There’s argument about why ‘high fat’ diets cause deleterious effects on the microbiota. Anything we eat but do not absorb fully will potentially feed the bugs (bacteria, fungi, whatever), which we can generally call fermentation.
The effect of fermentation (positive, negative) depends on the selectivity of the feeding (which bugs eat what), which depends on the strains present and the foodstuffs being fermented.
Almost everything can be fermented.
Simple sugars can be fermented by almost everything, so the benefit goes to the bugs which are faster growers and dividers (generally more pathogenic); hence why glucose or fructose mal-absorption is big trouble.
Various fibers can be fermented, and there is broad variability in the effect, since some fibers (such as some types of ‘resistant starch’ and fructooligosaccharides like inulin) preferentially feed the good guys (like bifido) and some longer chain carbs preferentially feed the bad guys.
Protein is less universally fermented, which highly advantages the bugs which can eat nitrogen compounds efficiently, like klebsiella and clostridium. Thus, too much protein, overtime, can lead to an increase in pathogenic strains.
Fat is, as I understand, not fermented (at least negligibly so). But the bile acids used to digest fat are fermented selectively by a relative few strains which have adapted to this, which includes the newly discovered Bilophilia.
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12820.html
In the case of the high fat diet, at least two things are going on here:
1) The increase in bile acids needed for fat digestion increase the presence of bugs that can eat bile acids (like bilophilia)
2) The high fat diet was also low in carbs, and therefore low in substrates that would feed non-fat-eating bugs. Thus, these bacteria, including bifido and other generally-accepted-to-be ‘good bugs’ would be starved.
Some believe that the latter is far more important than the former, and that a high fat diet that is also high in inulin or resistant starch type fibers would suffer ZERO or NEARLY ZERO deleterious effects.
http://humanfoodproject.com/sorry-low-carbers-your-microbiome-is-just-not-that-into-you/
One could ask the questions: so what?
Well, I think this is important to note how many long-time low carbers have some serious problems after months to years of low carbing, including autoimmune and metabolic issues. In fact, in the one year all-meat diet at Bellevue Hospital, I believe it was Andersen who ate a sandwich on his first day back from the year of only meat, and ended up in the hospital the next day needing intravenous antibiotics for a serious pneumonia infection. The researchers didn’t know what to make of that, but they added that comment into the end of the paper.
I think we now know what to make of it: the zero carb, high protein diet selectively bred relatively pathogenic, protein-consuming bugs, while it starved the good guys. As soon as he ate some easy-to-digest starch (everything can eat glucose and short glucose units), the bugs went wild. I think supplementing with inulin for a week or two as a transition from the low carb diet to the more typical diet could have prevented the whole shebang (my hunch).
To now get to the original question: are some people screwed? Yes. If the necessary strains are present but just dwindled in number, changing the diet may alleviate everything by re-balancing the proportions of the various strains. Eating more inulin, tubers, and fruits, and less simple sugars and protein (but still getting enough protein) will re-balance things within a few months to years. Even biofilms won’t stand a chance, since well-fed bifido can destroy pathogenic biofilms.
However, if the needed strains are simply NOT PRESENT, you’re screwed. My understanding is that many of the ‘needed’ strains don’t exist out-and-about, but only in our intestines. They have essentially been evolved for within our intestines, and they are only passed from one set of mucus membranes to another. So, vaginal births are good, C-sections bad. Prebiotics and vitamins good, antibiotics bad.
The best hope for someone without the proper strains is to eat as well as you can, minding your symptoms, and to have lots of mucus membrane contact with other, healthier people (kissing, sex of all types); and to potentially get a fecal transplant, though I would keep that on the back-burner since it is very new and many things are yet to be worked out with that.
This should not be thought of as exclusive to eating a nutrient-dense diet. The body has many tricks to deal with bacterial endotoxin and/or mycotoxin infiltration and so on when provided with ample nutrients. And also keep in mind, the deleterious effects of endotoxin (that is, the bad effects of bad bugs) are amplified in the presence of high PUFA, for several reasons including greater permeability of the intestines in the first place, and inability of the liver to be able to quickly and quietly detox the garbage coming in from the intestines.
So, eat well, have some hot sex, kiss everybody as if you were Italian, and go from there.