The Gut-Soil Connection

An Ecosystem Inside an Ecosystem

For most of human history, the invisible world was exactly that: invisible. We knew we digested food, we knew we got sick, we knew that some people seemed hardier than others, but the microbial universe operating at the center of all of it was beyond our ability to see. That changed over the past three decades as molecular biology developed the tools to sequence and catalog the trillions of microorganisms, bacteria, fungi, viruses, and other organisms that inhabit the human gastrointestinal tract.
What those tools have revealed is something genuinely surprising: the gut is not simply a digestive tube. It is a living ecosystem of extraordinary complexity, one that is deeply involved in immune function, metabolic regulation, the production of vitamins and neurotransmitters, the maintenance of the intestinal barrier, and, through what researchers now call the gut-brain axis, even mood and cognitive function.[1] The microbiome does not merely process our food. It participates in our biology in ways that researchers are only beginning to map.

And like any ecosystem, the gut microbiome is sensitive to what it is fed, what it is exposed to, and what has been done to the environment it depends on. A growing body of research suggests that the diversity of the human gut microbiome has declined significantly in industrialized populations, and that the food system responsible for what most Americans eat is a primary driver of that decline. Restoring that diversity, the science increasingly suggests, may be one of the most consequential things people can do for their long-term health.

What Your Gut Microbiome Actually Does

Before getting to the evidence on diversity loss and what drives it, it helps to understand what a healthy, diverse gut microbiome is actually doing for us, because the functions involved are more central to everyday health than most people realize.
The most well-established role of gut bacteria is the fermentation of dietary fiber. When fiber-rich foods reach the large intestine, gut bacteria break them down and produce short-chain fatty acids (SCFAs), particularly butyrate, propionate, and acetate, as byproducts. These molecules are not waste products. They are signals. Butyrate is the primary fuel source for the cells lining the colon, maintaining the intestinal barrier that keeps pathogens and inflammatory compounds from leaking into the bloodstream. Propionate and acetate travel to the liver and bloodstream, where they influence metabolism, appetite signaling, and blood sugar regulation. SCFAs also play a role in regulating immune cells throughout the body and, through the gut-brain axis, appear to influence neurological function.[2]

Gut bacteria also synthesize several B vitamins and vitamin K, train the immune system to distinguish between harmful pathogens and harmless food proteins, and produce neurotransmitters including serotonin, approximately 90 to 95 percent of the body’s serotonin is produced in the gut, not the brain.[3] They compete with pathogenic bacteria for resources, providing a first line of defense against infection. And they influence the expression of genes in the intestinal lining itself, shaping how the gut functions at a cellular level.

The key word throughout all of this is diversity. Different microbial species perform different functions, ferment different types of fiber, and produce different beneficial compounds. A microbiome with a wide range of species is more resilient, more metabolically capable, and more responsive to dietary change than a narrow one. When diversity falls, when the ecosystem becomes impoverished, the functions that depend on particular species begin to falter. This is what researchers mean when they talk about gut microbiome diversity as a marker of health: it is a proxy for the full complement of functions the gut ecosystem is capable of performing.

“The Hadza get 100 or more grams of fiber a day in their food, on average. We average 15 grams per day.” — Justin Sonnenburg, PhD, Stanford University School of Medicine

The Vanishing Microbiome: What Modern Life Has Cost Us

How diverse should a healthy human gut microbiome be? Researchers have tried to answer this question by looking at populations whose diets and lifestyles most closely resemble those of our evolutionary ancestors, specifically hunter-gatherer communities whose food supply has not been substantially altered by industrial agriculture.

The most studied of these populations is the Hadza of Tanzania, one of the world’s last groups living a traditional, nomadic, foraging lifestyle. Studies led by Justin Sonnenburg’s lab at Stanford, published in Science and Nature Communications, found that the Hadza carry a gut microbiome that is dramatically more diverse than that of people in industrialized societies, containing bacterial species rarely or never found in Western populations, and showing remarkable seasonal flexibility as the Hadza diet shifts between wet and dry season food sources.[4] The 2023 deep-sequencing study of the Hadza recovered more than 90,000 microbial genomes from their gut samples; of these, 44 percent had not been recorded in major global catalogues, and more than 1,000 were species entirely new to science.[5] Despite having no access to modern healthcare, the Hadza are largely free of the chronic diseases, cardiovascular disease, type 2 diabetes, metabolic syndrome, that define the modern health landscape.

