Microbiome quick guides series: Microbiome diversity

Years ago, one of the first questions scientists came together answer in the field of microbiome science was: what makes a microbiome “healthy”? But as the research progressed, scientists found the gut microbiomes of healthy adults turned out to be far more varied than expected—so despite hundreds of studies and several large-scale research initiatives, we still don’t have a clear idea what characterizes a healthy gut microbiota.

But we do know one thing: studies that compare healthy people to those with different chronic diseases tend to find that the healthy people show greater gut microbiota diversity. