Table 3 Association between significant microbiome genera and AD diagnosis from “best-fit” PRSice-2 model.

From: Genetic correlations between Alzheimer’s disease and gut microbiome genera

Genera

Samples

Threshold

R2

P

Coeff

SE

SNP#

SampleSize

Adlercreutzia*

ADc12

0.3705

0.0068

3.57E−04

− 1870.66

524.00

101798

2571

GenADA

0.0020

0.0036

3.91E−02

− 224.26

108.71

1684

1577

Alistipes

ADc12

0.1676

0.0080

1.04E−04

2581.83

665.28

67574

2571

GenADA

0.3246

0.0023

1.03E−01

− 2953.44

1810.61

99785

1577

Anaerostipes

ADc12

0.0032

0.0078

1.18E−04

− 469.15

121.86

2834

2571

GenADA

0.2989

0.0054

1.18E−02

4134.46

1641.01

96076

1577

Bacteroides*

ADc12

0.1792

0.0114

3.32E−06

3930.96

845.35

71984

2571

GenADA

0.0009

0.0037

3.68E−02

221.55

106.10

922

1577

Candidatus Soleaferrea*

ADc12

0.0002

0.0090

3.48E−05

− 71.29

17.22

177

2571

GenADA

0.0199

0.0020

1.28E−01

− 404.97

265.96

12431

1577

Catenibacterium

ADc12

0.3839

0.0082

8.54E−05

− 1276.68

324.95

71434

2571

GenADA

0.0831

0.0080

2.11E−03

1068.34

347.56

25728

1577

Collinsella

ADc12

0.0002

0.0073

1.78E−04

125.63

33.51

230

2571

GenADA

0.0003

0.0143

4.36E−05

229.15

56.06

335

1577

Eisenbergiella*

ADc12

0.1049

0.0082

9.64E−05

− 858.39

220.13

42727

2571

GenADA

0.0439

0.0066

5.28E−03

− 1131.73

405.70

22002

1577

Eubacterium coprostanoligenes

ADc12

0.1020

0.0086

7.19E−05

− 1085.22

273.37

48130

2571

GenADA

0.0101

0.0038

3.36E−02

707.65

333.01

7483

1577

Eubacterium fissicatena

ADc12

0.0404

0.0070

3.00E−04

− 418.31

115.71

19567

2571

GenADA

0.0008

0.0090

1.17E−03

− 142.85

44.01

663

1577

Eubacterium nodatum*

ADc12

0.4353

0.0072

2.52E−04

− 1240.65

338.95

95579

2571

GenADA

0.1259

0.0025

8.82E−02

− 805.51

472.45

42817

1577

Gordonibacter*

ADc12

0.0330

0.0089

5.57E−05

− 254.45

63.13

16821

2571

GenADA

0.0116

0.0039

3.30E−02

− 351.65

164.98

7135

1577

Intestinibacter*

ADc12

0.1903

0.0154

1.01E−07

− 3014.37

566.17

70292

2571

GenADA

0.0024

0.0024

9.22E−02

− 246.05

146.10

2152

1577

Lachnospira*

ADc12

0.0034

0.0067

3.30E−04

530.79

147.83

2997

2571

GenADA

0.0004

0.0021

1.11E−01

113.71

71.44

439

1577

LachnospiraceaeUCG008

ADc12

0.0784

0.0081

1.08E−04

− 776.50

200.53

35344

2571

GenADA

0.0041

0.0017

1.57E−01

197.29

139.40

3224

1577

Oscillibacter

ADc12

0.0124

0.0068

3.08E−04

− 630.36

174.67

8305

2571

GenADA

0.0051

0.0027

7.55E−02

302.62

170.24

3884

1577

Prevotella9*

ADc12

0.0084

0.0075

1.57E−04

− 556.34

147.21

6609

2571

GenADA

0.0008

0.0031

5.47E−02

− 147.32

76.68

819

1577

Roseburia*

ADc12

0.2061

0.0100

1.35E−05

− 3564.78

819.18

78446

2571

GenADA

0.0037

0.0027

7.64E−02

− 366.88

207.02

3135

1577

Sutterella

ADc12

0.4928

0.0071

2.53E−04

3594.16

982.20

124985

2571

GenADA

0.0002

0.0009

3.08E−01

− 34.75

34.10

156

1577

Veillonella

ADc12

0.0070

0.0081

8.83E−05

539.94

137.72

5406

2571

GenADA

0.0021

0.0085

1.56E−03

369.43

116.78

1843

1577

  1. Genetic association between PRSs for top 20 microbiome genera and AD diagnosis from PRSice-2 “best-fit” model. The association from the “best-fit” threshold was generated from PRSice-2 with a range of p-value thresholds from 5 × 10−8 to 1 and incremental interval of 5 × 10−5; R2: Variance explained by the PRS model; P: p-value of model fit for the association; Coeff: Coefficient of the model; SE: standard error; # of SNPs: Number of SNPs included in the model at the specified threshold. Genera in bold are three genera identified to have a genetically significant association with AD in both discovery and replicate samples. *: indicated ten genera that have the same direction in both discovery and replicate samples. Seven genera, originally identified to be significantly associated with AD in the discovery sample, did not survive the replicate analysis due to the opposite direction in the replicate sample.
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