Parasites and Your Gut Issues: What To Know

Parasites were once a trendy topic to discuss in gut health, now small intestinal bacterial overgrowth (SIBO) is a buzzword. Both still play a real role and should be considered if you are struggling with dysbiosis, inflammation, or other chronic conditions. Parasites may fuel changes in the microbiome, but can also take advantage of an already compromised gut. Holistic solutions and supporting the gut terrain are key. Frank pathogens should always be treated. Testing and treatment options are advancing, but still imperfect, so diagnoses and protocols still rely on a medical professional’s best judgment.

Episode Intro

Dr. Michael Ruscio, DC: Hey everyone, welcome to Dr. Ruscio Radio. This is Dr. Ruscio. Today I’m here with Dr. Ilana Gurevich. And we’re going to be talking about the creepy, crawly world of parasites. So Ilana, welcome to the show.

Dr. Ilana Gurevich: Thank you so much for having me.

[Continue reading below]

Dr. R’s Fast Facts Summary

Testing for parasites and other gut pathogens

  • Ova and parasite test (FEA base and sugar/salt flotation base). These are older standard tests – not as sensitive therefore can be less accurate
  • PCR – predilection toward false positives
  • Immune fluoroscopy – washes out some of those false positives
  • GI-MAP is a good test but requires a professional to translate the nuanced results
  • Best thing to do is use an assortment of newer tests and older tests, reflect on results and use discretion

Treatment for pathogens and other gut bugs

Bugs you MUST treat:

  • Pathogens: Giardia, crypto, e.Hista
    • Any of the ones that we know are going to cause dysentery, bloody stools, etc.

Consider treating:

  • Opportunistic bugs: Blastocystis, Dientamoeba fragilis, Endolimax nana, Entamoeba coli
  • Commensal bugs: “friendly” bacteria

Natural treatment options

Rx treatment options

  • Alinia –  antiparasitic medication
    • 500 mg 2x/day, 10 days, 2 weeks off, then repeat
    • Works on some protozoa not all
  • A great resource for practitioners UpToDate database

Where to learn more

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In this episode…

Episode Intro … 00:00:40
The SIBO-Parasite Connection … 00:05:05
Parasite Testing Options … 00:08:15
Gray-Area Gut “Bugs” … 00:15:54
Best Parasite Tests … 00:28:36
Frank Pathogens Need Treatment … 00:33:10
Approaches for Opportunistic Pathogens … 00:39:50
Optimizing Immune and Gut Health … 00:51:19
When a Parasite Can’t Be Found … 00:56:45
Episode Wrap-Up …00:58:35

Download Episode  (Right click on link and ‘Save As’)

ParasitesDrMR: It’s great to have you here. And I heard some good chatter through the grapevine about a presentation you recently gave on the SIBO-parasite connection. This is something I have mixed thoughts about. I’m curious to get your perspective. I think maybe 10, 15 years ago, parasites were blamed for everything. And we didn’t have the level of sophistication to understand, or at least it wasn’t very commonly understood, the prevalence of SIBO. And I don’t believe the SIBO testing was as readily available.

So I think we used this broad catch-all for parasites and used many similar herbal treatments that were antibacterial, antifungal, antiparasitic, all in the same formula. When people responded to that, I’m assuming there were a number of cases that may have been yeast, that we weren’t able to detect prior, or SIBO that we were not able to detect prior. But somewhat improved from the “parasite treatment.” So we assumed parasites were at the root of a lot of problems when maybe they weren’t. But I do think that parasites are a problem. Not trying to say I don’t think they are at all. I think we’ve become a bit more nuanced.

Now SIBO is the cool guy, everyone’s talking about SIBO. And I think we sometimes forget about parasites.

DrIG: So I feel like the pendulum has swung in the opposite direction where everything now is SIBO. You see all these forums online. “I have these symptoms, I have those symptoms.” And SIBO realistically is extraordinarily easy to find and relatively cheap to test for. But you have all these patients getting these recalcitrant SIBO cases where they’re just not getting better. It’s because of that patient population that I started looking at what else I could find. That’s when I really started stumbling on the parasites and treating them, with pretty good success. And protozoa, helminths… I’m going to put them all in the same category as parasites.

DrMR: Yeah. That’s a good transition into your background. If you can expand a little bit on what you were saying a moment ago: I assume you were seeing these relapsing cases and then looking further into parasites. So tell people about your background just so they know what your credentials are. And then how and what the evolution of this looked like, on the ground floor, as you were looking into it.

DrIG: So I’m a naturopathic physician and an acupuncturist. And I have a couple of practices in Portland, Oregon. And I am very, very specialized in inflammatory bowel disease and functional GI disorders. It’s about 80% of who I treat. I have a pretty busy private practice. I train residents underneath me. I lecture. So all I really do is GI-based things.

When I went to Allison Siebecker’s first lecture, this teeny tiny lecture at NUNM, the naturopathic college, it really blew my world apart in treating inflammatory bowel disease patients. Before that, I was focusing on the inflammatory cascade and on the mucous membrane healing. But you have this subset of patients that just wouldn’t get better. And when I started testing SIBO for those patients, all of a sudden I was able to bring these really, really complicated patients into remission. And maintain them for years sometimes.Parasites

So I started aggressively treating SIBO. My world got busted open. I was testing everybody, treating everybody. I was using pharmaceutical protocols and natural protocols. And when you find something and  treat it, especially with herbs that are so broad spectrum, you get really good success. I was super excited. And then the years roll by and you start to see these patients again and again, because they get better and then they relapse. They get better, they relapse. I started having more and more of this patient population that was so recalcitrant. So I started looking for something different.

