs. These sequences, primarily derived from host-associated metagenomes, represent 759 bacterial species, including many clinically relevant pathogens. A multiplexed in vivo assay tested their ability to restore metabolic function and confer trimethoprim resistance in an Escherichia coli ∆folA strain. Half of the synthetic homologs rescued the phenotype without supplementation, and mutant variants with up to five amino acid substitutions increased rescue rates to 90%, highlighting DHFR's evolutionary resilience. Broad mutational scanning of DHFR homologs and 100,000 mutants revealed key insights into fitness and resistance, offering the most comprehensive analysis of complementation and inhibitor tolerance to date.},
}

@article {pmid40801952,
year = {2025},
author = {Eckl-Dorna, J and Pjevac, P},
title = {[Principles of microbiome research].},
journal = {HNO},
volume = {},
number = {},
pages = {},
pmid = {40801952},
issn = {1433-0458},
abstract = {Microbiome research in the ear nose and throat (ENT) field has substantially gained in importance in recent decades. Modern sequencing methods have largely replaced traditional cultivation. Standardized protocols are essential to ensure reliable and comparable data. The article explains key terms, such as microbiome (the entire microbial community and its environment) and microbiota (only living microorganisms), along with the microbial taxonomy. Important measures for microbiome assessment include the alpha-diversity (species richness and distribution within a sample) and beta-diversity (differences between samples). A differentiation is made between two main approaches to microbiome sequencing: 1) 16S rRNA gene amplicon sequencing (identifies microbial community composition by sequencing the PCR product of a specific gene), 2) metagenomic sequencing (sequences the entire genomic material of a sample, allowing deeper insights). As nasal microbiome biomass is low, careful study design and controls are crucial. Microbiome research is a rapidly growing field with great potential but it requires meticulous planning and bioinformatics expertise for meaningful results.},
}

@article {pmid40801731,
year = {2025},
author = {Jackowetz, JN and Hanson, CS and Michael, M and Tsoukalas, K and Villanueva, C and Kozak, PA},
title = {Effects of Ultrafine Bubble Water on Gut Microbiota Composition and Health Markers in Rats.},
journal = {Nanomaterials (Basel, Switzerland)},
volume = {15},
number = {15},
pages = {},
pmid = {40801731},
issn = {2079-4991},
abstract = {Ultrafine bubbles (UFBs) represent an emerging technology with unique physicochemical properties. This study investigated the effects of air-filled UFBs infused in drinking water on gut microbiota composition and the associated health markers in Sprague Dawley rats over a 12-week period. Using a two-phase design, UFB concentration was increased from 1.7 × 10[6] to 6.5 × 10[9] UFBs/mL at week 7 to assess dose-dependent effects. Administration of UFBs in drinking water induced significant shifts in gut microbiome populations, characterized by increased Bacteroidetes (+122% weeks 8-12) and decreased Firmicutes (-43% weeks 8-12) compared to controls. These microbial shifts coincided with enhanced short-chain fatty acid production (butyrate +56.0%, p ≤ 0.001; valerate +63.1%, p ≤ 0.01) and reduced inflammatory markers (TNF-α -84.0%, p ≤ 0.05; IL-1β -41.0%, p ≤ 0.05; IL-10 -69.8%, p ≤ 0.05). UFB effects demonstrated systematic concentration-dependent threshold responses, with 85.7% of parameters exhibiting directional reversals between low (1.7 × 10[6] UFBs/mL) and high (6.5 × 10[9] UFBs/mL) concentration phases rather than linear dose-response relationships. The systematic nature of these threshold effects, with 71.4% of parameters achieving statistical significance (p ≤ 0.05), indicates concentration-dependent biological mechanisms rather than random effects on gut biology. Despite current metagenomic techniques identifying only 25% of the total gut microbiome, the observed changes in characterized species and metabolites demonstrate UFB technology's therapeutic potential for conditions requiring microbiome modulation, providing new insights into UFB influence on complex biological systems.},
}

@article {pmid40801353,
year = {2025},
author = {Liang, T and Situ, J and Qin, H and Peng, J},
title = {Adynamic ileus as an atypical manifestation of Staphylococcus aureus meningitis confirmed by metagenomic next-generation sequencing: A case report.},
journal = {The Journal of international medical research},
volume = {53},
number = {8},
pages = {3000605251365895},
doi = {10.1177/03000605251365895},
pmid = {40801353},
issn = {1473-2300},
abstract = {Staphylococcus aureus is an uncommon cause of bacterial meningitis, and S. aureus meningitis complicated with adynamic ileus has not been previously documented. This report presents a rare case of a man in his late 30s who developed purulent meningitis and intestinal pseudo-obstruction secondary to a skin-derived S. aureus infection. The patient initially presented with persistent fever, headache, and altered mental status. Subsequently, he developed abdominal distention, vomiting, dysuria, and meningeal signs. Laboratory tests revealed hyponatremia and elevated cerebrospinal fluid pressure; however, conventional cerebrospinal fluid culture failed to detect any pathogen. Diagnosis was ultimately confirmed through metagenomic next-generation sequencing, which identified S. aureus as the causative agent. Targeted antimicrobial therapy with vancomycin and meropenem resulted in rapid clinical improvement. This case highlights the importance of considering central nervous system infections in patients presenting with unexplained gastrointestinal and autonomic symptoms. Moreover, it emphasizes the clinical utility of metagenomic next-generation sequencing in identifying pathogens in culture-negative, atypical infections. Early recognition and intervention are essential to improving outcomes in such complex presentations.},
}

@article {pmid40801302,
year = {2025},
author = {Guzman, JPMD and Mwamburi, SM and Lurkpranee, S and Koiwai, K and Kondo, H and Hirono, I},
title = {Machine Learning-Aided Meta-Analysis Reveals Changes in Penaeus vannamei Gut Bacterial Communities Upon Dietary Supplementation-Induced Immunostimulation.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e70043},
doi = {10.1111/jfd.70043},
pmid = {40801302},
issn = {1365-2761},
support = {22H00379//Japan Society for the Promotion of Science/ ; JPMJSA1806//Japan Science and Technology Agency/ ; },
abstract = {Gut bacterial communities play a key role in shrimp health; thus, their modulation has been a target of dietary supplements which also function in enhancing disease and stress resistance of shrimp. However, this also raised the question of whether immunostimulants yield distinct changes in the gut bacterial composition or whether there are consistent features across all treatments. Here, we performed a machine learning-aided meta-analysis of 16S rRNA gut bacterial community studies of immunostimulants for Penaeus vannamei. Sequence reads from the selected studies were obtained and processed through bioinformatics tools. While beta diversity analysis suggests similarities between the normal, infected and stimulated shrimp, alpha diversity indices showed higher species richness in the gut bacterial communities of shrimp fed with immunostimulants. Specific beneficial taxa were enriched upon immunostimulation, while potentially pathogenic taxa decreased in abundance. Random forest modelling also identified key predictor taxa which may be used to classify gut bacterial communities based on immune status, type of immunostimulant and the specific immunostimulant. Despite some shared patterns in differential abundance-having decreased relative abundances of Photobacterium and other members of Gammaproteobacteria-the influence of immunostimulation on gut bacterial community composition was type- and treatment-specific, as evident in the distinct abundance profiles of the predictor taxa. Functional prediction analysis also showed distinct pathways enriched in immunostimulated shrimp, as influenced by the type of the immunostimulant. This study highlighted the specific impacts of dietary supplementation-induced immunostimulation on gut bacterial communities and identified key features in immunostimulated shrimp which provide a novel perspective on the interplay between gut bacterial community and immunity.},
}

@article {pmid40801057,
year = {2025},
author = {Talibli, F and Voß, B},
title = {Metagenomic CRISPR Array Analysis Tool: a novel graph-based approach to finding CRISPR arrays in metagenomic datasets.},
journal = {microLife},
volume = {6},
number = {},
pages = {uqaf016},
pmid = {40801057},
issn = {2633-6693},
abstract = {Clustered Regularly Interspersed Short Palindromic Repeats and CRISPR-associated genes (CRISPR-Cas) is a bacterial immune system also famous for its use in genome editing. The diversity of known systems could be significantly increased by metagenomic data. Here we present the Metagenomic CRISPR Array Analysis Tool (MCAAT), a highly sensitive algorithm for finding CRISPR arrays in unassembled metagenomic data. It takes advantage of the properties of CRISPR arrays that form multicycles in de Bruijn graphs. We show that MCAAT reliably predicts CRISPR arrays in bacterial genome sequences and that its assembly-free graph-based strategy outperforms assembly-based workflows and other assembly-free methods on synthetic and real metagenomes. Our new approach will help to increase the diversity of known CRISPR-Cas systems and enable studies of spacer evolution within metagenomic data sets.},
}

@article {pmid40800620,
year = {2025},
author = {Partanen, V and Dekić Rozman, S and Karkman, A and Muurinen, J and Hiltunen, T and Virta, M},
title = {Use of sequence barcodes for tracking horizontal gene transfer of antimicrobial resistance genes in a microbial community.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf113},
pmid = {40800620},
issn = {2730-6151},
abstract = {One of the most important knowledge gaps in the antimicrobial resistance crisis is the lack of understanding regarding how genes spread from their environmental origins to bacteria pathogenic to humans. In this study our aim was to create a system that allows the conduction of experiments in laboratory settings that mimic the complexity of natural communities with multiple resistance genes and mobile genetic elements circulating at the same time. Here we report a new sequence-based barcode system that allows simultaneous tracking of the spread of antimicrobial resistance genes from multiple genetic origins. We tested this concept with an experiment in which we added an antimicrobial resistance gene to different genetic environments in alive and dead donors and let the gene spread naturally in an artificial microbial community under different environmental conditions to provide examples of factors that can be investigated. We used emulsion, paired-isolation, and concatenation polymerase chain reaction to detect the new gene carriers and metagenomic analysis to see changes in the genetic environment. We observed the genes moving and were able to recognise the barcode from the gene sequences, thus validating the idea of barcode use. We also saw that temperature and gene origin had effects on the number of new host species. Our results confirmed that our system worked and can be further developed for more complicated experiments.},
}

@article {pmid40800617,
year = {2025},
author = {Fuschi, A and Merlotti, A and Remondini, D},
title = {Microbiome data: tell me which metrics and I will tell you which communities.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf125},
pmid = {40800617},
issn = {2730-6151},
abstract = {In microbial community studies, analyzing diversity is crucial for uncovering ecological complexity. However, the intrinsic characteristics of Next-gen sequencing data challenge the use of Euclidean metrics for estimating proximity and correlation. Consequently, a variety of distance measures have been developed within ecological frameworks. In this study, we compare several of these metrics-including Bray-Curtis, Canberra, Jensen-Shannon, Hellinger, Euclidean, and Aitchison distances-demonstrating how the choice of metric can significantly influence the interpretation of microbial community structures. Among these, Aitchison distance specifically defined for compositional data shows markedly different behavior from the others, highlighting different features related to the data. We consider two real-world examples: the human gut microbiome sampled using 16S rRNA sequencing with multiple measurements for different patients (G-HMP2) and urban sewage environmental metagenomes collected over time at different sites through shotgun sequencing (E-WADES). We show that, for the same dataset-independently on the sequencing technique or on the sampling context-the community structure depends strongly on the choice of specific metrics. This can be explained by the mathematical properties of the chosen metrics and the specific characteristics of microbiome data, namely their high heterogeneity in species abundance. This provides clear insights into how distance metrics influence interpretation and assists in choosing the most appropriate one for the study objectives.},
}

@article {pmid40800117,
year = {2025},
author = {Bloemen, B and Gand, M and Ringenier, M and Bogaerts, B and Vanneste, K and Marchal, K and Roosens, NHC and Dewulf, J and Boyen, F and De Keersmaecker, SCJ},
title = {Overcoming challenges in metagenomic AMR surveillance with nanopore sequencing: a case study on fluoroquinolone resistance.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1614301},
pmid = {40800117},
issn = {1664-302X},
abstract = {INTRODUCTION: Antimicrobial resistance is an alarming public health problem, and comprehensive surveillance across environments is required to reduce its impact. Phenotypic testing and whole-genome sequencing of isolates are efficient, but culture-free approaches like metagenomic sequencing potentially allow for broader investigation of resistance gene occurrence, evolution and spread. However, technical challenges such as difficulties in associating antimicrobial resistance genes with their bacterial hosts and the collapse of strain-level variation during metagenome assembly, hinder its implementation.

METHODS: To illustrate how these challenges can be overcome, we applied Oxford Nanopore Technologies long-read metagenomic sequencing and novel bioinformatic methods to a case study focused on fluoroquinolone resistance in chicken fecal samples.

RESULTS: We demonstrate plasmid-host linking based on detecting common DNA methylation signatures. Additionally, we use new bioinformatic approaches for strain haplotyping, enabling phylogenomic comparison and uncovering fluoroquinolone resistance determining point mutations in metagenomic datasets.

DISCUSSION: We leverage long-read sequencing, including DNA methylation profiling and strain-level haplotyping, to identify antimicrobial resistance gene hosts, link plasmids to their bacterial carriers, and detect resistance-associated point mutations. Although some limitations remain, our work demonstrates how these improvements in metagenomic sequencing can enhance antimicrobial resistance surveillance.},
}

@article {pmid40797468,
year = {2025},
author = {Guo, T and Chang, L and Huang, PW and Yao, JP and Zhang, YC and Ren, CY and Bao, CQ},
title = {Investigating the mediating effect of plasma metabolites on the gut microbiome in influencing Behçet disease: A multi-omics validated Mendelian randomization study.},
journal = {Medicine},
volume = {104},
number = {32},
pages = {e42698},
pmid = {40797468},
issn = {1536-5964},
support = {Z202213//Wuxi Municipal Health Commission's research project/ ; },
abstract = {Although an established correlation between gut microbiota (GM) and Behçet syndrome exists, the potential mediating involvement of plasma metabolites remains unclear. Using the most recent statistical data from genome-wide association studies conducted in 2024, we investigated the causal relationships between 473 GM taxa, 233 circulating metabolites, and Behçet syndrome (Behçet disease [BD]) through a 2-sample Mendelian randomization approach. This analysis was further supported by incorporating transcriptome and metagenomic data related to BD. A 2-step methodology was employed to evaluate the extent to which the effect of GM on BD is mediated through plasma metabolites. These results were subsequently validated in a separate validation set. Our Mendelian randomization results demonstrated correlations between various GM and the risk of Behçet syndrome. The potential link between GM and BD risk may be mediated through plasma circulating metabolite levels. Specifically, for every standard deviation, an increase in the abundance of Turicibacter sp001543345 was correlated with a 403% increase in BD risk (odds ratio : 5.03 [95% confidence interval, 1.77-14.25]). Meanwhile, the cholesteryl esters to total lipids ratio in large very low-density lipoprotein and the total cholesterol to total lipids ratio in very large very low-density lipoprotein increased by 4%. The proportion of indirect effects is 3.026% and 3.338%, respectively. Our study established a causal link between distinct GM and BD and quantified the proportion of effects mediated through plasma metabolites. These findings provide further insights for the treatment of BD.},
}

@article {pmid40797356,
year = {2025},
author = {Rashwan, HH and Ali, MH and Mostafa, MM and Ramadan, R and Mysara, M},
title = {Insights into the tripartite relationship between cervical cancer, human papillomavirus, and the vaginal microbiome: a mega-analysis.},
journal = {Human genomics},
volume = {19},
number = {1},
pages = {89},
pmid = {40797356},
issn = {1479-7364},
abstract = {BACKGROUND: Cervical cancer (CC) is the fourth most prevalent malignancy among women worldwide, where 99.7% of the cases are linked to persistent human papillomavirus (HPV) infections. While emerging evidence suggests a role for vaginal microbiome dysbiosis in HPV-driven CC, the specific microbial alterations and their functional implications remain unclear. However, inconsistencies in identifying specific microbial signatures-largely due to heterogeneous study designs, targeted 16S rRNA regions, and data processing methods-have limited the generalizability of existing findings. To address these challenges, we conducted a standardized mega-analysis using a compositionality-aware approach to ensure consistency and minimize technical bias across studies.

