对……的泛基因组分析:一组多样的胆汁酸和类固醇代谢共生肠道细菌菌株。 (你提供的原文不完整,这里是按照现有内容翻译的,建议补充完整原文以便更准确翻译。)

Pangenome analysis of : a collection of diverse bile acid and steroid metabolizing commensal gut bacterial strains.

作者信息

Olivos-Caicedo Kelly Y, Fernandez Francelys, Daniel Steven L, Anantharaman Karthik, Ridlon Jason M, Alves João M P

出版信息

bioRxiv. 2024 Sep 6:2024.09.06.610859. doi: 10.1101/2024.09.06.610859.

Abstract

is a commensal gut bacterium capable of forming the secondary bile acids deoxycholic acid and lithocholic acid from the primary bile acids cholic acid and chenodeoxycholic acid, respectively, as well as converting glucocorticoids to androgens. Historically, only two strains, ATCC 35704 and VPI 12708, have been characterized and to any significant extent. The formation of secondary bile acids is important in maintaining normal gastrointestinal function, in regulating the structure of the gut microbiome, in the etiology of such diseases such as cancers of the GI tract, and in the prevention of infection. We therefore wanted to determine the pangenome of 34 cultured strains of and a set of 200 metagenome-assembled genomes (MAGs) to understand the variability among strains. The results indicate that the 34 strains of have an open pangenome with 12,720 orthologous gene groups, and a core genome with 1,630 gene families, in addition to 7,051 and 4,039 gene families in the accessory and unique (i.e., strain-exclusive) genomes, respectively. The core genome contains 39% of the proteins with predicted metabolic function, and, in the unique genome, the function of storage and processing of information prevails, with 34% of the proteins being in that category. The pangenome profile including the MAGs also proved to be open. The presence of bile acid inducible ( ) and steroid-17,20-desmolase ( ) genes was identified among groups of strains. The analysis reveals that strains are distributed into two clades, indicating the possible onset of separation into two species, confirmed by gene content, phylogenomic, and average nucleotide identity (ANI) analyses. This study provides insight into the structure and function of the pangenome, offering a genetic foundation of significance for many aspects of research on the intestinal microbiota and bile acid metabolism.

摘要

是一种共生肠道细菌,能够分别从初级胆汁酸胆酸和鹅去氧胆酸形成次级胆汁酸脱氧胆酸和石胆酸,还能将糖皮质激素转化为雄激素。从历史上看,只有ATCC 35704和VPI 12708这两个菌株在任何显著程度上得到了表征。次级胆汁酸的形成对于维持正常的胃肠功能、调节肠道微生物群的结构、胃肠道癌症等疾病的病因以及预防感染都很重要。因此,我们想要确定34株培养菌株的泛基因组以及一组200个宏基因组组装基因组(MAG),以了解菌株之间的变异性。结果表明,34株该菌具有一个开放的泛基因组,包含12,720个直系同源基因组,一个核心基因组包含1,630个基因家族,此外,附属基因组和独特(即菌株特异性)基因组中分别有7,051个和4,039个基因家族。核心基因组包含39%具有预测代谢功能的蛋白质,而在独特基因组中,信息存储和处理功能占主导,34%的蛋白质属于该类别。包括MAG在内的泛基因组图谱也被证明是开放的。在菌株组中鉴定出了胆汁酸诱导基因和类固醇17,20-裂解酶基因的存在。分析表明,该菌菌株分为两个进化枝,表明可能开始分化为两个物种,这一点通过基因含量、系统发育基因组学和平均核苷酸同一性(ANI)分析得到了证实。这项研究深入了解了该菌泛基因组的结构和功能,为肠道微生物群和胆汁酸代谢研究的许多方面提供了重要的遗传基础。

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