title: 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.
authors.affiliation: Universität Hamburg, Biozentrum Klein Flottbek, Abteilung für Mikrobiologie & Biotechnologie, Hamburg, Germany.
authors.forename: Nele
authors.initials: N
authors.lastname: Ilmberger
authors.affiliation: Universität Hamburg, Biozentrum Klein Flottbek, Abteilung für Mikrobiologie & Biotechnologie, Hamburg, Germany.
authors.forename: Simon
authors.initials: S
authors.lastname: Güllert
authors.affiliation: Universität Hamburg, Biozentrum Klein Flottbek, Abteilung für Mikrobiologie & Biotechnologie, Hamburg, Germany.
authors.forename: Joana
authors.initials: J
authors.lastname: Dannenberg
authors.affiliation: Universität Hamburg, Biozentrum Klein Flottbek, Abteilung für Mikrobiologie & Biotechnologie, Hamburg, Germany.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Rabausch
authors.affiliation: Universität Hamburg, Biozentrum Klein Flottbek, Abteilung für Mikrobiologie & Biotechnologie, Hamburg, Germany.
authors.forename: Jeremy
authors.initials: J
authors.lastname: Torres
authors.affiliation: Georg-August-University Göttingen, Institute of Microbiology and Genetics, Göttingen, Germany.
authors.forename: Bernd
authors.initials: B
authors.lastname: Wemheuer
authors.affiliation: University Medical Center Hamburg-Eppendorf, Bioinformatics Service Facility, Hamburg, Germany.
authors.forename: Malik
authors.initials: M
authors.lastname: Alawi
authors.affiliation: Georg-August-University Göttingen, Institute of Microbiology and Genetics, Göttingen, Germany.
authors.forename: Anja
authors.initials: A
authors.lastname: Poehlein
authors.affiliation: Universität Hamburg, Biozentrum Klein Flottbek, Abteilung für Mikrobiologie & Biotechnologie, Hamburg, Germany.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Chow
authors.affiliation: University of Vienna, CUBE - Division for Computational Systems Biology, Department of Microbiology and Ecosystem Science, Vienna, Austria.
authors.forename: Dimitrij
authors.initials: D
authors.lastname: Turaev
authors.affiliation: University of Vienna, CUBE - Division for Computational Systems Biology, Department of Microbiology and Ecosystem Science, Vienna, Austria.
authors.forename: Thomas
authors.initials: T
authors.lastname: Rattei
authors.affiliation: Universität Hamburg, Biozentrum Klein Flottbek, Abteilung für Mikrobiologie & Biotechnologie, Hamburg, Germany.
authors.forename: Christel
authors.initials: C
authors.lastname: Schmeisser
authors.affiliation: Novozymes A/S, Microbial Discovery, Bagsværd, Denmark.
authors.forename: Jesper
authors.initials: J
authors.lastname: Salomon
authors.affiliation: Novozymes A/S, Microbial Discovery, Bagsværd, Denmark.
authors.forename: Peter B
authors.initials: PB
authors.lastname: Olsen
authors.affiliation: Georg-August-University Göttingen, Institute of Microbiology and Genetics, Göttingen, Germany.
authors.forename: Rolf
authors.initials: R
authors.lastname: Daniel
authors.affiliation: Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany.
authors.forename: Adam
authors.initials: A
authors.lastname: Grundhoff
authors.affiliation: Novozymes A/S, Microbial Discovery, Bagsværd, Denmark.
authors.forename: Martin S
authors.initials: MS
authors.lastname: Borchert
authors.affiliation: Universität Hamburg, Biozentrum Klein Flottbek, Abteilung für Mikrobiologie & Biotechnologie, Hamburg, Germany.
authors.forename: Wolfgang R
authors.initials: WR
authors.lastname: Streit
mesh_terms: D000818:Animals; D018533:Biomass; D001942:Breast Feeding; D003625:Data Collection; D004606:Elephants / Q000382:microbiology*; D005243:Feces / Q000382:microbiology*; D005260:Female; D006026:Glycoside Hydrolases / Q000235:genetics / Q000378:metabolism*; D008297:Male; D056186:Metagenomics; D064307:Microbiota; D010802:Phylogeny; D010944:Plants
chemical_list: D006026:Glycoside Hydrolases