Figure 3. Associations between Trait-Descriptive Words and OGs for Two Illustrative Clusters.

“Heat maps” display word–OG association scores (scores greater than 0 are indicated; negative values are set to 0). We considered all words and OGs contributing to the respective cluster with at least one high-confidence association. Protein interaction networks, shown below, were derived from genomic context analysis (see Materials and Methods). (A) Traits and genes related to plant constituent degradation. Functional descriptions are: Plant-degr., involved in plant constituent degradation; Ox, putative oxidoreductases; Arg, Arginine degradation protein/predicted deacylase; UV, UV damage repair endonuclease; those with no description are uncharacterized. Terms related to sporulation reflect a domination of exo- and endospore-forming species from different genera (e.g., Streptomyces, Bacillus, and Clostridium) in these degradation processes. (B) Traits and genes related to food spoilage and poisoning. Some proteins have previously been implicated in virulence of food pathogens such as ManR (“T”), a transcriptional antiterminator involved in resistance to natural food preservatives, and some propanediol degradation proteins (“Prop-diol”). We suggest the involvement of additional proteins in pathogenicity: for example, ethanolamine degradation proteins (“Eth.-amine-usage”; the phospholipid phosphatidyl-ethanolamine, cleaved to ethanolamine by phospholipase, is abundant in the gut [14]); the cobalt chelatase CbiK (“C”; cobalt is an essential factor for propanediol and ethanolamine utilization [14]); a phosphotransferase system (“PTS”) involved in sorbitol transport [36] (sorbitol is an artificial food sweetener naturally found in fruits and may act as an additional carbon source; we suggest that alternatively the chemically similar inositol, cleavage product of another abundant phospholipid, may be utilized). Other proteins that may also be involved are a presumably anaerobically used butyrate kinase (“B”), gamma-glutamylcysteine synthetase (“G”), an electron transport complex protein (“O”), a predicted metal-binding enzyme (“E”), and several uncharacterized proteins (no description).