@article {pmid40663936,
year = {2025},
author = {Wang, Z and Rong, XL and Dai, CX and Wang, Q and Lu, LF and Zhang, WT and Zhang, L and Chen, QQ and Liu, EH},
title = {Fucoidan alleviates renal fibrosis in mice via Akkermansia muciniphila-mediated suppression of NEU1-TLR4-NFκB signaling axis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {145},
number = {},
pages = {157060},
doi = {10.1016/j.phymed.2025.157060},
pmid = {40663936},
issn = {1618-095X},
abstract = {BACKGROUND: Fucoidan, a bioactive sulfated polysaccharide, is renowned for its extensive range of biological activities, including anticancer activity, antioxidative properties, immune activation and has demonstrated supportive therapeutic effects in treating kidney ailments. However, the underlying mechanism related to renal fibrosis remains not fully understood.

PURPOSE: The aim of this study was to elucidate the protective effects and mechanism of FPS against renal fibrosis with a focus on gut-kidney axis.

METHODS: We established renal fibrosis models in mice using unilateral ureteral obstruction (UUO), folic acid (FA) challenge, or a microbiota-depleted, with continuous oral administration of FPS, Akkermansia muciniphila (AKK), or acetate at specified doses and intervals. Simultaneously, we examined the impact of FPS on epithelial mesenchymal transformation in cultured HK-2 and investigated the associated mechanisms.

RESULTS: In this study, we demonstrate that fucoidan administration reduces renal collagen deposition, inflammation, epithelial mesenchymal transformation and improves renal function in mouse models of renal fibrosis induced by UUO or FA. Metagenomics analysis showed that fucoidan significantly increases the abundance of AKK by promoting its growth in UUO-induced renal fibrosis. Oral administration of live AKK alleviates renal fibrosis in UUO and FA mouse models. Using oral antibiotic-treated mice, we found that the effect of fucoidan on renal fibrosis was weakened. Gas chromatography-mass spectrometry (GC-MS/MS) study results show that AKK produces the short-chain fatty acids (acetate), which protects against renal fibrosis by suppressing NEU1-TLR4-NFκB-mediated inflammation in the kidney.

CONCLUSION: Our findings establish a novel gut-kidney axis wherein fucoidan ameliorates renal fibrosis through AKK-mediated acetate production and subsequent NEU1-TLR4-NFκB pathway inhibition.},
}

@article {pmid40663918,
year = {2025},
author = {Vishwakarma, YK and Bhardwaj, N and Ram, K and Gogoi, MM and Banerjee, T and Mohanty, M and Singh, RS},
title = {Bioaerosol emissions from solid waste processing facilities at urban environment and their impact on human health.},
journal = {The Science of the total environment},
volume = {994},
number = {},
pages = {180049},
doi = {10.1016/j.scitotenv.2025.180049},
pmid = {40663918},
issn = {1879-1026},
abstract = {Waste management is one of the challenging issues in developing countries because of indiscriminate urbanization, huge population growth coupled with insufficient technology to manage it. The processing of waste and producing manure are good techniques for solid waste management. This study shows that during waste processing such as loading and unloading, sorting, mixing and leachate treatment, several types of bioaerosols, both bacterial and fungal, are emitted to the atmosphere. Here, both fungal and bacterial bioaerosol concentration near a waste processing facility is reported with metagenomic analysis and health assessment. Average bacterial bioaerosol concentration was noted to be 2979 ± 544 CFU/m[3], whereas the fungal bioaerosol concentration was 2288 ± 1128 CFU/m[3] at the waste processing site. Size distribution shows that the concentration of bacterial bioaerosol was mostly in the finer range (0.65-1.1 μm) while the fungal concentration was highest in the coarse size (between 3.3 and 7.0 μm). The metagenomic analysis of the bacterial bioaerosol sample revealed dominance of Alcaligenaceae (22 %), Stenotrophomonas (19 %), Bacillus (14 %) whereas, Fusarium (40 %), Epicoccum (23 %), Hypocreales (15 %), Coprinopsis (8 %), Cladosporium (4 %), Sarocladium (4 %), Tourlaspora (2 %), Alternaria (2 %) and Cryptococcus (2 %) were dominant fungal species. The top two dominant genera of bacterial strain expressed resistance towards azithromycin and cefixime. In the cross-sectional health survey near the waste processing site, participants including both workers on the site and people nearby, reported symptoms of respiratory, skin and eye irritation and bad smell. This study will help to improve the waste treatment process safety protocols and the health of the population around.},
}

@article {pmid40663882,
year = {2025},
author = {Khattak, F and Galgano, S and Pearson, R and Houdijk, JGM and Short, F and Leigh, A},
title = {Enhancing key broiler welfare indicators, meat quality, and gut microbiome composition using oxygen-enriched drinking water under commercially relevant housing conditions.},
journal = {Poultry science},
volume = {104},
number = {10},
pages = {105550},
doi = {10.1016/j.psj.2025.105550},
pmid = {40663882},
issn = {1525-3171},
abstract = {Water is a critical nutrient in poultry production, yet its quality, particularly dissolved oxygen (DO) content, is often overlooked. This study is the first to comprehensively evaluate the impact of oxygen-enriched drinking water on broiler welfare, breast muscle myopathies, and gut microbiome composition under commercially relevant housing conditions. A total of 840 male Ross 308 broiler chicks were randomly assigned to two treatment groups (oxygenated water vs. tap water), with 12 replicate pens per treatment. Oxygenated water was enriched to a DO level of approximately 32 mg/L, compared to around 9.5 mg/L in tap water. Birds were reared to 36 days of age. The consistently high performance of both treatment groups under controlled experimental conditions is demonstrated by final body weights and feed conversion ratios surpassing Ross 308 breed standards by approximately 19-22 % from day 24 onward. Although growth performance remained unaffected under these optimal conditions, oxygenated water significantly improved welfare indicators, including feather condition, hock burn scores, and breast cleanliness (P< 0.05). Birds on oxygenated water also showed lower abdominal fat (-12 %) and higher thigh yield (+2.6 %) without compromising breast yield. Carcass fat deposition was significantly lower (abdominal fat pad reduced by ∼12 %), and thigh yield was higher in the oxygenated water treatment (P < 0.05), although overall carcass weight and breast yield were unchanged. No major differences were detected in breast meat nutrient composition (P > 0.05). The prevalence of white striping in breast fillets was markedly reduced in birds receiving oxygenated water, 32 mg/L indicating enhanced muscle integrity (P < 0.05). Metagenomic analysis revealed that some bacterial lipid metabolism pathways where differentially abundant in oxygenated-water birds. Following up on previous knowledge suggesting the interplay between lipid metabolism and broiler welfare, these findings suggest that supplementing broiler drinking water with 32 mg/L DO levels may offer a practical, non-pharmaceutical strategy to mitigate breast muscle myopathies and improve overall animal welfare and meat quality.},
}

@article {pmid40663851,
year = {2025},
author = {Wang, P and He, D and Xiao, Z and Zhao, J and Jin, Q and Ma, X and Ma, J and Zheng, M},
title = {Dual sludge system driven NDFO-Feammox coupling: Optimization of the iron cycling network for sustainable and efficient nitrogen removal.},
journal = {Water research},
volume = {286},
number = {},
pages = {124186},
doi = {10.1016/j.watres.2025.124186},
pmid = {40663851},
issn = {1879-2448},
abstract = {This research addresses the significant reliance on carbon sources and high energy consumption in traditional biological nitrogen removal methods. It introduces sponge iron (SI) as a source of iron to drive the coupled nitrate-dependent Fe(II) oxidation (NDFO) and Fe(III)-mediated ammonium oxidation (Feammox) processes using activated sludge and anaerobic ammonium oxidation (Anammox) sludges. The findings indicate that supplementing with SI significantly enhances the nitrogen removal capacity of the system. The system achieved up to 87.1 ± 3.2 % removal of NH4[+]-N and 91.8 ± 2.7 % removal of NO3[-]-N. A dual-constraint mathematical model confirms that the NDFO pathway provides at least 66.1 % of the Fe(III) required for Feammox metabolism. This lays the theoretical foundation for constructing a sustainable, autotrophic iron-nitrogen cycling system under anaerobic conditions. To elucidate the mechanisms underlying the coupled nitrogen removal, batch kinetic experiments and metagenomic analyses were conducted. These analyses identified the dominance of Candidatus Brocadia in Feammox metabolism. It was also noted that Anammox genes were enriched with the addition of SI. Combined with the experimental observation of in situ Anammox activity restoration, this suggests a high degree of metabolic overlap between the Anammox and Feammox pathways. Unexpected metabolic couplings were also revealed. In particular, divergent trends in the relative abundances of gene clusters encoding Nar and Nir triggered partial NDFO metabolism, driving Candidatus Brocadia to engage in co-metabolism of Feammox and Anammox. This process diversifies nitrogen escape pathways. Further investigations showed that sustained NDFO metabolism benefited from the synergistic effects of extracellular iron oxidation, Feammox-mediated iron reduction, and iron regulatory networks. Additionally, Feammox metabolism established an iron turnover mechanism through iron storage, subsequently providing positive feedback to Feammox metabolism for high energy gain.},
}

@article {pmid40662898,
year = {2025},
author = {Budatala, JM and Purkrtova, S and Lopez Marin, MA and Appels, L and Bartáček, J},
title = {Fate of antibiotic resistance genes and resistant bacteria under various operating temperatures of sludge anaerobic digestion.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {92},
number = {1},
pages = {53-65},
pmid = {40662898},
issn = {0273-1223},
support = {SS01020112//Technologická Agentura České Republiky/ ; },
mesh = {*Sewage/microbiology ; Anaerobiosis ; Temperature ; *Bacteria/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Waste Disposal, Fluid/methods ; Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; },
abstract = {This study investigates the impact of varying temperatures on reducing antibiotic resistance genes (ARGs) during anaerobic digestion (AD) of mixed raw sludge in wastewater treatment plants. Employing three different operating temperatures, i.e., 37, 55, and 65 °C, the research aims to identify how these conditions affect the diminution of resistant genes. The results, based on quantitative PCR analysis and metagenomic sequencing, show that higher temperatures significantly enhance the reduction of ARGs, with the most substantial decreases observed at 65 °C. This temperature-dependent reduction correlates with changes in the microbial community structure, where specific bacterial genera like Alicycliphilus, Macellibacteroides, Dokdonella, Ahniella, Thauera, and Zoogloea associated with ARGs exhibit decreased abundance at elevated temperatures. The study infers that AD at higher temperatures could be a more effective strategy in mitigating the spread of antibiotic resistance in the environment, suggesting a pivotal role of operational temperature in optimizing wastewater treatment processes for ARGs attenuation. The findings highlight the need for further research to refine AD protocols, aiming to minimize the environmental impact of antibiotic resistance dissemination.},
}

*Sewage/microbiology
Anaerobiosis
Temperature
*Bacteria/genetics/drug effects
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics
Waste Disposal, Fluid/methods
Anti-Bacterial Agents/pharmacology
*Genes, Bacterial

@article {pmid40662820,
year = {2025},
author = {Qu, F and Peng, C and Guan, J and Wang, D and Sun, Y and Shang, J},
title = {GiantHunter: accurate detection of giant virus in metagenomic data using reinforcement-learning and Monte Carlo tree search.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {Supplement_1},
pages = {i30-i39},
doi = {10.1093/bioinformatics/btaf239},
pmid = {40662820},
issn = {1367-4811},
support = {//Hong Kong Research Grants Council/ ; 11209823//General Research Fund/ ; //City University of Hong Kong/ ; },
mesh = {*Metagenomics/methods ; Monte Carlo Method ; *DNA Viruses/genetics ; *Machine Learning ; *Software ; Genome, Viral ; Metagenome ; Algorithms ; },
abstract = {MOTIVATION: Nucleocytoplasmic large DNA viruses (NCLDVs) are notable for their large genomes and extensive gene repertoires, which contribute to their widespread environmental presence and critical roles in processes such as host metabolic reprogramming and nutrient cycling. Metagenomic sequencing has emerged as a powerful tool for uncovering novel NCLDVs in environmental samples. However, identifying NCLDV sequences in metagenomic data remains challenging due to their high genomic diversity, limited reference genomes, and shared regions with other microbes. Existing alignment-based and machine learning methods struggle with achieving optimal trade-offs between sensitivity and precision.

RESULTS: In this work, we present GiantHunter, a reinforcement learning-based tool for identifying NCLDVs from metagenomic data. By employing a Monte Carlo tree search strategy, GiantHunter dynamically selects representative non-NCLDV sequences as the negative training data, enabling the model to establish a robust decision boundary. Benchmarking on rigorously designed experiments shows that GiantHunter achieves high precision while maintaining competitive sensitivity, improving the F1-score by 10% and reducing computational cost by 90% compared to the second-best method. To demonstrate its real-world utility, we applied GiantHunter to 60 metagenomic datasets collected from six cities along the Yangtze River, located both upstream and downstream of the Three Gorges Dam. The results reveal significant differences in NCLDV diversity correlated with proximity to the dam, likely influenced by reduced flow velocity caused by the dam. These findings highlight GiantHunter's potential to advance our understanding of NCLDVs and their ecological roles in diverse environments.

The source code of GiantHunter is available via: https://github.com/FuchuanQu/GiantHunter.},
}

*Metagenomics/methods
Monte Carlo Method
*DNA Viruses/genetics
*Machine Learning
*Software
Genome, Viral
Metagenome
Algorithms

@article {pmid40662816,
year = {2025},
author = {Belcour, A and Megy, L and Stephant, S and Michel, C and Rad, S and Bombach, P and Dopffel, N and de Jong, H and Ropers, D},
title = {Predicting coarse-grained representations of biogeochemical cycles from metabarcoding data.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {Supplement_1},
pages = {i49-i57},
doi = {10.1093/bioinformatics/btaf230},
pmid = {40662816},
issn = {1367-4811},
support = {//European Partnership under Joint Call 2022/ ; GA N°101069750//European Commission/ ; //Norway, France, Czech Republic, and Saxon/ ; ANR-23-CETP-0002//ANR/ ; //International Society for Computational Biology/ ; },
mesh = {*Metagenomics/methods ; *DNA Barcoding, Taxonomic/methods ; Software ; Proteome/metabolism ; *Computational Biology/methods ; },
abstract = {MOTIVATION: Taxonomic analysis of environmental microbial communities is now routinely performed thanks to advances in DNA sequencing. Determining the role of these communities in global biogeochemical cycles requires the identification of their metabolic functions, such as hydrogen oxidation, sulfur reduction, and carbon fixation. These functions can be directly inferred from metagenomics data, but in many environmental applications metabarcoding is still the method of choice. The reconstruction of metabolic functions from metabarcoding data and their integration into coarse-grained representations of biogeochemical cycles remains a difficult bioinformatics problem today.

RESULTS: We developed a pipeline, called Tabigecy, which exploits taxonomic affiliations to predict metabolic functions constituting biogeochemical cycles. In a first step, Tabigecy uses the tool EsMeCaTa to predict consensus proteomes from input affiliations. To optimize this process, we generated a precomputed database containing information about 2404 taxa from UniProt. The consensus proteomes are searched using bigecyhmm, a newly developed Python package relying on Hidden Markov Models to identify key enzymes involved in metabolic function of biogeochemical cycles. The metabolic functions are then projected on coarse-grained representation of the cycles. We applied Tabigecy to two salt cavern datasets and validated its predictions with microbial activity and hydrochemistry measurements performed on the samples. The results highlight the utility of the approach to investigate the impact of microbial communities on biogeochemical processes.

The Tabigecy pipeline is available at https://github.com/ArnaudBelcour/tabigecy. The Python package bigecyhmm and the precomputed EsMeCaTa database are also separately available at https://github.com/ArnaudBelcour/bigecyhmm and https://doi.org/10.5281/zenodo.13354073, respectively.},
}

*Metagenomics/methods
*DNA Barcoding, Taxonomic/methods
Software
Proteome/metabolism
*Computational Biology/methods

@article {pmid40662809,
year = {2025},
author = {Singh, NP and Khan, J and Patro, R},
title = {Alevin-fry-atac enables rapid and memory frugal mapping of single-cell ATAC-seq data using virtual colors for accurate genomic pseudoalignment.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {Supplement_1},
pages = {i237-i245},
doi = {10.1093/bioinformatics/btaf234},
pmid = {40662809},
issn = {1367-4811},
support = {R01HG009937//National Institute of Health/ ; CCF-1750472//National Science Foundation/ ; CNS-1763680//National Science Foundation/ ; 252586//National Science Foundation/ ; 2024342821//National Science Foundation/ ; //Chan Zuckerberg Initiative DAF/ ; //Silicon Valley Community Foundation/ ; //Chan Zuckerberg Initiative Foundation/ ; },
mesh = {*Single-Cell Analysis/methods ; Algorithms ; *Software ; *Genomics/methods ; *Chromatin Immunoprecipitation Sequencing/methods ; *Chromosome Mapping/methods ; *Sequence Alignment/methods ; Humans ; },
abstract = {SUMMARY: Ultrafast mapping of short reads via lightweight mapping techniques such as pseudoalignment has significantly accelerated transcriptomic and metagenomic analyses with minimal accuracy loss compared to alignment-based methods. However, applying pseudoalignment to large genomic references, like chromosomes, is challenging due to their size and repetitive sequences. We introduce a new and modified pseudoalignment scheme that partitions each reference into "virtual colors." These are essentially overlapping bins of fixed maximal extent on the reference sequences that are treated as distinct "colors" from the perspective of the pseudoalignment algorithm. We apply this modified pseudoalignment procedure to process and map single-cell ATAC-seq data in our new tool alevin-fry-atac. We compare alevin-fry-atac to both Chromap and Cell Ranger ATAC. Alevin-fry-atac is highly scalable and, when using 32 threads, is 2.8 times faster than Chromap (the second fastest approach) while using only 33% of the memory required by Chromap. The resulting peaks and clusters generated from alevin-fry-atac show high concordance with those obtained from both Chromap and the Cell Ranger ATAC pipeline, demonstrating that virtual color-enhanced pseudoalignment directly to the genome provides a fast, memory-frugal, and accurate alternative to existing approaches for single-cell ATAC-seq processing. The development of alevin-fry-atac brings single-cell ATAC-seq processing into a unified ecosystem with single-cell RNA-seq processing (via alevin-fry) to work toward providing a truly open alternative to many of the varied capabilities of CellRanger.

Alevin-fry-atac is written in Rust and C++17, and is freely-available under a BSD 3-clause license. It is integrated into piscem (https://github.com/COMBINE-lab/piscem) and alevin-fry (https://github.com/COMBINE-lab/alevin-fry), and is also supported directly as part of simpleaf (https://github.com/COMBINE-lab/simpleaf).},
}

*Single-Cell Analysis/methods
Algorithms
*Software
*Genomics/methods
*Chromatin Immunoprecipitation Sequencing/methods
*Chromosome Mapping/methods
*Sequence Alignment/methods
Humans

@article {pmid40662747,
year = {2025},
author = {Touceda-Suárez, M and Ponsero, AJ and Barberán, A},
title = {Differences in the genomic potential of soil bacterial and viral communities between urban greenspaces and natural arid soils.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0212424},
doi = {10.1128/aem.02124-24},
pmid = {40662747},
issn = {1098-5336},
abstract = {Urban green spaces provide essential ecosystem services that are ever more important in arid cities. However, the design and management of these greenspaces often require physicochemical transformations, whose effect in the balance of the arid urban ecosystems is normally not accounted for. In this project, we leverage metagenomic data from soil microbial communities of urban greenspaces and neighboring natural areas in a city from the arid Southwestern USA (Tucson, Arizona) to understand the differences in microbial (bacterial and viral) community structure, taxonomy, and function in urban greenspaces compared to natural arid soils. We found bacterial and viral communities to be distinct between urban greenspace and natural arid soils, with urban greenspace bacteria displaying reduced metabolic versatility and higher genetic potential for simple carbohydrate consumption and nitrogen reduction. Moreover, bacteria in urban greenspaces exhibit higher genetic potential for resistance to heavy metals and certain clinical antibiotics. Our results suggest that the conversion of arid natural land to urban greenspaces determines the soil microbiome structure and functioning, and potentially its ability to adapt to the changing environment.IMPORTANCEUrban green spaces are critical for the sustainability of arid cities. Nevertheless, they require deep soil physicochemical transformations. Soil bacterial and viral communities are responsible for soil functioning and provision of some ecosystem services, but they are also highly influenced by changes in the soil environment. The significance of our research is in illustrating the structural and functional changes that microbial and viral communities undergo in urban soils of arid cities and their potential impacts on urban greenspace soil processes.},
}

@article {pmid40662533,
year = {2025},
author = {Jiang, J and Hu, D and Hu, S and Huang, K and Zheng, J and Pei, E},
title = {Age-Related Differences in Gut Microbiome and Fecal Metabolome of Captive African Penguins (Spheniscus demersus).},
journal = {Zoo biology},
volume = {},
number = {},
pages = {},
doi = {10.1002/zoo.70014},
pmid = {40662533},
issn = {1098-2361},
support = {//This study was supported by a Project of Shanghai Zoo (SZ220302) and Special Fund for Scientific Research of Shanghai Landscaping & City Appearance Administrative Bureau (G250407)./ ; },
abstract = {The purpose of the present study was to characterize the profiles of gut microbiota and fecal metabolites in African penguins (Spheniscus demersus) of different ages. The combination of metagenome and metabolome was performed on the feces of captive African penguins of varying age groups, including juvenile (1-3 years old), adult (4-15 years old) and senior (16-20 years old) individuals. The results of the metagenome showed that microbial abundance was significantly different between groups. Adult penguins had higher abundances of Gallilactobacillus and Ligilactobacillus compared to juvenile penguins. Senior penguins exhibited higher abundances of Gammaproteobacteria and Escherichia coli than adult penguins. We further identified differentially expressed metabolites across the groups using liquid chromatography-mass spectrometry analysis. Correlation analysis showed that age was correlated significantly with certain differential microbial species and fecal metabolites. The results revealed that age is a key factor influencing gut microbiota and metabolism in African penguins. Our results provide baseline information on gut microbial structure and fecal metabolite characteristics in African penguins of different ages, which is vital for the management and ex situ conservation of this endangered species.},
}

@article {pmid40661966,
year = {2025},
author = {Yao, C and Xue, X and Jia, Y and Li, M and Zhang, L and Yuan, H and Xue, H and Hu, R},
title = {Rosuvastatin ameliorates obesity-associated insulin resistance in high-fat diet-fed mice by modulating the gut microbiota and gut metabolites.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1593581},
pmid = {40661966},
issn = {2235-2988},
mesh = {Animals ; *Insulin Resistance ; *Gastrointestinal Microbiome/drug effects ; Diet, High-Fat/adverse effects ; *Obesity/drug therapy/complications/metabolism ; *Rosuvastatin Calcium/pharmacology/administration & dosage ; Mice, Inbred C57BL ; Male ; Mice ; Fatty Acids, Volatile/metabolism/analysis ; Disease Models, Animal ; Feces/microbiology/chemistry ; Metabolomics ; Metagenomics ; Bacteria/classification/genetics/drug effects ; },
abstract = {INTRODUCTION: Insulin resistance (IR) underlies metabolic diseases such as obesity and diabetes. Statins are lipid-lowering drugs that have also been studied to improve insulin resistance, but the mechanism is not well understood. Metagenomics and metabolomics were used to analyze the main species and metabolic pathways involved in intestinal microbes while improving insulin resistance in mice with rosuvastatin in this study.

METHODS: C57BL/6J male mice fed a high-fat diet were used to establish the insulin resistance (IR) mouse model. Rosuvastatin (RSV) was then administered for 8 weeks. Metagenomics and metabolomics were utilized to analyze the microbial composition and short chain fatty acid metabolites in intestinal feces of mice.

RESULTS: It was observed that insulin-resistant mice showed significant improvement in insulin resistance following treatment with RSV. In comparison to the HFD group, specific bacterial strains were significantly increased, and the levels of butyric acid, caproic acid, and isovaleric acid among the short-chain fatty acids were notably elevated in the RSV group. Through KEGG enrichment analysis, 19 dominant strains and 15 key enzymes involved in butyric acid metabolism were identified.

CONCLUSIONS: The results suggested that IR mice might enhance insulin sensitivity by promoting butyric acid synthesis via intestinal microbes following RSV treatment.},
}

Animals
*Insulin Resistance
*Gastrointestinal Microbiome/drug effects
Diet, High-Fat/adverse effects
*Obesity/drug therapy/complications/metabolism
*Rosuvastatin Calcium/pharmacology/administration & dosage
Mice, Inbred C57BL
Male
Mice
Fatty Acids, Volatile/metabolism/analysis
Disease Models, Animal
Feces/microbiology/chemistry
Metabolomics
Metagenomics
Bacteria/classification/genetics/drug effects

@article {pmid40661950,
year = {2025},
author = {Ma, Y and Suo, J and Sheng, S and Chen, L},
title = {PD-L1 deficiency exacerbates colitis severity by remodeling gut microbiota in inflammatory bowel disease.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1622744},
pmid = {40661950},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *B7-H1 Antigen/genetics/deficiency ; Mice ; Mice, Knockout ; *Colitis/pathology/microbiology/chemically induced/genetics/immunology/metabolism ; *Inflammatory Bowel Diseases/microbiology/immunology/pathology/genetics/metabolism ; Dysbiosis ; Disease Models, Animal ; Severity of Illness Index ; Mice, Inbred C57BL ; Dextran Sulfate ; Male ; },
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic autoimmune disorder driven by gut microbiota dysbiosis. As an essential immune checkpoint, Programmed death-ligand 1 (PD-L1) has been implicated in modulating gut microbiota composition. However, the precise role of PD-L1 in shaping metagenomic profiles during IBD-associated colitis remains unexplored.

METHODS: DSS-induced colitis was established in both PD-L1 knockout (Pdcd1lg1-/-) mice and wild-type (wt) control mice. Clinical parameters, including disease activity index (DAI), body weight changes, colon length, and histopathological alterations, were systematically evaluated using non-parametric Kruskal-Wallis tests and ANOVA to compare colitis severity between genotypes.

