Recently I interviewed Dr. Ami Kapadia, and we talked about the gut microbiome and discussed the foundations of good gut health, testing, and treatment for fungi, protozoa, and biofilms, common nutrient deficiencies and their impact on overall healing. If you would prefer to listen the interview you can access it by Clicking Here.
Dr. Eric Osansky:
I am very excited to chat with Dr. Ami Kapadia, as we are going to do a deep dive into the gut microbiome. We’ll be chatting about the foundations of the gut microbiome, including fungi, protozoa, biofilm. We’ll talk about testing as well as treatment options.
I’m going to start off by giving Dr. Ami’s bio. Dr. Ami Kapadia has practiced as a family medication and holistic medicine physician since 2005. She completed her residency at Thomas Jefferson University Hospital in Philadelphia and went on to work in varied settings, including an inner-city urban clinic, VA hospitals around the country, and urgent care clinics in the Portland area. She has been practicing in Portland, Oregon since 2015. Her practice focuses on digestive health and metabolic health. She pays particular attention to the role of nutrition, lifestyle, and food and environmental sensitivities in helping patients reach their health goals. Thank you so much for joining us, Dr. Ami.
Dr. Ami Kapadia:
Thanks, Eric. Good to be here.
Dr. Eric:
Let’s start out. I gave your bio, but if you go into a bit more of your background, how you started focusing on the gut microbiome.
Dr. Ami:
Sure. My family’s from India. I have informally been exposed to ayurvedic medicine for many years. Formally, I have been doing some education in that as well. The gut is the root of a lot of our problems. I shouldn’t say all, but most of our problems historically, some of the more ancient forms of healing as well as we are learning more and more with integrative, functional medicine and even in regular medicine about how so much of our immune system is dependent on our gut health, the gut/brain connection, the gut/skin connection. Basically, any issue you have, there is a gut connection component with autoimmune illness as well. It’s one of the areas that we find is foundational in helping anyone who’s dealing with any sort of health condition help to improve their health. Even though they might have a thyroid issue or autoimmune issue or mood issue, we’re always going to think about gut health as part of how we can help them.
Dr. Eric:
I agree. Most natural health care practitioners, holistic practitioners, functional medicine practitioners, we agree that you need a healthy gut for optimal health. There is that saying, “All health starts in the gut.”
You mentioned foundations. Can you talk about some of the foundations, and expand into dietary recommendations that you give to your patients?
Dr. Ami:
Sounds good. Something that we sometimes forget to do if someone has seen a lot of other practitioners is make sure that we aren’t skipping over foundational aspects of what we all need to do for health. When I meet someone, I try to make sure we’re not missing any of those really basic things, getting stuck on fancy testing and other things where we miss the boat.
Some of the things I try to make sure we touch on with everyone: dietary practices. The standard anti-inflammatory diet. That could mean different things for different people. At least doing organic, non-GMO. Removing added sugars is important.
Meal timing is important. Just not eating continuously all day and into the night. Having some spacing with meals, which is a tradition in ayurvedic medicine, as we learn about more with our migrating motor complex. It’s important to give our digestion time to work in between eating. Those are some of the foundational nutritional things that we go over.
Of course, stress in whatever management we can do. Everyone is under way too much stress. Not forgetting about the effects of that. Outdoor light exposure, exercise, sleep, all of those foundational things are really important to make sure we’re going to get the most bang for our buck in any digestive protocols that we’re doing. That’s where we start with a lot of patients, making sure we’re not having artificial sweeteners and chemicals and all of those things as best we can.
Dr. Eric:
Can you talk more about meal spacing? You mentioned the migrating motor complex. If someone has SIBO, I know a lot of practitioners recommend going four hours between meals. When you sleep, you will hopefully go at least 8-10 hours. Do you think in general, even if someone doesn’t have a condition like SIBO, they should go a number of hours between meals?
Dr. Ami:
I think it makes sense. We did disservice to patients. There was this trend of telling people to eat snacks all day. It’s one thing if they have hypoglycemia. They need a different type of dietary intervention.
For anyone who doesn’t have that, or having low blood sugar symptoms frequently, ideally, they’re having a couple main meals, maybe a snack if needed, and trying not to eat overnight for at least 12 hours is what’s been found, even with Dr. Bredesen’s work with dementia. Giving our system a break overnight helps with things like autophagy and these processes we are learning more and more about. Historically, we recommend people would do that. Now we have more science about intermittent fasting.
I try to keep it simple. A 12-hour overnight fast is great. We just don’t want to be eating up until the minute we go to bed and then eating first thing in the morning. If you stop a couple hours before bedtime, that can get you a 12-hour overnight fast. Then trying to have a couple of regular meals and not just snacking throughout the day is good for everyone in general if you don’t have things like SIBO and overgrowth.
Dr. Eric:
Even if someone is incorporating a 16/8 fast, for those who are not familiar with it, going 16 hours fasting and having an eight-hour eating window, you wouldn’t recommend continuously eating during those eight hours. You would still space it out, have a couple of meals.
