Figure 5.

SGBs and Single Reconstructed Genomes Associated with Westernized and Non-Westernized Lifestyles

(A) 49 total large (>10 genomes) SGBs were significantly enriched (Fisher's test) in the set of 112 Madagascar gut metagenomes sequenced for this study, and 20 were significantly depleted (Fisher's test) relative to Western gut microbiomes (complete results in Table S6). Most Madagascar-enriched SGBs are uSGBs or contain only isolate sequences that were themselves assembled from other metagenomes in other studies.

(B) 232 total SGBs were differentially present with respect to the total set of non-Westernized populations, again with the 40 most significant—excluding those already reported in (A)—shown here (Fisher's test, complete results in Table S6).

(C) The intra-SGB genetic structure of Succinatimonas spp., the bacterium most associated with non-Westernized lifestyles (multidimensional scaling [MDS] on percentage nucleotide distances between genomes). The few genomes assembled from Westernized countries are tightly clustering together, while strains from non-Westernized populations are distinct and not well represented by the only available co-assembled (but not cultivated) strain.

(D) MDS of the two uSGBs (ID 19692 and ID 19694) enriched in the Madagascar cohort and available isolate genomes for the containing Elusimicrobia phylum (phylogeny in Figure S5A). The metagenomically assembled genomes in Elusimicrobia SGBs greatly diverge from the non-human-associated isolate genomes in the phylum.

(E) Significant differences in functional potential between the 25 SGBs most strongly associated with Westernized and non-Westernized populations. We report the differential KEGG pathways (Fisher's test Bonferroni-corrected p < 0.05, full list in Table S6) whose components are found in the set of representative genomes for the 50 species (only three genomes per SGB).