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

Journal Article · · Microbiome
 [1];  [2];  [2];  [2];  [3];  [4];  [4];  [5];  [5];  [6];  [2];  [2];  [2]
  1. Michigan State University, East Lansing, MI (United States); DOE/OSTI
  2. Michigan State University, East Lansing, MI (United States)
  3. Argonne National Laboratory (ANL), Argonne, IL (United States)
  4. Marine Biological Laboratory, Woods Hole, MA (United States)
  5. University of Chicago, IL (United States)
  6. University of Michigan, Ann Arbor, MI (United States)
+ Show Author Affiliations
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. 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. 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.
Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Organization:
National Institutes of Health (NIH); USDOE Office of Science (SC), Biological and Environmental Research (BER); University of Chicago
Grant/Contract Number:
AC02-06CH11357
OSTI ID:
1626686
Journal Information:
Microbiome, Journal Name: Microbiome Journal Issue: 1 Vol. 1; ISSN 2049-2618
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English

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Interleukin-15 promotes intestinal dysbiosis with butyrate deficiency associated with increased susceptibility to colitis journal September 2016
Anti-diabetic Effects of Clostridium butyricum CGMCC0313.1 through Promoting the Growth of Gut Butyrate-producing Bacteria in Type 2 Diabetic Mice journal August 2017
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Systemic availability and metabolism of colonic-derived short-chain fatty acids in healthy subjects: a stable isotope study: Short-chain fatty acid systemic availability and metabolism in humans journal September 2016
Ecological Patterns of nifH Genes in Four Terrestrial Climatic Zones Explored with Targeted Metagenomics Using FrameBot, a New Informatics Tool journal September 2013
The microbial basis of inflammatory bowel diseases journal August 2014
The response of canine faecal microbiota to increased dietary protein is influenced by body condition journal December 2017
Mechanisms Linking the Gut Microbiome and Glucose Metabolism journal April 2016
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Intestinal Metagenomes and Metabolomes in Healthy Young Males: Inactivity and Hypoxia Generated Negative Physiological Symptoms Precede Microbial Dysbiosis journal March 2018
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59 BASIC BIOLOGICAL SCIENCES
butyrate
gene-targeted metagenomics
human microbiome project
pouchitis
ulcerative colitis