Best Time to Take Probiotics: What The Science Tells Us and What Can Work Best for You

by Lindsay Christensen, M.S., CNS, CKNS

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Probiotic consumption is associated with a host of beneficial health effects, including gut and brain health benefits. However, the question remains, when exactly you should take probiotics. Should probiotics be consumed with or without food? Should you take probiotics if you have an infection? Is it better to take probiotics with prebiotics? Read on to learn more about the science behind when you should take probiotics to achieve the best health effects possible. 

Does Your Health Status Influence the Best Time to Take Probiotics?

Your current health status has a significant bearing on whether or not you should take probiotics or potentially hold off on consuming them. Below are some examples of health conditions that could affect probiotic use:

Irritable Bowel Syndrome

Irritable bowel syndrome (IBS) is, in many cases, caused by unfavorable shifts in the gut microbiome. Some cases of IBS develop after an acute gut infection (post-infectious IBS), while others involve bacterial overgrowth, sharing overlap with small intestinal bacterial overgrowth (SIBO). An overwhelming body of evidence indicates that probiotics are effective and safe for people with this type of IBS. (1) Probiotic treatment can reduce abdominal pain, bloating, and distension. (2) Probiotics may also regulate the intestinal immune system in IBS cases, ultimately protecting the gut. (3)

The topic of probiotics and SIBO is a bit more controversial. Some healthcare professionals and patients with SIBO argue that probiotics must be avoided, while others feel that probiotics improve SIBO. The truth appears to lie somewhere in between; some people with SIBO experience benefits from probiotics, such as the soil-based probiotic organism Bacillus clausii. (4)

However, other people with SIBO do not tolerate probiotics well and must proceed through antimicrobial treatment before weaving probiotics into their lives. If you have SIBO, talk with your Functional Medicine provider to determine whether probiotics are suitable for your situation.

General Constipation or Bloating

Evidence for the effectiveness of probiotics for general constipation is varied (5). Since the underlying causes of constipation are many, ranging from hypothyroidism to enteric nervous system dysfunction, probiotics on their own may have limited impact. That being said, experimentation with probiotics is an affordable, safe, and potentially beneficial intervention worth considering. 

Probiotics have clearly shown benefits for general bloating in the context of IBS, but alone may not be enough to resolve bloating caused by underlying conditions such as SIBO.

While Taking Antibiotics

Saccharomyces boulardii is a probiotic yeast that is beneficial to take during antibiotic treatment because it can prevent antibiotic-associated diarrhea, including diarrhea associated with antibiotic-induced Clostridium difficile overgrowth. (6)

Should you also take probiotics after antibiotic treatment? It’s long been believed that probiotic supplementation may help restore beneficial probiotic species to the gut after a course of antibiotic treatment. However, a couple of years ago, a study (7) made the rounds suggesting that probiotic supplementation after a round of antibiotics was detrimental, delaying the restoration of important microbial species in the gut. The study took healthy subjects and gave them high doses of two antibiotics, metronidazole and ciprofloxacin, for seven days. The subjects then underwent “evacuation therapy,” or manual clearance of stool from the colon, to obtain intestinal microbiota samples. The researchers observed that 10 to 15 intestinal bacterial species took longer to recover post-antibiotics in the group that received probiotics, compared to a group that did not receive probiotics, and a third group that received fecal microbiota transplantation. The conclusion that was drawn suggested that probiotic use after antibiotics may pose a threat to gut microbiota restoration. However, there were limitations to the study in that no clinical symptoms were measured during or after antibiotic treatment. Furthermore, this was just one study that looked at a single probiotic mixture.

Additionally, numerous studies contradict these results entirely, demonstrating significant benefits of probiotic usage after antibiotics. (8) Since the jury is out, a reasonable compromise might be to wait several weeks after completing a round of antibiotics to resume taking a probiotic.

You Have Candida or Other Bacterial Infections

Should you take a probiotic if you have an infection? Interestingly, a growing body of research indicates that probiotics may be beneficial as adjunct treatments for various types of infections, including Helicobacter pylori, drug-resistant infections (which are on the rise and quite scary!), and fungal infections.

