Mining of gene clusters for biosynthesis of secondary metabolites and analysis of genes encoding antibiotic resistance and virulence in 4 644 representative human gut strains.

Yeshi Yin; Hu Chen; Meihong Zhang; Linyan Cao; Huahai Chen

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Mining of gene clusters for biosynthesis of secondary metabolites and analysis of genes encoding antibiotic resistance and virulence in 4 644 representative human gut strains.

Author: Yeshi YIN ¹ ; Hu CHEN ¹ ; Meihong ZHANG ² ; Linyan CAO ¹ ; Huahai CHEN ¹
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1. Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Nanling Plant Resources Research and Development Hunan Engineering Research Center, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, Yongzhou 425199, Hunan, China.
2. State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Publication Type:Journal Article
Keywords: antibiotic resistance gene; gut microbiota; representative strains; secondary metabolites; virulence factors
MeSH: Humans; Virulence; Multigene Family; Bacteria; Drug Resistance, Microbial; Virulence Factors; Peptide Hydrolases
From: Chinese Journal of Biotechnology 2022;38(10):3682-3694
CountryChina
Language:Chinese
Abstract: Genome sequences of 4 644 representative strains from human gut microbiota were analyzed to mine gene clusters for biosynthesis of novel secondary metabolites, as well as genes encoding antibiotic resistance and virulence factors. AntiSMASH analysis showed that more than 60% of the representative strains encoded at least one secondary metabolite gene cluster, and 8 potential novel secondary metabolite gene clusters were identified from 8 unculturable bacteria. The secondary metabolite gene clusters in human intestine are mainly composed of nonribosomal peptide synthetase (NRPS), bacteriocin, arylpolyene, terpene, betalactone and NRPS like gene clusters distributed in Clostridia, Bacilli, Gammaproteobacteria, Bacteroidia, Actinobacteria and Negativicutes. PathoFact analysis showed that genes encoding antibiotic resistance and virulence factors are widely distributed in representative strains, but the frequency encoded by potential pathogens is significantly higher than that of non-potential pathogens. The frequency of genes encoding secretory toxins such as outer membrane protein, PapC N-terminal domain, PapC C-terminal domain, peptidase M16 inactive domain, and non-secretory toxins such as nitroreductase family, AcrB/AcrD/AcrF family, PLD-like domain, Cupin domain, putative hemolysin, S24-like peptidase, phosphotransferase enzyme family, endonuclease/ exonuclease/ phosphatase family, glyoxalase/ bleomycin resistance was high in potential pathogens. This study may facilitate mining new microbial natural products from the intestinal microbiome, understanding the colonization and infection mechanism of intestinal microorganisms, and providing targeted prevention and treatment of intestinal microbial related diseases.