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From Prebiotics to Probiotics — Demystifying Baby's Microbiome

By Sara Vance, Nutritionist and Author of The Perfect Metabolism Plan

The human body is host to trillions of bacteria (“microbes”) that live on our skin and in the gastrointestinal tract, mouth and eyes. They play an important role in our overall health. These bacteria are one part of a range of microorganisms that together form the microbiome, or microbiota.

The human digestive tract alone is estimated to contain 400 different species and subspecies of bacteria.[1] We often think of bacteria as “bad” — or something that we need to eradicate with antibacterial wipes and antibiotics. While it is true that some bacteria are pathogenic and can stimulate infection, many bacteria are beneficial.

Ideally, in a healthy microbiome, a balance exists between all of the different types of bacteria — so the probiotic bacteria (“good” bacteria) can keep the others in check. The word “probiotic” literally translated means “for life.”

For a microbiome to thrive, we must “seed and feed” it. Probiotics are the live microorganisms that seed our gut, while prebiotics feed the good bacteria, helping it to establish and flourish. Created through fermentation, probiotics can be found in fermented foods like kefir, as well as in supplements. Prebiotics are fibers, which can be found in fibrous foods and supplements.

It was recently discovered that the womb — once thought to be a sterile environment — has its own microbiome, with detectible bacteria found in most (but not all) placenta and amniotic fluid studied.[2] Therefore, a baby’s microbiome begins to develop before birth, although it is still immature at the time of birth. The most dramatic changes happen in the first year of life, with the first 6 months being a “critical window.”[3] Full colonization of a child’s microbiome happens by about age 3.

“Apart from the obvious gift of life, the seeding of the baby’s microbiome is perhaps the second greatest ‘gift’ a mother can give her baby.”

—Toni Harman, filmmaker of Microbirthand author of Your Baby’s Microbiome

The infant microbiome is influenced by a number of factors, both in and out of our control, including:

  • Maternal factors
    Exposure during pregnancy to high stress levels, dietary factors such as high sugar or processed foods, infections and antibiotic use, and obesity can all negatively impact the offspring’s microbiome.[3]
  • Vaginal or C-section birth
    Babies born vaginally have more bacterial diversity and lower levels of pathogenic bacteria.[3] Babies delivered by C-section are more likely to become obese later in life. Knowing the importance of the inoculation that occurs in the birth channel has led some doctors to swab the baby with maternal vaginal fluids after a C-section birth.[2][4]
  • Dietary and feeding patterns
    Breast vs. bottle feeding, weaning, and introduction of solids, dietary fiber, pre and probiotics can all affect a baby’s microbiome. Breastmilk-fed and formula-fed (even with prebiotics) infants have a significantly different microbiome.
  • Pre and postnatal antibiotic and antacid exposure
    Antibiotics given during pregnancy and delivery appear to reduce diversity in the infant’s microbiome. Recently, the common practice to give colicky infants antacids has come into question, as it was linked to an increase in allergies, likely due to its impact on the bacterial diversity of an infant.[5]
  • Environmental exposures
    Various environmental factors may influence the baby’s microbiome, such as skin-to-skin contact, pets in home, city vs. farm living, time spent in home vs. hospital, etc.[3]

A recent study discovered an increase in the pH of infant stools and a reduction in the Bifidobacterium strain of bacteria in the infant microbiome in the past century.[6] The researchers say that this trend may have contributed to the increased incidence of allergies and autoimmune diseases, although more studies are needed.[6]

The question is — what can we do to make sure our baby’s microbiome is balanced? Researchers are looking for ways to prevent and restore the diversity and population of beneficial bacteria in the infant microbiome, and one area of study is the supplementation of probiotics and prebiotics.


