Baby Gut Probiotics Guide
Medically Reviewed ✓
Baby Gut Probiotics Guide
Medically Reviewed By:
Dr. Alan Greene, MD, FAAP
Written By:
Tiny Health Team
June 17, 2020

Baby Gut Probiotics Guide

Table of Contents:

What are probiotics?
Why give probiotics to my baby?
When is it recommended that you give probiotics to your baby?
How to select the best product

What are probiotics?

Probiotics are defined as live microorganisms that benefit health when administered in adequate amounts [1]. 

While often used to support adult gut health, probiotics can also maintain a baby's health.

Why give probiotics to my baby?

Gut health, and most importantly the gut microbiota, is an important factor for immune development and a baby’s overall wellbeing. The development of a healthy gut microbiota begins with a baby's exposure to microbes during birth and continues over the first two years, also known as a baby’s first 1,000 days of life [2], [3]. 

Many factors can influence your baby's gut microbiota development [2], [3]. This includes, but is not limited to:

  • Mode of delivery, vaginal or c-section
  • Mode of feeding such as breastfed, bottle fed, or formula fed
  • Use of medications, like antibiotics

For example during normal vaginal delivery, babies are exposed to a mother’s vaginal and fecal microbes. Whereas babies who are born by C-section are colonized with microbes from a mother’s skin, mouth, and the surrounding environment [4]. This difference in a baby’s first exposure to microbes shapes how a baby’s gut develops.

In these very early stages, the gut microbiota of a healthy, vaginally delivered, and breastfed baby is characterized by a high diversity of Bifidobacterium species. These beneficial species are able to digest human milk oligosaccharides (HMOs), which are special sugars found in breast milk. This leads to the production of short chain fatty acids (SCFAs) that protect against inflammation and help to maintain a baby’s gut barrier [5], [6], [7]. 

Unlike the adult gut microbiota, which is rather stable over time, the baby gut microbiota continues to mature during the first two years of life [8]. 

This means that probiotics can support the development of your baby’s gut microbiota and play a pivotal role in the development of gut and immune health. 

Why probiotic species are important to consider for your baby

Most probiotic bacteria are selected from the genus Lactobacillus and Bifidobacterium. And it turns out that supplementing with beneficial bacteria can support your baby’s gut development. 


But it’s important to know that baby probiotics belonging to the Lactobacillus genus will most likely not colonize your baby’s gut.

This is because probiotic bacteria are not required to stick around in order to benefit health. In adults, Lactobacillus probiotics are mostly transient species, meaning they do not colonize the gut. Likewise, most probiotics designed for babies will benefit your baby by transiently passing through. During this time, they can support immune health and fight harmful microbes in the gut environment. However, once you stop using the probiotic, the Lactobacillus will soon disappear. Sometimes as quickly as within a couple of days. 

This means that if you want to see health benefits, it’s better to take probiotics for as long as possible. 

Keep in mind that both strain and person-specific persistence may also exist. Meaning probiotics have a unique effect on each one of us. With novel research techniques and longitudinal studies, some researchers have found Lactobacillus species that can colonize the gut for a longer period of time. However we need more information to be able to make a clear conclusion.


Probiotic bacteria belonging to the Bifidobacterium genus have been shown to colonize the baby gut, supporting baby health for a longer period of time. 

Bifidobacteria are one of the most important gut species for your baby. Using a Bifidobacteria probiotic will not only benefit your baby’s overall health [5],[6], but some of these species have also been shown to colonize the baby gut for a longer period of time — up to a couple of months after supplementing [7]. 

Bifidobacteria can easily colonize the baby gut because it’s not yet mature. This means more space, less competition, and more food such as human milk oligosaccharides (HMOs).

But not all probiotic bacteria are the same. For example, Bifidobacterium infantis has the ability to use all types of HMOs as a food source [9]. Other bifidobacteria, such as Bifidobacterium bifidum and Bifidobacterium breve, can use only some of the HMOs found in breast milk [9]. This ability of B. infantis gives it a competitive advantage to colonizing the baby gut and supporting health. Finally, some specific Bifidobacteria — such as B. longum AH1206  — can even colonize even the adult gut [10]. This shows that not all bacteria are the same. And not all provide the same benefits. 

When is it recommended that you give probiotics to your baby?

You may want to consider giving probiotics to your baby for the following reasons below.

  • When your baby has low levels of essential bacteria, like Bifidobacterium

You may want to consider giving probiotics to your newborn to increase low levels of beneficial gut bacteria, like Bifidobacterium. As described above, Bifidobacteria are essential for the use and benefits of HMOs [5].

