The Microbiome’s Role in Precision Medicine

Pictured are E. coli bacteria, one of the many species of bacteria present in the human gut.Pictured are E. coli bacteria, one of the many species of bacteria present in the human gut.

Inside the human body lives a complex community of microorganisms, bacteria, viruses and fungi known as the microbiome. Found primarily in the intestine, the microbiome plays an integral role in human health and wellness.

Researchers are mapping the microbiome in an effort to better understand disease treatment and prevention. And even to develop personal treatment plans based on an individual’s specific mix of microorganisms and bacteria. But just what is the microbiome? We asked local professors for insight.

Think of the microbiome as an “invisible organ,” said Jun Sun, associate professor of gastroenterology and hepatology at the University of Illinois College of Medicine. Like other organs in the body, the microbiome has “physical functions,” such as the digestion of food, stimulation of the immune system and protection against pathogens.

“There’s around 40 trillion bacteria cells in your body compared to about 35 trillion human cells,” said University of Chicago professor of surgery Jack Gilbert, the director of the Microbiome Center—a research partnership between the University of Chicago, the Marine Biological Laboratory and Argonne National Laboratory that launched in February.

“We’ve started to over the last 10 years really tease apart what that microbiome looks like and what those organisms do in a very rigorous and detailed way.”

In 2008 the Human Microbiome Project was established with the goal of identifying and describing the microorganisms that compose the microbiome in order to understand the microbiome’s role in health and disease.

The first phase of the HMP was to identify the different types of microorganisms found in the human microbiome through sequencing, which is still ongoing. As that continues, researchers are trying to understand how the microorganisms function in order to learn how to manipulate them to maximize health and wellness, as well as prevent and treat disease, said Sun.

Learn more about the human microbiome in the video below.


Because it’s a “major part” of the body and influences how the body functions, Gilbert is calling for precision medicine, or personalized medicine, to include a greater focus on the microbiome.

“Your microbiome is unique to you. Even your identical twin, if you had one, would have a different microbiome to you,” Gilbert said. “There’s no other person on the planet that has the same microbiome as you inside their body.”

In his 2015 State of the Union address, President Barack Obama announced the launch of the Precision Medicine Initiative, a research effort aimed at moving away from a “one-size-fits-all approach” to treatment and toward an individualized approach that takes into account differences in people’s genes, environments and lifestyles.

In a Jan. 30, 2015 speech, Obama called precision medicine “one of the greatest opportunities for medical breakthroughs.”

“Doctors have always recognized that every patient is unique, and doctors have always tried to tailor their treatments as best they can to individuals. You can match a blood transfusion to a blood type,” he said. “What if matching a cancer cure to our genetic code was just as easy? Just as standard?

“And that’s the promise of precision medicine, delivering the right treatments at the right time every time to the right person.” 

In the video below, President Barack Obama speaks about the Precision Medicine Initiative.


Though the microbiome is cited as one of the types of data the Precision Medicine Initiative should focus on, Gilbert says most research has focused on genetics.

“A lot of this started by trying to understand why certain people’s cancers didn’t respond to therapies and other people’s did,” he said of early precision medicine research. “By sequencing the genome of people’s cancers, we’ve been able to see that everyone’s cancer is slightly different and that the drugs affect certain cancers and not others.”

The microbiome can also be sequenced, which would allow researchers to stratify individuals based on the types of bacteria they have, Gilbert said. Knowing the types of bacteria present in a person’s microbiome could be used to complement genetics-based precision medicine, including drug response and interactions. 

When a person takes an oral medication, the drug is broken down by bacteria in the intestine. In some instances this can lead to an adverse effect. For example, when some people take Tylenol, bacteria break down the drug and produce compounds that lead to liver toxicity, Gilbert said.

If a person’s microbiome was screened first, he or she would know if Tylenol would be toxic for him or her, Gilbert said.

“There’s lots of very exciting ways the microbiome could be used to precisely deal with wellness, with health and also with treating disease.”

Universities receive grant to research connection between microbiome, breast cancer

Recently, the Department of Defense awarded researchers from UIC and U of C a three-year, $900,000 grant to investigate how the gut microbiome influences breast cancer. Sun and U of C professor Tao Pan are the principal investigators of the project.

Researchers will examine how a specific molecule produced by bacteria called queuine is related to breast cancer. Cells need queuine in order to modify tRNA – a type of molecule used by cells to translate genetic material into protein.

Queuine is “critical” to the process of turning genetic material into protein, according to Sun. “The imbalance of bacteria in the gut could potentially increase the risk of breast cancer.”

Past research has shown abnormal levels of tRNA are associated with an increased risk of breast cancer, but it remains unclear if and how queuine plays a role.

“Nobody actually really looked at how queuine contributes to breast cancer and how this could happen,” Sun said, adding that researchers are trying to uncover the link between the two.

Follow Kristen Thometz on Twitter: @KristenThometz


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