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.

herbal antibiotics

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.

antibiotic resistance

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.

efflux pumps

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.

dysbiosis

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!

gut infections cycle

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.

Solutions to Small Intestinal Bacterial Overgrowth (SIBO)

By Dr. Justin Marchegiani

I see patients every day walking to my clinic with small intestinal bacterial overgrowth (SIBO) symptoms. Have you ever felt your stomach pooch out after eating certain foods? Do you ever feel like you can’t quite digest your food all the way? Small intestinal bacterial overgrowth can also contribute to leaky gut syndrome!

There are millions of people with SIBO-like symptoms covering them up with medications that don’t fix the underlying problem. SIBO can affect our immune system and compromise our body’s ability to break down food and absorb nutrition.

gut health

Below are 5 signs you may have SIBO:

1. Burping or belching

2. Flatulence

3. Indigestion/low nutrient absorption (low B12, proteins, and fats)

4. Diarrhea or constipation

5. Abdominal pain

SIBO causes

What Causes SIBO?

1. A lack of stomach acid

When we have low stomach acid, or achlorhydria, our body lacks the ability to activate protein-digesting enzymes in our stomach, called pepsin. We need a low pH (acidic), right around 2, to ensure our body’s optimal digestive capabilities. This is why people on proton-pump inhibitors (drugs that block stomach acid) are at an increased risk for SIBO.

A low pH also provides an inhospitable environment for bad bacteria to grow. When bad bacteria overpopulate the stomach, it’s easy to see the increase in intra-abdominal pressure. This increase in intra-abdominal pressure can open up the esophageal sphincter and allow acids from the stomach to rise up and create irritation or burn the esophageal tissue. Without adequate levels of stomach acid, SIBO is almost certain!

2. Pancreatic insufficiency

Without adequate enzyme production, our body has a difficult time digesting proteins and fats. When our body doesn’t break down these proteins and fats fully, they putrefy, rancidify, and ferment in our intestinal track. This is not good!

HCl is the first important step for enzyme production. Without an acidic pH, the foods that are released from our stomach into our small intestine will not provide enough stimulation to trigger the gallbladder to release bile acids and pancreas to produce protein (trypsin and lipase) and fat-digesting enzymes. Without the crucial release of these enzymes, our body is at an increased risk for small intestinal bacterial overgrowth, or SIBO.

3. Chronic infections

Many infections are opportunistic and are able to take hold of the person’s body because of an accumulation of physical, chemical, and emotional stress. When this happens, we tend to have a decrease in immunoglobulin A (IgA). IgA is a protective mucous membrane barrier that lines our intestinal tract and plays an important role at preventing SIBO. Because 70 to 80% of our immune system is located in the lymphoid tissue in our intestinal tract, this has the ability to throw our immune system out of balance.

Chronic infections can lower stomach acid and decrease our body’s ability to break food down. With low IgA and a lack of stomach acid, our body is a sitting duck for an infection. Bacterial and parasitic infections are known to produce toxins (endotoxin and lithocolic acid) that can actually suppress our immune system. If you’re having chronic SIBO-like symptoms, feel free to click here to see if an infection connection is possible.

Other predisposing factors for SIBO

There are many other risk factors for SIBO, including fibromyalgia and IBS. These other conditions have common threads along with the main causes of SIBO that are above.

When our immune system is compromised by various infections, we have an inability to break down, absorb, and assimilate food due to an increase in physical, chemical, and emotional stress. This accumulation of stress eventually breaks the weak link in your chain. Because the gut is so central to the immune system, so many different conditions have a common link with small intestinal bacterial overgrowth. I would go as far to say that it is impossible to have a chronic disease without some type of gut dysfunction!

What Is SIBO?

SIBO is typically caused by a migration of bacteria from the large intestine making its way back upstream into the small intestine.

“SIBO may be accompanied by both maldigestion and malabsorption. Bacteria in SIBO might significantly interfere with enzymatic, absorptive and metabolic actions of a macro-organism.”

When our digestive system becomes stressed, our ileocecal valve can become loose. The slack in the ileocecal valve makes it easier for bacteria to migrate up the gastrointestinal tract. If more bacteria starts making its way up the GI tract, it makes it harder for the healthy gut bacteria in our small intestine to produce important nutrients, like vitamin K, vitamin D, iron, and various B vitamins.

