Table 1.

Ten uniformly processed 16S rRNA gene sequencing studies of the IBD mucosal/stool microbiomes. For longitudinal cohorts, numbers in parentheses indicate baseline sample size. For age, mean and standard error (parenthesized) are shown. Additional covariates are summarized in Additional file 3: Table S1

Study	Brief description	N subject	N sample	Phenotype(s)	Age	Gender	Sample type(s)
PROTECT [23]	Longitudinal cohort of newly diagnosed UC	405	1212 (539)	UC 405	12.71 (3.29)	Male 52%/Female 48%	Biopsy 22%/Stool 78%
RISK [7]	Pediatric cohort of treatment-naïve CD	631	882	CD 430/Control 201	12.16 (3.22)	Male 59%/Female 41%	Biopsy 72%/Stool 28%
Herfarth [26]	Densely (daily) sampled longitudinal cohort	31	860 (31)	CD 19/Control 12	36.03 (14.12)	Male 35%/Female 58%/Missing 6%	Stool
Jansson-Lamendella [22]	Longitudinal follow-up with fecal samples	137	683 (137)	CD 49/UC 60/ Control 28		Male 42%/Female 58%	Stool
Pouchitis [27]	Patients recruited underwent IPAA for treatment of UC or FAP prior to enrollment.	353	577	CD 42/UC 266/Control 45	46.19 (13.58)	Male 52%/Female 48%	Biopsy
CS-PRISM [28]	Cross-sectional cohort nested in PRISM	397	467	CD 215/UC 144/Control 38	41.68 (15.22)	Male 47%/Female 53%	Biopsy 29%/Stool 71%
HMP2 [9]	Large cohort of newly diagnosed IBD with multi-‘omics measurement.	81	177 (162)	CD 37/UC 22/Control 22	29.76 (19.63)	Male 51%/Female 49%	Biopsy
MucosalIBD [29]	Pediatric cohort with Paneth cell phenotypes	83	132	CD 36/Control 47	12.93 (3.65)	Male 58%/Female 42%	Biopsy
LSS-PRISM [30]	Longitudinal cohort nested in PRISM.	18	88 (19)	CD 12/UC 6	30.37 (10.52)	Male 39%/Female 61%	Stool
BIDMC-FMT [31]	FMT Trial design	8	16	CD 8	38.38 (12.73)	Male 62%/Female 38%	Stool