The SIBO-Parasite Connection

I know a bunch of people in that Lyme, Klinghardt-y world, and they would talk about parasites. So eventually I started looking at the literature to see what it tells us about this. What does the literature tell me about the testing and the predictability or sensitivity of different testing options? And what does the literature tell us about different protozoa and what they do to affect the microbiome and maybe predispose to SIBO? Or maybe be the underlying cause of SIBO? And looking at that, I found two really, really interesting studies.

The first one was a 2014 study that was in The Journal of Clinical Microbiology, which took a look at different protozoa. I think this one looked at Dientamoeba fragilis and Blastocystis hominis. And the theory is that what these species do is just change the microbiome enough to make the bacterial neighborhood a lot more pathogenic and predisposed to bacterial changes, both in the small bowel and in the large bowel.

And that got me thinking, maybe I should be looking a little more at these opportunistic protozoa and treating them a little more aggressively. What really changed my mind was this super interesting 2016 study. I tell patients about it all the time. This study looked at known Giardia samples (from patients who had known Giardia).Parasites

And they sent the stool to a lab tech who had been practicing for years, a very well-trained, well-seasoned lab tech. Which—just as a disclaimer—I think we have less and less of. Right now we rely on a lot of different technologies, so people who look at stool samples through an ova and parasite test don’t know what they’re looking for (as they used to before we had the really sensitive technologies). But the ova and parasite test is still our baseline test to look at different parasitic infections.

So this study had known Giardia samples given to well-seasoned lab techs. And they were trying to figure out: how sensitive were the tests? How likely were these lab techs to find Giardia in the stool? And the reality is… not very likely. The study looked at four different samples. It looked at two ova and parasite samples. One used an FEA base, and one used a sugar/salt flotation base. They compared that to immuno fluoroscopy and to PCR. They found that the likelihood of any of the ova and parasite testing to find Giardia in a known sample was extraordinarily low.

DrMR: And was there a certain methodology that reigned as successful? Was the DNA testing the best? Or were they all underperforming?

Parasite Testing Options

DrIG: For the FEA—the standard O&P, which we use when we send to, say, a Quest or a Labcorp—they found about 50 cysts per gram on average. For the sugar/salt flotation, they found 350 cysts per gram. For the immune fluoroscopy, they found 76,700 cysts per gram. And for the PCR, they found 316,000 cysts per gram. Huge, huge variation.

However, PCR was extremely sensitive and specific, but only found samples on average 56% of the time. So their finding was, the most reliable is using immuno fluoroscopy, because it washes out some of those false positives.

DrMR: Okay. And that was one of the questions I was going to ask. This is something that I’ve been seeing. So just for the audience, a little orientation. You have a few different tests your clinician can use. And there’s debate over which test is the best. I’ve seen enough fanfare about different tests to be a little bridled in my enthusiasm before jumping on any one test. When I say jumping on, I mean using one exclusively and abandoning other more traditional testing.

What I try to do is continue to use an assortment of newer tests and older tests. Reflect on the results. Reflect on how the results correlate with the patient’s symptoms. And if we’re retesting, see how the retesting matches with a patient’s evolution of their symptoms.

ParasitesOne of the things I’ve noticed with the DNA testing is sometimes you seem to—as you alluded to here, Ilana— find these false positives, where someone who looks generally healthy is still coming back with these readings. And maybe because the DNA is so sensitive at picking things up, you have this predilection towards false positives. Would you agree with that?

DrIG: I would totally agree with it. By the time somebody comes into my treatment room, they have been through the mill. It takes a while to get in with me. I’m getting a lot of my referrals from other practicing physicians in my area. So these people have been worked up and are still very symptomatic. I look at their broad history, all the other testing that they’ve done. When they come to me, I start looking at some of this DNA PCR testing earlier on in my process. I feel like it’s the one thing that hasn’t been checked. And when you treat the protozoa you find, some of the bacterial infections, generally I feel 70% of patients get improvement symptomatically.

DrMR: Gotcha. One thing I want to chime in on here—which I think is a good takeaway for clinicians—is if you’re ruminating on the results that you get, not looking at every lab test to be true, and making sure to correlate things, then I think—even if you’re using PCR—you won’t get pulled into the overzealous treatment of the PCR test.

The point I’m making is, don’t undercut how smart you are as a clinician. Just apply some common sense and juxtapose that with the lab result. Use your own brain and your own intuition as the final decision-maker for whether or not you’re going to move on a certain finding. I think we’re getting too debilitated by blindly relying on tests and not using our intuition: “Okay, this person is now feeling a lot better, but they’re still flagging for X, Y, or Z. Perhaps that’s a false positive. Perhaps they don’t need treatment.” I think that helps fill in the gaps, from just treating lab results to using lab results to help you treat a patient in a more holistic manner.

DrIG: I couldn’t agree more. I feel like the foundation of taking a workup is getting a really good history. Whenever I’m looking at my IBD population or even my SIBO IBS population, people don’t go from feeling completely fine to being really chronically sick. You know what I mean? There’s a history process that leads them to that place. And you have to ask and really challenge them. Patients will often forget what happened unless you push them to remember, push them to remember. But the history has to be the foundation of everything you do when you’re treating chronic GI patients.

