Any loving parent wants to give their child their best chance at life. But you don’t have to wait for them to walk or talk to pave the way to a healthy future. In recent years, more research has come to light on the important role gut bacteria play in the body, and microbiome-friendly products are filling the shelves. While most gut-focused products are geared towards adults, there is growing evidence that taking care of the infant microbiome has long-term benefits on a child’s development and health

The infant microbiome begins colonizing bacteria before birth. Metabolites that come from the mother’s microbes are transferred to the fetus in the amniotic fluid to the placenta. The largest amount of microbes gained is during delivery when the child is bathed in fecal microbes, skin microbes, and/or the vaginal microbiome. 

Related: Do I need to give my baby vitamins? A dietitian shares what you need to know

Throughout the pregnancy, a mother’s diet decisions and lifestyle choices impact the development of the infant microbiome. Once born, the surrounding environment influences the infant microbiome.

Motherly spoke with Ara Katz, co-founder of Seed, which just launched a kids' prebiotic and probiotic powder for ages 3 and up, on the best ways to shape your baby’s microbiome after birth. “We're only just understanding that there are clear and actionable things we can do every single day to maintain the health of this ecosystem so that it can maintain the health of us,” says Katz. Katz provided tips on infant probiotics that help baby microbiome.

Here’s how to help protect your baby’s microbiome after birth.

1. Try to avoid giving antibiotics to newborn babies

Doctors may prescribe your baby antibiotics if they suspect a bacterial infection. While warranted in many cases, if you can avoid using antibiotics on your infant in the first week of life, it’ll be better for their microbiome health in the long-run. The most common antibiotics given to infants are amoxicillin and gentamicin—both of which can be harmful to the infant microbiome. 

A February 2022 study published in Nature Communications found that newborns given antibiotics within 1 week after birth had lower amounts of the Bifidobacterium species compared to newborns who were not given antibiotics. 

Bifidobacterium are considered “good bacteria” (probiotics) that support the digestion of breast milk and the immune system. In another study, antibiotic exposure and the decrease in the Bifidobacterium species persisted until the baby turned 2 years old. 

Related: Ara Katz wants kids to love their microbiomes 

Researchers associate imbalance in the infant microbiome as a result of antibiotic use with future immune problems and an increased risk of catching a variety of infectious diseases.

The good news? If your infant does need antibiotics early on, breastfeeding or taking supplemental probiotics may help counteract the effects on their gut health. (More on both below.)

2. Aim to breastfeed, which transfers good bacteria from mother to infant

Breastfeeding is an excellent way to stimulate gut development in infants. Human breast milk has its own complex microbiome with prebiotic and probiotic properties. Because of the live cultures formed in breast milk, microbes from the milk transfer bacteria from the mother to the infant. Breastfeeding also helps the infant microbiome indirectly by transferring nutrients important for further bacterial growth, such as oligosaccharides and antibodies. 

“A third of the carbohydrates in breast milk aren't even digestible by the human part of the body,” Katz tells Motherly. “They're literally just food for the child's growing microbiome.” 

Breast milk carries long-term health benefits for the infant microbiome. A 2020 study found that giving breast milk to babies born prematurely improved their microbiome and was associated with improved neurodevelopment and a reduced risk for inflammatory diseases. 

Related: It’s science: Breast milk fights against bad bacteria

While not yet proven, there is some early research suggesting that breast milk contains tools that strengthen the gut barrier and, in turn, prevent allergies. 

Babies who were delivered via C-section may have a disrupted gut development because they are not exposed to the bacteria from the vaginal microbiome. However, research shows that breastfeeding helps to partially restore the microbiome from infants born via C-section. When breastfed, babies born via C-section had a lower risk of infection and a decrease in diarrhea.

If breastfeeding isn’t an option for you, Katz suggests looking for formulas that have probiotics and human milk oligosaccharides (HMOs), which are synthesized sugars and carbohydrates that are normally present in breastmilk. HMOs are important in shaping the gut’s role in immunity.

3. Consider adopting a pet, which diversifies the infant microbiome

Research shows that owning a cat or dog increases an infant’s microbial diversity, which is linked to the growth of ‘good’ bacteria such as Bifidobacterium pseudolongum, helping with constipation and intestinal problems. The infant’s immune system also further develops from pet-related microbial changes and is linked to a lower risk of allergies. 

Another study suggests exposure to pets as babies increases the number of Ruminococcus and Oscillospira in the microbiome, which‌ lowers the risk for childhood obesity and allergies. 

Additionally, a 2014 study found that early exposure to dogs creates a diverse microbial profile in household dust, leading to an increase in Lactobacillus johnsonii. This bacterial species helps protect against allergies and respiratory infections.

“People exposed to dogs are usually exposed to a more diverse amount of microbes, and having a dog in general [researchers] have seen people have more diverse microbiomes themselves,” explains Katz. 

4. Err on the side of caution when giving infants probiotics

Probiotics are an important source for the adult gut microbiome, but the benefits for infants are less understood. 

On one hand, there is evidence that probiotics help in shaping gut development. A 2021 study found that breastfed infants given the probiotic B. infantis—a gut microbe that helps to break down complex sugars—stays in the baby’s system for at least a year and continues to help the digestive tract. 

Another study found that infants delivered via C-section or who had early antibiotic exposure had their microbiomes restored when given a probiotic supplement with their formula or breast milk.

Related: Ara Katz shares what parents need to know about probiotics

However, one 2018 review suggests the benefits of probiotics for infants only last for a week, and long-term, can increase their risk for infection later in life. 

