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In this episode, you will learn about the various microbiomes in the human body and the impact of the sinubiome and oral biome on the broader microbiome.

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About My Guest

My guest for this episode is Dr. Haroldo Magarinos.  Haroldo Magarinos, ND, DDS is a Chilean dentist with expertise in Periodontics, Oral Medicine, and Surgical Implantology.  After a decade of conventional practice and university teaching, he followed his passion and became a board-certified naturopathic doctor.  Additionally, he has expertise in Integrative Biological Dental Medicine, Homeopathy, Live blood analysis, Peptide therapy, and Advanced Clinical Ozone therapy.  Dr. Haroldo has long been a strong advocate of the study of the human microbiome, with the conviction that treating patients with dysbiosis can prevent and even correct many prevalent forms of chronic disease.  Using his knowledge and experience in this field, he has been able to improve the lives of hundreds of people who wanted a deeper understanding and management of the underlying causes of their health problems.  He is the co-founder and clinical director of Revolution Gut Health, an online platform that provides counseling services to anyone interested in learning about and improving microbiome-related health conditions.

Key Takeaways

  • What is the microbiome?
  • How similar or different are the various microbiomes in the human body?
  • Is there a brain biome?
  • What is the bi-directional connection between the oral microbiome and the gut microbiome?
  • How important is brushing and flossing?
  • What role does mouth breathing play in impacting the oral microbiome?
  • What are the best type of dental implants?
  • Can tooth enamel be repaired?
  • What role do the sinubiome and the oral microbiome play on the gut microbiome and in SIBO/SIFO?
  • Do microbes such as H. Pylori and Clostridia warrant aggressive treatment?
  • What common themes have emerged from years of microbiome testing?
  • What role do viruses, fungi, and parasites play in our biome?
  • How might prebiotics, probiotics, postbiotics, and paraprobiotics be ordered in a protocol?
  • What role do lipopolysaccharides (LPS) and endotoxins play in chronic illness?

Connect With My Guest


Interview Date

July 17, 2023


Transcript Disclaimer: Transcripts are intended to provide optimized access to information contained in the podcast.  They are not a full replacement for the discussion.  Timestamps are provided to facilitate finding portions of the conversation.  Errors and omissions may be present as the transcript is not created by someone familiar with the topics being discussed.  Please Contact Me with any corrections.       


[00:00:01] ANNOUNCER: Welcome to BetterHealthGuy Blogcasts, empowering your better health. And now, here's Scott, your BetterHealthGuy.

The content of this show is for informational purposes only and is not intended to diagnose, treat or cure any illness or medical condition. Nothing in today's discussion is meant to serve as medical advice or as information to facilitate self-treatment. As always, please discuss any potential health-related decisions with your own personal medical authority.


[00:00:42] ANNOUNCER: Hello, everyone, and welcome to episode number 187 of the BetterHealthGuy Blogcast series. Today's guest is Dr. Haroldo Magarinos and the topic of the show is the Microbiome and Beyond.

Dr. Haroldo Magarinos is a Chilean dentist with expertise in periodontics, oral medicine, and surgical implantology. After a decade of conventional practice and university teaching, he followed his passion and became a board-certified naturopathic doctor. Additionally, he has expertise in integrative biological dental medicine, homeopathy, live blood analysis, peptide therapy, and advanced clinical ozone therapy.

Dr. Haroldo has been a strong advocate of the study of the human microbiome with the conviction that treating patients with dysbiosis can prevent and even correct many prevalent forms of chronic disease. Using his knowledge and experience in the field, he's been able to improve the lives of hundreds of people who wanted a deeper understanding and management of underlying causes of their health problems.

He is the co-founder and Clinical Director of Revolution Gut Health, an online platform that provides counseling services to anyone interested in learning about and improving microbiome-related health conditions.

And now my interview with Dr. Haroldo Magarinos.


[00:02:00] SCOTT: I am excited today to have Dr. Haroldo Magarinos with us to talk about all things microbiome. Thanks for being here today, Dr. Haroldo.

[00:02:09] DR. MAGARINOS: It's a pleasure to be here, Scott. Thank you.

[00:02:12] SCOTT: First, talk to us about the personal journey that brought you to your passion, your interest in the microbiome. How did your life's path lead you to the work that you're doing today?

[00:02:23] DR. MAGARINOS: Well, I was trained pretty allopathically. I went through all the training in terms of believing that drugs and traditional methods for addressing chronic illnesses was the only approach available. And I did believe that for many years.

But the truth really hit me in my face because I was treating people over and over using all the methods, everything that was supposedly was researched properly and was supposed to work. And I was not getting the results I wanted. And I was doing a lot of surgery for addressing chronic illnesses in the mouth especially. And so, I was using antibiotics and every other tool that you can imagine and it was not working. Patients were coming back about six months or a year after finalizing the treatment with the same type of condition.

And, of course, that gets you to the point of frustration. So you can do two things. Keep doing what you're doing and cashing the money and doing your life on the side or you have to go and dig deeper. And I'm the kind of person that doesn't really like an answer that it is what it is. And I was digging deeper. And I was very fortunate because I found people in my path that trained me and taught me things that was eye-opening.

And from that point, there was no way back. I quit my practice. I moved to the United States. I keep learning. And I'm dedicated full for trading microbiome right now. This is my job 24/7. This is what I am passionate about. And this has been the type of knowledge that gave me so much gratification. This is where I found all the answers that I was looking for for 15-plus years.

[00:04:17] SCOTT: So that leads me to my next question, which is what is a microbiome? What does our microbiome do for us? Why is it important? How many microbes do we have in the body compared to our own cells? And then maybe what is the balance between health-promoting and health-negating microbes in an average microbiome?

[00:04:41] DR. MAGARINOS: The human microbiome is comprised by viruses, bacterias, fungis all together, and parasites. And the whole collection of them is defined as the microbiome. And we have microbiomes in different areas of the body. Mouth, gut, skin, sinuses. Every single type of environment holds a different type of microbial diversity. And that actually creates our uniqueness in terms of how we modulate different pieces of information, which we can talk about that later more in extents.

But basically, we have this system that is in place for creating balance between the inner side of us and the outside world and also, for building things that we need for improving or making certain metabolic pathways in our cells, in our body that we can produce on our own.

We have this integrated model between microbes and human cells that are connected in a very tight way and they're constantly communicating. This is for me a communication system. It's an integrated communication system that we developed for purposes of evolution and for genetic understanding and amplifying the way we are able to produce things or create things with an adaptable, resilient basis. That's how I see the microbiome.

Now we have the latest research we have available says that we have equal amounts of human cells and microbes inside the body. The research is not consistent. It goes from 30 trillion to 100 trillion microbes inside the human gut. And there's different types of diversity in different areas of the body. Being the gut, the most diverse area of the body. But they're not really clear about. But we know that at least we have an equal amount of microbes compared to the amount of human cells we have inside the body at least. And that could be more for the microbes.

And the balance is key. And the balance is based on the terrain. If anyone that has been in touch with a lab, you'd grab a petri dish and you put a culture medium there. You put the food. You set up the temperature and you set up the oxygen level. And that makes the growth pattern of whatever you want to grow inside that petri dish.

The same way inside the body, that happens. Whatever we put inside in terms of the oxygen, pH, food will create different types of diversity, a different type of pattern of growth of microorganisms. If that goes off, then we have a terrain environmental problem because we're setting a different type of condition that is set in a different pattern of growth.

[00:07:46] SCOTT: We often talk about the microbiome. But I don't think we give a lot of thought to the fact that there can be many different biomes in the body. So the sinubiome and the sinuses, the oral microbiome, the gut microbiome, the skin microbiome. Probably other biomes in the body as well. So are these biomes throughout the body, are they more similar? Are they more different? Is their purpose to have more local effects or more systemic effects? How many different types of microbes do we think of in these various biomes throughout the body? How diverse are they? And is the diversity different in each of the different types of biomes?

[00:08:29] DR. MAGARINOS: Yes. Diversity changes. The type of microbes changes. And that is dictated by the availability of foods and the availability of oxygen we have and the pH. So those are the main variables that dictate the growth of the different microbes we can find in all these different environments.

For example, the sinuses, because this is an open airway, we will have more aerobic patterns of bacterias. And the mouth, same thing. But the mouth is super complex because it has so many different niches. That depending on where you look at, you can find different types of microorganisms. You have a wide array between aerobic to facultative anaerobics. The main ones I will say are Firmicutes, Actinobacteria, and Proteobacteria for the mouth.

Similar, we have dominantly Firmicutes and Actinobacteria on the sinuses. And we have in the gut the most diverse type of microbiome. And because we have different stages along the digestive tract that they vary in pH, and oxygen, and food availability.

And so, we have from facultative anaerobes to very strict anaerobes. And the populations usually increase while we're going deeper in the intestinal tract. The small bowel usually is less in diversity. And in the colon, we have probably the most ample variety and density of microbes.

[00:09:58] SCOTT: And when we think of the gut microbiome, I tend to think of it having broad systemic effects. Even producing nutrients for the body. Is that also true of the other more localized biomes like the sinuses? Or is their primary purpose to support that local tissue? And then extending on that, we haven't yet talked about the biome of the brain. So is there a biome of the brain? Are there organisms in the brain that are both potentially good and bad that are living in the brain? And how might we optimize the brain biome?

