6 Facts Or Myths About Probiotics - Are Probiotics Safe?


  • Probiotic regulation could be stronger in the United States. Be sure to choose a reputable product that states the dose of each strain and that supports its health claims with clinical trials. 
  • Probiotics are useful if you must take antibiotics. They may help reduce side effects such as gastrointestinal discomfort or diarrhea. 
  • Probiotics may reduce the diversity of your microbiome. However, they may still help to improve negative symptoms you are experiencing. 
  • Probiotics are safe for babies. Just be sure to choose a product that has been vetted for use in babies - as their microbiome is very impressionable at early ages.
  • Probiotics can contain antibiotic resistance genes. But they’re more likely to eliminate them.
  • Probiotics don’t work for everyone in the same way. Knowing the makeup of your microbiome is a great first step before choosing a probiotic.

Probiotics are defined as “live microorganisms that, when administered in adequate amounts, confer a health benefit on the host” [1]. 

But, with all of the options out there, it can feel difficult to know if and when a probiotic will improve your gut microbiome and support your health. Even worse - can probiotics make you sick? 

Here, we’re going to break down some science behind the facts and myths of probiotics. 

Everyone could use a probiotic 


Probiotics are best used to help build a healthy microbiome in babies and children who are missing key species, especially in the first 1,000 days of life. Probiotics also help with symptoms of diseases like eczema, and provide protection against the negative effects of antibiotics.

While it may seem like a good idea to try out a probiotic “just in case”, the use of probiotics in children and adults with a healthy gut microbiome will likely have little effect [2]. If you’re interested in boosting an already healthy microbiome, focus on eating plenty of foods that are high in fiber and whole grains, along with fermented foods, as these foods can help support beneficial bacteria and healthy diversity within your gut. 

Wondering if your baby needs a probiotic

It’s hard to know what’s in each probiotic and they could  be better regulated in the United States


Concerns about what is in a probiotic are very legitimate. Despite massive growth of the probiotic industry [3], regulations regarding the production of probiotics are still lacking.

Probiotics fall into three categories in the United States [4] - Foods, Drugs, and Dietary Supplements. Let’s take a look at these different types of probiotics: 

  • Foods: Some fermented foods, such as yogurt or kimchi, may naturally contain live bacteria. In addition, other foods may have bacteria added in. However, these bacteria may not be in high enough amounts to be considered a probiotic, and may not have defined health benefits for us, especially if the strains are unknown like in natural ferments. 
  • Drugs: Probiotics can also be sold as drugs (specifically, live biotherapeutic products) to treat or prevent a specific disease. To meet this classification, they must be backed by clinical trials that support their safety and ability to achieve their stated health benefits. At this time, there are unfortunately no probiotics that are approved by the Food and Drug Administration (FDA) to be marketed as drugs in the United States. Recent developments suggest we may be moving towards this however, as two fecal microbiota products were approved by the FDA in late 2022 (Rebyota) [5] and early 2023 (Vowst) [6] for the prevention of Clostridioides difficile infection.
  • Dietary Supplements: Dietary supplements are the most common way to take probiotics. However, when choosing a dietary supplement it is important to look for a product where the strains and amounts are stated, and ideally a product with clinically proven health benefits. 

Today, in the United States most probiotics are sold as dietary supplements. In 2007 the FDA established the Dietary Supplement Current Good Manufacturing Practice Rule (“the DS CGMP rule”) that requires testing for contaminants and sanitation in manufacture of supplements [7], [8], very similar to how a food product would be regulated.

However, it is only recommended, and not required, by the FDA that manufacturers report the dose of probiotic bacteria within their supplements.Trusted probiotic companies will always opt to follow this recommendation - so you should be able to find the dose of bacteria in the form of CFUs on the label of a good probiotic. In addition, probiotic supplements sometimes tout health benefits that have not been supported by clinical trials [9]. 

Unfortunately, lack of strict oversight on the composition of probiotics makes it difficult to be sure you are getting what you pay for. One 2016 study [10] showed that probiotic products may not contain all of the bacterial strains they claim to - which may result in you paying for a product that doesn’t have the strains you need to improve your gut health. In addition, in some cases bacterial strains have been detected in probiotic supplements that weren’t listed on the bottle [11]. 

Not in the United States? Every country independently regulates probiotics - so you may see different availability of probiotic classes and types of regulation in your country. Countries in Europe receive probiotic regulation from the European Food Safety Authority (EFSA). The EFSA requires [3]:

  • Known strain level characterization 
  • Proven health benefits
  • Benefits that can be extrapolated to the general population 

In Canada, probiotics may be in the form of natural health products (commonly known as dietary supplements) or in foods. All probiotics in Canada are regulated by Health Canada [12]. 

