The Human Microbiome: Megan Diddie interviews Dr. Eugene B. Chang

Special guest blog by Megan Diddie

Megan Diddie is an artist working in Chicago. Her work centers around the human body and its’ relationship to the environment.

This past year I started having numerous conversations with a dear friend about the human microbiome. She was in the process of rebuilding her gut flora and fauna through a change in diet. One of things that fascinated me about my friend’s process was thinking about the body in this more fluid state and how interconnected it is with the world – the things we eat, the air we breath, the bodies we touch, and then where those things come from and what they eat, and so on – this sort of endless unknown.

I recently created a series of pen and ink drawings inspired by the human microbiome called Things Get In You. Many of the images came about from questions and thoughts I’ve had about the microbiome. I was honored to converse with Dr. Eugene B. Chang who researches the human microbiome and explore some of those inquiries.

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M: Hi Eugene, thanks for speaking with me about the microbiome. Can you say a little about your background and what you do now?

E: Hi Megan – it’s a pleasure to speak with you and on one of my favorite topics. I am the Martin Boyer Chaired Professor of Medicine at the University of Chicago and have been studying the interactions between host (us) and gut microbes. I was originally trained in internal medicine and gastroenterology, but most of my efforts now have shifted away from patient care to translational and basic research. I now run a large research center at the University that focuses on digestive and metabolic diseases. The center is funded by a grant from the NIH (National Institutes of Digestive Diseases, Diabetes, and Kidney). When people ask me what my expertise lies, I say that I am an ‘experimentalist’ without boundaries and who learns whatever is necessary to pursue interesting research questions.

M: When did researchers first become aware of the human microbiome? It seems like there have been more articles and attention given to this topic lately. I’m also very curious to know about your own journey with the microbiome how did you come to focus on microbial interactions with the human intestine?

E: I am guessing that scientists knew that stool contained microbes for hundreds of years – perhaps as early as when the first microscopes that allowed them to visualize microorganisms.

In the modern age, growing awareness of the importance and complexity of gut microbes came with the advances in technology and computational analysis. These tools enabled scientists to gain fundamental insights into the relationship of gut microbes with host genetics and physiology. We then began to realize how important gut microbes were to our health and in causing diseases. We also realized the enormous impact of the gut microbiome on organ systems beyond the gut (e.g. brain, cardiovascular system, immune cells, etc), and how malleable it was by environmental factors, diet, and lifestyles changes.

We started studying the gut microbiome about 10 years ago. At that time, we were studying a unique class of proteins (heat shock proteins) that are highly expressed in certain regions of the gut and essential for maintaining the health of the intestine. When we discovered that gut microbes played a major role in maintaining their physiological expression, we had to learn more about the gut microbiome. We retooled the laboratory and teamed up with experts in the field who were soil and marine microbiologists. While this might seem odd, these folks had already developed the tools to study complex microbiomes in the environment. Over the years, we and others have come to appreciate the gut microbiome as a “microbial organ”, as important and essential as any other organ of the body. Not surprisingly, anything that causes malfunction of the microbial organ will have far reaching impact on other systems of the body. In this regard, our group has been particularly interested in how abnormalities in the gut microbiome affect our metabolic and immunological functions.

M: I’m very interested in the existence of a ‘microbial organ.’ Do the other organs have ‘microbial organs’ assisting their functions?

E: There are other microbiomes of the body (skin, vagina, lungs), but they don’t have the diversity and complexity of the gut microbiome and therefore are not likely to have the same impact and significance as an “organ.” This is not to say they aren’t important locally, but they are not likely to have the same systemic impact outside of their regional domain as the gut microbial organ.

M: As you were working with folks in the field of soil and marine microbiology did researchers discuss human’s microbial organs and the microbes in their surrounding environments? For example you write about malfunction in the microbial organ having a far reaching impact on other systems of the body. Does malfunction of the microbial system also reach out into our environment?

E: Very interesting and insightful question. One of my colleagues, Jack Gilbert (an environmental microbial ecologist), has done studies where he shows that we all contribute to the environmental microbiome – constantly and significantly. For instance, he reported that people and pets contribute to the microbiome of their homes, and, by doing so, their microbes interchange. Dogs in the house, for instance, are significant vectors for microbial transfer from one individual to another.

M: Do our environments’ microbial systems affect us?

E: Yes – if you travel abroad and stay for a while, you will begin to acquire microbes indigenous to that area.

M: I read that the microbes in our bodies the amount and the diversity has been waning with the introduction of antibiotics, hand sanitizer, and people spending less and less time outside. Any thoughts about this?

E: Most of us believe this to be true and studies of “ancient” human microbiomes, i.e. from stool samples from hundreds of years ago or from remote, civilization naïve populations have shown that their microbiomes are vastly different from those of individuals from modern industrialized societies. The concept of how westernization has changed the human microbe and host microbe interactions is the basis on which the hygiene hypothesis built.

M: Have the microbes of “ancient” human’s bodies gone extinct? Have new microbes come into existence with the rise of the industrial world?

E: Really great question. Many of the ancient strains may not have become extinct, but rather morphed into new strains because microbes constantly undergo genetic mutations and exchange of genetic materials. Microbes have the amazing ability to adapt to circumstances an environment to survive.

M: I’ve heard the gut microbiome referred to as the ‘second brain.’ How accurate a description is this?

E: Our studies support this notion. They show that the gut microbial organ is as important in controlling our metabolic networks (circadian rhythm) as the brain. Many of the metabolites produced by gut microbes are building blocks for neurotransmitters.

M: Thinking about the gut microbial organ and our metabolic networks I am wondering what happens when we die? Do our microbes die with us or do they go on to form new colonies in whatever environment we are laid to rest?

E: Some of the microbes will likely “die”, particularly as the environment we created for them deteriorates. However, many will likely survive the decay process and rejoin the environment depending on how the body is buried (or not). Cremation, for instance, will kill all the microbes of the body.

Prolonged chemical or casket entombment would likely kill or prevent the escape of microbes (which will eventually die). On the other hand, burying the body in the ditch will provide plenty of opportunity for microbes to rejoin the environment.