Your Guide to Probiotics And Exactly When to Take Them

Kelly Candela, MS, RD
Health Coach
July 1, 2019

Probiotics have come a long way from a handful of options at the drug store and ‘that stuff in your yogurt.’ Now you can find them in just about everything, from drinks and chocolate to trail mix and skincare. But not all probiotics are created equal—the brand, strain, and why and how you’re taking them, all make a difference in how effective they can be.

Probiotics play a key role as a potential therapy that can help rebalance the gut microbiome (the good and bad bacteria that live in your digestive tract). We’ll explore exactly the best time to take probiotics, the types to look for and what to consider if you’re going to experiment.

What is the gut microbiome?

To best understand what probiotics are and why they might be beneficial, it’s important to grasp the various roles microorganisms play in the body. For starters, it is estimated that there are about 39 trillion bacterial cells in the human body . This extensive ecosystem of bacteria and fungi-we’ll call it your gut flora or microbiome for short-helps to break down toxic byproducts of digestion and discourages the growth of ‘bad’ bacteria and yeasts that can cause digestive distress and make you sick. The gut bacteria also play a key role in the digestive process, aid in the absorption of nutrients, and produce essential vitamins B and K .

Things like a diet high in sugar, overly processed foods, a lack of sleep , and limited physical activity have been directly linked to promoting imbalance and a lack of diversity in gut bacteria, which lends way to digestive distress , depression , and the onset of disease .

What are probiotics?

So what do probiotics do and where do they come into play? Probiotics are living microorganisms including bacteria and yeasts (the same ones in your gut) that, when ingested, can maintain and help restore the balance of power in the gut. Probiotics can be consumed through nutritional supplementation or foods that have undergone bacterial fermentation (think: kombucha, sauerkraut, kimchi).

When you take probiotics, the live microorganisms encourage the repopulation of beneficial bacteria and fungi and allow the immune system to boost its response to harmful pathogens. In this way, they work by both changing the composition of gut bacteria and the metabolic activity of existing bacteria that live there.

When to take probiotics

Despite what you may think from the slew of products available with probiotics, not everyone needs a probiotic. There are a variety of specific conditions and cases in which probiotics may be advised by a doctor or healthcare practitioner. The most well studied and most commonly used medical uses of probiotics are to help reduce gastrointestinal symptoms in those with general digestive issues such as gas, bloating , diarrhea , and constipation . Specifically, probiotics have also proved to be beneficial for individuals with more serious gastrointestinal disorders such as irritable bowel syndrome, Crohn’s disease, ulcerative colitis, infectious diarrhea, Clostridium difficult colitis, and pouchitis.

There are a few more times when you may want to reach for a probiotic.

While on antibiotics

Several research studies suggest that taking probiotics while on antibiotics helps to reduce the likelihood of antibiotic-associated diarrhea. In some studies , reduction in diarrhea was as great as 42 percent. Conversely, another recent study found that treating the gut with probiotics while on antibiotics actually delayed the normal recovery process of the gut microbiome which further complicates the final verdict.

Because of these findings, we recommend checking with your doctor first to see if they advise taking the two together, based on which antibiotic you’re taking. If your doctor does recommend taking probiotics with antibiotics, ensure that you separate them by at least a few hours to prevent negative interaction.

During travel

When exposed to new and different bacteria in foreign countries through food and water, your gut can be more likely to react to changes. In fact, it is estimated that about 50-80 percent of traveler’s diarrhea is caused by pathogenic bacteria . To help reduce the incidence of food poisoning or digestive distress while traveling, probiotics can help to ward off harmful microbes and stabilize your intestine to prevent digestive issues so you’re less likely to suffer while away.

Internal imbalance (SIBO, yeast, vaginal, urinary)

Several medical issues are rooted in an imbalance between the good and bad bacteria or fungi. For these, probiotics can be particularly useful to help re-establish equilibrium. Good examples of this include vaginal yeast infections, bacterial vaginosis, urinary tract infections , small intestinal bacterial overgrowth (SIBO ) and gut dysbiosis . Utilizing probiotic supplements during these times can help to repopulate good bacteria in the body where the microbiome has been negatively impacted to help support a speedy return to normalcy.


Pregnancy can be a particularly important time to consider supplementation with probiotics. Studies have shown that using probiotics during pregnancy can have a positive impact on the future health of infants. This may in part be due to the fact that taking probiotics during pregnancy can help to balance and diversify the vaginal microbiome of the mother. With healthy vaginal flora, the infant is exposed to plentiful good bacteria through the birth canal that helps to form a strong foundation for their immune system. This theory is supported by research which has found that children delivered by cesarean delivery had significantly increased risk of immune disorders including asthma, systemic connective tissue disorders, juvenile arthritis, inflammatory bowel disease, immune deficiencies, and leukemia when compared with those delivered vaginally.

Skin Issues

Promising research has shown that probiotics may be particularly helpful for skin issues such as atopic eczema , acne, rosacea, and even anti-aging . They’re also being researched for the benefits of topical use in which bacteria are applied directly to the skin to restore balance and improve conditions at the site.

When to avoid probiotics

While the use of probiotics is generally considered safe, if you have a compromised immune system or are seriously ill, probiotics can be harmful. In a recent article in JAMA Internal Medicine , for example, probiotics increased the likelihood of infection among immune-compromised individuals. Additionally, because research on probiotics remains controversial with some findings pointing to benefits while others show little improvements or even detriment, it is always best to consult with your doctor prior to starting probiotics or any new nutritional supplements.

