The Phytobiome, Planetary Health, and Human Disease

Kalea Wattles, ND

We're all aware of the importance of the microbiome in human health, but other living organisms have microbiomes too, including plants. In recent years, research at the intersection of plant biology and human health has unveiled a fascinating and intricate relationship known as the phytobiome. This emerging field of study explores how plants, their associated microorganisms, the soil, and the environment collectively impact human and animal well-being. Today, we welcome IFM educator and 2024 AIC speaker Dr. Michael Ash to discuss what we know about the phytobiome and its potential implications for human health. Welcome to the show, Dr. Ash.

Michael Ash, DO, ND, BSc, RNT

Thank you very much.

Kalea Wattles:

At IFM, we love to talk about the latest research and look at things that might be new for many people. So right up front, I thought we should establish, what is the phytobiome, exactly?

Michael Ash:

Well, it's a great question. And you might imagine that the second half of its name gives you some sort of indication, and phyto is for plants. So the phytobiome is composed of plants with their interacting organisms and their environment, which together work to influence plant health and plant productivity. And I think probably we're going to cross this bridge a number of times, but you've mentioned already that most people listening to this are aware of the microbiome and its impact on human functionality. And the phytobiome has an equivalent level of responsibility within the soil and the plants. And we'll tease apart why that's relevant as we go along.

Kalea Wattles:

I always love to know what draws certain people to certain topics and how you find a love for researching and investigating certain things. What brought you to your own interest in studying the phytobiome?

Michael Ash:

Well, actually, that's quite an interesting story itself. So, 25 plus years ago, my clinical work was exploring a role in the early days of manipulating the commensal organisms in the gut to influence systemic immunity, initially with elite athletes to prevent seasonal breakdown during travel and then secondly, in neurodevelopmental cases. So for many years, I worked with individuals within the spectrum, and we did work to explore the role of the human microbiome and its influence on a variety of immune parameters, from cytokines to immunoglobulins and associated changes in behavior. 

So, think back 25 years, I've been interested in the idea that we are not alone. And as a consequence, we might be able to utilize what I like to think of as our generally underserved employees: the characters that reside predominantly in the lower colon but throughout our tissues that contribute to the way that we function and live. So when I stopped practicing full time, I began to look around to see what, apart from my educational work, what would we look at in terms of real root cause? Having dealt with thousands of patients that present with symptomology is consistent with a disrupted human microbiome, for which we try to utilize, at least in part, foods and food concentrates to correct. Where could we go from there? 

Circumstantially, I was already doing some work with some investors, and one of the investment projects that came up was looking at capturing and re-utilizing nutrients from beef abattoirs. And one of the components of that was to take the bone material and its mineral content and protein content, split those out, and then reconstitute the bone minerals with other waste matter and produce a multi-nutrient biodegradable fertilizer, effectively trying to provide a circular route. Animals consume the grass, extract the nutrients, animals are culled, their meat is then utilized, but there's a waste, and that waste was not being properly utilized. So that threw me into the world of fertilizer, about which I knew virtually nothing at the time. 

And so as a result, I began to work with an institute called the Rothamsted Research Institute in the UK, which is the oldest fertilizer research institute in the world. And we began to look at whether or not we could convert through a very complex rapid degradation of bone and other organic material to produce an organo-mineral fertilizer. And we did some early pot trials; I published or I co-authored some papers on exploring the impact of these carbon-rich micronutrient compounds on plant immune health and plant nutrient density, i.e., could we change the phytobiome or the soil constituents by introducing a carbon and an absorbable or utilizable nutrient? We refer to these as soluble nutrients because they get taken up by the organisms and transferred to roots quite quickly. Would that change plant composition? And the early studies we did showed that went well. We’ve subsequently done field trials, and we're running this into larger scale routes into the fertilizer market, with opportunities to develop this engineering project globally, because there are millions of cattle culled every year, and we dispose of or fail to utilize a large part of their assets, which is extracted from their bone. 

