Table 1. Summary of the 25 classification tasks derived from metagenomic datasets for case-control prediction.

ACDV: Atherosclerotic cardiovascular disease, AD: Alzheimer’s disease, BD: Behcet’s disease, CRC: Colorectal cancer, IBD: irritable bowel disease, T1D: Type 1 diabetes, T2D: Type 2 diabetes. We additionally considered the HMP_2012 dataset [10] for body site discrimination between gut (N = 414) and oral (N = 147) samples.

Dataset name	Body site	# controls	Cases	# cases	Reference
JieZ_2017	Gut	171	ACVD	214	[31]
ChngKR_2016	Skin	40	AD	38	[32]
YeZ_2018	Gut	45	BD	20	[33]
RaymondF_2016	Gut	36	Cephalosporins	36	[34]
QinN_2014	Gut	114	Cirrhosis	123	[35]
FengQ_2015	Gut	61	CRC	46	[36]
GuptaA_2019	Gut	30	CRC	28	[37]
HanniganGD_2017	Gut	28	CRC	27	[38]
ThomasAM_2018a	Gut	24	CRC	29	[39]
ThomasAM_2018b	Gut	28	CRC	32	[39]
VogtmannE_2016	Gut	52	CRC	52	[40]
WirbelJ_2018	Gut	65	CRC	60	[41]
YachidaS_2019	Gut	251	CRC	258	[42]
YuJ_2015	Gut	53	CRC	75	[43]
ZellerG_2014	Gut	54	CRC	61	[6]
LiJ_2017	Gut	41	Hypertension	99	[44]
IjazUZ_2017	Gut	38	IBD	56	[45]
NielsenHB_2014	Gut	248	IBD	148	[46]
GhensiP_2019_m	Oral	49	Mucositis	20	[47]
GhensiP_2019	Oral	49	Peri-implantitis	23	[47]
Castro_NallarE_2015	Oral	16	Schizophrenia	16	[48]
Heitz-BuschartA_2016	Gut	26	T1D	27	[49]
KosticAD_2015	Gut	89	T1D	31	[50]
KarlssonFH_2013	Gut	43	T2D	53	[51]
QinJ_2012	Gut	174	T2D	170	[52]