TABLE 3.

Permubiome performance against common microbiome biomarker discovery tools^a

Reference algorithm (no. of discriminated OTUs)	Permubiome OTUs (n = 8)
	Detectedb	Not detectedc	P valued
LEfSe (25)	6 [5 + 1] (LDA = 3.38 ± 0.38)	19 (LDA = 3.09 ± 0.43)	0.147
DESeq2 (38)	4 [4 + 0] (log2 FC = 1.45 ± 0.32)	34 (log2 FC = 1.62 ± 1.71)	0.627

^aConsensus OTUs detected were OTU13, OTU299, OTU662, and OTU680. LEfSe, linear discriminant analysis effect size; LDA, linear discriminant analysis; FC, fold change.

^bNumber of OTUs equally detected to be associated with lean and obese phenotypes by permubiome and the reference algorithms. Square brackets indicate those associated with lean and obese conditions.

^cNumber of OTUs detected to be associated with lean and obese phenotypes by reference algorithms but not by permubiome.

^dP values resulting from pairwise comparison between scores of OTUs detected and not detected by permubiome using Student t test (normally distributed data). The criterion used for selecting OTUs (P ≤ 0.05) in LEfSe analysis was an LDA of ≥2, whereas absolute log₂ FC was the criterion used in DESeq2.