So it grew out of a commercial and intellectual exercise. I knew that we could do something to change the quality of food. Obviously, there are various ways that people have been looking at food production over the years, but agrochemical industry tends to utilize a very blunt tool by using chemical composition fertilizers, and traditional methods of improving plant health also improve soil health, whereas the opposite happens now. So you've got to get an increased yield but at the cost of declining soil health and well-being. Why is that important to us? Well, ultimately, we are soil. I mean, what we extract and consume that grows in soil ultimately becomes us. And if that root becomes impaired, then the consequence to us is we get impaired health. 

Being a bit more philosophical about this rather than pragmatic, I think it also demonstrated to me a bit of a paradigm shift, and IFM loves a bit of paradigm being shifted to the left or right. So it's a new way or perhaps not so much a new way but another way of looking at the way that the world functions. We have traditionally separated ourselves from plants and animals. And we can say each of them may have a microbiome. Animals have microbiomes, we have microbiomes, and as you're learning, plants also do. But we're now really having to think that the idea is that they're all parts of a united meta-organism. And we all operate in concert with each other. So rather than thinking of us a bit like medicine has done for years in silos, their microbiome and my microbiome, I think it's important that what I'm trying to present at the conference is that there's a connectivity between all of these different processes. And there's a name given to this, one you may be familiar with, Kalea, but it's a name that's been around for a long time; it’s called holo-biont or holobiont. And the notion of holobionts looks to replace the concept that we're monogenomic, that we live in isolation, that effectively we protect and sustain ourselves as individuals, whereas in reality, we operate and engage with and survive because of the shared responsibility and engagement of all these different organisms across the planet. 

And I'll be looking at some old European researchers’ work over 200 years ago that were beginning to explain this. The contemporary analysis of how we function is making this much more quantifiable, but the notions are not that new. Naturally, it's a pretty big claim. We are stranger organisms, we’re sometimes thought of as a torus; we're a three-dimensional object with a hole for the middle. And that hole is the alimentary canal. And nearly all of that provides a home to these microbes. And the different parts have different inhabitants, but the majority of them, as you know, live in the lower gut. We're learning more and more. I don't think any subject matter in medicine these days doesn't touch upon the microbiome. And if we ask the big question, which is how did I get interested in this, so you just go back to that first question is, what happens before that? Why are we losing diversity? Why are we faced with so many consequential adverse health effects associated with dysfunctional microbiome? So I hope that wasn't too long, but that sort of should give you a bit of a snapshot.

Kalea Wattles:

That was quite the beautiful origin story and so much detail that I'd like to revisit. You've piqued my interest, as I live on a cattle ranch, we raise Highland cattle, my family does, and I'm listening to this fascinating work that you've done. And I have to wonder, are there some principles from the research you've done that farmers like me who focus on regenerative agriculture, can we take away some of the key principles of your work and apply it right away on the farm?

Michael Ash:

You can. I'm not sure how many listening to this will be farmers, but we'll offer a big picture. I'm on a farm as I speak to you now, but we're rewilding at the moment, rather than regenerate, or we're regeneratively improving the soil for rewilding. So let's answer the question with a slightly broader footprint here. Animals and plants engage or react with the soil, either by selective food grazing or by determined food grazing. So if we look at the lot farming, by animals who are positioned to operate within a confined space and they're fed a prepared food, those animals are denied access to the biodiversity that's naturally present in sward or pasture. And consequently, their food intake ultimately impacts across their own microbiome and then the quality of that food. If you have a grazing farm where you allow your animals to move and you're looking to employ regenerative strategies, there are numerous processes; you've probably come across Mr. Savory's work from Africa, which is where I am now, which is you do specific periods of intensive grazing and then you move animals. Their urine and manure contribute to a growth of biodiversity and improvement in the mycorrhizae and the microbial composition of the soil. So if you're not familiar with that, then this is not really specific to our clinical audience, but to the farming audience, Allan Savory has got a number of videos, and I certainly would recommend reviewing some of those. 

