@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.},
}

@article {pmid40787905,
year = {2025},
author = {Zhou, H and Zhang, L},
title = {Intracranial infection caused by Streptococcus intermedius and torque teno virus: A case report.},
journal = {The Journal of international medical research},
volume = {53},
number = {8},
pages = {3000605251363093},
doi = {10.1177/03000605251363093},
pmid = {40787905},
issn = {1473-2300},
mesh = {Humans ; Male ; *Torque teno virus/isolation & purification/pathogenicity/genetics ; Adult ; *Coinfection/microbiology/virology/diagnosis ; *Streptococcal Infections/microbiology/diagnosis ; *Streptococcus intermedius/isolation & purification/pathogenicity/genetics ; *DNA Virus Infections/diagnosis/virology ; Fatal Outcome ; },
abstract = {Infectious diseases of the central nervous system are commonly characterized by delayed diagnosis due to the diversity of pathogens, subtle clinical symptoms, and nonspecific early imaging findings. These diseases are associated with high morbidity and mortality rates. This report presents a rare case of intracranial mixed infection caused by co-infection with Streptococcus intermedius and torque teno virus. This report involves a retrospective analysis of the clinical features, laboratory investigations, and treatment outcomes of intracranial infection, along with diagnostic and therapeutic strategies for such rare mixed infections. The results demonstrated that cerebrospinal fluid metagenomic sequencing plays a crucial role in the microbiological diagnosis of intracranial mixed infection. This report describes the case of a man in his late 30s in whom Streptococcus intermedius and torque teno virus were simultaneously detected in the cerebrospinal fluid. The infection exhibited rapid progression and high aggressiveness, significantly increasing the risk of mortality. This study emphasizes the invasive clinical course of this infection. Despite active and intensive treatment, the patient ultimately succumbed to the illness. It remains unclear whether torque teno virus infection plays a direct role in the pathogenesis or contributes to the severity of the intracranial mixed infection. This case highlights the importance of multidisciplinary collaboration in the diagnosis and treatment of complex intracranial infections, providing clinicians with a novel approach for the differential diagnosis of mixed infections and increasing the clinical awareness and understanding of such rare mixed infections involving the central nervous system.},
}

Humans
Male
*Torque teno virus/isolation & purification/pathogenicity/genetics
Adult
*Coinfection/microbiology/virology/diagnosis
*Streptococcal Infections/microbiology/diagnosis
*Streptococcus intermedius/isolation & purification/pathogenicity/genetics
*DNA Virus Infections/diagnosis/virology
Fatal Outcome

@article {pmid40787162,
year = {2025},
author = {Li, C and Xiao, NS and Xiong, T and Li, S and Ke, BY and Lin, Y},
title = {Suppurative Spondylitis Misdiagnosed as Endplate Inflammation: A Rare Case Report.},
journal = {Clinical case reports},
volume = {13},
number = {8},
pages = {e70768},
pmid = {40787162},
issn = {2050-0904},
abstract = {Spinal infectious diseases are difficult to diagnose and treat; we reported a case of pyogenic spondylitis misdiagnosed as terminal discitis and successfully treated. The application of metagenomic next-generation sequencing technology holds promise in greatly improving diagnostic efficiency.},
}

@article {pmid40786849,
year = {2025},
author = {Hong, X and Zeng, L and Li, Q and Yang, T and Zhou, J and Li, H and Mo, Y and Zhuo, S and Ma, J and Cai, J and Xie, C},
title = {Infection of Enterocytozoon bieneusi in a Patient with Long-Term Immunosuppression after Liver Transplantation: A Case Report and Literature Review.},
journal = {Case reports in gastroenterology},
volume = {19},
number = {1},
pages = {556-567},
pmid = {40786849},
issn = {1662-0631},
abstract = {INTRODUCTION: Enterocytozoon bieneusi (E.b) can cause opportunistic infections in immunocompromised patients, especially HIV/AIDS recipients, but currently, there are still few case reports of E.b infections in solid organ transplant recipients. As E.b cannot be diagnosed by routine examination and culture, it is often overlooked as a possible cause of chronic diarrhea in transplant recipients. With no known established guidelines for E.b, the effective and available treatment options are limited.

CASE PRESENTATION: In this article, we reported a case of persistent chronic diarrhea and renal failure due to E.b infection after liver transplantation, which was definitively diagnosed using metagenomic next-generation sequencing (mNGS). Short course of albendazole was applied to the patient, resulting in rapid resolution of clinical symptoms and recovery of renal function.

CONCLUSION: The case demonstrates the advantages of mNGS for the diagnosis of rare pathogenic bacterial infections, and together with the previous case reports, further suggests albendazole may serve as an effective therapy for the treatment of E.b for some patient. This article reviews relevant literature and provides an updated and more comprehensive reference for the selection of E.b treatment drugs. To be note, the overview showed there may be individualized differences in the efficacy of albendazole, which needs more study.},
}

@article {pmid40786823,
year = {2025},
author = {Delikanli-Kiyak, B and Yilmaz, I and Guldas, M},
title = {Can Metagenomic Analyses Be Used Effectively in Safe Food Production?.},
journal = {Food science & nutrition},
volume = {13},
number = {8},
pages = {e70772},
pmid = {40786823},
issn = {2048-7177},
abstract = {This review aims to bring together current research on the importance, recent applications, and possible impacts of metagenomic analysis and emphasize that metagenomic analyses, which provide direct analysis of the genomes of the food itself and all the microbiota in its environment, are revolutionary approach for effective management of food safety requirements. The increasing health problems in recent years and the related developments regarding nutritional awareness have led people to seek safe food consumption. In order to ensure the quality and safety of food products and protect the health consumers worldwide, necessary preventive measure should be taken by conducting innovative control methods. Numerous microbial hazards threaten food safety worldwide. In this respect, rapid and accurate detection of pathogens is critical. Although traditional culture-based methods continue to be widely used, they often fail to detect organisms that are viable but cannot be cultured. This limitation has led to the increasing adoption of metagenomic analyses, which allow direct genome-level detection and provide a more comprehensive view of microbial communities in food systems. In this context, metagenomic analyses within new-generation technology has been inspired, as it can be a powerful tool to ensure food safety. In this study, for this purpose, the keywords 'metagenomics and food' and the studies on metagenomics published in English, peer-reviewed journals, and available in the Web of Science and Scopus databases were investigated. The years 2020-2024 were taken as a basis for the studies with the keywords identified and studies on antibiotic resistance and unrelated foods were excluded from the review's scope. This review brings together current research on the significance of metagenomics analysis in food safety, its latest applications, and possible effects. The study is a reference source for potential studies to be carried out in this context.},
}

@article {pmid40785991,
year = {2025},
author = {Takeuchi, H and Matsuishi, TF and Hayakawa, T},
title = {Metagenomic Insights Into the Role of Gut Microbes in the Defensive Ink "Tsunabi" of Physeteroid Whales.},
journal = {Ecology and evolution},
volume = {15},
number = {8},
pages = {e71910},
pmid = {40785991},
issn = {2045-7758},
abstract = {Whales of the superfamily Physeteroidea, which includes the genera Physeter and Kogia, exhibit a unique visual defense mechanism involving the release of dark reddish-brown feces (locally called "tsunabi-ink" in Japan) into the water to obscure themselves from predators and other threats. However, the mechanism underlying pigmentation remains unknown. Because physeteroids possess an enlarged distal colon that retains fecal material, a possible explanation is that symbiont microbial metabolism contributes to the feces pigmentation. To investigate this, we provided a shotgun metagenomic catalog of gut microbiomes from the intestinal tracts of eight cetacean species, including two physeteroids: a sperm whale (Physeter macrocephalus) and a pygmy sperm whale (Kogia breviceps). The colonic microbiome of physeteroids exhibited relatively high abundances of tryptophan metabolism genes, particularly indolepyruvate ferredoxin oxidoreductases (iorA and iorB), suggesting that physeteroids accumulate indole-3-pyruvate-derived pigments in their colons. Furthermore, bacterial members of the phyla Bacillota and Bacteroidota were identified in the physeteroid colon as primary taxa conferring heavy-metal resistance, which may be related to the primary predation of physeteroids on cephalopods, which bioaccumulate high levels of heavy metals. Prolonged fecal retention can expose gut microbes to chronic heavy-metal stress and colonize them as heavy metal-tolerant microbial communities, some of which may produce pigments to reduce their toxicity. Thus, we propose that tsunabi-ink is a metabolic byproduct of shifts in the gut microbial community, influenced by the host's digestive physiology and foraging behavior through sustained ecological interactions with gut symbionts. Moreover, we believe that further empirical investigation would validate this hypothesis.},
}

@article {pmid40785790,
year = {2025},
author = {Avila-Arias, H and Scharf, ME and Turco, RF and Jiménez, DJ and Simard, A and Richmond, DS},
title = {Metagenomic analysis reveals methanogenic and other archaeal genes in the digestive tract of invasive Japanese beetle larvae and associated soil.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1609893},
pmid = {40785790},
issn = {1664-302X},
abstract = {The linkage between methane emissions and the metabolic activity of archaeal species is broadly established. However, the structural and functional dynamics of this phenomenon within the scarab larval gut and associated host soil environment have not been investigated. In this study, we used shotgun metagenome sequencing to explore the archaeal communities associated with the digestive tract of third instar Japanese beetle (Popillia japonica Newman; Coleoptera: Scarabaeidae) (JB) larvae and its host soil. Our findings showed that both the JB gut compartment (midgut vs. hindgut) and experimental conditions (field vs. manipulative laboratory studies) significantly affect the composition of archaeal taxa. Moreover, gut compartment affected the functional profile. Results revealed an increase of methane metabolism-related taxa and gene sequences in the larval hindgut, supporting the hypothesis that methanogenesis is primarily maintained in that gut compartment. Methane production associated with the JB larval gut takes place primarily via CO2 reduction (~30%) and methanol methanation (4%) pathways. The presence of the same archaeal features in both soil and JB midgut suggests that the JB midgut archaeome may be environmentally sourced, with more tailored selection of the archaeome occurring in the JB hindgut. In turn, we found that JB larval infestation also increases the abundance of at least one methanogenic archaeon, Methanobrevibacter, in infested soil. Results underscore the potential impact of invasive root-feeding scarab larvae on the soil archaeome and highlight their potential contributions to climate change, especially in light of predicted global range expansion for this species.},
}

@article {pmid40785530,
year = {2025},
author = {Liang, J and He, J and Zhao, J and Yang, Y and Xu, W},
title = {Decline in the Relative Abundance of Antibiotic Resistance Genes in Long-Term Fertilized Soil and Its Driving Factors.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c03478},
pmid = {40785530},
issn = {1520-5118},
abstract = {The changes in antibiotic resistance genes (ARGs) in long-term fertilized soil remain controversial. We aimed to analyze the variation characteristics of ARGs in long-term fertilized soil using metagenomic sequencing. The relative abundance of ARGs did not increase significantly after 7 years of fertilization. However, a clear decline in the relative abundance of ARGs was observed compared to the data from the 4th year. Microbial adaptation strategies in response to changes in the ARG abundance were associated with shifts in microbiome composition and function. Among these, bacterial abundance was the primary driving factor. Additionally, total heavy metal content might serve as the most significant co-selective pressure influencing ARG number. We believe that increasing the selective pressure from heavy metals and antibiotics might result in the loss of certain microbial species and a decrease in ARG abundance. This study provides novel insights into the variations of soil resistance genes under long-term fertilization.},
}

@article {pmid40785091,
year = {2025},
author = {Kinsella, P and Thursky, K and Slavin, MA and Reynolds, GK},
title = {From guesswork to guidelines: advancing diagnostic stewardship in immunocompromised hosts.},
journal = {Expert review of anti-infective therapy},
volume = {},
number = {},
pages = {},
doi = {10.1080/14787210.2025.2545504},
pmid = {40785091},
issn = {1744-8336},
abstract = {INTRODUCTION: Diagnostic stewardship, the optimization of diagnostic testing to improve patient outcomes, is a rapidly evolving field; however, data relating to immunocompromised hosts are scarce.

AREAS COVERED: This review examines recent advances in diagnostic stewardship and explores best practice principles for key clinical scenarios in immunocompromised patients, including febrile neutropenia, central nervous system infections, invasive fungal infections, cytomegalovirus, and Clostridioides difficile.

EXPERT OPINION: Key challenges remain, including optimizing test utilization without compromising patient safety, interpreting advanced diagnostics in the context of immunosuppression, and demonstrating cost-effectiveness. A multidisciplinary approach incorporating both diagnostic and antimicrobial stewardship principles is essential to improve outcomes in this complex patient population. Future research should focus on prospective evaluation of diagnostic stewardship interventions and their impact on clinical and economic outcomes in immunocompromised hosts.},
}

@article {pmid40785047,
year = {2025},
author = {Shi, H and Wu, M and Wu, X and Liu, Z and Jiang, S and Li, G and Yang, Y and Fu, Y and Wang, Q and Zhang, G and Cheng, L},
title = {Multi-omics integration reveals functional signatures of gut microbiome in atherosclerosis.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2542384},
doi = {10.1080/19490976.2025.2542384},
pmid = {40785047},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Atherosclerosis/microbiology/genetics/metabolism ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Transcriptome ; Metabolomics ; Multiomics ; },
abstract = {Atherosclerosis (AS), a predominant contributor to global cardiovascular disease burden, exhibits complex interplay with gut microbiota dysbiosis. While the associations between microbial imbalance and AS pathogenesis are well-documented, the pathophysiological mechanisms governing microbe-host crosstalk remain incompletely characterized. Current research limitations stem from methodological heterogeneity across studies and the absence of consensus regarding disease-specific microbial signatures. In this study, we conducted an integrated multi-omics analysis to characterize the functional signatures of gut microbiome in AS. We collected all public AS-related 6 microbiome datasets and 8 peripheral blood host transcriptomic datasets from across the world, comprising 456 metagenomic samples and 111 16S rRNA gene sequencing samples for microbial profiling, alongside 118 RNA-Seq samples and 302 microarray samples. We systematically characterized AS microbial taxa and computationally inferred the metabolic potential for the gut microbiome using metabolomic-related data. Metabolite-host gene interactions were further predicted based on the synergistic effects between microbiome and host transcriptome in AS. Five "microbe-metabolite-host gene" tripartite associations related to AS were identified involving 5 microbial genera (Actinomyces, Bacteroides, Eisenbergiella, Gemella, and Veillonella), 2 metabolites (Ethanol and H2O2), and 2 host genes (FANCD2 and GPX2), and the reliability of these associations was validated. Five microbial genera demonstrated robust diagnostic potential as noninvasive biomarkers, with 5-fold cross-validation, study-to-study transfer validation, and leave-one-study-out (LOSO) validation confirming good diagnostic performance. Additionally, the specificity of the biomarkers was validated against hypertension, inflammatory bowel disease (IBD), diabetes, and obesity cohorts. Our study unveiled the functional characteristics of gut microbiota interacting with AS host genes and highlighted the potential of gut microbiota as both diagnostic biomarkers and therapeutic targets for AS. However, the findings should be interpreted considering the inherent heterogeneity of the integrated datasets and the preliminary diagnostic value of the biomarkers.},
}

*Gastrointestinal Microbiome/genetics
Humans
*Atherosclerosis/microbiology/genetics/metabolism
*Bacteria/classification/genetics/isolation & purification/metabolism
Dysbiosis/microbiology
RNA, Ribosomal, 16S/genetics
Metagenomics
Transcriptome
Metabolomics
Multiomics

@article {pmid40784938,
year = {2025},
author = {Winder, JC and Poulton, S and Wu, T and Mock, T and van Oosterhout, C},
title = {Environmental adaptations in metagenomes revealed by deep learning.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {252},
pmid = {40784938},
issn = {1741-7007},
support = {BB/T008717/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T008717/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T008717/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Deep Learning ; *Metagenome ; *Environment ; *Adaptation, Physiological/genetics ; },
abstract = {BACKGROUND: Deep learning has emerged as a powerful tool in the analysis of biological data, including the analysis of large metagenome data. However, its application remains limited due to high computational costs, model complexity, and difficulty extracting biological insights from these artificial neural networks (ANNs). In this study, we applied a transfer learning approach using the ESM-2 protein structure prediction model and our own smaller ANN to classify proteins containing the domain of unknown function 3494 (DUF3494) by their source environments. DUF3494 is found in a diverse group of putative ice-binding and substrate-binding proteins across a range of environments in prokaryotic and eukaryotic microorganisms. They present a compelling test case for exploring the balance between prediction accuracy and interpretability in sequence classification.

