Table 3.

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

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

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.