RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments

Methane is formed by methanogenic archaea in the rumen as one of the end products of feed fermentation in the ruminant digestive tract. To develop strategies to mitigate anthropogenic methane emissions due to ruminant farming, and to understand rumen microbial differences in animal feed conversion e...

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Main Authors: Henning Seedorf, Sandra Kittelmann, Gemma Henderson, Peter H. Janssen
Format: Article
Language:English
Published: PeerJ Inc. 2014-08-01
Series:PeerJ
Subjects:
Online Access:https://peerj.com/articles/494.pdf
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spelling doaj-7b6fc212107d40fdb7a3cb2bde6a41c02020-11-24T22:18:59ZengPeerJ Inc.PeerJ2167-83592014-08-012e49410.7717/peerj.494494RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environmentsHenning Seedorf0Sandra Kittelmann1Gemma Henderson2Peter H. Janssen3AgResearch, Grasslands Research Centre, Palmerston North, New ZealandAgResearch, Grasslands Research Centre, Palmerston North, New ZealandAgResearch, Grasslands Research Centre, Palmerston North, New ZealandAgResearch, Grasslands Research Centre, Palmerston North, New ZealandMethane is formed by methanogenic archaea in the rumen as one of the end products of feed fermentation in the ruminant digestive tract. To develop strategies to mitigate anthropogenic methane emissions due to ruminant farming, and to understand rumen microbial differences in animal feed conversion efficiency, it is essential that methanogens can be identified and taxonomically classified with high accuracy. Currently available taxonomic frameworks offer only limited resolution beyond the genus level for taxonomic assignments of sequence data stemming from high throughput sequencing technologies. Therefore, we have developed a QIIME-compatible database (DB) designed for species-level taxonomic assignment of 16S rRNA gene amplicon data targeting methanogenic archaea from the rumen, and from animal and human intestinal tracts. Called RIM-DB (Rumen and Intestinal Methanogen-DB), it contains a set of 2,379 almost full-length chimera-checked 16S rRNA gene sequences, including 20 previously unpublished sequences from isolates from three different orders. The taxonomy encompasses the recently-proposed seventh order of methanogens, the Methanomassiliicoccales, and allows differentiation between defined groups within this order. Sequence reads from rumen contents from a range of ruminant-diet combinations were taxonomically assigned using RIM-DB, Greengenes and SILVA. This comparison clearly showed that taxonomic assignments with RIM-DB resulted in the most detailed assignment, and only RIM-DB taxonomic assignments allowed methanogens to be distinguished taxonomically at the species level. RIM-DB complements the use of comprehensive databases such as Greengenes and SILVA for community structure analysis of methanogens from the rumen and other intestinal environments, and allows identification of target species for methane mitigation strategies.https://peerj.com/articles/494.pdfMethanogenArchaeaTaxonomyRumenIntestinal microbiotaReference database
collection DOAJ
language English
format Article
sources DOAJ
author Henning Seedorf
Sandra Kittelmann
Gemma Henderson
Peter H. Janssen
spellingShingle Henning Seedorf
Sandra Kittelmann
Gemma Henderson
Peter H. Janssen
RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments
PeerJ
Methanogen
Archaea
Taxonomy
Rumen
Intestinal microbiota
Reference database
author_facet Henning Seedorf
Sandra Kittelmann
Gemma Henderson
Peter H. Janssen
author_sort Henning Seedorf
title RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments
title_short RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments
title_full RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments
title_fullStr RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments
title_full_unstemmed RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments
title_sort rim-db: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments
publisher PeerJ Inc.
series PeerJ
issn 2167-8359
publishDate 2014-08-01
description Methane is formed by methanogenic archaea in the rumen as one of the end products of feed fermentation in the ruminant digestive tract. To develop strategies to mitigate anthropogenic methane emissions due to ruminant farming, and to understand rumen microbial differences in animal feed conversion efficiency, it is essential that methanogens can be identified and taxonomically classified with high accuracy. Currently available taxonomic frameworks offer only limited resolution beyond the genus level for taxonomic assignments of sequence data stemming from high throughput sequencing technologies. Therefore, we have developed a QIIME-compatible database (DB) designed for species-level taxonomic assignment of 16S rRNA gene amplicon data targeting methanogenic archaea from the rumen, and from animal and human intestinal tracts. Called RIM-DB (Rumen and Intestinal Methanogen-DB), it contains a set of 2,379 almost full-length chimera-checked 16S rRNA gene sequences, including 20 previously unpublished sequences from isolates from three different orders. The taxonomy encompasses the recently-proposed seventh order of methanogens, the Methanomassiliicoccales, and allows differentiation between defined groups within this order. Sequence reads from rumen contents from a range of ruminant-diet combinations were taxonomically assigned using RIM-DB, Greengenes and SILVA. This comparison clearly showed that taxonomic assignments with RIM-DB resulted in the most detailed assignment, and only RIM-DB taxonomic assignments allowed methanogens to be distinguished taxonomically at the species level. RIM-DB complements the use of comprehensive databases such as Greengenes and SILVA for community structure analysis of methanogens from the rumen and other intestinal environments, and allows identification of target species for methane mitigation strategies.
topic Methanogen
Archaea
Taxonomy
Rumen
Intestinal microbiota
Reference database
url https://peerj.com/articles/494.pdf
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