The Paramount Role of Regenerative Agriculture on the Human Microbiome

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jeremy princi

Written by Sasha Frate

September 2, 2022

Rodney Dietert, Ph.D. is an internationally known author, lecturer, scientist, media personality, and educator. While a professor and now a professor emeritus at Cornell University in the Department of Microbiology and Immunology and a faculty member in the Cornell Institute for Comparative and Environment Toxicology, Dr. Dietert has published peer-reviewed papers in more than seventy scientific journals ranging from environmental health and pediatric medicine publications to nutrition, metabolism, immune, neurological, and reproductive journals. He has been president of the Immunotoxicology Specialty Section of the Society of Toxicology and previously led Cornell’s programs in immunology, toxicology, and risk reduction of breast cancer.

His current book, The Human Superorganism: How the Microbiome is Revolutionizing the Pursuit of a Healthy Life, focuses on the microbiomes throughout the human body and their critical role in maintaining the equilibrium of our health. In part one of Face the Current’s fascinating discussion with Dr. Dietert, he shares his thoughts on topics including our current soil practices and regenerative agriculture, pre and probiotics, the effects of cesarian sections on microbiome development, the impact of travel on our body’s microbes, and the negative effects of emulsifiers on the gut.

Rodney Dietert
The Human Superorganism microbiome

Sasha Frate: Many people believe that ancient ways of doing things do not fit with today’s modern living. When it comes to ancient foods, can you explain how and why we should still be modeling certain food practices? What should we return to and how might our species’ health look different in the future if we were to return to these foods and practices?

Rodney Dietert: The important thing to recognize is that we’re complex organisms. The microbiome contributes to most of our genes—ninety-nine percent of all our genes and metabolic potential comes from our microbes, not from the human chromosomes. 


Our ancestors had certain food practices, but the twentieth century brought us the capacity to have frozen foods shipped everywhere. This changed things a lot, including our diet and how our food is produced—what we’re really consuming. In the end, this has not been to our benefit. So, there are practices we need to revisit because the microbes that we inherited were rich, diverse, and functioning because of those food practices.

Japanese fermented food microbiome

An example of this is fermented foods. If you look around the world through time, every single culture in Asia, Africa, Europe, South America, etc., had particular fermented foods. Of course they were fermenting foods because it helped to preserve them, but at the same time, it produced bacteria that were friendly and helped the metabolism and physiology of our ancestors. In modern times, we have gotten away from that. In my own family, my paternal grandfather was from Europe and he grew up regularly eating sauerkraut. My father ate it as well when he was a child, but in my family, my mother didn’t really know how to prepare it and she didn’t particularly like the aroma. This eating practice waned, and by the time I was born my parents weren’t eating it much anymore and so it was lost. I’m finding that my story with those two generational changes is very common. I talk to a lot of people and they say, “Yeah, my ancestors used to eat kimchi,” or other ancestral foods like miso. Current generations have gotten out of that habit, but now we’re trying to return to it.

fermented foods kimchi

While that’s a very good thing, we need to test drive these foods because it could turn out that some of them work better for you than others. This is part of the conditioning that happened over thousands of years through your ancestral line. For instance, if my European ancestors and their microbes were not used to digesting certain Asian food components, the actual result for my health might not go as well in reality as it might look on paper. So, test drive them; you’ll be able to tell! The gut’s a good reflection of whether you’re doing something useful.

There is also a rich tradition of how foods were produced with soil that was microbiome-rich and practices that diversified crops. If you’re talking about food-producing animals, you can either have a phytonutrient depleted source of beef and chicken or you can have one that’s very rich. It literally depends upon the foodstuffs that go into the animal feed as well as the grazing practices. Regenerative agriculture is so critical!

The Paramount Role of the Human Microbiome with Dr. Rodney Dietert

“I advocate: revisiting fermented foods and participating as much as you can in regenerative agriculture.  In fact, get your hands out in the (non-glyphosate treated) soil when you can, too!”

