Comparative genome analysis of strains of clostridium scindens: A bile acid and cortisol metabolizing gut bacterium

Fernandez Materan, Francelys Viviana

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https://hdl.handle.net/2142/125645 Copy

Description

Title

Comparative genome analysis of strains of clostridium scindens: A bile acid and cortisol metabolizing gut bacterium

Author(s)

Fernandez Materan, Francelys Viviana

Issue Date

2024-07-19

Director of Research (if dissertation) or Advisor (if thesis)

Ridlon, Jason M.

Department of Study

Animal Sciences

Discipline

Bioinformatics

Degree Granting Institution

University of Illinois at Urbana-Champaign

Degree Name

M.S.

Degree Level

Thesis

Keyword(s)

• Clostridium scindens
• bile acids
• steroid desmolase
• comparative analysis

Abstract

Clostridium scindens (Csci) is one of a few species determined to be responsible for bile acid (BA) dehydroxylation and oxidoreduction, as well as cortisol conversion into androgens. Excess production of secondary BAs is mechanistically associated with cancers of the GI tract. Csci strains ATCC 35704 (Csci35704) and VPI 12708 (Csci12708) are models to study the BA-inducible (bai) regulon and steroid-17,20-desmolase (des operon) activity, where each strain varies in their steroid metabolic activity. However, comparative genomics between these strains, and a broader comprehensive computational analysis of Csci strains has not been performed to date. Thus, a computational analysis of Csci strain genomes was performed to identify shared and unique representative genomic and metabolic capabilities in Csci. The genomic data was retrieved from the NCBI database, annotated by Prokka and pangenome analysis performed by Roary. Average Nucleotide Identity (ANI) was calculated using FastANI tool. Functional annotation was assessed with eggNOG, and orthology with OrthoFinder. Metabolic pathways were predicted with KEGG, and CRISPR-Cas systems with CRISPRCasFinder. We determined that by distance matrix of the SSU rRNA genes, Csci strains are ≥ 98.6%, suggesting a single species. However, phylogenomic and average nucleotide identity determined that Csci35704 and Csci12708 belong in distinct phylogenomic groups that share only 94.909% of nucleotide identity, indicating distinct species, despite sharing 99.67% identity in their 16s rRNA genes. About 23% of Csci12708 group shared genes are related to carbohydrates and energy metabolism, whereas 37% of Csci35704 group genes feature genes predicted to import, metabolize, or biosynthesize coenzymes as well as the import and integration of metal ions. Core genome functional annotation shows ~39% of genes are related to metabolic processes, especially carbohydrate and amino acid metabolism. Metabolic pathways involved in monosaccharide metabolism such as Embden-Meyerhof-Parnas pathway is complete, but not the Entner–Doudoroff pathway. However, like other Clostridia, Csci is predicted to harbor an incomplete TCA cycle known as the “horseshoe”, lacking succinate dehydrogenase (E.C.1.3.5.1) and succinyl-CoA synthetase (E.C.6.2.1.4). Amino acid biosynthesis pathways are mostly present, except for tryptophan, which was previously shown to be the only required amino acid in C. scindens ATCC 35704. Besides thiamine, vitamin biosynthetic ability was not part of the core genome of Csci strains. The Hylemon-Björkhem Pathway for the metabolism of primary bile acids to secondary derivatives (LCA and DCA) was found to be present in the core genome of Csci. CRISPR type I subtype C was detected as part of the mobilome systems in Csci, where the Csci12708 group (but not this strain) harbors more rudimentary CRISPR-Cas systems. This analysis provides an insight into the genomic content and variability among Csci strains denoting metabolic differences and important genetic variability influenced by the presence of des genes. Two limitations of the current study include (1) the sample size to accurately define pangenome and core genome in the specie, and (2) functional annotation relaying in the most updated version of the databases. There is still a need for future work to aid in the understanding of the effect of strain variation on host physiology and the role of strains variations in microbe-microbe interactions, such as the well-known inverse relation between Csci and Clostridium difficile.

Graduation Semester

2024-08

Type of Resource

Thesis

Handle URL

https://hdl.handle.net/2142/125645

Copyright and License Information

Copyright 2024 Francelys Viviana Fernandez Materan

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