RESULTS: Our ANN analysed 50,669 DUF3494 sequences from publicly available metagenomes, and successfully classified a large proportion of sequences by source environment (polar marine, glacier ice, frozen sediment, rock, subsurface). We identified environment-specific features that appear to drive classification. Our best-performing ANN was able to classify between 75.9 and 97.8% of sequences correctly. To enhance biological interpretability of these predictions, we compared this model with a genetic algorithm (GA), which, although it had lower predictive ability, provided transparent classification rules and predictors. Further in silico mutagenesis of key residues uncovered a vertically aligned column of amino acids on the b-face of the protein which was important for environmental differentiation, suggesting that both methods captured distinct evolutionary and ecological aspects of the sequences. Feature importance analysis identified that steric and electronic properties of the protein were associated with predictive ability.

CONCLUSIONS: Our findings highlight the utility of deep learning for classification of diverse biological sequences and provide a framework for combining methods to improve model interpretability and ecological insights.},
}

*Deep Learning
*Metagenome
*Environment
*Adaptation, Physiological/genetics

@article {pmid40784769,
year = {2025},
author = {Kim, HS and Kim, BH and Nam, B and Oh, SJ and Park, SK and Lee, SW and Lee, JY and Jo, S and Lee, YA and Lee, JY and Park, DI and Kim, TH and Lee, CK},
title = {Oral-gut microbiome axis in a Korean cohort with inflammatory bowel disease and ankylosing spondylitis (INTEGRATE): a prospective and observational study protocol.},
journal = {BMJ open},
volume = {15},
number = {8},
pages = {e092075},
doi = {10.1136/bmjopen-2024-092075},
pmid = {40784769},
issn = {2044-6055},
mesh = {Humans ; *Gastrointestinal Microbiome ; Prospective Studies ; *Spondylitis, Ankylosing/microbiology ; Republic of Korea ; Observational Studies as Topic ; *Crohn Disease/microbiology ; RNA, Ribosomal, 16S ; *Inflammatory Bowel Diseases/microbiology ; Female ; Adult ; *Mouth/microbiology ; Dysbiosis ; Male ; *Colitis, Ulcerative/microbiology ; Saliva/microbiology ; },
abstract = {INTRODUCTION: The global burden of chronic immune-mediated inflammatory diseases (IMIDs) is increasing, and rising prevalence rates significantly affect socioeconomic factors and quality of life. Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), along with ankylosing spondylitis (AS), are prominent chronic IMIDs that share overlapping pathophysiological mechanisms. Recent research has highlighted the importance of the gut microbiota in the pathogenesis of these diseases, suggesting that shared microbial dysbiosis may contribute to their development. Comprehensive research focusing on the gut and oral microbial characteristics and environmental factors is essential to elucidate the fundamental pathophysiology and develop personalised management strategies for IBD and AS. In-depth analyses and insights based on multiomics approaches are required to achieve these objectives.

METHODS AND ANALYSIS: This protocol describes a nationwide prospective observational study of CD, UC and AS in a Korean population. Over 5 years, we aim to recruit at least 900 patients with IBD and 200 first-degree relatives (FDRs), 500 patients with AS and 200 of their FDRs, and 2244 healthy controls. We will systematically collect clinical data and biological samples, including saliva, stool, blood and tissue biopsies, for integrative multiomics analyses focusing primarily on the microbiome. Highly advanced full-length 16S ribosomal RNA gene sequencing and shotgun metagenomics will be used to characterise the microbial composition of saliva and stool samples. Quantitative microbiome profiling will be used to address the pathological, physiological and ecological differences between microbial groups that may be masked by their relative abundance. Metabolomic analyses will be conducted on saliva, stool and plasma samples to assess functional metabolic profiles. Culturomics will be used to isolate, identify and characterise the diversity of microbial species, including rare or previously unrecognised species, to provide a comprehensive understanding of the microbiota associated with these diseases.

ETHICS AND DISSEMINATION: Ethical approval was obtained from the Ethics Committee of Kyung Hee University Hospital, Hanyang University Hospital, Kangbuk Samsung Hospital, Yeungnam University Hospital, Kyungpook National University Hospital, Chonnam National University Hospital, Wonkwang University Hospital, Catholic University Daejeon St. Mary's Hospital, Soon Chun Hyang University Hospital Cheonan, Chung-Ang University Hospital, Inje University Haeundae Paik Hospital, Dankook University Hospital, Hanyang University Guri Hospital, Kyung Hee University Hospital at Gangdong, Chung-Ang University Gwangmyeong Hospital and Keimyung University Dongsan Hospital. Our research team will provide detailed information about the study, including an information sheet explaining its aims and procedures, prior to enrolment. Prospective participants will be informed that they have the right to withdraw from the study at any time, without penalty. Participants will be assured of the anonymity and confidentiality of any data they provide throughout the study, using participant numbers and the storage of sensitive data in locked cabinets. Participants will be enrolled in the study only after providing written informed consent to the research staff. The results of this study will be disseminated to healthcare and academic professionals through publications in peer-reviewed journals and presentations at international conferences.

TRIAL REGISTRATION NUMBER: This prospective observational study is registered at ClinicalTrials.gov ((ID: NCT06124833, data first posted: 9 November 2023); (ID: NCT06076083, data first posted: 21 November 2023) and (ID: NCT06183697, data first posted: 27 December 2023)).},
}

Humans
*Gastrointestinal Microbiome
Prospective Studies
*Spondylitis, Ankylosing/microbiology
Republic of Korea
Observational Studies as Topic
*Crohn Disease/microbiology
RNA, Ribosomal, 16S
*Inflammatory Bowel Diseases/microbiology
Female
Adult
*Mouth/microbiology
Dysbiosis
Male
*Colitis, Ulcerative/microbiology
Saliva/microbiology

@article {pmid40784643,
year = {2025},
author = {Yang, R and Jiang, J and Wu, S and Jin, J and Din, MFM and Sanjaya, EH and Chen, H and Liu, Z and Wang, B},
title = {Calcium synergy in the enhancing single-stage partial nitritation-anammox process for high-strength ammonium wastewater treatment.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122543},
doi = {10.1016/j.envres.2025.122543},
pmid = {40784643},
issn = {1096-0953},
abstract = {The single-stage partial nitritation-anammox (PNA) process is widely regarded as a sustainable strategy for nitrogen removal from high-strength ammonium wastewater, yet its stability remains challenged under elevated ammonium conditions. In this study, a lab-scale airlift inner-circulation reactor with a working volume of 1.9 liters was continuously operated for 247 days to evaluate the synergistic effects of calcium ion addition on process performance, microbial structure, and gene expression. The influent ammonium concentration was progressively increased from 850 mg/L to 1800 mg/L, while calcium ion concentration, added as calcium chloride dihydrate, was raised from 0 mg/L to 100 mg/L. Moderate calcium addition between 40 mg/L and 100 mg/L promoted significant sludge granulation, with mixed liquor volatile suspended solids nearly tripling and sludge volume index decreasing markedly, indicating enhanced biomass retention and sedimentation. Accompanying this, the secretion of extracellular polymeric substances, particularly tightly bound protein and polysaccharides, was substantially stimulated, resulting in a more compact and cohesive matrix. High-throughput 16S rRNA gene sequencing revealed that Ca[2+] addition selectively enriched key autotrophic taxa, such as Candidatus Brocadia and Nitrosomonas, while metagenomic analysis showed upregulation of functional genes. The increased abundance of these genes suggests an enrichment of functional microorganisms involved in autotrophic nitrogen metabolism, which may contribute to enhanced nitrogen transformation capacity, thereby supporting stable total inorganic nitrogen removal performance above 85 % despite increasing ammonium stress. These findings deepen the mechanistic understanding of calcium's synergistic role in reinforcing microbial aggregation, regulating EPS biosynthesis, and enhancing nitrogen-converting functionality, providing theoretical guidance for the robust application of PNA systems in treating ammonium-rich industrial wastewaters.},
}

@article {pmid40784428,
year = {2025},
author = {Mellon, DG and Mahjoub, N and Dudoignon, E and Dépret, F and Gabassi, A and Osinski, N and Mimoun, M and Mercier-Delarue, S and Plaud, B and Ghelfenstein-Ferreira, T and Caméléna, F and Goff, JL and Salmona, M},
title = {Assessment of air infectious contamination during wound care in a burn intensive care unit using Shotgun metagenomics.},
journal = {American journal of infection control},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajic.2025.08.003},
pmid = {40784428},
issn = {1527-3296},
abstract = {BACKGROUND: Airborne microbial contamination in burn intensive care units (BICUs) poses a significant risk to immunocompromised patients. Wound care procedures, including dressing removal, may contribute to the aerosolization of pathogens and antimicrobial resistance genes. This study employs clinical metagenomics (CMg) to analyze the microbial composition of air during wound care in a BICU.

METHODS: Air and skin samples were collected over three days from a BICU patient with extensive burns (70% total body surface area). Air sampling was performed using three high-efficiency aerosol samplers. Microbial analysis included multiplex PCR for respiratory and herpes viruses, bacterial and fungal cultures, and metagenomic sequencing for taxonomic and resistome profiling.

RESULTS: HSV-1 DNA was detected in air samples on days when dressing removal occurred, with the highest viral loads observed during intensive wound care. Bacterial diversity and antibiotic resistance gene prevalence were also highest on these days, with Enterobacterales and Micrococcales dominating the bacterial profile. Candida albicans was detected in skin cultures but not in air samples, likely due to its reduced airborne persistence.

CONCLUSION: This study demonstrates the significant impact of wound care on airborne microbial contamination in BICUs. Clinical metagenomics provides an advanced culture-independent approach to assess aerobiological risks, supporting improved infection control strategies in healthcare settings.},
}

@article {pmid40784361,
year = {2025},
author = {Debroas, D and Hennequin, C and Bricheux, G},
title = {The Air Plasmidome: A Discreet Route for Pathogens and the Transmission of Antibiotic Resistance Genes?.},
journal = {Environmental microbiology},
volume = {27},
number = {8},
pages = {e70166},
doi = {10.1111/1462-2920.70166},
pmid = {40784361},
issn = {1462-2920},
support = {//Fédération des Recherches en Environnement-Clermont-Ferrand/ ; },
mesh = {*Plasmids/genetics ; *Bacteria/genetics/drug effects/isolation & purification ; *Air Microbiology ; Metagenome ; *Drug Resistance, Microbial/genetics ; COVID-19/transmission ; *Drug Resistance, Bacterial/genetics ; SARS-CoV-2 ; Humans ; },
abstract = {Since the COVID-19 pandemic started, preventing airborne microorganism transmission has become everyone's concern. Viruses, bacteria, and fungal spores are airborne biological particles referring to bioaerosols. Through bacteria, a panel of genes (e.g., resistance or metabolic genes) might be found in bioaerosols and disseminated. Genes found on plasmids are potentially more exposed to the risk of transmissibility than those harboured by chromosomes. From 2422 air metagenomes analysed across various studies on bacteria, Proteobacteria were the most abundant microorganisms identified in air, with pathogens representing between 0.2% and 35.3% of the bacterial community per country. We identified 674,495 representative plasmids; 63,564 of them were linked to 5679 metagenome-assembled genomes. Among them, 89 plasmids were defined as keystones in terms of location numbers and plasmid coverage being more universal. Accessory traits of plasmids allow bacteria to adapt to their environment and contribute to host fitness. Antibiotic resistance genes represented < 1% of predicted plasmid genes and were mainly genes encoding efflux pumps. The plasmid similarity was significantly linked to the location and the microbial community (p < 0.001). Based on CRISPR detection, we determined that plasmids of bacteria coming from built environments and soils were overrepresented.},
}

*Plasmids/genetics
*Bacteria/genetics/drug effects/isolation & purification
*Air Microbiology
Metagenome
*Drug Resistance, Microbial/genetics
COVID-19/transmission
*Drug Resistance, Bacterial/genetics
SARS-CoV-2
Humans

