Early Life Exposure to Gut Bacteria: The Timing Matters

I’ve read before that there is a possibility that the timing and order of exposure to various bacteria at birth will ultimately make a huge difference in the final makeup of the microbiota. I just finished reading a pretty telling paper[i] on this that is definitely worth sharing.

These researchers, from the University of Alberta, inoculated genetically identical infant mice in sequence with two “seed communities” (bacteria from adult mice), “A” first and then “B,” or vice versa. In a second experiment, they inoculated the pups with a cocktail of 4 bacterial strains and a seed community.  In summary, they discovered that, “…colonization order influenced both the outcome of community assembly and the ecological success of individual colonizers.”  Whatever was introduced first had the strongest influence on the ultimate composition of the bacterial microbiome when the pups reached adulthood.

At this time, scientists believe that genetics, diet, environment, lifestyle and psychological are responsible for only 30% of the variation found in the microbiomes of humans.  How this was determined, I don’t know but…if true, that leaves a gaping hole in our knowledge of how individual microbiomes develop.

We already know that disruption of the early, developing microbiota is associated with chronic disease.  I wrote about this just last week, in regards to autism, for example.  It is pretty scary how many things can go wrong  in the creation of the biome, leading to a life time of health issues. Research like this is proving more and more that what we come in contact with starting at birth is permanent.  Looking at the bright side though for a moment, says the lead researcher on this study, “Having long-term persistence of microbes when they colonize in the gut early in life means that a health-promoting biome could potentially be established by introducing beneficial bacteria straight after birth.”[ii]

But what about those who were not fortunate enough to be introduced to the good stuff very early in life?  In my last blog post, I wrote about those Israeli studies on probiotics, one of which suggests that they may not colonize some people well, as some microbiomes appear more resistant to change than others.

From the conclusion of the paper:

“Given the importance of historical contingency for gut microbiota assembly, clinical and medical interventions early in life (e.g. antibiotics, C-sections, formula feeding) are likely to have longer lasting consequences, driving not only inter-individual differences but potentially also aberrant patterns of colonization that could potentially be prevented by an adjustment of clinical practices to avoid priority effects….As the understanding of the health-promoting attributes of gut bacteria continues, it will be important to evaluate how they can be established more permanently. Once assembled, the gut microbiota is extremely resilient to therapeutic modulations, dietary changes and moderate doses of antibiotics, and colonization resistance constitutes a major barrier to introducing beneficial microbes….More permanent persistence can be achieved if microbes are introduced early in life. In addition, the findings demonstrated that early introduction of just a few species can divert the entire trajectory of the microbiota. If such shifts can be introduced reproducibly, then early colonizers could be selected to deliberately control microbiome assembly to obtain predictable outcomes….priority effects will favor bacteria that are introduced first, thereby providing an opportunity to potentially prevent aberrant microbiomes, and by doing so, dysbiosis-related diseases.”

My mentor, the functional medicine guru, Dr. Sidney Baker, used to tell me that, “The hardest thing in the world to fix is bad gut flora.”  He most certainly hit the nail on the head there.  Still, considering that I have seen diet work, helminths work, high dose probiotics work, etc., I have to believe that we have at least SOME control – some ability to heal the microbiota.


[i] Inés Martínez, Maria X Maldonado-Gomez, João Carlos Gomes-Neto, Hatem Kittana, Hua Ding, Robert Schmaltz, Payal Joglekar, Roberto Jiménez Cardona, Nathan L Marsteller, Steven W Kembel, Andrew K Benson, Daniel A Peterson, Amanda E Ramer-Tait, Jens Walter. Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly. eLife, 2018; 7 DOI: 10.7554/eLife.36521

[ii] https://www.sciencedaily.com/releases/2018/09/180918114441.htm

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