#93 The Best Gut Health Testing - with Dr. Ken McGrath
The Holistic Nutritionists Podcast
"Anything larger than bacteria isn't going to be evenly distributed in a stool, so the best gut microbiome test kits always require a large amount of stool to analyze. More than just a swab you need to have several grams or even 10s of grams of material to test before you really start to see parasites in a sample. And because parasites go through a cyclical shedding process, you also need to test stool samples across multiple days."
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In Episode 93 of The Holistic Nutritionists Podcast, Natalie Douglas and her guest, Dr. Ken McGrath (Clinical Liaison Manager for Microba), discuss the benefits of microbiome analysis and what is the best gut microbiome test available.
- The main types of gut testing available
- The difference between culture based stool testing and DNA based stool testing (+ what the heck it all means)
- DNA testing further explained + knowing which type of DNA based gut test is best
- What we get through the GP when requesting basic gut testing and what can and can’t that tell us
- Microbiome sequencing – what it does and doesn’t tell us
- The kinds of conditions, symptoms or presentations that can benefit from comprehensive microbiome testing
- How long it takes for our gut to change after implementing dietary and lifestyle changes
- How often we should get testing be done
- Are you looking for 1-to-1 support and a step-by-step healing process to overcome your chronic gut health issues? Take a look at my signature program, “Gut Rescue” today.
Dr. Ken McGrath
Clinical Liaison Manager for Microba
Hello and welcome to The Holistic Nutritionists Podcast, with your hosts Natalie K. Douglas, Thyroid Healer, and Kate Callaghan, The Holistic Nutritionist. Nat and Kate are degree-qualified dietitians and nutritionists, certified fitness instructors, speakers, and authors. If you love unfiltered banter, unedited bloopers, and authentic heart-sharing, then we are your ladies! Now it’s time to sit back, relax, and get ready for our latest tips on living your healthiest life possible.
Natalie K. Douglas 0:37
Hello, lovely friends. I thought I would jump in here quickly and introduce our podcast guests for today, which as always, I am very excited about and it is none other than Ken McGrath, who is the Clinical Liaison Manager with Microba. He obtained his PhD in biochemistry in molecular pathology from the University of Queensland and has a research background in microbial genomics including human microbiomes and metagenomic analysis. Ken was the manager of a DNA sequencing lab 10 years prior to join Microba and is a member of several international microbiome research projects, including global pathogen detection and monitoring, and Ken is now helping Microba bringing the latest gut microbiome technology to healthcare practitioners, and educate and inform them of how the information can benefit their patient management. And as you all know, I absolutely love talking about poo, and gut testing, and all things microbiome. So I found this interview really really fascinating, and I hope that you guys get a lot out of it as well. Just a quick reminder here that if you are interested in having any gut testing done yourself, or you currently have gut issues, or you’re just curious about the little bugs that are in there and want to know if your diversity is a good one or it needs some work, then I do offer the service during my one-on-one consultations. So feel free to book in a consultation or reach out, and I am more than happy, let’s be honest, more than happy to analyze your poo. So without further ado, see what I did there? Let’s jump into today’s interview. Okay, Ken, welcome to the podcast. The question we always start the podcast off with is, what is your current morning routine. And this may be a little bit different for you given that you are currently in quarantine.
Dr. Ken McGrath 2:40
That’s right. So, unfortunately, because of the whole global issue around COVID-19, I’m stuck at home Nat. I’m actually, I got back from New Zealand for a conference last Monday, it’s been nine days now. So doing the right thing and self-isolating. So my morning routine at the moment is quite limited but it still starts with coffee, you know, it’s important thing with caffeine to get the grain waking up and things and normally that our breakfast is some muesli and some yogurt, often or some some nut classes or something like that, typically. And that gets you sort of kick-started and on the way, but normally my routine would be taking our dogs for a walk two Staffies, Hercules and Zeus.
Natalie K. Douglas 3:21
Oh, I love it. Nice names.
Dr. Ken McGrath 3:23
Take for a walk down to the dog park most mornings. So that would be then, back home showering on the way into work. That’s my standard morning.
Natalie K. Douglas 3:34
I love it. I love it. And I love dogs. So someone else walking them at the moment, I assume?
Dr. Ken McGrath 3:38
Yeah, that’s right. My partner’s out walking.
