Adapted from episode 141 of The Perfect Stool podcast with Dr. Shayne Morris of Systemic Formulas and Alimentum Labs, sponsors of this episode, and edited for readability with Lindsey Parsons, EdD.
Lindsey:
Before you reached out to me about the podcast, I had not really heard of Systemic Formulas and Alimentum Labs. So can you just give a very brief background about those two entities and how and by whom your products are developed?
Dr. Shayne Morris:
Yeah, the Systemic Formulas products have been around since we started in 1984, and this gave us a really early entrance into the direct-to-clinician model, or the niche. It was started by my grandfather. He, in fact, started it back in the ’70s. Of course, it evolved, and it ultimately landed on Systemic Formulas* (use Doctor Referral Code: AZPA11 to access products). Clearly there was a need for some clinician-trained use for what we call dietary supplements or nutritional components, as well as herbal mixtures—therapeutic herbs. Ultimately, that led to the science of it all. My grandfather started in what we call ethnobotanical medicine, where he was traveling the globe learning about how these various herbs and other natural products were being used medicinally, mainly from native people of South America, the Polynesian islands, and Asia. He brought all that back.
What was exciting for us was that it was early. We say it was early, but it was only early for us—these things have been around for millennia, and yet they had really lost favor, being replaced by other, more modern approaches. But they were so powerful, and that’s kind of what led me into it. I started as a young child working with my grandfather, but I went back to school and really pursued the sciences—the hard sciences of natural products: biochemistry, molecular biology, genetics, and microbiology, which is now the microbiome.
Each and every one of these products benefits us through processes that are designed within us. These herbs have a particular medicinal benefit because of the way our body interacts with them. For anybody that doesn’t really gather that concept, you simply have to look at psychedelics. Natural product psychedelics clearly have an impact on our physiology. Some psychedelics can create hallucinations in our brain. So there’s this really intimate relationship between us and microbes and plants and fungi.
That’s what led me into this path as well, and Alimentum became a brand within the Systemic Formulas family that focuses on human genetics—the impact of nutrition on our genetics, on our cells. We call that cell-based nutrition, as well as the microbiome. The microbiome covers things like prebiotics, probiotics, and many of these really important nutrients that microorganisms need in order to maintain our health, protect us, manage our systems. We have all these axes—we refer to gut-brain, gut-lung, gut-heart. All these axes have to be well maintained. That’s really where Alimentum was born, about 12 years ago.
Lindsey:
And are you the one that develops the products?
Dr. Shayne Morris:
I do a lot of it, yes. We have a number of really amazing people here. We also have a research branch. So, there’s the family of Alimentum and Systemic that’s on the education, product, and sales side—which includes our sales team, marketing team, manufacturing, and education. There are some incredibly brilliant people in that area. But we also have a research and testing branch with a separate lab. It handles a lot of QC and R&D testing, and the scientists over there help me develop a lot of these things.
Lindsey:
Okay, cool. So today we’re going to be talking a lot about these keystone probiotics. Can you talk about what keystone probiotics are and how they differ from traditional probiotic strains found in typical supplements?
Dr. Shayne Morris:
It’s a really phenomenal topic. Whenever we talk about the microbiome, it can be understood in two ways. We’ve all heard it’s the collection of microorganisms that colonize us on every surface—sometimes even systemically. These amazing communities, or ecosystems, help keep us healthy. They support immune function, manage mucosal systems, and even impact neurological function through hormones and cellular signaling.
But there’s just so much information that people often simplify it down to “eat properly” or “take probiotics” or “eat fermented foods”—all great things, but they don’t always address the deeper issue. What’s the difference between a healthy, average, or dysbiotic microbiome? And that can apply anywhere in or on the body.
Keystone species have only been identified since we gained access to next-gen tools—ones that analyze not just microbial genetics, but also metabolites: what these microbes produce, what they’re doing, and how they benefit us. Keystone species are generally low in number—they don’t dominate—but they regulate the entire community structure. They’re essential to the structure of a healthy microbiome.
They’re necessary even in small amounts and produce compounds that are functionally important—not just for the other microbes but for us as hosts. They have a disproportionate impact. When you lose one, you often see surrounding organisms collapse.
My best analogy is a coral reef. Introduce one or two invasive species and it can collapse the whole ecosystem—destroy coral, push out fish, predators leave. But bring back the keystone species, and the whole thing rebounds: coral, invertebrates, fish, and so on. Over the past century, we’ve tried to reduce pathogen exposure, but in doing so, we’ve wiped out many keystone species. We want to bring them back to restore diversity and ecosystem stability.