[00:10:35] DR. MAGARINOS: I've been trying to find answers to actually the last question, the brain biome. Because there's not conclusive evidence about the fact that we have a brain microbiome. What we know is that there has been findings in terms of microbes inside the brain. We know that. But we need more than that to call that a biome.

We need integrated communication. We have a symbiotic relationship. We need quorum sensing. We need communication between those microbes to understand that they are living organisms, that they are playing a role in certain functions or a certain degree of interaction with that place of the human body.

We don't know that yet. We know that we found – there was some alpha proteobacteria found in the brain. We know that that was found on healthy subjects without any at least known chronic illnesses, especially neurological conditions. So we speculate that there's a healthy pattern of microbes that can be found in healthy subjects. That's what we know. And I will say that's kind of what I can responsively say about the brain microbiome.

Now why I am a little bit skeptical about brain microbiome? Because for me this is a processing engine. This is modulating information and sending responses all along the body. And it actually gets modulated by the molecules that are made on the gut. So the gut brain axis is a very powerful and very active pathway that we use for modulating responses on the central nervous system based on the information that is provided through the gut microbiome and the gut microbiome interaction with the enteric nervous system.

Dimensioning the amount of information that crosses that gut-brain access any given minute, I don't see the need of processing directly through microbial activity information in the brain itself. That's from my perspective completely arguable. But that's what I believe.

Now I think there's a certain degree of immune tolerance that is being built by a certain degree of presence of microbes that can be activating certain pathways on the microglial cells. In any event of leaking membranes, which we know is pretty common right now, we have leaky gut. We have leaky brain.

If our barriers in the brain are leaking in a small degree, we don't trigger very active, very acute inflammatory responses that can compromise the person's health. I believe that's more for immune tolerance than anything else. But I don't see the role really in terms of pathway activation.

[00:13:35] SCOTT: And when we have these various biomes, would you say that all of them, whether it's to sinubiome or the oral biome, would you say that they all have a role in systemic health whether that's in the good direction or in a negative direction? Or are some of the biomes really primarily focused on supporting that local function or local tissue in the body?

[00:14:00] DR. MAGARINOS: It is both. So we have a localized action of those microbes maintaining integrity with the membranes and the communication with the immune cells localized in those different areas. We are integrating information locally and systemically.

We know that via metabolites or direct passage of those microbes into other areas of the body, we can get that information but also passed to other areas of the immune system. And that gets modulated. The core piece of the immune system is located in the gut.

And eventually, by swallowing or breathing, everything arrives there. And those pieces of information, they're supposed to get modulated and crossed to reference to our immune cells so they can promote the corresponding responses. We know that from COVID actually, we know that COVID-19 virus was interacting with immune cells in the alveolus of the lungs. And those cells were sending signals to the gut microbiome. Therefore, the gut microbiome was sending or just analyzing those pieces of information and sending signals to the immune system to create the proper response for taking care of that viral infection.

We know everything is integrated in a certain degree. Of course, the passage should be also modulated. Because if you dump the whole amount of microbes from one side to another or you pass too many of them at any given time, you can overwhelm this communication pathways as well and the immune system will react differently.

[00:15:42] SCOTT: Let's talk a little bit more about these communications that are occurring between different biomes. Talk to us about the bi-directional connection between the oral microbiome and the gut microbiome. How does the oral microbiome impact the gut microbiome and vice versa?

[00:16:00] DR. MAGARINOS: I love that. That's kind of my favorite topic because it's quite new and it's very exciting. Because we tend to think that this has nothing to do – the mouth has nothing to do with the gut or very little. That's the common narrative. Whatever happens in the mouth, mouth stays in the mouth. And that is really not true.

We swallow microbes. We swallow billions, hundred billions of microbes every day. So we swallow a massive amount of microbes that they arrive into the stomach. And in the stomach, they get filtered. Similar to the conversation with ghost probiotics. They get killed but that doesn't mean that they don't play a role. These death microbes carrying DNA are analyzed by our gut microbiome and they provide information that is useful for our immune system to then go back or anticipate whatever immune challenges could be arriving. This is the entry point of the body. So it's very important from that perspective.

But also, an ineffective or digestive system that is not properly working will pass microbes now alive because you're not producing enough stomach acid or bile. And therefore, you're not killing those microbes properly enough. If that's the case, now you're going to have translocation. And that translocation will create also a different type of modulation in terms of the immune system. It will become more immune active and that will trigger very likely. And actually, we have very consistent evidence of a lot of chronic illnesses that they get activated or the progression gets more chronic or more acute if we have presence of oral microbes in the gut.

And we're talking about colorectal cancer. We're talking about RA, rheumatoid arthritis, we're talking about prostatic cancer or pancreatic cancer. We're talking about multiple very serious chronic illnesses. Non-alcoholic fatty liver is another one.

Now, also, we know that the microbiome of the mouth gets fed by the absorption of nutrients that occurs on the gut. And it's quite logical because we don't have enough time in the mouth. We're sustaining the life of the second most diverse ecosystem we have in the body. Of all these microbes, we don't have enough time. We chew foods probably for – I don't know. 30 seconds. If we're proper chewers, maybe less. And everyone is eating on the run. So probably it's like five seconds in average.

And those foods, they don't really stay in the mouth. And if we are relying on whatever can get attached to another – some structure in the mouth will be very inefficient and very inconsistent in terms of feeding our microbes. We have really a very direct connection between what we absorb in the gut that goes through the enteric circulation back to the salivary glands. And now you're feeding your mouth microbes.

And the problem has been that we have been researching all these nutrients separately. I have no at least acknowledgment of a meta-analysis that is putting all these nutrients together to establish a nutritional pathway for feeding the oral microbes through salivary glands from nutrient absorption in the gut.

But we know, if you look at the nutrients in the salivary glands, you have vitamins, you have minerals, you have amino acids all pre-digested in the gut. Now if you have lack of efficiency in your digestive system, if you're not eating the right foods, if you're not breaking down those nutrients properly, if you have leaky gut, now you're affecting the way you're nourishing your mouth microbiome.

Now your mouth microbiome becomes dysbiotic, your mouth microbiomes start looking for alternative food sources, changes the compositional patterns. And now you have dysbiotic bacterias. Now this dysbiotic bacterias, now you're swallowing them. They're going back into the gut. And now they're creating different immune responses because they're not the typical patterns that the microbiome of the gut will recognize as healthy.

You can see that you can circle back and forth in this vicious circle of chronic activation of the immune system and changing the patterns of the microbiome of the mouth and the gut all together just because of these impairments in the barriers and our nutrient absorption in the gut. They're heavily connected.

[00:20:51] SCOTT: This is fun for us because you are also a biological dentist in addition to a naturopathic doctor. So you have a really unique perspective on how these all connect. So I want to talk a little bit about just maybe a little diversion into dental contributors to chronic illness and what we can do to optimize our oral microbiome.

First, I think you have maybe a unique perspective. I want to hear your thoughts on brushing, flossing, toothpaste, mouthwash. When are antimicrobials appropriate versus potentially damaging in the oral microbiome? And where do you stand on oil pulling?

[00:21:27] DR. MAGARINOS: From tooth brushing and flossing, I think it is a necessary practice, especially nowadays with the consistency and the types of foods we're eating in average. But I don't think that we need to do that so frequently. Because we want to sustain a good diversity in the mouth microbiome as well. And those things are challenging, the diversity and the build-up of biofilms. And I know that biofilms had been so demonized and they're actually so foundational for us.

Biofilms, they need to be sustained in a healthy way. If you keep attacking them mechanically or chemically, they will respond accordingly and they will defend themselves. So you're going to be creating more aggressive patterns of microbes in the long run.

Now if we think about the standard recommendations, we start using antimicrobials and standard oral care products from two years old and one year old in some cases. So we have a long time of exposure to mechanical and chemical disruptors. And definitely, that will alter the composition of your microbiome.

I'm a proponent of brushing your teeth. Yes, you don't have to use toothpaste really. You can clean your surfaces interproximally. But you don't need to use any other chemical or additive for doing that mechanical cleansing. It's more about trying to rebalance a little bit the growth patterns of those microbes so we don't have overgrowth or we don't have plaque. That can be also from another perspective has a lot of affinity with certain minerals and can get calcified. And it can create more acidic environments. Definitely, we don't want that. But we don't want to go so intense in our cleansing method that we're going to be disrupting our oral microbiome so frequently. Three times per day I think is too much. I think that once a day could be potentially a good idea.

We know from old research, this is when I was studying dentistry, that gingivitis doesn't occur until you stop brushing your teeth for three days. So you need three days to start seeing some inflammatory signs on the gums. Before that, we know our microbiome pretty much holds up. Once a day is not crazy. And if you actually do toothbrushing every three days, you're going to be fine. But I don't want to say that so openly because dentists are not going to love me for that. But I have a point there and there's research backing up what I'm saying. I'm not just saying this out of nowhere.

Oil pulling and antimicrobials are necessary sometimes. But they have to be seen in the same way you will use an antibiotic for a very justified reason in a very small time frame. Beyond that, you will create an alter resilience. You will create activation of defense mechanisms. Phages, you know those. They're going to get activated to protect the microbes they use as hosts. And you can have more aggressive patterns in your microbiome ultimately.