@article {pmid40784283,
year = {2025},
author = {Zhao, J and Wang, Q and Zhao, Y and Guo, J and Ji, Z and Huang, Y and Shen, Q and Liu, Y and Bai, Y and Qi, W and Liu, H and Chen, Y},
title = {Chronic exposure to environmentally-relevant sulfamethoxazole alters ammonia-oxidizing microbial communities in managed aquifer recharge systems.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124298},
doi = {10.1016/j.watres.2025.124298},
pmid = {40784283},
issn = {1879-2448},
abstract = {Managed aquifer recharge (MAR) is a critical technology for water resource management and purification, yet its capacity to remove antibiotics remains limited. Understanding the response of ammonia-oxidizing microorganisms (AOMs) to antibiotics exposure is essential for optimizing MAR-based antibiotic mitigation strategies. This study investigated the long-term effects of sulfamethoxazole (SMX, ∼500 ng/L) on AOM communities through a 20-month controlled MAR column experiment. Results showed that AOMs (0.4-3.7 % of total microbial abundance) were dominated by ammonia-oxidizing archaea (AOA, 10.2-82.9 %) and complete ammonia oxidizers (comammox, 15.4-89.7 %), with negligible ammonia-oxidizing bacteria (AOB, <2.4 %). Chronic effects of SMX resulted in a 60-67 % reduction in amoA genes across AOA, AOB, and comammox populations, indicating a significant threat to nitrogen cycling. Specifically, SMX suppressed 2-7 AOA metagenome-assembled genomes (MAGs) (e.g., Nitrosotenuis) by 57-95 % and 4-5 comammox MAGs (e.g., Nitrospira) by 23-82 %. Conversely, SMX increased 4-7 AOA MAGs (e.g., Nitrosarchaeum) by 1.4-24.3-fold and 2 comammox MAGs (e.g., Nitrospira) by 1.9-2.0-fold, revealing taxon-specific tolerance. Notably, AOA lineages demonstrated superior resilience to SMX compared to comammox. These findings advance our understanding of antibiotic-driven microbial community dynamics in MAR systems and provide valuable insights for enhancing their performance in antibiotic-polluted environments.},
}

@article {pmid40784175,
year = {2025},
author = {Duan, S and Qiao, Z and Chen, Y and Shen, Y and Du, Z and Dong, J and Yu, L and Li, Y and Yang, R and Fang, C},
title = {Ultrasound-assisted extraction and flavor quality assessment of in vitro biomimetically fermented Kopi Luwak.},
journal = {Ultrasonics sonochemistry},
volume = {120},
number = {},
pages = {107499},
doi = {10.1016/j.ultsonch.2025.107499},
pmid = {40784175},
issn = {1873-2828},
abstract = {Kopi Luwak, renowned for its distinctive flavor profile, has long been esteemed in specialty coffee circles; however, the conventional animal digestive process is fraught with significant ethical and sustainability controversies. Building upon these findings, the present study established a tightly controlled in vitro biomimetic fermentation system, complemented by ultrasound-assisted extraction and multi-omics analyses, to faithfully reconstruct and elevate the hallmark flavour of civet coffee. Leveraging metagenomic data from the civet gut, thirty core functional strains were selected from 1870 isolates to create a synthetic symbiotic consortium. Fermentation parameters were optimised in three stages-single-factor experiments, Box-Behnken response-surface design, and a genetic-algorithm-artificial-neural-network (GA-ANN) model. Fermentation products were recovered by ultrasound-assisted extraction (40 kHz, 400 W, 10 min); volatile and non-volatile metabolites were quantified in both targeted and untargeted modes via GC-MS and UHPLC-MS/MS, and their temporal dynamics were deciphered through time-series clustering and metabolic-network analysis. The optimal conditions-16.5 % inoculum, initial pH 6.25, 33 ℃, 135 h-yielded an average SCA cupping score of 82.92, with a maximum of 85.25, significantly higher than those of natural fermentation and conventional civet coffee (P < 0.05). Total acidity increased to 0.78 g L[-1], total polyphenol content reached 225.3 mg L[-1], and key bioactive compounds remained stable. GC-MS quantification showed 1.9-2.3-fold increases in 2,3-dimethoxyphenol, phenylethanol, and 5-methylfurfural, alongside 63 % and 41 % reductions in 2-methylpyrazine and caffeine, respectively. Multi-omics evidence indicated that lipid β-oxidation, the amino-acid Ehrlich pathway, and esterification jointly enriched fruity, nutty, and floral notes; the elevated copy numbers of ndmA/B and pyoA/B genes underpinned the attenuation of bitter compounds. Relative to conventional solvent and Soxhlet extraction, ultrasound-assisted extraction improved volatile recovery by approximately 28 %, reduced energy consumption by ≥66 %, and halved solvent usage. Overall, this work achieves a high-fidelity in vitro replication of the civet gut microbiome and its metabolic functions, enables precision flavour modulation through intelligent optimisation and green extraction, and demonstrates industrial feasibility-the processing cost per kilogram of raw beans is 76.7 % lower than that of the traditional animal-derived method.},
}

@article {pmid40784097,
year = {2025},
author = {Lin, Y and Wang, X and Zhao, D and Zhou, H and Wang, Y and Gao, Y and Lin, Y and Xu, G and Ni, K and Yang, F},
title = {Waterlogging-induced restructuring of phyllosphere microbiota associated with mycotoxin accumulation.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {118821},
doi = {10.1016/j.ecoenv.2025.118821},
pmid = {40784097},
issn = {1090-2414},
abstract = {As waterlogging events intensify and become more frequent in the future, understanding their impact on plant physiology and associated microbes is crucial for alleviating stress in vulnerable species and ecosystems. Despite its importance, our understanding of how phyllosphere microbiota react to waterlogging stress remains limited. This study utilized metagenomic sequencing to assess the effects of waterlogging on microbial diversity and functional activities in different tissues of the maize phyllosphere, focusing specifically on leaves and ears. Our findings indicated that waterlogging significantly affected the maize phyllosphere microbial communities. Also, waterlogging altered the microbial interaction networks by increasing network complexity, enhancing negative interactions, and shifting the relative abundance of key bacterial and fungal genera. Moreover, metagenomic analysis revealed upregulated signaling pathways and oxidative stress responses, particularly within the fungal communities associated with maize ears. Crucially, we identified a higher abundance of genes related to mycotoxin production under waterlogged conditions, leading to elevated mycotoxin levels in ear tissues. These results suggest that waterlogging-induced changes in fungal communities may heighten the risk of mycotoxin contamination in maize. The distinct microbial responses noted between maize leaves and ears further highlight the tissue-specific dynamics of these communities.},
}

@article {pmid40784060,
year = {2025},
author = {Zhang, H and Wang, C and Gong, Y and Zhu, Y and Zhang, M and Li, D and Tian, Y and Han, R and Guo, Y and Zhang, Y and Kang, X and Jiang, R},
title = {Changes in pathogenicity of gut microbiota during fasting-induced molting in laying hens and their impact on spleen immune function.},
journal = {Poultry science},
volume = {104},
number = {10},
pages = {105526},
doi = {10.1016/j.psj.2025.105526},
pmid = {40784060},
issn = {1525-3171},
abstract = {Fasting-induced molting (FIM) leverages the natural molting mechanism of aging laying hens to enhance their egg production and egg quality. However, fasting may also increase the risk of pathogen infection and activate immune regulation in the spleen. Understanding the specific types of pathogen infections triggered during FIM and their impacts on the spleen's immune regulation mechanisms is crucial for enhancing the immunological resilience of poultry. A total of 90, aged 60 weeks, late-laying hens were randomly assigned to undergo FIM. During FIM, hens kept regular feed and 16 hours light initially. A 3-day fast with 8 hours light followed. Then, they gradually resumed water and feed, increasing from 30 g to 120 g daily, with light returning to 16 hours. This study investigates the effects of FIM on the gut microbiota and metabolites through metagenomic sequencing and metabolomics. Additionally, blood routine tests and ELISA assays were conducted to measure serum Ig concentrations. Real-time quantitative PCR and ELISA were used to detect the expression of inflammatory factors and immune cell markers in the spleen. The study also analyzed gene expression levels in the PI3K/AKT pathway, systematically exploring fasting's regulatory impact on gut-spleen immunity. Results showed that during FIM, the abundance of pathogens utilizing non-carbohydrates as an energy source initially increased and then decreased, while the abundance of pathogens relying on carbohydrates as an energy source declined. Correspondingly, with beneficial metabolites initially decreased before increasing, while harmful metabolites exhibited the opposite trend. During fasting, the concentration of eosinophilic leukocytes in serum significantly increased (P < 0.05), while the concentration of IgA significantly decreased (P < 0.05). In the spleen, significant increase in the expression of immune-related metabolites, including NF-κB, IFN-β, iNOS, IL-1β, and IFN-α, were observed, along with significant increases in the secretion of TNF-α, TGF-β, IL-1, and IL-8, suggesting a significant activation of the immune response. After refeeding, these factors in serum and spleen returned to pre-fasting levels. Notably, the PI3K/AKT signaling pathway was significantly activated during fasting, indicating that fasting exerts broad effects on the immune system via the PI3K/AKT pathway. This study holds significant theoretical and practical value for enhancing the immunity of molting laying hens, reducing pathogenic bacterial infections, and optimizing production performance.},
}

@article {pmid40783881,
year = {2025},
author = {Maldonado-Gómez, JC and Rincón-Molina, FA and Rincón-Rosales, R and Manzano-Gómez, LA and Gen-Jiménez, A and Rincón-Molina, CI},
title = {Diversity and plant growth-promoting properties of rhizospheric and endophytic bacteria associated with Agave americana.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {40783881},
issn = {1678-4405},
support = {21914.25-P//Tecnológico Nacional de México/ ; 22004.25-P//Tecnológico Nacional de México/ ; },
abstract = {Plant-microbe interactions play a critical role in maintaining plant health, enhancing soil fertility, and sustaining ecosystem functionality. Agave americana (Asparagales, Asparagaceae, L.), a crassulacean acid metabolism (CAM) species known for its remarkable drought tolerance and diverse industrial uses, represents a valuable model for exploring the ecological and functional dynamics of these associations. This study explores the diversity and functional potential of bacterial communities associated with A. americana and their role in promoting plant growth. A combination of culture-dependent techniques and metagenomic sequencing was employed to isolate and characterize rhizospheric and endophytic bacteria. Prominent bacterial genera identified included Acinetobacter, Bacillus, Rhizobium/Mesorhizobium, and Microbacterium. Metagenomic analyses revealed a high abundance of Actinobacteria, Proteobacteria, and Chloroflexi, highlighting their roles in nutrient cycling and organic matter decomposition. Plant growth-promoting assays demonstrated that Rhizobium sp. 34 A produced significant levels of indole-3-acetic acid (IAA), enhancing nutrient availability and plant growth. Mesorhizobium sp. 28 A had the greatest overall impact, significantly increasing total fresh weight, chlorophyll content, and sugar profiles, surpassing the effects of chemical fertilizers. Furthermore, Bacillus sp. T12C12, in combination with other plant growth-promoting bacteria (PGPB), exhibited the highest nitrogenase activity, as measured through acetylene reduction assays (ARA). These findings suggest that bacterial inoculants can enhance the nutritional and agronomic value of Agave species, which are of significant agro-industrial and food importance, providing a sustainable alternative to chemical fertilizers. This study offers valuable insights into sustainable agricultural practices by leveraging microbial communities to enhance crop productivity and resilience.},
}

@article {pmid40783398,
year = {2025},
author = {Shen, Y and Sun, D and Chen, K and Jiang, J and Shao, D and Yang, L and Sun, C and Liu, D and Ke, Y and Wu, C and Walsh, TR and Shen, J and Lv, Z and Wang, Y},
title = {High-fat and low-fiber diet elevates the gut resistome: a comparative metagenomic study.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {156},
pmid = {40783398},
issn = {2055-5008},
support = {81991535//National Natural Science Foundation of China/ ; 32141002//National Natural Science Foundation of China/ ; 2022YFD1800400//National Key Research and Development Program of China/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects/genetics ; Animals ; *Dietary Fiber/administration & dosage ; *Diet, High-Fat ; Mice ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Metagenomics/methods ; Male ; Humans ; Anti-Bacterial Agents/pharmacology ; Feces/microbiology ; Interspersed Repetitive Sequences ; Female ; },
abstract = {Antimicrobial resistance (AMR) is a global health challenge. The gut microbiome, a major reservoir for AMR, is influenced by dietary habits. However, the specific impact of dietary patterns on gut resistome remains poorly understood. This study aimed to assess the effects of high-fat/low-fiber and high-fiber/low-fat diets on the development of AMR in the gut microbiome. The shift from a normal diet to a high-fat/low-fiber or a high-fiber/low-fat diet in mice resulted in corresponding increases and decreases in the relative abundance of the resistome (0.14 to 0.25, p < 0.001 vs. 0.14 to 0.09 p < 0.05), virulence genes (VGs) (0.56 to 0.91, p < 0.001 vs. 0.58 to 0.50, p < 0.05), and mobile genetic elements (MGEs) (0.20 to 1.66, p < 0.001 vs. 0.22 to 0.13, p < 0.05), respectively. Network analyses identified bacteria such as Bacteroides, Parabacteroides, and Alistipes as hosts of ARGs and VGs, with changes in their abundance closely associated with shifts in ARG and VG levels. Mobile genetic elements such as Tn916, ISBf10, IS91, and intl1 were linked to these variations, including genes conferring resistance to vancomycin and capsule-related VGs. In humans, a similar trend was observed, with high-fat diets correlating with higher resistome levels, while high-fiber diets were associated with lower resistome levels compared to a normal diet group. ARGs were more prevalent in pathogenic genera such as Enterococcus spp., Klebsiella spp., Pseudomonas spp., and Staphylococcus spp. The high-fat/low-fiber diet increased the bacterial resistome and VG abundance compared to a high-fiber/low-fat diet. Therefore, adopting a high-fiber/low-fat diet may be an effective strategy to reduce the AMR burden in the human gut, providing a valuable insight for public health recommendations.},
}

*Gastrointestinal Microbiome/drug effects/genetics
Animals
*Dietary Fiber/administration & dosage
*Diet, High-Fat
Mice
*Bacteria/genetics/drug effects/classification/isolation & purification
Metagenomics/methods
Male
Humans
Anti-Bacterial Agents/pharmacology
Feces/microbiology
Interspersed Repetitive Sequences
Female

