Category: Science


Healthy Gut Bacteria – Diversity is the Key

I recently had the opportunity to interview Dr. Mark Plotkin, a renowned ethnobotanist who has spent almost three decades studying traditional plant use with the traditional healers of tropical America. Previously, he served as Research Associate in ethnobotanical conservation at the Botanical Museum of Harvard University and now serves as president of the Amazon Conservation Team, an organization dedicated to studying and raising global awareness of the ever-increasing rates of bio-diversity loss in the Amazon region.

Dr. Plotkin made it very clear to me that it is this diversity that allows the Amazon region to respond to changes in climate and other environmental pressures. He further revealed how the diversity of flora and fauna in the Amazon actually influences the health of the entire planet, providing a measure of resilience, or lack thereof, in terms of responding to environmental changes.

This interview really stuck with me. These concepts moved me, and resonated greatly with the understanding we have  of what goes on within each and every one of us. Like the Amazon, we are, in great measure, very much dependent upon the diversity of the organisms that live within us. Diversity equals resilience.

Unfortunately, research is now revealing that those of us living in cosmopolitan, industrialized nations, by and large, have populations of gut bacteria that are dramatically compromised, in terms of their diversity, and this translates into a significant loss in our ability to adapt to the profound number of environmental stresses to which we are exposed on a daily basis.

Many factors conspire to reduce the diversity of the bacteria that live within us. These include the use of antibiotics, other medications such as acid-blocking drugs, stress, and various environmental toxins. But far and away the biggest factor is the choices we make each and every day when it comes to the food on our plate. The diet we choose is the most influential factor in terms of the health and diversity of the hundred trillion microbes that live within us. To be clear, these microbes play a pivotal role in determining our health destiny.

Recently, Drs. Erica and Justin Sonnenberg from the Department of Microbiology at Stanford University conducted a fascinating study. They used “humanized” laboratory mice, meaning mice that had been born without any gut bacteria and were then inoculated with bacteria from healthy humans. The researchers studied the effects of dietary changes on the diversity of the bacterial species in these animals.

They found that when the animals were deprived of prebiotic fiber, the level of diversity dropped quickly and dramatically. However, they also showed that once prebiotic fiber was introduced into the diet, the level of diversity of the gut organisms significantly improved. Even more compelling was their finding that when they repeated this experiment over four generations, the level of bacterial diversity continued to worsen. Even more startling, even when prebiotic fiber was given, there was less and less recovery. The authors concluded that after several generations, some bacterial species actually became extinct, hence the title of the study, “Diet-induced extinctions in the gut microbiota compound over generations”.

There is so much being written these days about the importance of probiotics for health and wellness, and a lot of emphasis is being placed on looking at specific bacterial species, in terms of their particular effects on our physiology. But what is really exciting is the incredible explosion of research focusing on the long neglected health benefits of prebiotic fiber. We know that nurturing our probiotic friends by giving them healthy dosages of prebiotic fiber allows them to do so many of the things that they do to enhance our health, like manufacturing vitamins and balancing immunity. And this new research, showing how critical prebiotic fiber is to maintaining and even reclaiming bacterial diversity, adds so much to our appreciation of how important a role prebiotic fiber plays in paving the way for a healthy future.

While the Sonnenbergs demonstrated that reduction of dietary prebiotic fiber has a profound and detrimental effect on bacteria by reducing diversity, the upside is that they clearly showed that when prebiotic fiber is reintroduced into the diet, diversity can recover.

I believe there is some very empowering information in this research. We can pretty well assume that our diets are not ideal for nurturing diversity of our gut bacteria. That said, it certainly makes sense to do everything you can to enhance the amount of prebiotic fiber that you consume on a daily basis. Foods rich in prebiotic fiber include jicama (Mexican yam), dandelion greens, onions, garlic, asparagus, chicory root, cashews, pistachios, lentils, kidney beans, and Jerusalem artichoke.

These days, prebiotic fiber is available as a nutritional supplement. The best sources of prebiotic fiber include acacia gum and baobab fruit, and prebiotic supplements made from these sources are widely available in health food stores and online.

So remember, prebiotic fiber enhances gut bacterial diversity, and it is this diversity that can redirect your health destiny for the better.

  • Ri

    excellent thank you for this reminder about the importance of prebiotics in our diet. I have yet to find jicama and chicory root in my local grocery store though and I do see artichokes but just regular ones not Jerusalem ones is there even a difference?

    • SSE

      Yes, Jerusalem artichokes are a tuber. They can be called “sunchokes” in some stores.

  • Paradigm Change

    For those with IBS (or maybe IBD) though, purposely excluding these foods through the low-FODMAP diet now has some solid studies behind it and is advised to patients by institutions such as Stanford.

    I’d like to hear your thoughts on this.

  • Steven Roberts

    Great article.
    I am experimenting with making my own kombucha and sauerkraut.
    I am also training for a marathon on a ketogenic diet.

  • Larry B.

    Resistant starch (i.e. potato starch) is another food source for gut bacteria (when eaten cold). Potato starch is the 3rd ingredient (after water and brown rice flour) in my gluten-free waffle so I let it cool and load it with seed butter, coconut, flax, pumpkin seeds and a few raisins to reduce blood sugar spike.

  • cmans6282

    Is it true that prebiotics provide food for the ‘bad’ bacteria of SIBO?

  • Jackie Caldwell

    Thank you for all your great information. I am a nutrition coach and help people with digestive disease learn to eat grain free. I talk about probiotics a lot and have just really started talking to my clients about prebiotics and their importance. Thank you again!

  • Nanook

    What are “Kidney Brans”?

    • Sandra Olivia Frost

      Kidney BEANS, dark red kidney shaped beans !

  • Good Morning Dr. Perlmutter – What are your thoughts of plant based probiotics? I found one made from Pediococcus Live Culture that they say is more effective than lactobacillus strains. Not sure how to research what type of probiotics to use for the gut and if this plant based one is the best for my needs. Any suggestions where to start and your comments on the Pediococcus strains would be helpful.

  • Quinn

    What is the best dosage of the 5g prebiotic fiber product. How much and how many times a day?

  • Caroline Jacobs

    Larry B. Are u saying that potato starch is resistant starch?

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