Natalie K. Douglas 3:39
Yeah, good. I know the poor dogs in all of this day, that needs to like they probably don’t understand what’s going on. They have to stay home a lot of the time as well but.
Dr. Ken McGrath 3:48
They must think it’s the best thing ever. Like all of a sudden they have to stay at home every day all the time. They’re going, I don’t know what’s going on but this is amazing.
Natalie K. Douglas 3:55
Yeah, yeah, hundred percent. And probably the kids are a little bit like that too or a mix. I know a lot of my friends with children are equal, like equal parts going crazy versus like it would be hard to occupy your children for so many hours.
Dr. Ken McGrath
Yeah, well, I mean, it’s like school holidays, but with an unknown end to when it will go back. So, it is it’s very surreal. And at the same time very concerning what’s happening too so.
Natalie K. Douglas
Dr. Ken McGrath 4:23
Um, stay at home, wash your hands. I guess that’s the kind of message.
Natalie K. Douglas 4:26
Yeah, hundred percent. And I think it’s a timely thing that we’re talking about gut-related things considering how much connection there is between our gut and immune system. And we actually, as you know, spoke to one of your colleagues, Elena, on the podcast and we talked about, we kind of did a part one of talking about what actually makes a healthy gut and all those kinds of things. So listeners can go and have a look at that or listen to that rather when they want to. But today, I really wanted to dive into the testing side of things. I feel like even as a practitioner, navigating this space sometimes can be quite confusing, especially as testing evolves, and there are lots of different types of testing available. So where I thought we would start is on exactly that point, what type, what are the main types of gut microbiome testing available at the moment to the public?
Dr. Ken McGrath 5:23
Yeah, sure. So it’s really important to realize there are different kinds of tests available. And they really answer different questions about the gut. And they’re all useful in their own context. So they’ve all got some kind of purpose, I guess. But when someone says, I’ve done a stool test, I’ve had that done. That’s really not the right answer, because it’s what kind of stool tests they had done, that lets you know what kind of information they’ve got available. And we can start with some of the like, the really critical ones for health like the, the fecal occult blood screening the government does. So when you turn 50, the Australian Government sends out a swab, and it’s basically a dipstick, you put in the sample in your stool, you send back to a lab, and they test the stool but that’s actually testing very specifically for blood in the stool, and in fact, it’s an antibody test against hemoglobin. So that’s looking for the presence of blood, which is a marker for cancer. So that information is really important to understand. And if you get to one of those tests, so you get someone by the government do that, because it’s going to tell you if you’ve got any risks of cancer in the colon. The thing about that test, though, it won’t tell you anything about the bacterial community, it won’t tell you what kind of microbes you’ve got living inside you. And so to start to get some information about that topic, you need to look at something that specifically checks for the bacteria and other organisms that are in the gut. Now the most, I guess common, or the oldest method to do that is something called culture-based screening. So things like the agar plates, where they’ll take a sample and plate it out the stool sample and see what grows on culture, often referred to as CDSA test. These will essentially start to look at the bacteria but there’s a bit of a catch. We’ve learned recently that most of the bacteria that live in your gut don’t like growing on little plates and Petri dishes, in fact, they really only grow well in human guts. And so, if you’re using a culture-based approach, you’re really looking at a narrow range of organisms that can grow. Typically, it’s the pathogens and, and a number of reasons, including pathogens real-life oxygen, and that’s why they get into the body, and they use it oxygen to help live. And so, most of your gut is actually anaerobic, and filled with things that don’t like oxygen at all. And they work very really well on these carts and plates. So this is where you start to see a bias. So you don’t get the complete picture, you’re seeing a very small portion of the bacteria in a gut when you’re doing the culture-based screening. Still, it can pick up pathogens fairly well. So if you do have some kind of really nasty organism growing in you, like some of the E. coli strains and Shiga toxin-producing E. coli, it can be useful.
Natalie K. Douglas 8:16
And a question, two questions actually, just on that. So backtracking first to the tests that were sent out when we’re 50 to screen for bowel cancer. If it’s looking at where the presence of blood in stool outside of, of cancer, like if someone gets a positive result from that, besides of being like a marker of cancer, are there other things that it could indicate, like I’m thinking of patients who maybe have hemorrhoids, and there’s blood in their stool, like is it exclusive to a risk factor for cancer or can there be other reasons why there might be blood in someone’s stool on that test?
