Addressing Reoccurring H. Pylori Infection | Podcast #238

H. Pylori is a bacterial infection. This kind of infection is something that we always see in our patients with gut issues or poor digestion, or mood and energy issues. H. Pylori is anywhere between 20 to 50 percent of the population that could have this infection.

Know more about more symptoms that could lead to H. Pylori infections, advanced tests and medications, added symptoms, and a lot more.

Dr. Justin Marchegiani

Dr. Justin Marchegiani

In this episode, we cover:

00:57 What is H. Pylori Infections

02:49 Antibiotic Resistance

03:19 H. Pylori Medications, Tests

08:13 H. Pylori Symptoms

14:31 Other H. Pylori complications



Dr. Justin Marchegiani: Hey there it’s Dr. We are live. Evan, how are we doing today? 

Evan Brand: Hey man I’m doing good. Happy Monday to you. 

Dr. Justin Marchegiani: Very good. Happy Monday to you as well. Well we talked about today we’re going to be chatting about H pylori and H pylori infections. The topic that we see weekly in our office of patients coming in with gut issues or poor digestion and even patients that don’t even have gut or digestive issues that have just strictly mood and energy issues. H pylori is anywhere between 20 to 50 percent of the population could have this infection and I see it a lot in my clinic.

Evan Brand: Yeah I would rate this is one of the top five roadblocks to achieving optimal health. You know you and I will zoom in and focus on maybe smaller more nuanced topics. But to me this is like one of the biggest roadblocks there is, mainly because of the mechanism that H pylori is doing on the body which is reducing your ability to produce stomach acid.

Dr. Justin Marchegiani: 100 percent. So H pylori is a bacterial infection. H stands for helico so it’s like a helix shape and they can kind of like burrow and turn and twist into that gut lining it can create inflammation and there are virulence factors that we look at the big ones are gonna be [inaudible]. These are cytotoxic proteins that are being produced by H pylori by the bacterial infection and they can create more inflammation. It’s a good sign that the H pylori stronger. It’s a big player to be creating a lot more problems. I do see patients still have issues that don’t have these various factors but if we see them it’s a good idea that we want to clear them out by knocking out the infection. And it’s.. for me it just kind of like puts the infection at a higher level in priority in the treatment protocol.

Evan Brand: Worst case scenario with H pylori and those virulence factors you can develop gastric ulcers, you can develop gastric cancer, you can have major damage to your esophagus, so this stuff can get pretty nasty. And we’ve seen cases like that where someone comes to us where they’ve already had an ulcer diagnosis by doing like a barium x ray where you drink a terrible chalky drink they do an x ray on you and they can visualize the ulcers and then the gastro doc in that case generally they’re just gonna put you on acid blocking medication. So I think maybe we should spend just a minute here talking about conventional treatment for this stuff. It’s not very pretty. Triple or quadruple therapy is often used which is three or four antibiotics used at the same time. Now we know that that doesn’t work. Number one, because the CDC admitted that antibiotic resistance is happening. But number two, you and I measure antibiotic resistance on our stool testing and we find a lot of positives which would indicate, hey if you take this antibiotic, you throw it down the hatch you try to treat the H. Pylori with it. It won’t work. 

Dr. Justin Marchegiani: Yeah I see that a lot as well. I also see a lot of the antibiotic resistance even clear after herbal treatments. Do you see that at all?

Evan Brand: I do too and I’ve always been interested in that. And people asked me and I don’t ever have a good answer to why 

Dr. Justin Marchegiani: Yeah I’ll have to call the lab about that and figure out why that is. But I think —

Evan Brand: I think I know the answer yes. So if we clear the H. Pylori, maybe they can’t test the resistance of the antibiotic towards it because the actual bacteria that showed positive flow.

Dr. Justin Marchegiani: And that very well could be maybe you need enough of that bacteria there to actually test the resistance against other antibiotics. Now that it’s low enough we don’t have enough of that sample, it’s possible. I think that’s a possible theory. But we see H pylori frequently. Now we’ve been testing the DNA. And that’s a good way to test the PCR, the polymerase chain reaction testing is the newer DNA technology to assess the infection. It’s about two to three thousand times more sensitive than the previous gold standard which was the antigen testing. So antigen means it’s the foreign. It’s a piece of the H Pylori. They use a specific stain and they visualize it under a microscope. That was kind of the old type of testing.

Evan Brand: Or remember about five years ago, you and I were just starting to get into the DNA PCR testing but we were still using the old antigen testing where it took three days of stool samples. Remember that?