SF: There’s so much that goes into all of it—it’s not so cut and dry. I feel like we’re lacking a lot of education, even in basic nutrition, but then we’re also missing these other important elements. So, it’s a holistic picture that needs to be treated on all these different levels, because it’s not just the food we eat. We must look at the agriculture and the food processes, and like you said, food storage is critical. It’s also about the process of storing food after it’s grown, including length of storage, delivery method, and whether food is seasonal.

regenerative agriculture

RD: Absolutely. I can give you one example of people not even realizing or knowing about that. Currently I’m working in human health and am professor emeritus in the veterinary college at Cornell, but I was hired in the seventies into the poultry department. The focus then was to have naturally healthier chickens and they wanted me to breed and produce naturally healthier chickens that didn’t need lots of drugs—including prophylactic antibiotics. There was a salmonella outbreak in the late eighties into the early nineties and it affected a lot of the U.S., particularly the east coast. It was devastating because eggs and meat were contaminated, and it put humans at risk. 

The solution came from a Finnish scientist’s research. He posited that in commercial chicken operations, since we control the lighting, housing, and feed, why not modify the diet? Why not add useful bacteria to the feed that will block salmonella? This concept was originally called “competitive exclusion”, but now it’s called “colonization resistance”. This is a broader way of defending against potentially dangerous microbes that could infect you and cause inflammation. In this case, they used Lactobacillus acidophilus in the chickens and it solved the problem. The meat and eggs were now safe to eat.

We hear a lot about the horrific practice of prophylactic antibiotic use in animal feed, and it truly was terrible, but we don’t actually hear about the probiotic use that started in the eighties in major commercial poultry production as a natural defense.

We need to pay attention to that lesson because one of the problems we have right now is the emphasis on a frontline defense against infectious agents. We’re in the middle of the COVID pandemic, and not many people are talking about having a balanced immune system beginning with defenses within the microbiome, i.e., colonization resistance. The frontline defense is managing your microbes in the gut, in the airways, urogenital tract, and on the skin, and we don’t see that message as much as we should. We need to start embracing our microbes and taking care of them and insisting that our physicians do the same.

farm fresh eggs microbiome

SF: Right—wonderful! You mentioned in your book, The Human Superorganism, that we are not a single species ourselves, but rather we are comprised of numerous species that make us whole. How do you see viewing humanity from this perspective will change our understanding and our approach to move beyond the familiar notions of treating the whole human?

RD:  You might notice that the locations of the microbiome are what an infectious disease microbiologist would say are the “portals of entry”. They are where pathogens like viruses, bacteria, and fungi can get in such as the airways, the gut, the genital tract, and the skin barrier. This is where microbiomes are and they serve as our filters and gatekeepers. For instance, the microbiome filters the food we eat and determines what metabolites we’re going to get out of food. Even further, if we ingest some water that happens to have some arsenic in it, its danger varies among different individuals based on their gut microbiome because some gut bacteria make incredibly toxic products from the arsenic while others protect you against the arsenic. When you pay attention to managing those microbes for better health, you get real personalized medicine.

There’s also a plant-derived heart drug called digoxin that has been used for decades. It has a very narrow efficacy range, so physicians have to be very careful—it can be effective, ineffective, or lethal. We now know that the actual dose delivered to the patient is determined by one single species of bacteria in their gut. By measuring the level of that bacteria and then adjusting the dose of the medication or the level of the bacteria, lethal outcomes can be avoided.

Quite frankly, we should be doing that in every case with drugs! A large percentage of drugs affect the microbiome and that can be important because some need the microbiome. For instance, cancer therapeutics need microbiome metabolism to work, and in the UK it was determined that fifty percent of patients benefited from cancer therapeutics while the other half did not—and that’s the data over a decade! The efficacy can be closer to a hundred percent if we install the required bacteria to metabolize those drugs. This is a clear example of a situation that should be approached in a microbiome-first manner for better health.

