Your Health & Microbiome Balancing

Today we’ll explore novel techniques in the exploration of our microbiome and the impact in can have on health. Our guest, Alex Zaharakis, is a a licensed and board-certified Radiation Oncology Physicist and, grateful husband and father of two beautiful children.

Alex’s interest and motivation for answers in the microbiome is driven by his son’s regressive autism at 17 months after a culmination and spark of timely medical insults, several of which were microbiome focused.

Alex’ microbiome analysis and balancing protocols are highly sophisticated and individualized and are comparable to a 23andMe test, but for our bacteria. Let’s find out what it’s all about. Please visit our website for further info. Alex’ FB group is here.

What does microbiome balancing really mean? Is it a superior technology? What is the difference to the tests we have come accustomed to over the last 2 decades from stool tests like Great Plains Laboratory, Genova or Diagnostic Solutions?

EP6 Microbiome Balancing Transcripts
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Dr. Bogner:
Yeah, so what’s interesting that we know that in autism, up to 90% of patients have a gut-related problem. It’s very difficult to navigate through this because we know that we have, I think, more bacteria making our bodies than actually human cells. It’s about, as far as I know, about three and a half pounds of bacteria, about the weight of our brain, that we have inside of us. A lot of different bacterial species, I think about 20,000 different species that makes up what is essentially called our microbiome. And there’s a balance. There needs to be a balance in all that bacteria keeping each other in check. They’re dividing species, and they keep each other in check. And there seems to be problems, probably influenced by the environment, antibiotics, or chemicals, herbicides, glyphosate. All of these are factors that potentially could lead to clinical problems such as autism.
Over the years, I have utilized certain what we call gut tests that check for bacteria. One of them is Genova or GI-MAP. Many of you probably know those. I moved away from this, because it didn’t really help in regards to … You know, I didn’t know what to do with the results. If you have a bacteria that’s part of you and it’s overgrown, what are you going to do? Are you going to treat it with an antibiotic? That doesn’t make sense. There are a lot of interrelationships between bacteria. If one is low, maybe another one starts growing.
So about two years ago, I got to know about Alex Zaharakis. He’s a father of an autistic child as well. He’s a licensed and board-certified radiation oncology physicist, and he has a big interest in researching the microbiome. He has created a gut balancing model which is currently used by several doctors and practitioners. He provides an analysis of the microbiome using his software that he developed, and has his own Facebook group called Gut Balancing and Healing.
So we wanted to invite him today to pick his brain in regards to what he is doing, what he has observed in the samples that he’s analyzed, what kind of techniques, what makes his analysis different than the conventional testing that most of us have been implicating or used in the past. I know it’s called 16S sequencing. It doesn’t really tell us much what that is. So I wanted to see what we can find out in that regards, that makes it different, and what results has he seen in regards to applying this knowledge with patients.
So welcome, Alex. I am thankful to have met you. We have many discussions every day, almost, researching. And I know your scope goes beyond just the microbiome. Of course, we know about the gut-brain connection and all of that, genetics, and so forth. So I want to welcome you to our podcast here today, and wanted to know your background a little bit, where you’re coming from, what sparked your interest in this, in the microbiome in general, and then we go from there. I’ll ask you a couple questions in regards to what you see and go from there.
Alex Zaharakis, MA, MS, DABR:

Sure. Thanks so much. It’s a pleasure to be here and a pleasure to collaborate and share information and learn from you. So yeah, I’d be happy to talk about the 16S test versus some other tests and what I do. I guess I could talk a little bit about my background first. Obviously, I have some skin in the game with regard to my son, who has autism and regressed at a early age, and very noticeable GI problems. Obviously, we did some interventions, but similar to what you’ve hit on, that it just seems that the testing and the analysis, or the perspective on how to use the test and intervene, was incomplete in certain areas.