Dr. Ken McGrath 8:56
Certainly. So there are many reasons why blood might be in stool. And that’s why the result of a fecal occult blood test is not that you’ve got cancer, it’s that you should go and get checked, and often do a colonoscopy or some other kind of exploratory method to see what’s really going on. You can imagine even just a tear in the lining of the gut in the intestinal wall could result in blood coming in. There are lots of other reasons and you’ve alluded to a few as well, but it’s not a case of it always being cancer and the only the only reason.
Natalie K. Douglas
Dr. Ken McGrath
Yeah, it’s just okay, there is blood, let’s go and do further exploration in the hope that it’s not cancer and roll it out.
Natalie K. Douglas 9:37
Yep. Perfect. And my second follow-up question just on the culture-based stool testing. So with CDSAs, where often you know, it’s often said, or at least it’s what I’ve been taught is if you’re doing a CDSA, looking for parasites to do it on consecutive days, because parasites have life cycles. Is there truth to that, and if someone is actively looking for a parasite in their gut and is going to do a CDSA or a culture-based test, should they be doing a multiple days to stool sample?
Dr. Ken McGrath 10:13
So parasites are really interesting and there’s a lot of detail in about how to screen for them. We do know that many parasites have shedding cycles. And so often they really will be intermittently shared in a stool sample, because of that, that multiple tests or multiple samples across multiple days really are recommended for screening of those parasites particularly your blastocyst is another illnesses because you might not capture them. The flip side of all this is that blastocyst is probably isn’t a pathogen. And lots of studies out now, in fact, one just last year from Northern Europe showing that you see it more commonly in people who are well and less commonly in people who are unwell. And so, that aligns with, in fact, the Australian guidelines of testing for that is not that useful clinically. Now, if you dig even further beneath that, it turns out there are many different strains or even species of blastocysts that exist in the gut. And it may be that some of those strains or species are correlated with disease, and others are correlated with health. And so, when you have a test that just looks at the level of blastocystis, you don’t get to tease apart those kinds of correlations. And so, we may be in fact blinded to what’s going on, we just don’t know yet. It’s an active area of research and something that microbe is quite interested to because our test is able to start to differentiate these different blastocystis as types. And as we do that, we’re hoping we get enough information together to start to see correlations between certain types of blastocytis, and health or disease states. So from one question, we’ve gone quite deep down into the reasons here, but there are other parasites too. And, again, the same thing applies. Anything that’s kind of larger than a bacteria. So macroscopic levels really aren’t going to be evenly distributed in a stool test. And you should be looking at, firstly, a large amount of stool. So more than just a swab, you need to have, you know, several grams or even even 10s of grams of material to really start to see parasites in a sample. And then because of the cyclical shedding, you should look across multiple days.
Natalie K. Douglas 12:35
Yep. Yeah. And, you know, in Australia, you may or may not know the answer to this, and it’s fine. But in Australia, when someone goes to the GP and asked for a stool test, are they using culture-based stool testing or are they using DNA-based stool testing?
Dr. Ken McGrath 12:53
Look, the most common stool test for pathogens in Australia would probably be the Faecal Multiplex PCR.
Natalie K. Douglas 13:00
Yeah, that’s what I see a lot too. Is that DNA-based?
Dr. Ken McGrath 13:04
It is DNA-based, and it’s something called a panel. So a DNA panel or a PCR panel, what that is doing is that’s asking the question, are these 10 or 15 organisms in the sample? And so that’s a very specific question, rather than saying, what’s in the sample?
Natalie K. Douglas
Dr. Ken McGrath
Or actually going, are these exact list of species and organisms in this sample? And so what that does is people have designed something called PCR primers, that small bits of DNA that bind to very specific regions of those target organisms, and through the process of PCR can amplify the DNA from them. And essentially, then, if an organism is present, the DNA can amplify and you get a positive result. If that organism is not present, there’s no amplification, you get a negative result. And it does that for that specific list. So a very targeted panel of organisms, and you get yes and no answers if they’re there or not. Now again, that’s incredibly useful. If your question is, of these specific organisms in this sample that won’t tell you about the overall picture, not looking at the microbiome as a whole. So really useful for pathogen panels, not so useful for looking at overall gut health and the state of the microbiome.
