Microbiome: The first 1,000 days

Allan Walker, MD


In the United States and other developed countries, we have seen a shift over the past several decades in the types of illness people struggle with. Public health campaigns around vaccination, sanitation, and judicious use of antibiotics have largely eradicated many infectious illnesses. As the nature of disease has shifted to inflammatory conditions, we’ve seen a striking increase in allergy and autoimmune conditions such as diabetes, obesity, inflammatory bowel disease, celiac disease, and multiple sclerosis. The microbiome — the varied and teeming colonies of gut bacteria inside of us — may be helping to drive this shift.

What is the microbiome?

Colonization occurs within the first two years of life. It passes through stages: some exposure in utero occurs with bacteria from the mother’s intestine passing through the placenta into amniotic fluid. Major colonization begins with delivery, when the fetus either passes through the birth canal or is born by cesarean section. Each mode of delivery produces a different colonization pattern. Colonization is further affected by diet (breast milk vs. formula) and weaning to solid foods. Maternal illness during pregnancy and infant illness with the use of antibiotics can disrupt the process. With complete colonization at two years of life, each individual has a unique signature of billions of organisms residing principally in their colon. The nature of colonizing bacteria differs based on geographic location in the world.

Why are the first 1,000 days of life such a critical time?

Public health doctors and primary care physicians now recognize that appropriate initial bacteria colonization of the gastrointestinal tract, and good nutrition from the time of conception until the second year of life (the first 1,000 days), may profoundly affect our health during infancy and childhood through adulthood.

Recent research published in Nature Medicine underscores the importance of the large number of bacteria (billions of organisms) that colonize the intestinal tract and can contribute to the development of protective and metabolic functions in the body. In essence, the colonizing bacteria function as an additional body organ by providing protective metabolites and antibacterial substances.

During the first 1,000 days the developing fetus and newborn goes through major developmental changes in its body organs, particularly the gastrointestinal tract. The colonizing bacteria or its secretions interact with developing body functions in ways that can have long-term effects on how the infant, child, and adult respond to environmental stimuli such as diet, pets, and antibodies. Ultimately, this may help a person stay healthy or cause a chronic disease, such Type 1 diabetes or inflammatory bowel disease.

The microbiome and the process of tolerance

A newborn must appropriately colonize the intestine to accomplish reactions that are necessary to both harmful and nonharmful stimuli. Tolerance — the process of distinguishing between potentially harmful and harmless stimuli — is the means by which this occurs. An example of this is distinguishing between a harmful infectious agent such as E. coli and food substances (milk, vegetables, etc.) that aren’t harmful unless an inappropriate response occurs (autoimmune disease).

However, in cases where inappropriate bacteria colonize the intestines, even harmless stimuli — such as antibiotics, food components, or harmless bacteria — could cause inflammation. This may lead to conditions such as allergy and inflammatory bowel disease.

What does this mean for expectant and new parents?

A mother at the time of conception should be healthy. Ideally during gestation, she should gain weight appropriately, continue to exercise, and hopefully be free of infections which require use of antibiotics. This results in a balanced intestinal colonization. When a baby is born by natural means, a large bolus of colonizing bacteria comes from the ingestion of the mother’s intestinal and vaginal organisms. After birth, an infant rapidly colonizes its intestine under the influence of breast milk, hopefully given exclusively for the first four months of life. Breast milk contains bacteria from the mother’s intestine and nutrients that stimulate proliferation of health-promoting bacteria (probiotics). Ideally an infant should be free of infections requiring antibiotics, which interfere with the natural bacterial colonization process.

In subsequent blogs I will provide further recommendations about how new parents can help their baby improve bacteria colonization during the first 1,000 days of life.

Allan Walker, MD, is the the author of Eat, Play and Be Healthy.


  1. Stacy

    So you recommend use of probiotics in infants? My 5 month old has dairy/soy intolerance and showed minor reaction to egg yolk. Our pediatric GI specialist was against direct use of probiotics. I’ve been taking probiotics since pregnancy – he has been exclusively breastfed

  2. Kathie

    What effect do vaccines have on the microbiome?

    • Allan Walker, MD
      Allan Walker, MD

      There are no studies that I know of that look at vaccine versus no vaccine during the first year of life. Since almost all babies are vaccinated by the same schedule, the studies that have been done looking at the sequential appearance of microbiota during the first and second year of life probably suggest that there is not a major effect effect of vaccines. However, that needs to be specifically looked at before we can answer that question.

  3. Talya

    Similar to the above question, what is the effect on a newborn who was given antibiotics immediately post birth to avoid any potential infection (since 24 hours had passed from breaking waters to birth)? Vaginal delivery.

    • dokterpebri

      What effect do vaccines have on the microbiome?

    • Allan Walker, MD
      Allan Walker, MD

      A potential newborn whose mother has been give antibiotics or a baby who has been given antibiotics because of the amniotic fluid being discharged when sac broke up to 24 hours before delivery will probably have some disruption in the colonizing of it’s intestine. As stated in this blog a major influence in colonization comes from vaginal colonic bacteria mother provides in a vaginal delivery. The use of antibiotics during pregnancy or after birth is going to disrupt the microbiota. The longer the antibiotic is used and the more broad-spectrum the antibiotic the more likely it is that there is going to be a major disruption. In each of these cases, I think it works to give that mother or child or both a probiotic for a period of about ten days after antibiotics have been used in order to try to balance the health promoting bacteria with potential pathogens. A subsequent blog will discuss the impact of antibiotics used during pregnancy and in the first year of life on the microbiome and in turn it’s influence on health and disease.

  4. Jessie

    For women who have strep B and have to take antibiotics during labor – what affect does this have on the baby’s microbione?

    • Allan Walker, MD
      Allan Walker, MD

      This situation necessitates that antibiotics be given. To try to counteract the effect of antibiotics on the transmission of maternal bacteria from mothers vaginal and intestinal cavities to the young baby mothers can be given a probiotic during their breastfeeding or the baby can be treated with a probiotic. Antibiotics when indicated are necessary. It is just that they are excessively used during the course of pregnancy and the newborn infant’s lifestyle. To counteract the effects of antibiotics on intestinal microbiota probiotics can be used.

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