Infants and Microbes

Through Western culture we have been led to believe that bacteria on and in the body needs to be eliminated. When babies are born, we immediately scrub them clean and swaddle them up, rather than placing them skin-to-skin on the mother as traditional cultures have done for many millennia. Yet, finally, research is revealing how necessary it is for infants to be exposed to the microbes on mother rather than protected from them.

The current Western paradigm regards bacteria in the body as foreign or invasive. In recent decades the logic has been: “When foreign bacteria is removed or destroyed, disease is destroyed.” This has led to a heavy reliance on antibiotics and antibacterial products. The history behind why is quite intriguing – read more in our article on Pasteur and Bechamp. However, longstanding studies of human microbiome reveal a different story.

Humans serve as a host to evolving microbes in highly plethoric communities. Over 100 trillion microbes live in the body. Collectively these microbes are known as our microbiome. Microbes colonized in the gut help to metabolize sugar, synthesize vitamins and minerals, and break down hard to digest compounds. Bacteria on the skin produces a moisturizing film to prevent cracks in the skin. This film protects against invading pathogens.

Unfortunately, broad spectrum antibiotics may kill off precious bacteria that have co-evolved with us and are actively maintaining the health of our bodies. When prescribing antibiotics, doctors hope that beneficial bacteria killed off in this way will regenerate on their own. However, the microbial ecosystem that once flourished does not repopulate on its own. Once good bacteria is killed off, invasive species can flourish. Which is why reintroducing beneficial microbes to the system with a quality probiotic is critical after a round of antibiotics.

Mothers Promote the Health of Their Children by Shaping Their Microbiome

Scientists are finding that pregnant women pass significant microbes onto their infant while the infant passes through the birthing canal. She continues to pass this beneficial bacteria through breastfeeding. In an an NIH-funded study1, Dr. Kjersti Aagaard, an obstetrician at Baylor College of Medicine, examined the changes in vaginal microbiome during pregnancy. Her findings were the opposite of what she expected! Aagaard expected that the microbiome in the vagina would remain the same form of bacteria that existed prior to pregnancy. As early as the first trimester, the diversity of vaginal bacteria changes immensely. Species that were once quite abundant dissipate, and new species of bacteria arrive.

One species that forms in the vagina, Lactobacillus johnsonii is usually found only in the gut, where it produces enzymes that digest milk. Changing conditions in the vagina during pregnancy encourage this strain of bacteria to grow. “It’s an odd species to find proliferating in the vagina, to say the least,” states Dr. Aagaard.

During delivery, the baby will be covered by Lactobacillus johnsonii and even ingest some of it.

This inoculation prepares the infant to digest breast milk. The infant comes from a sterile environment, and once born is exposed to several environmental sources of beneficial bacteria immediately through maternal vaginal canal and feces, swallowing and breathing, skin to skin contact, maternal breastmilk, etc.1

The Mother Continues to Pass Beneficial Bacteria to Baby During Breastfeeding

Baby’s microbiome continues to develop during breast-feeding. In a study of 16 lactating women published last year,2 Katherine M. Hunt of the University of Idaho and her colleagues reported that the women’s milk had up to 600 species of bacteria, as well as sugars called oligosaccharides that babies cannot digest. The sugars serve to nourish several beneficial gut bacteria in infants, the scientists stated. The more good bacteria thrive, the harder it is for harmful species of bacteria to grow and flourish.

For the first approximately zero to seven days colostrum is provided to baby by the mother, a thicker form of human milk. Colostrum is composed of approximately 70% leukocytes. Leukocytes defend the body against infectious diseases and foreign materials. The mother produces antibodies to the diseases she has already acquired. Colostrum contains the antibodies produced by her body. The mother passes these antibodies through her colostrum and milk.

There are several antibacterial, antiviral, anti parasitic factors found in human milk (such as Secretory IgA and IgG) that actually kill off harmful bacteria such as e-coli, viruses, the flu as well as many other toxins and bad bacteria. Immunoglobulins present in both colostrum and mature milk protect the infant’s GI tract against penetration by organisms and antigens. Immunoglobulin A (aka IgA) binds to bacteria and prevents pathogens from binding to receptor sites and invading the gut. Lymphocytes and macrophages digest bacteria and make IgA and other protective substances.

The Microbiome Slowly Becomes More Complex

The immune system continues to mature throughout childhood. In a study published in the journal Science, Dr. Richard S Blumberg of Harvard and his colleagues reported:

Exposure to microbes during early childhood is associated with protection from immune-mediated diseases such as inflammatory bowel disease (IBD) and asthma. Here, we show that in germ-free (GF) mice, invariant natural killer T (iNKT) cells accumulate in the colonic lamina propria and lung, resulting in increased morbidity in models of IBD and allergic asthma as compared with that of specific pathogen-free mice.3

This and several other studies support the recognition that age-sensitive contact with commensal microbes is critical for healthy development of the immune system.

Science is discovering that babies are born through the vagina and near the anus for specific beneficial reasons, and that breastfeeding performs more complex functions than a supply of micro- and macro-nutrients.

This research leads us to question many Western interventions throughout pregnancy and lactation, such as elective cesarean section, not immediately placing baby on mother, not supporting breastfeeding, and routine antibiotic use before during and after pregnancy (especially broad-spectrum antibiotics). Microbes have more relevance to human health than we once realized, and can be crucial for us to understand when dealing with disease processes such as obesity, asthma, autoimmune conditions, and bowel dysfunction.

The microbial relationship between mother and baby are critical to successful infant inoculation.


  1. AAgaard K., Riehle,K, Ma J, Segata N, Mistretta, TA, Coarfa C, Raza S, Rosenbaum S, Van Den Veyver, I, Milosavljevic, A, Geyers D, Huttenhower C, Petrozeno J, Versalovic J (2012) A Metagenomic Approach to Characterization of the Vaginal Microbiome Signature in Pregnancy. DOI: 10.1371/journal.pone.0036466
  2. Hunt K, Foster J, Forney L, Schutte U, Beck D, Abdo Z, Fox L, Williams J, McGuire, M, McGuire MA (2001) Characterization of the Diversity and Temporal Stability of Bacterial Communities in Human Milk. DOI: 10.1371/journal.pone.0021313
  3. Olzsak T, An D, Zeissig S, Vera M, Richter J, Franke A, Glickman J, Siebert R, Baron R, Kasper D, Blumberg R (2012) Microbial Exposure During Early Life Has Persistent Effects on Natural Killer T Cell Function. Science Magazine Vol. 336 no. 6080 pp. 489-493