Dr. Justin Marchegiani: Yeah I remember that.

Evan Brand: So we it would test negative and then we’d have the DNA and we’d see positive and then we’d look at symptoms and we’d say Wow. So now, I mean you tell me if you if you’re doing it differently but I believe you and I both have ditched doing the antigen based testing pretty much completely because we used to run both because we were not sure which one was more accurate. Now we know the DNA is much better.

Dr. Justin Marchegiani: Yes, exactly, so the DNA is great. I will still every now and then if someone is, I think to have an H pylori infection but they’re not coming back up every now and then I will order a blood test where we’ll look at IGG IGA IGM to get a window into acute infections or chronic infections. Right. IGA IGM is more acute, IGG is more chronic. It’s possible that you had exposure to H Pylori. It’s cleared and the IGG still positive. You don’t ever want to treat based off of the IGG blood test for the H Pylori anyway. And then there are breath test, so breath test essentially work by testing and elevation in CO2. So essentially you have and they think they also may assess urea as well. So you have ammonia or you have protein in your tummy and that protein breaks down into urea. And when you have the ureae that’s elevated from H Pylori that urea is can cause that you re to break down into ammonia and CO2. And so you’re getting a lot of that CO2 that’s coming back positive as an indirect indication that H Pylori is active in the gut. So it’s that increase in CO2 that’s giving you that indirect measurement that H Pylori is there.

Evan Brand: Yeah. So one of the questions that we get from people is well, hey I tested positive on this stool test now you gave me this horrible protocol to address this infection. Can we just do a breath test because it’s cheaper or my doctor is going to run the breath test for me. Can’t we just do that to prove that we got rid of it. 

Dr. Justin Marchegiani: Right. So typically you always want to compare apples to apples so if we ran let’s say a genetic stool test and we came back with H Pylori we’d always want to compare apples to apples. We want to compare it to the other tests to assess the, to assess the veracity. So you came back with the G.I. map positive. We want to retest on the G.I. map.

Evan Brand: Now you could throw in the breath on top of it if you want to but I wouldn’t try to replace breath or blood. You know I wouldn’t try to use those to replace a stool panel. We still find the stool is most accurate and also too, you know when you’re looking at somebody who’s got it’s very rare to see H. Pylori by itself. Why don’t we discuss that? I mean, if we look at right now it’s on page two of the stool test. That’s where we see all these H Pylori markers we’ll look at the beneficial bacteria which are often low. But that’s not all. I mean usually there’s a handful of other things like Candida overgrowth that happens as kind of a, I would consider maybe a secondary issue that happened due to the primary H Pylori infection.

Dr. Justin Marchegiani: Oh totally, 100 percent. So just kind of looking at the breath test they are assessing urea but the big thing that does come up is carbon dioxide does come as a byproduct. So just to be clear they are looking at a lot of the urea and that’s a lot of the protein breakdown because H pylori does have that enzyme urea. So just kind of giving you an update of kind of what that breath test is looking at. So we have we have our genetic stool test that we like and they can also assess and look at the virulence factors, and they can also look at the antibiotic resistance. The big antibiotics are typically going to be a combination of triple or quadruple therapy usually it’s in to be Clarithromycin, Amoxicillin Prilosec or PPI and or Bismuth. And sometimes they’ll throw in Tetracycline or Doxycycline to pull those other antibiotics out. So that’s kind of the general triple slash quadruple therapy. And then on the IRB as we may use other things like or goldenseal or CLO or mastic gum or higher dose of oil oregano or even probiotic species can be very helpful at knocking down H Pylori. So there’s a lot of things that we may use to help knock down that H Pylori.

Evan Brand: I want to talk more about like confections that come with this. Yeah. So bacterial overgrowth you know we’ll talk about gut inflammation permeation of the gut barrier. But first why don’t we talk about symptoms because people may be hearing H Pylori all this talk and the like. OK well how the heck do you know besides testing that you have it. You mentioned some people may not show any symptoms at all but they still have a very high level of it. But most people that come to us they’re symptomatic right. They’re not just reaching out just for fun. They’re reaching out because they’re symptomatic. So I would see I would say weight loss or weight gain. In my case, I lost a bunch of weight with H Pylori where I just wasn’t digesting my proteins very well and so I lost muscle mass. I would say bloating, heartburn, gas burping, bad breath is pretty common your breath gets bad because your food’s rotting in petrifying in the gut, your nails my nails develop vertical ridges like my nails became more weak and at ridges because of my malabsorption. What else would you say symptom wise?

Dr. Justin Marchegiani: Can you talk a little closer to the mic? 

