Special Message for New Frontiers Listeners
Download the GI360 Sample Report and follow along with the podcast to uncover clinical pearls that can transform your patient care.
The centrality of gut health in total body health and aging means it’s a key topic for us to keep revisiting and updating our knowledge on. For instance, how confident do you feel about interpreting analytical indices such as phyla distribution, dysbiosis index, diversity score, as well as the myriad bacterial populations that can be resident in the GI tract? Join me and Dr. Julia Malkowski as we dive into advanced stool testing and how the insights gleaned from the GI360 test can tell us a lot about our patients’ health and lifestyle (ever wondered how the carnivore diet, long-term use of GLP-1 agonists, or chronic stress impact the gut?).
We also explore keystone bacterial species and their impact on systemic health, what is better than fiber for increasing microbiome diversity, different testing methods including the impressive MALDI-TOF Mass Spectrometry Technology and a ton of clinical pearls on tackling those report findings in clinical practice. There is something for everyone in this excellent conversation with Dr. Julia Malkowski, from the newly-minted to the seasoned functional medicine practitioner, and health-savvy consumers too. Tune in, grab your GI360 Sample Report and get ready to take notes!
~DrKF
In this episode of New Frontiers in Functional Medicine Dr. Kara Fitzgerald hosts an in-depth discussion with Dr. Julia Malkowski on the Doctor’s Data GI360 report, a cutting-edge tool for assessing gut health. Together they explore the intricacies of the gut microbiome and its far-reaching effects on overall health. Learn how the GI360 test offers a comprehensive view of gut health by analyzing microbiome composition, diversity, dysbiosis, and various gut-specific markers. Dr. Malkowski provides expert insights on interpreting the different components of the report, from phyla distribution to specific bacterial populations. She reviews the influence of dietary patterns on gut health, the impact of chronic stress on the microbiome, and the connections between gut health and systemic conditions, providing clinicians with actionable insights for patient care.
In this episode of New Frontiers, learn about:
- Latest Insights on Comprehensive Stool Testing: A deep dive into the advanced GI360 test, including how MALDI-TOF technology revolutionizes stool culture testing by offering advanced bacterial identification.
- Managing Self-Treatment Risks from Restrictive Diets: How carnivore, keto, or highly restrictive diets implemented professional guidance can impact the gut microbiome and gut health markers and strategies to mitigate negative outcomes.
- Importance of Microbiome Diversity: Interpreting the GI360’s Diversity Score and why higher diversity is generally associated with better health outcomes,
- Athletes, Chronic Stress, and Secretory IgA: Discussion on the impact of chronic physical (and psychological) stress and lower secretory IgA, leading to infections and gut imbalances.
- The Impact of Diet and Dietary Patterns on Microbiome Composition: How dietary patterns (e.g., Mediterranean, vegan, carnivore) produce distinct microbiome profiles and why fermented foods may be more effective than fiber alone in increasing microbiome diversity.
- Akkermansia as Keystone Species: Interpreting imbalances in Akkermansia muciniphila which could point to poor mucosal barrier integrity.
- GLP-1, Dysbiosis, and Obesity: Exploring whether dysbiosis may be contributing to the obesity epidemic by inhibiting natural GLP-1 production, and the impact of widespread GLP-1 agonist use on gut health.
- Chronic Stress, Intestinal Permeability, and the Microbiome: Discussion on microbiome imbalances, increased intestinal permeability, reduced secretory IgA, and compromised pancreatic enzyme production caused by chronic stress.
- Accurate Yeast Detection in the Gut: Novel insights into detecting yeast overgrowth (both in the colon and as SIFO), including the best evaluation methods.
- Interpreting Lab Results with Clinical Context: The importance of considering a patient’s diet and lifestyle when interpreting gut test results.
Dr. Kara Fitzgerald: (00:00:02) Hi, everybody. Welcome to New Frontiers in Functional Medicine, where we are interviewing the best minds in functional medicine and of course today is no exception. We are going to be doing a deep, deep, deep dive into the Doctor’s Data GI360 report. In fact, hit pause, go to the show notes page, and grab the sample report and have it in front of you so you can move through that document with us and then you’re really going to get to understand the utility of this particular lab.
Dr. Kara Fitzgerald: Let me introduce you to my expert. You can see her sitting next to me if you’re watching on YouTube. This is Dr. Julia Malkowski. She’s a ND and DC, and she has a bachelor’s in science. She began her career in functional medicine upon seeing excellent results with her infant son and then she went on to complete her bachelor’s degree in biomedical science, her doctorate in chiropractic, and her doctorate in naturopathic medicine, all while raising a healthy family. She remains committed to optimal health on both personal and professional levels, serving as a staff doctor of Clinical Education at Doctor’s Data and she maintains her own private functional medicine practice, Docere Health, outside of Chicago. Dr. Malkowski, welcome to New Frontiers.
Dr. Julia Malkowski: (00:01:25) Thank you so much for having me here. It’s an honor to be here and I look forward to having this conversation today.
Dr. Kara Fitzgerald: (00:01:31) Yeah. So again you guys, hit pause and grab the sample report because we’re going to dive in from the top looking at the GI360. There’s a saying from many moons ago, “All disease begins in the gut.” Now, we know from paper after paper the after paper, really validating the gut-systemic connection. Everywhere in the body is influenced by the microbiome. Talk to me about what we continue to learn in this arena, areas that you’re interested in, and how the GI360 works to really help us perceive what’s happening in the gut that may be influencing systemic health.
Dr. Julia Malkowski: (00:02:18) Absolutely, great point. Certainly the father of medicine, Hippocrates, would marvel at the GI360 and the technology that we really do have at our fingertips to understand this connection and also as a tool for our patients to understand.
Dr. Julia Malkowski: (00:02:33) The GI360 represents the microbiome. It represents microbiome abundance, diversity, dysbiosis, it can give us clues about intestinal permeability, it can give us clues about the patient’s diet, it can give us clues about compliance with our dietary recommendations, and it really does provide a tool to understand this connection. We know the gut microbiome is linked to chronic metabolic diseases, which account for 90% of healthcare expenditure right now, so this is a consideration that we can really help our patients with. We also know that Western diets, specifically the standard American diet, are connected to chronic disease, and the gut microbiome is a link right there.
Dr. Kara Fitzgerald: (00:03:20) Awesome. You just made the point that we can see what our patients are eating. It’s extraordinary. Many years ago when I was in the lab, we used to see a lot more trans fats. So on the fatty acid report we would look at omega-3s, omega-6s, trans fats, and saturated fats, and there were a lot more trans fats than we’re seeing today, actually. The industry has gotten a little savvier about removing them. But I could immediately see if I thought my patient was eating well or not just by looking at that data. Now, you guys have really created this cool opportunity for us to see how food and other interventions—medications, and so on and so forth—are influencing the gut microbiome. So speak to that. And again you guys, open your sample report now. I’ve got mine.
Dr. Julia Malkowski: (00:04:17) Yeah, absolutely. This is a great tool to understand what the research is telling us about the microbiome, about phyla, about specific keystone bacteria, and about functional groups of bacteria—we call them functional guilds of bacteria and they work together—so you can understand exactly where your patient is on these matrices that we’re hearing about in research.
