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

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.

Lignocellulose-Adapted Endo-Cellulase Producing Streptomyces Strains for Bioconversion of Cellulose-Based Materials

“…An enormous range of different habitats (Amore et al, 2013a) such as soil, compost, decaying plant materials (Zhang et al, 2006; Amore et al, 2013b), rumens (Dai et al, 2012), sewage sludge (Singh et al, 2011), termite guts (Warnecke et al, 2007), forest waste (Ventorino et al, 2013, 2016b), and wood processing plants (Dawkins and Esiobu, 2016), animal feces (Ilmberger et al, 2014), paper mills, and hot springs (López-López et al, 2013) have been so far investigated as sources of both aerobic and anaerobic bacteria producing several different enzymes of industrial interest. In particular, lignocellulosic biomass represents complex ecosystems in which environmental conditions influence living organisms.…”

Fibrobacter communities in the gastrointestinal tracts of diverse hindgut‐fermenting herbivores are distinct from those of the rumen

“…Since their original isolation from the rumen, cultureindependent studies have suggested the presence of Fibrobacter populations in diverse herbivore gastrointestinal tracts (Lin and Stahl, 1995;Matsui et al, 2010;Ilmberger et al, 2014). However, cultured representatives from most of these hosts are rare, and as a result, our understanding of their physiology is limited.…”

Recombinant RNA Polymerase from Geobacillus sp. GHH01 as tool for rapid generation of metagenomic RNAs using in vitro technologies

“…GHH01 were employed. Accordingly, metagenomic DNAs from elephant feces (Ilmberger et al, ), a biogas reactor (Güllert et al, ), and a microalgae culture (Krohn‐Molt et al, ) as well as gDNAs from E. coli , Bacillus subtilis , Propionibacterium acidipropionici , Paenibacillus sp., and Picrophilus torridus were used as templates for further transcription assays. A commercial E. coli RNAP holoenzyme from New England Biolabs was used according to manufacturer's recommendations to compare transcription profiles.…”