The use of microbiome testing – which analyzes the trillions of bacteria in and on the body – is on the move. It’s going from the research lab into the clinic to help guide patient care. DNA testing technologies have revolutionized researchers’ ability to identify individual bacterial strains driving disease. Now genomic testing is helping diagnose the source of infections, develop personalized diets, find new treatments for functional and inflammatory conditions of the gut and identify new screening tools for certain cancers.
For Purna Kashyap, M.B.B.S., this is just the beginning. As the Bernard and Edith Waterman co-director for the Mayo Clinic Center for Individualized Medicine Microbiome Program, Dr. Kashyap envisions the coming years as a pivotal time for moving the latest discoveries from the lab to new diagnostic tests and individualized microbiome-based therapies for patients.
“Just as genomics plays a key role in personalized medicine, the microbiome also affects our individual health – boosting our immune system, helping us digest food and influencing how we respond to medications. We are each born and live with a unique microbiome. But unlike our genes, the microbiome can be manipulated and changed. That’s why physicians need to consider the role of the microbiome, along with genetics and other factors, especially when treating patients with complex diseases like autoimmune disorders, gastrointestinal diseases, diabetes, obesity and many types of cancer,” says Dr. Kashyap.
Technologies developed in the lab provide answers in the clinic
A high fever, increased blood pressure and rapid heart rate – these are all symptoms that could be caused by an infection. But for some patients, traditional blood tests fail to identify the source of the illness. That’s where microbiome testing technologies developed in the laboratory are already helping to find answers for Mayo Clinic patients. Within a day and in some cases just hours, the testing is revealing the source of a previously undiagnosed infection, allowing for treatment with targeted therapies.
“We can now identify the specific bacteria causing serious infections even though we are not able to culture them” says Dr. Kashyap.
Test results can help physicians choose targeted therapies to treat infections and avoid the use of “dynamite” antibiotics explains Dr. Kashyap.
“Genomic testing allows us to select specific therapies to kill only the bacteria causing the infection, rather than prescribing an antibiotic that eliminates all of the gut bacteria, leaving the patient susceptible to other illnesses,” says Dr. Kashyap.
Next steps – identifying biomarkers to predict, diagnose and treat disease
To expand the use of microbiome testing, Dr. Kashyap and his colleagues are collaborating with the Center’s Clinomics Program to integrate microbiome testing into patient care as well as clinical trials. Their goal is to identify microbiome biomarkers that could be used to develop screening tests to detect early signs of disease or new individualized therapies, tailored to a person’s microbiome.
Going forward, microbiome testing may also provide important information about disease risk for healthy patients.
“This testing could provide healthy patients with information about disease risk and help define steps they can take to manage their health,” says Dr. Kashyap.
Eat this, not that – personalized diets
Dr. Kashyap and his colleagues have recently tested a model that successfully predicted changes in blood glucose (sugar) levels based on an individual’s age, lifestyle habits and microbiome.
“With the model, we can manage blood sugar levels by changing diet to match the microbiome rather than trying to change the microbiome which may take time”” says Dr. Kashyap.
Dr. Kashyap and his team have also uncovered a link between a person’s microbiome and their ability to lose weight.
“In a pilot study, we found that after switching to a lower-calorie-diet rich in fruit and vegetables, some people were able to lose weight more easily than others due to the type of bacteria in their gut.”
Learn more about the team’s research here.
Matching research to patient needs – a focus on gut health
Throughout his career as a gastroenterologist, Dr. Kashyap has focused on conducting research to meet the needs of his patients.
He has explored how gut bacteria control normal gut function and contribute to the development of gastrointestinal disorders, such as irritable bowel syndrome.
In addition, he has investigated how bacteria lead to opportunistic infections that can become life threatening, such as c. difficile, which can occur after a patient has had a prolonged stay in a hospital or nursing facility. The Mayo team has used new treatment approaches, including fecal transplants, to restore these patients' gut microbiome with healthy bacteria.
“Some patients have a microbiome composition that makes them more susceptible to c. difficile infection. We are working on strategies to prevent the infection as well as develop a treatment with a bacteria-containing pill.”
For Dr. Kashyap, these research efforts are just the tip of the iceberg. “As we learn more, we’ll be able to offer patients better screening and treatment for a wide range of diseases, tailored to their unique needs.”
Pushing the envelope to uncover causes, new treatments for colorectal cancer
Read the related article, highlighting Microbiome Program co-director Nicholas Chia, Ph.D., and his research to uncover early signs of colorectal cancer to improve screening and treatment for the disease.
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