Although more research is needed, there are some strains that may potentially be beneficial, with evidence that multi-strain probiotics could be more effective and more consistent with the microbiome than single-strain probiotics.[7]

  • Lactobacillus reuteri (reuteri)One of the best studied probiotics for infants with many reported benefits is L. reuteri. Research shows that L. reuteri given to the mother during week 26 of the pregnancy and then to the infant may help to reduce the risk of allergies.[8]According to a study published in Pediatrics, it may be useful in preventing and treating colic, although other studies found no benefit.[9] In addition, it may help resolve diarrhea.[10]
  • Lactobacillus rhamnosus (L. rhamnosus)
    If taken by the mother during and after pregnancy, rhamnosis was found to colonize the intestine of vaginally delivered, breastfed infants until 1–2 years of life. It also increased the abundance of Bifidobacterium species in the infant gut.[2]
  • Bifidobacterium infantis (B.infantis) A study found that the infantis strain EVC001 lowered infant fecal pH, improved breastfed infants’ gut function and produced substantial changes in the intestinal biochemistry.[6]


  • Breastmilk contains prebiotic fibers called oligosaccharides that are important for feeding the good bacteria in the gut. While breast is the gold standard, studies have shown that prebiotic supplementation brings formula “one step closer to breastmilk.”[9][11] Studies have found that benefits of a prebiotic-enhanced formula included improved gut colonization and pH, more frequent stools with better consistency, and fewer pathogenic bacteria, compared to infants receiving a formula without prebiotics.[9][11] Other studies have linked prebiotic formulas to a reduction in allergies and eczema.[12]

According to Hippocrates, considered the Father of Modern Medicine, “All disease begins in the gut.” It stands to reason that the delicate balance of bacteria in our digestive tract may affect our health. We are just scratching the surface in our understanding of the importance of a healthy microbiome — but thankfully, bacteria’s role in various areas of health and wellness is increasingly being examined in scientific studies. Hopefully, as new information comes to light, it can help us to understand how our microbiome impacts our metabolism, digestion, disease risk, weight, immunity, and mental and neurological health and development — and what to do to improve it.

About the Author: A nutritionist and the author of The Perfect Metabolism Plan, Sara Vance is a passionate advocate for natural approaches to health. She regularly offers cooking and group classes and has developed a series of online courses to empower people to use foods to balance their metabolism and overall health. As a mom and a specialist in childhood nutrition, Sara loves working with kids, speaking frequently at school assemblies and leading children’s workshops. Sara is a frequent guest on the Fox 5 San Diego show, CBS Los Angeles, KUSI and CW 6. She has contributed to Delicious Living, Mind Body Green and Refinery29. Sara has also filmed videos for eHow and created a Kids Yoga series for GaiamTV.

References and Sources

  1. Microflora of the gastrointestinal tract: a review.
  2. The infant microbiome development: mom matters
  3. The Infant Microbiome: Implications for Infant Health and Neurocognitive Development
  4. Nurturing a Baby’s Microbiome, Before and After Birth
  5. Association Between Use of Acid-Suppressive Medications and Antibiotics During Infancy and Allergic Diseases in Early Childhood
  6. Elevated Fecal pH Indicates a Profound Change in the Breastfed Infant Gut Microbiome Due to Reduction of Bifidobacterium over the Past Century
  7. Evidence-based guidelines for use of probiotics in preterm neonates
  8. Lactobacillus reuteri, Infant Allergy Prevention and Childhood Immune Maturation
  9. The effect of a prebiotic supplemented formula on growth and stool microbiology of term infants.
  10. Lactobacillus reuteri as a therapeutic agent in acute diarrhea in young children.
  11. Prebiotics in infant formula.
  12. Prebiotics in infants for prevention of allergy.
  13. It might be possible to remodel a baby's microbiome
  14. Could baby’s first bacteria take root before birth?
  15. Diet during pregnancy and infancy and risk of allergic or autoimmune disease: A systematic review and meta-analysis
  16. Baby poop is changing, science reveals. Here's why it matters
  17. Bacteria in the Intestines May Help Tip the Bathroom Scale, Studies Show
  18. Scientists Discover That Antimicrobial Wipes and Soaps May Be Making You (and Society) Sick
  19. Antibacterial agent could cause pregnancy problems
  20. With a caesarean section, the path to obesity may begin at birth
  21. Probiotic and prebiotic supplementation for the prevention of neonatal necrotizing enterocolitis
  22. Lactobacillus reuteri to Treat Infant Colic: A Meta-analysis
  23. The developing gut microbiota and its consequences for health.


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