Figure 1. The gut microbiota is distinct between East Asian (EA) and White (W) subjects living in the Bay Area.

(A–C) Each point represents a single individual’s gut microbiota based upon 16S-seq. (A) Principal coordinate analysis of PhILR Euclidean distances reveals significant separation between ethnic groups (ADONIS test values shown). Additional distance calculations for complementary distance matrix calculations are shown in Supplementary file 1C. (B) Calculations of alpha diversity between EA and W subjects. p-values determined using Wilcoxon rank-sum tests. (C) CLR abundances of all bacterial phyla between EA and W subjects. p-values determined using Wilcoxon rank-sum tests. (D) Stacked bar plots showing the average percent relative abundances at the genus level for EA and W subjects, respectively. The most abundant taxa are shown as differently colored bars, with lower abundance taxa grouped as a single bar (Remainder). (E, F) Volcano plot of ALDEx2 differential abundance testing on (E) genera and (F) ASVs detected by 16S-seq in the gut microbiotas of EA versus W individuals. Significantly different (FDR<0.1) features are highlighted in black and labeled by genus or the most specific taxonomic assignment. (A–F) n=22 EA and n=24 W individuals. ASV, amplicon sequence variant; FDR, false discovery rate.

Figure 1—figure supplement 1. The gut microbiota can be used to predict ethnicity.

(A) A phylogenetic tree of all ASVs generated from 16S-seq is shown. Leaves are colored by phyla. The inner circle indicates differential abundance (EA_CLR-W_CLR) between ethnicities. The outer circle is colored by significance (p<0.05, gray, FDR<0.1, black, Welch's t-test; labeled in Figure 1F). (B-D) A random forest classifier was developed utilizing ASV data (B,C) and PhILR transformed ASV data (D) representing phylogenetic nodes on the tree visualized in panel A. 46 classifiers were trained on a subset of 45 individuals and then used to predict the remaining individual (leave-one-out cross-validation). (B) ASVs in the top 90th percentile for median mean decrease in Gini are plotted. Each dot represents the value for mean decrease in Gini for a given classifier (n=46 total classifiers made up of a subset of 45 samples). (C-D) Receiver operating characteristic curves for ASV data (C) and phylogenetic nodes obtained utilizing PhILR transformation (D) are plotted with values of area under the receiver operator curve (AUC) and 95% confidence intervals displayed. (E) CLR abundances of ASVs in the top 90th percentile of median mean decrease Gini, in the same order as shown in panel B (*p<0.05, Wilcoxon rank-sum test between ethnicity). (F) No significant difference in overall gut microbial colonization assessed by qPCR quantification of 16S rRNA gene copies per gram wet weight (n=13 EA, n=21 W, Wilcoxon rank-sum test).