Table 1 Data sets collected and processed through standardized pipeline

Dataset ID	Controls	N (controls)	Cases	N (cases)	Reference
Singh 2015, EDD	H	82	EDD	201	³⁵
Schubert 2014, CDI	H	154	CDI	93	³³
Schubert 2014, non-CDI	H	154	non-CDI	89	³³
Vincent 2013, CDI	H	25	CDI	25	³⁴
Youngster 2014, CDI	H	4	CDI	19	¹⁸
Goodrich 2014, OB	H	428	OB	185	⁴³
Turnbaugh 2009, OB	H	61	OB	195	⁴²
Zupancic 2012, OB	H	96	OB	101	⁴⁴
Ross 2015, OB	H	26	OB	37	⁴⁵
Zhu 2013, OB	H	16	OB	25	¹
Baxter 2016, CRC	H	172	CRC	120	²⁰
Zeller 2014, CRC	H	75	CRC	41	²¹
Wang 2012, CRC	H	54	CRC	44	⁸
Chen 2012, CRC	H	22	CRC	21	²³
Gevers 2014, IBD	non-IBD	16	CD	146	²⁶
Morgan 2012, IBD	H	18	UC, CD	108	²⁷
Papa 2012, IBD	non-IBD	24	UC, CD	66	¹⁹
Willing 2010, IBD	H	35	UC, CD	45	²⁸
Noguera-Julian 2016, HIV	H	34	HIV	205	³⁹
Dinh 2015, HIV	H	15	HIV	21	⁴¹
Lozupone 2013, HIV	H	13	HIV	23	⁴⁰
Son 2015, ASD	H	44	ASD	59	⁷
Kang 2013, ASD	H	20	ASD	19	²
Alkanani 2015, T1D	H	55	T1D	57	⁵⁹
Mejia-Leon 2014, T1D	H	8	T1D	21	⁶⁰
Wong 2013, NASH	H	22	NASH	16	⁶¹
Zhu 2013, NASH	H	16	NASH	22	¹
Scher 2013, ART	H	28	PSA, RA	86	⁵²
Zhang 2013, LIV	H	25	CIRR, MHE	46	⁵¹
Scheperjans 2015, PAR	H	74	PAR	74	⁹

Non-CDI controls are patients with diarrhea who tested negative for C. difficile infection. Non-IBD controls are patients with gastrointestinal symptoms but no intestinal inflammation. Data sets are ordered as in Fig. 1
ART arthritis, ASD autism spectrum disorder, CD Crohn’s disease, CDI Clostridium difficile infection, CIRR liver cirrhosis, CRC colorectal cancer, EDD enteric diarrheal disease, H healthy, HIV human immunodeficiency virus, LIV liver diseases, MHE minimal hepatic encephalopathy, NASH non-alcoholic steatohepatitis, OB obesity, PAR Parkinson’s disease, PSA psoriatic arthritis, RA rheumatoid arthritis, T1D type I diabetes, UC ulcerative colitis

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