Healthy Microbiome; How We Get Our Good Bacteria


What is a microbiome? Well, the short version is that our microbiome is the community of microorganisms that live within and on the human body. This includes organisms such as viruses and bacteria.  Some are commensal friendly bacteria and some are pathogenic bacteria that can cause disease. Although the bacteria is not only in our gastrointestinal tract or gut, that is what we will focus on here. The Human Micorbiome Project has helped our understanding of the importance of gut health.  Having a more varied species in your mircrobiome is linked with lower risks of disease and greater long term health.


So how do we get a variety of species? I recently watch the Mircobiome Series from Rebel Health Tribe and was blown away by the information. This came at the perfect time for me as I am about to bring another child into the world.  Understanding how an infant receives a variety of good bacteria is a very important topic to me. My 5 yr old had leaky gut (intestinal permeability) at the age of 3, eczema rashes and many food intolerances. I am hoping to avoid this situation with my second child. Unfortunately with my first child I was unaware of my own poor gut health before conceiving. Since the majority of an infant’s gut bacteria get passed down from their mother it is not surprising that she ended up with an unhealthy microbiome.


As a Functional Diagnostic Nutrition® practitioner we use functional lab work to look for underlying imbalances. In the process of trying to get to the root of my daughter’s eczema, we ran many labs. The most eye opening was when my daughter and I simultaneously ran a stool test to look for pathogens and our results were exactly the same. We both had an overgrowth of enterobacter. My daughter’s gut health was a mirror of mine.


Since I have focused on supporting my gut health for a couple years, I already know that my second baby will be much better off. We now know that the more diverse the species are living in your gut, the healthier you are overall. Each person has their own unique microbial community that is as different from one person to the next as their fingerprint. Even twins, born from the same mother in the same environment have different species in their gut. So let’s talk about how you get these different species in the first place.


How did we get our unique microbiome? We don’t have our full set of gut bacteria until we are about 2 ½ years old. If you want to get a more detailed understanding of this subject, I highly suggest that you watch the Mircobiome Series from Rebel Health Tribe.


  • It Starts in utero. We used to think that when a baby entered the world the gut was sterile but we now know that while in utero the baby’s gut has already started to be inoculated. Immune cells from the mother will grab the good bacteria and transfer it to the baby through the umbilical cord. This gets the baby ready for the biggest inoculum of bacteria as the baby passes through the birth canal.
  • The birth canal. At the end of the first trimester, the vaginal population of the pregnant mother starts to shift to mimic that of the gut bacteria. The bacteria that helps babies digest milk also starts to grow so that when the baby enters the world through the birth canal the baby gets bathed in this bacteria. This prepares the infant to be able to drink milk, it’s primary source of nourishment for the next 6 months.
  • Skin to Skin. Luckily skin–to-skin contact has become a popular practice right after a baby is born, first with the mother and then the father. This is the next step in populating the microbiome since this is how the baby gets the friendly skin based bacteria from the parents. The good bacteria on our skin is like an invisible layer of body army that alerts our immune system if something is about to attack.
  • Breastfeeding! Another incredibly powerful way that nature helps pass different bacteria on from the bother to the baby. Breast milk contains 400-600 different species of bacteria! But did you know that the most abundant nutrient in breast milk are actually oligosaccharides, which can’t be digested by the baby? Why would a baby’s only source of nutrition be made up of something that they can’t digest? The milk is heavy in oligosaccharides because it feeds the baby’s bacteria that it just got from mom and helps it make a permanent home. This shows how important the role of the bacteria is!
  • Community – Pass that baby around. Ever wonder why you just want to kiss and snuggle every cute little baby that you see? Cute kissable babies have an evolutionary advantage. The baby that gets passed around from relative to relative or among community members comes into contact with bacteria that their mother didn’t have. The more diverse the species that they acquire the better off they are. So put down that antibacterial hand sanitizer that you spray on your visitors and pass that baby around!!!
  • Environment. The environment is where baby gets the remainder of the bacteria to populate the microbiome.   Ideally we will find this environmental bacteria in nature that hasn’t been altered by man, such as in the pristine mountains and woods. Consider letting your children play freely, get dirty and even eat some dirt if they want to while camping or hiking. People living in rural environments tend to have more diverse species. This tip doesn’t just apply to babies, this is a great way for adults to repopulate with good bacteria. Take a hike!


How fascinating is this? Hopefully this will help you set up your little one for success. Now I know a lot of you might be thinking, but what if I had a c-section or couldn’t breastfeed? There are medical reasons when c-sections are necessary and they can save lives, so if this is your situation there is no need to beat yourself up about it. Just be aware that your baby might need a little extra help populating it’s microbiome. After all, I was a c-section baby and I have been able to restore my microbiome!!!



  • Sarah
    November 28, 2015

    Fascinating! Thank you for informative and concise post!

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