Evan Brand: Yes. So your audio right there. Your audio did the same thing it sounded like you were really far away but you weren’t I think then something. 

Dr. Justin Marchegiani: Okay. All right guys we’ll just keep it really close. Perfect. All right. So in general yes. So the low hanging fruit with H Pylori is gonna be getting enough stomach acid.  acid, super super important when it comes to H Pylori. Now it’s a double edged sword with H pylori because with H pylori your gut lining could be a lot thinner. It could be a lot more inflamed due.. due to its inflammation. So hydrochloric acid is like it’s like trying to get a massage for your back pain or an adjustment for your back pain when you have a sunburn like you may need it. It may be the right thing but it may be too much for the amount of inflammation that’s present in your body. So we it’s really important that you work with a clinician to have this kind of dialed in. So we may come in with very low dose on hydrochloric acid or maybe even not maybe just use some gentle bitters or enzymes to support the digestive process and then assess how much inflammation, make sure there’s no bleeding, make sure we add in things to kind of cool off the gap before we do anything on the acidic side. And everyone’s a little bit different. So it just depends I’m always airing on the side of talking to the general public in doing things that aren’t going to set you up for more pain or more inflammation and then work with a clinician that can help individualize things as you start to stabilize.

Evan Brand: Nausea is another symptom I forgot to mention. What about you? Do you have any other symptoms I mentioned the gas bloating burping– 

Dr. Justin Marchegiani: Your gas, your bloating, your constipation, your diarrhea, anytime enzymes or acids are affected motility can be affected. And then of course you have, there’s a couple of studies out there saying, hey look at these symptoms of H Pylori. They have nothing to do with digestive symptoms. These are mood issues, depression, anxiety, cognitive issues so you can have a lot of issues that aren’t H pylori driven, and they can be mood in emotional and cognitive stuff and this is hard because people are kind of like indoctrinated to think, oh I have to have acid burning, I have to have stomach pain, I have to have an ulcer for H pylori to be a problem, and you may not have no symptoms at all connected to digestion.

Evan Brand: Yeah absolutely. I had depression, I had anxiety, I had panic episodes. I mean I was a wreck when I had H Pylori. So I can agree and attest to the fact that yes there probably are some cognitive, psycho, emotional stuff involved and you know, your, your counselor is not going to tell you to go get a stool test for your depression.

Dr. Justin Marchegiani: Exactly yes. And that’s an important part. And why does this happen? What’s the mechanism? The mechanism is pretty simple. I think if we don’t have enough hydrochloric acid if we don’t have enough digestive support, we have to break down these amino acids, right? So think of like a necklace you’re wearing. Think of that as protein, right. If we go to break each pearl off of that necklace. Those are amino acids, and essentially digestive was we have to break those little pearls up so we can utilize, assimilate, and absorb them. And then of course in our body they get converted into a lot of our neuro chemicals, serotonin is going to be tryptophan, or five HDP, tyrosine will get converted to dopamine and adrenaline and norepinephrine and then you’re going to have some of these amino acids convert to GABA which will help you relax and wind down. So we have to essentially take this necklace and break each individual off so we can digest it absorbing assimilate.

Evan Brand: Yep. Well said. All right, so let’s go back to the point I mentioned earlier. So the Coinfections like what else happens with H Pylori, we often see Candida overgrowth happening. We often see bacterial overgrowth happening, so at that point maybe more GI symptoms will come on board, and it may not be the H Pylori directly. It may be know pseudomonas or streptococcus or Klebsiella. Some of these other bad guys. And then we know too that all this undigested food has collateral damage on the gut barrier, right? So we’re going to see the secretory IGA go low and then we know someone has a leaky gut situation. Now what about  Do you test Zonulin? I don’t because I just haven’t found it worth the extra expense for people. But some people this beg and plead that they want on when tested.

Dr. Justin Marchegiani: Yeah there is some data on it. I mean most of the data is kind of circular it comes from Alessio Fasano over at Harvard but there’s some good data that that’s good. That’s the number one protein forgot permeability so if I see a lot of auto immune people I will definitely run it just to assess how permeable the gut is. So Zonulin, this protein when it’s elevated it means the tight junctions are kind of getting unzipped in your gut and the epithelial lining, and then the more permeable your gut is, the more bacteria and infectious debris and or foods that aren’t broken down fully can get into your bloodstream, and create an immune response and create more inflammation, because your immune system not used to seeing all these foods not broken down in the bloodstream. So that creates a lot of immune stress. So it’s nice to have that. I’ll look at it more patients that are have a lot of autoimmune stuff going on just to assess if treatment brings it down. But again it’s not causation for me that’s more correlation. How does this improve as we do these things over here to get rid of inflammation or digest foods or get rid of other infections, so it’s kind of a corollary marker for me.

