Early Life Biome Depletion and a Lifetime of Health Issues

Yesterday, I found a great complimentary article[i] to my Tuesday post regarding lack of exposure to commensal organisms and the development of asthma in children.  This is another “it’s biome depletion not the darn ‘hygiene hypothesis’” kind of story!

Background information:   babies are exposed to their first major onslaught of commensal organisms during the birth process. In an ideal world, the breast milk they are then fed for those first crucial few months leads to the development of a robust infant microbiome (consisting mainly of bifidobacteria and lacobacilli) with the oligosaccharides (prebiotics) in the milk being crucial for the developing biome.

Using a mouse model, researchers at the Institut Pasteur and Inserm looked at what happens in infants when solid food is first introduced and it’s pretty amazing.

Apparently, when solid food is introduced – typically between 3 and 6 months in humans (equivalent to two to four weeks for mice) – the number of bacteria increases 10- to 100-fold, and this rapid increase “…triggers an intense immune response,” which these scientists call a “weaning reaction.”[ii] This reaction occurs at a very critical time in immune development.

This rapid change in the microbiota (which of course also includes a major increase in bacterial metabolites) and the subsequent immune response (which consists of a huge increase in regulatory cytokines, which are the off-switch to the inflammatory system) is critical to normal immune development. When the scientists treated the infant mice with antibiotics during this crucial time window, disrupting this weaning reaction, they found that the mice were far more likely to develop inflammatory disorders, including allergies, colon cancer and inflammatory bowel disease.  Thus, they conclude that if the microbiome is decimated by antibiotics very early in life, the weaning reaction will fail to occur…and since the production of regulatory cells during the weaning reaction requires bacterial metabolites, like short chain fatty acids, the infant is set up for low levels of Treg cells and an abnormal immune response throughout life.

Says Dr. Gerard Eberl, the lead author of the study, “This is what is known as pathogenic imprinting…that is to say, events occurring in early childhood determine future susceptibility to inflammatory disorders.”

During the many years I’ve worked as a nutritionist, I have noted that the single most common thread in the children I’ve seen – many of whom had autism and/or ADHD as well as gastrointestinal issues – was early introduction of antibiotics.  (My own son, Alex, who is autistic and has a history of major immune issues and inflammatory bowel disease) was put on 5 days of IV antibiotics starting at 36 hours old, during which time he ceased to breast feed and I was forced by the hospital staff to start him on formula.) I’ve read many articles over the years exploring the connection of early antibiotics to later immune issues and finally, 25 years later, it looks like scientists have finally discovered the mechanism of action.  As sometimes antibiotics cannot be avoided, with all my heart, I hope this rapidly leads to a therapeutic solution.


[i] https://www.eurekalert.org/pub_releases/2019-03/ip-doa031919.php

[ii] Al Nabhani, Z, et. al. A weaning reaction to microbiota is required for resistance to immunopathologies in the adult.  Immunity. 2019.  DOI:https://doi.org/10.1016/j.immuni.2019.02.014

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