RESULTS: Our mega-analysis consolidates findings from five case-control 16S rRNA ampilicon sequencing studies, encompassing 215 samples. Compared to healthy controls, CC patients exhibited significantly higher alpha diversity (Shannon index, p <0.005) and a shift from a Lactobacillus-dominant to a polymicrobial vaginal microbiome. This microbial dysbiosis was characterized by an increased abundance of Porphyromonadaceae, particularly Porphyromonas asaccharolytica, and other anaerobic bacterial species such as Campylobacter ureolyticus, Peptococcus niger, and Anaerococcus obesiensis (FDR <0.05). Functional profiling of the altered microbiome revealed enrichment in pathways associated with chronic inflammation, fatty acid biosynthesis, amino acid metabolism, cellular proliferation, invasion, and metastasis.

CONCLUSIONS: This mega-analysis presents the most methodologically homogeneous study to date of CC-associated vaginal microbiome using publicly available 16S datasets. Our findings not only deepen our understanding of microbial influences on CC but also pave the way for novel diagnostic and therapeutic approaches potentially enhancing patient outcomes in CC care. These insights open new avenues for clinical interventions that extend beyond conventional HPV-centric strategies.},
}

@article {pmid40797041,
year = {2025},
author = {Wu, K and Zhou, L and Liu, L and Yang, M and Li, J and Ma, S and Sousa, DZ and Cheng, L},
title = {Targeted isolation of H2-dependent methylotrophic methanogens by a cocktail approach.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {40797041},
issn = {1750-2799},
support = {92351301 and 32325002//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Methanogenic archaea play a crucial role in the global carbon cycle and in climate change. Recent metagenomic sequencing has revealed a considerable number of (putative) H2-dependent methylotrophic methanogens (HMMs) across the archaeal tree and in diverse environments. Traditional isolation methods, such as dilution-to-extinction and roll-tube techniques, fail to cultivate fastidious HMMs. Here, we describe a four-stage isolation strategy designed to selectively isolate HMMs by using a flexible combination of methods to systematically reduce microbial complexity to a pure culture. In the initial stage, the growth conditions for the target HMM were optimized through closed-batch cultivation encompassing >50 conditions. Second, HMM-containing cultures were serially diluted in 96-well plates combined with substrate limitation to eliminate non-target archaea. In stage 3, the bacterial diversity in the culture was further decreased to a single bacterium by treatment with antibiotics and lysozyme. Finally, a last bacterial contaminant was removed by repeated addition of antibiotic mixtures and successive dilution transfers, leading to the successful isolation of the first pure culture of Methanosuratincola petrocarbonis LWZ-6, an HMM of the phylum Thermoproteota. This protocol also describes molecular methods, including 16S rRNA gene amplicon sequencing, metagenome sequencing and quantitative PCR, to track microbial community shifts and assess the growth advantage of the target HMM, enabling monitoring of the stepwise elimination of non-target microorganisms and ultimately confirming the purification of the target HMM. The duration of the protocol will vary for different HMMs depending on their substrate utilization, growth rate and method selection.},
}

@article {pmid40796374,
year = {2025},
author = {Pan, S and Du, H and Zheng, R and Zhang, C and Pan, J and Yang, X and Wang, C and Lin, X and Li, J and Liu, W and Zhou, H and Yu, X and Mo, S and Zhang, G and Zhao, G and He, Z and Tian, Y and Jiang, C and Qu, W and Liu, Y and Li, M},
title = {A holistic genome dataset of bacteria and archaea of mangrove sediments.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
pmid = {40796374},
issn = {2047-217X},
support = {2023B0303000017//Guangdong Major Project of Basic and Applied Basic Research/ ; 92251306//National Natural Science Foundation of China/ ; 92051102//National Natural Science Foundation of China/ ; 92251307//National Natural Science Foundation of China/ ; 92351303//National Natural Science Foundation of China/ ; 32370055//National Natural Science Foundation of China/ ; 32200099//National Natural Science Foundation of China/ ; 32070108//National Natural Science Foundation of China/ ; 32225003//National Natural Science Foundation of China/ ; 31970105//National Natural Science Foundation of China/ ; 42303064//National Natural Science Foundation of China/ ; 42430707//National Natural Science Foundation of China/ ; JCYJ20200109105010363//Shenzhen Science and Technology Program/ ; KCXFZ20201221173404012//Shenzhen Science and Technology Program/ ; JCYJ20230808105711023//Shenzhen Science and Technology Program/ ; 20220809161641002//Shenzhen Science and Technology Program/ ; SML2023SP218/SML2023SP237//Southern Marine Science and Engineering Guangdong Laboratory/ ; 2022B002//Shenzhen University/ ; },
abstract = {BACKGROUND: Mangroves are one of the most productive marine ecosystems with high ecosystem service value. The sediment microbial communities contribute to pivotal ecological functions in mangrove ecosystems. However, the study of mangrove sediment microbiomes is limited.

FINDINGS: Here, we applied metagenome sequencing analysis of microbial communities in mangrove sediments across Southeast China from 2014 to 2020. This genome dataset includes 966 metagenome-assembled genomes with ≥50% completeness and ≤10% contamination generated from 6 groups of samples. Phylogenomic analysis and taxonomy classification show that mangrove sediments are inhabited by microbial communities with high species diversity. Thermoplasmatota, Thermoproteota, and Asgardarchaeota in archaea, as well as Proteobacteria, Desulfobacterota, Chloroflexota, Acidobacteriota, and Gemmatimonadota in bacteria, dominate the mangrove sediments across Southeast China. Functional analyses suggest that the microbial communities may contribute to carbon, nitrogen, and sulfur cycling in mangrove sediments.

CONCLUSIONS: These combined microbial genomes provide an important complement of global mangrove genome datasets and may serve as a foundational resource for enhancing our understanding of the composition and functions of mangrove sediment microbiomes.},
}

@article {pmid40796349,
year = {2025},
author = {Huang, WC and Probst, M and Hua, ZS and Szánthó, LL and Szöllősi, GJ and Ettema, TJG and Rinke, C and Williams, TA and Spang, A},
title = {Phylogenomic analyses reveal that Panguiarchaeum is a clade of genome-reduced Asgard archaea within the Njordarchaeia.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf201},
pmid = {40796349},
issn = {1537-1719},
abstract = {The Asgard archaea are a diverse archaeal phylum important for our understanding of cellular evolution because they include the lineage that gave rise to eukaryotes. Recent phylogenomic work has focused on characterising the diversity of Asgard archaea in an effort to identify the closest extant relatives of eukaryotes. However, resolving archaeal phylogeny is challenging, and the positions of two recently-described lineages - Njordarchaeales and Panguiarchaeales - are uncertain, in ways that directly bear on hypotheses of early evolution. In initial phylogenetic analyses, these lineages branched either with Asgards or with the distantly-related Korarchaeota, and it has been suggested that their genomes may be affected by metagenomic contamination. Resolving this debate is important because these clades include genome-reduced lineages that may help inform our understanding of the evolution of symbiosis within Asgard archaea. Here, we performed phylogenetic analyses revealing that the Njordarchaeales and Pangiuarchaeales constitute the new class Njordarchaeia within Asgard archaea. We found no evidence of metagenomic contamination affecting phylogenetic analyses. Njordarchaeia exhibit hallmarks of adaptations to (hyper-)thermophilic lifestyles, including biased sequence compositions that can induce phylogenetic artifacts unless adequately modelled. Panguiarchaeum is metabolically distinct from its relatives, with reduced metabolic potential and various auxotrophies. Phylogenetic reconciliation recovers a complex common ancestor of Asgard archaea that encoded the Wood-Ljungdahl pathway. The subsequent loss of this pathway during the reductive evolution of Panguiarchaeum may have been associated with the switch to a symbiotic lifestyle potentially based on H2-syntrophy. Thus, Panguiarchaeum may contain the first obligate symbionts within Asgard archaea.},
}

@article {pmid40796326,
year = {2025},
author = {Patel, SM and Farirai, J and Patel, MZ and Boiditswe, S and Tawe, L and Lekalake, S and Matshaba, M and Steenhoff, AP and Arscott-Mills, T and Feemster, KA and Shah, SS and Thielman, N and Cunningham, CK and David, LA and Murdoch, DM and Kelly, MS},
title = {Alterations of the upper respiratory microbiome among children living with HIV infection in Botswana.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf429},
pmid = {40796326},
issn = {1537-6613},
abstract = {Children living with HIV (CLWH) are at high risk of colonization and infection by respiratory pathogens, though this risk can be reduced by other microbes in the upper respiratory microbiome. The impact of HIV infection on the pediatric upper respiratory microbiome is poorly understood, and we sought to address this knowledge gap by identifying associations between HIV infection and the nasopharyngeal microbiomes of Batswana children. We enrolled Batswana CLWH (<5 years) and age- and sex-matched HIV-exposed, uninfected (HEU) and HIV-unexposed, uninfected (HUU) children in a cross-sectional study. We used shotgun metagenomic sequencing to compare nasopharyngeal microbiomes by HIV status. Among the 143 children in this study, HIV and HIV-associated immunosuppression were associated with alterations in nasopharyngeal microbiome composition, including lower abundances of Corynebacterium species associated with resistance to bacterial pathogen colonization. These findings suggest that the upper respiratory microbiome may contribute to the high risk of respiratory infections among CLWH.},
}

@article {pmid40796214,
year = {2025},
author = {Kopylov, U and Verstockt, B and Marigorta, UM and Noviello, D and Bossuyt, P and Mookhoek, A and Sinonque, P and El-Hussuna, A and Sahnan, K and Baumgart, DC and Noor, NM and Allocca, M and Carter, D and Ensari, A and Iacucci, M and Pellino, G and Soriano, A and de Laffolie, J and Daperno, M and Raine, T and Cleynen, I and Sebastian, S},
title = {Results of the 9th Scientific Workshop of the European Crohn's and Colitis Organisation (ECCO): Artificial Intelligence in medical management and precision medicine.},
journal = {Journal of Crohn's & colitis},
volume = {},
number = {},
pages = {},
doi = {10.1093/ecco-jcc/jjaf134},
pmid = {40796214},
issn = {1876-4479},
abstract = {BACKGROUND AND AIMS: Artificial intelligence (AI) is increasingly being applied in various fields of medicine, including Inflammatory Bowel Diseases (IBD). This systematic review, conducted as part of the ECCO 9th Scientific Workshop on AI in IBD, explores AI applications in multiomic precision medicine, large language models (LLMs) for textual tasks and utilisation of wearable and remote care technologies.

METHODS: A comprehensive systematic analysis of the literature was undertaken, emphasising three topics: multiomic predictive models in IBD; natural language processing (NLP) and LLMs for clinical practice, research and patient communication; and the role of remote monitoring and wearable devices.

RESULTS: Key areas of promise include the implementation of NLP and LLMs for case identification and differentiation, tracking disease activity, pharmacovigilance, quality assurance and patient support. Multiomic approaches, integrating genomics, transcriptomics, proteomics, metabolomics and metagenomics, show potential for developing more accurate diagnostic and risk prediction models and improving treatment response prediction and detection of actionable drug targets for future therapeutics. Wearables and remote monitoring technologies can transform IBD management from episodic assessments to continuous less biased tracking of patient-reported outcomes and physiological biomarkers.

CONCLUSIONS: While AI and multiomic approaches hold substantial promise for advancing IBD management and research, further refinement is necessary to ensure content validity and address safety concerns, thereby allowing integration of AI into clinical workflows and safeguarding of data privacy. Future research should prioritise the integration of diverse omic data, conduct of longitudinal studies and validation in large and diverse cohorts.},
}

@article {pmid40795932,
year = {2025},
author = {Teng, ZJ and Yuan, XJ and Liu, R and Xu, SC and Chen, XL and Chen, Y and Zhang, YZ},
title = {Inositol phosphates as an overlooked phosphorous source in marine ecosystems.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf161},
pmid = {40795932},
issn = {1751-7370},
abstract = {Inositol phosphates, common phosphorus storage compounds that are also crucial for eukaryotic cell signaling, constitute a significant portion of dissolved organic phosphorus in coastal waters. The hydrolysis of inositol phosphates could be an important contributor to phosphorus cycling in phosphorus-limited marine ecosystems, yet this process remains poorly understood in marine contexts. In this study, we reveal substantial concentrations of Inositol phosphates in marine macrophytes, including green, brown, and red algae as well as common seagrasses, suggesting that these organisms are likely major biological sources of inositol phosphates in the oceans. A comprehensive analysis of genes involved in inositol phosphates hydrolysis in global marine metagenomes and metatranscriptomes identified key roles for γ-, α-, and δ-proteobacteria, with additional contributions from Flavobacteriia. The degradation of marine inositol phosphates was predominantly mediated by alkaline β-propeller phytases, though genes associated with acidic cysteine phytases and purple acid phytases were also widely present. Community structure and functional traits linked to inositol phosphates degradation were shaped largely by stochastic processes. Further examination of enzyme activity at the protein and community levels indicated that phytate metabolism by marine microbes is likely a widespread phenomenon in the ocean. Overall, this study highlights inositol phosphates hydrolysis as an essential yet overlooked adaptation by marine microorganisms to address phosphorus limitations in ocean ecosystems.},
}

@article {pmid40795871,
year = {2025},
author = {Natsume-Kitatani, Y and Kobiyama, K and Igarashi, Y and Aoshi, T and Nakatsu, N and Tripathi, LP and Ito, J and Nyström-Persson, J and Kosugi, Y and Allendes Osorio, RS and Nagao, C and Temizoz, B and Kuroda, E and Standley, DM and Kiyono, H and Nakanishi, K and Uematsu, S and Hamaguchi, I and Yasutomi, Y and Kunisawa, J and Yamasaki, S and Coban, C and Yamada, H and Mizuguchi, K and Ishii, KJ},
title = {An adjuvant database for preclinical evaluation of vaccines and immunotherapeutics.},
journal = {Cell chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chembiol.2025.07.005},
pmid = {40795871},
issn = {2451-9448},
abstract = {Adjuvants are immunostimulators used to enhance vaccine efficacy against infectious diseases. However, current methods for evaluating their efficacy and safety are limited, hindering large-scale screening. To address this, we developed a prototype Adjuvant Database (ADB) containing transcriptome data, generated using the same protocols as the widely used Open TG-GATEs (OTG) toxicogenomics database, covering 25 adjuvants across multiple species, organs, time points, and doses. This enabled cross-database integration of ADB and OTG. Transcriptomic patterns successfully distinguished each adjuvant regardless of organs or species. Using both databases, we built machine learning models to predict adjuvanticity and hepatotoxicity. Notably, we identified colchicine's adjuvant activity and FK565's liver toxicity through data-driven analysis. Overall, ADB combined with OTG offers a framework for transcriptomics-based, data-driven screening of adjuvant candidates.},
}