Evan Brand: Makes sense. I mean I just generally look at the low secretory IGA. I’d say based on that hey you know probably a leaky gut situation. 

Dr. Justin Marchegiani: Yeah, 100 percent. So looking at the H Pylori right today’s podcast is on H Pylori. It’s going to be affecting the digestion of protein. It’s going to affect the lowering of that PH in the got that nice low PH does three things, it, one it makes it harder for bacteria to grow think of nice low PH as like bleach on a dirty picnic table. It kind of cleans things up and sterilize those things bacteria hates acidic environments to grow and likes actual the alkaline environments. Number two, it gets enzymes activated. So those nice active enzymes are PH sensitive so we drop down that nice PH. These enzymes perhaps energy and turns the peps in. We get these nice protein like enzymes going and then all that food that’s all kind of mushed up. That’s called kyme. All right that gets emptied into the small intestine and that nice low PH triggers a whole bunch of Bicarbonate from the pancreas, a whole bunch of enzymes, proteolytic enzymes, light ballistic enzymes that means protein and fat digesting enzymes. And it’s also gonna trigger that gallbladder to bruise a whole bunch of bile which will help you digest fat as well. So three things, right, it’s creating an environment that’s harder for bad critters to grow, it’s activating enzymes, right? And it’s activating a lot of our proteolytic portions and as well as getting the pancreas and the gallbladder involved so really important.

Evan Brand: Yeah, the whole domino effect has to happen with enough HCL which you can’t make if you have that infection, and we find 80 plus percent of partners share H Pylori too, so this is why sometimes we have to get the husband or the wife or even the kids involved too, because if someone gets better and then two to three months later, symptoms come back or issues return then we know it’s probably just a case of reinfection.

Dr. Justin Marchegiani: 100 percent. So if H Pylori is one of these predators that you know typically a lot of parasites the more fecal oral so we usually have to be a higher level of intimacy for that infection to pass back and forth outside of the fact maybe someone did wash their hands and they cook a meal for the family. That could happen every now and then. But the bigger thing with H Pylori that can be spread with saliva. So just you know a kiss between a mom and her son easily spread that, or sharing silverware or sharing a drink in a household– pretty common among family members so that could easily be spread. So, definitely if we see a husband or wife come in, I definitely want at least those two treated. And then we may look at what’s going on with the kids that have any issues that are kind of abnormal on the radar. Meanwhile a little bit deeper right.

Evan Brand: Yeah. Well said well I don’t think there’s anything else we need to cover on this subject. I’m sure we could, we could pick and add more things to the picture. I would you say if you don’t have gut symptoms that doesn’t mean that you’re clear. 

Dr. Justin Marchegiani: Correct. I think it’s good to look at that. And then if you have cognitive issues or let’s say you have mood issues and you’re on an SSRI, maybe a medication that may not be getting to the root cause, it’s stabilizing. Right. But let’s get to the root cause. And then, once we address that then you can go back to your prescribing doctor and look at tapering off that correctly but we always want to get to the root cause. 

Evan Brand: Absolutely. 

Dr. Justin Marchegiani: Now don’t find one thing here I’m just kind of highlight it is gluten is a big deal. I find the more inflamed we keep the gut it’s harder for H Pylori to be eradicated. So, in other words, if people don’t change their diets even with really good herbs it can be harder to knock out the infection. So the more we can keep inflammation down, the better the patient responds to a lot of these natural herbal treatments that.. you notice that too?

Evan Brand: Yeah. Well most of the people that come to us they’ve already changed their diet. So it’s rare that we have to have that, hey you need to be off gluten and dairy conversation. But yeah it does act as a roadblock, especially when we see teenagers that are going out and eating pizza and stuff like that. I don’t get as much success as quickly with them.

Dr. Justin Marchegiani: I agree I think it has to do with getting the inflammation in the gut and the digestive tract drops, but also I think it has a major effect on the immune system. I think if your immune system is continuing to be pounded with the entire course, eventually that performance would drop. 

Evan Brand: Good call. I didn’t think of the mechanism. What do you mean system that makes perfect sense. With the dairy piece especially, I could think of kids that are saying oh my skin is still bad you know cause skin issues can result from H Pylori too. Right. Because that rotting food will create some acne. OK. Well what are you eating and they say well I go out and eat pizza twice a week. Well there you go.

