Good Shit! Your Guide to a Healthy Intestinal Microbiome—Even on Antibiotics

Your source for quality supplements

Shop Now

Good Shit! Your Guide to a Healthy Intestinal Microbiome—Even on Antibiotics Image

This is a long article. The first part provides background on the importance of the intestinal microbiome and what helps, while on antibiotics, to keep your gut healthy. The second part of this article is Marty Ross, MD’s Gut Health Action Plan which lays out specific actions you can take.

  • You can skip to the action plan here.
  • Download a pdf version of the entire article here.

Key Actions of Your Intestinal Microbiome

At its most basic level, your gastrointestinal tract is a tube through which food you eat is digested, detoxified, absorbed, transported, and eventually discarded. But it really has so many other functions. In the last decade, the amount of research on the function and makeup of the intestinal microbiome is exploding. And we have only scratched the surface.


We now know there are numerous intestinal microbiome axes—where the intestinal microbiome manages or influences an organ or system, and the organ or system helps manage or influence the intestinal microbiome. Here are some of the key intestinal microbiota axes:

  • Immune system,
  • Brain,
  • Muscle,
  • Cardiovascular system,
  • Endocrine-Metabolic (diabetes, weight, and more), and
  • Bone.

According to Xue et. al.

The gut is the main digestive organ of the human body and absorbs the most nutrients It is also the largest immune and detoxification organ. The gut is also called the “gut brain” or “second brain” owing to its complex neural network of approximately 100 billion scattered nerve cells. The function of the gut is closely related to human health. The gut harbors a vast microbial community, which plays key roles in gut function. Gut microbes include bacteria, phages, viruses, protists, worms, and fungi. Bacteria are the main inhabitants of the gut and participate in physiological activities through intermediate metabolites or surface antigens. The gut flora plays an important role in substance metabolism and immune defense and is necessary to maintain human health. The gut flora communicates with the central nervous system through neural, immune, and endocrine pathways, affecting mood, behavior, and other brain functions. The gut flora is associated with sleep, memory, anxiety, and depression. Normally, the gut flora composition is relatively stable. Changes in the microbial abundance, composition, and levels of metabolites of gut flora lead to a variety of diseases, including cancer. (21)

A Variety and Abundance of Germs is Gut Healthy

The intestinal microbiome contains bacteria, viral phages, viruses, protozoa parasites, worms, and fungi including yeast. The number of germs is vast. By some estimates the genetic material of the intestinal microbiome germs makes up 90% of the total body DNA in humans.

The healthiest intestinal microbiome is both diverse and abundant in its varieties of organisms. Unhealthy intestinal microbiomes lose diversity or may have decreased levels of germs or both.

The Intestinal Microbiome in Lyme Disease

Sabine Hazan, MD found significantly decreased levels of important Bifidobacteria levels in people living with Lyme disease. It is unclear from her study whether Lyme and tick-borne infections or antibiotics cause the decreased levels. Dr. Hazan even wonders if low levels of Bifidobacteria allow for Lyme disease after a tick bite.

Bifidobacteria are a keystone species of intestinal bacteria that provides direction to the immune system. Without adequate direction, it is possible the immune system cannot eradicate Lyme after a bite—leading to the development of chronic Lyme disease, or even other tick-borne infections. In her study, Dr. Hazan only looked at Bifidobacteria levels rather than other intestinal keystone species like Akkermansia, or Lactobacillus.

Due to antibiotics, or even the effect of Borrelia or other tick-borne infections, the intestinal microbiome in individuals with chronic Lyme likely have decreased diversity and abundance of organisms. Some, like Dr. Hazan, even postulate that at a point, chronic Lyme disease or tick-borne infections may be due to disruption of the intestinal microbiome leading to disease or dysfunction in every organ or system influenced by the gut microbiome. Under this scenario, it is possible that months or years of antibiotics eradicate the germs, but the remaining illness is due to an injured intestinal microbiome.

Intestinal Dysbiosis

Intestinal dysbiosis means there is an unhealthy imbalance in healthy vs unhealthy organisms in the intestines. In dysbiosis there is a lack of diversity and abundance of healthy organisms while unhealthy bacteria, yeast, or other germs become more predominant. Dysbiosis affects the function of every gut-brain axis system and organ. More directly it has very local effects on the function of the intestinal wall and cells. This leads to leaky gut, food allergies and sensitivities, body-wide inflammation, and metabolic dysfunction (diabetes and weight gain).

