Open Access Research

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

Marius Vital1, Christopher R Penton1, Qiong Wang1, Vincent B Young2, Dion A Antonopoulos3, Mitchell L Sogin4, Hilary G Morrison4, Laura Raffals5, Eugene B Chang6, Gary B Huffnagle2, Thomas M Schmidt1, James R Cole1* and James M Tiedje1*

Author Affiliations

1 Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA

2 Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA

3 Argonne National Laboratory, Argonne, IL, USA

4 Marine Biological Laboratory, Woods Hole, MA, USA

5 Knapp Center for Biomedical Discovery, University of Chicago, Chicago, IL, USA

6 Department of Medicine, University of Chicago, Chicago, IL, USA

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Microbiome 2013, 1:8  doi:10.1186/2049-2618-1-8

Published: 4 March 2013

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.

Keywords:
Butyrate; Gene-targeted metagenomics; Human microbiome project; Pouchitis; Ulcerative colitis