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. 2022 Jul 1;55(1):196–218. doi: 10.4143/crt.2022.080

Fig. 4.

Fig. 4

Changes in the abundance ratio of the gut microbiome by AOM/DSS and TP addition: LEfSe analysis. (A–F) Bar plots of the LEfSe results, which were obtained based on the following criteria: (1) alpha value of the factorial Kruskal-Wallis H test between assigned taxa < 0.05; (2) the alpha value for the pairwise Wilcoxon test among the taxonomic members < 0.05; (3) threshold of the logarithmic LDA score for discriminative features < 2.0; and (4) a multi-class analysis set as all-against-all; (5) identifying and classifying the bacterial characteristics based on previous reports as “commensal bacteria,” “opportunistic pathogens,” and “not characterized”; (6) removal of non-overlapping bacteria from the “not characterized” microbiome; and (7) in the LEfSe plot, all commensal bacteria and opportunistic pathogens, and top ten “not characterized” bacteria were included. The color bars show the LDA scores of species that enriched in indicated conditions; (A) filled red bar (female control), (A, B) hatched blue bar (AOM/DSS-treated female), (B) blanked blue bar (AOM/DSS+TP-treated female), (C) filled red bar (male control), (C, D) hatched red bar (AOM/DSS-treated male), (D) blanked red bar (AOM/DSS+TP-treated male). (E) filled green bar (ORX control), (E, F) hatched green bar (AOM/DSS-treated ORX mice), (F) blanked green bar (AOM/DSS+TP-treated ORX mice). The color on the species name indicates the characteristics of each species: yellow for commensal bacteria, orange for opportunistic pathogens, and green for not characterized bacteria. Asterisks indicate the butyrate-producing bacteria. The p- and q-values were determined using the non-parametric factorial Kruskal-Wallis H test. (G) The ratio of commensal bacteria to opportunistic pathogens based on the LEfSe results in each comparison group. AOM, azoxymethane; DSS, dextran sulfate sodium salt; F, female; LDA, linear discriminant analysis; LEfSe, linear discriminant analysis effect size; M, male; NC, not calculated; ORX, orchiectomized; TP, testosterone propionate.