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Metagenomic Insights into Pigeon Gut Microbiota Characteristics and Antibiotic-Resistant Genes.
Biology (Basel)
January 2025
Department of Bioinformatics, Nanjing Medical University, Nanjing 211166, China.
Background: Antibiotics were extensively used in the pigeon breeding industry previously to promote growth and prevent disease, leading to the spread of antibiotic-resistant genes (ARGs) in gut microbes, which has become a major public health concern.
Methods: A metagenomic analysis was performed to investigate the gut microbial communities and ARGs in young and older pigeons in Nanjing, Jiangsu Province, China.
Results: There were obviously distinct gut microbiota and functional compositions between young and older pigeons.
Microbially produced imidazole propionate impairs prostate cancer progression through PDZK1.
Mol Med
January 2025
Wuxi School of Medicine, Jiangnan University, Wuxi, 214122, China.
Background: A close relationship exists between castration-resistant prostate cancer (CRPC) and histidine metabolism by gut microbes. However, the effects of the histidine metabolite imidazole propionate (IMP) on prostate cancer (PCa) and its underlying mechanisms are not well understood.
Methods: We first assessed the effects of IMP on cell proliferation and migration at the cellular level.
Increasing pesticide diversity impairs soil microbial functions.
Proc Natl Acad Sci U S A
January 2025
Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
Pesticide application is essential for stabilizing agricultural production. However, the effects of increasing pesticide diversity on soil microbial functions remain unclear, particularly under varying nitrogen (N) fertilizer management practices. In this study, we investigated the stochasticity of soil microbes and multitrophic networks through amplicon sequencing, assessed soil community functions related to carbon (C), N, phosphorus (P), and sulfur (S) cycling, and characterized the dominant bacterial life history strategies via metagenomics along a gradient of increasing pesticide diversity under two N addition levels.
View Article and Find Full Text PDFNRGCNMDA: Microbe-Drug Association Prediction Based on Residual Graph Convolutional Networks and Conditional Random Fields.
Interdiscip Sci
January 2025
Computer and Control Engineering College, Qiqihar University, Qiqihar, 161006, China.
The process of discovering new drugs related to microbes through traditional biological methods is lengthy and costly. In response to these issues, a new computational model (NRGCNMDA) is proposed to predict microbe-drug associations. First, Node2vec is used to extract potential associations between microorganisms and drugs, and a heterogeneous network of microbes and drugs is constructed.
View Article and Find Full Text PDFSystematic identification of secondary bile acid production genes in global microbiome.
mSystems
January 2025
State Key Laboratory of Genetic Engineering, Fudan Microbiome Center, School of Life Sciences, Fudan University, Shanghai, China.
Unlabelled: Microbial metabolism of bile acids (BAs) is crucial for maintaining homeostasis in vertebrate hosts and environments. Although certain organisms involved in bile acid metabolism have been identified, a global, comprehensive elucidation of the microbes, metabolic enzymes, and bile acid remains incomplete. To bridge this gap, we employed hidden Markov models to systematically search in a large-scale and high-quality search library comprising 28,813 RefSeq multi-kingdom microbial complete genomes, enabling us to construct a secondary bile acid production gene catalog.
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