H. pylori Infection

H. pylori is a bacterium that exists in several different “varieties” in the human body, residing primarily in the stomach but also appearing in the intestines: a type I virulent strain, the kind that causes severe infections; a type II reduced virulence strain(s); and intermediate strains. The virulence of H. pylori is classified based on the proteins, referred to as “virulence proteins,” that the bacterium makes. (9) Non-pathogenic H. pylori strains may serve beneficial roles, including protecting against asthma and Crohn’s disease. (10) However, the pathogenic varieties of this microorganism can cause gastritis and are even linked to gastric cancer. When harmful forms of H. pylori are at large, probiotic supplementation can be a helpful treatment. Lactobacillus casei and the probiotic yeast S. boulardii significantly improve H. pylori eradication rates. (11, 12) Lactobacillus gasseri LG21 may even help prevent H. pylori infection in the first place through the improvement of the commensal upper gastrointestinal tract microbiota. (13)

Drug-resistant Bacterial Infections

When combined with antibiotic therapies, probiotics are helpful allies in treating specific drug-resistant infections, such as Staphylococcus aureus and Pseudomonas aeruginosa. One study applied three strains of Lactobacillus probiotics from Bio-K+ (a commercially available probiotic), encapsulated the probiotics in a substance called alginate to protect them from antibiotics, and administered them in a preclinical study setting. The combination of the probiotics with antibiotics completely eradicated S. aureus and P. aeruginosa infections. (14) Furthermore, in a Caco-2 model, a model of the intestine, Lactobacillus fermentum 8711 significantly inhibited adhesion of methicillin-resistant S. aureus, the dangerous antibiotic-resistant form of S. aureus. (15)

Fungal Infections, Such as Candida Overgrowth

Vaginal yeast infections and intestinal Candida overgrowth are not uncommon and sometimes necessitate the use of an antifungal medication such as fluconazole or nystatin. While we often think of antibiotics as the leading pharmaceutical offenders that disrupt the gut microbiota, fluconazole (and possibly other antifungals) can also alter the gut microbiota. (16) While the effects of antifungals on the gut microbiota are not well understood yet, probiotics may be a more desirable alternative for addressing fungal infections in specific scenarios. Research shows that Lactobacillus probiotics help to reduce oral, vaginal, and enteric colonization by Candida fungal species, alleviating fungal overgrowth symptoms, such as itching and vaginal discharge. (17) Probiotics may thus be helpful tools in the treatment of fungal infections.

Probiotics can be a powerful tool when using it to recover patients from various gut issues and imbalances. However, it is vital to determine the root cause of gut imbalances before starting a treatment that includes probiotics and other supplements.

The ADAPT Practitioner Training Program offers functional medicine training that teaches doctors to treat patients by addressing their root cause of the problem instead of managing symptoms. Learn more and discover how functional medicine can help you lead your patients to a healthier and happier life.

Combining with Prebiotics

When probiotics and prebiotics are combined, we refer to them as “synbiotics.” Research indicates that synbiotics may be more helpful than taking probiotics alone; in fact, prebiotic fibers can improve the viability of probiotics. (18) Examples of prebiotic fibers included in synbiotic formulas or supplemented separately alongside probiotics, include inulin and fructooligosaccharides. (19)

Other Things to Consider

Taking Probiotics: With or Without Food?

The advice on whether probiotics should be taken with or without food is conflicting. However, the ideal timing of probiotic supplementation around food intake may depend on the type of probiotic you’re consuming. For example, spore-based probiotics can likely be taken with food since they are resistant to stomach acid and will likely survive the acidic environment of the stomach that occurs at mealtime as gastric acid is produced. On the other hand, it may be better to take Lactobacillus and Bifidobacteria probiotic supplements several hours away from food since these bacterial genera tend to be more sensitive to acidic conditions in the stomach. (20) However, the jury is honestly still out, and numerous studies demonstrate health benefits of taking Lactobacillus and Bifidobacteria probiotics without having provided any specific instructions for when subjects should take them. Beyond that, the research is inconclusive as to whether you should take probiotics several hours before or after meals; it’s likely fine to go either way—choose the strategy that is most convenient for you. The popular probiotic yeast S. boulardii is resistant to stomach acid, so it can be taken with food. (21)

The probiotics intrinsic to fermented foods, on the other hand, may remain viable despite being consumed with food since the strains of Lactobacillus probiotics found in these foods tend to tolerate a low pH. Furthermore, the “food matrix” of fermented foods may buffer the bacteria against the acidic conditions of the stomach. (22)

Interestingly, even if some of the probiotics found in probiotic supplements are killed by stomach acid, the “dead bodies” of the probiotics may still have beneficial effects! Dead probiotics with an ability to still stimulate beneficial health effects are referred to as “ghost probiotics.” (23)

Can Probiotics Be Taken with Herbs?