Dr. Justin Marchegiani: Exactly. Find the big thing in a lot of the skin issues are what happens because poor digestion is going to be a skin issue. That’s why you see, lots of people talking about improving. You know when they start adding apple cider vinegar into their diet because you’re asking. To see the gas and that’s helping to break down proteins and therefore you see improvement. Yes. That’s another mechanism. Why skin improves with better gut out, better acid and digestion, less putrefaction to the patient and the skin is always going to be used as a means to detoxify. So if you have stress and we can’t get it out giving you to deliver, the skins into the next organ system that’s going to be leaned upon to help with the thoughts of the patient.

Evan Brand: Yeah if I start to break out of my face, I start to think, OK what’s going on. Am I not doing something right. Is my gut? Is it my diet? Is it my liver? Like what’s going on.

Dr. Justin Marchegiani: Exactly. Good point. All right. So just kind of recapping the if someone’s struggling with issues that digestive side or even mood side and muscle look at that. That’s the H pylori infection connection. Make sure you click down below. Reach out to Evan at or Dr. Justin Marchegiani. Myself at  Links down below. We also have transcriptions available if you guys want to look at or read transcriptions there’s a great option for you. Make sure you click and subscribe as well so you get new great content that is coming out of your way. Right. Anything else you want to say here?

Evan Brand: No that’s it. I would just say get yourself tested. You never know until you test.

Dr. Justin Marchegiani: I totally agree. You’re not testing,  if you’re not testing, your guessing. Right. We want you to assess and getting that correct data so we can make the right.

Evan Brand: My daughter showed up with H Pylori. She had loose stool, and so we tested her around age 2 and she had H Pylori. So we gave her some liquid herbs. We retested her H Pylori, now gone. So I mean this doesn’t discriminate no matter how old or young. I mean, you could be two years old with this infection and that could lead into potentially issues with growth and development and all that. If you’re just not digesting, her gut inflammation was high with that as well. So I’m glad that we were able to catch it early and take care of it.

Dr. Justin Marchegiani: Awesome. Pretty cool. Well great podcast today. We’ll be back next week. You guys have a phenomenal day. Thanks guys. 

Evan Brand: Take care. Bye

Dr. Justin Marchegiani: Bye.


Audio Podcast:

Hashimoto’s Disease and The Infection Connection

hashimoto's disease

By Dr. Justin Marchegiani

Hashimoto’s Disease, is an autoimmune disease, a disorder in which the immune system turns against the body’s own tissues. In people with Hashimoto’s, the immune system attacks the thyroid. This can lead to hypothyroidism, a condition in which the thyroid does not make enough hormones for the body’s needs.

While a healthy immune system resists infection, a weakened immune system welcomes it in with open arms. Infections thrive in unhealthy environments. And once a bug (parasite, bacteria, fungus, or virus) moves in, it can be difficult to exterminate.

Infections can worsen autoimmune conditions of the thyroid (such as Hashimoto’s thyroiditis and Grave’s disease) and other parts of the body. It can also create inflammation, disrupt detoxification, and wreak havoc on the digestive system. So the bug has moved in—here’s what you need to know to minimize infection and protect your thyroid.

Bacteria in the Gut: The Good vs. the Bad

Our gut needs good bacteria to function and thrive. A ratio of 80% good bacteria and 20% bad is a healthy level of gut bacteria.

An imbalance in this bacteria (e.g., 80% bad and 20% good) is called dysbiosis. Overgrowths of yeast (such as Candida) or infections (such as H. pylori) can cause this imbalance.




Good bacteria consume toxins and send nutrients to the body. Bad bacteria consume nutrients and send toxins to the body. Those bad bacteria can lead to a leaky gut.

Small intestinal bacterial overgrowth (SIBO) is a condition that’s driven by bacteria that’s migrated from the large intestine into the small intestine. They’re in the wrong place. This can produce toxins in the gut and disrupt peristalsis (the wavelike contractions that move stool through our intestines).

If we have a delay in peristalsis, we can reabsorb a lot of the toxicity. This is called autointoxication.

Infections in the gut can be particularly challenging and difficult when they accompany an autoimmune condition.

If you are concerned that you might have a gut infection, please feel free to reach out here for help!

Infection with an Autoimmune Condition (Hashimoto’s)

When we have an autoimmune condition, this simply means the body is making antibodies that can’t tell the difference between the invader and the body itself. Antibodies are proteins that fight invaders such as bacteria and viruses. So while the antibody may fight the invader, it will also attack a specific part of the body.

