Gut Bacteria

#112 with Gastroenterologist Robynne Chutkan, MD and author of the Microbiome Solution

by Mike Mutzel


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Robynne Chutkan, MD

Dr. Robynne Chutkan is member of the faculty at Georgetown Hospital since 1997, Dr Chutkan founded the Digestive Center for Women (DCW) in 2004, an integrative gastroenterology practice that includes nutritional therapy, stress reducing techniques such as meditation, biofeedback and counseling, as well as gastrointestinal procedures like endoscopy, colonoscopy, and video capsule endoscopy. In addition to digestive disorders in women, her clinical areas of interest include alterations in gut bacteria (dysbiosis), inflammatory bowel diseases, irritable bowel syndrome, and food as medicine. She is a recognized leader in gastroenterology both nationally and internationally and Washingtonian magazine has consistently named her one of the top doctors in her field. Board certified in Gastroenterology, Dr Chutkan serves on numerous committees and boards and is actively involved in patient and physician education.

Contact Dr. Chutkan

Related Books

The Microbiome Solution: A Radical New Way to Heal Your Body from the Inside Out

Gutbliss: A 10-Day Plan to Ban Bloat, Flush Toxins, and Dump Your Digestive Baggage

Related Podcast

Show Notes

0:53 Dr. Chutkin’s Digestive Health Journey:  Her medical training embraced the usual pharmaceutical therapies.  She had the good fortune to study at Mt. Sinai where Crohn’s Disease was first discovered and other great breakthroughs were made in gastroenterology.  The emphasis at that time was pharmaceutical rather than diet and lifestyle.  People now want to know not only what their disease is, but why it is.  When she joined the faculty at Georgetown in 1997, and became the first woman in the department.  Women patients lined up to see her with the question “Why?”  She had few answers.  A few of her patients with ulcerative colitis and Crohn’s disease healed themselves through diet, not medication.  Because of her patients, she gradually shifted away from the standard diagnosis/drug therapies

4:54 Healing Through Diet:  Her patients were having great success doing some sort of Paleo or SCD (Specific Carbohydrate Diet).  Not only were their symptoms gone, but Dr. Chutkun could see the difference when doing colonoscopies on her patients.  In her practice now, she focuses on nutritional therapy.  She has found that the changes in inflammation are mediated through microbes.  The standard American diet is pro-inflammatory.  Shifting to an anti-inflammatory diet can effect far more than the gut.  It can help to heal other autoimmune diseases, arthritis, rosacea, eczema, and many other disorders.

7:51 The First Step is Diet and Lifestyle:  Dr. Chutkun believes in the utility of western medicine, though it is over-utilized and often the prescribed cure does not match the problem.  She always uses diet and lifestyle optimization, by trying to get her patients to stop eating junk and start eating plants and by getting them to relax using biofeedback.  Not all people’s illnesses respond to diet and lifestyle changes.  At that point, she can turn to western medicine.  Dr. Chutkun cautions her patients to continue with the diet and lifestyle modifications as a means to assist in healing and, perhaps, lessen the amount of medications needed.  She considers herself an integrative gastroenterologist.

12:47 A Personal Lesson on the Impact of Antibiotics:   Dr. Chutkun had the flu when her daughter, Sydney, was born by C-section.  Newborn Sydney was put into neonatal ICU and tested for infection.  Even though the thorough and invasive testing showed no infection, Sydney was given IV antibiotics just in case. With no gut microbes, her immune system was compromised. Sydney was a very sick child who was given many more antibiotics, which grew in potency as time progressed.  Dr. Chutkun realized that Sydney had had 16 courses of antibiotics by the time she was 2 ½.  By the time she was 3, they stopped going to the doctor for colds/flu.  Dr. Chutkun does not recommend this, but she is a doctor and would know when things got serious.  It took a lot of green vegetables, broth and rest, but Sydney’s immune system eventually did rebound.  Dr. Chutkun says that antibiotics are often prescribed for children to make the parent feel better.  Viral illnesses do not respond to antibiotics and most bacterial illnesses will run their course without antibiotics.  A 5 day treatment of an antibiotic like clindamycin will remove about 1/3 of your gut bacteria.  There is no guarantee that those gut bacteria will come back.  Antibiotics should be used for severe infection, not for just in case or we’re not sure.

20:54 The Development of Super Bugs:  We have a series of super bugs, for which we have no adequate antibiotic.  Infections become super infections because we have over-used antibiotics.  Bacteria are very smart and in the business of survival, so they quickly learn to hack the antibiotic.  This leads to the need for more aggressive antibiotics with more devastating and sometimes permanent damage to your microbes and your immune system.

22:55 Over-prescribing of Antibiotics:  Find a healthcare professional whom you trust and shares your philosophy.  Let them know that you want to avoid antibiotics. Pediatricians prescribe antibiotics for viral non-life threatening illnesses 65% of the time when parents expect it and only 7% when they don’t.  In her book, The Microbiome Solution, Dr. Chutkun has a list of 10 questions to ask your doctor if you are about to be prescribed an antibiotic.  She also provides a list of 10 things to do if you must take antibiotics.

24:05 Today’s Savvy Patient:  We are at a time where many patients know more about the gut microbiome than most gastroenterologists.  Dr. Chutkun believes that most physicians are not aware that 5 days of a broad spectrum antibiotic will kill 1/3 or your gut microbiota.  Nor do they understand why those gut bacteria are important. Some physicians are receptive to the knowledgeable patient and others are not.