Dr. Ami:
I think that would be better. Traditionally, what’s worked well for our digestion as well as some of the newer information we’re finding. They will still get that overnight fast benefit. It makes more sense to have a couple regular balanced meals than just to be eating continuously ideally.
Dr. Eric:
Sticking with the diet but talking more about elimination diet. I could be wrong, but do you do both elimination diet and incorporate food sensitivity testing? Do you essentially start everybody off with an elimination diet?
Dr. Ami:
I do both. For everyone, I do the normal gluten antibodies that you can get through Quest or LabCorps because it’s an easy screen. For some patients, I do advanced gluten sensitivity testing, but not everyone.
Beyond that, outside of removing added sugars, I give patients the option. Elimination diet is the gold standard, but it is hard to implement. It’s challenging with the busy lives everyone has. My favorite book for that is The Elimination Diet by Tom Malterre. He and his wife put together that book. It’s a good, at least one time in your life thing to do to get a sense of how food might be affecting you, if that’s possible with your lifestyle.
If someone can’t do that, ideally, we’ll do the gluten sensitivity testing, and then we will try to remove one or two of the more inflammatory foods, specifically cow dairy along with sugar, at least those couple things, to see if we can reduce inflammation.
The food sensitivity testing can be a useful tool if someone isn’t ready to go into an elimination diet. It’s certainly not 100% accurate. It has false positives and false negatives. But it is a tool. We can use that sometimes to help motivate someone to potentially try the elimination diet. Gluten, dairy, soy, eggs are some of the most common food sensitivities we see. Usually, someone does not need to avoid all of those long-term. We can find a couple that are irritating their system.
Dr. Eric:
I agree with the flaws. There is no perfect test. Even stool testing, someone could test negative for parasites but still have parasites. With food sensitivity testing, it is not exactly the same, but as you said, you can have false positives or false negatives. That being said, when you recommend food sensitivity testing, is it IGG?
Dr. Ami:
It’s IgG. I don’t have any affiliations.
Dr. Eric:
You can name the lab.
Dr. Ami:
It’s cost effective through Alcat. It’s a $95 IGG food panel for $100-$120. It’s quite affordable. It’s good overall. For some people, they might have a lot of food sensitivities, and I am getting a completely negative panel, so it does help me, kind of. Even though we might still explore that, because it’s not 100% accurate, it does lend itself some information to the overall picture of what we’re dealing with.
I know we’re going to dive into this, but this whole mast cell/histamine reactivity in the gut can look like food sensitivities when it’s not. That’s another topic that we could tackle if we get to it.
Dr. Eric:
Sounds good. How about nutrient deficiencies? Can you talk about some of the common nutrient deficiencies you find?
Dr. Ami:
Through routine lab work, through Quest or LabCorps, I routinely will check zinc, copper, ferritin for iron stores, and B12. I frequently find low or low normal levels for zinc, B12, and ferritin for a lot of my patients. That’s another easy screening to look for nutrient deficiencies.
Some people, even though they have been to lots of practitioners and have tried lots of things, surprisingly will have some benefit from simple nutrient repletion, moreso for B12 or iron. With zinc, I don’t have people notice immediate improvement, but it’s one of the things we replete to help in their overall healing. With the other ones, sometimes people do have a noticeable improvement in their symptoms.
Dr. Eric:
For B12, do you recommend serum B12 or methylmalonic acid?
Dr. Ami:
I’ve had good luck with checking a regular serum B12. If it’s less than 400, certainly consider repletion. If it’s less than 600, we sometimes will still consider improving optimizing levels. I often find low or normal levels with that, so I don’t always do the methylmalonic acid unless I am digging further.
Dr. Eric:
For zinc, is it serum zinc or RBC zinc?
Dr. Ami:
Plasma zinc/serum copper. There is a reason that intracellular zinc is not as accurate. One of the founders of functional medicine had given a talk many years ago, and I never fully remember all the details, but it has to do with an intracellular enzyme. Intracellular zinc, I have been taught is not as accurate, so I don’t go with the blood levels. Plasma zinc/serum copper.
That being said, when we order it through Quest, I can’t always get the one that I want. It still seems generally accurate with whatever they’re running for us, so I order as such. It’s been a helpful guide.
Dr. Eric:
I’m sure you do a comprehensive metabolic panel on the basics, the CBC. Some will say that if alkaline phosphatase is low, less than 60, that could indicate a zinc deficiency.
Dr. Ami:
Yeah, I’ve learned that, too. I can’t say I’ve always seen it correlate though. I do usually have a hepatic functioning panel and a zinc level. I typically do both because I don’t always see it correlate.
Dr. Eric:
That makes sense. Can we talk about microbes now?
Dr. Ami:
Sounds good.
Dr. Eric:
You know I want to talk to you about fungi and protozoa, maybe even H-pylori if we have time. Can you talk about opportunistic bacteria? I guess I should ask you first, do you do test for the gut? Do you do a comprehensive stool test?