What Type of Bacteria Is Found in SIBO?

Streptococcus 60%, Escherichia coli 36%, Staphylococcus 13%, Klebsiella 11% and others, as well as 117 anaerobes (Bacteroides 39%, Lactobacillus 25%, Clostridium 20%, and others) are found in SIBO.

How Do You Test for SIBO?

1. Hydrogen or methane breath test

A solution of glucose or lactulose is consumed. Hydrogen or methane levels are measured after the test, and if hydrogen or methane is found in amounts greater than or equal to 20 ppm, it is considered a positive test for SIBO. Ammonia is a common by-product from the intestinal bacteria. Ammonia has a pH of 11, so it’s easy to see how bacteria can affect intestinal pH!

2. Comprehensive stool test

The pathogenic bacteria mentioned above can be found in the stool by a comprehensive stool analysis. All lab companies are not created equal when it comes to this type of specialized testing. I recommend only using the best companies to ensure that you are getting accurate results. My three favorite lab companies for stool testing are Biohealth Diagnostics, Genova Diagnostics, and Doctors Data. If you are trying to get assessed for SIBO or any other infection, feel free to click here!

3. Organic acid test: This test can look for metabolic by-products of SIBO, including benzoate, hippurate, phenylacetate, phenylpropionate, p-hydroxybenzoate, p-hydroxyphenylacetate, indican, tricarballylate.

How do you treat SIBO?

Conventional Treatment Options

Conventional treatments typically consist of taking specific antibiotics, such as metronidazole and rifaximin. Antibiotics are powerful medicines, and I typically recommend a natural herbal approach first. The herbs tend to be more gentle on the body and don’t have all of the side effects.

Natural Treatment Options

There are many herbal medicines that can help eradicate SIBO. One of my favorites is oil of oregano. Other great herbs include berberine, artemisia, cat’s claw, colloidal silver, and ginger.

Sometimes it’s more than just SIBO causing the problem. If you are having any of the above symptoms, it’s good to get checked by a functional-medicine doctor to make sure there are no other infections driving the problem.

Some of these bacteria use biofilms as a means to protect themselves from the antimicrobials. It can get a little more nuanced when addressing the stubborn infections. Feel free to click here if you need help!

I find many patients do better at making diet and lifestyle changes first and addressing the adrenals and hormonal system second before addressing the gastrointestinal system. When patients go right to the GI system, the side effects tend to be much higher!

Dietary Interventions

FODMAPs: Removing fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAPs) from the diet is also important. These FODMAP sugars can fuel the pathogenic bacteria in the gut, which then leads to more toxic metabolic by-products. Many people notice great improvements in stomach distention, gas, and flatulence after removing these foods from the diet. I personally find a combination of diet, lifestyle, and herbal medicines tend to be the trick to addressing the underlying cause of the problem.

Resistant starch: Adding resistant starch type 2 or 3 into your diet can also help feed the beneficial bacteria in the gut. The beneficial bacteria in the gut produce a short-chain fatty acid called butyrate. Butyrate helps keep the pH in the gut lower, tightens the ileocecal valve, and provides fuel for the cells of the colon. Watch the above video for more information on how resistant starch can help improve your SIBO.

My Favorite Resistant Starch

  • Type 2 resistant starch—unripened banana flour by Wedo.
  • Type 3 resistant starch—potato flour by Bob’s Red Mill.

Instructions: If you have significant SIBO, start with just 1 tsp of resistant starch and work up to 2 tbs. If you have any significant gas or bloating after taking the resistant starch, half the dose the next day. When in doubt start slow. Gas and bloating are surefire signs that you have SIBO.

I can take 2 tbs of resistant starch two times per day without any symptoms. Some people may have to use herbal medicines to significantly knock down the SIBO before the resistant starch can be tolerated. Make sure you work with your functional-medicine practitioner to support you in the process.

On a low-carbohydrate diet, the E.rectale and the Roseburia bacteria can significantly decline. Adding in resistant starch can help prevent this decline in beneficial bacteria while maintaining a low-carbohydrate eating plan. Some people are carbohydrate sensitive and need to keep their carbohydrates down, and this provides an excellent option to get the best of both worlds.

Feel free to click here if you need help!


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.