SF: Just thinking of it in terms of being the filter or the translator—if you’re missing some of that filter because the microbiome is damaged or altered, then what’s happening in your body? It’s a very different perspective, because we generally think of ourselves as one being when we choose our diets and our lifestyle, but when you break it down, we’re actually many thousands of beings.

Rodney Dietert

RD: Right, and those species make vitamins like vitamin K that we absolutely need, so you do not want to be microbiome depleted. We have seen the outcomes in lab animals, so we know that it’s the starting point for a healthy life. We need to ensure that we have the microbes that should normally be there during development and adulthood as well.

microbiome gut health

SF: You’ve mentioned that we have destroyed our microbiome by about thirty-five to forty percent as a population in the United States, and this certainly has its ramifications. What have you identified as the primary causes of destruction and what are their common ramifications?

RD: I think we’re down by about forty percent as seen in research pioneered by Dr. Martin Blaser and his wife. First of all, we need to look at the rising numbers of elective cesarean sections, recognizing the medically necessary scenarios. C-section deliveries break the critical seeding of microbes from mom to baby and that may be the single most damaging thing that can occur. It’s not that it’s totally irreversible, but it’s a lot of work to correct the physiology and the state of the immune system. So, you get bigger bang for your buck by managing the pregnant woman, childbirth, and the first critical one hundred days. Physicians conducting short-term analyses may say, “Oh, the baby looks clean—we checked at six months and everything looks great.” What they don’t do is look at seven years and see type one diabetes, childhood obesity, asthma, and all the comorbid autoimmune, allergic and inflammatory conditions.

I’ve told OB-GYNs that they’re managing the health of two generations and they need to manage mom’s health microbially. If she’s carrying a so-called noncommunicable disease like diabetes, or if obesity or asthma are issues, then there’s a really good chance that the microbiome is dysbiotic. This means it’s out of balance; it’s less diversified and more restricted. There’s a community of bacteria that flourish and cause inflammation when things are not as diverse. Whatever mom has is what gets passed to the baby through natural childbirth, so mom’s the primary source for the baby’s bacteria. It’s not that other sources don’t exist, but with something like c-sections you then default to, “Well, it isn’t mom. So guess what? It’s the hospital.” The hospital environment and attendees are going to be contributing to the baby’s microbiome, and that’s probably not what you want for your baby’s health.

Second is food and the way we’ve changed it. My career was spent in safety testing for the immune system, particularly the infant immune system. I can tell you that because the microbiome was never considered in the safety testing design, food, environmental chemicals, and drugs were never screened for safety as they apply to the microbiome; we have had some very unpleasant surprises in the last five to eight years in terms of things that were deemed “safe” by the FDA or the EPA that are not.

The regenerative agriculture movement is helping a lot. For example, if you include meat in your diet and the animals are grazing on a huge diversity of plants, it turns out that the meat and the fat is very different in phytochemical storage. You can have a very phytochemical rich diet that will provide you with a lot of the co-factors that you need to support your microbiome and metabolism that is simply absent from feedlot-produced livestock.

SF: When some of these things have been implemented at such a large scale, the challenge is that it’s difficult and costly to make changes. Some of the changes were implemented to help prevent food loss or improve crop production (pesticides, monocropping etc.). On that scale, it is definitely a challenge to make the shift toward healthier practices. But, the awareness is starting to increase and people are asking for that change with regenerative agriculture.

RD: Right. And you really must question why something like glyphosate was approved for worldwide, widespread use when it’s labeled as an antimicrobial. We know that’s what it does, and it does it through the food chain. So, that’s the kind of mistake that never should have been allowed, in my opinion.