You want to do that to the point that we don't really disrupt on the microbes so much. And oil pulling is another mechanism for doing that. But it's a little bit more gentle on the tissues. And I do encourage using oil pulling in very, again, specific moments. If you have a very severe imbalance and you want to restart the system and you want to re-inoculate your oral microbiome, changing your practices for becoming better in your oral health, maybe you can start with an oil pulling protocol and then following by changes in your diet and using other methods which will replenish your microbiome in a more healthy way. That will be my suggestion but just in a very specific way.

[00:25:35] SCOTT: How much of a role does dry mouth or mouth breathing play in oral health and our oral microbiome? I tend to like mouth-taping just because I find that it actually helps my sleep scores and I sleep more deeply when I'm mouth-taping. Wondering in this realm if you're a fan of mouth-taping and not only for sleep but also because it has potential benefits for our oral health.

[00:25:58] DR. MAGARINOS: I love mouth-taping. I think it's such a simple solution for a common problem we have right now. It's not the root cause solution. But it will help. And, yes, breathing by the mouth probably is one of the most disruptive problems we have right now for the mouth microbiome. And it has a ripple effect that will affect everything else. It's not just the microbiome of the mouth that gets affected.

And we have elevation in inflammatory markers in research done by mouth breathers compared to non-mouth breathers. And we know that causes inflammation and toxicity equally to be an active smoker. That's how bad it is. Or even worse actually if you compare the data.

Definitely, we don't want to be breathing by the mouth. Also, we know that there's something else underlying if we need to breathe by the mouth. Mouth-taping can be a very simple solution for addressing that. But the mouth microbiome will change.

Of course, if we open up the airway, this should be closed unless we're eating or talking. If we keep this constantly open or at night time open all the time for eight hours averagely, we're going to change the pH. We're going to change the oxygen. We're going to change the environmental setting that is needed for growth and balance of the mouth microbiome. So that will drive dysbiosis in the mouth. And again, dysbiosis in the mouth can trigger problems in the gut. And therefore, systemically as well. We know everything is connected.

[00:27:35] SCOTT: We're going to talk a little bit later about the BiomeFx that looks at the gut microbiome. Is there a clinically helpful tool available for assessing the oral biome like we can do with the gut microbiome? I just went to a presentation last week. I'm starting to hear about more practitioners talking about tests for looking at the oral microbiome. But my question to you is are those clinically useful yet or not?

[00:28:02] DR. MAGARINOS: I don't see much usefulness on them right now. And I don't want to become controversial because I know a lot of people are getting excited about having microbiome testing for the mouth. But we need to understand the mouth microbiome is pretty complex. It has so many different niches.

When we test for the oral microbiome, what we're testing for? Usually saliva. It's a salivary sample. And most of the microbes you can find in the salivary area are transient. You might have some reflection of something that is participant in the stable communities of the mouth. But you have mostly a blend of things.

I won't be able to determinate with a clear understanding that how my oral microbiome looks like based on salivary markers only. It will be very complex actually to analyze the mouth microbiome because I want to have the inner side of the cheeks. I want to have the sulcus. I want to have the three surfaces of the teeth. I want to have the saliva also included. I want to have the palate analyzed. Because we have data that every single niche has a different type of stability.

If you use Spearman correlation, you have different types of instability based on the different areas of the mouth. Being the palette, one of the most stable ones. And yes, we have salivary stability as well. But we're just looking one piece of the puzzle. So it's like looking at, "Okay, we're going to look at the transversal side of the column. That's it." And that's your gut microbiome. And it really doesn't reflect everything. We want to have a full assessment.

I don't know how that can be done. But until something like that is available, I know the information we're getting is very narrow-sided. Now, it is useful. Maybe. But we need to consider all these variables and factors to understand what we're looking at. If not, we can get very excited and not very specific.

[00:30:01] SCOTT: Yeah. I think it's very similar to we look at lots of things in the blood and run blood tests and then we kind of assume that it actually represents something meaningful. Like, if you're looking at thyroid hormone in the blood, that may or may not reflect the thyroid in the cells themselves, right? So it's kind of the same concept there.

I want to talk a little bit about how health-damaging other oral dental issues are like amalgams or root canals or, particularly, cavitations. I've been surprised over the years by how many people have cavitations. If you're working with someone that knows how to look for them, it doesn't seem like most dentists actually even know how to look for cavitations even if they have CBCTs, cone-beams, those types of things. They're not always able to interpret them. I'm wondering, where do you stand on the importance of addressing cavitations when they are present?

[00:30:57] DR. MAGARINOS: Oh, it's huge. It's absolutely necessary. I start working when I move to United States in a biological dentistry practice in Denver. And they were very good at that. And it's funny because we are not trained to see images, even 3D imaging like cone-beam with that angle. It's there. You can't deny it. You see the radiolucent images inside the bone and you can't explain that in any other way. There's no healing process going on. The bone itself, the density looks completely off. And yet, we don't see it in regular dental practices. Because nobody thought that we need to see that area with that approach. When you see that for the first time, it's eye-opening. It's like, "Wow. This is a new world."

Now when you do a surgery, and I've been in those, and you open the bone where you detected the cone-beam cavitation and you see what's there, I wish every single dentist will be able to see that. Because, probably, they will not overlook that anymore. It's necrotic jawbone. It's full gases and the malodor there is clear that there's an active infection that is not healing.

And that has so many implications for systemic health. We look at the meridian pathways process, all these areas. We look at the inflammatory responses you're going to be creating both by having an active, non-resolving infection in the jawbone. It's huge. From all the angles you want to look at that.

And the tools for fixing those are available mostly in every single dental practice. You need laser. You need some surgical instruments. Of course, I will add ozone, which is a huge aid for treating those. But addressing cavitations is a major thing for improving systemic health.

I've seen people with severe compromises in their systemic health that after – I'm very responsible saying this. After the cavitation surgery, they were completely different persons. They were able to function normally in many, many aspects that they couldn't before. And the only thing that changed it was addressing that chronic infection site in their jawbone. That was eye-opening for me. It was fascinating.

Amalgams, root canals, also, they promote hypertoxicity. Release of very, very toxic materials. Off-gassing of amines especially, like putrescine or cadaverine, which are metabolites from anaerobic bacterias, which is normal. But in those amounts, they become very, very toxic. And all of them, they're disruptive for our feedback mechanism, for immune system functionality, for everything you can imagine that is connected to human health.

[00:33:59] SCOTT: Dental implants are another common area of Interest most seem to be titanium-based, which, as I understand, can actually stimulate the immune system in a negative or reactive direction in some people. I think zirconia is more commonly used now by biological dentists. What are your thoughts on dental implants? And I actually believe that you're an implantation specialist as well, if I recall.

[00:34:22] DR. MAGARINOS: Zirconia will be my way to go. That will be my first statement. If I have to choose for myself or for any of my loved ones, zirconia. Any of my patients as well. But it is the only material that is showing long-term biocompatibility for the body tissues.

Titanium has adherence to the bone but creates a rust layer that can also be immune-reactive. So over time actually, we have a progressive bone loss around the titanium implant. And that is telling you that the bone is reacting from an immunological point. And if that's happening means that the biocompatibility and the reaction of the immune system is not a healthy one.

Now implants were never, never meant to be used as a single tooth replacement in the first place. They were always meant to be used for a full denture structure. That was the initial intention of the dental implants. We changed it that later on and we start seeing more failure because we decided to change the way they were intended to be used.

Now I don't know the by the laws of mechanics that are implied in this problem, zirconia will respond equally or not or responds better. I know that from a immunological standpoint has better outcome than a titanium implant. But from a mechanical standpoint, I think, still, we need to see that in research. And I don't have enough available data on that.

But I understand the importance of replacing and being efficient in the mastication process and how detrimental can be not being able to chew your foods properly for many, many reasons. I think that dental implants are a necessity for many people. And my option will be always zirconium. That's the most biocompatible material.

[00:36:29] SCOTT: One of the common things that I see people doing, and, unfortunately, I did this as well, is kind of clinching or grinding on one side and eventually causing some wear patterns, some damage on one side of the mouth. I wanted to get your insights around how to support damaged enamel once somebody's getting to a place that they actually maybe have some exposed dentin. Can we improve that situation? Can we reduce further damage?

I see lots of products these days with nanohydroxyapatite. Do those have a place? And then I know that vitamin K2 potentially is relevant in this conversation. And of course, we couldn't talk about supporting enamel without also asking for your thoughts on fluoride and how that fits into the discussion.

[00:37:15] DR. MAGARINOS: I will start with fluoride. Fluoride is a nutrient, first of all. It's a basic mineral. We need that. But not in the way that is used or presented in the dental care products. It's the different conversation. Between the trace minerals that we have available in nature, fluoride is part of it. We need fluoride.

But in the mega those things that are used or in the way we expose the tooth structure, it's not probably the healthiest way. And the consequences on the side in terms of bioaccumulation in other parts of the body through the absorption through the membranes of systemic absorption of fluoride is huge. I don't think that it poses a benefit compared to the negative sides that you can find in fluoride activity in the way, again, that is used in the common dental industry.

