We all take antibiotics. Staph infections, Strep throat, etc. and they get the job done. Within two or three days, sometimes a week, you’re cured and infection-free. But is that really best for us?

Microbiomes are what make us so unique and individual. In fact, we have more bacteria cells that human cells in a 10 to 1 ratio. We have different microbiomes for different parts of the body; our mouth has a different microbiome than our skin microbiome which has a different microbiome than our gut microbiome. We can influence our microbiomes by what we eat, or rather they influence us based on what we eat. As part of an evolutionary benefit, our microbiomes adapt to newly introduced food within days, which we previously thought took years to change. In other words, if you didn’t eat carrots for three years and sporadically ate carrots one day, your microbiome would activate bacteria that was previously dormant to digest the carrots within days. Think for a moment: a bacteria your body hadn’t made in three years is suddenly recolonized and active in helping you digest within a few days. It’s truly amazing! However, the rest depends on how you were born.

If you were vaginally born, your first encounter with bacteria (bacteria from the placenta is still controversial as to whether babies acquire some of their intestinal bacteria before birth) was in the birth canal, which is exactly where you get your microbiota colonies from. If you were Cesarean born, you might find that you have a higher chance of chronic conditions like asthma or Celiac’s disease simply because you received your mother’s skin microbiome instead of her vaginal microbiome. If you were not breast fed, you are more likely to contract similar conditions because breast milk contains nutrients that cannot be broken down by your digestive track. Rather, they surpass your digestive track and nourish microbiota. Formulas were unaware of this and therefore did not contain everything necessary for your microbiota health, but formulas have been making adaptions to fully mimic these qualities of breast milk.

Say you did all of the right things: you eat whole, unprocessed foods that can nourish your microbiome, you were vaginally born and you were breastfed. It’s completely possible that you have a wonderful, flourishing microbiome. However, you likely do not.  Processed foods do not contain enough prebiotic nutrients (food for microbes). Although one associates Western civilization with nutrition and health, we are actually considered “impoverished” in the world of microbiomes.

The big problem with the Western diet is that it doesn’t feed the gut, only the upper G I. All the food has been processed to be readily absorbed, leaving nothing for the lower G I. But it turns out that one of the keys to health is fermentation in the large intestine. Stephen O’Keefe

Those with no contact to the Western world and its medicine, pesticides, sterility and processed foods have a rich and diverse microbiome. Not to mention the growth hormone in cows, which changes the microbiota for a hastened growth as well as the metabolism of the liver. They even stimulate an increase in body fat. Western medicine, however, affects us in less visible manner. Our antibiotics are too strong for our own good; they destroy the pathogenic bacteria, yes, but they also destroy the health-promoting ones. Therefore, some argue that we should improve our diagnostics to prescribe fewer and narrow-spectrum antibiotics to kill the harmful bacteria while reducing the collateral damage. (Dr. Blaser) These heavy duty antibiotics not only destroy the healthy, diverse microbiota, but have a permanent effect if used for a second course; the microbiome will bounce back but it will not be able to return to its original state. In addition to this, antibiotics have been trying to eliminate H. pylori since 1983 when they found it could lead to stomach cancer or peptic ulcers, when in fact its disappearance could be contributing to acid reflux and obesity. Due to our continual efforts to eliminate H. pylori from the microbiome, it is unlikely that we will see it in upcoming microbiomes due to antibiotics, and “each generation is [already] passing on fewer of this microbes.” Prevotella, for example, is a gut bacteria extremely difficult to find in Western society but relatively common in underdeveloped countries. One woman had unusually high levels of this bacteria in her microbiome, but after one course of antibiotics for oral surgery, her wonderful microbiome was reduced to the average American bacterial standards. 

One of the more striking results from the sequencing of my microbiome was the impact of a single course of antibiotics on my gut community. My dentist had put me on a course of Amoxicillin as a precaution before oral surgery. (Without prophylactic antibiotics, of course, surgery would be considerably more dangerous.) Within a week, my impressively non-Western “alpha diversity” — a measure of the microbial diversity in my gut — had plummeted and come to look very much like the American average. My (possibly) healthy levels of prevotella had also disappeared, to be replaced by a spike in bacteroides (much more common in the West) and an alarming bloom of proteobacteria, a phylum that includes a great many weedy and pathogenic characters, including E. coli and salmonella. What had appeared to be a pretty healthy, diversified gut was now raising expressions of concern among the microbiologists who looked at my data.

Her bacterial composition will return to something that somewhat resembles her original microbiome, but every course after that will decrease potential microbial recovery and also decrease invasion resistance (keeps pathogens from gaining a toehold by occupying potential niches or otherwise rendering the environment inhospitable to foreigners e.g. H. pylori regulates stomach acid to make the environment unfavorable to other bacteria that wants to colonize; vaginal pH is kept low so the environment is too acidic for foreign bacteria to colonize, etc.) So the next time you take an antibiotic, ask yourself: what am I doing to my microbiome?