The World Within Us

How the Microbiome Influences Human Disease and Patient Outcomes

As a child, Ami Bhatt, MD, PhD (assistant professor, Hematology, and assistant professor, Genetics), found herself drawn to science. “I was always curious, and I wanted to apply my curiosity in a way that could help people,” she recalls. These dual instincts led her to medicine, where she found her calling as a physician-scientist. Today Bhatt runs her own laboratory at Stanford, where she studies how shifts in the microbiome—the vast community of bacteria and other microscopic life that live on the body—affect human disease and patient outcomes.

Bhatt first became interested in the intersection of infection and malignancy as a medical student at UCSF. “At UCSF I saw a lot of patients with HIV who died of opportunistic infections,” she explains.  Several years later she encountered a similar trend while on rotation for Brigham and Women’s Hospital’s bone marrow transplantation service.  “A lot of the bone marrow transplant patients were getting sick with syndromes that seemed like infections, but we weren’t able to identify the infectious triggers because we didn’t know what we were looking for.”

Bhatt’s search for answers led her to the laboratory, where she used genomics to understand the diseases that had presented in those bone marrow transplantation patients. Her investigation led to an important discovery—the genome of a new bacterium—and set the stage for her current research. “That’s the moment when my eyes started to open. I realized that there are many more types of bacteria and viruses and fungi that live within us, in our microbiome, than we know about.”

Bhatt and her colleagues use cutting-edge genetic sequencing technologies and a sophisticated understanding of diseases to try to “solve mysteries that occur in immunocompromised patients. The fundamental thesis that drives our research,” she explains, “is that patient outcomes are manipulated or modified by the alterations in their microbiota, and that we can discover these microbes using sequence-based technologies.” Once the microbes are identified, Bhatt’s team works to clarify the mechanistic underpinnings of the microbiota-disease relationship. This information is then used to alter the microbiota through targeted drugs or treatments.

Another of Bhatt’s initiatives aims to unravel a particularly interesting question: What molecular changes occur during a fecal microbiota transfer? To answer this, Bhatt and her colleagues have developed a computational pipeline that will provide a time-based characterization of what actually happens during a transfer.

While her research goals are ambitious and varied, the source of Bhatt’s passion remains the same. “I’m still committed to the idea of being able to help people using science,” she says. “It’s been exciting to see our lab grow from just me in an empty room to a vibrant, interactive environment. We currently have eight talented staff members from all over the world. It’s a fun and bustling place. I feel like I am one of those lucky few who get to do exactly what they want to do.”