. Author manuscript; available in PMC: 2013 Feb 11.

Published in final edited form as: J Microbiol Methods. 2009 Sep 29;79(3):266–271. doi: 10.1016/j.mimet.2009.09.012

Table 2.

Comparison of oral phyla abundance obtained using different classification tools.

Phylum	Percentage of total sequences classified
	Saliva+throat swab			Saliva (Keijser et al., 2008)
	GAST^a	MG-RAST^b	RDP^c	Saliva (Keijser et al., 2008)
Firmicutes	61.2	28.6	39.3	40.7
Proteobacteria	29.3	29.9	27.8	21
Actinobacteria	4.9	4.1	2.8	6.3
Fusobacteria	2.9	0.93	1.6	2.9
TM7	1.2	1.2	0.0063	1.9
Bacteroidetes	0.027	0.026	0.021	27.2
BRC1	0.07	0.076	0	0
OP10	0.12	0.040	0	0
Spirochaetes	0.20	0.20	0.064	0.2
Cyanobacteria	0.0007	0.0020	0.0016	0.020
SR1	0.013	0	0.0013	0.014
Acidobacteria	0.0018	0	0	0.049
OP3	0.0006	0	0	0
Unclassified Bacteria	0.023	35	28.5	0.2

NR, not reported.

≤30% divergent from their nearest reference sequence.

Maximum e-value 10⁻¹⁰ and minimum alignment length of 50 nucleotides.

80% confidence cutoff applied at the phylum level.