Testing the canine healthy soil hypothesis

Is healthy soil the secret ingredient to better health for dogs? Learn about the groundbreaking research being done by the Canine Healthy Soil Project.

Many veterinarians have shared with us that they still see a lack of optimal health in their canine patients, even those on balanced, species-appropriate, fresh food diets. We theorize that something is still missing: the ancestral microbes, their “old friends”, found in nutrient-rich soil and other ancestral environments. The Canine Healthy Soil Hypothesis states that exposure to healthy soil, especially as a young puppy, can help restore a dog’s ancestral microbial communities and therefore enhance his overall health.

We define healthy soil as that which is quality tested, sustainable and produced through regenerative agricultural methods. Healthy soil may be nature’s ultimate probiotic for all dogs, from young puppies to older canines. The dog’s microbiota — the community of microscopic organisms on and in his body — likely influences a tendency toward health or disease, including, but not limited to, the following conditions: allergies, obesity, diabetes, dental disease and gingivitis, dermatitis, cancer, arthritis, and cognitive decline and disease.

Is this hypothesis accurate?

We are a volunteer group of pet food professionals, veterinarians, regenerative agriculture specialists and microbiologists who want to know if the Canine Healthy Soil Hypothesis is true. Steve Brown (see below for more info) is leading the program’s start-up.

If the hypothesis is true, we can help take a major step toward understanding how to promote good health in dogs, and perhaps humans too, while raising awareness of the global benefits of healthy soil for all living beings.

“The diseases most people die of have been attributed to unhealthy lifestyles. But evidence now suggests bacteria are to blame, heralding a revolution in medicine.”1


The Canine Healthy Soil Hypothesis start-up team

  • Steve Brown is a renowned formulator of ancestral-type diets for dogs, as well as a researcher, author of two books on canine nutrition, developer of several best-selling leading edge canine dog foods and treats, and the developer of the Animal Diet Formulator™ program.
  • Dr. Natasha Lilly, DVM, is co-founder of the Royal Animal Health University and an Adjunct Professor College of Agriculture, Cal Poly University, San Luis Obispo.
  • James Pendergast is a commercial pet food formulation consultant, and the veterinary sales director for a leading fresh food diet company.

Technical advisors include:

  • Dr. David C. Johnson, PhD, Soil Microbiologist/Molecular Biologist, New Mexico State, College of Engineering, Institute for Sustainable Agricultural Research
  • Dr. Tim LaSalle, PhD, Co-Founder of CSU Chico, Center for Regenerative Agriculture; Director of Outreach & Development; Adjunct Professor
  • Dr. Holly Ganz, PhD, microbial ecologist who studies how microbes and mammals interact; CEO and founder of AnimalBiome, a biotech company based in the San Francisco Bay Area.

Call for volunteers

In order to test this hypothesis, we need volunteers to be part of our research and sign up their dogs for testing. The more dogs that participate, the more all of us can learn. Testing will begin in the spring of 2020. Everyone who participates will become part of the team, and if we prove the hypothesis, everyone is part of the revolution in our understanding of what makes dogs, and possibly also humans, healthy.


Defining healthy soil

Healthy soil is highly biodiverse; one gram, ¼ teaspoon, may contain 10 billion microbes, and 2,000 to 50,0002 species per gram, though some studies estimate as many as 10,000,000.3 Healthy soil is clean, not treated with herbicides, pesticides or chemical fertilizers, and sustainable, preferably produced on polyculture farms through Regenerative Agriculture methods. Regenerative Agriculture is a holistic land management practice that produces healthy microbe-rich soil for healthy plants, animals, humans and the environment.The canine healthy soil team will provide healthy soil for the initial set of preparatory tests (see step two under “How”). We will also provide healthy soil for the veterinarian-guided tests (step three under “How”), but our goal is to get enough participants that we can examine other more local sources of healthy soils.Adult dogs will be inoculated with healthy soil as a topper to food, with an estimated dose of ½ gram per day for a 10 lb dog. For breeders, we will test several methods of inoculating very young puppies, including the application of healthy soil to whelping areas so that litters will be born in soil, much like their ancestral relatives were.


The science

The canine ancestral environment was full of microbe-rich soil. Starting at birth, soil-based microbes colonized every canine environmental niche, externally and internally. Today, most puppies are born inside, in a radically different environment often full of harsh cleaning chemicals, antimicrobial soaps, and the accompanying indoor microbes that thrive in such environments. Many puppies may never play in soil until they get to their new homes, if then. They are not exposed to their ancestral microbes.

Why healthy soil?

Just as we find that most dogs are healthiest when they consume their ancestral diets, we think they are healthiest when they have their natural — ancestral — microbial populations. Dogs co-evolved with the trillions of microbes that are in and on their bodies. The dogs who possessed the greatest harmony between their genes and the microbes to which they were exposed were the fittest and most successful. From a Darwinian perspective, the canine genes selected for were those that fit best with the microbes in the dogs’ environment.