Natalie K. Douglas 14:22
And with that, just to clarify, so when it’s a DNA-based test, you people don’t have to do multiple stool samples. Is that correct?
Dr. Ken McGrath 14:30
No, that the bacterial population is actually quite homogenized. And it’s quite interesting to see. Microba has done some work when we look at the same stool sample and swab the the end of the middle and the other end, and look at the homogeneity of that sample. And it’s an incredibly consistent, you do see some fluctuations and small shifts in the ratios of the organisms. So one might have a little bit more of one organism than the other end has a little bit less, but they’re typically all present across the sample. So that is what your microbiome is typically. It’s the same combination of organisms, but just slightly different ratios of those bacteria and other organisms.
Natalie K. Douglas 15:09
Fascinating. Okay, cool. Thank you for clarifying that. So, within kind of the DNA testing of the microbiome, are there different technologies used, and which one is kind of better, or, you know, more helpful for us?
Dr. Ken McGrath 15:27
So certainly, there are different tests. And if you think of that DNA-based tests, there really are differences and nuances in that, so start to understand what kind of test you’re using. We already talked about the PCR screens, the PCR panels, or multiplex PCR, that’s that specific test of is this list of organisms in a stool sample. To start to go beyond that, and understand the different organisms in total are there, you can move towards something that’s still a PCR-based test, but it’s a PCR for a gene called 16S. Now, 16S is the name of a gene that’s fairly common, it’s almost universal in organisms. And so pretty much all bacteria have a copy of that gene. And it’s conserved, which means that the genetic sequence is very similar across most bacteria, and even archaea. So the idea is that if you target that gene and amplify it up, and then use DNA sequencing, to read through the gene, you can start to identify what kinds of organisms you have in a sample. And this is the first way people were able to look at the whole community. And typically, you’re looking around, maybe, you know, somewhere between 50 to 80% of organisms, you can identify in this way. So you’re seeing a lot more of the picture, you know, it’s not complete, it’s not total, there are still black spots in 16S, and that comes down to those primers not being perfect for all organisms, they won’t bind to everything. They’re not, they’re not truly universal, but they’re they’re okay. So now you’re starting to look at that overall community structure. And you’re able to tell, you know, on a high level, the different combinations of bacteria that you have in the gut, this can be useful, but it’s still a little bit low resolution. And 16S is accepted that it’s at a genus level, not a species-level on identity. And what that means is, you could say, you can tell for an example that you have the E part of E. coli, the Escherichia part. You wouldn’t know which exact species it is, whether it’s coli or some other form. To get that level of resolution, you need to use a different technology. And that’s something that doesn’t just sequence a region of a single gene, you start to sequence the entire genome. And that’s something called metagenomics, which is the technology that Microba uses. So we’re not looking at PCR in a specific target, we sequence every fragment of DNA. We get out of the sample and then reconstruct the genomes of organisms to identify them, it’s really powerful because you’re no longer having a bias. So you no longer going to miss things that may not have been able to bind with PCR primers, you capture everything that’s there. And it gives you species-level identity. So you know, with absolute precision, the species that are in that sample, but beyond that, you know what they’re doing, you’re not just looking at that identity region that 16S part of the gene to get the name of the organism. Sequencing all the different functional genes that constitute that organism’s genome. So an example, you can tell if an organism is able to produce butyrate or not because we’ll be able to see the gene that produces butyrate.
Natalie K. Douglas
Dr. Ken McGrath
Well, you could tell if an organism is going to produce lipopolysaccharide, which has an inflammatory compound or not, because we’ll be able to detect the gene that produces LPS. And with that level of detail, you’re really getting a full functional profile back of the microbiome. And it’s funny that you can almost stop learning all the Latin names, and not have to pronounce things like for coli, bacteria, and prostate.
Natalie K. Douglas
Dr. Ken McGrath
That’s not the important bit. The important bit is it’s a butyrate producer. And that’s what’s going to keep your gut healthy and happy. And even to the point of some of these species that don’t have names yet, right? That are undiscovered, that Microba season the data. We actually can still tell, well, we’ve got no idea what to call it, but it’s a butyrate producer because we see it has the gene that produces butyrate. And so you really start to get the full complete picture of what’s going on in a person’s gut. And that functional information is so powerful when you’re really trying to understand your patient’s microbiome and understand where their strengths or deficiencies might lie.
