Well, if you believe that  humans have been cooking "for far longer than paleo advocates admit", then you have a bit of a problem. All solid  archaeological evidence re cooking shows that cooking got invented c.250,000 to 300,000 years ago or so. The only real guru who claims otherwise is the pro-vegetarian chimpanzee researcher Richard Wrangham, who has  grudgingly but openly admitted that there is no actual valid palaeoanthropological evidence to support his claims. He  was the one who theorised that cooking got invented c.1.8-1.9  million years ago.
Of course, length of time is not actually relevant either, in terms of  likelihood of  evolutionary adaptation. For example, pandas have been eating mostly bamboo for  several millions of years and still have a carnivorous digestive system despite that.
Plus there are various toxins such as advanced glycation end products, polycyclic aromatic hydrocarbons, nitrosamines and heterocylic amines, all produced by cooking and there are now plentiful scientific studies showing how very  harmful these substances are to human health over time. If humans were genuinely adapted to cooking, one would expect humans to be somehow fully  immune to such toxins, yet this is not the case.
Other than that, human gut flora levels and types change considerably  depending on one's particular diet  at the time. Hunter-gatherers are  often  known to eat some raw animal food  as part of their diet, so they would be getting in plenty of  extra bacteria that way and be able to replenish any needed gut flora. It does not seem to make sense that ancient bacteria are somehow "better" than current modern  bacteria. After all, bacteria are one of the few organisms with a really fast ability to adapt on an evolutionary level as they reproduce so very quickly.
Raw, palaeolithic dieters find it very easy to replenish gut flora, if they ever need to do so. They just eat raw, aged meat, what is generally referred to as "high-meat".
Geoff








> Date: Thu, 26 Mar 2015 07:25:27 -0300
> From: [log in to unmask]
> Subject: You don't have the gut (microbes) to stomach a real paleo diet
> To: [log in to unmask]
> 
> This is pretty much obvious because we already knew that...
> 
>  a) Intestinal flora varies quite a lot between different
>     populations
>  b) Antibiotics and industrial foods have already made
>     parts of our gut flora extinct
> 
> But now some researchers have done the difficult legwork of
> analyzing the intestinal flora of some genuine, minimal
> contact hunter gatherers:
> 
> 
> http://news.sciencemag.org/biology/2015/03/ancient-bacteria-found-hunter-gatherer-guts
> 
> Personally I've long been a paleo-skeptic... I believe that
> a "modern paleo" diet has *some* health benefits and is useful
> for weight-loss and to resolve some other specific issues, but
> overall probably isn't the *healthiest* diet for modern
> humans.  I think humans have cooked food much longer
> than most paleo advocates admit, and also that evolution
> works much more rapidly than paleo people give it credit for.
> And our gut microbiomes evolve along with us (or you could
> say that their changes *are* a way of us evolving) and are
> part of us, and sad as it may sometimes seem, we can never
> go back.
> 
> The real hardcore paleo nuts may now dream of getting a
> fecal transplant from an Amazonian Indian, but I must warn
> you that most Indians would kill you in a heartbeat if you
> even suggest that you want to absorb some of their essence
> in that way!
> 
> Cheers...