The article is about surface external bacteria - which are very, very different to the bacterial colonies which live inside your digestive system (and also only there - if any of those get inside your circulatory system that's where most "flesh eating bacteria" horror stories start from).
There's a naturalistic fallacy heavily at play here, because humans have never before lived in such close proximity in such high density dwellings as they do today. The idea that this doesn't merit some forward thinking on how we manage personal hygiene standards is ridiculous.
Do you have any evidence for your beliefs? Skin flora is largely beneficial to hosts. Like internal bacteria, it can be disrupted and become pathogenic.
Do you know of any studies that show that frequent washing with soap decreases pathogens and promotes beneficial skin flora?
The anecdotal experience of people like me who stop washing with soap is that we smell better. This suggests that soap was disturbing our skin flora.
I'm willing to be proven wrong on that point, but you need actual evidence. Calling something "a naturalistic fallacy" without evidence of your own is a perfect example of a fallacy fallacy.
Edit: To be clear, I'm not just saying I smell good. Women spontaneously tell me "you smell good!" without knowing about my non-soap habit.
A naturalistic fallacy is simply appealing to "this is way it is before we do anything". Others have presented the counter-evidence - i.e. human hygiene and life-expectancy and disease rates got way better with the introduction of hand-washing and soap.
I'd think carefully about your anecdotal evidence. The social contract is we don't comment on matters of hygiene directly, and I know I couldn't smell how bad me and my schoolmates smelt after a couple of days field-trip out camping. That didn't mean we didn't.
I edited my response to clarify that I've had spontaneous compliments on how I smell, particularly since I switched. This is without people knowing I don't use soap.
And I thing hand-washing is good. We have clear evidence it works.
But is there any evidence that washing the whole body with soap on a daily basis is beneficial? The counter-evidence you speak of refers only to hand-washing.
Wikipedia distinguishes them, and that's in line with my understanding, although I don't know that my understanding wasn't derived at some point from Wikipedia or a descendent source.
As Wikipedia (and, apparently, G. E. Moore) would have us believe, the "naturalistic fallacy" is believing that you can reduce good/bad to natural states, and seems more closely related to Hume's "is-ought problem" than to the "appeal to nature". I actually think this comes down to disagreement about what is meant by "good/bad" more than substance, though.
Clearly, some do use "naturalistic fallacy" to mean "appeal to nature", and I'm not certain the original use of the term is worth preserving as distinct from Hume, but I'd encourage "appeal to nature" for clarity since that seems to have no ambiguity.
There's a naturalistic fallacy heavily at play here, because humans have never before lived in such close proximity in such high density dwellings as they do today. The idea that this doesn't merit some forward thinking on how we manage personal hygiene standards is ridiculous.