Fig. 3

Signature modules of species networks associated with NAFLD phenotype for NAFLD-O and NAFLD-L. A Venn diagram of significantly different in abundance species using ANCOM-II (cutoff = 0.6) adjusted by age gender BMI HOMA-IR and SBP for the comparisons of NAFLD-O vs CTRL-NAFLD-O and NAFLD-L vs CTRL-NAFLD-L. The amount of common significantly different species of each case, with other metabolic disease comparisons is displayed as a percentage under the Venns circles with arrows. Differentially abundant species analysis for metabolic diseases was done using ANCOM-II adjusting for a set of clinical data depending on the disease-control comparison (Methods). B Multiscale embedded correlation network analysis illustrates the differential correlation of species in NAFLD-O vs CTRL-NAFLD-O and NAFLD-L vs CTRL-NAFLD-L. Only species pairs with significant differential correlations (empirical P < 0.01) were included. The color of the link indicates the type of correlation change in control/NAFLD. Sparse canonical correlation analysis (sCCA) was used to evaluate the contribution of each species to the correlation between the module and NAFLD-related clinical parameters (P < 0.05), which is displayed by the color of the nodes (blue: negative, red: positive). ANCOM-II was used to find a significant difference in abundance species (cutoff = 0.6) adjusting for a set of clinical data depending on the disease-control comparison (Methods). Species found significantly different in abundance uniquely in NAFLD comparisons are marked with a triangle whereas a diamond is used if the species also appears significant in the comparison of any other metabolic diseases. The size of the node indicates the magnitude of the W statistic generated by ANCOM-II. C Table summarizing the numbers for each type of correlation change for the two modules in B. The types are depicted as from control to NAFLD (control/NAFLD) and colored differently as in B