Education hasn’t filtered through. This is just my opinion, but a physician will see a potential disease and counter with a prescription that is medically coded for that issue. But no one’s paying attention to what that means over a lifetime and that’s the problem. What we now know is there is a cascade of so-called comorbid diseases that occur and nobody’s taking responsibility for that. I would contend it’s the treatment of the symptom rather than the curing of the condition that causes that.


regenerative agriculture

For example, with asthma you want to reduce the symptoms and make them manageable, but how many physicians correct the immune problem—the inflammatory response—that allows asthma to persist?  If we don’t do that, many asthmatics are going to end up with other conditions that will need drugs and medical or caregiver assistance, resulting in polypharmacy. To me, that is the epitome of healthcare failure. So, I think we need that education—we need to provide tools because there are very few doctors’ offices where microbiome is the first thing discussed, and yet it should be.

SF: Yes, absolutely. Whether it’s to get back to work right away, for the sake of convenience, to get baby in childcare, or just to return to a former lifestyle, another trend in infancy that I’ve noticed is shortening the breastfeeding period. I do know that some people have health issues that prevent them from breastfeeding, but a lot of people are going to formula very fast. So, if you have a cesarean and reduced breastfeeding periods, I think that there’s a lack of education and awareness around that joint effect.

RD: The reason that breastfeeding is so critical is there is now recognized to be Bifiodobacterium longum sspinfantis (B. infantis), one specific bacterium that is critically important for the infant and is provided through breast milk. It becomes a predominant resident in the newborn’s gut and is one of the best metabolizers of human milk oligosaccharides. The majority of the food in breast milk cannot be digested by our intestines, and these complex sugars can only be digested by microbes—particularly B. infantis and its friends in the gut. The baby immediately needs B. infantis and it needs the human milk oligosaccharides to feed it and nurture the progression of the microbes in the gut and the development of the immune system. What’s been found in the last two years is that B. infantis, digesting human milk oligosaccharides, reduces gut inflammation. It also reduces the risk of allergy and autoimmune disease later in life. Nature is telling us how important it is.

Seven years ago I was asked at a pharmaceutical conference, “So is this microbiome thing a fad?” I said, “Only if you think breast milk is a fad, because those sugars are not for us—they’re for the microbes.” That’s how critical they are—the first thing that’s going to get fed are the microbes.

SF: What is the current recommended period for breastfeeding?

RD: I’m not the be-all, end-all expert in that area, but I think you really want to get six months if you can. When you start introducing food there’ll be a progression off of B. infantis, but the amazing thing is the breastmilk microbes evolve during the breastfeeding process. If you shorten the nursing period, you are not getting the later bacteria and the shift in the milk oligosaccharides that would feed those bacteria.

SF: For those who may not have the option, what are some alternatives to compensate for the ideal pathway?

RD: Milk banks do give you the sugars, and there are companies that have B. infantis probiotics that show promise. They’re a way to try and achieve colonization. If pediatricians are not telling moms those things, then we’re going to miss windows of development. You’ve got to shift the immune system if you want the balance that will give lifelong health.

SF: There’s a lot of discussion about the gut-brain axis, so is that something that would be related to newborns developing microbiomes through the breast milk and vaginal delivery?

breastfeeding microbiome immune system

RD: Yes, I focused on the immune system because that’s my expertise, but all the physiological systems are impacted. The microbiome exerts huge regulatory influences on liver metabolism and even the neurochemistry in the brain. The gut makes more neurotransmitters than the brain, but the microbes are able to control the amount of neurotransmitters from their production in the gut to the brain. So, yes, the gut-brain axis is huge and it’s something that is controllable. There are even groups working on psychobiotics that have shown that the solution for major depressive disorder, anxiety solutions, and other neurodevelopmental issues are gut microbes that you need to adjust. Some promote serotonin, some promote dopamine, others norepinephrine etc.

SF: You mentioned that when howler monkeys are transferred from their wild habitat into captivity in American zoos, their diet goes from about fifty-seven species of plants to one species of plant. They also get their microbiomes from the zoo handlers, so how does this impact the howler monkeys? And what would you say is a comparable scenario with humans?

