Are you experiencing gas, bloating, abdominal pain, and digestive issues? Chances are, you are dealing with a microbiome imbalance. Microbiome imbalance is a common root cause of not only gut health issues, but also other chronic symptoms, inflammatory conditions, and autoimmunity.

I recommend following a nutrient-dense diet with lots of prebiotics and probiotics. This is common advice to improve microbiome imbalance. For most people, however, we may be missing a key ingredient to microbiome health: sulfur.

In fact, sulfur deficiency may be driving the overgrowth of harmful bacteria, causing microbiome imbalance. Improving your sulfur levels with MSM supplementation may be the missing piece you’ve been seeking.

I learned about the importance of sulfur from a colleague, Kathleen Janel, ND who’s brilliant work on this topic is featured in her book called, GI Janel.

Let’s talk about the connection between sulfur deficiency and your microbiome health and how to improve it naturally.


Sulfur Deficiency

Parts of the  Gut

Your gastrointestinal (GI) tract, or gut, is a system of organs that food and liquid travel through. Food gets digested, nutrients get absorbed, and waste products leave at the end. Your GI tract includes your mouth, throat (pharynx), esophagus, stomach, small intestine, large intestine, rectum, and anus. Together they form your digestive system.

This is a complex system, so you can imagine a lot of things can go wrong: often in your small or large intestines. You may develop gut microbiome imbalance (more on that in a second!) and gut health issues in either or both areas.

Your small intestine is the part of your gut where food gets broken down into liquid. Most nutrients also get absorbed there. From here, waste products get moved to your large intestine.  Usually there are little to no bacteria or fungi in the small intestines. Small intestinal bacterial overgrowth (SIBO) and small intestinal fungal overgrowth (SIFO) are conditions where too many bacteria or fungi have grown in the wrong place, leading to symptoms related to your small intestine.

Your large intestine is a part of your gut where partly digested food passes through. By this time, most digestion and nutrient absorption is over. In your large intestine, your body can absorb water and salt from the remaining materials. Then the waste product can move to the rectum to be released through the anus. Common gut health issues that may affect your large intestines include irritable bowel syndrome (IBS), leaky gut syndrome, ulcerative colitis, and Crohn’s disease. Crohn’s disease may affect both your large and small intestines.

Using sulfur may be particularly helpful for small intestinal microbiome balance and for improving SIBO or SIFO. It may also help to improve your gut lining, gut motility, large intestinal health, and symptoms that affect your large intestines. But before I jump into the potential gut health benefits of sulfur, let’s talk a bit more about your microbiome health.


Microscope in Laboratory

Importance of the Microbiome

Your gut is the home of trillions of microbes, including bacteria, viruses, fungi, and other microorganisms. Your body actually has more bacteria than human cells (1, 2). This means that the bacteria and other microorganisms living in your gut greatly affect your health and well-being.

Thus, the composition of these bacteria and microbes is critical. The Integrative Human Microbiome Project published a study in Cell Host & Microbe in 2014 which found that the average human gut is home to about 1,000 different species of bacteria (3). Some of these bacteria are beneficial and supportive to your health. Others are more harmful and may lead to chronic symptoms, inflammation, and disease (3).

Though having harmful bacteria and microbes in your gut is normal at a certain level, it’s important to have a healthy balance between beneficial and harmful microbes. If you have too many bad bacteria and too few good ones, your gut microbiome will be off-balance and you will develop gut dysbiosis. Gut dysbiosis or gut microbiome imbalance can lead to chronic inflammation, leaky gut syndrome, digestive issues and other chronic symptoms, inflammatory conditions, autoimmune issues, and other health problems.

Taking care of your gut microbiome health is clearly important. Most people have heard about the importance of probiotics and prebiotics, but there is one nutrient we don’t really talk about, yet it may be the key to microbiome balance.

I’m talking about sulfur.


Sulphur crystals

What Is Sulfur?

Sulfur is a nonmetabolic chemical element and mineral found in soil, plants, food, and water. Though sulfur is one of the most abundant minerals in your body, along with calcium and phosphorus, your body cannot make it on its own. You have to get sulfur from your diet or water from certain resources. Or you can apply it topically, as in sulfur mineral baths or mud soaks (4). I grew up near Saratoga Springs, NY, which was famous for its sulfurous healing mineral water. From local Indian tribes, such as the Mohawk and Iroquois, to the wealthy Vanderbilts and Whitneys, people throughout the centuries have bathed and drank this carbonated mineral water for health reasons.  Now we can explore how this mineral works.


Benefits of Sulfur

Sulfur is an essential mineral for your health. Potential functions and benefits of sulfur may include (5):

  • Providing protection against oxidative stress and cellular damage (6)
  • Supporting building and repairing DNA (7)
  • Aiding the synthesis of antioxidants (8)
  • Reducing inflammation and supporting immune health (9)
  • Decreasing joint pain (10)
  • Supporting heart health (11)
  • Supporting nitrogen balance (12)
  • Fighting certain harmful bacteria (13)


Wheat field on modern farm

Causes of Sulfur Deficiency

Not eating enough sulfur-rich foods can lead to low sulfur levels, as is often the case for SIBO patients who find that sulfur rich foods increase their symptoms.