More About Leaky Gut, Food Allergies and Sensitivities, Body Inflammation

In leaky gut syndrome, the normal protective layer of mucin that covers intestinal cells thins or breaks down. Mucin is produced in intestinal goblet cells under the direction of Akkermansia muciniphila. If there is a shortage of Akkermansia, then the mucin layer thins. In addition, gaps develop between intestinal cells allowing microscopic food particles, toxins and even germs through the intestinal barrier. Keep in mind around 70% of the immune cells in the body sit under the intestinal lining. In leaky gut, the substances that leak through the wall trigger immune cell activation including mast cells that make allergy histamine and T white blood cells that make histamine. So, leaky gut can lead to increased food sensitivities and even food allergies plus body-wide cytokine inflammation.

Metabolic Dysfunction

Some cells that line the intestines make glucagon-like protein 1 (GLP-1). You may be familiar with drugs like semaglutide that people take to manage diabetes and weight through actions at GLP-1 receptors in the body. GLP-1 is made in the intestinal lining under the direction of Akkermansia muciniphila. Akkermansia makes a protein that directs production of GLP-1. So low levels of Akkermansia may lead to diabetes, weight gain, and metabolic syndromes.

Building Blocks for a Healthy Intestinal Microbiome


Definition. Probiotics are healthy germs which a person takes to improve intestinal and overall health. According to the World Health Organization definition from 2001, probiotics are "live micro-organisms which, when administered in adequate amounts, confer a health benefit on the host."

Explanation. Some probiotic species like Akkermansia, Bifidobacteria, and Lactobacillus can implant and grow in the intestines. Others, like spore forming Bacillus spp, do not implant. All probiotics release chemical metabolites and messengers that support good intestinal microorganisms and the health of the body and its systems, like the immune system. Some that implant, compete with unhealthy germs for territory pushing out the bad bacteria.


Definition. Prebiotics are non-digestible plant fibers composed of various kinds of sugars that are fermentable by intestinal bacteria.

Explanation. The products of fermentation are short chain fatty acids (SCFAs) like butyrate, propionate, and others that support other bacteria in the intestines, communicate with the various body organ systems, including the brain and immune systems, and support a healthy, non-leaking, intestinal lining.

Common prebiotics in supplements that are derived from plant fibers include

  • pectin,
  • chitin,
  • fructo-oligosaccharides (FOS),
  • galacto-oligosaccharides (GOS),
  • Inulin, and
  • beta glucan.

Food based prebiotics include most fibers found in whole-food (non-processed) vegetables, berries and fruits, beans, legumes, nuts, and seeds.


Definition. Polyphenols are antioxidant chemicals found in colorful vegetables, berries and fruits, tree nuts and seeds, coffee, chocolate, and teas that promote healthy intestinal bacteria while suppressing unhealthy germs.

Explanation. Evolving science shows polyphenols support healthy intestinal bacteria like Akkermansia and Bifidobacteria. Top sources of polyphenols include peppermint, oregano, sage, rosemary, blueberries, black currants, plums, cherries, pomegranates, black and green olives, artichokes, red onions, spinach, flaxseeds, hazelnuts, pecans, almonds, walnuts, dark chocolate, red wine, coffee, green and black teas. Over 90% of polyphenols reach the large intestine where they are metabolized by bacteria releasing chemicals and messengers that affect the healthy character of the intestinal microbiome and major systems in the body, like the immune system.


The best way to support a healthy intestinal microbiome is through diet. A whole foods plant forward diet that uses high fiber foods and does not include fast foods, processed foods, or alcohol is best. Prebiotic fiber and polyphenols in diets support healthy intestinal bacteria. In fact, fiber is the best prebiotic.

Foods that are rich in fiber and polyphenols include colorful fruits and berries, vegetables, beans, legumes and whole grains. Polyphenols come from dark chocolate, coffee and teas as well. Ideally a person should consume 30 grams of fiber a day which can come from five servings of these foods. And it is best to avoid alcohol which is a general toxin to the microbiome. To see if you are getting enough fiber, consider tracking your food choices using apps like MyFitnessPal. Fermented foods like yogurt, kombucha, sauerkraut, and kimchi can supply probiotics in the diet too, but they generally provide small amounts compared to probiotic supplements.


Definition. According to The International Scientific Association of Probiotics and Prebiotics, postbiotics are a “preparation of inanimate microorganisms and/or their components that confers a health benefit on the host.”

