I think the implication of the bacteria screwing up metabolism and the signaling mechansims for fat storage/fat burning impacts the "simple physics" approach of calories in and calories out.
If you put $10 worth of gas in your vehicle every day but don't drive much, it starts to fill up with gas and you start towing an extra tank of it around with you. (I'll call that the 'trailer', which is fed from an overflow condition in your truck's normal tank). If you drive more and fill up less your truck's tank will run low, and this will cause it to start drawing fuel from the trailer to bring the level back to normal, but slowly emptying the trailer. It's kind of like having a reversible fuel pump between the truck's tank and the trailer, and that's kind of how fat storage is supposed to work. If you're used to your vehicle working properly, it runs trim and has a tiny little trailer behind it. When you see people hauling around big semi-truck trailers of gas you think they couldn't be driving very much, and when they do it's just between gas station because all they do is fill up.
But the gut bugs produce a compound that screws up the fuel sensors (probably by evolutionary design), so that the truck's fuel-tank pump always tries to pump fuel into the trailer, whether the truck's tank is really full or not, and won't ever pump fuel from the trailer back to the regular tank. The fuel transfer pump is stuck on, and in one direction, perhaps because the truck's tank level always says "full" and the trailer's sensor always says "empty."
So whenever the defective truck fills up, it immediately starts pumping gas into the trailer, emptying the regular tank earlier, and if driven around like a normal vehicle it just runs out of gas sooner, and won't feed from the trailer, ending up stuck on the side of the road. Simple physics says it has plenty of gas to drive half-way across the country, but it just doesn't seem to tap into the supply to burn any of it. Instead the truck rolls into the nearest gas station and fills up, because to the sensors, and to the carburator, it's out of gas - even though it's towing an entire semi-trailer of fuel around.
For such people, losing weight through the normal mechanisms (which are based on having a working cross-feed system) would be like trying to shrink a tumor by exercising, on the theory that it will eventually burn off.