How To Select An Infant Daycare That’s Safe For Your Baby’s Microbiome


  • Daycare attendance can shape the microbial composition of your growing child.
  • Consider searching for a nature-oriented daycare to help boost your child’s immune system and increase gut diversity.
  • Don’t be afraid to ask some hard questions. This can help provide more insight into the child care philosophy of a daycare center, and if it will benefit your baby’s microbiome.

Leaving your precious child at an infant daycare (or toddler daycare) can bring up complex feelings: letting go of your loved one and trusting them to the care of others can be a heart-wrenching experience, and at the same time it can feel liberating to regain some independence. Whether it is your first or your third child, it is never easy. Beyond providing child care help, it’s helpful to remember that daycare can offer some incredible benefits to children, especially if they’re allowed to play outdoors or in nature [6].

Benefits of infant and toddler daycare

Daycare enrollment can have a positive influence on your children’s development. For example, a study showed that high-quality early daycare enrollment can support a child’s social and emotional growth [2].

In addition, early socialization with other children has been shown to promote prosocial behavior. This socialization can blossom in daycare centers. Early appearing prosocial behavior can take many forms, including:

  • Helping
  • Cooperating
  • Sharing
  • Informing
  • Comforting [2]

Early infant and toddler daycare attendance can also improve school readiness [2]. Research shows that children that attended high-quality early childhood education programs are more likely to graduate from high school, and less likely to be placed in special education and be retained in a grade [4].

Daycare attendance may not only be beneficial for your child’s development, but also for your child’s microbiome development.

Benefits of infant and toddler daycare on the microbiome

Daycare centers can play a significant role in influencing a child’s gut microbial composition [4].

A recent study found that daycare may contribute to gut microbiome maturation and make-up in early childhood [5]. The study followed 61 children who entered daycare for the first time and were under 3 years old. Researchers also compared the gut microbiome of daycare vs homecare children. The children’s stool samples were collected at several time points through the course of the year and the gut microbiome was analyzed.

The research study found that children who attended daycare had a different gut microbiome composition compared to homecare children. Daycare children were also found to have bacterial taxa in their gut that were more commonly found in adults.

During the early months, keeping a low microbiome maturation is ideal for your baby. This is especially true if they are under 4 months of age, as an early gut maturation has been linked with a higher BMI (body mass index) later in life [6].

As your baby begins weaning from breastmilk, eating solid foods, and receiving exposure to more environments, their gut microbiome will begin to shift towards a more mature adult-like gut composition. This stablizes around 3-5 years of age [6], [7].

A more mature microbiome composition will have a greater balance of different species, also known as alpha-diversity. The more variety and evenness of bacteria your baby has in their gut, the more likely they will have a healthy metabolism. You can read more about a baby’s gut microbiome development in our guide.

This may mean that daycare attendance can be a positive environment in shaping the microbial composition of your growing child [5].

Even where your children play in daycare can affect their microbiomes. For example, one study in which children had contact with nature five times a week for a month, engaging in guided activities like planting in planter boxes, crafting natural materials, and climbing and digging with peat blocks found several health benefits.

Nature-oriented daycare centers were found to have benefits, such as:

  • Improved immune system
  • Diverse skin microbiome
  • Diverse gut microbiome

Finding a daycare is hard, let alone finding one that promotes a healthy gut microbiome, but we are here to help you along the way.

Infections at daycare: scourge or gift?

While your little tots are learning to share toys, they’re also sharing microbes. Research has shown that the risk of getting sick is higher in children attending daycare [6], [7]. The downside to your baby or toddler going to daycare is that daycares can be superspreader spots for unwanted infections, which can be stressful for children and parents.

Although it’s true that daycare attendance may cause more frequent illness, research has shown that there is no significant difference in the development and growth of children in home-care versus daycare settings [6]. This means your child will continue growing normally, regardless of those sniffles.

There is a light at the end of the tunnel.

Although attendance at daycare before the age of 2½ years old is associated with increased infections during that time, it seems to protect against infections later in life, especially during the elementary school years [8].

This may mean that infections during the first years of child care may help boost your child’s immune system which is likely to decrease the risk of sickness later in life.

How to choosing an infant or toddler daycare that’s good for the microbiome

1. Research

Put on your detective hat and begin the search for a great daycare for your child. Finding the best fit daycare for you, your baby, and your family, may seem daunting at first.

But you are not alone. In the U.S., 59% of children aged 5 and younger have at least one weekly care arrangement [8].

Consider using a  search engine to look for toddler or infant daycare centers in your area. You can also ask friends, family, neighbors, or even your pediatrician for recommendations of group daycare centers. Compile a list of all potential daycare centers that may fit the needs of your family.  

2. Interview

Once you have compiled a couple of daycare centers, consider reaching out through phone or email to schedule an interview. This can provide more insight whether a group daycare center’s philosophy aligns with your values and needs for your baby.

If time permits, you may even consider checking out the daycare center in-person. This can further reveal if the daycare center is the right fit for your baby. An in-person interview can provide information about the environment, daycare cleaning practices, and activities that your baby may be exposed to.

During your interview, ask about numbers. Specifically, the number of caregivers looking over the children.

The number of caregivers looking over a number of children at a daycare is known as the child-to-adult ratio. This is important because the attention of a caregiver is split by the number of children they are looking after. Currently, the American Academy of Pediatrics recommends that child care centers have no more than 3 infants under 12 months old per one adult caregiver.

