My understanding of the gut microbiome is that it consists of over a 1000 different bacteria which each one deals with different parts of the food eaten. Things you eat a lot of will have more relevant bacteria, as their food supply is greater. If you stopped eating that item, the bacteria diminish as the food supply drops. If you change your diet completely, your microbiome changes the ratios of bacteria dependent on diet. this is why we suffer gut problems for a few days when eating a totally different diet, as the bacteria need to increase or decrease accordingly.
from the info i've seen, they are looking at how your gut handles fat, so if your diet is highish in fat, the recommendation should be to continue as you are as you should have the correct ratios of the fat handling bacteria.