Human beings have a very special relationship with microbes, especially bacteria. Together, humans and bacteria have co-evolved for millions of years. Human survival is dependent on bacteria despite the few, fearsome species; and bacteria are dependent on a human host.

Very recently on that timeline, Science has discovered that a person’s microbiome is the front-line immune system. Thus we could say that a person has THREE immune systems—the innate, acquired (adaptive), and microbiome.

The gut microbiome is an integral part of innate (non-specific) immune system as a first responder to invading pathogens ingested or acquired from the external environment.

And should a pathogen or antigen involve the body’s internal cells, there is a subset of the humoral/acquired immune system called cell-mediated. Each immune system employs specialized cells and overlaps with the other immune responses.

Ultimately, they all work together to preserve the host’s life. The microbiome works in symbiosis with the innate, adaptive, and cell-mediated immune responses to provide the protection the body needs.

So where did the microbiome—an important and integral part of the human immune system come from?

In-Utero Bifido

For hundreds of years, Medicine assumed the infant-in-utero had a “clean slate,” sterile Gastro Intestinal (G.I.) Tract. Recently, Science found a few probiotic bifidobacilli in an unborn fetus sparking interest in how a bacteria crossed the blood/placental barrier. Seems that Nature has its ways to ensure life and perpetuation of the species. Even for infants as Will Shakespeare noted “from his mother’s womb untimely ripp’d” via Caesarian Section.

Babies are born with special bifidobacillus in their G.I. Tracts. Such species would already bear the stamp of approval from the infants’ genes and developing immune system.

Recently, Science has discovered that the vernix caseosa (the whitish, cheesy coating on a neonate’s skin) develops in weeks 19 through 34 of pregnancy. It serves as a food for gut bacteria (the baby swallows some while in the womb). Other benefits include lubrication for passage through the birth canal and skin-protection at the time of birth. It also helps proliferate the probiotic species the baby will acquire in the birth canal.

Birth Canal – A Gauntlet of Probiotic Seeding

Right before birth, the mother’s vaginal microbiome goes through a rapid, massive proliferation of a variety of probiotic species. This serves to inoculate the infant with front-line immune support based on the mother’s inherent probiotic species’ DNA. The infant leaves the womb’s safe, sequestered haven and is thrust out into the world of both friendly and fearsome microbes.

Passage through the birth canal seeds the infants skin for protection against yeast-fungus (candida), pathogenic bacteria, virus, and other microbes. The birth process also seeds the oral, gastro-intestinal, ocular, nasal/sinus, and auricular microbiomes as well.

Baby’s Bacteria Bath

We could say that, after the in-utero amniotic bath, baby’s second bath is in probiotic bacteria. Seeding the nasal probiotic microbiome during birth is important to infant survival. The scent of vernix and bacterial presence are thought to trigger neural connections in the baby’s brain needed to initiate breastfeeding.

As obstetrics applies modern scientific discoveries to childbirth, the vernix should not be immediately washed off should be left on the baby for a while after birth, except in cases of chorioamnionitis, HIV, and hepatitis where it could harbor unwanted microbes.


Historically, breast milk was considered sterile. Now science finds abundant “commensal” bacteria (species that Science has not yet found a pro-health function) and probiotics1. In fact, breast milk is a microbiome all its own.

Science speculates that “somehow” G.I tract probiotic species migrate (via an entero-mammary pathway) to the breasts to seed infants’ bodies with health-supportive microbes (bifidobacteria, lactobacillus, streptococcus). Breast milk provides both prebiotics (human oligosaccharides) and probiotics making breast milk a synbiotic.

For the infant, breast milk is Nature’s perfect food. It feeds baby’s cells as well as the gut microbiome. It also provides immunoglobulins and anti-microbial peptides as well as Nature’s perfect nutrients for the baby’s health and growth.

Historically, modern medicine advocated NOT breastfeeding and use of synthetic “baby formula” often made with corn syrup, synthetic vitamins, rock-minerals, and complex vegetable proteins. Now the trend is “the breast is best,” as Science delves deeper into discovering that Nature had it right all along.

Holding, Touch, Cuddling, Playing In The Dirt

While holding the infant close to the skin, the mother, father, and other’s impart elements of their microbiome. Contact with animals and the soil imparts more species. Infants often ingest dirt and likely a few insect microbiomes. Life is exploration and contact with many varied microorganism species—some beneficial, some threatening—and the body learns something from each encounter.

So where does the microbiome come from? It starts before birth with the mother and then the birth process. It continues with enhancements by breastfeeding. It’s further enhanced and augmented by contact with the Earth’s flora and fauna.

Over time, the developing child’s immune system helps control and mutate bacterial species to best support the various microbiomes as well as proper regulation of the brain’s neurotransmitter processes (gut-brain connection). All through this journey the microbial input helps develop proper immunological responses to the environment.

Support, Don’t Destroy, Your Best Friends

One could say that, even more than canines and diamonds, the microbiome is a person’s best friend. Yet, for the past 500 years, humanity has errantly been on a witch-hunt to damage and stamp-out the very bacteria that support life on Planet Earth. Living in fear of 120 pathogenic species, Science is now learning about the myriad of other species that support a healthy ecology—for the person, the food supply, and planet.

Today we find a new respect for the microbiomes emerging. As demonstrated during the global viral pandemic, people with healthy microbiomes have superior immune system processes2 in place to help handle the challenges of the microbial environment.


  1. Lyons KE, Ryan CA, Dempsey EM, Ross RP, Stanton C. Breast Milk, a Source of Beneficial Microbes and Associated Benefits for Infant Health. Nutrients. 2020;12(4):1039. Published 2020 Apr 9. doi:10.3390/nu12041039
  2. Research: Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19 gutjnl-2020-323020 Journal: Gut