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Good bacteria—those that live in symbiosis with us—are nourished by fruit and veggies, grains, and beans, whereas dysbiosis—bad bacteria that may contribute to disease—are fed by meat, junk food and fast food, seafood, dairy, and eggs. Typical Western diets can “decimate” our good gut flora.

We live with trillions of symbionts—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 “lipocalin-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 “Bilophila wadsworthia [associated with inflammatory bowel disease and] A. putredinis [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, anticancer 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 is eaten raw; and so, some seaweed bacteria may have made it into their colons. But, how could some marine bacteria thrive in the human gut? They didn’t need to; they 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 microbe[s]”—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 carnitine 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 adoptive response of the gut microbiota in omnivores.” They are what we feed them.

It’s like if you give people cyclamate, a synthetic artificial sweetener. Most of our bacteria don’t know what to do with it. But, you feed it to people for ten days, and select for the few bacteria that were hip to the new synthetic chemical. Eventually, three-quarters of the cyclamate you eat is metabolized by the bacteria into another new compound called cyclohexylamine. But, stop eating it, and those bacteria die back. Unfortunately, cyclohexylamine 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 cyclamate once in a while, it wouldn’t turn into cyclohexylamine, 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, 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.

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