I agree that it's likely microbiome changes. The microbiome is part of our body's functioning, so changes there can affect other functions of the body, and other parts of the body can affect the microbiome. I've had two instances where a change in my gut microbiome has worsened my ME symptoms. One was fixed by probiotics (pure luck that one of 14 strains in the capsule was the one that I had somehow lost). The other was fixed by food poisoning (coconut milk was a bit off), which gave my guts a good flushing out. Correcting such a problem can be as easy as taking a single probiotic capsule, or require drastic antibiotic treatments, FMTs or other such techniques, and I don't think there's any easy way to determine what is required.
You could experiment with diet, which can alter microbiome balance. Keeping a food/activity/symptoms journal is important, since human memory is too fallible for that. Maybe you'll find some food to add or avoid that will provide some improvement in your symptoms.