Dr. Julia Malkowski: (00:04:44) The first thing we see on the profile are the six main phyla that are well-researched and you can actually tell your patient’s levels of these phyla. This is important because some phyla are more inflammatory, while others have anti-inflammatory properties. So you want to see not only where your patient is with those phyla, but where your patient is in regards to the relationship between the phyla and that’s when we’re talking about diversity. That’s how they interact with each other and lay with each other. You don’t want a heavy load of pro-inflammatory phyla such as Proteobacteria and maybe Bacteroidetes, and you want an abundance of those healthy, anti-inflammatory phyla, such as Actinobacteria, Firmicutes, and also Verrucomicrobia.
Dr. Kara Fitzgerald: (00:05:30) Having the sample report open, there’s a cool hexagon with these phyla represented. At a glance, I can see this individual is biased toward a more pro-inflammatory phyla distribution. Then, as we look down at the dysbiosis index below we can see that this individual has some pretty serious dysbiosis.
Dr. Kara Fitzgerald: (00:05:58) So, talk to me about the nutrients influencing this. I guess at a glance, we can see it’s biased toward pro-inflammatory. If this is all we had, what would we do? How would we change what they’re eating to shift this diversity summary?
Dr. Julia Malkowski: (00:06:20) Exactly. As you’re mentioning, this is at-a-glance information and you can tell that right away from that hexagon. It’s also a great tool to show your patient their results.
Dr. Kara Fitzgerald: (00:06:30) What are they eating? Tell me about that.
Dr. Julia Malkowski: (00:06:34) So, their “web” is the white reference, and it’s superimposed on the green hexagon, which is the normal biotic reference range. For this patient, they are lower in the top left corner for Actinobacteria—you can see that point of the web is pulled in.
Dr. Kara Fitzgerald: (00:06:51) Very low. Yeah.
Dr. Julia Malkowski: (00:06:52) The same goes for Verrucomicrobia in the top right corner and that’s pulled in as well. We like to think about what these phyla enjoy eating. For Actinobacteria, that top left hand corner, they like eating vegetables and soluble fiber is in that category as well, but really vegetable consumption, especially cruciferous vegetables. And then the top right hand corner, Verrucomicrobia, they really like polyphenols. With the polyphenols we’re thinking about Akkermansia muciniphila and we’re also thinking about pomegranates, and those types of things. So, this individual is deficient in vegetables and polyphenols.
Dr. Kara Fitzgerald: (00:07:34) Interesting. So you could just at-a-glance tweak this. I want to get to this, but I’ll put a pin in it for now and we’ll further analyze what’s going on in this individual based on their lab data. If you didn’t have any data other than this, would you be assuming this person is eating a standard American diet, maybe higher in fat and processed, nutrient-void carbs? What does this data tell you they’re probably consuming?
Dr. Julia Malkowski: (00:08:13) Potentially. One of the key findings for the standard American or Western diet, high in processed foods, is that bottom right hand corner, Proteobacteria, will be pulled down and skewed toward that section. You will see that quite often for patients on a standard American diet. That’s a red flag, if you will, for this diet. Conversely, you will also see lower Actinobacteria and Verrucomicrobia as well. Yet, you can see nuances in some individuals, even in vegan diets. When we think of vegan or vegetarian diets, these are highly educated or health-conscious individuals. Sometimes you will see lower levels of Actinobacteria and Verrucomicrobia because they are eating processed foods and they’re not eating those whole foods.
Dr. Kara Fitzgerald: (00:09:00) That’s really interesting. So you could actually see higher Proteobacteria or Firmicutes in vegans too. Then you’d say, okay, we know you’re a vegan, but you’re not actually eating vegetables. Interesting. So they’re eating, like, lab burgers and a bunch of pasta…
Dr. Julia Malkowski: (00:09:21) Yeah. Toast.
Dr. Kara Fitzgerald: (00:09:22) That’s so fascinating. We’re jumping ahead to a question I had for you later, but what does a carnivore diet look like?
Dr. Julia Malkowski: (00:09:30) Oh, good question. With carnivore diets, I tend to notice dysbiosis. We’ll talk in a minute about the dysbiosis index, but as you might consider, these individuals are not consuming produce and they’re not consuming legumes , so they tend to be lower in Actinobacteria and Verrucomicrobia. They tend to be lower in Bacteroidetes and Firmicutes, but that’s a nuanced phyla because there’s a lot of bacteria within there. And it’s certainly skewed down toward Proteobacteria, as we mentioned. These are very inflammatory profiles. And then we’ll talk about other findings on the report, but I do note, and you’ve seen this in your practice as well, that sometimes individuals are trying to self-treat their IBS or their IBD with a carnivore diet, because it’s that ultimate elimination diet, but they’re actually making their situation worse as you can see on the phyla there.
Dr. Kara Fitzgerald: (00:10:31) That’s an incredible pearl. Without question I will use a very strict keto diet when I’m trying to aggressively address certain conditions—maybe somebody who’s on the diabetic continuum. We’ve used the Tom Seyfried calorie-restricted ketogenic diet. We’ve used a similar dietary pattern when we’re treating individuals with refractory epilepsy and so forth. I’ve also seen research on keto diets for bipolar disorder. So, it seems to me that these dietary patterns have their place, but when you and I were talking offline, you talked about pulsing it or paying attention to how the intervention is influencing the microbiome. It makes sense that when we do an extreme dietary pattern, obviously we have to pay attention to nutrient repletion systemically and we really need to be paying attention to the gut microbiome as well. If symptoms warrant, i.e. if we can increase veg in this individual and maybe lower the quantity of protein, we could switch this pattern and really make this prescription safer. What are your thoughts on that?
Dr. Julia Malkowski: (00:11:58) Exactly. I wholeheartedly agree with that. I certainly agree with the concept of cycling, and I certainly agree with addressing an individual’s motivation for a specific diet. You’re speaking to medically recommended diets, and that make sense. A lot of people are hearing anecdotal evidence about carnivore and ketogenic diets and doing them without the guidance of a physician.
Dr. Kara Fitzgerald: (00:12:20) Yeah. And I’m sure you have seen that there can be some pretty horrific fallout when someone’s adopted this dietary pattern long-term. We could have our whole conversation on it. What you guys have created over at Doctor’s Data is awesome– this at-a-glance tool. I love it. And then we can see below the dysbiosis index. It’s no great surprise that this individual is raging with dysbiosis, and accompanying that is a drop in diversity. So speak about that. Is the dysbiosis severe in this individual? What do you commonly see? And then, what does the diversity score tell us?
Dr. Julia Malkowski: (00:13:06) Absolutely. These are excellent matrices. The dysbiosis index is a marker that’s characterizing the information about abundance and diversity, and looking at the key bacteria we’ll talk about later, such as Akkermansia muciniphila and Faecalibacterium prausnitzii. Those are really heavy hitters in the gut microbiome. Their populations are heavily weighted in the computed algorithm to create the dysbiosis index, but it is looking at all the bacteria detailed on pages two, three, and four of the report. The way GI360 is organized is that the first page has all of the data, the pertinent findings and that first piece of information we have is phyla. That’s broad information and then we get more and more detailed.
Dr. Julia Malkowski: So, the dysbiosis index is there. As you mentioned, the scores go from 1 to 5. A score of 1 to 2 indicates a normal, healthy gut, which is really where you want your patients to be, 3 is moderate, so you could consider interventions at this point, and then 4 to 5 is dysbiotic. And as this patient shows, the dysbiosis index of 5 is significant. This is significant dysbiosis. This score specifically has been studied in populations with IBS, IBD, obesity, diabetes… And then you’ll find many peer reviewed journal articles about microbiome dysbiosis in general so you can extrapolate this information to those concepts.
