How can we use the genome of a microbe to infer its metabolism?

Question

What will be an ideal response?

Answer 1

Now that so much metabolism is understood in model organisms, much of the metabolic capacity of other organisms can be deduced by comparison of their genomes.
As an example, the TCA cycle, in whole or in part, is found in all microbial species except for degenerately evolved pathogens that are dependent on host metabolism, such as Treponema pallidum, the cause of syphilis. The genome encodes key enzymes of glycolysis, as well as those of fermentation to lactate or acetate. However, enzymes of the TCA cycle are completely absent, as are the proteins of electron transport. Thus, T. pallidum can generate ATP only by substrate-level phosphorylation, such as the ATP formation steps of glycolysis.

In addition, human gut bacteria (strains of Bacteroides plebeius), have obtained genes from marine bacteria enabling digestion of marine seaweed polysaccharides such as porphyran. Analyzing from individuals with a long dietary history of eating Porphyra seaweed (nori, used to wrap sushi), research has shown that their intestinal bacteria include a strain of Bacteroides plebeius whose genes encode enzymes and Sus-like proteins for digestion of the sulfonated polysaccharides unique to the seaweed. The genes show homology with similar genes from marine bacteria associated with the seaweed (Zobellia and Microscilla). In effect, the human-associated bacteria appear to have "learned" to digest the seaweed by picking up the necessary genes through horizontal transfer. Humans who have never consumed the seaweed lack bacteria with these particular genes. However, in individuals who consume a lot of seaweed, the genomes of their gut bacteria are functionally part of their human metagenome.