Metagenomic analysis of the fecal microbiome of an adult elephant reveals the diversity of CAZymes related to lignocellulosic biomass degradation

The resident microbial population responsible for lignocellulosic biomass assimilation in the gastrointestinal tract of animals is a rich source for discovering novel biocatalysts finding application in the production of value-added commodities. Herbivorous animals, such as elephants, consume a variety of lignocellulosic materials in bulk amounts to support their high energy requirements. Since the interdependence of host diet and its microbiome is well established, it is necessary to explore the potential resident microbes of obligate herbivores like elephants belonging to different age classes and habitats for mining enzymes involved in complex biomass deconstruction. In the present study, metagenomic analysis of an adult elephant fecal sample using whole-genome shotgun library preparation indicated the dominant representation of microbes belonging to the phylum Proteobacteria. Subsystem- and KEGG-based analyses revealed a high potential for carbohydrate metabolism and membrane transport. CAZy database analysis identified similar to 55,000 ORFs that had either catalytic domains or carbohydrate-binding modules (CBMs) in the metagenomic data set. Moreover, CBMs and carbohydrate-active enzymes (CAZymes), such as glycoside hydrolases (GHs), glycosyltransferases (GTs), carbohydrate esterases (CEs) were most abundant in microbes of phylum Proteobacieria, and among them, the majority of GHs and GTs were from Bacillus subtilis and Escherichia coli. A comparative GH analysis with other gut metagenomic datasets of herbivorous animals revealed the presence of several unique GHs of the beta-glucosidase, endoglucanase, and exoglucanase families thus providing a comprehensive understanding of the diverse CAZymes present in the gut microbiome of an adult elephant.