Clostridium scindens ATCC 35704: Integration of nutritional requirements, the complete genome sequence, and global transcriptional responses to bile acids

Saravanan Devendran, Rachana Shrestha, João M.P. Alves, Patricia G. Wolf, Lindsey Ly, Alvaro Gonzalo Hernandez, Celia Méndez-García, Ashley Inboden, J'nai Wiley, Oindrila Paul, Avery Allen, Emily Springer, Chris L. Wright, Christopher J Fields, Steven L. Daniel, Jason M Ridlon

Research output: Contribution to journalArticle

Abstract

In the human gut, Clostridium scindens ATCC 35704 is a predominant bacterium and one of the major bile acid 7α-dehydroxylating anaerobes. While this organism is well-studied relative to bile acid metabolism, little is known about the basic nutrition and physiology of C. scindens ATCC 35704. To determine the amino acid and vitamin requirements of C. scindens, the leave-one-out (one amino acid group or vitamin) technique was used to eliminate the nonessential amino acids and vitamins. With this approach, the amino acid tryptophan and three vitamins (riboflavin, pantothenate, and pyridoxal) were found to be required for the growth of C. scindens. In the newly developed defined medium, C. scindens fermented glucose mainly to ethanol, acetate, formate, and H2. The genome of C. scindens ATCC 35704 was completed through PacBio sequencing. Pathway analysis of the genome sequence coupled with transcriptome sequencing (RNA-Seq) under defined culture conditions revealed consistency with the growth requirements and end products of glucose metabolism. Induction with bile acids revealed complex and differential responses to cholic acid and deoxycholic acid, including the expression of potentially novel bile acid-inducible genes involved in cholic acid metabolism. Responses to toxic deoxycholic acid included expression of genes predicted to be involved in DNA repair, oxidative stress, cell wall maintenance/metabolism, chaperone synthesis, and downregulation of one-third of the genome. These analyses provide valuable insight into the overall biology of C. scindens which may be important in treatment of disease associated with increased colonic secondary bile acids.

Original languageEnglish (US)
Article numbere00052-19
JournalApplied and environmental microbiology
Volume85
Issue number7
DOIs
StatePublished - Apr 1 2019

Fingerprint

Clostridium scindens
nutritional requirement
Nutritional Requirements
Clostridium
bile acids
Bile Acids and Salts
nutrient requirements
genome
Genome
Vitamins
acid
Cholic Acid
Amino Acids
vitamins
formic acid
Deoxycholic Acid
vitamin
deoxycholic acid
cholic acid
amino acids

Keywords

  • Bile acid
  • Clostridium scindens
  • Defined medium
  • Deoxycholic acid
  • Growth factor requirements
  • RNA-Seq

ASJC Scopus subject areas

  • Biotechnology
  • Food Science
  • Applied Microbiology and Biotechnology
  • Ecology

Cite this

Clostridium scindens ATCC 35704 : Integration of nutritional requirements, the complete genome sequence, and global transcriptional responses to bile acids. / Devendran, Saravanan; Shrestha, Rachana; Alves, João M.P.; Wolf, Patricia G.; Ly, Lindsey; Hernandez, Alvaro Gonzalo; Méndez-García, Celia; Inboden, Ashley; Wiley, J'nai; Paul, Oindrila; Allen, Avery; Springer, Emily; Wright, Chris L.; Fields, Christopher J; Daniel, Steven L.; Ridlon, Jason M.

In: Applied and environmental microbiology, Vol. 85, No. 7, e00052-19, 01.04.2019.

Research output: Contribution to journalArticle

Devendran, S, Shrestha, R, Alves, JMP, Wolf, PG, Ly, L, Hernandez, AG, Méndez-García, C, Inboden, A, Wiley, J, Paul, O, Allen, A, Springer, E, Wright, CL, Fields, CJ, Daniel, SL & Ridlon, JM 2019, 'Clostridium scindens ATCC 35704: Integration of nutritional requirements, the complete genome sequence, and global transcriptional responses to bile acids', Applied and environmental microbiology, vol. 85, no. 7, e00052-19. https://doi.org/10.1128/AEM.00052-19
Devendran, Saravanan ; Shrestha, Rachana ; Alves, João M.P. ; Wolf, Patricia G. ; Ly, Lindsey ; Hernandez, Alvaro Gonzalo ; Méndez-García, Celia ; Inboden, Ashley ; Wiley, J'nai ; Paul, Oindrila ; Allen, Avery ; Springer, Emily ; Wright, Chris L. ; Fields, Christopher J ; Daniel, Steven L. ; Ridlon, Jason M. / Clostridium scindens ATCC 35704 : Integration of nutritional requirements, the complete genome sequence, and global transcriptional responses to bile acids. In: Applied and environmental microbiology. 2019 ; Vol. 85, No. 7.
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abstract = "In the human gut, Clostridium scindens ATCC 35704 is a predominant bacterium and one of the major bile acid 7α-dehydroxylating anaerobes. While this organism is well-studied relative to bile acid metabolism, little is known about the basic nutrition and physiology of C. scindens ATCC 35704. To determine the amino acid and vitamin requirements of C. scindens, the leave-one-out (one amino acid group or vitamin) technique was used to eliminate the nonessential amino acids and vitamins. With this approach, the amino acid tryptophan and three vitamins (riboflavin, pantothenate, and pyridoxal) were found to be required for the growth of C. scindens. In the newly developed defined medium, C. scindens fermented glucose mainly to ethanol, acetate, formate, and H2. The genome of C. scindens ATCC 35704 was completed through PacBio sequencing. Pathway analysis of the genome sequence coupled with transcriptome sequencing (RNA-Seq) under defined culture conditions revealed consistency with the growth requirements and end products of glucose metabolism. Induction with bile acids revealed complex and differential responses to cholic acid and deoxycholic acid, including the expression of potentially novel bile acid-inducible genes involved in cholic acid metabolism. Responses to toxic deoxycholic acid included expression of genes predicted to be involved in DNA repair, oxidative stress, cell wall maintenance/metabolism, chaperone synthesis, and downregulation of one-third of the genome. These analyses provide valuable insight into the overall biology of C. scindens which may be important in treatment of disease associated with increased colonic secondary bile acids.",
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