It's worth noting that the study[1] does not suggest that. It says that there has been some "circumstantial evidence for a connection between cravings and the composition of gut microbiota" and notes that there would be evolutionary pressure on microbes to be able to influence cravings, but gives no evidence on this point.
The thing the study was actually researching was ways microbes could influence cravings, not whether or not any of them actually were.
Meanwhile, it does appear you can noticeably change the expression of your microbiome by long term changes in your diet, but the effects we've actually found are still fairly subtle (at least in terms of metabolic outputs), and I've found no studies that indicate you can change cravings due to those changes. For example, in [2], "chocolate desiring" subjects had noticeably different microbiomes than "chocolate indifferent" subjects, but that difference was significant even when on the exact same diet (which was necessary for the study's methods).
You have to be careful not to extrapolate from actual data to "what makes sense". Spurlock's stuff appeals at a gut instinct level, but that's often the most dangerous kind of thing for science since our brains desperately want to make patterns out of data even when there isn't one.
[1] http://onlinelibrary.wiley.com/doi/10.1002/bies.201400071/fu...
The experiments basically fed gut bacteria from thin creatures, (mice / humans) to fat ones (mice) and they lost weight and visa versa for fat to thin. I guess you could extend that experiment quite easily to mice and chocolate though I'm not sure it's been done yet. Maybe if anyones got some experimental mice and bars of chocolate knocking around they could report back?
But i'm not saying that there is no such thing as the microbiome directly influencing your brain, bacteria produce a wide array of by-products. In which way these by-products affect our bodies is exactly the question. I just want to point out that there are types of dysbioses that can reduce the ability to absord certain nutrients and by that could exacerbate the problem of cravings.
Are you sure you really want that extra side of chips? Or has your gut biome decided it wants that extra fat, and influences you to eat it.
Additionally, you can "reseed" your gut biome by changing your diet. Do you crave greasy food? Go vegan for 2 weeks. The new gut biome that develops and takes hold may soon have you start craving healthier foods. A change in diet can change your biome in as little as 4 days. (2) You can witness this phenomena in the movie Super Size Me. At the start of the movie Spurlock is disgusted by eating McDonalds for every meal. But, by the end of his experiment, his gut biome has significantly changed, and you can literally see his mood darken when he is not eating greasy fries and burgers. He craves, or should I say, his microbiome craves those happy meals, and is influencing both his taste receptors, health, and general mood in order to manipulate him in to a trip to the drive though.
1. http://www.theatlantic.com/health/archive/2014/08/your-gut-b... 2. http://www.scientificamerican.com/article/the-guts-microbiom...