TY - JOUR
T1 - Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities
AU - Kittelmann, Sandra
AU - Seedorf, Henning
AU - Walters, William A.
AU - Clemente, Jose C.
AU - Knight, Rob
AU - Gordon, Jeffrey I.
AU - Janssen, Peter H.
N1 - Funding Information:
Two of the authors are from AgResearch Ltd., which is a Crown Research Institute, and is funded by the Pastoral Greenhouse Gas Research Consortium (PGgRc) to develop means of mitigating ruminant methane emissions. PGgRc's members are AgResearch, Fonterra, Fert Research, PGG Wrightson, DairyNZ, Deer Research, Beef+Lamb New Zealand, Landcorp, NIWA, the Ministry for Primary Industries, and the Ministry of Science and Innovation (formerly Foundation for Research, Science and Technology). The publication of the data reported here is at the discretion of the PGgRc. The PGgRc did not control which data were presented or how these data were interpreted within this paper. This does not alter the authors' adherence to all the PLOS ONE policies on sharing data and materials. The other authors have declared that no competing interests exist. There are no patents, products in development or marketed products to declare.
PY - 2013/2/8
Y1 - 2013/2/8
N2 - Ruminants rely on a complex rumen microbial community to convert dietary plant material to energy-yielding products. Here we developed a method to simultaneously analyze the community's bacterial and archaeal 16S rRNA genes, ciliate 18S rRNA genes and anaerobic fungal internal transcribed spacer 1 genes using 12 DNA samples derived from 11 different rumen samples from three host species (Ovis aries, Bos taurus, Cervus elephas) and multiplex 454 Titanium pyrosequencing. We show that the mixing ratio of the group-specific DNA templates before emulsion PCR is crucial to compensate for differences in amplicon length. This method, in contrast to using a non-specific universal primer pair, avoids sequencing non-targeted DNA, such as plant- or endophyte-derived rRNA genes, and allows increased or decreased levels of community structure resolution for each microbial group as needed. Communities analyzed with different primers always grouped by sample origin rather than by the primers used. However, primer choice had a greater impact on apparent archaeal community structure than on bacterial community structure, and biases for certain methanogen groups were detected. Co-occurrence analysis of microbial taxa from all three domains of life suggested strong within- and between-domain correlations between different groups of microorganisms within the rumen. The approach used to simultaneously characterize bacterial, archaeal and eukaryotic components of a microbiota should be applicable to other communities occupying diverse habitats.
AB - Ruminants rely on a complex rumen microbial community to convert dietary plant material to energy-yielding products. Here we developed a method to simultaneously analyze the community's bacterial and archaeal 16S rRNA genes, ciliate 18S rRNA genes and anaerobic fungal internal transcribed spacer 1 genes using 12 DNA samples derived from 11 different rumen samples from three host species (Ovis aries, Bos taurus, Cervus elephas) and multiplex 454 Titanium pyrosequencing. We show that the mixing ratio of the group-specific DNA templates before emulsion PCR is crucial to compensate for differences in amplicon length. This method, in contrast to using a non-specific universal primer pair, avoids sequencing non-targeted DNA, such as plant- or endophyte-derived rRNA genes, and allows increased or decreased levels of community structure resolution for each microbial group as needed. Communities analyzed with different primers always grouped by sample origin rather than by the primers used. However, primer choice had a greater impact on apparent archaeal community structure than on bacterial community structure, and biases for certain methanogen groups were detected. Co-occurrence analysis of microbial taxa from all three domains of life suggested strong within- and between-domain correlations between different groups of microorganisms within the rumen. The approach used to simultaneously characterize bacterial, archaeal and eukaryotic components of a microbiota should be applicable to other communities occupying diverse habitats.
UR - http://www.scopus.com/inward/record.url?scp=84873684861&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0047879
DO - 10.1371/journal.pone.0047879
M3 - Article
C2 - 23408926
AN - SCOPUS:84873684861
SN - 1932-6203
VL - 8
JO - PLoS ONE
JF - PLoS ONE
IS - 2
M1 - e47879
ER -