Natalie K. Douglas 0:16
And I, I think that’s so important, because I think for, at least, like naturopathically and nutritionally there, and even medically, like, there has been this real kind of, in my experience and opinion, too much of this, like, kill kill kill approach, as opposed to looking at the terrain. And I think there’s been many instances where I’ve had patients come to me, after going through other several other practitioners. And for example, like you were saying before, at the first sign of like, there’s blasto in their stool, straight on to antibiotics or really strong antimicrobials when perhaps it’s not a problem, or you know, perhaps if we rebalance the microbiome it doesn’t become anything that is problematic. And I think that we more, the more we focus on the terrain, the I feel like the healthier our gut becomes, in an oversimplified sense. Has that been your experience in relation to, do you feel like that it’s more important to look at the terrain, then just go off to killing things that we just happen to find?
Dr. Ken McGrath 1:26
Yeah, so we like to think of it as an ecosystem or a rainforest where you’ve got all these different animals and plants and butterflies and bugs and lizards growing in a community with lots of diversity, ideally, and that’s a healthy ecosystem. And if you’ve got like a couple of weeds that are creeping in on the side, typically, they’re not going to be able to do much, because every niche in that ecosystem is occupied. And it really won’t be able to grow much, that’s not a concern. If you clear the space, I’ve got a bulldozer and cleared an entire region of that rainforest and left it vacant, the weeds have a free space to jump into and start to grow into. And that’s where problems and dangers can occur and the gut is very similar to that. So within that balance, we may think that encouraging the growth of the good things is a really strong way. However, if you’ve got a pathogen if you’ve got something really nasty in your gut, then getting rid of it is still important too. So I think there are very clear cases where antibiotic usages is needed and warranted, certainly. But in the absence of pathogens or true pathogens. Certainly, you can support your microbiome by growing up the healthy guys, which will crowd out and essentially reduce the numbers of the less beneficial species. And that’s a really powerful approach and one that Microba does support.
Natalie K. Douglas 2:51
Hmm, yeah. I love that and completely agree. In relation to looking at, like the testing methodology that Microba use, does it pick up parasites, or is that exclusive to looking at more culture-based or the PCR testing?
Dr. Ken McGrath 3:08
So Microba’s technology, because we’re looking at all the DNA in a sample. We do detect parasites if they’re in the sample but it goes back to what I was talking about earlier that we sample at Microba such a small amount of stool, it’s a swab of a bit of used toilet paper.
Natalie K. Douglas 3:25
Yes, it is very tiny.
Dr. Ken McGrath 3:27
Natalie K. Douglas
Yeah, it’s so convenient.
Dr. Ken McGrath
It’s not messy, and it you know, it’s not something that people avoid, because it’s it’s not an issue but when you’re talking about such a small amount of stool, the chance of there being a parasite in that even in an active infection is low. And so we would even say, look, if this parasite is there, it will be in the report that you may not capture it. So look at tests that actually sample larger amounts of stool across multiple days, because then you’re really going to account for that heterogeneity in the sample, as well as that cyclical shedding that many parasites exhibit.
Natalie K. Douglas 4:07
Hmm, yeah. Perfect. So in in like a, an ideal situation. If someone was, for example, really symptomatic in relation to showing presentations of what might be a parasitic infection, doing the culture-based testing across multiple days and doing microbial alongside it would be perfect because you’re picking up the parasite and also you’re looking at the terrain because that’s also a really important part of treatment, is that correct?
Dr. Ken McGrath 4:38
And they’re answering different questions.
Natalie K. Douglas
Dr. Ken McGrath
So if your question is, is there a parasite present? Things like your culture or even some parasite PCR tests would be appropriate but if your question is, what is the microbiome doing, and is it doing the right functions for this patient or not? That’s where Microba really comes into its own.
Natalie K. Douglas 4:55
Yeah, and I think more and more as we learn more about the microbiome and how many roles it has, even outside of just what we first think of, you know, as gut health being I mean, its relationship to the immune system to mental health to so many different things. So what kind of like in that same vein, what kind of conditions, symptoms, or presentations would this type of testing be helpful in, like, what’s even your experience at Microba about the types of people that are looking to look at their microbiome?
