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

普氏粪杆菌 丁酸盐 生物 蔷薇花 真细菌 基因 微生物群 微生物学 丁酸梭菌 遗传学 细菌 乳酸菌 粪便 生物化学 发酵
作者
Marius Vital,C. Ryan Penton,Qiong Wang,Vincent B. Young,Dion Antonopoulos,Mitchell L. Sogin,Hilary G. Morrison,Laura H. Raffals,Eugene B. Chang,Gary B. Huffnagle,Thomas M. Schmidt,James R. Cole,James M. Tiedje
出处
期刊:Microbiome [BioMed Central]
卷期号:1 (1) 被引量:142
标识
DOI:10.1186/2049-2618-1-8
摘要

Abstract Background Butyrate, which is produced by the human microbiome, is essential for awell-functioning colon. Bacteria that produce butyrate are phylogeneticallydiverse, which hinders their accurate detection based on conventional phylogeneticmarkers. As a result, reliable information on this important bacterial group isoften lacking in microbiome research. Results In this study we describe a gene-targeted approach for 454 pyrotag sequencing andquantitative polymerase chain reaction for the final genes in the two primarybacterial butyrate synthesis pathways, butyryl-CoA:acetate CoA-transferase( but ) and butyrate kinase ( buk ). We monitored theestablishment and early succession of butyrate-producing communities in fourpatients with ulcerative colitis who underwent a colectomy with ileal pouch analanastomosis and compared it with three control samples from healthy colons. Allpatients established an abundant butyrate-producing community (approximately 5% to26% of the total community) in the pouch within the 2-month study, but patternswere distinctive among individuals. Only one patient harbored a community profilesimilar 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 fourthpatient displayed abundant communities containing both genes. Most butyrateproducers identified in previous studies were detected and the general patterns oftaxa found were supported by 16S rRNA gene pyrotag analysis, but thegene-targeted approach provided more detail about the potential butyrate-producingmembers of the community. Conclusions The presented approach provides quantitative and genotypic insights intobutyrate-producing communities and facilitates a more specific functionalcharacterization of the intestinal microbiome. Furthermore, our analysis refines but and buk reference annotations found in centraldatabases.
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