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The Questions I Get Asked Most About The Microbiome: A Gastroenterologist Explains

Robynne Chutkan, M.D., FASGE
August 27, 2015
Photo by Michael Benabib
August 27, 2015

It seems like every week there's a new article out on the microbiome. As an integrative gastroenterologist and founder of the Digestive Center for Women, I'm asked about the microbiome all the time. So to clear up some confusion, I’m sharing the 10 questions I hear most often, and what I tell my patients.

1. So, what exactly is the microbiome?

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The word “microbiome” refers to all the bacteria, viruses, and fungi that live in or on your body. That's over 100 trillion microbes in total.

Your unique microbial footprint, which develops over your lifetime, can reveal a lot about you: your parents’ health, how and where you were born, what you’ve eaten, where you’ve lived, your occupation, personal hygiene, past infections, exposure to chemicals and toxins, medications and hormone levels. The mix is so distinctive that your microbiome is actually a more accurate identifier of you than your DNA.

2. Why is it so important?

Think of microbes as worker bees that perform most of the important functions in your body. They help to digest your food, train your immune system to distinguish between friend and foe, turn your genes on and off, synthesize important vitamins that your body can’t make on its own, aid in detoxification, neutralize cancer-causing compounds, plus many other things.

3. What are some of the problems associated with an unhealthy microbiome?

Damage to the microbiome — what we call dysbiosis — is the root cause of a broad range of diseases. That includes gastrointestinal disorders like Crohn’s, ulcerative colitis and irritable bowel syndrome, but also autoimmune diseases like thyroid disorders, multiple sclerosis, and type-1 diabetes.

Studies have demonstrated an altered microbiome in many children with autism. Research has also shown that anxiety and obesity can both be induced in germ-free mice by transferring microbes from mice who are anxious or obese.

4. What can I do to support my microbiome health?

  • Avoid antibiotics, unless absolutely necessary.
  • Eat lots of fibrous plants.
  • Skip the hand sanitizer.
  • Get a pet. We just got a puppy and he’s already helping to rewild the whole family with lots of dirt and licks!
  • Plant a garden. You’ll get your hands dirty and be able to eat the veggies you grow!

5. What should I be eating for a healthy microbiome?

Indigestible plant fiber. It’s the preferred food of the healthy bacteria living in our gut. We should be eating foods that are high in inulin — a form of soluble dietary fiber — like leeks, garlic, onion, artichokes, asparagus, lentils and oats. Fermented foods, like sauerkraut, kimchi and pickles, are also great because they act as a prebiotic, meaning they provide food for our gut bacteria, and the fermentation process also produces additional live bacteria.

6. How do lifestyle choices impact our microbiome?

Microbial disruptors are everywhere: in the food we eat, the water we drink, the medicine we take, the products we use on our bodies and in our homes. Even our thoughts can be a threat: stress wreaks havoc on the microbiome.

We spend a lot of time scrubbing away healthy microbes on our skin with too much anti-bacterial products, and using hand sanitizers that contain the microbial disruptor triclosan. Foods full of chemicals and artificial sweeteners can also be harmful to gut bacteria.

7. How do I know when I need to take an antibiotic?

Antibiotics are one of the most frequently prescribed class of drugs, and it can be confusing trying to figure out when they’re truly necessary, versus when we can skip them and still be OK.

To help decide, here are some questions I recommend asking your health care provider:

  • Is the antibiotic prescribed for me absolutely necessary?
  • Is it being used to treat an actual infection, or to prevent one?
  • What would be the natural course of my illness if I didn’t take an antibiotic?
  • Is there a narrow-spectrum antibiotic such as penicillin I can take instead of the more powerful broad-spectrum antibiotic I’ve been prescribed?
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8. Do I need to take a probiotic?

The right probiotic may offer real promise for people with a damaged microbiome — but not all probiotics are created equal. It’s important to take the correct strains of bacteria for the condition you’re trying to treat, and to make sure that they’re present in adequate amounts. I recommend discussing this with your doctor first. My book, The Microbiome Solution, also explains how to pick the right probiotic, and offers a detailed list of which conditions are most likely to be helped by each.

9. Will stool transplants soon become mainstream?

Absolutely! Once you get over the yuck factor, it’s clear that when it comes to gut bacteria, going straight to the source makes perfect sense.

Fecal microbiome transplant, or FMT, has already proven1 to be the most effective therapy for certain types of intestinal infections, like Clostridium difficile colitis.

FMT isn’t without risk though, so it’s important to weigh the risks and benefits before deciding if this therapy is right for you.

10. What's the biggest threat to our microbiome?

The overuse of antibiotics and our processed, nutrient-poor diet. We’re killing off our microbes with unnecessary antibiotics, and then starving the ones that remain by not feeding them the right stuff.

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Robynne Chutkan, M.D., FASGE
Robynne Chutkan, M.D., FASGE

Robynne Chutkan, M.D., FASGE, is the author of the recently published book The Microbiome Solution (Penguin 2015) and Gutbliss (Penguin 2013). She received her bachelor’s degree from Yale University and her medical degree from Columbia College of Physicians and Surgeons. Board certified in gastroenterology, Robynne has been on the faculty at Georgetown University Hospital in Washington DC since 1997. In 2004 she founded the Digestive Center for Women, an integrative practice that incorporates nutritional optimization, exercise physiology, biofeedback and stress reduction as part of the therapeutic approach to digestive disorders.

A regular guest on the Dr. Oz Show, Robynne is also a member of the medical advisory board for the show. She has made national appearances on CBS This Morning, The Today Show, The Early Show, and The Doctors and is frequently interviewed as a medical expert for the Washington Post and women's health magazines.

Robynne is the founder of – a digestive wellness space that provides science-based, integrative GI information and products with a proven track record for improving digestive health. On a personal note, she is an avid runner and snowboarder and enjoys Vinyasa yoga. She is passionate about helping her patients live not just longer, but better lives.