4 Ways to Support Your Baby's Microbiome in the First Few Months of Life

The first months to years of an infant’s life are critical for the development of their microbiome—a complex system of bacteria, fungi, and other microorganisms that plays a key role in digestion, immunity, and overall health. With the sleep deprivation and constant adjustments of new parenthood, it’s easy to wonder, “Am I doing enough to support my baby’s microbiome?” The great news is that you are likely already doing many things that support their microbiome, and if not, I’m here to show you how to integrate simple, effective practices into your day without adding more stress to your plate.

If you're new to this page, I often talk about the importance of the first 1,000 days—this is the window of time when the microbiome is developing and adapting the most. The choices we make in these early days can shape the microbiome in profound ways that affect our child’s health long into adulthood. It’s truly amazing how much power we have as parents to positively influence this crucial system. So, while the first few months may feel like a whirlwind of feeding, changing, and calming, there are specific things you can do to nurture and support your baby’s microbiome right from the start. Let’s dive in!

1. Skin-to-Skin Time, Which Can Also Double as Tummy Time!

Skin-to-skin time is truly one of the best things you can do for both your baby’s neurodevelopment and microbiome development. While I could go on and on about the benefits of skin-to-skin, I want to highlight some key points for you. If you only get to one activity a day, let it be this, and here’s why:

Skin-to-skin contact is one of the most effective ways to transfer beneficial microbes from the parent’s skin to the baby, promoting the establishment of a diverse and healthy microbiome. This early microbial exposure helps strengthen the baby’s immune system, aids digestion, and may reduce the risk of allergies and gastrointestinal issues later in life.

I also love skin-to-skin because it can serve as an effective form of tummy time! During skin-to-skin, when the baby is placed on their parent's chest, they engage their neck, back, and shoulder muscles as they try to lift their head and push against their parent’s body. Tummy time is important for:

• Strengthening the neck, shoulder, and arm muscles needed for milestones like lifting the head, rolling over, sitting up, and crawling.
• Exposure to different textures and sensations, helping babies develop body awareness, spatial orientation, and sensory processing abilities.
• Enhancing visual development by giving babies a chance to look around and focus on objects at different angles, supporting both visual fixation and tracking. 

2. Don’t Overly Clean and Be Cognizant of the Products in Your Home

Many people think that having an overly clean home, free from any dirt, debris, or germs, is good for an infant, but the opposite is true (within reason, of course!). Early microbial exposure in a baby’s environment, particularly from surfaces, pets, and family members, is crucial for helping them build a diverse and healthy gut microbiome. Over-sanitizing and using harsh cleaning products can limit this exposure, reducing the opportunity for beneficial microbes to interact with the baby’s developing system.

That being said, over-sanitizing and frequently disinfecting surfaces in the home, while often done with good intentions, can inadvertently sterilize the environment and limit exposure to microbes that help "train" the immune system. In fact, studies have shown that babies who are exposed to a broader range of microbes (for example, those who grow up with pets or spend time in nature) tend to have lower rates of allergies and better immune function.

What to do instead? Find a balance that works for you. Maybe, for you, wiping down toys that were dropped on the floor in public is important, but skipping the daily Clorox wipes on the changing table feels like a better balance for your family. My goal is to always give you the information and encourage you to find systems and routines that work best for your family.

In my home, I typically use Branch Basics solution or blueland cleaning tablets for my all-purpose spray. These are both made with gentle ingredients, and I know they won’t greatly impact my baby’s neurodevelopment and microbiome. I also make my own solution using the recipe below:

• 1 cup distilled white vinegar
• 1 cup water
• 1 tablespoon baking soda
• 10-15 drops of whichever essential oil I have handy (such as lemon, lavender, or tea tree oil for added antibacterial properties)

3. Use Safe Personal Care Products

Personal care products we bring into our homes can have profound effects on both an infant’s neurodevelopment and microbiome development. If you're feeling overwhelmed by this category, let me assure you that you are not alone! There are so many products on the market with far too many ingredients, which can leave parents feeling confused and unsure—me included!

An online survey by the Environmental Working Group (EWG) revealed that children are exposed to an average of 27 chemicals daily through body care products. Once you become more educated in this area and remove these chemicals from your home, you'll be amazed at how sensitive you become to them, especially fragrances. There’s no place for many of these, particularly around our little infants.

Many personal care products, such as lotions, shampoos, and detergents, contain parabens, phthalates, and fragrances, which are linked to long-term negative health effects. Since babies have higher absorption rates through their skin and their detoxification systems are still developing, they are much more vulnerable to these chemical exposures, making the first few months particularly sensitive. Exposure to these chemicals can impair nervous system development and affect behavior, cognition, and motor skills, as well as interfere with the natural microbial colonization process by killing both harmful and beneficial bacteria.

