Microbial diversity in the rumen, reticulum, omasum, and abomasum of yak on a rapid fattening regime in an agro-pastoral transition zone

다국어 초록 (Multilingual Abstract)

The ruminant digestive system harbors a complex gut microbiome, which is poorly understood in the case of the four stomach compartments of yak. High-throughput sequencing and quantitative PCR were used to analyse microbial communities in the rumen, reticulum, omasum, and abomasum of six domesticated yak. The diversity of prokaryotes was higher in reticulum and omasum than in rumen and abomasum. Bacteroidetes predominated in the four stomach compartments, with abundance gradually decreasing in the trend rumen > reticulum > omasum > abomasum. Microorganism composition was different among the four compartments, all of which contained high levels of bacteria, methanogens, protozoa and anaerobic fungi. Some prokaryotic genera were associated with volatile fatty acids and pH. This study provides the first insights into the microorganism composition of four stomach compartments in yak, and may provide a foundation for future studies in this area.

참고문헌 (Reference)

1 Ramsak, A., "Unravelling the genetic diversity of ruminal bacteria belonging to the CFB phylum" 33 : 69-79, 2000

2 Lozupone, C., "UniFrac: a new phylogenetic method for comparing microbial communities" 71 : 8228-8235, 2005

3 Edgar, R.C., "UCHIME improves sensitivity and speed of chimera detection" 27 : 2194-2200, 2011

4 Kittelmann, S., "Two different bacterial community types are linked with the low-methane emission trait in sheep" 9 : e103171-, 2014

5 Qiu, Q., "The yak genome and adaptation to life at high altitude" 44 : 946-949, 2012

6 Orpin, C.G., "The rumen anaerobic fungi;The rumen microbial ecosystem" Springer 140-195, 1997

7 Newbold, C.J., "The role of ciliate protozoa in the rumen" 6 : 1313-, 2015

8 Hong, Y., "The impact of orally administered phages on host immune response and surrounding microbial communities" 6 : e1211066-, 2016

9 Bartlett, P.C., "Temporal patterns of lost milk production following clinical mastitis in a large Michigan holstein herd" 74 : 1561-1572, 1991

10 Osborne, J.M., "Synergism in degradation and utilization of intact forage cellulose, hemicellulose, and pectin by three pure cultures of ruminal bacteria" 55 : 2247-2250, 1989

11 Belanche, A., "Study of methanogen communities associated with different rumen protozoal populations" 90 : 663-677, 2014

12 Kim, M., "Status of the phylogenetic diversity census of ruminal microbiomes" 76 : 49-63, 2011

13 Gulino, L.M., "Shedding light on the microbial community of the macropod foregut using 454-amplicon pyrosequencing" 8 : e61463-, 2013

14 Aschenbach, J.R., "Ruminant nutrition symposium: role of fermentation acid absorption in the regulation of ruminal pH" 89 : 1092-1107, 2011

15 Nagaraja, T.G., "Ruminal acidosis in beef cattle: The current microbiological and nutritional outlook 1, 2" 90 : E17-E38, 2007

16 Akin, D.E., "Rumen fungi: morphological types from Georgia cattle and the attack on forage cell walls" 21 : 385-391, 1988

17 Guirong, Su, N.R., "Rumen ciliated protozoan fauna of the yak (Bos grunniens) in China with the description of Entodinium monuo n. sp." 47 : 178-182, 2000

18 Puniya, A.K., "Role of live microbial feed supplements with reference to anaerobic fungi in ruminant productivity: A review" 14 : 550-560, 2015

19 Lee, S.S., "Relative contributions of bacteria, protozoa, and fungi to in vitro degradation of orchard grass cell walls and their interactions" 66 : 3807-3813, 2000

20 Denman, S.E., "Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane" 62 : 313-322, 2007

21 Caporaso, J.G., "QIIME allows analysis of high-throughput community sequencing data" 7 : 335-336, 2010

22 Yang, L.Y., "Phylogenetic analysis of 16S rRNA gene sequences reveals rumen bacterial diversity in yaks (Bos grunniens)" 37 : 553-562, 2010