Many probiotics contain well studied and clinically tested Bifidobacterium species. Taking a product like this might help to increase the levels of beneficial bacteria in your baby’s gut. 

Look especially for products that contain B. infantis. As described above, studies have shown that this species can colonize a baby’s gut, use all types of HMOs, and support baby microbiota development by stopping the growth of harmful microbes [9].

  • When your baby is prescribed antibiotics

Antibiotics kill both harmful bacteria and beneficial gut microbiota, which can lead to gut dysbiosis. 

Changes in microbiota after antibiotic use can last for months and even years. When it comes to early life exposure to antibiotics, the effects can be even more dramatic. For example, antibiotic use in a baby can lead to long lasting changes in the gut microbiota that impacts health later in life [11]. You can find out more in our guide about the effects of early life antibiotic use.  

It’s highly recommended to take probiotics the first day you start your antibiotic treatment and continue during the entire period of antibiotic treatment. We also recommend that you continue taking probiotics for at least an additional one to two weeks after you stop the antibiotics.  

Because antibiotics can also kill probiotic bacteria, make sure to separate antibiotic and probiotic treatment with at least two hours.

  • When your baby has digestive troubles such as colic, diarrhea, and gas 

If your baby has any digestive complaints, you can also use probiotics. 

Certain probiotics have been shown to help with colic in newborn babies along with other digestive troubles such as diarrhea and constipation [12], [13]. 

  • When your baby has eczema or diaper rash

During their very first months of life, many newborn babies suffer from eczema, also known as atopic dermatitis. It’s been shown that the symptoms of eczema can be relieved by giving your baby certain probiotics, which can steer gut microbiota development and reduce inflammation [14], [15].

Probiotics can even help with diaper rash, a condition often caused by yeast in babies [12].

  • To protect against necrotizing enterocolitis (NEC) 

Necrotizing enterocolitis (NEC) is a life-threatening intestinal condition that occurs in premature babies, usually between 2 and 8 weeks of age. NEC causes an intestinal inflammatory process that can lead to tissue damage and even death. As a result, many premature babies go through surgery to remove diseased bowel. 

It has been scientifically proven that some probiotic strains can reduce the risks of NEC, reducing infections and even death and when given prophylactically to premature babies [16]. 

Always discuss with your physician about NICU’s policy and rationale of using probiotics for NEC or in preterm infants.

How to select the best product

Probiotics can be one of the most important interventions for a baby’s health. Because the market is overloaded with products, it sometimes isn't easy to find the best probiotic for your needs. 

To help navigate market shelves, our scientists have compiled a list of baby probiotic products for you.

If there’s a credible probiotic in the market that you’d like us to include on this list, please email us at

We’ve also created a checklist of questions to ask yourself when selecting a product [17], [18]:

  • Is it backed by science?

Look for a product that has been studied in human clinical studies and has been shown to be effective. 

Sounds like a lot of work? Don’t worry, our research team has compiled an in-depth list of products that are easy to find. 

  • Is it an effective dose? 

Probiotic concentration is usually measured as colony forming units (CFU), which you’ll find on the label. The best dose is the one that has been tested in clinical trials and proven effective. Most probiotic products have been tested at a concentration between 1-10 billion CFU/day.

Keep in mind that more is not always better.

Many products are offered as superior only because they contain higher dosage, but this doesn’t always mean that the product is more effective than a product with a lower amount of bacteria. 

  • Is it specific enough for the benefits you are looking for? 

No two bacterial strains are the same, similar to probiotic bacteria. Even though they may have the same name, each has different properties and benefits. For example, some strains might be beneficial for baby gut function, while others may help to fight vaginal infections. 

Select a product that has sufficient evidence for what you’d like to address. 

The label has to contain the names of the probiotic microorganisms since no two species are the same. 

Quality products always include the genus, the species, and the strain name. For example, probiotic strain Lactobacillus rhamnosus GR-1: Lactobacillus is the genus name, rhamnosus is the species name and GR-1 is the strain name. Make sure that the product you buy mentions all of them.

In addition to the names of the probiotics in the product, look for a label that also: 

  • Clearly states the exact CFU per dose till the expiration date
  • Describes the recommended use and for which indication you can expect to see a beneficial effects
  • Points towards the recommended dose
  • Describes the storage conditions
  • Has company contact information where you can get more information about the product

Do I need to buy products with more than one strain? Are they more effective?

