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http://care.diabetesjournals.org/content/33/10/2277.full
A little light reading.
I don't doubt that all of the overweight prisoners the allies found in the concentration and prison camps near the end of WWII suffered from these same gut flora issues.
You can throw up all sorts of links to research that supports whatever it is you want to claim. But I'm the last person who is going to believe that you've read through and fully understand what they've done here, and have taken the time to slog your way through all of the references. Yeah, sure.
Again, if a person consumes less energy than they burn, they will lose weight. It will take some people longer to do so, but in the end, you cannot deny thermodynamics. Not even gut flora can do it. Sorry.