How to Treat Gut Infections: Antibiotics or Natural Herbs?

By Dr. Justin Marchegiani

Gut infections are common, and they can prohibit healing and cause a leaky gut. They must be treated to keep the body healthy, but are antibiotics the right choice for you? For some serious infections, antibiotics might be a good choice, but there are deleterious side effects.

Let’s explore why antibiotics have side effects; why antimicrobial, or natural, medicines may be a better choice. And also, what the benefits are of natural medicines.

Antibiotics Pros & Cons

Antibiotics are one of the true miracles of the twentieth century. The invention of penicillin and other antibiotics over the last 50-75 years have saved thousands if not millions of lives!

We live in a world today where antibiotics are handed out like candy, and as a result our gut biome and our health are finally paying for it. Most conventionally trained physicians are still not recommending a round of probiotics after an antibiotic treatment. In my professional opinion, this is an absolute must if antibiotics are ever to be used.

There is a phenomenon known as antibiotics resistance where we are creating superbugs from excessive antibiotic use. I saw a patient just last week who over a 10-year period was given over 100 prescriptions!

This excess antibiotic use causes rebound overgrowth in the digestive tract, essentially causing the bad or sometimes pathogenic bacteria to proliferate. As a result, it will take up most of the space in our GI tract.

If you use the garden analogy for our gut bacteria, everyone knows it takes virtually no effort for weeds to grow, yet, it takes good eating habits, stress reduction, and sometimes supplements to keep the good bacteria predominating. In the garden analogy, the healthy plants or vegetables growing.

When to take Antibiotics?

The bad bacteria in our gut can produce toxins and make it harder for us to absorb nutrients from food. In acute serious infections, antibiotics may be the right choice. With these chronic everyday situations, herbal medicines have a longer and safer track record and tend to be more selective to the bad bugs without causing as many side effects.

I was in a serious situation this last summer with a hand infection from a cat scratch and I was very close to using an antibiotic to treat the infection. I actually had the prescription in my possession, yet after 3 days of natural herbs, the infection resolved. If the infection hadn’t started resolving so soon, I would have had no hesitation to use the prescribed antibiotic.

What Are Efflux Pumps?

Bacteria or infections have a phenomenon known as efflux pumps. The antibiotic enters the cell, where it is metabolized. The efflux pumps then force the antibiotic out of the cell and into the extracellular space or back into the gut.

Imagine you’re in a canoe on a river, and the canoe has a hole in it. The canoe starts taking in water. Your natural response would be to grab a bucket and start bailing water from the canoe.

Efflux pumps are very similar to the bucket. The bucket takes the water that shouldn’t be in the canoe and bails it back into the river.

The same thing happens with the bacteria. That bacteria wants to thrive, and it knows the antibiotic isn’t good for it, so it takes the antibiotic. Just like you’d bail water from your canoe, the bacterial will shoot it’s way back into the intestinal track where it thinks it belongs.

Our goal, however, is to kill the bacteria, so we must inhibit the efflux pumps. If we inhibit the efflux pumps, the bacteria will retain the drug or the antimicrobial, which will procure its demise. If the canoe is analogous to the bacteria, we want the canoe to take on water faster. So knocking out the person with the bucket (the analogous efflux pump) is the goal.

Do you think you have an infection, click here!

How Can We Block the Efflux Pump?

When we create protocols to knock out these infections, how to block the efflux pump is the question that is first and foremost in mind. There is a family of herbs called berberines, and it includes the following:

• Goldenseal
• Oregon grape
• Barberry

These herbs have efflux-inhibiting properties. They have been used in cancer medications, infection-treatment plans, and other treatments. They actually block the function of the efflux pumps.

If you’re going to use an antibiotic, at least use it with a gram of goldenseal to block the efflux pump. This will prevent the bacteria from shooting the antibiotic back out into the extracellular space or the gut.

However, a better choice, which may give a far superior result, could be to take a combination of berberines and other herbs. This is especially effective if you are in relatively good health and making good dietary changes. This healthier lifestyle will boost the immune system, giving you a better chance of responding to the herbs.

What Are Natural Ways to Address Gut Infections?

•  Local killer: Goldenseal is one local killer that will target the area of the infection.
•  Systemic killer: Artemisia or wormwood are systemic killers that will get in the blood and target the whole system.
• Infection-specific killer: Herbal cocktails are created specifically to fight a certain infection. If you have a virus, we may use silver; If you have a Lyme disease coinfection, we may use neem or noni; And if you have a gut-bacteria issue, we may use oil of oregano.

There is an excellent synergistic effect when combining local and systemic killers—wormwood and Artemisia combined with goldenseal. The goldenseal makes the Artemisia stronger.

The Viscous Cycle of Infections:

Most people with a chronic unaddressed infection are kept trapped in a viscous cycle of a weakened immune system, nutrient malabsorption, and a leaky gut.

Our body needs nutrients to run its energy systems, and we derive those nutrients primarily from food. With a chronic leaky gut due to infections, we are assured to develop food allergens to even so-called healthy foods, like broccoli and beef. Thus, our diet becomes more restrictive as the root cause to many of these gut issues gets commonly missed.

