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. 2007 Jun 19;5(7):e156. doi: 10.1371/journal.pbio.0050156

Figure 2. Sensing, Regulatory, and Carbohydrate Metabolism Genes Are Enriched among All Gut-Associated Bacteroidetes.

Figure 2

The number of genes assigned to each GO term from each genome is shown. Significant enrichment is denoted by pink (p < 0.05) or red (p < 0.001), whereas depletion is indicated by light blue (p < 0.05) or dark blue (p < 0.001), as calculated by a binomial comparison followed by Benjamini-Hochberg false-discovery rate correction (see Materials and Methods).

(A) Genes assigned to GO terms related to core metabolic functions are enriched in the subset of common gut-associated Bacteroidetes orthologs shared with non-gut Bacteroidetes (seven-way comparison; abbreviated 7w), compared to the reference set of 1,416 orthologs common to the five sequenced gut Bacteroidetes genomes (5w), suggesting that all Bacteroidetes have inherited a core metabolome from their common ancestor. The set of orthologs that is not shared with non-gut–associated Bacteroidetes (five-way unique; 5wU) is enriched, relative to all orthologs (5w), for genes in three classes—amino acid biosynthesis; membrane transport; and two-component signal transduction systems—suggesting that these genes were important in the process of adaptation to the gut and/or other habitats by the common ancestor of gut Bacteroidetes.

(B) Various GO terms related to environmental sensing, gene regulation, and carbohydrate degradation are enriched in gut Bacteroidetes relative to Cy. hutchinsonii (Ch). A similar pattern is observed relative to P. gingivalis (Pg) (unpublished data). Note that these same classes of genes are depleted in the subset of shared gut Bacteroidetes orthologs ([A] 5w) relative to the full B. thetaiotaomicron (Bt) genome ([A] Bt-G). Thus, these classes of genes, though enriched in all gut Bacteroidetes, are widely divergent between them. Other classes of genes vary between species: B. distasonis (Bd) and B. vulgatus (Bv) show an expanded repertoire of proteases, whereas B. thetaiotaomicron lacks genes involved in synthesis of cobalamin. 6w refers to the orthologs shared by the five sequenced gut Bacteroidetes genomes (Bt, Bv, Bd, plus two B. fragilis strains [NCTC 9343 (BfN) and YCH 46 (BfY)] and Pg.