(By Grace Rollins, MS, LAc) Antibiotics may have saved my life as an infant, when I had an infection in my neck that necessitated surgery. After that, probably much like many of you, I was on antibiotics as a kid every year, if not multiple times, for strep throat or bronchitis. And in a way that had nothing to do with fighting infections or saving my life, I also consumed antibiotics as part of my conventional American, fast-food diet, since approximately 70% of our antibiotics are used to accelerate growth in livestock and end up contaminating our meat and farmed fish.

Sadly, the unnecessary antibiotic saga continued: while in college, I contracted a serious gastrointestinal infection while traveling abroad, and underwent a course of a powerful antibiotic called Cipro (part of a class known for major side effects and now partially banned in Europe). After it didn’t help my infection symptoms at all, the doctor decided to run a simple stool test that determined I had a parasitic protozoan called Giardia, not a bacterium susceptible to antibiotics (a proper, if belated, diagnosis that finally led to a proper treatment).

As with many young people who grow up on a diet of antibiotics (and are exposed to innumerable other microbiome disruptors, like pesticides, herbicides and processed food additives), I was plagued with allergies and acne from the time of puberty well into adulthood. Becoming a vegan in those college years opened my eyes to a lot of new foods, but since I was still also eating a lot of junk, including artificial sweeteners, sugar and conventional grains laced with pesticides, my symptoms stayed pretty much the same. The allergies and congestion were just a way of life for me. But eventually, sick of drenching my face with benzoyl peroxide every night, after I got out of college I finally saw a dermatologist about the acne. The doctor immediately prescribed an oral and a topical antibiotic for me to use daily... indefinitely.

My breakfast at a budget hotel in Tokyo

Looking back, I’m just happy I didn’t get taken to a dermatologist when I was younger, which would have started me on that regimen even earlier in life. I stayed on those antibiotics for at least a year. It made me UV-light sensitive (I was supposed to stay out of the sun) and gave me dry eyes. It wasn’t until I started going to an acupuncturist and he dropped a couple of gentle hints about the harm it might be doing me, that I decided to get off the stuff. That was actually the last antibiotic I took, over 20 years ago.

Those childhood and young adult experiences with antibiotics are all too common, as were the health issues I experienced of allergies, asthma, skin issues, struggles with weight, and susceptibility to upper respiratory infections. I also had immediate family members with fibromyalgia, obesity, alcoholism, depression, Hashimoto’s thyroiditis, multiple food sensitivities, asthma, environmental allergies and more. What I know now is that all of these issues have one glaring thing in common: disruptions in the body’s microbiome.

I went to high school and started college in the 90s when microbiome research was just a tiny blip on the radar. What was really hot at the time was genetics. In high school I was very interested in molecular biology and had a job for a few months at the Human Genome Project office in Boston. The trending idea in those days was that mapping the genome completely would lead to huge breakthroughs in medical science. It turned out to be a little anticlimactic, though. As soon as we learned more about the genome, we began to realize that it’s largely about how the environment interacts with the existing genes that turns their functions on and off– that is, epi-genetics. This, in a way, put everything back at square one, implicating the things we already knew were effective ways of lowering risk factors for all major diseases– adequate sleep, regular exercise, managing stress, curtailing pollution, and healthy food choices. Sorry, no silver bullet there.

However, the expansion of the field of molecular biology also opened up a new frontier of research into the human microbiome. This is where things have actually become pretty hot and exciting since the early 2000s. Researchers are finding it’s not just about how your habits and food interact with your genes, but also about how they interact with your germs. And how those germs interact with your genes. And so forth.

Based on the emerging science, we now know the status of the microbiome to be influential, if not pivotal, to many common health conditions. This includes nuisances like acne, eczema and allergies, for sure, but also includes obesity, cardiovascular disease, IBS and GERD, autoimmune diseases, and even neurodegenerative diseases like Alzheimer’s and Parkinson’s. Virtually all of the prevalent, stubborn, treatment-resistant health conditions in our day and age seem to have at least some sort of tie-in to the health of the microbiome. Which makes sense, in a way, because the human microbiome has never been so disrupted, so topsy-turvy, as it has become in our current age, thanks to the ubiquity of antibiotics, chemical disruptors, refined and processed food, and many other factors that have changed our evolutionary, ancestral microbiome into an utter wildcard.

*Another budget hotel breakfast in Japan*

Around the time I began to study acupuncture and nutrition in the early 2000s, I started to pay more attention to this concept and what we could do to repair my disrupted microbiome. Focusing in on natural, traditional foods, dialing in my lifestyle practices (and getting regular acupuncture) eventually cleared up my skin, regulated my weight and minimized my seasonal allergies. After that I even stopped catching the flu and rarely caught anything beyond a mild cold, let alone a more serious infection. Fun fact about me: the only sick day I’ve had to take in my 15+ years as an acupuncturist was the time I caught COVID last summer, from which I fully recovered after four days, without complication.

