The human body plays host to trillions of microorganisms. In the gut, teeming communities of bacteria, fungi and other microbes interact with one another and with host cells, affecting immune response and creating metabolites that influence both health and disease. Scientists who map the gut microbiome have learned it varies tremendously from person to person — even region to region, diet to diet — and over the course of a life. Yet mounting evidence shows correlations between microbiota and health problems as varied as heart disease, life-threatening infections and inflammatory bowel disease.

Hera Vlamakis, PhD, is a research scientist and senior group leader for the Infectious Disease and Microbiome Program at the Broad Institute of MIT and Harvard. She answers three questions for executive education about the ever-expanding impact of microbiome research and the value it adds to traditional drug development programs.

Interview condensed and edited for clarity

Do you think the larger impact of microbiome research will be microbes as drugs themselves, or microbes as improving our understanding of disease?

The answer has to be both. We know microbes can have an effect on the host: they can train our immune response, they can alter our immune response. From early life, they can change how we react to different insults or how we’re going to respond if we’re predisposed to a disease or are exposed to a pathogen. I can imagine using microbes that we know can train your immune system as a probiotic early in life.

And certainly, we’re finding lots of associations with diseases. We know that in inflammatory bowel disease (IBD), for example, there are microbes associated with the disease that are increased or decreased. We’re starting to understand how those microbes are interacting with host cells. Once we know what they’re doing, we can target those processes.

How far away is an FDA-approved diagnostic or therapy based on the microbiome, and what hurdles does the field need to overcome to get there?

The gut microbiome is affected by environmental factors, diet, where you live and different exposures people have. Findings in one population may not translate to another population. So part of what needs to happen before we can start using microbiome-based diagnostics or therapies in a really definitive way is more studies with diverse groups of people.

As far as microbiome-based therapies go, they’re already using fecal microbiota transplants (FMT) to treat Clostridum difficile infections with FDA guidance, though not approval. C. difficile is extraordinarily difficult to treat. Studies have shown that a transplantation of the microbiome can clear the infection very quickly — and this is for people who have been suffering for a long time.

In the work we’ve done, there’s a lot of information on potential diagnostics. We look at which microbes and microbial metabolites are present in certain diseases. We’ve made lots of associations that this bacteria or molecule is present in a disease, but not in a healthy individual. I’m thinking particularly of IBD, a disease that manifests in lots of different ways clinically. Right now, no one knows why some patients have stricturing in their colon, develop fibrotic disease or require a colectomy. And no one knows why only 40% of individuals respond to any given treatment. I think where microbiome research will become super-relevant is in trying to parse out those individuals to subclassify diverse diseases like IBD in order to guide what treatment to give.

How can microbiome research add value to traditional drug discovery and development programs?

By understanding the bacteria that are present, we’ll be able to see how those microbes are altering our responses to different drugs. Bacteria can change your immune response, but they can also directly modify therapeutic drugs: they can degrade them or activate them. So, you can imagine not just giving a therapeutic, but also giving a probiotic at the same time. Or, if you know you have a microbe that degrades your therapeutic, you might give antibiotics at the same time. I can see this being very relevant and altering clinical practice.

Continue the conversation on Twitter by connecting with us @HMS_ExecEd. Learn more about the exciting opportunities the microbiome has to offer in our Spring 2019 program The Microbiome: Emerging Opportunities for Biopharma.

— Francesca Coltrera