darryl where did you get this info "oligofructose (onions, leeks, garlic etc) increases Akkermansia 100-fold" ?
As an isolated supplement, given to genetically obese mice consuming high fat lab diets. I don't believe it would have anywhere near this effect taken as a supplement in ordinary human diets. However mice on HFD is such a common protocol to induce chronic Western diseases, and the diets are so well defined, that its probably a relevant model to humans eating highly refined Western diets.
Everard et al, 2013. Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proceedings of the National Academy of Sciences, 110(22), pp.9066-9071.
I'm not persuaded there's anything special about oligofructose, as it appears any microbiota-available carbohydrate that increases intestinal short chain fatty acids (oligofructose, bean α-galactosides, arabinoxylan, resistant starch) will increase mucin and thence feed Akkermansia. The studies on cranberry polyphenols and metformin suggests that compounds with mostly antimicrobial action also have limited positive impact, perhaps by impairing competing species.
As for the effects of onions and garlic on the human gut microbiota, there just been one non-compliance compromised pilot study that demonstrated significant effects on Bifido, Lactobacillus, C. diff and Bacteroides, but didn't identify whether the high onion diet raised or lowered amounts compared to the low onion diet.
Just because something has antimicrobial properties doesn't mean its an antiseptic. In many cases it just selects for resistant species. Hominins have probably been eating bulb vegetables for several million years. Plenty of time for the normal microbiota to adapt, though perhaps not enough for opportunistic intestinal pathogens to do so.
More on SFCAs and mucin production:
Willemsen et al, 2003. Short chain fatty acids stimulate epithelial mucin 2 expression through differential effects on prostaglandin E1 and E2 production by intestinal myofibroblasts. Gut, 52(10), pp.1442-1447.
Burger-van Paassen et al, 2009. The regulation of intestinal mucin MUC2 expression by short-chain fatty acids: implications for epithelial protection. Biochemical Journal, 420(2), pp.211-219.
Edited by Darryl, 29 October 2016 - 10:17 AM.