TY - JOUR
T1 - Gene-targeted metagenomic analysis of glucan-branching enzyme gene profiles among human and animal fecal microbiota
AU - Lee, Sunghee
AU - Cantarel, Brandi
AU - Henrissat, Bernard
AU - Gevers, Dirk
AU - Birren, Bruce W.
AU - Huttenhower, Curtis
AU - Ko, Gwangpyo
N1 - Funding Information:
This work was supported by the National Institutes of Health grant R01HG005969 (CH) and by the National
Funding Information:
Research Foundation of Korea (NRF) grant funded by the Korean government (MEST) 2010-0029113 (SL and GK).
PY - 2014/3
Y1 - 2014/3
N2 - Glycoside hydrolases (GHs), the enzymes that breakdown complex carbohydrates, are a highly diversified class of key enzymes associated with the gut microbiota and its metabolic functions. To learn more about the diversity of GHs and their potential role in a variety of gut microbiomes, we used a combination of 16S, metagenomic and targeted amplicon sequencing data to study one of these enzyme families in detail. Specifically, we employed a functional gene-targeted metagenomic approach to the 1-4-α-glucan-branching enzyme (gBE) gene in the gut microbiomes of four host species (human, chicken, cow and pig). The characteristics of operational taxonomic units (OTUs) and operational glucan-branching units (OGBUs) were distinctive in each of hosts. Human and pig were most similar in OTUs profiles while maintaining distinct OGBU profiles. Interestingly, the phylogenetic profiles identified from 16S and gBE gene sequences differed, suggesting the presence of different gBE genes in the same OTU across different vertebrate hosts. Our data suggest that gene-targeted metagenomic analysis is useful for an in-depth understanding of the diversity of a particular gene of interest. Specific carbohydrate metabolic genes appear to be carried by distinct OTUs in different individual hosts and among different vertebrate species' microbiomes, the characteristics of which differ according to host genetic background and/or diet.
AB - Glycoside hydrolases (GHs), the enzymes that breakdown complex carbohydrates, are a highly diversified class of key enzymes associated with the gut microbiota and its metabolic functions. To learn more about the diversity of GHs and their potential role in a variety of gut microbiomes, we used a combination of 16S, metagenomic and targeted amplicon sequencing data to study one of these enzyme families in detail. Specifically, we employed a functional gene-targeted metagenomic approach to the 1-4-α-glucan-branching enzyme (gBE) gene in the gut microbiomes of four host species (human, chicken, cow and pig). The characteristics of operational taxonomic units (OTUs) and operational glucan-branching units (OGBUs) were distinctive in each of hosts. Human and pig were most similar in OTUs profiles while maintaining distinct OGBU profiles. Interestingly, the phylogenetic profiles identified from 16S and gBE gene sequences differed, suggesting the presence of different gBE genes in the same OTU across different vertebrate hosts. Our data suggest that gene-targeted metagenomic analysis is useful for an in-depth understanding of the diversity of a particular gene of interest. Specific carbohydrate metabolic genes appear to be carried by distinct OTUs in different individual hosts and among different vertebrate species' microbiomes, the characteristics of which differ according to host genetic background and/or diet.
KW - 1-4-α-glucan-branching enzyme (gBE) gene
KW - carbohydrate metabolism
KW - gene-targeted metagenomics
KW - glycoside hydrolase family 13
KW - gut microbiota
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U2 - 10.1038/ismej.2013.167
DO - 10.1038/ismej.2013.167
M3 - Article
C2 - 24108330
AN - SCOPUS:84894298679
SN - 1751-7362
VL - 8
SP - 493
EP - 503
JO - ISME Journal
JF - ISME Journal
IS - 3
ER -