Table 1. An overview of statistical methods and their properties.

Method	Method name	Number of experimental factors allowed	Parametric	Multivariate	Univariate	Provides output at community level	Statistics for ranking OTUs	Reference
ALDEx2	ANOVA-like differential expression tool for high-throughput sequencing data	any	yes	no	yes	no	p-values or effect sizes	[26]
ANCOM	Analysis of composition of microbiomes	main factor + covariates	yes	no	yes	no	W-stat for the main variable	[28]
ANOSIM	Analysis of similarities	one	no	yes	no	yes	no	[15]
ASCA	ANOVA-simultaneous component analysis	any	yes	yes	no	yes	loadings or PLS-DA regression coefficients	[33]
DESeq2	Differential gene expression analysis based on the negative binomial distribution	any	yes (GLM)	no	yes	no	p-values or effect sizes (coefficients)	[30]
FFMANOVA	Fifty-fifty multivariate ANOVA	any	yes	yes	yes (rotation tests)	yes	p-values	[35]
PERMANOVA	Permutational multivariate analysis of variance	any	no	yes	no	yes	no	[14]
SIMPER	Similarity percentage	two-group comparison	no	yes	no	no	permutation p-values	[15]

ANOVA—analysis of variance; GLM—generalized linear model; OTU—operational taxonomic unit; PLS-DA—partial least squares discriminant analysis.