@article {pmid40783071,
year = {2025},
author = {Proal, A and VanElzakker, M},
title = {Pathogens accelerate features of human aging: A review of molecular mechanisms.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {102865},
doi = {10.1016/j.arr.2025.102865},
pmid = {40783071},
issn = {1872-9649},
abstract = {(250 words) Many models of aging assume that processes such as cellular senescence or epigenetic alteration occur under sterile conditions. However, humans sustain infection with viral, bacterial, fungal, and parasite pathogens across the course of a lifetime, many of which are capable of long-term persistence in host tissue and nerves. These pathogens-especially members of the human virome like herpesviruses, as well as intracellular bacteria and parasites-express proteins and metabolites capable of interfering with host immune signaling, mitochondrial function, gene expression, and the epigenetic environment. This paper reviews these and other key mechanisms by which infectious agents can accelerate features of human aging. This includes hijacking of host mitochondria to gain replication substrates, or the expression of proteins that distort the signaling of host longevity-regulating pathways. We further delineate mechanisms by which pathogen activity contributes to age-related disease development: for example, Alzheimer's amyloid-β plaque can act as an antimicrobial peptide that forms in response to infection. Overall, because many pathogens dysregulate mTOR, AMPK, or related immunometabolic signaling, healthspan interventions such as low-dose rapamycin, metformin, glutathione, and NAD+ may exert part of their effect by controlling persistent infection. The lack of diagnostics capable of detecting tissue-resident pathogen activity remains a critical bottleneck. Emerging tools-such as ultrasensitive protein assays, cfRNA metagenomics, and immune repertoire profiling-may enable integration of pathogen detection into biological age tracking. Incorporating infection into aging models is essential to more accurately characterize drivers of senescence and optimize therapeutic strategies that target both host and microbial contributors to aging.},
}

@article {pmid40782961,
year = {2025},
author = {Chen, Y and Wang, F and Gao, J and Liu, Q and Guo, J and Liu, H},
title = {Enhancing phyto-microbial remediation of petroleum-contaminated soil using sophorolipid-modified biochar: Metagenomic and metabolomic insights.},
journal = {Environmental research},
volume = {285},
number = {Pt 3},
pages = {122525},
doi = {10.1016/j.envres.2025.122525},
pmid = {40782961},
issn = {1096-0953},
abstract = {We developed KOH-activated biochar (K-BC) and sophorolipid-modified K-BC (S-K-BC) for enhancing phyto-microbial remediation of petroleum hydrocarbon (PH)-contaminated soil using Iris lactea Pall. Subsequently, three remediation systems were established: KBC-SLs (Iris lactea Pall. + 2 wt% S-K-BC), KBC + SLs (Iris lactea Pall. + 2 wt% K-BC + 3 × 10[-4] mol SLs), and KBC (Iris lactea Pall. + 2 wt% K-BC) to study the enhancing effect on phyto-microbial remediation. The removal ratio of petroleum hydrocarbons (PHs) in KBC-SLs, KBC + SLs and KBC were 64.0 %, 53.6 % and 46.7 %, respectively, which were higher than that of the plant alone treatment group (27.8 %). After 90 days of remediation experiments, metagenomics showed that KBC-SLs increased the abundance of PH-degrading bacteria (Actinomycetota +34.3 %, Acidobacteriota +23.3 %) and key genes (alkB +32.3 %, nidB +49.8 %, xylC +33.4 %). Metabolomics revealed that KBC-SLs boosted PHs degradation by upregulating fatty acid and polycyclic aromatic hydrocarbons (PAHs) metabolic pathways. Association analysis of metagenomics and metabolomics showed strong positive correlations between PHs metabolites and PHs degrading microorganisms, such as palmitic acid with Bacteroidota, myristic acid with Acidobacteriota. And, strong positive correlations were observed between PHs metabolites and PHs degradation genes, such as m-toluic acid with nahE (K14585) and xylM (K15757). Additionally, KBC-SLs had enhanced the phyto-microbial remediation of PH-contaminated soil by boosting plant growth, root activity, soil enzymes, and plant-microbe synergy. This study confirms that S-K-BC effectively enhances the phyto-microbial remediation of PH-contaminated soil, providing valuable insights into green and sustainable remediation technologies.},
}

@article {pmid40782819,
year = {2025},
author = {Nguyen-Tran, H and Park, SW and Vogt, MR and Permaul, P and Spaulding, AB and Hernandez, ML and Bohl, JA and Godbole, S and Ruckwardt, TJ and Krug, PW and Moss, DL and Derrien-Colemyn, A and Chowdhury, A and Dziubla, G and Wang, L and Castro, M and Narpala, SR and Longtine, ER and Henry, AR and Ngo, TB and Dzantiev, L and Sigal, GB and Metcalf, CJ and Kimberlin, DW and Dominguez, SR and Mittelman, A and McDermott, AB and Serebryannyy, LA and Grenfell, B and Messacar, K and Douek, DC},
title = {Dynamics of endemic virus re-emergence in children in the USA following the COVID-19 pandemic (2022-23): a prospective, multicentre, longitudinal, immunoepidemiological surveillance study.},
journal = {The Lancet. Infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/S1473-3099(25)00349-4},
pmid = {40782819},
issn = {1474-4457},
abstract = {BACKGROUND: The Pandemic Response Repository through Microbial and Immune Surveillance and Epidemiology (PREMISE) programme was established to translate knowledge gained from global immunoepidemiological surveillance into a better understanding of population-level dynamics of emerging and re-emerging infections, as well as into the discovery and development of biomedical countermeasures against potential pandemic threats. As proof of principle for this approach, we conducted a longitudinal immunoepidemiological study in children in the USA, focusing on enterovirus D68 (EV-D68) infection dynamics but also capturing surveillance of a broad array of other endemic respiratory pathogens. Serendipitously, our sampling spanned the lifting of widespread COVID-19 non-pharmaceutical interventions (NPIs) in 2022-23, following a unique period during which virus exposure markedly diminished.

METHODS: This prospective, multicentre, longitudinal, immunoepidemiological surveillance study enrolled children aged 10 years or younger and weighing at least 8 kg at three US university sites. Blood specimens collected from January to June, 2022 (visit 1; pre-enterovirus season), and from January to June, 2023 (visit 3; post-enterovirus season), were tested in a multiplex assay for antibody binding to EV-D68 (prespecified primary objective) and a panel of 15 other respiratory viruses (exploratory objectives), and for neutralising activity against EV-D68, enterovirus A71, and respiratory syncytial virus (RSV; for antibody binding assay validation). Respiratory mid-turbinate swabs collected from children with symptomatic illness who participated in symptom surveys during July-December, 2022 (visit 2; enterovirus season), underwent metagenomic sequencing for pathogen detection. Serological data for EV-D68 were incorporated into epidemiological models based on case data from national surveillance to predict future transmission dynamics.

FINDINGS: Of 488 eligible children approached, 174, with a median age of 3·4 years (IQR 1·9-6·4), were enrolled and followed up longitudinally from January, 2022, to June, 2023. Three children withdrew before study completion and 51 were lost to follow-up between visits 1 and 3. 90 paired serological samples and 73 respiratory swabs were tested. Mean antibody binding and neutralisation titres against all viruses tested increased over the study period, most notably in younger children with lower initial titres. The highest exposure rates (seroconversion or antibody boosting) were seen with SARS-CoV-2 (51 [59%] of 87), EV-D68 (36 [41%] of 87), RSV (36 [41%] of 87), and influenza (35 [40%] of 87), whereas the pathogens most frequently detected by respiratory swab sequencing were EV-D68 (clade B3), rhinovirus A, and rhinovirus C (n=7 each). Incorporating EV-D68 serological data into epidemiological models resulted in an 82% reduction in the range of prediction errors and a 33% reduction in median prediction errors for longer-term EV-D68 circulation dynamics compared with national pathogen surveillance data alone.

INTERPRETATION: In this study, we captured immunological evidence of endemic virus re-emergence in children following lifting of pandemic NPIs, which revealed high rates of exposure to endemic respiratory pathogens in a large group of seronegative, predominantly younger, children. This study demonstrates the feasibility and utility of immunoepidemiological surveillance to enable more precise and accurate modelling of pathogen circulation dynamics to predict and prepare for future waves of disease.

FUNDING: Intramural Research Program of the National Institute of Allergy and Infectious Diseases-Vaccine Research Center, and the National Cancer Institute, National Institutes of Health.},
}

@article {pmid40782752,
year = {2025},
author = {Liang, M and Li, J and Zhang, J and Zhang, Q and Zhang, X and Wang, D},
title = {Sustainable in-situ arsenic immobilization in paddy soils using magnetic biochar and the role of microbial functional genes.},
journal = {Journal of environmental management},
volume = {392},
number = {},
pages = {126916},
doi = {10.1016/j.jenvman.2025.126916},
pmid = {40782752},
issn = {1095-8630},
abstract = {Arsenic (As) contamination in paddy soils poses a threat to both rice safety and human health. To address this challenge, we developed and evaluated an in-situ remediation approach using magnetic iron oxide biochar (MBC) for paddy soils with varying As contamination levels, aiming to reduce As accumulation in rice grains. MBC significantly altered soil physicochemical properties [pH, dissolved organic carbon (DOC), soil organic matter (SOM), and Free iron oxides (Fe-ox)] at both tillering and maturity stages. Reduced available As by 31-65 % across low (136.68 mg kg[-1]), moderate (214.22 mg kg[-1]), and high (254.21 mg kg[-1]) contamination levels, and suppressed As translocation to rice grains by 62 %, ensuring brown rice As levels below the Chinese national safety threshold (GB 2762-2022, ≤0.35 mg kg[-1]). The paddy soils' metagenomic analysis revealed MBC-enriched Pseudomonadota and Actinomycetota with arsM and arsC genes, transitioning microbial networks from modular (tillering stage) to interconnected (maturity stage), enhancing arsenic detoxification and organic matter degradation. MBC enables efficient As immobilization and redox transformation, offering a scalable, eco-friendly solution for reconciling soil remediation with safe rice production in various As-contaminated regions.},
}

@article {pmid40782750,
year = {2025},
author = {Yang, H and Fan, S and Jiang, M and Hu, Y and Chen, X and Chen, C and Liu, W and Zeng, Y and Peng, K and Wang, Y and Wang, G and Wu, Y},
title = {Biochar-organic fertilizer synergy drives microbial-mediated C-sequestration and N-cycling in mixed forests toward sustainability.},
journal = {Journal of environmental management},
volume = {392},
number = {},
pages = {126892},
doi = {10.1016/j.jenvman.2025.126892},
pmid = {40782750},
issn = {1095-8630},
abstract = {Fertilizer management in artificial mixed systems is generally regarded as an efficacious approach to enhance soil fertility and sustain soil health. Nevertheless, research on the impacts of incorporating 600 g biochar (BC) with 1500 g organic fertilizers (OF) in the subsoil on the functional characteristics of short-term soil nutrient cycling in artificial mixed woodland soils remains scarce. This study investigated the effects of BC, OF, and (600 g BC + 1500 g OF) their mixture (OFBC) on soil properties and microbial functions in Cyclobalanopsis glauca and Pinus massoniana plantations. The results indicated that, compared to the control group, the contents of soil organic carbon (SOC) and total phosphorus (TP) increased by 248.33 % and 199.37 %, respectively, after the application of OFBC. Under the treatment of organic fertilizer (OF), the content of total nitrogen (TN) increased by 292.30 %. Metagenomic analysis revealed that BC-OF synergy (1) Upregulated C-fixation genes (e.g., cbbL): but suppressed C-degradation (celB, GAM1) and CH4-metabolism genes (pmoA, mmoX), promoting C-sequestration; (2) Enhanced N-cycling gene abundance (e.g., nifH, hao, nosZ), accelerating N-turnover efficiency beyond additive effects. Soil pH and β-glucosidase activity (increased by 1255.52 %) were key mediators of microbial functional shifts. The study provides critical insights into leveraging organic amendments to enhance ecosystem services while advancing sustainable forestry practices.},
}

@article {pmid40782414,
year = {2025},
author = {Li, C and Zhang, T and Xie, Y and Wei, R and Wu, W},
title = {Multisystem inflammatory syndrome in children (MIS-C) with secondary intestinal cytomegalovirus infection: A case report.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {4},
pages = {117038},
doi = {10.1016/j.diagmicrobio.2025.117038},
pmid = {40782414},
issn = {1879-0070},
abstract = {Multisystem inflammatory syndrome in children (MIS-C) constitutes a severe pediatric disorder temporally linked to SARS-CoV-2 infection. Although SARS-CoV-2 may induce cytomegalovirus (CMV) reactivation, MIS-C cases with secondary intestinal CMV infection are exceptionally rare. We describe a pediatric patient with MIS-C treated initially with intravenous immunoglobulin (IVIG) and methylprednisolone, following clinical improvement, sudden high fever and worsening abdominal symptoms occurred. Symptomatic resolution occurred following ganciclovir administration, with CMV infection confirmed by colonic histopathology and metagenomic next-generation sequencing (mNGS).},
}

@article {pmid40782151,
year = {2025},
author = {Kumari, P and Tripathi, BM and Eo, KY and Kimura, J and Yamamoto, N},
title = {Spatioseasonal Comparison of Fecal Resistome and Pathogenome of Raccoon Dogs in Korea.},
journal = {EcoHealth},
volume = {},
number = {},
pages = {},
pmid = {40782151},
issn = {1612-9210},
support = {2021R1F1A1060259//National Research Foundation of Korea/ ; },
abstract = {The raccoon dog (Nyctereutes procyonoides) is a medium-sized omnivore native to Asia. Because they live close to human habitation, and therefore, there is likely bidirectional influence between raccoon dogs and humans, it is important to investigate their potential risks. Here, to identify potential risks of carriage of antimicrobial resistance (AMR) and human pathogens by raccoon dogs, we investigated spatioseasonal patterns of fecal resistome (collection of antimicrobial resistance genes: ARGs), pathogenome (collection of virulence factor genes: VFGs), and microbiome (collection of bacterial species) of raccoon dogs inhabiting an urban forest area and a rural rice paddy area in Korea. Metagenomic sequencing revealed that the compositions of fecal resistome, pathogenome, and microbiome were all patterned by season, and we hypothesize that the observed patterns are due to seasonal changes in the diet of omnivorous raccoon dogs. Furthermore, although less pronounced than the seasonal differences, we also observed the geographical differences in the resistome, with aminoglycoside resistance genes being more prevalent in the rural area, which may reflect the geographical difference in selective pressures for AMR emergence, such as the use of manure that may contain antimicrobials in rice cultivation in agricultural areas. Additionally, our network analysis revealed that specific antimicrobial resistance genes were linked to specific bacterial pathogens, e.g., tetA-P to Clostridium. Overall, our study successfully revealed for the first time that not only the microbiome, but also the resistome and pathogenome of wild animals change spatioseasonally, and that the risk of AMR in bacterial pathogens laden by raccoon dogs is spatioseasonal.},
}

