Table 1.

Human loci associated with microbial abundance

Approach	Chromosome	SNP	Gene	Microbe	Target	Sample size	Reference
Twin Studies	11	rs651821	APOA5	Bifidobacterium	16S V4	655	(Lim et al. 2017)
Twin Studies	3	rs2276731	ALDH1L1	Unclassified SHA‐98	16S V4	1126	(Xie et al. 2016)
	2	rs6730157	RAB3GAP1	Bifidobacterium
	2	rs2164210	LCT	Bifidobacteria
	7	rs1360741	CD36	Blautia
	11	rs1506977	OR6A2	Cc 115 (family Erysipelotrichaceae)
	7	rs1182182	GNA12	SMB53 (family Clostridiaceae)
	11	rs1506977	rs1506977	Cc 115 (family Erysipelotrichaceae)
	7	rs1182182	GNA12	SMB53 (family Clostridiaceae)SS
Genetic association	16	rs2066847, rs2066844, rs2066845,	NOD2	depletion of Bacteroidetes and Firmicutes (particularly Clostridium taxa)	16S V1‐V9	178	(Frank et al. 2011)
	2	rs2241880	ATG16L1	depletion of Bacteroidetes and Firmicutes (particularly Clostridium taxa)	16S V1‐V9
Genetic association	19	rs601338	FUT2	Alistipes, unclassified Lachnospiraceae, and Coprococcus	16S V1‐2	47	(Rausch et al. 2011)
Genetic association	19	rs601338	FUT2	Bifidobacteria	16S V6‐V8	71	(Wacklin et al. 2011)
Genetic Association	6		HLA‐DRB1	Prevotella copri	16S V1‐V2	114	(Scher et al. 2013)
Genetic Association	16	rs2066844, rs2066845, rs5743277, rs5743293, rs104895431, rs104895467	NOD2	Enterobacteriaceae	16S V4	474	(Knights et al. 2014)
GWAS	3	rs4894707	PLD1	Akkermansia	16S V4	114	(Davenport et al. 2015)
GWAS	2	rs56064699	LCT	Bifidobacterium	16S V3‐5	93	(Blekhman et al. 2015)
	2	rs1050115	UBXN4	Bifidobacterium
	3	rs1110168	PLXND1	Prevotella
	11	rs1966834	OR1S1	Prevotella
	14	rs8019270	TBPL2	Prevotella
	20	rs2274669	PCED1A	Alistipes
	7	rs10248138	EPDR1	Lachnobacterium
GWAS	1	rs12137699	VANGL1	Family Sutterellaceae	WGS	1514	(Bonder et al. 2016)
	2	rs7605872		Species Dialister invisus
	6	rs4548017		Class Methanobacteria
	9	rs1081306616	LINGO2	Genus Blautia
	10	rs1889714		Species Dialister invisus
	11	rs16913594		Species Bacteroides xylanisolvens
	11	rs17115310		Family Acidaminococcaceae
	12	rs10743315		Species Lachnospiraceae bacterium 1 1 57FAA
	21	rs2834288		Family Oscillospiraceae
GWAS (replicated)	2	rs62171178	UBR3	Rikenellaceae			(Turpin et al. 2016)
	3	rs1394174	CNTN6	Faecalibacterium
	1	rs59846192	DMRTB1	Lachnospira
	18	rs28473221	SALL3	Eubacterium
	4	rs3775467	MMRN1	Weissella
	12	chr12:136,228 39:D	LINC01559 RNA5SP353 GRIN2B	Weissella
	1	rs6666120	ACTL8	Methanobrevibacter
GWAS (followed TWIN)	3	rs7433197	FHIT	Clostridiales (OTU 181,702)	16S V4	3666	(Beaumont et al 2016; Le Roy et al. 2018)
	6	rs1433723	TDRG1	Clostridiales (OTU 25,576)
	1	rs2480677	ELAVL4	Blautia (OTU 194,733)
GWAS	1	rs938295	FBLIM1	Unclassified Enterobacteriaceae	16S V1‐V2	1812	(Wang et al. 2016)
	1	rs75036654	LINC01137	Unclassified Acidaminococcaceae
	1	rs597205	C1orf183	OTU13305 Fecalibacterium Species‐level OTU
	2	rs4669413	RP11‐ 521D12.1	Blautia genus
	2	rs79387448	SLC9A2	Blautia genus
	2	rs10928827	HS6ST1	Bacilli class/Lactobacillales order
	2	rs4621152	AC007557 1	Gammaproteobacteria class
	2	rs56006724	C2orf83	Unclassified Acidaminococcaceae
	3	rs11915634	CNTN6	Marinilabiliaceae family/Unclassified Marinilabiliaceae