Dr. Kara Fitzgerald: (00:14:31) And, conversely, you and I were talking about it offline, when we see a diverse gut and we see a lot of those keystone players like Akkermansia, the dysbiosis index is lower, and that’s associated with longevity.
Dr. Julia Malkowski: (00:14:49) Yeah. That’s one of my favorite findings about the Blue Zone information that we have now: maintaining microbiome diversity for longevity is really important.
Dr. Kara Fitzgerald:It’s cool.
Dr. Julia Malkowski: Yeah. Microbiome diversity is also on the GI360, and that’s a really unique marker.
Dr. Kara Fitzgerald: (00:15:08) So, walk us through the diversity score and what you’re seeing in this individual. But by the way, before we go into diversity, with the dysbiosis index– You’ve looked at thousands of these reports as an in-house clinician and educator at Doctor’s Data and you have your own practice as well. What extent of dysbiosis do you see routinely?
Dr. Julia Malkowski: (00:15:35) Yeah, it’s a fairly nuanced topic because I do tend to see the cases involving metabolic syndrome, where there’s that consideration of symptoms, as well as GI conditions, so I really see the scores of 3 or 4, sometimes 5, sometimes 2, and 1 is not too common. I have some excellent cases of 1 where an individual has remediated a standard American diet. Generally in those cases it’s going to be on a recommended, potentially modified Mediterranean diet, which has a lot of good components that are very nourishing to the gut microbiome.
Dr. Kara Fitzgerald: 00:16:17 Oh, that’s cool. Good to know. All right. And so the diversity score.
Dr. Julia Malkowski: 00:16:22 Yeah, diversity is really important and it’s not a well-known marker. Right now, there are over 5,000 peer-reviewed journal articles associating microbiome diversity with health outcomes so it’s actually well studied. Clinically, though we’re not applying it as much as we could yet. The diversity score in the colon is like any ecosystem. Think of the diversity of the rainforest or the Great Barrier Reef. You want an abundance of multiple bacteria in your colon. It’s the same concept. It’s a foundational component and is not only associated with GI health directly but it’s also associated with systemic physiology. This has been studied in conditions such as chronic disease, colic in infancy, extroverted behavior, and disordered eating. We know that individuals on a standard American diet display decreased microbiome diversity and individuals with higher microbiome diversity previously, before immigrating to North America, they end up with a decrease in microbiome diversity, and this actually exaggerates with each succession of each generation.
Dr. Kara Fitzgerald: 00:17:37 Oh, that’s pretty interesting. Wow.
Dr. Julia Malkowski: 00:17:39 Yes. And then one last thing about diversity that I think is important—there is one study where they noted that individuals with lower microbiome diversity did not show a benefit from probiotic therapy. We’re using probiotic therapy quite ubiquitously in our clinics, and I think it’s important to be aware of that. (Correction: probiotics do not increase microbiome diversity, regardless of baseline microbiome diversity.)
Dr. Kara Fitzgerald: 00:17:59 So if that’s the case, how are we going to best influence the diversity score?
Dr. Julia Malkowski: 00:18:07 Good question. That same group of researchers did another study where they took two groups of individuals and allocated them to either a high-fiber group or a high-fermented food group. They were able to study these individuals over a 12-week period. The individuals in the high-fiber group needed to add 20g of fiber per day, and the individuals in the fermented food group needed to add at least two servings so by the end of the study, they were averaging about 4 to 6 servings of fermented foods per day.
Dr. Julia Malkowski: 00:18:44 What happened at the end of the study was that the fiber group did not note a significant increase in microbiome diversity, whereas the fermented food group did note a significant increase in microbiome diversity and they noted a decrease in 19 inflammatory proteins, including interleukin-6 and cytokines. So potentially there is a connection here with increased improvement in microbiome diversity and decreasing inflammation. So again, we’re connecting it to the chronic disease and root cause considerations.
Dr. Kara Fitzgerald: 00:19:17 Okay. That’s fabulous. I certainly appreciate fermented foods. But we prescribe fiber all the time. We prescribe fiber in the form of a good whole-food diet. The Mediterranean dietary pattern that you referenced before is a good high-fiber dietary pattern. So what was remiss in this study to not see favorable outcomes with the fiber intervention? I’m really curious. What were they doing? And what were they doing in the cohort that did respond? What were the specific fermented foods? Why the difference? Were they just throwing a bunch of psyllium in the fiber group to kind of hit that target of 20 grams? Why are we seeing such different outcomes?
Dr. Julia Malkowski: 00:20:07 Yeah. Not psyllium. I would actually be interested in a psyllium study. The largest category of fiber was fruit, so it seems to be self-directed. The individuals were just told to add 20g of fiber and put this in your food–
Dr. Kara Fitzgerald: 00:20:21 Here’s what you can do.
Dr. Julia Malkowski: 00:20:22 Yeah. So, given the choice, individuals largely chose fruit. Vegetables and grains were also options. Legumes are certainly an option, but when I look at the data from the individuals, legumes are a small portion of what they added. And that’s key because there is a difference between soluble and insoluble fiber. Additionally, the researchers noted that their ratio of insoluble to soluble fiber increased, which makes sense to me since they chose fruit. So quick information on fiber, because it’s so important—I agree with you. Generally speaking, if we’re talking about produce, it’s going to be one-third soluble fiber to two-thirds insoluble. And if we talk about the difference between those, we need both.
Dr. Julia Malkowski: (00:21:23) Insoluble fiber is the indigestible portion. That portion does not dissolve in water and it basically helps move the bowel movement through. I think of this when I think of a stalk of celery, you can take off that long stringy fibrous portion, right? You’re not going to digest that. That’s that extracellular matrix—that’s insoluble fiber. The additional portion is soluble fiber and soluble fiber is this gelatinous substance that dissolves in water and this is what the bacteria eat. You need both but if you want to feed the bacteria specifically, you really need to increase your soluble fiber.
Dr. Kara Fitzgerald: (00:21:57) Interesting. And 20g is not the greatest amount. If you really wanted to improve a diversity score in your practice, what would you do? I mean, you would—yeah, go ahead.
Dr. Julia Malkowski: (00:22:14) No, I agree. 20g is potentially not enough because the average American is getting about 10g of fiber total per day. So remember what we said– about a third of that is going to be soluble fiber, so that’s only about 3g of soluble fiber, but our microbiome really needs 10 to 15g of soluble fiber per day. That is the key—making sure we hit that level of soluble fiber daily intake.
Dr. Kara Fitzgerald: (00:22:40) So if it’s a third, then we’re looking at around 45g of fiber if we really want to diversify our microbiome. And then layer in some fermented foods. What did they use for fermented foods in this particular study?
Dr. Julia Malkowski: (00:22:52) Yes, beautiful. I love 45g of fiber. I love that. The fermented foods were everything from kombucha to vegetable brine drink, and then fermented vegetables, cottage cheese, kefir, and yogurt. One thing as well, they did give a macronutrient breakdown and the fermented food group slightly increased their protein intake because they were consuming more yogurt, whereas the fiber food group slightly decreased their protein intake because they were consuming more fruits. There are a few nuances with the study, and the researchers hypothesize that it just wasn’t a long enough time.
