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Development of a phylogenetic microarray for comprehensive analysis of ruminal bacterial communities
Author(s) -
Kim M.,
Wang L.,
Morrison M.,
Yu Z.
Publication year - 2014
Publication title -
journal of applied microbiology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.889
H-Index - 156
eISSN - 1365-2672
pISSN - 1364-5072
DOI - 10.1111/jam.12598
Subject(s) - rumen , biology , 16s ribosomal rna , bacteria , phylogenetic tree , ruminant , microarray , operational taxonomic unit , metagenomics , gene , microbiology and biotechnology , genetics , food science , gene expression , ecology , fermentation , crop
Aims The aim of the study was to develop a microarray dedicated to comprehensive analysis of the diverse rumen bacteria. Methods and Results All the 16S r RNA gene ( rrs ) sequences of rumen origin were retrieved from the RDP database, and operational taxonomic units (OTUs) were calculated at 97% sequence similarity. A total of 1666 OTU‐specific probes were designed and synthesized on microarray slides (referred to as RumenBactArray) in a 6 × 5 k format with each probe being represented in triplicate. The specificity, sensitivity and linear range of detection were determined using pools of rrs clones of known sequences. The RumenBactArray detected as few as approx. 10 6 copies of a target and had a linear detection range of >4 orders of magnitude. The utility of the RumenBactArray was tested using fractionated rumen samples obtained from sheep fed two different diets. More than 300 different OTUs were detected across the four fractionated samples, and differences in bacterial communities were found between the two diets. Conclusions This is the first phylochip dedicated to analysis of ruminal bacteria, and it enables comprehensive and semiquantitative analysis of ruminal bacteria. Significance and Impact of the Study RumenBactArray can be a robust tool to comparatively analyse ruminal bacteria needed in nutritional studies of ruminant animals.