Figure 5.

Combined overview of the microbiota shows that CD4⁺ T cell depletion alters gut bacterial structure, diversity, and composition

(A) Significant differences in the bacterial composition and structure (Aitchison distance) between the groups: PBS, RGDOX + indoximod + anti-CD4, and RGDOX + indoximod + IgG (PERMANOVA p = 0.003). The features that strongly influence the clustering of the groups are highlighted in the compositional biplot, where Bifidobacterium is responsible for sample clustering of the RGDOX + indoximod + IgG group. (B) There are no differences in richness (Chao1 index) or diversity (Shannon index) between groups (KW p > 0.05), although animals treated with the oncolytic virus and indoximod with depleted CD4⁺ T cells have a tendency toward lower richness and diversity compared with viroimmunotherapy-treated mice with functional CD4⁺ T cells. (C) The F/B ratio for the experimental groups. This ratio is slightly reduced, but not significantly (WRST p > 0.05), in RGDOX/indoximod without CD4⁺ T cell depletion mice compared with all other groups, whereas animals administered PBS showed a very high F/B ratio. (D) Taxonomic composition of gut bacteria at the phylum and genus levels between groups, where mice treated with combination therapies that had CD4⁺ T cell depletion had a decreased abundance of Actinobacteria highlighted by lower levels of Bifidobacterium and Lactobacillus. See also Table S6.