RESULTS: PD-L1 knockout mice exhibited exacerbated colitis, manifesting significantly greater weight loss (p<0.05 vs. wt_DSS), colonic shortening (p<0.05), and DAI scores (p<0.05) and inflammatory changes. PD-L1 knockout mice showed distinct dysbiosis, with enriched pathobionts (Escherichia coli, p=0.006; Bacteroides thetaiotaomicron, p=0.015) and depletion of commensals (Tritrichomonas foetus, p<0.001; Ligilactobacillus murinus). Alpha diversity analysis using Chao1 index revealed statistically significant differences between experimental groups (p=0.05). The transporters downregulate anti-inflammatory SCFA metabolism. KEGG enrichment analysis of differentially expressed genes (DEGs) revealed significant associations with immune and inflammatory pathways in PD-L1 knockout mice.

CONCLUSION: PD-L1 deficiency aggravates colitis by driving pathogenic microbiota alterations and impairing microbial metabolic homeostasis, highlighting its dual regulatory roles in immune homeostasis and microbiome dynamics.},
}

Animals
*Gastrointestinal Microbiome/immunology
*B7-H1 Antigen/genetics/deficiency
Mice
Mice, Knockout
*Colitis/pathology/microbiology/chemically induced/genetics/immunology/metabolism
*Inflammatory Bowel Diseases/microbiology/immunology/pathology/genetics/metabolism
Dysbiosis
Disease Models, Animal
Severity of Illness Index
Mice, Inbred C57BL
Dextran Sulfate
Male

@article {pmid40661024,
year = {2025},
author = {Xia, ZW and Zhao, H and Liu, TT and Li, Y and Huo, JS and Guo, X},
title = {[Research progress of childhood obesity based on genomic and epigenomic biomarkers].},
journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]},
volume = {59},
number = {7},
pages = {1125-1130},
doi = {10.3760/cma.j.cn112150-20240729-00606},
pmid = {40661024},
issn = {0253-9624},
support = {Leading talent-01-09//Beijing Municipal Health Commission High-level Public Health Technical Talent Construction Project/ ; },
mesh = {Humans ; *Pediatric Obesity/genetics ; Child ; *Epigenomics ; Genomics ; *Epigenesis, Genetic ; Biomarkers ; },
abstract = {Obesity represents a complex, heritable condition shaped by interactions among genetic, epigenetic, metagenomic, and environmental factors. Nevertheless, the mechanistic contributions of genetic variation and epigenetic regulation to obesity pathogenesis remain incompletely elucidated. Advances in molecular profiling technologies have enabled the identification of numerous biomarkers associated with childhood obesity phenotypes. These discoveries facilitate understanding of obesity etiology and its links to chronic diseases. This review synthesizes current research on genomic and epigenomic biomarkers influencing childhood obesity susceptibility, advances our comprehension of etiological heterogeneity and intervention strategies, and offers conceptual frameworks for precision prevention based on epigenetic mechanisms.},
}

Humans
*Pediatric Obesity/genetics
Child
*Epigenomics
Genomics
*Epigenesis, Genetic
Biomarkers

@article {pmid40661021,
year = {2025},
author = {Zhen, BJ and Zhang, P and Guo, XC and Zhang, J and Zhang, Y and Gao, X and Wang, F and Li, J and Zou, L},
title = {[Genomic characterization of a case of enterovirus D68 infection in a child from Tongzhou District, Beijing City].},
journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]},
volume = {59},
number = {7},
pages = {1108-1112},
doi = {10.3760/cma.j.cn112150-20250326-00247},
pmid = {40661021},
issn = {0253-9624},
support = {2020-2-1012//Optimization of Primer Selection and Effect Verification for Enhanced Viral Detection Using Metagenomic Next-Generation Sequencing Technology/ ; },
mesh = {Humans ; *Genome, Viral ; Phylogeny ; *Enterovirus Infections/virology ; Infant ; Male ; *Enterovirus D, Human/genetics/isolation & purification ; China ; Beijing ; Genomics ; },
abstract = {A throat swab sample from a pediatric case in Tongzhou District, Beijing was identified as enterovirus; the patient was a 1-year-and-8-month-old male sporadic case. Whole-genome sequencing revealed a viral genome length of 7 436 bp. BLAST alignment confirmed the serotype as EV-D68. Phylogenetic analysis of the whole genome indicated that this strain belongs to the B3 clade, showing closer genetic proximity to the 2018 Shanghai strain MW697453 with 99.53% whole-genome nucleotide homology. Genetic and amino acid variation analysis demonstrated that the B3 subclade to which this strain belongs exhibits a nucleotide deletion at positions 718-726, differing from deletion sites observed in other B3 clade strains. A key neuropathogenic amino acid site, T650A, was found to have undergone mutation. Recombination analysis confirmed no cross-clade recombination events in this strain. This study conducted genetic characterization of the strain's evolutionary relationship with EV-D68 strains from different regions and years in China, providing data support for formulating prevention and control measures against EV-D68 infection.},
}

Humans
*Genome, Viral
Phylogeny
*Enterovirus Infections/virology
Infant
Male
*Enterovirus D, Human/genetics/isolation & purification
China
Beijing
Genomics

@article {pmid40660868,
year = {2025},
author = {Lin, F and Liu, Q and Zhao, Y and Chen, Y and Wang, R and Miao, C and Zhang, Q},
title = {He's Yangchao Formula Ameliorates Premature Ovarian Insuf-ficiency via Remodeling Gut Microbiota to Promote Granulosa Cell Glycolysis.},
journal = {Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. Medical sciences},
volume = {},
number = {},
pages = {1-10},
doi = {10.3724/zdxbyxb-2024-0604},
pmid = {40660868},
issn = {1008-9292},
abstract = {OBJECTIVES: To investigate the molecular mechanism by which He's Yangchao Formula improves ovarian function in premature ovarian insufficiency (POI) mice through intestinal flora modulation.

METHODS: Forty female ICR mice (aged 6-8 weeks) were intraperitoneally injected with cyclophosphamide (150 mg/kg) to establish a POI model, while 10 untreated mice served as the blank control. Successfully modeled mice were randomly divided into four groups (n=10/group): low-dose He's Yangchao Formula (6 g crude herb/kg), high-dose He's Yangchao Formula (25 g crude herb/kg), positive control (estradiol), and model control (distilled water). Treatments were admin-istered daily by gavage for 6 weeks. Vaginal exfoliated cells were stained with Wright-Giemsa solution to monitor estrous cycles. Serum estradiol and follicle-stimulating hormone (FSH) levels were measured by ELISA. Ovarian FSH receptor (FSHR) expression was assessed by immunohistochemistry. Glycolysis-related proteins pyruvate kinase M2 (PKM2) and glucose transporter 4 (GLUT4) were analyzed by Western blotting and immuno-fluorescence. Fecal samples from blank control, model control, and high-dose groups underwent metagenomic sequencing to evaluate intestinal microbiota diversity and com-position.

RESULTS: He's Yangchao Formula restored estrous cyclicity, increased serum estradiol (P<0.05), decreased serum FSH (P<0.05), and upregulated FSHR expression in granulosa cells (P<0.05). Metagenomic analysis revealed significant structural differences in intestinal flora among blank control, model control, and high-dose groups (P<0.01). The high-dose group showed reduced abundance of conditional pathogens (e.g., Alistipes, Prevotella, Odoribacter, Blautia, Rikenella) compared to the model control (P<0.05). Functional enrichment analysis indicated involvement of glycolysis-related pathways. Concordantly, PKM2 and GLUT4 expression was downregulated in the model control but upregulated in He's Yangchao Formula groups (P<0.05).

CONCLUSIONS: He's Yangchao Formula ameliorates POI in mice by remodeling intestinal flora structure, enhancing glycolytic activity, improving ovarian sex hormone secretion, increasing granulosa cell FSHR expression, and restoring estrous cyclicity.},
}

@article {pmid40660333,
year = {2025},
author = {Yang, Z and Zhang, Y and Ran, S and Zhang, J and Gao, Y and Zhang, Y and Li, X and Ai, B and Wei, S and Tian, F and Jia, G and Lin, H and Chen, Z and Zhang, Z},
title = {Exposure to ambient air pollution over developmental stages induced neurodevelopmental impairment in mice offspring via microbiome-gut-brain axis.},
journal = {Particle and fibre toxicology},
volume = {22},
number = {1},
pages = {20},
pmid = {40660333},
issn = {1743-8977},
support = {2024A1515010465//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2022A1515010695//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 82203988//National Natural Science Foundation of China/ ; 2023A04J2071//Guangzhou Municipal Science and Technology Project/ ; 23qnpy107//Fundamental Research Funds for the Central Universities of Sun Yat-sen University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Female ; *Air Pollution/adverse effects ; Mice ; Male ; *Neurodevelopmental Disorders/chemically induced/microbiology ; Pregnancy ; *Prenatal Exposure Delayed Effects/chemically induced ; *Brain/drug effects/growth & development ; *Air Pollutants/toxicity ; Mice, Inbred C57BL ; Behavior, Animal/drug effects ; *Brain-Gut Axis/drug effects ; },
abstract = {Exposure to air pollution has been increasingly recognized as a risk factor for neurodevelopmental disorders, and gut microbiome may play a critical role. However, current evidence still remains scarce. In the present study, mice were exposed to real-time ambient air pollution from conception through young adulthood, with neurobehavioral performance and gut microbiome being assessed across different developmental stages. Neurodevelopmental changes including emotional and cognitive impairments were observed in behavioral tests, accompanied by pathological and inflammation changes in brain, which were more pronounced in adolescence than in young adulthood. Alterations in the compositions and functions of gut microbiome were also revealed by fecal metagenomic sequencing. Mediation analysis showed that gut microbiome alterations significantly contributed to the observed neurodevelopmental changes induced by air pollution. Furthermore, after antibiotic (ABX) intervention, the observed neurobehavioral, pathological and inflammatory differences between the exposed and control groups diminished. These findings indicate that the gut microbiome mediates the neurodevelopmental damage caused by exposure to air pollution during developmental stages, adding novel insights on the underlying mechanisms linking air pollution and neurodevelopmental disorders.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Female
*Air Pollution/adverse effects
Mice
Male
*Neurodevelopmental Disorders/chemically induced/microbiology
Pregnancy
*Prenatal Exposure Delayed Effects/chemically induced
*Brain/drug effects/growth & development
*Air Pollutants/toxicity
Mice, Inbred C57BL
Behavior, Animal/drug effects
*Brain-Gut Axis/drug effects

@article {pmid40660160,
year = {2025},
author = {Chae, JB and Kim, WG and Song, S and Chae, JS},
title = {Molecular characterization of ten viral pathogens causing calf diarrhea in Hanwoo (Bos Taurus coreanae) by next generation sequencing.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {464},
pmid = {40660160},
issn = {1746-6148},
support = {122061-2//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/ ; 122061-2//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/ ; 122061-2//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/ ; },
abstract = {BACKGROUND: Calf diarrhea remains a significant concern in the global cattle industry, leading to considerable economic losses. Infectious pathogens are among the primary causes of this disease. In this study, the prevalence of 7 pathogens—bovine rotavirus (BRV), bovine coronavirus (BCV), bovine viral diarrhea virus (BVDV) types 1 and 2, Cryptosporidium parvum, Giardia spp., and Eimeria spp.—associated with calf diarrhea was investigated using polymerase chain reaction (PCR). A metagenomic approach was also applied to identify additional RNA viral pathogens from unknown causes of diarrheic fecal samples in the Republic of Korea (ROK).

RESULTS: A total of 810 fecal samples from Hanwoo calves (Bos taurus coreanae) were collected, consisting of 526 normal samples (267 with a fecal score of 0 and 259 with a fecal score of 1) and 284 diarrheic samples (178 with a fecal score of 2 and 106 with a fecal score of 3). All 7 pathogens were detected by PCR in feces and their detection rates and mean fecal scores for each were as follows: BRV (14.0%, 1.41), BCV (3.2%, 1.42), BVDV1 (2.1%, 1.35), BVDV2 (4.9%, 1.33), C. parvum (9.8%, 1.66), Eimeria spp. (1.9%, 1.73), and Giardia spp. (0.9%, 0.71). Among these pathogens, BRV (p = 0.004), C. parvum (p < 0.001), and Eimeria spp. (p = 0.027) showed an increase in prevalence with higher fecal scores. Twenty-one fecal samples negative for all pathogens were randomly selected and subjected to high-throughput sequencing to identify RNA viral pathogens associated with calf diarrhea. This approach led to the identification of nearly complete genomic sequences for bovine astrovirus, bovine enterovirus, bovine kobuvirus, bovine nebovirus, bovine norovirus, bovine boosepivirus B, bovine parechovirus, bovine torovirus, C. parvum virus 1, and hunnivirus.

CONCLUSIONS: This study represents the first investigation of hunnivirus presence and provides a comprehensive description of the nearly complete genomes of 10 viruses associated with calf diarrhea in the ROK. The findings contribute to a better understanding of the epidemiology and molecular characteristics of calf diarrhea-associated pathogens in the ROK, highlighting the potential application of high-throughput sequencing for diagnosing other diseases.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12917-025-04926-2.},
}

@article {pmid40659786,
year = {2025},
author = {Lin, NY and Fukuoka, S and Koyama, S and Motooka, D and Tourlousse, DM and Shigeno, Y and Matsumoto, Y and Yamano, H and Murotomi, K and Tamaki, H and Irie, T and Sugiyama, E and Kumagai, S and Itahashi, K and Tanegashima, T and Fujimaki, K and Ito, S and Shindo, M and Tsuji, T and Wake, H and Watanabe, K and Maeda, Y and Enokida, T and Tahara, M and Yamashita, R and Fujisawa, T and Nomura, M and Kawazoe, A and Goto, K and Doi, T and Shitara, K and Mano, H and Sekiguchi, Y and Nakamura, S and Benno, Y and Nishikawa, H},
title = {Microbiota-driven antitumour immunity mediated by dendritic cell migration.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40659786},
issn = {1476-4687},
abstract = {Gut microbiota influence the antitumour efficacy of immune checkpoint blockade[1-6], but the mechanisms of action have not been fully elucidated. Here, we show that a new strain of the bacterial genus Hominenteromicrobium (designated YB328) isolated from the faeces of patients who responded to programmed cell death 1 (PD-1) blockade augmented antitumour responses in mice. YB328 activated tumour-specific CD8[+] T cells through the stimulation of CD103[+]CD11b[-] conventional dendritic cells (cDCs), which, following exposure in the gut, migrated to the tumour microenvironment. Mice showed improved antitumour efficacy of PD-1 blockade when treated with faecal transplants from non-responder patients supplemented with YB238. This result suggests that YB328 could function in a dominant manner. YB328-activated CD103[+]CD11b[-] cDCs showed prolonged engagement with tumour-specific CD8[+] T cells and promoted PD-1 expression in these cells. Moreover, YB238-augmented antitumour efficacy of PD-1 blockade treatment was observed in multiple mouse models of cancer. Patients with elevated YB328 abundance had increased infiltration of CD103[+]CD11b[-] cDCs in tumours and had a favourable response to PD-1 blockade therapy in various cancer types. We propose that gut microbiota enhance antitumour immunity by accelerating the maturation and migration of CD103[+]CD11b[-] cDCs to increase the number of CD8[+] T cells that respond to diverse tumour antigens.},
}

@article {pmid40659687,
year = {2025},
author = {Zhang, N and Zhao, Y and Zhang, Z and Zhan, M and Zhao, X and Zhang, Y and Sun, J and Zhang, Y and Teng, L and Liu, Z},
title = {Metagenomic and Transcriptomic Datasets of Plateau Brown Frogs (Rana kukunoris) from the Helan Mountains.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1219},
pmid = {40659687},
issn = {2052-4463},
support = {32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32071649//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Transcriptome ; Metagenomics ; *Ranidae/genetics/microbiology ; *Metagenome ; Climate Change ; Microbiota ; China ; Adaptation, Physiological ; },
abstract = {Global climate change has become a primary driving factor behind the biodiversity crisis in amphibians, making it crucial to understand how climate change affects species and their potential responses. The plateau brown frog (Rana kukunoris) is often regarded as an ideal ecological indicator species, yet research on its environmental adaptation mechanisms based on transcriptomic and microbiomic studies remains limited. Therefore, this study investigates the adaptation strategies of the plateau brown frog to environmental changes, providing extensive transcriptomic and the first comprehensive metagenomic dataset from two distinctly different environmental regions (eastern and western slopes of the Helan Mountains). We gathered transcriptomic data from three tissues (blood, liver, and muscle), resulting in 294,962 unigenes and 570,192 transcripts. Metagenomic sequencing identified major bacterial groups, including Firmicutes, Proteobacteria, Bacteroidetes, Spirochetes, and Actinobacteria. In summary, the results of this study can be used to further explore the associations among microbiota, host, and environment, which are crucial for comprehending the mechanisms of environmental adaptation in this species and contributing to the conservation of amphibian biodiversity.},
}

Animals
*Transcriptome
Metagenomics
*Ranidae/genetics/microbiology
*Metagenome
Climate Change
Microbiota
China
Adaptation, Physiological

@article {pmid40659683,
year = {2025},
author = {Li, P and Wu, Z and Liu, T and Deng, C and Liu, Q and Ni, J},
title = {The defensome of prokaryotes in aquifers.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6482},
pmid = {40659683},
issn = {2041-1723},
support = {U2240205//National Natural Science Foundation of China (National Science Foundation of China)/ ; 51721006//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Groundwater/microbiology ; *Bacteria/genetics/immunology/virology ; China ; *Prokaryotic Cells ; Metagenomics ; Bacteriophages ; CRISPR-Cas Systems/genetics ; Ecosystem ; Metagenome ; Phylogeny ; },
abstract = {Groundwater harbors a pristine biosphere where microbes co-evolve with less human interference, yet the ancient and ongoing arms race between prokaryotes and viruses remains largely unknown in such ecosystems. Based on our recent nationwide groundwater monitoring campaign across China, we construct a metagenomic groundwater prokaryotic defensome catalogue (GPDC), encompassing 190,810 defense genes, 90,824 defense systems, 139 defense families, and 669 defense islands from 141 prokaryotic phyla. Over 94% of the defense genes in GPDC are novel and contribute vast microbial immune resources in groundwater. We find that candidate phyla radiation (CPR) bacteria possess higher defense system density and diversity against intense phage infection, while microbes as a whole exhibit an inverse relationship between defense systems and adaptive traits like resistance genes in groundwater. We further identify five first-line defense families covering 69.2% of the total defense systems, and high-turnover accessory immune genes are mostly conveyed to defense islands by mobile genetic elements. Our study also reveals viral resistance to microbial defense through co-localized anti-defense genes and interactions between CRISPR-Cas9 and anti-CRISPR protein. These findings expand our understanding of microbial immunity in pristine ecosystems and offer valuable immune resources for potential biotechnological applications.},
}

*Groundwater/microbiology
*Bacteria/genetics/immunology/virology
China
*Prokaryotic Cells
Metagenomics
Bacteriophages
CRISPR-Cas Systems/genetics
Ecosystem
Metagenome
Phylogeny

@article {pmid40659674,
year = {2025},
author = {Ren, M and You, B and Gong, X and Zhang, P and Wang, J},
title = {Microbial genomic database of the Yangtze River, the third-longest river on Earth.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1222},
pmid = {40659674},
issn = {2052-4463},
support = {42372353, 42225708, 92251304, 92351303, 42002304//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Rivers/microbiology ; China ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; *Microbiota ; Metagenomics ; *Genome, Archaeal ; Databases, Genetic ; *Genome, Bacterial ; },
abstract = {Microbes play an important role in mediating the nutrient cycling in the river ecosystem as a hotspot for biogeochemical processes. Due to scattered sampling efforts, however, there is a lack of a systematic study of the diversity of prokaryotic genomes in the Yangtze River, the third longest river on Earth. Here, we collected 602 metagenomic datasets of water, sediment and riparian soil samples spanning the Upper, Middle, and Lower basins of the Yangtze River over a 6,300 km continuum. We reconstructed 8,110 qualified genomes represented by 927 species-level genomes at the 95% ANI threshold, spanning 31 bacterial and five archaeal phyla. We further showed that more than half of these species (61.3% ~ 82.4%) were novel according to the genomic comparison against the curated databases, greatly expanding the known diversity of river prokaryotes. This dataset depicts an overview of microbial genomic diversity in the Yangtze River and provides a resource for in-depth investigation of metabolic potential, ecology, and evolution of riverine microbiomes.},
}

*Rivers/microbiology
China
*Archaea/genetics/classification
*Bacteria/genetics/classification
*Microbiota
Metagenomics
*Genome, Archaeal
Databases, Genetic
*Genome, Bacterial

@article {pmid40659339,
year = {2025},
author = {Singh, A and Juyal, G and Gacesa, R and Joshi, MC and Midha, V and Thelma, BK and Weersma, RK and Sood, A},
title = {Cross-ethnic evaluation of gut microbial signatures reveal increased colonization with oral pathobionts in the north Indian inflammatory bowel disease cohort.},
journal = {Intestinal research},
volume = {},
number = {},
pages = {},
doi = {10.5217/ir.2024.00216},
pmid = {40659339},
issn = {1598-9100},
abstract = {BACKGROUND/AIMS: Inflammatory bowel disease (IBD) has become a global health concern. With the growing evidence of the gut microbiota's role in IBD, studying microbial compositions across ethnic cohorts is essential to identify unique, populationspecific microbial signatures.

METHODS: We analyzed stool samples and clinical data from 254 IBD patients (226 ulcerative colitis, 28 Crohn's disease) and 66 controls in northern India using metagenomic shotgun sequencing to assess microbiota diversity, composition, and function. Results were replicated in 436 IBD patients and 903 controls from the Netherlands using identical workflows. Using machine learning, we evaluated the generalizability of Indian IBD signals to the Dutch cohort, and vice versa.

RESULTS: Indian IBD patients exhibited reduced bacterial diversity and an abundance of opportunistic pathogens, including Clostridium, Streptococcus, and oral bacteria like Streptococcus oralis and Bifidobacterium dentium. There was a significant loss of energy metabolic pathways and distinct co-occurrence patterns among microbial species. Notably, 39% of these signals replicated in the Dutch cohort. Unique to the Indian cohort were oral pathobionts such as Scardovia, Oribacterium, Actinomyces dentalis, and Klebsiella pneumoniae. Both Indian and Dutch IBD patients shared reduced butyrate producers. Machine-learning diagnostic models trained on the Indian cohort achieved high predictive accuracy (sensitivity 0.84, specificity 0.95) and moderately generalized to the Dutch cohort (sensitivity 0.77, specificity 0.69).

CONCLUSIONS: IBD patients across populations exhibit shared and unique microbial signatures, suggesting a role for the oral-gut microbiome axis in IBD. Crossethnic diagnostic models show promise for broader applications in identifying IBD.},
}

@article {pmid40658318,
year = {2025},
author = {Yu, S and Li, J and Ye, Z and Zhang, M and Guo, X and Wang, X and Liu, L and Wang, Y and Zhou, X and Fu, W and Zhang, MQ and Chen, YG},
title = {Identification of a 10-species microbial signature of inflammatory bowel disease by machine learning and external validation.},
journal = {Cell regeneration (London, England)},
volume = {14},
number = {1},
pages = {32},
pmid = {40658318},
issn = {2045-9769},
support = {2023YFA1800603//National Key Research and Development Program of China/ ; 31988101//Natural Science Foundation of China/ ; 92354306//Natural Science Foundation of China/ ; Z231100007223006//Beijing Science and Technology Plan/ ; B2302022//Shenzhen Medical Research Fund/ ; 20224ACB209001//Natural Science Foundation of Jiangxi Province/ ; O0390302//Guangdong Provincial Postdoctoral Science Foundation/ ; },
abstract = {Genetic and microbial factors influence inflammatory bowel disease (IBD), prompting our study on non-invasive biomarkers for enhanced diagnostic precision. Using the XGBoost algorithm and variable analysis and the published metadata, we developed the 10-species signature XGBoost classification model (XGB-IBD10). By using distinct species signatures and prior machine and deep learning models and employing standardization methods to ensure comparability between metagenomic and 16S sequencing data, we constructed classification models to assess the XGB-IBD10 precision and effectiveness. XGB-IBD10 achieved a notable accuracy of 0.8722 in testing samples. In addition, we generated metagenomic sequencing data from collected 181 stool samples to validate our findings, and the model reached an accuracy of 0.8066. The model's performance significantly improved when trained on high-quality data from the Chinese population. Furthermore, the microbiome-based model showed promise in predicting active IBD. Overall, this study identifies promising non-invasive biomarkers associated with IBD, which could greatly enhance diagnostic accuracy.},
}

@article {pmid40658106,
year = {2025},
author = {Chen, G and Wang, Y and Zhang, X and Jiang, K and Yu, M and Fang, L and Li, F},
title = {Periphyton-Driven Arsenic Methylation in Paddy Soils: The Crucial Role of Trophic Interactions.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c06047},
pmid = {40658106},
issn = {1520-5851},
abstract = {Arsenic (As) methylation facilitated by periphyton in paddy soils is crucial for its biogeochemical cycling and thus its bioavailability. However, the key functional taxa and underlying interactive metabolisms remain unclear due to the high complexity of the periphytic microbiome. Here, we employ DNA-stable isotope probing with metagenomic binning analysis to uncover the critical role of intrinsic trophic interactions in stimulating As methylation within the periphyton in association with soil inorganic carbon. Abundance of As-methylating microorganisms in the periphyton increases by 2.1-fold after bicarbonate addition. Members of phototrophs are predominantly responsible for regulating the stability of the periphytic microbiome, of which photoautotrophs (e.g., Oscillatoriales) initiate carbon fixation and constitute a major portion of As-methylating populations. These phototrophs further offer requisite organic substrates such as polysaccharides for heterotrophic bacteria (e.g., Chitinophagales) that in return foster the growth of the periphytic community, while these taxa simultaneously detoxify As through biomethylation to secure their ecological niches in periphyton. Such a symbiotic metabolism between phototrophs and heterotrophs facilitates carbon sequestration and shapes the functional community, collaboratively determining methylated As production in paddy soils. These findings offer new insights into the influence of trophic interactions within the periphyton on As speciation with potential implications for element cycling and soil remediation in paddy soils.},
}

@article {pmid40657968,
year = {2025},
author = {Morandi, SC and Uldry, AC and Eldridge, N and Kreuzer, M and Herzog, EL and Zinkernagel, M and Zysset-Burri, DC},
title = {Toward the Characterization of the Human Core Ocular Surface Microbiome.},
journal = {Investigative ophthalmology & visual science},
volume = {66},
number = {9},
pages = {40},
doi = {10.1167/iovs.66.9.40},
pmid = {40657968},
issn = {1552-5783},
mesh = {Humans ; *Microbiota/genetics ; Middle Aged ; Adult ; *Tears/microbiology/metabolism ; *Conjunctiva/microbiology ; Female ; Male ; Tandem Mass Spectrometry ; *Eyelids/microbiology ; *Bacteria/genetics/isolation & purification ; Chromatography, Liquid ; Eye Proteins/metabolism ; },
abstract = {PURPOSE: The field of ocular surface microbiome (OSM) research suggests its involvement in ocular surface (OS) health and disease. However, existing OSM data are heterogeneous. This study aims to provide a whole-metagenome shotgun sequencing-based description of the healthy core ocular surface microbiome (COSM), encompassing all taxonomic kingdoms at species-level resolution.

