Why Does Our Microbiome Undergo an Unhealthy Shift with Age?

In the last several blogs we looked at the research on the human microbiome which corresponds to the onset of the many diseases that become more prevalent with age.  Keep in mind “with age” does not mean after the age of 60-70 but rather gradually beginning between age 30-40.

This shift is hallmarked by the diminishing quantity of a few key species led by Akkermansia muciniphila and Clostridium butyricum, species that up until recently have not been available in supplemental form.  Early studies which restored these species with either fecal medical transplant or supplementation have shown improvements in several disorders related to increasing inflammation such as type two diabetes.

The last question we need to address is perhaps why do these species diminish with age.  Understanding that has implications regarding preventing age related inflammation and disease.  The known and suspected causes include:

  • Caesarean birth
  • Formula fed versus nursed
  • Early life antibiotic use
  • Antibiotic use
  • Diet
  • Toxic environmental exposures

In terms of which factor has the most detrimental effect, early life and any antibiotic use seems to be the greatest impact.  The difference between these two are discussed below:

Caesarean birth

Passage through the birth canal provides the initial seeding of our microbiome so a normal vaginal birth is an important step in setting our microbiome.  This is complicated by the fact that the makeup of the mother’s microbiome will be the composition that is shared with the infant.  Mothers with highly altered microbiomes related to any of the above list of causes can only share a less than ideal microbiome.

Formula fed versus nursed

The second support for building of the infants microbiome is through the mother’s milk during nursing.  Complications that prevent or limit nursing limit the transfer of microbes to the infant developing their microbiome.  The above comments regarding a less than ideal maternal microbiome will also affect this source of infant microbes.

Early life antibiotic use

It is thought that the main growth of the seeding microbes from the mother into a full, healthy infant microbiome occurs primarily in the first 3 years of life.  Antibiotic use during that interval as is common with reoccurring ear infections is particularly disrupting.

Any antibiotic use

Antibiotics generally have a non-specific effect meaning that while they may target an infection in the lung, they disrupt all of the microbes in our system including the healthy gut microbiome.  It has long been the misconception that the normal microbiome simply repopulates on its own after antibiotic use, but this is a misguided assumption.  While that may happen in a limited number of persons, most will suffer some ongoing degree of imbalance in the normal microbiome after antibiotic use.  This problem is called dysbiosis.  Supplementing with standard probiotics or foods such as yogurt attempts to restore only a limited number of species and not the keystone species we now know are paramount.


The relationship between diet and the health of the microbiome is simple yet complex.  The simplicity is that the microbes “share” our food with us.  An unhealthy diet as is the norm in the developed world is unhealthy for the microbiome just as it is for us.  The microbiome needs high quality fermentable fiber which they ferment into short chained fatty acids, signaling molecules which help reduce inflammation, maintain a healthy gut barrier and several other important functions. The microbiome also metabolizes phytonutrients in our diet converting them into disease preventing metabolites that we absorb.  Both fermentable fiber and phytonutrients such as polyphenols are largely absent in highly processed food.

Toxic environmental exposures

There are thousands of chemicals approved for use in the U.S.  Several hundred are approved for use in food.  While they are tested for relatively large, short-term exposure, chronic, low level exposure as occurs is not.  Others not approved for use in food find their way into food such as herbicide and pesticide residues used in agriculture.  

Glyphosate, the primary herbicide used in food agriculture has been shown to disrupt the shikimate metabolic pathway, a major metabolic pathway used by over 50% of the human microbiome. (1)  When these microbes cannot nourish through metabolism, they perish – dysbiosis.

So, a lot said about why and prevention.  We have no control over the early life factors that should have developed our healthy microbiome.  We do however, have a significant amount of influence over that for our offspring.  At times, antibiotic use may be necessary and it is important to appreciate the impact that will have on the microbiome and take the proper steps to rehabilitate this population.

Diet and the majority of environmental exposure we have great control over.  Eating a diverse diet full of colorful fruits and vegetables which supply fermentable fiber and phytonutrients is a must.  Eating organic produce is the best protection to minimize food based chemical exposure as those foods are certified free of chemical treatment. 

The other chemicals that we are exposed to through air and many other pathways should be adequately eliminated by a strong population of liver enzymes called P450 enzymes.  Those enzymes we must constantly regenerate, something done by many of the same phytonutrients we share with our microbiome that should come in healthy food.  It is literally that feeding us well, feeds them; and feeding them well, feeds us.  That seems to be the natural plan.

Puigbo et al.  DOES GLYPHOSATE AFFECT THE HUMAN MICROBIOTA?  Life (Basel), 2022 May;12(5):707.