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Written by
Amy Brownstein
Medically Reviewed by
Dr. Danielle Desroche

The gut microbiome influences many aspects of our health, from appetite to energy to how we respond to illness. Ensuring we have a robust and diverse gut microbiome is one way to maintain good health. We can alter the makeup and diversity of our gut microbiota with probiotics, living microorganisms that benefit health.

Research is promising on the use of probiotics for inflammation and autoimmune disorders, with their positive effects specific to both bacterial strain and health condition. But when is the best time to take probiotics, and how should these supplements be taken for us to reap the benefits? In this article, we’ll discuss all things probiotics — the health benefits, why these microbes should be part of your supplement regimen, and the best time to take probiotics. (Source, Source)

The Gut Microbiome

The human gastrointestinal tract is home to an estimated 100 trillion microorganisms, including bacteria, fungi, and viruses, that make up our gut microbiome. Environmental factors such as diet, medications, method of birth, and individual body measurements and structure contribute to our microbiota composition. Thankfully, a healthy microbiome adapts and responds to these environmental factors. (Source, Source) 

What Are Probiotics? 

Probiotics Are Living Microorganisms

Probiotics are living microorganisms that benefit health when taken in adequate amounts, although not all microbes are probiotics. Probiotics found in dietary supplements and some kinds of cultured foods provide beneficial bacteria to the small intestine and the colon. There are many strains of probiotics, each with different health effects. (Source, Source, Source

For a microorganism to be used as a probiotic, it must meet the requirements for safety, functionality, and usefulness. Functionality refers to the ability of the microorganism to survive its journey from the mouth to the gut, and its ability to retain its health properties when being manufactured into a consumable product. Usefulness refers to whether the microorganism is easy to produce and whether it is stable in the final probiotic product. And for safety, a probiotic must not be antibiotic resistant and must not be expected to cause infection. (Source)

There Are Many Strains of Probiotics

Some of the most common probiotics belong to the Lactobacillus and Bifidobacterium genuses. Both groups are among the first microbes to colonize the gut following a vaginal birth, and there is evidence they are transferred from mother to baby through breast milk. Strains from the Lactobacillus and Bifidobacterium groups have been associated with positive effects on health such as promoting immune function, strengthening the gut barrier, and inhibiting the growth of pathogens. (Source, Source, Source)

Lactobacillus inhabits the mouth, intestines, and vagina. It can withstand the stomach’s acidic environment, so it is ideal for use in probiotics. Lactic acid produced by Lactobacillus is also used to cultivate cheese, yogurt, and other fermented foods. Bifidobacterium, found in the intestinal tract, vagina, and mouth, ferments complex carbohydrates to contribute to digestion. (Source, Source)

Saccharomyces boulardii, a species of yeast, is frequently used as a probiotic and is naturally resistant to antibiotics, stomach acid, and digestive enzymes. (Source)

yogurt with almonds, granola, and blueberries, when is the best time to take probiotics

Sources of Probiotics

Food Sources

Knowing how much of a probiotic you are getting from food is tricky. Probiotics in food products are often in the form of free cells (probiotics that have not been encapsulated to protect the microorganisms), meaning they are more susceptible to destruction as they move through the digestive tract. Food labels are not required to list the quantity of probiotics in a product. The food matrix — the microscopic structural arrangement and interaction of molecules found in foods — can influence the digestion, survival, and health benefits of probiotic food sources. (Source, Source, Source

Live microorganisms are used to ferment food products such as yogurt, cheese, sourdough, and kimchi, among other items. Food processing after fermentation can destroy live cultures, though, so products such as sourdough and pickles end up not containing live microorganisms.

Even in unprocessed fermented foods, we may not get the health benefits associated with live microorganisms. Some fermented food products, including kimchi, kombucha, miso, and sauerkraut, do not contain proven probiotic microorganisms. Furthermore, some live microorganisms that help stabilize fermented products are destroyed during digestion. However, some probiotic strains in foods such as yogurt can survive the digestive tract. (Source)


Supplements provide a targeted and effective way to consume probiotics. Supplements are formulated for microbial strain and strength to ensure viability (the ability to survive). Some microbial strains have a greater survival rate than others, so more probiotics reach the intestines. Many supplements come in the form of beads, capsules, and tablets with enteric coatings. These protective coatings help probiotics survive the harsh conditions of the digestive tract. (Source)

What Do Probiotics Do for Us and Why Should We Take Them?