Explanation. So postbiotics do not have living germs, but only the metabolites and messengers produced by those germs. One way to create a postbiotic is to collect stool samples from healthy donors and then kill living germs through high heat leaving only the chemical messengers and metabolites. By some estimates postbiotics from human intestines may include 800 or more of these messengers and metabolites. Some of the chemicals are SCFAs mentioned above in the prebiotics section, some are peptides, and a whole lot more. These messengers support a healthy intestinal microbiome and provide signals affecting most of the body's systems like the immune system and brain. Postbiotics can even rehabilitate the variety and abundance of organisms in the intestinal microbiome.

Fecal Microbiota Transplant

Definition. A fecal microbiota transplant (FMT) uses stool which includes living organisms and their chemical messengers which is then given to a person either rectally or orally.

Explanation. FMT is governed by the US Food and Drug Administration (FDA). FDA only allows FMT for the treatment of C. difficile overgrowth causing diarrhea. Under experimental protocols, FMT can treat other conditions.

The problem with using universal FMT from general donors is every person has a different intestinal microbiome. The chemicals and germs in one person’s intestinal microbiome are different from another person’s. Ideally a transplant would use a donor with a similar intestinal microbiome to the recipient.

Sabine Hazan, MD is doing research showing healthy family members often have similar microbiomes. In her presentations, she shows benefit using the stool of one donor from a family to make up for the deficits in another family member. 

Non-dietary Lifestyle Factors

Regular exercise, sleep, and stress reduction all work to support a healthy intestinal microbiome. Regarding exercise, movement at a level you can tolerate is helpful.

Stressors and Destroyers of Healthy Intestinal Microbiome

The leading disruptor of a healthy intestinal microbiome is the use of antibiotics. Additional stressors include cancer medications, alcohol, environmental toxins, and chronic infections with or without antibiotic treatment.

Risks of Antibiotics vs Benefits

Whether to take antibiotics or not always involves weighing risks and benefits. For those with chronic tick-borne infections that require prolonged antibiotics, the benefits of killing infections has to be weighed against harm to the intestinal microbiome and the body systems it supports like the immune system and the brain.

Fortunately, if you choose antibiotics, there are steps you can take to protect the gut microbiome which I review later in this article. As I explain below, my impression based on my practice is that herbal antibiotics are not as harmful as prescription antibiotics to the intestinal microbiome.

The Good Bacteria and Yeast in Existing Probiotic Products

There are a variety of bacteria and yeast species and strains that are currently found in probiotic supplements. Except for spore forming Bacillus species, which are not found naturally in human intestines, probiotic species and strains can implant. What follows is a description of key functions of the various species and strains found in probiotics.

Akkermansia muciniphila

This bacterium naturally occurring in humans may

  • Support healthy intestinal wall mucin layers,
  • Improve GLP-1 production leading to greater insulin sensitivity, glucose control, appetite regulation, and healthy weight,
  • Improve energy through better metabolism due to increased GLP-1,
  • Support digestive health,
  • Recondition the intestinal microbiome by promoting microbial diversity and maintaining key health promoting gut bacteria through metabolites and SCFAs,
  • Implant in intestinal wall increasing Akkermansia intestinal colonization, and
  • Decrease inflammation in the gut and body.

Bifidobacterium spp and Lactobacillus spp

These bacteria that naturally occur in humans may

  • Ferment probiotic sugar fibers to key SCFAs like butyrate, pyruvate, and lactate,
  • Recondition the intestinal microbiome by promoting microbial diversity and maintaining key health promoting gut bacteria through metabolites and SCFAs,
  • Implant in intestinal wall increasing intestinal colonization,
  • Support digestive health, and
  • Support healthy immune function.

Saccharomyces boulardii

This healthy intestinal yeast that naturally occurs in humans may

  • Promote healthy intestinal IGA levels,
  • Aid in antibiotic-associated diarrhea,
  • Implant in the intestinal wall increasing Saccharomyces colonization, and
  • Support the growth and function of healthy intestinal microbes.

Bacillus spp Spore Formers

Spore forming probiotics are found in soil. They do not naturally occur in humans and do not appear to colonize human intestines either. They may

  • Support healthy immune function,
  • Recondition the intestinal microbiome by promoting microbial diversity and maintaining key health promoting gut bacteria through chemical messengers,
  • Improve actions of the intestinal barrier,
  • Decrease abdominal discomfort, and
  • Support digestive health

Bacillus spp is stable in high heat and the stomach acid. This means Bacillus spp products do not require refrigeration and have a great chance to get through the acid of the stomach to reach the intestines.

Anaerobutyricum hallii, Clostridium beijerinckii, and Clostridium butyricum Butyrate Producers

These butyrate producing strains of bacteria that naturally occur in humans may

  • Support the production of butyrate, the key cell food for intestinal lining, and
  • Decrease leaky gut and improve intestinal wall cell function through Increased butyrate production.