Finally, the World Health Organization alongside the International Probiotics Association have made recommendations for probiotic companies worldwide [11].

Probiotics can slow down the natural recovery of the microbiome


After using antibiotics, it can take months or even years for our microbiome to return to its original state. Probiotics are thought to help speed up this process, by increasing the amount of beneficial bacteria (and preventing the emergence of unfriendly bacteria) in your gut. 

However, a 2018 study [13] treated healthy participants with antibiotics, and showed that they were slower to recover to their original microbiome composition if they were given probiotics, compared to others in the study who received a fecal microbiota transplant made from their own preserved stool, or were allowed to recover naturally. While it’s perhaps unsurprising that the introduction of new species can slow the return to an original microbiome composition, these results do raise concern about the ability of probiotics to rescue a microbiome from dysbiosis. However, this study didn’t assess the ability of probiotics to reduce symptoms associated with gut dysbiosis, such as gastrointestinal discomfort or diarrhea. 

On the flip side, it is possible for probiotics to improve symptoms without changing the microbiome, as evidenced by a 2020 study [14] that showed even non-viable bacteria could help improve gastrointestinal symptoms present in irritable bowel syndrome.

Other studies present good evidence that probiotics can rescue a microbiome from dysbiosis, particularly in babies. These studies showed that probiotics, especially those enriched with Lactobacillus or Bifidobacterium, can help set your baby’s gut microbiome back on track after a c-section birth or antibiotic use [15], [16]. The benefits of taking these probiotics may be even greater if you also follow practices like breastfeeding to support the probiotic bacteria’s growth. 

At Tiny Health, we recommend that you take probiotics throughout a course of antibiotics, and for one or two weeks after you stop the antibiotics to give you the best chance of avoiding negative symptoms.

Probiotics decrease microbiome diversity

SOMETIMES - it depends on the microbiome

The adult microbiome contains hundreds of different bacterial strains, and probiotic supplements at most contain just a few. 

If the microbiome is decimated by a course of antibiotics, followed by the use of a probiotic with just a few species, it’s not a surprise that the microbiome may be less diverse at this stage. However, some probiotic strains have been shown to help with symptoms like diarrhea and bloating that can follow antibiotics [17], so in some cases it may still be helpful to take them while the microbiome recovers naturally [18]. This recovery can be aided by a diet that includes vegetables and fermented foods to increase species diversity [19]. However, probiotics are not ‘one size fits all’ and it is possible that their introduction to an already vulnerable and perturbed microbiome may result in adverse effects [20].

In other cases, probiotics are used to supplement just one or two highly beneficial bacteria that may be absent in an otherwise healthy microbiome. In these cases, a drop in overall microbiome diversity is unlikely [21]. That’s because healthy microbiomes are relatively stable and robust.  

Probiotics aren’t safe for babies


In fact, a variety of probiotics are actually formulated with babies in mind. 

A baby’s microbiome over the first 1000 days of life will set them up for lifelong health. A baby’s microbiome is typically low-diversity, with just a few major players. This means carefully considered probiotics have the room to generate a great positive impact.  


Bifidobacterium probiotics support gut health and can also prevent the emergence of unfriendly gut bacteria [22], [23], [24]. Probiotics containing bacteria within the Bifidobacterium genus are a great choice for your baby - the best options are those with clinical evidence in babies, such as Bifidobacterium infantis, which has a unique ability to use any type of human milk oligosaccharide (HMO) for fuel [25]. 


At birth, the baby receives microbes directly from their mom. Lactobacillus, a vaginal bacterial genus present in the majority of women, is one of the microbes that may pass directly to a babies’ gut. Lactobacillus are transient microbes in the gut, meaning that they arrive and provide benefits for the gut microbiome, but then pass through quickly [26], [27]. Even though they may not hang around for long, Lactobacillus probiotics are a great option for improving gut health.

But premature babies may be a different story. 

When born premature, babies may not have a strong enough immune system to protect against the unfriendly bacteria that exist in their environment. In addition, premature babies often have extended stays in neonatal intensive care units, or NICUs, to support their growth while in this vulnerable state. The time they spend in a NICU is likely life-saving, but it also reduces their chances of receiving beneficial microbes from their mom during this important window in early life. 

