It has now been established that breast milk, similar to the intestinal tract, has its own microbiome containing possibly hundreds of bacterial species. In addition, breast milk produces its own indigestible sugars called oligosaccharides that babies cannot digest. These sugars become the food (prebiotics) for the bacteria residing in the breast tissue and milk. During breastfeeding these healthy bacteria relocate to the baby’s mouth and intestinal tract, where they establish healthy communities of bacteria that become the baby’s own microbiome.

Another microbiome that changes early in the first trimester is the vaginal microbiome. There are shifts in numbers and types of bacteria, especially Lactobacillus strains. One notable strain, Lactobacillus  johnsonii, begins to dominate the vaginal microbiome.  This strain of Lactobacillus is designed to digest milk in the intestinal tract. L. johnsonii moves to the vagina as the pregnancy progresses, so that with vaginal births the baby will be orally inoculated with it to help the baby digest breast milk or formula.1

At the time of birth the infant is inoculated with many strains of beneficial bacteria as (s)he passes through the birth canal, and will be exposed to many more with breastfeeding. However, it is the high level of diversity of mother’s diverse microbiomes (mouth, intestine, breast, vagina, skin and lungs) that through direct contact with the baby will develop a strong and well balanced immune system.1 Unfortunately, it has been shown that the more obese the mother, the lower the diversity of her intestinal microbiome and the more likely she is to pass bacteria to the baby that promote fat storage.2

So here are some tips to consider during pregnancy:

  • Eat an 80 to 90% plant-based diet: more alkalinity, more probiotic bacteria (they thrive on plant based foods), and more magnesium (good to decrease inflammation). Animal food should ideally be organic. Include pre- and probiotics in your diet.
  • Moderate exercise: Resistance, aerobic, and stretching
  • Good hydration: At least 6 to 8 glasses of water daily
  • Manage stress and sleep well: It supports your beneficial bacteria; get stressed and watch your Bifido and Lacto bacteria decrease!
  • Consider a vaginal culture during last month of pregnancy. If Lactobacillus species are low, increase probiotics orally or intravaginally.  (If you are found to have Group D Streptococcus on vaginal culture, they will insist on IV antibiotics, which are certainly less than ideal at the time of delivery).
  • Supplement with fish oil and vitamin D, and have your doctor monitor them with an Omega-3 Index test and a 25-OH vitamin D blood test.

Adding these tips to your pregnancy will help to ensure a healthy baby.



  1. K. Aagaard, et al., “A metagenomic approach to characterization of the vaginal microbiome signature in pregnancy.” PLoS One. 2012;7(6):e36466.
  2. R. Cabrera-Rubio, et al., “The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery.”  Am J Clin Nutr. 2012 Sep;96(3):544–51.