ParasitesDrMR: History, and monitoring them as they improve, right? And I’m sure you see this also: sometimes a treatment that you wouldn’t necessarily expect to work well works really well. Sometimes the labs tend to correlate really tightly. Other times perhaps they don’t correlate super tightly. But it sounds like you’re finding that the PCR testing is more of a tight correlation. I’m assuming you also see cases where the testing doesn’t fully match, and sometimes you end up more treating the patient empirically than you do by labs. But perhaps you don’t. Would you agree with that?

DrIG: Well, for sure. I practice in Portland, Oregon, where I have really good script rights. The big question is, if you treat and they’re not getting better, are you using the wrong treatment? Or is your treatment not strong enough? Because that is also in the realm of possibility.

The longer I practice and really, the more lazy I get, the more I move to pharmaceutical medications that have relatively low risks, but more risks than some herbs.

And the way that I go about this is, if they’re 70% better, 80% better, I’m done treating their bugs and I’m moving on to GI restoration, microbiome. Also using probiotics. Or mucin regeneration or just mucus membrane regeneration. I’m not going to retest. I don’t find the financial value of retesting, because the testing is expensive.

ParasitesDrMR: Right. You’re preaching to the choir there.

DrIG: Yeah. If they’re not better, then I have to figure out why they’re not better. Was my treatment not appropriate? And that’s within the realm of possibility: if a test finds a parasite, parasites are really hard to treat. Medication isn’t as effective for them through the ova formation. You have to be a little bit more aggressive with your treatments. So my big question is, if you’re not getting better, why aren’t you getting better? Did I not use a broad enough treatment?

DrMR: There are several things here I want to come back and dig into. More specifics on the testing, more specifics on the treatment. But I want to take a step backward, to touch on something you said. It’s more of a philosophical construct, but I think will be helpful for people to understand.

Gray-Area Gut “Bugs”

For the audience, if you don’t know what a protozoa is—and perhaps, Ilana, you can give a more technical definition—I describe them to my patients as more advanced bacteria. For some protozoa, like Blastocystis hominis, for example, the Mayo Clinic’s position (at least a couple of years ago) was to treat in someone who has symptoms. And for someone that does not have symptoms, you may not need to treat it. And I think there is a degree of these bugs in that gray area. They really can cut both ways. If someone’s not eating the proper diet, not exercising, or exercising too much, not sleeping enough, if they have a lot of stress, they have a much higher predilection towards those gray-area bugs causing problems.

ParasitesAnd if you do what you can, then I think these potential commensals or these gray area bugs don’t necessarily pose a problem. As you said, gut restoration (which I thought was a nice term) takes a holistic approach, which I talk about in Healthy Gut, Healthy You, and you try to cultivate healthy soil like a gardener. Now you have a really healthy soil and ostensibly healthy microbes to help police out these bugs that may be problematic.

So that’s how I look at this. But would you amend this philosophical point at all?

DrIG: So I’m a naturopathic physician, which means that my first rule is to do no harm. And I feel like when you’re a neonate in school, the message that they shove down our throats is, “It’s not the bug, it’s the terrain. It’s not the bug, it’s the terrain.” Like the Blastocystis hominis, Dientamoeba fragilis, Entamoeba histolytica: all of these fall under the opportunistic pathogen. Which means they can be in somebody’s gut and that person can be completely fine, totally asymptomatic.

DrMR: Oh, even with Entamoeba histolytica? Because I understood that was an overt pathogen.

DrIG: I feel like it’s changing right now. Literally, in my inbox two days ago, I got an email from Medscape. I get updates from where I’ve put what I’m interested in into Medscape: I have GI, I have probiotics, stuff like that. They send me all of the latest studies and continuing ed about it. Just two days ago I got one from Medscape that was a list of the most common parasites found in the U.S. and in the world. But the whole point of this little tutorial was that parasites are a lot more common than we think they are. And when you have symptoms you should treat the parasites.

And in the message they had Dientamoeba fragilis, which for me up until recently I always thought was more of the opportunistic pathogen. Now, as of two days ago, Medscape is putting it into the frank parasite category. So I think whenever we’re looking at these parasites, it’s this spectrum: do we know for a fact that this is a known pathogen that’s going to cause issues like Giardia? Which wasn’t a known pathogen 25 or 30 years ago.

Editorial Note: Dr. Ruscio feels that Entamoeba histolytica is a frank pathogen, and should always be treated.

DrMR: Okay. Then perhaps it was because of my introduction to that critter, having had it myself, that I was under the impression. I also know that that bug can cause dysentery death in Third World countries. But yeah, there’s this gray line delineating overt pathogens, potential commensal, or just opportunists. So it’s not always as black and white as I think patients wish that it would be.

And I think that’s okay. It’s just good for us to recognize that, so that patients don’t feel like their provider is evading a question. It’s not always black and white. And I’m sure some providers struggle with that. Hopefully you can have your patients listen to this discussion.

DrIG: And as the testing becomes more sensitive and we’re able to find these pathogens a little more readily, it will most likely change our perspectives. These pathogens oftentimes are relatively difficult to find if you’re relying on standard older technology. But the flip side of that is, these pathogens might falsely come up positive if you’re relying only on the newer technology.

DrMR: Right. It’s a balance. And I’ve seen quite a few clinicians fall into over-extrapolating from DNA tests. Looking at them too literally. And I do use the DNA tests and I like some of them. But you have to know the pros and the cons of the tests that you’re using. If you use a lactulose SIBO breath test and you see only positive at the very, very end, that may not be a true positive. And if you see a positive on a PCR DNA test and it doesn’t seem to fit, that may be a false positive. Hopefully we’re getting better and better.

