Table 2

Logistic regression model for IBS versus control

	Genus				Species
		OR	95% CI	P value		OR	95% CI	P value
Taxa*	Streptococcus	1.12	1.06 to 1.18	<0.01	Streptococcus agalactiae	1.15	1.02 to 1.30	0.02
	Gardnerella	1.13	1.03 to 1.23	0.01	Gardnerella vaginalis	1.16	1.04 to 1.28	0.01
	Tyzzerella	0.94	0.88 to 0.99	0.02	Tyzzerella nexilis	0.90	0.84 to 0.96	<0.01
	Lactobacillus	1.07	1.02 to 1.13	0.01	Lactobacillus jensenii	1.18	1.04 to 1.34	0.01
					Lactobacillus salivarius	1.24	1.04 to 1.48	0.02
	Slackia	1.05	1.01 to 1.10	0.03	Slackia piriformis	1.07	1.00 to 1.14	0.05
	Anaerostipes	0.93	0.86 to 1.00	0.04	Anaerostipes hadrus	0.92	0.85 to 0.99	0.03
	Acidaminococcus	1.05	1.00 to 1.11	0.04	Acidaminococcus intestini	1.06	1.00 to 1.13	0.04
	Parabacteroides	1.09	1.03 to 1.16	<0.01	Dorea formicigenerans	1.09	1.03 to 1.15	<0.01
	Oscillibacter	1.10	1.03 to 1.16	<0.01	Flavonifractor plautii	1.10	1.04 to 1.17	<0.01
	Faecalibacterium	0.94	0.90 to 0.98	0.01	Blautia hydrogenotrophica	1.10	1.03 to 1.17	0.01
	Veillonella	1.09	1.02 to 1.16	0.01	Faecalimonas umbilicata	1.09	1.02 to 1.17	0.01
	Anaerotruncus	1.08	1.01 to 1.15	0.02	Anaerococcus provencensis	1.14	1.03 to 1.27	0.01
	Merdibacter	0.92	0.85 to 0.99	0.03	Prevotella copri	1.06	1.01 to 1.10	0.01
	Coprococcus	0.94	0.89 to 0.99	0.03	Staphylococcus aureus	0.89	0.80 to 0.98	0.01
	Metaprevotella	1.09	1.01 to 1.17	0.03	Corynebacterium pyruviciproducens	1.12	1.02 to 1.22	0.02
					Bacteroides finegoldii	1.06	1.01 to 1.11	0.03
					Bilophila wadsworthia	1.05	1.01 to 1.11	0.03
					Clostridium perfringens	1.16	1.00 to 1.35	0.05
Sex	Male	1.09	0.76 to 1.58	0.64	Male	1.00	0.68 to 1.48	1.00
	Female	Referent	–	–	Female	Referent	–	–
Age	>34 to 42	1.06	0.79 to 1.41	0.72	>34 to 42	0.99	0.73 to 1.34	0.95
	>42 to 52	1.02	0.76 to 1.38	0.88	>42 to 52	0.97	0.71 to 1.32	0.84
	>52 to 81	1.35	0.99 to 1.83	0.05	>52 to 81	1.17	0.85 to 1.61	0.34
	18–34	Referent	–	–	18–34	Referent	–	–
Sex–age interaction	Male:age (>34 to 42)	0.70	0.42 to 1.17	0.17	Male:age (>34 to 42)	0.78	0.46 to 1.32	0.36
	Male:age (>42 to 52)	0.61	0.35 to 1.04	0.07	Male:age (>42 to 52)	0.64	0.36 to 1.11	0.11
	Male:age (>52 to 81)	0.54	0.31 to 0.93	0.03	Male:age (>52 to 81)	0.70	0.39 to 1.24	0.22
Race	African–American	1.33	0.57 to 3.08	0.51	African–American	1.10	0.47 to 2.60	0.82
	Asian/Oceania/Pacific Islander/Hawaii	0.52	0.32 to 0.85	0.01	Asian/Oceania/Pacific Islander/Hawaii	0.54	0.32 to 0.91	0.02
	Latin American/Hispanic	0.54	0.31 to 0.93	0.03	Latin American/Hispanic	0.52	0.29 to 0.91	0.02
	Mixed	0.45	0.26 to 0.78	<0.01	Mixed	0.41	0.23 to 0.73	<0.01
	Unknown	0.87	0.72 to 1.05	0.16	Unknown	0.85	0.69 to 1.03	0.1
	Caucasian/European/American	Referent	–	–	Caucasian/European/American	Referent	–	–
History of antibiotic use in the preceding year	Penicillins	1.24	0.98 to 1.58	0.07	Penicillins	1.32	1.03 to 1.68	0.03
	Tetracyclines	1.73	1.17 to 2.56	0.01	Tetracyclines	1.82	1.21 to 2.74	<0.01
	Cephalosporins	1.88	1.11 to 3.17	0.02	Cephalosporins	1.85	1.07 to 3.19	0.03
	Quinolones	2.06	1.37 to 3.10	<0.01	Quinolones	1.94	1.27 to 2.96	<0.01
	Lincomycins	2.24	0.98 to 5.14	0.06	Lincomycins	2.01	0.86 to 4.70	0.11
	Macrolides	1.46	1.04 to 2.05	0.03	Macrolides	1.42	1.00 to 2.03	0.05
	Sulfonamides	1.62	0.79 to 3.32	0.19	Sulfonamides	2.06	0.99 to 4.28	0.05
	Glycopeptides	4.81	0.58 to 39.96	0.15	Glycopeptides	4.54	0.47 to 43.82	0.19
	Aminoglycosides	1.09	0.17 to 6.87	0.92	Aminoglycosides	1.33	0.19 to 9.02	0.77
Family history of gut disorders	IBS	5.15	3.80 to 6.98	<0.01	IBS	5.46	3.97 to 7.50	<0.01
	Ulcerative colitis	0.96	0.54 to 1.68	0.88	Ulcerative colitis	1.01	0.56 to 1.83	0.97
	Crohn’s disease	1.25	0.91 to 1.71	0.18	Crohn’s disease	1.38	0.99 to 1.92	0.06
	Diverticulitis	0.96	0.56 to 1.67	0.89	Diverticulitis	0.95	0.54 to 1.70	0.87

*Only significant taxa at the genus and species level are shown here for brevity. Some species are shown at p=0.05 due to rounding (full models shown in online supplementary material table A2, table A4, and table A6).
IBS, irritable bowel syndrome.