Katz says that the problem with most probiotics on the market is that they are highly ineffective because they either have incorrect strains or low dosages that do not exert an effect on the body or reach certain areas of the GI tract. She advises talking with your child’s doctor or a medical professional who’s really familiar with a child’s medical history when you’re starting new.

“We should move away from talking about probiotics generically and start thinking about what you want them to do and looking at strain specificity. You’ll next have to look at whether a strain can get through the GI tract and remain viable to ‌do what it's meant to do,” Katz tells Motherly.

5. Take your child outside as much as possible

Science shows that infants who spend time in nature grow up to have diverse microbiomes filled with ‘good’ bacteria, such as proteobacteria, found in plants. 

Spending time outside could also restore some of the microbial effects lost when your child is fed with formula rather than breast milk. A 2020 study found that formula-fed children who lived within 500 meters of natural spaces like a park had greater microbial diversity than those who did not. 

“Children who grow up in nature and who are touching soil all the time are exposed to more of the microbes that are found in the natural environment,” Katz explains. “This is a time when your immune system is developing and your gut microbes can start to help your body recognize things and make sure that later they aren’t misfiring around things that aren’t really bad.” 

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Featured expert

Ara Katz is the author of A Kids Book About Your Microbiome and the co-founder and co-CEO of Seed Health, a microbial sciences company pioneering applications of microbes for human and planetary health. A serial entrepreneur, it was Ara’s breastfeeding experience that led her to the microbiome and inspired her personal mission to explore the importance and impact of microbes.


Fujimura KE, Demoor T, Rauch M, Faruqi AA, Jang S, Johnson CC, Boushey HA, Zoratti E, Ownby D, Lukacs NW, Lynch SV. House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus infection. Proceedings of the National Academy of Sciences. 2014 Jan 14;111(2):805-10. doi:10.1073/pnas.1310750111

Granger CL, Embleton ND, Palmer JM, Lamb CA, Berrington JE, Stewart CJ. Maternal breastmilk, infant gut microbiome and the impact on preterm infant health. Acta Paediatrica. 2021 Feb;110(2):450-7. doi:10.1111/apa.15534

Guo C, Zhou Q, Li M, Zhou L, Xu L, Zhang Y, Li D, Wang Y, Dai W, Li S, Zhang L. Breastfeeding restored the gut microbiota in caesarean section infants and lowered the infection risk in early life. BMC pediatrics. 2020 Dec;20(1):1-6. doi:10.1186/s12887-020-02433-x

Kim H, Sitarik AR, Woodcroft K, Johnson CC, Zoratti E. Birth mode, breastfeeding, pet exposure, and antibiotic use: associations with the gut microbiome and sensitization in children. Current allergy and asthma reports. 2019 Apr;19(4):1-9.

Korpela K, Salonen A, Vepsäläinen O, Suomalainen M, Kolmeder C, Varjosalo M, Miettinen S, Kukkonen K, Savilahti E, Kuitunen M, de Vos WM. Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants. Microbiome. 2018 Dec;6(1):1-1. doi:10.1186/s40168-018-0567-4

Nielsen CC, Gascon M, Osornio-Vargas AR, Shier C, Guttman DS, Becker AB, Azad MB, Sears MR, Lefebvre DL, Moraes TJ, Turvey SE. Natural environments in the urban context and gut microbiota in infants. Environment International. 2020 Sep 1;142:105881.

O’Brien CE, Meier AK, Cernioglo K, et al. Early probiotic supplementation with B. infantis in breastfed infants leads to persistent colonization at 1 year. Pediatr Res 91, 627–636 (2022). doi:10.1038/s41390-020-01350-0

Quin C, Estaki M, Vollman DM, Barnett JA, Gill SK, Gibson DL. Probiotic supplementation and associated infant gut microbiome and health: a cautionary retrospective clinical comparison. Sci Rep. 2018;8(1):8283. Published 2018 May 29. doi:10.1038/s41598-018-26423-3

Reyman M, van Houten MA, Watson RL, et al. Effects of early-life antibiotics on the developing infant gut microbiome and resistome: a randomized trial. Nat Commun 13, 893 (2022). doi:10.1038/s41467-022-28525-z

Tun HM, Konya T, Takaro TK, Brook JR, Chari R, Field CJ, Guttman DS, Becker AB, Mandhane PJ, Turvey SE, Subbarao P. Exposure to household furry pets influences the gut microbiota of infants at 3–4 months following various birth scenarios. Microbiome. 2017 Dec;5(1):1-4. doi:10.1186/s40168-017-0254-x

Uzan-Yulzari A, Turta O, Belogolovski A, et al. Neonatal antibiotic exposure impairs child growth during the first six years of life by perturbing intestinal microbial colonization. Nat Commun 12, 443 (2021). doi:10.1038/s41467-020-20495-4

Van den Elsen LW, Garssen J, Burcelin R, Verhasselt V. Shaping the gut microbiota by breastfeeding: the gateway to allergy prevention?. Frontiers in pediatrics. 2019 Feb 27;7:47. doi:10.3389/fped.2019.00047

Yang I, Corwin EJ, Brennan PA, Jordan S, Murphy JR, Dunlop A. The Infant Microbiome, Nursing Research: January/February 2016 - Volume 65 - Issue 1 - p 76-88 doi:10.1097/NNR.0000000000000133

A version of this story was published April 13, 2022. It has been updated.