But what if you have a healthy diet and eat plenty of those foods? Unfortunately, you may still develop sulfur deficiency.

The sulfur cycle plays an important role in cellular regeneration.  Unfortunately, modern farming practices, such as monocropping and using pesticides and chemicals to increase production, have changed the normal sulfur cycle in food production. This has led to lower sulfur levels in previously higher-sulfur crops (14). A 2016 study published in the Journal of Environmental Quality found that sulfur levels have declined so much in our rivers, watersheds, and soils that farmers may have to consider adding sulfur to the soil (15). Hopefully, regenerative farming practices will improve this sulfur depletion problem. I’m excited to learn more about these farming practices and how they may change our world for the better.

So, even if you are able to eat “sulfur-rich foods”, they may no longer contain these levels of sulfur your body needs, leading to sulfur deficiency even if you eat a healthy diet. A 2021 study published in Communications Earth and Environment found that sulfur depletion may lead to nutrient deficiencies (16). Since sulfur is so important for your gut and other areas of your health, low sulfur levels can pose a health risk. Improving your sulfur levels may be critical.


Woman with gut imbalance

Sulfur, Gut Health, and Microbiome Balance

Chronic microbiome imbalance, chronic gut infections, small intestinal overgrowth, and chronic digestive symptoms can take a serious toll on your body. But what if I told you that you could improve your gut microbiome, relieve gas and bloating, and improve your overall health with sulfur? It sounds pretty miraculous!  Though more research is needed on the topic, some doctors believe that sulfur deficiency is one of the most common nutrient deficiencies (17). Addressing it may improve your health on many levels, including your gut health.


Sulfur and Your Gut Lining

Since your body cannot make or store sulfur, you have to maintain normal levels through a constant intake of sulfur through supplementation, since our diets are no longer sufficient to supply the necessary amount. Methylsulfonylmethane, or MSM, is the oxidized form of dimethyl sulfoxide (DMS), which is an organic sulfur compound. MSM is biologically available for your body and is essential for building glycosaminoglycans (GAG). GAGs serve as a basis for your connective tissues. GAGs help to form collagen, which helps to form connective tissues (18).

It’s not surprising that MSM is a commonly used supplement for joint, cartilage, and bone health (19, 20). However, connective tissues also form the gut barrier. Using sulfur in the form of MSM may help to improve gut mucous lining, repair cell-to-cell connections, improve cell permeability and elasticity, and support motility in your gut (21, 22).


Sulfur and Your Gut Microbiome

Beyond supporting your intestinal lining, sulfur may also help to improve your gut flora. And this is where the story gets really interesting! Sulfur is commonly used as a natural antimicrobial in the food industry and as a natural antifungal in organic farming (23, 24).

If used correctly, MSM sulfur may help to reduce bacterial and yeast overgrowth in the gut and improve symptoms of small intestinal bacterial overgrowth (SIBO) and small intestinal fungal overgrowth (SIFO). A 2022 animal study published in Frontiers in Microbiology found that MSM supplementation may improve the gut microbiome in cats (25).

We still need more research, including human studies, to understand this better. However, anecdotal evidence and the experience of some functional medicine doctors suggest that using MSM sulfur may be beneficial for those with gut infections and gut dysbiosis (26).

Your gut is an anaerobic environment. This means that there is no oxygen. In such an environment, sulfate-reducing bacteria may use elemental sulfur or sulfate as a receptor to get energy. Microbes in your gut may ferment pyruvate, which is a metabolic product of carbohydrate breakdown. Sulfur or sulfate may serve as electron receptors in this process.

This helps energy production. It also causes the production of ethanol and gases. This may explain why adding too much sulfur to your diet or supplementation protocol may cause gas. Your body needs to acclimate to therapeutic levels of sulfur. Starting at a low dose and increasing it gradually over time may reduce gassiness and may even eliminate gas completely once your microbiome reaches balance.

Think about it this way.  The body has innate wisdom and our microbiome works in synergy with our bodies.  If we are sulfur deficient, the microbiome shifts to contain more sulfate-reducing bacteria in order to provide our bodies with more sulfur!  If we replenish the sulfur through supplementation, then when your body has enough sulfur, it doesn’t need sulfur-producing bacteria anymore! The sulfate-reducing bacteria in your gut will start dying off, leaving more room for beneficial microbes and gut microbiome balance. Symptoms of gut microbiome imbalance can finally improve, resolving your SIBO for good, and improving your overall health.


Woman with brain fog from sulfur decificieny

Sulfur Intolerance and Sulfur Deficiency

Sulfur intolerance should not be mistaken for sulfa drug allergy or sulfite intolerance. They are not the same thing.

