Dysbiosis & Antibiotics: Can Yeast Probiotics Help?

Written by: Sarah Glinski, RD

Updated: January 15th, 2025

Your gut is home to trillions of microorganisms, and your health depends on the delicate balance of viruses, fungi, and bacteria in the gut. This ecosystem, collectively called the gut microbiota, plays a vital role in digestion, immune function, and overall well-being. However, antibiotics can disrupt this delicate balance. While effective at killing harmful bacteria, they can also disrupt the balance between beneficial and harmful gut microbes, leading to a condition known as gut dysbiosis.

Gut dysbiosis can lead to various health issues, including digestive problems. Read on to learn about how dysbiosis and antibiotics are related and the potential for yeast probiotics to restore the microbiota and counteract the adverse effects of antibiotics.

What is Dysbiosis?

Typically, a healthy gut contains a diverse and balanced population of microorganisms that help with digestion, nutrient absorption, immune function, and protection against harmful microorganisms. Dysbiosis occurs when this balance is disrupted, often due to factors such as antibiotic use, dietary changes, stress, illness, or environmental factors.

Consequently, when the balance is disrupted, it can lead to a decrease in beneficial microbes and an overgrowth of harmful microbes, which can lead to various health issues.

Symptoms of Dysbiosis

According to the Cleveland Clinic, there are several symptoms associated with gut dysbiosis, including:

Gas
Bloating
Poor digestion
Lower abdominal pain
Diarrhea
Constipation

What Causes Dysbiosis?

Dysbiosis can be caused by various factors, including diet and stress.

High Simple Sugar Diet

Studies in rats show that bacterial diversity decreases and potentially harmful bacteria increase when fed a high sugar diet. In addition, inflammatory chemicals and lipopolysaccharide (an inflammatory compound produced by certain bacteria) increase. This demonstrates how the gut microbiota is capable of causing inflammation if it’s unbalanced.

High Protein Diet

High protein diets can be low in carbohydrates and therefore fibre. Certain bacteria can metabolize fibre into short-chain fatty acids (SCFAs), which are compounds that provide fuel to the cells in your colon and may reduce inflammation. High protein diets are associated with decreased beneficial SCFA-producing microbes (likely due to lower fibre intake) and increased bacteria that break down protein. The breakdown of proteins by bacteria produces compounds that may be harmful to the health of colon cells.

High Fat Diet

A high fat diet (45%-65% of calories from fat) is associated with dysbiosis. Specifically, it is associated with decreased beneficial Bacteroidetes and increased Firmicutes and Proteobacteria in mouse experiments. It is also associated with an increase in bacteria that create substances that weaken the gut barrier, leading to increased intestinal permeability (i.e., “leaky gut”).

Stress

Studies in frontline healthcare workers during the COVID-19 pandemic showed that stress significantly disrupts the makeup of the gut microbiota. This gut dysbiosis persisted for at least half a year after the source of stress was removed.

Alcohol Misuse

Alcohol misuse is associated with dysbiosis and intestinal bacterial overgrowth in both animal studies and people struggling with alcohol misuse. This dysbiosis can lead to the development of liver disease.

Other Causes of Dysbiosis

Other causes of dysbiosis include malnutrition, gut infections, old age, receiving liquid or IV nutrition, having diabetes or metabolic syndrome, and smoking.

Can Antibiotics Cause Dysbiosis?

In addition to the other causes discussed, antibiotics can also cause dysbiosis. In particular, antibiotics can cause a loss of microbial diversity, changes in the abundance of certain groups of microbes, and the growth of antibiotic-resistant bacteria.

Treatment with common antibiotics is associated with the depletion of beneficial microbes such as Bifidobacterium and Lactobacillus species. These changes may weaken the gut barrier, which is an integral part of the immune system.

How to Diagnose Dysbiosis

Several tests are available for diagnosing dysbiosis, but not all are accurate.

Small intestinal bacterial overgrowth (SIBO), a type of small intestine infection, can be diagnosed by taking a fluid sample from the small intestine and seeing which microbes can be grown from it in a lab. Alternatively, a test in which you breathe into a tube and measure the amount of hydrogen or methane produced can be used to diagnose SIBO.

Stool tests may also be used to determine the overall balance of bacteria and yeasts in the gut. A process called Polymerase Chain Reaction (PCR, a technique that makes many copies of a specific DNA segment, like a photocopier for genetic material) can determine the ratio of beneficial bacteria to harmful bacteria. However, a limitation of this method is that we still don’t know what constitutes a “healthy” gut microbiota. While we are learning what dysbiosis looks like, it’s harder to define a healthy gut microbiota.

In addition to testing which types of microbes are present, certain compounds can give us clues about the health of our gut microbiota. They include compounds like trimethylamine-N-oxide (TMAO), SCFAs, and zonulin (a protein found in the gut barrier). For example, TMAO could indicate the presence of harmful bacteria, while SCFAs indicate the presence of beneficial bacteria.

Can Dysbiosis Cause Other Chronic Diseases?

In addition, dysbiosis is associated with several medical conditions, including small intestinal bacterial overgrowth (SIBO), inflammatory bowel disease (IBD), and atherosclerosis (plaque buildup in the arteries).

Small Intestinal Bacterial Overgrowth

SIBO occurs when bacteria that typically inhabit the colon are present in the small intestine in large amounts. It’s associated with symptoms like abdominal pain, gas, bloating, diarrhea, and irregular bowel movements. If left untreated, SIBO can lead to malabsorption of nutrients and nutritional deficiencies.

Inflammatory Bowel Disease (IBD)

Dysbiosis is commonly observed in people with inflammatory bowel disease (IBD), but we’re still learning whether dysbiosis is a cause of the disease or a consequence.

