— Invited Review — Metagenomic investigation of gastrointestinal microbiome in cattle

Minseok Kim, Tansol Park, Zhongtang Yu
<span title="2017-11-01">2017</span> <i title="Asian Australasian Association of Animal Production Societies"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5x4vaquupnaarlclnfczoqwwd4" style="color: black;">Asian-Australasian Journal of Animal Sciences</a> </i> &nbsp;
The gastrointestinal (GI) tract, including the rumen and the other intestinal segments of cattle, harbors a diverse, complex, and dynamic microbiome that drives feed digestion and fermentation in cattle, determining feed efficiency and output of pollutants. This microbiome also plays an important role in affecting host health. Research has been conducted for more than a century to understand the microbiome and its relationship to feed efficiency and host health. The traditional
more &raquo; ... research elucidated some of the major metabolism, but studies using molecular biology techniques conducted from late 1980's to the late early 2000's greatly expanded our view of the diversity of the rumen and intestinal microbiome of cattle. Recently, metagenomics has been the primary technology to characterize the GI microbiome and its relationship with host nutrition and health. This review addresses the main methods/techniques in current use, the knowledge gained, and some of the challenges that remain. Most of the primers used in quantitative real-time polymerase chain reaction quantification and diversity analysis using metagenomics of ruminal bacteria, archaea, fungi, and protozoa were also compiled. Open Access 1516 www.ajas.info ) Asian-Australas J Anim Sci 30:1515-1528 to reveal the glycoside hydrolases in the rumen of dairy cows [13] and to evaluate the diversity of bacteria in the rumen and feces of beef cattle [14] . By now, hundreds of metagenomic studies have been reported to address different aspects of the rumen microbiome, such as the effect of feed additive or diets on the rumen microbiome, early patterns of colonization of young rumen, and the diversity of the enzymes, especially glycoside hydrolases. In this review, we discussed metagenomic investigation of gastrointestinal (GI) microbiome in cattle using quantitative real-time polymerase chain reaction (qPCR), phylogenetic microarrays, and NGS. The limitations and future perspectives of metagenomic studies of GI microbiome are also discussed.
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