It’s not necessary to buy products with more than one strain. Just like with probiotic concentration, more is not always better. 

Many studies have shown health benefits of using single-strain probiotic formulation; others have shown an effect when using multispecies probiotic formulations. It all comes down to whether the product is clinically studied and shown to have health benefits. 

Always remember that no two strains are the same, so look for products that are backed by science.

Why should you look for probiotics with clinical results on the entire formulation?

Many probiotic products on the market contain a mixture of different strains. Such products are known as multispecies probiotics. When only one bacterial strain is included, these are monospecies probiotics. 

Scientists study many different bacteria by looking into the properties of one single strain. This would mean that some strains, especially if they were discovered a long time ago, will have a substantial amount of research. This includes clinical data indicating the health benefits of the strain. 

These days consumer companies buy probiotic strains from probiotic providers and mix up different strains with proven efficacy in clinical trials. In the end some companies add multiple different strains and claim they are clinically tested. Although this is most of the time true, companies refer to studies which have been performed for a single strain but not for the entire formulation that they are selling.

Ideally, you want to see proven efficacy of the entire formulation. Or the end product on the market. The reason for this is that we don’t know how strains will affect each other when combined and if they will still show the same efficacy. 

For example some strains may prevent other strains from growing and performing their desirable effect. 

This explains why it’s important to perform studies on the end formulation. However, many probiotic products contain strains that have been well studied and tested in clinical studies, but the end product has not been clinically proven. 

In our guide we have included products that seem very promising on the market, but for which tests on the end formulation are not provided. 

Final note to keep in mind

No matter the strain source, the number of different strains, the potency, or the probiotic combination, there will always be responders and non-responders to probiotic supplementation. Similar to standard drug treatments available today.

For more information about  probiotics, how to use them, and what to look for when buying products, you can refer to the website of the International Scientific Association for Probiotics and Prebiotics.


  1. Hill, C. et al. (2014) 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 11, 506–514
  2. Robertson, R.C. et al. (2019) The Human Microbiome and Child Growth – First 1000 Days and Beyond. Trends in Microbiology 27, 131–147
  3. Selma-Royo, M. et al. (2019) Shaping Microbiota During the First 1000 Days of Life. In Probiotics and Child Gastrointestinal Health 1125 (Guandalini, S. and Indrio, F., eds), pp. 3–24, Springer International Publishing
  4. Dominguez-Bello, M.G. et al. (2010) Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proceedings of the National Academy of Sciences 107, 11971–11975
  5. Fukuda, S. et al. (2011) Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 469, 543–547
  6. O’Neill, I. et al. (2017) Exploring the role of the microbiota member Bifidobacterium in modulating immune-linked diseases. Emerging Topics in Life Sciences 1, 333–349
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  8. Stewart, C.J. et al. (2018) Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature 562, 583–588
  9. Turroni, F. et al. (2018) Glycan Utilization and Cross-Feeding Activities by Bifidobacteria. Trends in Microbiology 26, 339–350
  10. Maldonado-Gómez, M.X. et al. (2016) Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome. Cell Host & Microbe 20, 515–526
  11. Aires, J. (2021) First 1000 Days of Life: Consequences of Antibiotics on Gut Microbiota. Front. Microbiol. 12, 681427
  12. Dimitratos, S.M. et al. (2021) Symptomatic relief from at-home use of activated Bifidobacterium infantis EVC001 probiotic in infants: results from a consumer survey on the effects on diaper rash, colic symptoms, and sleep. Beneficial Microbes 12, 333–340
  13. Szajewska, H. et al. (2013) Lactobacillus reuteri DSM 17938 for the Management of Infantile Colic in Breastfed Infants: A Randomized, Double-Blind, Placebo-Controlled Trial. The Journal of Pediatrics 162, 257–262
  14. Kalliomäki, M. et al. (2001) Probiotics in primary prevention of atopic disease: a randomised placebo-controlled trial. Lancet 357, 1076–1079
  15. Durack, J. et al. (2018) Delayed gut microbiota development in high-risk for asthma infants is temporarily modifiable by Lactobacillus supplementation. Nature Communications 9, 707
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Take Home Points
  • Probiotics can be a great way to boost your baby gut microbiome since they contain beneficial Bifidobacterium and Lactobacillus species 
  • Probiotics can have different health benefits, but these characteristics are specific to certain species and strains. So select the best products for your baby’s needs.
  • Look for probiotic products that meet scientific and industry requirements.
  • Look for clinically tested probiotic products, which are properly labeled.

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