METHODS: Swabs from the conjunctiva and lower lid margin, and tear fluid of 27 individuals without OS disease aged 40 to 60 years were collected at 3 time points. The OSM was sequenced and taxonomically and functionally profiled using Kraken2 and HUMAnN3, respectively. To validate sequencing results, human and microbial proteins of the tear fluid, termed the tear proteome (TP), were characterized by nano liquid chromatography-tandem mass spectrometry (nLC-MS/MS) and profiled by gene ontology. The COSM was defined as the microbiome present in most of the study population over time. Therefore, species present in > 50% of all samples across the three time points were considered to form the COSM.

RESULTS: At species level, Cutibacterium acnes, Malassezia restricta, and Staphylococcus epidermidis formed the COSM, with Corynebacterium segmentosum additionally being part of the core lid microbiome (LM). No significant differences in the OSM and human TP were observed between the left and right eyes on individual levels. However, the variance between subjects mostly exceeded that between eyes within subjects, suggesting an individual-specific COSM and TP.

CONCLUSIONS: The description of the COSM provides the basis for future OSM research and potential targets for preventive and therapeutic interventions of the OS and associated diseases.},
}

Humans
*Microbiota/genetics
Middle Aged
Adult
*Tears/microbiology/metabolism
*Conjunctiva/microbiology
Female
Male
Tandem Mass Spectrometry
*Eyelids/microbiology
*Bacteria/genetics/isolation & purification
Chromatography, Liquid
Eye Proteins/metabolism

@article {pmid40657866,
year = {2025},
author = {Babiker, A and Van Riel, J and Lohsen, S and Page, A and Strudwick, A and Wilber, E and Woodworth, M and Satola, S},
title = {Evaluation of swabbing methods for culture and non-culture-based recovery of multidrug-resistant organisms from environmental surfaces.},
journal = {Infection control and hospital epidemiology},
volume = {},
number = {},
pages = {1-8},
doi = {10.1017/ice.2025.10214},
pmid = {40657866},
issn = {1559-6834},
abstract = {OBJECTIVES: Sponge-Sticks (SS) and ESwabs are frequently utilized for detection of multidrug-resistant organisms (MDROs) in the environment. Head-to-head comparisons of SS and ESwabs across recovery endpoints are limited.

DESIGN: We compared MDRO culture and non-culture-based recovery from (1) ESwabs, (2) cellulose-containing SS (CS), and (3) polyurethane-containing SS (PCS).

METHODS: Known quantities of each MDRO were pipetted on a stainless-steel surface and swabbed by each method. Samples were processed, cultured, and underwent colony counting. DNA was extracted from sample eluates, quantified, and underwent metagenomic next-generation sequencing (mNGS). MDROs underwent whole genome sequencing (WGS). MDRO recovery from paired patient perirectal and PCS-collected environmental samples from clinical studies was determined.

SETTING: Laboratory experiment, tertiary medical center, and long-term acute care facility.

RESULTS: Culture-based recovery varied across MDRO taxa, it was highest for vancomycin-resistant Enterococcus and lowest for carbapenem-resistant Pseudomonas aeruginosa (CRPA). Culture-based recovery was significantly higher for SS compared to ESwabs except for CRPA, where all methods performed poorly. Nucleic acid recovery varied across methods and MDRO taxa. Integrated WGS and mNGS analysis resulted in successful detection of antimicrobial resistance genes, construction of high-quality metagenome-assembled genomes, and detection of MDRO genomes in environmental metagenomes across methods. In paired patient and environmental samples, multidrug-resistant Pseudomonas aeruginosa (MDRP) environmental recovery was notably poor (0/123), despite detection of MDRP in patient samples (20/123).

CONCLUSIONS: Our findings support the use of SS for the recovery of MDROs. Pitfalls of each method should be noted. Method selection should be driven by MDRO target and desired endpoint.},
}

@article {pmid40657495,
year = {2025},
author = {Bruins-van Sonsbeek, LGR and Verschuren, MCM and Kaal, S and Lindenburg, PW and Rodenburg, KCW and Clauss, M and Speksnijder, AGCL and Rutten, VPMG and Bonnet, BFJ and Wittink, F},
title = {Correction: Rhinoceromics: a multi-amplicon study with clinical markers to transferrin saturation levels in ex-situ black rhinoceros (Diceros bicornis michaeli).},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1644681},
doi = {10.3389/fmicb.2025.1644681},
pmid = {40657495},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1515939.].},
}

@article {pmid40657403,
year = {2025},
author = {Akram, F and Safdar, M and Shabbir, I and Fatima, T and Ikram-Ul-Haq, },
title = {Insight into the eminent biotechnological applications of xylanolytic enzymes for sustainable bioprocessing.},
journal = {3 Biotech},
volume = {15},
number = {8},
pages = {249},
pmid = {40657403},
issn = {2190-572X},
abstract = {Xylan is one of the most abundant polysaccharides in nature and presents a structural complexity characterized by a heterogeneous polymer composition. Comprising various sugar subunits and associated acids linked through a diverse array of bonds, xylan poses challenges for complete degradation. This review article provides a comprehensive overview of xylan's structure, the role of xylanolytic enzymes in its degradation, and the industrial applications of xylanases in sectors, such as paper and pulp, food, textiles, and pharmaceuticals. Furthermore, it also discusses the use of advanced biotechnology tools, such as nano-biotechnology and genetic engineering, particularly through CRISPR/CAS technology, for enhancing the thermostability of xylanases. This article also provides insights into emerging trends in xylanase research, including bioprospecting novel thermostable xylanases from metagenomes, protein engineering, synthetic biology, and the integration of biorefinery. Finally, it highlights the importance of regulatory frameworks and standardization initiatives for ensuring the quality and the sustainability of xylanase-based technologies. Overall, this review offers valuable insights into the multifaceted role of xylanases in biotechnology and industrial bioprocessing while outlining future directions for research and innovation in this field.},
}

@article {pmid40657278,
year = {2025},
author = {Chen, Q and Gao, B and Guo, W and Liu, H and Guo, J},
title = {Clinical Features of Patients with Tropheryma Whipplei Detected in Lower Respiratory Tract Samples in China.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {3439-3448},
pmid = {40657278},
issn = {1178-6973},
abstract = {INTRODUCTION: Tropheryma whipplei (TW) can cause various infections that are relatively rare worldwide. With the development of molecular biology, the ability to detect TW has increased in recent years. However, its significance in lower respiratory tract samples remains unclear.

PATIENTS AND METHODS: We collected the clinical data of 5 patients admitted to a tertiary care hospital in Beijing with TW detected by bronchoalveolar lavage fluid (BALF) mNGS and reviewed all case reports of TW-related pneumonia in China (up to November 2024) to analyse the features of this disease among Chinese patients.

RESULTS: A total of 41 articles reporting 55 cases were identified. Fifty-two (94.5%) patients had respiratory symptoms. Fifteen (27.3%) patients developed severe pneumonia. Confirmation of TW infection was achieved through methods including the assessment of TW reads and relative abundance (63.6%), empirical treatment (18.2%), lung biopsy histopathology (14.5%), and qPCR confirmation (3.6%). Fifty (90.9%) patients received antibiotic therapy. Fifty-one (92.7%) patients had a good prognosis.

CONCLUSION: TW can enter the lower respiratory tract through multiple routes. When TW sequences are detected in lower respiratory tract samples, it is important to consider not only the read and relative abundance but also histopathological findings such as interstitial pneumonia and the presence of PAS- or PASM-positive bacilli within foamy macrophages as they can aid in diagnosing TW infection. MDT discussions and empirical antibiotic therapy targeting TW are viable options when a patient's condition deteriorates. Microbiological testing of saliva, gastric fluid, blood, and faeces may help clarify the source of TW.},
}

@article {pmid40657275,
year = {2025},
author = {Fu, Y and Zhou, J and He, P and Li, X},
title = {A Rare Case Report of Tropheryma Whipplei-Induced Acute Respiratory Distress Syndrome in an Immunocompetent Patient.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {3409-3414},
pmid = {40657275},
issn = {1178-6973},
abstract = {Tropheryma whipplei is a rare gram-positive bacterium traditionally associated with Whipple's disease, primarily presenting with gastrointestinal symptoms. Pulmonary involvement, particularly acute respiratory distress syndrome (ARDS), is extremely rare and poses diagnostic challenges, especially in immunocompetent individuals. We report a rare case of ARDS caused by Tropheryma whipplei in a 28-year-old immunocompetent male with no significant medical history. Traditional diagnostic methods failed to identify the causative pathogen. However, metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid enabled rapid and accurate detection of T. whipplei, allowing timely initiation of targeted antimicrobial therapy with ceftriaxone and trimethoprim-sulfamethoxazole. The patient demonstrated marked clinical improvement and was discharged with no relapse at follow-up. This case highlights the critical diagnostic value of mNGS in atypical ARDS cases and emphasizes the importance of considering T. whipplei in the differential diagnosis, even among immunocompetent individuals.},
}

@article {pmid40656756,
year = {2025},
author = {Huang, Y},
title = {Investigation of protists in Momoge wetland (China) through metagenomic next-generation sequencing.},
journal = {Biodiversity data journal},
volume = {13},
number = {},
pages = {e153721},
pmid = {40656756},
issn = {1314-2828},
abstract = {The Momoge wetland plays an important role in maintaining the ecosphere and protist is an indispensable component of it. In order to reveal community structure and diversity of protists in Momoge wetland, metagenomic next-generation sequencing (mNGS) was performed. The main results are as follows: 1) A total of 224 species were identified, belonging to 17 phyla, 32 classes, 75 orders, 94 families and 146 genera. Among them, Bacillariophyta, Evosea, Oomycota, Rhodophyta, Ciliophora, Haptophyta, and Salpingoecarosetta, Guillardiatheta, Polarellaglacialis, Cladocopiumgoreaui were the dominant phyla and species, respectively; 2) Most of them were species adapted to the saline-alkali environment, and the protists of Momoge wetland had higher diversity, fewer dominant species, and higher evenness than those of the harsher environment; 3) KEGG analysis showed that some protistan pathways were related to the saline-alkali environmental adaptation. This research is beneficial to ecological protection and provides valuable information for future studies.},
}

@article {pmid40656634,
year = {2025},
author = {Hieta, J and Benchraka, C and Pärnänen, K and Houttu, N and Mokkala, K and Lotankar, M and Kataja, EL and Lahti, L and Laitinen, K},
title = {Perinatal depressive and anxiety symptoms are associated with gut microbiota in pregnant women with overweight and obesity.},
journal = {Brain, behavior, & immunity - health},
volume = {47},
number = {},
pages = {101042},
pmid = {40656634},
issn = {2666-3546},
abstract = {The associations of gut microbiota with depressive and anxiety symptoms have been investigated mainly in non-pregnant humans, and currently there is a significant gap in research on pregnant women, especially those who are living with overweight and thus at a higher risk for experiencing perinatal mental health problems. In this study, we used shotgun metagenomic sequencing to analyze the gut microbiota of pregnant women with overweight and obesity, both in early and late pregnancy. We compared gut microbial diversity, composition, and function across groups with different trajectories of depressive (n=419) and anxiety (n=408) symptoms. Depressive symptoms were assessed using the Edinburgh Postnatal Depression Scale (EPDS), and anxiety symptoms were evaluated with the Symptom Checklist 90 (SCL-90, anxiety subscale) at five time points spanning from early pregnancy to one year postpartum. Latent growth mixture modeling (LGMM) was used to model symptom trajectories from early pregnancy until one year postpartum and further symptom sum scores at five time points cross-sectionally. We observed differences in several bacterial species abundances between the trajectory groups and in cross-sectional analyses, including higher abundance of Hungatella hathewayi in the Moderate and increasing depressive symptoms group (FDR<0.25), and Bacteroides clarus in the High and decreasing depressive symptoms group (FDR<0.25) and in women experiencing clinically significant postpartum anxiety symptoms (FDR<0.05). No differences were found regarding the gut microbiota diversity (α or β) or function. The results suggest that maternal gut microbiota, particularly the increased abundance of possible pro-inflammatory species, could be one of the factors affecting perinatal distress.},
}

@article {pmid40655931,
year = {2025},
author = {Redondo, MA and Jones, CM and Legendre, P and Guénard, G and Hallin, S},
title = {Predicting gene distribution in ammonia-oxidizing archaea using phylogenetic signals.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf087},
pmid = {40655931},
issn = {2730-6151},
abstract = {Phylogenetic conservatism of microbial traits has paved the way for phylogeny-based predictions, allowing us to move from descriptive to predictive functional microbial ecology. Here, we applied phylogenetic eigenvector mapping to predict the presence of genes indicating potential functions of ammonia-oxidizing archaea (AOA), which are important players in nitrogen cycling. Using 160 nearly complete AOA genomes and metagenome assembled genomes from public databases, we predicted the distribution of 18 ecologically relevant genes across an updated amoA gene phylogeny, including a novel variant of an ammonia transporter found in this study. All selected genes displayed a significant phylogenetic signal and gene presence was predicted with an average of >88% accuracy, >85% sensitivity, and >80% specificity. The phylogenetic eigenvector approach performed equally well as ancestral state reconstruction of gene presence. We implemented the predictive models on an amoA sequencing dataset of AOA soil communities and showed key ecological predictions, e.g. that AOA communities in nitrogen-rich soils were predicted to have capacity for ureolytic metabolism while those adapted to low-pH soils were predicted to have the high-affinity ammonia transporter (amt2). Predicting gene presence can shed light on the potential functions that microorganisms perform in the environment, further contributing to a better mechanistic understanding of their community assembly.},
}

@article {pmid40655380,
year = {2025},
author = {Siraj, K and Kaliyaperumal, KA and Gururajan, G and Saravanan, TG},
title = {Metagenomics Analysis of Microbiota in Raw Chicken Stored at Different Temperature over Storage Time in Chennai.},
journal = {Indian journal of microbiology},
volume = {65},
number = {2},
pages = {955-960},
pmid = {40655380},
issn = {0046-8991},
abstract = {Poultry meat consumption nowadays demands the need for efficient storage practices for safe and healthy meat. Studying the putative microorganisms for meat spoilage therefore necessitates the effectiveness of storage Microbial types. In this study, poultry meat from Chennai was analyzed for spoilage considering the Microbial types of temperature (- 18 °C and 0-5 °C) and storage time (2, 4, 6 months). Conventional pour plate method was assisted with next generation sequencing to analyze the microbiota and potent spoilage bacteria. Irrespective of the storage temperature, all the samples showed bacteria of phyla Proteobacteria, Actinobacteria, Firmicutes, Bacteroidota predominantly. Hafnia-Obesumbacterium and Wohlfahrtiimonas (nearly 10%), Enterococcus (~ 5%), Moellerella and Bacillus (~ 1%) genera were observed in sample stored at the slightly higher temperature. This preliminary study points out that storage temperature is important to maintain shelf life of chicken sample and sample stored at even slightly raised temperature will be spoiled within 10 days. In addition, the need for equipping metagenomics analysis along with conventional method would be required to observe the spoilage at intricate levels.},
}

@article {pmid40655373,
year = {2025},
author = {Sabarish, S and Dhanasekaran, D},
title = {Bacterial Community Profile of Bovine Mastitis Infected Dairy Cow Milk by 16S rRNA Amplicon Sequencing.},
journal = {Indian journal of microbiology},
volume = {65},
number = {2},
pages = {1142-1151},
pmid = {40655373},
issn = {0046-8991},
abstract = {UNLABELLED: The prevalence of Bovine mastitis, an important disease of cow, causing huge economic loss in dairy industries, was tested in cows and other types of breeds reared at Salem and Trichirappalli district. It was interesting to note that the country breed cow was free from disease. The presence of mastitis microbes was identified by culture dependent method. Staphylococcus aureus, Staphylococcus agalactiae, Klebsiella sp. and Pseudomonas sp. were the most common bacteria found in mastitis-infected milk. Opportunistic anaerobic bacteria such as Fusobacterium necrophorum and Porphyromonas levii were found in abundance in mastitis milk samples, but not in non-mastitis milk samples. Milk samples from a mastitis-infected Jersey cow and healthy cow as a control cow were utilized to construct V3-V4 sections of 16S rRNA gene profiles, which were compared to bacterial diversity and abundance. A total of 16,000 sequence numbers were acquired from the 16S rRNA dataset, with a cumulative length of base pairs (bp) of 250. About 321 OTUs were created from these readings. Among these, 190 OTUs are similar in milk from both uninfected healthy and infected Jersey cow. A total of 70 OTUs and 61 OTUs were unique to milk obtained from healthy milk and mastitis infected milk respectively. The hierarchically clustered heat map depicted the overall perspective of the found relationships of bacterial populations among milk samples. The relative abundance of the Ochrobactrum, Pseudomonas and Stenotrophomonas (Kamilari) were associated in the milk. The Shannon index of a healthy cow milk sample was greater (4.136), suggesting the quantity and evenness of the microbial species present. The Simpson index also revealed that during a cow infection, the species richness and evenness declined. Metagenomic analysis can help us better understanding the pathophysiology of bovine mastitis, and it has the potential to be employed as a diagnostic tool as well.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01310-w.},
}

@article {pmid40655366,
year = {2025},
author = {Yadav, S and Kapley, A},
title = {Profiling of Pharmaceutical Sludge Microbiome, Resistome and Secondary Metabolites Using Metagenomics.},
journal = {Indian journal of microbiology},
volume = {65},
number = {2},
pages = {1181-1200},
pmid = {40655366},
issn = {0046-8991},
abstract = {UNLABELLED: Antibiotic manufacturing sites act as the hotspot for the dissemination of antibiotic resistance. The present study explores the resistome and secondary metabolites profile associated with the sludge of two pharmaceutical industries located in Delhi and Mysore, India. It confirmed that the pharma sludge contains complex microbiome and resistome. The presence of antibiotic-resistant genes (ARGs), class I integrons, and secondary metabolite genes (NRPs and PKs) was confirmed using PCR. Metagenomic tools like ResFinder 3.2, DeepARG, BusyBee, MG-RAST, and CoMET universe were used to analyze pharmaceutical sludge metagenome. Proteobacteria was found abundant in both metagenomes, followed by firmicutes & bacteriodetes. KEGG analysis predicted the expression of vancomycin, Pandrug, antifolate resistance pathway in both metagenomes. Resfinder predicted the presence of aminoglycoside, macrolide, and sulphonamide resistance genes in both metagenomes. DeepARG analysis classified ARGs in 28 (Arbro) & 27 (Mysore) ARG category and 431 & 368 ARG class. Further, CoMET universe indicated the presence of biosynthetic gene clusters like type II polyketide biosynthesis, Nonribosomal polypeptide biosynthesis, vancomycin & tetracycline, and macrolide biosynthesis. The present study provides primary insight about the diversity of secondary metabolites clusters present in pharmaceutical sludge. Microbes residing in such environment grows under higher selection pressure and produce various secondary metabolites. These metabolites could be exploited for the discovery of novel metabolites with antimicrobial potential and combating AMR. In future, the author aims to clone metagenome in expression vector (BAC/YAC vectors) for the discovery of novel secondary metabolites.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01349-9.},
}

@article {pmid40655305,
year = {2025},
author = {Yuan, X and Wang, Q and Ding, H and Li, H and Fang, X and Zhang, W and Huang, Z},
title = {The Role of Applying Metagenomic Next-Generation Sequencing (mNGS) in Periprosthetic Joint Infection with Sinus Tract: A Retrospective Study.},
journal = {International journal of general medicine},
volume = {18},
number = {},
pages = {3787-3795},
pmid = {40655305},
issn = {1178-7074},
abstract = {BACKGROUND: Diagnosing periprosthetic joint infection (PJI), especially with sinus tracts, is challenging using traditional cultures. Metagenomic next-generation sequencing (mNGS) offers a culture-independent diagnostic approach. We evaluated mNGS's role in diagnosing and guiding treatment for PJI with sinus tracts.

METHODS: This retrospective analysis included 52 PJI patients (2019-2024). An mNGS group (n=43; 18 sinus PJI, 25 non-sinus PJI) was compared to a non-mNGS control group (n=9; all sinus PJI, culture-diagnosed). We compared pathogen detection rates. For sinus PJI patients (two-stage revision), 2-year cure rates and antibiotic duration were compared between mNGS-guided and non-mNGS-guided therapy.

RESULTS: In sinus PJI cases (n=18), mNGS achieved significantly higher pathogen detection (88.9%, 16/18) versus culture (50.0%, 9/18) (Relative Risk [RR] 1.78; P=0.027). mNGS also detected more polymicrobial infections (38.9%, 7/18) compared to culture (5.6%, 1/18) (RR 7.00; P=0.041). For sinus PJI treatment, mNGS-guided therapy yielded a significantly higher 2-year cure rate (94.4%, 17/18) than non-mNGS therapy (55.6%, 5/9) (Absolute Risk Increase 38.9%; RR 1.70; P=0.03). Mean antibiotic duration was significantly shorter with mNGS guidance (35.62 ± 5.42 vs 47.11 ± 6.53 days; difference 11.49 days; P<0.01), with a trend towards fewer antibiotic-related complications (11.1% vs 55.6%; P=0.23).

CONCLUSION: mNGS significantly improves pathogen detection, especially polymicrobial infections, in sinus tract PJI. mNGS-guided therapy for sinus PJI is associated with substantially improved cure rates and shorter antibiotic duration, highlighting its utility in guiding targeted anti-infection strategies for these complex cases.},
}

@article {pmid40655196,
year = {2025},
author = {Fuentes-Santander, F and Curiqueo, C and Araos, R and Ugalde, JA},
title = {BugBuster: a novel automatic and reproducible workflow for metagenomic data analysis.},
journal = {Bioinformatics advances},
volume = {5},
number = {1},
pages = {vbaf152},
pmid = {40655196},
issn = {2635-0041},
abstract = {SUMMARY: Metagenomic sequencing generates massive datasets that capture the complete genetic content of a sample, enabling detailed characterization of microbial communities. Yet the software and processes necessary to transform raw data into biologically meaningful results have become increasingly complex, limiting accessibility for researchers without specialist expertise. In this work, we present a novel modular a reproducible workflow developed to facilitate the analysis of metagenomic data. BugBuster is a fully containerized, modular, and reproducible workflow implemented in Nextflow. The pipeline streamlines analysis at level of reads, contigs, and metagenome-assembled genomes, offering dedicated modules for taxonomic profiling and resistome characterization. Thanks to the use of containers, BugBuster can be deployed with minimal configuration on workstations, high-performance clusters, or cloud platforms. Together, these features allow the robust, scalable, and reproducible analysis of metagenomic datasets.

