Table 2.

Diversity and richness of the tonsillar microbial communities

	# Reads	# OTUsa	Chao-1b	Shannonc	Simpsond	Simpson evennesse
Pig E	43770	582	980	3.14	0.10	0.02
Pig F	11386	197	268	3.40	0.07	0.07
Pig G	16519	485	820	3.73	0.05	0.04
Pig H	28219	730	1224	3.42	0.11	0.01
Herd 2 Time 1	99894	1525	2513	3.58	0.06	0.01
Pig A	12268	128	161	2.37	0.21	0.03
Pig B	14885	190	235	3.17	0.09	0.05
Pig C	9392	182	237	2.81	0.14	0.04
Pig D	18387	135	291	3.23	0.07	0.11
Herd 1 Time 1	54932	453	628	3.23	0.07	0.03
Pig J	5523	122	191	3.26	0.07	0.12
Pig K	2760	67	88	2.70	0.11	0.14
Pig L	6295	167	233	3.12	0.09	0.06
Pig M	1351	57	87	2.45	0.15	0.11
Herd 1 Time 2	15929	273	382	3.23	0.08	0.05
Pig J Brush	13361	155	228	2.04	0.29	0.02
Pig K Brush	5672	102	141	2.38	0.14	0.07
Pig L Brush	9380	251	465	2.35	0.26	0.01
Pig M Brush	11265	136	164	2.83	0.11	0.06
Herd 1 Brush	39678	418	650	2.53	0.18	0.01

^a number of OTUs (based on 0.03 cut-off) found in each sample or herd

^b the estimated richness of an environment based on 0.03 cut-off

^c computed at the RDP Pyrosequencing Pipeline

^d calculated with MOTHUR [21] using a distance matrix computed at RDP Pyrosequencing Pipeline

^e derived from Simpson's Index where E = (1/D)/S, D is the Simpson's Index and S is the total number of species (OTUs)