TABLE 2.

Results of conventional microbiology cultures and 16S rRNA gene library analyses on bighorn sheep BAL specimens

Animal	Aerobic bacterial culture		16S rRNA gene library analysis
	Species	Level	Species (% identity)a	Proportionb
06OR02	Pasteurella multocida	Very many	Uncultured bacterium (89-94)	0.34
	Pasteurella trehalosi	Many	Fusobacterium necrophorum (99)	0.25
	Moraxella sp.	Many	Uncultured Firmicutes (88-93)	0.16
			Streptococcus sp. (95-97)	0.13
			Cilium-associated respiratory bacterium (98)	0.09
			Fusobacterium sp. (96)	0.03
06OR03	Pasteurella multocida	Many	Pasteurella multocida (99)	0.34
	Arcanobacterium pyogenes	Few	Mycoplasma ovipneumoniae (99)	0.31
	Mixed bacterial growth		Moraxella sp. (97)	0.31
	Mycoplasma ovipneumoniae (reculture)	Positive	Pasteurella trehalosi (98)	0.03
06SM90	Pasteurella trehalosi	Many	Uncultured rumen bacterium (93-99)	0.81
	Pasteurella multocida	Few	Uncultured bacterium (89-99)	0.19
	Moraxella sp.	Very many
	Enterococcus sp.	Very many
	Arcanobacterium pyogenes	Very many
	Mycoplasma ovipneumoniae (reculture)	Positive
06OR04	Pasteurella trehalosi	Moderate	Mycoplasma ovipneumoniae (99)	1.00
06OR05	Mannheimia haemolytica	Moderate	Helcococcus sp. (99)	0.50
	Possible Aerococcus sp.	Many	Fusobacterium necrophorum (99)	0.33
	Streptococcus suis	Few	Cilium-associated respiratory bacterium (98)	0.17
	Pasteurella trehalosi	Few
	Coliforms	Few
06WA03	Pasteurella trehalosi	Many	Fusobacterium necrophorum (96-99)	0.28
	Streptococcus sp., beta-hemolytic	Many	Pasteurella trehalosi (96-99)	0.25
	Mycoplasma ovipneumoniae	Positive	Mycoplasma ovipneumoniae (99-100)	0.22
	(reculture)		Cilium-associated respiratory bacterium (97-98)	0.09
			Unidentified spp.	0.09
			Streptococcus suis (99)	0.06
06WA06	Pasteurella trehalosi	Very many	Bacteroides pyogenes (98-100)	0.28
	Pasteurella multocida	Few	Uncultured rumen bacterium (92-99)	0.25
	Mixed bacterial growth		Fusobacterium necrophorum (99)	0.17
			Unidentified spp. (86)	0.17
			Miscellaneous spp. (98-99)	0.14
06WA08	Pasteurella trehalosi	Very many	Uncultured rumen bacterium (89-99)	0.43
	Pseudomonas aeruginosa	Very many	Fusobacterium necrophorum (99)	0.23
	Streptococcus sp., nonhemolytic	Very many	Unidentified. spp. (83-91)	0.20
	Arcanobacterium pyogenes	Many	Prevotella sp. (96%)	0.11
	Bacillus sp.	Low	Miscellaneous spp. (98-99)	0.03
	Mycoplasma ovipneumoniae (reculture)	Positive
07OR06	Pasteurella trehalosi	Many	Not determined
	Mycoplasma ovipneumoniae	Positive
07OR07	Pasteurella trehalosi	Few	Not determined
	Alpha-hemolytic Streptococcus sp.	Few
	Mycoplasma ovipneumoniae	Positive
07WA03	Coliform	Few	Not determined
	Staphylococcus sp., coagulase negative	Few

^aBest BLAST matches with identities of >98% are reported to species level, and those with 95 to 98% identity are reported to genus level. Types representing <4% of the sequenced clones are reported as miscellaneous species.

^bProportion of clones identified as the corresponding species.