"We know quite a lot about associations between food and health, we know a bunch of associations between food and microbes, and we know a bunch about associations between microbes and health," says microbiome researcher Rob Knight.
What researchers don't yet know is how to put the whole picture together.
Are certain vegetables good because they have a positive effect on our microbiome? Or do they have a more direct effect on our metabolism? "That's still very much an emerging area of research," Knight tells The Salt.
Still, some foods look promising. Dietary fiber serves as food for many of the bacteria that live in our guts, says microbiome researcher Jeff Leach of the Human Food Project. "It doesn't hurt as a general rule to eat more fiber," Leach tells The Salt.
Too little fiber could starve the bacteria we want around. "When we starve our bacteria they eat us," Leach says. "They eat the mucus lining – the mucin in our large intestine."
Knight adds that when we do keep our bacteria well fed, they, in turn, give off nutrients that nourish the cells that line our guts. Fiber, Knight says, "is thought to be good for your gut health over all."
There are a lot of different ways to get fiber. Leach recommends getting it from vegetables. Eat a variety of veggies, and eat the whole thing, he recommends. "If you're going to eat asparagus, eat the whole plant, not just the tips," he says.
Fiber was also central to Leach's suggestion to Stein to eat more garlic and leek. Those vegetables contain high levels of a type of fiber called inulin, which feeds actinobacteria in our guts. In fact, inulin is considered a prebiotic, since it feeds the good bacteria, or probiotics, that live inside us.
Garlic actually has antimicrobial properties, which paradoxically, could also be good thing for our microbiomes. One study shows that garlic hurts some of the bad bacteria in our guts while leaving the good guys intact.
Whole grains are another good source of fiber — but evaluating its benefits is a bit trickier. Whole grain consumption seems to be associated with high levels of a type of bacteria prevotella, Leach says. "Prevotella has been associated with inflammation in HIV patients [and] it's been associated with rheumatoid arthritis." We don't know why that is, Leach says. "So the jury's still out on whole grains."
Another way to build a better microbiome may be to eat foods that naturally teem with probiotics. Michael Pollan mentions the puported benefits of organic veggies fresh from the soil in his piece on the microbiome for The New York Times Magazine.
But this can get tricky, Knight says. In the absence of pesticides, a lot of veggies turn on their natural defenses in order to fight off insects, and those defenses can be toxic to humans.
Fermented foods like kimchi, saurkraut and yogurt might be surer sources of probiotics. Researchers are unclear about whether these have any lasting effect on the composition of our microbiome, but in some cases they do seem to help.
"Epidemiologically there seems to be some evidence that eating fermented food is beneficial rather than harmful," Knight says. But researchers are still trying to figure out why.
Still, the big question is whether we can actually reshape our microbiomes by changing our diets. "Short term dietary interventions," Leach says, "don't have a dramatic impact." And slightly tweaking your diet probably isn't going to do much either.
"The question is how dramatically are you changing your diet," Leach says. "If you go from eating 10 to 15 grams of fiber a day to eating 40 or 50, you may see some changes."