Dr. Ami:
When I’m doing stool testing, we’ll talk about blood markers I use for candida. For stool testing, specifically I’m looking for protozoa. I’m not fully convinced that the technology we have for stool testing is giving me the best picture of bacterial imbalance, if and when it’s there. I assume everyone has some bacterial imbalance. Part of the treatments we use are broad spectrum botanicals that hopefully will be helping to resolve yeast imbalance and bacterial imbalance when it’s there.
I think the stool testing we have could be helpful. My go-to is Parawellness stool testing, which looks at identifying protozoa because it’s one organism which I feel like we can treat and move past, whereas these yeast and bacterial imbalances can sometimes be a longer treatment plan to help rebalance over time.
Dr. Eric:
I will add that I don’t do stool testing on every single person. When I do a comprehensive stool test, almost always we are going to find some type of dysbiosis, imbalance in the gut flora. Very common to see Streptococcus and Staphylococcus and sometimes Klebsiella pseudomonas. Even if we put someone on a treatment protocol, it’s not like their gut is going to look perfect. There will still be imbalances. I think that’s a good approach, not to go crazy and do testing on everybody and treating everybody for opportunistic bacteria. I just wanted to pick your brain.
Dr. Ami:
It’s tricky because if we see it, we know it’s there, but we still don’t know if it’s causing the person’s symptoms. Is it worth doing an intervention for that? We’ll get into protozoa, but even for example, patients with Giardia, some of the studies show a significant number of people just have Giardia, and they don’t have any symptoms. Other people are incredibly symptomatic from it. It’s this weight of are we going to test? If we are going to test, are we ready to do a treatment? What are the risks and benefits of subjecting someone to that treatment?
Dr. Eric:
It’s funny you mention that. I had someone test positive for Giardia. I was asking about gastrointestinal symptoms. She didn’t have anything that would indicate she has Giardia infections. I forgot where I heard it, but you can be a carrier for Giardia or salmonella.
Dr. Ami:
Right. With Giardia, again, it’s tricky because if someone’s had it for a long time, some of those patients I’ve had had much more chronic constipation. We of course learn about it as causing acute diarrhea. It’s tricky to know exactly what’s doing what sometimes.
Dr. Eric:
Let’s talk about fungi. What are the consequences of fungal overgrowth? Fungi by itself isn’t bad. We want to have yeast. We don’t want to have too much of it. If you can dive into that.
Dr. Ami:
The way I typically explain it with patients is with our microbiome, there is protozoa, bacteria, yeast, and some of these other archaea and such, but those are the primary three organisms we are working on. There is usually some combination of those being out of balance.
The consequences of if yeast is out of balance, it can cause quite a bit of digestive symptoms and systemic symptoms due to the breach of the leaky gut and causing symptoms in other organ systems, such as symptoms that sound like allergy or skin reactivity, brain fog, as well as common IBS symptoms.
The symptoms that patients can get are very similar to SIBO. It’s tricky to sort out is this from bacterial overgrowth or yeast overgrowth or a chronic protozoa infection? We talk about trying to work with whichever of those is the most easily identified and goes along with that person’s history, and reevaluating to see where we are with that.
I do test for that frequently with the standard blood markers through Quest. I check a candida immune complex and antibodies. While you can’t prove that someone has an overgrowth, it gives me clues and puzzle pieces. If those, particularly the IgG or candida or the immune complex are elevated, and they are having gut symptoms or a lot of systemic reactivity that we talked about. It may be worth doing a trial of anti-yeast medication or botanicals.
The advantage of using botanicals like we talked about is they can work on other organisms as well. We can see where we are after that. I know we will talk about protozoa as well. If I find both, I typically will treat protozoa first just because I find a higher success rate of treating that over the short term with pharmaceuticals usually. We can get that treated. Again, the yeast imbalance, bacterial imbalance can be a longer-term proposition. We usually have to spend more time with that.
Dr. Eric:
Protozoa you treat first. Then it sounds like for that, you don’t use botanicals. Usually, you go to pharmaceuticals like metronidazole, for example?
Dr. Ami:
For example, the most common ones we find are Giardia and Cryptosporidium. If someone has one of those, it is always important to remember I have them filter their water to make sure we are not having reexposure.
For treatment, I typically use pharmaceuticals unless they prefer botanicals just because it’s usually a couple-day treatment. I use tinidazole more than metronidazole. It seems to be better tolerated. It has quite good efficacy for Giardia as well.
For Cryptosporidium, there is no perfect medication. Nitazoxanide can work well for that in conjunction. For that one, I use botanicals as well because there is no pharmaceutical that is anywhere close to 100% at eradicating that as far as I know. I will sometimes do nitazoxanide pulsed with some botanicals, and then a second round of nitazoxanide and then more botanicals for that one.
For Giardia, it has a pretty good success rate with standard pharmaceuticals, either metronidazole, tinidazole, nitazoxanide. I would say tinidazole is my go-to that I start with based on my preference.
Dr. Eric:
I want to get back to the fungi, but what are your thoughts on Blastocystis hominis?
Dr. Ami:
That’s a good question. I have wavered over the years. On my website, there is a section on protozoal and parasitic infections, where I list some of the studies looking at what we can use for eradication.