About Probiotic Effectiveness While on Antibiotics

Do probiotics work to protect the gut while on herbal or prescription antibiotics? There are a couple of meta-analysis papers pooling together numerous research studies to see if probiotics work. The two studies give conflicting results. One showed that probiotics worked to protect intestinal microbial abundance and diversity in the intestines while a person was on short course (less than two weeks) antibiotics. The other showed no benefit.

It is hard to generalize these studies to the health of the intestinal microbiome in treating chronic tick-borne infections using months or years of antibiotics.

My own clinical observation is probiotics work. People on probiotics while taking antibiotics get less intestinal yeast infections and tend to have better gut function. It is possible with the recent findings about the benefits of polyphenols, actions of spore-forming bacteria, and Akkermansia, etc that there is a great chance of protecting the intestinal microbiome during treatment. And at the end of treatment, there are good ways to rehab the gut.


Marty Ross, MD’s Gut Health Action Plan

Here is an action plan to protect and rehabilitate your intestinal microbiome. For a complete understanding of my recommendations, you will need to be familiar with the background information I provided above.

In Part I you will consider whether you should even take antibiotics or whether it is best for you to use herbal or prescription antibiotics.

Parts II through IV lay out your daily gut health action plan that should

  • Provide sleep and movement discussed in Part II,
  • Feed good intestinal bacteria with polyphenols and prebiotic fibers discussed in Part III, and
  • Use a specific probiotic species and strains based on your health issues discussed in Part IV.

Part I. Choose the Timing and Type of Antibiotics Wisely

Rule One. Do not use herbal or prescription antibiotics if you do not have symptoms from the infection.


If you have a positive test without symptoms, it could

  • be a false positive test, or
  • your immune system either got the infections under control, or
  • even eradicated the germs.

Using antibiotics may disrupt the function of your immune system that is keeping your various infections under control or even eradicating your infections. 

We have no long-term studies showing us if treating non-symptomatic infections prevents long-term activation of the infections or harm from them. Basically, the immune system can keep many infections we cohabitate with under control. Such infections can be tick-borne infections, mycoplasma, or chlamydia.

Rule Two. When possible, choose herbal over prescription antibiotics.


In my experience treating people living with tick-borne illness over the last 20 years, prescription antibiotics tend to have a much greater chance than herbal antibiotics of clinically disrupting the good intestinal microbiome. I find most people on prescription antibiotics, at some time will develop intestinal yeast overgrowth. People on herbal antibiotic regimens develop yeast overgrowth rarely. Research about the effect of herbal antibiotics used for tick-borne infections on the intestinal microbiome is missing.

For information on herbal antibiotics see Best Herbal Antibiotic Plans for Lyme, Bartonella, and Babesia.

Rule Three. Before you start herbal or prescription antibiotics, make sure you do not have intestinal dysbiosis due to yeast overgrowth from Candida albicans, and if you do, treat it with herbal or prescription antifungals.


Prescription and herbal antibiotics can decrease healthy intestinal bacteria which can lead to intestinal yeast overgrowth. It is best to get this problem under control before adding fire to the problem with antibiotics. When you have intestinal yeast overgrowth, there is a high possibility of having leaky gut as well—leading to mast cell activation with allergy and histamine symptoms and increased inflammation cytokines causing body wide symptoms.

See A Silent Problem - Is It Yeast? and Kills and Prevents Yeast: A Brief Guide for more information about diagnosing and treating intestinal yeast overgrowth.

Part II. Non-Dietary Lifestyle Steps

Sleep and movement support a healthy intestinal microbiome. Make sure these two lifestyle steps are part of your gut health action plan.

  • Sleep seven to nine hours a night. Work with healthy sleep practices, supplements, or prescription medicines as needed. For more information see the Sleep Section of my Online Lyme Guide.
  • Move or exercise to tolerance. The key here is to move or exercise to tolerance. In tick-borne infections, mold toxicity, fibromyalgia, long covid, and chronic fatigue syndrome, too much exercise can set you back. The key is to find a level of activity that does not set you back the next day.

Part II. Feed Your Intestinal Microbiome with Polyphenols and Prebiotic Fibers

Polyphenols, prebiotic non-digestible fibers and sugar support a healthy gut microbiome. Make sure you build these into your gut health action plan. My preference is to get the polyphenols and prebiotic fibers in your diet, but I realize that is not always possible, especially if it is too hard to cook due to illness.