ParasitesBut again, I think the theme here is that we don’t want to look at these tests 100% literally. This is why I’m not a big fan of some of these companies offering direct-to-consumer testing. Because without the interpretation, it’s very easy to get lost and misled with some of these.

DrIG: I also find that it’s just as easy to over-treat herbally or pharmaceutically.

DrMR: Sure. I think over-treatment’s a big problem. Completely.

DrIG: And that also can do more harm than good in some cases, if you’re not paying attention to the full picture.

DrMR: Yep. So we have our monthly clinicians’ training newsletter. And we had a few clinicians wondering why I didn’t treat a lab finding, a positive PCR/DNA test for H. pylori, in a patient who is now completely asymptomatic after just changing their diet and using probiotics. And it’s because—even though H. pylori has more of a dictum attached to it to always treat it—with the PCR I’m suspicious whether this is potentially a false positive.

And also, there is some evidence showing that probiotics can help change the milieu of the gut to help support the healthier bacteria, to help police out the H. pylori or police it to a more acceptable level. Because the game with H. pylori may not be strict eradication but reestablishing of a healthy equilibrium.

MissingMicrobesDrIG: Did you read that book Missing Microbes?

DrMR: I read bits and pieces of it.

DrIG: It’s a very interesting theory that has slowed me down in treating H. pylori with asymptomatic, not frank ulcer or frank upper GI issues. The whole theory is that H. pylori might play a key role in the microbiome. And you only should treat it when there’s an overgrowth.

DrMR: Right. We reviewed some of this information in my book also: the data on H. pylori don’t show it to be overtly problematic. There’s some evidence showing that it can be beneficial. Now, there is a little bit of a potential skewing of that data. Some of the data that show association of H. pylori to healthier people may be because H. pylori was turned to a proxy for a dirtier environment, meaning people with a less hygienic living situation. Plus, giving them all this exposure to bacteria that tunes the immune system may make them more prone to have H. pylori. So it may not be the H. pylori, it may be the environment.

So we have to be a little bit bridled. But I think, yes, there’s definitely that potential that these things we thought were bad may be good. I think worms are a shining example of that. We’re now literally running select clinical trials in the States and other countries putting worms back into people. And as someone who focuses on IBD, I’m sure you’re privy to that. And there are also these patients who you got better, and then you go to treat the lab result, and then they get worse.

So I’ve learned—and I say this to patients all the time—not to be greedy when someone’s feeling well. Because if the goal is to get you feeling well and you’re feeling well, if there’s something in the lab that you don’t want there and then you just treat that lab, you may lose the “I’m feeling well now.” And that’s a real travesty when that occurs.

DrIG: So you know that theory, is it the chicken or the egg with the H. pylori? Is this the predictor of a worse environment where you’re more exposed? Or is this the frank underlying cause for the pathogen? I’m not sure that’s so untrue with a lot of those opportunistic protozoa that I’m finding a lot of.


At this point my stance is that if I have somebody who is clinically, symptomatically doing very poorly and I find one of these protozoa in higher amounts—for a lot of this testing, you can have a microbiome, a bacterial picture and a fungal picture as well as the protozoa and the helminth—if I’ve ruled out all of the organic diseases that could possibly be causing it and we’re in a frank functional world, I am going to go after the protozoa. Being aggressive with going after it has made a difference in my clinical findings in the office.

DrMR: Sure. And I definitely link up with you there, which is why I have fallen into a pattern of often treating empirically. There may not be definitive lab results or there may be questionable lab results. And I’ve learned that sometimes people need more rounds of antimicrobial treatments or more aggressive or potentially adjunctive antibiofilm agents. So yes, I agree with you there.

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Best Parasite Tests

DrMR: Let’s go back to testing for a minute. Is it your position that PCR testing is the best testing to pin this down? What labs do you like?


DrIG: At this point, I’m almost exclusively using the GI-MAP, which I like a lot. I’ve been in practice treating GIs for 10 years. So I think I’ve done all of them on the market. At this moment, I’m relying most heavily on the GI-MAP. Before this, I was using ParaWellness Research. Do you know that lab?

DrMR: No, I don’t, actually.

DrIG: This guy runs a standard ova and parasite test. He’s a medical doctor and he was a family practice doctor for years. Then he retired. He was a military doctor and he used to run their microbiology department. So after he retired, just for his friends, he started re-running ova and parasite. He runs FEAs and SSMs, plus iodine stains. So he does three different forms of ova and parasite testing. And the difference between a standard ova and parasite test and his is that he will look at every sample well over a thousand times.

So it’s an ova and parasite test. But he is looking a lot, and he’s been doing it since the ’70s or ’80s. He doesn’t do any advertising. This was completely his retirement project. It’s a little bit of a funny test because it’s not a CLIA-certified test. So that’s one. Two, he makes you join some membership group. So I used to use a lot of his. He finds a lot of Giardia, a lot of Crypto, a lot of the opportunistic protozoa. Then I switched to GI-MAP, mainly because I think that PCR is better-studied. I think GI-Map is a CLIA-certified test. And it gives me a bunch of the functional findings as well.

I’m giving a talk at the Hawaii Doc Talks Conference. So I’m in the process of putting together this presentation looking at the usefulness of the functional GI markers. Like elastase, for example. And what I like about the GI-Map in particular is it gives me all of the bacteria. It gives me all of the fungi. It gives me the helminths. But also, it gives me this functional look to see where I need to supplement and what I need to not worry so much about.

