Genome sequences of nine
            <i>Clostridium scindens</i>
            strains isolated from human feces

Fernandez-Materan, Francelys V.; Olivos-Caicedo, Kelly Yovani; Daniel, Steven L.; Walden, Kimberly K. O.; Fields, Christopher J.; Hernandez, Alvaro G.; Alves, Joao M. P.; Ridlon, Jason M.

doi:10.1128/mra.00848-24

Microbiol Resour Announc

2024

DOI: 10.1128/mra.00848-24

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Genome sequences of nine Clostridium scindens strains isolated from human feces

Francelys V. Fernandez-Materan,

Kelly Yovani Olivos-Caicedo,

Steven L. Daniel

et al.

Abstract: Clostridium scindens is an important member of the gut microbiome. Strains of C. scindens are model organisms for bile acid and steroid metabolism studies. The genome sequences for nine C. scindens strains isolated from human feces are reported. Genomes ranged from 3,403,497 to 4,318,168 bp, 46.5% to 48% G+C content, and 3,386 to 4,137 protein-coding total genes.

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Cited by 2 publications

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Clostridium scindens: an endocrine keystone species in the mammalian gut

Daniel,

Ridlon

2024

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Clostridium scindensis a keystone human gut microbial taxonomic group that, while low in abundance, has a disproportionate effect on bile acid and steroid metabolism in the mammalian gut. Numerous studies indicate that the two most studied strains ofC. scindens(i.e., ATCC 35704 and VPI 12708) are important for a myriad of physiological processes in the host. We focus on both historical and current microbiological and molecular biology work on the Hylemon-Björkhem pathway and the steroid-17,20-desmolase pathway that were first discovered inC. scindens.Our most recent analysis now calls into question whether strains currently defined asC. scindensrepresent two separate taxonomic groups. Future directions include developing genetic tools to further explore the physiological role bile acid and steroid metabolism by strains ofC. scindens, and the causal role of these pathways in host physiology and disease.

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Clostridium scindens: an endocrine keystone species in the mammalian gut

Daniel,

Ridlon

2024

Preprint

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

Olivos-Caicedo,

Fernandez,

Daniel

et al. 2024

Preprint

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Clostridium scindensis 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,C. scindensATCC 35704 andC. scindensVPI 12708, have been characterizedin vitroandin vivoto 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 ofClostridium difficileinfection. We therefore wanted to determine the pangenome of 34 cultured strains ofC. scindensand a set of 200 metagenome-assembled genomes (MAGs) to understand the variability among strains. The results indicate that the 34 strains ofC. scindenshave 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 (bai) and steroid-17,20-desmolase (des) genes was identified among groups of strains. The analysis reveals thatC. scindensstrains are distributed into two clades, indicating the possible onset ofC. scindensseparation into two species, confirmed by gene content, phylogenomic, and average nucleotide identity (ANI) analyses. This study provides insight into the structure and function of theC. scindenspangenome, offering a genetic foundation of significance for many aspects of research on the intestinal microbiota and bile acid metabolism.

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Genome sequences of nine Clostridium scindens strains isolated from human feces

Cited by 2 publications

References 18 publications

Clostridium scindens: an endocrine keystone species in the mammalian gut

Clostridium scindens: an endocrine keystone species in the mammalian gut

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

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