Abstract
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it contains a set of 2,379 almost full-length chimera-checked 16S rRNA gene sequences, including 20 previously unpublished sequences from isolates from three different orders.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.
Highlights
Ruminants such as sheep and cattle are among the most numerous farmed animals, and enteric methane formation in their rumens contributes substantially to global greenhouse gas emissions (Yusuf et al, 2012), as well as being a conversion of part ofHow to cite this article Seedorf et al (2014), Rumen and Intestinal Methanogen Database (RIM-DB): a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments
We wanted to develop a taxonomic framework for rumen methanogens and methanogens residing in other intestinal habitats based on long (>1,200 bp) 16S rRNA gene sequences that resolves taxonomic groups that are currently unresolved by taxonomies such as Greengenes or SILVA
Within the Methanobacteriales, the genera Methanobrevibacter and Methanosphaera have primarily been detected in the rumen; and both genera contain species that have been found in a variety of other intestinal environments
Summary
Ruminants such as sheep and cattle are among the most numerous farmed animals, and enteric methane formation in their rumens contributes substantially to global greenhouse gas emissions (Yusuf et al, 2012), as well as being a conversion of part ofHow to cite this article Seedorf et al (2014), RIM-DB: a taxonomic framework for community structure analysis of methanogenic archaea from the rumen and other intestinal environments. Formate, and methyl-compounds that are among the products formed during the degradation and fermentation of ingested feed through the combined activities of bacteria, fungi, and protozoa. To mitigate emissions of methane from ruminants into the atmosphere, interventions are being developed to reduce the number or activity of methanogenic organisms in the rumen (Buddle et al, 2011). Tools based on DNA markers (Kittelmann et al, 2013) are being used to monitor the effects of experimental interventions or to uncover differences in microbial community structures in animals with different productivity traits, such as differences in feed conversion efficiency (Carberry et al, 2014; Zhou, Hernandez-Sanabria & Guan, 2009; Zhou, Hernandez-Sanabria & Guan, 2010). The accurate identification and classification of rumen methanogens is an important step, whether to identify target methanogens, for subsequent community analysis during the development and testing of mitigation technologies, or to uncover details of rumen community differences in animals with different production characteristics
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