A comparative metagenome survey of the fecal microbiota of a breast- and a plant-fed Asian elephant reveals an unexpectedly high diversity of glycoside hydrolase family enzymes

PLoS One. 2014 Sep 10;9(9):e106707. doi: 10.1371/journal.pone.0106707. eCollection 2014.

Abstract

A phylogenetic and metagenomic study of elephant feces samples (derived from a three-weeks-old and a six-years-old Asian elephant) was conducted in order to describe the microbiota inhabiting this large land-living animal. The microbial diversity was examined via 16S rRNA gene analysis. We generated more than 44,000 GS-FLX+454 reads for each animal. For the baby elephant, 380 operational taxonomic units (OTUs) were identified at 97% sequence identity level; in the six-years-old animal, close to 3,000 OTUs were identified, suggesting high microbial diversity in the older animal. In both animals most OTUs belonged to Bacteroidetes and Firmicutes. Additionally, for the baby elephant a high number of Proteobacteria was detected. A metagenomic sequencing approach using Illumina technology resulted in the generation of 1.1 Gbp assembled DNA in contigs with a maximum size of 0.6 Mbp. A KEGG pathway analysis suggested high metabolic diversity regarding the use of polymers and aromatic and non-aromatic compounds. In line with the high phylogenetic diversity, a surprising and not previously described biodiversity of glycoside hydrolase (GH) genes was found. Enzymes of 84 GH families were detected. Polysaccharide utilization loci (PULs), which are found in Bacteroidetes, were highly abundant in the dataset; some of these comprised cellulase genes. Furthermore the highest coverage for GH5 and GH9 family enzymes was detected for Bacteroidetes, suggesting that bacteria of this phylum are mainly responsible for the degradation of cellulose in the Asian elephant. Altogether, this study delivers insight into the biomass conversion by one of the largest plant-fed and land-living animals.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Biomass
  • Breast Feeding*
  • Data Collection
  • Elephants / microbiology*
  • Feces / microbiology*
  • Female
  • Glycoside Hydrolases / genetics
  • Glycoside Hydrolases / metabolism*
  • Male
  • Metagenomics*
  • Microbiota*
  • Phylogeny
  • Plants*

Substances

  • Glycoside Hydrolases

Associated data

  • BioProject/PRJNA240141
  • SRA/SRP040073

Grants and funding

This work was in part funded by the ministry of education and research “Bundesministerium für Bildung und Forschung” (BMBF; http://www.bmbf.de/) within the network program ExpresSys and the grant FKZ 0315586F to WRS. JT was funded by the German Academic Exchange program (DAAD; https://www.daad.de/de/index.html). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.