@article {pmid40766562,
year = {2025},
author = {Zulk, JJ and Robertson, CM and Ottinger, S and Kambal, A and Tostado, AR and Fleck, RC and Shea, AE and Coarfa, C and Blutt, SE and Maresso, AW and Patras, KA},
title = {Human bladder organoids model urinary tract infection and bacteriophage therapy.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {40766562},
issn = {2692-8205},
abstract = {Urinary tract infections (UTIs), primarily caused by uropathogenic Escherichia coli (UPEC), are among the most common antibiotic-resistant infections. Despite this, currently available preclinical UTI models lack the breadth of morphotypic and heterogenous cell populations of the human bladder, impairing the development of novel therapies. To address these limitations, we developed human bladder organoids derived from the bladder stem cells of multiple healthy donors which recapitulate cellular diversity of the urothelium. Using bulk and single cell RNA-sequencing, we characterized organoid responses to UPEC and phage exposure individually and in combination to model phage therapy. Although phage minimally affected the uroepithelium in the absence of infection, during UTI, phage treatment reduced bacterial burdens and dampened inflammatory responses and barrier disruption. Collectively, our findings highlight human bladder organoids as a tool for capturing conserved and individual-specific uroepithelial responses to infection while also providing preclinical efficacy and safety testing for therapeutic development.},
}

@article {pmid40795850,
year = {2025},
author = {Cano-Gamez, K and Maclean, P and Inoue, M and Hussainy, S and Foss, E and Wainwright, C and Qin, H and McKechnie, S and Song, CX and Knight, JC},
title = {The circulating cell-free DNA landscape in sepsis is dominated by impaired liver clearance.},
journal = {Cell genomics},
volume = {},
number = {},
pages = {100971},
doi = {10.1016/j.xgen.2025.100971},
pmid = {40795850},
issn = {2666-979X},
abstract = {Circulating cell-free DNA (cfDNA) is a promising molecular biomarker, but its role in severe infection is unclear. Here, we profile cfDNA from sepsis patients and controls, demonstrating a 41-fold increase during disease. Methylation-based deconvolution revealed similar cfDNA compositions in the two groups, suggesting that cfDNA accumulation during disease is due not to excess cell death but to impaired hepatic clearance. Fragmentation and end-motif patterns both support this hypothesis, suggesting prolonged exposure of cfDNA to circulating nucleases. In addition, we show that cfDNA retains nucleosome footprints informative of gene activity. By developing a novel method to quantify these footprints and integrate them with single-cell data, we report an increase in cfDNA from Kupffer cells and liver parenchyma in patients with liver dysfunction. Finally, we show that cfDNA contains pathogen-derived material, highlighting its diagnostic potential. This high-throughput, multimodal study provides a reference for understanding cfDNA's role in sepsis and critical illness.},
}

@article {pmid40795737,
year = {2025},
author = {Zhao, J and Kou, X and Liu, H and Wu, T and Li, J and Wang, Y and Xie, H and Wang, M and Wu, L and Wen, L and Wang, L},
title = {Microbial community responses and functional shifts in carbon degradation driven by water-salt gradients in lakeshore wetlands of semi-arid lakes.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {126893},
doi = {10.1016/j.jenvman.2025.126893},
pmid = {40795737},
issn = {1095-8630},
abstract = {Wetlands, especially lakeshore ecosystems, play an essential role in global carbon (C) cycling and are strongly influenced by dynamic water-salt gradients. However, the mechanisms by which these gradients shape microbial communities and affect soil organic C (SOC) degradation remain incompletely understood. Here, we aimed to elucidate microbial mechanisms driving C degradation shifts along water-salt gradients. We investigated microbially mediated SOC degradation potential in Daihai Lake wetlands by metagenomic profiling of carbohydrate-active enzyme (CAZyme) genes. Our results demonstrated a significant shift in CAZyme gene abundances across the gradients. Genes involved in plant-derived C (cellulose, hemicellulose, lignin) degradation decreased with increasing soil salinity and moisture, while those related to microbial-derived C (chitin, peptidoglycan, glucans) decomposition were significantly enriched. Concurrently, the microbial community composition shifted toward greater abundance of salt-tolerant taxa, notably Proteobacteria and Bacteroidetes, while Actinobacteria and Firmicutes declined under higher water-salt conditions. Statistical analyses revealed strong correlations between key environmental factors (soil salinity (EC), soil moisture (SM), and pH) and both microbial community structure and CAZyme gene abundances (p < 0.001). Random Forest analysis further identified EC and SM as primary factors influencing C-degrading microbial functions. This study highlights the importance of water-salt gradients in regulating microbial-mediated C cycling in wetlands, providing critical insights into microbial adaptation strategies and their implications for wetland C dynamics under environmental change.},
}

@article {pmid40795730,
year = {2025},
author = {D'Ugo, E and Mukherjee, A and Resitano, M and Giuseppetti, R and Fortini, D and Bruna Matturro, and Chirico, M and Pisanu, ME and Tucci, M and Pozzi, R and Lovecchio, N and Slawomir, O and Iosi, F and Villa, L and Iorio, E and Aulenta, F and Viggi, CC and Bertuccini, L and Magurano, F},
title = {Fishing out microorganisms for bioremediation using metagenomics: Isolation and whole-genome sequencing of the metabolically versatile Rhodococcus erythropolis LP27217 strain from oil spill lake.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139463},
doi = {10.1016/j.jhazmat.2025.139463},
pmid = {40795730},
issn = {1873-3336},
abstract = {Isolating microorganisms from oil spill-contaminated environments is essential for advancing bioremediation strategies and discovering novel bioprocesses for hydrocarbon degradation. In this study, we report the isolation of a novel strain, Rhodococcus erythropolis LP27217, from Pertusillo Lake (Italy) on february 2017. Water samples were collected during an oil spill event and microbial community was previously characterized using 16S rRNA gene-targeted metagenomic analysis and functional prediction. The Rhodococcus genus was identified as the dominant member of this microbiome, and functional predictive analyses guided the isolation of the R. erythropolis LP27217 strain under various growth conditions, including the presence of hydrocarbons and in Liquid Microbial Fuel Cell (L-MFC) systems. This strain exhibits a versatile hydrocarbon-degrading and transforming metabolism, effectively addressing pollutants such as crude oil, polycyclic aromatic hydrocarbons (PAHs), and dibenzothiophene (DBT), even under psychrophilic conditions. Additionally, R. erythropolis LP27217 demonstrated the ability to produce lipopeptide biosurfactants and lipophilic polymers, with the latter being associated with the formation of an electrogenic hydrocarbonoclastic biofilm at the anoxic oil-water interface. Overall, this study demonstrated that R. erythropolis LP27217 is a promising candidate for sustainable applications, including in situ bioremediation of oil spills in lake ecosystems and the biosynthesis of innovative polymers and biosurfactants for biotechnological and environmental purposes. Furthermore, its ability to operate across oxic and hypoxic conditions, at the oil-water interface and within the water column, highlights a novel microbial mechanism with significant ecological and industrial potential.},
}

@article {pmid40795725,
year = {2025},
author = {Zhang, FL and Li, AY and Zhu, KX and Zhang, K and Tian, Z and Wang, T and Zhang, XH and Zang, J and Sun, XF and Shen, W and Li, L},
title = {Integrated multi-omics analysis uncovers Zearalenone-induced ovarian and intestinal inflammation is mediated by the tumor necrosis factor-α.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139476},
doi = {10.1016/j.jhazmat.2025.139476},
pmid = {40795725},
issn = {1873-3336},
abstract = {As a widely encountered foodborne mycotoxin, Zearalenone (ZEN) has the potential to accumulate along the food chain, posing threats to public health and safety. However, the precise mechanisms by which ZEN causes tissue damage remain incompletely understood. Here, we established in vivo (40 μg/kg) and in vitro (30 μM) models to elucidate the underlying processes of ZEN-induced damage to the ovary and intestine. Our results demonstrated that, following ZEN exposure, pro-inflammatory signaling factors, including NLR family pyrin domain containing 3 (NLRP3) and Interleukin 6 (IL6), were significantly elevated in both ovarian and intestines. Metagenomic analysis revealed dysbiosis of the gut microbiota, which was closely associated with tumor necrosis factor (TNF)-α signaling pathway. Transcriptomic results further indicated that inflammatory response are intricately linked to TNF signaling pathway. Additionally, the Tnf-α knockout mouse model showed a marked resistance to ZEN-induced ovarian and intestinal injuries. In vitro, RNA interference targeting TNF-α attenuated the inflammatory response in IPEC-J2 cells. Moreover, dysregulated expression of the hormone synthesis genes, including KISS-1 metastasis suppressor (Kiss1) and gonadotropin releasing hormone 1 (Gnrh1), was observed, suggesting that ZEN-induced microbial dysbiosis and ovary damage may be interconnected through hormonal disruption. In summary, our results emphasize the role of TNF-α in causing ovarian and intestinal damage after ZEN exposure.},
}

@article {pmid40795332,
year = {2025},
author = {Aguilera-Campos, KI and Boisard, J and Törnblom, V and Jerlström-Hultqvist, J and Behncké-Serra, A and Cotillas, EA and Stairs, CW},
title = {Anaerobic breviate protist survival in microcosms depends on microbiome metabolic function.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf171},
pmid = {40795332},
issn = {1751-7370},
abstract = {Anoxic and hypoxic environments serve as habitats for diverse microorganisms, including unicellular eukaryotes (protists) and prokaryotes. To thrive in low-oxygen environments, protists and prokaryotes often establish specialized metabolic cross-feeding associations, such as syntrophy, with other microorganisms. Previous studies show that the breviate protist Lenisia limosa engages in a mutualistic association with a denitrifying Arcobacter bacterium based on hydrogen exchange. Here, we investigate if the ability to form metabolic interactions is conserved in other breviates by studying five diverse breviate microcosms and their associated bacteria. We show that five laboratory microcosms of marine breviates live with multiple hydrogen-consuming prokaryotes that are predicted to have different preferences for terminal electron acceptors using genome-resolved metagenomics. Protist growth rates vary in response to electron acceptors depending on the make-up of the prokaryotic community. We find that the metabolic capabilities of the bacteria and not their taxonomic affiliations determine protist growth and survival and present new potential protist-interacting bacteria from the Arcobacteraceae, Desulfovibrionaceae, and Terasakiella lineages. This investigation uncovers potential nitrogen and sulfur cycling pathways within these bacterial populations, hinting at their roles in syntrophic interactions with the protists via hydrogen exchange.},
}

@article {pmid40795028,
year = {2025},
author = {Park, HS and Chavarria, X and Shatta, A and Kang, D and Oh, S and Choi, DY and Choi, JH and Kim, M and Cho, YH and Yi, MH and Kim, JY},
title = {Distinct microbial communities of drain flies (Clogmia albipunctata) across sites with differing human influence.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf078},
pmid = {40795028},
issn = {1574-6968},
abstract = {Drain flies (Clogmia albipunctata) are insects that thrive in humid urban environments such as bathrooms drains and sewage systems. While their role in pathogen transmission has been suggested, little is known about their microbiome or ecology in non-clinical contexts. Using 16S rRNA gene metabarcoding, we characterized the bacterial communities of drain flies from three locations in South Korea, public bathrooms from a college in Seoul, a rural port in Ulleungdo island, and a highly frequented public park in Yeouido. In total, we obtained 221 families and 1 474 features. We found significant differences in microbiome composition and diversity as well as a small core microbiome shared among locations, with environmental bacteria such as Pseudomonas and Ralstonia being the dominant taxa across samples. The majority of the detected amplicon sequence variants (ASV) were not shared among locations. These findings suggest drain fly transport a location-specific environmental bacteria. Notably, we also identified ASVs of potential clinical relevance, including Mycobacterium, Acinetobacter baumanii, Providencia, and Nocardia. This is the first metagenomic insight into the microbiome of this species and adds to a renewed interest in the role that non-hematophagous insects play in urban microbial ecology and the spread of microbes.},
}

@article {pmid40794955,
year = {2025},
author = {Dai, Y and Qian, Y and Qu, Y and Guan, W and Xie, J and Wang, D and Butler, C and Dashper, S and Carroll, I and Divaris, K and Liu, Y and Wu, D},
title = {Decoding longitudinal microbiome trajectories: an interpretable machine learning approach for biomarker discovery and prediction.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
pmid = {40794955},
issn = {1477-4054},
support = {1R03DE034507-01/NH/NIH HHS/United States ; U01DE025046/NH/NIH HHS/United States ; },
mesh = {Humans ; *Machine Learning ; *Biomarkers ; *Microbiota ; Longitudinal Studies ; Gastrointestinal Microbiome ; },
abstract = {Information generated from longitudinally sampled microbial data has the potential to illuminate important aspects of development and progression for many human conditions and diseases. Identifying microbial biomarkers and their time-varying effects can not only advance our understanding of pathogenetic mechanisms, but also facilitate early diagnosis and guide optimal timing of interventions. However, longitudinal predictive modeling of highly noisy and dynamic microbial data (e.g. metagenomics) poses analytical challenges.To overcome these challenges, we introduce a robust and interpretable machine-learning-based longitudinal microbiome analysis framework, LP-Micro, that encompasses (i) longitudinal microbial feature screening via a polynomial group lasso, (ii) disease outcome prediction implemented via machine learning methods (e.g. XGBoost, deep neural networks), and (iii) interpretable association testing between time points, microbial features, and disease outcomes via permutation feature importance. We demonstrate in simulations that LP-Micro can not only identify incident disease-related microbiome taxa, but also offers improved prediction accuracy compared with existing approaches. Applications of LP-Micro in two longitudinal microbiome studies with clinical outcomes of childhood dental disease and weight loss following bariatric surgery yield consistently high prediction accuracy. Moreover, LP-Micro highlights critical time points and associated microbial changes: oral microbial changes, including Streptococcus mutans, are most informative for predicting childhood dental disease at around 39 months of age, while gut microbial changes shortly after bariatric surgery strongly predict future weight loss. These findings are both informative and aligned with clinical expectations. The tool LP-Micro can be seen at https://github.com/IV012/LPMicro.},
}

Humans
*Machine Learning
*Biomarkers
*Microbiota
Longitudinal Studies
Gastrointestinal Microbiome

@article {pmid40794939,
year = {2025},
author = {Kannan, EP and Venkatachalam, P and Gopal, J and Sarkaraisamy, P and Muthu, M},
title = {Temporal shift of bacterial communities in poultry litter during the course of broiler chicken rearing: A 16S rRNA based metagenomic study.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf199},
pmid = {40794939},
issn = {1365-2672},
abstract = {AIM: To decipher the bacterial community transitions of poultry litter at various time frames over a six-week rearing cycle in a commercial broiler chicken poultry farm in Marakkanam, Tamil nadu, India.