The first question is should we be trying to eradicate this? Is it causing problems? There are studies showing that if someone is symptomatic with IBS, eradication of Blastocystis hominis can improve symptoms. It’s not my first priority to go after that.
If we have done other treatments, and they’re still symptomatic, it’s worth a trial of treatment. I used to do a longer course of nitazoxanide for that because there was studies on that. Then I found that shorter courses had almost the same eradication rate.
I don’t love putting someone on pharmaceuticals for any longer than we have to. My standard Cryptosporidium three-day treatment of nitazoxanide, now repeated two weeks later if we are going to use pharmaceuticals.
There are also botanicals that can work for that. Some of the standard ones that we use for protozoa: artemisia, berberine, things like that can be helpful. Sometimes, I’ll do a combination treatment like I do for Cryptosporidium.
I’m not convinced it’s causing problems for everyone. It’s so ubiquitous. Again, if they have been treated a lot of other things, we will talk about treating this and seeing if they get symptomatic improvement.
Dr. Eric:
In a situation where you’re just focusing on the protozoa, and the person just wants the botanicals, how long on average? You mentioned the advantage of medications knocking it out in a few days. Are we typically looking at a few weeks or a few months when it comes to protozoa and botanicals?
Dr. Ami:
It is rare that I just use botanicals for protozoa. If I do, I’ll usually do at least a month or so, and then we’ll see where we are with treatment. Again, I don’t have any affiliations, but I use a lot of Supreme Nutrition products. They have artemisia supreme, mimosa supreme, melia, which is neem, and a berberine, which is coptis supreme. I don’t use all of those by any means. I’ll pick one or two.
Beyond Balance also has some really nice protozoal treatments that are very safe for kids and adults.
I’ll typically pick one or two, do a bottle of that, and see how they feel. I don’t like to continue it for longer than that. We usually will pause if they are doing better and see if we need longer treatment. We gauge their symptoms before proceeding with more than a month or so of treatment.
Dr. Eric:
Great. Getting back to the fungi. Have you seen where someone has a yeast overgrowth, yet the antibodies are negative?
Dr. Ami:
Yes. There is no perfect test for it. Often, patients will come in with a stool test or these blood markers that I’m talking about, and I try to remind them that we still don’t know if this is causing your symptoms. We want to stop and reevaluate each time. Whatever yeast overgrowth someone has is not going to be sensitive to all of the botanicals or pharmaceuticals. Just because we treat it and it doesn’t improve, we could either be using the wrong agent for what they have, or we could be on the wrong track. I will typically try two or three different things if we don’t get a response with the first intervention that we do before giving up on yeast overgrowth as a piece of what’s going on for that person.
Dr. Eric:
What do you think about organic acids testing? Looking at arabinose and other yeast markers.
Dr. Ami:
Some of my mentors used a lot of that, and I like it. I couldn’t find a lot of research backing up that usage outside of the companies that offer it. I think it’s another helpful tool. If someone has done it, I can use that information. If those are elevated, and I have elevated immune complex, and it’s showing up on a stool test, again, while none of those are definitive, because we all have yeast in our stool, and there is no concentration level that indicates an overgrowth, putting those pieces together gives us more clues as to it might be worth going after this.
Dr. Eric:
When it comes to focusing on the gut, how about other types of fungi? If someone has toenail fungus, would you treat the toenail directly? Is the root cause still the gut in this example?
Dr. Ami:
I’ve seen that be its own thing a lot of times. When I’ve worked with veterans, for example, if they had to wear boots a lot and were sweating a lot, the conditions of external moisture can be there. Other people, there has been shown to be a genetic component for your body having what I generically say is trouble controlling yeast and fungi.
I don’t see toenail fungus to be necessarily correlated to any sort of internal issue. Of course, it could be. But I tend to treat that specifically, usually with pharmaceuticals. The standard protocols as well as some compounded topical antifungal prescriptions that we can get from our compounding pharmacy. That’s worked well for a lot of our patients.
Dr. Eric:
How about vaginal candidiasis?
Dr. Ami:
I do see that often having the person also has a gut imbalance. There has also been some studies showing some women are genetically prone to getting that because we’ve had some patients where they have been on so many antibiotics, and they never get a yeast infection. Other people go on one course and get this recurrent problem. With those patients, I do often see a GU component and a GI component. We are working on this full spectrum treatment that we’re talking about.
Dr. Eric:
With the treatments, again, you’re more likely to use botanicals with the fungi than protozoa, but there are times when you recommend the antifungal meds. Could you talk about when you would use nystatin versus diflucan?
Dr. Ami:
If someone hasn’t responded to botanicals, and I’m still wondering if they have fungal imbalance in the gut, I will typically start with nystatin. It’s not systemically absorbed. It’s very safe. The benefit is it acts on the mucus membranes that it hits, so if they have an oral or esophageal issue, you can get compounded nystatin capsules and empty that in water. It doesn’t taste good, but you can swish and swallow that. If you’re doing the commercial tablets or capsules, that will act in the gut where it’s hitting. It’s not systemically absorbed, and it’s concentrated in the gut imbalance area we are trying to treat. That is usually where I start.
