TABLE 1.

Definitions and descriptions for alpha and beta diversity measures applied in this study.

Diversity measure	Index	Weighting	Description	References
Alpha	Observed richness	Not weighted	Number of ASVs detected per sample	NA
	Faith’s PD	Phylogeny-weighted	Sum of the branch lengths of the phylogenetic tree connecting all microbial taxa present within a sample	Daniel, 1992; Chao et al., 2015
	Shannon	Abundance-weighted	A diversity index based on the number of ASVs present and their abundance distribution (evenness)	Shannon, 1948
	BWPD	Phylogeny- and abundance-weighted	Abundance-weighted extension of phylogenetic diversity	McCoy and Matsen, 2013
Beta	Jaccard	Not weighted	Variability in microbial composition among sampled communities, with composition measured by which ASVs are present or absent	Jaccard, 1912
	Unweighted Unifrac	Phylogeny-weighted	Variability in microbial composition among sampled communities based on the lineages they contain	Lozupone and Knight, 2005
	Morisita	Abundance-weighted	Variability in microbial composition among sampled communities based on ASV presence and abundance. Sensitive to the most abundant species	Morisita, 1959; Chao et al., 2006
	Weighted Unifrac	Phylogeny- and abundance-weighted	Abundance-weighted extension of Unweighted Unifrac	Lozupone et al., 2007