Option 1. Use Supplements

  • Polyphenol 2 capsules one time a day. I prefer Polyphenol Booster by Pendulum.*
  • Prebiotic non-digestible sugars 1 to 2 pills 3 times a day. I prefer MegaPre by Multibiome Labs.*

Option 2. Eat a Plant-forward Whole Food Diet

  • Include polyphenols and prebiotic plant fibers in your diet by eating a whole food diet rich in colorful berries and fruits, vegetables, beans, legumes, nuts and seeds. Aim for at least 30 grams of plant-based fiber a day which you can track using an app like MyFitnessPal or by having at least 5 servings a day of the various foods types listed above. In choosing a whole-foods plant-forward diet, it is ok to use animal proteins or plant-based proteins for your protein source.

Part III. Choose Your Probiotic or Postbiotic Based on Your Health Goals and Health Problems

As I noted earlier, there are many types of probiotics available in various products. These probiotic types include:

  • Akkermansia muciniphila,
  • Bacillus spp spore formers,
  • Bifidobacterium spp and Lactobacillus spp fiber fermenters,
  • Anaerobutyricum hallii, Clostridium beijerinckii, and Clostridium butyricum butyrate producers, and
  • Saccharomyces boulardii.

All these probiotic types, to some degree, support and promote the health of all good bacteria in the intestines. But each of these types has different advantages based on your health goals and health problems.

Option 1. No Leaky Gut Syndrome Symptoms

If you do not have any intestinal symptoms of leaky gut, this option is for you.

Symptoms suggesting leaky gut can include intestinal gassines, bloating, or cramping, or multiple food sensitivities. The general probiotics I recommend here support and promote the health and growth of most healthy intestinal bacteria.

  • Bacillus spp spore forming probiotic 1 to 2 pills 1 time a day. I prefer Corebiotic and Corebiotic Sensitive by Researched Nutritionals or MegaSporeBiotic by Multibiome Labs.*

Comment. In my experience, probiotic supplement products deliver more probiotics than fermented food sources. I chose a spore-forming probiotic because they are easier to use as they do not require refrigeration. They also do a great job of microbiome rehab and may work even when a person is on antibiotics.

Substitution Consideration. If you have diabetes or are overweight, consider substituting Akermansia mucinphila for the Bacillus spp spore forming probiotic. As I noted above Akkermansia may raise GLP-1 leading to weight loss and better sugar control. It also supports other intestinal microbiome bacteria like Bacillus spp. Its major drawback is that it is better refrigerated.

  • Akkermansia muciniphila 1 or 2 pills one time a day instead of Bacillus spp. I prefer the Akkermansia product by Pendulum.*

Option 2. Leaky Gut Symptoms with or without Intestinal Yeast Overgrowth or Dysbiotic Bacteria Overgrowth.

If you have intestinal symptoms, this option is for you.

If you have intestinal symptoms like gassiness, bloating, or cramping; or multiple food sensitivities, work to rebuild the intestinal lining and mucin layers while promoting the health and growth of good intestinal bacteria. Use this probiotic option regardless of whether you are treating yeast or bacterial intestinal dysbiosis with targeted antimicrobials.

  • Akkermansia, Bifidobacterium, Anaerobutyricum hallii, Clostridium beijerinckii, and Clostridium butyricum blend 1 pill 2 times a day. I prefer the Metabolic Daily product by Pendulum.*

Comment. With leaky gut there is injury to the mucin layer of the intestines that covers intestinal cells. Additionally, the intestinal lining develops gaps between the cells. Akkermansia builds the mucin layer. Bifidobacterium, Anaerobutyricum hallii, Clostridium beijerinckii, and Clostridium butyricum produce butyrate which is the leading fuel source for intestinal cells. Mucin in combination with butyrate helps heal the gaps between the intestinal cells.

Dysbiosis Consideration due to Yeast or Bad Bacteria. If your leaky gut symptoms do not improve using this option within 1 to 2 months

  • consider if you have intestinal yeast overgrowth using my guide here;
  • talk with your provider about having a comprehensive stool test, (GI Map or Genova GI Effects) to determine the levels of various intestinal bacteria; and
  • consider testing for small intestinal bacterial overgrowth (SIBO).

Option 3. Repeated Intestinal Yeast Overgrowth or Unresolving Leaky Gut Symptoms

When the probiotic, polyphenol, and prebiotic regimens above do not resolve GI symptoms, or if you keep getting repeated yeast overgrowth while on one of these regimens, consider adding a postbiotic. As I noted above, postbiotics contain over 800 messenger chemicals that

  • support the various GI axes including the immune system and brain,
  • promote growth of healthy intestinal bacteria, and
  • improve function of the intestinal wall to fix leaky gut. 

