A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community

Marius Vital, Christopher R. Penton, Qiong Wang, Vincent B. Young, Dion A. Antonopoulos, Mitchell L. Sogin, Hilary G. Morrison, Laura E. H. Raffals, Eugene B. Chang, Gary B. Huffnagle, Thomas M. Schmidt, James R. Cole, James M. Tiedje

Research output: Contribution to journalArticle

62 Citations (Scopus)

Abstract

Background: Butyrate, which is produced by the human microbiome, is essential for a well-functioning colon. Bacteria that produce butyrate are phylogenetically diverse, which hinders their accurate detection based on conventional phylogenetic markers. As a result, reliable information on this important bacterial group is often lacking in microbiome research. Results: In this study we describe a gene-targeted approach for 454 pyrotag sequencing and quantitative polymerase chain reaction for the final genes in the two primary bacterial butyrate synthesis pathways, butyryl-CoA:acetate CoA-transferase (but) and butyrate kinase (buk). We monitored the establishment and early succession of butyrate-producing communities in four patients with ulcerative colitis who underwent a colectomy with ileal pouch anal anastomosis and compared it with three control samples from healthy colons. All patients established an abundant butyrate-producing community (approximately 5% to 26% of the total community) in the pouch within the 2-month study, but patterns were distinctive among individuals. Only one patient harbored a community profile similar to the healthy controls, in which there was a predominance of but genes that are similar to reference genes from Acidaminococcus sp., Eubacterium sp., Faecalibacterium prausnitzii and Roseburia sp., and an almost complete absence of buk genes. Two patients were greatly enriched in buk genes similar to those of Clostridium butyricum and C. perfringens, whereas a fourth patient displayed abundant communities containing both genes. Most butyrate producers identified in previous studies were detected and the general patterns of taxa found were supported by 16S rRNA gene pyrotag analysis, but the gene-targeted approach provided more detail about the potential butyrate-producing members of the community. Conclusions: The presented approach provides quantitative and genotypic insights into butyrate-producing communities and facilitates a more specific functional characterization of the intestinal microbiome. Furthermore, our analysis refines but and buk reference annotations found in central databases.

Original languageEnglish (US)
Article number8
JournalMicrobiome
Volume1
Issue number1
DOIs
StatePublished - Mar 4 2013
Externally publishedYes

Fingerprint

Butyrates
Genes
Microbiota
Acidaminococcus
Colon
Clostridium butyricum
Coenzyme A-Transferases
Eubacterium
Colonic Pouches
Colectomy
Ulcerative Colitis
rRNA Genes
Acetates
Databases
Bacteria
Polymerase Chain Reaction
butyrate kinase
Research

Keywords

  • Butyrate
  • Gene-targeted metagenomics
  • Human microbiome project
  • Pouchitis
  • Ulcerative colitis

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)

Cite this

Vital, M., Penton, C. R., Wang, Q., Young, V. B., Antonopoulos, D. A., Sogin, M. L., ... Tiedje, J. M. (2013). A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community. Microbiome, 1(1), [8]. https://doi.org/10.1186/2049-2618-1-8

A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community. / Vital, Marius; Penton, Christopher R.; Wang, Qiong; Young, Vincent B.; Antonopoulos, Dion A.; Sogin, Mitchell L.; Morrison, Hilary G.; Raffals, Laura E. H.; Chang, Eugene B.; Huffnagle, Gary B.; Schmidt, Thomas M.; Cole, James R.; Tiedje, James M.

In: Microbiome, Vol. 1, No. 1, 8, 04.03.2013.

Research output: Contribution to journalArticle

Vital, M, Penton, CR, Wang, Q, Young, VB, Antonopoulos, DA, Sogin, ML, Morrison, HG, Raffals, LEH, Chang, EB, Huffnagle, GB, Schmidt, TM, Cole, JR & Tiedje, JM 2013, 'A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community', Microbiome, vol. 1, no. 1, 8. https://doi.org/10.1186/2049-2618-1-8
Vital M, Penton CR, Wang Q, Young VB, Antonopoulos DA, Sogin ML et al. A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community. Microbiome. 2013 Mar 4;1(1). 8. https://doi.org/10.1186/2049-2618-1-8
Vital, Marius ; Penton, Christopher R. ; Wang, Qiong ; Young, Vincent B. ; Antonopoulos, Dion A. ; Sogin, Mitchell L. ; Morrison, Hilary G. ; Raffals, Laura E. H. ; Chang, Eugene B. ; Huffnagle, Gary B. ; Schmidt, Thomas M. ; Cole, James R. ; Tiedje, James M. / A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community. In: Microbiome. 2013 ; Vol. 1, No. 1.
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