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

作者：Marius Vital, C. Ryan Penton, Qiong Wang, Vincent Bensan Young, Dion Antonopoulos, Mitchell L. Sogin, Hilary G. Morrison, Laura H. Raffals, Eugene B. Chang, Gary B. Huffnagle, Thomas Mitchell Schmidt, James R. Cole, James M. Tiedje · 发表于：Microbiome · 年份：2013 · DOI：10.1186/2049-2618-1-8 · 被引用次数：166 · 研究领域：Gut microbiota and health、Probiotics and Fermented Foods、Antibiotic Resistance in Bacteria

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, ...