METHODS AND RESULTS: The bacterial consortia of poultry litter was elucidated using 16S rRNA based metagenomic oxford nanopore sequencing method, followed by taxonomic assignment using kraken2 tool. Our findings unveiled the varied dominance patterns of bacteria in poultry litter (P1-P6) with Sphingobacterium sp. 21 (53%) in P1, Amphibacillus xylanus dominated in P2 (∼12%), Oceanimonas sp.GK1 in P3 (∼14%) and P6 (>50%), Anaerococcus prevotii in P4 (∼10%) and Marinobacter hydrocarbonoclasticus (∼15%) in P5. Importantly various bacteria involved in key biogeochemical cycles including Nitrosomonas eutropha (Nitrogen cycle), Bacillus subtilis (Phosphorous cycle), and Acidithiobacillus caldus (sulphur cycle) were detected indicating a strong potential of utilizing the poultry litter as an effective biofertilizer. On the other hand, harmful human pathogens including Mycobacterium tuberculosis, Escherichia coli, Salmonella enterica and Streptococcus pneumoniae were also detected indicating significant public health concern associated with the application of poultry litter as fertilizer.

CONCLUSIONS: This study offers knowledge to both leverage the usefulness of poultry litter as biofertilizer, to mitigate transmission of harmful pathogens harboured by poultry litter.},
}

@article {pmid40794845,
year = {2025},
author = {Heber, K and Tian, S and Betancurt-Anzola, D and Koo, H and Bisanz, JE},
title = {StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf440},
pmid = {40794845},
issn = {1367-4811},
abstract = {MOTIVATION: Synthetic microbial communities offer an opportunity to conduct reductionist research in tractable model systems. However, deriving abundances of highly related strains within these communities is currently unreliable. 16S rRNA gene sequencing does not resolve abundance at the strain level and other methods such as quantitative PCR (qPCR) scale poorly and are resource prohibitive for complex communities. We present StrainR2, which utilizes shotgun metagenomic sequencing to provide high accuracy strain-level abundances for all members of a synthetic community, provided their genomes.

RESULTS: Both in silico, and using sequencing data derived from gnotobiotic mice colonized with a synthetic fecal microbiota, StrainR2 resolves strain abundances with greater accuracy and efficiency than other tools utilizing shotgun metagenomic sequencing reads. We demonstrate that StrainR2's accuracy is comparable to that of qPCR on a subset of strains resolved using absolute quantification.

AVAILABILITY: Software is available at GitHub and implemented in C, R, and Bash. Software is supported on Linux and MacOS, with packages available on Bioconda or as a Docker container. The source code at the time of publication is also available on figshare at the doi: 10.6084/m9.figshare.29420780.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Source code and required resources to regenerate in silico reads are available via GitHub. Sequencing data is available via the NCBI Sequence read archive under BioProject PRJNA1038784.},
}

@article {pmid40794770,
year = {2025},
author = {Chia, M and Pop, M and Salzberg, SL and Nagarajan, N},
title = {Challenges and Opportunities in Analyzing Cancer-Associated Microbiomes.},
journal = {Cancer research},
volume = {},
number = {},
pages = {},
doi = {10.1158/0008-5472.CAN-24-3629},
pmid = {40794770},
issn = {1538-7445},
abstract = {The study of cancer-associated microbiomes has gained significant attention in recent years, spurred by advances in high-throughput sequencing and metagenomic analysis. Microbiome research holds promise for identifying non-invasive biomarkers and possibly new paradigms for cancer treatment. In this review, we explore the key computational challenges and opportunities in analyzing cancer-associated microbiomes (in tumor/normal tissues and other body sites, e.g. gut, oral, skin), focusing on sequencing-driven strategies and associated considerations for taxonomic and functional characterization. The discussion covers the strengths and limitations of current analysis tools for identifying contamination, determining compositional bias, and resolving species and strains, as well as the statistical, metabolic, and network inferences that are essential to uncover host-microbiome interactions. Several key considerations are required to guide the choice of databases used for metagenomic analysis in such studies. Recent advances in spatial and single-cell technologies have provided insights into cancer-associated microbiomes, and AI-driven protein function prediction might enable rapid advances in this field. Finally, we provide a perspective on how the field can evolve to manage the ever-growing size of datasets and to generate robust and testable hypotheses.},
}

@article {pmid40794299,
year = {2025},
author = {El-Halim, HMA and El-Hadidi, M and Fouad, N and Hamed, RR and Megid, IA and Taha, MH and Radwan, KH},
title = {Metagenomic insight into drought-induced changes in the Egyptian wheat rhizosphere microbiome.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {8},
pages = {310},
pmid = {40794299},
issn = {1573-0972},
mesh = {*Triticum/microbiology ; *Rhizosphere ; *Droughts ; Egypt ; *Microbiota/genetics ; Soil Microbiology ; Phylogeny ; *Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; Stress, Physiological ; RNA, Ribosomal, 16S/genetics ; Metagenome ; },
abstract = {Wheat is one of the most important cereal crops and an important source of food for billions of people worldwide. However, drought stress can pose a real threat to its productivity and lead to significant yield losses, especially in Egypt. The rhizospheric microbiome of wheat can play an important role in drought stress and help wheat to respond to this abiotic stress. Understanding this microbiome is therefore also important to improve drought stress resilience and productivity. In this study, a metagenomic analysis was performed to investigate how the composition and diversity of microbial communities associated with the wheat rhizosphere change under drought. Taxonomic and phylogenetic analyses revealed a shift in microbial abundance, with Actinobacteria, Bacteroidetes, Proteobacteria and Verrucomicrobia being the four most abundant phyla of the ethnic microbiota. Remarkably, other classes, including Alphaproteobacteria and Cytophagia, were significantly enriched under drought, which could be a promising enhancement of plant stress altruism. Differential abundance analysis showed that the control samples had higher abundance of microbial taxa such as OD1, WS2, Chlorobi, ABY1 and SHA-109 compared to the drought-treated genotypes. Functional prediction analysis using PICRUSt showed that an uncharacterized ATP-binding protein within the AAA + superfamily is overrepresented under drought conditions. This suggests that these genes may play a role in stress adaptation, possibly via energy-dependent regulation of cellular processes involved in plant survival. Our results expand our understanding of the complexity of responses of the wheat rhizosphere microbiome to drought and have practical implications for the development of microbial target combinations to improve wheat tolerance and productivity in the context of climate change challenges.},
}

*Triticum/microbiology
*Rhizosphere
*Droughts
Egypt
*Microbiota/genetics
Soil Microbiology
Phylogeny
*Metagenomics
*Bacteria/classification/genetics/isolation & purification
Stress, Physiological
RNA, Ribosomal, 16S/genetics
Metagenome

@article {pmid40793873,
year = {2025},
author = {Manning, S and Hackney, E and Dunneram, Y and Hull, MA and Mitra, S and Stewart, CJ and Louca, P and Meader, N and Sharp, L and Rees, C},
title = {Systematic Review: The Relationship Between the Faecal Microbiome and Colorectal Neoplasia in Shotgun Metagenomic Studies.},
journal = {Alimentary pharmacology & therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1111/apt.70252},
pmid = {40793873},
issn = {1365-2036},
support = {//Guts UK/ ; },
abstract = {BACKGROUND: The human gut microbiome is of academic and clinical interest. Associations between certain organisms and colorectal neoplasia have been reported, but findings have limited reproducibility in different populations.

METHODS: We performed a systematic review of whole metagenome shotgun sequencing studies using faecal samples from patients with colorectal neoplasia and control populations. Searches were performed on 30th June 2023. We identified 26 studies, reporting on 22 study populations (13 from Asia, five from Europe and four from North America). Study size ranged from 14 to 971 individuals (mean 170).

RESULTS: Some reproducible data were identified, such as the significant enrichment of Fusobacterium nucleatum and Parvimonas micra in colorectal cancer patients compared to controls (in 10 and nine studies, respectively). However, 21 out of 26 studies scored poorly on quality appraisal, specifically surrounding selection of cases and controls. Definitions of controls varied; some studies used individuals with normal endoscopic investigations, some used 'healthy' individuals where no colonoscopy was performed, and one used those with non-neoplastic findings (haemorrhoids). There was even less reproducibility of data in studies where individuals with colorectal polyps were compared to controls, possibly because of heterogeneity in these patient groupings as a variety of definitions for 'polyp cases' were used.

CONCLUSIONS: Heterogeneity and potential for bias indicates that findings should be interpreted with caution. Standardised protocols to ensure robust methodology and allow pooling of large-scale data are required before these findings can be used in clinical practice (PROSPERO: CRD42023431977).},
}

@article {pmid40793781,
year = {2025},
author = {Cifuentes, SG and Graham, J and Trueba, G and Cárdenas, PA},
title = {Hi-C untangles the temporal dynamics of the children's gut resistome and mobilome, highlighting the role of transposable elements.},
journal = {mBio},
volume = {},
number = {},
pages = {e0113425},
doi = {10.1128/mbio.01134-25},
pmid = {40793781},
issn = {2150-7511},
abstract = {Many metagenomic studies lack the ability to measure the temporal dynamics of the intestinal resistome (the collection of antibiotic resistance genes [ARGs]) and mobilome (the collection of all mobile genetic elements that enable their transfer) and link the genetic features to specific species in the gut. We applied Hi-C sequencing and shotgun metagenomics to study fecal matter from children (n = 15) living in semi-rural communities of Quito, Ecuador. We sampled at three different periods, with a 4- to 6-month interval between each sample collection. To understand the dynamics of ARGs from different genetic perspectives, we focused on identifying classes of mobile ARGs that are classified as high risk to human health. We selected those ARGs that appeared at least twice across sampling periods in the same child and focused the longitudinal analysis on the subset of children (n = 6) where these high-risk ARGs were consistently detected. The study demonstrated the temporal dynamics of these mobile ARGs from the taxonomic, plasmid, and transposable element perspectives, including insertion sequences and transposons. Our findings reveal that while plasmid composition fluctuates over time, transposons play a crucial role in the stability and dissemination of ARGs. Specifically, aph(3″)-Ib and aph(6)-Id genes were consistently mobilized by transposons across multiple multidrug-resistant Escherichia coli strains. These results highlight the importance of transposons in shaping the gut resistome and suggest that tracking regionally significant transposons could improve our understanding of ARG transmission in small geographic areas.IMPORTANCEAntibiotic resistance (ABR) is a growing global challenge, and particularly high-risk antibiotic resistance genes (ARGs) are a threat to public health. While plasmids are often considered the cornerstone of the spread of ARGs, our study emphasizes the critical role of transposons in the persistence and mobility of ARGs within the gut microbiota. By integrating Hi-C sequencing and shotgun metagenomics, we show that transposons mediate the transfer and persistence of ARGs across different Escherichia coli lineages, while plasmid composition changes over time. Recognizing the impact of transposons on resistome dynamics can help refine strategies to mitigate ABR transmission, particularly in regions where the impact of resistance is most significant, such as low- and middle-income countries. Our findings provide new insights into the mechanisms driving the persistence of ABR in the human gut, which are essential for developing more effective public health interventions and incorporating transposable elements into surveillance efforts.},
}

@article {pmid40793780,
year = {2025},
author = {Hull, JA and Fusco, RM and Tan, J and Ochoa, MA and Hall, A and Wan, X and Loeb, E and Asokan, A},
title = {Functional orthogonality of parvoviral phospholipase A2 domains in adeno-associated virus transduction.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0079925},
doi = {10.1128/jvi.00799-25},
pmid = {40793780},
issn = {1098-5514},
abstract = {Dependoparvoviruses, which belong to the family Parvoviridae, are being developed as viral vectors for gene transfer. Notably, different adeno-associated viral (AAV) serotype capsids have been utilized to generate pseudotyped recombinant vectors. While capsid surface regions mediate host cell interactions, buried structural domains have been implicated in parvoviral infectivity and post-entry trafficking. In this regard, the functional diversity of highly conserved group XIII phospholipase A2 domains (PLA2) located within the N-terminal capsid domain of different parvoviruses is of particular interest. Here, we developed a massively parallel screen to evaluate a diverse panel of rationally engineered and naturally derived parvoviral PLA2 domains incorporated within the human isolate, AAV9. In vitro infectious cycling of chimeric virions revealed a functional bias toward parvoviral PLA2 domains of mammalian and avian origin and decreased preference for PLA2 domains of insect, ungulate, or metagenomic origin. Notably, wild-type chimeric AAV9 virions carrying avian dependoparvovirus PLA2 domains demonstrate increased replication over other chimeras. The best-performing recombinant avian/human origin chimera (UNY47950.1/AAV9) shows improved transduction with both single-stranded and self-complementary vector genomes. This observation is accompanied by improved cytoplasmic uptake and nuclear entry of chimeric virions compared to parental AAV9, as evidenced by subcellular fractionation and confocal microscopy. Overall, this study highlights the functional orthogonality of distinct parvoviral PLA2 domains incorporated into AAV capsids. These chimeric virions present an opportunity to gain deeper insight into the infectious biology of parvoviruses and potentially enable new approaches to improve post-entry trafficking of AAV vectors for gene transfer applications.IMPORTANCEThis study explores the functional overlap of phospholipase domains located within the capsid lumen across the parvovirus family. The findings provide insights into parvovirus-host interactions across different genera within the context of this highly conserved capsid region and underscore its essential role in viral trafficking to the nucleus. Furthermore, incorporation of orthogonal phospholipase domains derived from diverse parvoviral family members may expand the recombinant vector toolkit of adeno-associated viruses for gene transfer applications.},
}

@article {pmid40790469,
year = {2025},
author = {Qin, M and Ding, W and Qin, L and Liang, R and Guo, Y and Zhao, Y and Xu, H and Wen, Y and Pang, Y and Li, L},
title = {Dysbiosis associated with enhanced microbial mobility across the respiratory tract in pulmonary tuberculosis patients.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {499},
pmid = {40790469},
issn = {1471-2180},
support = {2022TFC2304803//National Key Research and Development Program of China,China/ ; },
abstract = {BACKGROUND: The microbiota is actively engaged in interaction networks both with the host and among its own constituent members. However, comprehensive studies examining the microbiome profiles across various respiratory sites in pulmonary tuberculosis (PTB) are lacking. Here, we explored the diversity of the microbiome in PTB patients across multiple respiratory sites and investigated potential interactions between the microbiomes of these sites.

METHODS: A total of 130 respiratory tract samples were collected from multiple sites of 22 patients with PTB and 14 healthy individuals, including the oral cavity, trachea, and both the healthy and affected sides of the lungs. These samples were subjected to metagenomic sequencing to analyze the characteristics and diversity of the respiratory microbiome.

RESULTS: We found that the respiratory tract of PTB patients had higher microbial diversity than seen in the healthy individuals (8,182 vs 6,465). Among them, Rothia, Prevotella and Actinomyces exhibited higher proportions in PTB. The characteristics of high diversity features in the oral site were more prominent with PTB, especially the notable difference of Rothia mucilaginosa. Additionally, Streptococcus, Neisseria, Prevotella and Fusobacterium have strong interactions with other species at present at various sites of PTB patients, as well as frequent communication between these species during migration in the upper and lower respiratory tract.