It was probably about two years ago that I had come across a particular type of 16S test. I guess I could talk a little bit about that, compared to the other tests. But the main implication for really driving my interest and trying to harness my skills was that with these types of tests, you have access to what’s called the raw data, or the entirety of what has been sequenced. We’ll talk a little bit about that. But that really sparked my interest, because I quickly realized that I could leverage some of my analytical skills and my background as a physicist and different encounters throughout my education and professional life, having to work with large datasets and numbers and doing different types of analyses. I started to get a picture in my head of the potential of the problem that was being faced in my son, but also several other tests that I had seen of children on the spectrum.
Some of these traditional tests, like you mentioned the GI Effects or things like that … There was an evolution of technology. It started with culture-based testing. That really has a limitation, because the culture-based test, when you take a sample, it’s going to be effectively grown on a medium that they have to choose that’s appropriate to whatever microbe they’re trying to analyze, so that they can get enough of it and they can actually identify what it is. If you think of the totality of the problem, in a stool sample, you’re having, in a gram of stool, trillions of microbes. And from the bacterial perspective, the microbiome, which we know the most of, even though we don’t completely know everything, there’s hundreds, potentially close to a thousand different microbes. So trying to be able to culture a thousand different microbes is a very tall order. But there’s also complications where it’s heat-sensitive, it’s time-sensitive, what you send to the lab can change. So you’re really limited in what you can look at.
That evolved into some other technology called qPCR, quantitative PCR, where they were leveraging some sequencing, looking actually at the DNA structure, to identify microbes. With those types of test, you need to know what you’re looking for. For instance, if I’m looking for something like COVID, well, I need to know the sequence so that I can find it and match it in my sample. Obviously, there’s an advantage to doing that, because you can get clear identification. The amplification takes place in this PCR process where we’re taking a small amount of DNA or microsomal RNA and amplifying it so that you can actually quantify it.
But the problem there is, like I said, you really need to know what you’re looking for. So over time we developed an idea of what might be good and what might be bad, and some of these qPCR tests, they typically limit to about 30 or 100 different microbes. And the process of the amplification really is somewhat specific to the primer used for each microbe. So it’s really hard to get a comparison of percentage, like a percentage of a pizza pie, if you will, of what is taking what. Really what we know is good or bad in those cases and the bounds are just based on probing the population and seeing what might be abnormal or normal, or what we think.
But the 16S type testing, and this technology really became feasible in the era of 23andMe, it’s the same type of technology where they’re sequencing DNA. They’re probing this 16S gene, which is a ribosomal RNA common to bacteria, and it’s termed conserved, meaning that it’s found in all of the microbes. The necessity for it to be there is such that if it doesn’t have this particular gene, the microbe doesn’t function. So you’re picking apart a smaller piece of DNA that you can harness and say, “Hey, this sequence corresponds to this microbe,” and so on and so forth, distinct enough that you can tell between different microbes. But it’s similar enough, the sequences for each of these microbes, that when you don’t know what it is, you can still give it some level of classification.
So it really depends on the database that you have to compare against and identify, but if we come across, for instance, a particular microbe where we don’t have in our database, because of the similarities in this region, we can say, “Oh, it’s actually part of this genus.” We get some information, whereas something with qPCR, if we’re not looking for it, we won’t know that it’s there. We won’t see it. So what we effectively get with the 16S type testing is almost like a percentage of the stool sample, percentage abundance, and what is occupying what.

