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J Microbiol Biotechnol. 2018 Oct 28;28(10):1700-1705. doi: 10.4014/jmb.1803.03002.

Effects of Sampling Techniques and Sites on Rumen Microbiome and Fermentation Parameters in Hanwoo Steers.

Author information

1
Animal Nutrition and Physiology Team, National Institute of Animal science, Rural Development Administration, Wanju 55365, Republic of Korea.
2
Department of Pet Science, Seojeong College, Yangju 11429, Republic of Korea.
3
Department of Animal Science, College of Agriculture and Life Sciences, Chonnam National University , Gwangju 61186, Republic of Korea.

Abstract

We evaluated the influence of sampling technique (cannulation vs. stomach tube) and site (dorsal sac vs. ventral sac) on the rumen microbiome and fermentation parameters in Hanwoo steers. Rumen samples were collected from three cannulated Hanwoo steers via both a stomach tube and cannulation, and 16S rRNA gene amplicons were sequenced on the MiSeq platform to investigate the rumen microbiome composition among samples obtained via 1) the stomach tube, 2) dorsal sac via rumen cannulation, and 3) ventral sac via rumen cannulation. A total of 722,001 high-quality 16S rRNA gene sequences were obtained from the three groups and subjected to phylogenetic analysis. There was no significant difference in the composition of the major taxa or alpha diversity among the three groups (p> 0.05). Bacteroidetes and Firmicutes represented the first and second most dominant phyla, respectively, and their abundances did not differ among the three groups (p> 0.05). Beta diversity principal coordinate analysis also did not separate the rumen microbiome based on the three sample groups. Moreover, there was no effect of sampling site or method on fermentation parameters, including pH and volatile fatty acids (p > 0.05). Overall, this study demonstrates that the rumen microbiome and fermentation parameters are not affected by different sampling techniques and sampling sites. Therefore, a stomach tube can be a feasible alternative method to collect representative rumen samples rather than the standard and more invasive method of rumen cannulation in Hanwoo steers.

KEYWORDS:

16S rRNA gene amplicon sequencing; cannulation; fermentation parameters; rumen microbiome; stomach tube

PMID:
29996593
DOI:
10.4014/jmb.1803.03002
[Indexed for MEDLINE]
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