The contrast with industrialized populations is stark. Researchers have consistently documented that microbiome diversity is lower in people eating Western diets high in ultra-processed foods and low in fiber-rich whole foods. A 2024 scoping review in People and Nature synthesized the evidence plainly: gut microbial diversity has decreased in parallel with urbanization and the global loss of dietary diversity, and this decline coincides with the rising prevalence of chronic, non-communicable inflammatory diseases in industrialized societies.[6] The correlation is not proof of causation, and researchers are careful to say so, but the pattern is consistent enough across independent populations and study designs to represent a serious scientific signal.

A key mechanism appears to be fiber deprivation. The average American consumes approximately 15 grams of dietary fiber per day, against a recommended 25 to 38 grams and the Hadza’s 100 or more. Fiber is the primary food source for the gut bacteria that produce SCFAs and support microbial diversity. Without adequate fiber, and especially without a diversity of fiber types from different plant sources, populations of beneficial bacteria decline, diversity contracts, and the gut ecosystem becomes less metabolically capable.[7]

Thirty Plants a Week: The Most Accessible Finding in Microbiome Science

Among all the research findings to emerge from the microbiome field in the past decade, one has proven particularly accessible and actionable: the 30-plants-per-week finding from the American Gut Project, one of the largest citizen science microbiome studies ever conducted.

The American Gut Project, led by researchers at UC San Diego, analyzed gut microbiome samples from thousands of participants across the United States and the United Kingdom alongside detailed dietary surveys. One of the clearest findings: people who reported eating 30 or more different types of plants per week had significantly more diverse gut microbiomes than those who ate fewer than 10 different plant types. This held true regardless of whether participants identified as vegan, vegetarian, or omnivore. The diversity of plants consumed mattered more than the general category of diet.[8]

The finding makes biological sense. Different plants contain different types of fiber, different polyphenols, different prebiotic compounds, and different structures. Different gut bacteria specialize in fermenting different plant components. The more varied the plant inputs, the wider the range of microbial species that are fed and supported. A diet built around a handful of the same vegetables week after week, however healthy those vegetables are, feeds a narrower range of microbial species than one that cycles through a wide diversity of seasonal plants.

This is worth sitting with, because it reframes what a healthy diet means in a microbiome context. The question is not just whether you are eating enough vegetables. It is whether you are eating a wide enough variety, rotating through different species, different colors, different textures, different seasons, to sustain a genuinely diverse gut ecosystem. That is a different kind of dietary goal than traditional nutrition advice has tended to offer, and it has direct implications for how we think about what neighborhood farms provide.

Fermented Foods: The Other Piece of the Puzzle

Fiber diversity is one major driver of gut microbiome health. Fermented foods appear to be another, and the evidence for their role was sharpened significantly by a landmark 2021 clinical trial at Stanford.

The study, published in Cell by Justin and Erica Sonnenburg and their colleagues, randomized 36 healthy adults to one of two dietary interventions for ten weeks: a diet high in fermented foods (yogurt, kefir, kimchi, sauerkraut, fermented cottage cheese, kombucha, and vegetable brine drinks), or a diet high in dietary fiber from fruits, vegetables, legumes, and whole grains. The results surprised even the researchers. The fermented food group showed a consistent, significant increase in gut microbiome diversity, measured across all participants, and a broad reduction in 19 inflammatory proteins in the bloodstream. The high-fiber group showed no significant change in overall microbiome diversity during the trial period, though they showed increased microbiome-encoded capacity to ferment carbohydrates.[9]

