LEfSe highlights pathways consistently differential between bacterial microbiomes and viromes within diverse environmental subclasses. (a) Using the SEED  catalog of functional pathways, LEfSe reports Nucleoside and nucleotide metabolism and Respiration to differ consistently between bacterial microbiomes and viromes across environmental samples described in . The former is significant using the strictest all-subclasses test, the latter in the more lenient one-subclass test. (b) A two-level cladogram reporting the significant pathway differences as visualized using the SEED hierarchy (see Additional file 3 for the three-level cladogram and detailed differences). (c) Metastats  reports four additional pathways differential among these data (Carbohydrates, DNA metabolism, Membrane transport and Nitrogen metabolism). Using only the KW test portion of LEfSe (α = 0.05), we obtain results consonant with Metastats (excluding Nitrogen metabolism). However, as shown here, an overview of the abundance histograms of these subsystems demonstrates them to be less consistent across environments (for example, Coral and Hyper-saline subclasses in the Carbohydrates, Membrane transport and Nitrogen metabolism) and to lose significance within individual subclasses (as for the DNA metabolism subsystem).
Segata et al. Genome Biology 2011 12:R60 doi:10.1186/gb-2011-12-6-r60