You may even consider dropping by unannounced. This can reveal how a center runs when no one is looking. This may mean the cleanliness of the infant daycare center or even how caregivers interact with your child. Ensuring that you know how a daycare center operates behind closed doors can give you some peace of mind when you drop off your child.

3. Licensing

Consider asking about the group daycare’s license. Though a license doesn’t necessarily equate to a daycare’s quality, you can rest reassured that they will meet standard criteria. Different states have different licensing requirements. You can learn more about your individual state's licensing requirements at the National Resource Center for Health and Safety in Child Care and Early Education or at Child Care Aware of America [9].

For higher standards, you may consider an infant or toddler daycare center accredited by the National Association for the Education of Young Children (NAEYC).

The criteria has taken into account:

  • Ratio of adults to babies
  • Turnover of caregivers
  • Health, safety, and development of kids

Potential questions to ask for a microbiome safe daycare

Asking some of the following questions can reveal if a daycare aligns with your child care philosophy, as well as whether a daycare center is safe for your child’s gut microbiome.

What food are kids fed in daycare?

You are what you eat. The age-old proverb holds a lot of truth, especially for your children’s nutrition. Consider asking to see a menu or list of foods and snacks provided to your child.​​ Ensuring that your child is fed with healthy wholesome snacks and meals can potentially help their health and gut microbiome in the long-term.

Is your child still taking breastmilk or infant formula? Consider asking if the daycare has a feeding protocol in place for breastmilk and infant formula. You may even consider asking if the caregivers have also been trained in proper handling and storage of breastmilk and infant formula [10]. Ensuring proper handling and storage of your child’s breastmilk or infant formula while at daycare can help to avoid illness.

Ask to see a feeding schedule for the children and whether feeding times are adjusted for children of different ages. This is because children of different ages have different nutritional requirements to help with growth and development. For instance, children under 6 years old should be offered food every 2 to 3 hours [9].

If your child has special dietary requirements, ask if the daycare can accommodate your child’s dietary needs. For instance, if your child has food allergies, the daycare may need separate cutting boards and kitchen utensils for food preparation to avoid cross-contamination with allergens.

Do children play outdoors or in nature?

When searching for daycares, you may consider one that is nature focused. A nature-oriented group daycare may help boost your child’s immune system and increase gut diversity.

Children exposed to green spaces have been associated with beneficial effects on brain development and cognitive function [11]. Even exposure to nature during childhood, has been associated with better mental wellness in adulthood [12].

What cleaning products are used?

While cleaning is important, certain harsh chemicals often found in household cleaners may have a negative effect on your health, as well as your gut microbiome. Consider asking the daycare center what kinds of cleaning products are used.

What are health requirements for caregivers?

Consider asking the health requirements for the caregivers at daycare. Do caregivers require medical checkups and completed immunizations? Are the caregivers up-to-date with their vaccinations? Ensuring that caregivers have medical clearance can ensure that sicknesses and diseases are not spread to your child.

Daycare may not be for everyone. If you are considering a daycare, doing your research can help ease any doubts that your daycare provides a healthy atmosphere for your little one.

This can help guarantee that the daycare you select will best fit the needs for you, your child, your family— and their gut microbiome.  

Running a home daycare? Tiny Health was recently featured as a contributor of nutrition best practices in Porch's home daycares article.


[1] E. A. Donoghue et al., “Quality Early Education and Child Care From Birth to Kindergarten,” Pediatrics, vol. 140, no. 2, p. e20171488, Aug. 2017, doi: 10.1542/peds.2017-1488.

[2] “Prosocial Behavior in Infancy: The Role of Socialization - Brownell - 2016 - Child Development Perspectives - Wiley Online Library.” (accessed Jan. 16, 2022).

[3] D. C. McCoy et al., “Impacts of Early Childhood Education on Medium- and Long-Term Educational Outcomes,” Educ. Res., vol. 46, no. 8, pp. 474–487, Nov. 2017, doi: 10.3102/0013189X17737739.

[4] A. Amir et al., “Gut microbiome development in early childhood is affected by day care attendance,” Npj Biofilms Microbiomes, vol. 8, no. 1, pp. 1–10, Jan. 2022, doi: 10.1038/s41522-021-00265-w.

[5] M. I. Roslund et al., “Biodiversity intervention enhances immune regulation and health-associated commensal microbiota among daycare children,” Sci. Adv., vol. 6, no. 42, p. eaba2578, Oct. 2020, doi: 10.1126/sciadv.aba2578.

[6] U.S. Department of Education, “Early Childhood Program Participation: 2019 (NCES 2020-075REV),” National Center for Education Statistics. (accessed Jan. 16, 2022).

[7] “Selecting a Child Care Program: Visiting and Asking Questions |” (accessed Jan. 05, 2022).

[8] “CACFP Trainer’s Tools: Feeding Infants: Handling and Storing Breastmilk and Infant Formula in a Child Care Site | Food and Nutrition Service.” (accessed Jan. 20, 2022).

[9] P. Dadvand et al., “The Association between Lifelong Greenspace Exposure and 3-Dimensional Brain Magnetic Resonance Imaging in Barcelona Schoolchildren,” Environ. Health Perspect., vol. 126, no. 2, p. 027012, Feb. 2018, doi: 10.1289/EHP1876.

[10] M. Preuß et al., “Low Childhood Nature Exposure is Associated with Worse Mental Health in Adulthood,” Int. J. Environ. Res. Public. Health, vol. 16, no. 10, p. E1809, May 2019, doi: 10.3390/ijerph16101809.