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I have been thinking about this a lot. I think this is a huge area that is under studied. I do think fast food and other "factory foods" as my dad calls them promote a specific guy flora that makes people gain weight and not process foods properly. Also, preservatives keep certain bacteria from digesting foods, and that could heavily skew how your gut works if you eat a lot of prepared or non fresh food.
The most convincing study to me, was a case study of a woman who got a fecal transplant. A fecal transplant is to replace microorganisms in the gut after they have been killed with antibiotics. A thin woman got a fecal transplant from an overwight woman, and she ballooned up immediately even though her diet did not change.
http://www.iflscience.com/health-an...bese-after-fecal-transplant-overweight-donor/
Are you saying that the promotion of the "bad" bacteria is deliberately, or just a side-effect of that kind of food?