Scientists unlock predictive healthcare with innovative gut microbiome analytical tool

09 Sep 2024 --- A new computational tool can assess and distinguish healthy individuals from those with any disease at 80% accuracy by analyzing their gut microbiome. Researchers at the Mayo Clinic, US, who developed the tool, dubbed the Gut Microbiome Wellness Index 2 (GMWI2), note that it can even detect subtle changes in gut health to identify if a person may progress toward or recover from a disease.

The new tool is an enhanced version of a prototype developed by the same team. It overcomes the limitations in classifying non-healthy people associated with the earlier version and is available as an open-source tool. 

“The GMWI2 holds significant potential as a preventive tool in healthcare by identifying early gut health disturbances before they manifest as serious disease symptoms,” Jaeyun Sung, Ph.D., the senior author and computational biologist at Mayo Clinic Center for Individualized Medicine’s Microbiomics Program, tells Nutrition Insight. 

“It could guide interventions such as dietary changes, the use of probiotics or modifications in lifestyle to restore gut balance, potentially preventing the onset of chronic diseases like autoimmune disorders or metabolic conditions. Additionally, in clinical scenarios like fecal microbiota transplants, GMWI2 could aid in selecting donors with optimally healthy gut microbiomes, thus improving patient outcomes.” 

He adds that further research is required to move toward therapeutic applications. Studies must correlate specific microbial shifts detected by GMWI2 with clinical outcomes across various diseases. 

“Large-scale longitudinal studies would also be essential to validate its efficacy in preventing disease or guiding therapeutic decisions in areas like rheumatoid arthritis and inflammatory disorders.”

To develop the tool, the researchers tested it against 8,069 stool metagenomes from 54 published studies across 26 countries in six continents to identify gut taxonomic signals linked to disease presence or absence. 

Personalized, proactive healthcare

The new tool, presented in Nature Communications, is a “pivotal advancement in gut microbiome research,” says Sung. It offers a scalable, quantitative tool that captures the health status of the gut microbiome across a wide range of diseases. 

“It highlights the gut microbiome’s potential not just as a diagnostic tool for specific conditions but as a broader indicator of overall health. As we move toward more personalized, data-driven healthcare, tools like GMWI2 may be crucial in preventive medicine, helping people maintain their health long before they experience disease symptoms.”

The tool can guide preventive lifestyle or dietary interventions by identifying microbial imbalances before symptoms emerge.He explains that GMWI2 serves as an early warning system for detecting adverse changes in gut microbiome health, “much like a canary in a coal mine.” The tool can guide preemptive lifestyle or dietary interventions by identifying microbial imbalances before clinical symptoms emerge. Sung stresses that this can “potentially stop the progression of early gut disturbances into more serious diseases.” 

“For instance, if a person’s gut health begins trending toward a diseased state, GMWI2 could prompt personalized recommendations, such as dietary modifications or probiotic supplementation, to restore balance. 

“This proactive approach empowers individuals to manage their health before more invasive or expensive medical interventions are necessary. It also has the potential to inform clinicians of subtle health shifts in patients undergoing treatments, such as monitoring for early signs of disease flares in autoimmune conditions.”

How to build a healthy gut

The gut microbiome is crucial in healthy digestion, metabolism and immunity. Research links gut microbiome diversity to improved health, while imbalance or dysbiosis has been associated with disease or health risks.  

Sung notes that a combination of dietary, environmental and lifestyle factors influence the healthiness of a person’s gut. 

“Diet is a key determinant of microbiome composition. High-fiber foods, particularly those rich in prebiotics, can promote the growth of beneficial microbes. Fermented foods rich in probiotics also enhance gut health.”

“Exposure to diverse environments, including varied microbial ecosystems, plays an important role in enhancing gut microbial diversity, which is associated with better health outcomes.”

Sung notes that diet is a key determinant of microbiome composition, pointing to high-fiber foods and fermented foods.He also points to the potential of chronic diseases and the overuse of medications like antibiotics to disrupt the microbial balance. “A balanced immune response and limited exposure to environmental toxins or chronic inflammation also contribute to a healthy gut.”

Finally, Sung underscores the importance of regular physical activity and stress management, as these “have been shown to positively influence gut microbiome composition by fostering the growth of health-promoting bacteria.” 

Tool development

The GMWI2 can screen a gut microbiome sample and quantify how much it resembles a healthy (disease-free) or non-healthy (diseased) person. After testing the index on 8,069 microbiome samples, the researchers validated their work on a new cohort of 1,140 samples. 

They also tested the tool across clinical scenarios to demonstrate its ability to detect shifts in gut health, for example, in people who had undergone fecal microbiota transplantation and individuals who changed dietary fiber intake or were exposed to antibiotics. 

Sung highlights that the tool builds significantly upon existing knowledge to improve accuracy. “Prior studies have identified associations between the gut microbiome and various chronic diseases, but accurately tracking gut health in a way that can be applied across multiple conditions has remained challenging.” 

“The original GMWI was a breakthrough in quantitatively assessing gut microbiome health, but it had limitations in classifying non-healthy individuals due to its reliance on prevalence-based strategies. The refined tool addresses these limitations by incorporating a broader dataset, applying weighted species associations and using more advanced bioinformatics techniques.” 

In the long-term, the team aims to embed GMWI2 into larger health monitoring systems to benefit individual health trajectories.The new tool can detect subtle microbiome shifts that signal improving or deteriorating gut health, providing a comprehensive and disease-agnostic approach to understanding the gut’s role in overall wellness.

Future plans

The research team is planning to further develop GMWI2, such as “expanding its dataset to represent a broader spectrum of populations, diseases and geographic regions,” Sung continues. 

“This will enhance its generalizability and accuracy across diverse patient groups. Integrating more sophisticated artificial intelligence (AI) techniques will further refine the index’s predictive power.” 

“The long-term vision for GMWI2 is to embed it into larger health monitoring systems, combining data from wearables, multi-omics and other health measurements to offer comprehensive insights into individual health trajectories,” he concludes. 

“This integration could usher in a new era of personalized healthcare, where early detection of health issues and preventative strategies are driven by real-time data from the gut microbiome.”

By Jolanda van Hal