Probiotics are sometimes used as a strategy to remedy this missed opportunity; today about 10% of low birth weight babies in NICUs will receive a probiotic [28]. However, despite the increase in use of probiotics for premature babies, both the health benefits and potential negative outcomes are not completely understood. Clinical trials in vulnerable populations such as premature babies are limited [29]. Luckily, some probiotics have been formulated and tested to be safe for premature babies [30], so they may be an option for your premature or low birth-weight baby.

The vulnerability of premature babies, and the naivety of their gut microbiome, put them at an increased risk for the negative side effects of probiotics, such as infection. As these probiotic bacteria will be the pioneering microbes within the babies’ gut, it is also important to consider that they will likely continue to influence the microbiome of your baby for years to come [31].

Need more help deciding if your baby needs a probiotic

Probiotics can contain antibiotic resistant genes 


Any bacteria, including probiotic bacteria, can carry genes that enable resistance to antibiotics

There are growing concerns that even beneficial microbes could be carrying negative qualities that they could potentially pass on to other members of our microbiome. 

Antibiotic resistance is a frightening example of this. Antibiotic resistance is a very dangerous situation in which a specific bacteria can no longer be killed by an antibiotic. Sadly, thousands of people die each year from infections related to antibiotic-resistant bacteria [32].

Past reports have highlighted a concern that probiotic bacteria, while beneficial, can carry antibiotic resistance genes that they could pass to unfriendly resident bacteria within our guts [33], making us vulnerable to an antibiotic-resistant bacterial infection. 

Despite these concerns, it actually is more likely that probiotics will reduce the amount of antibiotic resistant bacteria you carry in your gut. This is because genes that cause antibiotic resistance are often found in unfriendly bacteria, and probiotics work to edge out these unwelcome visitors [24]. 

Probiotics don't work for everyone the same way


There is a chance you won't respond to a probiotic, simply because all people and all  microbiomes are different.

Each person’s microbiome is as unique as their fingerprint [34]. This cool fact has a difficult implication - it can be hard to know which probiotic your microbiome needs. Taking probiotics without the appropriate strains for your gut microbiome could be a waste of effort.

Probiotics are best used to supplement or support beneficial bacteria that are missing or at low levels, so knowing the makeup of your microbiome is the first step. Consider using Tiny Health’s gut or vaginal microbiome test to explore the makeup of your microbiome before picking a probiotic off the shelf. 

It may still be hard to decide if you’d like to use a probiotic. That’s okay! 

Prebiotics may be a good alternative if the risks of probiotics are overwhelming. Prebiotics are consumed products or foods that are selectively utilized by our microbiome for fuel [35], [4]. They support the growth of beneficial bacteria already in your gut.

Babies who consume breastmilk will receive natural prebiotics in the form of HMOs, which are sugars that bacteria like Bifidobacterium thrive on [22].

Adults or children can try prebiotic foods [36] including: 

  • Whole grains such as rye and barley
  • Carbohydrate-rich vegetables such as asparagus, cabbage, or eggplant 
  • Foods with lots of dietary fiber, such as inulin


[1] C. Hill et al., “Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic,” Nat. Rev. Gastroenterol. Hepatol., vol. 11, no. 8, pp. 506–514, Aug. 2014, doi: 10.1038/nrgastro.2014.66.

[2] N. B. Kristensen, T. Bryrup, K. H. Allin, T. Nielsen, T. H. Hansen, and O. Pedersen, “Alterations in fecal microbiota composition by probiotic supplementation in healthy adults: a systematic review of randomized controlled trials,” Genome Med., vol. 8, p. 52, May 2016, doi: 10.1186/s13073-016-0300-5.

[3] R. L. Day, A. J. Harper, R. M. Woods, O. G. Davies, and L. M. Heaney, “Probiotics: current landscape and future horizons,” Future Sci. OA, vol. 5, no. 4, p. FSO391, 2019, doi: 10.4155/fsoa-2019-0004.

[4] “Office of Dietary Supplements - Probiotics,” National Institutes of Health. https://ods.od.nih.gov/factsheets/Probiotics-HealthProfessional/ (accessed Jun. 22, 2023).

[5] “Ferring Receives U.S. FDA Approval for REBYOTATM (fecal microbiota, live-jslm) – A Novel First-in-Class Microbiota-Based Live Biotherapeutic,” Ferring Pharmaceuticals USA, Nov. 30, 2022. https://ferringusa.com/?press=ferring-receives-u-s-fda-approval-for-rebyota-fecal-microbiota-live-jslm-a-novel-first-in-class-microbiota-based-live-biotherapeutic (accessed Jun. 22, 2023).

