One of the problems with observational studies just occurred to me, after reading a couple of articles about "the obesity problem" -- people who don't want to face what modern foods do to us grab at straws of conceivable "causation" and waste a SHITLOAD of professional time exploring absolute nonsense.
...Like "food reward." While ignoring the PHYSICALLY addictive properties of grains and sugars. Significant difference.
...Like demonizing "high-fat" foods such as the large McDonalds' combos ... without observing that they're MUCH higher in carbs than fats.
People believe what they want to believe, no matter how much data piles up that their ideas don't pan out in real life. This is why obese people who don't *like* low-carbing insist that carbohydrates are necessary -- they love their "fix" too much to abstain long enough to kick the habit, i.e. find out how much better they'll feel without it.
I feel that this is the cogent bit about the microbiome hypothesis of obesity. Yes, sick people have sick intestines. Yes, children born via C-section are more likely to be one of those people. Yes, swapping gut-bugs between fat, sick people and lean, healthy people makes an impact on the wellbeing of both types.
But I think of the microbiome as just another red herring. What lurks in your colon depends ENTIRELY upon what YOU, as an adult, have ingested. Get a candida overgrowth after a single high-carb day? It's because of what foods, drinks, and antibiotics YOU took in, sometime in your history.
Modern-day African hunter-gatherers with great health have an entirely different set of "bugs" in their poop than the average American? WHY THE BLOODY HELL SHOULD THAT BE ANY SURPRISE TO ANYONE? I'll bet the most perfectly healthy American ALSO has an entirely different set of "bugs" from the Africans'. The latter got their mothers' bugs at birth, never took antibiotics, drink non-tap-water, eat tubers grown in entirely different soils having entirely-different bacteria in them....
Red herring. Too many variables. Inconclusive.
WHAT people eat is the important part. Diet composition sets the stage for EVERYTHING that comes after. Eat things that feed bad gut-bugs and you'll have bad gut-bugs. Eat an all-meat diet and the bugs that love sugar will languish. IF you eat an all-meat diet, you don't NEED the bugs that a fibre-eater REQUIRES. Why try to cultivate them? They're COMPLETELY SUPERFLUOUS.
We of the "western world" too often think we should be able to do/have/eat anything we want. FREEDOM!TM ya know? That's just plain stoopid. This is like the lactose-intolerant insisting on the "right" to drink milk, or celiacs demanding their share of the wheat supply without the repercussions. Ought we ALL to think we should be able to drink alcohol, despite the existence of people who haven't the enzymes to metabolize it properly, and despite the existence of alcoholics?
Many people -- many many MANY -- simply behave like spoiled children. If we can't eat our cake and have it too, it's NOT FAIR. Sorry, but biology doesn't work like that.
If your biology calls for a low-carb Paleolithic diet and what you *want* is the SAD, you can whine and deny all you like, but your genotype will win every argument, every single time. Trying to find a loophole -- chasing the "perfect" microbiome might distract you for awhile; you might even improve a little for awhile; but it's NOT going to solve all your problems because it is very unlikely to be the main thing wrong with your physiology.