One study suggests that choline feeds bacteria in meat (red, white, fish, eggs, but not dairy) eaters, that produce TMAO that damages liver and promotes atherosclerosis; but this is mitigated in vegetarians who consume little L-carnitine and choline in their diet.
Eating foods rich in these nutrients (including supplements) would seem to have some serious known negative effects along with the postulated positive effects. Continuous dosing may lead to continuous high TMAO levels, and with it the stereotypical cascade of "Western" metabolic disorders.
In one study I read that Anaerococcus hydrogenalis, Clostridium asparagiforme, Clostridium hathewayi, Clostridium sporogenes, Escherichia fergusonii, Proteus penneri, Providencia rettgeri, Edwardsiella tarda were implicated in TMA production from choline. These germs can be pathological on their own.
- A. Hydrogenalis eats meat
- E. Fergusonii eats glucose and produces flatulance and eats other L-sugars as well and has been detected in clinical settings in human blood and spinal fluid
- Clostridium species seem to eat meat and the lab medium is usually cooked meat
- P. Penneri eats meat and sugar and prefers an alkaline environment in contaminated meat products, is implicated in kidney stone formation, and doesn't metabolize citric acid; E tarda is a meat eater and infects fish
- P. rettgeri eats glucose and other sugars and sugar alcohols and has been found on meat products
Probiotics such as inulin (artichokes, garlic, leeks, chicory, asparagus) may supress these organisms by promoting other strains of microorganisms. Maintaining an acidic gut via acid-producing beneficial microorganisms, keeping to a more consistently vegetative diet, and/or shifting protein to vegetative sources and dairy consumption may shift the balance away from the pathogenic TMA producing strains and toward more beneficials.
Sorry not to cite all my sources in the text, but as I said these are just my notes. I did jot down a few of the papers, but any search engine can show you more, particularly if you search PubMed for papers.