Can you change your gut microbiota by changing your diet? Would that affect calorie uptake?

Question

I have seen peer-reviewed papers mentioning the daily changes in gut microbiota composition according to dietary changes. See for example this paper:

http://genomebiology.com/2014/15/7/R89

My question is related to this one:

Relationship between our microbiome and personalized nutrition

If, according to these recently published scientific results, it takes a day to change the gut microbiota to adjust to the dietary change, and the presence of certain microbes makes food assimilation more effective,

Does this mean that alternating a protein-rich meat and dairy diet with a carbs-rich diet every day would make our microbiota switch daily and not have time to increase calorie uptake?

Answer 1

Firstly, it should be noted that a stable, healthy microbiome is generally thought to be a marker of health; actively disrupting it through diet in an attempt to fight with it over nutrients is therefore not necessarily a good idea, as it can affect the health of not only your gut but also your immune system, etc.

Dysfunctional microbiomes are for example associated with behavioral problems in eating disorders.

Nonetheless, diet shifts have been used as a tool to attempt to control the microbiome and put it in a "healthy state". You can indeed use consumption of some foods to shift microbiome composition. Presumably if you did this in a sufficiently disjointed way, you could throw your microbiome into a sort of ecological chaos.

However, it would be much simpler to just constantly take antibiotics to ensure that your gut load of microbes was generally low. This still isn't a good idea, as it can lead to Clostridium difficile or E. coli infections or other bad things, but it would be a much more straightforward way of getting to the desired end state.