TABLE 2.

Sources of taxonomic information and its value at different levels in the taxonomic hierarchy

Source of information	Methoda	Use for taxonomic rank:
		Genus or above	Species	Subspecies or below
Genotypic data
Chromosomal DNA	Base composition (mol% G+C)	√	√
	DNA-DNA hybridization		√	√
	Restriction patterns (PFGE, RFLP, AFLP)		√	√
	Whole-genome sequences	√	√	√
DNA segments	DNA probes	√	√	√
	DNA sequencing (e.g., gyrB and recA genes, MLST)	√	√	√
	PCR-based DNA fingerprinting (e.g., PCR-RFLP, RAPD, REP-PCR)		√	√
Ribosomal RNA	DNA-rRNA hybridization	√	√
	Nucleotide sequences	√	√
	Ribotyping, ARDRA		√	√
Phenotypic data
Proteins	Amino acid sequences	√	√
	Electrophoretic patterns		√	√
	Multilocus enzyme electrophoresis			√
	Serological comparisons	√	√	√
Chemical markers	Fatty acids	√	√
	Isoprenoid quinones	√	√
	Lipoglycans	√	√
	Mycolic acids	√	√
	Peptidoglycan	√
	Polar lipids	√	√
	Polyamines	√	√
	Polysaccharides	√	√
	Teichoic acids	√	√
Whole-organism chemical fingerprinting	Dispersive Raman spectroscopy		√	√
	FT-IR		√	√
	PyMS		√	√
Whole-organism expressed features	Morphology	√	√
	Physiology	√	√
	Rapid enzyme tests		√	√

^aAbbreviations: PFGE, pulsed-field gel electrophoresis; RAPD, randomly amplified polymorphic DNA fingerprints; REP-PCR, repetitive DNA PCR; MLST, multilocus sequence typing; RFLP, restriction fragment length polymorphism; ARDRA, amplified rDNA restriction analysis; AFLP, amplified fragment length polymorphisms.