“Many microorganisms in the intestine seem to have developed in sync with their host animals over millions of years.”4

“Given the ongoing extinction of our ancient commensal organisms, the future of a healthy human microbiome may include restoration of our ancestral microbial ecology.”5

The asthma-protective effect of polyculture farms and the Amish dust studies

Amish dust studies and similar research using dust from organic polyculture farms show that exposure to highly biodiverse soil and dust reduce the symptoms of allergies. In the Amish dust studies, scientists bred a variety of mice that suffered from a chronic inflammatory disease akin to allergic asthma. The mice developed asthma symptoms when exposed to egg proteins. The team divided the mice into three groups: one group had egg proteins sprayed in their environment for inhalation every two or three days for a month; the second had egg proteins plus dust from organic monoculture farms; and the third group had egg proteins plus dust from Amish farms. The mice exposed to just egg protein suffered allergic responses as did the mice exposed to egg protein and organic monoculture farm dust. But the mice exposed to egg protein and Amish dust had almost no allergic responses.6 The allergy- and asthma-protective effects of dust from polyculture farms have been replicated with human infants7 and piglets.8

Most studies on mammal microbiota are conducted with humans, mice, pigs and rats; just a few have been done with dogs. Studies suggest, though, that bacteria can reasonably be expected to function similarly in the digestive tracts of different species. The results we find with dogs may eventually help humans.“The structural and functional similarity of the dog microbiome to the human one implies that, as human studies are predictive of results in dogs, dog studies may be predictive of results in humans. Thus, dog studies provide a double benefit: for dogs directly and for their potential to generalize to humans.”9

Early exposure is important: why we need to work with dog breeders

“The composition of the gut microbiota in early life is emerging as a factor in helping achieve and maintain good health in the years to come.”10

“Our findings show that a key timing of exposure to the microbiota and microbiota metabolites may actually be very early in life.”11

Again, most puppies are born indoors now, in an attempt to create sterile environments. Microbes that can withstand harsh chemicals populate the puppies; these are not their ancestral microbes. It is possible that a small inexpensive change in the way breeders raise their puppies — adding small amounts of healthy soil to whelping areas — can have a significant long-term beneficial effect on the puppies’ lives. We need your help in testing this.

Why not just give probiotics?

Probiotics do not address the high level of species diversity present in healthy soil. They also often over-represent a fewer number of species (see Canine Healthy Soil Hypothesis Corollary sidebar below).

Participate in the program


The project’s four components

STEP 1: Recruiting study participants. Pet parents and veterinarians will sign up more than 2,000 dogs to complete oral cavity testing before and after exposure to healthy soil microbiota. At least ten breeders will sign up for testing genetically-similar litters with and without early exposure to healthy soil.

STEP 2: Completing preparatory work. We will recruit sufficient sponsorship to pay for the extensive preparatory work and for testing with breeders. The preparatory work includes quality testing and approval of the healthy soil, determining dosage and frequency of exposure, and identifying marker microbes. Once we know more about our marker microbes, we can provide more information regarding the duration of the soil administration and timing of re-tests.

STEP 3: Testing the oral cavities of participants. Our testing will focus on exposure to the oral cavity for the following reasons: recent studies suggest that good health begins in the mouth; oral cavity examinations by veterinarians are routine; the eruption of puppy and adult teeth are ideal times for exposure and testing; the human oral microbiota has already been well-studied; and canine dental care can be expensive. “The worst culprits, which seem to play a role in the widest range of ailments, are the bacteria that cause gum disease. This is the most widespread disease of aging — in fact, “the most prevalent disease of mankind.”12

“Oral microbiome data suggest that a single-pathogen model cannot account for either caries or periodontitis: in these diseases, many constituents of the bacterial community are perturbed.”13

STEP 4: Doing data collection, analysis, and publishing. Our goal is to finalize analyses and publish results two years after commencing the study.


We need veterinarians and dog parents to sign up now. Individual dog testing will begin in the spring of 2020 — see sidebar for details.



2Raynaud A, Nunan N. “Spatial Ecology of Bacteria at the Microscale in Soil”.  PLOS doi.org/10.1371/journal.pone.0087217. January 2014.

3Roesch LFW, et al. “Pyrosequencing enumerates and contrasts soil microbial diversity”. The ISME Journal. 2007;1:283–290.

4Youngblut ND, Reischer GH, Walters W, et al. “Host diet and evolutionary history explain different aspects of gut microbiome diversity among vertebrate clades”. Nature Communications. 2019; 10 (1) DOI: 10.1038/s41467-019-10191-3.

5The ancestral and industrialized gut microbiota and implications for human health”. Nature Reviews. June 2019.

6Best described in Never Home Alone by Rob Dunn.

7“The asthma-protective effect of farms appears to be associated with rich home dust microbiota; Farm-like indoor microbiota in non-farm homes protects children from asthma development”. Nature Medicine. 2019.

8“Amish (Rural) vs. non-Amish (Urban) Infant Fecal Microbiotas Are Highly Diverse and Their Transplantation Lead to Differences in Mucosal Immune Maturation in a Humanized Germfree Piglet Model”. Frontiers in Immunology. July 2019.

9“Similarity of the dog and human gut microbiomes in gene content and response to diet”. Microbiome. 2018;6:72. microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0450-3.

10Ishiguro, E, et al. Gut Microbiota, Interactive Effects on Nutrition and Health. Academic Press, 2018; p41.

11Harusato A, Viennois E, Etienne-Mesmin L, et al. “Early-Life Microbiota Exposure Restricts Myeloid-Derived Suppressor Cell–Driven Colonic Tumorigenesis”. April, 2019;DOI: 10.1158/2326-6066.CIR-18-0444.

12New Scientist. August 7, 2019; newscientist.com/article/mg24332420-900-have-we-found-the-true-cause-of-diabetes-stroke-and-alzheimers/#ixzz5w2U72l28.

13Ishiguro, E, et al. Gut Microbiota, Interactive Effects on Nutrition and Health. Academic Press, 2018; p57.


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