CONCLUSIONS: The diversity and translocation of microbiota across the respiratory tract in PTB patients are associated with increased susceptibility of microbiome. The predominance of Rothia, Prevotella, and Actinomyces may represent progression-associated microbial signatures, warranting mechanistic studies on their pathogenic potential through host-microbe interactions to guide therapeutic targeting.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04206-x.},
}

@article {pmid40792511,
year = {2025},
author = {Pokšāne, A and Ķimsis, J and Pētersone-Gordina, E and Vilcāne, A and Gerhards, G and Ranka, R},
title = {Characterization of ancient DNA preservation in copper-patinated human bone and tooth samples from Latvia.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0270524},
doi = {10.1128/spectrum.02705-24},
pmid = {40792511},
issn = {2165-0497},
abstract = {UNLABELLED: Bronze and copper-containing alloys are known to possess antibacterial properties, which, besides mineralization, might contribute to the observation of better preservation of bone, teeth, and other organic materials in close proximity to bronze artifacts in archaeological contexts. Often, the selection of preserved hard tissue material from burials for ancient DNA (aDNA) analysis is limited due to the sampling strategies used at the time of excavations or poor preservation in general. This study assessed the suitability of samples with copper patination for in-depth human and bacterial aDNA analysis. To characterize the difference between patinated and unpatinated samples, a qualitative assessment of human DNA preservation and metagenomic analysis using Kraken2 and MEGAN Alignment Tool was performed. For patinated samples, a very low proportion of endogenous DNA preservation was observed. Only one-the least patinated-out of five analyzed samples could be authenticated to be containing human aDNA with confidence. A patinated sample of specific bacterial genera was affiliated with soil and aquatic, mostly marine environmental, microorganisms. In conclusion, due to mineralization processes that occur during the patination of hard tissue, endogenous DNA preservation is seen to be greatly affected, thus making heavily patinated samples a compromised source of endogenous aDNA. Future in-depth research is needed, including the assessment of chemical composition of patinated tissues.

IMPORTANCE: Ancient DNA research has recently become a very powerful tool for archaeological and historical research, enabling the discovery of information about various aspects of our predecessors' lives, but it is limited by the availability of material to be sampled. To our knowledge, there is no previous study focused on effects of copper patination on ancient DNA preservation and metagenomic profiles of archaeological teeth and bone samples. Our results suggest that patination should be considered an influential factor during sample selection, as it affected human endogenous DNA preservation and metagenomic diversity within analyzed samples.},
}

@article {pmid40792268,
year = {2025},
author = {Zhong, J and Li, J and Liao, J and Ma, Y and Li, Z and Yang, L and Chang, W and Miao, M},
title = {Alpine radish rhizosphere microbiome assembly and metabolic adaptation under PBAT/PLA humic acid biodegradable mulch films.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1623052},
pmid = {40792268},
issn = {1664-302X},
abstract = {INTRODUCTION: Alpine agroecosystems present unique crop production challenges due to extreme environmental conditions, where rhizosphere microbiomes significantly influence plant adaptation.

METHODS: To investigate mulch-induced microbial changes in high-altitude agriculture, this study analyzed a radish field in China using SMRT sequencing (16S rRNA/ITS) and metagenomics, comparing PBAT/PLA biodegradable films with/without humic acid (HA) at varying thicknesses.

RESULTS: Results demonstrated that radish cultivation selectively enriched Proteobacteria and Acidobacteriota while depleting Chloroflexi and Actinobacteria, with fungal communities shifting from Basidiomycota-to Ascomycota-dominance. Notably, HA-amended mulches enhanced bacterial diversity and specifically promoted polymer-degrading microbes (Chitinophagaceae, Candidatus_Udaeobacter, Chaetomiaceae). Metagenomic profiling revealed thickness-dependent increases in functional genes related to carbohydrate and amino acid metabolism in HA-treated soils.

CONCLUSION: These findings advance our understanding of how biodegradable mulch formulations can be optimized to enhance microbial ecosystem services in alpine farming systems.},
}

@article {pmid40792258,
year = {2025},
author = {Chen, Q and Mo, P and Yang, R and Xu, H and Liu, H and Zhang, Z and Du, Q and Jiang, Q and Guo, Q and Chen, L and Zhang, Y and Xiong, Y and Deng, L},
title = {Analysis of microorganisms and drug-resistance mutations detected by probe-capture metagenomics among HIV-infected patients with pneumonia.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1616937},
pmid = {40792258},
issn = {1664-302X},
abstract = {BACKGROUND: Probe-Capture Metagenomics is a newly developed method for detecting infectious pathogens. However, its application in HIV-infected patients with pulmonary infection remains limited. This study utilized Probe-Capture Metagenomics to analyze lung microbiomes and Drug Resistance Mutations of HIV and bacteria in people living with HIV (PLWH) with pneumonia.

METHODS: We retrospectively investigated lung microorganisms in PLWH hospitalized at Zhongnan Hospital of Wuhan University. A combination of bronchoalveolar lavage fluid Probe-Capture Metagenomics and conventional microbiological tests were performed in all patients.

RESULTS: A total of 91 patients were included in the study. Excluding the EB and Torque teno virus, at least two organisms were identified in 85 patients using Probe-Capture Metagenomics combined with conventional microbiological tests. The top six detected organisms were CMV, Pneumocystis jirovecii, Mycobacterium tuberculosis complex, HHV-7, Candida albicans and Aspergillus. For specific organisms, the detection rate of CMV and Candida albicans by Probe-Capture Metagenomics was significantly higher than that of conventional microbiological tests (p < 0.0001). Moreover, the detection rates of CMV (p = 0.0167) and Pneumocystis jirovecii (p = 0.04) in patients with CD4[+]T count ≥ 200 cells/μL were higher than that with CD4[+]T count < 200 cells/μL. Importantly, Probe-Capture Metagenomics can uncover potentially clinically relevant drug-resistance mutations linked to HIV and bacteria.

CONCLUSION: Probe-Capture Metagenomics provides a promising method of detecting suspected opportunistic infections in PLWH with pneumonia, especially for mixed infections and rare microorganisms. In addition, Probe-Capture Metagenomics was a potential valuable tool for genotyping resistance testing of HIV and bacteria.},
}

@article {pmid40792257,
year = {2025},
author = {Xie, Z and Wu, Z and Liu, Y and Gu, Y and Niu, J and Lv, K},
title = {Intratumoral microbiota: implications for cancer progression and treatment.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1551515},
pmid = {40792257},
issn = {1664-302X},
abstract = {The human body has a diverse range of microbiota that influences human physiological processes and alters disease risk, involving cancer. Metagenomic sequencing investigations have revealed that the microbiota is an element of the tumor microenvironment, affecting tumor proliferation and responsiveness to current anticancer treatments. The notion of intratumoral microbiota was subsequently introduced. Intratumoral microorganisms have been identified in kinds of cancer, including pancreatic, colorectal, liver, esophageal, breast, and lung malignancies. Microbiota may inhabit tumor tissues by mucosal breakdown, neighboring tissue migration, and hematogenous spread, influencing the biological behavior of tumors as a significant component of tumor's microenvironment. The intratumoral microbiota may facilitate the onset and progression of malignancies through DNA mutations, activation of carcinogenic pathways, alteration of anticancer medication metabolism, and commencement of metastasis. This document is to present an overview of intratumoral microbiota, their prevalence and progression in cancer, their detection and therapy, and to evaluate the potential and limitations of research in this domain. We intend to generate ideas for investigating intratumoral microbiota as possible treatment targets and biomarkers for tumor assessment, prognosis, and detection.},
}

@article {pmid40792105,
year = {2025},
author = {Han, W and Zhou, Y and Wang, Y and Liu, X and Sun, T and Xu, J},
title = {Exploring fecal microbiota signatures associated with immune response and antibiotic impact in NSCLC: insights from metagenomic and machine learning approaches.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1591076},
pmid = {40792105},
issn = {2235-2988},
mesh = {Humans ; *Machine Learning ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Metagenomics/methods ; *Feces/microbiology ; *Carcinoma, Non-Small-Cell Lung/immunology/microbiology/drug therapy/therapy ; *Lung Neoplasms/immunology/microbiology/therapy/drug therapy ; Immunotherapy ; Male ; Female ; Middle Aged ; Aged ; Bacteria/classification/genetics/drug effects ; },
abstract = {BACKGROUND: Substantial interstudy heterogeneity in cancer immunotherapy-associated biomarkers has hindered their clinical applicability. To address this challenge, we performed a comprehensive integration of publicly available global metagenomic datasets. By leveraging metagenomic profiling and machine learning approaches, this study aimed to elucidate gut microbial signatures associated with immune response in lung cancer (LC) and to evaluate the modulatory effects of antibiotic exposure.

METHODS: A systematic literature search was conducted to identify relevant datasets, resulting in the inclusion of 209 fecal metagenomic samples: 154 baseline samples (45 responders, 37 non-responders, and 72 healthy controls) and 55 longitudinal samples collected during immunotherapy. We performed taxonomic and functional characterization of gut microbiota (GM) differentiating responders from non-responders, delineated microbiome dynamics during treatment, and assessed the impact of antibiotics on key microbial taxa. Among eight machine learning algorithms evaluated, the optimal model was selected to construct a predictive framework for immunotherapy response.

RESULTS: Microbial α-diversity was significantly elevated in responders compared to non-responders, with antibiotic administration further amplifying this difference-most notably at the species level. Integrative multi-omics analysis identified two pivotal microbial biomarkers, s_Bacteroides caccae and s_Prevotella copri, which were strongly associated with immunotherapy efficacy. A random forest-based classifier achieved robust predictive performance, with area under the curve (AUC) values of 0.82 and 0.79 at the species and genus levels, respectively. Notably, P. copri was further enriched in responders with poor progression-free survival (PFS <3 months), indicating a potential deleterious role. Antibiotic exposure significantly influenced the abundance and functional potential of these key taxa. KEGG-based functional analysis revealed the enrichment of amino acid metabolism pathways in responders. Additionally, CARD database annotation demonstrated that the majority of antibiotic resistance genes were associated with Bacteroidetes and Proteobacteria, implicating these taxa in shaping microbial-mediated therapeutic responses.

CONCLUSIONS: This study represents the first large-scale, cross-cohort integration of metagenomic data to identify reproducible GM signatures predictive of immune checkpoint inhibitor efficacy in LC. The findings not only underscore the prognostic relevance of specific taxa but also establish a foundation for developing microbiome-informed, personalized immunotherapeutic strategies.},
}

Humans
*Machine Learning
*Anti-Bacterial Agents/therapeutic use/pharmacology
*Gastrointestinal Microbiome/drug effects
Metagenomics/methods
*Feces/microbiology
*Carcinoma, Non-Small-Cell Lung/immunology/microbiology/drug therapy/therapy
*Lung Neoplasms/immunology/microbiology/therapy/drug therapy
Immunotherapy
Male
Female
Middle Aged
Aged
Bacteria/classification/genetics/drug effects

@article {pmid40792101,
year = {2025},
author = {Lu, Y and Sun, Y and Li, Y and Wang, Y and Wu, D and Li, Z and Guo, X},
title = {A breakthrough Trichosporon asahii infection in an immune thrombocytopenia patient during caspofungin and isavuconazole combined therapy: a case report.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1625007},
pmid = {40792101},
issn = {2235-2988},
mesh = {Humans ; *Caspofungin/therapeutic use/administration & dosage ; *Antifungal Agents/therapeutic use/administration & dosage ; *Nitriles/therapeutic use/administration & dosage ; *Trichosporonosis/drug therapy/diagnosis/microbiology ; *Triazoles/therapeutic use/administration & dosage ; *Trichosporon/isolation & purification/drug effects/genetics ; *Pyridines/therapeutic use/administration & dosage ; Drug Therapy, Combination ; Male ; Amphotericin B/therapeutic use/administration & dosage ; Treatment Outcome ; Voriconazole/therapeutic use ; Immunocompromised Host ; High-Throughput Nucleotide Sequencing ; Basidiomycota ; },
abstract = {Trichosporon infection is a rare but highly lethal infectious disease. Clinically, Trichosporon asahii is the strain most commonly isolated from patients with Trichosporon infections. T. asahii is an opportunistic pathogen that can cause local or invasive infections in immunocompromised patients. In this article, a case of breakthrough T. asahii infection in an immune thrombocytopenia (ITP) patient during caspofungin and isavuconazole combined therapy is reported. Metagenomic next-generation sequencing (mNGS) played a crucial role in the diagnosis of the breakthrough infection in this patient. Upon receiving combined therapy with intravenous voriconazole and nebulized amphotericin B, the patient demonstrated significant clinical improvement and was subsequently discharged.},
}

Humans
*Caspofungin/therapeutic use/administration & dosage
*Antifungal Agents/therapeutic use/administration & dosage
*Nitriles/therapeutic use/administration & dosage
*Trichosporonosis/drug therapy/diagnosis/microbiology
*Triazoles/therapeutic use/administration & dosage
*Trichosporon/isolation & purification/drug effects/genetics
*Pyridines/therapeutic use/administration & dosage
Drug Therapy, Combination
Male
Amphotericin B/therapeutic use/administration & dosage
Treatment Outcome
Voriconazole/therapeutic use
Immunocompromised Host
High-Throughput Nucleotide Sequencing
Basidiomycota

@article {pmid40791803,
year = {2025},
author = {Altaie, AM and Venkatachalam, T and Patil, K and Al-Marzooq, F and Rawat, SS and Qabbani, AA and Alsaegh, MA and Samaranayake, LP and Soliman, SSM and Hamoudi, R},
title = {Integrated metagenomics and transcriptomics analysis reveals pathways associated with oral periapical lesions formation and progression.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100443},
pmid = {40791803},
issn = {2666-5174},
abstract = {Periapical abscesses, radicular cysts, and periapical granulomas are among the most frequently identified pathological lesions in the alveolar bone. Although many studies have investigated bacterial metagenomics in periapical abscesses, little is known about the genome mining of abundant bacteria in periapical lesions and its correlation to human transcriptome. This study aims to explore the enriched metabolic environment of periapical lesions associated with microbial diversity and their role in lesion progression. Bacterial DNA and human RNA were isolated from periapical lesions and healthy pulp tissue and sequenced using next-generation sequencing (NGS). The sequences of the most abundant bacteria were then analyzed to identify secondary metabolites, pathogenic proteins, and their associated metabolic pathways. The results revealed that Fusobacterium nucleatum was the predominant bacterium in periapical abscesses and radicular cysts, whereas Porphyromonas endodontalis was the most abundant in periapical granulomas. Integrated bacterial and human metabolic pathways indicated that the augmentation of similar pathways is important in lesions pathogenesis. In periapical abscesses, inflammatory response, humoral immune response, positive regulation of cell migration, and hemopoiesis were enriched. In radicular cysts, pathways linked to NABA matrisome associated, inflammatory response, immune response-regulating signaling pathway, neutrophil degranulation, and P73 pathway were enriched. Meanwhile, periapical granulomas exhibited significant enrichment of pathways related to response to bacterium, regulation of immune effector process, and positive regulation of cell migration. In conclusion, this study is the first to elucidate the interplay between microbial and human metabolic activity associated with inflammation in abscesses, apoptosis in cysts, and inflammatory regulation in granulomas. These findings have significant clinical implications for the early diagnosis, prevention, and treatment of periapical lesions.},
}

@article {pmid40791778,
year = {2025},
author = {Tamayo-Estebaranz, N and Muñoz-González, C and Gil-Valcárcel, AM and Calvo López-Dávalos, P and Martín-Vacas, A and Paz-Cortés, MM and Aragoneses, JM},
title = {Salivary microbiota profile in adult and children population according to active dentin caries: a metagenomic preliminary analysis.},
journal = {Frontiers in oral health},
volume = {6},
number = {},
pages = {1599925},
pmid = {40791778},
issn = {2673-4842},
abstract = {OBJECTIVES: The aim of this study was to investigate the relationship between active dentin caries (ADC), salivary biochemical parameters, and salivary microbiota composition in Spanish children and adults.