It may also be important to take probiotic supplements away from foods and herbs that contain “quorum sensing inhibitors.” What are quorum sensing inhibitors? First, it will help to understand what quorum sensing is. Quorum sensing is a process by which bacteria monitor their population through the production, exchange, and detection of signaling molecules unique to their species. When members of a probiotic strain are concentrated enough, they send out a strong chemical signal called a “quorum sensing signal” that ultimately allows them to change their morphology (form) and potentially implant and make a colony in the intestine. This is precisely what we want probiotic bacteria to do in our guts. Quorum sensing inhibitors are compounds (many are plant compounds found in medicinal herbs) that inhibit this inter-microorganismal communication, thus interfering with morphology changes and successful implantation of the probiotics. You may want to avoid consuming quorum sensing inhibitors, such as quercetin, luteolin, cinnamon, garlic, and many other medicinal herbs, several hours before and after taking a probiotic supplement. Food sources of quercetin include red onions and capers, while luteolin is found in a variety of vegetables and herbs, including parsley, peppers, and celery.

How Often to Take Probiotics

There are several viewpoints on how often probiotics should be consumed. Some healthcare professionals feel that probiotics should be consumed daily since many of their health benefits may be conferred transiently, as the probiotics are passing through the gut. However, other professionals argue that probiotics should be consumed in less frequent, albeit much higher, doses to promote quorum sensing, the process by which bacteria communicate with each other and give the “all clear” to take up residence in the gut. Since there is, as yet, no official answer on this, it may be best to try taking probiotics both ways and see which strategy works best for you.

”It’s like when you switch from a super-high-refined carb, Standard American type of diet to a whole-foods diet, there is usually an adjustment period.”

Raja Dhir, cofounder of Seed probiotics

Interactions between Probiotics and Other Nutrients

Because probiotics may facilitate the absorption of certain micronutrients, it could be beneficial to take your probiotics in proximity to specific nutrients. Probiotics and iron are one such example of a beneficial probiotic and micronutrient pairing. The probiotic Lactobacillus plantarum 299v (the 299v part refers to the specific strain of L. plantarum) has been found to increase iron absorption from an iron-rich beverage by 50 percent and from iron-containing meals. (24, 25) Probiotics may increase iron absorption by enhancing the conversion of ferric iron to ferrous iron, the form of iron that our intestines are capable of absorbing. Combining probiotic intake with iron-rich foods may thus be beneficial for individuals who need to improve their iron status. In this case, consuming probiotics with a meal, instead of away from food, appears ideal.



Certain probiotics may also improve the absorption of another mineral, calcium. In animal studies, supplementation with L. casei, Lactobacillus reuteri, and L. gasseri probiotics are linked to greater calcium absorption and improved bone mass. This finding creates a strong argument for consuming fermented dairy products, which contain both calcium and naturally occurring probiotic cultures, if you can tolerate dairy. One mechanism through which probiotics may improve calcium absorption is by creating short-chain fatty acids, which have the effect of solubilizing minerals, making them more absorbable. (26) If you want to improve your absorption of calcium, consider adding probiotics to your routine. It’s unclear whether probiotics need to be consumed close to calcium to enhance absorption. However, since probiotics may have more opportunities to establish themselves in the gut when taken away from food, you may opt for this approach.

Excitingly, probiotics may also enhance vitamin D absorption! This is good news for those looking to optimize our vitamin D status for healthy, balanced immune function. Oral supplementation with L. reuteri NCIMB 30242 increases circulating 25-OH vitamin D3, suggesting a positive effect on vitamin D. (27) One proposed mechanism of action is that the probiotic enhances vitamin D absorption in the intestine by increasing intraluminal (“within the gut”) lactic acid production.

Key Takeaway

There are a surprising number of factors to consider when determining when to take probiotics! However, giving the timing of your probiotic consumption some thought may help you get more “bang for your buck” from the probiotic supplements you take.

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