And it became very clear to me, because a lot of the history or the consensus in autism was that there were these pathogenic things that need to be eradicated, and those are the reasons or the causes for certain issues, inflammation and LPS, lipopolysaccharide, inability to absorb nutrients, or toxic metabolites. But it become very quickly to me that in many of the individuals, the problem was in essence a little more simpler than that, that there was a couple of microbes taking up a large piece of the pie. So where maybe some of these other tests were focusing on these pathogens … And for instance something like strep bacteria, streptococcus genus, we might say over a percent of the sample, it starts to become not an ideal situation. And certainly you can find it higher than that. But there was these other microbes that you don’t necessarily classify as being good or bad all the time, making up maybe 10, 20, 30, 40% of the pie.
So it became apparent to me that if we were able to strike a balance … And that involves shifting of some of these neutral microbes, replenishing or feeding some of these missing good microbes, targeting some of these pathogenic microbes. The combination of those things would allow us to reach a more stable microbiome. Rather than just trying to, if you will, weed out the crime in a neighborhood, how do you prevent it? Bring in the jobs, bring in the good schools, have a good government, nurse the economy. Then you can have a more stable environment that is going to prevent these pathogenic things from taking over.
So it became apparent to me that the problem was really both simpler than what we were thinking, but at the same time more complex, because rather than focusing on, hey, getting down this bad thing, we need a tailored approach. That kind of sums up the differences between the tests and how the 16S test looks at sequencing.
Dr. Bogner:
It’s clear to me that this technology of 16S is clearly superior than the conventional PCR that’s used by most commercial laboratories. Now let me ask you this. How many samples do you think you have analyzed now in regards to autism, and have you seen patterns in regards to what you see in the abnormal distribution of a particular bacteria?
Alex Zaharakis, MA, MS, DABR:
Yeah, so it’s probably over … Sometimes the individuals will do multiple tests. So total samples, probably close to a thousand, half of them directly analyzed and provided suggestions from me, and the other half nourished and trained through different practitioners, but still being analyzed by me. But even though that there’s such variability, there are some clear patterns that emerge. Where my mind goes to first is that, you know, what could go wrong? Well, certainly I would say probably one of the most common ones is this overgrowth of this particular microbe called Prevotella copri, which not only is it very common, it’s very alarming and jarring when you look at the percentage that it takes up of the samples, some 30 to even in extreme situations 90% of the sample. And there’s implications that this microbe has connections or a synergistic relationship with the microbiome and fungi.
But there’s other situations where there can be … For instance, very common to see little to no Bifidobacterium, which I think is very important. There’s literature to show that it is pH regulating, has implications in the immune system. But I find that as we are able to regenerate it, that is particularly the genus that seems to tip the stability into a direction where we have now a better chance of rewriting the narrative.
Certainly there can be certain overgrowths that lead to things where gas is produced, like hydrogen sulfide or methane gas, which you would commonly associate with a SIBO. There are situations where clostridium and pseudo-clostridium … And I say that because some of the other advantages to this type of testing is that the technology and the individuals that are responsible for doing the sequencing, it’s just the nature of the beast, they’re in tune with the bacterial naming, which changes over time. For instance, I was asked by a practitioner about clostridium one time, and I made the comment that there’s about 15 or 20 different clostridium species that are no longer considered clostridium. They’ve been put into other genuses, like Lachnospira or Ruminiclostridium. The way the bacteria are named, they’re kind of like naming a star, right? Somebody discovers it, they give it a name, they classify it, and then after further research they put it into the more appropriate category. That doesn’t necessarily change the pathogenicity of it, but to talk about apples and apples, it certainly helps to make sure that you’re talking about the same thing. So we see a lot of those pseudo-clostridium and clostridium being elevated. There can be strep.
Dr. Bogner:

I know that when you get the samples with the raw data, you have developed your own software to spit out the data into a very snackable charting system and a distribution of those to give you a good overview of what we’re looking at in regards to the most critical overgrowth. But throughout your last two years of analyzing these samples, what have you seen in regards to your suggestions in regards to intervention? You mentioned you want to feed some. I think what you’re talking about, the term is prebiotics, correct? And I know that you also incorporate probiotics and different minerals and other just naturally occurring substances. When you make your recommendations to your patients that engage with you, what do you usually expect, or what do you see in regards to improvements, and what timeframe and what percentage of the population do you see? If you could give us a rough estimate in regards to improvement, and what kind of improvements do you observe?