Lindsey:
Yeah, in my experience looking at stool tests, I often see species disappear after people go through multiple rounds of antibiotics or strong herbal antimicrobials. Akkermansia muciniphila and Faecalibacterium prausnitzii are big ones. I was blown away to see F. prausnitzii in one of your probiotics—I didn’t even know that was commercially available. I’d love to hear more about that and the other keystone species you’ve got in your probiotics.
Dr. Shayne Morris:
Yeah, we’ve got a number. It’s taken us—really since about 2009—when we got heavily involved in microbiome projects. We knew about some of these species academically, but we didn’t yet know the future of probiotics. I mean, probiotics have been around for decades. We’ve all used some form of Lactobacillus, Bifidobacterium, Streptococcus, even yeasts like Saccharomyces.
These mostly came from the food industry—cheese, dairy, other fermented foods. So we always embraced the idea that living microbes could be beneficial, not just in themselves, but also through the metabolites they produce.
As the microbiome field exploded—it’s probably one of the most actively researched areas globally—we went from a handful of publications a decade ago to around 20,000 a year. With all that interest, we started trying to understand keystone species better. How do we go from identifying them in stool or saliva or the urogenital tract to actually growing them in stable, viable conditions?
That was our focus from 2009 to around 2017–2018. It was exciting, but also painful. The tech needed to grow these is tough—most are strict anaerobes and extremely sensitive ot oxygen-sensitive, even more than water. So that technology took us a bit.
But along the way, we also asked: what feeds them? What keeps them alive? What makes them want to take up residence—not just pass through? That’s where we started experimenting with different prebiotics. We used a lot of plant compounds: flavonoids, polyphenolics. Then we discovered they also need basic nutrients—certain B vitamins, glutathione, even a little carbon. These are the small but critical details we learned over time.
So we realized we not only wanted to support keystone species—we needed to educate people on the full scope of what a prebiotic can be. The current definition is a fiber or a microbial-accessible carbohydrate, but it’s much broader. It includes polyflavonoids, alkaloids, cyanidins—you’ve probably heard of ellagitannins or ellagic acid converting into urolithin A. That’s a keystone-driven microbial reaction with real physiological benefits.
So along with our probiotic work, we took the prebiotic journey too, incorporating a range of compounds—some not traditionally thought of as prebiotics, including human-derived ones like mucin and glycosaminoglycans.
Lindsey:
Let’s get into some specifics on the keystone species in your probiotics.
Dr. Shayne Morris:
Yeah. So the way we’ve approached organizing these keystone species is by identifying the systems where they’re most impactful. For example, we have something called Terra Terrain. While not all of them are keystones per se, they’re part of a larger need for soil-based organisms. Many of those are spore-forming. There are about five common commercial ones, but there are many more.
Looking more deeply into Europe, Africa, and Asia, you’ll find other species with real probiotic benefits—ones we’ve largely ignored in the U.S. But if you sequence healthy people eating from their gardens or local farmers markets, you’ll see these show up. Just a few examples: Bacillus lichenformis, Bacillus amyloliquefaciens, Priesta megaterium, Paenibacillus mucilaginosus, Bacillus indicus, which is more commercially recognized, there’s Paenibacillus polymyxa. These are all unique SBOs that we now have.
We’ve also partnered with people using kefir grains and kombucha SCOBYs from various places. We use the live organisms from the SCOBY and the kefir grains to then round out these more transient organisms. That’s one way we’ve incorporated the fermented food world.
Then we get into the actual keystone species. I’m going to list some of these off for you, but they’re their names are crazy. I have to say that microbiologists are not the greatest at naming things. But we have things like Micrococcus luteus and Staphylococcus epidermidis. Luteus is a gut-based keystone species, but it seems to have a benefit to our skin. It produces certain carotenoid pigments that end up in the skin, creating a UV protection, not unlike recommending the carotenoids from beta carotene to gamma, alpha, delta. Or you may have heard of other types of blueberry compounds or blackberry compounds that are protective in the skin. Well, we have microorganisms that produce similar compounds.
