Table 3.

Prevalence and proportion of total reads for “species” detected in at least 10% of samples.

Species	Prevalence/126(%)	% total reads	Reads
Lactobacillus sp.	93 (73.8%)	0.3	3,470
Lactobacillus iners	84 (66.7%)	30.9	327,884
Lactobacillus crispatus	82 (65.1%)	33.7	358,089
Lactobacillaceae	80 (63.5%)	0.0	444
Lactobacillus helveticus	46 (36.5%)	0.0	260
Lactobacillus sp.	42 (33.3%)	0.2	2,514
Ureaplasma parvum	38 (30.2%)	1.8	18,741
Atopobium vaginae	36 (28.6%)	3.3	35,148
Lactobacillus psittaci	36 (28.6%)	0.5	5,604
Lactobacillus jensenii	35 (27.8%)	3.6	38,601
Gardnerella vaginalis	31 (24.6%)	0.4	4,761
Prevotella timonensis	31 (24.6%)	0.7	7,661
Dialister micraerophilus	31 (24.6%)	0.5	5,368
Prevotella bivia	28 (22.2%)	1.4	15,402
Prevotella sp.	27 (21.4%)	0.0	344
Lactobacillus vaginalis	26 (20.6%)	0.0	356
Megasphaera sp.	24 (19.0%)	2.0	20,893
Lactobacillus kitasatonis	24 (19.0%)	0.0	85
Lactobacillus ultunensis	23 (18.3%)	0.0	85
Veillonellaceae	22 (17.5%)	0.0	72
Dialister sp.	21 (16.7%)	0.2	2,311
Aerococcus christensenii	21 (16.7%)	0.1	1,053
Prevotellaceae	21 (16.7%)	0.0	154
Atopobium sp.	21 (16.7%)	0.0	72
Megasphaera sp.	20 (15.9%)	0.0	133
Lactobacillus gasseri	18 (14.3%)	2.2	23,384
Peptoniphilus indolicus	18 (14.3%)	0.0	326
Sneathia sanguinegens	17 (13.5%)	0.7	7,535
Coriobacteriaceae	17 (13.5%)	0.2	1,745
Microbacterium laevaniformans group	17 (13.5%)	0.1	705
Leptotrichia amnionii	16 (12.7%)	2.8	29,310
Lactobacillus rodentium	16 (12.7%)	0.0	254
Lactobacillus sp.	16 (12.7%)	0.0	61
Lactobacillales	16 (12.7%)	0.0	20
Streptococcus anginosus	15 (11.9%)	1.1	12,176
Dialister sp.	15 (11.9%)	0.0	48
Gordonia sputi group	14 (11.1%)	0.4	4,004
Lactobacillus sp.	14 (11.1%)	0.1	649
Propionibacterium acnes	14 (11.1%)	0.0	50
Ruminococcaceae	13 (10.3%)	0.2	1,672
Prevotella sp.	13 (10.3%)	0.0	480
Dialister propionicifaciens	13 (10.3%)	0.0	73
The Remainder species		12.7	136,080