TABLE 2.

Characteristics of rpoB data sets and phylogenies for different taxonomic levels^a

Taxonomic group	Taxonomic level	No. of taxa	Saturated codon position(s)	rpoB (complete gene)			Resolutionb	rpoB (DGGE fragment)			Resolutionb
				No. of nucleotide positions	G	I		No. of nucleotide positions	G	I
Bacteria	Domain	50	All	774 (aa)	0.67	0.05	26/47	126 (aa)	0.65	0.08	8/47
Actinobacteria	Phylum	11	None	3,336	1.73	0.30	6/8	390	2.83	0.34	5/8
Chlamydiaceae	Family	7	None	3,756	0.59	0.30	2/4	387	1.13	0.56	2/4
Firmicutes	Phylum	33	3rd	1,978	0.82	0.16	19/30	262	1.61	0.30	10/30
Bacillales	Order	11	3rd	2,308	1.64	0.62	4/8	262	0.39	0.24	5/8
Lactobacillales	Order	12	3rd	2,336	0.74	0.37	5/9	262	0.87	0.36	4/9
Streptococcus	Genus	9	None	3,546	0.71	0.37	4/6	393	0.49	ND	6/6
Mycoplasmataceae	Family	6	None	2,679	1.7	0.18	2/3	354	1.34	0.15	1/3
Proteobacteria	Phylum	46	1st, 3rd	1,147 (aa)	0.57	0.08	35/43	127 (aa)	0.52	0.10	23/43
Alphaproteobacteria	Class	9	None	3,993	0.4	ND	4/6	387	1.88	0.31	2/6
Gammaproteobacteria	Class	29	3rd	2,660	0.89	0.36	19/26	258	0.89	0.36	11/26
Enterobacteriales	Order	14	None	4,020	1.27	0.34	11/11	387	0.56	0.22	5/11
E. coli/S. flexneri	Species	5	None	4,026	ND	ND	2/2	387	ND	ND	1/2

^aND, value cannot be defined (data set is too small and/or lacks informative positions).

^bNumber of nodes resolved (>80% bootstrap support value) out of the total nodes, with bold type indicating the gene (rpoB or 16S rRNA) displaying the most resolved node.