And then you have things Staphylococcus epidermidis, which is a skin commensal. And it’s brilliant, because it out competes Staphylococcus aureus. Now aureus is the problem child, and its main enemy, believe it or not, is staph epi (epidermis) is what we call it, and the competition between those two is significant. Epidermidis creates what we call bacteriocins that only reduce the aureus population—it has no impact on other organisms, just aureus. So when you see people that are suffering from Staphylococcus aureus issues, they likely lack epidermis in their skin. And that’s a really, when . . .
Lindsey:
And those are all in the Derma µBiomic?
Dr. Shayne Morris:
Derma µBiomic and the Derma Serum. Epidermidis is in there.
Lindsey:
So you have a topical for that? Wow, that’s awesome.
Dr. Shayne Morris:
Yeah, it’s a plant-based oil where we’ve tried to mimic a lot of the oils we secrete from the sebum, and then we’ve lyophilized the epidermis and also included Staphylococcus xylosus, another commensal. These are found on the skin in various regions, and they are protective in the fact that your immune system needs to know they’re there. It educates them. But they’re also protective against invading.
Lindsey:
And what does a skin infection with Staph aureus look like?
Dr. Shayne Morris:
The most familiar one is atopic dermatitis, especially in children. There’s a brilliant scientist, I forget her name, out of UC Davis or maybe Stanford. She studies pediatric skin conditions like psoriasis and atopic dermatitis. And she’s published a number of amazing studies showing that most atopic dermatitis on children is essentially an overgrowth of Staphylococcus aureus. And one of the unique features that differentiates aureus is when you have a rash that fills and looks like atopic dermatitis and it itches, the itch is somewhat indicative of Staph aureus, because they actually that organism actually sends a signal to create itching into our skin. It’s kind of devious, right?
Lindsey: Cool that you have a serum that fights it.
Dr. Shayne Morris:
Yeah, and for really recalcitrant versions, we actually tell people to open up Derma and Immune capsules and make a paste and lather it on top of the issue prone area to really try to get these colonies to push back against the non-desirable. . .
Lindsey:
I can already think of a client who needs this…
Dr. Shayne Morris:
It’s incredible that—I mean, for me, it’s always an incredible journey to not only keep up with the ever-increasing and ever-amazing world of the microbiome and these organisms, but also the clinical applications that really range from our metabolism to our neurological health to our lungs and our kidneys and liver, etc., right? Some of these are really amazing at destroying metabolites—I mean, helping us metabolize xenotoxins, for example. It’s going to be an area that is ever-growing and ever-improving. And this is where we’re at the tip of the iceberg, but we’re excited to be here because it’s taken us a while to get here.
But let’s jump to, let’s say, on the immune front. So we know that the microbiome is incredibly powerful when it comes to our immune education, our immune evolution, and just navigating new threats all the time. And, you know, our keystone species in that regard are some interesting names. Again, we have some Bacteroides species—one of them is ovatus. We have uniformis, also Bacteroides. We have Roseburia hominis, which is a pretty fun one.
Lindsey:
I was very impressed to see that in there because that’s another one that often is depleted in people’s microbiomes.
Dr. Shayne Morris:
Right. And then we have another one called Collinsella aerofaciens. Again, a very unique keystone that has this incredible ability to help educate not only the area of the gut, which, you know, can be inflamed—the gut is, of course, overwhelmed by things like invading organisms, invading food, invading toxins, etc.—so it helps manage a lot of that immune/epithelial tissue regulation to keep things as managed as possible and healthy. It lowers inflammation, for example.
And then from the hormone front, we were able to get Bacteroides uniformis. We have Lactobacillus crispatus—a version of that that’s ours. That one, I believe, is now commercially available, one strain. And then we have Lactobacillus vaginalis, which is also a really important urogenital organism. And I oftentimes get the question: okay, we call it hormone balance in the microbiome, so we call it Hormone µBiomic and Hormone Superfood. Although there are a number of organisms that benefit women, no doubt, men also benefit. And in women, oftentimes people don’t realize that the organisms that colonize the urogenital tract are also found—or can transit—from the gut into the urogenital tract, likely because of the close proximity.
And when you study the consumption of pre- and probiotics to help improve the urogenital tract in women, taking them orally works. You can also use these in a suppository way, which is completely normal and healthy and fine. But you can also just rely on oral ingestion, and they will colonize. When that is their place, the body has this beautiful innate ability to help traffic these organisms to where they need to be. It’s quite a unique process. When they’re available and you’re feeding them properly, the body will do the rest in many cases. But for people that are struggling, we oftentimes recommend oral as well as suppository urogenital support.