@article {pmid40782126,
year = {2025},
author = {Andeta, AF and Lema, NK and Debel, GL and Misganaw, FW and Ifa, AC},
title = {Evaluating food safety of traditionally fermented kocho: microbial profiling through classical methods and PacBio SMRT sequencing technology.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {9},
pages = {127},
pmid = {40782126},
issn = {1572-9699},
support = {CRP/ETH20-03_EC//International Center for Genetic Engineering and Biotechnology (ICGEB)/ ; CRP/ETH20-03_EC//International Center for Genetic Engineering and Biotechnology (ICGEB)/ ; CRP/ETH20-03_EC//International Center for Genetic Engineering and Biotechnology (ICGEB)/ ; CRP/ETH20-03_EC//International Center for Genetic Engineering and Biotechnology (ICGEB)/ ; CRP/ETH20-03_EC//International Center for Genetic Engineering and Biotechnology (ICGEB)/ ; },
mesh = {*Fermented Foods/microbiology ; *Food Safety ; *Bacteria/classification/genetics/isolation & purification ; *Food Microbiology ; Ethiopia ; Fermentation ; Cross-Sectional Studies ; Fungi/isolation & purification/classification/genetics ; Microbiota ; },
abstract = {Enset (Ensete ventricosum) serves as a staple or co-staple food crop for over 20 million people in Southern, Southwestern, and Central Ethiopia, significantly contributing to regional food security. Despite its importance, food safety concerns surrounding its fermented product, kocho, remain largely unaddressed. This study aimed to evaluate the food safety of traditionally fermented kocho samples collected from districts in the Gamo Zone using a cross-sectional study design. The microbial community composition was analyzed through both culture-based methods and PacBio sequencing. The physicochemical properties exhibited slight variations in acidity, fermentation stage, and moisture content among samples from different districts. Culture-based microbiological analysis indicated total viable aerobic counts ranging from 5.76 to 7.13 log CFU/g, yeast and mold counts between 5.20 to 8.53 log CFU/g, and Enterobacteriaceae counts ranging from 5.03 to 6.13 log CFU/g. Metagenomic analysis revealed that Proteobacteria and Firmicutes were the predominant phyla, with Acetobacter and Lactobacillus as the most prevalent genera. Notably, potential pathogenic bacteria, including Klebsiella pneumoniae, Klebsiella terrigena, Dysgonomonas capnocytophagoides, and Clostridium paraputrificum, were identified. The coexistence of beneficial microorganisms and potential pathogens underscores the urgent need for enhanced food safety measures in the traditional production of kocho.},
}

*Fermented Foods/microbiology
*Food Safety
*Bacteria/classification/genetics/isolation & purification
*Food Microbiology
Ethiopia
Fermentation
Cross-Sectional Studies
Fungi/isolation & purification/classification/genetics
Microbiota

@article {pmid40782046,
year = {2025},
author = {Bradley, ES and Stansky, C and Zeamer, AL and Huang, Z and Cincotta, L and Lopes, A and Potter, L and Fontes, T and Ward, DV and Bucci, V and McCormick, BA and Haran, JP},
title = {The urinary microbiome distinguishes symptomatic urinary tract infection from asymptomatic older adult patients presenting to the Emergency department.},
journal = {Virulence},
volume = {},
number = {},
pages = {2546063},
doi = {10.1080/21505594.2025.2546063},
pmid = {40782046},
issn = {2150-5608},
abstract = {Older adults suffer from a high rate of asymptomatic bacteriuria (ASB), in which urinalysis may appear positive (presence of bacteria, white blood cells, and nitrates), often triggering initiation of antibiotics in acute care settings, without actual urinary tract infection (UTI) present. To investigate the urinary microbiome of older adults being tested for UTI, we enrolled a convenience sample of 250 older adult Emergency Department patients who had microscopic urinalysis ordered as part of their routine clinical care. Urinalysis results were classified as positive or negative, and patients were classified as being symptomatic or asymptomatic based on established diagnostic guidelines. We sought to determine if features of the urinary microbiome differed between positive and negative urinalysis (UAs) and symptomatic and asymptomatic patients with positive UAs. The same urine sample used for clinical testing was sequenced and analyzed for bacterial taxa, metabolic pathways, and known bacterial virulence factors. After exclusion for anatomical abnormalities and filtering for sequencing quality, 152 samples were analyzed (5 negative UAs, 147 positive UAs, among which 68 were asymptomatic, and 79 symptomatic). Positive UA samples showed significantly lower alpha diversity (2.29 versus 0.086, p < 0.01) and distinct community composition based on beta-diversity (PERMANOVA on Bray-Curtis distance p < 0.01). Alpha and beta diversity did not significantly differ between asymptomatic and symptomatic patients. Machine learning classifiers combining clinical covariates other than specific signs and symptoms and microbiome features (taxa, metabolic pathways, or virulence factors) revealed mostly microbiome features as predictive of symptomatic UTI over clinical features.},
}

@article {pmid40781723,
year = {2025},
author = {Escobar-Prieto, JD and Van Goethem, MW and Vernooij, B and Antony, CP and Cheng, L and Mishra, H and Marasco, R and Daffonchio, D},
title = {Microbial diversity and functional potential of the Halobates melleus (Heteroptera: Gerridae) microbiome from the Red Sea coastline.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {103},
pmid = {40781723},
issn = {2524-6372},
support = {CRG-7-3739//King Abdullah University of Science and Technology/ ; CRG-7-3739//King Abdullah University of Science and Technology/ ; CRG-7-3739//King Abdullah University of Science and Technology/ ; },
abstract = {BACKGROUND: Halobates, commonly known as sea skaters, are predatory Hemipterans uniquely adapted to tropical marine environments. Their ability to thrive in oligotrophic and environmentally extreme habitats, such as the open ocean surface and marine coastal areas, suggests the evolution of specialised adaptations, possibly including symbiotic associations with microorganisms that can support nutrition, niche adaptation, and stress resilience. To explore this hypothesis, we analysed the bacterial communities associated with Halobates melleus, a species inhabiting the Red Sea coastal mangroves in Saudi Arabia.

RESULTS: Amplicon sequencing of the 16S rRNA gene and metagenomic analyses of composite body and gut samples from adult H. melleus revealed a population-level bacterial community dominated by Wolbachia and Spiroplasma, consistent with patterns observed in several terrestrial predatory insects. Members of Providencia and Swaminathania were also detected, along with other minor taxa that may represent transient environmental commensals. The identified bacteria encoded genes for the biosynthesis of essential vitamins and prosthetic groups, such as riboflavin and heme-compounds typically not synthesised de novo by insects-as well as amino acids, likely contributing to the host's nutritional requirements. Notably, the Wolbachia metagenome-assembled genome from H. melleus clustered within the supergroup B, showing high genetic similarity to strains from phylogenetically distant Dipteran and Lepidopteran hosts that nonetheless inhabit common ecological niches, i.e., mangrove and tropical environments. This extends the known ecological breadth of Wolbachia symbioses to marine insects, underscoring their evolutionary and environmental versatility.

CONCLUSION: Our findings highlight the potential nutritional and metabolic roles of the Halobates-associated bacterial microbiome, particularly members of the Wolbachia genus. This emphasises the importance of microbial symbionts in the ecological success and adaptation of marine insects, offering a perspective complementary to previously studied terrestrial insect microbiomes.},
}

@article {pmid40781499,
year = {2025},
author = {Kumari, J and Uthaman, A and Bose, S and Kundu, A and Sharma, V and Dutta, S and Dhar, A and Roy, S and Srinivasan, R and Pande, S and Vinothkumar, KR and Gayathri, P and Palani, S},
title = {Distinct filament morphology and membrane tethering features of the dual FtsZ paralogs in Odinarchaeota.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {40781499},
issn = {1460-2075},
support = {IA/I/21/1/505633//Wellcome Trust DBT India Alliance (India Alliance)/ ; IA/S/23/1/506755//Wellcome Trust DBT India Alliance (India Alliance)/ ; IA/I/20/1/504921//Wellcome Trust DBT India Alliance (India Alliance)/ ; BT/INF/22/SP33046/2019//Department of Biotechnology, Ministry of Science and Technology, India (DBT)/ ; DBT/PR12422/MED/31/287/2014//Department of Biotechnology, Ministry of Science and Technology, India (DBT)/ ; SRG/2021/001600//DST | Science and Engineering Research Board (SERB)/ ; STARS2/2023-1015//Ministry of Education STARS grant/ ; RTI 4006//Department of Atomic Energy, Government of India (DAE)/ ; },
abstract = {The Asgard phylum has emerged as a model to study eukaryogenesis because of their close relatedness with the eukaryotes. In this study, we use FtsZ proteins from a member of the class Odinarchaeia as representatives to investigate the probable origin, evolution, and assembly of the FtsZ/tubulin protein superfamily in Asgard archaea. We performed a comparative analysis of the biochemical properties and cytoskeletal assembly of FtsZ1 and FtsZ2, the two FtsZ isoforms in the Odinarchaeota metagenome. Our electron microscopy analysis reveals that OdinFtsZ1 assembles into curved single protofilaments, while OdinFtsZ2 forms stacked spiral ring-like structures. Upon sequence analysis, we identified an N-terminal amphipathic helix in OdinFtsZ1, which mediates direct membrane tethering. In contrast, OdinFtsZ2 is recruited to the membrane by the anchor OdinSepF via OdinFtsZ2's C-terminal tail. Overall, we report the presence of two distant evolutionary paralogs of FtsZ in Odinarchaeota, with distinct filament assemblies and differing modes of membrane targeting. Our findings highlight the diversity of FtsZ proteins in the archaeal phylum Asgardarchaeota, providing valuable insights into the evolution and differentiation of tubulin-family proteins.},
}

@article {pmid40781093,
year = {2025},
author = {Kojima, CY and Henson, MW and Coelho, JT and Lanclos, VC and Bañuelas, D and Thrash, JC},
title = {Metagenomes and 1,313 metagenome-assembled genomes from a northern Gulf of Mexico coastal time series.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1388},
pmid = {40781093},
issn = {2052-4463},
support = {OCE-1931113//National Science Foundation (NSF)/ ; Simons Investigator in Aquatic Microbial Ecology Award//Simons Foundation/ ; Faculty Innovation Research Award//USC | Wrigley Institute for Environmental Studies, University of Southern California (USC Wrigley Institute for Environmental Studies)/ ; },
mesh = {Gulf of Mexico ; *Metagenome ; },
abstract = {Coastal and estuarine systems are hotspots of microbial diversity, activity, and biogeochemical cycling. Despite their importance, we have few comprehensive datasets of microbial populations across space and time from these ecosystems. To improve our understanding of these systems, we generated metagenomes averaging 46 M reads per sample (nearly 389 Gbp total) from four coastal/estuarine locations in the northern Gulf of Mexico across seven timepoints spanning nine months. Using standard methodology combined with a unique assembly and binning approach called subtractive iterative assembly (SIA), we generated 1,313 non-redundant metagenome-assembled genomes (MAGs) with 5% contamination or less and at least 75% completeness. We produced approximately a third of the MAGs through SIA. Actinobacteria and Proteobacteria were represented most. We recovered MAGs of great ecological significance including SAR11, Marine Group I (Thaumarcheaota), Marine Group II Euryarchaeota, SAR324, and Asgardarchaeota. We describe both our methodology using the SIA approach as well as the 28 metagenomes and 1,313 MAGs that provide a rich spatiotemporal dataset with which to study coastal and estuarine microbiology.},
}

Gulf of Mexico
*Metagenome

@article {pmid40780971,
year = {2025},
author = {Boulanger, N},
title = {Tick and host microbiotas: immunomodulators in tick-borne diseases?.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2025.07.009},
pmid = {40780971},
issn = {1471-5007},
abstract = {Vector-borne diseases have a growing impact on human and animal health. Metagenomics has been largely used to characterize the microbiome and has highlighted the key role of the microbiota in modulating the vector competence of insects. Currently, an integrated approach combining vector control, vaccine prevention, and drug treatment is being developed to limit the transmission of insect-borne pathogens. This is more complex for tick-associated diseases, considering the biology of the tick and the possibility of modifications of its microbiota in vector control. Conversely, because the skin is an essential interface in tick-borne diseases, an in-depth study of the precise role of the tick and host microbiota during tick bite and pathogen inoculation opens up new prospects for controlling these diseases.},
}

@article {pmid40780525,
year = {2025},
author = {Wang, X and Wang, H and Tian, Y and Lv, S and Li, M and Shi, L and Wang, J},
title = {Adaptation mechanism of anammox granular sludge to high ammonia nitrogen mixed nutrient wastewater: Regulating metabolism function through particle size differentiation.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122544},
doi = {10.1016/j.envres.2025.122544},
pmid = {40780525},
issn = {1096-0953},
abstract = {Organic matter is prevalent in real wastewater and affects the anaerobic ammonia oxidation (anammox) nitrogen removal process. Anammox granular sludge (AnGS) can effectively enrich anammox bacteria and improve its resistance to organic stress, but its macroscopic response and microscopic regulatory mechanisms have not been clarified. In this study, AnGS particle size classification driven by real mixed nutrient wastewater was revealed, and the adaptive regulation mechanism of different particle sizes (G1: < 1.18 mm, G2: 1.18-2.8 mm, G3: 2.8-4.75 mm, G4: > 4.75 mm) to organic matter was discussed. Mixed nutrients promoted extracellular polymeric substance secretion, especially polysaccharides, continuously increasing the AnGS particle size. Large particle size has high specific anammox specific activity, while the dominant role of anammox was strongest in G3, and the associated bacteria increase in G4. The dominant genus involved in anammox in G1-G3 was Ca. Kuenenia, which transited to Ca. Brocadia in G4 where the tightest and most active microbial community network was established. Metagenomics further elucidated the strategic differences of AnGS of different sizes in responding to organic stress. G3 enhanced the multi-pathway metabolic activity of Ca. Kuenenia through AnAOB stress response, while G4 maintained stable treatment performance by promoting metabolic coupling between Ca. Brocadia and associated bacteria. This study highlights organic matter regulated the diverse metabolic pathways of AnAOB by driving the particle size evolution, providing more insights into the complex ecological adaptation mechanisms of AnGS.},
}

@article {pmid40780487,
year = {2025},
author = {Fang, X and Cai, Y and Zhang, C and Li, W and Huang, Z and Zhang, W},
title = {Microbial Culture and Metagenomic Next-Generation Sequencing Results-Oriented Antibiotic Regimen (MCM-ROAR) Improve Clinical Outcomes of Periprosthetic Joint Infection.},
journal = {The Journal of arthroplasty},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.arth.2025.07.071},
pmid = {40780487},
issn = {1532-8406},
abstract = {BACKGROUND: This study aimed to assess the utility of a microbial culture and metagenomic Next-Generation (mNGS) sequencing results-oriented antibiotic regimen (MCM-RORA) in the management of periprosthetic joint infection (PJI).