METHODS: Saliva samples were collected from 80 subjects (40 adults and 40 children) divided between ADC and non-ADC. Salivary biochemical determination was performed by analysing total protein content (TPC) and total antioxidant activity (TAC) in saliva supernatants. DNA was obtained from the pellet of saliva samples using the Bacterial DNA kit and analysed with the Illumina NextSeq platform from all participants. Alpha diversity (Chao, Observed Features, Shannon and Simpson indices) and beta diversity (PCoA plot and PERMANOVA procedure) were analysed. In addition, Linear Discriminant Analysis Effect Size (LEfSe) was used to identify differential taxa between groups. All statistical analysis were performed with a 95% confidence level (p < 0.05).

RESULTS: No significant associations were found between ADC and salivary biochemical markers in either the adult or pediatric age group, suggesting that these parameters alone may not sufficiently reflect cariogenic activity. Microbiota analysis at the phylum level did not show significant correlations with ADC; however, distinct associations appeared at the genus and species levels. In adults, several genera (Corynebacterium, Porphyromonas, Tannerella, Catonella, Filifactor, Parvimonas, and Dialister) were positively associated with ADC, reflecting a shift towards a dysbiotic microbiome composition that overlaps with periodontal and endodontic pathologies. Conversely, Haemophilus was negatively correlated with ADC, potentially indicating a protective role. At the species level, a positive correlation with ADC was found with Porphyromonas gingivalis, Porphyromonas endodontalis, Peptostreptococcus stomatis, Leptotrichia buccalis, Prevotella oris, or Corynebacterium matruchotii in the adult population. In children, microbial associations with caries were more limited, with Scardovia, a well-known acidogenic genus, positively correlated with ADC, and P. stomatis showing a negative association. Interestingly, P. stomatis exhibited opposite correlations in adults and children, possibly reflecting age-specific ecological roles. No significant differences in alpha or beta diversity were found either in adults or children participants.

CONCLUSIONS: Overall, these findings highlight a stronger and more diverse association between salivary microbiota and caries in adults compared to children. These results underscore the importance of age-specific microbial signatures in the aetiology of dental caries. The obtained differences suggest that caries development in adults may involve broader dysbiosis involving proteolytic and anaerobic organisms in addition to acidogenic species.},
}

@article {pmid40791674,
year = {2025},
author = {Nadimpalli, ML and Sehgal, N and Rojas-Salvatierra, L and Gilman, RH and Earl, AM and Worby, CJ and Schwab, M and Pickering, AJ and Pajuelo, MJ},
title = {Role of the gut microbiome in frequent gut colonization with extended-spectrum β lactamase-producing Enterobacterales among Peruvian children.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.11.06.24316595},
pmid = {40791674},
abstract = {Gut colonization with extended-spectrum beta lactamase-producing Enterobacterales (ESBL-E) is increasingly common among children in low and middle-income countries. Some children nevertheless remain never or rarely colonized during early life. Understanding how this protection is conferred could be helpful for designing future interventions to protect children's health. Here, we investigated whether differences in gut microbiome development could underlie differential susceptibility to ESBL-E gut colonization over time among children in peri-urban Lima. Weekly stool and daily surveys were collected from 345 children <3 years old during a 2016-19 study of enteric infections. A subset of children (n=12) were rarely gut-colonized with ESBL-E from 1-16 months of age. We performed short-read metagenomic sequencing of stool collected at 3, 6, 7, 9, 12, and 16 months from these children and a random subset of 42 frequently colonized children, and characterized differences in their exposures and gut microbiomes. No differences in gut taxa or functional pathways were identified over time, though children harbored differentially abundant taxa, more unique E. coli strains, and a higher abundance of bla CTX-M gene copies at ESBL-E-positive versus negative timepoints. Differing patterns of ESBL-E colonization over time among children in peri-urban Lima do not appear to be related to differences in gut microbiome development.},
}

@article {pmid40791429,
year = {2025},
author = {Flor, S and Dost, T and Haase, M and Simon, R and Ederer, S and Kadibalban, AS and Taubenheim, J and Olecka, M and Walker, A and Zimmermann, J and Marinos, G and Franzenburg, S and Schmitt-Kopplin, P and Baines, J and Riege, K and Hoffmann, S and Best, L and Frahm, C and Kaleta, C},
title = {Multi-omics analysis highlights the link of aging-related cognitive decline with systemic inflammation and alterations of tissue-maintenance.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.13.662751},
pmid = {40791429},
issn = {2692-8205},
abstract = {Aging-related cognitive decline is associated with changes across different tissues and the gut microbiome, including dysfunction of the gut-brain axis. However, only few studies have linked multi-organ alterations to cognitive decline during aging. Here we report a multi-omics analysis integrating metabolomics, transcriptomics, DNA methylation, and metagenomics data from hippocampus, liver, colon, and fecal samples of mice, correlated with cognitive performance in the Barnes Maze spatial learning task across different age groups. We identified 734 molecular features associated with cognitive rank within individual data layers, of which 227 features remain when integrating all data layers with each other. Among the single-layer predictors, several host and microbial features were highlighted, with host-associated markers being predominant. Host features associated with cognitive function mainly belong to innate and adaptive inflammatory activity (inflammaging) and developmental processes. Our findings suggest that cognitive decline in aging is tightly coupled to systemic, age-associated inflammation, potentially initiated by microbiome-driven gastrointestinal inflammatory activity, emphasizing a link between peripheral tissue alterations and brain function.},
}

@article {pmid40791349,
year = {2025},
author = {Kim, KJ and Garcia, M and Romero, AS and Jin, Y and Chi, J and Campen, MJ and Gu, H and Richardson, JR and Castillo, EF and Cui, JY},
title = {In vivo exposure of mixed microplastic particles in mice and its impacts on the murine gut microbiome and metabolome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.15.664901},
pmid = {40791349},
issn = {2692-8205},
abstract = {Microplastics (MPs) are emerging environmental contaminants due to increasing global plastic production and waste. Microplastics, defined as plastic particles less than 5 mm in diameter, are formed through degradation of larger plastics via sunlight, weathering, and microbes. These plastic compounds are widely detected in water, soil, food, as well as human stool and blood. The gut microbiome, often referred to as our second genome, is important in human health and is the primary point of contact for orally ingested microplastics. To investigate the impact of ingested MPs on the gut microbiome and the metabolome, 8 weeks-old male and female C57/BL6 mice were orally gavaged mixed plastic (5 um) exposure consisting of polystyrene, polyethylene, and the biodegradable/biocompatible plastic, poly-(lactic-co-glycolic acid) twice a week for 4 weeks at 0, 2, or 4 mg/week (n = 8/group). Fecal pellets were collected for bacterial DNA extraction and metagenomic shotgun sequencing, and serum was subjected to targeted and untargeted metabolomics. MPs exposure resulted in significant sex-specific and dose-dependent changes to the gut microbiome composition along with substantial regulation of the predicted metabolic pathways. Untargeted metabolomics in serum showed that a low MPs dose displayed a more prominent effect on key metabolic pathways such as amino acid metabolism, mitochondrial function, and inflammation. Additionally, SCFA-targeted metabolomics showed significant changes in neuroprotective SCFAs levels in both sexes by MPs exposure. In conclusion, our study has demonstrated that microplastics dysregulate the gut microbiome and serum metabolome, providing critical insights into potential human disease risks associated with microplastic contamination.},
}

@article {pmid40791337,
year = {2025},
author = {Fichorova, RN and Cezar-de-Mello, PFT and Dreyfuss, JM and Yamamoto, H and Chen, PL and Hui, P and Gao, X and Morrison, C and Barbieri, R and Doncel, GF},
title = {Abnormal Vaginal Microbiota Associated with miRNA Targeting the HIV-Host Interactome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.18.665639},
pmid = {40791337},
issn = {2692-8205},
abstract = {Understanding the molecular mechanisms underlying the ability of vaginal dysbiosis to alter the mucosal barrier to HIV acquisition is an essential step toward prevention. We hypothesized that micro(mi)-RNAs dysregulated by vaginal pathobiont bacteria epigenetically control host pathways exploited by the virus. The impact of these endogenous non-coding short RNAs on the anti-viral mucosal barrier function in the female reproductive tract is largely unknown. This study utilized cervicovaginal specimens collected during the luteal and follicular phase of the menstrual cycle along with data on age, race, ethnicity, education, and body mass index from 141 healthy reproductive-age women confirmed negative for sexually transmitted infections. Vaginal microbiota was classified by Nugent scoring. Shot-gun vaginal microbiome sequencing and metagenome taxonomic classification was performed on a subset of 21 women. Levels of miRNAs in exosomes isolated from cervicovaginal secretions were quantified using the EdgeSeq-NextGen global transcriptome platform. Differential expression (DE) was determined using R. Epigenetic target prediction was performed using MirTarBase. MiRNA profiles varied by both Nugent score categories (0-3 scores = normal, 4-6 = intermediate, and 7-10 = bacterial vaginosis, BV) and by metagenome classification. Higher microbiome diversity was associated with higher number of significantly dysregulated miRNAs (588 in BV compared to Nugent 0-3 versus 42 in Nugent 4-6 compared to Nugent 0-3, false discovery rate FDR<0.01) affecting over 400 experimentally validated genes targeted for post-transcriptional regulation. The miRNAs dysregulated by G. vaginalis -dominated compared to L. crispatus -dominated metagenomes included 24 DE miRNAs (92% overlap with BV by Nugent score) and 112 validated target genes. BV-dysregulated miRNA mediated the immunosuppressive effects of BV on cytokine levels previously associated with HIV acquisition risk. The gene ontology predictions based on BV-dysregulated miRNAs identified enrichment for 445 downregulated and 50 upregulated genes previously validated as part of the HIV-host interactome. miRNAs mediation revealed a mechanism of suppressed immunity by BV predictive of HIV risk. In conclusion, miRNAs dysregulated by vaginal dysbiosis may facilitate immune imbalance and cellular pathways associated with HIV risk.},
}

@article {pmid40790818,
year = {2025},
author = {Li, S and Strous, M and Diao, M},
title = {Groundwater Nitrogen Fixation Is Associated with Methane and Sulfur Cycling.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c02298},
pmid = {40790818},
issn = {1520-5851},
abstract = {Nitrogen fixation is an energy-intensive process critical for microbial survival in nitrogen-depleted environments. Groundwater, the Earth's largest accessible freshwater reservoir, is typically oligotrophic. However, recent studies have identified productive groundwater habitats where nitrogen fixation may become important to support the productivity. This study investigated the diversity, activity, and metabolisms of diazotrophs in groundwater through 25 metagenomes and five proteomes. We identified 203 nonredundant nitrogenase iron proteins (NifH) and 140 diazotroph genomes. They were affiliated with diverse bacterial and archaeal taxa and could comprise half of the community. Methanotrophic Methylomonadaceae emerged as the most abundant and active diazotrophs in methane-rich groundwater systems. These microorganisms, along with diazotrophic methanogens, anaerobic methanotrophs, and methylotrophs, highlighted a strong linkage between nitrogen fixation and the methane cycle. In addition, sulfur-cycling diazotrophs, including chemoautotrophic and heterotrophic sulfur oxidizers and sulfate reducers, were ubiquitous and showed metabolic versatility in varying geochemical conditions. Proteomes further suggested active nitrogen fixation by both methane- and sulfur-associated diazotrophs. This study highlights nitrogen fixation as an important process in groundwater, especially in aquifers where nitrogen-depleted methane, produced by methanogens, serves as a major carbon source.},
}

@article {pmid40790604,
year = {2025},
author = {Kale, V and Baldi, G and Beracochea, M and Clausen, C and Escobar-Zepeda, A and Leanti La Rosa, S and Lecaudey, LA and Li, S and Mak, SST and Martin, MD and Martin Bideguren, G and Pless, LA and Rasmussen, JA and Rogers, AB and Sveier, H and León, AV and Verissimo, A and Gilbert, MTP and Richardson, L and Limborg, MT and Finn, RD},
title = {A bacterial and viral genome catalogue from Atlantic salmon highlights diverse gut microbiome compositions at pre- and post-smolt life stages.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {85},
pmid = {40790604},
issn = {2524-4671},
support = {817729//European Union's Horizon 2020 research and innovation programme/ ; 817729//European Union's Horizon 2020 research and innovation programme/ ; 817729//European Union's Horizon 2020 research and innovation programme/ ; 817729//European Union's Horizon 2020 research and innovation programme/ ; 817729//European Union's Horizon 2020 research and innovation programme/ ; 817729//European Union's Horizon 2020 research and innovation programme/ ; 817729//European Union's Horizon 2020 research and innovation programme/ ; 817729//European Union's Horizon 2020 research and innovation programme/ ; 817729//European Union's Horizon 2020 research and innovation programme/ ; 817729//European Union's Horizon 2020 research and innovation programme/ ; 817729//European Union's Horizon 2020 research and innovation programme/ ; 817729//European Union's Horizon 2020 research and innovation programme/ ; 817729//European Union's Horizon 2020 research and innovation programme/ ; 817729//European Union's Horizon 2020 research and innovation programme/ ; 817729//European Union's Horizon 2020 research and innovation programme/ ; 817729//European Union's Horizon 2020 research and innovation programme/ ; 817729//European Union's Horizon 2020 research and innovation programme/ ; 817729//European Union's Horizon 2020 research and innovation programme/ ; 817729//European Union's Horizon 2020 research and innovation programme/ ; },
abstract = {Resolving the microbiome of the Atlantic salmon Salmo salar gut is challenged by a low microbial diversity often dominated by one or two species of bacteria, and high levels of host contamination in sequencing data. Nevertheless, existing metabarcoding and metagenomic studies consistently resolve a putative beneficial Mycoplasma species as the most abundant organism in gut samples. The remaining microbiome is heavily influenced by factors such as developmental stage and water salinity. We profiled the salmon gut microbiome across 540 salmon samples in differing conditions with a view to capture the genomic diversity that can be resolved from the salmon gut. The salmon were exposed to 3 different nutritional additives: seaweed, blue mussel protein and silaged blue mussel protein, including both pre-smolts (30-60 g salmon reared in freshwater) as well as post-smolts (300-600 g salmon reared in saltwater). Using genome-resolved metagenomics, we generated a catalogue of 11 species-level bacterial MAGs from 188 input metagenome assembled genomes, with 5 species not found in other catalogues. This highlights that our understanding of salmon gut microbial diversity is still incomplete. A prevalent bacterial genome annotated as Mycoplasmoidaceae is present in adult fish, and a comparison of functions revealed significant sub-species variation. Juvenile fish have a different microbial diversity, dominated by a species of Pseudomonas aeruginosa. We also present the first viral catalogue for salmon including prophage sequences which can be linked to the bacterial MAGs.},
}