If I’ve done that and am still not sure if they have a problem, because we haven’t had a clear response, it’s possible that the overgrowth they have is not susceptible to nystatin. Sometimes, I will do a couple weeks of fluconazole. I don’t like to do that long-term. It has a lot of drug interactions. I think using it on a broad scale for a lot of patients with digestive disorders isn’t a great idea, given we don’t have a lot of good antifungals, and this whole resistance issue. I will sometimes do a couple-week trial, and if we get a really good response, I will try to find some other agents that can be helpful for them. But it can help us decide if we are on the right track or not.
Dr. Eric:
That sounds good. I know you’ve mentioned botanicals for parasites. Did you mention what you like for yeast?
Dr. Ami:
For yeast, the good part is that some of them overlap. I find berberine or coptis to be really helpful for bacterial overgrowth, yeast overgrowth, and protozoa, depending on the person.
The other ones I will frequently try are neem, which can have an effect on all of those. undecylenic acid is another one. Thorne makes a compound that’s been around for a long time. I will use that one for yeast a lot.
Beyond Balance makes MYCOREGEN, which I’ll also use for yeast a lot, as trials of more yeast specific therapy. Those are some of my favorites I use. Olive leaf can also be really helpful.
Dr. Eric:
I was going to ask you about olive leaf, which I know can help with viruses and other things, too. How about oregano?
Dr. Ami:
One of my mentors was not a fan of oregano, just because it’s so strong. I’ve had patients where they’ve told me it’s been quite helpful. If it’s helped them in the past, we will consider using it again.
My personal bias is I don’t use it as much because of personal teachings from one of my mentors. I don’t think it’s wrong to use it. It is very strong, so I would not use it for a prolonged period of time.
Dr. Eric:
Yeah, I agree. It’s good to at least briefly mention that some of these could have a potential negative- Just because it’s natural doesn’t mean it’s completely harmless. Arguably, it’s better than taking an antibiotic. Still, like you said, you wouldn’t want to be on oregano oil for six months.
Dr. Ami:
Before I learned about mast cell activation and histamine reactivity, I was treating some patients with botanicals over and over, and it was helping. It didn’t seem like that was the root cause. If we’re treating someone over and over, and they tend to improve but not fully, and it keeps coming back, we can talk about how to go after the biofilm issue because sometimes, that’s the issue.
Sometimes, it’s this mast cell reactivity in the gut which can mimic the symptoms of any of these abnormal gut flora issues with diarrhea, constipation, bloating. Sometimes, it’s worth a trial of very simple H1/H2 blockers to see if that helps. Sometimes, that’s helped a lot more than any of the dysbiosis protocols that I’ve done. We just have to remember to think about it as part of our differential. If someone is having ongoing gut or other symptoms, that might be another avenue to think about, in addition to biofilms causing resistance.
Dr. Eric:
With mast cell activation syndrome, you mentioned earlier how someone might not have food sensitivities but mast cell activation syndrome or histamine intolerance. They’re not exactly the same. Is that what you were talking about just now as well?
Dr. Ami:
It’s this spectrum of disorders, specifically for gut health but also allergic and skin conditions and all sorts of issues where it wasn’t in my differential until the last five/six years. I was missing it.
There are mast cells throughout our body, and they contain histamine and all of these other mediators. It’s been found in patients with IBS that mast cell reactivity is higher in the gut compared to other patients. It may be that there is this overall sensitization and reactivity as opposed to “I’m reacting to egg or dairy or soy.” It might be just whatever they’re eating, their gut is hyperreactive, so calming that down can help prevent having to restrict their diet as much. It’s something to think about.
Some of the most effective treatments, if it works for the patients, like cromolyn. For some patients, it doesn’t do anything, and for some, it’s reduced 75% reactivity to foods. Not because they were reacting to all of those foods, but because their histamine reactivity was up.
The tricky part is what is causing the histamine reactivity and mast cell reactivity? That is all of those things we’re talking about. These gut bugs can do it. Food sensitivities can do it. Stress can do it. We still have to go digging. But it can certainly help stabilize symptoms. We can buy ourselves some time and improve quality of life.
Dr. Eric:
Definitely agree you want to address the cause of the problem. You said H1/H2 blockers. As you just mentioned, you don’t want to just give these blockers; you want to do things to address what we’re talking about. Also incorporate diet and lifestyle factors.
I’m sure there might be some people listening who are wondering about quercetin. Can I just take quercetin instead of these blockers? I’m guessing it’s probably not strong enough in many cases of mast cell activation syndrome.
Dr. Ami:
A lot of us do prefer natural botanical, food-based interventions. In my community, what we’ve found is that the natural agents, we can circle back around to them, but we’re not getting as clear or definitive of a response. If we’re really trying to figure out if this person is suffering from mast cell reactivity, we’ve just had a lot more success using pharmaceuticals, at least for a 3-6-month trial. Then we can say, “This is helping or not.” If the person prefers botanicals, we can try to regroup and go that route. I haven’t seen those same results with quercetin, for example.
