I think you may have misread. The article is suggesting that a high-fat, fast food diet has a negative effect on gut flora, in both mice and humans.
To be honest, I’m not a fan of Michael Pollan and I don’t think he has enough evidence to support some of his claims, and I also don’t think there’s much to gain, at least at this point, from trying to manipulate our gut flora.
But I think it’s also important to avoid fatalism. Obviously, life isn’t fair, and some of us have it easier than others in the health department (and no doubt some of us get better gut bacteria from our mothers), but we can all work to improve ourselves. There is no excuse to give up.
I don’t agree with the article in every respect, but it would still be wrong to interpret it to mean that some people are screwed, as did the OP (though maybe he was joking). If you accept Pollan’s ideas about our microbiota, the article also points out that diet can be used to change it. We’re not doomed by our genome.