Simultaneous Amplicon Sequencing to Explore Co-Occurrence Patterns of Bacterial, Archaeal and Eukaryotic Microorganisms in Rumen Microbial Communities

PLoS One

Sandra Kittelmann¹  Henning Seedorf²  William A. Walters²  Jeffrey I. Gordon³  Rob Knight³  Jose C. Clemente⁴  Peter H. Janssen⁵ 

[1] AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand;Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, United States of America;Department of Chemistry and Biochemistry and BioFrontiers Institute, University of Colorado, Boulder, Colorado, United States of America;Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, United States of America;Howard Hughes Medical Institute, Boulder, Colorado, United States of America

关键词: Anaerobic bacteria;    Archaea;    Bacteria;    Protozoans;    Ribosomal RNA;    Fungi;    Sequence databases;    Methanogens;   

DOI  :  10.1371/journal.pone.0047879

学科分类：医学（综合）

来源: Public Library of Science

【 摘 要 】

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.

【 授权许可】

CC BY