Dr. Eric:
Great, thanks. Before we get into biofilm, I do want to ask you: Getting back to how we spoke about oregano being a little bit harsh on the gut microbiome, what are your thoughts on berberine? You have mentioned it. I interviewed one specific practitioner who wasn’t too high on using berberine, but the more recent research seems to show a beneficial effect with berberine on the gut microbiome.
Dr. Ami:
I know. That’s gone around and around. We have some patients where we are using botanicals more long-term. I would love to know if there are any studies showing that it’s causing disruption of the microbiome.
I remember one of my first integrative medicine conferences like 15-20 years ago, I asked the speaker who was talking about berberine for blood sugar, “Are you worried about using this long-term with patients?” He was one of the most well-known senior doctors, and he said, “We monitor, but we haven’t seen it.”
It is strong. I don’t like to use it indefinitely. I haven’t seen studies showing it has a negative effect on the microbiome, and there have been studies showing it has a positive effect on the microbiome, and it helps with blood sugar.
Maybe we wouldn’t use coptis long-term. That has stronger activity than some of the other berberine-containing herbs, I believe. I have not seen data showing that we’re causing a disruption. Clinically, from my Chinese medicine colleagues, I learned it is a cold-forming herb. I would be cautious about using it with a certain constitution of patients. I haven’t seen data on negative effects.
Dr. Eric:
Okay. Let’s talk about biofilm. When do you use biofilm? What are some of your favorite biofilm disruptors?
Dr. Ami:
Some of my mentors have had very drastically different views on biofilm. Dating back 15-20 years ago, some of them said, “Don’t mess with biofilms. They’re there for a reason. It’s our body’s way of walling off things.” Other mentors have had the opposite view. I’m in the middle.
I don’t start with biofilm treatment. I think we do have to be cautious, especially with someone who has had symptoms for a long time. That being said, I don’t give it with the first round of treatment. If someone is having non-responsive symptoms or recurrent symptoms, it’s definitely one of the things we think about. Do they have biofilms? That may be why the agents we’re giving them, be they pharmaceutical or botanical, are not getting where we want them to go.
I will introduce biofilm treatment cautiously. We usually use it. Dr. Paul Anderson has some really good information on some of the products he’s formulated. There are some over the counter and some prescription ones. I typically start with over the counter. Some of the ones I’ve used moreso are some of the enzymes, like lumbrokinase and nattokinase as well as Priority One—I have no affiliation. They have a biofilm phase one or something like that. They have a product I’ve found helpful. Those are some of the ones I’ll start with.
If we are still not getting to where we want to be, and it seems like the patient is tolerating those, but we didn’t get anywhere, and I want a yes or no answer if biofilm is part of what is going on, then we will use a prescription compounded version that Dr. Anderson has formulated. Various compounding pharmacies use it. It’s a bithionol complex that is quite strong. That will give me an answer. If someone has an exacerbation of symptoms or improves, then we know that biofilms are part of why they haven’t responded.
You want to start them on that complex, and then have botanical support on board because if we are opening up these biofilms, we want to make sure we’re helping to treat whatever is in there, whether it’s protozoa or yeast or bacteria or whatever else might be part of that biofilm community.
Typically, we’re looking for some sort of response. Did they get worse or better on the biofilm treatment? As opposed to “I took it for a month and didn’t feel any different,” then there probably isn’t a biofilm component to why they’re not responding.
Dr. Eric:
You mentioned Dr. Anderson. A number of years ago, he spoke about taking a biofilm disruptor 7-10 days before doing a stool test, just to reduce the chances of getting false negatives. I’m thinking you’re probably not doing that with the Parawellness, but I don’t know if you heard him talk about that.
Dr. Ami:
I haven’t. I used to do that with certain stool tests. With Parawellness, I get so many positives as is, so I haven’t needed it. If I have a patient who prefers a different type of stool test, I do think it’s a good idea. They probably are not looking themselves under the microscope, like the director of Parawellness is looking microscopically. There are different technologies being used with other stool tests. I think it’s a good idea.
It’s a 7-10-day protocol, and then you collect your stool after that, unless you have an aggravation of symptoms. Then you stop it and collect your sample.
Dr. Eric:
What do you think of NAC as a biofilm disruptor? It’s not just for that purpose. A lot of people take it, including myself. I recommend it for supporting glutathione as a precursor. In some cases, it can be used as a biofilm disruptor.
Dr. Ami:
I think it can be useful. I would say it’s not strong enough to give me a yes or no answer. If you’re using it as one of those initial ones to gently get into biofilms, it’s a good idea. I still hesitate to use it long-term because there are healthy biofilm communities. I do find it is useful for if someone is having a respiratory infection, and we are trying to thin secretions. As a precursor, it can have a role. I tend to avoid it longer-term for theoretical risk of disrupting healthy biofilm communities.
Dr. Eric:
I’m glad we’re having this conversation. I do commonly recommend NAC. If you’re trying to support detoxification, would you tend to go more toward a liposomal glutathione because of what you just mentioned?
