Open AccessDesign and in vitro evaluation of new rpo B‐DGGE primers for ruminants
Author(s) -
Perumbakkam Sudeep,
Craig A. Morrie
Publication year - 2011
Publication title -
fems microbiology ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.377
H-Index - 155
eISSN - 1574-6941
pISSN - 0168-6496
DOI - 10.1111/j.1574-6941.2011.01042.x
Subject(s) - rpob , biology , rumen , 16s ribosomal rna , phylum , primer (cosmetics) , population , microbiology and biotechnology , bacteria , genetics , food science , fermentation , chemistry , demography , organic chemistry , sociology
Two new primer sets based on the rpo B gene were designed and evaluated with bovine and ovine rumen samples. The newly developed rpo B‐DGGE primer set was used along with the 16S rRNA gene‐V3, and another (old) rpo B‐DGGE‐based primer set from a previous study to in vitro compare the bovine and ovine rumen ecosystems. The results indicate a significant ( P <0.001) difference in the microbial population between the two ruminants irrespective of the primers used in the analysis. Qualitative comparison of the data provides evidence for the presence of similar phyla profiles between the 16S rRNA gene and the newly developed rpo B primers. A comparison between the two rpo B‐based primer sets (old and new) showed that the old rpo B‐based primers failed to amplify phylum Bacteroidetes (a common phylum in the rumen) in both bovine and ovine rumen samples. The old and new rpo B‐DGGE‐based primers amplified a large number of clones belonging to phylum Proteobacteria , providing a useful insight into the microbial structure of the rumen. ChaoI, ACE, Simpson, and Shannon–Weaver index analysis estimated the bovine rumen to be more diverse than the ovine rumen for all three primer sets. These results provide a new insight into the community structure among ruminants using the newly developed primers in this study.