Research over the past few decades has revealed that we humans host a bewildering variety of invisible creatures, our microbiota. We can almost envision the collective genome of all these microbes, the microbiome, as a sort of second genome for human individuals. Unlike our human genome, the microbiome can be altered based on our diet and factors such as whether we have taken antibiotics.

The exact balance of microbes in our intestinal ecology varies from one person to another. It may be time to jettison the old notion that all microbes are “germs” that will do us harm and learn how to appreciate microbial diversity. How does our microbiota influence our health?

Where Do the Microbes Come From?

How does a baby acquire its intestinal inhabitants? How do they change throughout the life cycle? The microbiota has significant effects on behavior, cognition and the immune system, as well as digestive well-being. Since the health of our microbiota is intimately linked to our own health, how should we be caring for it?

Can You Reprogram Your Microbiota?

Doctors begin to suspect that imbalances in the microbiota may be at the root of serious problems such as inflammatory bowel disease. The classic example of microbiota imbalance causing digestive disease is C diff infection. This diarrheal disease often occurs when many of the gut microbes are wiped out by antibiotic treatment. As a result, Clostridium difficile has an open niche to exploit. Once firmly established, these bacteria can be hard to eradicate. Recently, doctors have resorted to fecal microbiota transplant from healthy donors to treat serious C diff infections.

Taking Care of Our Microbiota:

How do we take care of our microbiota so it can take good care of us? One approach is to make sure we eat what the microbiota wants. Mostly, that means a high-fiber plant-based diet with relatively little red meat or sugar. In addition, fermented foods can be helpful. When we consume foods with live bacteria such as kombucha, kimchi, kefir, sauerkraut, real pickles or yogurt, we are getting living probiotics that may bolster the microbiota. What else should you be doing?

This Week’s Guests:

Justin Sonnenburg, PhD, is currently an associate professor in the Department of Microbiology and Immunology at the Stanford School of Medicine.

Erica Sonnenburg, PhD, is currently a senior research scientist at the Stanford University School of Medicine in the Department of Microbiology and Immunology, where she studies the role of diet on the human intestinal microbiota.

Drs. Sonnenburg are co-authors of The Good Gut: Taking Control of Your Weight, Your Mood, and Your Long-Term Health.


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  1. barbara

    I am interested in diet (food) on the microbial; i.e. dietary changes that are beneficial to the microbiome. Would like basic information on how our diet affects the microbiome.

  2. Carolyn H.

    A wonderful book suggestion: “Never Home Alone” by Rob Dunn. He explains in language we can all understand about the living things in our homes and bodies that affect us in so many ways. So interesting it is a hard book to put down!

    • Terry Graedon

      Tune in March 16, 2019. Rob Dunn will be answering questions on The People’s Pharmacy radio show!

  3. Rich
    Houghton MI

    Fecal microbiota transplant is slow to help with inflammatory bowel disease because it is caused mainly by trauma, something I haven’t heard a lot about on your show. It would be awesome to hear what the effect of trauma is on the microbiota. Any disease which has an inflammation component will be mainly caused by our body being stuck in stress states. Talk to Stephen Porges, Robert Scaer, or Vincent Felitti for expert insight on diseases that have strong trauma/toxic stress contribution.

  4. David F.
    Wheaton Illinois

    How wonderful would it be to have a bottle of pills full of antibodies specific for C. diff?
    IGY Immune Technologies & Life Sciences can produce it. We need an impact investor to partner with us.

  5. Daniel

    Are there studies linking human hormonal and other bio-regulator levels to microbiota diversity? The states of stress, fertility, abundance, age affects so much human biochemistry is there evidence these factors influence one’s microbiota?

  6. Matthew

    What are the effects of drugs such as nexium on the microbiota? Long term?

  7. Daniel

    Is there evidence that microbiota alters seasonally? Primitive man’s diet was totally reliant on seasonal produce. Winter diet in particular would be hugely different from a harvest season diet. Seems logical certain micro-organisms in a microbiota would ebb and flow based on their own metabolism?

  8. Kathleen C.

    Hi – I am curious as to how someone who has had gastric bypass – roux-en-y – is affected with their gut?

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