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Fig. 4 | Microbiome

Fig. 4

From: Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires

Fig. 4

Relationship between reaction content, phylogeny, and phenotype. The metabolic distance was determined according to the presence of specific reactions in the model (A,B). COG (C) and Pfam (D) functional differences were assessed by comparing the presence/absence of COG functions and Pfam domains for all genomes, respectively. The phylogenetic distance is based on the cophenetic distance of the maximum likelihood tree (rooted with two methanogenic archea) calculated from the sequence similarity of 400 selected essential genes (a, c, d). The phenotype divergence was represented by the difference in essential nutrients, which were determined by removing the nutrient of interest from the in silico medium and subsequently checking for growth/no growth with flux balance analysis (b). The shading of the points (ad) represents the density of all pairwise comparisons between the microbe models (n = 45.150). The blue line (ad) represents the moving average over the data points. The goodness of fit for both regression models (a, b) can be found in Table 2. The means of the phylogenetic (a, c, d) and metabolic distances (b) for each taxonomic category are indicated by dashed red lines

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