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
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...
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| Veröffentlicht in: | PloS one 2014-09, Vol.9 (9), p.e106707-e106707 |
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| creator | Ilmberger, Nele Güllert, Simon Dannenberg, Joana Rabausch, Ulrich Torres, Jeremy Wemheuer, Bernd Alawi, Malik Poehlein, Anja Chow, Jennifer Turaev, Dimitrij Rattei, Thomas Schmeisser, Christel Salomon, Jesper Olsen, Peter B Daniel, Rolf Grundhoff, Adam Borchert, Martin S Streit, Wolfgang R |
| description | 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. |
| doi_str_mv | 10.1371/journal.pone.0106707 |
| format | Article |
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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.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0106707</identifier><identifier>PMID: 25208077</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Animals ; Aromatic compounds ; Bacteroidetes ; Biodegradation ; Biodiversity ; Bioinformatics ; Biology ; Biology and life sciences ; Biomass ; Breast Feeding ; Cellulase ; Cellulose ; Data Collection ; Deoxyribonucleic acid ; DNA ; Ecosystem biology ; Ecosystems ; Elephants ; Elephants - microbiology ; Elephas maximus ; Enzymes ; Fecal microflora ; Feces ; Feces - microbiology ; Female ; Fermentation ; Firmicutes ; Fruits ; Genes ; Genetics ; Genomes ; Glycoside hydrolase ; Glycoside Hydrolases - genetics ; Glycoside Hydrolases - metabolism ; Growth hormone ; Herbivores ; Hydrolase ; Male ; Metagenomics ; Microbiota ; Microorganisms ; Phylogeny ; Physiology ; Plants ; Polymers ; Polysaccharides ; Proteobacteria ; rRNA 16S ; Sequences ; Transfer RNA</subject><ispartof>PloS one, 2014-09, Vol.9 (9), p.e106707-e106707</ispartof><rights>2014 Ilmberger et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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Altogether, this study delivers insight into the biomass conversion by one of the largest plant-fed and land-living animals.</description><subject>Animals</subject><subject>Aromatic compounds</subject><subject>Bacteroidetes</subject><subject>Biodegradation</subject><subject>Biodiversity</subject><subject>Bioinformatics</subject><subject>Biology</subject><subject>Biology and life sciences</subject><subject>Biomass</subject><subject>Breast Feeding</subject><subject>Cellulase</subject><subject>Cellulose</subject><subject>Data Collection</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Ecosystem biology</subject><subject>Ecosystems</subject><subject>Elephants</subject><subject>Elephants - microbiology</subject><subject>Elephas maximus</subject><subject>Enzymes</subject><subject>Fecal microflora</subject><subject>Feces</subject><subject>Feces - 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Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ilmberger, Nele</au><au>Güllert, Simon</au><au>Dannenberg, Joana</au><au>Rabausch, Ulrich</au><au>Torres, Jeremy</au><au>Wemheuer, Bernd</au><au>Alawi, Malik</au><au>Poehlein, Anja</au><au>Chow, Jennifer</au><au>Turaev, Dimitrij</au><au>Rattei, Thomas</au><au>Schmeisser, Christel</au><au>Salomon, Jesper</au><au>Olsen, Peter B</au><au>Daniel, Rolf</au><au>Grundhoff, Adam</au><au>Borchert, Martin S</au><au>Streit, Wolfgang R</au><au>Bereswill, Stefan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>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</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2014-09-10</date><risdate>2014</risdate><volume>9</volume><issue>9</issue><spage>e106707</spage><epage>e106707</epage><pages>e106707-e106707</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><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.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>25208077</pmid><doi>10.1371/journal.pone.0106707</doi><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2014-09, Vol.9 (9), p.e106707-e106707 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1561282730 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Public Library of Science (PLoS) Journals Open Access; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Animals Aromatic compounds Bacteroidetes Biodegradation Biodiversity Bioinformatics Biology Biology and life sciences Biomass Breast Feeding Cellulase Cellulose Data Collection Deoxyribonucleic acid DNA Ecosystem biology Ecosystems Elephants Elephants - microbiology Elephas maximus Enzymes Fecal microflora Feces Feces - microbiology Female Fermentation Firmicutes Fruits Genes Genetics Genomes Glycoside hydrolase Glycoside Hydrolases - genetics Glycoside Hydrolases - metabolism Growth hormone Herbivores Hydrolase Male Metagenomics Microbiota Microorganisms Phylogeny Physiology Plants Polymers Polysaccharides Proteobacteria rRNA 16S Sequences Transfer RNA |
| 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 |
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