Dr. Kara Fitzgerald: (00:23:34) That’s pretty interesting. It would also be interesting to look at the details on the fruit and maybe take a look at blood sugar levels and some of the systemic influence of that much sugar, and the influence of sugar on the microbiome also and how it shifts the growth pattern of gut bugs. Obviously yeast is going to be feasting on some fruit. Candida is going to be feasting on fruit along with many other players.
Dr. Kara Fitzgerald: (00:24:00) I want to say that you have the sample report from our website, from the show notes page sitting in front of you. All of the information that we’re talking about, the way they compile the scores is by looking at the rest of the data from the labs. So as clinicians, if you want to know exactly what the growth patterns or presence of these particular bacteria look like, you can look at the balance of the report and get that information exactly. For example, if this person has a lot of Proteobacteria, you can flip over to that section and actually see what’s going on. What about the rest of page one and this fabulous summary report?
Dr. Julia Malkowski: 00:24:47 Yeah. Page one is excellent because depending on how much time you have in your office or how much time you have with your patient, you can simply utilize page one. You can go into as much detail as you like as well. It’s really your choice. So again, we started with the web and then we have the Dysbiosis and Diversity score. Then the next piece of information we have, that last row, is separated into two pieces of information. We have the GI Health Markers and then we have the Key Findings. The GI Health Markers is microbiome data. This is functional guilds of bacteria. We are looking at bacteria that work together. As an example, the first group is the butyrate-producing bacteria. That’s the Faecalibacterium and the Eubacterium.
Dr. Julia Malkowski: 00:25:31 These are the bacteria that create butyrate. If it is within range for your patient you have a green toggle. If it is outside the reference range you have a yellow toggle. So you would know right there to make a clinical intervention for the butyrate producing bacteria. You could utilize the soluble fiber feeding approach, because when you feed those bacteria soluble fiber, they ferment it and create butyrate.
Dr. Julia Malkowski: The next group is the gut barrier protective bacteria. Within this category we have that keystone bacteria Akkermansia muciniphila. In this case it’s toggled yellow meaning it’s imbalanced, so we know that Akkermansia is outside reference intervals and that’s potentially compromising mucosal barrier integrity. So then right here at this juncture, you could support Akkermansia populations by using probiotics, polyphenols or using the two together. And then you could also do your gut barrier protective protocol. I would do that as well because we know intestinal permeability is associated with so many of the conditions, you know, chronic disease like we were talking about. And then the next piece of information–
Dr. Kara Fi tzgerald: 00:26:41 Before you jump into the Key Findings I just wanted to make a point on this. First of all, I just have to circle back to your earlier mention of probiotics not making a difference to diversity in that same study group. And by the way, folks, that paper will be on our show notes as well. We do we prescribe probiotics all the time. So this is evidence perhaps, I mean it depends on what probiotic they use, but this is evidence, obviously, for leaning on dietary changes as really being where the heavy lift is and diversifying the fiber choices. I think if they were primarily eating fruit– and it also depends on what fruit they were eating– they just didn’t do a good job at designing or prescribing the amount needed, as you already identified. But we use probiotics all of the time and there’s some pretty good research out there. I’m just curious your thoughts on that and if you’re using probiotics and how you might be prescribing them.
Dr. Julia Malkowski : (00:27:39) Yeah, great point. Excellent point. I certainly use probiotics. I think there’s absolutely a place for probiotics, especially when a patient has a Dysbiosis Index score of 5, or when a patient has low abundance, especially if there’s a specific probiotic like Akkermansia or Lactobacillus and that’s low. I certainly think that makes sense. I like to layer things, right? So we’re using the probiotic, we’re using the fermented foods, and we’re having those together. I think it makes sense to get the probiotic in there, but then feed the probiotic with soluble fiber, polyphenols, and fermented foods. It makes sense because you’re giving your patient a dietary recommendation alongside those targeted nutraceutical supplements, of which the probiotic falls into that category.
Dr. Kara Fitzgerald: (00:28:22) Yeah, for sure. I routinely use Akkermansia or Akkermansia combination products for the barrier issue, as you and I have spoken about in the past. And then I use them for some of the cool data around GLP, blood sugar control, A1c, etc., etc. So that’s a very different reason for prescribing them.
Dr. Kara Fitzgerald: (00:29:04) Okay. Let’s talk about the Key Findings on this report. Well talk about the key findings in general, but I’m still looking at the sample paper here, and yeah, this person is in rough shape. They’ve got C. diff present, they’ve got a couple of different not-so-good Klebsiellas, and they’ve got inflammation, etc., etc. But talk about those Key Findings.
Dr. Julia Malkowski: (00:29:29) Yeah, exactly. GI360 is not only talking about the microbiome, we’re looking for targeted bacteria, yeast, stool chemistries, parasites, inflammatory markers, and immunology markers. Any findings there outside those parameters would be printed on this first page. Exactly as you mentioned, not only does this patient have significant dysbiosis, they have two species of Klebsiella, and those are directly cultured.
Dr. Julia Malkowski: (00:30:02) At the end of the report, you will find direct sensitivities. That means in the laboratory, they took your patient’s bacteria or yeast, if applicable, and in the laboratory, the microbiologist put that in vitro with natural and pharmaceutical agents so you have another opportunity here for individualized medicine, for targeted treatment.
Dr. Kara Fitzgerald: (00:30:23) Okay. That’s cool. So going through the sample report we can see that for this person the Klebsiella pneumoniae would respond to colloidal silver if they wanted to go natural, possibly caprylic acid, and all of the antibiotics would be able to eradicate the Klebsiella with the exception of ampicillin. Okay, good. That’s a nice complement of different interventions—oregano, golden seal, olive leaf, uva ursi, caprylic acid, black walnut. But really, for the most part, none of them—actually, ionic silver and colloidal silver both responded, with a distant third being caprylic.
Dr. Julia Malkowski: (00:31:06) Yeah. And just a note, of course, in the laboratory, we test them individually, but we know that there’s potentially a synergistic effect. So if you have a formula that has more than one in there, it’s potentially going to show greater efficacy than what we can see on the report, if that makes sense.
Dr. Kara Fitzgerald: (00:31:21) Yeah. You’re testing literally one by one. Right. What are we going to look at using this report to get a good understanding of intestinal permeability? What are the players we’re going to be looking at? And there are some other tests we can add on if we need to.
Dr. Julia Malkowski: (00:31:44) Absolutely. Intestinal permeability is so important and we see it actually increasing in the clinic, and I’m sure you’ve seen that. Intestinal permeability—we cannot directly measure it on this report. To directly measure it, you could simply add on the fecal zonulin. The zonulin family proteins do measure that. Yet, we do know on this report that gut bacteria— Akkermansia muciniphila, Faecalibacterium prausnitzii— they significantly contribute to mucosal barrier. So if those are outside the reference interval, that is a key that you have mucosal barrier integrity. And again, that is going to be indicated by that gut barrier protective toggle there so it’s quite straightforward to understand. If you wanted to implement a mucosal barrier integrity protocol, it’s right there.
Dr. Kara Fitzgerald: (00:32:34) Nice. And then you can just, at a glance, scroll over to page four and see that the Akkermansia on this individual is really low. It’s significantly low. So one of our interventions is definitely going to be some of the polyphenols you mentioned earlier that can really help stoke Akkermansia growth. And then, you know, we could consider using Akkermansia or an Akkermansia combination product.