Dr. Ken McGrath 5:32
It certainly goes well beyond the gut. And I think that’s one of the most amazing things in the last sort of 5 to 10 years. We’ve realized that the gut microbiome is not just related to gut-based conditions and that pretty much every system in the body seems to have some kind of connection to the gut. We can think of the gut’s involvement in mental health. And so the gut-producing compounds like butyrate, and propionate, which have been shown to correlate with offsetting anxiety and depression, even serotonin production that occurs in the gut and 90% of the body’s serotonin is made in the cells that line your intestine. Microbiome can produce GABA, which is a neurotransmitter, or even consume it and break it down. These are the kinds of connections that are emerging, you’ve got the connection now with liver disease in the gut microbiome, and nonalcoholic fatty liver disease are now having some kind of connection with certain organisms in the gut that may be triggering that, and not necessarily through alcohol production too, there seems to be some other mechanisms at play there. You’ve got the skin condition in the microbiomes now having correlations. And so, certain profiles of the microbiota tend to be related to atopic dermatitis. In fact, one of the bacteria that’s often thought to be a really beneficial one. And there’s a certain species of that now, that has been shown to be connected to dermatitis. And so, that kind of realization that, oh, wow, just because it’s got the same kind of name doesn’t mean it’s a good bacteria to have. When you get that level of those genes and those functions and what every strain is doing, that’s when you start to see what’s really happening.
Natalie K. Douglas 7:20
Yeah, and so. So helpful, so helpful for, for treatment, for understanding, and I think the really exciting thing is that I was talking to Elena about is that we have so much, you know, ability to to change the terrain through what we choose to consume. In terms of food, even if we even just start there. There’s, it’s I love, I’m a big fan of testing that can change treatment. And I really think that gut microbiome testing like Microba, where we are looking at that whole terrain, this is where food as medicine can be so beneficial in actually causing a shift in that in a really positive way and understanding what’s going on or at least beginning to because the gut is just still this evolving field of, you know, of just new things coming all of the time, which I’m sure you guys are at the forefront of even just seeing all these different samples all the time.
Dr. Ken McGrath 8:17
Certainly, and it’s exciting to know that food is the primary driver of your microbiome and the profile you get back. And so through food, you can really have quite a powerful tool to shift someone’s microbiome. And now we’re not to the level of being able to say, with absolute certainty, or here’s your profile, so this exact diet is going to shifted in this exact direction. There’s still a little bit of trial and error that we had there. But you’ve got the right tools in your hands and what Microba does give you are these directions to start trying. So for example, if you’re low in butyrate production, we know that butyrate production is driven by resistant starches. And so by focusing on that area, and things like legumes, or cooked and cooled starches can really start to focus on that topic, and drive the bacterial production of butyrate in the gut and start to correct that. And, and there are plenty of examples like that Microba’s report actually gives you food suggestions to start to try an approach to make the corrections in a person’s gut microbiome and really start to bring about that change. I mean, foods are a bigger driver of change that even supporting antibiotics.
Natalie K. Douglas 9:29
Yeah, it’s fascinating, and it is a really helpful report that you guys create. I really love it. It takes away a lot of the hard work for us practitioners actually. It really presents it fantastically. So in in terms of if someone is doing testing, and they’ve done a Microba test, for example. And then they’ve implemented the changes that have been suggested by the test results itself or by a practitioner that’s helping them with that. How long can we actually expect to, for it to take to see changes in the microbiome that’s kind of worth reassessing? Like if someone wanted to assess progress, how long would they wait between testing?
Dr. Ken McGrath 10:14
So the answer to this is more about human psychology and behavioral change than it is about the microbiome. The microbiome can change quite rapidly. So if you completely and fundamentally change your diet, within a couple of days, you’ll see changes and that will persist, and the changes will become stronger over time. The thing is that, what you’re really wanting to see those is the person has taken on the suggestions and really made them part of their lifestyle. And it’s not just a fad that they’re doing salad for a week and their back on their old diet. And so for that, we actually recommend around three months is the appropriate time to wait to retest because, at that point, that person either has or hasn’t adopted those changes as part of their lifestyle, and really understand if that change is something that set him down, it’s part of who they are, or if they’ve just gone back to their old ways. And so three months is the recommended kind of time frame that we would say to to make the changes and have them persist beyond just a short-term fad.