Alex Zaharakis, MA, MS, DABR:
Yeah. Good question, complex question. I guess it can come from the other end, is that everyone completes a survey with potentially these questions on there. What improvement that they feel that they have experienced after doing a round. A round is the six weeks of targeted prebiotics program and herbs specific to the profile. There are specific questions on certain symptoms.
My overall impression based on the results of those is that you can … And this is kind of subjective, and also anecdotal per the individual. But I would say 10 to 30% improvement over the course of three rounds. Some people, it’s quite dramatic, that they report significant improvements. And I think the worse the sample, the more upside. Others, slight improvements, and then in a second round, there’s a jump there. But I think not an unreal expectation is 10 to 30% over the course of three rounds. I like to suggest, and this is based on my opinion, my belief, but there’s also some literature to show that the changes that you can make in the microbiome may have implications in making some other therapies more beneficial or more able to be realized or provide improvement.
Actually, in the world that I work in, in oncology, there was a study that came out two years ago for individuals who received immunotherapy, which is a type of therapy that the aim is to promote the immune system to target the cancer. This is actually a very successful therapy, but the biggest conundrum for a long time is that it seems to either be extremely helpful or not helpful at all. In this trial, they took a set of individuals that were non-responders to this immunotherapy, and they performed them a FMT, fecal microbiotic transplant, which is essentially … You know, think of a gut recharge, if you will. And these non-responders became responders.
I think the mechanism there is to say that even though we might be able to see 10 to 30% directly through these gut interventions, it might have a compound effect in something else that you try later. Maybe if you need an antifungal, it might be more successful after your microbiome is in a better place.
Certainly the anecdotal experiences from parents, many of them have told me their children often never really get sick before, like a cold or a common bug, and they would start to do this and they noticed that it’s almost like the immune system was kicking on. It’s the first time that they’ve ever had a cold since they regressed. Which, obviously, nobody wants their child to have a cold, but there’s some indication there that things are moving in the right direction.
Dr. Bogner:
Yeah, yeah. No, children, they need to get sick. Fever is essentially the immune system training against some very common pathogens so you don’t get sick again, right? That’s great, really. I know you are also extending your research into a technology called 18S. That’s what we consider the mycobiome. It’s essentially not looking at bacterial metabolites or bacteria, but the mold, correct? Mold and yeast. I know that there’s very little information on that, and I know you are looking into that type of research. Is that correct?
Alex Zaharakis, MA, MS, DABR:
Yeah. I was actually asked about this the other night. With the fungal world, so there’s a technology out there, the 18S or ITS. You can use that particular gene to probe fungi similarly 16S with the bacteria. Unfortunately, it tends to be more complicated for different reasons. For instance, with the fungi there’s a lot more variability in the lengths of the DNA sequences, which poses some challenge. The database that we have, it’s much less complete, the dictionary, if you will, of bacteria versus fungi. So that poses a challenge.
And then, as I was asked this question the other night, the knowledge [inaudible 00:27:26] said that even if the sequencing was great and the database was complete, meaning that we can identify everything we find, the intervention at the end of the day, I don’t know that I would do much different approach, because we don’t have the same kind of experience with fungi in the entirety of the medical community as we do … We’re just kind of getting in tune with this in the last couple of years. There’s just so much more literature on bacteria.
But that doesn’t mean that we shouldn’t be pursuing it. So I have been running some of these tests under my own expense, my own time, to try to work the problem backwards with some severe cases and see if I can find some common trend. But I do think that this is the way forward. This is the kind of thing that you have to do to take apart the problem.
Dr. Bogner:
Yeah, I think it’s fascinating. Especially it seems like a kind of an upgrade of what we’ve seen over the last two decades in regards to testing the microbiome. I know there is a very large interest in academia, and I know there’s some very excited things in the pipelines with you in regards to that. But let our listeners know where we could find out … I know you give a lot of talks that are free on YouTube. So tell us, where can we find your work in regards to finding out more about this and the more extended version of you explaining this to anybody who’s interested?
Alex Zaharakis, MA, MS, DABR:
Yeah, there is a YouTube channel. You can look me up. My first name and last name, Alex Z-A-H-A-R-A-K-I-S. There’s some videos there. There is a Facebook group, Microbiome Balancing and Biomedicine, ASD, that they share some information there. I do have a profile on Biomesight, which is one of these companies that provides the 16S testing. There are some links there. And you know, I have some homework to do. A lot of this stuff takes time. But my goal is to get the like minds together and pick this apart and see where we can bring improvement.
Dr. Bogner:
Very cool.
Alex Zaharakis, MA, MS, DABR:
There’s multiple things implicated. The microbiome, it seems to be a big piece, but it’s not the whole piece. But if you can get 10, 15%, 20% here, and then with another therapy, another 10%, improvement breeds improvement. I think that that’s the way forward.
Dr. Bogner:
Well, very nice. Alex, you’re on my website for anybody that wants to find out more, And I’m glad to be collaborating with you. I’m looking forward to what the future brings in regards to that. I want to thank you for your time. I’m sure we’ll have more discussion in the future.
Alex Zaharakis, MA, MS, DABR:
It’s been a pleasure. Thanks so much, Christian. Take care.
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