But we need a balance, electrolyte balance, to replenish the structure, the hard surface of the tooth structure. We need electrolyte balance for that. And K2 plays a huge role because this is centrifuge movement inside the pulp, inside the teeth, inside the tooth that is structure. That can create bioaffinity for minerals or can pull away minerals from the tooth structure.

And it will depend on the direction that this is spinning. And we know that K2 interacts with the pituitary gland for fixing the direction of the centrifuge movement inside the tubules, inside the pulp, so we can grab minerals from the environment. And that is beautiful. And this is actually pretty new knowledge.

We know that D3 with K2, they contribute for the remineralization process. We know that we need magnesium for the same purpose. And we know that we need all the other trace minerals for making that happen.

Now gum recession, when it's mechanically induced, unfortunately, it's very hard to be recovered because the gums – gums are nourished by the bone. If your bone recedes, the gums will adjust correspondently to keep getting the nutrition. And, of course, there's a limitation in terms of vertical nutrition from the bone structure to your gums. They can go that high if you lose certain amount of bone. Your gums will always be very close to the bone structure. We're talking about three millimeters approximately from the crest of the alveolar bone. You can go for that. You can have a huge – unless you're inflamed. Inflammation will of course enhance the gum appearance. But not from a healthy perspective.

There's ways though. We can mineralize that structure to become less sensitive to help people alleviating with the pain and temperature sensitivity. But unfortunately, the exposed root has dentin, not enamel, as the crown. And we have something called cement. But it's very fragile. So, usually, it doesn't last whenever we have a problem with grinding or clenching teeth. It usually breaks up and you have exposed dentin. And this dentin is permeable. All these nerve endings inside these chemicals, inside these tubules from the dentine will get exposed and now you get all this pain reaction because you're triggering one of the most actually active nerve endings you can have in the body, the trigeminal nerve. Yes. But we can also remineralize this.

Nanohydroxyapatite can actually. I think that there's a place for using hydroxyapatite in certain dental formulations. My concern is that the smaller the size of the particle you go can cross barriers and get to other places. And I'm worried about always getting intracellular levels of hydroxyapatite because the particle size is too small.

Beyond that, it has been proven that it can be very effective for improving remineralization process in an exposed surface or in the cavity problem. And I think that there's a usage for hydroxyapatite. And it will be much better, much safer than using fluoride.

And again, but if we're not putting the right nutrients, we're not putting the right minerals in our body, we're not remineralizing our body systemically, we are not going to get those minerals pushed into the mouth cavity through the salivary gland. And if we're missing those vitamins like D3 and K2, we're not going to push the process to grab the minerals and put them in the tooth structure. It's a very, very orchestrated systemic process in terms of nutrition that is needed for remineralization of the tooth structure. It's not just localized treatments.

[00:42:24] SCOTT: How much vitamin K2 would you recommend for someone that was focused more on dental health? Are we talking a hundred micrograms? Are we talking higher than that? What's the sweet spot for K2?

[00:42:38] DR. MAGARINOS: I think that consistency is better than dosing. And I know there's a lot of conversation about dosings. And if we're using a hundred micrograms of K2 vitamin I think is enough. Because that's how much we can grab from the bioavailability of that vitamin.

The delivery method matters. And we know that those vitamins are liposoluble. We need to have a lipidic absorption of those vitamins. Meaning that the food that contains K2 should be eaten in conjunction with the supplementation of vitamin K2. We can just take the vitamin and having a plant-based smoothie probably will not work that much. Still, maybe. But we need to always push the body's pathways in the same direction of our nutrients. If we're eating certain foods and we're supplementing at the same time, we need to have corresponding or matching nutrients in the foods and in the supplements at the same time to optimize absorption. It will be actually a contradiction even for the body to understand that we are trying to absorb a liposoluble vitamin drink in a fruit juice. This doesn't make too much sense. The pathways are going to get activated with the food that naturally contains that nutrient, if it makes sense.

[00:44:03] SCOTT: You mentioned that from a gum health perspective that that can be in some cases tied into the bone health. Products are emerging in the oral probiotic realm with lozenges and other things. I'm wondering if those potentially have some role in maybe reducing inflammation that might be a contributor to gum recession or other oral health issues. And do you find oral probiotics shift the microbiome in a positive direction in the mouth?

[00:44:33] DR. MAGARINOS: There's evidence about it. Right now, we see that, especially slow-delivered probiotics in the mouth locally, not systemically. Systemically, it doesn't make any sense. But the local delivery of certain probiotics can be actually beneficial for improving the mouth microbiome. It's all about the interaction with our own biofilms and the information we're providing there. But it's only going to be as good as how we set up the environmental conditions.

If you're a mouth breather and you're putting this lozenge inside your mouth and the tablets, dissolving tablets, I don't think you're going to get so much benefits. But the reported benefits through the research that has been done using locally-delivered probiotics are quite limited.

This is not something that we see in a long-term study yet. We see only that we can get some improvements on a short run, like a few months of testing. It's been very limited data about the improvements. But there's data, which is promising. Because I would love to see more intention on improving the mouth microbiome status.

This has to be done in conjunction with dietary changes also. Because no matter what type of microbes you're putting in tablet, if you don't provide the nutrients, really, nothing will happen at the end of the day. That's my conclusion there.

[00:45:55] SCOTT: Many of our listeners are dealing with biotoxins and illnesses such as chronic Lyme disease or mold illness, also known as CIRS or Chronic Inflammatory Response Syndrome. The sinuses can have bacterial or fungal overgrowths or colonization. The sinubiome can affect the oral and gut microbiomes as well. So talk to us about how we optimize the sinubiome? And where do you stand on using antimicrobial nasal sprays? Whether they're pharmaceutical or natural. Like, maybe propolis, for example, which I think has some potential in this conversation? What are your thoughts on using probiotics in the sinuses even?

[00:46:36] DR. MAGARINOS: I think that we need to breathe healthy microbes. And that's something that we can do even with a nebulizer. You can use spores there and breathe them. Spores are abundant in natural settings. That's not something foreign for us. We can put in the nebulizer and we can inhale those spores. And definitely, they will play a role in improving and modulating proper changes on the microbial composition of the sinuses. That's one strategy.

I don't like to alter diversity so dramatically. I'm not a really huge fan of antimicrobials locally or systemically delivered. I know there's a place in time for those. I'm not saying 100% no. I'm just saying look for any other option before. And if nothing else works or the imbalance is critical enough that is creating a very complicated infection, okay. Well, I understand. That might be a good route to follow. But if you have alternatives, use them first.

Propolis and other more natural antimicrobials are definitely my choice. Even colloidal silver could be used in certain cases. And it's much more probably safer than strong antimicrobials. Even though colloidal silver in certain dosages can be very strong as well. But it's not so hard for the membranes, which is one of my main concerns with other antimicrobials. They create more immune reactions, more impermeability in the membranes. More damage in the structures. I tend to go more naturally for that purpose.

But you can breathe spores. You can use fluvic acid, humic acid compounds. That can be nasally delivered. Liquid form. You can spray those inside your nose trails and try to reach the sinus area. And that definitely can help closing the gaps of the leaking membranes that you can find easily on compromised sinuses.

And those strategies actually work amazingly well. They don't really comprise using an antimicrobial. But again, if we have to, propolis and other natural antimicrobials will be my option if we need to.

[00:48:56] SCOTT: Using a nasal spray that has humic or fulvic type acids in it, what comes to mind is the Zach Bush products. The ION Biome products that I think there is a nasal spray as well. Is that something that you're talking about in that realm? And then to get spores into the sinuses, I know some people will actually just open a capsule of MegaSpore and put it in some nasal saline and then use that in a spray as well. What are your thoughts on those two options potentially?

[00:49:26] DR. MAGARINOS: I like both. I think that those are good strategies for replenishing and rebalancing the microbiome of the sinuses. They both play a role. One in the communication pathways and the integrity of the membranes. And the other one for modulating microbial changes in the microbiome composition of the sinuses. Lowering pathogenic species and improving the beneficial ones.

And there's a natural intelligence in the spores that is fantastic. It's fascinating. And yes, you can open up the capsules and breathe them in. And you can do that at daily practice or at least weekly practice, especially if you live in this urban setting. You're not going to get much in those environments compared to if you live in the woods or close to nature.

If you go and you have the chance of going outside, do breathing practices outside. Go to the woods. Go for a hike. Go to the beach and leave 10 minutes, 15 minutes, no more, just for a conscious breathing. And that will be so impactful for replenishing microbes in the sinus area as well. That's super important.

[00:50:37] SCOTT: I want to talk a little bit about how the sinubiome and the oral biome impact the gut microbiome. So you talked about we're swallowing billions of these organisms. So if we have pathogenic organisms in our sinuses, in our oral cavity, we're swallowing those around the clock, could that potentially be a contributor to SIBO or SIFO? It seems to me that there is really a need in SIBO and SIFO to kind of look beyond just killing and look at the vagus nerve, and the migrating motor complex and bile flow, which you mentioned. Things like bitters and phosphatidylcholine. Working with the nervous system, for example.

I think there's more involved than just the organism. I don't think they're necessarily the cause of SIBO or SIFO. Maybe they're the result of some of these more upstream things. But I'm wondering how you view the microbial contribution of the mouth and the sinuses to the gut in terms of the potential for the development of SIBO or SIFO.

