In Defense of Dirty Produce

This Week’s Research Highlight

Your grocery store produce is teeming with bacteria.

One analysis found that a single organic apple contains over 100 million bacteria — not just on the skin, but buried deep inside the flesh and core. That’s 100 million microbial signals, delivered in a single bite.

To most people, that sounds…kind of gross. We’ve been taught to be wary of bacteria, especially on our food. But here’s the twist: These microbes may be vital for keeping the immune system from overheating as we age.

A new study of nearly 8,000 older adults found that those who ate the most microbe-rich foods — including raw produce and fermented foods — had a significantly lower risk of death, especially from cardiovascular disease.

Not because of vitamins. Not even because of fiber. But because of the bacteria.

Let’s take a look.

What the Researchers Did

To investigate how microbial exposure through diet might shape longevity, researchers analyzed data from the National Health and Nutrition Examination Survey (NHANES) — a nationally representative U.S. health study that combines in-home interviews with physical exams conducted at mobile centers.

They focused on 7,882 adults aged 60 and older, tracking deaths and causes of death over eight years. Participants were grouped by their intake of dietary live microbes — a category that includes more than just probiotics.

In this study, live microbes referred to all viable microorganisms naturally present in food, including:

• Fermented foods like yogurt, kefir, and sauerkraut

• Raw fruits and vegetables, especially unpeeled or minimally processed produce

Microbial exposure was estimated using 24-hour dietary recall data and a food classification system based on microbial load:

• Low (<10⁴ CFU/g): cooked, processed, or sterile foods

• Medium (10⁴–10⁷ CFU/g): fresh, raw foods

• High (>10⁷ CFU/g): fermented or microbe-rich produce

Participants were then sorted into low, moderate, or high intake groups based on the total weight of medium- and high-microbe foods consumed. The researchers also identified users of probiotic and prebiotic supplements using text mining on supplement labels.

Their goal: to determine whether higher microbial intake — from food or supplements — was linked to a lower risk of death, especially from cardiovascular disease.

Microbe-Rich Diets Linked To Longer Life

Among the 7,882 older adults included in the study:

• 31% had a low intake of microbe-rich foods

• 48% fell into the moderate range

• Only 21% consistently consumed a high level of these foods.

Those in the high-intake group — the top 21% — had the lowest risk of death over the eight-year follow-up. Compared to those with the lowest intake, they had:

• a 21% lower risk of all-cause mortality, and

• a 29% lower risk of cardiovascular mortality

These associations held up even after adjusting for key health and lifestyle factors, including age, body weight, smoking status, and chronic disease.

Higher intake was associated with greater survival over time.

Participants with the highest intake had the lowest risk of cardiovascular death.

When the Immune System Forgets to Turn Off

Why would exposure to foodborne microbes — the very thing we’ve been taught to fear — reduce the risk of death in older adults? Because microbial contact helps regulate the immune system. Not just in childhood, but throughout life.

With age, the immune system doesn’t simply weaken. It loses balance. Instead of reacting selectively to real threats, it starts responding to harmless ones — fueling a background hum of chronic inflammation.

This phenomenon, known as inflammaging, is a powerful driver of age-related disease.

At the center of this breakdown in immune balance are a special class of immune cells called regulatory T cells, or Tregs.

Tregs act like a brake pedal: they shut down inflammation after a threat has passed and prevent the immune system from attacking friendly microbes, food proteins, or the body itself.

With age, the dynamics of Tregs shift. The body produces fewer naïve Tregs — the kind trained to recognize new threats — while memory Tregs accumulate. But these aging Tregs often lose precision. Their ability to suppress inappropriate immune responses weakens.

The result: an immune system that’s more reactive, less discerning — and harder to shut off.

And it’s not just aging that drives this loss of tolerance. It’s also the environment we age in.

The immune system evolved in constant contact with the microbial world — low-level exposures to bacteria in soil, on food, and throughout the gut. These signals helped it learn what to ignore, and what to fight.

Today, that microbial education is being cut short:

• We eat sterilized, ultra-processed foods

• We scrub and peel our produce

• We cook most of what we eat

• We filter out the everyday microbes our bodies evolved with

Deprived of those cues, the immune system starts to misfire, treating friendly microbes, dietary proteins, and even the body itself as enemies.

In short, aging drives inflammation not because of infection — but because the immune system forgets how to turn off.

And this quiet overactivation slowly wears the body down: damaging blood vessels, disrupting cognition, weakening muscle, and accelerating the very decline we’re trying to avoid.

Rebuilding the Immune System’s Brakes

Live microbes in food may help retrain the immune system — restoring the balance it needs to age more gracefully. And that calibration starts in the gut.

Though we think of the gut as a digestive organ, it’s also one of the body’s most important immune hubs. It contains over 70% of all immune cells, spread across 200 square meters of surface area — about the size of a tennis court!

That surface is lined with sensors, constantly sampling what passes through — from food particles to microbial fragments — and adjusting immune behavior in real time.

The gut isn’t just a filter. It’s a classroom: where the immune system learns to tell friend from foe.

