I can't be bothered to write a complete takedown, but two things come to mind:
1) The author falls prey to the naturalistic fallacy:
> We can actually achieve a good mixture of gut bacteria very similar to that of our hunter-gatherer ancestors by adopting a good diet high in fiber and low in processed foods.
2) I've read studies to the effect that some infectious diseases can affect intelligence. Particularly when children are young - apparently there is a mechanism to either further develop the immune system or the brain depending on the environment (this might partially explain the Flynn Effect). I can't find the exact study (this used to be in this section - https://en.wikipedia.org/wiki/Impact_of_health_on_intelligen... - but I think it was edited out at some point).
Your point one sounds like a fallacy fallacy, i.e., just because some conditions of a fallacy are present, does not mean it applies.
The article does not state that every aspect of the hunter gather microbiome is superior to the modern day ancestor, rather just acknowledges the complex and long process of evolving mutually beneficial microbiota which is being disrupted by modern technology. That statement is not as controversial as you imply.
Perhaps when you aren't so busy reading Hacker News, you might be "bothered" to give a more complete reposte.
Ironically, I think you may have fallen victim to a kind of fallacy fallacy fallacy, because the fallacy fallacy concerns the interpretation of an argument assuming a valid fallacy in it does exist. At least according to Wikipedia's definition of fallacy fallacy.
Rather, in this case the parent post merely misidentified a fallacy.
That's not a naturalistic fallacy. The author's claiming that our ancestors had lower incidence of bowel disease or were perhaps healthier in other ways. Feel free to refute that claim, but don't attack a strawman.
Well, the author has to back that claim first. The burden of proof is on the one who brings the original claim (despite modern advances in hygiene and medicine), not on me.
1) The author falls prey to the naturalistic fallacy:
> We can actually achieve a good mixture of gut bacteria very similar to that of our hunter-gatherer ancestors by adopting a good diet high in fiber and low in processed foods.
2) I've read studies to the effect that some infectious diseases can affect intelligence. Particularly when children are young - apparently there is a mechanism to either further develop the immune system or the brain depending on the environment (this might partially explain the Flynn Effect). I can't find the exact study (this used to be in this section - https://en.wikipedia.org/wiki/Impact_of_health_on_intelligen... - but I think it was edited out at some point).