23 Radaelli, E., "Outbreak of bovine clinical mastitis caused by Mycoplasma bovis in a North Italian herd" 91 : 251-253, 2011

24 Soest, P.J.V., "Nutritional ecology of the ruminant" Comstock Publishing 1994

25 Kokotovic, B., "Mycoplasma alkalescens demonstrated in bronchoalveolar lavage of cattle in Denmark" 49 : 1-3, 2007

26 Mccann, J.C., "Induction of subacute ruminal acidosis affects the ruminal microbiome and epithelium" 7 : 701-, 2016

27 Salonen, A., "Impact of diet on human intestinal microbiota and health" 5 : 239-262, 2014

28 Peng, S., "First insights into the microbial diversity in the omasum and reticulum of bovine using Illumina sequencing" 56 : 1-9, 2015

29 Wei, Y.Q., "Fiber degradation potential of natural co-cultures of Neocallimastix frontalis and Methanobrevibacter ruminantium isolated from yaks (Bos grunniens) grazing on the Qinghai Tibetan Plateau" 39 : 158-164, 2016

30 Guo, W., "Evaluation of composition and individual variability of rumen microbiota in yaks by 16S rRNA high-throughput sequencing technology" 34 : 74-79, 2015

31 Chen, Y.B., "Effect of DNA extraction methods on the apparent structure of yak rumen microbial communities as revealed by 16S rDNA sequencing" 64 : 29-36, 2015

32 Leng, J., "Dominant bacterial communities in the rumen of gayals (Bos frontalis), yaks (Bos grunniens) and yunnan yellow cattle (Bos taurs) revealed by denaturing gradient gel electrophoresis" 38 : 4863-4872, 2011

33 Stevenson, D.M., "Dominance of Prevotella and low abundance of classical ruminal bacterial species in the bovine rumen revealed by relative quantification real-time PCR" 75 : 165-174, 2007

34 Griswold, K.E., "Diversity of extracellular proteolytic activities among Prevotella species from the rumen" 39 : 187-194, 1999

35 Fliegerova, K., "Diversity of anaerobic fungi within cow manure determined by ITS1 analysis" 55 : 319-325, 2010

36 Sylvester, J.T., "Development of an assay to quantify rumen ciliate protozoal biomass in cows using real-time PCR" 134 : 3378-3384, 2004

37 Denman, S.E., "Development of a real-time PCR assay for monitoring anaerobic fungal and cellulolytic bacterial populations within the rumen" 58 : 572-582, 2006

38 Creevey, C.J., "Determining the culturability of the rumen bacterial microbiome" 7 : 467-479, 2014

39 Makoto Mitsumori, "Control of Rumen Microbial Fermentation for Mitigating Methane Emissions from the Rumen" 아세아·태평양축산학회 21 (21): 144-154, 2008

40 Wang, Y., "Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies" 4 : e7401-, 2009

41 Jami, E., "Composition and similarity of bovine rumen microbiota across individual animals" 7 : e33306-, 2012

42 Gu, Z., "Complete sequence of the yak (Bos grunniens) mitochondrial genome and its evolutionary relationship with other ruminants" 42 : 248-255, 2007

43 Huang, X.D., "Comparison of methanogen diversity of yak (Bos grunniens) and cattle (Bos taurus) from the Qinghai-Tibetan plateau, China" 12 : 237-, 2012

44 Ishii, S., "Coaggregation facilitates interspecies hydrogen transfer between Pelotomaculum thermopropionicum and Methanothermobacter thermautotrophicus" 71 : 7838-7845, 2005

45 Mao, S., "Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function" 5 : 16116-, 2015

46 Fu, L., "Cd-hit: accelerated for clustering the next-generation sequencing data" 28 : 3150-3152, 2012

47 Xue, D., "Analysis of the rumen bacteria and methanogenic archaea of yak (Bos grunniens) steers grazing on the Qinghai-Tibetan Plateau" 188 : 61-71, 2016

48 Tamaki, H., "Analysis of 16S rRNA amplicon sequencing options on the Roche/454 next-generation titanium sequencing platform" 6 : e25263-, 2011

49 Liu, J.H., "A high-grain diet causes massive disruption of ruminal epithelial tight junctions in goats" 305 : R232-R241, 2013