[00:51:38] DR. MAGARINOS: It's one of the key pieces of SIBO. I have a different way of seeing SIBO/SIFO in terms of the root cause. And I know there's some other people that are in the same page. It's a little bit controversial. I don't think that the overgrowth is the root cause. It's the consequence.

The root cause is probably niche in three major factors and complete imbalance or very important imbalance in the autonomic nervous system and negative impact on the digestive barriers, especially bile flow and stomach acid production. And a translocation of oral microbes and sinus microbes, why not, into the gut, into the small intestine due to the lack of barriers, especially, again, from those two fluids. And that sets the perfect storm for signaling the body differently.

And just as an example, you know that if we have more diversity in a certain area, then we're going to produce more byproducts. But we're not enzymatically able to break down these byproducts so fast. From an immunological standpoint, there's going to be an alert, a red alert. And usually, that shuts down because of the endotoxemia that is created because of those issues and others of course. The direct passage or the indirect passage of inflammatory molecules from one side to the other or the direct microbes that are getting there and creating immune responses.

Now you're sending signals increasing interleukin-6. Shutting down a lot of the pathways between the gut and the brain. Now your MMC and your peristaltic movements, they get slower. Now you have this food sitting there becoming rotten and toxic. And you create, of course, an increased amount of gas, and bloating and all these other – all the symptoms coming from that situation.

Now bile is support in antimicrobial. And if you're not producing enough, you're not correcting the overgrowth of these microbes at the same time. And toxins, which are also supposed to be filtered in a certain way in the mouth and the sinuses. If you have dysbiotic sinuses, the things we're breathing in, all these particles from the environment, for example, are going to get leaked into deeper places in the body eventually coming to the gut also and triggering a lot of these problems.

We have a lot of integration between what's passing through the mouth, the sinuses. What's being modulated in the small bowel? And eventually, creating SIBO. But for me, it's one of the major factors, the passage of oral bacterias into the small bowel. And I've seen this from a metagenomic analysis perspective every single time. It's so connected that I think it's undeniable at this point.

[00:54:48] SCOTT: I love those observations. And that's very powerful. And I think it's important to look at SIBO and SIFO differently than just killing a bug.

You have been a clinical consultant for Microbiome Labs for several years working with thousands of BiomeFx, stool microbiome tests. What are some of the common themes or observations that have emerged from that work? What did you observe that maybe you didn't expect to? Are there some key things from looking at these tests that we should stop doing and some key things that we should start doing? What are we getting right and what are we getting wrong?

[00:55:26] DR. MAGARINOS: We're getting a lot of things wrong, unfortunately. And also, we're doing a lot of good things because now we have much more information that we have available before. This is probably the main explanation to every single chronic illness we see today.

I think that we have a beautiful amount of knowledge for improving human health from the microbial perspective. Again, I think that we're getting right now pieces of information that are powerful. First of all, the translocation problem that I was just mentioning. You can see it's streptococcus. You can see patterns of actinobacteria. You can see increased flow of other microbes like … protobacteria-derived microbes that are naturally living in the mouth more than the gut. Where you can see ...

Just mentioning some of the most common families you will see on a microbiome sample that they're supposed to be more abundant in the mouth. And now you see that huge presence in the gut that you can't explain otherwise the translocation problem.

The other thing is the balance between the major groups. And we can see movement between the FB ratio, Firmicutes/Bbacteroides ratio in one direction or the other based on the dietary preferences. And this is huge. It's critical to understand that we need a diverse diet to equally feed all our microbes.

And I've seen, for example, that we have over-abundance of Bacteroides whenever a person is more prone for a Carnivore diet. And we see Firmicute elevation when there's autoimmune, which is actually the opposite. Firmicute elevation can trigger autoimmune. They're highly connected to the chronic illnesses we can see from the person's baseline and explains a lot. Because these microorganisms, they have different preferences in terms of the living setting that is needed for them to survive the foods that they eat.

All these things, all these variables are usually implied in the person's condition. For example, bile is a huge buffer. Has a pH of 11. If we flush bile normally, we will buffer the acidity of the gut to a certain level. And there are microbes that are needing a more alkaline environment to survive. If we don't push enough bile, we're creating more acidic environment favoring the more acidic microorganisms, which they tend to be actually Firmicute-derived microorganisms.

Now we're creating a better setting for a Firmicute overgrowth. And therefore, we're setting the environment and the growth of these microbes for triggering autoimmune. Now bile becomes crucial for treating autoimmune conditions because you need that buffer capability.

Just as an example of how you can connect the dots between overgrowth or patterns of growth of different microorganisms and the things that they are required for balancing them out and the conditions that will be triggered if you're not efficient in doing so.

[00:58:44] SCOTT: That's really an amazing observation. That's why my friend, Ann Louise Gittleman, says “bitters are better”. And bitters are so critical. But it's amazing. That's a connection you just made for me to think, "Oh, I'm taking some bitters before meals," I may actually be reducing the potential for autoimmune development. That's an incredible insight.

How do we know when we get a biome effects test back and we see something like H. pylori or Clostridia? How do we know when it warrants treatment versus maybe being a healthy part of a broader ecosystem? I know some people suggest that H. pylori actually may have some beneficial implications for the immune system.

And one of the hesitations that I have is a lot of times you see people will get a H. pylori positive test and then they're on triple antibiotics. And they're just really being super aggressive. Putting all these bombs into their gut and hoping that that's going to improve things. Do we always want to kill these organisms that we perceive to be bad? Or might they still have some health-promoting properties as well?

[00:59:53] DR. MAGARINOS: Yeah. Me, here, triple antibiotic when I was a kid. Well, not kid actually. I was probably 20 years old. And actually, I relate that to a lot of health issues that I got later in my life. Just from a personal perspective, we don't want to kill those microbes. And actually, it's unrealistic. We can't. We will kill whatever. H. pylori will survive mostly. It has some better chances than many other microbes. And if we kill that means that we did a massive damage to the mouth, to the microbiome of the body.

Clostridium, the same thing. Clostridium difficile, for example, is a spore-forming bacteria. You try to kill that, you will fail. It will go to a sporulated form. It will kill everything else when the antibiotic treatment finished. Now you're going to have this C. diff looking at the environment like, "Hey, thank you for giving me all this room for growth." And they also – of course, the whole balance of the ecological conditions are going to be changing.

But from a perspective of treatment, H. pylori I think has some protective role in the colon that has been proven. And there's some research done by NYU actually, but don't quote me because I might be wrong, that we're looking at colorectal cancer protective role of H. pylori.

And so, we know that everything has a role in balance. C. diff produces vitamins for us. It has a balancing role in the microbiome. It's actually commensal. If the problem is that we tend to create these abnormal terrains that they will favor the growth.

For example, H. pylori is a mucus-degrading organism. Yes. Let's say we are putting things that are mucus-forming. We're over-feeding now that microbe along with others because we're producing more mucus to protect the gut lining from that detrimental or damaging element.

It is the H. pylori problem. No. It is what we're doing for affecting the terrain in a certain way that will favoring the growth of multiple microorganisms. And ultimately, when we look at pathogens or potentially pathogenic bacterias, the problem is that we look for what we know. This is the tip of the iceberg of a major imbalance.

But because these organisms were cultured and grown in a lab and we study them, now we can identify them better. And because we start doing this linear connection that I don't like at all, I hate, it's just, "Oh, okay. This organism is high. This is the person's condition. Okay. This must be the causative agent."

When most of the times this is a very personal belief. These microorganisms, when they're overgrowing, they're the consequence of the terrain imbalance that trigger the problem. Now we're seeing the reflection. And maybe why not? They might be trying to solve the problem in a certain degree.

[01:03:06] SCOTT: I love that. I love everything that you just said. Those are such profound insights.

When we're looking at testing of the microbiome, it seems to me we have more of a focus on bacterial organisms versus fungal overgrowth, parasites. Maybe even the virome or viruses in our microbiome and how those influence health. Do all of these categories or classes of organisms have the same potential to negatively impact our health and our microbiome? Which of them might be more concerning?

[01:03:42] DR. MAGARINOS: Unfortunately, we don't know much about the others. The easier ones for analyzing and understanding are bacterias because of the size and because they are more able to be controlled in a laboratory setting. Unfortunately, we're aiming most of our resources for bacterias only. The mycobiome, the virome, and protozoa might play a huge role. And that's my belief in the homeostasis of the microbiome itself. In the balance of the microbiome itself. But we don't know much.

From a clinical perspective, when we see overgrowth of certain bacteria, we have tools. We don't have to rely on antimicrobials anymore. We can use spores. We can use immunoglobulins. We can use many, many supplements and tools for fixing those overgrowth or abnormal patterns.

When it comes to fungi, for example, we just go directly into antifungials because we don't know much. How we can predict that the fungis we're killing are actually not beneficial for us? We're going after Candida. There's so much more. There's like 33,000 types of fungis only in the Ascomycota phylum. And we don't know much about them.

I'm hugely concerned that we are coming to the practices that created this antibiotic resistance and all these other microbial diversity problems on the bacterial world now in the fungis and other microorganisms. I'm concerned about that. And because we don't understand even the correlations so much. But we know all of them, they play a role. We know all they are all talking to each other. We know there's communication. There's symbiosis. That quorum sensing doesn't end on the bacterial side. That is expanded to viral communication.

