How to Establish a Healthy Microbiome for Your Little One

If you’re a new parent, you may be worried about exposing your little one to bacteria, however not all bacteria are considered “bad for you!” In fact, the human body has trillions of bacteria, viruses and fungi that live in the gut-microbiome, and they all play a very important role in health. 

A healthy microbiome has a balance of “good” and “bad” bacteria. Lactobacillus and Bifidobacterium are the most common groups of beneficial bacteria (also known as probiotics) that are found naturally in both you and your child’s body, as well as in various foods. These probiotics work together to boost your little one’s health by protecting/strengthening the immune system, helping with absorption of nutrients, and assisting your LO’s ’s gut development. 

A growing body of research has found that early establishment of infants’ gut microbiomes can shape their metabolic and immune-related health. 

The Latest Study: 

  • A 2018 study done by researchers at Baylor College of Medicine (Houston, USA) analyzed 12,005 stool samples that were collected from 903 children between 3 months and 46 months of age.

  • Researchers found that “breastfeeding was significantly associated with 121 different bacterial species, with higher levels of B. bifidum, B. breve, B. dentium, Lactobacillus rhamnosus and Staphylococcus epidermidis, (good bacteria) and lower levels of Escherichia coli, Tyzzerella nexilis, Eggerthella lenta, Ruminococcus torques and Roseburia intestinalis” (bad bacteria) in infants.”

  • They also discovered that “B. breve and B. bifidum, have distinct profiles of sugar utilization, suggesting that the different nutrient availability between infants can promote the colonization of specific Bifidobacterium species” (healthy bacteria).

  • Also, “birth mode was significantly associated with microbiome development over the first year of life, with higher levels of Bacteroides spp. (healthy bacteria) in infants that were delivered vaginally.”

In summary, the study found that the first few years of life are important for microbiome establishment and is affected by several factors such as delivery mode (cesarean delivery vs. vaginal delivery), breast milk vs. formula feeding, and introduction of nutritious solid foods during weaning. 

The study elucidates the importance of infant nutrition and gives insight into how it affects the development of an infant's microbiome. Therefore, when your LO is ready for solids, it is important to provide nutritious foods that naturally contain both pre and probiotics. Prebiotics are the “food” for probiotics. In other words, they are not living microorganisms but rather the nutrients that help feed the probiotics and help them flourish in the gut. 

Some examples of foods rich in pre and probiotics: 

  • Yogurt (especially with added probiotics) 
  • Kefir 
  • Aged cheeses (cheddar or gouda) 
  • Whole foods with high fiber content (whole-grain breads/cereals, berries, bananas, apples, broccoli, peas, beans, potatoes, etc). 
  • Other fermented food products 

Other tips for improving gut health include: 

  • Limit intake of processed foods 
  • Avoid yogurts that are high in sugar (unsweetened is best) 

Bottom Line:

Building a healthy microbiome for your LO can be boosted by choosing whole foods with high fiber content and limiting processed foods that are high in sugar/salt. Foods such as oats, berries, yogurt, and broccoli are just a few examples of foods high in pre-and probiotics. These foods also contain important nutrients like protein, calcium, and vitamin D, which are additional reasons they are good choices. However, it's important to note that every baby is different and grows at their own pace. There is no right or wrong method when feeding your baby. How to support good bacteria in your LO’s tummy is up to you!  


  1. “Probiotics: What You Need To Know.” National Center for Complementary and Integrative  Health, U.S. Department of Health and Human Services, 22 Aug. 2019,
  2. Stewart, Christopher J., et al. “Temporal Development of the Gut Microbiome in Early Childhood from the TEDDY Study.” Nature News, Nature Publishing Group, 24 Oct.  2018,
  3. Shreiner, Andrew B, et al. “The Gut Microbiome in Health and in Disease.” Current Opinion in      Gastroenterology, U.S. National Library of Medicine, Jan. 2015,


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