DrMR: I’d be very interested in a follow-up with you about the functional GI markers. Because I think some are helpful and some I feel to be red herrings. So I’d be curious to see, when you dig into it, what you like and what you’re leaving by the wayside.

DrIG: I agree. And just as an aside—I was writing the presentation this morning—there’s a study I was looking at from 1994 to 1996, and they compared elastase with chymotripsin. You know if you’ve been running functional GI stool tests, chymotripsin used to always be included. It is a kind of pointless marker. It tells us almost nothing.


DrMR: Yeah, and there are only a select few functional markers that I’d look closely at. I did a cursory check in the literature for some of the markers, and I was really shocked at how little evidence there was for many of them. There are a few, and I think the inflammatory bowel disease markers probably have the most potential.

DrIG: But you also have to know how to use those. Like, calprotectin is extremely predictive for Crohn’s, colitis, or ulcerative colitis. But very low predictability for ileum colitis, or ileum Crohn’s, and these patients are 80% of Crohn’s.

And if you’re relying on the calprotectin for your patients and you don’t have it linked to a colonoscopy, you might be assuming the patients are okay when they’re not.

DrMR: Right. Yeah, there’s definitely a nuance with using some of those markers. And sometimes—I speak for myself, where some patients I’m consulting with are out of state, so we don’t have a local GI we can refer with, or their local GI doesn’t want to do a repeat—there can be challenges getting the data you’d like and you have to do the best you can with the data you have. But agreed that I think the inflammatory bowel disease markers are probably leading the pack, in terms of the ones that I look at for a functional marker.

So you like the GI-MAP. That’s easy for people, so now there’s a test there that they can look to.

Frank Pathogens Need Treatment

What about the treatment options? And maybe some of the findings that you feel to be the most important to move on? Like, if you saw Endo-Nana compared to E-Histo, I’m assuming that you’re going to look much more strongly at one. And I know this might be a little bit meticulous, but to whatever degree that you can, if there’s a list of any of these definitely need to be treated, so people can have a list to go to.

DrIG: So yes, absolutely. If you find Giardia, you’ve got to treat it. If you find Crypto, you’ve got to treat it. Entamoeba histolytica, any of the ones that we know are going to cause dysentery, bloody stools, that always gets the top of your list. Below that is these opportunistic bugs. And so that would be the Blastocystis, the Dientamoeba fragilis–


DrMR: And these are broken out, I believe, by pathogens to opportunistic—just for people who may have gotten their own GI-Map and are trying to interpret this—right? They are divided out nicely, correct?

DrIG: Yes. And I like the organization of the test as well. The way the test is broken up is, the first page is bacterial pathogens that are frank. Parasitic pathogens that are frank. And viral pathogens that are frank. And then we have H. pylori markers with virulence factors. This is a really interesting nuance. If I have a positive H. pylori, but any of the virulence factors are not positive and the patient is not symptomatic in the traditional H. pylori way, I’m not going to treat that.

DrMR: I really like that. It’s funny you say that, because I’ve been doing that without even really realizing I’ve been doing that. And I especially look at the CAGA, because there was recently a study published showing that that virulence factor correlated with thyroid autoimmunity. Whereas without that virulence factor, but with H. pylori, there was no correlation of thyroid autoimmunity. So there’s definitely this nuance in H. pylori. It’s exciting to think where we’re going to be in another, maybe, five years with being able to say, “H. pylori, here are the virulence factors you treat. Here are the ones that you don’t treat.” And have a much clearer perspective on this.

DrIG: There is something to be said about specializing. When anybody first starts practice in the alternative healthcare field, you see everybody. And you’re smart on everything, but you don’t know a lot about anything. I feel like when you can specialize, focus, and get into the nitty-gritty to understand all of the nuance, first of all, it’s incredibly exciting for a provider, because then they can keep up and keep afloat. And second of all, for patients: unless you’re working with a specialist, there are a lot of superficial things that people know but don’t know how to get deep into.

DrMR: No, I love the fact that you say that. This is one of the things I’ve talked about in our clinicians’ training newsletter and in various talks I’ve given to clinicians. I think this is where natural and functional and integrative medicine needs to go. Because in my experience, if you’re trying to do everything, you’re only going to be able to help those small slice of people who have the simplest cases. Which is all fine and good, but the problem is that oftentimes people need more than that.

And I’ve found that my office runs much more efficiently in every regard, from time to finances to how quickly we get patients better, to patient problems and troubleshooting. In every regard, there have been better results as I’ve had a niche that I focus in, rather than trying to be too broad. And I think this is really important, especially for newer practitioners. Don’t try to be everything, because I think that may cause some practitioners to flounder. They’re never wanting to say no to one patient, because understandably you just finished school. You have no money. You have a lot of debt. And you’re trying to grow your practice as much as you can.

“If I have a positive H. pylori, but any of the virulence factors are not positive and the patient is not symptomatic in the traditional H. pylori way, I’m not going to treat that.”tweet e1540485375388

But, in my opinion, you’re much better off focusing. Because, again, you’ll struggle. You’ll have all these protocols to use, but you won’t know when you’re using the protocol the right way. When you’re not using the protocol the right way. When you’re actually treating the right thing. When you need to make a lateral move to another system. And it can be very hard to really get the traction that you’re looking for when you’re doing Lyme, thyroid, gut, mold, adrenal, hormone, right? It can be very challenging.