“This is a stunning finding,” said Justin Sonnenburg at the time. The study was notable not only for its results but for what it suggested about mechanism: fermented foods appear to introduce new microbial species into the gut, or support the expansion of low-abundance species already present, in a way that dietary fiber alone does not, at least not over short timeframes. The researchers also noted that the two interventions may work synergistically: fiber feeds the microbes already present, while fermented foods can expand the community itself. Larger and longer trials are needed to fully characterize the relationship, but the signal was clear enough to shift how researchers and clinicians think about the relative contributions of fiber and fermentation to gut health.[10]

The Soil Connection: A Developing Framework

So far, the research described is well-established, the core findings on SCFA function, microbiome diversity and chronic disease, the 30-plants finding, and the fermented foods trial are among the most cited and replicated results in the field. But there is a newer and still-developing body of research that is beginning to draw a direct line between the health of the soil in which food is grown and the health of the gut microbiome in the people who eat it. This is the next frontier.

A 2024 report from the National Academies of Sciences, Engineering, and Medicine, titled Exploring Linkages Between Soil Health and Human Health, synthesized the emerging evidence on this connection. Among its key findings: fruits and vegetables have been identified as sources of what researchers call human gut microbial seeding, meaning that the microorganisms living on and in the produce we eat appear to contribute to the composition of our gut microbiomes.[11] A single apple, one study found, contains approximately 100 million bacterial cells, and the microbial richness of that apple is shaped by the agricultural management practices used to grow it.[12]

This has significant implications. Organically and regeneratively grown produce has been documented to carry a measurably different microbial profile than conventionally grown produce treated with synthetic pesticides and fungicides, which are, by definition, designed to reduce microbial populations.[13] Cover crops, compost, no-till practices, and polyculture planting, the tools of regenerative agriculture, all build soil microbial diversity. A 2023 review in Frontiers in Agronomy documented that regenerative agriculture practices consistently improve soil microbial richness and diversity compared to conventional tillage and synthetic input systems.[14]

A 2025 paper in Nature Communications framed this more explicitly as the soil-plant-human gut microbiome axis: a continuum of microbial community interaction spanning from the soil through the plants grown in it, through the food those plants become, and into the gut of the person who eats that food.[15] The research is still developing, establishing direct causal links between specific soil practices and specific human gut microbiome outcomes is methodologically complex, and the field has not yet resolved these questions. But the framework is biologically coherent, supported by parallel bodies of evidence, and being actively pursued by some of the most credible institutions in microbiome research. It suggests that the health of the soil is not merely an agricultural concern. It is a human health concern.

“Foods can be a key linkage between the environmental microbiome, including the soil microbiome, and the human microbiome.” — National Academies of Sciences, Engineering, and Medicine, 2024

What Neighborhood Farms Are Actually Growing

When you look at the farms in the Neighborhood Farms USA network through the lens of microbiome science, something comes into focus: the practices that define these farms are precisely those that the research identifies as most likely to support both soil microbial diversity and the gut health of the people they feed.

The farms NFUSA highlights and supports are market gardens and community farms built on regenerative principles: no synthetic pesticides or fertilizers, active composting, cover cropping, no-till or minimal-till soil management, and the kind of diverse, polyculture planting that builds the living biology of the soil season by season. These are not incidental features, they are the defining characteristics of how these farms operate. Compost, in particular, is a critical bridge: the microbiologically rich material produced by a well-managed compost system inoculates the soil with beneficial bacterial and fungal communities, which in turn colonize plant root zones, shape the microbial profile of the produce that grows in those soils, and ultimately, if the framework developing in the research literature is correct, contribute to the gut microbiome of the consumer.

Equally significant is what these farms grow. A typical NFUSA community farm or market garden does not grow two or three commodity crops at scale. It grows dozens of varieties of vegetables, fruits, herbs, and legumes, rotating through the seasons, including heirloom varieties selected for nutritional depth and flavor rather than shelf life, incorporating edible flowers, culinary herbs, and lesser-known greens that rarely appear in conventional produce aisles. A well-designed CSA share from a neighborhood farm in any region of the country naturally moves toward 30-plus plant varieties per week without any deliberate effort on the consumer’s part, because that is simply what a seasonally diverse farm produces.