Irritable Bowel Syndrome (IBS)

As many as 10% of people with IBS had a gut infection leading to gut dysbiosis, which resulted in the development of IBS. This is known as postinfectious IBS. It demonstrates how dysbiosis can have long-lasting effects on our health.

Atherosclerosis

Atherosclerosis is the leading cause of heart disease worldwide. Gut dysbiosis has been shown to contribute to the development of atherosclerotic cardiovascular disease (ACVD) through several pathways.

The gut microbiota produces metabolic byproducts such as trimethylamine (TMA), which gets converted into trimethylamine-N-oxide (TMAO). This compound promotes hardening of the arteries.

In addition, SCFAs reduce inflammation and atherosclerosis. If there aren’t enough SCFA-producing microbes, chronic low-grade inflammation may persist and lead to the development of conditions associated with atherosclerosis, such as metabolic syndrome and type 2 diabetes.

How to Treat Dysbiosis

There are many emerging treatments for dysbiosis. It’s best to discuss these potential treatments with a healthcare provider to ensure you choose a treatment that’s right for your specific circumstances.

Prebiotics

Prebiotics are substances that are selectively used by beneficial gut microbes to provide health benefits. Think of them as fertilizers that create an optimal environment for good gut microbes to thrive. Recently, there has been interest in using prebiotics to treat conditions caused by dysbiosis.

Prebiotics can be obtained through the diet. Chicory root, whole grains, onion, garlic, asparagus, banana, and Jerusalem artichoke are all good sources of prebiotics. Make sure to add them to your diet slowly, as increasing your intake too quickly can lead to gas and bloating.

Yeast Probiotics

While most probiotics used to treat dysbiosis are beneficial bacteria, a growing body of evidence suggests yeast probiotics such as Saccharomyces boulardii CNCM I-745 can effectively prevent antibiotic-associated dysbiosis and diarrhea.

Yeast probiotics are particularly beneficial for preventing antibiotic-associated diarrhea because, unlike bacteria probiotics, yeast probiotics are not killed by antibiotics. This means you can take them at the same time as probiotics. Studies show that when taken simultaneously with antibiotics, S. boulardii effectively reduces the risk of antibiotic-associated diarrhea in adults and children.

S. boulardii works by coating the bowel lining with billions of microorganisms, preventing the overgrowth of harmful bacteria in the gut. In other words, the yeast cells act as a temporary shield within the gut, which allows for the faster reestablishment of a healthy microbiota.

Omega-3 Fatty Acids

Growing evidence suggests that omega-3 fatty acids (such as those found in flaxseeds or fatty fish) can alter the gut microbiota and increase the amount of beneficial microbes in the gut. Some researchers even suggest that omega-3 fatty acids be considered as prebiotics (like certain types of fibre).

Fecal Microbiota Transplantation (FMT)

In cases of severe gut dysbiosis (such as Clostridioides difficile infection or IBD), fecal microbiota transplantation has been successfully used to treat dysbiosis. FMT is a procedure where stool from a healthy donor is transferred to the gut of a person with gut dysbiosis. It’s like planting healthy bacteria from one person’s gut into another to help restore their microbiota balance. However, research regarding the safety and effectiveness of FMT is ongoing. More clinical trials in humans are needed before this treatment can be recommended to treat dysbiosis.

FAQs

Can antibiotics cause diarrhea?

Yes, antibiotics can cause diarrhea due to their negative effect on the gut microbiota.

Do antibiotics cause constipation?

Antibiotics typically don’t cause constipation. In fact, there is emerging evidence that antibiotics can be used to treat chronic constipation and constipation-predominant IBS.

Can you take probiotics with antibiotics?

A Cochrane review suggests that taking probiotics with antibiotics prevents antibiotic-associated diarrhea. The probiotics most often suggested for this purpose are Lactobacillus rhamnosus and S. boulardii.

Can you take too much probiotics?

Most probiotics contain high doses of beneficial bacteria and yeasts, which are typically well-tolerated. While less is known about whether there is an upper limit to how many probiotics you can take, it’s best to follow the advice of your healthcare provider or the directions provided with your probiotic.

What is a SIBO diet?

Some people recommend a low-FODMAP diet for SIBO. FODMAPs are carbohydrates that are fermented by the gut microbes. It’s thought that temporarily eliminating these foods can “starve” the microbes in your small intestine. However, this diet may also cause unfavourable changes to your beneficial gut microbes and should only be followed under the supervision of a healthcare provider.

Key Takeaways

Your gut is home to trillions of microorganisms, and maintaining a balance between beneficial and harmful microbes is vital for digestion, immune function, and overall well-being.
Dysbiosis can be triggered by factors ranging from poor diet to stress to antibiotics, causing symptoms like gas, bloating, and diarrhea.
While antibiotics effectively kill harmful bacteria, they can also disrupt the balance of beneficial microbes in your gut, leading to dysbiosis and digestive problems.
Yeast probiotics such as S. boulardii can help restore the balance of microbes in your gut by preventing antibiotic-associated diarrhea and promoting a healthy gut environment.

Conclusion

Maintaining a healthy gut microbiota is essential for overall well-being, especially when factors like antibiotic use can disrupt the balance. By recognizing the symptoms of dysbiosis and understanding its causes, you can take proactive steps to restore your gut health. Yeast probiotics, like S. boulardii offer a promising way to counteract the negative effects of antibiotics and support a healthy gut.

If you’re experiencing digestive issues or taking antibiotics, consider incorporating yeast probiotics into your routine and consult a healthcare provider for personalized advice.

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