DrIG: I will also say I have the luxury of being in Portland, Oregon, and we are the natural medicine capital of the world, probably. And so I do have the luxury of saying, “I don’t do that but I know you can find another natural health provider that does.”

When I was practicing in New York for a very short time, nobody did what I did there. People were dying to see anybody who knew natural medicine. So when I was practicing there I didn’t have the luxury of specializing. And so it’s this interesting dance where if you’re in this unlicensed state and you’re the only one who does what you do, you kind of have to do a little more of everything. But I feel it is to the detriment of the patient. I don’t think it’s going to hurt the patient, but it’s definitely going to cause them to spend a lot more money.

DrMR: Yeah. Again, well said. I agree completely. Okay, so we have the pathogens sections.

DrIG: Also, can I just make a correction? I said Entamoeba histolytica earlier, what I meant was endolimax nana. Sorry about that.

*Endolimax nana and Entamoeba coli fall into the opportunistic category. And the Entamoeba histolytica is the frank pathogen.

DrMR: Gotcha. And GI-Map does do a good job of breaking these out into those different categories for people. So the bottom line here is—and feel free to amend this if you want to—anything that’s labeled as a pathogen, yes, that needs to be taken care of.

DrIG: Has to be treated.

DrMR: The commensals and the opportunists, they may pose a problem. They may not pose a problem. This is where context is much more important.

DrIG: Anything that’s a frank pathogen, there is no discussion. No matter what provider you see, they are going to say say treat. Period. Full stop. The commensals, that’s where we go into the gray.

Approaches for Handling Opportunistic Pathogens

DrMR: Right. Now, how do you get the gray? That’s a big question. But any pearls there?

DrIG: So honestly, the first thing that I’m looking for is, is there any gray? Am I finding any protozoa at all? You know what I mean?

DrMR: Mm-hmm.

DrIG: Like, am I finding a positive Blastocystis hominis? Am I finding Dientamoeba fragilis? Or Endolimax nana? So if there’s any gray, and they’re showing me symptoms that would correlate with what those opportunistic pathogens would present as (and they’re not correlating with any organic disease picture or we’ve done testing to rule out the likelihood of an organic disease), I’m going to go after those protozoa.


DrMR: Okay. So I want to push you on one a little bit here. Because there’s something that I’ve had to constantly broaden my openness on.

Say you see a commensal that could be problematic, one of these gray area bugs. And let’s say it typically manifests as joint pain, but the person only has brain fog and insomnia (I’ve seen so many cases of problems in the gut manifest in this bewildering array of non-gut symptoms that don’t always line up the same way). And SIBO I think is a great model for that, shown to cause anything from restless leg all the way to problems with the skin to problems with joints to constipation. Problems in the gut can manifest in a wide array of symptoms.

If someone has done everything else—we’ve isolated our variables and diet, and lifestyle’s all in check, we’ve worked them up the therapeutic pyramid—and now we’re finding this potential problem bug with this symptom that doesn’t necessarily line up to it, I will almost always treat that bug. And I’ll observe and look to their symptoms improving to tell me that it was the cause. Are you also doing that?

DrIG: I’m going to start by giving you the disclaimer that I am so specialized. Mainly people walk into my office with GI problems. So I’m going to start there. I feel like a better question for my specialization would be, if these people are coming up positive with these protozoa but showing up with constipation—which generally is not how these protozoa present, they generally present as diarrhea—would I treat those constipation-positive people? And my response is: absolutely.

DrMR: Gotcha. And I should add the context that I think we have a similar patient population. Though it sounds like my patient population might be a little different, in that there’s a subset of my patients who don’t have anything digestive or very minor digestive issues. But they’re saying, “I’d like to have a gut check to see if X, Y, Z symptoms are being driven by a problem in the gut.” And that’s where I’ve been cautious.

But man, there was one case study we wrote up where this patient had this idiopathic, unidentified chapping and swelling of her lips that would just come and go. And no one could figure out what it was. And she had some type of protozoa. We treated that, and four weeks later it was gone and never came back. So I’ve really tried to be open-minded, because I’ve seen some remarkable cases.

DrIG: So I’m also a Chinese medicine practitioner. It’s a very, very old system of medicine. And there is an entire school of Chinese medicine where the whole premise was: treat the gut and the rest of the body gets better. My first day of naturopathic school, we were in histology. And the professor basically said, “Every single person sitting in this room is a large tube with hands and feet to walk them around.”

DrMR: I’ve heard that before. Yeah.

DrIG: In my opinion, if you treat the GI—and I will definitely cop to the fact that my view is very narrow—the rest of them gets better.

DrMR: Right. Well, again, I agree. And I think we both make that statement, not thinking that that’s an absolute rule, but it’s a great place to start.

DrIG: I might think it’s an absolute rule.

ArtemisininDrMR: Okay, fair enough. So regarding treatment options, do you have—and I know sometimes this might be specific to the organism—a few natural and a few prescription that you like? And I’d like to lead that question with, I found Artemisinin, when paired with a broad-spectrum antimicrobial herbal blend, and in recalcitrant or stubborn cases and antibio formation, to work really well. But wondering what you’re liking here?

DrIG: So I’m going to say again, I practice in a fully-licensed state and I am lazy. And I think that either I am not a good enough herbalist, which is definitely true, or my herbal education was lacking in a lot of these low-dose or toxic botanicals. So oftentimes, if I find a protozoa and it is responsive to Alinia, it’s my favorite, favorite, favorite anti-parasitic medication. Mainly because it has no known long-term side effects. Which is kind of amazing when you’re working with any drug. When you look up Alinia—you will feel bad when you take the drug—literally there is (at this exact moment) no long-term risk.