This matters in a specific, measurable way. The American Gut Project finding that 30 plant varieties per week significantly increases gut microbiome diversity was not about eating more spinach. It was about eating a wider range of plants, different colors, different fiber types, different polyphenol profiles, that collectively feed a broader community of gut microbes. A CSA box filled with purple sweet potatoes, rainbow chard, fresh turmeric root, snap peas, three varieties of tomato, a bunch of cilantro, and a head of Romanesco broccoli is not a nutritional luxury. It is, by the best available evidence, exactly the kind of dietary input that supports a resilient, diverse gut microbiome.

And then there are the fermented products. Farms in the NFUSA network that incorporate fermentation, producing live-culture krauts, kimchi, farm-fresh kefir, or probiotic vegetable brines from their own harvests, are providing something the Stanford Cell trial identified as one of the most potent known stimuli for increasing gut microbiome diversity. Fermented farm products, made from produce grown in biologically rich regenerative soils, represent the convergence of both pathways the research points to: diverse plant inputs and live-culture microbial inoculation.

The Nutrient Density Dimension: What Regenerative Soil Produces That Conventional Soil Cannot
There is a third layer to what regeneratively grown neighborhood farm produce offers that goes beyond microbial seeding and dietary diversity: measurably higher concentrations of the very compounds that gut bacteria depend on to do their work. A 2025 narrative review published in Nutrients, synthesizing research from 2000 to 2025, documented consistent increases in vitamin C, zinc, and polyphenols in crops grown under regenerative organic systems compared to conventional equivalents, including leafy greens, grapes, and carrots.[16] This is not the same data covered in our earlier piece on nutrient density in the food system. That story was about what the industrial system removes from food through soil depletion and distance from harvest. This is about what regenerative soil actively adds.

Polyphenols, the broad class of plant compounds that give fruits and vegetables their colors, bitter notes, and antioxidant properties, are particularly significant in this context, because they are not just nutrients for the human body. They are food for the gut microbiome. A 2025 review in Frontiers in Nutrition documented the reciprocal relationship between polyphenols and gut bacteria in detail: gut microbiota transform polyphenols into bioactive metabolites that in turn influence microbiome diversity, selectively promoting beneficial species while suppressing pathogenic ones.[17] Plants produce more polyphenols under conditions of mild environmental stress, inconsistent rainfall, varied soil biology, competition with neighboring plants, exactly the conditions that characterize a diverse regenerative farm, and the opposite of the controlled, input-optimized environment of industrial production. Crops from conventional monocultures, grown under uniform conditions with synthetic inputs that eliminate stress, consistently show lower polyphenol concentrations than those grown in biodiverse, regeneratively managed soils. The zinc and magnesium that regenerative soils deliver more abundantly are not incidental either: zinc is essential for the function of hundreds of gut enzymes, and magnesium deficiency is associated with dysbiosis and increased gut permeability. A CSA share from an NFUSA regenerative market garden is, in this sense, providing not just more types of food for the gut microbiome, but richer, more potent versions of each type.

Feeding Your Microbiome: What the Evidence Suggests

The science points toward a few clear, actionable priorities. Aim for 30 or more different plant types per week, rotating greens, legumes, root vegetables, herbs, and grains, because plant diversity drives microbial diversity more than any other single dietary factor. Prioritize fiber from varied whole-food sources rather than supplements, since different fiber types feed different bacterial species. Add fermented foods regularly: yogurt, kefir, kimchi, sauerkraut, and live-culture vegetable brines have the strongest direct evidence for increasing microbiome diversity. Choose regeneratively grown produce where accessible, both for its richer microbial profile and its higher polyphenol and mineral content. And reduce ultra-processed foods, which crowd out the whole-food diversity a healthy microbiome depends on while introducing emulsifiers that disrupt the gut environment. A seasonal CSA share from a local regenerative farm addresses all five of these simultaneously, which is the simplest summary of what the research, taken together, points toward.