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, 30 (11), 1515-1528

Metagenomic Investigation of Gastrointestinal Microbiome in Cattle


Metagenomic Investigation of Gastrointestinal Microbiome in Cattle

Minseok Kim et al. Asian-Australas J Anim Sci.


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 cultivation-based 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.

Keywords: Cattle; Gastrointestinal; Metagenomics; Microbiome; Nutrition; Rumen.

Conflict of interest statement


We certify that there is no conflict of interest with any financial organization regarding the material discussed in the manuscript.


Figure 1
Figure 1
A diagram showing the alternate conserved regions and hypervariable regions of the 16S rRNA genes. C1–C10, the 10 conserved regions; V1–V9, the 9 hypervariable regions. Alignments with high sequence similarity are highlighted in black, whereas alignments with low sequence similarity are highlighted in gray.
Figure 2
Figure 2
A flowchart for meta-analysis of gastrointestinal (GI) microbial diversity in cattle.
Figure 3
Figure 3
A flowchart outlining the process of bioinformatic analysis of 16S rRNA gene amplicons sequenced using next-generation sequencing (NGS). Either QIIME or Mothur can be used.

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