Researchers are even finding that the susceptibility to COVID infection, and the ability to recover afterwards, is highly linked to the health of the individual’s microbiome. COVID, in turn, may stimulate pathological changes in the microbiome that can later complicate matters. (See a few recent research citations below.) Another fun fact about me: in spite of working in close quarters with patients throughout the pandemic, the only time I caught COVID was while on vacation in Mexico, when I was already suffering from bacterial food poisoning and my gut biome had been unbalanced for a few days (I was at a dinner party with someone who the next day tested positive). I could just be lucky, of course, but given my track record over the past decades and what the latest research is saying, it’s also highly likely that my current microbiome confers me some protection against viral infection. COVID just happened to catch my gut on a bad day, after the classic bozo move of eating contaminated street food.

I’m not saying all of this to boast– I don’t take my current health for granted, and we never know what’s around the corner for us. I also know my current microbes are far from perfection, which may be but a pipe dream after the abuse they went through (and who knows what they suffered in the generations before I was born and innoculated). However I do know what a contrast my current state of disease resistance is to what many people I know go through on a regular basis. And I also know how different my diet and lifestyle practices are from those of many other Americans.

There is a great deal that still remains a mystery about the microbiome. It’s hugely intricate and complex in and of itself– when we try to understand how it interacts with the substances we consume, the gut lining and the rest of the systems in the human body, it becomes infinitely more complex. Mending our microbiome is not always a simple process, but we do know a lot about what can be done to promote better balance. My own experience, even after my antibiotic-enriched early life, holds out hope that this is possible for others to achieve in a way that has a meaningful impact on health.

*Holiday Inn breakfast buffet in the US*

As an afterword, I’ll mention that while the microbiome of just about everyone outside of remote hunter-gatherer villagers is a complete departure from that of our ancestors, the microbiome of the average American scores even a few ticks worse, and it's likely related to our country's high rates of obesity and chronic disease. I recently got back from Japan, where I snapped pictures of a couple of the typical breakfasts I received in the hotels I stayed in (see the photos above). This was nothing unusual compared to my past experiences in Japan.
There, even at a low-budget business hotel, the breakfast buffets usually offer hand-made dishes that include a wide variety of fresh, cooked and pickled vegetables, multiple types of seaweed, fermented soy like miso soup and natto, fresh fish, fresh eggs, rice and fruit, in addition to the common Western food options like toast, pastries, sweets and processed meat. I'm not saying all Japanese folks eat like monks, but please compare and contrast these everyday offerings to what you might find available at a budget hotel in the US, or even a higher end one.

Some of what we have to do as Americans to repair our public health is really no mystery, but it takes wresting our awareness back from commercial interests that have trained us to harbor certain attitudes towards food, leisure activity and life's priorities. Opening our eyes to the practices of our ancestors, and to traditional practices in other cultures, is a great place to start.

Join me for more discussion on this topic in my class Mending the Microbiome, live or on Zoom, on April 26, 2023 (or sign up by that date to receive the recording link).

Sarkar, A., Harty, S., Moeller, A. H., Klein, S. L., Erdman, S. E., Friston, K. J., & Carmody, R. N. (2021). The gut microbiome as a biomarker of differential susceptibility to SARS-CoV-2. Trends in molecular medicine, 27(12), 1115–1134. https://doi.org/10.1016/j.molmed.2021.09.009

De, R., & Dutta, S. (2022). Role of the Microbiome in the Pathogenesis of COVID-19. Frontiers in cellular and infection microbiology, 12, 736397. https://doi.org/10.3389/fcimb.2022.736397

Yamamoto, S., Saito, M., Tamura, A., Prawisuda, D., Mizutani, T., & Yotsuyanagi, H. (2021). The human microbiome and COVID-19: A systematic review. PloS one, 16(6), e0253293. https://doi.org/10.1371/journal.pone.0253293

Haran, J. P., Bradley, E., Zeamer, A. L., Cincotta, L., Salive, M. C., Dutta, P., Mutaawe, S., Anya, O., Meza-Segura, M., Moormann, A. M., Ward, D. V., McCormick, B. A., & Bucci, V. (2021). Inflammation-type dysbiosis of the oral microbiome associates with the duration of COVID-19 symptoms and long COVID. JCI insight, 6(20), e152346. https://doi.org/10.1172/jci.insight.152346

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