  • Sulfa drugs or sulfonamides, including sulfonamide antibiotics, thiazide diuretics, loop diuretics, sulfonylureas, and carbonic anhydrase inhibitors, are a group of medications used for treating bacterial infections. Allergies to sulfa drugs are common.
  • Sulfites are naturally occurring, sulfate-containing molecules that are produced during fermentation and are used as preservatives in foods, including jam, pickled foods, soup mixes, gravies, canned vegetables, baked goods and wine. Some people experience reactions to sulfites.
  • Sulfates are salts of sulfuric acid. They are found in some supplements, medicines, and personal care products.
  • Sulfur is a chemical element that’s essential for your health. Sulfur-containing nutrients include methylsulfonylmethane (MSM), allicin, alpha-lipoic acid (ALA), glucosamine sulfate, S-adenosylmethionine (SAMe), chondroitin sulfate, and certain antioxidants, including glutathione, dimethyl-sulfoxide (DMSO), and N-acetylcysteine (NAC).

Sulfur is an essential element for your health. Without sulfur, your body couldn’t possibly be alive and function well. This means that you cannot be allergic to sulfur.

However, there are some people who cannot tolerate sulfur well. Sulfur intolerance is a rare condition that leads to systematic symptoms when exposed to dietary sulfur. Symptoms may be similar to histamine reactions and may include flushing, hives, headaches, nausea, brain fog, or asthma-like symptoms.

Having sulfur intolerance doesn’t mean, however, that your microbiome health can’t benefit from sulfur. If you begin with very low doses and move up gradually, you may eventually tolerate sulfur supplements at a higher level.

There are some genetic variants that may make it more difficult to tolerate sulfur, such as CBS  and SUOX genes. If you know that you have these gene variants or find that you are struggling to add sulfur, the addition of supportive nutrients such as molybdenum and selenium are co-factors and support sulfur metabolism.

Though there is no current scientific research backing it up, sulfur deficiency may be a potential explanation behind sulfur intolerance. As hydrogen sulfide species are being released and sulfur levels are replenished, your microbiome balance will shift too. The healthier your microbiome becomes, the more likely you may be able to tolerate higher doses of sulfur and sulfur-rich foods.

So what can you do about sulfur deficiency? Sulfur-rich foods and supplementation may help. My recommendations were inspired by Kathleen Janel, ND’s work.


Sulfur Deficiency

Food Sources of Sulfur

Consuming sulfur-rich foods can be very beneficial for your gut and overall health. Due to our depleted soils, it may not be enough, especially if you are dealing with gut microbiome imbalance and related symptoms. However, you still shouldn’t forget about dietary sources of sulfur, even if you are taking MSM sulfur supplements.


Food sources of sulfur include:

  • Meat, poultry, and fish, especially beef, chicken, turkey, organ meat, most fish, shrimp, mussels, and scallops
  • Eggs and dairy
  • Legumes, especially kidney beans, black beans, white beans, split peas, and lentils
  • Nuts and seeds, especially Brazil nuts, walnuts, sesame seeds, and pumpkin seeds
  • Cruciferous vegetables, including broccoli, Brussels sprouts, cauliflower, radishes, and radishes
  • Allium vegetables, especially garlic, onion, leek, scallion, and chives
  • Leafy greens, including red cabbage, watercress, kale, and turnip tops
  • Certain whole grains, especially oats, barley, and wheat
  • Certain spices and condiments, especially ginger, curry powder, and horseradish
  • Certain beverages, especially coconut milk, grape juice, tomato juice, wine, and cider


Sulfur Deficiency

Supplementation, Dosage, and the Herx Response

There is no recommended daily intake for sulfur. The National Academies Food and Nutrition Board recommends 0.2 to 1.5 grams a day (27). A 2017 review published in Nutrients found that up to 3 to 6 grams a day may be safe and well-tolerated (28). However, if you are dealing with gut microbiome imbalance, starting with a high dose can lead to digestive issues instead of improvements.

We must not forget about the Herxheimer reaction or Herx reaction when it comes to sulfur supplementation. The Herx reaction refers to the idea that you will feel worse before you feel better. Killing any excess harmful bacteria or yeast can be difficult on your body at first. As these microorganisms die, your body may become overwhelmed by trying to remove all the toxic waste. Some people may refer to this reaction as the detox response.

Based on the book, ‘GI Janel: Permanent IBS/SIBO Resolution’ and some personal experimentation, I found that starting with a low dose of MSM sulfur and gradually increasing your dose may help your body to ease into things (29). This approach may minimize the Herx reaction and help you get better gradually.

I recommend starting with around 0.5 grams of MSM. Gradually increase your dose with 0.5 grams at a time. Once you reach 8 to 12 grams, you can start increasing your dose a bit faster. Your goal is to reach up to 24 grams. However, every body is different. It’s important to listen to yours. A knowledgeable functional medicine practitioner can be a helpful guide on your journey.


Dr. Kelly McCann

Next Steps

Are you interested in improving your sulfur levels to rebalance your microbiome? If you are experiencing symptoms of IBS or SIBO or gut microbiome imbalance, and want support with your nutrition, I welcome you to schedule a functional nutrition consultation with my nutritionist, Sarah.  Visit our store for products to support your GI health.

And stay tuned for more information to help you uncover the root cause of your health issues, to improve your nutrition, repair your body, and regain your health naturally.

You can schedule your consultation with Sarah here.