What we're always looking to do in regenerative work is we're trying to say, much the same way we say about our colon or our small intestine, the greater the diversity of organisms, both bacteria, mycorrhizae, worms, et cetera, that live in that soil, the greater the capacity the soil has to absorb water, transfer nutrients to plants, have those plants consumed by animals in your case, so they're not a cash crop, they're eating it to consume it, absorb those nutrients into their tissues, and then those tissues will ultimately be transferring that value to the person that consumes them. And the same for their bones. 

With plants, their immune system is highly dependent upon the ability of the organisms to stimulate something called jasmonic acid. It's not the only chemical, but let's just concentrate on one that we can review. So jasmonic acid is generated through tissue in plants for exactly the same reason as we don’t want to be eaten. They would like to survive long enough to produce progeny and continue functioning. That jasmonic acid contains compounds, which our immune system has spent millennia developing receptors to translate that information into inducing various types of defenses and other tissue repair chemicals in our own gastrointestinal tract. So if we improve the soil through reduced impact of grazing but concentrated grazing, we do no-till or reduced till where we're looking to farm, we reintroduce carbon back into that ground by allowing cover crops to grow so that nitrogen is held in roots, that we introduce, one of the ways you can look at this is introducing microbial agents to soil. There's a variety of companies that offer that. I think that’s another subject for today, but there's risks with that and there's also potential benefits. 

If you get involved in the regenerative agricultural movement, you'll discover there's a whole host of wonderful individuals that have developed all sorts of strategies, some of which are consistent, some of which are not, but ultimately the same thing applies with soil as it does with human gastrointestinal functionality. If you don't feed that soil with the nutrients necessary to propagate, promulgate, and sustain the life of the phytobiome, just like the microbiome, there's a diminished capacity to function, and with that comes a diminished quality of health.

Kalea Wattles:

We're starting to see all these parallels between the microbiome and the phytobiome, and you mentioned this microbial balance, and like the microbiome, I imagine that there are likely some beneficial organisms and some pathogenic ones that might affect the phytobiome. Do we know much about this balance yet?

Michael Ash:

Yes and no. So in much the same way as there is a tendency, and it still exists for the human analysis of the microbial population inside the gastrointestinal tract to be qualified in a rather simplistic ‘good or bad’ nature. I think all of us are aware that there are fluctuations within the pathogenicity or the functionality of those organisms depending on population, growth, the ratios between different organisms, and their immediate environment and also the food substrates that are available to them. So what we can see is that there are far more organisms in soil than there are in us. To be able to quantify and qualify their role individually is an emerging field. Some of them are very old, some of them not so old. 

And what we can say is that both seeds and soils have their own microbiome, and therefore, organisms present both in and on are slightly different. And they depend on different environmental pressures, just like it does for us. So if you have an area that's been biotically stressed, i.e., too much heat, not enough water, it's the same as us. If we're biotically stressed, we're placed in an environment where we're not adequately nourished, there's a compositional change in the organism's structure. And what we are seeing is that there's an increased prevalence of plant-based pathogens starting to appear in the human gut. So if you take a biologically stressed plant, so that pathogenic organisms are not being defeated by a normal innate immune system and therefore they are carried into the food chain and they are consumed by somebody whose own innate and bacterial defense mechanisms are compressed, the risk for cross-infection increases. 

And so early studies now in different countries are showing that the incidence of plant-based pathogens is increasing where there's a decrease in the quality of the soil and the quality of the plant. And that results in the production of -cides or herbicides or fungicide, et cetera, which comes with a lot of unintended consequences in much the same way as we see with antibiotics. So again, I've tried to do these parallels because the two are connected, and I think they make sense in that we are familiar with the life-saving capacity of different types of antibiotics and also the declining effectiveness as antibiotic resistance grows. Herbicides, pesticides, fertilizer, which are operating in synergy to try and increase yield because we have a rapidly growing population, generate the same unintended consequences. We end up with more and more soils becoming dirt, and dirt doesn't grow things. Soil is required to grow things. You can artificially grow something temporarily or you can artificially suppress an infected state of the gut, but they have unintended consequences, and that's something that society is only really just beginning to become aware of.

