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.
M: With more research being done to uncover the gut microbial organ and its relationship with the brain do you think that ideas of consciousness will ultimately change? I was thinking about how the brain as a symbol in philosophy and human culture is often used to justify our difference from the natural world of animals, plants, minerals, etc. One of the things that intrigues me about the human microbiome is it seems to break away from this hierarchy and support a more integrative way of existing with the surrounding world.
E: I am not sure I can answer this question because we’re just at the cusp of realizing that there is a relationship between brain and microbes – we haven’t navigated sufficiently the nature and extent of this relationship. Nevertheless, let me offer you one clinical insight that might be telling. Patients with end stage liver disease (cirrhosis) can develop a condition called hepatic encephalopathy, characterized by derangements in consciousness, behavior, motor (neuromuscular) function, and judgement.
With severe cirrhosis, the blood vessels from the intestine to the liver have to find another pathway because the liver is essentially blocked (from the scarring). Abnormal blood vessels then form that bypass the liver. This results in toxic metabolites made by gut microbes entering the bloodstream (normally the liver detoxifies these compounds). When these patients are treated with antibiotics or compounds that alter the gut microbiome, they “wake up” and have return of many of the disordered functions. Antibiotics work because they reduce the number of toxin-forming bacteria, thereby reducing the toxin levels in the blood.
M: Wow that’s super interesting. So, while the relationship between the brain and microbes is still being uncovered there is this example of how gut microbes, in the wake of disease, are another intricate area that is adversely affected and need to be considered in treatment.
E: Yes, that’s right. I view our gut microbes as an “organ” of the body that has evolved with human biology and is inherently tied into other organ systems. Disturbances of the gut microbial organ can affect and contribute to disease just as it does with other organ systems (heart, lungs, etc). In the same vein, disturbances and disease of other organs will affect the gut microbial organ. To make the body whole again, there may be instances where we have to restore normal function to gut microbes.
M: Since antibiotics kill bacteria and hinder growth they also kill microbes, but do they destroy all microbes or just devastate certain communities? Does the body rebuild microbial communities after it has been treated with antibiotics or does it need assistance?
E: Antibiotics are indiscriminate and kill good and bad microbes. If potent combinations of antibiotics are used, microbial armageddon can result. Recovery can occur, but how fast and complete it is depends on how deeply the microbial suppression was, whether antibiotic-resistant microbes bloom and dominates, and on the individual’s state of health. Not infrequently, help is needed to restore the gut microbiota, For example, fecal microbial transplant is now being used in severe cases and appears to be effective.
M: Has researching the gut microbiome made you reevaluate what you eat in any way?
E: Definitely. I pay attention to what, how much, and when I eat. I don’t go to extremes, but use common sense and good judgment.
M: When you say ‘when I eat’ are you implying that gut microbes are affected by not only what we eat but when we eat? If so, I’d be curious to know a little bit more about this.
E: Our studies support what many dietitians have been telling us to do for years – eat smaller, regular meals and avoid the midnight snack. Regularity in when we take meals is critically important because our biological systems are synchronized to harvest the energy to meet our metabolic needs during the course of the day. Having the midnight snack for most of us is the wrong time. Our metabolic machinery at that time is essentially in the off mode and the calories we ingest are not burned, but stored as fat.
M: In your introduction you wrote, “I am an experimentalis without boundaries and who learns whatever is necessary to pursue interesting research questions.” What is something you are pursuing now or in the recent past that has brought forth some interesting results?
E: Our studies have shown that the gut microbiome has effects and functions beyond the gastrointestinal tract, e.g. Brain, cardiovascular system, immune system, bone development, liver function, metabolism, diabetes, and obesity. We find new clues and pieces of the puzzle every week. For me, this is exciting. We are at the forefront of discovery. I believe our research will make a difference in improving human health and curing disease.
M: Thank you so much Eugene for your time and thought-provoking answers ! There is still so much to uncover and I’m looking forward to reading and learning more in the future.