METHODS: Patients suspected of PJI at our center were included in the study. Synovial fluid and periprosthetic tissues were collected for microbial culture and mNGS, and the results were interpreted by a panel of PJI experts. Following surgical intervention, patients were treated with antibiotics according to the MCM-RORA procedure recommended by the panel and received regular follow-up care. Data on medical records, infection control practices, and rates of antibiotic-related complications were documented and analyzed for comparison.

RESULTS: The study included 216 PJI cases, among which 143 underwent both microbial culture and mNGS testing. Of these, 100 cases were culture-positive, while 43 cases were culture-negative. Overall, a total of 53 (37.0%) PJI cases that underwent both microbial culture and mNGS testing modified their antibiotic regimens based on mNGS results. The overall infection control rate was approximately 86.8% (131 of 151) in culture-positive PJI cases and 81.5% (53 of 65) in culture-negative PJI cases. In culture-negative PJI cases, mNGS testing and modification of antibiotic regimens based on mNGS results significantly improved infection control rates compared with PJI cases without mNGS testing (94.4 versus 63.6%; P = 0.009), while decreasing the incidence of antibiotic-related complications (8.8 versus 36.4%; P = 0.017).

CONCLUSION: In conclusion, mNGS is an instructive diagnostic tool for PJI, and treating PJI with MCM-ROAR could markedly improve the clinical outcomes of PJI.},
}

@article {pmid40780374,
year = {2025},
author = {Mao, Z and Liu, C and Ni, J and Huang, M and Qu, W and Chen, W and Shen, Y and Qin, T and Gao, M and Zheng, S and Chen, Y},
title = {Gut derived (S)-Equol mitigates influenza viral pneumonia by modulating macrophage polarization via Nrf2 mediated AKT/ERK/NF-κB signaling pathways.},
journal = {Free radical biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.freeradbiomed.2025.08.004},
pmid = {40780374},
issn = {1873-4596},
abstract = {Respiratory virus including influenza A virus (IAV) infection induces alterations in gut microbiota structure and function, which in turn plays an essential role in the pathogenic process. Alterations in gut microbiota are usually accompanied with changes in metabolites. The specific relationship between dynamic changes in gut microbiota and serum metabolites in influenza remains unclear. In this study, we depicted dynamic changes in composition of gut microbiota by using metagenomic sequencing in an influenza mouse model. Through mass spectrometry based metabolomic, we identified (S)-Equol as a notable protective metabolite derived from intestinal flora. Serum (S)-Equol level decreased from the initial infection phase and increased gradually during the convalescence phase, which was positively associated with the changes in some Eggerthella and Bifidobacterium species. Antibiotic treatment reduced serum (S)-Equol level and exacerbated lung pathological damage. Oral administration of (S)-Equol relieved disease severity and controlled inflammatory infiltration. Mechanistically, (S)-Equol activated Nrf2 in macrophages, thereby inhibited AKT, ERK and NF-κB phosphorylation. The inhibition of these signaling pathways ultimately restrained pro-inflammatory cytokines release and repressed pro-inflammatory macrophage polarization. Moreover, serum (S)-Equol level was lower in influenza patients at progressed phase and was negatively correlated with serum levels of IL-6, IL-1β, and TNF-α. Collectively, our data highlighted gut derived (S)-Equol a promising postbiotic for alleviating influenza pneumonia.},
}

@article {pmid40780365,
year = {2025},
author = {Yang, R and Liu, Z and Liu, Y and Yang, Z and Wang, Z and Zhang, Y and Lei, J and Han, T and Wang, J and Li, Z},
title = {Coupling mechanisms of community assembly and pollutant removal in algal-bacterial granular sludge systems.},
journal = {Bioresource technology},
volume = {437},
number = {},
pages = {133122},
doi = {10.1016/j.biortech.2025.133122},
pmid = {40780365},
issn = {1873-2976},
abstract = {This study comparatively assessed algal-bacterial granular sludge (ABGS) decontamination performance and microbial community mechanisms under two cultivation modes: flocculated sludge transformed into ABGS (AS_ABGS) and aerobic granular sludge transformed into ABGS (AGS_ABGS). The results indicated that, AS_ABGS achieved superior pollutant removal (COD: 92.2 %, TN: 82.1 %, TP: 61.5 %) versus AGS_ABGS (COD: 96.3 %, TN: 75.1 %, TP: 53.3 %). Microbial community analysis revealed deterministic assembly dominated AS_ABGS, narrowing niches, and enhancing functional specialization of N/P-removing taxa. AS_ABGS exhibited higher modularity, robustness, and stronger positive algal-bacterial interactions (52.32 %). Conversely, stochastic assembly in AGS_ABGS yielded weaker interactions (50.45 %). Metagenomics confirmed AS_ABGS enriched N/P metabolic genes (amo, acc) may be driven by Thauera, Micavibrio, and Aquisediminimonas, while AGS_ABGS favored Amaricoccus and Rhodovulum but showed lower N/P gene abundance. This study highlights the effect of algal-bacterial ecological interactions mediated by functional genes on the decontamination efficiency of ABGS and provides valuable insights for advancing this method.},
}

@article {pmid40780319,
year = {2025},
author = {Wan, S and Liu, H and Zhu, G and Geng, Y and Li, W and Chen, L and Zhang, Y and Han, G},
title = {Decoding oxygen preference: Machine learning discovers functional genes in Bacteria.},
journal = {Genomics},
volume = {},
number = {},
pages = {111095},
doi = {10.1016/j.ygeno.2025.111095},
pmid = {40780319},
issn = {1089-8646},
abstract = {Predicting bacterial oxygen preference and identifying associated genes is critical in microbiology. This study developed a machine learning model using genomic features to predict bacterial oxygen preference and discover potential functional genes. Trained on a dataset of 1813 bacterial genomes, a Random Forest model achieved 90.62 % accuracy in predicting oxygen preference, outperforming prior methods. Feature analysis pinpointed key protein domains and candidate genes. Experimental overexpression of model-identified genes (encoding SOD, SAM radical enzyme, GCV-T, FDH domains) in Escherichia coli enhanced growth under aerobic conditions, validating their role in oxygen adaptation. Applying the model to rumen metagenomes revealed a predominantly anaerobic community. This work establishes machine learning as an effective strategy for bacterial oxygen preference prediction and functional gene identification, offering a novel strategy and tool for in-depth understanding of bacterial oxygen adaptation mechanisms, discovering key functional genes, and efficient exploration of uncultured microbial resources.},
}

@article {pmid40779937,
year = {2025},
author = {Xu, X and Jia, Y and Dong, Y and Yu, M and Xu, M and Zhang, C and Zhou, P and Yu, B and Lu, W and Liu, J},
title = {Viral-community-induced antibiotic resistance gene regulation throughout the process of sewage sludge composting and its subsequent application to a phosphate mining wasteland: A three-year, large-scale field study.},
journal = {Water research},
volume = {287},
number = {Pt A},
pages = {124308},
doi = {10.1016/j.watres.2025.124308},
pmid = {40779937},
issn = {1879-2448},
abstract = {The application of sewage sludge compost to phosphate mining wastelands improves soil quality, and provides a viable solution for sludge disposal. However, attention must be paid to antibiotic resistance genes (ARGs) in sewage sludge. Based on a large-scale field study, we comprehensively profiled the antibiotic resistome throughout the process of sewage sludge composting and its subsequent application to a phosphate mining wasteland. The trend of the ARG abundance in the phosphate mining wasteland after applying sewage sludge compost was consistent with the priming effect. The total ARG abundance in the phosphate mining wasteland increased by 38.3 % in the 1st year of soil reclamation but significantly decreased in the 3rd year. Nevertheless, multi-resistant plasmids persisted in the reclaimed soil. Our findings also support the contribution of viral communities to ARG regulation in phosphate mining wastelands, and the virus-ARG interactions were lifestyle- and host-dependent. Moreover, there was an overlap between the ARG and phage hosts, and phylogenetic coherence of ARG hosts against bacitracin, sulfonamide, macrolide-lincosamide-streptogramin, polymyxin, and rifamycin was observed.},
}

@article {pmid40779699,
year = {2025},
author = {Bao, Y and Ho, YW and Shen, Z and Lam, EY and Fang, JKH and Leung, KMY and Lee, PKH},
title = {Ecological Roles and Shared Microbes Differentiate the Plastisphere from Natural Particle-Associated Microbiomes in Urban Rivers.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c06538},
pmid = {40779699},
issn = {1520-5851},
abstract = {The "plastisphere," comprising microbes associated with microplastics (MPs), may have substantial ecological impacts on riverine ecosystems. However, little is known about how the microbiomes associated with anthropogenic MPs compare with those associated with natural particles (NPs) in urban rivers with varying MP pollution levels. We therefore conducted a comparative analysis of the metagenomes associated with MPs and NPs (100-5000 μm) and river water (RW) across 10 urban river systems. Although we found similarities in taxonomic and functional compositions between the microbiomes associated with MPs and NPs, the plastisphere exhibited distinct associations with specialized taxa and life-history strategies. These unique traits enhanced the potential of the plastisphere for complex carbohydrate and plastic degradation, nitrate and nitric oxide reduction, and antibiotic resistance and virulence compared with the NP or RW microbiomes. Furthermore, MPs supported the sharing of unique microbes with the surrounding RW; these shared microbes possessed enhanced horizontal gene transfer capabilities and potentially could disperse traits of the plastisphere into the broader RW microbiomes. This study highlights the distinct ecological roles and shared microbes of the plastisphere, indicating that MP pollution may substantially and uniquely impact the function and health of riverine ecosystems.},
}

@article {pmid40778433,
year = {2025},
author = {Li, W and Pan, S and Qian, J and Xia, Y and Han, G and Liu, J and Wang, Y and Peng, L and Huang, S and Chen, Y and Xie, Y and Xu, J and Zhang, W and Zhou, C},
title = {Comparisons of blood, upper respiratory tract and gut viromes from patients with lung cancer and healthy persons.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.70075},
pmid = {40778433},
issn = {1097-0215},
support = {TZKY20230204//Clinical Research Project of Taizhou Clinical Medical College, Nanjing Medical University/ ; TZKY20230305//Key Research Project of Taizhou Clinical Medical College, Nanjing Medical University/ ; 24142202800//Shanghai Science and Technology Innovation Action Plan/ ; 82341106//National Natural Science Foundation of China/ ; },
abstract = {Lung cancer is the leading cause of cancer-related mortality globally. Although some studies have proposed a potential association between viral infections and lung cancer pathogenesis, the evidence remains inconclusive. This study characterized the virome in blood, upper respiratory tract, and gut samples from 200 lung cancer patients and 75 healthy controls, with the goal of identifying potential microbial biomarkers for lung cancer, using viral metagenomics. Significant differences in viral diversity and composition were observed between cancer and healthy groups, with lower similarities in blood, respiratory, and gut viromes. Notably, LUSC and LUAD groups showed high similarity, with LUAD exhibiting the most diverse virome. In blood, Anelloviridae dominated in cancer patients, while Retroviridae was more abundant in specific subgroups. The upper respiratory tract virome in cancer patients was enriched with Siphoviridae and Myoviridae, contrasting with Retroviridae in healthy individuals. Gut viromes were dominated by Podoviridae and Virgaviridae in cancer patients, with Virgaviridae showing higher abundance compared to healthy controls. Alpha and beta diversity analyses indicated significant differences in blood and respiratory viromes but not in gut viromes. STAMP and LEfSe analyses identified Anelloviridae and Siphoviridae as potential biomarkers for lung cancer. Additionally, 242 anelloviruses with complete ORF1 were isolated, revealing high genetic diversity. These findings highlight distinct virome profiles in lung cancer patients, offering insights into potential diagnostic and therapeutic targets.},
}

@article {pmid40778208,
year = {2025},
author = {Ma, W and Lian, L and Guo, L and Wu, Y and Huang, L},
title = {A synbiotic combination of mixed probiotics and oligofructose restores intestinal microbiota disturbance in DSS-induced colitis in mice.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1582155},
pmid = {40778208},
issn = {1664-302X},
abstract = {Both probiotics and prebiotics can regulate gut microbiota and produce metabolites that are beneficial to the host, showing potential therapeutic prospects for ulcerative colitis (UC). This study aimed to investigate the therapeutic effects and mechanisms of low-, medium-, and high-dose probiotic mixtures (Bifidobacterium animalis subsp. lactis XLTG11: Lactobacillus paracasei Glory LP16: Lactiplantibacillus plantarum CCFM8661) combined with oligofructose (FOS) on DSS-induced colitis mice. Male BALB/c mice were induced with 2.5% DSS for colitis and then treated with low-, medium-, and high-dose mixed probiotics and oligofructose synbiotics (6 × 10[6] CFU probiotics + 1.5 mg FOS synbiotics/day, 6 × 10[7] CFU probiotics + 1.5 mg FOS synbiotics/day, and 6 × 10[8] CFU probiotics + 1.5 mg FOS synbiotics/day) for 1 week. Colonic inflammation was evaluated by body weight, diarrhea index, immune organ index and colon length; the protective effect of synbiotics on the intestinal barrier was evaluated by HE staining, ELISA and RT-qPCR to detect the degree of intestinal tissue damage, inflammatory cytokines, intestinal permeability and tight junction proteins. In addition, the intestinal microbiota and short-chain fatty acids (SCFAs) were estimated by metagenomics and LC-MS, respectively, to analyze the mechanism of action of synbiotics in alleviating colitis. The results showed that the combination of mixed probiotics and oligofructose could significantly alleviate the symptoms of colitis in mice, improve the weight loss symptoms of DSS mice, reduce the diarrhea index, restore the colon length, reduce tissue pathological damage, and improve the integrity of the intestinal barrier. In addition, through metagenomic data analysis, mixed probiotics combined with oligofructose can enhance the diversity and richness of gut microbiota, increase the abundance of beneficial bacteria Bifidobacterium and Lactobacillus, promote the production of SCFAs, and enhance intestinal barrier function. It is worth noting that the therapeutic effect of synbiotics depends on the dose of mixed probiotics. This study explored the alleviating effect of synbiotics containing mixed probiotics and oligofructose at different doses on UC, and provided a theoretical basis for guiding the development and use of synbiotic preparations that regulate the homeostasis of gut microbiota.},
}