Kalea Wattles:

So it sounds like we're still in the early stages of understanding the phytobiome and how it can influence human health. But as of this point, will you tell us some of the ways in which we think that the phytobiome might influence human health and well-being?

Michael Ash:

Right, so it might initially seem a bit of a jump. We're talking about initially soils and plants, animals, and then humans. I've given you one indication of when things might go awry. So there's a lateral transfer of pathogens from either animals or plants into humans. What I think, depends on how big a scale we want to go, Kalea. Let's do a big picture. First of all is that we all live on a planet that we try to co-evolve with and sustain a mix of both natural and manmade experiences. If you're a farmer, I think you will, and you come from a farming background, you're aware that the intricacies of every day’s experience expressed through natural episodes have to be translated into a different type of interpretation. If you're living in a building and you're operating in a city, these sort of subtle variations in weather changes and climatic changes and food production changes pass you by because you're really focusing on end product, i.e., the finished goods, whereas farmers are focusing on the starting product, which is essentially the soil and the plants. But there's a transfer at every stage from growth to consumption that will determine the possibility of transferring information to the end user, which is us. 

So I think we're all familiar at IFM with the idea that food can be medicine, and used correctly, it can unwind people's dysbiotic or dysfunctional health. But the power of that medicine rests in the strength, health, and vitality of the soil. You can't create a medicinal food if you grow it in a substrate that's absent both of the microbial components and all the other elements that were required by that plant to be beneficially useful, not just to itself, but also to us. So the direct link is that, unfortunately, around the world, we are losing topsoil. We're degrading the production of plants in part because of environmental pressures, including the increased exposure to plants of carbon dioxide in the air or atmospheric carbon dioxide, changes in water availability and capacity to rear plants, and the pressures on food production systems to meet growing demand from around the world. And at the same time, the somewhat dysfunctional, and this is not just unique to the US or to the UK, but the dysfunctional way that governments have tried over many years to favor certain types of plant or animal production over others. So we move into monocultural loss of diversity. So the very big picture is we're degrading, damaging, and disorienting many of the essential components of nature that constitute the joy of us living in our world. At the micro level, we see disordered communities of organisms that are dependent upon an environment just as we are to survive, to transfer benefit through the plant system to us as humans.

Kalea Wattles:

The theme of the 2024 Annual International Conference is from the macro to the micro, and this topic seems particularly well-suited to fit under that theme.

Michael Ash:

When we were thinking through how could we start to create a connection that has some traceable, quantifiable analytics back to the soil, it's to me where everything now sits. I think once you become aware, as you drive around, again, if you're not exposed to agricultural land, it's sometimes difficult to imagine. This could be a garden, it could be an allotment, it could even be a small collection of pops in your house. The environment in which you plant whatever it is you wish to grow, whether it's a food or just a plant to enjoy, the environment in which that lives is sensitive, dynamic, and vulnerable. 

And when we think at a scale, when you drive through the Midwest, for example, and you just drive after mile after mile after maize or corn or wheat, all of which are commodity crops grown because we convert them into foods that are convenient and packaged and processed, we are looking and witnessing at a commercialization of a resource, which we only have a limited amount of, which is our soils. There are movements that are looking to increase the understanding of why the microorganisms and that tiny complex world at the micro level in soil is just as important as that which is in the oceans or in the atmosphere or is in us as humans. I think every country goes through challenges of understanding about soil. America is an unusual country. They've already experienced one massive loss during the 1930s when there was a large quantities of the Midwest that became damaged and destroyed. And we're witnessing it again right now is that there is a strong commercial demand to continue to force our co-hosts on this planet to produce food for our ultimate consumption. 