Lindsey:
And have you seen that using these species in the Hormone µBiomic has some impact on hormones?
Dr. Shayne Morris:
Yeah, right now we’re conducting some observational preclinical work. So everything I have on the hormone—especially in women in childbearing years, as opposed to perimenopausal or menopausal—is anecdotal. But we’re getting some really good anecdotal data, very positive, improving urogenital health in regards to recurrent UTIs, just overall health of the urogenital tract, as well as the gut simultaneously.
Now we’re moving into sequencing samples and trying to follow these more specifically. And of course, there is a lot of really good data just surrounding the crispatus and the vaginalis that help us follow the academic work. So we’re kind of on a parallel path with academia as well regarding these.
And you’ve probably heard that female urogenital tracts have been classified into about five different classifications. The first four are essentially Lactobacillus-dominant ecosystems, and the fifth one is pretty much lacking Lactobacilli. It’s not as common, especially in industrialized countries, but it is just every bit as healthy—it just has a whole separate ecosystem or community that we look at. So in that case, you would support the gut, and then that unique person would have to feed and really encourage the growth of these other unique keystone organisms outside of the Lactobacilli that we can actually provide directly.
Lindsey:
Yeah, and those are also in that Hormone µBiomic?
Dr. Shayne Morris:
Yeah.
Lindsey:
And what’s the predominant species in that fifth type?
Dr. Shayne Morris:
Oh, the fifth type—those we don’t have. Those are unique. And so far, the work that’s been done and the work that we’re following—they’re not organisms that we’ve been able to culture and, of course, run the safety studies, etc., and get them ready to bring to commercial. But by employing the probiotics that are keystone—and especially the prebiotic world, so a lot of these superfood prebiotics—you can actually encourage the reconstitution of that particular urogenital classification through what we call nutritional intervention.
It helps bring back all of the external factors that drive dysbiosis in the urogenital tract of women. You bring that back. You make sure you understand whether or not they’re using cleansing products, or if their partner is healthy at the moment—avoiding a lot of the disruptive things—as well as reintroducing these healthy pre- and probiotics that help the GI manage the UTI. Because there is a connection.
And of course, the piece I can’t speak to at length today—because it’s a whole different topic—but you also have to monitor hormones. Hormone variations can absolutely disrupt the female urogenital microbiome. They’re intimately connected. If a woman is highly estrogenic—carrying way too much estrogen—we want to look first at their GI microbiome. Because if they have the enzymes—you’ve probably heard of these, these glucuronidases and galactosidases—they will re-cycle estrogen that’s being excreted. That increases the estrogen load in their bloodstream, which does, in fact, impact the epithelial lining of the female urogenital tract and can disrupt the microbiome.
Now, conversely, if there’s not enough estrogen, it will also impact the urogenital microbiome. That’s an area that needs to be looked into when there’s a recurrent urogenital problem in women. You’ve also got to look at the hormones, for sure.
Lindsey:
and how about the Metabolic µBiomic?
Dr. Shayne Morris:
Yeah. So we have, of course, our two—the last two—and we’re coming out with more, by the way. So this won’t be the end of the story. We’re about 70% through. The Metabolic µBiomic and its Superfood: we tried to take what was known, as well as our own research, and say, okay, metabolically, there’s a number of impactful things. We know that the microbiome has the ability to metabolize our food, whether it’s processed food or whole food. There’s a certain metabolic function that our microbiome has, and if that’s disrupted—one, by diet, and two, by the population or the ecosystem—it’s extremely impactful and detrimental on our metabolic uptake, the way we store lipids, the way we metabolize and sense sugar, and other areas of hormone production. And these neuropod cells that communicate directly to the brain through the vagal nerve and maybe even through the central nervous system.
This is a very, very enormous part of the microbiome’s job—and perhaps one of the more significant after the immune system—where, when you have a dysbiotic gut, you find that everything else, the number of hormones that you’re signaling, the number of neurotransmitters you’re making, the number of systems that are connecting through the vagal nerve and managing all of our endocrine system, our neuroendocrine system, as well as our detox systems—these are all starting to fail us. And this is why we have the chronic epidemics that we do. It’s one of the main features.
