Table 1 Loci associated with gut microbiome composition at study-wide significance

From: Genome-wide association analyses highlight the role of the intestinal molecular environment in human gut microbiota variation

Variant

Microbiome feature

Model

Swedish studies

HUNT

Locus

Lead variant

Chr: Pos37

EA/OA

Effect prediction

EAF

Trait

Prev

Beta

s.e.

P

Beta

s.e.

P

OR51E1–OR51E2

rs10836441

11:4689742

T/C

Intergenic

0.52

Richness

NA

Linear

−0.06

0.01

1.9 × 10−9

−0.04

0.01

2.1 × 10−3

LCT

rs4988235

2:136608646

A/G

Intron (MCM6)

0.72

Negativibacillus sp000435195

(NCBIa: Clostridium sp. CAG:169)

28.1

Logistic

0.23

0.03

2.9 × 10−13

0.09

0.04

0.04

rs4988235

2:136608646

A/G

intron (MCM6)

0.72

Phocea massiliensis

75.7

Linear

0.08

0.01

1.4 × 10−11

0.08

0.02

5.1 × 10−6

rs182549

2:136616754

T/C

Intron (MCM6)

0.72

Bifidobacterium adolescentis

90.0

Linear

−0.10

0.01

1.7 × 10−16

−0.14

0.02

1.4 × 10−14

rs6754311

2:136707982

T/C

Intron (DARS)

0.72

Copromonas sp000435795

(NCBIa: Alitiscatomonas acetii)

67.7

Linear

0.08

0.01

3.2 × 10−11

0.10

0.02

2.4 × 10−8

FOXP1

rs17007949

3:70920041

C/G

Intergenic

0.32

Intestinibacter sp900540355

(NCBIa: Clostridium sp. 1001270J_160509_D11)

55.9

Linear

0.07

0.01

5.1 × 10−11

0.03

0.01

7.3 × 10−3

MUC12

rs4556017

7:100632790

T/C

Intron (MUC12)

0.83

Coprobacillus cateniformis

26.9

Logistic

0.34

0.04

3.3 × 10−17

0.38

0.06

1.7 × 10−11

ABO

rs9411378

9:136145425

A/C

Intron (ABO)

0.28

Mediterraneibacter torques

(NCBI*: [Ruminococcus] torques)

86.9

Linear

0.11

0.01

1.4 × 10−18

0.12

0.01

1.0 × 10−16

rs550057

9:136146597

T/C

Intron (ABO)

0.31

Faecalibacterium longum

96.6

Linear

0.08

0.01

3.8 × 10−11

0.08

0.02

1.6 × 10−9

CORO7–HMOX2

rs8182173

16:4420787

T/C

Intron (CORO7)

0.23

Clostridium saudiense

40.2

Logistic

−0.22

0.03

7.8 × 10−13

−0.11

0.05

0.02

rs4785960

16:4453319

C/G

Intron (CORO7)

0.26

Turicibacter sanguinis

53.9

Linear

−0.08

0.01

2.0 × 10−12

−0.04

0.01

1.7 × 10−3

SLC5A11

rs55808472

16:24931691

A/G

Noncoding transcript exon (AC008731.1)

0.06

Agathobaculum butyriciproducens

98.3

Linear

0.15

0.02

2.4 × 10−11

0.16

0.03

4.3 × 10−9

FUT3–FUT6

rs708686

19:5840619

T/C

Upstream gene (FUT6)

0.30

Clostridium sp900540255

(NCBIa: uncultured Clostridium sp.)

36.3

Logistic

−0.20

0.03

4.5 × 10−13

−0.11

0.05

0.02

FUT2

rs679574

19:49206108

C/G

Intron (FUT2)

0.56

Clostridium sp001916075

(NCBIa: C. lentum)

31.2

Logistic

0.17

0.03

2.5 × 10−11

0.15

0.05

1.6 × 10−3

rs492602

19:49206417

A/G

Synonymous (FUT2)

0.56

Blautia A obeum

(NCBIa: B. obeum)

96.4

Linear

0.07

0.01

1.6 × 10−11

0.08

0.01

7.6 × 10−10

rs681343

19:49206462

T/C

Stop gained (FUT2)

0.44

Clostridium sp900540255

(NCBIa: uncultured Clostridium sp.)

36.3

Logistic

−0.22

0.03

2.2 × 10−18

−0.19

0.04

1.1

  1. Associations shown here were those at study-wide significance after Bonferroni correction of the genome-wide threshold, that is, P < 1.7 × 10−8 for richness and P < 5.4 × 10−11 for species. Bold type indicates those robustly replicated in HUNT at a Bonferroni-corrected P = 3.3 × 10−3. Betas are regression coefficients in standard deviation richness or species abundance per effect allele (calculated using a linear regression model) or log odds of species presence per effect allele (calculated using a logistic regression model). Tests were two-sided. Locus, manually assigned locus name based on previous GWAS assignment or function of nearby genes if new; Lead variant, reference SNP identifier of the locus lead variant (that is, the variant with the lowest P value); Pos37, human genome GRCh37 position on the chromosome; EA, effect allele; OA, other allele; EAF, mean effect allele frequency across studies; Trait, microbial species richness or species name; Model, GWAS regression model; Prev, mean species prevalence across studies (based on rarefied relative abundances for logistic models and nonrarefied relative abundances for linear models); Swedish studies P, P value in Swedish studies SCAPIS, SIMPLER-V, SIMPLER-U and MOS (discovery); HUNT P, P value in HUNT (replication).
  2. aNational Center for Biotechnology Information (NCBI) equivalents refer to the unfiltered NCBI taxonomy of GTDB species representative as of 2024-04-24. This was only added for species for which the name of the NCBI equivalent was different than GTDB.
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