Dr. Ami:
Yeah. Detoxification, I used to do very complex protocols. I’ve gone back to more simple things again. Some people feel amazing on acetyl glutathione or liposomal glutathione. I’ve had an equal number of patients who don’t feel good on them. I don’t think it’s essential to use. I think it can be helpful. We’ll try it, if we’re doing a very targeted detoxification treatment.
I’ve gone back toward trying to ensure someone is having good elimination, using food forms of fiber, like cilium, chia, flax to get bile binding that way. Sauna therapy, if they tolerate it. Outdoor exposure.
If I am going to do a targeted detox protocol, I think what you’re doing sounds really good. Trials of NAC or glutathione, maybe just not using it as longer-term. With the glutathione, letting patients know some people feel better, and some people feel worse. Let’s see how you do. I start with those more minimalistic interventions, and then I see, do we still need more detoxification support after that, particularly if someone can’t sweat or do a lot of movement? Everything you’re talking about definitely can be part of the toolbox.
Dr. Eric:
Great. A few questions getting back to yeast when talking about fungi. A lot of people want to know, if someone has candida overgrowth, should all sugar be avoided? Should they avoid fruit? Or is it just minimizing sugar consumption?
Dr. Ami:
I use the protocol that one of my mentors, Dr. Leibowitz, came up with in the ‘80s. We remove added sugars. We allow fresh or frozen fruit. Stevia is fine. Sugar alcohol tends to aggravate GI symptoms, but it doesn’t feed yeast per se. I tell them to remove all added sugars, but fresh and frozen fruit are fine. Carbohydrates are fine. The healthy forms, if they tolerate them. That tends to work well. Patients would always ask about honey or maple syrup.
I have an FAQ list. All of those can still make dysbiosis in any form worse and can negatively affect our health. Part of it is a teaching tool of reading labels.
I tell them not to drive yourself crazy. If you’re eating out, there might be some sugar in the dressing. Don’t worry about it. When you’re preparing your food, you don’t want to add sugar. That’s a long-term lifestyle change. I tell people if you tolerate dark chocolate, the higher the percentage, the less the sugar. That’s fine.
A couple grams of sugar here and there, once we have gotten through the protocol. While we’re doing our first couple weeks, it’s helpful for patients to see how they feel when they’re not doing any processed added sugars outside of fresh or frozen fruit.
Dr. Eric:
Do you minimize fresh and frozen fruits? Like a couple of servings. Or not necessarily?
Dr. Ami:
I tell them to use reasonable judgment. Don’t eat 10 bananas a day. A couple servings of fruit is generally tolerated and fine. Unless they’re doing something unusual, they’re not eating that much fruit. A couple of servings a day if they ask is totally fine for most people.
Dr. Eric:
How about fermented foods for yeast overgrowth?
Dr. Ami:
I have people do this old protocol that Sidney Baker came up. It’s a five-day yeast/mold elimination challenge diet. I tell patients these foods are not bad for you; they don’t feed yeast, but you may react to them, either because you’re reactive to high histamine foods, or because they are moldy. You can remove them for five days and then eat whatever of those you frequently eat. The most common are fermented vegetables, vinegar, nutritional yeast. See how you feel. If you don’t react, you need to remove them. If you do react, we keep them out for the first few weeks of the protocol.
The other way I do it is for some people, it’s just easier to remove them for the first 2-3 weeks of our protocol, and then add them back.
We have a more comprehensive list. The main ones are fermented vegetables, vinegar, dried fruit, alcohol, sugar, and yeast. The sugar, we keep out for everyone. The other ones, we only keep out if they’re reacting, or if we want to keep them out for the first couple weeks because it’s easier than doing the elimination challenge.
Dr. Eric:
I don’t know if you know this off the top of your head. What percentage would you say of your patient population have protozoa, on Parawellness? Same thing with fungi. I don’t know if you want to include mold.
Dr. Ami:
It’s always tricky because we have such a biased patient population. Everyone has symptoms. I would love to have 100 of these test kits to test 100 people in my community and see. I’m sure my results are not representative of the general population.
I would say of my patients, 80% have a protozoal infection. Of the candida blood testing I do, at least 50% will show up positive for one of those I mentioned. Those aren’t definitive, but they are puzzle pieces. It’s a very high percentage. A lot of them have had SIBO testing done already. That’s often a piece of our overall landscape, but it’s been done already. Probably at least 50% of them have had that imbalance.
I try to reorient what we’re doing. These are the three main pathogens or organisms that can be out of balance in the gut. Our overall goal is to help make your system less likely to be having an overgrowth or infection of any of these, as well as eradicating protozoa and rebalancing those other micro-organisms as part of our whole approach. It’s a very high percentage of patients that I test that have those.
Dr. Eric:
I know you have no affiliation with Parawellness. Is it just because that’s what they focus on is parasites, and they have been doing it for a long time, that makes it superior to other stool tests?