Well, phages, for example. There's a huge example of how viruses are controlling and interacting with bacterial populations. But fungis, the same thing. They set up the environment. They talk to other bacterias. They have this symbiotic relationship. We know that from candida only or mostly. But there's other things that can be involved in that conversation as well.

[01:06:03] SCOTT: I think there's a lot of conversation around the potential contribution of parasites in our microbiome. It seems to me that, for the most part, testing for parasites is just so incredibly poor. And since we can't see it, we assume it's not present. I think parasites are missed very commonly when we're talking about the microbiome. Do you think that parasites play a bigger role than we're giving them consideration for at this point?

[01:06:31] DR. MAGARINOS: This is something I been trying to find information about but there's not much. But from an evolutionary standpoint, we're not that clean. Probably, parasites were way more abundant in our gut ecosystem that it is right now from all the triple washing and avoidance of any contact with nothing that looks like dirt or not clean.

But if you go to certain settings, certain populations, other countries and different parts of the world, they have a way more direct contact with things that are not so clean. They have more contact with soil and not-so-clean water, which we know is loaded with parasites. Actually, the actual US testing for parasites is very small percentage. I can't remember the exact number of the total parasite spectrum that humans know. And it could be way more. But we only test for a fraction of the amount of parasites we can get exposed to. That's why a lot of the overseas infections with parasites are not seen on the common testing in US.

But if you think about those populations which are not foreign, they're native for that setting, that environment, which are interacting with these parasites all the time, they're not falling apart. They don't have this huge health issues or digestive symptoms. It's when we go there that we can't integrate this. But probably, there is a more deeper interaction with these parasites that are living in those natural settings that we neglect for so many years that now we can't relate to. And maybe we're missing them. Why not?

[01:08:12] SCOTT: It sounds like, in part, it's that because we haven't had exposure to them, we don't have the ability to create tolerance or have an integration with them as part of a healthy microbiome that they potentially then create some problems.

[01:08:28] DR. MAGARINOS: Yes. I believe so.

[01:08:30] SCOTT: High levels of Akkermansia has been associated with conditions such as multiple sclerosis. I heard this a couple of years ago and it was really interesting to me. It seemed unlikely to me that the Akkermansia was a contributor to MS. But maybe that the body upregulates the Akkermansia as a protective response. So that if you have an autoimmune condition, you have MS, maybe that's actually beneficial. I'm wondering what your perspective is. And if Akkermansia is already elevated in someone, do we need to be a little more cautious about doing things that might further increase it? Or is there not a downside of high levels of Akkermansia?

[01:09:12] DR. MAGARINOS: Akkermansia is incredibly important for us, especially the keystone species Akkermansia muciniphila. Now, Akkermansia is a gram-negative mucin-degrading bacteria and degrades mucin 2 along with the whole Verrucomicrobiota filum that is included in. We have a big filum in our gut microbiome that is Verrucomicrobiota. And within that microbiome filum, we have Akkermansia, and Akkermansia muciniphila is one of those microbes.

And all of them, they're mucin 2 degraders. They degrade mucin 2 layer, which is incredibly important for a proper relationship between the outside and the inside world of our bodies. And of course, that implies immune modulation.

Now we know that there's a linear direct correlation between the growth rate of a bacteria and the amount of substrate, of food, that is available. When we have more mucin 2, we can exponentially grow more Akkermansia because we have more substrate. And Akkermansia will grow more because it needs to take care of the degradation process of the mucin 2 layer in a faster rate to avoid this overabundance that can compromise the communication system between the mucin 2 layer and the immune system and the microbes. This is the intermediate layer that creates a healthy interaction without exposing the gut lining, which is pretty sensitive. It's actually sterile and has no microbes in it. But we have all these microbes on the outside layer of the mucin 2 degrading this mucin 2. And on the inside, we have all these immune cells talking to these microbes on the other side. And there's a lot of interaction happening there.

Now MS is an autoimmune. It's an advanced autoimmune. So if you have high markers of Akkermansia, for me, there's probably an overgrowth of mucin 2. And why this could be happening? Well, mucin 2 will be produced more if there's a damaging element that is constantly passing or getting inside the gut.

Now some of the most significant damage in elements we can think about are foods, especially mucus-forming foods. Not so good quality dairy. Certain denaturalized proteins. And of course, sugars and other additives and chemicals in processed foods.

Toxins. If you have a poor detoxification process, those toxins are going to be flushed back to the gut instead of being eliminated properly. And now you're exposing your gut to this very damaging molecules. And the proper response will be, "Okay, let's create a thicker layer that will protect the gut lining from this exposure."

And now, Akkermansia has to come into the play to degrade the mucin 2 in larger amounts. And then when you check for Akkermansia levels, you will see a pattern. I believe that the connection between an improper communication between the immune system and the microbiome and overgrowth of Akkermansia because of an expanded amount of mucin 2. And the exposure in a chronic way for these damaging elements is all connected.

Healthy levels of Akkermansia on the other side, if this is not coming from an autoimmune or another chronic illness, will be actually a beneficial thing. But if you have autoimmune and high levels of Akkermansia, doesn't make sense in terms of healthiness.

[01:12:48] SCOTT: If we have autoimmune and high levels of Akkermansia, should we then not be doing things to further increase it? Or is there still not a downside?

[01:12:56] DR. MAGARINOS: I think that what we need to do is find out what is the damaging element that is triggering protective mechanisms towards the gut lining? And I think that 90% of the times we'll find those in toxins. I standardly run a toxicological analysis for all my clients because it's probably one of the main root causes for every single disorder or imbalance in the body.

[01:13:23] SCOTT: I think this is another key message that you have shared in this conversation that most people don't talk about. When you talk about ways to optimize or improve the microbiome, very few people are going to say detoxification, right? And what you're saying is that we need to really consider the terrain that we need to be doing things to minimize the impact of these environmental toxicants on our microbiome through implementation of various tools for optimizing and upregulating our detoxification capacity.

[01:13:58] DR. MAGARINOS: Yes. 100%.

[01:14:00] SCOTT: That's huge. That's a huge, huge message. I love that. Dr. Ritchie Shoemaker, he talks about Actinobacteria and endotoxins now as more primary contributors to chronic inflammatory response syndrome, to biotoxin illness even more than mold and mycotoxins at this point. And so, I'm wondering if you find higher levels of Actino bacteria in the gut biome effects testing in those people dealing with CIRS that have exposure to a building that may have high levels of Actinos.

And then kind of tying that into some thoughts that Dr. Neil Nathan has shared, a lot of times people tend to jump to functional medicine approaches for working with the gut. And his observation and guidance has been that if someone has exposure to mold mycotoxins, potentially actinobacteria, things in the environment, that we really want to address the external environment first to really set the stage for optimization of the internal environment. I'm wondering what your thoughts are on that.

[01:15:05] DR. MAGARINOS: I can't agree more with both of them. Actually, I'm a huge fan of Neil Nathan. He's huge. And I learned a lot from his lectures about hyper toxicity. And that led me actually, at least partially, to understand the environmental factors contributing to microbial imbalances.

Actinobacteria is also highly present in the mouth microbiome. Going back to the mouth. Now mycotoxins will trigger imbalances in the digestive system pathways. If we want to connect – because I know that's their expertise for both of the doctors you mentioned. Mycotoxins, when they're present and our detoxification pathways are not properly working, they will disrupt digestive pathways and they will disrupt the ability for producing stomach acid and bile and all the other things that are contained in the passage of mouth microbes.

Now, you're setting the perfect ground for translocation. And then what you're going to be passing the most is what you have the most in the place of origin, which will be in this case Actinobacteria, Proteobacteria, and Firmicutes. But Actinobacteria being one of the most dominant groups in the mouth.

Now you will have an amplification of those populations in the gut that are highly immune reactive and triggering all these chronic inflammatory responses that we're talking about. And of course, the environment then plays a huge role in balancing the gut. You can't balance the gut if you have a toxic environment because it's completely connected. They're integrated. It's just one thing.

That's why, again, detoxification, avoidance and elimination of toxins all together should be phase one of every gut protocol. If you jump into probiotics and other strategies, you usually get frustrated. You don't get the benefits you're looking for. And the reason is because you're not removing the imbalancing agent or the disruptive agent to create the environmental conditions you need for those microbes to thrive.

[01:17:22] SCOTT: In those people that have high levels of Actinobacteria that you see in the stool testing, and you said that a lot of that comes from the oral cavity, is it possible that if there are higher levels of Actinobacteria in their home, for example, coming from the drain pipes, which is one of the common areas that we see these or coming from bedding and pillows. And there's certain sources now where we're seeing also that, environmentally, there's these Actinomycetes or Actinomycetes that are common contributors to biotoxin illness. So do you think that if the external environment has higher levels of those organisms, that then it's logical to say that also is contributing to higher levels in the mouth that then is potentially impacting the gut? How direct might that correlation be to the external environment in our home and what we're then seeing from an actinobacteria perspective ultimately in our gut?