In the autoimmune condition Hashimoto’s thyroiditis, the body makes antibodies to thyroid peroxidase (TPO) causing thyroid breakdown. In Grave’s disease, the body makes antibodies to thyroxine-binding globulin (TBG) causing thyroid breakdown.

Infection Leads to Leaky Gut Leads to Thyroid Breakdown (Hashimoto’s)

The bad bacteria (overgrowths of infection) in the gut pave the way to a leaky gut.

When our gut becomes leaky, undigested food particles pass through “leaks” in the gut and enter the bloodstream. The surface proteins on gluten, for example, can look very similar to the thyroid and cases of “mistaken identity”. This is known as molecular mimicry. This is true for other body tissues as well. Dairy can look like the pancreas, for example.

So the immune system starts making antibodies for the thyroid because it can’t tell the difference. And then know, the thyroid is under attack.

Infection and a leaky gut are two of the prime mechanisms that exacerbate the breakdown of the thyroid.


immune system


Infections That Impact the Gut and Thyroid

A few common infections that are found when dealing with leaky gut and thyroid issues follow:

  • Helicobacter pylori (H.pylori)—This bacteria is common in greater than 50% of the population. It can drive autoimmunity in Hashimoto’s. Also, it is linked to other autoimmune conditions. It is transmitted through saliva or fecal contamination.
  • Borrelia burgdorferi (Lyme disease)—This bacteria looks similar to the thyroid, so it can exacerbate autoimmunity. It can be acute or chronic and is transmitted by the deer tick.
  • Yersinia enterocolitica—This parasitic infection can trigger thyroid conditions and autoimmunity. It is transmitted through contaminated food and water.
  • Candida—This fungal infection disrupts digestion, throws off good-bad gut bacteria balance, and creates constipation. It is transmitted through direct contact and can be spread by contact with contaminated objects.
  • Epstein-Barr virus (mono, the kissing disease)—This virus causes an imbalance in the immune system and is present in 80–90% of the population. It’s connected to many autoimmune conditions, including Hashimoto’s. It is transmitted through saliva.

Removing the Infection Isn’t the First Step

Addressing infections can be stressful on the body. Being unhealthy means having an imbalance in gut bacteria, poor gut function, adrenal issues, energy issues, a bad diet, poor sleep habits, etc. When we are unhealthy and we knock out an infection, our body has to deal with the dead debris.

The infections are like soldiers fighting on a battlefield. We introduce our natural or herbal antibiotics to destroy the infections. Massive numbers of soldiers (the infections) are falling all over the battlefield.

Our immune and detoxification systems have to send out the medics to help pull the soldiers off the battlefield, but there are just too many soldiers (too much infection debris). The medics (our immune and detox systems) get backed up. And there’s a huge line of soldiers that still need help.

Once our immune and detox systems are backed up, this creates a Herxheimer reaction. In this reaction, the harmful biotoxins from the infectious debris accumulate. Then, they start creating stress on our immune, detoxification, and lymphatic systems. The medics are stressed—they can’t keep up.

To eliminate the stress of infection debris on the body, removing infection should be the fourth step in a five-step (the 5Rs) strategy that can be found in detail at this link, and briefly below:

  1. Remove hyperallergenic foods.
  2. Replace enzymes, acids, and bile salts.
  3. Repair with healing nutrients and adrenal support.
  4. Remove infections
  5. Reinoculate with probiotics.

Removing infections can leave the gut empty. It will even knock out some good stuff, too. And weeds (bad bacteria) tend to grow automatically in this world. Gardeners don’t go to Home Depot to pick out weeds to plant. Weeds just happen. So it’s important to reseed the gut with the good bacteria after removing infections.


Studies have shown that when certain infections are removed, we see a significant decrease in the amount of thyroid antibodies. This means that these infections are driving the immune system to destroy the thyroid faster. So if we can knock out the infections, ideally naturally, herbally, and safely, we can reduce the self-destruction of our thyroid tissue. That’s the goal.

Determining if you have a thyroid and infection connection can be difficult. Please don’t self-diagnose, but feel free to click here for help.


Featured image from

Benvenga S, Guarneri F, Vaccaro M, et al. Homologies between proteins of Borrelia burgdorferi and thyroid autoantigens. Thyroid, 2004 Nov; 14 (11): 964–66.

Corapçioğlu D, Tonyukuk V, Kiyan M, et al. Relationship between thyroid autoimmunity and Yersinia enterocolitica antibodies. Thyroid, 2002 Jul; 12 (7): 613–17.