But like I said at the beginning, we have employees that live inside of us. If we don't provide them adequate care, pay them appropriately, give them a nice home in which to live, they go on strike or they start protesting. And they do that by inducing inflammation, which becomes systemic. We see the same thing happening in soils, except they go sterile. So soils essentially say, we can't support your demands, and our organisms can no longer do it. The cost of that ultimately is for the demise of all life. And so when we look at the micro level at a global scale, it's very, very significant. And I think hopefully you'll learn over the conference that there are people that are working to correct that. But if we're not aware of it, we just wander around unaware that right around us, right now, there are microorganisms pleading for our assistance outside of us but responsible for those that are inside of us.

Kalea Wattles:

I love this mental model of thinking of our microbes as our employees. That really works well for my brain. Will you talk to us a little bit about how the microbes in plants might influence our own gut flora?

Michael Ash:

Yeah, well, I think there's some, I gave a few indications that there are compounds that plants will utilize for the purpose of defense. And there's quite a lot of research and interest in how plants develop and evolve relationships with each other. I'm sure by now, if not you, then probably a lot of people listening to this are aware that there are massive, interconnected populations of trees and plants that share a communication pathway, often through fungal spores, but also through their roots. And the idea that we have a holobiont of plants where they're sharing information between each other is exemplified further by the defense mechanisms that can be triggered by one component within that group being triggered. And so if you were to threaten, either by sun, water, or some form of insult occurring at trees operating these large communications, you'll see that there are subtle changes sequentially across those trees. 

Think about that when we look at our primary source of the food groups that most people consume derived from wheat, which is a hybridized version of wheat, which I'll do a little bit of explanation about on the presentation, it's a hybridized version facilitated in growth by an artificial stimulation from an extraction of a powerful source of energy to produce nitrogen, other chemicals as well, but let's just choose the wheat and the nitrogen. If you introduce a single chemical or even two or three chemicals into that environment of the soil to stimulate growth, you do so at a cost. Growth comes at a loss of diversity. Those plants are less efficient at defending themselves, they carry less messengers to the receptors in our body that we have spent thousands and thousands, hundreds of thousands of years developing. The consequential loss is reflected in an absence of diversity in a westernized society gut compared to those operating in a hunter-gatherer environment. They have probably twice as many, as I'll demonstrate, twice as many different species in a hunter-gatherer's gut than in a westernized gut. 

What's the implication for that? Well, one, we metabolize food differently, we end up storing probably more effectively than our hunter-gatherers, but at a molecular level, what I've been able to track and trace for years is that the genetic stimulation of immune defenses in our mucosal tissues decline. The consequences for that vary from one person to another, but the link here is a phytobiome-deficient soil produces a microbially and immune-deficient plant. The chemicals that would normally defend that plant are essential for our human receptors to utilize to defend against infections and chronicity and inflammation. We see a cascade of reduced capacity to maintain the human holobiont in its traditional form, and we end up making compensations through a diminution of our functionality.

Kalea Wattles:

Wow, I'm wondering if, knowing how these interactions are influencing things like our immune function, can we make a link to certain diseases or physiologic dysfunctions? I'm thinking autoimmune disease. Can we make some linkages here between the foods that one is eating and how these processes are manifesting in the human body?

Michael Ash:

The direct correlation is occurring more in the infectious area, as I mentioned earlier. So you can trace and track a single or multiple pathogenic organism. I think the area in which functional medicine sits most comfortably is the system's dysfunctionality. Often one system may be more out of line than another. Commonly, obviously, we all like to look at the gastrointestinal tract as an anchor point for intervention. But the reason why we can often intervene in a range of systems and still affect the beneficial outcome for somebody is because of the interconnectivity of it all. So if we see, as we do most commonly, a decline in microbial diversity, which is a related connection to a decline in plant and soil diversity, i.e., if you have a plant that's grown in nutrient-deficient, microbially deficient soils, its ability to sustain, promulgate, and transfer organisms of value to us declines.

So, as I was saying, where we have our hunter-gatherers who I refer to demonstrate around 760 different types of species differentiation from people in Italy. And the reason that has an impact is for exactly the same things that many of your previous guests will have been discussing. We change the dynamic defense processes in our body. We increase the production of defense molecules, particularly inflammatory cytokines, and diminish those that can retain and maintain a normal homeostatic mechanism. Our homeodynamic cell becomes disordered. Stepping away from there, Kalea, you can immediately see where the path is going. Every single NCD that we look at can be traced back to a disordered immune inflammatory cascade. And we are relying on end products that are nutritionally poor when produced and then manufactured into a less efficient form to try and sustain a homeodynamic system that's now out of condition.