For repeated intestinal yeast overgrowth or unresolving leaky gut symptoms I suggest a probiotic and postbiotic combination.

  • Postbiotic supplement 1 pill 1 to 2 times a day with food. The only postbiotic supplement on the market is Thaenabiotic.* This product is available through a limited number of healthcare providers who must have visits with you. I am working with Thaena to open their product for sale directly to consumers through ecommerce sites. I am very hopeful this will happen. When it does, I will carry it through Marty Ross MD Supplements.
  • Akkermansia, Bifidobacterium, Anaerobutyricum hallii, Clostridium beijerinckii, and Clostridium butyricum blend 1 pill 2 times a day. I prefer the Metabolic Daily product by Pendulum.*

Option 4. Gut Rehab at The End of Treatment

It is important to rebuild a healthy gut at the end of a prolonged antibiotic treatment. I suggest using this probiotic-postbiotic option for six months to a year. There is no research that backs how long to do this. My observation in my practice using just probiotics, is that the best results for intestinal microbiome health can take 6 months or more to return.

  • Postbiotic supplement 1 pill 1 to 2 times a day with food. The only postbiotic supplement on the market is Thaenabiotic.* This product is only available through healthcare providers who must have visits with you. Thaena is considering ecommerce sales without provider involvement in the future. When that happens, we plan to carry the product at Marty Ross, MD Supplements.
  • Akkermansia, Bifidobacterium, Anaerobutyricum hallii, Clostridium beijerinckii, and Clostridium butyricum blend 1 pill 2 times a day. I prefer the Metabolic Daily product by Pendulum.*

One other option instead of using the probiotic-postbiotic option above is to have a Fecal Microbiota Transplant (FMT).

  • FMT from a family household member or another person with a similar intestinal microbiota. As I noted earlier in this article, FMT to rehab the gut is only allowed by the FDA in an experimental setting. FDA only allows FMT to treat C. difficile diarrhea, but not other conditions. If you are interested in pursuing this further, consider a visit with Dr. Sabine Hazan through one of her programs at Progenabiome.

Comment: It is best to have your donation from a healthy family or household member because their intestinal microbiota is most likely to be similar to a healthy microbiome you would have had if not for tick-borne disease and antibiotics. FMT from random donors may have a variety of microbiota organisms that are not like those you would have in a healthy situation.

Option 5. C. Difficile Intestinal Diarrhea

Clostridium difficile (C. diff) overgrowth in the intestines causes diarrhea. This is a bacterium, which lives in our intestines and can grow too much when a person is on prescription antibiotics. Here are the steps to treat and prevent this condition.

C. Difficile Prevention in Lyme Disease

You can help prevent C. diff by taking probiotics. This is very important in someone who has a history of C. diff diarrhea. In this type of situation, Sacro B is very effective at preventing another episode of C. diff.

  • Saccharomyces boulardii (Sacro B).* Start at 4 pills 1 time a day for active diarrhea. Once you have had a C. diff infection, you should remain on this at 4 pills 1 time a day while you are on herbal or prescription antibiotics for Lyme to prevent C. diff from causing diarrhea again.
  • Akkermansia, Bifidobacterium, Anaerobutyricum hallii, Clostridium beijerinckii, and Clostridium butyricum blend 1 pill 2 times a day. I prefer the Metabolic Daily product by Pendulum.*

C. Difficile Diarrhea Treatment in Lyme Disease

When diarrhea occurs due to C. diff, herbal and prescription antibiotics for Lyme and the co-infections must be stopped. There are three antibiotics that treat C. diff infection to resolve the diarrhea. Use vancomycin or fidaxomicin first. If they do not work, then consider metronidazole. While metronidazole is much cheaper than the other antibiotics, it is much less effective and has more potential for side effects. In addition, use an effective probiotic and Sacro B.


  • Vancomycin 125 mg 1 pill 4 times a day for 10 days.
  • Fidaxomicin 200 mg 1 pill 1 time a day for 10 days.
  • Metronidazole 500 mg 1 pill 3 times a day for 10 days.


