TABLE 3.

Expected vs. actual classification of bacterial (n = 13) and archaeal (n = 3) sequences included in reference standard by four databases at a bootstrapping threshold of 80.

Sequence	Expected Classification	GTDB	RDP	SILVA	RefSeq +RDP
1	Eubacterium ruminantium	FF	FF	FF	UE
2	Methanobrevibacter millerae	EE	EF	EF	EE
3	Methanobrevibacter olleyae	EE	EF	EF	EE
4	Peptostreptococcus anaerobius	FF	EE	EE	EE
5	Pseudobutyrivibrio ruminis	EE	EF	EF	EE
6	Propionibacterium sp.	EF	EF	EU	EE
7	Ruminococcus albus	EE	EE	EE	EE
8	Butyrivibrio fibrisolvens	FF	EE	EE	EE
9	Megasphaera elsdenii	EE	EF	EF	EF
10	Methanogenic archaeon strain ISO4-H5 Methanomassiliicoccales	UU	UU*	UU*	EE**
11	Streptococcus bovis	EU	EF	EF	EU
12	Lachnospira multipara	EU	EF	EF	EE
13	Fibrobacter succinogenes	EE	EE	EE	EE
14	Clostridium aminophilum	FF	UF	UF	EE
15	Selenomonas ruminantium	EE	EE	EE	EE
16	Prevotella ruminicola	EF	EE	EE	EE

F, database failed to assign ASV to taxonomic level. E, database assigned ASV to the expected taxonomic level. U, database assigned ASV to the unexpected taxonomic level. ^∗Both the RDP and SILVA database gave a genus, but not a species, level classification. ^∗∗RefSeq + RDP database was unable to classify ASV beyond phylum.