Howler monkey microbiome

RD: If howler monkeys don’t get their rich diet and have the microbiome diversity, they get things like kidney stones. There’s terrific medical care in zoos, so they can still have long lives, but it’s comparable to lab mice and rats who also have a reduced diversity of the microbiome compared with their wild counterparts. In the howler monkey, the reduced diversity essentially means that they don’t get the metabolites that they need, creating a better chance of pathobionts occurring—the pathogens that take advantage of not being blocked. When this happens there is a greater likelihood of infections and inflammation, compromised gut lining, and additional health issues. In the end, captive howler monkeys with severely restricted diets are fragile and they lack the resiliency of the microbiome diversity found in the wild population.

Howler monkey microbiome

A study found that at least one level of analyzing the gut microbes in mice and rats showed that the facility the animals were in made even more difference than their specific breeding. Environment does matter when you’re talking about the microbiome. Where you live, what you put in your body, and the chemicals in your household like cleaners matter a lot. It’s not that your genetics don’t matter, but your environment’s pretty important in terms of your microbiome. If lab mice and rats (whose microbiomes are influenced by their building, their diet, their caging/bedding, and their animal handlers) are moved to a new building, scientists have trouble reproducing their experiments’ results in the new location. The change in building changes the animals’ microbiomes because each lab animal building has its own specific microbial environment.  

I call us the Johnny Appleseeds of microbes. That’s why humans are microbes’ best friend because we travel. When you go into a hotel room, you’re picking up microbes from the prior occupant and you’re leaving behind some of your own. When we have a restricted microbiome in terms of diversity and we don’t have good colonization resistance, then just one little thing like a life-stressor, a different food, or a new exposure to a microbial community can have an effect.

Also, air travel is not known to be wonderful for your microbiome. Recycled air is not necessarily a great thing. You can’t ensure that you’ll never get sick when you travel, but with preventative medicine, we really should be helping people better protect themselves.

SF: As far as how that’s impacting you with negative side effects, it is probably dependent on how strong your system is prior to or during those travels.

RD: You can get hit with a stressful travel or a different diet and a pathogen you haven’t encountered before, and that can tip the scales. Then it’s a matter of building it back. If a physician prescribes antibiotics, there are few that are single bacterial species specific or strain specific. So, if they indiscriminately kill your bacterial friends that are producing metabolites that you need, your physician needs to restore those. This is currently not part of an antibiotic treatment regime that enough physicians have on their plate, but they really need to be doing that.

SF: Yes, very important. What would you say are some of the major factors that need to shift within our food systems and our diets? Do you see the regenerative agriculture movement helping us with this?

RD: Yes. The regenerative agriculture movement is helping a lot. For example, if you include meat in your diet and the animals are grazing on a huge diversity of plants, it turns out that the meat and the fat is very different in phytochemical storage. You can have a very phytochemical rich diet that will provide you with a lot of the co-factors that you need to support your microbiome and metabolism that is simply absent from feedlot-produced livestock.

regenerative agriculture role on microbiome

Besides sugar, if I had to point to an evil component of food at the moment, it would be emulsifiers. The major food emulsifiers are incredibly destructive for the microbiome. They wipe out a keystone bacteria species called Akkermansia muciniphila which regulates your mucin layer by way of the one-cell-thick gut lining that keeps pathogenic inflammatory-generating bacteria away from your intestinal immune cells.

Emulsifiers like polysorbate 80, carboxymethyl cellulose, and carrageenan kill Akkermansia. This causes leaky gut and activates the innate immune system immediately adjacent to the gut. It’s a good idea to pay attention to that crosstalk between the gut microbiome and the immune system because that’s where your cells are. Once your macrophages are activated, they produce a cytokine storm of inflammation that becomes one of the best paths to metabolic syndrome.