[6] “FDA Approves First Orally Administered Fecal Microbiota Product for the Prevention of Recurrence of Clostridioides difficile Infection,” FDA, Apr. 28, 2023. https://www.fda.gov/news-events/press-announcements/fda-approves-first-orally-administered-fecal-microbiota-product-prevention-recurrence-clostridioides (accessed Jun. 22, 2023).

[7] “Small Entity Compliance Guide: Current Good Manufacturing Practice in Manufacturing, Packaging, Labeling, or Holding Operations for Dietary Supplements,” U.S. Food and Drug Administration, May 13, 2023. https://www.fda.gov/regulatory-information/search-fda-guidance-documents/small-entity-compliance-guide-current-good-manufacturing-practice-manufacturing-packaging-labeling (accessed Jun. 22, 2023).

[8] A. Zawistowska-Rojek, T. Zaręba, and S. Tyski, “Microbiological Testing of Probiotic Preparations,” Int. J. Environ. Res. Public. Health, vol. 19, no. 9, p. 5701, May 2022, doi: 10.3390/ijerph19095701.

[9] P. A. Cohen, “Probiotic Safety—No Guarantees,” JAMA Intern. Med., vol. 178, no. 12, pp. 1577–1578, Dec. 2018, doi: 10.1001/jamainternmed.2018.5403.

[10] Z. T. Lewis et al., “Validating bifidobacterial species and subspecies identity in commercial probiotic products,” Pediatr. Res., vol. 79, no. 3, pp. 445–452, Mar. 2016, doi: 10.1038/pr.2015.244.

[11] D. Mazzantini, M. Calvigioni, F. Celandroni, A. Lupetti, and E. Ghelardi, “Spotlight on the Compositional Quality of Probiotic Formulations Marketed Worldwide,” Front. Microbiol., vol. 12, p. 693973, Jul. 2021, doi: 10.3389/fmicb.2021.693973.

[12] Health Canada, “Questions and Answers on Probiotics,” Government of Canada, Apr. 16, 2009. https://www.canada.ca/en/health-canada/services/food-nutrition/food-labelling/health-claims/questions-answers-probiotics.html (accessed Jun. 22, 2023).

[13] J. Suez et al., “Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT,” Cell, vol. 174, no. 6, pp. 1406-1423.e16, Sep. 2018, doi: 10.1016/j.cell.2018.08.047.

[14] V. Andresen, J. Gschossmann, and P. Layer, “Heat-inactivated Bifidobacterium bifidum MIMBb75 (SYN-HI-001) in the treatment of irritable bowel syndrome: a multicentre, randomised, double-blind, placebo-controlled clinical trial,” Lancet Gastroenterol. Hepatol., vol. 5, no. 7, pp. 658–666, Jul. 2020, doi: 10.1016/S2468-1253(20)30056-X.

[15] C. L. Garcia Rodenas, M. Lepage, C. Ngom-Bru, A. Fotiou, K. Papagaroufalis, and B. Berger, “Effect of Formula Containing Lactobacillus reuteri DSM 17938 on Fecal Microbiota of Infants Born by Cesarean-Section,” J. Pediatr. Gastroenterol. Nutr., vol. 63, no. 6, pp. 681–687, Dec. 2016, doi: 10.1097/MPG.0000000000001198.

[16] K. Korpela et al., “Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants,” Microbiome, vol. 6, no. 1, p. 182, Oct. 2018, doi: 10.1186/s40168-018-0567-4.

[17] A. C. Ouwehand et al., “Probiotics reduce symptoms of antibiotic use in a hospital setting: a randomized dose response study,” Vaccine, vol. 32, no. 4, pp. 458–463, Jan. 2014, doi: 10.1016/j.vaccine.2013.11.053.

[18] W. E. Anthony et al., “Acute and persistent effects of commonly used antibiotics on the gut microbiome and resistome in healthy adults,” Cell Rep., vol. 39, no. 2, p. 110649, Apr. 2022, doi: 10.1016/j.celrep.2022.110649.

[19] H. C. Wastyk et al., “Gut-microbiota-targeted diets modulate human immune status,” Cell, vol. 184, no. 16, pp. 4137-4153.e14, Aug. 2021, doi: 10.1016/j.cell.2021.06.019.

[20] D. Kothari, S. Patel, and S.-K. Kim, “Probiotic supplements might not be universally-effective and safe: A review,” Biomed. Pharmacother. Biomedecine Pharmacother., vol. 111, pp. 537–547, Mar. 2019, doi: 10.1016/j.biopha.2018.12.104.