27:10 Getting the Gut and Immune System Back on Track:  Dr. Chutkun continues to work with Sydney to improve her microbiota and immune system.  They avoid antibiotics.  It can be unnerving when she spikes a fever, but there have been no positive cultures and everything has run its course.  They do not 100% eliminate anything from her diet, but they do not eat gluten at home.  They eat low gluten, low dairy and low sugar.  Sydney cooks from recipes on  They have trained their pallets to appreciate healthy ingredients and are now turned off by the refined sugar and chemicals in processed foods.  The focus is not on what you eliminate, it is about eating real food with an emphasis on vegetables.

31:51 Good News.  You Can Change Your Gut Microbes:  Much of our health and wellness depends upon our gut microbes.  They are constantly changing.  You are stuck with your genes, but your gut microbes are what change your genes, activate them and deactivate them.  It takes about 30 hours for your microbes to shift from changes in your diet.  Different genes, studies show, are turned off and on with different diets in the same people.  People find that when they cut out the junk processed foods, and shift to a whole foods diet, cravings disappear within a few days.  Many of your cravings are mediated by gut bacteria.  In many ways, our gut microbes drive our behavior.  Different strains of gut bacteria will overthrow others in dominance. It is like Game of Thrones happening in the gut.

35:28 The Mysteries of Sweat and Morning Breath:  Because we sleep with our mouth’s closed, cutting off much of the oxygen, the bacteria in our mouths shift and give us morning breath.  We have two kinds of sweat glands.  Eccrine glands are all over our bodies.  They release water, sweat, that helps to cool our body. It is basically odorless.  We also have the apocrine sweat glands, which are located under our arms, in our groin, and other hairy areas of the body.  They release a milky white substance in response to stress.  The white substance doesn’t smell bad, but bacteria act quickly upon it and that is what makes smelly body odor.

38:13 Your Poop has a Smell and that’s Generally Okay:  During a colonoscopy, Dr. Chutkun can smell the inflammation of Crohn’s disease and ulcerative colitis, even when there is none visible.   No one’s stool smells good, but when it smells really bad, something is off.

40:24 Your Body Gives You Feedback:  You get feedback from your body all the time and we tend to ignore it. How you feel, how your body smells, how your poop smells and its conformation are all important.

41:23 Fecal Matter Transplantation:  Is it Right for You? FMT, or stool transplant, is the ultimate probiotic.  FMT has been done for a long time.  A few years ago a study compared FMT with antibiotics in the treatment of patients with C-diff (clostridium difficile bacterial infection).  We have C-diff in our colons.  We can contract the infection from others who have it, but often we get it from the use of antibiotics, when good guy bacteria are reduced and it becomes dominant, causing active inflammation in the colon. Standard treatment for C-diff has been, you guessed it, antibiotics.  FMT crowds out the C-diff by providing trillions of good guys, healthy bacteria from the stool of a healthy person who meets very stringent criteria.  The study found that the FMT treatment was so profoundly more successful that they had to stop the study because it was unethical not to treat the patients with FMT.

44:35 Fecal/Stool Transplantation for Other Illnesses:  With the great success against C-diff, people began to question whether FMT would also work with ulcerative colitis or Crohn’s disease.  The difference is that C-diff is an active infection that can be cured with one stool transplant.  Autoimmune diseases are diseases, chronic illnesses.  FMT can help with inflammatory bowel diseases, but it takes frequent regular FMT treatments. It is a long term commitment and there are risks, like risk of infection or other unknown risks from undetected disease or from transferring the bacterial genome of one person to another. About 50% of the stool is bacteria, but there are toxins, viruses and other things in your stool that your body is eliminating.  In addition, you may not be able to get a medical professional to do the transfer for these conditions, though it can be done at home.  In her book, Dr. Chutkun outlines the risk/benefit ratio.

48:52 Dr. Chutkun’s Morning Routine:  She aspires to get up early.   Dr. Chutkun starts her day with a smoothie containing things like kale and coconut water. She then steel cut oats with raisins and walnuts, or, if she thinks she may not get to have lunch, she may have salmon and eggs.  She tries to work out in the morning or sometime during the day, perhaps weights, yoga or a run.  Sweating a little every day is important.  She does more of a rinse than a soapy scrub in the shower. As she says, “Live Dirty, Eat Clean”.  She also makes quite meditation time for herself in the morning.

52:13 One Nutrient, Herb, Botanical or Food Substance She Cannot Live Without:   Dr. Chutkun says that her one thing is the leafy green.  She doesn’t love to eat leafy greens, but she feels much better when she eats them and can tell the difference in how she smells and in her bowel movements. They are the most under-represented food in the American diet.  Spinach is her number one choice.  It is great in a smoothie.  It makes it less sweet, but not bitter.  It is full of iron, calcium, and many other micronutrients.

54:07 One Health Policy Issue for America:  Access to healthcare does not mean access to insurance.  We need to educate people of all ages how to take care of themselves, not just how to get your hospital bill or prescription paid. We need to teach people how to eat and the importance of exercise, promoting health literacy.  Most people do not understand how to care for themselves.  People need to understand the connection between how they are living and how they are feeling.  This disconnect and inability to proactively maintain health runs the full socio-economic spectrum.  It should be a health policy issue.



  1. Great interview Mike!!! 100% agree with Dr.Robynne Chutkan… This country needs nutritional literacy !!!!!
    How wonderful if several of you health practitioners could join forces & get financial backing to create a country wide 1/2 hour power packed informational intro into the food & health connection on TV, Internet & billboards . I say 1/2 hour to keep interest with the non believers to at least hear ” some” that hopefully sticks & they can process as the days go by.

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