DrMR: And I did both herbals and Alinia for my amoeba. I will never forget, I was in school at the time. I was driving home over the San Mateo Bridge. And just the sun setting was bright enough, because my eyes just felt so toxic–

DrIG: And it will change the color of your contacts. One of my patients just told me that.

DrMR: Yeah. And I don’t wear contacts, but my eyes felt glossed over and puffy. I remember feeling terrible. But sometimes you have to go through a little bit of storm to get to the tranquil seas on the other side.

DrIG: And if I have a bug that responds to Alinia—not all bugs do—I’m generally going to start there. I also dose higher and longer. I studied with Simon Yu, who is this integrated medical doctor in St. Louis, Missouri. And he’s another veteran. He used to do these really long, really intense protocols. So the protocol that I’ll use for Alinia is 500 mg twice a day for 10 days. And then I’ll take about a week and a half off, and then repeat that dose, hoping to catch bugs in the ova and the parasite phase.

I will also say, I will treat around the new moon and the full moon. Not because I have any literature, but I have a ton of folklore. So I try to do these protocols where I’ll have them take it for seven days before the next full or new moon. And then two days after, with the tenth day in the middle. And then take a week and a half off. And then starting two days before the next full or new moon, and take it for another 10 days. So I’ll do those longer protocols. If the bug is known to respond to Alinia, I’m really happy.

DrMR: And is the GI-Map providing a list?

DrIG: No.

DrMR: Okay, so how do you have a list of responders/non-responders?

DrIG: UpToDate. UpToDate will often provide a good PubMed search. Will often tell you if it responds to Alinia or not.

DrMR: Just for the practitioners: UpToDate is a great database that I use, by the way. It’s a subscription required, and I think it’s absolutely worth it. I think it’s $40, maybe $49 a month.

DrIG: I feel like I pay $900 for three years, and I get every ounce of worth out of it.

DrMR: Yeah. And you can just look up the conventional consensus on a given treatment or test in that database. It’s a great tool to have.

ParasitesDrIG: Yeah. So that’s where I start. If Alinia doesn’t work, I have plenty of people who don’t want to take pharmaceuticals. So then I’ll use Artemisia, wormwood. I’ll use Jamaican Quassia, so Picrasma excelsa. It’s in a product I use called Para-Gard by ITI. That’s a pretty good formulation. Black walnut, stuff like that.

If you’re going to do it in tincture form, it’s going to be really, really strong. Really, really bitter. From a Chinese medicine perspective, that’s a really good thing. I’ll still use berberines, garlics, stuff like that, naturally. Oregano is pretty good broad spectrum. My thought process is, most likely if any of these protozoa are here, with them they have a lot of other dysbiotic things that they’re carrying along.

The way I describe it to patients is: you live in a neighborhood. And if the mafia lives in your neighborhood but doesn’t do business there, you’re okay. But if the mafia lives in your neighborhood and does business there, you’ve got a bad new neighbor. That’s why I think the herbs are a lot more helpful because they’re so broad spectrum.

View Dr. Ruscio’s Additional Resources

Optimizing Immune and Gut Health

DrMR: All right, I have two final questions I want to ask you. I’ll bundle these two into one, because they actually touch one another. There are some cases where someone is convinced that they have a parasite. Or convinced that they still have some type of dysbiosis, even though it can’t be found. Which I am 100% open to because I do know that occurs.

I always use the example of SIFO (small intestinal fungal overgrowth). We know it occurs. We know in roughly 30% of non-responsive IBS cases that SIFO—at least according to one study by Satish Rao—may be the underlying cause. So totally open to that, and I’m open to treating someone empirically without any lab findings and using their symptomatic response to guide us. Totally on board.

But my hypothesis that I’ve been developing is that you may have gotten the microbiota in pretty good shape. And the problem might be the immune system. And I pull this from what I learned when writing Healthy Gut, Healthy You. It was really a newfound respect for how these early life developmental factors can skew someone’s immune system for their entire life.

H. pylori

So I’ve been wondering… For some of these people, they had a touch of SIBO. They had H. pylori. And maybe they had Blastocystis hominis. And we’ve now treated that and they’ve gotten better. But they’re still seeing some symptoms or they’re still occasionally relapsing. Not as bad as they were before, but there’s still something there. They still need to advance. And I wonder, perhaps, if we’ve gotten the microbiota as good as we can, but now we need something that helps to tone down and attenuate this overzealous immune response. And this is where I think various immunoglobulin formulas or antihistamines may have impact.

So the question I’m leading to here with this long prelude is, do you see the merit in potentially treating the immune system on occasion?

DrIG: Yeah.

DrMR: And are you doing anything there?

DrIG: If the patient wants me to treat but there is no found pathogen, I do not feel comfortable treating with anything except really mild, gentle herbs. These herbs especially are known to have GI mucosal repair. That feels pretty safe to me, like I’m not going to do harm. The war on drugs was a really, really good idea. It panned out really, really poorly, because you just focus on the war. I feel like we have the possibility of doing the same thing with the GI. It’s this beautiful, intense orchestra. Supporting its function is much more valuable than just carpet-bombing everything.

So I feel like if I find something and it matches the symptomatic picture, I’ll treat that. And then following up that treatment, you have to do the restoration of the lumen of the GI. You have to. It’s invaluable.