[01:18:19] DR. MAGARINOS: Again, the barriers, the systemic barriers are are huge here. And we know that those microbes are going to be, of course, less concerning if we have proper balance in the production of bile and stomach acid, salivary flow, everything that we have here in the mouth that is containing immunoglobulins. And the stomach acid, the pH difference, will create a barrier for those microbes to arrive into the gut when they will be more immune-compromising, of course. That's where most of your immune system is.

Definitely, there's a connection between environmental agents, the filtering barriers we have and the immune triggers that we can get from the exposure to those microbes. Also, there's another factor included. Actinobacterias and facultative anaerobe. Meaning that it can tolerate more oxygen than the strict anaerobic forms we have in the gut.

That can actually give Actinobacteria more opportunities to colonize areas that they're not getting so low in oxygen, especially in small intestine. In the colon, we tend to have more lower oxygen because of the fermentation process. The entry point of colonization is easier because there's less distance to arrive into the environment that they can actually grow in compared to other microbes, which are strict anaerobic and they can't – or they need long-distance traveling for getting into an environment that they will actually survive.

[01:19:53] SCOTT: I want to get your thoughts on biofilms. I think it's fairly common to have biofilm breaking enzymes in many gut pathogen protocols. And I'm interested in the potential benefits and potential downsides of biofilm-dissolving agents. You talked about this earlier, that biofilms are important.

And I'm thinking along the lines of if a person also has systemic biofilms that maybe are housing chronic infections like Lyme disease or environmental toxicants, that if we get too aggressive with biofilm breaking, even if we think we're just doing that in the gut, that we have the potential to be breaking down systemic biofilms. Releasing infections. Releasing toxicants. Triggering the inflammatory cascade. Triggering the mast cells. And that we can actually make people feel much worse. What are your thoughts on the need for breaking down biofilms as part of a microbiome optimization strategy?

[01:20:54] DR. MAGARINOS: I have a different perspective. And because I believe biofilms are fundamental for the normal functioning of the body. And I know they have been demonized because they're so efficient in the communication pathways and adapting and becoming resilient.

Then, of course, when you have abnormal or pathogenic bacterias, for example, you will have them included in the biofilm, it's going to be very hard for taking them out or rebalancing. And so, we think, "Okay, we need to take care of these biofilms," breaking them. And then we might be able to control better these overgrowing patterns of this potentially pathogenic or detrimental bacterias.

I tend to think differently. I think that this adaptability of the biofilms can be used for our purpose for improving the health conditions that are related to these abnormal growth patterns. The same way that microbes are sensing through quorum sensing, the environmental conditions that might be triggering imbalances or pathogenic overgrowth within those biofilms, we can push better or optimize the environment to create or reverse this biofeedback.

And now with the same quorum sensing, telling this microbiome, this biofilm, "You know what? Things are going well here. There's abundance of nutrients. The oxygen levels are fine. The pH is the one you require. You don't need to go to these aggressive patterns anymore because the environment is more benign for you."

And we know how to control that because we know that the regulatory agents are common for everyone. Bile, lymphatic system, the nutrient intake, the stomach acid production, the enzymes, pancreas functioning, the kidney clearance. All those organs are supporting the environment of the gut itself. And if we contribute for a healthy status of all these organs and systems, we're going to change the environment and the biofilms will adapt accordingly.

I will always push that idea more than trying to disrupt biofilms from my perspective. And again, there's different ways for doing things. And all of those ways could be effective. But I think, on the long run, attacking biofilms will always create more aggressive patterns. And if we go to the knowledge we have about phages, for example, we know that if we start killing microbes to a certain extent, phages are going to go into the play and they're going to activate more defense mechanisms inside the microbes.

I want to create my microbiome in the most benign, in the most resilient way possible with a proper integration of the microbes and immune cells without this aggressive patterns that can trigger immune responses. And I think that the regulation of the terrain is much more powerful to create long-lasting effects than using biofilm disruptive agents.

[01:24:18] SCOTT: I love that. So you're a thought disrupter. Not necessarily a biofilm disruptor.

[01:24:23] DR. MAGARINOS: Exactly.

[01:24:25] SCOTT: As we come into our last several minutes together, I want to hit on a few last topics. I, personally, am a big fan of MegaSporeBiotic. I find it very helpful. Well-tolerated for many people. However, I had taken it for several years and still didn't have quite the optimization or diversity of my microbiome that I would have liked when I did the biome effects testing a couple years ago. My question is do we need more than just the spores to really get a broad diverse microbiome? And what are some of your favorite probiotics in the marketplace today?

[01:25:01] DR. MAGARINOS: Yeah. Well, one of them is actually MegaSporeBiotic. I've been with the company externally as a consultant. But I wouldn't be able to be with them if I don't believe in what they do and what they're researching about. Definitely, a huge fan of them.

I think spores are the fundamental regulatory agents for the microbiome whenever it gets established as an adult microbiome. Before that, we can combine and get more – we can grab more microorganisms from the environment. But when we have this fixed microbiome completed around three years old, that's when spores are contributing for keeping the regulatory process. This is powerful.

But environmental settings are required for them to work properly. If the environment is not in the same place, their regulatory activity of the spores is going to have a limitation. That's when detoxification and, again, improvement of the drainage pathways, detoxification pathways, lymphatic system circulation, everything else we spoke about, is so important. That's crucial for maintaining the ecological conditions for our native commensal bacterias to grow in the right direction. And then the spores can become super powerful.

I like MegaSpore. I also like BiotiQuest from Martha Carlin. I've been connecting with her for many years and I like the intention that she has behind her formulations. And Microbiome Labs and BiotiQuest, they share something in common that I do encourage everyone that is using probiotics to look after research. Both of them, they're researching and expanding knowledge and trying to improve what they're doing already. That's super important.

But both of them, they contain spores. And you can get also benefits from Lactobacillus and Bifidobacterium. Those are ghost probiotics. But always keep in mind, information is key. We don't need the active bacteria most of the times. We just need that piece of information that will tell something that is missing on our own microbiome. And the microbiome then we'll grab that information and do whatever is needed.

[01:27:11] SCOTT: I am a huge fan of Microbiome Labs too. I think, definitely, one of my top five companies that when they come out with something new I'm definitely listening and interested.

If we think about prebiotics, probiotics, post-biotics, and maybe even paraprobiotics, and I tend to think of that similar – that paraprobiotics very similar to ghost probiotics. Maybe you can differentiate them for us if they are different. How would you suggest introducing those types of tools into a health optimization program?

My observation has been that it seems that people tolerate post-biotics and paraprobiotics better early on than they might prebiotics and probiotics. When's the right time for each of these tools?

[01:27:57] DR. MAGARINOS: It's hard to say actually. It's one of the most challenging questions. And every single person is different to a certain extent. But I agree with you. I think that the inactive form can be more beneficial initially. I think prebiotics are usually less tolerated at the initial phases of any treatment plan because you require a proper activation of the fermentative pathways of the enzymatic pathways needed for utilizing them.

Yes, they play a huge role. But also, you need more balance in the microbiome itself and the digestive pathways for getting benefits out of them. Prebiotics, when it comes to spores, I think that we need to use more individualized approaches using one strain at a time or two. Don't go crazy in multiple types of strains right away because we're going to be operating different types of pathways. We put too much mechanisms in activation right away, it could cause havoc in your rebalancing process. Every type of rebalancing agent will create an immune reaction. More pathways, more immune reactions. We try to avoid, of course, side effects as much as possible.

And so, again, probiotic, ghost biotics. Let's talk about those. I believe they're – for me, they're pretty much the same, are these information carriers. We don't need the actual bacteria. We just need this piece of information needed for telling the story to the microbiome we have to optimize the functioning. That makes so much sense. And it will be less immune reactive than put in an actual living bacterium in the body.

And from the standpoint of supplements, prebiotics are probably my last thing to include in any type of protocol I use if I use them. I'm not saying there's no benefits. But we can feed the good, the bad, and the ugly with the same ones.

Actually, Klebsiella pneumoniae which is pretty huge sometimes in SIBO and other type of issues and IBS, loves fructooligosaccharides. You put anything with inulin in there and it's going to make a party for Klebsiella.  Definitely, we want to rebalance the microbiome. The terrain first. And then we might introduce prebiotics.

[01:30:22] SCOTT: Instead of very high level, I know we could have a whole separate conversation about this. But what are your thoughts on FMT or fecal microbiota transplants either now or in the future as a tool for balancing the biome? It seems to me that it comes with some potential benefits. But also, some potential risk.

[01:30:40] DR. MAGARINOS: Yeah, it is risky. Because the amount of information that we're putting together, and a couple of those things of this fecal matter transplant, it's huge. How many pathways we're going to be interacting with from neurotransmitters, to protein fatty acid production, to endocrine system function? There's so many things implied in the overall composition of the microbiome.

And thinking fecal matter, put it somewhere else, in someone else's microbiome, will have a huge impact on those communication pathways. There's also a regulatory process. And I think that the die off and other regulatory systems within the person who is receiving the FMT is diminishing a little bit that huge impact that we can create.

There was a reported that trial that was from a person that apparently had depression or was going through a very complicated time in his life. And they used him as a donor and the person who received the sample actually got in a very sad state. Was depressed and everything else. Because we pass more information that we are actually aware of. I see benefits. Don't get me wrong. I think that there's potential benefits for use in FMT. But that also comes with more understanding. And that's something that we're still working on.

