Open/Close Menu Supporting Research at the University of Chicago Medicine Digestive Diseases Center

The human microbiome is a complex ecosystem made up of bacteria, viruses, and other microscopic organisms. In recent decades, scientists have recognized that the microbiome is a factor in inflammatory bowel diseases and other gastrointestinal illnesses. Support from GIRF is enabling A. Murat Eren, PhD, known as “Meren,” and his team to use sophisticated computational methods and novel studies to gain a deeper understanding of the microbiome. Their unique approach could transform how scientists understand the relationship between microbes and human health.

Thanks to GIRF, Meren’s lab was able to obtain advanced genetic sequencing equipment and hire lab personnel, allowing them to take a new, in-depth approach to analyzing microbial DNA.

Most current studies of the microbiome use a method called “shotgun sequencing” to analyze the DNA of entire communities of microbes. While this method allows for rapid analysis of many pieces of genetic information from many types of microbes, it is limited in its ability to provide a detailed and complete picture of the genetics of individual microbial strains.

Meren’s team is now investigating a new technology, “long-read sequencing,” to analyze longer strands of DNA. Compared with the shotgun method, this approach involves analyzing a smaller number of microbes, but it provides more in-depth, complete, and accurate information about how genetic information is organized in the genomes of specific strains, which may provide critical insights regarding their role in health and disease.

Meren and his colleagues are developing strategies to use long-read sequencing to analyze microbes that come directly from the critical interface between host and microbe. To do this, he is working with gastroenterologist Joel Pekow, MD, to collect microbial samples from the linings of the intestines. Meren’s lab is currently testing the equipment and methods that they will use to conduct the long-read sequencing of these valuable samples. Their focused, in-depth analysis of the gut microbes could lead to breakthroughs in our understanding of which microorganisms promote health or trigger disease, and how normally harmless microbes change their behavior and contribute to illness. This could lead to new treatments for a wide range of gastrointestinal illnesses.

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