人体肠道4 644株代表菌次级代谢产物生物合成基因簇挖掘与耐药及毒力基因分析

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

摘要:

为了更好地从肠道微生物组中挖掘新的次级代谢产物、了解肠道微生物组编码的抗生素耐药基因和毒力因子情况，本研究基于4 644株人体肠道微生物代表菌的基因组序列，对其编码的次级代谢产物基因簇、抗生素耐药基因和毒力因子进行了预测分析。经antiSMASH预测分析发现，超过60%的代表菌编码至少1个次级代谢产物基因簇，并从8个未可培养菌中发现了8个潜在的新颖次级代谢产物基因簇。人体肠道中的次级代谢产物主要由梭菌纲（Clostridia）、芽孢杆菌纲（Bacilli）、γ-变形菌纲（Gammaproteobacteria）、拟杆菌纲（Bacteroidia）、放线菌纲（Actinobacteria）和厚壁菌纲（Negativicutes）6类细菌编码的非核糖体多肽合成酶（nonribosomal peptide synthetase，NRPS）、细菌素、芳基多烯类化合物、萜烯、β-丙内酯、NRPS-样蛋白组成。经PathoFact预测分析发现，抗生素耐药基因和毒力因子在代表性菌株中分布广泛，但潜在病原菌编码频率更高。潜在病原菌中编码外膜蛋白、PapC N-端结构域、PapC C-端结构域、肽酶M16失活结构域等分泌型毒素和硝基还原酶家族、AcrB/AcrD/AcrF家族、PLD-样结构域、Cupin结构域、假定溶血素、S24-样肽酶、磷酸转移酶家族、内切核酸酶/外切核酸酶/磷酸酶家族、乙二醛酶/博莱霉素抗性等非分泌型毒素的频率较高。该研究将为进一步从肠道微生物组中挖掘新的微生物天然产物、了解肠道微生物的定殖与感染机制，为肠道微生物相关疾病提供靶向防治策略等奠定基础。

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.