Dr. Julia Malkowski: (00:32:59) Yeah. And another potential finding would be potentially low fecal secretory IgA. There may be many underlying considerations when we’re talking about low fecal secretory IgA, but that’s another potential clue. In this report, we have a high fecal secretory IgA, yet that would be considered functionally high because you do have two Klebsiella and then that C. diff, so it’s actually appropriately elevated in this case.
Dr. Kara Fitzgerald: (00:33:27) It’s responding to the potentially pathogenic organisms present, and C. diff is there as well so it’s appropriate. It’s good. This person doesn’t feel well in this sample report—they’re not happy with all of those findings. But plenty of times in clinical practice, we see people who’ve got chronic dysbiosis, and secretory IgA just hits a wall and it can really no longer sustain producing that much. Our bodies—we just don’t produce it, and we see low secretory IgA.
Dr. Julia Malkowski: (00:34:05) I see that quite often, and also in individuals that are under psychological stress that’s also a finding that you may find.
Dr. Kara Fitzgerald: (00:34:13) Athletes will drop secretory IgA after the stress of their season. and then they’re all out there, routinely getting sinus infections, upper respiratory infections, things that aren’t surprising that would be associated with the fallout of low secretory IgA. And yeah, you could certainly see dysbiosis and gut issues creep in.
Dr. Julia Malkowski: (00:34:38) That makes sense. It’s a really good point. Yeah.
Dr. Kara Fitzgerald: (00:34:42) So you look at Akkermansia, you’re able to measure low, you’re also able to measure high. What are your thoughts on high Akkermansia? This is somewhat of a hot topic among functional medicine geeks.
Dr. Julia Malkowski: (00:34:56) Yeah. We discussed that there are a few studies out there that suggest Akkermansia may be potentially higher in certain conditions, and it may confer a protective benefit. We don’t necessarily know the exact mechanism of action for that. And then I would say that when it is elevated, it is associated with dysbiosis. So when it’s too high, it’s associated with dysbiosis, which brings me back to the fact that the microbiome really works synergistically and together. So if you have an elevated Akkermansia on your patient’s report, there will be other findings to be addressed. I do not recommend eradicating that. As a matter of fact, nothing on that web or the first few pages of the report—pages two, three, and four—do we eradicate. We’re talking about feeding the microbiome and bringing things back into balance.
Dr. Kara Fitzgerald: (00:35:46) Awesome. I so appreciate that. I do think some clinicians are anxious about elevated Akkermansia. It is a keystone strain engaged in incredibly, incredibly important activity, both locally in the gut—from maintaining barrier integrity to stimulating production of GLP-1 to systemic influence body-wide. It isn’t titled a keystone strain for naught. And yeah, to your point, I definitely wouldn’t recommend an aggressive eradication intervention. I have thought that maybe there’s an aggressive sloughing off of the mucin layer, and that’s why you’re seeing more Akkermansia in the fecal bolus. Or maybe there is an attempt of the Akkermansia to kind of respond to recycling damaged mucin. I mean, it’s probably a surrogate marker of something else and not, in and of itself, a pathogenic player. And that, I’m getting, is what you think as well?
Dr. Julia Malkowski: (00:36:55) Yeah, absolutely. And you bring up an excellent, nuanced point about that sloughing off of that mucosal layer, because that mucosal layer is just so important in regards to physiology, because it really is modulating where our internal environment meets our external environment. The body makes two liters of that every single day so it’s a very important system. And we do see that some individuals do tend to slough that off. They tend to be very symptomatic GI-wise, but maybe even systemic physiology as well.
Dr. Kara Fitzgerald: (00:37:29) Sure. Yeah. Intestinal permeability being associated with pretty much everything. Very interesting. So the early pages in this report where we’re measuring all of those different phyla, the specific players and the different phyla, again, I just want to underline—you don’t want to kill them. Don’t go in for the assault via aggressive antibiotic interventions or botanical interventions. Rather, you want to nuance and balance.
Dr. Julia Malkowski: 00:38:00 Yeah. Absolutely. Exactly. We want to feed the bacteria that we need there, those anti-inflammatories and when we want to starve those inflammatory bacteria. It’s really largely about diet and remediating that diet. Yep.
Dr. Kara Fitzgerald: 00:38:14 Stress. So everybody’s under chronic amounts of it. How do we perceive chronic stress? Like short -term stress can actually be this beautiful, hormetic experience that could be beneficial for the microbiome, I would imagine. But this chronic grading stress of a tough job, not enough sleep, stuck in traffic, etc., etc.. How does that show up in changes to what’s happening in the gastrointestinal tract and with the microbiome?
Dr. Julia Malkowski: 00:38:47 Yeah, absolutely. Stress certainly influences the microbiome. So stress itself can induce intestinal permeability. So it is a risk factor for that. As you mentioned, acute stress is appropriate so you may see compensatory fecal Secretary IgA, but over time, what we see is chronic decreasing fecal Secretary IgA. Chronic stress downregulates fecal secretary IgA, and then of course, elastase, because you cannot be in fight or flight and rest and digest at the same time. Another consideration here is eating hygiene, making sure individuals are sitting down and relaxed and practicing mindful eating. But certainly stress does wreak havoc in the microbiome.
Dr. Julia Malkowski: 00:39:38 When we are under the influence of these stress catecholamines, they can actually spill over into the microbiome and these pathogenic bacteria, such as E. coli and Salmonella, they actually really enjoy those stressful catecholamines. That environment can really increase their growth, and it can increase their ability to adhere to enterocytes, which of course, we don’t want because once they adhere to enterocytes, they can translocate, and we can get LPS into systemic circulation, which leads to further maladaptive physiology. So stress certainly influences the microbiome. The other thing is, as you mentioned, if individuals are stressed due to our everyday considerations, it actually takes six hours— I saw one study that’s at six hours, another study that said two weeks— for the environment in the microbiome to remediate itself.
Dr. Kara Fitzgerald: 00:40:41 It’s incredible how potent the stress response can be. And to your point, if we’re in a fight or flight, we’re not going to be dumping out the necessary compounds. We’re not going to be dropping our stomach acid to a sufficient degree to really allow for digestion to happen. Also to your point, we’re not going to be releasing sufficient elastase or the other pancreatic exocrine enzymes that are essential for the appropriate breakdown of foods.
Dr. Kara Fitzgerald: The other piece— just because I teach part of the immune module at IFM, and I’m thinking about allergic disease— we see the same kind of occurrence with insufficient digestion ushering in allergies because those proteins are abnormal to our immune system. So if we’re in this fight or flight and we shut down digestion, as we should, but we’re also eating, those food compounds can become pathogenic to our system. The system will identify those proteins as not safe and mount an inflammatory or an allergic response. There were some pretty cool studies looking specifically at proton pump inhibitors and increasing the aggressiveness of allergic reaction or actually bringing on new allergic reactions.
Dr. Julia Malkowski: Wow. That’s fascinating.
Dr. Kara Fitzgerald: 00:42:11 It’s super fascinating and we’re prompting a similar effect with the stress response. So let’s talk about GLP-1 agonists. They’re the rage; physicians are prescribing them all over the place. Patients want them, big time. I have a couple of questions for you. First of all, you’ve had the chance to look at the laboratory data of people on GLP-1 and I’m really curious what you see—how these potentially modify not just the microbiome, but some of the additional chemistries– if you see changes and what happens. And then I want to talk to you about the fact that GLP-1 is stimulated by Akkermansia and Clostridium butyricum, probably other important strains as well and this epidemic of dysbiotic guts may really be the underlying issue in the obesity epidemic that we’re in because we’re not making GLP-1. So two questions I have there about GLP: dysbiosis playing a role in sort of inhibiting GLP-1 production and in this era of lots of GLP-1 use, what you’re seeing in the gut microbiome.