[21] R. L. Washburn, D. Sandberg, and M. A. Gazdik Stofer, “Supplementation of a single species probiotic does not affect diversity and composition of the healthy adult gastrointestinal microbiome,” Hum. Nutr. Metab., vol. 28, p. 200148, Jun. 2022, doi: 10.1016/j.hnm.2022.200148.

[22] D. A. Mills, J. B. German, C. B. Lebrilla, and M. A. Underwood, “Translating neonatal microbiome science into commercial innovation: metabolism of human milk oligosaccharides as a basis for probiotic efficacy in breast-fed infants,” Gut Microbes, vol. 15, no. 1, 2023, Accessed: Apr. 06, 2023. [Online]. Available: https://www.tandfonline.com/doi/full/10.1080/19490976.2023.2192458

[23] B. M. Henrick et al., “Colonization by B. infantis EVC001 modulates enteric inflammation in exclusively breastfed infants,” Pediatr. Res., vol. 86, no. 6, pp. 749–757, 2019, doi: 10.1038/s41390-019-0533-2.

[24] G. Casaburi et al., “Early-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria,” Antimicrob. Resist. Infect. Control, vol. 8, p. 131, Aug. 2019, doi: 10.1186/s13756-019-0583-6.

[25] R. M. Duar et al., “Comparative Genome Analysis of Bifidobacterium longum subsp. infantis Strains Reveals Variation in Human Milk Oligosaccharide Utilization Genes among Commercial Probiotics,” Nutrients, vol. 12, no. 11, p. 3247, Oct. 2020, doi: 10.3390/nu12113247.

[26] P. S. La Rosa et al., “Patterned progression of bacterial populations in the premature infant gut,” Proc. Natl. Acad. Sci. U. S. A., vol. 111, no. 34, pp. 12522–12527, Aug. 2014, doi: 10.1073/pnas.1409497111.

[27] J. E. Koenig et al., “Succession of microbial consortia in the developing infant gut microbiome,” Proc. Natl. Acad. Sci., vol. 108, pp. 4578–4585, Mar. 2011, doi: 10.1073/pnas.1000081107.

[28] B. Poindexter et al., “Use of Probiotics in Preterm Infants,” Pediatrics, vol. 147, no. 6, p. e2021051485, Jun. 2021, doi: 10.1542/peds.2021-051485.

[29] D. Merenstein et al., “Emerging issues in probiotic safety: 2023 perspectives,” Gut Microbes, vol. 15, no. 1, p. 2185034, 2023, doi: 10.1080/19490976.2023.2185034.

[30] S. Bajorek et al., “B. infantis EVC001 Is Well-Tolerated and Improves Human Milk Oligosaccharide Utilization in Preterm Infants in the Neonatal Intensive Care Unit,” Front. Pediatr., vol. 9, p. 795970, 2021, doi: 10.3389/fped.2021.795970.

[31] C. Milani et al., “The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota,” Microbiol. Mol. Biol. Rev. MMBR, vol. 81, no. 4, pp. e00036-17, Dec. 2017, doi: 10.1128/MMBR.00036-17.

[32] “Antibiotic Resistance Threats in the United States, 2019,” Centers for Disease Control, 2019. https://www.cdc.gov/drugresistance/biggest-threats.html (accessed Jun. 22, 2023).

[33] A. Crits-Christoph, H. A. Hallowell, K. Koutouvalis, and J. Suez, “Good microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome,” Gut Microbes, vol. 14, no. 1, p. 2055944, Dec. 2022, doi: 10.1080/19490976.2022.2055944.

[34] E. A. Franzosa et al., “Identifying personal microbiomes using metagenomic codes,” Proc. Natl. Acad. Sci., vol. 112, no. 22, pp. E2930–E2938, Jun. 2015, doi: 10.1073/pnas.1423854112.

[35] M. E. Sanders, D. J. Merenstein, G. Reid, G. R. Gibson, and R. A. Rastall, “Probiotics and prebiotics in intestinal health and disease: from biology to the clinic,” Nat. Rev. Gastroenterol. Hepatol., vol. 16, no. 10, pp. 605–616, Oct. 2019, doi: 10.1038/s41575-019-0173-3.

[36] “Food as Medicine: Prebiotic Foods,” Children’s Hospital of Philadelphia, Dec. 21, 2022. https://www.chop.edu/health-resources/food-medicine-prebiotic-foods (accessed Jun. 22, 2023).