DrMR: Yep, I agree. And to clarify for people who are wondering, I typically don’t do a lot of gut soothing, repair nutrients, immunoglobulins, or things like that, until after I’ve addressed dysbiosis. Because I’ve found until you’ve addressed that, the results have been lackluster. And I also have noticed that sometimes—maybe the majority of cases—after you address dysbiosis or the infection, there’s not any need for repair and soothing nutrients. In a lot of cases, that was the thing driving the problem. And now they’re in good shape.

DrIG: So I’m playing around with it a little differently. That’s how I used to do it almost exclusively. And right now, I’m starting to think maybe I was waiting too long to introduce the GI lumen support. I’m playing around with doing them simultaneously. The other big “aha” moment that I’ve had in the last year, four months, is I feel like I have been underdosing a lot of my GI restoration agents. I started looking at the literature and I’m positive I was underdosing my glutamine, my NAG, my vitamin E. I think I wasn’t seeing as much efficacy, because I was underdosing it.

So right now I’m either treating antimicrobials and immediately following it with some of those GI supportive nutrients, or I’m doing it simultaneously. A, I feel like it helps with side effects of the medications. And B, I feel like that way, as soon as we get rid of the underlying cause of the pathogen, the body can restore.

DrMR: It’s so funny you say that. Because as I was making that comment, I was grappling inside my head. Do I say that, every once in a while, I deviate from waiting to use the gut repair nutrition until after? It’s always a challenge in these conversations how much of the nuance I build into the narrative. Because if we’re too nuanced then we won’t ever get anywhere.


It’s great how we’re both specializing in this area and seeing some of the same things. Which is really nice to see, because there have been more cases where I’ve been doing that lately. The subset I’m looking at is patients who seem to have symptoms that revolve around histamine sensitivity (that’s not very helpful because it is a broad assortment of symptoms).

But when I have the intuition that someone is histamine intolerant or histamine sensitive, that subset especially, I’ve been using some of these compounds a little earlier. Just to see what kind of assistance we can give. We’ve been experimenting in a similar vein with CBD. Too early to tell just yet, because I’m only a month or so in. I’m curious to see what kind of impact we see from that.

DrIG: Yep. I would absolutely agree.

When A Parasite Can’t Be Found

DrMR: Okay. So, last question—before I ask you about your website or wherever you’d like to point people to learn more about your work, which I think is great—you kind of answered this, but I just want to ask it for certain audience members listening. Every once in a while I come across someone who is convinced they have a parasite. And even after we’ve done numerous types of the best tests, which would include a DNA test, like the GI-MAP, these patients are just convinced.

And it’s always disheartening, because I think they’ve convinced themselves that the problem is X. And I understand when you have a strong hunch. But if you have a strong hunch that you are unwilling to move off of, in light of even compelling evidence, it’s challenging. These patients often say, “Well, I’ve read that you’ll never find them. And you try to treat them and they move. And even the best labs…”Parasites

So I have to say, “I don’t know what you want me to do.” Because if there’s this thing that there’s no way of quantifying and no way of treating, what do you do?

Do you have anything for these people that you think might be helpful?

DrIG: I’m sure we both have plenty of these patients. Where I usually start is, if I can’t find it, I’m not willing to treat it. But that doesn’t mean we can’t work on restoring the GI microbiome and the GI lumen, and explain it’s not necessarily the bug, it’s the terrain. If I can’t find the bug, let me work on treating the terrain for a little bit. And let me see if we can get improvement treating that. Maybe that will help us see the bug, if there is no improvement.

DrMR: Yeah, I think that’s fair.

Episode Wrap-Up

All righty. Well, where can people learn more from you?


DrIG: So—I was telling Dr. Ruscio earlier—I just launched my website this week. It’s And it’s ridiculous that it took me a decade to launch it, but it’s up and running. Please be patient, because I’m trying to fill it up as I go. But that’s the best place to find me. And then my clinic is Kwan Yin Healing Arts Center. You’ll get ported there if you go to That’s where I see patients. And it takes a little while to get in with me, but I have residents working under me who are really, really well-trained and we review all their cases. So we can usually get you in to see somebody.

It’s always better to see me in person. I feel like taking that history and sitting with somebody face-to-face just gives us a lot more information. But we do some consultations as well.

DrMR: Awesome. Thank you again for taking the time. I didn’t know that we were going to see eye to eye on so much. But if you’re specializing in the space, and you’re open-minded and doing a good job with fact-checking, reflecting, and learning, I guess you’re going to be led to similar waters. So I’m glad that we are kind of similar in a lot of our thought processes. This has been a fantastic conversation. I really appreciate it.

DrIG: And I just want to say yet again, I am loving what you are doing. I’m loving your view on it and how you put in the literature. And I know for a fact that you are providing such a good service for patients. But for me as a physician, when you’re in this field, learning something new is incredibly exciting. And so I just want to thank you again for everything you do.

DrMR: Awesome. Well, thank you. And if anything new comes your way and you want to come back on the podcast, just let me know and we’ll set that up.

DrIG: Okay, great. Thanks so much.

What do you think? I would like to hear your thoughts or experience with this.

Dr. Ruscio is your leading functional and integrative doctor specializing in gut related disorders such as SIBO, leaky gut, Celiac, IBS and in thyroid disorders such as hypothyroid and hyperthyroid. For more information on how to become a patient, please contact our office. Serving the San Francisco bay area and distance patients via phone and Skype.


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