@article {pmid40790378,
year = {2025},
author = {Flores-Gallegos, FA and García-Guevara, F and Vega-Alvarado, L and Lara, P and Jiménez-Jacinto, V and Juárez, K},
title = {Microbial diversity and metabolic potential in long-term Cr(VI) polluted soil during in situ biostimulation: a pilot effective assay.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {40790378},
issn = {1614-7499},
support = {IN208912//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; FOINS4785//Consejo Nacional de Ciencia y Tecnología/ ; },
abstract = {Excess industrial Cr(VI) waste and its improper disposal have resulted in the contamination of diverse environments, including soils and aquifers. To contend with high concentration of Cr(VI), a dangerous mutagen and oxidizing agent, diverse bacteria have developed a broad spectrum of metabolic strategies, mainly through chromate efflux pumps and reduction of Cr(VI) to Cr(III), which is less toxic and unable to cross biological membranes. In this study, we performed an in situ biostimulation assay in a highly alkaline and saline soil from a long-term contaminated site in Guanajuato, México. Four percent molasses was an effective treatment in promoting the Cr(VI) reduction by indigenous microorganisms. Initial Cr(VI) concentration was 5.6 to 12.4 g per kg of soil; After biostimulation assay (20 days), Cr(VI) was reduced from 0.75 to 3.02 g per kg of soil. DNA and RNA extraction from biostimulated samples was performed to carry out metagenomic and metatranscriptomic studies. Furthermore, 16S rDNA V3 and V4 amplicons were sequenced using illumina MiSeq technology complementing the study. The results showed an enrichment at Class level of Gammaproteobacteria, Alphaproteobacteria, Actinobacteria, Nitriliruptoria and Bacilli. The enrichment of Halomonas spp. during the biostimulation assay was remarkable, reaching 92% of the population and becoming the most dominant genus. On the other hand, comparative metagenomic and metatranscriptomic analysis was carried out in order to know the whole microbial population and the genes expressed during the reduction of Cr(VI) to Cr(III). We identified reductase genes associated with various bacterial groups. Interestingly, all the expressed reductase genes were exclusively from the genus Halomonas, which are related with our taxonomic assignment analysis. This study improves our understanding of the response of bacterial communities to high exposure to chromate and offers an alternative to the restoration of environments severely contaminated with this powerful toxic agent.},
}

@article {pmid40790223,
year = {2025},
author = {Ren, Y and Zhang, P and Yu, H and Li, S and Jiang, H},
title = {Metagenome-based characterization of the gut virome in patients with schizophrenia.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {895},
pmid = {40790223},
issn = {1479-5876},
support = {82170755//National Natural Science Foundation of China/ ; LHYYKYQD20240307//Scientif Research Foudation of People's Hospital of Longhua of Shenzhen/ ; },
mesh = {Humans ; *Schizophrenia/virology/microbiology ; *Virome/genetics ; *Gastrointestinal Microbiome/genetics ; Male ; *Metagenome/genetics ; Female ; Adult ; Feces/virology/microbiology ; Middle Aged ; Case-Control Studies ; },
abstract = {BACKGROUND: Schizophrenia (SCZ) is a multifactorial psychiatric disorder increasingly linked to gut microbial dysbiosis. While bacterial alterations have been widely studied, the role of the gut virome in SCZ remains largely unexplored. This study aimed to characterize the gut virome in SCZ and identify potential viral biomarkers associated with the disease.

METHODS: We analyzed fecal metagenomic data from 171 individuals (90 SCZ patients and 81 controls) using the Chinese Gut Virus Catalog (cnGVC). We assessed gut virome diversity, identified SCZ-associated vOTUs, explored virus-bacteria correlations, and evaluated diagnostic potential using random forest models. In addition, we examined follow-up samples from SCZ patients to assess the impact of antipsychotic treatment on the gut virome.

RESULTS: We identified 171 vOTUs that differed significantly between SCZ patients and controls, with 124 enriched in SCZ-mainly from Siphoviridae and Flandersviridae. Correlation analysis revealed altered virus-bacteria interactions in SCZ, including disease-specific associations with Akkermansia and Clostridia. A random forest classifier based on virome features achieved an AUC of 93.2%, outperforming the bacterial model. External validation using ASD and PD cohorts yielded lower AUCs (61.2-67.0%), suggesting disease specificity. In follow-up samples collected after three months of treatment, we observed partial changes in alpha diversity, while beta diversity remained stable, indicating that antipsychotic therapy may alter specific viral taxa without broadly reshaping the overall gut virome structure.

CONCLUSIONS: This study provides evidence of distinct gut virome alterations in SCZ and identifies specific viral markers with strong diagnostic potential. These findings highlight the underappreciated role of the gut virome in psychiatric disorders and support its utility as a non-invasive biomarker for SCZ diagnosis and future therapeutic development.},
}

Humans
*Schizophrenia/virology/microbiology
*Virome/genetics
*Gastrointestinal Microbiome/genetics
Male
*Metagenome/genetics
Female
Adult
Feces/virology/microbiology
Middle Aged
Case-Control Studies

@article {pmid40790136,
year = {2025},
author = {Zhang, T and Yu, J and Zhao, Z and Yang, C and Chen, X and Yao, L},
title = {Fermentation quality improvement of cigar wrapper inoculated with exogenous strain Staphylococcus capitis S1.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {29396},
pmid = {40790136},
issn = {2045-2322},
support = {110202201040(XJ-11)//China Tobacco Corporation/ ; 110202201040(XJ-11)//China Tobacco Corporation/ ; 110202201040(XJ-11)//China Tobacco Corporation/ ; },
mesh = {*Fermentation ; *Staphylococcus/metabolism/genetics ; Volatile Organic Compounds/analysis ; Gas Chromatography-Mass Spectrometry ; Odorants/analysis ; Wine/microbiology ; Food Microbiology ; },
abstract = {The cigar wrapper leaves (CWLs), as a symbol of the intrinsic quality and appearance of cigars, reflects the overall quality of the cigar. The Shaoxing-flavored T3 Jiuqu used in Shaoxing wine production contains a large number of high-quality microorganisms, such as molds and yeasts, which play a significant role in enhancing flavor and quality. Among these microorganisms, several positively promote the fermentation of CWLs. A dominant strain, S1, was isolated and identified from the T3 Jiuqu and inoculated into the fermentation of CWLs. Gas Chromatography-Mass Spectrometry (GC-MS) was employed to analyze the volatile aroma components in the CWLs. The results showed that the contents of substances such as Phenethyl alcohol, Dihydroactinidiolide, Sclareol, and Farnesyl acetone were significantly increased compared to pre-fermentation (NF) and the natural fermentation with only water (WF) group. Specifically, Phenethyl alcohol content increased by 261.63% compared to WF group during the same turning-over period, while Farnesyl acetone content increased by 144.99%. The proportions of sugars and nicotine also increased significantly. Metagenomic analysis of the microbial samples on the surface of CWLs revealed that inoculating S1 significantly improved and altered microbial community structure. At the phylum level, the proportion of Pseudomonadota increased dramatically to 17%, while the proportion of Uroviricotasharply decreased sharply from 9% to 0. At the genus level, the previously dominant Staphylococcus genus was replaced by a balanced coexistence of Pantoea, Enterobacter, Cronobacter, and Aspergillus. This balanced microbial distribution significantly improved the quality of the CWLs.},
}

*Fermentation
*Staphylococcus/metabolism/genetics
Volatile Organic Compounds/analysis
Gas Chromatography-Mass Spectrometry
Odorants/analysis
Wine/microbiology
Food Microbiology

@article {pmid40790086,
year = {2025},
author = {Wu, L and Lian, W and Bai, R and Chen, H and Wu, J and Li, H and Zhao, L},
title = {METTL3 facilitates colorectal cancer growth through altering the abundance of intestinal Akkermansia muciniphila.},
journal = {Cancer gene therapy},
volume = {},
number = {},
pages = {},
pmid = {40790086},
issn = {1476-5500},
support = {82203607//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2022M721540//China Postdoctoral Science Foundation/ ; 2021A1515111186//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; 2024A04J6605//Guangzhou Municipal Science and Technology Project/ ; },
abstract = {Colorectal cancer (CRC) is a prevalent malignant tumor that poses a significant threat to human health; however, the precise mechanism underlying its onset remains elusive. In this study, we utilized metagenomic sequencing to reveal the dysregulation of intestinal microbiota caused by CRC. Single-cell sequencing data showed elevated mRNA expression of methyltransferase-like protein 3 (METTL3) in CRC, which was correlated with the abundance of intestinal microbiota. Furthermore, we found that METTL3 promotion of CRC progression is microbiota-dependent. Using induced METTL3[fl/fl] Vil1-cre[+/-] mice, we identified the microbiota regulated by METTL3 in CRC. Our research indicates that METTL3 leads to high expression of HIF1α, which promotes the expression of lipocalin 2 (LCN2) in CRC cells, inhibiting the abundance of Akkermansia muciniphila, thereby promoting CRC progression.},
}

@article {pmid40790024,
year = {2025},
author = {Kiguchi, Y and Hamamoto, N and Kashima, Y and Runtuwene, LR and Ishizaka, A and Kuze, Y and Enokida, T and Tanaka, N and Tahara, M and Kageyama, SI and Fujisawa, T and Yamashita, R and Kanai, A and Tuda, JSB and Mizutani, T and Suzuki, Y},
title = {Giant extrachromosomal element "Inocle" potentially expands the adaptive capacity of the human oral microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7397},
pmid = {40790024},
issn = {2041-1723},
support = {22fk0108538s0201//Japan Agency for Medical Research and Development (AMED)/ ; },
mesh = {Humans ; Saliva/microbiology ; *Microbiota/genetics ; Metagenomics/methods ; *Mouth/microbiology ; Female ; Male ; Colorectal Neoplasms/microbiology ; Head and Neck Neoplasms/microbiology ; Metagenome ; Adult ; DNA, Bacterial/genetics ; *Bacteria/genetics ; Middle Aged ; Streptococcus/genetics ; },
abstract = {Survival strategy of bacteria is expanded by extrachromosomal elements (ECEs). However, their genetic diversity and functional roles for adaptability are largely unknown. Here, we discover a novel family of intracellular ECEs using 56 saliva samples by developing an efficient microbial DNA extraction method coupled with long-read metagenomics assembly. Even though this ECE family was not hitherto identified, our global prevalence analysis using 476 salivary metagenomic datasets elucidates that these ECEs reside in 74% of the population. These ECEs, which we named, "Inocles", are giant plasmid-like circular genomic elements of 395 kb in length, including Streptococcus as a host bacterium. Inocles encode a series of genes that contribute to intracellular stress tolerance, such as oxidative stress and DNA damage, and cell wall biosynthesis and modification involved in the interactions with oral epithelial cells. Moreover, Inocles exhibit significant positive correlations with immune cells and proteins responding to microbial infection in peripheral blood. Intriguingly, we examine and find their marked reductions among 68 patients of head and neck cancers and colorectal cancers, suggesting its potential usage for a novel biomarker of gastrointestinal cancers. Our results suggest that Inocles potentially boost the adaptive capacity of host bacteria against various stressors in the oral environment.},
}

Humans
Saliva/microbiology
*Microbiota/genetics
Metagenomics/methods
*Mouth/microbiology
Female
Male
Colorectal Neoplasms/microbiology
Head and Neck Neoplasms/microbiology
Metagenome
Adult
DNA, Bacterial/genetics
*Bacteria/genetics
Middle Aged
Streptococcus/genetics

@article {pmid40790018,
year = {2025},
author = {Wang, K and Wang, J and Yang, X and Sun, W and Sheng, G and Wang, Y},
title = {Structural insights into Type II-D Cas9 and its robust cleavage activity.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7396},
pmid = {40790018},
issn = {2041-1723},
support = {Z231100007223004//Beijing Municipal Science and Technology Commission/ ; 32330055, 31930065, 22121003, 32071198, 32071444//National Natural Science Foundation of China (National Science Foundation of China)/ ; 5232022//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; XDB0570000, XDB37010202//Chinese Academy of Sciences (CAS)/ ; },
mesh = {*CRISPR-Associated Protein 9/metabolism/chemistry/genetics/ultrastructure ; Cryoelectron Microscopy ; DNA/metabolism/chemistry/genetics ; RNA, Guide, CRISPR-Cas Systems/metabolism/genetics/chemistry ; DNA Cleavage ; CRISPR-Cas Systems ; Gene Editing ; *Bacterial Proteins/metabolism/genetics/chemistry ; Catalytic Domain ; },
abstract = {Type II-D Cas9 proteins (Cas9d) are more compact than typical Type II-A/B/C Cas9s. Here, we demonstrate that NsCas9d from Nitrospirae bacterium RBG_13_39_12 derived from a metagenomic assembly exhibits robust dsDNA cleavage activity comparable to SpCas9 in vitro. Unlike typical Cas9 enzymes that generate blunt ends, NsCas9d produces 3-nucleotide staggered overhangs. Our high-resolution cryo-EM structure of the NsCas9d-sgRNA-dsDNA complex in its catalytic state reveals the target and non-target DNA strands positioned within the HNH and RuvC catalytic pockets, respectively. NsCas9d recognizes the 5'-NRG-3' protospacer adjacent motif (PAM), with 5'-NGG-3' showing the highest cleavage efficiency. Its sgRNA structure, resembling the 5' end of IscB ωRNA, along with structural features shared with other Cas9 variants, suggests that Cas9d are hypothesized to resemble evolutionary intermediates between other Cas9 sub-types and IscB. These findings deepen our understanding of Cas9 evolution and mechanisms, highlighting NsCas9d as a promising genome-editing tool due to its compact size, DNA cleavage pattern, and efficient PAM recognition.},
}

*CRISPR-Associated Protein 9/metabolism/chemistry/genetics/ultrastructure
Cryoelectron Microscopy
DNA/metabolism/chemistry/genetics
RNA, Guide, CRISPR-Cas Systems/metabolism/genetics/chemistry
DNA Cleavage
CRISPR-Cas Systems
Gene Editing
*Bacterial Proteins/metabolism/genetics/chemistry
Catalytic Domain

@article {pmid40789383,
year = {2025},
author = {Rout, AK and Rout, SS and Panda, A and Tripathy, PS and Kumar, N and Parida, SN and Dey, S and Dash, SS and Behera, BK and Pandey, PK},
title = {Potential applications and future prospects of metagenomics in aquatic ecosystems.},
journal = {Gene},
volume = {},
number = {},
pages = {149720},
doi = {10.1016/j.gene.2025.149720},
pmid = {40789383},
issn = {1879-0038},
abstract = {Metagenomics plays a vital role in advancing our understanding of microbial communities and their functional contributions in various ecosystems. By directly sequencing DNA from environmental samples-such as soil, water, air, and the human body-metagenomics enables the identification of previously uncultivable or unknown microorganisms, offering key insights into their ecological functions. Beyond taxonomic classification, metagenomic analyses reveal functional genes and metabolic pathways, facilitating the discovery of enzymes, bioactive compounds, and other molecules with applications in agriculture, biotechnology, and medicine. This review discusses the wide-ranging applications of metagenomics in environmental monitoring, including sample collection, high-throughput sequencing, and data analysis and interpretation. We review different sequencing platforms, library preparation methods, and advanced bioinformatics tools used for quality control, sequence assembly, and both taxonomic and functional annotation. Special focus is given to the role of metagenomics in evaluating microbial responses to environmental stress, contaminant degradation, disease emergence, and climate change. The use of microbial bioindicators for aquatic ecosystem monitoring and toxicological assessments is also examined. A comprehensive evaluation of current bioinformatics pipelines is provided for their effectiveness in processing large-scale metagenomic datasets. As global environmental pressures intensify, integrative meta-omics approaches, including whole-genome metagenomics, will be crucial for understanding the complexity, functions, and dynamics of microbiomes in both natural and affected ecosystems.},
}

@article {pmid40789238,
year = {2025},
author = {Geng, B and Zhu, C and Cui, Z and Chen, Y and Zhang, Q and Shi, H and Min, L and Zhu, S and Zhang, W and Zhao, M and Zhang, S and Xu, J},
title = {Maslinic acid alleviates ulcerative colitis by inhibiting the colitis-aggravating pathogen Clostridium perfringens and modulating gut microbiota.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {146},
number = {},
pages = {157144},
doi = {10.1016/j.phymed.2025.157144},
pmid = {40789238},
issn = {1618-095X},
abstract = {BACKGROUND: Ulcerative colitis (UC), a prevalent form of inflammatory bowel disease, continues to pose therapeutic challenges due to the limitations of conventional drugs and their inability to prevent relapse. Emerging evidence highlights the crucial role of gut microbiota dysbiosis in UC pathogenesis, yet our understanding of specific harmful microbes and their contributions to disease development remains limited.