Anything that’s smooth, has a long shelf life, and doesn’t want to separate contains emulsifiers. Sauces, salad dressings, some peanut butter, margarine, mayonnaise, ice cream, bread, and processed meats/foods are likely to contain emulsifiers. We need warning labels that say, “This is a risk factor for metabolic syndrome, which can be life threatening.” Consumers need to know that this will damage a key protecting bacteria.

asparagus microbiome

“To help your gut, look for chicory root, dandelion greens, Jerusalem artichoke, garlic, onions, leeks, asparagus, bananas, cocoa, seaweed, and flax seed. They all have prebiotics; food for beneficial microbes.” 

A lot of the probiotic supplements that exist come with prebiotics loaded in as well. To get the benefit from them, you have to feed the microbes you want to metabolize in your gut, on your skin, and in your airways.

SF: Probiotic foods like kefir, yogurt, and even alternative milks are widely available, but the term prebiotic is still lesser known. People aren’t quite as aware of how important prebiotics are and why we should be incorporating them into our diets along with probiotic foods.

RD: The foodstuffs that I mentioned, like leeks, do have high amounts of prebiotics and they are the components that the friendly bacteria will use to grow and reproduce in the gut or in the airways. If you’re eating junk food and a lot of sugar, you will have some bacteria, but they will not be the ones you want, and that’s where you’re going to get into pathogenic inflammatory problems.

But be careful with fiber—not everyone responds exactly the same way to a given fiber-containing food. That’s why I don’t like the one-size-fits-all recommendations. If you can find the right fiber-containing mix for you, then that’s fantastic and it’s the easiest way to support your microbes: install and feed them.

leeks prebiotics microbiome

SF: With typical western diets, there is not enough vegetables and fruits, so the variety is already reduced. Fast foods and processed foods also include animal products that don’t have enough phytochemicals, so many people are lacking in phytochemicals through a shortage of vegetables and fruits and through meat consumption.

RD: Absolutely, it can be, and that’s the cycle we’ve gone through. You are the microbes that grew up from what you ate! If you want to grow a lot of pathogens that’ll give you metabolic syndrome and heart disease and cancer, then that’s what will happen.

kids farm animals microbiome

You need to get your kids out to animal petting zoos and animal farms to get them some early experience in those exposures that’ll protect them against allergic and autoimmune diseases. It helps to balance the immune system out and that is critical. If pregnant women live on an animal farm or the infant is born and grows up there, the infant has a reduced risk of allergic disease. However, this is not the case if there was pesticide exposure. You need those bacterial exposures to make you healthier, but pesticides will wipe out all the benefits.

SF: Diversifying our diets also means looking at the soil that our produce is grown in as far as the phytonutrients and nutrient density, and also what is being fed to the animal products.

RD: Yeah, absolutely. Where do your food animals come from and what is “meat quality”? We need meat products that are loaded with phytonutrients and things that are really going to support your body and your microbes. And we haven’t talked about the environment—the urban wasteland of microbes—which is terrible.

You need to get your kids out to animal petting zoos and animal farms to get them some early experience in those exposures that’ll protect them against allergic and autoimmune diseases. It helps to balance the immune system out and that is critical. If pregnant women live on an animal farm or the infant is born and grows up there, the infant has a reduced risk of allergic disease. However, this is not the case if there was pesticide exposure. You need those bacterial exposures to make you healthier, but pesticides will wipe out all the benefits.

If you’re thinking of getting a furry pet and your family is not atopic or already allergic, you need to get the new pet sooner rather than later (e.g. for the newborn and/or infant). It is protective to have a new pet already in place as the young immune system rebalances. Whereas if you think, “I’ll wait until the child’s is six or seven—that’ll be great,” that’s a prescription for a higher risk of pet-driven asthma.

In terms of soil, there is a Mycobacterium vaccae that is an anxiety reducer. It helps PTSD. Touching it with your skin and breathing it in will improve your neurological status and it’ll help elevate the production of serotonin in the prefrontal cortex.

soil and microbiome

For more info on Rodney Dietert and his work, you may visit his website or read his book The Human Superorganism: How the Microbiome is Revolutionizing the Pursuit of a Healthy Life.

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