With the additional stress to our digestive system, we also lose the ability to make adequate levels of enzymes and HCL. These compounds help break our food down, but they also help kill potential foreign invaders in our food, like bacteria and parasites.

As you can see, it’s common for people, over the years, to collect their gut infections like souvenirs on their mantle. The more gut bugs or infections you have, typically the longer it takes to recover.

If you want to break the viscous cycle of gut infections, click here!

Conclusion

Efflux pumps are the real problem, and that’s why a lot of antibiotics have side effects. The protocol for most antibiotics is only about 10–14 days. With a natural antimicrobial program, the protocol can be 60–90 days, allowing us to slowly break down the whole efflux pump system.

Natural programs include using specific herbs, like the goldenseal, and utilizing the synergistic effect of stacking local, systemic, and infection-specific herbs.

Use Mother Nature’s natural herbs first and foremost. Antibiotics can be beneficial when used in combination with the appropriate natural herbs, but antibiotics should be the last-resort approach.

If you have a gut infection, tough-to-remove parasite, H.pylori infection, or viral infection, these are common blocks that keep you from healing and cause a leaky gut. If you need more help to eliminate these gut infections, click here.

Leaky Gut Syndrome and the Autoimmune Disease Connection

By Dr. Justin Marchegiani

Leaky gut syndrome (gastrointestinal permeability) is a phenomenon that occurs within the intestinal tract where the epithelium tissue’s tight junctions open slightly, allowing undigested food particles and potential bacteria (endotoxin) to make its way into the bloodstream. These compounds are typically only found in the gut, so our immune system goes on high alert when it starts seeing new and unusual things. Our immune system reacts by creating various immune cells called antibodies to inspect what’s going on (and potentially attack)! These antibodies are equivalent to our navy, marine corps, air force, and army; their job is to tag these various particles for destruction. When our immune system attacks some of these foreign proteins (antigens), various organs can get caught up in the scuffle. This accidental tagging is a case of mistaken identity, or the scientific term molecular mimicry.

How Does Molecular Mimicry Work? 

There are amino acid sequences on these antigens (foreign particles) that are similar to other tissues in the body. Our immune system reads these antigens by the sequence of its surface proteins. It’s kind of like getting pulled over by a policeman that is out looking for a similar make and model of the car you drive because a suspected criminal was seen driving the same car earlier that day. Foods like gluten can easily cause your immune system to start attacking the thyroid gland, brain, intestinal tract (celiac, Crohn’s, ulcerative colitis), or other nervous-system tissue based on similarity and genetic predisposition. There’s a good deal of research showing that autoimmune disease cannot occur without a leaky gut. This is why people with a chronic illness need to have their gut checked. Click here to get your gut checked!

Gluten and Cross-Reactivity

When these proteins have a similar shape to other proteins, cross-reactivity can occur. These proteins have the ability to bind into other receptor sites, just like with casein and gluten. As you can see by the picture below, the shape of the antigen can be enough to confuse the immune system.

Foods containing things like casein from dairy products can cause the immune system to start attacking the pancreas. Casein can also cross-react with gluten too! Cross-reaction is where the immune system starts responding to other proteins as if they are gluten. This is the reason why some people who only remove some grains from their diet may not recover fully. The consumption of other cross-reactive foods outside of gluten can be enough to prevent your thyroid from healing.

It All Comes Down to Genetics

Wherever the weak link in your genetic chain is, may be the deciding factor regarding what autoimmune condition you express. The tighter you pull your genetic chain, the increased chance those weak links will be exposed and break. The tightness is equivalent to the stress in your life, while the weak link is symbolic of your genetic susceptibility.

Some people may get Hashimoto’s (autoimmune thyroid condition) while others may develop multiple sclerosis or Parkinson’s disease. There tends to be a genetic link regarding what condition you may express. If Parkinson’s or Hashimoto’s runs in your family, this may be a good indicator of what you are predisposed for.

Genetic predisposition is not a death sentence but merely a strong warning you need to heed. I personally have an autoimmune thyroid condition and also have many other autoimmune conditions that run in my family. Because of this, I pay close attention to my diet, emotional stress, physical stress, and chemical stress. The stressors, or allostatic load, in your life have a huge impact on your epigenetics. Your epigenetics control what genes your body expresses, kind of like turning a light switch on or off. So in other words, you have the ability to control what genes you express or don’t express.

So if you have a predisposition toward chronic degenerative autoimmune conditions, it’s really important that you develop other healthy habits that keep those genes from expressing themselves. The more our immune system is fired up, the more inflammation occurs in our body. The additional inflammation and undigested food proteins put additional stress on our detoxification system, causing our liver to have to work harder to filter out all those extra antigens and toxins in our blood stream.

What Causes Leaky Gut?

Inflammation is the underlying cause of leaky gut. Below I will talk more specifically about what the underlying drivers of inflammation are.

