Figure 3. Participants consuming fiber exhibit shifts in the functional profile of the microbiome.

(A) Observed number of amplicon sequence variants (ASVs) from 16S rRNA amplicon sequencing; no significant changes during any intervention time point compared to baseline (Week −2 or Week 0) (paired t-test).

(B) Proteins measured using LC-MS (Gonzalez et al., 2020) were categorized as human or microbe derived using the HMP1 database (The Human Microbiome Project Consortium, 2012). Microbe proteins as a percent of total stool proteins increase from baseline to end of maintenance phase (Week 10, p-value=0.003 from Week −2, p-value=0.01 from Week 0, paired t-test).

(C) CAZymes identified from metagenomic sequencing as significantly changing in relative abundance from baseline to end of maintenance phase (FDR ≤ 0.05, q-value ≤ 0.1, SAM two-class paired). CAZymes were annotated using dbCan and assigned to functional categories (Yin et al., 2012; Cantarel et al., 2012).

(D) Significant decreases in two branched chain fatty acids and valeric acid in stool (p-value=0.044, 0.033, 0.033, paired t-test). Outliers not plotted but all values were included for statistical analysis testing (see Methods).

(E) Total fiber intake (grams) correlated with percentage of carbohydrates in stool using linear mixed effects (LME) model (p-value=8e-4).