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 | Â | 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 |