There is widespread research on the gut bacteria composition and evidence for microbiome adaptation, which must be simply from your diet. 

Rapid compositional shifts: Studies show the gut microbiome can begin changing within 24-48 hours of dietary modification, with significant alterations visible within 3-5 days. Long-term dietary patterns create stable microbial ecosystems adapted to available substrates.
Grain-loving bacteria: Chronic grain consumption enriches populations of bacteria that efficiently ferment starches and produce enzymes to break down complex carbohydrates – particularly Bacteroidetes species and certain Firmicutes. These bacteria thrive on the resistant starches and fibers in grains.
Metabolic signalling: Here’s where it gets interesting – these microbes produce metabolites (short-chain fatty acids, particularly acetate and propionate) that can influence host appetite and food preferences through gut-brain axis signalling. Some research suggests they may actually create cravings for the substrates they prefer.

The Transition Challenge

When you shift to low-carbohydrate eating, you’re essentially “starving out” a significant portion of the established bacterial population.

This creates:
Die-off symptoms: As carbohydrate-fermenting bacteria decline, they release endotoxins – contributing to temporary fatigue, brain fog, and cravings
Competitive dysbiosis: The ecosystem destabilises before new populations establish
Metabolic withdrawal: Reduced production of certain SCFAs the body had adapted to

This is likely part of what people experience as “keto flu” beyond just electrolyte shifts.

The Evolutionary Perspective

Populations with multi-generational grain consumption (post-agricultural revolution) do show distinct microbiome signatures compared to hunter-gatherer populations. The Hadza people of Tanzania, for example, have dramatically different gut bacterial profiles than Western grain-consuming populations.
For your GAPS protocol work: This microbial adaptation is precisely why the transition period is challenging but necessary. The 3-4 week adaptation window you likely observe isn’t just metabolic switching – it’s ecosystem remodelling at the microbial level.