So as we were developing this, we decided to pivot. We knew the keystone organisms we wanted—and of course, foremost has been the Akkermansia. We have two different strains of Akkermansia, and they both—you know, we won’t get into strains too deeply—but they both impact. They have separate… when you think of you and I’s genetic potential, there’s going to be different things that you and I do genetically. Even though we might be 99.9% identical genetically, we have these little nuances—these things that you and I can do differently or better or worse—and each species of organism has the same potential. So you might have Akkermansia muciniphila, two of them, but they both maybe perform something a little bit differently. That’s the ongoing knowledge that we’re getting from these strains.
So we have two Akkermansia muciniphila. We have a Butyricoccus pullicaecorum, and that’s a really complicated name, again, and just from the name you can tell that it’s very much involved in maintaining small chain fatty acids from a number of food sources. So it’s Butyricoccus because it produces butyrate—and it produces butyrate that we really need to manage a lot of our epithelial metabolism in the gut. And then, of course, that becomes a systemic benefit as well. And in maintaining that, it creates an integrity in our gut lining that, of course, not only impacts the inflammatory process, but it helps us then manage our metabolic switches—whether we’re letting a lot of glucose in or we’re keeping it out, we’re triggering the L cells to produce more GLP-1 along with the Akkermansia, or do we want to produce PYY or CCK. And these are all what we call satiety hormones. These help us manage our metabolic uptake and the way we store it, and it’s critical.
And of course, now that’s blown up with this new generation of GLP-1 agonists, we can now have that conversation more, I guess, candidly, because the candor around GLP-1 is—it’s out there. And there are more than just GLP-1. Like I say, there’s a number of—you know—the ghrelin, the leptin, the PYY and the CCK. These are all hormones that our body has used, intimately related to our microbiota and our diet, to manage a healthy metabolic process. And we’ve disrupted all of those. So bringing it back to some of these organisms that help us do that is critical. And it’s been phenomenal science. So—excited about that.
Lindsey:
Curious, because I had only previously been familiar with the Pendulum products that had Akkermansia in them. And I know from their original experiments that after supplementing—I think their study maybe was two or three months—after supplementing it didn’t implant. And so I know they have a protocol that’s a bit longer now. So I’m curious, have you looked at implantation of Akkermansia and how long it takes and what you need to do to make that actually happen?
Dr. Shayne Morris:
Yeah, we have. In fact, we’re in the process of doing that right now as we speak. We’ve done it a few times. The work we’ve done so far has shown that pretty much every one of these has implanted and lasted over 60 days. Now beyond that, we didn’t run those further out, which we are doing now. We’ve only done it against one of the Akkermansia strains, so we only have data on one of the strains. The other strain, we have not looked at its—not only implantation—but what we call it taking up residency.
Lindsey:
And how long did they supplement for before you ran the 60 days?
Dr. Shayne Morris:
We ran stool at—so supplemented for 30 days—and then we ran it again at 60, and then at 90, and then we followed that washout period for another 60 days. We were seeing the organisms. After 30 days, we were seeing them regularly.
Lindsey:
Implant at the dose that’s in your product? At the recommended dosage?
Dr. Shayne Morris:
Yeah. Okay, yeah, exactly. And what we found just as fascinating in that—because that’s something we were looking for, right? That’s an experiment where you’re looking for something, you’re doing it. One of the surprising outcomes with these—and keep in mind, we were also giving them the prebiotic, the superfood at the same time. That was a requirement. We didn’t just do probiotic. We did a pre and a pro together. And my hypothesis is that’s an important feature we underappreciated. That if you just supplement a probiotic and then follow it—if you’re not giving it the nutrients that it requires—it will not really engraft and become a resident, because there’s no priority for it to. If it’s not getting its food, it’s going to leave—it’s going to bail.
So we’ve always run our studies with the pre and pro together. And what we found is not only were we seeing really healthy outcomes with the keystones, we started seeing the emergence of a lot of other keystone species that we don’t have, that no one has—but they were growing as a consequence of the pre and the pro journey. And we don’t know if they were just caught in there and they were just surviving at some low level, or if they were being introduced through contact with humans and food. We don’t know. We just know that in our dataset, we not only saw the organisms we were looking for, but we started seeing a lot of new organisms show up that were beneficial organisms. And we saw the reduction of the non-beneficial organisms—or essentially the pathobionts or pathogens—would decrease. And that’s because the whole ecosystem was becoming more competitive, and we weren’t feeding those, right? We were not feeding organisms that don’t belong there—we were feeding the ones that do. It was quite exciting.
