Icahn School of Medicine at Mount Sinai
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Focus Areas The Microbiome

The Microbiome

The microbes that live in and on our bodies -- known as our microbiota -- have both beneficial and deleterious effects on our health. The influence of microbes is particularly acute in our intestines, where they are so abundant that they create one of the densest ecosystems on the planet. Our intestines harbor a few hundred species of bacteria. These species remain stably colonized in our intestines for much of our adult lives. Researchers want to ascertain which of these microbes are beneficial and which are harmful in the context of each person's unique genome and lifestyle.

At the Icahn Institute for Genomics and Multiscale Biology, we are developing the next generation of software tools, experimental technologies, and animal models to deepen our understanding of the role of microbiota in human health. We are focusing on identifying diseases in which changes in the microbiota are correlated with disease, verifying in animal models if those changes play a causative role in disease, and identifying the microbes that are responsible. Our goal is to set the stage for a new type of medicine that encompasses both our human genomes and the genomes of our microbes to understand how together they influence health. Just as chemotherapy is more effective when it is targeted to a patient's unique cancer, future treatments for numerous diseases will take into account our personal microbiome so that the right microbes (i.e., next generation probiotics) can be added or removed from their microbial communities to improve health.

Resources at the Icahn School of Medicine at Mount Sinai that enable this work include the QIIME software pipeline - one of the leading software tools for analyzing high-throughput microbiome data. Scientists at the Icahn Institute for Genomics and Multiscale Biology are continually making improvements to QIIME. These improvements are immediately made available to the entire scientific community at the Icahn School of Medicine through the Minerva computing cluster at the Icahn Institute for Genomics and Multiscale Biology. We have developed anaerobic robotics capabilities to isolate and identify microbes of patients in an automated manner. In addition, we have constructed a germ-free facility to house mice that are free of microbes and live in sterile "bubbles." By colonizing germ-free animals with different microbes, we will be able to investigate how particular bacterial strains can cause disease or potentially be used as a treatment for conditions of interest.

Scientists in the Icahn Institute for Genomics and Multiscale Biology are particularly interested in the potential role of our gut microbes in inflammatory bowel disease, allergies, and cancer. Working with the Immunology Institute, the Division of Gastroenterology, and other research institutes and clinical scientists at Mount Sinai, we hope to usher in novel therapies and diagnostics that target our microbes.

Learn more about the labs of two of our foremost experts on the microbiome: José Clemente, PhD and Jeremiah Faith, PhD.

Our scientists have contributed to the following research papers:

Science Advances (April 2015): "The Microbiome of Uncontacted Amerindians."

Science (November 2013): "Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States."

For their work on "Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States," Jose Clemente, PhD, and his co-authors were featured in Wired's "Best Scientific Visualizations of 2013" (December 2013)

Science (September 2013): "Gut microbiota from twins discordant for obesity modulate metabolism in mice." 

Science (July 2013): "The long-term stability of the human gut microbiota."

Nature (June 2012): "Human gut microbiome viewed across age and geography."

Cell (March 2012): "The impact of the gut microbiota on human health: an integrative view."

Science (July 2011): "Predicting a human gut microbiota's response to diet in gnotobiotic mice."