Off the Cuff: Curtis Huttenhower

“The microbiome consists of all the microorganisms that live anywhere in and on the human body—bacteria, viruses, fungi, and others—that can influence human health. For simplicity, I’ll refer to all of these together as ‘bugs’—not to be confused with insects! In the context of public health, much of our work ends up being on the bacteria in the gut. Even at population scale, there’s remarkable personalization of the microbiome: There’s typically only about a 10 percent overlap in gut microbial species between any two otherwise similar individuals, in contrast to 99.9 percent genetic similarity. Even then, everyone has different strains of those microbes. Ultimately, we hope to be able to profile microbial communities starting at the population level, figure out which bugs are there, what they are doing chemically, and how we can change any one individual’s microbial ecology for the better.

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One of the most common ways the gut microbiome relates to health is in chronic disease, such as inflammatory bowel diseases, as well as allergies, diabetes, arthritis, and cancer. We generally use DNA sequencing of whole microbial communities—referred to as a metagenome—with computational algorithms and statistical tools to determine what the organisms are doing, how they’re evolving, how they’ve perturbed a disease, and how that relates to the human outcome. Many autoimmune or inflammatory diseases seem to promote the growth of certain bugs that ‘like’ inflammation, which in turn kick out more beneficial, anti-inflammatory microbes. Removing or avoiding these bacteria provides potential new routes for treatment, and we can use the presence of these bugs as microbial signatures to give us early detectors of risk.

One of the most promising therapies to change the microbiome is through fecal transplants, and in the future we expect therapies to include long-term dietary preventatives or short-term targeted antibiotics as well. There has been research into using fecal transplants to ‘add in’ bugs that will activate the immune system in such a way to make more people responsive to these therapies, thus allowing them to target cancer tumors more effectively.

Some researchers in the Microbiome Center address nutrition; for example, how microbes might affect weight gain or loss. We’re looking at how people respond in different ways to the same food or dietary supplement, since our personal microbiomes can change the chemistry of things we eat. The microbiome also helps metabolize pharmaceuticals, explaining different responses among individuals to the same drug. We also study the microbiome in infectious diseases and the degree to which lifetime exposure to different microbes can prime the immune system in different ways. That priming affects how people respond differently to exposure to infectious diseases, for example, as well as to certain vaccines. Ultimately, we hope that by understanding how the microbiome affects such a wide range of systems in the body, we will be able to target it to improve health and well-being.”