Dr. Julia Malkowski: 00:43:40 Yeah, absolutely. So certainly with the dysbiotic gut, we do tend to see that lower Akkermansia, which would potentially decrease GLP-1 production. Another consideration is actually soluble fiber. As soluble fiber is in the colon, this can potentially interact with the enteroendocrine L cells and there is a mechanoreceptor on there, so when they’re providing a lingering physical tone, this can stimulate the L cells to release GLP-1. So in individuals that are fiber deficient and dysbiotic, they’re potentially at risk for perturbing both of those mechanisms of action. As far as individuals on GLP-1 agonist medications, there’s a variety of findings. Again, not every diet is created equally. One of the worst dysbiosis scores I had seen was on an individual who was on a GLP-1 for a few years and who was not eating throughout the day—simply having an apricot throughout the day and coffee—but then at night would binge on carbohydrates and alcohol.
Dr. Kara Fitzgerald: 00:44:48 Wow. And it was the worst dysbiosis score you saw. Woop, woop. That’s huge. The worst dysbiosis score you saw was on an individual on a years-long GLP-1 therapy who had just adopted a pretty damaging dietary pattern. Wow, that’s fascinating. Layer that on to muscle loss and some of the other issues and they are certainly a less healthy individual now. Wow. With the use of GLP-1, a lot of folks are talking about how it needs to be accompanied by resistance training and sufficient protein to inhibit muscle loss or muscle wasting even. But, to your point, we can really damage the microbiome.
Dr. Julia Malkowski: 00:45:40 Yeah, exactly. And so then that patient is going to be decreasing their endogenous production of GLP-1 even further. So they really need to remediate that. As you’re mentioning, when patients are on these medications—because they are so popular—it makes sense to take a look at their microbiome and adjust and support them along the way.
Dr. Kara Fitzgerald: 00:45:59 There’s a lot of cool opportunities out there. A lot of clinicians in the functional medicine space are thinking about how you might toggle between tending to the gut microbiome, an appropriate whole foods diet, some of the various interventions to support increasing GLP-1 endogenously, and then tapering down to the lowest necessary dose of the GLP-1 agonist drug. We can use this as a guide. You know, we can use the information from the GI360 as a guide. That was really interesting. As we come to the homestretch of our conversation, why don’t you just review again what is on the GI360. Just run through what we already went through and then the things that we haven’t touched on yet.
Dr. Julia Malkowski: 00:46:53 Yeah. So again, that first page is really a summary of the findings. You have that phyla information, you have the Dysbiosis Index, Diversity Score, and then you have that left column there—that’s the GI Health Markers, so we’re getting detailed information about key bacteria from the microbiome.
Dr. Julia Malkowski: 00:47:10 And then you have that second column—that’s the Key Findings. So any positive findings here you could address. In this case, the patient has a pathogen. GI360 is also doing PCR testing for direct pathogens such as C. diff, as we see here, so those are the acute considerations. Then we are also seeing the information on here of the stool chemistries: lysozyme, secretory IgA, and the short-chain fatty acids.
Dr. Julia Malkowski: We know that short-chain fatty acids are so important because they’re really a link between the gut microbiome and those systemic considerations regarding physiology. They are the microbial mediators that travel from the colon and stimulate organ physiology, so it’s really important to look at those. We look at valerate, propionate, acetate, and butyrate, so those are on there as well. pH is on there as well. And then, of course, beta-glucuronidase is on the report— a very important consideration, especially when we’re talking about estrogen metabolism and when we’re talking about individuals that are in perimenopause, or have PCOS and endometriosis. In those conditions beta-glucuronidase does play a role.
Dr. Julia Malkowski: 00:48:26 And it’s important when we’re talking about toxin elimination and endogenous detoxification because it’s tagging those conjugates and releasing them, so then there’s potential for re-uptake into systemic circulation to be reabsorbed. So, there’s potential reabsorption of toxins and hormones if beta-glucuronidase is too high. It’s good to take a look at that indication and there’s potentially a link between this level and breast cancer.
Dr. Kara Fitzgerald: 00:48:58 Are we mostly concerned about beta-glucuronidase if it’s elevated? That’s my understanding. A low beta-glucuronidase is reported on this sample report. In the sphere of what’s going on with this individual, how concerned are we about that?
Dr. Julia Malkowski: 00:49:18 Right. We’re concerned with elevated beta-glucuronidase clinically. It is known that low beta-glucuronidase levels are potentially associated with low diversity. So when you have–
Dr. Kara Fitzgerald: 00:49:33 Ah. Interesting. Okay. So you want some beta-glucuronidase hanging around; you just don’t want a lot of it. And low may be a surrogate marker of something else going on. Okay, good.
Dr. Julia Malkowski: 00:49:43 Yep. Now, there is some newer information that it may be associated with IBS and IBD, but I would not say definitively yet, so let’s hold off on that.
Dr. Kara Fitzgerald: 00:49:52 Oh, interesting. Okay. There’s plenty to do here on this sample report. So we don’t really have to worry about the beta-glucuronidase levels or what we need to do. And I would bet that when you treat the overall gut and you get this person back to balance and you tweak their diet, etc., etc., you’ll see that beta-glucuronidase just sort of bounce back into a normal range. Would you agree?
Dr. Julia Malkowski: 00:50:12 Yes, I would 100% agree with that. Absolutely.
Dr. Kara Fitzgerald: 00:50:15 Okay, cool. All right. So walk us through the next sections and then spend a minute or two on the ones that we actually haven’t really talked about.
Dr. Julia Malkowski: 00:50:22 Sure. So pages two, three, and four are summaries of the information. So if you wanted to take a look at the specific bacteria—let’s say Bifidobacterium or Lactobacillus or Akkermansia—you have those levels there, so that’s an important finding. Page five is going to be the pathogens information. So we’re looking for viruses, pathogenic bacteria, and parasites on that page. We’re looking for those pathogens. And then pages six and seven is the parasitology. It is important that this is the ova and parasitology. This is still the gold standard for parasitology information. So any finding on there is a positive finding.
Dr. Kara Fitzgerald: 00:51:17 Actually, I’m back. I’m at the pathogenic bacteria. This is where we can see that the individual has C. diff present. You’re looking at viruses, and again, as you said, the parasites as well.
Dr. Julia Malkowski: 00:51:30 Yeah. So everything is covered. And then sometimes the parasites could be found in their cyst or their ova, and a positive finding is a positive finding. So if you see ova, that’s the parasite there.
Dr. Kara Fitzgerald: 00:51:42 Okay, okay. And then what else do we have?
Dr. Julia Malkowski: 00:51:45 So we have other markers, and these other markers can be fairly nuanced. We’re looking at yeast under the microscope. This yeast is non-viable. The expert parasitologists and microbiologists are looking under the microscope and they see the cellular structure of yeast. Further on the report, we will have cultured yeast. These are distinguished because yeast that’s cultured is active and alive, and it’s growing in the colon. Yeast here can be associated with yeast that’s been cultured. If you have cultured yeast, it goes together in life cycles; some of them are alive, some of them are dead. It makes sense. But if you have a patient that presents with yeast symptoms and you don’t have anything cultured, but you see it on the microscopy, you can consider small intestinal fungal overgrowth (SIFO). In that case, it’s not cultured in the colon; it’s in the small intestine, but you can see it under the microscope here.