And so we’re repeating some of those just to see how far we can take this. And when we did that, we only had probably about a dozen of the Keystones, and we now have more. So as we do this in the future, we can start adding more of these to see how we’re doing. And more of the pre and probiotics, like the superfood for the Metabolic, not only has plant-based compounds, it has a number of what we call human oligosaccharides or human polysaccharides that our body produces to maintain our own microbiome. And, you know, that’s important. It’s an important feature of our uniqueness—not just from a diet perspective, but from your own body’s ability to regulate the microbiome through the production of food for these guys.
Lindsey:
And I think we still have one left—the Neuro, is it?
Dr. Shayne Morris:
Yeah, the Neuro. The Neuro one is a really exciting one. This one was—in fact, a version of this was launched first. So back in 2018, we did a beta of the Neuro. Now, we’ve added since then, but key players in that were, of course, the Faecalibacterium and we had Parabacteroides—but we’ve added to this one since. In the early launch, we had the Neuro and the first version of the Neuro superfood. We called it Neurobiome. But both those together, again, we got really great anecdotal feedback. We got some good stool feedback.
And because we knew it was early on, we went through the beta, collected all the data—I think I had somewhere around 4,000 data points from practitioners using it in their clinics during the beta test. And then we went and reset it. We actually reformulated it in 2021 to get a better result than we got the first time. But we’d also learned more from academia. I mean, there are these two researchers in Ireland—Dinan and Cryan*—who are phenomenal. They coined the term “psychobiotics,” so we follow their work, and it helped guide us in this new direction.
But in that product, of course, we now have Parabacteroides distasonis, Agathobaculum butyriciproducens—again, that’s a butyrate producer but it’s a unique keystone. You probably haven’t heard that name. It’s a unique name—Agathobaculum. That’s pretty cool. We have M. Vaccae, and of course we have an L. farciminus. So there’s a number of unique ones there as well—and more to come.
And really, what we’re looking for there—we have a GABA producer in there. It is a Lactobacillus, but it produces GABA. We know that from looking at the studies, and that’s actually from work with a supplier—a group that creates probiotics. And then a number of these organisms are known to produce what we call neurotransmitters or neurochemicals. They don’t all cross the blood-brain barrier, but they still do what they need to do systemically—your serotonin producers, your dopamine producers, the L-DOPA process, as well as the GABA and glutamine and glutamate.
So there are some pretty amazing organisms that we’ve now utilized in this approach to their neurological microbiome with the Neurobiome—or the psychobiome.
Lindsey:
There’s a lot of exciting stuff there. And I’m honestly quite excited to know about these products and to think about who I’m already working with who could probably use some of these. So I’m curious about the specific foods—because we did talk about polyphenols and cyano… whatever they’re called, cyano-something or others, yeah—but when people are actually eating food, what kind of foods are going to most help nourish and support these keystone strains?
Dr. Shayne Morris:
Yeah, that’s a great question. And to be honest with you, I love whole foods. But you’re right—it’s going to depend on where people are starting from. So if you take a relatively healthy 20- or 30-something who’s already been on a wellness journey, they’re going to be able to start with some pretty nutrient-dense, fiber-rich foods—these microbial accessible carbohydrates. That can be from the brassicas. They can start incorporating, at a minimum—we all need to get to the point where we’re utilizing at least 30 to 60 different vegetables and fruits per week, at a minimum. That’s quite an ask, right, when you think about it.
This can include a decent dose of what we call non-staple foods. So we can all increase the amount of broccoli, beets, asparagus, radishes, various squashes—the gourds, the pumpkins. We can all increase the leafy greens, the strawberries, the blueberries, the blackberries. We all have access to those—and hopefully to good, clean versions of them.
But on top of that, there are these unique ingredients we get from other plants—plants we wouldn’t normally include in our diet. Herbs and spices—we might think of them as medicinal, like turmeric, ginger, ginseng, resveratrol from chicory root. These are compounds we’ve thought about medicinally, but I want people thinking about them from a microbiome perspective.
A lot of these—especially tubers—are important when it comes to microbiota. The resistant starches, you’ve probably heard that term. We really encourage including resistant starch-based foods. A purple potato or sweet potato or yam—if you cook them twice or cook and freeze them, that process creates what we call resistant starch. So you drop the glucose impact on the body and increase the microbiome benefit.
And then we use other plants that bring in things like glucomannan, galactooligosaccharides, xylooligosaccharides, polymethoxylated flavones. We use dragon fruit, larch extract with arabinogalactans, baobab pulp, Indian kino, turmeric, Poria (a mushroom)—all high in medicinal value and amazing for the microbiome. Things we don’t normally think of, but that exist in mushrooms and other plants—especially tubers—are all involved in what we call our prebiotic presentation.
