August 31, 2016

School of Medicine scientists design experimental method for studying host-microbiome interactions

Individual genetic and microbial makeup could be matched to personalize therapy

(Left) Francesca Luca, Ph.D., and the study’s first author, postdoctoral scholar Allison Richards, Ph.D.

DETROIT – Researchers in the Center for Molecular Medicine and Genetics at the Wayne State University School of Medicine have developed a novel approach to studying host-microbiome interactions, the first step toward learning the cause-and-effect relationship between the microbes that live in our gut and our gut cells using a functional genomic approach.

(Full study is viewable here).

The new experimental method allows researchers to identify the changes in human gene expression in cells of the colon that are determined by the presence of the microbiome. They also can determine whether these changes will be the same across individuals or may differ depending on an individual DNA sequence. The human gut microbiome, which is the community of microorganisms living in our gastrointestinal tract, plays an important role in human health and disease, but current science lacks specific information on the causal effect of the microbiome on humans.

“We know for example that specific gut microbiome taxa are associated with obesity in humans, but we don't know if they contribute to causing obesity or if instead they live preferentially in the gut of obese individuals. Essentially, we don't know how the microbes in the gut affect the human cells they interact with,” said WSU Assistant Professor of Molecular Medicine and Genetics and of Obstetrics and Gynecology Francesca Luca, Ph.D., who co-led the study with Ran Blekhman, Ph.D., assistant professor of Genetics, Cell Biology, and Development at the University of Minnesota.

Clinically, manipulating the microbiome – through fecal microbiome transplants for example – is emerging as a new treatment area. Identifying which disease mechanisms are modulated by specific microbiome taxa could lead to therapies that target both sides of the interaction.

“In the upcoming world of personalized genomics, collecting information on an individual genetic and microbial makeup can then be matched to a specific therapeutic strategy with the highest chance of success,” Dr. Luca said. “This opens a large avenue of future studies that will be able to precisely discriminate causes and effects in the interaction between our cells and our microbes.”

“Genetic and transcriptional analysis of human host response to healthy gut microbiota” is published in the current issue of mSystems, an open access journal of the American Society of Microbiology.

The idea for the novel system was born out of informal conversations between Drs. Luca and Blekhman at a scientific meeting in 2014. Dr. Luca and WSU Assistant Professor of Molecular Medicine and Genetics and of Obstetrics and Gynecology Roger Pique-Regi, Ph.D., had already developed a high-throughput approach to profile the gene expression response to a large number of treatments through RNA-sequencing. At the same time, Dr. Blekhman had developed an interest in understanding how host genetics influences microbiome composition.

“Through those conversations we reached the understanding that to bring the study of host-microbiome interactions to a level beyond association analysis and to really understand how the microbiome can affect human cells and at the same time see how the DNA sequence in those cells influences their response, the fields of functional genomics and human microbiome studies had to come together,” Dr. Luca said.

The work was partially funded by the American Cancer Society Institutional Research Grant (124166-IRG-58-001-55-IRG53) and the Randy Shaver Cancer Research and Community Fund to Dr. Blekhman; and by the National Institutes of Health’s National Institute of General Medical Sciences (R01GM109215) to Drs. Luca and Pique-Regi.

The study team is now applying the method to further studies. Members recently submitted a proposal for a grant aimed at studying host-microbiome interactions in obesity and plan to extend the novel approach to organoid cultures, which more closely resemble the 3D structure of the human gut, Dr. Luca said.

For more information on the Luca laboratory, visit

About Wayne State University School of Medicine

Founded in 1868, the Wayne State University School of Medicine educates more than 1,000 medical students in all four classes. In addition to undergraduate medical education, the school offers master’s degree, Ph.D. and M.D.-Ph.D. programs in 14 areas of basic science to about 400 students annually.  

Wayne State University is a premier urban research institution offering more than 380 academic programs through 13 schools and colleges to more than 27,000 students.


Andrea Westfall
Phone: 586-871-9630

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