PURPOSE: This study aims to (1) investigate the therapeutic potential of maslinic acid (MA), a food-derived natural compound, in colitis mice models; (2) elucidate the previously underestimated pathogenic role of Clostridium perfringens in UC development; and (3) reveal the molecular mechanisms underlying both C. perfringens pathogenesis and MA-mediated protection.

METHODS: We examined the therapeutic effect of MA using DSS-induced colitis model and performing metagenomic sequencing; elucidated the pathogenic role of C. perfringens using GMrepo database, clinical stool samples, and in vivo infection models. Additionally, we revealed its mechanism using inhibitors and markers of various cell death and inflammation pathways. The bactericidal effect of MA on C. perfringens was studied through in vitro experiments and two in vivo colitis models.

RESULTS: MA alleviates DSS-induced colitis and restores gut microbiota. C. perfringens is enriched following DSS administration while significantly decreased after treatment with MA. C. perfringens contributes to the development of colitis and induces ZBP1-mediated PANoptosis in intestinal epithelial cells, while stimulates inflammation through NOD2 activation. MA has direct bactericidal activity against C. perfringens through ROS induction. It can almost completely rescue the exacerbation of colitis-related pathological and physiological phenotypes caused by C. perfringens in two mice colitis models.

CONCLUSIONS: Our study reveals that MA effectively mitigates DSS-induced colitis by inhibiting the colitis-aggravating pathogen C. perfringens and modulating gut microbiota. Furthermore, it elucidates the previously underestimated role and mechanism of C. perfringens in the development of UC. It also highlights the therapeutic potential of MA in preventing and treating UC, particularly in patients who are C. perfringens positive.},
}

@article {pmid40788839,
year = {2025},
author = {Spottiswoode, N and Neyton, LP and Mick, E and Kalantar, KL and Hao, S and Lydon, EC and Narendra, R and Serpa, PH and Caldera, S and Gomez, A and Hendrickson, C and Kangelaris, K and Liu, KD and Sinha, P and DeRisi, JL and Matthay, MA and Calfee, CS and Langelier, CR},
title = {Host-Microbe Multiomic Profiling Predicts Mortality in Sepsis.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1164/rccm.202410-1996OC},
pmid = {40788839},
issn = {1535-4970},
abstract = {RATIONALE: Sepsis is a leading cause of mortality and involves a dysregulated host response to infection. Host and microbe have historically been considered independently in studies of sepsis, limiting our understanding of key relationships driving mortality.

OBJECTIVES: We sought to identify host and microbial factors associated with sepsis mortality and build prognostic classifiers.

METHODS: We studied 321 critically ill adults and adjudicated sepsis status. From whole blood collected within 24 hours of admission we performed transcriptional profiling, and from plasma we carried out proteomics and metagenomics. We evaluated associations between in-hospital mortality and gene expression, protein levels and microbial metagenomic data, and built support vector machine-based prognostic classifiers.

MEASUREMENTS AND MAIN RESULTS: In patients with sepsis, mortality associated with increased expression of genes related to neutrophil degranulation, lower expression of genes related to T cell signaling, and higher interleukin-8. Mortality also associated with higher microbial mass and greater bacterial relative dominance. Similar findings were observed in a broader group that also included patients with culture-negative sepsis or indeterminate sepsis status. An integrated host-microbe metagenomic classifier predicted sepsis mortality with an area under the curve (AUC) of 0.79, and a host transcriptomic classifier performed comparably with an AUC of 0.75. Both performed better (p<0.05 by paired DeLong tests) that the APACHE-III score (AUC of 0.69).

CONCLUSIONS: Taken together, our findings provide a conceptual advance in the understanding of host and microbial factors associated with mortality in critical illness and demonstrate a new approach to mortality prediction in sepsis.},
}

@article {pmid40788706,
year = {2025},
author = {Israel, A and Israel, S and Weizman, A and Ashkenazi, S and Vinker, S and Magen, E and Merzon, E},
title = {Atovaquone-proguanil and reduced digestive cancer risk: a Toxoplasma gondii connection.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2545412},
doi = {10.1080/19490976.2025.2545412},
pmid = {40788706},
issn = {1949-0984},
mesh = {Humans ; Middle Aged ; *Atovaquone/therapeutic use/pharmacology ; *Toxoplasma/isolation & purification/drug effects/genetics ; Adult ; Male ; Aged ; Female ; Retrospective Studies ; *Proguanil/therapeutic use/pharmacology ; Drug Combinations ; Gastrointestinal Microbiome/drug effects ; Feces/parasitology/microbiology ; *Colorectal Neoplasms/epidemiology/prevention & control/parasitology ; Toxoplasmosis ; Incidence ; Metagenomics ; },
abstract = {Emerging evidence suggests microbial pathogens contribute to digestive cancer risk. Atovaquone - proguanil (A-P), an antimalarial with antiparasitic activity, has been associated with a reduced risk of colorectal cancer (CRC). We conducted a retrospective cohort study using the TriNetX US Collaborative Network, including over 100,000 individuals aged 40-69 years who received A-P, matched 1:1 to controls who received other medications. Incident digestive cancers were analyzed using Cox proportional hazards models. Additionally, we performed a metagenomic analysis of 1,044 fecal samples from 156 individuals to assess the abundance of Toxoplasma gondii in CRC-associated microbiota. A-P use was associated with a significant reduction in digestive cancer incidence across all age groups: hazard ratios (HRs) ranged from 0.49 to 0.53 (all p < 0.001). Protective associations extended to pancreatic cancer (HR range, 0.50-0.72). In metagenomic analysis, T. gondii was the most discriminatory microbial species for CRC (p = 1.8 × 10[-16]), detected above threshold in 22.6% of CRC samples versus 1.6% of controls (odds ratio 18.2, 95% CI, 8.2-47.6, p = 2.3 × 10[-22]). These findings suggest T. gondii may be an overlooked microbial risk factor for digestive cancers, and that A-P may offer chemopreventive effects through antiparasitic activity. Prospective studies are needed to evaluate its preventive potential.},
}

Humans
Middle Aged
*Atovaquone/therapeutic use/pharmacology
*Toxoplasma/isolation & purification/drug effects/genetics
Adult
Male
Aged
Female
Retrospective Studies
*Proguanil/therapeutic use/pharmacology
Drug Combinations
Gastrointestinal Microbiome/drug effects
Feces/parasitology/microbiology
*Colorectal Neoplasms/epidemiology/prevention & control/parasitology
Toxoplasmosis
Incidence
Metagenomics

@article {pmid40788461,
year = {2025},
author = {Torres, MC and Breyer, GM and da Silva, MERJ and de Itapema Cardoso, MR and Siqueira, FM},
title = {Metagenomic approaches for the quantification of antibiotic resistance genes in swine wastewater treatment system: a systematic review.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {816},
pmid = {40788461},
issn = {1573-4978},
support = {408693/2022-3//Conselho Nacional de Desenvolvimento Científico e Tecnológico,Brazil/ ; },
mesh = {Swine ; *Wastewater/microbiology ; Animals ; *Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; Metagenome/genetics ; Bacteria/genetics/drug effects ; *Drug Resistance, Bacterial/genetics ; Water Purification/methods ; Computational Biology/methods ; Anti-Bacterial Agents/pharmacology ; },
abstract = {This systematic review aims to identify the metagenomic methodological approaches employed for the detection of antimicrobial resistance genes (ARGs) in swine wastewater treatment systems. The search terms used were metagenome AND bacteria AND ("antimicrobial resistance gene" OR resistome OR ARG) AND wastewater AND (swine OR pig), and the search was conducted across the following electronic databases: PubMed, Scopus, ScienceDirect, Web of Science, Embase, and Cochrane Library. The search was limited to studies published between 2020 and 2024. Of the 220 studies retrieved, eight met the eligibility criteria for full-text analysis. The number of publications in this research area has increased in recent years, with China contributing the highest number of studies. ARGs are typically identified using bioinformatics pipelines that include steps such as quality trimming, assembly, metagenome-assembled genome (MAG) reconstruction, open reading frame (ORF) prediction, and ARG annotation. However, comparing ARGs quantification across studies remains challenging due to methodological differences and variability in quantification approaches. Therefore, this systematic review highlights the need for methodological standardization to facilitate comparison and enhance our understanding of antimicrobial resistance in swine wastewater treatment systems through metagenomic approaches.},
}

Swine
*Wastewater/microbiology
Animals
*Metagenomics/methods
*Drug Resistance, Microbial/genetics
Metagenome/genetics
Bacteria/genetics/drug effects
*Drug Resistance, Bacterial/genetics
Water Purification/methods
Computational Biology/methods
Anti-Bacterial Agents/pharmacology

@article {pmid40788149,
year = {2025},
author = {Cui, Y and Yang, Y and Li, X and Wang, J and Jin, H and Liao, H and Wang, X and Shi, K and Huang, S and Zhou, T and Löffler, FE and Yan, J},
title = {Complete genome sequence of Dehalococcoides mccartyi strain NK, an acid-tolerant organohalide-respiring bacterium.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0063325},
doi = {10.1128/mra.00633-25},
pmid = {40788149},
issn = {2576-098X},
abstract = {Dehalococcoides mccartyi strain NK reductively dechlorinates tetrachloroethene to ethene at pH 5.5. The metagenome-assembled strain NK genome is 1.51 Mb in size with a G + C content of 48.6%.},
}

@article {pmid40787980,
year = {2025},
author = {Ormaasen, I and Kjos, M and Simpson, MR and Øien, T and Snipen, L and Rudi, K},
title = {Tracing of streptococcal strains from infant stools across human body sites links site-specific prevalence to adhesins.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0019625},
doi = {10.1128/aem.00196-25},
pmid = {40787980},
issn = {1098-5336},
abstract = {Streptococci colonize various human body sites, both as commensals and as pathogens. They are early gut colonizers, but we lack strain-level information about the origin and persistence of streptococci in the non-diseased gut. To gain a greater insight into commensal streptococci in the infant gut and their presence in other body habitats, we analyzed samples from mother-infant pairs collected from multiple body sites (stool, oral cavity, vagina, breast milk). We performed whole-metagenome sequencing and isolated streptococci from 100 infant stool samples (collected at 10 days of age). To trace the streptococci at the strain level, we designed selective quantitative PCR (qPCR) primers for seven streptococcal strains, which were then used to screen the corresponding samples from the other body sites of the infants and their mothers. We found that two of the strains investigated, one Streptococcus parasanguinis strain and one Streptococcus vestibularis strain, were highly prevalent in stool samples obtained from infants and their mothers. Interestingly, the screening revealed that another S. parasanguinis strain, closely related to the stool-prevalent strain, displayed a completely different prevalence pattern, being most prevalent in vaginal swabs, breast milk, and oral swabs. A genotypic comparison of these two S. parasanguinis strains revealed major differences in genes encoding adhesins, suggesting that host surface attachment could be a key factor for the observed differences in body site specificity. Together, our extensive tracing of streptococci across the body sites of 100 infants and their mothers provides strain-level insight into patterns of distribution and identifies streptococcal strains prevalent in stool.IMPORTANCEStreptococci thrive on mucosal surfaces and colonize multiple human body sites, including the gut. To understand how streptococci colonize and spread between body site habitats, strain-level information about their prevalence is required; however, such knowledge is currently lacking. In this study, we isolate streptococci and perform metagenome sequencing and quantitative PCR (qPCR) on samples from a large cohort of mother-infant pairs to trace streptococcal strains in different habitats. We demonstrate how different strains prefer specific habitats. For example, we show that two closely related strains, both isolated from stool, are distributed differently across the human body, with one of them prevalent in stool samples and the other more prevalent in other samples. These results emphasize the necessity of strain-level analysis for the identification of true colonizers of a habitat.},
}

@article {pmid40787979,
year = {2025},
author = {Liu, Y and Zhao, X and Feng, X and Zhu, W and Feng, S and Ren, M and Tu, Y and Niu, G and Zhu, Y},
title = {Diversity and evolutionary analysis of viruses carried by mosquitoes in Shandong, China.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0101825},
doi = {10.1128/spectrum.01018-25},
pmid = {40787979},
issn = {2165-0497},
abstract = {UNLABELLED: Arboviruses represent a growing threat to global public health, as climate change is exacerbating the spread of these vectors and thereby increasing the transmission potential of arboviruses. As primary vectors, mosquitoes harbor remarkably diverse virus populations, broadly classified into mosquito-borne viruses and mosquito-specific viruses. Although metagenomic sequencing has revolutionized viral discovery, geographical variations in mosquito viromes remain poorly characterized. In this study, we conducted comprehensive viral surveillance on 5,051 mosquitoes representing six medically important species (grouped into 14 taxonomic units) collected from Shandong, China, in 2021. Using next-generation sequencing, we generated 3.7 billion clean reads and identified 10 distinct virus species spanning eight virus families. Phylogenetic analyses revealed substantial genomic diversity and complex evolutionary relationships, including two completely novel virus species and several incompletely characterized known viruses. Notably, Culex quinquefasciatus mosquitoes exhibited significantly greater viral diversity than other species, although we observed considerable overlap in viral communities across mosquito taxa, suggesting non-host-specific viral maintenance. The presence of two novel viruses in field populations was confirmed by RT-qPCR screening, wherein minimum infection rates of 0.16% and 0.38% were established. Our findings substantially expand the known diversity of mosquito-associated viruses in East Asia and provide critical baseline data for arbovirus surveillance programs. This work highlights the value of systematic virome characterization for predicting emerging arboviral threats and understanding virus-mosquito ecology in changing environments.

IMPORTANCE: Ten viruses, including two novel ones, were found in a study performed on mosquitoes in Shandong, China. It shows viral diversity and coexistence in different species, highlighting host impact on viral communities. The new viruses are prevalent locally, with infection rates of 0.38% and 0.16%. This work advances viral ecology understanding and has public health significance. This study sheds light on the circulation of the identified viruses in Shandong.},
}