And I don't like the idea of using antibiotics prior to the FMT, which is something that's commonly done. I don't like that. And if you're going to use probiotics, stand on the probiotic side. Don't kill microbes to get more or others included. I know it makes sense. But it doesn't create the benefits we're looking for.

[01:32:25] SCOTT: I want to talk a little bit about lipopolysaccharides and endotoxins. Talk through how lipopolysaccharides get from the gut into the body. The potential problems that they create. And does the focus on addressing intestinal hyperpermeability improve the absorption or translocation potentially of these lipopolysaccharides and endotoxins? What kind of tools are we thinking about here to minimize the impact of LPS? Are we talking about bovine immunoglobulins? Are we talking about other things? What are your thoughts on LPS and endotoxins?

[01:33:00] DR. MAGARINOS: We know they're huge in playing a role for initiation and progression of multiple chronic illnesses. That's something that has been very well researched to this point. Lipopolysaccharides are naturally occurring in everyone's microbiome. It's not something foreign for us.

Actually, we have dominance naturally speaking in a healthy subject of gram-negative bacterias, which are the ones that are containing in their membranes this lipopolysaccharide molecules. But it's the nature of them and the abundance. And also, our scavenging pathways, our elimination pathways, that makes the whole thing go in the right direction or the wrong direction.

If we put together leaking membranes or leaky gut, if we have an overabundance of gram-negatives, which by the way can be coming from gram-negative bacterias from the mouth which also is dominant in gram-negative bacterias. If we have those and we have a low ability for producing immunoglobulins from our immune system, all those things combined can create this leaking problem and hyper endotoxemia that thrives into a lot of issues including neurological situations like depression, anxiety, mood disorders. But way even more than that, we can have so many autoimmunes and other chronic situations because of that increased circulating levels of lipopolysaccharides.

By being a huge fan of using immunoglobulins, I think that those are the most effective way for improving the scavenging process of lipopolysaccharides. But also, we want to increase the receptors in the gut for also downgrading the immunological expression of the lipopolysaccharide activity.

And for that reason, we use strains like Bifidobacterium Longum 1714 that you can find in some biome, for example. That product is fantastic for correcting those receptors. And therefore, cutting down this vicious loop of activation on interleukin 6 going back to the brain and all the cortisol activity that increases in membrane permeability in the gut.

Lipopolysaccharides are definitely something we need to take care of from the beginning if they were detected high or we have higher abundance of gram-negative populations in the gut. That's why I like to test for microbiome analysis because I can see these patterns and take action rapidly. But immunoglobulins have been shown to be very effective, especially in high doses. And they're very safe, especially if they are derived from bovine serum.

Colostrum is another great alternative. And you have naturally occurring immunoglobulins there. Some people are a little bit hesitant of using colostrum for dairy reasons, dairy sensitivity reasons. I found none of the patients that they reported their re-sensitivity to be immune reactive to colostrum. By the way, it's not on the side. And I use pretty high doses of colostrum when it's needed.

[01:36:12] SCOTT: Yeah, I think it's interesting the bovine immunoglobulin. We can kind of think of them as a binder. We think about charcoal, and bentonite, and all these other things. But when it comes to a number of materials that we have in the gut that we don't want there, these immunoglobulins are essentially kind of a binding agent. Is that a reasonable way to think of them?

[01:36:31] DR. MAGARINOS: Yeah. Definitely. They work as a binding. They're specifically biological binders for lipopolysaccharides.

[01:36:37] SCOTT: Before we get to our wrap-up question, I want to just touch a little bit on your thoughts about diet and the microbiome. I think many people now are promoting high protein, high fat. We talked about Carnivore briefly where people are eating meat almost exclusively. How much does diet change or impact the microbiome? And then how important is it to have, let's say, carbohydrates in order to support a healthy microbiome?

[01:37:05] DR. MAGARINOS: Carbohydrates are essential. And this is something that bothers me when I hear Carnivore-promoting diets, physicians. Because I understand the relevance of proteins and fats. I do. We can't deny that from a nutritional perspective. But this is when we get narrow-sided. Because we're looking at the benefits of the cellular needs, human cells needs. But we're not looking at the microbial needs.

And you can't feed in a diverse way your microbiome using a couple of fruits and honey. That's stated on the Carnivore diet. And on the other side, the main problem is that how do you know how optimized are you for managing proteins and fats? And I see so many people right now with digestive efficiency problems from an enzymatic standpoint from hydrochloric acid production that we can assume that everyone can eat huge or big amounts of proteins on a daily basis without getting problems on the side, especially immunological problems. And that will be derivative from the over-fermentation of those proteins that is not supposed to occur in large amounts. Proteins are fermented naturally in a small amount. So we get amines and we get phenols, we get hydrogen sulfide in small amounts. We get these molecules that we need. Ammonia. Those things, they play a role in our health. But in large amounts, they're inflammatory. All of them.

How you can predict what's going to be the direction that those proteins are going to be used in terms of amounts or quality? We can't. But there's definitely going to be a huge risk of that person becoming unable to use them properly. And then they're going to be partially digested. Becoming damaging or toxic for your gut environment. Or they're going to be over-fermented. Creating more inflammatory molecules. A lot of things can go wrong.

And from a nutritional standpoint, how much we need really compared to what we need from the microbiome? The microbiome, 70% of the microbiome needs complex carbs. And I'm not talking also about – I'm talking about overwhelming the microbiome eating a big bowl of salad with 20 different fruits and vegetables every day. I'm talking about that we need to sustain a diverse, consistent amount of carbohydrates, hopefully seasonally-oriented in our diet to feed our microbiome accordingly.

And definitely, we went through starvation periods of times for the microbiome. And we were more carnivores sometimes. We're more vegan other times. We had that resilience established from an evolutionary standpoint. Definitely, we can get benefits when we are in a carnivore diet. We can get benefits when we're in a more vegetarian diet.

But ultimately, in a lifespan, we need to have both coming in and out. And again, even better if it's coming from a seasonal perspective and a local perspective. That will be even better. But using a consistent long-term carnivore diet for me is set in the perfect storm for disaster. It's not a good thing.

[01:40:25] SCOTT: I think people listening to this will be interested in finding out how they can work with you. Tell us a little bit about Revolution Gut Health. And do you consult one-on-one with people? What if people are feeling drawn to work with you more, how can they do that?

[01:40:40] DR. MAGARINOS: Revolution Gut Health is an online platform that coaches people for improving their gut microbiome needs, especially oriented for improving chronic illnesses. Conditions that are rooted on the gut microbiome. That's what I do on a daily basis.

I love what I do and I feel passionate about helping people to improve their health. I'm a huge fan of testing. So people who look for us, we are going to be testing initially a lot. But that allows us to understand what's going on and what needs to be corrected from the beginning. We become more efficient at the end of the day. They can work one-on-one with me.

We're expanding the team right now. We're trying to – we're becoming more busy and bigger. But for now, I'm taking care of a big portion of all the consultations. And I love that. And even though maybe not directly participating in all of the consultations, I'm always involved in the process. I like to participate. And I learn from my clients as much as I try to provide solutions and answers for them.

[01:41:43] SCOTT: Beautiful. Beautiful. My last question is the same for every guest. And that is what are some of the key things you do on a daily basis in support of your own health?

[01:41:51] DR. MAGARINOS: I tend to be very realistic to what I do. I don't do really crazy things. I tend to try to be outside as much as possible. It's hard sometimes with work. But I promote that as a huge piece of becoming healthy. You need to be in contact with the soil, with the air, with everything around you. And that has been a huge piece of my life. And I come from a place that nature is everywhere. I try to get that in my daily routines as much as possible and planning even to move to a place that I can get that more frequently even.

My wife has been super supportive in that. She's always pushing me out even when I'm working between 15 minutes, "Go 15 minutes out. That's going to be great for you. You can disconnect a little bit." It's great to have that right hand promoting this.

And my other huge thing, I'm a huge fan of cooking. My house, I'm very social. I like to be with people. I like to eat – every guest that comes to my house, you're going to get a good meal with it, with the invitation. I like to cook for my family, for my guests, whoever comes into my house. I take a good time of my day, I will say an hour, for eating, cooking and having a good decent meal with the right time and the right social interaction. If you do that, you improve your digestive pathways. You improve your serotonin naturally. You enjoy what you're eating. Your nutrient absorption goes way higher than eating in the run. And eventually, that is one of the most potent I found healing therapies that you can get.

[01:43:29] SCOTT: Absolutely amazing, Dr. Haroldo. Not only did I love your brain, but I love your curious mind. I can tell you're having fun with this. That you're still putting pieces together. That you're curious. That you're still looking for more solutions and more answers. And lucky to be on the receiving end of the benefits of all the thoughts that I'm sure are going through your head every day.

Thank you so much for being generous with your time today and for sharing just some fantastic information. Some new ideas. New thoughts. And connecting a lot of dots for us. I really appreciate it.

[01:44:05] DR. MAGARINOS: Yes. God, it was real pressure being here. I love this conversation. It has been an amazing opportunity for talking about so many interesting things. Thank you so much for this. Anytime.


[01:44:15] SCOTT: To learn more about today's guest, visit RevolutionGuthHealth.com. That's RevolutionGuthHealth.com. RevolutionGuthHealth.com.

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