Health Benefits of Probiotics

Probiotics are important for sustaining a healthy gut microbiome. Gut dysbiosis, an alteration in gut microbiota, has been linked to multiple health conditions. Probiotics help restore the composition of gut microbiota, increasing microbial diversity and supporting beneficial bacteria. By strengthening our gut lining, probiotics support a healthy digestive tract and may help prevent leaky gut syndrome. (Source, Source, Source)


Probiotics may also help manage food allergies, fungal infections, and dental cavities. Antibiotic therapy can take a toll on the gut microbiome, causing gastric upset and diarrhea, and probiotics may help restore normal microbial balance. Independent of the gut microbiome, probiotics boost vitamin and mineral absorption. Some probiotic strains are even natural producers of B vitamins. (Source, Source)  

Research has shown that probiotics may have a beneficial effect on improving heart and metabolic health (the ability to process and generate energy), reducing inflammation, and preventing upper respiratory infections. Markers of metabolic syndrome — body mass index, fasting blood glucose, and cholesterol levels — have been shown to improve following probiotic supplementation. Probiotics may help increase the body’s immune response to pathogens, and may inhibit the release of inflammatory cytokines, small proteins involved in cell signaling, while activating anti-inflammatory cytokines. (Source, Source,, Source

How Do Probiotics Work?

Probiotics have many ways of working in the body. They act beyond the microbiome, exerting a holistic effect on health through immunomodulation and affecting pathogen growth.

  • Probiotics act as antagonists by releasing antimicrobial substances. As an antagonist, probiotics interfere with the normal growth and behavior of other, usually pathogenic, bacteria. Probiotics secrete substances that make the gut environment unwelcoming to pathogens, preventing these organisms from settling and wreaking havoc on our bodies. (Source, Source)
  • Probiotics compete with pathogens to attach to the intestinal lining and for nutrients. There is limited space available for bacteria to colonize in our intestines; by adhering to our intestinal lining, probiotics limit the space available for pathogens. Probiotics and pathogens also need the same nutrients, and a vigorous community of beneficial microorganisms helps deprive the harmful ones of needed food. (Source, Source
  • Probiotics are involved in immunomodulation, influencing the body’s response to inflammation and stimulating phagocytosis, a process by which viral or infected cells are engulfed and destroyed. (Source, Source)

Autoimmune Disease and Probiotics

Research is evolving on the role of the gut microbiome in the development of autoimmune diseases, but evidence suggests probiotics may reduce symptoms associated with some conditions. Altered gut microbiota contributes to the onset and progression of inflammatory bowel disease, and studies have shown a decrease in symptoms and overall remission when following a probiotic rich diet, such as the autoimmune protocol. Studies have shown that taking probiotic supplements can lead to ulcerative colitis remission, but they don’t seem to have the same effect on Crohn’s disease. (Source, Source)

Increasing evidence supports the role of gut microbiota in the development of multiple sclerosis. It is possible probiotics may prevent, lessen, or delay symptoms of multiple sclerosis by affecting inflammatory pathways. Research suggests a relationship between gut microbiota and rheumatoid arthritis, but further research is needed to understand the role probiotics may play as a complementary treatment for the disease. (Source, Source)


Therapy for autoimmune diseases often includes antibiotics, which can modify the gut microbiota composition. It is unclear whether antibiotics for these health conditions just suppress harmful bacteria or also accidentally remove beneficial bacteria. If you are concerned about the effects of antibiotics on the gut microbiome, you might want to talk to your health care provider about trying natural antimicrobials. (Source, Source, Source)


When Is the Best Time to Take Probiotics?

We’ve looked at the health benefits of probiotics, but when is the best time to take them? 

A probiotic is only successful if it can survive the digestive tract. Gastric acid, digestive enzymes, and bile are released following a meal to help break down the food we just ate. These secretions and the movement of food through the gastrointestinal tract create a harsh and acidic environment. Probiotics need to remain intact until they reach the colon, where the microbes can colonize and exert their health benefits. (Source)

One study in the journal Beneficial Microbes found it best to take non-enteric coated probiotic supplements either 30 minutes before a meal or with a meal containing fat, but other studies have had different results. A small study of healthy individuals conducted in Italy found that food did not influence the effect of probiotics. Participants who took a probiotic supplement 30 minutes before breakfast had the same gut microbial changes as those who took a probiotic supplement 30 minutes after breakfast. (Source, Source)


Should You Eat Before Taking a Probiotic?

Currently, there is no consensus on the best time of day to take a probiotic supplement. However, research suggests it matters whether or not they are taken with food. 

