Table 3

Summary of the pyrosequencing data and statistical analysis of bacterial and archaeal microbial communities in the rumens of Hanwoo steers (two growth stages), Holstein cows, and Korean native goatsa

Entry (rumen sample type)Sample no.No. of readsNo. of high-quality readsAvg read length (bp)OTUShannon-Weaver index (H′)Chao1 indexEvenness (E)No. of phylaNo. of genera
1 (bacteria in HGS)19598314984035.627710.941222
22,8582,2774977816.111,3450.921239
33,3292,6214978966.291,4190.931539
2 (bacteria in HFS)13,5542,8424949096.201,4730.911640
22,4741,8394977136.051,3270.921437
31,4901,1544975295.919820.941430
3 (bacteria in HDC)11,5291,1384975205.949550.951335
21,1469994964695.828620.951428
31,2701,1064965195.948440.951234
4 (bacteria in KNG)17646935001674.013320.78519
22,7321,9524973224.484690.761030
31,6071,2675001593.752510.74720
5 (archaea in HGS)15,3234,025453832.51990.5711
25,1393,850453552.26600.5711
34,0143,180452412.30450.6212
6 (archaea in HFS)14,0072,856453402.29620.6211
23,4102,170454291.88320.5612
34,0962,657453342.28410.6521
7 (archaea in HDC)12,6921,899453321.91370.5521
24,3872,777455321.86460.5421
33,1202,220453271.92480.5821
8 (archaea in KNG)11,7751,28645270.4380.2211
21,4661,03245280.47110.2311
37,0511,891452110.17120.0711
  • a Ruminant abbreviations are as defined in Table 1, footnote a. Three replicate animals were examined per treatment. OTU, operational taxonomic units. OTU were calculated by the RDP pipeline with a 97% OTU cutoff of the 16S rRNA gene sequences. Diversity indices of the microbial communities and numbers of phyla and genera were calculated using the RDP pyrosequencing pipeline based on the 16S rRNA gene sequences. In the last two columns, all unclassified phyla or genera were counted as one phylum or genus.