Natalie K. Douglas 11:16
Hmm. I love it. And I’ve just thought of a completely random, not random but a backtrack question that I forgot to ask you before that popped to mind that I know people would be curious about. So we’ve talked about, you know, Microba testing, picking up a lot of different bacteria. Does it pick up any kind of yeast or fungus, or fungi, or viral pathogens or anything like that?
Dr. Ken McGrath 11:42
Yes. So again, coming back to the fact that Microba sequences all the DNA in a sample. So we do pick up yeast and other fungi. They’re actually not that common in the gut and it’s, it’s challenging our thinking about the prevalence of some of these bacteria. It may be the case that you sort of have fungi are present at really low levels below the detection limit of Microba’s test, which is, you know, it’s down to around .05 percent at the moment of abundance, and we’ve got new technology coming out, that will bring that down closer to .01 in the future. And that’s, that’s a scaling thing of how much DNA sequencing we do to produce it, as well as the analysis techniques we use but we do see yeast, and we certainly pick them up and report them in our reports of saccharomyces and other organisms. On the viruses’ side of things, we do have the capacity to detect and report DNA-based viruses. The tricky thing is it’s such an understudied area, that currently if we started reporting it, it would make no clinical sense. Most of the viruses are actually bacteriophages, so they’re are viruses that infect bacteria. And in terms of the science behind it, it’s an unknown space. We don’t even know how to classify some of these viruses yet. So Microba has a project on where we are trying to build a database and we’re doing this constantly. But until we have that database complete, and we’re able to really make sense of that viral world, we’re not going to be recording information.
Natalie K. Douglas
Dr. Ken McGrath
It is a topic that we want to get released in the product. And so, it’s an active area of research for us. And hopefully in a few months’ time, we’ll have this viral element in our report. I think it’s also prudent to note that we won’t be reporting RNA-based viruses because they’re not looking at the RNA side of things.
Natalie K. Douglas
Dr. Ken McGrath
And so at least in the current climate, the the virus that’s getting the headlines at the moment is an RNA-based virus. And so that would not appear in a DNA-based test.
Natalie K. Douglas 13:49
Yeah, that makes sense. And when you’re, when you’re looking at the results, so when someone gets their report, and they’re looking at the result, you know, when it’s giving you an idea, as most tests do, especially functional tests, where you see it within, you know, are you low, are you average, are you high? Where are you pulling that data from, like, who is the, who is the population that is normal, that dictates those ranges? Is it based on the kinds of that like all of the data that you’re getting or is it some some other data?
Dr. Ken McGrath 14:20
Yeah, so Microba’s comparison group is actually a defined healthy cohort where we’ve gone through our information and found people that are at least self-reporting to be quite healthy. And so there’s a number of criteria, including they’re in a certain BMI range, that they’re eating fruit and vegetables every day, that they’re not smoking, they haven’t had antibiotics for the last six months. They’re not on any ongoing medications and haven’t had any major medical conditions. That’s a sort of a general overview. So arguably, fairly healthy, also some physical activity, so they’ve been doing a certain amount of physical activity each day. Currently in our healthy cohort. I think it’s around 150 people, we’ve got that group, and but it is something we update and we expand that increase all the time. So there’s probably an iteration coming out soon that will increase the numbers.
Natalie K. Douglas
Dr. Ken McGrath
We’re finding now, we’re at the point that as we increase the numbers, the values are changing too much. So we are approaching some kind of consensus on what a person or a healthy person’s microbiome looks like. And the key thing is that’s functionally, all of those healthy people have very different microbiomes in terms of the species that are in them and are like fingerprint really, they’re unique to them. But when we start to look at the functional capacity, there is far more consensus. And we know that a healthy microbiome does produce butyrate and produce propionate. They don’t produce much LPS, they don’t produce much trimethylamine, and all those kinds of things. So other people say we don’t know what healthy is, that’s true in terms of species, but it’s starting to form now that functionally, a picture of health doesn’t merge.
Natalie K. Douglas 15:56
Yeah. Sorry, you continue.
Dr. Ken McGrath 15:57
Yeah, in our reports, as well, you do have the option of changing away from that healthy group to the entire testing population. And so this is actually many thousands of people that you want. There’s a sidebar that a lot of people aren’t aware of that actually lets you change to specific age groups or even gender. So you can look at a male microbiome profile compared to female, and that is actually using our entire cohort data. So several thousand people in there. The issue with that is that those people mostly have come to Microba because they’ve got issues.