@article {pmid40778207,
year = {2025},
author = {Ren, M and Wang, J},
title = {Biogeography of soda lake microbiome and uneven cross-continent transition rates.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1614302},
pmid = {40778207},
issn = {1664-302X},
abstract = {Microbial dark matter in soda lakes has been increasingly illuminated, however, much remains unknown about microbial biogeography at the global scale and underlying mechanisms. To study microbial biogeography and dispersal patterns, we analyzed 51 soda lake metagenomes collected from key global regions, including 37 from the Kulunda Steppe in South Siberia, Mongolia, and the Cariboo Plateau in Canada, as well as 14 newly sequenced samples from the East African Rift Valley. We found that there were 575 widespread taxa such as the dominant archaeal Haloarchaeota and actinobacterial Nitriliruptor persistently inhabiting global soda lakes. We further identified 1,217 region-specific taxa, with Africa containing the highest proportion of geographical endemism (66.72%). Such effects of dispersal limitation on microbial assembly of global soda lakes were supported by the significant distance-decay relationships for taxonomic and functional composition, and genomic similarity. For example, microbial genomic divergence was closely associated with their geographical distance, showing that both inter- and intraspecies genome similarities decayed with distance. This concurs with the uneven dispersal history among continental microbiomes, indicated by the at least one order of magnitude lower transition rates between Africa and other continents than between Asia and North America. Our results revealed that the global biogeography of soda lake microbial communities across three continents and their distinct transition history between continents. These findings highlight the critical role of microbial evolutionary history associated with dispersal limitation in shaping their geographical distribution in extreme environments.},
}

@article {pmid40777923,
year = {2025},
author = {Ramos, SF and Siguenza, N and Zhong, W and Mohanty, I and Lingaraju, A and Richter, RA and Karthikeyan, S and Lukowski, AL and Zhu, Q and Nunes, WDG and Zemlin, J and Xu, ZZ and Hasty, J and Dorrestein, PC and Panda, S and Knight, R and Zarrinpar, A},
title = {Metatranscriptomics Uncover Diurnal Functional Shifts in Bacterial Transgenes with Profound Metabolic Effects.},
journal = {Cell host & microbe},
volume = {33},
number = {7},
pages = {1057-1072},
pmid = {40777923},
issn = {1934-6069},
support = {R01 EB030134/EB/NIBIB NIH HHS/United States ; R01 HL148801/HL/NHLBI NIH HHS/United States ; I01 BX005707/BX/BLRD VA/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 CA236352/CA/NCI NIH HHS/United States ; P30 DK063491/DK/NIDDK NIH HHS/United States ; U24 CA248454/CA/NCI NIH HHS/United States ; R01 AI163483/AI/NIAID NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; U01 CA265719/CA/NCI NIH HHS/United States ; P30 CA014195/CA/NCI NIH HHS/United States ; R01 DK136117/DK/NIDDK NIH HHS/United States ; R01 CA258221/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; *Circadian Rhythm ; Mice ; Cecum/microbiology ; *Transgenes ; Escherichia coli/genetics/metabolism ; *Gastrointestinal Microbiome/genetics ; *Transcriptome ; Diet, High-Fat ; Metagenomics ; Metagenome ; Mice, Inbred C57BL ; Male ; *Bacteria/genetics/metabolism ; Gene Expression Profiling ; },
abstract = {Diurnal rhythmicity in the gut maintains gut integrity, circadian rhythms, and metabolic homeostasis. However, existing studies focus on microbial composition rather than transcriptional activity. To understand microbial functional dynamics, we characterize diurnal fluctuations in the mouse cecal metatranscriptome and metagenome under high-fat diet and time-restricted feeding (TRF). We show that metatranscriptomics uncover TRF-induced time-dependent microbial functional shifts that are undetectable with metagenomics alone. We also found bile salt hydrolase (bsh) from Dubosiella newyorkensis exhibits diurnal expression in the TRF group. Engineering this bsh, along with other candidates, into a native E. coli chassis reveals distinct differences in deconjugation and amidation activities, underscoring functional specificity. In vivo, a D. newyorkensis bsh improves insulin sensitivity, glucose tolerance, and body composition, suggesting a direct role in TRF metabolic benefits. This study highlights how coupling metatranscriptomics with engineered bacterial systems is a powerful approach for uncovering time-dependent bacterial functions related to health and disease.},
}

Animals
*Circadian Rhythm
Mice
Cecum/microbiology
*Transgenes
Escherichia coli/genetics/metabolism
*Gastrointestinal Microbiome/genetics
*Transcriptome
Diet, High-Fat
Metagenomics
Metagenome
Mice, Inbred C57BL
Male
*Bacteria/genetics/metabolism
Gene Expression Profiling

@article {pmid40777436,
year = {2025},
author = {Shrestha Gurung, BD and Rayamajhi, M and Maharjan, N and Do, T and Bhandari, D and Yadav, R and Aryal, S and Gnimpieba, EZ},
title = {Forecasting Urban Wastewater Microbiome Dynamics Using a Digital Twin Framework.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.21.666059},
pmid = {40777436},
issn = {2692-8205},
abstract = {Urban wastewater microbiomes are complex and temporally dynamic, offering valuable insight into community-scale microbial ecology and potential public health trends. However, existing wastewater-based studies often remain descriptive, lacking tools for predictive modeling. In this study, we introduce a digital twin framework that forecasts microbial abundance trajectories in urban wastewater using an interpretable generative model, Q-net. Trained on a 30-week longitudinal metagenomic dataset from seven wastewater treatment plants, the model captures temporal microbial dynamics with high fidelity (R [2] > 0.97 for key taxa; R [2] = 0.998 at the final timepoint). Beyond accurate forecasting, Q-net provides transparent model structure through conditional inference trees and enables simulation of realistic microbial trends under hypothetical scenarios. This work demonstrates the potential of digital twins to move wastewater microbiome studies from static snapshots to dynamic, predictive systems, with broad implications for environmental monitoring and microbial ecosystem modeling.},
}

@article {pmid40777250,
year = {2025},
author = {Burkhart Colorado, AS and Nusbacher, NM and O'Connor, J and Marden, T and Higgins, J and Neff, CP and Fiorillo, S and Campbell, TB and Borok, M and Boyd, K and Sterrett, J and Palmer, BE and Lozupone, C},
title = {The impact of western versus agrarian diet consumption on gut microbiome composition and immune dysfunction in people living with HIV in rural and urban Zimbabwe.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.18.665619},
pmid = {40777250},
issn = {2692-8205},
abstract = {BACKGROUND: People living with HIV (PLWH) suffer from chronic inflammation even with effective antiretroviral therapy (ART). A high-fat, low-fiber western-type diet has been linked with inflammation, in part through gut microbiome changes. In sub-Saharan Africa (SSA), a region with high HIV burden, urbanization has been linked with a shift from traditional agrarian towards westernized diets, and with changes in food security. To explore the relationship between diet, inflammation, and the gut microbiome in PLWH, we enrolled 1) ART Naïve PLWH who provided samples before and after 24 weeks of ART, 2) PLWH on ART at both timepoints and 3) HIV-seronegative controls. Individuals were evenly recruited from rural and urban Zimbabwe (locations were 145 kilometers/90 miles apart). Using a food frequency survey designed to measure intake of agrarian versus western-type food items in Zimbabwe, we determined how diet differs with urbanization, HIV-infection and treatment, and is related to inflammation and the gut microbiome.

RESULTS: Individuals residing in a rural area of Zimbabwe less frequently consumed high-fat, low-fiber western type food items and had lower consumption of diverse food items overall, except for sadza-a subsistence staple-processed from home-grown grains. Consumption of a more western-type diet correlated with lower CD4+ T cell percentage in untreated and treated PLWH and with increased T cell exhaustion in PLWH on ART. PLWH on ART at time of enrollment also consumed diverse food items at a lower frequency and more often were underweight. Low food consumption correlated with muted improvements in T cell exhaustion after 24 weeks of ART. Individuals residing in the rural area had more Prevotella -rich/ Bacteroides -poor microbiomes, but this did was not significantly mediated by diet. western diet consumption reduced the diversity of carbohydrate substrate degradation capabilities in the microbiome, based on predictions made using metagenomic polysaccharide utilization loci.

CONCLUSIONS: Taken together, this work supports that consumption of more high-fat/low-fiber type food items has the potential to exacerbate HIV pathogenesis in a sub-Saharan setting where HIV burden is high and reinforces the importance of nutritional support for promoting immunologic response to ART in PLWH in SSA.},
}

@article {pmid40778068,
year = {2023},
author = {Moreland, RB and Choi, BI and Geaman, W and Gonzalez, C and Hochstedler-Kramer, BR and John, J and Kaindl, J and Kesav, N and Lamichhane, J and Lucio, L and Saxena, M and Sharma, A and Tinawi, L and Vanek, ME and Putonti, C and Brubaker, L and Wolfe, AJ},
title = {Beyond the usual suspects: emerging uropathogens in the microbiome age.},
journal = {Frontiers in urology},
volume = {3},
number = {},
pages = {1212590},
pmid = {40778068},
issn = {2673-9828},
abstract = {The advent of sensitive enhanced culture (metaculturomic) and culture-independent DNA-based (metagenomic) methods has revealed a rich collection of microbial species that inhabit the human urinary tract. Known as the urinary microbiome, this community of microbes consists of hundreds of distinct species that range across the entire phylogenetic spectrum. This new knowledge clashes with standard clinical microbiology laboratory methods, established more than 60 years ago, that focus attention on a relatively small subset of universally acknowledged uropathogens. Increasing reports support the hypothesis that this focus is too narrow. Single uropathogen reports are common in women with recurrent urinary tract infection (UTI), although wider disruption of their urinary microbiome is likely. Typical "UTI" symptoms occur in patients with "no growth" reported from standard culture and sometimes antibiotics improve these symptoms. Metaculturomic and metagenomic methods have repeatedly detected fastidious, slow growing, and/or anaerobic microbes that are not detected by the standard test in urine samples of patients with lower urinary tract symptoms. Many of these microbes are also detected in serious non-urinary tract infections, providing evidence that they can be opportunistic pathogens. In this review, we present a set of poorly understood, emerging, and suspected uropathogens. The goal is to stimulate research into the biology of these microbes with a focus on their life as commensals and their transition into pathogens.},
}

@article {pmid40777179,
year = {2025},
author = {Yu, X and Huang, L and Wang, Y and Li, L and Lu, W and Zhang, Z and Wang, H},
title = {Bifidobacterium longum subsp. infantis CCFM1426 enhances the anti-colitic effect of vitamin A via retinoic acid restoration and gut microbiota modulation in ulcerative colitis mice.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1644649},
pmid = {40777179},
issn = {2296-861X},
abstract = {BACKGROUND: Ulcerative colitis (UC) is a chronic inflammatory bowel disease with increasing global prevalence, making it a significant health concern. Although vitamin A (VA) plays a beneficial role in UC management, its therapeutic efficacy is limited by impaired absorption and disrupted retinoic acid (RA) metabolism. Gut microbiota are known to influence VA metabolic pathways, offering potential targets to enhance VA bioavailability and efficacy.

METHODS: A dextran sulphate sodium (DSS)-induced mouse model of colitis was established to evaluate the therapeutic effects of co-administering Bifidobacterium longum subsp. infantis CCFM1426 with vitamin A. Body weight, disease activity index (DAI) and colon length were monitored in mice with DSS-induced colitis. Serum levels of intestinal injury markers, inflammatory cytokines, antioxidant enzymes and colonic RA levels were measured using ELISA kits. Metagenomic analysis investigated gut microbiota composition.

RESULTS: It was indicated that the VA and CCFM1426 combination significantly improved colon length and DAI, enhanced serum levels of intestinal injury markers (lipopolysaccharide-binding protein, intestinal fatty acid-binding protein, diamine oxidase) and cytokines (IL-6, TNF-α, IL-10), and restored antioxidant capacity. The combination demonstrated superior efficacy in colonic RA levels and contributed to gut microbiota diversity restoration. Metabolomics analysis showed that colitis mice treated with the combination had higher levels of eicosapentaenoic acid, adenosine and anandamide.

CONCLUSION: These findings provide novel evidence that co-administration of CCFM1426 and VA synergistically alleviates colitis by enhancing RA bioavailability through microbiota-dependent pathways.},
}

@article {pmid40776919,
year = {2025},
author = {Chen, K and Lyu, X and Liu, X and Bi, Y and Wang, Z},
title = {Case Report: Endogenous endophthalmitis caused by Listeria monocytogenes infection in patients with end-stage renal disease.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1643137},
pmid = {40776919},
issn = {2296-858X},
abstract = {PURPOSE: This paper reports a rare case of endogenous Listeria monocytogenes endophthalmitis caused by hemodialysis in end-stage renal disease (ESRD).

METHODS: The patient was a 70-year-old female. The best-corrected visual acuity (BCVA) was light perception (LP). Endogenous endophthalmitis was diagnosed based on clinical manifestations and auxiliary examinations. Pathogenic microbial metagenomic detection of intraocular aqueous was used to identify Listeria monocytogenes. As multiple investigations showed no source of infection, a standardized treatment plan was proposed.

RESULTS: The treatment included the local application of antibiotics, glucocorticoids and cycloplegic drugs, vitrectomy, intravitreal injection of vancomycin and ceftazidime, anterior chamber irrigation, and systemic antibiotic treatment after the operation. After treatment, the inflammation subsided, and the BCVA at discharge was hand movement (HM).