Understanding probiotic strains for specific medical conditions?

There are hundreds of types of bacteria classified as probiotics and different strains can have varying effects. For the greatest probiotic benefits, it’s imperative to select a probiotic that has specific strains that have been studied to help support the health issues you’re dealing with.
The two most recognized and utilized probiotics come from either the genus Lactobacillus or the genus Bifidobacterium. These are the most studied strains of bacteria from these families and when they can be particularly helpful in addition to a popular probiotic yeast called Saccharomyces boulardii.

Lactobacillus acidophilus: Studies have positively associated L. acidophilus with helping to aid in digestion , reduce cholesterol levels , improve immunity , reduce symptoms of eczema , and prevent vaginal infections .

Lactobacillus reuteri: When used therapeutically, one study showed that it decreased the oral bacteria that cause tooth decay. Other studies have linked L. reuteri to improving symptoms of acid reflux , reducing respiratory and gastrointestinal infections and managing women’s health issues such as urinary tract infections , yeast infections and overall improvement of the vaginal flora .

Lactobacillus rhamnosus: Studies have found that L. rhamnosuscan help in specific conditions such as eczema , cystic fibrosis , allergic rhinitis , and bacterial vaginosis . More generally, supplementation with this strain has shown to reduce digestive discomfort and other symptoms of IBS . Lastly, in regards to cancer, Lactobacillus rhamnosus has been studied to help prevent colon cancer and reduce chemotherapy induced diarrhea .

Bifidobacterium animalis: Research has found B. animalis is useful in helping with gastrointestinal issues such as reducing bloating , preventing constipation and fighting food-borne bacteria . It’s also been shown to have positive effects on the immune system and metabolism in animal studies.

Bifidobacterium lactis: Specific strains of B. lactishave been linked to supporting the digestive tract , reducing allergies and relieving occasional constipation .

Bifidobacterium longum: B. longum is most known for its antioxidant properties and the ability to aid in digestion by breaking down carbohydrates . Studies have shown that this strain can help reduce depression and anxiety and help reduce symptoms of IBS . Similar to L. acidophilus, B. longum also helps maintain healthy cholesterol levels .

Saccharomyces boulardii: This particular probiotic is actually a yeast, which is a type of fungus. Saccharomyces boulardii has been clinically studied to help treat a variety of gastrointestinal disorders and symptoms in addition to acne , high cholesterol, urinary tract infections, and yeast infections.

While specific strains have specific benefits, there is a clear overlap in many of their uses. This is often why probiotics are created to be “broad spectrum” meaning they contain a combination of multiple, well-studied strains to provide optimal and diversified benefits. At Parsley Health , our doctors often recommend high tech specialty lab testing such as stool cultures and microbiome testing to help identify which strains would be most beneficial to help restore, replenish, and diversify your unique community of gut flora.

What are the best food sources of probiotics

Supplements are not the only way to get your daily dose of probiotics. There are various foods loaded with these cultures of good bacteria. Probiotic-rich foods must undergo bacterial fermentation and be refrigerated to ensure the beneficial bacteria stay alive.

The top sources include fermented vegetables such as sauerkraut, kimchi, and pickles in addition to yogurt, kefir, kombucha, and miso. Keep in mind that once heated, the special bacteria found in these foods are killed so to reap the benefits, ensure you eat them raw, cultured and unheated.

Because it can often be difficult to get enough probiotic-rich foods in the diet to meet your needs, supplementation can often be helpful.

What to look for when purchasing a probiotic supplement

When it comes to picking out a probiotic supplement, here’s what to look for before purchasing your next dose of good bacteria.

Opt for a reputable source.

With so many different probiotics available at your local pharmacy alone, it’s extremely important to determine if the supplement manufacturer is reputable. Parsley Health doctors recommend pharmaceutical-grade probiotics that are third-party tested to ensure optimal quality and purity.

Get the right dose.

One of the most important considerations for a quality probiotic is the number of viable organisms in the product. Probiotics are measured in colony-forming units, or CFUs, which estimate the number of viable bacteria or fungal cells present. Ideally, you want a probiotic that ranges from at least 50 million to more than 100 million CFUs per serving to be consumed each day to yield benefit.

Be mindful of storage and expiration.

Because probiotics are living microorganisms, they sometimes require refrigeration and inevitably lose their effectiveness after a certain date. Others are freeze dried and shelf-stable, so check the label for instructions and expiration date. Additionally, as live organisms probiotics inevitably lose their effectiveness after a certain date so being mindful of expiration is another important consideration.

Know your strains.

Ensure you’re including the best probiotic strains for your particular health concerns. We always recommend consulting with a doctor to find the right supplement for you.

Kelly Candela, MS, RD
Health Coach

Kelly Candela is a registered Dietitian Nutritionist with six years of experience in the health and wellness field, four of which have been spent right here at Parsley Health supporting members with everything from gut issues and autoimmune disease to cardiometabolic health concerns and fertility. She holds a Master's of Science in Nutrition from one of the leading science-based natural medicine schools in the country, Bastyr University, and completed her dietetic internship at Sea Mar Community Health Center in Seattle, WA.

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