Hi BadBoy. One of the things microbial influence.com shows for treatments is antibiotic use, but as you can see they don't advocate it as those bad bacteria come back, typically in greater numbers when the antibiotic use is over.
Something you may want to look into is the specific carbohydrate diet, or SCD for short.
The premise of the SCD is that complex carbs, ie those in starchy foods, require various digestive procceses to break down those carbs into simple sugars (the only kind of carbs the body absorbs). What happens is the digestive tract isn't able to break it down fully when the digestive tract is compromised (think leaky gut), so what's left over goes to the lower intestine and feeds bacteria. Causing bacterial overgrowth of bad strains of bacteria.
What the SCD does allow is simple carbs. Simple carbs require virtually no digestive process, since they're simple carbs they're immediately absorbed in the upper intestine. Leaving no carbs to feed bacteria. There's even an entire list of legal and illegal carbs. If you want to follow a raw diet, while still doing SCD, you just eat the raw scd legal carbs.
Something recommended on the SCD is 24 hour yogurt, which is high in probiotics. It's not very paleo, and you'd be getting a bunch of strains that aren't likely to colonize the gut of someone on a natural diet. What I recommend is various fermented foods. Besides high meat, you could look into the book "Wild Fermentation." The book has tons of ferments you can make with SCD legal ingredients.
The purpose of the fermented food is to replenish with good bacteria as the bad bacteria die off. You'd be eating SCD legal carbs raw, with high quality animal foods raw. And various fermented foods like sauerkraut, pickles, fermented honey, high meat, and anything else you can ferment for the good bacteria.
Here's a link with the science behind the diet -
http://www.breakingtheviciouscycle.info/p/science-behind-the-diet/Here's the legal/illegal list (legal foods are allowed, illegal ones aren't).
http://www.breakingtheviciouscycle.info/legal/listing/Something that makes Raw-SCD even better than regular SCD is that the makers of the SCD didn't consider animal food digestibility. This is just theory. But since raw animal foods digest so much better, maybe cooked animal foods still feed bacteria in the gut. It's a possibility, and can explain why it takes some SCD'ers so long to recover.
Something else that's interesting to note, is that on the eat wild website under food safety -
http://www.eatwild.com/foodsafety.html - it shows how grass fed cows have very low levels of e.coli, and various other bad bacteria. It makes sense that grass is the cow's natural diet, so bad bacteria don't thrive in their digestive tracts. But when you feed them grains, the bacteria mutate into dangerous strains.
The same is true for humans, and that's the exact premise of the SCD. And raw SCD is even better than regular SCD.
I suggest reading "Breaking the Vicious Cycle." The book will give you an understanding of just how strict you need to be for the diet to work. As well as the real science behind it. Of course, your goal would be to eat 100% raw-SCD. However if you HAD to cheat for whatever reason, you'd stay within the bounds of the SCD. Which would essentially still be paleo (SCD is like strict paleo). So your cheat meal would be cooked meat with SCD legal seasonings. Not french fries.