Dr. Ami:
From what I’ve been told, talking about standard labs, even our specialty labs, the training is not necessarily there as far as literally making the stool samples to look at under a microscope. The director at Parawellness must have looked at tens of thousands by now of stool samples under the microscope, so it’s a subjective skill in some ways, to be able to pick out these organisms.
It’s the way it used to be done. There were many lab changes over the last couple decades, where that’s not the way most labs are looking for protozoa anymore. They don’t have a technician that’s been trained for years on how to do this. It’s an antigen test. It’s an objective measure, which doesn’t always correlate with the subjective looking under the microscope and having that skillset. That’s my understanding of why the prevalence is so much higher with that actual microscopy skill.
Dr. Eric:
Very interesting. Is it just that one technician there? Has he trained others?
Dr. Ami:
I don’t know. It seems like a large volume of specimens to look at. I don’t know if there is a whole staff. At some point, I want to observe, as I have the same questions. It’s panning out in the patient resolution of symptoms. I know there are practitioners who question it. Clinically, it’s made sense.
I have had patients have completely negative specimens, especially when I’ve had patients who say they’re not having a lot of symptoms. What else can we do? “I have this autoimmune condition or this or that, and I just want to make sure.” I have had fully negative test results at times, typically in patients who aren’t manifesting any symptoms.
Dr. Eric:
You’ve seen autoimmune cases where you address the protozoa. If they have fungi, you address that. And then they get into remission by doing that?
Dr. Ami:
Autoimmune is usually not just those things. It’s this whole thing we’re talking about. It’s stress, lifestyle, all of the things that we talk about in integrative and functional medicine. It’s rare that I have someone who has- It’s so hard to dial in those other factors for all of us, even us as practitioners, that “just fixing the microbiome” is a huge feat in itself. It can’t get fully rebalanced without addressing all those areas.
Yes, I have had patients with autoimmune conditions go into remission. I can’t recall a case when it was easy.
Dr. Eric:
It’s not just follow this parasite protocol. I get it. It’s definitely complex.
Dr. Ami:
I’ve had patients with alopecia arietta where it did go into remission, but it goes into remission on its own sometimes. My patient and I thought it was from everything we did. Would it have gone into remission anyway? I don’t know. But it did go into remission after we treated her protozoa. She was someone who didn’t have a lot of lifestyle factors that were impeding our progress. It was a lot of gut stuff. It was great to see her hair growth come back. We were both super excited. Was it what we did? Who knows?
Dr. Eric:
Can I ask you one last question? H-pylori. You knew I wanted to ask you about this, too. What is your approach? Do you test for it? If someone is positive, do you treat it?
Dr. Ami:
The first thing to remember is I only want to test for it if someone has symptoms of H-pylori. I don’t want to test for it just because they’re having, for example, typical IBS symptoms. So many people are colonized with it worldwide, and the treatment protocols can be pretty aggressive. I only test for it if someone is having typical symptoms like reflux, gastric pain, low stomach acid, and we are trying to dig into that particular symptom picture.
Typically, we use a stool antigen test although there is urea breath testing. If someone has had an endoscopy, they will have had biopsies for it. If it is positive, we will typically treat it because we have usually done the test because they are symptomatic.
I will have patients often ask about botanical options. The pharmaceutical options are aggressive. It’s a proton pump inhibitor with a couple of antibiotics and bismuth sometimes. I give patients both options.
If we’re going to use a botanical option, it’s definitely really important to retest and make sure we’ve eradicated it. There are potential long-term consequences of untreated H-pylori in someone where it’s causing symptoms. There is a Thorne product I’ve used that has some of the things we’ve talked about, like berberine and bismuth. It’s called Pepti-Guard. Most of the companies we use have some sort of H-pylori life formula.
I think that option is totally fine as long as we’re retesting to make sure we’ve treated. I do have patients where we’ve done the botanical program, and it has been eradicated on retesting. I definitely think it works for the right patient.
Dr. Eric:
All right. I know there is so much more we could talk about, but I do want to ask: Is there anything I should have asked you that I didn’t ask you? Anything else you want to talk about?
Dr. Ami:
I feel like you touched on everything, Eric. In 15-20 years of seeing patients now, if we’re getting into all of these details of that supplement or this supplement or why isn’t this working, I find it helpful to take a step back and make sure we’re looking at those foundational pieces we talked about as well as this histamine/mast cell component and biofilm component. If we’re getting stuck and spinning our wheels, there is usually something in those three areas that we’ve missed the boat on. When I revisit those, that’s where we can often find something that will work when we’re getting stuck in the older paradigm of treating these bugs over and over again.
Dr. Eric:
Dr. Ami, thank you so much for your time. Can you let the audience know where they can learn more about you?
Dr. Ami:
My website is AmiKapadia.com. I have a resource tab that has a lot of the handouts I’ve made for patients and resources on there. I see patients in Oregon, so if you live in Oregon or southwest Washington, feel free to reach out to our clinic if you do need help. Thank you for having me.
Dr. Eric:
Thank you so much. It was a great conversation. I’m sure the listeners learned a lot. As usual, I learned a lot, too.
Dr. Ami:
Thanks, Eric. It was nice talking with you.
