 Good bacteria, those that live in symbiosis with us, are nourished by fruits and veggies, grains and beans, whereas dysbiosis, bad bacteria that may contribute to disease, are fed by meat, junk food, fast food, seafood, dairy, and eggs. Typical Western diets can decimate our good gut flora. We live with trillions of symbiotes, good bacteria that live in symbiosis with us. We help them, they help us. And a month on a plant-based diet results in an increase of the good guys, and a decrease in the bad, the so-called pathobionts, the disease-causing bugs. Given the disappearance of pathobionts from the intestine, one would expect to observe a reduction in intestinal inflammation. So they measured stool concentrations of lipochilin-2, which is a sensitive biomarker of intestinal inflammation. And within a month of eating healthy, it had declined significantly, suggesting that promotion of microbial homeostasis, or balance by a strict vegetarian diet, resulted in reduced intestinal inflammation. And this rebalancing may have played a role in the improved metabolic and immune system parameters. On an animal-based diet, you get growth of disease-associated species, like bilofila-whadworthia, associated with inflammatory bowel disease, and apute-treatiness, found in abscesses and appendicitis, and a decrease in fiber-eating bacteria. Eat fiber, and the fiber-munching bacteria multiply, and we get more anti-inflammatory, anti-cancer, short-chain fatty acids eat less fiber, and our fiber-eating bacteria starve away. They are what we eat. Eat a lot of phytates, and your gut flora get really good at breaking down phytates. We assumed this was just because we were naturally selecting for those populations of bacteria that could do that, but it turns out our diet can teach old bugs new tricks. There's one type of fiber in nori seaweed that our gut bacteria can't normally break down, but the bacteria out in the ocean that eat seaweed have an enzyme to do so. When it was discovered that the enzyme was present in the guts of Japanese people, it presented a mystery. Sure, sushi isn't raw, and so some seaweed bacteria may have made it into their colons, but how could some marine bacteria thrive in the human gut? It didn't need to. It transferred the nori-eating enzyme to our own gut bacteria. Consequently, the consumption of food with associated environmental bacteria is the most likely mechanism that promoted the enzyme update into our own gut microbes, almost like a software update. We have the same hardware, the same gut bacteria, but they just updated their software to chew on something new. Hardware can change, too, though. The reason this is called the way to a man's heart is through his gut microbiota is because they were talking about TMAO. Certain gut flora can take carnation from the red meat we eat, or the choline concentrated in dairy and seafood and eggs, and convert it into a toxic compound which may lead to an increase in our risk of heart attack, stroke, and death. This explains why those eating more plant-based diets have lower blood concentrations of the stuff, but they also produce less of the toxin, even if you feed them a steak. You don't see the same conversion, suggesting an adaptive response of the gut microbiota in omnivores. They are what we feed them. It's like if you give people cyclomata, a synthetic artificial sweetener. Most of our bacteria don't know what to do with it, but if you feed it to people for 10 days and select for the few bacteria that were hip to the new synthetic chemical, eventually three-quarters of the cyclomate you eat is metabolized by the bacteria into another new compound called the cyclohexalamine, but stop eating it, and those bacteria die back. Unfortunately, cyclohexalamine may be toxic, and so was banned by the FDA in 1969, whereas regular Kool-Aid, evidently, is completely safe. But if you just ate cyclomate once in a while, it wouldn't turn into cyclohexalamine, because you wouldn't have fed and fostered the gut flora specialized to do so, and the same with TMAO. Those that just eat red meat or eggs or seafood once in a while would presumably make very little of the toxin because they hadn't been cultivating the bacteria that produces it.