Figure 2.

LEfSe results on human microbiomes. (a-c) Mucosal body site analysis. Mucosal microbial communities are diverse, while non-mucosal body sites are characterized by several clades, including the Actinobacteria. The analysis reported here is carried out on initial data from the Human Microbiome Project [55,56] assigning the main body sites to mucosal and non-mucosal classes, and using the body sites as subclasses. These graphical outputs were generated by the publicly available LEfSe visualization modules applied on the analysis results and integrating microbial taxonomic prior knowledge [58]. (a) Histogram of the LDA scores computed for features differentially abundant between mucosal and non-mucosal body sites. LEfSe scores can be interpreted as the degree of consistent difference in relative abundance between features in the two classes of analyzed microbial communities. The histogram thus identifies which clades among all those detected as statistically and biologically differential explain the greatest differences between communities. (b) Taxonomic representation of statistically and biologically consistent differences between mucosal and non-mucosal body sites. Differences are represented in the color of the most abundant class (red indicating non-mucosal, yellow non-significant). Each circle's diameter is proportional to the taxon's abundance. This representation, here employing the Ribosomal Database Project (RDP) taxonomy [58], simultaneously highlights high-level trends and specific genera - for example, multiple differentially abundant sibling taxa consistent with the variation of the parent clade. (c) Histogram of the Actinomycetales relative abundances (in the 0[1] interval) in mucosal and non-mucosal body sites. Subclasses (specific body sites) are differentially colored and the mean and median relative abundance of the Actinomycetales are indicated with solid and dashed lines, respectively. (d,e) Aerobiosis analysis. The cladograms report the taxa (highlighted by small circles and by shading) showing different abundance values (according to LEfSe) in the three O₂-dependent classes as described in Results; for each taxon, the color denotes the class with higher median for both the small circles and the shading. (d) The strict (all classes differential) version of LEfSe detects 13 biomarkers whereas (e) the non-strict (at least one class differential) version of LEfSe detects 60 microbial biomarkers with abundance differential under aerobic, anaerobic, or microaerobic conditions. Additional file 2 reports the non-strict version of LEfSe focused on the Firmicutes phylum, highlighting several low-O₂ specific genera within Ruminococcaceae and Lachnospiraceae.