You have to be careful with microbiome research because it’s a buzzword that gets crammed into a lot of research papers to imply something bigger. This is a single paper from Nestle Research Center (yes that Nestle) from 2007 that doesn’t even cite a number of people sampled in the abstract.

They didn’t run any experiments trying to change the diet or microbiome. They just correlated dietary preferences with some markers that might be correlated with the microbiome.

The paper does not say anything about how changing the microbiome might change preferences. The simplest and most well tested explanation is that dietary preference are driving the microbiome.

There’s a lot of woo-woo microbiome discussion out there that misses the really obvious basics of how the microbiome comes to exist and thrive: What you eat is what the microbiome eats, so changing what you eat will change the composition of bacteria that thrive. People who prefer chocolate are correlated with people who prefer sweet diets. High sugar intake is proven to alter the microbiome.