Even things like pectins, cassava, butterfly pea flower, cranberry—certainly important for women—these are all what we call plant-based carbohydrates. But it’s not just the carbohydrate we care about—it’s the phyto constituents, the phytochemicals like polyphenolics, polyglucosinolates, and others.
Across our prebiotics, for me personally—and this was a personal journey—it was really hard to get my 50 to 60 veggies and fruits per week. So I wanted to incorporate all of those into our prebiotics. Doesn’t mean you can’t do it with whole foods. Someone really dedicated can source many of these organically—especially if they live where you can grow food year-round, without harsh winters. But we dry and include them in our prebiotics.
If I take two or three of my prebiotics a week, I’m hitting 30+ plants and fruits and vegetables, and I feel much better about it. I encourage people to eat whole foods and also use pre- and probiotics. It’s tough to jump right into this. Depending on where someone is starting, if they’ve been really neglectful of diet, then they need to introduce prebiotics slowly—even if they’re food-based. Ginseng, fruit, saccharide-containing foods, onions, garlic, broccoli, etc.—introduce them slowly so the microbiome can catch up.
If not, you might get a rebound effect—microbes aren’t happy, convert things into gases, you might get bloating, cramping, gas, changes in bowel movements. So you’ve got to go slow to let the microbiome adapt. The most I’ve seen someone need is about two weeks—by then they’re feeling great, no more pushback, and they can begin rotating in more.
I rotate monthly—different versions, different diets. I always tell people: eat for the season, eat for your ancestry. There’s a genetic component to this. So eat your ancestry, eat your seasonal—both help guide where you’re headed.
Lindsey:
Does that mean—because I’ve got Italian in me—I can eat a lot of pasta?
Dr. Shayne Morris:
You can eat good pasta. And really, if you’re getting pasta from Italy, those grains are absolutely healthy. I mean, there are a number of studies that have shown how the ancient grains—especially heirloom grains grown in areas that are still healthy, without glyphosates and other high-production food treatments—are phenomenal for the microbiome, and especially supportive of both your ancestry and your microbiome. And then you can just infuse that with Italian plants, and you’ll feel amazing from that.
Lindsey:
So what should consumers know when they’re using probiotic supplements? Because there’s such a variety—some are refrigerated, some not. There are different types. How do you sort it all out?
Dr. Shayne Morris:
Yeah, it’s a lot. I’m glad you asked because it can be so frustrating. With this microbiome revolution, everyone’s trying to understand probiotics, prebiotics, postbiotics, synbiotics… it keeps expanding.
My take is—work through clinicians. Clinicians can stay on top of the education and understanding, and that helps patients get better input and outcomes. When you’re looking at probiotics and prebiotics in the mass market, it takes work to sort them out. The growing field has created a marketing machine. So even if you don’t want to work with a clinician long-term, at least consult one. Don’t just rely on marketing. The marketing is one thing—but the data is another.
A lot of probiotics out there are still old-school, transient types. They come from the dairy industry—cheese, milk, yogurt. And while those aren’t bad, they don’t necessarily generate the outcome you might want. When you take a probiotic, it could offer general benefits. But probiotics can also be used as a precision tool. If you’re taking a general probiotic from a fermented food source that’s not human-based, it might have a general, transient benefit. It can help shift nutrients and encourage growth of existing organisms. Things like kefir, kombucha, kimchi, sauerkraut—all of those can do that.
But when you need precision, you have to understand what’s in the product. Do they contain keystone organisms? Are they human-based, clinically studied organisms like Lactobacillus and Bifidobacterium? The ones we use in Alimentum, if they’re Lactobacillus or Bifido, they’re still human-origin—not dairy-origin. That allows you to be more precise, especially for things like IBS, IBD, gut-liver axis, gut-brain axis, etc.
So you really need to dig into the label, talk to your clinician, and understand the formulation to get that benefit. Otherwise, you see people saying, “I took a probiotic for a few weeks and didn’t feel better, so I gave up,” or “I took a prebiotic and felt worse, so I stopped.” That’s not what we want. We know the benefit is there—we just have to use them appropriately.
Lindsey:
Right. There are so many different types. And like you said, the strains are different. So it’s crazy to think, “Oh, I got this one from CVS,” versus the ones you’ve got. It’s like the difference between eating an apple and eating a bag of chips. There’s no comparison.
