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

Vital M, Penton CR, Wang Q, Young VB, Antonopoulos DA, Sogin ML, Morrison HG, Raffals L, Chang EB, Huffnagle GB, Schmidt TM, Cole JR, Tiedje JM - Microbiome (2013)

Bottom Line: As a result, reliable information on this important bacterial group is often lacking in microbiome research.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.Furthermore, our analysis refines but and buk reference annotations found in central databases.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA. colej@msu.edu.

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.

No MeSH data available.


Related in: MedlinePlus

Nonmetric multidimensional scaling analysis of the total butyrate-producingcommunity - butyryl-CoA:acetate CoA-transferase (but)and butyrate kinase (buk) genes together - based onindividual patients. For explanation see text. Ellipses represent the95% confidence interval on standard errors of means. Shepard plot forclustering is shown in Additional file 1: FigureS7.
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Figure 3: Nonmetric multidimensional scaling analysis of the total butyrate-producingcommunity - butyryl-CoA:acetate CoA-transferase (but)and butyrate kinase (buk) genes together - based onindividual patients. For explanation see text. Ellipses represent the95% confidence interval on standard errors of means. Shepard plot forclustering is shown in Additional file 1: FigureS7.

Mentions: Nonmetric multidimensional scaling analysis of the total butyrate-producing community(but and buk genes together) revealed a unique community patternfor individual patients, which all clustered distinct from the healthy controlsamples (Figure 3). However, the successional trend wasdifferent for all patients (Additional file 1: Figure S8).Diversity calculations also did not reveal a consistent successional pattern. WhereasShannon diversity increased for patients 200 and 206, no change was detected for 207,and 210 demonstrated a decrease over time (Figure 4). Atthe fourth visit, all communities analyzed displayed a comparable diversity value,which was similar to that of the healthy control samples.


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

Vital M, Penton CR, Wang Q, Young VB, Antonopoulos DA, Sogin ML, Morrison HG, Raffals L, Chang EB, Huffnagle GB, Schmidt TM, Cole JR, Tiedje JM - Microbiome (2013)

Nonmetric multidimensional scaling analysis of the total butyrate-producingcommunity - butyryl-CoA:acetate CoA-transferase (but)and butyrate kinase (buk) genes together - based onindividual patients. For explanation see text. Ellipses represent the95% confidence interval on standard errors of means. Shepard plot forclustering is shown in Additional file 1: FigureS7.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4126176&req=5

Figure 3: Nonmetric multidimensional scaling analysis of the total butyrate-producingcommunity - butyryl-CoA:acetate CoA-transferase (but)and butyrate kinase (buk) genes together - based onindividual patients. For explanation see text. Ellipses represent the95% confidence interval on standard errors of means. Shepard plot forclustering is shown in Additional file 1: FigureS7.
Mentions: Nonmetric multidimensional scaling analysis of the total butyrate-producing community(but and buk genes together) revealed a unique community patternfor individual patients, which all clustered distinct from the healthy controlsamples (Figure 3). However, the successional trend wasdifferent for all patients (Additional file 1: Figure S8).Diversity calculations also did not reveal a consistent successional pattern. WhereasShannon diversity increased for patients 200 and 206, no change was detected for 207,and 210 demonstrated a decrease over time (Figure 4). Atthe fourth visit, all communities analyzed displayed a comparable diversity value,which was similar to that of the healthy control samples.

Bottom Line: As a result, reliable information on this important bacterial group is often lacking in microbiome research.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.Furthermore, our analysis refines but and buk reference annotations found in central databases.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Microbial Ecology, Michigan State University, East Lansing, MI, USA. colej@msu.edu.

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.

No MeSH data available.


Related in: MedlinePlus