Molina V, Shoenfeld Y. Infection, vaccines and other environmental triggers of autoimmunity. Autoimmunity 2005 May; 38 (3): 235–45.

Tomer Y, Davies TF. Infection, thyroid disease, and autoimmunity. Endocr Rev, 1993 Feb; 14 (1):107–20.

Wentz, Izabella. Hashimoto’s Thyroiditis: Lifestyle Interventions for Finding and Treating the Root Cause. Wentz, 2013: 238–241.

What Causes H. Pylori Infection…The Most Insidious Infection Around?

By Dr. Justin Marchegiani

What causes H. pylori infection? Did you know that over 50% of the population has an H. pylori infection (1)? Dr. Marshall, the scientist who discovered H. pylori, won the Nobel Prize in medicine in 2005 for his discovery. His initial research was done on himself, as he infected himself to prove the bacteria’s causal connection with gastritis (inflammation of the stomach).

H. pylori is an opportunistic infection that spreads more rapidly in people that have a compromised immune system. This is why there are higher rates of all parasite infections in Third World countries. In the United States, we are seeing an increase in chronic stress and poor eating habits, which compromises our immune function and makes us open for an attack.

How Do You Get an H. pylori Infection?

H. pylori, unlike other parasitic infections, can be spread very easily via saliva and doesn’t require sexual intimacy per se. This is why it’s very common to see an entire family test positive for an H. pylori infection. Things like sharing a drink or silverware can be enough to spread the infection in a compromised individual.

What does H. pylori do to our body?

One of the biggest problems with H. pylori is its production of a specific enzyme called urease, which essentially neutralizes hydrochloric acid due to its increased production of ammonia. Hydrochloric acid is needed to help digest protein, ionize minerals, and create an acidic environment in the guts to stimulate bile release from the gallbladder, which aids in fat digestion in the small intestine.


h. pylori infection

If we can’t ionize our minerals properly, this will lead to a whole host of issues, including osteoporosis, immune problems, thyroid problems, and anemia. Lack of hydrochloric acid will also lead to indigestion, malabsorption, gas, bloating, and a catabolic physiology (your body breaking down faster than it can build up).

A large percentage of H. pylori infected patients will not present with any symptoms, so it’s possible you could be feeling great and still have an infection. This is also why my recommendation for anyone with an H. pylori infection is to supplement with hydrochloric acid and enzymes to ensure optimal digestion, even if no digestive symptoms are present.

It’s important to note that the enzymes and hydrochloric acid by themselves will not be enough to eradicate the infection. A proper assessment should be made by your functional-medicine doctor regarding your primary physical, chemical, and emotional stressors to ensure long-term eradication of the infection.

Click here to eradicate your H pylori infection!

h pylori and inflammation

H. pylori also irritates the stomach lining, hence its connections with gastric ulcers. This essentially creates silent inflammation, and now your adrenal glands have to come to the rescue to put out the smoldering fire in your gut. Your body uses cortisol from the adrenal glands to help put out the fire. But as your adrenals become more fatigued, cortisol will lose its capability of keeping the fire under control. This is the point where you will start to see the exacerbation of your symptoms. Many people can have this infection for a long period of time and not necessarily have any symptoms until their adrenals drop into stage III adrenal fatigue.

What Makes H. pylori Different?

H. pylori is a gram-negative bacteria. What this means is that H. pylori has two cell walls while most bacteria (gram positive) only have one cell wall (see picture below). When there are two cell walls, it makes it harder for antimicrobial medicines and herbs to eradicate the infection. This is analogous to a castle with stone walls for protection also being surrounded by a moat, which makes it more difficult for any intruders to invade.

Efflux Pumps and Antibiotics

In between the first and second cell wall, there is something known as efflux pumps. These pumps have the ability to disperse the antibiotic medicines that were given to the patient back outside into the gastrointestinal tract. These efflux pumps are believed to significantly contribute to antibiotic resistance, which is so prolific today (2).

When the antibiotics are pumped back into the gastrointestinal tract, patients can experience more die-off reactions. These reactions can include fatigue, nausea, bloating, flu-like symptoms, and diarrhea. H. pylori has obviously adapted in a way that has made it more resistant to antibiotics. This is one of the main reasons why I’m such a fan of herbal medicines, as they can be used for longer periods of time and don’t seem to have the same side effects as antibiotics.

