Figure 4. Positive association between community diversity and gene loss in Human Microbiome Project (HMP) time series.

(A) Scatter plots showing the relationship between Shannon diversity at time point 1 (tp1) and gene loss between tp1 and tp2 within each of the nine most prevalent species in HMP. (B) Scatter plots showing the relationship between species richness at tp1 and gene loss between tp1 and tp2 within each of the nine most prevalent species in HMP. Significant linear correlations are shown with red trendlines (Pearson correlation, p<0.05); non-significant trend lines are in gray. The Y-axis is plotted on a log10 scale for clarity. Results of generalized linear mixed models (GLMMs) predicting gene loss in a focal species as a function of (C) Shannon diversity, (D) species richness estimated on all data, and (E) species richness estimated on rarefied sequence data. p-Values (likelihood ratio test) are displayed in each panel. Shaded areas show the 95% confidence interval of each model prediction. The Y-axis is plotted on the link scale, which corresponds to log for negative binomial GLMMs with a count response. GLMMs are based on data from 54 bacterial species across 154 HMP stool donors sampled at more than one time point. See Supplementary file 1g and Supplementary file 2 section 10 for detailed model outputs.