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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.

A gene-targeted approach to investigate the intestinal butyrate-producing bacterialcommunity