FIGURE 4.

Within-subject alpha diversity of samples shown separately for chronic disruption of rhythms (CDR) conditions and normal light:dark conditions (NLD), as measured by (A,B) Faith’s phylogenetic diversity, (C,D) Shannon’s index, and (E,F) number of distinct features over time. Data represent treatment group means ± standard errors of the means of alpha diversity in fecal samples from days –1, 48, and 62 of mice in five independently tested cohorts of mice. Analyses were performed on 16 small subunit ribosomal RNA (16S rRNA) gene V4 amplicon data at a rarefaction depth of 15,000 reads per sample. 16S rRNA, 16 small subunit ribosomal RNA; CDR, chronic disruption of rhythms; Mv, Mycobacterium vaccae NCTC 11659; NLD, normal light:dark conditions; SD, social defeat; SHC, single-housed home cage control condition; Veh, borate-buffered saline vehicle. For sample sizes of each group at each time point, see Supplementary File S1; for definitions of symbols used to indicate significant post hoc pairwise comparisons, see Table 4.