Dr. Shayne Morris:
Exactly. It’s very different. And that’s the future of this—we need people to know the benefit is there. But they need to know how to use it. I’d love to make it simple—but it isn’t. It’s powerful, and we have to understand it. Because if it’s misused or used out of context, you don’t get the result. And then people lose faith—and that’s not what we want. We want them to get the benefit, but we have to start with appropriate use.
Lindsey:
Brief segue into another topic. I saw on your website you have a product called Pseudo Vyrome—and I noticed it’s a bacteriophage that specifically targets Pseudomonas aeruginosa, which I know can be a lung pathogen. I had a client with a chronic lung infection with this bacterium. Could you briefly explain what bacteriophages are and talk about Pseudomonas aeruginosa?
Dr. Shayne Morris:
Yeah, it’s such a unique part of our microbiota. So, what are bacteriophages? They’re probably the most dominant micro—I’m going to call it a microorganism—even though it’s not technically alive. It’s in the virus world. A phage is a virus that only targets bacteria.
In us and on us, we have bacteria, bacteriophage, eukaryotic fungi, some parasites, and mammalian viruses. But the vast majority are bacteria and phages. Phages are viruses that target specific bacteria. They live in us and move through us. You’re exposed to trillions of them in the ocean, lakes, soil—just pulling a carrot out of the ground, for example.
Phages help manage bacterial populations. If a bacterium grows out of control, phages grow alongside them to bring the numbers down. Without that control, bacteria could overwhelm us or any animal or plant. Phages attack and destroy bacteria. And they’re super specific—there’s a phage for E. coli, Salmonella, Pseudomonas, Bacteroides, Lactobacillus, Bifidobacterium—pretty much every bacterium we’ve looked for.
We use phages nutritionally as a kind of prebiotic—to help maintain a healthy ecosystem. They help promote eubiosis and reduce dysbiosis. Research is still limited, especially here in the U.S., but there’s a long history of phage use in Eastern Europe. Now the science is growing again in the U.S. and Europe.
So we’re using phages to help maintain balance in the gut, skin, and maybe other areas, though we still know very little about their role in organs like the lungs, liver, or kidneys.
Lindsey:
I suggested it to my client—so I’ll let you know if he has any positive effects!
Dr. Shayne Morris:
Please do, yeah. It’s amazing.
Lindsey:
Where can listeners learn more about your work, your research, and the products?
Dr. Shayne Morris:
We’ve got social media—my Instagram is @drshaynemorris. Also Alimentum and Systemic have social platforms. And there’s a website: alimentumlabs.com* (use Doctor Referral Code: AZPA11 to access products). Also systemicformulas.com. We’ve got another one called NBResults—that’s more on the DNA side and will be the future for microbiome testing.
We’re creating more all the time. We’re just getting to the point where we can really get out and tell the story. We’ve been in the lab for 12 years, and now we’re emerging from it so we can start sharing all of this.
Lindsey:
Everybody should check the show notes for all the specific links and such. Thank you so much for sharing all this information with us!
Dr. Shayne Morris:
Yeah—thank you for having me on. It was such a pleasure.
Lindsey:
If you’re interested in accessing these probiotics with unique keystone species, there’s a link* and referral code (AZPA11) to register for an account on Systemic Formulas.
But I highly recommend setting up a consultation with me first—and doing a stool test—to figure out which species you most need to replenish and whether you need to address any pathogens first.
If you’re dealing with gut health issues of any type (diarrhea, constipation, bloating, SIBO, IMO, H2S SIBO/ISO, IBS, IBD, gastritis, GERD, H pylori, diverticulitis, candida, etc.) or have an autoimmune disease and need some help, I see individual clients to help them resolve their digestive issues or reverse autoimmune disease naturally, You’re welcome to set up a free, 30-minute breakthrough session to see if you’d like to work with me. I also have my own two products, Tributyrin-Max, which is particularly helpful for loose stool and diarrhea as it slows your motility and firms up your stool, and SBI powder, which is an all around gut pathogen binder, which is super safe and won’t harm beneficial bacteria, and is usually the first line of treatment I educate my clients about in order to avoid stronger antimicrobial herbs.
*Product and dispensary links are affiliate links for which I’ll receive a commission. Thanks for your support of the podcast by using these links. As an Amazon Associate, I earn from qualifying purchases.