BugBuster was written in Nextflow-DSL2. The program applications, user manual, example data and code are freely available at https://github.com/gene2dis/BugBuster.},
}

@article {pmid40654884,
year = {2025},
author = {Wirbel, J and Hickey, AS and Chang, D and Enright, NJ and Dvorak, M and Chanin, RB and Schmidtke, DT and Bhatt, AS},
title = {Discovering Broader Host Ranges and an IS-bound Prophage Class Through Long-Read Metagenomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.09.652943},
pmid = {40654884},
issn = {2692-8205},
abstract = {Gut bacteriophages profoundly impact microbial ecology and human health, yet they are greatly understudied. Using deep, long-read bulk metagenomic sequencing, a technique that overcomes fundamental limitations of short-read approaches, we tracked prophage integration dynamics in 12 longitudinal stool samples from six healthy individuals, spanning a two-year timescale. While most prophages remain stably integrated into their host over two years, we discover that ∼5% of phages are dynamically gained or lost from persistent bacterial hosts. Within the same sample, we find evidence of population heterogeneity in which identical bacterial hosts with and without a given integrated prophage coexist simultaneously. Furthermore, we demonstrate that phage induction, when detected, occurs predominantly at low levels (1-3x coverage compared to the host region). Interestingly, we identify multiple instances of integration of the same phage into bacteria of different taxonomic families, challenging the dogma that phage are specific to a host of a given species or strain. Lastly, we describe a new class of phages, which we name "IScream phages". These phages co-opt bacterial IS30 transposases to mediate their integration, representing a previously unrecognized form of phage domestication of selfish bacterial elements. Taken together, these findings illuminate fundamental aspects of phage-bacterial dynamics in the human gut microbiome and expand our understanding of the evolutionary mechanisms that drive horizontal gene transfer and microbial genome plasticity in this ecosystem.},
}

@article {pmid40654764,
year = {2025},
author = {Myers, JM and Schulz, F and Rahimlou, S and Yadav, V and Amses, KR and Simmons, DR and Sun, S and Orozco-Quime, M and Heitman, J and Stajich, JE and James, TY},
title = {Discovery of giant viruses as past and present infections of zoosporic fungi.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.01.04.574182},
pmid = {40654764},
issn = {2692-8205},
abstract = {Giant viruses of the phylum Nucleocytoviricota have emerged as particularly notable due to their increasingly recognized impacts on eukaryotic genome evolution. Their origins are hypothesized to predate or coincide with the diversification of eukaryotes, and they have been detected in hosts that span the eukaryotic tree of life. But surprisingly, such viruses have not been definitively found in Kingdom Fungi, though genomic and metagenomic work suggests a putative association. Here we report both "viral fossils" and active infection by giant viruses in fungi, particularly in the zoosporic phyla Blastocladiomycota and Chytridiomycota. The recovered viral genomes span up to 350 kb, encode over 300 genes, and form a monophyletic family-level clade within the Nucleocytoviricota related to orders Imitervirales and Algavirales , which we name Mycodnaviridae . We observed variation in infection status among the isolates including apparent active infection and transcriptionally-suppressed states, suggesting that viral activation may be constrained to certain life stages of the host. Our experimental findings add to the limited natural virus-host systems available in culture for the study of giant viruses. These viruses may have shaped the early evolution of these fungal lineages by the shuttling of genes between major kingdoms and domains of life. Our findings expand the known host range of Nucleocytoviricota into a new kingdom that contains many model species. Mycodnaviridae have a global distribution, which invites inquiry into the implications of these infections for host traits, host genome evolution, and the metabolic impacts to ecosystems.},
}

@article {pmid40654740,
year = {2025},
author = {Azhieh, A and Hernandez, P and Anderson, AC and Sychantha, D and Verster, AJ and Whitney, JC and Ross, BD},
title = {Rapidly evolving orphan immunity genes protect human gut bacteria from intoxication by the type VI secretion system.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.03.651265},
pmid = {40654740},
issn = {2692-8205},
abstract = {Bacteria encode diverse mechanisms for mediating interbacterial antagonism through the exchange of toxic effector proteins. Although the structure, function, and regulation of these pathways has been well established for many organisms, an understanding of their ecological and evolutionary dynamics lags behind. Type VI secretion systems (T6SS) deliver effectors between competing Gram-negative bacteria, including among mammalian gut Bacteroidales, resulting in the evolution of elaborate defense mechanisms that protect against T6SS attack. One such mechanism is the r ecombinase-associated a cquired interbacterial d efence (rAID) system, which harbors arrays of orphan immunity genes that diverge in sequence from T6SS-associated cognate immunity genes. It is not known if such sequence divergence impacts rAID orphan immunity function, or how rAID distribution across microbiomes relates to the T6SS. Here, we show that divergent rAID orphan immunity factors that possess SUKH domains allow bacteria to survive intoxication by cognate effectors. Such protection is due to high affinity protein-protein interactions between orphan immunity and effector that are comparable to that of cognate effector-immunity. Unlike other examples of T6SS effector-immunity interactions, we find that the binding interface is comprised of electrostatic interactions with a high degree of redundancy underlying its protective capacity. Finally, we quantify orphan immunity and effector gene abundance and dynamics across human gut metagenomes, revealing patterns of co-occurrence indicative of positive selection. Population genetic analyses of longitudinal data suggests that orphan immunity genes accumulate non-synonymous mutations that lie at the predicted effector-immunity interface. Together, our findings establish rAID orphan immunity genes as important bacterial fitness determinants in the human gut.},
}

@article {pmid40654714,
year = {2025},
author = {Carmichael, MM and Valls, RA and Soucy, S and Sanville, J and Madan, J and Surve, SV and Sundrud, MS and O'Toole, GA},
title = {Profiling Bile Acids in the Stools of Humans and Animal Models of Cystic Fibrosis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.08.651222},
pmid = {40654714},
issn = {2692-8205},
abstract = {UNLABELLED: Cystic fibrosis (CF) is associated with dysbiosis of the gut microbiome, alterations in intestinal mucus production, aberrant bile acid (BA) metabolism, fat malabsorption, and chronic inflammation. As little is known about BAs in CF, we performed both comprehensive and targeted BA profiling in stool of children with or without CF. Our results reveal that select BA species and metabolites are significantly different between children with CF (cwCF) and healthy controls. There is also a trend towards higher primary cBA and total BA levels for cwCF. Matched bacterial metagenomic analyses showed no change in alpha-diversity between groups in our small cohort, at odds with previous studies, whereas changes in relative abundance of Bacteroides (lower) and E. coli (increased) species is consistent with prior reports. A robust trend was noted toward reduced abundance of bsh gene families (Wilcox test, p = 0.052), a key rate-limiting enzyme required for bacterial synthesis of secondary BAs, in cwCF. Modest changes in both BAs and microbial BA metabolism-related gene abundances may be attributable to small sample sizes, but also suggest likely combination defects in both host and microbial BA metabolic pathways in cwCF. Importantly, although fecal BA profiles from both ferret and mouse CF models showed significant differences from human BA profiles, only the ferret model reproduced significant differences between CF and nonCF animals, highlighting ferrets as a potentially more appropriate model for studying BA in stool in the context of CF. Together, these results provide new insights into CF-related BA dysmetabolism in cwCF, and highlight limitations of CF animal models for BA functional studies.

IMPORTANCE: Changes in the abundance and/or composition of intestinal bile acids (BAs) may contribute to dysbiosis and altered gastrointestinal physiology in CF. Here, we report shifts in select fecal BA classes and species for children with CF (cwCF). Matched metagenomic analysis suggest possible defects in both host intestinal BA absorption and gut microbial BA metabolism. Additional analyses of mouse and ferret CF stool for BA composition suggest great care must be taken when interpreting BA functional studies using these animal models. Together, this work lays technical and conceptual foundations for interrogating BA-microbe interactions in cwCF.},
}

@article {pmid40654689,
year = {2025},
author = {Zhang, J and Thomas Backet, RV and Sekela, JJ and Zeller, MJ and Sellers, RS and Redinbo, MR and Gulati, AS and Bhatt, AP},
title = {Commercially Purchased and In-House Bred C57BL/6 Mice with Different Gut Microbiota Exhibit Distinct Indomethacin-Induced Toxicities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.01.651704},
pmid = {40654689},
issn = {2692-8205},
abstract = {Non-steroidal anti-inflammatory drug (NSAID)-induced toxicities are a significant clinical problem, yet the factors influencing these outcomes remain incompletely understood. Here, we investigated the impact of mouse vendor on indomethacin-induced injury using C57BL/6 mice from different breeding facilities (in-house "Tar Heel" and commercial Charles River). We found that Tar Heel mice exhibited significantly enhanced susceptibility to indomethacin toxicity, characterized by greater body weight loss, increased ileal ulceration, elevated fecal lipocalin-2 levels, and higher goblet cell numbers in ileum compared to Charles River mice. Importantly, whole genome metagenomic analysis revealed distinct baseline gut microbiomes between the two types of mice. Notably, Tar Heel mice showed higher abundances of β-glucuronidase (GUS)-producing bacteria, particularly those expressing Loop-1 GUS enzymes, and elevated levels of mucolytic enzyme-encoding bacteria. These differences suggest that enhanced indomethacin toxicity observed in Tar Heel mice may be related to functional changes in their gut microbiome, which may predispose to an exaggerated response to NSAID exposure. Together, our findings demonstrate that vendor-specific differences significantly influence NSAID-induced intestinal toxicity and highlight the importance of considering mouse sources and gut microbial compositions in experimental design. Moreover, we highlight potential functional roles that gut microbes play in host-indomethacin interactions.},
}

@article {pmid40654580,
year = {2025},
author = {Chen, J and Du, Y and Sun, L and Dai, Y and Zhang, L and Ding, X and Liu, T and Yang, K and Han, X and Li, M and Zhou, X},
title = {The boundaries between PML and PML-IRIS: difficult to define, pathology may predict.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1607428},
pmid = {40654580},
issn = {2235-2988},
mesh = {Humans ; *Leukoencephalopathy, Progressive Multifocal/pathology/diagnosis/virology ; Male ; Adult ; Female ; *Immune Reconstitution Inflammatory Syndrome/pathology/diagnosis ; Middle Aged ; JC Virus/genetics/isolation & purification ; Viral Load ; CD4 Lymphocyte Count ; Immunohistochemistry ; Brain/pathology ; },
abstract = {BACKGROUND: Progressive multifocal leukoencephalopathy (PML), caused by John Cunningham (JC) virus reactivation, represents a critical neurological complication in AIDS-related immunosuppression. This single-center study conducted a clinicopathological analysis of 19 confirmed PML cases in an AIDS cohort (16 biopsy; 3 surgical specimens), employing comprehensive neuropathological evaluation. Immunohistochemical testing included SV40, NF, NeuN, P53, Ki-67, GFAP, Oligo-2, and CD68. Myelin architecture was evaluated through Luxol fast blue staining, complemented by molecular diagnostics incorporating quantitative JC viral load PCR and metagenomic next-generation sequencing (mNGS).

RESULTS: Notably, 63.2% (12/19) of them had blood CD4+ T-cell counts < 200 cells/μl, and 36.8% (7/19) had ≥ 200 cells/μl. 52.9% (9/17) of the patients had elevated CSF protein, 5.3% (1/19) had decreased CSF glucose. Statistical analysis revealed significant correlations between mass effect and both blood CD4+ T-cell counts (P = 0.022) and CSF protein levels (P < 0.001). It also demonstrated significant positive correlations between the duration of HIV diagnosis and the degree of inflammatory infiltration (P = 0.038) and perivascular inflammatory infiltration (P = 0.005), as well as plasma cell infiltration (P = 0.011). The degree of inflammatory infiltration was significantly positively correlated with antiretroviral therapy (ART) (P = 0.036). The degree of inflammatory infiltration, the presence of plasma cells, and perivascular lymphocytic cuffing were significantly associated with contrast enhancement on imaging studies (P = 0.044, P = 0.011, and P = 0.018, respectively). These cases display characteristics that deviate from the classic PML previously reported, exhibiting a tendency towards MRI enhancement and histologically indicating a more severe inflammatory response, especially for patients following ART treatment.

CONCLUSION: Our findings suggest that PML and PML-immune reconstitution inflammatory syndrome (IRIS) represent a continuous pathological spectrum, potentially bridged by an intermediate stage with distinct clinicopathological features. This transitional phase may constitute a critical link in the continuum between classic PML and fully developed PML-IRIS. Importantly, it implicates synergistic mechanisms of viral oncogenesis and immune reconstitution, which could redefine therapeutic strategies for this emerging PML variant.},
}

Humans
*Leukoencephalopathy, Progressive Multifocal/pathology/diagnosis/virology
Male
Adult
Female
*Immune Reconstitution Inflammatory Syndrome/pathology/diagnosis
Middle Aged
JC Virus/genetics/isolation & purification
Viral Load
CD4 Lymphocyte Count
Immunohistochemistry
Brain/pathology

@article {pmid40654574,
year = {2025},
author = {Yang, S and Sun, Y and Wang, M and Xu, H and Wang, S},
title = {Risk factors for identifying pulmonary aspergillosis in pediatric patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1616773},
pmid = {40654574},
issn = {2235-2988},
mesh = {Humans ; Risk Factors ; Retrospective Studies ; Male ; Female ; Child ; Child, Preschool ; Infant ; ROC Curve ; *Pulmonary Aspergillosis/diagnosis/epidemiology/microbiology ; Adolescent ; Logistic Models ; China/epidemiology ; },
abstract = {OBJECTIVES: This study aimed to identify the independent risk factors and develop a predictive model for pulmonary aspergillosis (PA) in pediatric populations.

METHODS: This retrospective study compromised 97 pediatric patients with pulmonary infections (38 PA cases and 59 non-PA cases) at Children's Hospital Affiliated to Shandong University between January 2020 and October 2024. Multivariate binary logistic regression was used to identify PA-associated risk factors. Receiver operating characteristic (ROC) curves, calibration plots, and Brier scoring were used to evaluate the diagnostic model.

RESULTS: 8 clinical variables significantly differed between the PA and non-PA groups. Multivariate binary logistic regression analysis identified six significant independent risk factors: a history of surgery (OR: 9.52; 95% CI: 1.96-46.23; P = 0.005), hematologic diseases (OR: 11.68; 95% CI: 0.89-153.62; P = 0.062), absence of fever (OR: 8.244; 95% CI: 1.84-36.932; P = 0.006), viral coinfection (OR: 15.99; 95% CI: 3.55-72.00; P < 0.001), elevated (1, 3) -β -D-glucan levels (BDG, > 61.28 pg/mL; OR: 7.38; 95% CI: 1.26-43.31; P = 0.027), and shorter symptom-to-admission interval (< 4.5 days; OR: 38.68; 95% CI: 5.38-277.94; P < 0.001) were risk factors for PA. The predictive model demonstrated excellent discrimination (AUC 0.93, 95% CI 0.88-0.98) and calibration (Hosmer-Lemeshow p=0.606, R²=0.96, Brier score 0.097). metagenomic next - generation sequencing (mNGS) revealed significantly higher rates of polymicrobial infections in PA cases (86.84% vs 18.64%, p<0.001).

CONCLUSIONS: This study established and validated a high-performance predictive model incorporating six clinically accessible parameters for the diagnosis of pediatric PA.},
}

Humans
Risk Factors
Retrospective Studies
Male
Female
Child
Child, Preschool
Infant
ROC Curve
*Pulmonary Aspergillosis/diagnosis/epidemiology/microbiology
Adolescent
Logistic Models
China/epidemiology

@article {pmid40654462,
year = {2025},
author = {Yu, JJ and Hernandez-Kapila, Y and Wang, CW},
title = {Probiotics to reduce microbiota-related dental stains: A potential approach.},
journal = {Journal of dental sciences},
volume = {20},
number = {3},
pages = {1890-1893},
pmid = {40654462},
issn = {2213-8862},
abstract = {Adult extrinsic black stains on teeth, caused by bacterial colonization, impact aesthetics and confidence. Conventional treatments can be abrasive and have a high recurrence rate. This pilot case study explores probiotics as an adjunctive approach. Direct application of probiotic powder over the black stains of the teeth was carried out prior to routine home care. Results showed black stain removal was possible with tooth brush and dental floss. Saliva and biofilm samples were analyzed via 16S rRNA sequencing. Microbiome revealed a noticeable reduction in Corynebacterium, a key black stain-associated bacterium, with slight shifts in major phyla like Actinobacteriota and Firmicutes. This case study aimed to evaluate the potential of probiotics in reducing black stains on teeth and assess the associated microbiome changes.},
}

@article {pmid40653865,
year = {2025},
author = {Wang, W and Dong, Y and Wang, HB and Xue, DH and Zhang, HF and Li, ZJ and Wang, H and Bo, HJ and Zhang, WJ and Zhang, BH and Xiong, YC and Zhang, Q and Jin, DS},
title = {Long-Term Legume Cultivation Affects the Soil Bacterial Community via Altering the Soil Pore Structure in Coal Mine Reclamation Agroecosystems.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70063},
pmid = {40653865},
issn = {1365-3040},
support = {//This research was supported by the Research Start-up Project of Shanxi Agricultural University for Recruited Talents (2023BQ120), Promotive Scientific Research Fund for New PhD Graduates working in Shanxi Province (SXBYKY2023038), Youth Science and Technology Research Program of Shanxi Province Basic Research Program (202303021222077; 202303021212104), Merit-based Open Competition Project of Shanxi Major Science and Technology Special Program (202201140601028-4). Open Project Funding Project of the Engineering Technology Innovation Center for Ecological Protection and Restoration of the Middle Reaches of the Yellow River, Ministry of Natural Resources (2025080)./ ; },
abstract = {Legume cultivation has great potential for improving soil microbial communities and soil quality in reclaimed ecosystems. However, little is known about the effects of long-term legume cultivation on the soil microbial community structure in agroecosystems in coal mine reclamation areas. To address this issue, we used metagenomics to examine the variations in the soil bacterial community composition and functionality under three leguminous crops in a 10-year reclamation experiment. After 10 years, we found dissimilarity in the microbial communities between the control and leguminous crops. Furthermore, three legume cultivation greatly promoted the diversity and abundance of the dominant bacteria The keystone phyla of the soil bacterial communities in the reclamation area included Proteobacteria, Acidobacteriota, Gemmatimonadota and Myxococcota. In particular, soil pore structure was the main factor influencing the variation in the bacterial community. Therefore, long-term legume cultivation can significantly improve the soil microbial community structure, which likely serves as the basis for soil microbial abundance and functionality and soil health. This study confirmed the ability of the spongy structure formed by legumes to optimize resource use in a nutrient-impoverished mine reclamation agroecosystem. These findings may have important implications for assessing microbial multifunctionality in agroecosystems in coal mine reclamation areas.},
}

@article {pmid40653476,
year = {2025},
author = {Bi, BY and Lin, L and Huang, L and Zhou, J and Yan, WJ and Huang, L and Wang, J and Li, XB},
title = {Effects of arabinoxylan on BDNF/TrkB/p-CREB signaling pathway in the prefrontal cortex and intestinal microbiome in post-stroke depressed rats.},
journal = {BMC neuroscience},
volume = {26},
number = {1},
pages = {40},
pmid = {40653476},
issn = {1471-2202},
support = {No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; No. S2018073,No. S2021003//Guangxi Medical and Health Appropriate Technology Development and Promotion Application/ ; },
mesh = {Animals ; *Prefrontal Cortex/metabolism/drug effects ; *Brain-Derived Neurotrophic Factor/metabolism ; *Gastrointestinal Microbiome/drug effects ; Male ; Signal Transduction/drug effects ; Rats ; Receptor, trkB/metabolism ; *Depression/metabolism/drug therapy/etiology ; *Xylans/pharmacology ; Rats, Sprague-Dawley ; *Stroke/complications/metabolism ; Cyclic AMP Response Element-Binding Protein/metabolism ; },
abstract = {AIM: To explore the effects of arabinoxylan on the BDNF/TrkB/p-CREB signaling pathway in the prefrontal cortex of post-stroke depressed rats, and to explore its neuronal protective effects through the microbial-gut-brain axis in the regulation of this pathway.

METHODS: The rat model of post-stroke depression (PSD) was established by middle cerebral artery occlusion (MCAO) combined with chronic unpredictable mild stimulation (CUMS). They were randomly divided into 5 groups (blank control, post-stroke depression, arabinoxylan, fluoxetine hydrochloride, fluoxetine hydrochloride combined arabinoxylan). The rats were treated differently for 28 days according to their grouping. Body mass, sugar and water consumption experiments and open-field experiments were used to evaluate the behavior of rats. The pathological changes were observed by H&E staining. The expression levels of amine neurotransmitters were detected by ELISA. The expression levels of BDNF mRNA and BDNF, TrkB and p-CREB were detected by RT-PCR and Western blot. The analysis of intestinal metagenomics was conducted by 16 S rDNA sequencing.

RESULTS: Compared with the post-stroke depression group, the body weight, activity and sugar water consumption rate of the arabinoxylan group were increased. The expression levels of 5-HT in the prefrontal cortex, colon and serum levels of 5-HT, DA and NE were increased. The expression levels of BDNF mRNA and BDNF, TrkB and P-CREB in the prefrontal cortex were also upregulated. The number of neurons in the prefrontal cortex increased; Colon mucosal injury and inflammatory cell infiltration decreased, the intestinal microbial diversity increased; The relative abundance of probiotics such as bifidobacterium, Christensenia, Dubosiella New York and ruminococcus increased. The relative abundance of Prevotella NK3B31 group was reduced. The level of 5-HT in the prefrontal cortex was negatively correlated with the abundance of Prevotellaceae NK3B31 group.

CONCLUSION: Arabinoxylan improved depressive-like behavior in rats and its neuroprotective role was achieved by promoting the growth of intestinal probiotics, improving the intestinal barrier, affecting the BDNF/TrkB/p-CREB signaling pathway, and increasing the expression levels of monoamine neurotransmitters 5-HT, DA and NE.},
}

Animals
*Prefrontal Cortex/metabolism/drug effects
*Brain-Derived Neurotrophic Factor/metabolism
*Gastrointestinal Microbiome/drug effects
Male
Signal Transduction/drug effects
Rats
Receptor, trkB/metabolism
*Depression/metabolism/drug therapy/etiology
*Xylans/pharmacology
Rats, Sprague-Dawley
*Stroke/complications/metabolism
Cyclic AMP Response Element-Binding Protein/metabolism

@article {pmid40653257,
year = {2025},
author = {Shantha, JG and Moussa, K and Laovirojjanakul, W and Yeh, S and Tsui, E and Chen, JL and Vitale, AT and Shakoor, A and Larochelle, M and Niemeyer, K and Mentreddy, A and Livnat, I and Safo, M and Ao, W and Choo, C and Yan, D and Zhong, L and Chen, C and Da Silva, K and Reddy, AK and Lee, J and Sura, A and Crowell, EL and Qian, Y and Sharon, Y and Hinterwirth, A and Porco, T and Arnold, BF and Gonzales, J and Acharya, NR and Lietman, TM and Doan, T and , },
title = {The Effect of Metagenomic Sequencing on Patient Clinical Outcomes for Intraocular Infections: A Multicenter Randomized Controlled Trial.},
journal = {American journal of ophthalmology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajo.2025.07.003},
pmid = {40653257},
issn = {1879-1891},
abstract = {OBJECTIVE: To determine whether the addition of an unbiased test, metagenomic sequencing of intraocular fluid, compared to standard-of-care diagnostics alone, leads to better patient outcomes in presumed infectious intraocular inflammatory eye diseases.

DESIGN: A randomized controlled trial was conducted from May 2022 through February 2024.

PARTICIPANTS: Eligible participants had intraocular inflammation concerning for an infectious etiology, were 18 years or older, and had vision better than no light perception (NLP). This study enrolled participants at 6 tertiary referral eye centers in the United States (5 sites) and Thailand (1 site).

INTERVENTIONS: Participants were randomized to have their physicians have access to deep sequencing results or not.

MAIN OUTCOMES AND MEASURES: The main outcomes were 1) clinical improvement on examination at 4 weeks after randomization and 2) appropriate therapy administered by the treating physician as determined by an independent expert panel.

RESULTS: Among the 100 participants enrolled (median [IQR] age, 62.0 [47.5-71.0] years; 57 (57.0%) were women), 92 participants completed the study. Forty-one (41.0%) participants had resolution of inflammation at their 2-week follow-up and 23 (23.0%) participants had a pathogen identified with routine diagnostics and exited the study. Twenty-one (21.0%) participants met the criteria for randomization. At the primary endpoint, 8 (88.9%) patients in the metagenomic sequencing group had clinical improvement compared to 7 (63.6%) patients in the no metagenomic sequencing group (risk difference, 30% [95% CI: 0.6% to 59.1%]; relative risk (RR)=1.35 [95% CI: 1.01 to 1.81]; P=0.045). Eight (88.9%) patients were considered to receive the appropriate therapy in the metagenomic sequencing group compared to 11 (100%) patients in the no metagenomic sequencing group (risk difference, -12.0% [95% CI: -38.0% to 14.0%]; RR= 0.89 [95% CI: 0.68 to 1.15]; P=0.37). There were 3 non-study related adverse events.

CONCLUSIONS: Having access to metagenomic sequencing results modestly improved clinical outcomes in a subset of patients with suspected intraocular infections. Larger studies are needed to determine the long-term impact on management and clinical outcomes.

TRIAL REGISTRATION: https://clinicaltrials.gov/ct2/show/NCT05286203.},
}

@article {pmid40652761,
year = {2025},
author = {Gupta, A and Saleena, LM and Sivachandran, A},
title = {Genomic insights into antibiotic resistance in dental caries among the south indian population: A bioinformatics approach with abrit AMR.},
journal = {Computers in biology and medicine},
volume = {196},
number = {Pt A},
pages = {110753},
doi = {10.1016/j.compbiomed.2025.110753},
pmid = {40652761},
issn = {1879-0534},
abstract = {OBJECTIVE: This research aims to explore the prevalence, diversity, and impact of Antibiotic Resistance Genes (ARGs) in dental caries within the South Indian population, as well as their association with microbial communities, with the goal of improving treatment outcomes and management strategies.

METHODS: Metagenomic shotgun sequencing was performed on 24 dental caries samples using the Illumina NovaSeq platform. The quality assessment was done using the FASTQC tool. The assembly of sequences was conducted using MEGAHIT and Velvet, which generate contigs, with MEGAHIT producing longer contigs than Velvet. ARGs were identified using AbritAMR (NCBI AMRFinderPlus) with a 90 % similarity threshold. Taxonomic profiling was conducted using SqueezeMeta (Silva database).

RESULTS: The analysis revealed a total of 55 distinct antibiotic resistance genes (ARGs), including 9 efflux pump genes, 8 beta-lactam resistance genes, 4 aminoglycoside resistance genes, and 4 tetracycline resistance genes. Fourteen metal resistance genes were identified, of which copper and mercury resistance genes were the most prevalent. Taxonomic profiling revealed Pseudomonas, Stenotrophomonas, and Acinetobacter as common genera associated with ARGs in dental caries samples from the South Indian population.

CONCLUSION: This is the first study to uncover a significant number of ARGs using shotgun metagenomic sequencing of dental caries samples in the South Indian population. This work contributes to our knowledge of the genetic foundation of antibiotic resistance in dental caries in the South Indian population. To address antibiotic resistance in oral health conditions, unique ARGs and their associations with bacterial taxa offer important new insights for future study and the creation of focused treatment approaches.

