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Altering Our Gut Bacteria for Autoimmune Disease


I’ve written articles about the microflora (gut bacteria), and how the bacteria in our gut influences our immune system and autoimmunity. That article can be found here. There is strong evidence showing the bacteria in the gut affects autoimmunity, but this article will focus on how bacteria populations may change for the worst.

First off, genetic predisposition and the environment a person lives in are significant factors [1]. We can’t change our genes, but we can influence how our genes present.

Diet is huge.

Proof that our diet influences our gut bacteria is evident in the early days of food introduction in babies. When a baby switches from a liquid based diet (milk or formula) to solid foods, they experience major gut bacteria changes [1]. By simply switching to solid foods, we see a reduction in bifidobacteria and enterobacteria [1].

Not only do we see ages early in life, but as we age, bacteria change too. We tend to see a drop off in bifidobacterial once again [1].

Throughout our lives, as we change our diet, our microflora will change with it. The changes are not always immediate either; varying from 8 weeks to up to 1 year. This is one reason dietary changes wont always provide benefit right away [1].

The fibers we eat (a type called prebiotics) also serve an important role. Various types of fibers will promote growth of beneficial species of bacteria.

Overuse of Antibiotics

Antibiotics are a medical miracle; they’ve transformed modern medicine and saved millions of lives. However, when used inappropriately, they can impair gut health in a huge way.

One of the most important characteristics of normal microbiota is the capacity to compete with infectious pathogens. By removing the good bugs with antibiotics, that may allow the detrimental growth of pathogenic bacteria populations and increase the probability of infection [1].

Constant exposure to antibiotics can allow certain pathogenic (bad) bacteria to acquire genetic resistance, leading to multi-drug resistance [1].

Correcting the effects of antibiotic overuse can take months to even years. Even then, there’s some speculation it may not be restored to the same state as it was before [1]. This is not to say it cannot be restored, but it may end up being different than it used to be.


As mentioned above, when pathogenic (bad) bacteria are allowed to flourish, gut health will suffer. Keeping good bacteria strong will keep bad bacteria at bay.

There is alot of evidence certain bacteria can serve as a trigger for autoimmune disease. Learn more about this topic here.


The gut bacteria, or microbiome plays a huge role in autoimmune disease. Research has shown changes in the gut can directly influence the presence of disease. It works by modulating the immune system and inflammation.

There are various ways the immune system may change for the better or worse. Understanding these relationships is key to treating any gut disease and especially autoimmune disease.


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