The microbiome includes all the microorganisms in your body — bacteria, fungi, parasites, viruses, and arachnids. It covers your skin, respiratory tract, and genital tract, and it is most abundant in your gastrointestinal tract.
We can think of the gastrointestinal tract as a transit system, like the New York City subway. Food, the passengers in this case, goes for a ride along the route, and at certain stops, gets off or is absorbed or excreted in our body. But this is not entirely the correct picture: those “stations” where the passengers, or food, exit are deeply influenced by their environment — in our case, the gut microbiome.
The most important station along the gut transit system is the duodenum, which is 11 to 13 inches long and the first part of the small intestine. This relatively short area does an incredible amount of work to absorb partially digested nutrients. Also, the small intestine is where the microbiome and the immune system play a key role in our overall health.
The key to a robust, healthy microbiome is diversity. Dr. Mark Pimentel, a leading gastroenterologist at UCLA, has conducted some of the most groundbreaking research showing that diversity is the key to a strong immune system. He has also demonstrated how diet, medications, stress, and metabolic conditions all affect our microbiome
Dr. Pimentel eloquently describes the importance of the microbiome’s diversity in his book The Microbiome Connection: “Imagine a vast microbiome city in your small intestine. This city has many inhabitants with different jobs — plumbers, doctors, and sanitation workers among them. As long as the city’s microbiome stays in balance and remains diverse, the city functions well. But if you take an antibiotic and fire all the sanitation workers, the city fills with trash.”
Thank goodness for sanitation workers!
Where Does Candida Fit Into This Overall Microbiome Picture?
Candida is a single-cell fungus, not a bacterium. It seems like bacteria and viruses are the stars among microorganisms; they get all the attention. Maybe it’s because bacteria came on the scene about a billion years before fungi, but scientists have come to respect how, in many ways, fungi can be more robust and resistant to treatment than bacteria.
After all, fungi can change forms, going from a filament shape to a spore that forms a protective coating, which prevents its demise. Our microbiome has evolved to harbor Candida, bacteria, and viruses in harmony as long as there aren’t insults from drugs or dietary factors that alter the immune balance. Candida lines the oral mucosa, the intestinal lining, the vaginal mucosa, and the skin.
What confuses doctors is Candida is considered a normal part of our flora. It is a commensal, meaning that it lives within our bodies without causing harm. So, you start to understand why doctors think Candida causing a disease is farcical. But Candida can become our enemy: if the micro-biome’s diversity is harmed or disrupted by antibiotics, strong proton-pump acid blockers, steroids, or even estrogens in birth control pills. This leads to Candida overgrowth. It is this overgrowth that now causes inflammation or infection in the body.
Doctors who care for AIDS patients, cancer patients who are undergoing or have undergone chemotherapy or radiation, or patients on immunosuppressant drugs know that when the immune system is suppressed, Candida and other opportunistic organisms, especially other fungi and viruses, can cause severe infections. What most doctors struggle with is understanding that Candida overgrowth triggers inflammation in the body, leading to a variety of symptoms.
The Effects Of Diet And Medications On Candida
As mentioned, Candida is a yeast, a simple single-cell organism, and its diet depends on one thing: glucose (sugar). Candida doesn’t need protein or fats to exist. So, the more our sugar intake feeds the Candida that is existing quietly within our system, the more we are feeding the Cookie Monster from Sesame Street.
It’s important to understand that sugar is a carbohydrate, but that doesn’t mean all carbohydrates are bad and cause Candida overgrowth. A metric called glycemic load is based on a food’s carbohydrate content and how much it increases the body’s insulin response, which results from our blood sugar rising.
But what is important to remember is that Candida overgrowth typically occurs in the perfect storm situation, meaning if you have been taking antibiotics for an extended period and you are eating a high-carbohydrate diet, the possibility exists that Candida will jump out of its niche and start to dominate the microbiome.
In addition to diet, many common medications, whether prescribed by a doctor or available over the counter, can contribute to Candida overgrowth and should concern you if you take them regularly. Medications seem to play a significant role in Candida overgrowth. For example, antibiotic quinolones like Cipro (ciprofloxacin) and Levaquin (levofloxacin) are like cluster bombs when they kill bacteria. They don’t just kill the bad guys. They often kill a lot of good guys as well. This is a disaster for the gut microbiome, and I believe it can be avoided.
Excerpted from Conquering Candida: The New 30-day Protocol for Restoring Your Microbiome and Health by Dean Mitchell, MD, with Joelle Mitchell, RD. Reprinted with permission of Healthwise Books. Copyright © 2025.
Dean Mitchell, MD, has been practicing medicine in New York City for over thirty years. He is an adjunct clinical assistant professor at Touro College of Osteopathic Medicine, and the author of Dr. Dean Mitchell’s Allergy and Asthma Solution (Marlow, 2006).
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