Kalea Wattles:

Well, I think we can all understand how important the phytobiome is, and we're starting to see these connections between human health. As a consumer or as a clinician who advises consumers, can I purchase foods that are grown or harvested in a way that honors the phytobiome? Is it just purchasing foods that are local and organic? How do I make these choices that honor these processes?

Michael Ash:

Well, again, much of this is familiar in terms of what is practical. How do you persuade somebody that their investment into a different type of consumption is going to pay off? I sometimes think of this as a pension plan. You know, when you're 21, the idea that you should form a pension plan seems pretty alien because it's a long way away before you imagine you're ever going to need it. But the people who start pension plans when they're 20 are generally in a much better position when they retire than those who start when they're 40 or 50. So I try to persuade people that we need to think of this as a long-term investment. It's not normally you're going to see a change in days, but you'll see a change over months or years. And what I explain is that the transfer of value that occurs from an early investment is multiplied by its utilization over time. So if you do choose foods that are organic in nature, they may be slightly more expensive. It may be that the taste is not that different. They may even appear less attractive than some of the more commercially ground products. But what you can't see is the value add. You can't see the metabolites that become muscles and fat in you, the biochemicals, the phytochemicals that transfer that message to promote health. Eating phytochemically rich herbs, spices, vegetables, and fruits provide an expanded set of compounds that are produced from these plants and ultimately consumed by animals as well.

So if we want to dampen down oxidative stress and inflammation, think with conditions such as cancer, cardiovascular disease, metabolic syndrome, the challenges that we have as a world of feeding eight to ten million people over the next few years cannot only be predicated by yield. If we continue to pursue the process that you only eat foods that are easy to access rather than eating foods that are beneficially going to assist your health generation, we end up with a tier of people, which we see now, particularly in the US and UK, where the majority of the population has at least one, in many cases, three chronic diseases. And that will bankrupt the countries, it will bankrupt the healthcare system, and it will diminish productivity right across. So I say, every time you purchase a locally produced, preferably organic or from a regenerative farm where you can find them, food, you're making a deposit for your future health pension. It's difficult to see it growing on day one, but if you can put five or six portions a week into that deposit box, then you will end up with a much healthier future or a much richer health pension fund.

Kalea Wattles:

Beautifully said. This has been such a fascinating conversation, and as we come to a close, are there some takeaways that you really hope the functional medicine clinicians who are listening will take back to their practice? Any principles you hope that they'll put into play immediately?

Michael Ash:

Well, the biggest takeaway is this: we as clinicians and everybody in functional medicine tends to focus on the finished product, and there's a very good reason for doing so. The processed foods, the finished products carry with them a message of destruction when they're consumed. They're not adding value to us, they're temporary beneficial reductions of hunger, but they're messages of human destruction. What plants grown in rich soils using organic or regenerative methods do is the opposite. They transfer beneficial growth messages; they inhibit or prevent or reduce or even reverse chronicity. So I think we need to think that we're having an edible microbiome present in the plants and meats that we consume that are grown on farms that are trying their very best to return to a more traditional, thousands of years old practice of utilizing and appreciating and valuing the strength and quality of the soil.

Kalea Wattles:

This has been such an amazing preview to your lecture that you will deliver at the 2024 Annual International Conference. Thank you for sharing these clinical insights that will help us to invest in our future, invest in our planet. It's just been such a pleasure to spend time with you today. Thank you so much for being on the show.

Michael Ash:

Well, thank you, Kalea. And I look forward to seeing you at the AIC.

Discover the latest research and innovative clinical practices at IFM’s Annual International Conference, May 29 through June 1, 2024, at the Bellagio in Las Vegas. For more information, visit aic.ifm.org.