What Makes a Healthy Microbiome?

Why do some people develop chronic diseases such as cancer, Rheumatoid Arthritis, and Ulcerative Colitis, while others stay healthy? A major clue could be in the gut microbiome. That’s exactly why scientists decided to develop the Gut Microbiome Health Index. Now, you can find out if you have a healthy microbiome – or not.

Our microbiomes are so vastly complex, that it can be difficult to diagnose or easily define health status just by testing the gut microbiome. There are countless details to decode when we look at our data. Luckily, the development of the Gut Microbiome Health Index makes things a whole lot easier.

The Gut Microbiome Health Index

Created by researchers at Mayo Clinic, the index is composed of a mathematical formula that can be biologically-interpreted. The research team analysed over 4000 publicly available human stool shotgun metagenomes, meaning they could decode all the genes in the stool sample. They then pooled the samples into healthy and non-healthy groups. They found that some microbes were more common in different groups. This analysis lead them to make a microbiome signature of a healthy human gut, based on 50 microbial species. 

Discovering this healthy gut microbiome signature led the team to develop a mathematical formula to predict how closely a gut microbiome sample resembles healthy or non-healthy conditions. They established a ratio between species that were more health-abundant or health-scarce. The higher the number, the higher the chances were that the microbiome sample in question came from a healthy person.

You can view it as a ‘credit score for your gut.’

So a higher number is going to tell you: ‘Oh, you look very healthy. Your microbiome resembles that of a healthy population,'” says Dr Sung, assistant professor and corresponding author. “But a low number reveals: ‘Oh, we can’t tell yet exactly which disease you may have, but we can tell that something looks off. Your microbiome resembles very close to what a microbiome would be in a disease population.’ And that’s what we call the Gut Microbiome Health Index. You can view it as a ‘credit score for your gut.‘”

The index makes it possible to take a gut microbiome profile from a person’s stool sample, and actually tell what the likelihood is of having a disease – independent of clinical diagnosis1.

The index makes it possible to take a gut microbiome profile from a person’s stool sample, and actually tell what the likelihood is of having a disease

Taking the index out in practice, an independent validation cohort found that, in close to 700 human subjects, healthy samples were correctly selected from non-healthy samples 74% of the time.

Healthy Gut, Healthy Heart

During the investigation, Dr Sung discovered something else: a link between the Gut Microbiome Health Index and high-density lipoprotein (HDL) or “good cholesterol” in the blood. 

The higher the Gut Microbiome Health Index, the higher your HDL level is,” Dr Sung explained. “That we were able to find this correlation with a marker of cardiovascular health is really exciting, as now we’re connecting gut microbiome information with clinical data. One area of research in my group is to identify how the gut microbiome talks to various tissues in the body through chemical signals. Currently, we’re far from being able to conclude on specific mechanisms, but we have some promising leads we’d like to further pursue.”

Overall, the team believes that this heart connection highlights the potential of the index to act as a powerful and consistent predictor of health. Soon enough, the researchers believe the time will come where microbiome testing will be as routine as a check-up at the doctor.


  1. Gupta, V., Kim, M., Bakshi, U., Cunningham, K., Davis, J., Lazaridis, K., Nelson, H., Chia, N. and Sung, J., 2020. A predictive index for health status using species-level gut microbiome profiling. Nature Communications, 11(1).
  2. Harvard Publishing, 2018. Healthy Gut, Healthy Heart? – Harvard Health. [online] Harvard Health. Available at: <https://www.health.harvard.edu/heart-health/healthy-gut-healthy-heart> [Accessed 11 October 2020].