CLINICAL SIGNIFICANCE: The detection of unique ARGs and their association with specific bacterial taxonomy offers valuable insights for developing more effective interventions against antibiotic resistance in oral health.},
}

@article {pmid40652718,
year = {2025},
author = {Tang, R and Luo, X and He, W and Cai, X and Huang, L and Zhou, L and Yuan, Y},
title = {Microbial electrotrophs-driven molecular transformations of dissolved organic matter in paddy soil.},
journal = {Journal of environmental management},
volume = {391},
number = {},
pages = {126562},
doi = {10.1016/j.jenvman.2025.126562},
pmid = {40652718},
issn = {1095-8630},
abstract = {Microbial electrotrophs are key players in biogeochemical cycles, but the impact of electrotrophic communities on the diverse chemical composition and properties of dissolved organic matter (DOM) molecules in paddy soils has not been comprehensively explored. Herein, we investigated the response of DOM molecules in paddy soil-based microcosms to electrotrophic communities using microbial electrosynthesis systems (MESs), high-resolution mass spectrometry, and genome-centric metagenomics techniques. Compared to the open-circuit control, the closed-circuit system exhibited a 2.6-fold increase in dissolved organic carbon concentration after 120 days of incubation in the MESs, with aromatic and tannin molecular abundances rising by 3.5-fold and 4.4-fold, respectively. These results indicate that electrotrophic activity enhances both the structural complexity and aromatization (humification degree) of soil DOM. Functional annotation revealed significant enrichment of the reductive tricarboxylic acid (rTCA) cycle and Calvin-Benson-Bassham (CBB) cycle, demonstrating active CO2 assimilation by electrotrophs into complex organic compounds. Electrotrophic genera such as Pseudomonas, Hyphomicrobium, Phenylobacterium, Achromobacter, Geobacter, Anaeromyxobacter, and Magnetospirillum were substantially enriched under the closed-circuit conditions, with relative abundances increasing from 0.02-0.72 % to 1.65-13.68 %. These microbes likely facilitated DOM stabilization by coupling extracellular electron uptake with CO2 fixation, thereby transforming labile organic carbon into more stable molecular structures. These findings elucidate the impact of electrotrophic bacteria in regulating the DOM transformation, providing a deeper understanding of the transformation mechanisms of DOM in paddy soils.},
}

@article {pmid40652689,
year = {2025},
author = {Schaeffer, J and Indio, V and Troja, F and Desdouits, M and de Cesare, A and Le Guyader, FS},
title = {Use of capture based metagenomic to assess human enteric virus diversity in sewage and shellfish samples.},
journal = {Marine pollution bulletin},
volume = {220},
number = {},
pages = {118417},
doi = {10.1016/j.marpolbul.2025.118417},
pmid = {40652689},
issn = {1879-3363},
abstract = {Human sewage is the main source of contamination of environmental waters with human enteric viruses, that can contaminate food such as shellfish. Metagenomic represents a new way of analyzing viral diversity through an a priori massive parallel sequencing approach. However, the precise identification of enteric viruses in sewage or shellfish matrices, is still challenging due to the low viral load, large diversity of viral genera and the large amounts of matrix masking viral sequences. This work compared three commercial kits using capture-based enrichment during the library preparation, for the diversity of detected enteric viruses and for the identification of viral strains in sewage and shellfish samples, focusing on four families impacting human health. Triplicate libraries were prepared for each sample and each kit. All three kits allowed the characterization of a variety of viral genera. In sewage samples, a large number of long contigs was obtained allowing a precise identification of more than 35 strains. In shellfish samples, long contigs were rarer but allowed the identification of one human astrovirus and one norovirus strains. Of the tested kits, one displayed lower variation between replicates, allowed to sequence a higher diversity of viruses from the four families of interest and yielded a higher number of nearly-whole genomes.},
}

@article {pmid40652650,
year = {2025},
author = {Meng, X and Chen, S and Liu, Z and Cheng, L and Hu, Y and Huang, X},
title = {Mechanism of electro-acclimation shaped microbiota facilitating phosphorus release from iron-containing sludge: microbial reduction and induced dissolution.},
journal = {Water research},
volume = {286},
number = {},
pages = {124197},
doi = {10.1016/j.watres.2025.124197},
pmid = {40652650},
issn = {1879-2448},
abstract = {Iron-based Chemically Enhanced Primary Treatment (Fe-CEPT) can efficiently concentrate phosphorus (P) from municipal wastewater into sludge; however, unfavorable P release efficiency impedes P recovery from Iron-based Chemically Enhanced Primary Sludge (Fe-CEPS). This study developed an electro-digester by applying controlled potentials to bio-electrodes. The electro-acclimated microorganisms on bio-electrodes achieved efficient P release due to microbial Fe(III) reduction and microbial metabolism-induced P-Fe complexes dissolution. In P release potential tests, 53.2 % of total P was released within 60 h after +1.0 V acclimation, 2.2-fold of the control. P fractionation analysis revealed that the proportion of Fe(II)-P, Fe(III)-P, and Reductant-P in Fe-CEPS (substrate) decreased by 9.7 %, 44.8 %, and 37.5 % after P release, respectively, combined with X-ray diffraction analysis, indicating P-release process followed Fe(III)-P and reductant-P first being reduced to Fe(II)-P and then dissolved into P(liquid), while inherent Fe(II)-P directly dissolved into P(liquid). The enhanced electron transfer capacity of electro-acclimated microorganisms, demonstrated by cyclic voltammetry analysis, promoted Fe(III)-P reduction. The lower pH (a minimum of 5.7) in mixed liquor, achieved by the enhanced metabolism of electro-acclimated microorganisms and elevated enzyme activities relating to hydrolysis-acidification, facilitated the dissolution of Fe(II)-P into the liquid phase. These two steps were dominated by enriched iron-reducing bacteria as Deferribacteraceae and fermentative bacteria as Clostridiaceae in electro-acclimation shaped microbiota. Metagenomic analysis showed consistent results as genes encoding cellular respiratory, metabolism and electron transportation upregulated significantly. These findings provided an eco-friendly, cost-effective solution for treating iron-containing chemical sludge and recovering valuable P resources.},
}

@article {pmid40652649,
year = {2025},
author = {Kong, T and Sun, X and Gao, P and Huang, W and Guan, X and Xu, Z and Li, B and Sun, W},
title = {Investigation of the ecological roles of the plastisphere microbiome in metal-contaminated river sediments: elucidation of their metabolic versatilities for plastics mineralization and metal resistance.},
journal = {Water research},
volume = {286},
number = {},
pages = {124170},
doi = {10.1016/j.watres.2025.124170},
pmid = {40652649},
issn = {1879-2448},
abstract = {Both plastics and heavy metal(loid)s (HMs) are ubiquitous environmental contaminants, and their frequent interactions in aquatic environments are observed globally. These interactions could result in adsorption of HMs onto plastics, thereby altering the environmental behavior of both contaminants. The change of physicochemical property of plastics surfaces, due to HM adsorption, inevitably impacts the plastisphere microbiome, as well as the fate of plastics in the environment. However, our understanding of how plastisphere microbiomes respond to HMs stress, and the subsequent impacts on the fate of plastics and HMs, remain in its infancy. The current study identified keystone taxa of the plastisphere microbiome and identified their ecological roles in HM metabolism. Members of Mycobacterium were identified as the keystone taxa in the HM contaminated plastisphere. Metagenomic binning and pangenome analysis demonstrated that Mycobacterium encoded essential genes for plastics biodegradation and HM resistance. Pure isolates of Mycobacterium further confirmed that the bacteria can mineralize plastics under arsenic exposure, with plastics biodegradation rates remaining unaffected by environmentally relevant As concentrations (up to 0.5 mM). In summary, the metabolic potentials of HM detoxification as well as the mineralization of plastics by the keystone taxa of the plastisphere microbiome may play important environmental service to promote the bioremediation of the co-contamination of HMs and plastics.},
}

@article {pmid40652256,
year = {2025},
author = {Tang, Y and Zhan, P and Wu, Y and Zhang, T and Yin, D and Gao, Y and Yu, Y and Qiu, S and Zhao, J and Zhang, X and Ma, Z and Chen, Y and Zhao, L and Mao, S and Huang, J and Chen, WH and Liu, J},
title = {Landscape of mobile genetic elements and their functional cargo across the gastrointestinal tract microbiomes in ruminants.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {162},
pmid = {40652256},
issn = {2049-2618},
mesh = {Animals ; *Ruminants/microbiology ; *Gastrointestinal Microbiome/genetics ; *Interspersed Repetitive Sequences ; Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Plasmids/genetics ; Gene Transfer, Horizontal ; *Gastrointestinal Tract/microbiology ; Metagenome ; },
abstract = {BACKGROUND: Mobile genetic elements (MGEs) drive horizontal gene transfer and microbial evolution, spreading adaptive genes across microbial communities. While extensively studied in other ecosystems, the role of MGEs in shaping ruminant gastrointestinal microbiomes-especially their impact on diversity, adaptation, and dietary responsiveness-remains largely unexplored. This study systematically profiles MGE distribution and functionality across gastrointestinal regions in multiple ruminant species to advance our understanding of microbial adaptation.

RESULTS: Across 2458 metagenomic samples from eight ruminant species, we identified 4,764,110 MGEs-a ~ 216-fold increase over existing MGE databases. These elements included integrative and conjugative elements, integrons, insertion sequences, phages, and plasmids, with mobilization patterns largely confined to closely related microbial lineages. The distribution of MGEs varied by GIT regions, often reflecting nutritional gradients. In a validation cohort, GH1-carrying plasmids enriched in carbohydrate-active enzymes were found to predominate in the stomach, showing notable responsiveness to forage-based diets. All annotated MGEs have been compiled into a publicly accessible database, rumMGE (https://rummge.liulab-njau.com), to support further research.

CONCLUSIONS: This study substantially expands the catalog of known MGEs in ruminants, revealing their diverse roles in microbial evolution and functional adaptation to dietary changes. The findings provide a valuable resource for advancing research on microbial functionality and offer insights with potential applications for enhancing ruminant health and productivity, through strategies aimed at modulating the microbiome in agricultural contexts. Video Abstract.},
}

Animals
*Ruminants/microbiology
*Gastrointestinal Microbiome/genetics
*Interspersed Repetitive Sequences
Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Plasmids/genetics
Gene Transfer, Horizontal
*Gastrointestinal Tract/microbiology
Metagenome

@article {pmid40652235,
year = {2025},
author = {Wang, Z and Piao, Y and An, Z and Piao, H},
title = {Pneumonia due to scrub typhus infection: a case report.},
journal = {BMC pulmonary medicine},
volume = {25},
number = {1},
pages = {340},
pmid = {40652235},
issn = {1471-2466},
support = {Nos.2024A060//Health Science and Technology Ability Improvement Program of Jilin Province/ ; },
mesh = {Humans ; *Scrub Typhus/complications/diagnosis/drug therapy ; Female ; Middle Aged ; *Orientia tsutsugamushi/isolation & purification/genetics ; Doxycycline/therapeutic use ; Anti-Bacterial Agents/therapeutic use ; Bronchoalveolar Lavage Fluid/microbiology ; *Pneumonia, Bacterial/drug therapy/diagnosis/microbiology ; High-Throughput Nucleotide Sequencing ; Bronchoscopy ; },
abstract = {BACKGROUND: Scrub typhus is an acute febrile illness caused by the rickettsial bacterium Orientia tsutsugamushi, transmitted to humans through infected mite bites. Patients typically present with sudden onset high fever, headache, myalgia, and eschar formation at the site of the bites. Respiratory symptoms, such as cough and shortness of breath, can also occur, especially in severe cases that lead to pneumonia or acute respiratory distress syndrome (ARDS). This report presents a case of scrub typhus pneumonia, diagnosed by metagenomic next-generation sequencing (mNGS) on bronchoalveolar lavage fluid(BALF).

CASE PRESENTATION: A 58-year-old woman was admitted with cough, sputum production, and fever. Imaging revealed pneumonia. During hospitalization, bronchoscopy was performed to identify the causative pathogen. mNGS of the bronchoalveolar lavage fluid confirmed Orientia tsutsugamushi infection. Patient's pneumonia was improved after oral administration of doxycycline(100 mg two times daily) for 1 month.

CONCLUSION: This report highlights the diagnostic challenges of scrub typhus-induced pneumonia and demonstrates usefulness and the advantages of mNGS in identifying rare pathogens.},
}

Humans
*Scrub Typhus/complications/diagnosis/drug therapy
Female
Middle Aged
*Orientia tsutsugamushi/isolation & purification/genetics
Doxycycline/therapeutic use
Anti-Bacterial Agents/therapeutic use
Bronchoalveolar Lavage Fluid/microbiology
*Pneumonia, Bacterial/drug therapy/diagnosis/microbiology
High-Throughput Nucleotide Sequencing
Bronchoscopy

@article {pmid40652142,
year = {2025},
author = {Fang, H and Yu, Y and Su, Y and Li, H and Gao, H and Li, D and Xia, D and Liu, C and Mao, D},
title = {Characterization of Human Viral Diversity and Adenovirus Isolates in a Sewage Treatment Plant in Tianjin: Implications for Public Health and Advanced Monitoring.},
journal = {Food and environmental virology},
volume = {17},
number = {3},
pages = {39},
pmid = {40652142},
issn = {1867-0342},
support = {42077382//National Natural Science Foundation of China/ ; 42377426//National Natural Science Foundation of China/ ; },
mesh = {*Sewage/virology ; Humans ; China ; Phylogeny ; *Adenoviruses, Human/isolation & purification/classification/genetics ; Public Health ; *Adenoviridae/classification/isolation & purification/genetics ; Wastewater/virology ; Genetic Variation ; Environmental Monitoring ; },
abstract = {This study focuses on the characterization of human viral diversity within a major Wastewater Treatment Plant (WWTP) in the central area of Tianjin, China, with a particular emphasis on adenoviruses due to their robust survivability and potential health implications. By employing metagenomic sequencing, targeted sequencing, quantitative polymerase chain reaction (qPCR) analysis, and cell culture methodologies, we identified a broad spectrum of human viruses, encompassing 25 viral families and 45 viral genera, including enteric, respiratory, and contact viruses. Our findings demonstrate that adenoviruses were stably present in sewage from January to May and retained their infectious activity. The temporal analysis of viral loads across different months revealed no significant changes, suggesting a consistent risk of exposure. Additionally, our phylogenetic analysis of adenoviruses isolated from A549 cell cultures provides insights into their genotypic diversity and potential transmission dynamics. This comprehensive assessment underscores the critical need for improved viral surveillance in urban wastewater systems to mitigate public health risks and highlights the importance of advanced treatment technologies to address the challenges posed by adenoviruses and other pathogenic viruses in municipal wastewater.},
}

*Sewage/virology
Humans
China
Phylogeny
*Adenoviruses, Human/isolation & purification/classification/genetics
Public Health
*Adenoviridae/classification/isolation & purification/genetics
Wastewater/virology
Genetic Variation
Environmental Monitoring

@article {pmid40651825,
year = {2025},
author = {Kenney, GE},
title = {Genome mining with hypothetical proteins.},
journal = {Methods in enzymology},
volume = {717},
number = {},
pages = {199-240},
doi = {10.1016/bs.mie.2025.04.004},
pmid = {40651825},
issn = {1557-7988},
mesh = {Biological Products/metabolism ; *Data Mining/methods ; *Genomics/methods ; Bacteria/genetics/metabolism ; Biosynthetic Pathways/genetics ; Computational Biology/methods ; Genome, Bacterial ; },
abstract = {Natural products are diverse compounds made by many organisms, though bacteria, fungi, and plants are particularly prolific producers. While they have a range of biological roles, bioactive natural products have long been of interest as drug candidates. With the advent of accessible genome mining tools like antiSMASH, it is possible to search through genomes and metagenomes, identifying genes associated with natural product production and even predicting potential structures for experimentally uncharacterized compounds. However, most genome mining tools rely on similarity to previously characterized natural product pathways, and so they can fail to detect unusual or novel pathways and pathways that rely on "hypothetical proteins" for key biosynthetic steps. This is unfortunate, because natural products from new classes or with potentially divergent scaffolds are of particular interest in efforts to identify compounds with antibiotic and anticancer activity. This chapter will document some of the approaches that can be used to explore and develop biosynthetic hypotheses for these challenging-to-detect natural product pathways.},
}

Biological Products/metabolism
*Data Mining/methods
*Genomics/methods
Bacteria/genetics/metabolism
Biosynthetic Pathways/genetics
Computational Biology/methods
Genome, Bacterial

@article {pmid40651702,
year = {2025},
author = {Yu, PF and Wang, D and Fu, YB and Ma, XG and Zheng, H and Han, LY and Wang, A and Jiang, DL and Sun, HW and Jin, X},
title = {The recovery mechanism of granular sludge fragmentation and re-granulation caused by long-term high-concentration organic matter erosion in the SAD process: performance, sludge evolution, and metagenomic sequencing.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132966},
doi = {10.1016/j.biortech.2025.132966},
pmid = {40651702},
issn = {1873-2976},
abstract = {The Simultaneous Anammox and Denitrification (SAD) process effectively removes organic carbon sources, the impact of high-concentration carbon sources on the SAD process remains unclear. This study investigated the performance, sludge characteristics, microbial community correlations, and metagenomic sequencing of the SAD system under conditions of excessive organic matter exposure. The results showed that the organic matter metabolism ability of SAD granular sludge increased from 90.16 ± 1.16 % to 95.2 ± 2.3 %. The Mantel test revealed that Anaerobic Ammonium Oxidation Bacteria (AnAOB) (Candidatus_Kuenenia) were positively correlated with VSS/SS and instability coefficient, while Denitrifying Bacteria (DNB) (Truepera, Ottowia, Deniratisoma, Arenimonas) were negatively correlated with wet density, settling velocity, granule size, protein/polysaccharides (PN/PS) ratio, and the complete coefficient. Following the recovery of the SAD system, the bacterial community correlations increased, and the stability and mechanical strength of the granular sludge were enhanced. Metagenomic sequencing showed that a decrease of Quorum sensing (QS) and the increase of c-di-GMP levels led to up-regulation of exopolysaccharide and extracellular protein expression, resulting in the disintegration of SAD granular sludge. As the sludge aggregated, recombined, and re-granulated, the system up-regulated the expression of the hzs gene in AnAOB nitrogen metabolism via c-di-GMP and QS signals. It also up-regulated the expression of genes such as Dissimilatory Nitrate Reduction to Ammonium (DNRA) and potential denitrification pathways, enhancing the metabolism of AnAOB and symbiotic bacteria.},
}

@article {pmid40651701,
year = {2025},
author = {Zhu, C and Wang, H and Liu, R and Yuan, H and Li, X},
title = {Response of anaerobic digestion of cattle manure to continuous temperature transitions: Process performance, microbial succession, key enzymes, and metabolic pathways.},
journal = {Bioresource technology},
volume = {435},
number = {},
pages = {132953},
doi = {10.1016/j.biortech.2025.132953},
pmid = {40651701},
issn = {1873-2976},
abstract = {This study investigated the effect of continuous temperature transitions on the anaerobic digestion (AD) performance of cattle manure (CM) and microbial response mechanisms. Experiments were conducted in a completely-stirred tank reactor (CSTR) for over 390 days with a fine 3 °C gradient from 35 °C to 65 °C. The results showed that AD achieved optimal performance at R47 (47 °C). Microbial analysis indicated that 47 °C was thecritical temperaturefor the transition from mesophilic to thermophilic communities. Metagenomic analysis revealed that, compared with R38 (38 °C) and R53 (53 °C), R47 enhanced the hydrolysis efficiency of refractory components by upregulating key enzyme expression in glycolysis and pyruvate metabolism. At R47,elevatedexpression of key enzymes inboth acetate/butyrate metabolic pathways and methylotrophic methanogenesis pathway contributed to the highest methane yield. The optimal temperature determined for CM provides important parameters for practical AD operations.},
}

@article {pmid40651403,
year = {2025},
author = {Gao, Z and Zhou, H and Han, C and Wang, Z and Hu, X and Jia, M and Wang, Z and Zhang, G and Han, G},
title = {Long-term grazing does not increase antibiotic resistance genes in the soil in an Inner Mongolia desert steppe.},
journal = {Journal of environmental management},
volume = {391},
number = {},
pages = {126545},
doi = {10.1016/j.jenvman.2025.126545},
pmid = {40651403},
issn = {1095-8630},
abstract = {Antibiotic resistance due to overuse of antibiotics is one of the biggest challenges to global health. Furthermore, antibiotic resistance genes (ARGs) can enter the environment, for example, via the accumulation of animal excreta. However, the effect of different levels of livestock grazing under natural grazing conditions on soil ARGs is not yet clear. In this study, we examined soil ARGs from a long-term experiment manipulating levels of grazing intensity in an Inner Mongolian desert steppe using metagenomic sequencing technology. We found little influence of increasing grazing intensity on the abundances of soil ARGs. We did, however, find decreases in the absolute abundance of aminoglycoside ARGs with light grazing and increases of vancomycin ARGs under heavy grazing. We found that grazing indirectly affects soil ARGs by altering soil physicochemical properties (moisture, C/N) and bacterial diversity. Our study suggests that long-term grazing will not significantly increase ARGs in the soil of the desert steppe of Inner Mongolia. At the same time, we also believe that the risk of spreading ARGs is lower under light grazing.},
}

@article {pmid40651382,
year = {2025},
author = {Wang, H and Zeng, H and Zhang, J and Zhou, Q},
title = {Single-chamber differs from dual-chamber bioelectrochemical systems in wastewater treatment and methane recovery under combined exposure to microplastics and antibiotics.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139175},
doi = {10.1016/j.jhazmat.2025.139175},
pmid = {40651382},
issn = {1873-3336},
abstract = {The coexistence of microplastics (MPs) and antibiotics in wastewater poses important threats to microbial ecosystems and methane recovery during anaerobic digestion (AD). This study systematically compares the methanogenic performance and microbial response of single- and dual-chamber bioelectrochemical systems (BES) (0.8 V) exposed to a mixture of MPs (10 mg/L) and antibiotics (1 mg/L). Results demonstrated that single-chamber BES significantly enhanced methanogenesis, achieving a 21.19 % increase in methane production compared to conventional AD, while dual-chamber BES exhibited limited activity due to ammonia inhibition and acetate accumulation. Meanwhile, pollutant exposure dramatically altered the functional enzyme activities and microbial community structure. Metagenomic analysis revealed that methane was primarily produced via the acetoclastic pathway mediated by Methanothrix, with electrical stimulation promoting direct interspecies electron transfer. Pollutant exposure drastically altered microbial communities, reducing Euryarchaeota and enriching fermentative bacteria (e.g., Proteiniphilum). Notably, antibiotic resistance genes (ARGs) increased across all systems, with electrode carriers amplifying ARGs proliferation. However, single-chamber BES showed superior resistance to horizontal gene transfer of ARGs. Key metabolic pathways (e.g., glycolysis, TCA cycle) were markedly inhibited, highlighting the cascading effects of pollutants on microbial energetics. These findings highlight the potential of single-chamber BES for treating co-contaminated wastewater, providing critical insights for optimizing BES configurations.},
}

@article {pmid40650758,
year = {2025},
author = {Kearns, R},
title = {Gut modulation to regulate NF-κB in colorectal and gastric cancer therapy and inflammation.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {74},
number = {8},
pages = {264},
pmid = {40650758},
issn = {1432-0851},
mesh = {Humans ; *NF-kappa B/metabolism ; *Gastrointestinal Microbiome/immunology ; *Stomach Neoplasms/therapy/immunology/metabolism/microbiology/pathology ; *Inflammation/metabolism ; *Colorectal Neoplasms/therapy/immunology/metabolism/microbiology/pathology ; Animals ; Dysbiosis ; Fecal Microbiota Transplantation ; Signal Transduction ; },
abstract = {The nuclear factor-kappa B (NF-κB) pathway plays a pivotal role in cancer progression, immune regulation, and inflammation. Aberrant activation of this pathway, often driven by gut microbiota dysbiosis, contributes to tumorigenesis, therapy resistance, and chronic inflammation. Emerging evidence highlights the bidirectional interaction between gut microbiota and NF-κB signalling, suggesting that microbiota modulation may enhance cancer treatment efficacy and reduce treatment-induced inflammation. This review explores the mechanistic underpinnings of gut microbiota-mediated NF-κB regulation, focusing on microbial metabolites such as short-chain fatty acids (SCFAs) and microbial-associated molecular patterns, including lipopolysaccharides (LPS). It examines how conventional cancer treatments, chemotherapy, radiotherapy, and immune checkpoint inhibitors, exacerbate dysbiosis and NF-κB-driven inflammation, further complicating treatment outcomes. Additionally, this review evaluates the therapeutic potential of gut-targeted interventions, including probiotics, prebiotics, faecal microbiota transplantation (FMT), and dietary modifications, in restoring microbial homeostasis and modulating NF-κB signalling. Despite promising findings, challenges remain regarding the clinical translation of microbiota-based therapies, including the need for standardised microbiota profiling, regulatory frameworks, and long-term safety assessments. Advances in metagenomics and metabolomics are proposed as essential tools to personalise gut-targeted interventions and optimise cancer treatment strategies. Integrating gut modulation into oncology represents a paradigm shift, offering a holistic, patient-centric approach to cancer therapy. However, further research is required to validate these strategies and ensure their efficacy in clinical applications.},
}

Humans
*NF-kappa B/metabolism
*Gastrointestinal Microbiome/immunology
*Stomach Neoplasms/therapy/immunology/metabolism/microbiology/pathology
*Inflammation/metabolism
*Colorectal Neoplasms/therapy/immunology/metabolism/microbiology/pathology
Animals
Dysbiosis
Fecal Microbiota Transplantation
Signal Transduction

@article {pmid40650567,
year = {2025},
author = {Wallenius, AJ and Venetz, J and Zygadlowska, OM and Lenstra, WK and van Helmond, NAGM and Martins, PD and Slomp, CP and Jetten, MSM},
title = {A ubiquitous and diverse methanogenic community drives microbial methane cycling in eutrophic coastal sediments.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf075},
pmid = {40650567},
issn = {1574-6941},
abstract = {Coastal areas contribute over 75% of global marine methane emissions, a proportion predicted to increase with anthropogenic eutrophication and deoxygenation. Prolonged low oxygen and high organic matter input can disrupt the methane cycle, favoring methane production over oxidation. However, factors influencing this imbalance remain unclear. Here, we show that methanogenesis dominates microbial methane cycling in the anoxic sediments of eutrophic coastal marine Lake Grevelingen (NL) after summer stratification. A shallow sulfate-methane transition zone (SMTZ; 5-15 cm depth) was observed, with high methane concentrations below. Methane was produced in all investigated layers, while methane oxidation was restricted to the narrow SMTZ. Amplicon sequencing, metagenomics, and incubations revealed a metabolically and phylogenetically diverse methanogenic community with niche separation, and methylotrophic methanogenesis prevalent in all layers. Two clades of ANME archaea, ANME-2a/b and ANME-3, were restricted to a narrow zone together with their putative syntrophic sulfate-reducing bacteria, coinciding with the observed methane oxidation activity. Our results suggest that eutrophication and deoxygenation will further contribute to rising methane emissions, tilting the microbial methane cycle towards increased methanogenesis and decreasing the efficiency of the microbial methane filter.},
}

@article {pmid40650408,
year = {2025},
author = {Beau, A and Natividad, J and Benoit, B and Delerive, P and Duboux, S and Feng, Y and Jammes, M and Barnel, C and Sequino, G and Pinteur, C and Glorieux, G and Fouque, D and Vidal, H and Koppe, L},
title = {A specifically designed multi-biotic reduces uremic toxin generation and improves kidney function.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2531202},
doi = {10.1080/19490976.2025.2531202},
pmid = {40650408},
issn = {1949-0984},
mesh = {Humans ; *Uremic Toxins/metabolism ; *Renal Insufficiency, Chronic/microbiology/therapy ; Animals ; *Probiotics/administration & dosage ; Feces/microbiology/chemistry ; *Gastrointestinal Microbiome ; Male ; Cresols/metabolism ; *Kidney/physiology ; Prebiotics/administration & dosage ; Female ; Middle Aged ; Lactobacillus/metabolism/growth & development ; *Uremia ; Cellobiose/metabolism ; Rats ; Indican ; Bacteria/metabolism/genetics/classification ; Disease Models, Animal ; },
abstract = {Chronic kidney disease (CKD) is characterized by accumulation of uremic toxins (UTs), such as p-cresyl sulfate and indoxyl sulfate, generated through the transformation of tyrosine and tryptophan by the gut microbiota. Using an ex vivo Simulator of the Human Intestinal Microbial Ecosystem (SHIME) colonized with fecal samples from eight CKD patients or nine healthy volunteers, a higher bacterial generation of p-cresol and indoles post-amino acid enrichment, as well lower basal butyrate levels, in the feces of CKD patients were found. Through in silico data mining, we selected a probiotic strain lacking the capacity to produce UT, i.e. without genes for tryptophanase, tyrosinase and urease. In vitro, we confirmed the potential of cellobiose as a prebiotic supporting the growth of this strain. We further designed a novel specific multi-biotic for CKD (SynCKD) [containing a probiotic Lactobacillus johnsonii NCC533, a prebiotic (1% cellobiose), and a postbiotic (1% short and medium chain triglycerides C4-C8, a source of butyrate)]. SynCKD effectively curtailed UT precursor generation ex vivo. The in vivo efficacy of SynCKD (and the synergic effect) was established in two uremic rodent models, demonstrating lower plasma levels of UTs and enhancing kidney function after 6-8 weeks of treatment. These effects were linked to better gut microbial ecology. Metagenomic analysis revealed reduced microbial genes for tryptophan/tyrosine degradation. This study lays the foundation for SynCKD as a potential therapy to mitigate CKD progression.},
}

Humans
*Uremic Toxins/metabolism
*Renal Insufficiency, Chronic/microbiology/therapy
Animals
*Probiotics/administration & dosage
Feces/microbiology/chemistry
*Gastrointestinal Microbiome
Male
Cresols/metabolism
*Kidney/physiology
Prebiotics/administration & dosage
Female
Middle Aged
Lactobacillus/metabolism/growth & development
*Uremia
Cellobiose/metabolism
Rats
Indican
Bacteria/metabolism/genetics/classification
Disease Models, Animal

@article {pmid40650352,
year = {2025},
author = {Rios, N and Shi, Y and Chen, J and Zhan, X and Xue, L and Li, Q},
title = {Composition-On-Composition regression analysis for multi-omics integration of metagenomic data.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf387},
pmid = {40650352},
issn = {1367-4811},
abstract = {MOTIVATION: Compositional data are frequently encountered in many disciplines, such as in next-generation sequencing experiments widely used in biomedical studies. Regression analysis with compositional data as either responses or predictors have been well studied. However, when both responses and predictors are compositional, the inventory of analysis tools is surprisingly limited, especially in the high-dimensional setting. Among the few existing methods, most of them rely on a log-ratio transformation to move compositional data from the simplex to real numbers. Yet, a serious weakness of these methods is their failure to handle the substantial fraction of zeroes observed in data collected from next-generation sequencing experiments.

