Table 2.

Differential taxa abundance associated with PD compared to two different control groups (total and household only)

Taxa	Main Analys isa (N=170)			Sensitivity Analys is 1b (N=153)			Sensitivity Analys is 2c (N=100)			Sensitivity Analys is 3d (N=170)
	Log2FCe	SE	Adj p	Log2FCe	SE	Adj p	Log2FCe	SE	Adj p	Log2FCe	SE	Adj p
Proteobacteria (phylum)	1.37	0.35	0.0007	1.40	0.41	0.0055	0.17	0.31	0.8341	1.20	0.26	0.0001
Verrucomicrobiota (phylum)	1.23	0.40	0.0078	1.34	0.47	0.0163	1.31	0.42	0.0270	1.05	0.30	0.0033
Actinobacteriota (phylum)	1.02	0.37	0.0135	−0.07	0.44	0.8730	0.82	0.34	0.0918	0.57	0.26	0.0884
UBA1819 (Ruminococcaceae family genus)	2.27	0.39	0.0000	1.98	0.46	0.0018	0.40	0.35	0.8345	1.51	0.27	0.0000
DTU089 (Ruminococcaceae family genus)	3.08	0.81	0.0078	NAg	NA	NA	−0.90	0.78	0.8345	2.06	0.63	0.0073
Akkermansia (genus)	1.43	0.42	0.0213	1.96	0.48	0.0021	1.50	0.41	0.0197	0.97	0.29	0.0066
Enterococcus (genus)	3.65	1.11	0.0252	2.79	1.25	0.1925	2.61	1.86	0.7327	NAf	NA	NA
Hungatella (genus)	2.54	0.80	0.0312	3.56	0.96	0.0070	1.86	0.67	0.1306	2.11	0.56	0.0014

^aIncluded both community controls and population controls; adjusted for sex, race, age, and sequencing platform. DESeq2 was used to perform the analysis.

^bIncluded both community controls and population controls; adjusted for sex, race, age, and sequencing platform and constipation status. DESeq2 was used to perform the analysis.

^cIncluded household controls only: PD patient and household control pair was treated as random effect. Adjusted for sex, race, age, and sequencing platform. MaAsLin2 was used to perform the analysis.

^dIncluded both community controls and population controls; adjusted for sex, race, age, and sequencing platform. MaAsLin2 was used to perform the analysis.

^eCoefficient indicates the difference in the log-transformed relative abundances between PD and Control.

^fThis taxon was removed from the sensitivity analyses due to small cell count. Log2FC, Log2 fold change; SE, standard error; Adj, adjusted.