Thankfully, there are many trusted products you can swap out in your home to create a safe environment for your growing babe. With any personal care product I bring into my home, I run it through the EWG database so I can educate myself on the ingredients. Here are the ones I used with my son from birth.

• Body wash + shampoo
• Diaper balm
• Detergent
• Light lotion
• Thick lotion
• Baby wipes
• The only EWG certified diaper (watch this video for a good review on diapers in general) I personally never committed to a single diaper brand. I tried them all—from Coterie to Hello Bello to Kirkland. Diapers are a tough industry, so just do your best and find the one that works best for you.

4. Navigating Probiotics for the Infant Microbiome

There’s a lot of mixed information out there about probiotics for infants, so I want to share my general thoughts. While the decision to use probiotics varies from infant to infant, here’s how I approach it:

For Breastfed Infants:
Whether partially or exclusively breastfed, I typically never recommend probiotic supplementation. Breastmilk is rich in naturally occurring probiotics, prebiotics, and bioactive compounds that can’t be replicated by any formula or supplement—no matter how good the marketing may be! ;)

For Formula-Fed Infants:
This is where things get more nuanced. The decision to supplement depends heavily on the infant’s health status and individual circumstances. With any supplement, it’s not just about the active ingredient; fillers and additives can also impact the infant’s microbiome. Here are a few important considerations:

• Was the infant born via c-section or vaginal delivery?
• Did the infant or mother require antibiotics during delivery or shortly after?
• Is the infant experiencing health challenges such as eczema, reflux, or colic?

In general, I prioritize the following when considering probiotics for formula-fed infants:

• Using only well-researched strains tested for the infant’s specific age group such as bifidobacterium infantis.
• Selecting high-quality, third-party-tested supplements.

My General Approach for Exclusively Formula-fed babies:
In most cases, I lean toward adding a probiotic rather than not, as the research largely supports the beneficial outcomes—especially in formula-fed infants or those with specific health needs. However, the choice should always be individualized, taking into account the unique circumstances of each baby.

Probiotics are not a one-size-fits-all solution, but with the right guidance and a thoughtful approach, they can be a valuable tool in supporting an infant’s gut health.

I hope this information was more valuable than overwhelming!

My goal is always to help you become an informed parent, and this is never meant to make you feel like you're not doing enough. Rather, I want to empower you to realize that your efforts truly matter in shaping your baby’s future health! Find your balance as a parent and, above all else, always stay true to what feels right for you. And one final reminder: all your baby needs at the end of the day is you.

References

• O'Hara, M., et al. (2020). "The Influence of Skin-to-Skin Contact on the Microbial Colonization of Newborns." Frontiers in Pediatrics. https://doi.org/10.3389/fped.2020.00315

• Zimmermann, P., et al. (2019). "The Hygiene Hypothesis—An Explanation for the Increased Frequency of Allergic Disease." Frontiers in Pediatrics.
  https://doi.org/10.3389/fped.2019.00512

• Hesselmar, B., et al. (2013). "Pet-Keeping in Early Life Reduces the Risk of Allergy Development." Clinical & Experimental Allergy.
  https://doi.org/10.1111/cea.12201

• Dodson, R. E., et al. (2012). "Endocrine Disruptors and Infant Exposure to Personal Care Products." Journal of Exposure Science & Environmental Epidemiology.
  https://doi.org/10.1038/jes.2012.9

• Steinemann, A. C., et al. (2017). "Household Cleaning Products and Asthma: A Review of the Evidence." Environmental Health Perspectives. https://doi.org/10.1289/EHP.1510

• Bäckhed, F., et al. (2016). "Microbial Exposure and the Development of the Infant Gut Microbiome." Nature Reviews Gastroenterology & Hepatology. https://doi.org/10.1038/nrgastro.2016.108

• Chiarelli, F., et al. (2014). "Probiotics for Treating Gastrointestinal Symptoms in Infants and Children: A Review of the Literature." Current Pediatric Reviews. https://doi.org/10.2174/1573396314666141218233901

• Dimitri, P., et al. (2017). "The Role of Probiotics in the Management of Colic in Infants." Journal of Perinatology. https://doi.org/10.1038/jp.2017.66

• Bäckhed, F., et al. (2015). "Gut Microbiota and Infant Health: Lessons from Probiotics and Beyond." Nature Reviews Gastroenterology & Hepatology. https://doi.org/10.1038/nrgastro.2015.48