In my family, there are several with CFS/ME and/or the usual co-morbid disorders. We grew up and live in different cities and countries. I also have a relative in the same branch of the family who battled lymphoma. This and related conditions are too prevalent in my family not to be genetic, especially without other common factors (such as local diet, places of birth, places of living). But I agree in part: microbiome will turn out to be one influential factor.
Basically, I think all of the physical prerequisites need to happen all together in genetically susceptible people to create the perfect immune storm. I realize now that @halcyon pointed out, that Dr, Chia has focused mostly on enteroviruses as the cause.
I will look at @halcyon 's Dr. Chia links and your micribiota/viral susceptibility link. I'm definitely curious to read them. I'm also reading through Dr. Chia's site and found this:
....
From this explanation, it seems he thinks there's an underlying immune problem, which makes patients more susceptible to the infections.
Family members share much more than just genes. Research into metagenome - bacteria, viruses etc, all non-human DNA, being passed from parents to children and interchanged between family members is in its infancy but one of the most exciting areas of 'general' modern science.
So when diseases (or susceptibility to diseases) are inherited or running in the family this does not automatically exclude infectious agents. On the contrary, those seem to be part of our family heirloom.
Regarding the question of genes vs gut microbiome playing a central part in immune reactions, there was a study recently that found past CMV infections played a much larger role than genes in one's immune responses.