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 goats^a

Entry (rumen sample type)	Sample no.	No. of reads	No. of high-quality reads	Avg read length (bp)	OTU	Shannon-Weaver index (H′)	Chao1 index	Evenness (E)	No. of phyla	No. of genera
1 (bacteria in HGS)	1	959	831	498	403	5.62	771	0.94	12	22
	2	2,858	2,277	497	781	6.11	1,345	0.92	12	39
	3	3,329	2,621	497	896	6.29	1,419	0.93	15	39
2 (bacteria in HFS)	1	3,554	2,842	494	909	6.20	1,473	0.91	16	40
	2	2,474	1,839	497	713	6.05	1,327	0.92	14	37
	3	1,490	1,154	497	529	5.91	982	0.94	14	30
3 (bacteria in HDC)	1	1,529	1,138	497	520	5.94	955	0.95	13	35
	2	1,146	999	496	469	5.82	862	0.95	14	28
	3	1,270	1,106	496	519	5.94	844	0.95	12	34
4 (bacteria in KNG)	1	764	693	500	167	4.01	332	0.78	5	19
	2	2,732	1,952	497	322	4.48	469	0.76	10	30
	3	1,607	1,267	500	159	3.75	251	0.74	7	20
5 (archaea in HGS)	1	5,323	4,025	453	83	2.51	99	0.57	1	1
	2	5,139	3,850	453	55	2.26	60	0.57	1	1
	3	4,014	3,180	452	41	2.30	45	0.62	1	2
6 (archaea in HFS)	1	4,007	2,856	453	40	2.29	62	0.62	1	1
	2	3,410	2,170	454	29	1.88	32	0.56	1	2
	3	4,096	2,657	453	34	2.28	41	0.65	2	1
7 (archaea in HDC)	1	2,692	1,899	453	32	1.91	37	0.55	2	1
	2	4,387	2,777	455	32	1.86	46	0.54	2	1
	3	3,120	2,220	453	27	1.92	48	0.58	2	1
8 (archaea in KNG)	1	1,775	1,286	452	7	0.43	8	0.22	1	1
	2	1,466	1,032	452	8	0.47	11	0.23	1	1
	3	7,051	1,891	452	11	0.17	12	0.07	1	1

^aRuminant 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.