Olivos-Caicedo Kelly Y, Fernandez-Materan Francelys V, Daniel Steven L, Anantharaman Karthik, Ridlon Jason M, Alves João M P
Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, Brazil.
Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL 61801, USA.
Microorganisms. 2025 Apr 9;13(4):857. doi: 10.3390/microorganisms13040857.
is a commensal gut bacterium capable of forming the secondary bile acids as well as converting glucocorticoids to androgens. Historically, only two strains, ATCC 35704 and VPI 12708, have been characterized to any significant extent. The formation of secondary bile acids is important in the etiology of cancers of the GI tract and in the prevention of infection. We determined the presence and absence of bile acid inducible () and steroid-17,20-desmolase () genes among strains and the features of 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 cultivars have an open pangenome with 12,720 orthologous gene groups and a core genome with 1630 gene families, in addition to 7051 and 4039 gene families in the accessory and unique (i.e., strain-exclusive) genomes, respectively. The pangenome profile including the MAGs also proved to be open. Our analyses reveal that strains are distributed into two clades, indicating the possible onset of separation into two species, as suggested 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.
是一种共生肠道细菌，能够形成次级胆汁酸以及将糖皮质激素转化为雄激素。历史上，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。次级胆汁酸的形成在胃肠道癌症的病因学以及预防感染方面都很重要。我们确定了菌株中胆汁酸诱导基因（）和类固醇17,20-裂解酶基因（）的有无，以及34株培养菌株和一组200个宏基因组组装基因组（MAG）的泛基因组特征，以了解菌株间的变异性。结果表明，这些培养菌株有一个开放的泛基因组，包含12720个直系同源基因组，一个核心基因组有1630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7051个和4039个基因家族。包括MAG在内的泛基因组图谱也被证明是开放的。我们的分析表明，菌株分为两个进化枝，这表明从基因含量、系统基因组学和平均核苷酸同一性（ANI）分析来看，可能开始分化为两个物种。这项研究深入了解了该菌株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。