RESULTS: To investigate associations between two high-dimensional multi-omics compositions, we propose a Composition-On-Composition (COC) regression analysis method which does not require log-ratio transformations and hence can handle zeroes in the data. To account for high dimensionality, we estimate regression coefficients using a penalized estimation equation approach. Finally, inference procedures for COC regression are also proposed. Superior performance of COC is demonstrated through both comprehensive numerical simulations and case studies.

Source R codes to implement COC method is available at https://github.com/nrios4/COC.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid40649719,
year = {2025},
author = {Popov, IV and Manakhov, AD and Gorobets, VE and Diakova, KB and Lukbanova, EA and Malinovkin, AV and Venema, K and Ermakov, AM and Popov, IV},
title = {Metagenomic Investigation of Intestinal Microbiota of Insectivorous Synanthropic Bats: Densoviruses, Antibiotic Resistance Genes, and Functional Profiling of Gut Microbial Communities.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
pmid = {40649719},
issn = {1422-0067},
support = {23-14-00316//Russian Science Foundation/ ; 075-10-2025-017//Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {Animals ; *Chiroptera/microbiology/virology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; Phylogeny ; *Metagenome ; },
abstract = {Bats serve as key ecological reservoirs of diverse microbial communities, including emerging viruses and antibiotic resistance genes. This study investigates the intestinal microbiota of two insectivorous bat species, Nyctalus noctula and Vespertilio murinus, at the Rostov Bat Rehabilitation Center in Southern Russia using whole metagenome shotgun sequencing. We analyzed taxonomic composition, functional pathways, antibiotic resistance genes, and virulence factors. Densoviruses, especially those closely related to Parus major densovirus, were the most dominant viral sequences identified. Metagenome-assembled densovirus genomes showed high sequence similarity with structural variations and clustered phylogenomically with viruses from mealworms and birds, reflecting both dietary origins and the potential for vertebrate infection. Functional profiling revealed microbial pathways associated with cell wall biosynthesis, energy metabolism, and biofilm formation. A total of 510 antibiotic resistance genes, representing 142 unique types, mainly efflux pumps and β-lactamases, were identified. Additionally, 870 virulence factor genes were detected, with a conserved set of iron acquisition systems and stress response regulators across all samples. These findings highlight the ecological complexity of bat-associated microbiota and viromes and suggest that synanthropic bats may contribute to the circulation of insect-associated viruses and antimicrobial resistance in urban settings.},
}

Animals
*Chiroptera/microbiology/virology
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Drug Resistance, Microbial/genetics
Phylogeny
*Metagenome

@article {pmid40649382,
year = {2025},
author = {Dasí-Delgado, P and Andreu, C and Del Olmo, ML},
title = {Strategies Used for the Discovery of New Microbial Metabolites with Antibiotic Activity.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {13},
pages = {},
pmid = {40649382},
issn = {1420-3049},
mesh = {*Anti-Bacterial Agents/pharmacology/chemistry ; *Drug Discovery/methods ; *Bacteria/metabolism/drug effects/genetics ; Metagenomics/methods ; Humans ; Drug Resistance, Bacterial ; },
abstract = {The discovery of new microbial metabolites is essential to combat the alarming rise in antimicrobial resistance and to meet emerging medical needs. This work critically reviews current strategies for identifying antimicrobial compounds, emphasizing the potential of microorganisms as a rich source of bioactive secondary metabolites. This review explores innovative methods, such as investigating extreme environments where adverse conditions favor the emergence of unique metabolites; developing techniques, like the iChip, to cultivate previously uncultivable bacteria; using metagenomics to analyze complex samples that are difficult to isolate; and integrates artificial intelligence to accelerate genomic mining, structural prediction, and drug discovery optimization processes. The importance of overcoming current challenges, such as replicating findings, low research investment, and the lack of adapted collection technologies, is also emphasized. Additionally, this work analyzes the crucial role of bacterial resistance and the necessity of a holistic approach involving new technologies, sustained investment, and interdisciplinary collaboration. This work emphasizes not only the current state of metabolite discovery but also the challenges that must be addressed to ensure a continuous flow of new therapeutic molecules in the coming decades.},
}

*Anti-Bacterial Agents/pharmacology/chemistry
*Drug Discovery/methods
*Bacteria/metabolism/drug effects/genetics
Metagenomics/methods
Humans
Drug Resistance, Bacterial

@article {pmid40647714,
year = {2025},
author = {Lampou, M and Trull, EC and Warren, HM and Ghebremichael, MS and Nakka, R and Floyd, DJ and Fathi, AT and Brunner, AM and Mansour, MK},
title = {Clinical Utility of Plasma Microbial Cell-Free DNA Surveillance in Neutropenic Patients with Acute Myeloid Leukemia Undergoing Outpatient Chemotherapy: A Case Series.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {13},
pages = {},
pmid = {40647714},
issn = {2075-4418},
support = {R01 AI132638 and R01 AI176658//NIH grant/ ; },
abstract = {Background/Objectives: The main objective of the study is to assess the clinical utility of microbial cell-free DNA (mcfDNA) in neutropenic patients diagnosed with acute myeloid leukemia (AML) undergoing chemotherapy in the outpatient setting. Neutropenia is a common complication in this patient cohort and enhances the risk of fatal opportunistic bacterial and fungal infections. Accurate and timely diagnosis of these infections in outpatient asymptomatic individuals is critical. Methods: Fourteen patients were studied in this prospective observational case series. Traditional blood cultures (BCs) were obtained when clinically indicated and blood samples were collected for plasma mcfDNA metagenomic sequencing up to two times a week at outpatient oncology appointments. Results were compared in identifying potential infectious agents. Results: BCs identified pathogens in only two patients, despite several cases where infection was suspected. In contrast, mcfDNA testing detected pathogens in 11 of the 14 patients, including bacteria, such as Staphylococcus aureus, and invasive fungi, such as Candida and Aspergillus species, and Pneumocystis jirovecii. Conclusions: In the outpatient setting, mcfDNA surveillance offers a more reliable method for detecting pathogens. This approach identified actionable microbiologic results in immunocompromised individuals who did not meet standard clinical criteria for suspicion of infection. Further research is required to confirm the potential of mcfDNA surveillance in an outpatient setting to guide more accurate treatment decisions, reduce extensive clinical investigations, and improve neutropenic patient outcomes.},
}

@article {pmid40647338,
year = {2025},
author = {Decembrino, N and Scuderi, MG and Betta, PM and Leonardi, R and Bartolone, A and Marsiglia, R and Marangelo, C and Pane, S and De Rose, DU and Salvatori, G and Grosso, G and Di Domenico, FM and Dotta, A and Putignani, L and Capolupo, I and Di Benedetto, V},
title = {Microbiota-Modulating Strategies in Neonates Undergoing Surgery for Congenital Gastrointestinal Conditions: A Narrative Review.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
pmid = {40647338},
issn = {2072-6643},
mesh = {Humans ; Infant, Newborn ; *Gastrointestinal Microbiome/drug effects ; Probiotics/administration & dosage/therapeutic use ; Dysbiosis/microbiology/prevention & control ; Prebiotics/administration & dosage ; *Gastrointestinal Diseases/surgery/microbiology/congenital ; Anti-Bacterial Agents/therapeutic use ; Milk, Human ; *Digestive System Surgical Procedures ; Enteral Nutrition ; },
abstract = {Background/Objectives: The gut microbiota (GM) is pivotal for immune regulation, metabolism, and neurodevelopment. Infants undergoing surgery for congenital gastrointestinal anomalies are especially prone to microbial imbalances, with a paucity of beneficial bacteria (e.g., Bifidobacteria and Bacteroides) and diminished short-chain fatty acid production. Dysbiosis has been associated with severe complications, including necrotizing enterocolitis, sepsis, and feeding intolerance. This narrative review aims to critically examine strategies for microbiota modulation in this high-risk cohort. Methods: An extensive literature analysis was performed to compare the evolution of GM in healthy neonates versus those requiring gastrointestinal surgery, synthetizing strategies to maintain eubiosis, such as early nutritional interventions-particularly the use of human milk-along with antibiotic management and supplementary treatments including probiotics, prebiotics, postbiotics, and lactoferrin. Emerging techniques in metagenomic and metabolomic analysis were also evaluated for their potential to elucidate microbial dynamics in these patients. Results: Neonates undergoing gastrointestinal surgery exhibit significant alterations in microbial communities, characterized by reduced levels of eubiotic bacteria and an overrepresentation of opportunistic pathogens. Early initiation of enteral feeding with human milk and careful antibiotic stewardship are linked to improved microbial balance. Adjunctive therapies, such as the administration of probiotics and lactoferrin, show potential in enhancing gut barrier function and immune modulation, although confirmation through larger-scale studies remains necessary. Conclusions: Modulating the GM emerges as a promising strategy to ameliorate outcome in neonates with congenital gastrointestinal surgical conditions. Future research should focus on the development of standardized therapeutic protocols and the execution of rigorous multicenter trials to validate the efficacy and safety of these interventions.},
}

Humans
Infant, Newborn
*Gastrointestinal Microbiome/drug effects
Probiotics/administration & dosage/therapeutic use
Dysbiosis/microbiology/prevention & control
Prebiotics/administration & dosage
*Gastrointestinal Diseases/surgery/microbiology/congenital
Anti-Bacterial Agents/therapeutic use
Milk, Human
*Digestive System Surgical Procedures
Enteral Nutrition

@article {pmid40647144,
year = {2025},
author = {Sreenesh, B and Varghese, E and Kubatka, P and Samuel, SM and Büsselberg, D},
title = {Prebiotic Potential of Dietary Polyphenols in Colorectal Cancer Immunomodulation.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
pmid = {40647144},
issn = {2304-8158},
support = {NPRP14S-0311-210033//Qatar National Research Fund/ ; },
abstract = {Molecular crosstalk between the gut microbiome and human diet represent a potential therapeutic avenue requiring further investigation as it can be applied to human health management and treatment. Colon cancer, the third leading cause of cancer mortality, is often linked to the gut microbiome. In vitro and in vivo studies and metagenomic research have revealed alterations in gut microbial flora among diseased individuals. The human diet is connected to these changes in microbial inhabitants related to the pathophysiology underlying colorectal cancer (CRC). Polyphenols are well-studied, naturally occurring plant secondary metabolites recognized for their anti-inflammatory and antioxidant properties. The anticancer activities of these compounds are increasingly reported, offering insights into the administration of these natural molecules for managing various types of cancer and developing novel medications from them. Recent investigations have highlighted the prebiotic-like effects of these compounds on gut microbial dysbiosis and their metabolism concerning colorectal cancer, influencing colon cancer by interfering with multiple signaling pathways. This review will focus on the existing literature regarding the prebiotic potential of dietary polyphenols, and further research in this area would be valuable, as the integration of artificial intelligence (AI) and machine learning (ML) can enable analysis of the connections between unique gut microbiome profiles and other dependent factors such as physiological and genetic variables, paving the way for personalized treatment strategies in gut microbiome-based health management and precision medicine.},
}

@article {pmid40647099,
year = {2025},
author = {Krongdang, S and Sawongta, N and Pheepakpraw, J and Ngamsomchat, A and Wangtueai, S and Wongsa, J and Parametthanuwat, T and Charoenphun, N and Chitov, T},
title = {Comprehensive Analysis of Bacterial Communities and Microbiological Quality of Frozen Edible Insects.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
pmid = {40647099},
issn = {2304-8158},
support = {Fundamental Fund: Grant no. 31/2567//(i) Burapha University (BUU), (ii) Thailand Science Research and Innovation (TSRI), (iii) National Science Research and Innovation Fund (NSRF) (Fundamental Fund: Grant no. 31/2567), and was partially supported by Chiang Mai University./ ; },
abstract = {Edible insects are gaining traction worldwide; however, the existing data regarding their microbiological quality remain inadequate. This study investigated the bacterial communities and microbiological quality of five types of frozen edible insects commercially available in Thailand. Amplicon sequencing revealed Firmicutes (Bacillota) and Proteobacteria (Pseudomonadota) as the main phyla across all samples; Bacteroidota was predominant in house crickets, Actinobacteriota in silkworms, and Desulfobacterota was exclusively found in house and mole crickets. Culture-based assays showed total viable counts, lactic acid bacteria, yeasts-molds, and spore-formers ranging from 3.41-6.58, 2.52-7.41, 1.83-5.62, to 2.00-4.70 log CFU·g[-1], respectively. In some samples, Enterobacteriaceae and Escherichia coli, key hygiene indicators, reached 5.05 and 2.70 log CFU·g[-1], respectively. Among foodborne pathogens, presumptive Bacillus cereus was found to vary from <1.70 to 3.93 log CFU·g[-1], while Clostridium perfringens and Staphylococcus aureus were under the quantitation limit, and Salmonella was absent. Overall, the results indicate significant variation in microbial diversity and quality among different insect types. The high levels of microbial hygiene indicators and foodborne pathogens in some samples raised food safety concerns and point to the need to develop or implement production guidelines and microbiological criteria for frozen edible insects to ensure food safety.},
}

@article {pmid40647045,
year = {2025},
author = {Zhang, J and Li, Q and Liu, S and Wang, N and Song, Y and Wu, T and Zhang, M},
title = {Lactobacillus rhamnosus LRa05 Alleviates Constipation via Triaxial Modulation of Gut Motility, Microbiota Dynamics, and SCFA Metabolism.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
pmid = {40647045},
issn = {2304-8158},
support = {2022YFF1100201//the Key Research and Development Program of China/ ; 24PTLYHZ00020//2024 Tianjin "the Belt and Road" Innovation Platform Project/ ; 24JCQNJC00740//Natural Science Foundation of Tianjin Municipality/ ; },
abstract = {Constipation, a widespread gastrointestinal disorder, imposes significant burdens on healthcare systems the and global health-related quality of life, yet current options remain suboptimal due to limited mechanistic understanding and efficacy limitations. Given the pivotal significance of the interactions between the gut microbiota and the host on governing bowel movement, we employed a multi-modal approach integrating animal experiments, ELISA, histopathology, qRT-PCR, GC-MS, and 16S rRNA metagenomics to evaluate the functional potential of Lactobacillus rhamnosus LRa05 against loperamide-induced constipation in mice. LRa05 treatment markedly alleviated constipation symptoms, as evidenced by reduced first black stool expulsion time, increased fecal moisture, and enhanced intestinal motility. Mechanistic investigations revealed that LRa05 balanced gastrointestinal regulatory peptides. It also downregulated aquaporin (AQP4/AQP8) mRNA levels and activated the SCF/C-Kit signaling pathway. These effects contributed to the restoration of intestinal peristalsis. Furthermore, LRa05 rebalanced gut microbiota composition by enriching beneficial, including Alloprevotella and Lachnospiraceae NK4A136, key SCFA producers. Thus, LRa05 could boost short chain fatty acid (SCFA) production, which is vital for stimulating intestinal motility, improving mucosal function, and relieving constipation. These findings demonstrated that LRa05 could mitigate constipation through a multi-target mechanism: regulating motility-related gene transcription, restructuring the microbial community, balancing gastrointestinal peptides, repairing the colonic mucosa, and promoting SCFAs for fecal hydration. Our study positions LRa05 as a promising probiotic candidate for constipation management.},
}

@article {pmid40646857,
year = {2025},
author = {Zhu, W and Guo, J and Li, X and Li, Y and Song, L and Li, Y and Feng, B and Bao, X and Li, J and Gao, Y and Xu, H},
title = {Effects of Gallic Acid on In Vitro Ruminal Fermentation, Methane Emission, Microbial Composition, and Metabolic Functions.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
pmid = {40646857},
issn = {2076-2615},
support = {QN2025134//Science Research Project of Hebei Education Department/ ; HBCT2023180207//Hebei Dairy Cattle Innovation Team of Modern Agro-industry Technology Research System/ ; HBCT2024230205//Hebei Dairy Cattle Innovation Team of Modern Agro-industry Technology Research System/ ; 202202F016//Construction of the Weichang Yidukou Smart and Circular Agriculture and Animal Husbandry Demonstration Zone/ ; C2024204012//Natural Science Foundation of Hebei Province/ ; 6012018//The Top Talent Project of Hebei Province/ ; YJ2021053//Research Special Project for Talent Introduction of Hebei Agricultural University/ ; KY2024003//Research Project Funding for Basic Scientific Research of Universities in Hebei Province/ ; CARS-36-20//CARS-36-20/ ; },
abstract = {The objective of this study was to assess the effects of gallic acid (GA) on nutrient degradability, gas production, rumen fermentation, and the microbial community and its functions using in vitro fermentation methods. An in vitro experiment was conducted to test GA dose levels (0, 5, 10, 20, and 40 mg/g DM) in the cow's diet. Based on the results of nutrient degradability, gas production, and rumen fermentation, the control group (0 mg/g DM, CON) and the GA group (10 mg/g DM, GA) were selected for metagenomic analysis to further explore the microbial community and its functions. The degradability of dry matter and crude protein, as well as total gas production, CH4 production, CH4/total gas, CO2 production, and CO2/total gas, decreased quadratically (p < 0.05) with increasing GA doses, reaching their lowest levels at the 10 mg/g DM dose. Total volatile fatty acid (VFA) (p = 0.004), acetate (p = 0.03), and valerate (p = 0.03) exhibited quadratic decreases, while butyrate (p = 0.0006) showed a quadratic increase with increasing GA doses. The 10 mg/g DM dose group had the lowest levels of total VFA, acetate, and valerate, and the highest butyrate level compared to the other groups. The propionate (p = 0.03) and acetate-to-propionate ratio (p = 0.03) linearly decreased with increasing gallic acid inclusion. At the bacterial species level, GA supplementation significantly affected (p < 0.05) a total of 38 bacterial species. Among these, 29 species, such as Prevotellasp.E15-22, bacteriumP3, and Alistipessp.CAG:435, were less abundant in the GA group, while 9 species, including Aristaeella_lactis and Aristaeella_hokkaidonensis, were significantly more abundant in the GA group. At the archaeal species level, the relative abundances of Methanobrevibacter_thaueri, Methanobrevibacter_boviskoreani, and Methanobrevibactersp.AbM4 were significantly reduced (p < 0.05) by GA supplementation. Amino sugar and nucleotide sugar metabolism, Starch and sucrose metabolism, Glycolysis/Gluconeogenesis, and Pyruvate metabolismwere significantly enriched in the GA group (p < 0.05). Additionally, Alanine, aspartate and glutamate metabolism was also significantly enriched in the GA group (p < 0.05). GA use could potentially be an effective strategy for methane mitigation; however, further research is needed to assess its in vivo effects in dairy cows over a longer period.},
}

@article {pmid40646853,
year = {2025},
author = {Liu, H and Xiao, L and Liu, Z and Deng, Y and Zhu, J and Yang, C and Liu, Q and Tian, D and Cui, X and Peng, J},
title = {Impacts of Captive Domestication and Geographical Divergence on the Gut Microbiome of Endangered Forest Musk Deer.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
pmid = {40646853},
issn = {2076-2615},
support = {No. 31470570//The People's Republic of China Wildlife Protection Program of the Central Forestry Reform and Development Fund of the State Forestry Administration, and the National Natural Science Foundation of China/ ; },
abstract = {Forest musk deer (Moschus berezovskii Flerov), a critically endangered ruminant species, faces extinction risks, with captive populations further threatened by prevalent digestive and immune disorders. This study utilized comparative metagenomic sequencing to assess intestinal microbiota structure and functional profiles between wild populations in Chongqing and Hunan and captive individuals. Wild populations exhibited a Pseudomonadota-dominated gut microbiota (significantly more abundant than in captive counterparts), enriched with lignin-degrading genera Novosphingobium and Acinetobacter. In contrast, the captive group demonstrated increased abundances of Bacillota/Bacteroidota, alongside abnormal proliferation of Escherichia and Clostridium. Both alpha and beta diversity analyses confirmed significant compositional divergences among the three groups, with wild populations maintaining higher diversity than captive populations. Notably, while substantial disparities in microbial abundance existed between wild populations (attributed to habitat vegetation differences), core microbial diversity and carbohydrate metabolic functions exhibited convergence. Functional analyses marked divergences in metabolic pathways: Captive microbiota showed enrichment in translation and glycan metabolism pathways, whereas wild populations displayed pronounced enrichment in immune regulation and environmental sensing pathways. These findings establish a theoretical foundation for optimizing wild population conservation strategies and developing science-based captive management protocols.},
}

@article {pmid40646844,
year = {2025},
author = {Kerek, Á and Szabó, Á and Jerzsele, Á},
title = {Amoxicillin Resistance: An In Vivo Study on the Effects of an Approved Formulation on Antibiotic Resistance in Broiler Chickens.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
pmid = {40646844},
issn = {2076-2615},
support = {RRF-2.3.1-21-2022-00001//National Research, Development and Innovation Office/ ; },
abstract = {Background: Antimicrobial resistance (AMR) is a growing global concern in poultry production, where antibiotic use can disrupt gut microbiota and enrich antimicrobial resistance genes (ARGs). Objectives: This study aimed to assess the in vivo effects of a veterinary-approved amoxicillin formulation on gut microbiome composition and ARG profiles in broiler chickens. Methods: A total of 120 Ross-308 broiler chickens were randomly allocated into 12 experimental groups (n = 10 per group), with three replicates per treatment. Birds received either full-dose (1×), a subtherapeutic quarter-dose (¼×) of amoxicillin, a placebo (starch), or no treatment. Cloacal swabs were collected on days 0, 14, and 28 for shotgun metagenomic sequencing. One-way ANOVA was used to evaluate treatment effects on body weight, with significant differences observed from day 14 onward (p < 0.0001). Results: The ¼× dose caused a more pronounced microbiome shift than the 1× dose, with a marked reduction in Pseudomonadota and increase in Bacillota and Bacteroidota. ARG abundance declined in the ¼× group (from 1386 to 1012). While TEM-type ESBL genes were ubiquitous, CTX-M-1 emerged only after ¼× treatment. Worryingly, 20 types of vancomycin resistance genes were detected across all samples. Plasmid-borne ARGs and mobile genetic elements decreased in the ¼× group. Conclusions: Even subtherapeutic antibiotic exposure significantly reshapes the gut microbiota composition and ARG landscape, highlighting the need for refined risk assessments and microbiome-conscious antimicrobial policies in poultry farming.},
}

