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. 2020 May 19;11:2500. doi: 10.1038/s41467-020-16366-7

Fig. 3. Phylogenetic analysis of MAGs from 50 rural Ethiopian metagenomes.

Fig. 3

a Occurrence of the 20 most prevalent SGBs among 50 previously sequenced Ethiopian gut metagenomes highlights the presence of many previously identified but largely uncharacterized species-level genome bins (uSGBs) and the identification of few additional MAGs (unassigned) that are not recapitulated in any already defined SGB. The presence/absence profiles are clustered using average linkage with Euclidean distances. b Multidimensional scaling ordination using the t-SNE algorithm on phylogenetic distances from PhyloPhlAn 3.0's tree of eight Ethiopian E. coli MAGs (kSGB 10068) integrated with 200 automatically selected E. coli reference genomes using 3246 UniRef90 gene families for phylogenetic reconstruction. c PhyloPhlAn 3.0 phylogeny of Ethiopian MAGs assigned to uSGB ID 19436 including all reference genomes for the closest phyla (589 in total) according to the prokaryotes tree-of-life in Fig. 4. Phylogeny reconstruction used 400 universal markers selected by PhyloPhlAn 3.0 for deep-branching phylogenies. Portions of the tree collapsed are labeled and numbers in parentheses represent the number of genomes in the collapsed subtrees. Uncollapsed phylogeny is available in Supplementary Fig. 4.