  • Saccharomyces boulardii (Sacro B)*. Start at 4 pills 1 time a day for active diarrhea. Once you have had a C. diff infection, you should remain on this at 4 pills 1 time a day while you are on herbal or prescription antibiotics for Lyme to prevent C. diff from causing diarrhea again.
  • Akkermansia, Bifidobacterium, Anaerobutyricum hallii, Clostridium beijerinckii, and Clostridium butyricum blend 1 pill 2 times a day. I prefer the Metabolic Daily product by Pendulum.*


This is a very effective way to treat C. diff if one or two rounds of antibiotics do not work. Studies show it works about 90 percent of the time. It can be administered in a physician’s office or the home by enema. Another option is to take 30-40 freeze dried pills a day for about 10 days. FMT for C. diff is FDA approved. This is usually offered by a GI specialist.


If there is a recurrence of C. diff after initial antibiotics, then adding bezlotoxumab to the next antibiotic treatment may help to prevent further relapses. Bezlotoxumab is a monoclonal antibody against the C. difficile toxin.

  • Bezlotoxumab 10mg/kg IV 1 time.


The ideas and recommendations on this website and in this article are for informational purposes only. For more information about this, see the sitewide Terms & Conditions.

* These statements have not been evaluated by the Food and Drug Administration. These products are not intended to diagnose, treat, cure, or prevent any disease.