Dr. Kara Fitzgerald: 00:52:38 Well, that’s pretty interesting. So in a symptomatic individual, if yeast is present but they’re not culturing, this could just suggest SIFO.
Dr. Julia Malkowski: 00:52:50 Yeah. And we can’t provide sensitivities, obviously, because to do sensitivities we’re taking that live isolate.
Dr. Kara Fitzgerald: 00:52:55 Yeah, for sure. Yeah. Okay, okay. And what else are we looking at here?
Dr. Julia Malkowski: 00:53:01 Red blood cells and white blood cells and we are also looking at muscle fibers and vegetable fibers. We spoke briefly about the carnivore diet. I do tend to see red blood cells and muscle fibers in the carnivore diet due to the red meat consumption. With red blood cells, one of the considerations is also hemorrhoids. So this is fresh blood. This is fresh in the colon. Of course, you can see that with considerations of IBS and IBD, so the markers here really need to be considered in the context of the other findings.
Dr. Kara Fitzgerald: 00:53:30 Okay. And the person and what’s happening with them clinically and so forth. So red blood cells could be active hemorrhoids; it could be an active bleed somewhere, and in a carnivore diet person, it could be evidence of eating a whole lot of meat. So you need to just do further investigation to confirm or rule that out. Okay. What else do we have?
Dr. Julia Malkowski: 00:53:49 Again, we have the muscle fibers and vegetable fibers. The Charcot-Leyden Crystals are going to be associated with parasitology and then pollen is really going to be an incidental finding. It can be associated with allergies, but it’s really just a finding that is of note within the colon.
Dr. Kara Fitzgerald: 00:54:06 So it’s not anything that’s going to inform your clinical decision-making?
Dr. Julia Malkowski: 00:54:11 Not at this point. It’s more of an observation. Correct.
Dr. Kara Fitzgerald: 00:54:15 Okay. And then there’s the macroscopic appearance, be it the color, the consistency, and the presence of mucus.
Dr. Julia Malkowski: Exactly.
Dr. Kara Fitzgerald: Any comments on those?
Dr. Julia Malkowski: 00:54:26 Not to discount those. Those aren’t the flashy findings, but they can provide us information.
Dr. Kara Fitzgerald: 00:54:33 Sure. It could be evidence of constipation. There could be mucus, obviously inflammation for sure. Yeah. And in this individual and the sample report, I think it’s loose, as it should be if you’ve got a C. diff infection. Okay, okay. All right. What else do we have?
Dr. Julia Malkowski: 00:54:48 The next page is the culture page. And this page I will tell you, of all the years and all the GI360s I’ve seen, I’ve never seen two pages alike. This is really individualized. The first section is the pathogenic bacteria— the Aeromonas through Yersinia— that will always be printed there because we’re always going to culture and let you know if those are found.
Dr. Julia Malkowski: The next group is going to be imbalanced bacteria. With the imbalanced bacteria, you can really see anything here from 0 to 12. These bacteria take up space in the colon. They’re not significant players, but they do take up residence in the colon. You’ll potentially see more of these imbalanced bacteria if there’s less of an abundance of the bacteria from the first section of the report. The other consideration here is that this is identified via the MALDI-TOF library. And that library is updated every six months, so as microbiology evolves and we can understand these bacteria more to species level, sometimes these names are actually updated.
Dr. Kara Fitzgerald: 00:55:54 Oh interesting. Can you just speak to what the MALDI-TOF technology and the MALDI-TOF library are?
Dr. Julia Malkowski: 00:56:01 Yeah. So the MALDI-TOF technology is essentially identifying the genomic fingerprint of each bacteria. Once it’s cultured, it’s using that dataset that is a global library that is associated with research facilities and laboratories all over the world. It identifies the bacteria, the genomic fingerprint that was identified, and it’s matching it to the library. And even at Doctor’s Data we’ve had one discovery of the Laribacter hongkongensis and it was the first one in the world.
Dr. Kara Fitzgerald: 00:56:33 Wow! Congratulations. Did you guys get an award? That’s pretty cool. I think that maybe we can throw a little something on the show notes about the MALDI-TOF technology. That would be nice to make available to people because this is the next generation culture, right? If you’re using culture, it should be done in this way. Would you agree?
Dr. Julia Malkowski: 00:57:00 Oh, absolutely. Yes.
Dr. Kara Fitzgerald: 00:57:03 So this imbalanced bacteria, would that also have any influence on the dysbiosis or the diversity score? Could this directly or indirectly influence page one?
Dr. Julia Malkowski: 00:57:15 This is going to potentially be a byproduct of page one. As you’ll see here, we have a Corynebacterium. We have bacteria that we see on the skin. We have a lot of Staph and Strep and those are bacteria that… You know, we are a very bacteria-rich organism and so sometimes you’ll have something in the oral cavity or on the skin that goes along for the ride in the colon. It’s not really going to significantly influence colonic health or systemic physiology, but as you know, the colon can’t have any empty spaces. It has to be filled with bacteria. So if we don’t have those good bacteria that we want–
Dr. Kara Fitzgerald: 00:57:52 Ah. There’s room. That’s pretty interesting. So maybe if they were very high you would be a little more suspect, but for the most part, it’s more an incidental finding would you say?
Dr. Julia Malkowski: 00:58:04 Yes. That’s correct.
Dr. Kara Fitzgerald: 00:58:04 Okay. All right. Go ahead.
Dr. Julia Malkowski: 00:58:07 Now those bacteria, we have some that are value-driven. Some bacteria in smaller amounts, such as Citrobacter and Klebsiella, would be considered imbalanced. But if they’re larger, we kick them over to the next category, the dysbiotic category. These bacteria are categorized as those that will contribute to GI symptomatology in your patients so these patients might not feel well; they may have diarrhea, stomach pain, things like that.
Dr. Kara Fitzgerald: 00:58:37 And in this one, we see both of the Klebsiellas that were reported on the first page.
Dr. Julia Malkowski: 00:58:43 Exactly. Yes, correct. And then last but not least, we have yeast. In this case, there’s no yeast grown, but if there was yeast grown, it would be put here. And then yeast outside the reference interval will also be provided with direct sensitivities.
Dr. Kara Fitzgerald: 00:58:59 Cool. And then one of my favorite parts of the report—I love the chemistries. And there are a ton of chemistries on the GI360. Why don’t you run through those.
Dr. Julia Malkowski: 00:59:12 Yeah, I always say this page has a wealth of information, right?
Dr. Kara Fitzgerald: 00:59:15 It does. Yeah.
Dr. Julia Malkowski: 00:59:16 The first section is going to be Digestion / Absorption, as we touched upon. There’s elastase, a pancreatic enzyme and we have a fat stain for individuals with fat malabsorption issues. I’d also pay attention to diet. Right? We talked about ketogenic and carnivore because sometimes individuals are consuming a lot of fats, and conversely, there are still individuals who are eschewing fats and abiding by low-fat diets, so that might not give you the best clinical information because it would still be none in those cases.