CONCLUSION: Our study highlights the importance of rapid pathogenic microbial metagenomic detection and timely standardized intervention in the treatment of endogenous endophthalmitis.},
}

@article {pmid40776541,
year = {2025},
author = {Hyun, TK},
title = {Composition, Diversity, and Functional Roles of the Rhizosphere Microbiome in Panax ginseng.},
journal = {The plant pathology journal},
volume = {41},
number = {4},
pages = {425-436},
doi = {10.5423/PPJ.RW.02.2025.0027},
pmid = {40776541},
issn = {1598-2254},
support = {RS-2024-00333380//National Research Foundation of Korea/ ; },
abstract = {The rhizosphere microbiome of Panax ginseng plays a crucial role in promoting plant growth, enhancing stress resilience, and facilitating the biosynthesis of pharmacologically significant ginsenosides. However, continuous monocropping disrupts the microbial community balance, leading to soil degradation, the proliferation of soilborne pathogens, and decreased crop productivity. Advanced multi-omics technologies, such as metagenomics and metabolomics, have provided valuable insights into the structure and function of the ginseng rhizosphere microbiome. These studies highlight its potential for nutrient mobilization, disease suppression, and stress mitigation. Root exudates, including phenolic acids and ginsenosides, influence microbial composition; however, they may also exacerbate soil imbalances by promoting pathogenic fungi. Conversely, beneficial microbes, such as phosphate-solubilizing bacteria and siderophore-producing strains, enhance nutrient availability, mitigate heavy metal toxicity, and suppress pathogens through bioactive metabolites. This review emphasizes the functional roles of the ginseng rhizosphere microbiome and highlights knowledge gaps in leveraging microbial interactions for sustainable cultivation. A more comprehensive understanding of plant-microbe interactions, coupled with the integration of microbiome-driven strategies, can enhance ginseng productivity, boost bioactive compound yields, and support environmentally sustainable agricultural practices. These findings provide a foundation for advancing microbiome research and addressing challenges in ginseng cultivation.},
}

@article {pmid40776036,
year = {2025},
author = {Upadhyay, U and Dhar, E and Bomrah, S and Syed-Abdul, S},
title = {Unraveling the Role of Gut Microbiota in Colorectal Cancer: A Global Perspectives and Biomarkers as Early Screening Tool for Colorectal Cancer.},
journal = {Studies in health technology and informatics},
volume = {329},
number = {},
pages = {1145-1149},
doi = {10.3233/SHTI251018},
pmid = {40776036},
issn = {1879-8365},
mesh = {*Colorectal Neoplasms/diagnosis/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Early Detection of Cancer/methods ; *Biomarkers, Tumor ; Metagenomics ; },
abstract = {Colorectal cancer (CRC), the second deadliest cancer globally, is closely tied to gut microbiota, opening doors for early detection and treatment. This review of 45 studies (2018-2024) highlights microbial biomarkers like Fusobacterium nucleatum, Bacteroides fragilis, and Parvimonas micra, with strong diagnostic accuracy (AUC >80%) across populations. Techniques like 16S rRNA sequencing, metagenomics, and shotgun sequencing revealed these links. Gut-based diagnostics offer a non-invasive, cost-effective alternative to colonoscopy and FIT for spotting early CRC and precancerous lesions. Yet, regional microbial differences and inconsistent methods-sample processing and sequencing-hinder comparability. Standardizing approaches and exploring fungi and viruses are key to unlocking microbiota's full potential in CRC prevention, diagnosis, and therapy.},
}

*Colorectal Neoplasms/diagnosis/microbiology
Humans
*Gastrointestinal Microbiome
*Early Detection of Cancer/methods
*Biomarkers, Tumor
Metagenomics

@article {pmid40775451,
year = {2025},
author = {Crognale, S and Amalfitano, S and Casentini, B and Di Pippo, F and Fazi, S and Tonanzi, B and Rossetti, S},
title = {Microbial signature of groundwater mixing in geothermal areas: insights from the Cimino-Vico volcanic system (central Italy).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {28941},
pmid = {40775451},
issn = {2045-2322},
support = {CN_00000033//Ministero dell'Università e della Ricerca/ ; CN_00000033//Ministero dell'Università e della Ricerca/ ; },
mesh = {*Groundwater/microbiology ; Italy ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Water Microbiology ; *Hot Springs/microbiology ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The complex structure and dynamics of geothermal ecosystems strongly affect the spatial distribution and activity of aquatic microbial communities. The interactions between groundwaters and thermal waters represent an additional selective factor. A deeper understanding of microbial diversity, metabolic potential, and ecological interactions in groundwater mixing zones is essential for evaluating their impact on biogeochemical cycles (such as sulfur, nitrogen, and carbon) and predicting the ecological consequences of water mixing on ecosystem functioning. In this study, the taxonomic diversity and metabolic potentialities of microbial communities in groundwater and thermal waters revealed the occurrence of novel thermophiles able to cope with extreme physical-chemical conditions and high concentrations of toxic elements, such as arsenic, characteristics of the studied area. Furthermore, a core microbiome composed of the families Burkholderiaceae, Caulobacteraceae, Halothiobacillaceae, and Sulfurovaceae was identified as markers of the interaction between the two water compartments. Our findings emphasize the key role of microbial communities in S-, As-, and N-related biogeochemical cycles of geothermal areas.},
}

*Groundwater/microbiology
Italy
*Microbiota
*Bacteria/classification/genetics/isolation & purification
*Water Microbiology
*Hot Springs/microbiology
Ecosystem
RNA, Ribosomal, 16S/genetics

@article {pmid40774824,
year = {2025},
author = {Lee, I and Kim, BS and Suk, KT and Lee, SS},
title = {Gut Microbiome-Based Strategies for the Control of Carbapenem-Resistant Enterobacteriaceae.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2406017},
doi = {10.4014/jmb.2406.06017},
pmid = {40774824},
issn = {1738-8872},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Carbapenem-Resistant Enterobacteriaceae/drug effects/physiology ; Humans ; Fecal Microbiota Transplantation ; *Enterobacteriaceae Infections/prevention & control/microbiology/therapy ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Animals ; Carbapenems/pharmacology ; Antimicrobial Stewardship ; },
abstract = {Carbapenem-resistant Enterobacteriaceae (CRE) represent a critical antimicrobial resistance threat due to their resistance to last-resort antibiotics and high transmission potential. While conventional strategies-such as infection control, antimicrobial stewardship, and novel antibiotic development-remain essential, growing attention has shifted toward the gut microbiome, which plays a central role in mediating colonization resistance against CRE. Disruption of the intestinal microbiota-primarily driven by antibiotic exposure and further exacerbated by non-antibiotic drugs such as proton pump inhibitors-reduces microbial diversity and impairs functional integrity, facilitating CRE acquisition, prolonged carriage, and horizontal transmission. In response, microbiome-based strategies-including microbiome disruption indices (MDIs), fecal microbiota transplantation (FMT), and rationally designed symbiotic microbial consortia-are being explored as novel approaches for CRE prevention and decolonization. Mechanistic studies have shown that colonization resistance is mediated by both direct mechanisms (e.g., nutrient competition, short-chain fatty acid production) and indirect mechanisms (e.g., immune modulation via IL-36 signaling). Advances in metagenomics, metabolomics, and culturomics have enabled high-resolution profiling of gut microbial communities and their functional roles. Emerging preclinical and clinical evidence supports the potential of microbiome-informed interventions to predict infection risk, enhance antimicrobial stewardship, and guide the development of next-generation probiotics targeting CRE. Longitudinal studies continue to evaluate the efficacy of FMT and synthetic microbial consortia in eradicating intestinal CRE colonization. Collectively, these insights underscore the promise of gut microbiome science as a complementary and innovative strategy for CRE control in the post-antibiotic era.},
}

*Gastrointestinal Microbiome/drug effects
*Carbapenem-Resistant Enterobacteriaceae/drug effects/physiology
Humans
Fecal Microbiota Transplantation
*Enterobacteriaceae Infections/prevention & control/microbiology/therapy
Anti-Bacterial Agents/pharmacology/therapeutic use
Animals
Carbapenems/pharmacology
Antimicrobial Stewardship

@article {pmid40774611,
year = {2025},
author = {Mohammadi, MR and Moradkasani, S and Latifian, M and Esmaeili, S},
title = {Coxiella burnetii: Emerging threats, molecular insights, and advances in diagnosis and control measures.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107213},
doi = {10.1016/j.mimet.2025.107213},
pmid = {40774611},
issn = {1872-8359},
abstract = {Coxiella burnetii, a Gram-negative, obligate intracellular bacterium and causative agent of Q fever, is a re-emerging zoonotic pathogen with a complex transmission cycle involving livestock (cattle, sheep, and goats), diverse terrestrial and aquatic wildlife, arthropod vectors (ticks and fleas), and resilient environmental reservoirs, such as free-living amoebae. Humans are mainly infected by inhaling contaminated aerosols, especially during parturition. This review offers an integrative synthesis of current research across six key domains: ecological reservoirs, diagnostic strategies, molecular epidemiology, therapeutic challenges, vaccine development, and the One Health approach. We first examined emerging insights into host and vector diversity, including underexplored aquatic and semi-aquatic species, and environmental factors sustaining endemicity. We then assessed recent diagnostic innovations, such as multiplex and digital PCR, LAMP, metagenomic sequencing, and immunohistochemistry, alongside conventional serological tools, such as ELISA and IFA. Given the taxonomic complexity introduced by genetically related Coxiella-like endosymbionts, we highlight the necessity of high-resolution molecular typing platforms, such as MLVA, MST, and SNP analysis, for accurate strain discrimination. In clinical and environmental contexts, sample matrices now include blood, milk, feces, urine, respiratory secretions, and ectoparasites, enabling more sensitive surveillance. Despite this progress, Q fever control remains challenging because of nonspecific symptoms, diagnostic delays, chronic complications, and reliance on prolonged antibiotic therapy. Advances in antimicrobial testing and evolving vaccine strategies offer hope; however, durable cross-strain protection remains elusive. Adopting a One Health approach, this review highlights the key knowledge gaps and strategic priorities for reducing the global burden of C. burnetii across human, animal, and environmental health sectors.},
}

@article {pmid40774558,
year = {2025},
author = {Li, Y and Dai, L and Zhang, L and Shen, X and Zhang, X and Yang, Y and Guan, Y},
title = {Metagenomic insights into the changes of runoff water quality in a deep tunnel drainage system.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122509},
doi = {10.1016/j.envres.2025.122509},
pmid = {40774558},
issn = {1096-0953},
abstract = {Deep tunnel retrofitting of conventional urban drainage systems represents a pivotal strategy for mitigating stormwater pollution and combating flooding. While microbial-driven biogeochemical cycles in stormwater are constrained by taxonomic diversity and environmental variability, the interplay between hydrogeochemical dynamics and microbial functional genes during storage remains poorly characterized. In this study, an in situ stormwater self-purification system was constructed to investigate seasonal water quality evolution, microbial community dynamics, and functional gene regulation in Shenzhen, China. Compared with continuous rainfall events, initial postdrought stormwater events resulted in significantly elevated pollutant loads. Dissolved organic matter analysis revealed that endogenous contaminants accounted for 76% of the total contaminants, characterized by high microbial bioavailability and low humification after 14 days of storage. The storage of samples favors the enrichment of functional microorganisms such as Plancomycetota, Verrucomicrobiota and Proteobacteria. A quantitative assessment of 62 functional genes linked to carbon (C)/nitrogen (N)/sulfur (S) cycling identified temperature, oxidation‒reduction potential ammonia nitrogen, chemical oxygen demand and total nitrogen as critical drivers of microbial community succession and gene abundance. N cycle genes presented heightened sensitivity to environmental fluctuations, with increased stability and metabolic activity observed in wet season samples. Comparative analysis demonstrated that deep tunnel samples presented more stable functional gene profiles and enriched microbial consortia relative to their surface counterparts. These findings elucidate the mechanistic relationships between hydrogeochemical variables and microbial functional resilience in stormwater storage systems. This work advances the process-level understanding of biochemical cycles mediated by C, N and S transformations, offering actionable insights for optimizing urban drainage infrastructure and microbial-mediated pollution control strategies.},
}

@article {pmid40774536,
year = {2025},
author = {Wang, Y and Chen, C and Cheng, L and Jiang, C and Zhou, B and Zhang, Y and Qin, J and Huang, J and Li, X},
title = {Wastewater-based surveillance reveals distinct resistome profiles in younger and older populations.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126950},
doi = {10.1016/j.envpol.2025.126950},
pmid = {40774536},
issn = {1873-6424},
abstract = {Antimicrobial resistance (AMR) poses serious health risks, especially to the older population. In this study, differences in antibiotic resistance genes (ARGs) between younger and older populations were investigated using wastewater-based surveillance. Wastewater samples were collected from four nursing homes, three high schools, and two residential areas in Changshu, China. Metagenomics was used to analyze the diversity and abundance of ARGs and their host characteristics, with a focus on pathogen-related ARGs. The age representativeness of the wastewater samples was verified by examining the expression levels of senescence-related genes and species composition. The results showed that the diversity of ARGs in wastewater samples from the nursing homes was higher than that from schools and residential buildings, with 1264, 986, and 1002 subtypes, respectively. Besides, ARG abundance was also higher in the samples from nursing homes, particularly for those clinically relevant β-lactam resistance genes (e.g., blaVEB, blaTEM, and blaCTX-M families). Pathogen-related ARGs also had similarly higher diversity and coverage in the samples from nursing homes. Key pathogens (e.g., Escherichia coli and Klebsiella pneumoniae) had more complex resistance profiles in nursing home samples. These observations unequivocally indicate that the older population has a higher overall resistance level than the younger population. This study also demonstrates that wastewater-based surveillance can effectively assess the level of ARG carriage in specific subgroups, providing an important basis for supplementing clinical surveillance and developing targeted prevention and control strategies.},
}

@article {pmid40774442,
year = {2025},
author = {Qiu, H and Wang, Y and Bai, M and Zhao, W and Zhang, J and Yang, C and Su, S and Qin, Y and Wang, C and Zhao, Z},
title = {Novel side-stream-enhanced biological phosphorus removal system for highly efficient nitrogen and phosphorus removal: performance, microorganisms, and mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133085},
doi = {10.1016/j.biortech.2025.133085},
pmid = {40774442},
issn = {1873-2976},
abstract = {A novel side-stream-enhanced biological phosphorus removal system was successfully operated for 203 days, with controlled influent carbon-to-phosphorus ratio (25.8), side-stream influent (20 %), and oxidation-reduction potential (-150 to - 300 mV). This system facilitated synergistic collaboration of Candidatus Accumulibacter, Dechloromonas, and side-stream fermentative microorganisms, without relying on Tetrasphaera. During two-stage operation, COD and PO4[3-]-P removal efficiencies increased from 73.7 % and 75.3 % to 83.2 % and 91.8 %, respectively. The system exhibited high biological activity, with peak phosphorus release of 49.3 mg·L[-1], a 66 % increase from Phase I. Microbial analysis revealed the enrichment of Candidatus Accumulibacter (12.9 %) and Dechloromonas (6.2 %) in the mainstream reactor. Key genes and enzymes related to phosphorus removal were also enriched. Overall, the experiment achieved stable system operation, with Candidatus Accumulibacter and Dechloromonas effectively collaborating with fermentative microbes. Future research will focus on optimizing parameters and evaluating their potential for large-scale wastewater treatment applications to enhance stability and reduce costs.},
}