Effects of Sampling Techniques and Sites on Rumen Microbiome and Fermentation Parameters in Hanwoo Steers
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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.
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.
참고문헌 (19)
- Kim M, "Status of the phy logenetic diversity census of ruminal microbiomes", FEMS Microbiol. Ecol, 76, pp.49~63 (2011)
- Laflin SL, "Rumen cannulation: procedure and use of a cannulated bovine", Vet. Clin. North Am. Food Anim. Pract, 24, pp.335~340 (2008)
- Lodge-Ivey SL, "Technical note: bacterial diversity and fermentation end products in rumen fluid samples collected via oral lavage or rumen cannula", J. Anim. Sci, 87, pp.2333~2337 (2009)
- Terré M, "Short communication: comparison of pH, volatile fatty acids, and microbiome of rumen samples from preweaned calves obtained via cannula or stomach tube", J. Dairy Sci, 96, pp.5290~5294 (2013)
- Ramos-Morales E, "Use of stomach tubing as an alternative to rumen cannulation to study ruminal fermentation and microbiota in sheep and goats", Anim. Feed Sci. Technol, 198, pp.57~66 (2014)
- Paz HA, "Rumen bacterial community composition in Holstein and Jersey cows is different under same dietary condition and is not affected by sampling method", Front. Microbiol, 7, pp.1206~ (2016)
- Shen JS, "Insertion depth of oral stomach tubes may affect the fermentation parameters of ruminal fluid collected in dairy cows", J. Dairy Sci, 95, pp.5978~5984 (2012)
- Geishauser T, "A comparison of rumen fluid sampled by oro-ruminal probe versus rumen fistula", Small Ruminant Res, 21, pp.63~69 (1996)
- Duffield T, "Comparison of techniques for measurement of rumen pH in lactating dairy cows", J. Dairy Sci, 87, pp.59~66 (2004)
- Yu Z, "Improved extraction of PCRquality community DNA from digesta and fecal samples", Biotechniques, 36, pp.808~812 (2004)
- Herlemann DP, "Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea", ISME J, 5, pp.1571~1579 (2011)
- Magoc M, "FLASH: Fast length adjustment of short reads to improve genome assemblies", Bioinformatics, 27, pp.2957~2963 (2011)
- Caporaso JG, "QIIME allows analysis of high-throughput community sequencing data", Nat. Methods, 7, pp.335~336 (2010)
- Haas BJ, "Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons", Genome Res, 21, pp.494~504 (2011)
- DeSantis TZ, "Greengenes, a chimerachecked 16S rRNA gene database and workbench compatible with ARB", Appl. Environ. Microbiol, 72, pp.5069~5072 (2006)
- Edgar RC, "Search and clustering orders of magnitude faster than BLAST", Bioinformatics, 26, pp.2460~2461 (2010)
- Price MN, "FastTree 2 -Approximately maximum-likihood trees for large alignments", PLoS One, 5, pp.e9490~ (2010)
- Erwin ES, "Volatile fatty acid analyses of blood and rumen fluid by gas chromatography", J. Dairy Sci, 44, pp.1768~1771 (1961)
- Benson AK, "Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors", P. Natl. Acad. Sci. USA, 107, pp.18933~18938 (2010)