Natalie K. Douglas
Dr. Ken McGrath
So you’re not really looking at a healthy group anymore. You’re looking at just the testing population, which does bias towards unhealthy people. So that was why my crevasse default report doesn’t show that comparison because we think it’s a good indicator of where a person sits for their targets and their goals to be healthy.
Natalie K. Douglas 16:51
Yeah, and that makes sense because, you know, the goal is to be healthy and and functionally well. So I like that it’s done that way because I think that it’s, I mean, a really example, a really common example is a lot of a lot of labs that, you know, people go to do blood tests that several of the reference ranges that are developed for certain markers are based on that labs, you know, population, and you know, what is normal within that, and I think that most people going to the doctor’s office aren’t going because they feel amazing. And that’s not to say, I know that that doesn’t isn’t true across the board for every single reference range for every single test, but it certainly does still happen. And I think, you know, looking at it, from the view of what does a healthy gut look like, is just so, so helpful to at least have something to aim towards. So I really really like that. Fantastic. Well, that is all of the questions I have for you. I mean, I could ask you a billion more but I think that’s given us a really really good understanding. And I will pop the links to the Microba website for people to be able to go on there, have a look, order test kits if they wish to. And yeah, start to analyze their microbiome and, and develop all of the understanding and actionable steps they can take to improve that because I think that in a time where a lot of us are concerned about our immune system are wanting to optimize our health. It’s I always think that good health starts from the gut, that’s for sure.
Dr. Ken McGrath 18:31
Certainly, and I think a lot of people are going to be really focusing on health in the coming months and years certainly so. Microba’s testing being available at home and being really well supported digitally, because the reports are digital, and you can use them in remote services quite well. I think that’s quite a useful approach now, as people will be isolating a bit more, and I think health will move to digital forum more so in the coming months and years.
Natalie K. Douglas 19:00
Yeah, and I would be happy, self-isolated, analyzing microbiome tests. I’m a big fat nerd. And I love when someone’s report comes in any of my patients. So it’s, and it’s just so helpful. So thank you for joining us and thank you for all the work you’re doing at Microba. And I’m sure we’ll get you back on the podcast as more information comes to light on the microbiome and as Microba grows as a company with their testing. So thank you so much.
Dr. Ken McGrath 19:29
Wonderful. Thanks, Nat.
Thanks for tuning in to The Holistic Nutritionists Podcast. Remember, we love to make the show relevant to you. If you have any questions or topics you’d like us to discuss, just submit them to [email protected] and we’ll get them answered for you. Also, don’t forget to subscribe, rate, and review the podcast on iTunes and share it with your friend. And if you’re looking for more info about how we can accelerate your journey to your optimal health, you can find me, Nat, over at NatalieKDouglas.com, and Kate, at TheHolisticNutritionist.com. See you next time!
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Natalie K. Douglas | Thyroid Healer
Natalie K. Douglas ("Nat") is a Holistic Dietitian and Nutritionist dedicated to Thyroid, gut and hormone healing.
Nat shows stressed, burnt out, overwhelmed women how to value their worth again, change their mindset habits, prioritize healing, and reclaim their vitality. Guaranteed.
Her clients say she’s the right girl to see if you’ve tried the conventional approach and nothing has worked.
Kate Callaghan | The Holistic Nutritionist
Kate Callaghan is a Holistic Nutritionist, Personal Trainer and Lifestyle Coach who specializes in women's hormone healing.
She recognizes that there is no “one size fits all” diet or “magic bullet” which is going to cure all illnesses.
She focuses on having a thorough understanding of your personal goals, needs, likes/dislikes, support networks and lifestyle in order to create a food and lifestyle approach that suits YOU.
Dr. Ken McGrath | Clinical Liaison Manager for Microba
Dr. Ken McGrath is the Clinical Liaison Manager with Microba. He obtained his PhD in Biochemistry and Molecular Pathology from the University of Queensland, and has a research background in microbial genomics, including human microbiomes and metagenomic analysis. Ken was the manager of a DNA sequencing laboratory 10 years prior to joining Microba, and is a member of several international microbiome research projects, including global pathogen detection and monitoring. Ken is now helping Microba bring the latest gut microbiome technology to healthcare practitioners and educate and inform them of how the information can benefit their patient management.