Regular exposure to live microbes helps restore that education process. Even if these microbes don’t stick around long-term, their presence is enough to stimulate immune tolerance through several key mechanisms:

• They promote the development and function of regulatory T cells, helping suppress unnecessary inflammation

• They reinforce oral tolerance, teaching the immune system to ignore harmless inputs like food and commensal bacteria

• They dial down innate immune receptors, which otherwise amplify inflammation in response to microbial fragments

We’re even starting to see how this plays out in clinical studies. In one tightly controlled trial, participants adhered to a diet high in microbes for 10 weeks. Compared to controls who were fed a high fiber diet, they showed a significant drop in key inflammatory markers, including IL-6 and CRP, as well as a measurable shift in immune cell profiles, suggesting enhanced immune tolerance.

From Wastyk et al, 2022.

Hitting the Sweet Spot

Understanding the mechanisms is important — but theory only goes so far. The practical question is: how much microbial exposure does it take to see a benefit?

Let’s circle back to the original study.

The researchers found something striking: the relationship between microbial intake and mortality wasn’t linear. Risk didn’t keep dropping with each additional serving.

It dropped sharply from low to moderate intake — then leveled off.

This inverted L-shaped curve points to a threshold effect. Most of the benefit came from simply restoring a baseline level of microbial exposure — a bare minimum that many people today fall short of. Getting past that low-exposure zone appears to switch on key protective systems, from immune regulation to gut barrier integrity.

More might help! But hitting the threshold consistently is what matters most.

This curve shows the relationship between microbe-rich food intake and all-cause mortality. Intake is expressed as a “MedHi score”, a measure based on the total daily weight of medium- and high-microbial foods consumed. Risk drops sharply from low to moderate intake, then levels off around MedHi 3, suggesting that most of the benefit comes from restoring a baseline level of microbial exposure.

A Daily Microbial Dose Made Easy

In the study, participants in the highest intake group consumed around 500–550 grams of microbe-rich foods daily.

That’s roughly 4 to 5 cups of raw fruits, vegetables, and fermented foods — super easy to achieve with a few small shifts:

Breakfast

• ¾ cup plain yogurt with live cultures (150g)

• Handful of fresh berries (50g)

Lunch

• Raw vegetable salad with carrots, spinach, and cherry tomatoes (200g)

Snack or Dinner Side

• 2 tablespoons sauerkraut or kimchi (30g)

• 1 apple, unpeeled (150g)

Total: ~580g

This mix lands squarely in the intake range linked to reduced mortality — no pills, powders, or overthinking required.

💡 Tip: Choose raw over cooked when you can, and look for “live and active cultures” on fermented food labels. Organic produce may also be richer in dietary microbes than conventional counterparts.

Summary: An analysis of 7,882 older adults from the nationally representative NHANES dataset found that higher intake of microbe-rich foods — including raw fruits, vegetables, and fermented foods — was associated with significantly lower risk of death over an 8-year period. Compared to those with the lowest intake, participants in the highest group had a 21% lower risk of all-cause mortality and a 29% lower risk of cardiovascular mortality. These findings suggest that regular intake of live microbes from whole foods may support longevity by modulating immune function and restoring the body’s capacity to regulate inflammation.

Random Trivia & Weird News

⚾  A Canada goose made headlines this week after building a nest in the center-field bleachers at Chicago’s Wrigley Field.

Ballpark staff were quick to accommodate the unexpected fan, roping off the surrounding area and even sending in “geesekeepers” to protect her.

“Protecting our fans, and our feathered guest, is our top priority,” a Cubs spokesperson told reporters.

In a stadium famous for baseball folklore, she may have already earned a spot in Wrigley legend.

Photo: Paul Sullivan / Chicago Tribune / Tribune News Service via Getty Images

Podcasts We Loved This Week

• Alan Flanagan & Danny Lennon: Crucial ideas for understanding nutrition science. Via Sigma Nutrition Radio.

• R. Alexander Bentley: COVID modeling reveals new insights into ancient social distancing. Via The Conversation.

Products We Like

Misfits Market

Misfits Market delivers customizable boxes of organic produce and pantry staples directly to your door — no mystery box roulette. Unlike traditional CSAs, you choose what goes in.

The “misfit” fruits and veggies come in all shapes and sizes: some ginormous, some tiny, some a little weird-looking. But in my experience, the flavor holds up fine despite the occasionally gnarly appearance. And by opting for raw, unpeeled produce, you naturally increase your intake of beneficial microbes that support immune balance.

humanOS Catalog Feature of the Week

The Mediterranean Diet

The Mediterranean Diet isn’t just a heart-healthy pattern — it’s a microbiome-supporting, inflammation-lowering, cell-rejuvenating powerhouse.

In this course, you’ll learn how this time-tested way of eating:

• Feeds beneficial gut microbes and promotes key anti-inflammatory metabolites

• Supports healthy aging and cognitive function

• Improves stress resilience and endurance performance — sometimes in as little as 4 days!

Plus, we unpack the real science behind olive oil, fiber, polyphenols, and a little-known molecule called spermidine — and show you how to Mediterranean-ize any style of cooking.

To Access:

1. Log in to humanOS.
2. See Mini-Courses in navigation on the left-hand side
3. Click Mediterranean Diet

Also, you can search “mediterranean diet” in the search field after you’ve logged in:

Wishing you the best,