If you prefer to take your probiotic with meals, choose one with an enteric coating. Enteric coating, or encapsulation, provides a barrier around a medication or supplement to protect it from being destroyed by stomach acid. Limited research exists on the effect of food on enteric coated probiotics, but studies show encapsulation helps these beneficial microorganisms survive the gastric journey when food is present. (Source)

Non-enteric coated probiotics, on the other hand, are better taken before a meal, when the environment of the intestinal tract is less harsh. Taking a non-enteric coated probiotic on an empty stomach, when there is less acid present, helps protect the probiotic bacteria and increase its viability. Taking a non-enteric coated probiotic with food causes greater degradation because of the increase in acid and digestive enzymes that occur with eating. (Source)

Drinking milk with your probiotic may improve microbial survival because it acts as a buffer, reducing the acidity of the stomach and intestinal tract. Additionally, the food matrix of milk may act as a protective environment for probiotics. Though milk may benefit microbial survival, dairy products are avoided on the autoimmune protocol due to its inflammatory effects. If you are following the autoimmune protocol diet, eliminating dairy from your diet is essential. (Source, Source)

At the end of the day, consistency matters most when taking supplements. Choose a probiotic supplement and time of day that fits with your routine. 

Can You Take Probiotics With Other Medications?

Antibiotics target the microbiome, altering the diversity, strength, and composition of its microbes. Probiotics may help reduce the effect of antibiotics on the microbiota, and research has shown that pairing probiotics with antibiotics may help prevent and treat antibiotic-related diarrhea. (Source, Source, Source)


If you want to support your gut health while taking antibiotics, consider starting probiotic supplements within the first few days of beginning antibiotic treatment, and continuing for 1 to 4 weeks after the antibiotic regimen ends. If you choose to do this, research recommends taking the probiotic and antibiotic at least 2 hours apart to prevent each canceling out the other’s effect. (Source)



Choosing a Probiotic

When choosing a probiotic, look at the amount of bacteria in the supplement. Bacteria are measured in colony-forming units (CFU), which indicates the amount of viable microbial cells present. Most clinical studies use a dosage of 10 million to 10 billion CFU per capsule taken 1 to 3 times per day. Some studies have shown that at least 100 million to 1 billion CFUs must reach the intestine for beneficial health effects. (Source, Source, Source)

A higher CFU doesn’t necessarily guarantee greater health benefits, though. There’s no consensus on the dose or duration needed to keep bacterial colonies thriving and supporting health after a probiotic is discontinued. (Source, Source, Source)

When selecting a probiotic, consider the time of day when you’ll take the supplement. Choose an encapsulated supplement if you are more likely to take the probiotic around meal time. Our care team at WellTheory can review your health history and help you choose the best probiotics for your lifestyle so you can reclaim your health now

Probiotic Side Effects

Probiotics are categorized by the U.S. Food and Drug Administration (FDA) as GRAS, or generally recognized as safe. This means experts have enough good information to determine that probiotics are safe when used as intended. Reported side effects are minimal but may include abdominal pain, nausea, gas, and soft stools. Because probiotics contain living microorganisms, people with compromised immune systems and other serious medical conditions could be at risk of developing infections from probiotic use. (Source)

Probiotic Supplements Are Not Regulated by the FDA

The FDA does not approve dietary supplements before they are sold, the way it does medications. Supplement manufacturers must use truthful and clear labeling and guarantee their products are safe when used as intended, but they don’t have to provide evidence to the FDA. Dietary supplement labels may suggest they provide health-related benefits. However, labels must also disclose that the FDA has not evaluated the products and that they are “not intended to diagnose, treat, cure, or prevent any disease.” Generally speaking, FDA oversight is limited to making sure supplement makers follow good manufacturing practices, don’t produce dangerous products, and don’t make misleading claims about them. (Source, Source)

Consult Your Health Care Provider Before Starting Probiotics

Before starting a probiotic, consult your health care provider. Discuss which probiotic strain may be best suited for your particular needs and health condition. If you are immunocompromised, review the safety of probiotics. Some probiotic supplements may contain additional, potentially harmful, strains that are not listed on the label. (Source)


The Bottom Line on the Best Time to Take Probiotics

To get the most out of your probiotic, choose an enteric coated supplement that contains 100 million to 1 billion CFUs of the bacteria strain that is most associated with your health condition. The best time to take probiotics depends on the supplement form and your schedule. Enteric coated supplements can be taken at any time of day. Non-enteric coated supplements should be taken 30 minutes before a meal or with a meal. Before starting probiotics, it is helpful to consult a health care provider to make sure your unique medical history and diet are taken into consideration. 

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