Yep, I think you're right in thinking about the gut microbiota.
I'd first want to identify what foods set things off. E.g., sugar usually promotes the bad microbes, which then take over - like weeds in a lawn.
Because oil of oregano is a powerful microbe-killer, I'd look up Herxheimer (die off) effect, then try it wisely.
Some other things to be aware of are probiotics, prebiotics, SIBO... and leaky gut causing general immune activation.
Or maybe you have a food intolerance, such as with lactose or others. Or maybe least likely: an outright gut infection.
Well thanks, lool. It's nice when people reply :)
So let me expand on this a little, simply --> "...leaky gut causing general immune activation."
Your gut is a barrier against bad things getting in, just like your skin is. When your gut lining is disrupted (say, from overgrowth of bacteria or yeast), then bad chemicals and bad proteins can get into your bloodstream. That causes your immune system to react, and things get all stirred up. Just like all the bad symptoms you get if you have a cold, which is your immune system reacting/activating. There can be a very large variety of effects.
Good luck with your self-experiments. Let me know how it goes.