@article {pmid40646819,
year = {2025},
author = {Lv, X and Qiao, Z and Chen, C and Hua, J and Zhou, C},
title = {Exploration of Multi-Source Lignocellulose-Degrading Microbial Resources and Bioaugmentation Strategies: Implications for Rumen Efficiency.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
pmid = {40646819},
issn = {2076-2615},
support = {DKYJ202303//High-level Talents Introduction Project of Anhui Science and Technology University/ ; 32261143467//Projects of International Cooperation and Exchanges NSFC/ ; 2022YFD1300805//National Key Research and Development Program/ ; },
abstract = {Utilizing straw feed is an effective strategy to optimize straw resource utilization by incorporating microbial degradation agents to expedite lignocellulose breakdown and enhance feed efficiency. Lignocellulose-degrading species and microbial communities are present in various Earth ecosystems, including the rumen of ruminants, insect digestive tracts, forest soil, and microbial populations in papermaking processes. The rumen of ruminants harbors a diverse range of microbial species, making it a promising source of lignocellulose-degrading microorganisms. Exploring alternative systems like insect intestines and forest soil is essential for future research. Current studies primarily rely on traditional microbial isolation techniques to identify lignocellulose-degrading strains, underscoring the necessity to transition to utilizing microbial culturomics and genome-editing technologies for discovering and manipulating cellulose-degrading microbes. This review provides an overview of lignocellulose-degrading microbial communities from diverse environments, encompassing bacterial and fungal populations. It also delves into the use of metagenomic, metatranscriptomic, and metaproteomic approaches to pinpoint highly efficient cellulase genes, along with the application of genome-editing tools for engineering lignocellulose-degrading microorganisms. The primary objective of this review is to offer insights for further exploration of potential lignocellulose-degrading microbial resources and high-performance cellulase genes to enhance roughage utilization in ruminant rumen ecosystems.},
}

@article {pmid40646273,
year = {2025},
author = {Mikolas, M and Fauszt, P and Petrilla, A and Nemeth, P and David, P and Szilagyi-Tolnai, E and Szilagyi-Racz, A and Stagel, A and Gal, F and Gal, K and Sohajda, R and Szoke, Z and Hossain, SA and Stundl, L and Biro, S and Remenyik, J and Paholcsek, M},
title = {Analysis of ICU resistome dynamics in patients, staff and environment for the identification of predictive biomarkers of sepsis and early mortality.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25080},
pmid = {40646273},
issn = {2045-2322},
mesh = {Humans ; *Intensive Care Units ; *Sepsis/mortality/microbiology ; Biomarkers/analysis ; Male ; Female ; Middle Aged ; Anti-Bacterial Agents/pharmacology ; Aged ; *Drug Resistance, Multiple, Bacterial ; Health Personnel ; Oropharynx/microbiology ; Bacteria/drug effects/genetics ; Microbiota ; Drug Resistance, Bacterial ; },
abstract = {Antimicrobial resistance (AMR) is a global crisis, posing a critical challenge to healthcare systems, particularly in intensive care units (ICUs), where multidrug-resistant organisms (MDROs) threaten patient survival. This study offers a unique, real-world perspective on AMR dynamics by analyzing 96 metagenomic samples from three key sources: oropharyngeal and rectal swabs of deceased ICU patients (both postadmission and antemortem), healthcare workers, and high-touch ICU surfaces. Findings revealed the ICU environment as a major AMR reservoir, with oropharyngeal swabs carrying the highest AMR burden. While healthcare staff facilitated MDRO spread, they were not primary sources. Staff microbiomes' MDRO pattern closely resembled environmental samples. Key AMR species included B. fragilis, E. coli, S. pneumoniae, S. aureus, with P. aeruginosa persisting on high-touch surfaces. Tetracycline resistance was the most prevalent, with common resistances comprising 36.1% of all detected AMR markers. Staff microbial community exhibited higher resistance to macrolides, fluoroquinolones, lincosamides, and cephamycins. A 10-day survival threshold distinguished early (EM) and late mortality (LM) groups. EM patients exhibited unique AMR species in the oropharynx, suggesting respiratory-driven infections, while LM patients showed greater gut-associated resistance. Higher rectal AMR counts correlated with prolonged survival. Notably, four key MDROs (L. monocytogenes, M. tuberculosis, S. haemolyticus, and S. agalactiae) were enriched in sepsis patients, suggesting early risk markers. Fewer new resistances emerged in rectal than oropharyngeal swabs, likely due to antibiotic selection pressure. Vancomycin and levofloxacin, frequently co-administered, exerted stronger selective pressure in the oropharynx, possibly explaining the high MRSA prevalence in patient and environmental samples.},
}

Humans
*Intensive Care Units
*Sepsis/mortality/microbiology
Biomarkers/analysis
Male
Female
Middle Aged
Anti-Bacterial Agents/pharmacology
Aged
*Drug Resistance, Multiple, Bacterial
Health Personnel
Oropharynx/microbiology
Bacteria/drug effects/genetics
Microbiota
Drug Resistance, Bacterial

@article {pmid40645966,
year = {2025},
author = {Kim, S and Park, MS and Kang, I and Cho, JC},
title = {Microbial metagenomes from Lake Soyang, the largest freshwater reservoir in South Korea.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {1201},
pmid = {40645966},
issn = {2052-4463},
support = {NRF-2022R1A2C3008502//National Research Foundation of Korea (NRF)/ ; NRF-2022R1C1C2004070//National Research Foundation of Korea (NRF)/ ; },
mesh = {Republic of Korea ; *Lakes/microbiology ; *Metagenome ; *Microbiota ; Metagenomics ; Ecosystem ; Fresh Water/microbiology ; },
abstract = {Lake ecosystems play a fundamental role in the global biogeochemical cycling of essential elements such as carbon, nitrogen, and phosphorus. Microorganisms within these ecosystems mediate key processes that regulate these cycles. Metagenomic analyses provide valuable insights into the taxonomic and functional diversity of microbial communities in various environments, including freshwater habitats. Here, we present a comprehensive metagenomic dataset derived from Lake Soyang, the largest freshwater reservoir in South Korea. A total of 28 metagenomes were generated from water samples collected across two distinct sampling periods: the first set (n = 8) was obtained between April 2014 and January 2015 from two depths (1 m and 50 m) in four different seasons, while the second set (n = 20) was collected between January 2019 and November 2019 from five depths (1, 10, 20, 40, and 90 m) over four seasons. Metagenomic sequencing yielded 9.3-21.8 Gbp per sample. This dataset provides a valuable resource for future studies exploring the ecophysiological characteristics of microbial communities in pelagic freshwater environments.},
}

Republic of Korea
*Lakes/microbiology
*Metagenome
*Microbiota
Metagenomics
Ecosystem
Fresh Water/microbiology

@article {pmid40645948,
year = {2025},
author = {Calayag, AM and Priest, T and Oldenburg, E and Muschiol, J and Popa, O and Wietz, M and Needham, DM},
title = {Arctic Ocean virus communities and their seasonality, bipolarity, and prokaryotic associations.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6427},
pmid = {40645948},
issn = {2041-1723},
mesh = {Arctic Regions ; Seasons ; *Seawater/virology/microbiology ; Metagenome ; *Virome/genetics ; Oceans and Seas ; *DNA Viruses/genetics/classification/isolation & purification ; Biodiversity ; Bacteria/virology/genetics ; Host Microbial Interactions ; },
abstract = {Viruses of microbes play important roles in ocean environments as agents of mortality and genetic transfer, influencing ecology, evolution and biogeochemistry. However, we know little about the diversity, seasonality, and host interactions of viruses in polar waters. Here, we study dsDNA viruses in the Arctic Fram Strait across four years via 47 long-read metagenomes of the cellular size-fraction. Among 5662 vOTUs, 98% and 2% are Caudoviricetes and Megaviricetes, respectively. Viral coverage is, on average, 5-fold higher than cellular coverage, and 8-fold higher in summer. Viral community composition shows annual peaks in similarity and strongly correlates with prokaryotic community composition. Using network analysis, we identify putative virus-host interactions and six ecological modules associated with distinct environmental conditions. The network reveals putative novel cyanophages with time-lagged correlations to their hosts (in late summer) as well as diverse viruses correlated with Flavobacteriaceae, Pelagibacteraceae, and Nitrosopumilaceae. Via global metagenomes, we find that 42% of Fram Strait vOTUs peak in abundance in high latitude regions of both hemispheres, and encode proteins with biochemical signatures of cold adaptation. Our study reveals a rich diversity of polar viruses with pronounced seasonality, providing a foundation for understanding viral regulation and ecosystem impacts in changing polar oceans.},
}

Arctic Regions
Seasons
*Seawater/virology/microbiology
Metagenome
*Virome/genetics
Oceans and Seas
*DNA Viruses/genetics/classification/isolation & purification
Biodiversity
Bacteria/virology/genetics
Host Microbial Interactions

@article {pmid40645526,
year = {2025},
author = {Xu, J and Zhang, Y and Wang, X and Xu, W and Chen, S and Pan, L and Gao, J},
title = {A P2X7 receptor antagonist alleviates PTSD-like behaviors in adolescent rats through gut microbiota modulation and hippocampal transcriptomic remodeling.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {119859},
doi = {10.1016/j.jad.2025.119859},
pmid = {40645526},
issn = {1573-2517},
abstract = {Post-traumatic stress disorder (PTSD) is a debilitating psychiatric disorder that frequently manifests during adolescence, a critical neurodevelopmental period. Although the P2X7 receptor is implicated in the pathophysiology of PTSD, its role in adolescent-onset PTSD, particularly concerning gut microbiota dysbiosis and hippocampal transcriptomic alterations, remains unclear. This study investigated the effects of the P2X7 receptor antagonist Brilliant Blue G (BBG) on PTSD-like behaviors, gut microbiota, and hippocampal transcriptomic profiles in adolescent rats subjected to single prolonged stress and electric foot shock (SPS&S). BBG treatment significantly ameliorated SPS&S-induced fear- and anxiety-like behaviors and spatial working memory deficits. Metagenomic analysis revealed that BBG partially reversed SPS&S-induced gut microbiota dysbiosis, significantly enriching key bacterial taxa (e.g., Bacteroidota) and modulating functional pathways related to immunity and metabolism. Hippocampal transcriptomic analysis demonstrated that BBG normalized a majority of SPS&S-induced differentially expressed genes; these corrected genes were significantly enriched in pathways for extracellular matrix organization, neural differentiation, and PI3K-Akt signaling pathway. Integrated multi-omics correlation analyses revealed significant correlations among key microbial abundances, hippocampal gene expression, and behavioral outcomes, supporting a gut-brain axis mechanism underlying the therapeutic effects of BBG. These findings position the P2X7 receptor as a promising therapeutic target for adolescent PTSD and highlight the crucial role of gut microbiota in modulating stress-related neuropathology via the gut-brain axis.},
}

@article {pmid40645301,
year = {2025},
author = {Melamed, E and Rungratanawanich, W and Liangpunsakul, S and Maki, KA and McCullough, RL and Llorente, C},
title = {Alcohol, Aging, and the Gut Microbiome: Intersections of Immunity, Barrier Dysfunction, and Disease.},
journal = {Alcohol (Fayetteville, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.alcohol.2025.07.001},
pmid = {40645301},
issn = {1873-6823},
abstract = {Alcohol consumption exerts complex, dose- and context-dependent effects on human health, particularly by influencing the gut microbiome, intestinal barrier integrity, immune regulation, and aging processes. Genetic variation and advancing age are two major, and often interacting, factors that modify the risk of alcohol-related diseases. Among genetic factors, the prevalent aldehyde dehydrogenase 2 polymorphism (ALDH2*2) compromises acetaldehyde clearance, driving toxic metabolite accumulation, oxidative stress, and increased intestinal permeability that disrupts gut microbial communities, even at low levels of alcohol consumption. Heavy and chronic alcohol use further disrupts gut microbial communities, erodes mucosal integrity, and drives systemic inflammation, contributing to alcohol-associated liver disease (ALD), neuroinflammation, and multi-organ injury. Aging independently worsens these effects by promoting chronic low-grade inflammation and impaired immune responses, heightening susceptibility to alcohol-induced pathology. In specific contexts, such as certain autoimmune diseases, low to moderate alcohol intake may exert immunomodulatory effects and influence the gut microbiome, potentially contributing to reduced inflammation and alterations in microbial composition. This review synthesizes current mechanistic insights into how alcohol, host genetics, the gut microbiome, immune regulatory pathways, and aging intersect to influence disease risk. As global populations age and the burden of alcohol-related health issues rises, there is an urgent need for integrated, systems-level approaches. Future research should prioritize precision-based, gut-targeted strategies aimed at restoring microbial balance, maintaining intestinal barrier integrity, and mitigating alcohol-related harm across the lifespan.},
}

@article {pmid40645053,
year = {2025},
author = {Zhao, M and Xiong, S and Du, T and Xu, X and Li, H and Zhang, L and Xu, Y and Wei, T and Xiong, T and Xie, M},
title = {Elucidating microbial succession dynamics and flavor metabolite formation in korean style spicy cabbage fermentation: Integration of flavoromics, amplicon sequencing, and metagenomics.},
journal = {Food chemistry},
volume = {492},
number = {Pt 2},
pages = {145464},
doi = {10.1016/j.foodchem.2025.145464},
pmid = {40645053},
issn = {1873-7072},
abstract = {Korean style spicy cabbage (KSC) is a prominent fermented vegetable consumed globally. Nevertheless, microbial succession dynamics, interactions, and flavor-core microbiome correlations lack comprehensive understanding. Metabolomics revealed eight taste-active compounds and sixteen aroma-active compounds as key flavor determinants throughout fermentation. Amplicon sequencing elucidated dynamic shifts in bacterial and fungal community structures during KSC fermentation, with subsequent analyses identifying free sugars as the primary drivers of microbial succession. Spearman correlation analysis further identified Psychrobacter, Latilactobacillus, Weissella, Pseudomonas, Rothia, Candida, Vishniacozyma, Kazachstania, and Cutaneotrichosporon as core microbes driving the formation of characteristic flavor metabolites in KSC. Through metagenomic analysis, we reconstructed the metabolic network underlying the formation of characteristic flavor compounds. Our study elucidates microbial diversity dynamics and flavor metabolite formation during KSC fermentation, offering actionable insights for identifying critical fermentation phases and optimizing inoculated starter culture.},
}

@article {pmid40645041,
year = {2025},
author = {Pei, J and Chen, S and Yu, K and Liang, J and Zhang, R and Li, P and Hou, Z and Fu, L and Ma, H},
title = {Microbial regulation of dissolved organic matter revealed by integrated metabolomics and metagenomics in the World's deepest blue hole.},
journal = {Marine environmental research},
volume = {210},
number = {},
pages = {107354},
doi = {10.1016/j.marenvres.2025.107354},
pmid = {40645041},
issn = {1879-0291},
abstract = {Dissolved organic matter (DOM) is central to marine biogeochemical cycles, with its composition and dynamics closely linked to microbial communities. In oxygen-stratified extreme environments, however, the ecological relationships between DOM and microbes remain insufficiently explored. This study explores the dynamics of DOM and microbial communities in the Sansha Yongle Blue Hole, the world's deepest ocean blue hole, using an integrated metabolomics and metagenomics approach. Our findings elucidate significant alterations in microbial communities and DOM composition in response to variations in oxygen concentrations. Specifically, various DOM components, including dissolved organic sulfur (DOS) and dissolved organic nitrogen (DON), along with a spectrum of small molecule metabolites, were affected by microbial metabolic activities. Higher concentrations of DOS in the anoxic layer were positively correlated with increased sulfur metabolism in microbial communities, whereas lower concentrations of DON in the chemocline were associated with the coupling of nitrification and denitrification processes. Additionally, metabolites such as lipids, amino acids, isovalerylcarnitine, and peptides, associated with microbial physiological functions, energy metabolism, and signal transduction processes, varied with oxygen stratification. These findings contribute to a deeper understanding of the intricate relationships between microbial communities and DOM dynamics in extreme marine environments.},
}

@article {pmid40644847,
year = {2025},
author = {Zhang, H and Jiang, H and Yin, J and Wang, T and Zeng, W and Lin, D and Xu, B and Bai, L and Liang, H and Ng, HY},
title = {Biofilm response in potential difference-enhanced membrane-aerated biofilm systems for accelerated antibiotic removal and ARG mitigation.},
journal = {Water research},
volume = {285},
number = {},
pages = {124154},
doi = {10.1016/j.watres.2025.124154},
pmid = {40644847},
issn = {1879-2448},
abstract = {A membrane-aerated bio-cathode configuration was engineered, leveraging counter-diffusion biofilm architecture to physically segregate oxygen from cathode reactions. This design minimized electron diversion to oxygen (a competing terminal electron acceptor), thereby optimizing electron allocation for antibiotic co-metabolism. Further, the biofilms self-regulation and the molecular dynamics (MD) mechanism of antibiotic/antibiotic resistance genes (ARGs) reduction were simultaneously investigated. At 80 V/m potential difference, anode biofilms exhibited enhanced protein secretion (2.31-fold increase versus controls), which mitigated SMX-induced static quenching of tyrosine-like fluorophores by shifting to dynamic quenching mechanisms. Concurrent cathode analyses revealed substantial ARG suppression, with sul1 (-1.25 log2) and sul2 (-1.22 log2) reductions attributed to host genus inactivation (Nitrateductor, Pseudomonas, Methylobacterium abundance undetectable). MD simulations elucidated critical interaction mechanism: Reduced polar solvation energy (ΔGPB=-31.363 kJ/mol) promoting Sul1-encoded protein and SMX interactions strengthened, enhancing resistance sustainability under ARGs reduction. Besides, Flavin mononucleotide activation promoted SMX degradation via Cytochrome P450, likely driving rapid SMX removal under electric fields, with a 1.5-fold SMX removal rate enhancement versus conventional MABR.},
}

@article {pmid40644733,
year = {2025},
author = {Zhou, Y and Wen, C and Zhang, Q and Gu, Z and Lian, L and Xue, K and Xu, T and Lin, Z and Wang, W and Zhu, H},
title = {Characteristics of oral microbiomics with soldiers in the army before and after high-intensity physical training.},
journal = {Archives of oral biology},
volume = {178},
number = {},
pages = {106347},
doi = {10.1016/j.archoralbio.2025.106347},
pmid = {40644733},
issn = {1879-1506},
abstract = {OBJECTIVES: This paper aims to investigate the changes in soldiers' oral microbiome and metabolic levels after a month of high-intensity training.

DESIGN: We collected saliva samples from 10 soldiers with good oral health and hygiene habits before and after training. Subsequently, DNA extraction, metagenomic sequencing, and phylogenetic analysis of the oral microbiome were conducted.

RESULTS: 7733 bacterial species from 113 known bacterial phyla and 2017 genera detected in 20 samples. The diversity and richness of saliva microorganisms before and after training were similar (p > 0.05), while beta diversity analysis showed structural differences in microbiota at the phylum and genus levels (p < 0.05). The relative abundance of 27 genera such as Proteobacteria, Neisseria, Morococcus cerebrosus and Eikenella in soldiers' saliva significantly increased after high-intensity training (p < 0.05). Conversely, the relative abundance of 20 genera such as Bacteroidota, Veillonella, Parvimonas micra, Prevotella oris, Peptostreptococcus, and Treponema decreased (p < 0.05). At the metabolic level, training resulted in a relative increase (p < 0.05) in various pathways, including amino acid metabolism, sulfur metabolism, glutathione metabolism, and Tyrosine metabolism. By comparison, after training, carbohydrate metabolism, glycan biosynthesis, metabolism, the HIF-1 signaling pathway, and necroptosis revealed a relative decrease (p < 0.05).

CONCLUSIONS: This paper reveals the changes in the saliva microbiome of soldiers after one month of high-intensity training, in which the relative abundance of biomarkers of periodontal disease, caries, and other oral diseases represented by peptostreptococcus, prevotella oris, treponema, etc., are significantly reduced, suggesting that long-term high-intensity training may have a positive effect on oral health.},
}

@article {pmid40643937,
year = {2025},
author = {Jenkins, MC and Parker, C and Campos, P and Grimm, K and Davies, C and Tucker, MS and Heeder, C and Quist, M and Thompson, P},
title = {Use of Deep Amplicon Sequencing Based on the Cytochrome Oxidase I Gene to Quantify the Relative Percentages of Eimeria spp. Oocysts in Poultry Litter.},
journal = {Avian diseases},
volume = {69},
number = {2},
pages = {177-182},
doi = {10.1637/aviandiseases-D-25-00006},
pmid = {40643937},
issn = {1938-4351},
mesh = {Animals ; *Eimeria/genetics/isolation & purification/classification ; *Chickens ; Oocysts ; *Coccidiosis/veterinary/parasitology ; *Poultry Diseases/parasitology ; *Electron Transport Complex IV/genetics/metabolism ; *High-Throughput Nucleotide Sequencing/veterinary ; *Protozoan Proteins/genetics/metabolism ; Housing, Animal ; },
abstract = {The purpose of this study was to evaluate a deep amplicon sequencing approach for estimating the relative abundances of different Eimeria spp. oocysts in litter from commercial broiler farms that may or may not be experiencing necrotic enteritis (NE) infections. Oligonucleotide primers directed to the mitochondrial cytochrome oxidase I (COI) gene, a sequence that is conserved among all chicken Eimeria spp., were first used to PCR amplify Eimeria acervulina, Eimeria maxima, and Eimeria tenella oocyst DNA. COI amplification was applied to samples containing either a single Eimeria species or an equal mixture of E. acervulina, E. maxima, and E. tenella oocysts. Amplicon sequencing and mapping to the relevant COI sequences in the GenBank database confirmed the expected ∼100% mapping to the appropriate Eimeria sp. and in approximately equal percentages (∼33%) for mixtures of equal numbers of Eimeria spp. oocysts. This approach was then applied to DNA derived from Eimeria oocysts obtained at 0, 2, and 4 wk after chick placement (growout) from a total of 20 individual houses on six different commercial broiler farms. Of the seven Eimeria spp. known to infect chickens, only five were consistently found in litter at each collection time point: E. acervulina, E. maxima, Eimeria mitis, Eimeria praecox, and E. tenella. The relative numbers of E. maxima and non-E. maxima (Eamipt) oocysts in all litter samples as estimated by COI deep amplicon sequencing showed a modest correlation with the respective E. maxima or Eamipt oocyst counts (R ∼ 0.30). The results revealed an interesting phenomenon that supports the role of E. mitis in predisposing chickens to NE. In this study, the percentage of E. mitis as estimated by deep amplicon sequencing at 0, 2, and 4 wk growout showed a strong positive correlation with NE incidence (0 wk, R = 0.57; 2 wk, R = 0.52; 4 wk, R = 0.61). This study provides evidence for the usefulness of a deep amplicon sequencing approach to estimating the relative abundances of different Eimeria oocysts infecting chickens because it allows reactions to take place in a single tube, thus avoiding the time-consuming, labor-intensive, species-specific internal transcribed spacer 1 (ITS1) PCR analyses. More importantly, it allows one to explore relationships between NE incidence and the abundance of minor Eimeria species, which would have been missed by oocyst counting or ITS1 PCR because most Eimeria species are not distinguishable by microscopy, and ITS1 PCR is not quantitative.},
}

Animals
*Eimeria/genetics/isolation & purification/classification
*Chickens
Oocysts
*Coccidiosis/veterinary/parasitology
*Poultry Diseases/parasitology
*Electron Transport Complex IV/genetics/metabolism
*High-Throughput Nucleotide Sequencing/veterinary
*Protozoan Proteins/genetics/metabolism
Housing, Animal

@article {pmid40643235,
year = {2025},
author = {Wang, X and Lv, Y and Zhao, W and Xiao, X and Wang, J},
title = {D-amino acid metabolic versatility as a common adaptive strategy in the Mariana Trench microbiome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0058125},
doi = {10.1128/msystems.00581-25},
pmid = {40643235},
issn = {2379-5077},
abstract = {UNLABELLED: Hadal trenches, the Earth's deepest marine environments, harbor thriving microbial communities that promote the turnover of recalcitrant dissolved organic matter (RDOM) under extreme conditions. However, the effects of microbes on D-amino acid (D-AA) reservoirs, which are important components of deep-sea RDOM, remain largely unknown. To address this knowledge gap, we curated a comprehensive reference database of D-AA functional genes for accurate identification of D-AA metabolic potential from metagenomic data. Using this database, we identified the presence of various D-AA anabolic and catabolic genes that were closely correlated with central carbon metabolism and ammonia oxidation genes throughout the water column and in the sediment of the Mariana Trench. Furthermore, 93.6% of the recovered bacterial and archaeal genomes contained at least one of these D-AA functional genes, substantially expanding our understanding of potential D-AA utilizers. Notably, we discovered that glutamate racemase, an enzyme previously thought to be exclusive to bacteria, is ubiquitously present in ammonia-oxidizing archaea. This finding suggests that D-glutamate could be integrated into hadal carbon and nitrogen cycling by this crucial microbial taxon. Finally, we observed an increase in both D-AA production and degradation potential with water depth, with higher levels in near-bottom seawater than in sediment. These findings suggest that diverse microbial taxa promote increased D-AA turnover in hadal zones, potentially representing a common adaptive response to extreme hadal conditions.