The other major issue with gram-negative bacteria is that the outside of the bacteria is toxic. This toxin is known as lipopolysaccharide (LPS), or endotoxin, which is actually toxic to the liver. The more H. pylori becomes eradicated from your body, the more your detoxification pathways become stressed from the toxic debris! This is why I find removing the infection over a longer period of time and using additional herbs to help with drainage and detoxification can be beneficial in reducing those die-off reactions.


gram negative bacteria

The most common or conventional symptoms of H. pylori infection:

  • Abdominal pain
  • Bloating and fullness
  • Dyspepsia or indigestion
  • Feeling very hungry one to three hours after eating
  • Mild nausea (may be relieved by vomiting)

Less common symptoms of H. pylori infection:

  • Neurological pain
  • Anemia (B12 or iron)
  • Leaky gut (gastrointestinal permeability)
  • Depression and anxiety: All of the neurotransmitters in our body are made from proteins and amino acids.
  • Constipation and diarrhea: Inflammation can disrupt motility in the GI tract.
  • Crohn’s, ulcerative colitis, or any other digestive disorder
  • Explainable weight gain.
  • Fatigue or thyroid disorder: H. pylori is linked to autoimmune thyroid disease (6).

gut healthExams and Tests for H. pylori

  1. Blood tests: These tests are indirect and assess the specific immune responses to the H. pylori infection. The immune responses that are measured are H. pylori and IgA, IgG, and IgM antibodies. If you test positive for IgA or IgM, you can be confident that you have an active H. pylori infection. Research has shown that test results in patients that are positive for IgG antibodies tend to drop within six months of H. pylori removal (5).
  2. H. pylori breath test: This test measures increased levels of CO2, which is the by-product of urease and nitrogen. H. pylori breath tests tend to only show acute infections.
  3. Stool testH. pylori stool tests are the gold standard and are the only tests that look for the actual particles of the H. pylori bacteria.
  4. Endoscopy: This test is the most invasive and tends to be the least reliable, especially if you have no overt symptoms. This test can be good at assessing cancer as well as damage to the stomach, duodenum, and esophagus. For most individuals this test is unnecessary and is only recommended for high-risk patients.

Conventional Treatment Options and the Prevpac

Patients who have H. pylori and also have an ulcer are most likely to benefit from being treated. The treatment does not work in all patients.

Treatment must be taken for 10 to 14 days. Medications may include the Prevpac, which is a combination of three antibiotics.

  1. Clarithromycin (Biaxin)
  2. Amoxicillin, tetracycline, or metronidazole (Flagyl)
  3. Proton-pump inhibitors, such as omeprazole (Prilosec), lansoprazole (Prevacid), or esomeprazole (Nexium)
  4. Optional: Bismuth subsalicylate (Pepto-Bismol), in some cases

Natural Treatment Options

  1. Mastica (3)
  2. Burberines (4)
  3. Oil of oregano
  4. Wormwood
  5. Neem
  6. Olive leaf
  7. Black walnut hulls
  8. Burdock
  9. Probiotics (4)
  10. Vitamin C (4)

It’s very important the right combination of herbs as well as the right dosage of herbs are used. I strongly recommend a customized program by a functional-medicine doctor specific to your needs. This will give you the best chance of removing the infection the first time without terrible die-off reactions. If you have any of the symptoms mentioned in this article, click here to schedule a complimentary consult.


1. Yale J Biol Med. 1998, Helicobacter pylori: the Middle East scenario.

2. Biochemical Pharmacology 2000, Antibiotic Efflux Pumps Francoise Van Bambeke et al.  

3. Phytomedicine. 2010, The effect of mastic gum on Helicobacter pylori: a randomized pilot study.

4. Alernative medicine review 2001, Alan Gaby M.D, Helicobacter pylori Eradication: Are there alternative to antibiotics?

5.  J Clin Microbiol. 2001, Short-Term Follow-Up by Serology of Patients Given Antibiotic Treatment for Helicobacter pylori Infection.

6. Acta Med Iran. 2013 May, The association of Helicobacter pylori infection with Hashimoto’s thyroiditis.


The entire contents of this website are based upon the opinions of Dr. Justin Marchegiani unless otherwise noted. Individual articles are based upon the opinions of the respective author, who retains copyright as marked. The information on this website is not intended to replace a one-on-one relationship with a qualified health care professional and is not intended as medical advice. It is intended as a sharing of knowledge and information from the research and experience of Dr. Justin and his community. Dr. Justin encourages you to make your own health care decisions based upon your research and in partnership with a qualified healthcare professional. These statements have not been evaluated by the Food and Drug Administration. Dr. Marchegiani’s products are not intended to diagnose, treat, cure or prevent any disease. If you are pregnant, nursing, taking medication, or have a medical condition, consult your physician before using any products.