Gut Health Without the Supplement Aisle

The bottle has a number of billions on the front, and the person holding it in the supplement aisle wants to know if it’s the right one. I liked that question when I worked retail. The honest answer sent most people two aisles over, to the beans and the yogurt, and it still does.

A crowd, mostly in the colon

Your microbiome is the crowd of bacteria and other microbes living mostly in your large intestine. For years the line was that they outnumber your own cells ten to one. A careful recount in 2016 put it closer to even, around 38 trillion bacteria to about 30 trillion human cells, weighing a little under half a pound all together, with nearly all of them packed into the colon.¹ Still a crowd, just a smaller one than the slogan.

“The honest answer sent most people two aisles over, to the beans and the yogurt, and it still does.

They live on what you don’t digest, mostly fiber, and people who eat more kinds of plants carry a more varied set of them.² It isn’t an organ with one number I can read, the way I read an A1C. There’s no lab value for it that would change what I’m about to suggest, so I don’t order one. And it isn’t fixed. The trial I’ll get to below moved it in ten weeks with groceries.

Where thirty plants a week comes from

The “30 plants a week” idea comes from the American Gut Project, a citizen-science study that collected stool samples and diet questionnaires from more than 11,000 people. The people who reported eating more than 30 different kinds of plants a week had a more varied set of gut bacteria than those who ate 10 or fewer, along with lower levels of some antibiotic-resistance genes in their samples.²

The headline leaves a few things out. The comparison was 42 people against 43, the two extremes of a much larger group. The diets were self-reported. And it’s an observation, so it can’t tell us the plants did it; people who eat 30 kinds of plants differ from people who eat 10 in a dozen other ways, and nobody randomized them.

I use the number anyway, because it changes the shopping list rather than the scale. Most of us aren’t getting anywhere near enough fiber to begin with. More than 90 percent of women and 97 percent of men in this country don’t meet the recommended intake.³ Most of that gap is in the cart, and the cart is the part I can help with.

“Plant” is broader than produce. Herbs, spices, nuts, seeds, beans, and whole grains all count. A bunch of cilantro, a jar of cumin, and a handful of pepitas are three. A frozen bag of mixed vegetables is usually three or four. Masoor dal and chana dal count separately, and so do black beans and pintos. Nobody has to hit 30. Reaching for a different plant than last week is the habit I’m after.

The fermented-food trial

In 2021 a group at Stanford ran a small trial I think about every time I pass the refrigerated case.⁴ Thirty-nine healthy adults were assigned to two groups, and thirty-six finished. One worked up to a high-fiber diet. The other worked up to a diet heavy in fermented foods, meaning yogurt, kefir, fermented cottage cheese, kimchi and other fermented vegetables, vegetable brine drinks, and kombucha, reaching about six servings a day by the end. Over ten weeks the fermented-food group’s gut bacteria grew steadily more diverse, and 19 of the 93 inflammatory proteins measured in their blood went down, including interleukin-6.

The fiber group surprised the researchers. Diversity across that group didn’t budge, and how someone’s immune markers responded depended on where their microbiome started.⁴ More fiber is still a good idea; it’s the thing most of us are shortest on. It just didn’t do what the fermented foods did in ten weeks.

The trial was small. Eighteen people per group, all healthy, ten weeks, and nobody was tracking whether anyone got sick less; the well-being questionnaires they did collect didn’t move. The fermented-food group did report more bloating in the first weeks, and it had faded by the end.⁴ Six servings a day is a lot of kimchi. I’d want a second trial at a serving or two a day, which is what most people would manage. What I take from it is the direction. The fermented foods changed something measurable in healthy people, and they did it from the refrigerated case.

Where a probiotic has evidence

Fermented food and probiotic are different words, and the scientists who study them are firm about it.⁵ A fermented food is anything made through desired microbial growth, sourdough and sauerkraut alike. A probiotic is a named strain that a trial has shown does one particular thing at one dose. Plenty of fermented foods carry no live microbes at all by the time you eat them, among them bread, wine, most beer, soy sauce, and any kimchi or sauerkraut that’s been pasteurized for the shelf-stable aisle.⁵

The American Gastroenterological Association went through the probiotic evidence in 2020 and came back with a short list.⁶ For irritable bowel syndrome, Crohn’s disease, and ulcerative colitis, it recommends probiotics only inside a clinical trial, because the evidence so far is too thin to call. For children with a stomach bug, it suggests against them. Where it does say yes, the recommendation is conditional and rests on low-certainty evidence, and it’s narrow and strain-specific, meaning a few named strains to lower the chance of a C. difficile infection while you’re on antibiotics, and particular strains for preterm infants in the hospital.⁶

So the bottle with the big number on the front is making a promise that mostly hasn’t been tested. If you’re on antibiotics and want to try one, bring the bottle to your pharmacist and ask whether the strain on the label is one of the ones in the guideline. If you have Crohn’s, colitis, or a weakened immune system, ask your doctor before you start anything.

A fermented-food grocery list

The food side is cheaper, and it’s where the trial above got its result, so this is where I’d spend. Cold case first, since the fermented foods that still have their microbes are refrigerated rather than shelved. If you’re pregnant or your immune system is weakened, the ask-your-doctor line above covers home ferments and unpasteurized kombucha too.

• Plain yogurt or dahi, with “live and active cultures” on the carton. A yogurt that’s been heat-treated after culturing has to say “does not contain live and active cultures” on the label, so it’s easy to tell.⁷ Dahi is the Indian set yogurt, sold in tubs at any Indian grocery and easy to make at home from a spoonful of the last batch.
• Kefir, drinkable and tart, the same idea as yogurt with a different mix of microbes. It goes over oats where milk would.
• Kimchi and sauerkraut from the refrigerated case. The shelf-stable jars have been heated, and heat is the end of the microbes, so cold case only.⁵
• Curtido, the Salvadoran cabbage relish served with pupusas all over Houston. The fermented kind is sour from the cabbage itself; the quick kind is sour from vinegar. Ask, or make it yourself from cabbage, carrot, onion, and oregano with about 2 percent salt by weight, roughly a tablespoon of fine salt for two pounds of vegetables. Pack it under its own brine, leave it at cool room temperature for three or four days, then refrigerate it. Toss it if it grows fuzzy mold or smells off rather than sour.
• Tepache, the Mexican pineapple drink, made from the peel and piloncillo left to ferment a few days under a cloth rather than a tight lid, then refrigerated once it’s fizzy. It’s a little alcoholic, so it’s a grown-up drink.
• Dosa or idli batter, rice and urad dal ground and left overnight until the batter domes and smells sour. The griddle kills the microbes, so this is a fermented food without live ones, like sourdough.⁵ It’s still dinner with fiber and protein in it, and the fermentation is where the tang comes from.
• Miso and kombucha, both from the refrigerated case. Unpasteurized miso is a live food until it’s boiled, which is why it goes into soup at the end, and kombucha is live unless the label says pasteurized.⁵

Two or three of these in the cart on an ordinary week, next to the beans, is the plan. The vegetable ferments and miso are salty, so if you’re watching sodium, lean on yogurt, dahi, and kefir and treat kimchi as a condiment. Start with the one you already like.