The gut microbiome is highly individual and is shaped by diet, lifestyle, medication use, the environment and disease. Now, researchers have developed a way to condense some of that complexity into a single score that may help reflect overall health.

The study, published in Gut Microbes, examined 893 adults who underwent detailed annual medical check-ups.

Researchers combined clinical records, laboratory results, medication data, cardiac stress testing, lifestyle questionnaires, dietary information and stool microbiome analysis to investigate how a Microbial Health Index, or MHI, relates to physical and mental well-being.

How the Index Works

The MHI was originally developed through large-scale analyses comparing gut microbiomes across different diseases. It is calculated as the logarithmic ratio of 97 bacterial variants associated with health to 31 variants associated with disease, producing a single score for each person.

In the new study, researchers tested whether this measure could also reflect differences in lifestyle and health among adults, rather than simply distinguish between disease groups. The associations remained evident across the full cohort, among participants without documented disease and among those with conditions such as hypertension and dyslipidaemia.

Diet and Fitness Were Linked to Higher Scores

Several lifestyle factors were associated with a healthier microbial profile.

Higher fibre intake and closer adherence to a Mediterranean-style diet were linked to higher MHI scores. Better physical fitness also showed a positive association. Researchers assessed exercise capacity using metabolic equivalents, or METs, measured during cardiac stress testing with the Bruce protocol.

Participants with higher fitness levels tended to have healthier microbiome scores, suggesting a relationship between exercise capacity and microbial composition. However, the observational findings do not prove that improving fitness directly causes the microbiome to become healthier.

By contrast, greater consumption of ultra-processed foods and higher levels of markers associated with low-grade inflammation were linked to lower MHI scores.

Blood Lipids Showed Similar Patterns

The researchers also examined lipid profiles in a subgroup of participants. Triglyceride levels were positively associated with greater consumption of ultra-processed foods. By contrast, higher intake of unsaturated fats, olive oil and nuts was associated with lower triglyceride levels.

These findings suggest that diet, blood lipids and microbial composition may reflect overlapping aspects of metabolic health rather than functioning as entirely separate indicators.

Could the Score Change With Lifestyle?

Using statistical models that accounted for age, lifestyle factors and existing medical conditions, the researchers estimated how changes in modifiable behaviours might affect an individual’s MHI. They also compared these estimates with earlier dietary intervention studies and found that microbiome scores could change relatively quickly following dietary changes.

The models were used to estimate the degree of behavioural change that might be associated with a 0.5-point improvement in the index. However, this figure should not be interpreted as a guaranteed clinical target, and the MHI is not currently a standard diagnostic test.

A Possible New Health Marker

The researchers suggest that the gut microbiome could eventually serve as another indicator of health alongside measures such as blood pressure or cholesterol.

The appeal of the MHI lies in its simplicity: rather than examining hundreds of bacterial variants individually, researchers and potentially clinicians can work with a single composite score.

At the same time, the findings highlight an important distinction. Bacteria associated with poorer health may reflect a person’s diet, lifestyle or medical condition rather than directly causing disease.

For now, the index is best viewed as a research tool rather than a clinical diagnostic measure. Its value lies in showing how closely the gut microbiome appears to track everyday factors such as diet, exercise and metabolic health — while also revealing how much remains to be understood about what those microbial patterns actually mean.