	3	rs3925158	SLC22A13	OTU10032 unclassified Enterobacteriaceae Species‐level OTU
	3	rs13096731	FLNB	Escherichia Shigella
	3	rs59042687	LINC00879	Lactobacillales order
	3	rs9831278	LINC00973	Unclassified Marinilabiliaceae
	3	rs62295801	LINC01192	Lactobacillales order
	3	rs7646786	LOC344887	Bacilli class
	4	rs7656342	DRD5	Unclassified Porphyromonadaceae
	4	rs11724031	SHROOM3	Marinilabiliaceae family
	4	rs17421787	RP11‐ 422J15.1	Erysipelotrichaceae family
	5	rs9291879	CD180	Unclassified Porphyromonadaceae
	5	rs249733	SPRY4	OTU10032 unclassified Enterobacteriaceae
	7	rs17661843	ABCA13	Unclassified Acidaminococcaceae
	8	rs13276516	TGS1	OTU10032 unclassified Enterobacteriaceae
	8	rs2318350	COL22A1	OTU10032 unclassified Enterobacteriaceae Species‐level OTU
	9	rs17085775	C9orf71	OTU10032 unclassified Enterobacteriaceae
	10	rs7083345	RP11‐ 554I8.2	Lactobacillales order/Bacilli class
	11	rs7113056	RP11‐ 166D19.1	Lactobacillales order
	12	rs479105	PRMT8	Bacilli class
	12	rs1009634	AKAP3	OTU10032 unclassified Enterobacteriaceae Species‐level OTU
	13	rs9300430	RAP2A	Gammaproteobacteria class
	14	rs9323326	SLC35F4	Proteobacteria phylum
	14	rs986417	SIX6	Unclassified Acidaminococcaceae
	14	rs11626933	C14orf102	Unclassified Erysipelotrichaceae
	15	rs12442649	TMCO5A	OTU15355 Dialister Species‐level OTU
	15	rs35275482	BNIP2	Enterobacteriaceae family
	16	rs12149695	FLJ21408	OTU10032 unclassified Enterobacteriaceae
	16	rs1362404	TOX3	Lactobacillales order
	18	rs11877825	NAPG	Erysipelotrichaceae family
	19	rs148330122	SIPA1L3	Bacilli class
	20	rs2071199	HNF4A‐AS1	Bacilli class
	21	rs34613612	KRTAP8‐1	Actinobacteria class
GWAS	9	rs150018970	RAPGEF1	Ruminococcus	16S V4	3890	(Hughes et al. 2020)
	1	rs561177583		Coprococcus
	16	rs55808472	ARHGAP17	Butyricicoccus
	11	rs4494297	EXT2	Sutterellaceae
	11	rs7118902	SORl1	Dialister
	13	rs35980751	ABCC4	Porphyromonadaceae
	6	rs13207588	FOXP4	Parabacteroides
	2	rs6733298	CCDC85A	Erysipelotrichaceae
	15	rs116865000		Gammaproteobacteria
	9	rs11788336	IKBKAP	Firmicutes
	6	rs34656657	ATXN1	Firmicutes
	4	rs116135844	SPOK3	Bacteroidales
	15	rs117338748	LIPC	Veillonella
GWAS	16	rs3803713	HS3ST4	Faecalibacterium	16S V3‐V4	1,068	(Ishida et al. 2020)
	21	rs2839417	C2CD2	Erysipelotrichaceae
	2	rs6545786	2p16.1	Prevotella
	10	rs1033781	10p15.1	Oscillospira
	18	rs885034	18q12.2	Alpha diversity index
GWAS		rs182549	LCT	Bifidobacterium	16S Various	18,340	(Kurilshikov et al. 2021)
	3	rs9864379		Gastranaerophilales	V4, V3‐V4, V1‐V2
	3	rs75754569	IRF1	Peptococcus
	3	rs4428215	FNDC3B	Oxalobacteraceae
	4	rs10805326		Intestinibacter
	4	rs11098863		Enterorhabdus
	7	rs10805326		Eubacterium coprostanoligenes
	9	rs602075	PCK5,RFK, GCNT1	Allisonella
	9	rs736744		Oxalobacter
	10	rs12781711		Ruminococcaceae UCG013
	10	rs61841503	CUBN	Peptostreptococcacea e
	11	rs10769159		Ruminococcus1
	12	rs12320842		Faecalibacterium
	12	rs11110281		Streptococcus
	13	rs7322849		Bifidobacterium
	14	rs8009993		Ruminococcaceae UCG009
	17	rs7221249		Erysipelatoclostridium
	19	rs67476743		Tyzzerella3
	19	rs830151		Candidatus Soleaferrea
	19	rs35866622	FUT2‐FUT1	Ruminococcus torques