Gene-targeted metagenomic analysis of 1-4-α-glucan branching enzyme gene profiles among human and animal fecal microbiota

Organismal and functional aspects of the gut microbiota are of great interest in human microbiome studies. Although 16S rRNA gene sequence-based phylogenetic and whole-genome shotgun (WGS) data analysis are frequently used for assessment of genetic diversity, these techniques pose biological challenges for in-depth understanding of metabolic genes related to the gut microbiota. Phylogenetic analyses of 16S rRNA gene sequences provide limited information on their involvement in metabolic pathways. WGS data provide useful information on metabolic functions; however, this technique generates a large amount of data unrelated to the gene of interest at a high cost. In this study, we employed a metagenomic approach targeting the 1-4-α-glucan branching enzyme (gBE) gene of four host species (chicken, cow, pig, and human). Glycoside hydrolases (GHs) are key enzymes associated with the gut microbiota and its metabolic functions. The gBE gene, belonging to GH family 13, is responsible for glycogen branching and determines its solubility and subsequent catabolic metabolism. In addition to 16S rRNA gene-based phylogenetic analyses, an average of 1,200 reads of gBE were generated from fecal microbiota samples from human (n = 16), chicken (n = 18), cow (n = 15) and pig (n = 20). Each of the hosts showed distinct 16S rRNA and gBE sequence profiles. Human and pig exhibited both unique and common characteristics of operational taxonomic units (OTUs) and gBE profiles. Interestingly, the OTUs identified from the 16S rRNA and gBE gene sequences differed among the host species, suggesting the presence of different gBE genes in the same OTU in 16S rRNA sequences of 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. Moreover, specific OTUs in the gut may contain metabolic genes the characteristics of which differ according to host genetic background and/or diet.