Dr. Kara Fitzgerald: 00:59:49 But we would see people who are doing sort of a fat bomb, you know, a peanut butter, nut, olive oil breakfast or whatever, you can see a really high fat, and you don’t have to worry about steatorrhea or fat malabsorption.
Dr. Julia Malkowski: 01:00:04 Well, I wouldn’t say you don’t have to, but you can’t differentiate those, but yes, it would make sense that that’s going to be your first thought.
Dr. Kara Fitzgerald: 01:00:13 So confirm that with your patient and then if you are concerned, I guess you’d have to do a follow-up. One of the things you could do—if you remember, and I’ll admit that I don’t often advise people before testing—you could say, look, don’t eat anything high fat before you obtain your stool specimen.
Dr. Julia Malkowski: 01:00:33 Yep, yep. That’s certainly a consideration. And then the next one is carbohydrates. So carbohydrate malabsorption we can see that there. So that’s the Digestion/Absorption and the next section is the inflammatory markers. Here are the markers associated with inflammation. The first one that I would consider is lysozyme. It’s in the middle there because lysozyme is nonspecific. If we have elevated lysozyme, as we do in this case, we don’t know why. We have to look at the other findings on the report to see. Now, it makes sense because there’s that C. diff, we have two dysbiotic bacteria, and then we have a high dysbiosis score, so this is an inflamed gut.
Dr. Kara Fitzgerald: 01:01:17 Okay. That’s consistent with that. Yep.
Dr. Julia Malkowski: 01:01:20 Yeah, absolutely. And then lactoferrin and calprotectin are specific for IBD.
Dr. Kara Fitzgerald: 01:01:26 Or in the case of super high levels, calprotectin could be colon cancer actually, right?
Dr. Julia Malkowski: 01:01:32 Yeah. And another consideration would actually be if you potentially have a malignant enteropathogen, you can see those markers as well. It is a marker of destruction of the colonocytes.
Dr. Kara Fitzgerald: 01:01:46 Okay. Okay. Both of them.
Dr. Julia Malkowski: Yep.
Dr. Kara Fitzgerald: Okay. Then we’ve got the immunology.
Dr. Julia Malkowski: 01:01:54 Yeah. Fecal secretory IgA, which is a very important biomarker, as we’ve been discussing. In this case, it’s elevated appropriately. More often than not, you will see low fecal secretory IgA, and the considerations that we’ve discussed—stress, mucosal barrier integrity—and then of course, the considerations of vitamin D, vitamin A, and zinc status; those play a role as well.
Dr. Kara Fitzgerald: 01:02:19 Interesting. So this is good that this person has a high IgA in the face of all of the other elements that are happening, so they’re able to respond to the assault with IgA. But if it wasn’t addressed, we would anticipate seeing this drop. Short-chain fatty acids.
Dr. Julia Malkowski: 01:02:38 Yeah. Short-chain fatty acids. These are intricately linked to that first section, the microbiome section, because they’re derived from the microbiome. Now, if you’ll notice, there are two pieces of information here. The first four markers are percentages. We have % Acetate, % Propionate, % Butyrate, and %Valerate. And again, this is important because we’re talking about balance in relation to one another. So we’re talking about those levels as they relate to one another. We don’t necessarily have a treatment protocol to say if acetate is higher, we need to absolutely do this. It’s about bringing everything into balance based on the microbiome’s abundance and diversity portion.
Dr. Julia Malkowski: The next piece of information is the absolute frank values. We have the frank value of butyrate and then the frank value of total short chain fatty acids. Because these are both so clinically relevant, we look at these absolute values here.
Dr. Kara Fitzgerald: 01:03:35 We want to make sure there’s enough butyrate and overall short-chain fatty acids given the incredibly important roles they play. Yeah. Okay. And then the balance of markers.
Dr. Julia Malkowski: 01:03:44 Yeah, so we have pH, and again, pH is associated with that information we saw at the beginning, the microbiome. We tend to see that lower pH commonly and sometimes you’re thinking of patients that have food sensitivities or lactose malabsorption. That can potentially be seen on here as well. And then we have that enzyme beta-glucuronidase, that important biomarker and then occult blood. Occult blood is different than red blood cells. Occult blood is hemolyzed, so this is coming from the upper GI—potentially an ulcer or esophageal varices. If this is positive, you do want to follow up with a second test in four weeks to confirm.
Dr. Kara Fitzgerald: 01:04:28 All right. And then let’s see what else we have here on this cool report. Oh. Then we go into the various sensitivities that we already talked about, where you guys test the natural ingredients as well as the prescriptive agents against the dysbiotic organisms.
Dr. Julia Malkowski: 01:04:47 Yes. We just updated this list. In collaboration with physicians like yourself, we updated the natural agents list to provide the ones that are applicable in clinical practice.
Dr. Kara Fitzgerald: 01:05:02 Nice. Nice. It is a good list. It’s a nice robust list. And then I want to just add that there’s a pretty long discussion section at the end talking about the imbalances in the individual. Right? So you don’t just dump everything; it’s specific to the report at hand. Is that correct?
Dr. Julia Malkowski: 01:05:24 Absolutely correct.
Dr. Kara Fitzgerald: 01:05:26 Awesome. So that’s useful too if you want to do a little bit of a drill-down into your patient case. Well, this has been fabulous. I really appreciate all the hard work that you’ve done. Any of the papers that we’ve referenced will be in the show notes. Again, the sample report will be over there, and we’ll get something about MALDI-TOF technology for you to read about if you’re curious about that cultured methodology they’re using over at Doctor’s Data. Do you have anything to add to this conversation today, Dr. Malkowski, before we say goodbye?
Dr. Julia Malkowski: 01:05:59 No. Thank you so much for having this conversation. It’s been excellent to have this opportunity to talk about the microbiome.
Dr. Kara Fitzgerald: 01:06:05 Awesome.
Dr. Malkowski began her career in Functional Medicine upon seeing excellent results restoring the health of her infant son. She went on to complete her bachelor’s degree in biomedical science, Doctorate in Chiropractic and Doctorate in Naturopathic Medicine, while raising her healthy family. She remains committed to optimal health on a personal and professional level as Staff Doctor of Clinical Education at Doctor’s Data, Inc., and maintains her own private functional medicine practice Docere Health outside Chicago, IL.
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Doctor’s Data GI360 Publications
Test and Address: The Clinical Importance of Direct Assessment of Gut Microbial Abundance and Diversity, The Townsend Letter, January 2023 Issue.
Study: Gut-microbiota-targeted diets modulate human immune status
Study: Gut Microbiome in Progressive Multiple Sclerosis.
Study: Role of Akkermansia in Human Diseases: From Causation to Therapeutic Properties. Nutrients.
Study: Microbial endocrinology: host-bacteria communication within the gut microbiome
Study: The influence of perceived stress on the human microbiome.
Study: Proton pump inhibitors in allergy: benefits and risks
How MALDI-TOF Mass Spectrometry Technology Contributes to Microbial Infection Control in Healthcare Settings
Doctor’s Data Webinars
Some Diseases Do Begin in the Gut: The Gut Microbiome and Chronic Disease
Podcast: Breast Health and Beyond: A Practitioner’s Guide to Functional Testing
Podcast: Utilizing Salivary and Urinary Hormone Testing for Comprehensive Patient Support
Podcast: Evidence-Based Dietary Approach to Improve Health and Stress Resiliency Through the Microbiome
DrKF Clinic: Patient consults with DrKF physicians including Younger You Concierge