TABLE 4.

Permutational analysis of variance to determine influence of extraction method on microbial communities (both taxonomy and predicted function) stratified by sample type.

Outcome	Metric	Covariate	All samples		Stool only		Sputum only		Dust only
			R2	p-value	R2	p-value	R2	p-value	R2	p-value
Taxonomy	Bray-Curtis	Extraction method	0.017	< 0.001	0.030	< 0.001	0.123	< 0.001	0.121	0.018
Taxonomy	Bray-Curtis	Sample type	0.477	< 0.001
Taxonomy	Bray-Curtis	Extraction × Sample	0.023	< 0.001
Taxonomy	Bray-Curtis	Subject	0.407	< 0.001	0.923	< 0.001	0.726	< 0.001	0.551	< 0.001
Taxonomy	Bray-Curtis	Residuals	0.076		0.047		0.151		0.328
Taxonomy	Aitchison	Extraction method	0.021	0.002	0.039	0.003	0.092	0.026	0.156	0.002
Taxonomy	Aitchison	Sample type	0.47	< 0.001
Taxonomy	Aitchison	Extraction × Sample	0.028	0.024
Taxonomy	Aitchison	Subject	0.352	< 0.001	0.886	< 0.001	0.688	< 0.001	0.415	< 0.001
Taxonomy	Aitchison	Residuals	0.128		0.075		0.219		0.429
Function	Bray-Curtis	Extraction method	0.011	0.003	0.066	0.002	0.108	0.031	0.226	< 0.001
Function	Bray-Curtis	Sample type	0.755	< 0.001
Function	Bray-Curtis	Extraction × Sample	0.018	< 0.001
Function	Bray-Curtis	Subject	0.179	< 0.001	0.864	< 0.001	0.715	< 0.001	0.557	< 0.001
Function	Bray-Curtis	Residuals	0.037		0.070		0.177		0.217
Function	Aitchison	Extraction method	0.021	0.021	0.054	0.017	0.133	0.048	0.152	0.022
Function	Aitchison	Sample type	0.531	< 0.001
Function	Aitchison	Extraction × Sample	0.032	0.055
Function	Aitchison	Subject	0.268	< 0.001	0.844	< 0.001	0.454	< 0.001	0.398	< 0.001
Function	Aitchison	Residuals	0.148		0.102		0.412		0.449

Bray-Curtis dissimilarity index and the Aitchison distance results are presented.