Food allergens

All grains, especially gluten-containing grains, such as wheat, barley, rye, oats, spelt, and Kamut, can be hyperallergenic. Other foods can also cross-react with gluten, such as dairy products (especially milk products that are higher in casein) and legumes (soy, beans, and peanuts). Butter, heavy whipping cream, and ghee tend to be OK. Some people who are autoimmune need to avoid everything but ghee. Many of these allergens tend to be a little controversial.

Most people think of allergies as the kinds that close up your throat, like when someone who has a peanut allergy eats peanuts. That type of allergy is known as an IgE-mediated immune response, or in the above peanut example, an anaphylactic response. We tend to know about these allergens in childhood because of some type of traumatic experience that may have included a blocked airway, itching, and/or hives. The allergenic response I am talking about comes from a different part of the immune system. Essentially, a low-grade inflammation that occurs because of a cross-reactivity or an IgA–, an IgG–, or a T-cell–mediated immune response. These types of immune responses can cause leaky gut and contribute to thyroid imbalances, adrenal fatigue, brain fog, weight gain, and other digestive symptoms.

Low stomach acid

We need HCl, or stomach acid, to help break down our proteins and ionize minerals. If we don’t have enough stomach acid, we can’t break down and absorb zinc. If we don’t have enough zinc, this can affect our immune system, sex hormones, and our ability to make stomach acid. As you can see, a downward spiral is occurring that causes our body to break down even faster with no end in sight!

Infections

With inadequate stomach acid, we are also prone to gut infections (bacterial, parasitic, fungal, and viral) and small intestinal bacterial overgrowth (SIBO). Many of these infections produce biotoxins/endotoxins that can affect hormone metabolism and nutrient absorption and can contribute to fatigue of the thyroid and adrenal glands. Chronic infections tend to play a role with autoimmune conditions as well as leaky gut.

How Do We Fix Leaky Gut?

When getting to the bottom of leaky gut, it’s essential to incorporate a 5R program (remove, replace, repair, remove, and reinoculate). Just like baking a cake, the order in which things are done is very important to making the recipe tasting great. Just like when addressing chronic leaky gut autoimmune conditions, the order and how we address the underlying cause is important to preventing relapse as well as to feeling as good as you possibly can during the process. Again, I want to stress that it’s very important to address underlying hormonal imbalances, including adrenal, thyroid, and female hormone issues, before getting to the chronic infection.

I personally find that patients will fall apart during the treatment if this isn’t done. This is dependent on how long the person is sick and how sick the person is, and there are exceptions to every rule. If the person’s hormonal system is not supported adequately when removing the infection, the chance of a die-off reaction is higher. Die-off reactions may feel something like fatigue, headache, nausea, and/or chills. Some people may notice nothing when the infection is being removed while others may have significant die-off reaction symptoms. There are various techniques and herbal medicines that can mitigate die-off or Herxheimer reactions.

The 5R program follows:

Remove

This part’s pretty simple. Remove the foods that are creating inflammation. Some people may need to be on a stricter autoimmune Paleo type of diet. Some may need to remove FODMAPs (a group of carbohydrates the small intestine has trouble absorbing). For others, a clean Paleo diet may be enough. An elimination provocation diet is the easiest way to be specific and avoid expensive and sometimes unnecessary allergy testing.

Replace

People with chronic stress can have low stomach acid. When there’s low stomach acid, there is typically low enzyme and bile salt production as well. It’s always good to work up to a patient’s stomach-acid tolerance so we can ensure the patient is breaking down proteins, fats, and minerals optimally. We need to make sure the building blocks are present, broken down, and absorbed so the person can heal.

Repair

Depending on how stressed or inflamed a patient is, adding additional healing and/or soothing nutrients can be helpful. Sometimes just making the above changes is enough to help facilitate healing. Others may need additional compounds, such as L-glutamine, slippery elm, zinc, aloe vera, and deglycerized licorice.

Remove

This is the place where we remove the infection. As you can see, the infection is one of the last things we address. This helps prevent die-off reactions from overwhelming the detoxification system, immune system, and lymphatic system. I find that removing the infection at the end tends to be the most effective.

Reinoculate

This is where we add the probiotics back in. Many people have a dysbiosis (or SIBO) in the gastrointestinal tract. This is when there is an overwhelming amount of bad bacteria in relationship to good bacteria. Adding in probiotics when there is a high amount of bad bacteria can cause problems, such as gas, bloating, and gastrointestinal pain. Removing the infections and bad bacteria first, allows the good bacteria to flourish. The analogy is weeding the garden before you plant the seeds—you never put seeds into a garden full of weeds.

Hidden barriers

Chronic infections can encase themselves in the slime known as biofilms. These biofilms are resistant to antibiotics; therefore, the conventional approach to treating these infections tends to not be as successful. Working with a skilled functional-medicine doctor that can combine the right antimicrobial herbs for your infection with some well-known biofilm busters is an important ingredient to removing the infection in the long run.

What Should I Do Next?

If you’re suffering from an autoimmune condition, fatigue, digestive problems, and/or hormonal imbalances, there is a good chance that leaky gut is playing a part. If you want to take a closer look into what’s causing your health issues, feel free to click here for a complimentary consultation.