View Citations

  1. Azad MAK, Sarker M, Li T, Yin J. Probiotic Species in the Modulation of Gut Microbiota: An Overview. Biomed Res Int. 2018;2018:9478630. Published 2018 May 8. doi:10.1155/2018/9478630 (View)
  2. Chaudhary PP, Kaur M, Myles IA. Does "all disease begin in the gut"? The gut-organ cross talk in the microbiome. Appl Microbiol Biotechnol. 2024;108(1):339. Published 2024 May 21. doi:10.1007/s00253-024-13180-9 (View)
  3. Davani-Davari D, Negahdaripour M, Karimzadeh I, et al. Prebiotics: Definition, Types, Sources, Mechanisms, and Clinical Applications. Foods. 2019;8(3):92. Published 2019 Mar 9. doi:10.3390/foods8030092 (View)
  4. Dimidi E, Cox SR, Rossi M, Whelan K. Fermented Foods: Definitions and Characteristics, Impact on the Gut Microbiota and Effects on Gastrointestinal Health and Disease. Nutrients. 2019;11(8):1806. Published 2019 Aug 5. doi:10.3390/nu11081806 (View)
  5. Éliás AJ, Barna V, Patoni C, et al. Probiotic supplementation during antibiotic treatment is unjustified in maintaining the gut microbiome diversity: a systematic review and meta-analysis. BMC Med. 2023;21(1):262. Published 2023 Jul 19. doi:10.1186/s12916-023-02961-0 (View)
  6. Elshaghabee FMF, Rokana N, Gulhane RD, Sharma C, Panwar H. Bacillus As Potential Probiotics: Status, Concerns, and Future Perspectives. Front Microbiol. 2017;8:1490. Published 2017 Aug 10. doi:10.3389/fmicb.2017.01490 (View)
  7. FAO/WHO. Health and nutritional properties of probiotics in food including powder milk with live lactic acid bacteria, Report of a Joint FAO/WHO expert consultation on evaluation of health and nutritional properties of probiotics in food including powder milk with live Lactic acid bacteria. Córdoba, Argentina: 2001.
  8. Fernández-Alonso M, Aguirre Camorlinga A, Messiah SE, Marroquin E. Effect of adding probiotics to an antibiotic intervention on the human gut microbial diversity and composition: a systematic review. J Med Microbiol. 2022;71(11):10.1099/jmm.0.001625. doi:10.1099/jmm.0.001625 (View)
  9. Fitzgerald K. All About Akkermansia: The keystone bacteria critical to gut health and longevity. Lecture presented at: Longevity FEST 2023 Leveling Up Healthcare; December 15, 2023; Las Vegas, NV.
  10. Fu J, Zheng Y, Gao Y, Xu W. Dietary Fiber Intake and Gut Microbiota in Human Health. Microorganisms. 2022;10(12):2507. Published 2022 Dec 18. doi:10.3390/microorganisms10122507 (View)
  11. Hazan S, The Microbiome and Disease. Lecture presented at: Breaking Barriers: Advancing Treatment for Complex Chronic Illness; March 1, 2024; Austin, TX.
  12. Hazan, Sabine MD1; Dave, Sonya PhD2; Goudzwaard, Amelia3; Barrows, Brad DO1; Borody, Thomas J. MD, PhD, DSc, FACG4. S551 Loss of Bifidobacteria in Lyme Disease: Cause or Effect. The American Journal of Gastroenterology 117(10S):p e389-e390, October 2022. | DOI: 10.14309/01.ajg.0000858844.94374.43 (View)
  13. Hidalgo-Cantabrana C, Delgado S, Ruiz L, Ruas-Madiedo P, Sánchez B, Margolles A. Bifidobacteria and Their Health-Promoting Effects. Microbiol Spectr. 2017;5(3):10.1128/microbiolspec.BAD-0010-2016. doi:10.1128/microbiolspec.BAD-0010-2016 (View)
  14. Holscher HD. Dietary fiber and prebiotics and the gastrointestinal microbiota. Gut Microbes. 2017;8(2):172-184. doi:10.1080/19490976.2017.1290756 (View)
  15. Marzorati M, Van den Abbeele P, Bubeck S, Bayne T, Krishnan K, Young A. Treatment with a spore-based probiotic containing five strains of Bacillus induced changes in the metabolic activity and community composition of the gut microbiota in a SHIME® model of the human gastrointestinal system. Food Res Int. 2021;149:110676. doi:10.1016/j.foodres.2021.110676 (View)
  16. Olteanu G, Ciucă-Pană MA, Busnatu ȘS, et al. Unraveling the Microbiome–Human Body Axis: A Comprehensive Examination of Therapeutic Strategies, Interactions and Implications. Int J Mol Sci. 2024;25(10):5561. Published 2024 May 20. doi:10.3390/ijms25105561 (View)
  17. Salminen S, Collado MC, Endo A, et al. The International Scientific Association of Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics [published correction appears in Nat Rev Gastroenterol Hepatol. 2021 Jun 15;:] [published correction appears in Nat Rev Gastroenterol Hepatol. 2022 Aug;19(8):551]. Nat Rev Gastroenterol Hepatol. 2021;18(9):649-667. doi:10.1038/s41575-021-00440-6 (View)
  18. Shapiro D, Kapourchali FR, Santilli A, Han Y, Cresci GAM. Targeting the Gut Microbiota and Host Immunity with a Bacilli-Species Probiotic during Antibiotic Exposure in Mice. Microorganisms. 2022;10(6):1178. Published 2022 Jun 8. doi:10.3390/microorganisms10061178 (View)
  19. Waitzberg D, Guarner F, Hojsak I, Ianiro G, Polk DB, Sokol H. Can the Evidence-Based Use of Probiotics (Notably Saccharomyces boulardii CNCM I-745 and Lactobacillus rhamnosus GG) Mitigate the Clinical Effects of Antibiotic-Associated Dysbiosis?. Adv Ther. 2024;41(3):901-914. doi:10.1007/s12325-024-02783-3 (View)
  20. Wang X, Qi Y, Zheng H. Dietary Polyphenol, Gut Microbiota, and Health Benefits. Antioxidants (Basel). 2022;11(6):1212. Published 2022 Jun 20. doi:10.3390/antiox11061212 (View)
  21. Xue C, Li G, Gu X, et al. Health and Disease: Akkermansia muciniphila, the Shining Star of the Gut Flora. Research (Wash D C). 2023;6:0107. doi:10.34133/research.0107
  22. Yang J, Qin S, Zhang H. Precise strategies for selecting probiotic bacteria in treatment of intestinal bacterial dysfunctional diseases. Front Immunol. 2022;13:1034727. Published 2022 Oct 20. doi:10.3389/fimmu.2022.1034727 (View)
  23. Zhou, Q., Zhang, Y., Wang, X. et al. Gut bacteria Akkermansia is associated with reduced risk of obesity: evidence from the American Gut Project. Nutr Metab (Lond) 17, 90 (2020). (View
Marty Ross MD Image

Follow Marty Ross MD

See full profile: on LinkedIn.
See the latest: on Twitter, YouTube, and Instagram.

About The Author

Marty Ross, MD is a passionate Lyme disease educator and clinical expert. He helps Lyme sufferers and their physicians see what really works based on his review of the science and extensive real-world experience. Dr. Ross is licensed to practice medicine in Washington State (License: MD00033296) where he has treated thousands of Lyme disease patients in his Seattle practice.

Marty Ross, MD is a graduate of Indiana University School of Medicine and Georgetown University Family Medicine Residency. He is a member of the International Lyme and Associated Disease Society (ILADS), The Institute for Functional Medicine, and The American Academy of Anti-Aging Medicine (A4M).

keep up with our LATEST!

Subscribe to receive our FREE pdf download book: How to Successfully Treat Lyme: Key Info before You Treat or Treat Again & The Ross Lyme Support Protocol; health tips; updates; special offers; and more.