IMPORTANCE: Deep-sea microorganisms play a crucial role in the turnover of RDOM. In this study, we investigated the metabolic potential of D-AAs, which are important constituents of RDOM and are used for indicating the recalcitrance of organic matter. By elucidating the genetic profiles of D-AA metabolism and associated microbial taxa, we observed that D-AA metabolism is a fundamental ecological function that is prevalent in the deepest ocean. Our finding of higher D-AA turnover potentials in deeper environments challenges the conventional view of the constant recalcitrance of D-AAs, suggesting that D-AA turnover may be environmentally dependent. This insight provides a new paradigm for understanding RDOM turnover, with broad implications for marine biogeochemistry.},
}

@article {pmid40643197,
year = {2025},
author = {Xu, T and Wu, X and Zhang, Y and Cai, Y and Zhang, X and Zeng, Q and Luo, J and Wei, J and Chen, T},
title = {L-Tryptophan Produced by Bifidobacterium pseudocatenulatum NCU-08 Delays Aging in SAMP8 Mice by Activating the Sirt1/P53/P21/Rb Signaling Pathway.},
journal = {Aging cell},
volume = {},
number = {},
pages = {e70166},
doi = {10.1111/acel.70166},
pmid = {40643197},
issn = {1474-9726},
support = {32201250//National Natural Science Foundation of China/ ; 2024YFA1307103//National Key R&D Program of China/ ; 2024SSY07061//Jiangxi Province Key Laboratory of bioengineering drugs/ ; 20242BAB25464//Jiangxi Provincial Natural Science Foundation/ ; },
abstract = {Gut microbiota delays aging by regulating the immune, metabolic, and neurological functions of the host. However, current research on novel probiotics with antiaging properties significantly lags, impacting their application in clinical treatments. In this study, metagenomics, culturomics, and probiotic property screening were used to identify Bifidobacterium pseudocatenulatum NCU-08 as a potential probiotic with anti-aging properties. In addition, B. pseudocatenulatum NCU-08 effectively improved the behavioral characteristics, significantly reduced the levels of the age-related protein β-galactosidase (β-gal) (BP: M = 0.81 vs. 1.13, p < 0.05), attenuated neuronal damage in the hippocampus, and improved the composition of the gut microbiota of senescence-accelerated mouse tendency-8 (SAMP8) mice. The targeted metabolomics suggested that L-tryptophan (L-Trp) may be a key substance for B. pseudocatenulatum NCU-08 to exert anti-aging effects (BP: M = 14878.6 ng/mL vs. 5464.99 ng/mL, p < 0.01). Mechanistically, using the aging model of SAMP8 mice and HT22 mouse hippocampal neuronal cells, it was found that B. pseudocatenulatum NCU-08 might enter the intestine to regulate L-Trp, and then transport it to the brain. In the brain, L-Trp was metabolized to NAD[+], which activated the Sirt1/P53/P21/Rb signaling pathway, thereby exerting antiaging effects. Interestingly, this antiaging effect was inhibited after the intervention of the Sirt1 inhibitor EX-527. This study is the first to confirm the antiaging properties of NCU-08 isolated from the fecal samples of seven centenarians in Jiangxi Province, providing data support for the future development of probiotic preparations with antiaging effects.},
}

@article {pmid40642988,
year = {2025},
author = {Wang, F and Wu, Y and Ni, J and Xie, Q and Shen, J and Chen, H and Ma, C and Yao, Y and Wang, J and Xu, L and Xiang, Q and Zhao, Y and Chen, Y and Li, L},
title = {Gut microbiota links to histological damage in chronic HBV infection patients and aggravates fibrosis via fecal microbiota transplantation in mice.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0076425},
doi = {10.1128/spectrum.00764-25},
pmid = {40642988},
issn = {2165-0497},
abstract = {Gut microbiota dysbiosis has been observed in HBV-related cirrhosis, but its role in early-stage disease and its correlation with liver pathology remain unclear. Moreover, whether dysbiosis is a cause or consequence of liver cirrhosis is still debated. We recruited 20 treatment-naïve patients with chronic HBV infection, assessing liver injury via biopsy. Fecal metagenomic sequencing was used to analyze the correlation between gut microbiota and liver histology. To explore the causality, fecal samples from an HBV-related cirrhosis patient were transplanted into mice with CCl4-induced liver fibrosis. Patients with significant histological damage exhibited reduced alpha diversity and greater microbial homogeneity. Species such as Eubacterium_sp_CAG_180, Gemmiger_formicilis, and Oscillibacter_sp_ER4 had decreased abundance, while Parabacteroides_distasonis, Bacteroides_dorei, and Bacteroides_finegoldii were enriched. Mice receiving fecal transplants from the cirrhotic patient showed aggravated liver fibrosis, with increased collagen deposition; elevated ALT, AST, and ALP levels; and heightened hepatic inflammatory gene expression. Additionally, abnormal bile acid profiles with elevated unconjugated bile acids (e.g., GCA and CA) were observed. Gut microbiota dysbiosis is closely associated with liver histological damage in chronic HBV infection and may drive fibrosis progression via microbial-bile acid interactions. These findings suggest potential for gut microbiota-based assessment and treatment strategies in chronic hepatitis B.IMPORTANCEThis study elucidates a significant association between gut microbiota dysbiosis and liver histological damage in patients with chronic hepatitis B (HBV), potentially exacerbating fibrosis progression through bile acid interactions. By analyzing patient gut microbiota and conducting fecal transplant experiments in mice, researchers have identified that gut microbiota dysbiosis contributes to hepatic fibrosis during chronic HBV infection. These findings underscore the importance of the gut-liver axis in HBV disease progression, indicating that monitoring or modulating gut bacteria may facilitate early diagnosis or therapeutic interventions. This research bridges the gap in understanding whether microbial alterations drive disease progression or result from it, providing a foundation for developing therapies targeting the microbiome to mitigate liver damage in chronic HBV infections.},
}

@article {pmid40642980,
year = {2025},
author = {Jia, X and Xiong, Y and Xu, Y and Chen, F and Han, P and Qu, J and He, Q and Rao, G},
title = {Machine learning-selected minimal features drive high-accuracy rule-based antibiotic susceptibility predictions for Staphylococcus aureus via metagenomic sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0055625},
doi = {10.1128/spectrum.00556-25},
pmid = {40642980},
issn = {2165-0497},
abstract = {Antimicrobial resistance (AMR) represents a critical global health challenge, demanding rapid and accurate antimicrobial susceptibility testing (AST) to guide timely treatments. Traditional culture-based AST methods are slow, while existing whole-genome sequencing (WGS)-based models often suffer from overfitting, poor interpretability, and diminished performance on clinical metagenomic data. In this study, we developed an interpretable genotypic AST approach for Staphylococcus aureus using minimal genomic determinants. Analysis of 4,796 S. aureus genomes and AST data for 18 antibiotics revealed one to five key resistance genes per antibiotic, including two previously uncharacterized vancomycin resistance markers. These features enabled highly accurate rule-based predictions, achieving area under the curve (AUC) values ranging from 0.94 to 1.00. The model demonstrated an overall sensitivity of 97.43% and specificity of 99.02%, respectively, with a very major error (VME) rate of 2.57% and a major error (ME) rate of 0.98% for isolate-level testing. Furthermore, after optimization for shallow-depth metagenomic sequencing, the model achieved 81.82% to 100% accuracy in AST predictions for 59 clinical samples, bypassing the need for bacterial isolation and reducing diagnostic time by an average of 39.9 hours. By combining minimal feature selection with strong interpretability and adaptability to metagenomic data, this method offers a practical and transformative solution for rapid and reliable AST in clinical settings.IMPORTANCEAntimicrobial resistance (AMR) in Staphylococcus aureus poses a critical challenge to global health, necessitating rapid and reliable antimicrobial susceptibility testing (AST) for timely treatment decisions. Traditional culture-based AST is slow, while existing whole-genome sequencing (WGS)-based approaches often suffer from overfitting and poor interpretability. This study introduces a rule-based, interpretable genotypic AST model for S. aureus that leverages minimal genomic determinants, achieving over 97% accuracy in isolate-level testing and high accuracy in clinical metagenomic samples. By extracting key resistance features and applying a rule-based approach, our model enables faster AST predictions and enhances hospital surveillance of resistant strain outbreaks. This culture-independent method reduces diagnostic time by nearly 40 hours, providing a scalable and actionable solution for clinical AMR management.},
}

@article {pmid40642907,
year = {2025},
author = {Liu, H and Shi, K and Zhang, Y and Zhang, L and Chen, Y and Shi, Y},
title = {Foliar Application of Nanoselenium: A Novel Strategy to Enhance Tuber Quality, Yield, and Nitrogen Use Efficiency in Potato.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c03576},
pmid = {40642907},
issn = {1520-5118},
abstract = {Excessive nitrogen application reduces nitrogen use efficiency (NUE) and exacerbates environmental risks. Nanoselenium (nano-Se) has been shown to enhance plant nitrogen uptake efficiency. This study investigated nano-Se influences potato (Solanum tuberosum L.) tuber yield, quality, rhizosphere soil enzyme activity, and inorganic nitrogen content under different nitrogen application levels, integrating metabolomic, metagenomic, and soil metabolomic analyses. Results showed that the N2 + Se treatment matched the yield of the N3 + Se treatment but notably boosted vitamin C (Vc), starch content, and NUE. Metabolomic analysis showed that nano-Se promoted the accumulation of d-glucose-1-phosphate (a starch precursor) and amino acids (raw materials for protein) in tubers. Multiomics data indicated that nano-Se recruited beneficial rhizobacteria such as Flavobacterium and Pseudoxanthomonas by exuding l-tyrosine, l-valine, and 4-oxoproline. In addition, It promoted nitrate assimilation genes (narB and nirB) and suppressed nitrification genes (amoA and hao), reducing nitrogen losses.},
}

@article {pmid40641875,
year = {2025},
author = {Yu, F and Jin, J and Jin, X and Ding, X and Lou, Y},
title = {Altered upper respiratory tract microbiota in laryngeal cough attributed to lung yin deficiency and the modulatory effects of Yangyin Qingfei Oral Liquid.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1592294},
pmid = {40641875},
issn = {1664-302X},
abstract = {OBJECTIVE: This study investigates changes in upper respiratory tract microbiota in laryngeal cough patients with lung yin deficiency using high-throughput sequencing of the 16S rDNA gene. It also examines the modulatory effects of Yangyin Qingfei Oral Liquid (YYQFOL).

METHODS: We included 100 laryngeal cough patients and 65 healthy subjects, collecting throat swab samples for microbiota comparison. Patients were randomly assigned to a control group receiving methoxyphenamine capsules and an experimental group receiving YYQFOL and methoxyphenamine for 10 days. We assessed changes in microbiota, symptom scoring, and Leicester Cough Questionnaire (LCQ) results. Each group was divided into responders (R) and non-responders (NR).

RESULTS: Patients with laryngeal cough had significantly lower microbial abundance and diversity than healthy subjects (p < 0.05). After treatment, symptom scores and LCQ results improved significantly (p < 0.05), with responders in the experimental group (ER) showing significantly better improvement than those in the responders in the control group (CR) (p < 0.05). Post-treatment, the experimental group saw a significant reduction in Streptococcus, Haemophilus, and other genera, while Veillonella increased (p < 0.05).

CONCLUSION: Laryngeal cough patients with lung yin deficiency are imbalanced in the upper respiratory tract microbiota. Treatment with methoxyphenamine and YYQFOL improves microbiota composition and alleviates symptoms.},
}

@article {pmid40641865,
year = {2025},
author = {Nyimbo, WJ and Fallah, N and Mutombo, AM and Xu, H and Bin, Q and Makungu, JS and Lin, W},
title = {Exploring the change of coastal saline agroecosystem diversity, composition and predicted function of soil microbial community mediated by soybean and corn intercropping.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1427196},
pmid = {40641865},
issn = {1664-462X},
abstract = {INTRODUCTION: Soil microbial community is the key determinant of coastal agroecosystem soil health. However, the response of soil microbial community and its anticipated functions to soybean and corn intercropping in coastal saline agroecosystems is not well understood.

METHOD: Soybean and corn intercropping was done in Putian city of Fujian province. After harvest, soil total carbon (TC), total phosphorus (TP), total nitrogen (TN), total organic carbon (TOC), soil organic matter (SOM), salinity content and elemental ratios of C: N, C: P and N: P were examined. High-throughput sequencing was performed to investigate the community composition and diversity of rhizospheric bacterial and fungal communities as influenced by monoculture soybean (MS) and corn (MC), first (FP) and second (SP) intercropping pattern. LEfSe cladogram was generated to identify potential microbial markers and metagenome was annotated with the metabolic cycles and pathways in the KEGG database to predict the microbial function. The co-occurrence and RDA analysis assessed the correlation between microbes and soil microbes with soil chemical parameters.

RESULTS AND DISCUSSION: The intercropping patterns FP and SP significantly influenced soil TC, TP, TN, SOM, EC, pH and salinity content. The C: N, C: P, and N: P ratios were influenced by C, N, and P concentrations. Our investigation found that Chao1 was significantly higher in intercropping patterns than in monoculture patterns. Nevertheless, the Shannon index was substantially higher in monoculture than in intercropping patterns FP and SP indicating reduced bacterial and fungi diversity measured by species richness and evenness. The Non-Metric multidimensional scaling (NDMS) diversity showed that all samples were significantly clustered into four major groups, according to the bacteria and fungi communities of origin. Further statistical analysis revealed that cropping patterns strongly affected microbial communities. Furthermore, Proteobacteria, Actinobacteria, Acidobacteria, and Chloroflexi were enriched bacterial phyla in the rhizosphere of MS, MC, FP, and SP. Ascomycota, Mortierellomycota, and Basidiomycota were the most enriched fungi phyla in each intercropping pattern. These phyla were identified as sensitive biomarkers for soil nutrient circulation, ecosystem bioremediation and chemical degradation.

CONCLUSION: This study increases our understanding of soybean and corn intercropping in coastal saline agroecosystems microbiomes.},
}

@article {pmid40641180,
year = {2025},
author = {Echeveste Medrano, MJ and Su, G and Blattner, LA and Leão, P and Sánchez-Andrea, I and Jetten, MSM and Welte, CU and Zopfi, J},
title = {Methanotrophic Flexibility of 'Ca. Methanoperedens' and Its Interactions With Sulphate-Reducing Bacteria in the Sediment of Meromictic Lake Cadagno.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70133},
pmid = {40641180},
issn = {1462-2920},
support = {024.002.002//Dutch Research Council (NWO), Gravitation Grant SIAM/ ; VI.Vidi.223.012//NWO-VIDI Talent Grant/ ; 854088/ERC_/European Research Council/International ; },
mesh = {*Lakes/microbiology ; *Methane/metabolism ; *Geologic Sediments/microbiology ; Oxidation-Reduction ; Sulfates/metabolism ; Deltaproteobacteria/genetics/metabolism ; Phylogeny ; *Sulfur-Reducing Bacteria/metabolism/genetics ; *Microbial Interactions ; Metagenomics ; Electron Transport ; },
abstract = {The greenhouse gas methane is an important contributor to global warming, with freshwater sediments representing important potential methane sources. Anaerobic methane-oxidising archaea mitigate methane release into the atmosphere by coupling the oxidation of methane to the reduction of extracellular electron acceptors or through interspecies electron transfer with microbial partners. Understanding their metabolic flexibility and microbial interactions is crucial to assess their role in global methane cycling. Here, we investigated anoxic sediments of the meromictic freshwater Lake Cadagno (Switzerland), where 'Ca. Methanoperedens' co-occur with a specific sulphate-reducing bacterium, with metagenomics and long-term incubations. Incubations were performed with different electron acceptors, revealing that manganese oxides supported highest CH4 oxidation potential but enriched for 'Ca. Methanoperedens' phylotypes that were hardly present in the inoculum. Combining data from the inoculum and incubations, we obtained five 'Ca. Methanoperedens' genomes, each harbouring different extracellular electron transfer pathways. In a reconstructed Desulfobacterota QYQD01 genome, we observed large multi-heme cytochromes, type IV pili, and a putative loss of hydrogenases, suggesting facultative syntrophic interactions with 'Ca. Methanoperedens'. This research deepens our understanding of the metabolic flexibility and potential interspecific interactions of 'Ca. Methanoperedens' in freshwater lakes.},
}

*Lakes/microbiology
*Methane/metabolism
*Geologic Sediments/microbiology
Oxidation-Reduction
Sulfates/metabolism
Deltaproteobacteria/genetics/metabolism
Phylogeny
*Sulfur-Reducing Bacteria/metabolism/genetics
*Microbial Interactions
Metagenomics
Electron Transport

@article {pmid40640914,
year = {2025},
author = {Zhao, J and Kui, L and Huang, J and Deng, J and Liu, L and Zhu, C and Shi, Y and Li, C and Xiao, Y and Yu, J and Li, Q and Yang, B and Leng, B and Chan, H},
title = {Bifidobacterium animalis subsp. Lactis BX-BC08 modulates gut microbiota and secretes alpha-Ketoglutaric acid to alleviate MC903-induced atopic dermatitis.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {768},
pmid = {40640914},
issn = {1479-5876},
support = {SL2024A04J01394//Guangzhou Municipal Science and Technology Bureau Young Doctor "Qihang" Program/ ; },
mesh = {Animals ; *Dermatitis, Atopic/microbiology/chemically induced/drug therapy ; *Gastrointestinal Microbiome ; *Bifidobacterium animalis/physiology/metabolism ; *Ketoglutaric Acids/metabolism ; Mice ; Disease Models, Animal ; Female ; Probiotics ; Mice, Inbred BALB C ; },
abstract = {OBJECTIVE: Bifidobacterium is known to be depleted in patients with atopic dermatitis (AD). This study aims to investigate the potential prophylactic effects of Bifidobacterium animalis subsp. lactis BX-BC08 (B. lactis BX-BC08) in a murine model of AD.

DESIGN: The immunosuppressive and anti-inflammatory effects of BX-BC08 were evaluated in a MC903-induced AD mouse model. Gut microbiota composition was analyzed by metagenomic sequencing, while high-performance liquid chromatography-mass spectrometry (HPLC-MS) was employed to identify anti-inflammatory molecules produced by B. lactis BX-BC08.

RESULTS: BX-BC08 significantly attenuated pro-inflammatory responses, scaling and swelling in the MC903-induced AD like murine model compared to controls. Fecal microbial profiling revealed an enrichment of probiotics and a reduction of pro-inflammatory bacteria in BX-BC08 treated mice. Metabolic analysis of BX-BC08 bacteria culture supernatant and treated mice identified a significant enrichment of alpha-Ketoglutaric acid (AKG). Functional validation in the murine AD model demonstrated that AKG strongly suppressed T helper 2 (Th2)-driven pro-inflammatory responses.

CONCLUSION: BX-BC08 mitigates AD-like inflammation by producing the anti-inflammatory metabolite AKG. BX-BC08 could serve as a novel prophylactic agent for AD prevention.},
}

Animals
*Dermatitis, Atopic/microbiology/chemically induced/drug therapy
*Gastrointestinal Microbiome
*Bifidobacterium animalis/physiology/metabolism
*Ketoglutaric Acids/metabolism
Mice
Disease Models, Animal
Female
Probiotics
Mice, Inbred BALB C

@article {pmid40640502,
year = {2025},
author = {Liu, L and Firrman, JA and Narrowe, AB and Mahalak, KK and Lemons, JMS and Marzorati, M and Duysburgh, C and Rotsaert, C and Van de Wiele, T},
title = {Structural and functional characterization of a porcine intestinal microbial ecosystem developed in vitro.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24821},
pmid = {40640502},
issn = {2045-2322},
support = {8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; 8072-41000-108-00-D//USDA/ ; EOS-Homistasis project//FWO-FNR/ ; GOA-Microbes4Immunity//UGent-BOF/ ; },
mesh = {Animals ; Swine ; *Gastrointestinal Microbiome ; Metagenome ; Feces/microbiology ; *Bacteria/genetics/classification ; Metagenomics/methods ; Metabolomics ; *Intestines/microbiology ; Ecosystem ; },
abstract = {The mammalian digestive tract harbors a vast microbial community that has the potential to modulate numerous health-related processes. Multicompartment dynamic gut models have been developed to study microbial communities in a controlled environment. To verify the assumption that the experimental results produced in vitro in a mechanical device would be highly similar to those obtained from an in vivo study, in this study fecal samples from four pigs were inoculated in a simulator of the porcine intestinal microbial ecosystem (SPIME) and cultured until reaching steady state. The composition and structure of the resultant microbial communities, and the metabolites produced were compared with those harvested from the intestine of the same pigs. Taxonomic abundance identification based on shallow shotgun metagenomic sequencing revealed only 12.1% of species or 15% of metagenome-assembled genomes (MAGs) being shared across the colon compartments of the source pigs and the SPIME. Despite these overwhelming compositional shifts, higher functional conservation was indicated as measured by functional richness, MAG-level traits, CAZymes, and untargeted metabolomics. Environmental selection and bacterial functional redundancy were considered the two key elements in microbial compositional shifts and functional preservation.},
}

Animals
Swine
*Gastrointestinal Microbiome
Metagenome
Feces/microbiology
*Bacteria/genetics/classification
Metagenomics/methods
Metabolomics
*Intestines/microbiology
Ecosystem

@article {pmid40640272,
year = {2025},
author = {Xie, Y and Xiang, JY and Long, L and Ma, Y and Xing, Z and Wang, L and Shao, C and Liu, N and Li, F},
title = {Impact of different treatment methods and timings on soil microbial communities with transgenic maize straw return.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24820},
pmid = {40640272},
issn = {2045-2322},
support = {20230508091RC//Jilin Provincial Scientific and Technological Development Program/ ; 20230508091RC//Jilin Provincial Scientific and Technological Development Program/ ; },
mesh = {*Zea mays/genetics ; *Soil Microbiology ; *Plants, Genetically Modified ; *Microbiota ; Soil/chemistry ; Agriculture/methods ; Crops, Agricultural ; Metagenomics/methods ; },
abstract = {Understanding the impact of genetically modified (GM) crop straw return on soil ecosystems is crucial as GM crops become more prevalent. This study assesses the effects of straw mulching and deep tillage on soil microbial communities from GM and non-GM maize, highlighting potential ecological impacts. Shotgun metagenomic sequencing was utilized to analyze the microbial community structure and functional genes in soil samples collected at different times (30, 180, and 270 days) after straw mulching and deep tillage treatments. The study included insect-resistant transgenic maize varieties 2A-7 and CM8101 and their non-transgenic counterparts B73 and Zheng58. Different treatment methods significantly affect soil microbial alpha-diversity and beta-diversity, with deep tillage resulting in higher alpha-diversity compared to mulching, and the 180-day mark exhibiting the highest alpha-diversity across all sampling times. Early straw treatment prompted a rapid microbial response to nutrient availability, with notable changes in diversity and function over time. Straw treatments notably altered soil microbial functions, especially in carbon cycling and nutrient metabolism. Interestingly, the microbial effects of GM versus non-GM maize straw were similar, suggesting crop residue type under consistent soil management practices might not significantly alter microbial community structures. The methods and timing of straw treatments have a significant impact on soil microbial communities, surpassing the differences between GM and non-GM straw. These findings highlight the importance of straw management practices for sustainable agricultural ecosystem management.},
}

*Zea mays/genetics
*Soil Microbiology
*Plants, Genetically Modified
*Microbiota
Soil/chemistry
Agriculture/methods
Crops, Agricultural
Metagenomics/methods

@article {pmid40639969,
year = {2025},
author = {Shi, C and Wang, C and He, J and Zhang, M and Huang, W},
title = {Epichloë Endophytes Potentially Facilitate Host Plant Recruitment of Rhizosphere Microbiota Carrying Beneficial Traits.},
journal = {Physiologia plantarum},
volume = {177},
number = {4},
pages = {e70397},
doi = {10.1111/ppl.70397},
pmid = {40639969},
issn = {1399-3054},
support = {31760704//National Natural Science Foundation of China/ ; 2022D01A79//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; 23XJTRZW07//Xinjiang Key Laboratory of Soil and Plant Ecological Processes/ ; },
mesh = {*Rhizosphere ; *Endophytes/physiology ; Plant Roots/microbiology ; *Epichloe/physiology ; *Microbiota/physiology ; Soil Microbiology ; Symbiosis ; },
abstract = {Plant-microbe symbiotic relationships drive ecosystem evolution. This study employed metabolomics and metagenomic technologies to investigate the effects of the aboveground-restricted endophytic fungus Epichloë guerinii in the host plant Melica transsilvanica on the rhizosphere microbial community structure and functional traits. Our results revealed that the presence of E. guerinii significantly increased the secretion of organic acids, amino acids, and sugar alcohols from the host root system. These exudates correlated strongly with abundant, plant growth-promoting rhizosphere microorganisms like Pseudomonas, Bradyrhizobium, and Nitrospira. Functional genes that were significantly enriched in the host rhizosphere microbiota were predominantly associated with biofilm formation and organic acid metabolic pathways. Co-enrichment analyses of rhizosphere soil metabolites and genes highlighted pathways such as flagellar assembly and carbon/nitrogen/sulfur metabolism. Notably, the abundance of key genes governing the flagellar motor MotA protein in the host rhizosphere, as well as those involved in the reductive tricarboxylic acid (rTCA) cycle, nitrification, and thiosulfate oxidation, were significantly elevated. This study demonstrates that E. guerinii positively regulates rhizosphere microbial community functions by reprogramming the composition of host root exudates. These findings deepen the mechanistic understanding of Epichloë-plant-rhizosphere microbe interactions.},
}

*Rhizosphere
*Endophytes/physiology
Plant Roots/microbiology
*Epichloe/physiology
*Microbiota/physiology
Soil Microbiology
Symbiosis

@article {pmid40639658,
year = {2025},
author = {Ravelo, AD and Salfer, IJ and Caixeta, LS},
title = {GRADUATE STUDENT LITERATURE REVIEW: Contemporary perspectives and the use of omics techniques to improve our understanding of hyperketonemia in dairy cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-26542},
pmid = {40639658},
issn = {1525-3198},
abstract = {Hyperketonemia (HYK) is a metabolic disorder defined by increased ketone concentrations, particularly β-hydroxybutyrate (BHB). It is linked to increased disease risk and reduced milk production in dairy cows due to energy deficits during early lactation. Recently, omics approaches such as genomics, transcriptomics, proteomics, and metabolomics have been used to better understand mechanisms associated to HYK. These studies have helped characterize pathways associated to energy metabolism, lipid mobilization, insulin resistance, and immune response, with associated genes identified in several genome regions, including Bos taurus autosome 6. Omics studies have identified biomarkers, such as methanol, C16, and phosphatidylcholine acyl-alkyl C30:2, which have been associated with or predictive of HYK, with elevated levels detectable up to 4 weeks before calving. Limitations of omics studies include the small sample sizes of controlled study designs, standardizing sampling timelines, and translating the large amounts of data generated into practical applications. While global changes in other body fluids have been well-characterized, research focused on the role of the rumen fluid metagenome and metabolome is much more limited. Changes in rumen metabolites and microbes are important to consider in relation to HYK, as associated shifts in dry matter intake and diet can alter rumen function and subsequent nutrient metabolism and absorption. Shifts in microbial communities, such as Ruminococcaceae, and altered metabolite profiles, including increased butyrate in HYK cows, may offer insights to guide on farm decisions, such as dietary interventions or feed additive use. Overall, although HYK in dairy cows is a topic that has been extensively studied, improved understanding of its etiology and advances in 'big data' technologies have created continued opportunities to further understand HYK and the factors associated with it. Thus, the focus of this review is to provide an overview of omics methods and how they have been used to further describe HYK as well as explore new associations of omics methods and rumen parameters with HYK.},
}