September 19, 2024 | Researchers at the Mayo Clinic have developed a new tool that uses machine learning to analyze a stool sample to provide insights into your gut health. The tool, called the Gut Microbiome Wellness Index 2 (GMWI2), can detect subtle changes in the gut to see if one is progressing toward better health or possibly developing a disease.
Recent studies have shown links between the gut microbiome and a variety of chronic diseases (Nature Communications, DOI: 10.1038/s41467-024-51651-9). Because of this, researchers have long been interested in studying the gut microbiome to better understand a person’s health and wellbeing. This idea isn’t entirely new. In northeast Asian countries like South Korea, for example, doctors have been observing stool to monitor health for years. According to Jaeyun Sung, Ph.D., a computational biologist at Mayo Clinic and the senior author of the study, doctors in these countries often assess an infant’s health by examining stool to adjust diet, check for allergies, and more.
However, this method is not as taught and practiced in Western medicine, but it seems like that is starting to change. “More and more clinicians are getting questions from their patients on what to do about their gut microbiome,” says Sung.
GMWI2 is the second version of a tool designed to assess health based on the makeup of bacteria in your stool. The first version, GMWI (Nature Communications, DOI: 10.1038/s41467-020-18476-8), had some limitations—it didn’t perform as well for people with diseases compared to healthy individuals, and it didn’t properly account for the varying roles different bacteria play in health. GMWI2 addresses these issues and is much better at distinguishing between healthy (no disease) people and non-healthy (diagnosed with a disease) people using a gut microbiome profile.
For this study, the team downloaded over 8,000 gut microbiome data samples from public repositories, and using a penalized linear regression method, carefully parsed through the bacterial makeup of the samples. Certain bacteria were associated with gut microbiomes from healthy (disease-free) people, while others were linked to non-healthy people who had a clinical disease, such as colorectal cancer, rheumatoid arthritis, Crohn’s disease, and other autoimmune diseases and cancers. The team developed a scoring system based on this data, with scores ranging from –6 to +6. A higher score (+6) suggests a healthy gut microbiome, while a lower score (–6) indicates a microbiome more strongly associated with disease.
To confirm that GMWI2 works, the research team ran validation steps on the training set of 8,069 samples and on an independent cohort of 1,140 samples. They demonstrated that GMWI was able to distinguish people who had a clinical diagnosis of a disease versus those who were disease-free by at least 80% accuracy. This showed solid proof-of-concept that the gut microbiome can indeed be a reliable indicator of health.
To use GMWI2, a stool sample is sequenced to identify the various bacteria present. The GMWI2 tool then generates a score based on the makeup of your gut bacteria. This score can help you understand your overall gut health, allowing you to take proactive steps to improve it if necessary.
“We asked ourselves, ‘Can we create a score for gut health, similar to a credit score, that helps people understand their wellness?’” says Sung. “If we can, who wouldn’t want to know more about their health?”
A Proactive Approach to Health
Sung emphasizes that the tool is not meant to diagnose disease. “This wasn’t a disease-focused study,” he explains. “It’s more about health and wellness and knowing when it’s time to optimize that.”
For example, if someone gets a low score, like –4, it indicates a non-healthy gut microbiome. This alarm bell could encourage them to make changes, such as eating more fiber, exercising, and cutting down on processed foods, to improve their gut health before more serious health issues develop.
Even if someone is generally healthy, GMWI2 can be used as a tool to maintain their wellbeing by keeping an eye on their gut health over time. It could also be useful for people with a family history of diseases like cancer or autoimmune conditions, allowing them to monitor changes in their gut microbiome.
“Even if you feel fine, we want to make sure nothing is brewing in your gut,” says Sung. “And if everything looks good, great—let’s keep it that way.”
GMWI2 can also be helpful for doctors monitoring patients. For example, if a patient is taking antibiotics or undergoing chemotherapy, which can disrupt the gut microbiome, GMWI2 can help track changes in gut health and aid in their recovery.
Bringing the Tool to Market
The Mayo Clinic team hopes to eventually make GMWI2 available as an at-home health tracking app, but it seems like it is a long road ahead to get it to the commercial market. “There are a lot of regulations we need to navigate. It’s not like, ‘Hey, let’s do it, guys,’” jokes Sung. “I found that breaking barriers and getting people to embrace new paradigms is a lot harder than expected… you have to kind of change their mentality, as well, which is one of the hardest things to do. This is especially the case in medicine.”
For now, GMWI2 is available as an open-source tool for researchers with bioinformatics expertise. The long-term goal is to have people send in their stool samples for analysis at specialized facilities and receive their gut health score directly. Sung and his team hope to build a future where it’s common practice among clinicians to use the gut microbiome to monitor health and disease and guide treatment decisions. Sung also hopes that, as time goes on, the gut microbiome will be taught more in medical schools and more physicians will see it as an effective way to help treat and inform their patients.