E208: Improve your microbiome - Improve your Health

If you want to improve your digestion, your immune system, and your overall health, one might begin with a focus on a healthy gut microbiome. Today we're talking with Stanford University professor of microbiology and immunology Dr. Justin Sonnenburg, co-author of the book entitled, "The Good Gut: Taking Control of Your Weight, your Mood, and Your Long-Term Health." He and his wife, research scientists Dr. Erica Sonnenburg, argue that our typical modern diet has caused the microbial diversity or intestine to shrink substantially. Turns out that's a big problem.

Interview Summary

My impression is that this field of work on the microbiome is just exploding. It seems like every day something new comes out, something exciting, some kind of major breakthrough. It's wonderful to have a leading scientist like you to join us to help explain this. Let me begin with this question. I recently read something very interesting in the article that discussed your work, namely that you've hypothesized, and this is a quote from this article, "Humans may merely be elaborate vessels "designed for the propagation of bacterial colonies." Now that's pretty interesting. Tell us more if you would?

Yes, absolutely. I should note that this is an idea that has been propagated, just as microbes are propagated over time. I did say that, but I'm now attributing it to the great scientists that came before me. I will say that the microbes in our gut have been for a long time a curiosity. For hundreds of years we've known that they live there. Over time we've learned that they're affected by what we eat. We know that they're involved in digestion and gut health. But what is really phenomenal is, as you alluded to in the introduction just the ability of these microbes to impact so many dimensions of our health. Everything from our immune system, to metabolism, to things like moods, behavior, and neurodegeneration. When you start to think about microbes getting passed from generation to generation - because as a new baby is born, their gut is sterile in the womb, and then they're rapidly colonized when they come to this world largely by microbes from their mother and other adults around them - you start to realize that these microbes may actually be the ones calling the shots and dictating aspects of our biology to promote their growth through evolutionary time. It does change the way you think about this relationship in some ways.

One might jump to the conclusion that microbes are a bad thing, and you'd like to have fewer of them. That's in fact what antibiotics do, they get rid of them. But we need more rather than less, and it sounds like the shrinking diversity of the microbiome is really a problem. How do our diet and lifestyles damage the vitality of the human microbiome? I'm imagining this is a 'let me count the ways question,' but what are the leading concerns in your mind?

Yes, completely. I think you're right in that it's very hard to single out one particular factor, because as populations become more industrialized and embrace all of the technologies and medical practices that go along with the industrialized lifestyle, we have so many factors that can impact our microbiome. Certainly, diet is a major factor, and we can come back to this. But we know that most of the microbes in our gut reside at the far reaches of our digestive tract - at the very end of the line down in our colon in our large intestine. That means that if we're eating simple nutrients, like most of the things in a western diet - sugars, starch, fat, protein - a lot of those things get digested and absorbed in our small intestine, which leaves nothing remaining for the microbiota. It's really complex carbohydrates and dietary fiber, that serve as the major fuel for the microbiota because we can't digest those complex carbohydrates. The western diet has greatly reduced dietary fiber content, which has left a lot of our gut microbes starving. But there are other aspects of diet, certainly artificial sweeteners, emulsifiers, and probably the high fat content of the western diet are not great for our microbiome. Then beyond diet, antibiotics as you mentioned known to be great for fighting infectious diseases, but not so great for maintaining all of the friendly microbes that we harbor in our body. A variety of other factors like C-sections, baby formula, the incredible sanitation in our environment, again, a lot of these things are a trade-off because we have reaped a lot of benefits from a lot of the lifestyle medical practices technologies. But at the same time, we've implemented these in the absence of understanding the importance of our gut commensals, and the other commensals on our body for our health. Now we really need to start thinking about do we need to restore diversity to this community? Certainly, we need to start thinking about taking care of the community more diligently.

You mentioned in some detail how diet affects the gut, but how does it happen in the reverse? Is there a reciprocal relationship going on?

Yes, it's a great question, and there are some papers that have been published looking at how gut microbes can affect food choice in model organisms like fruit flies and other organisms that are studied in the lab. We kno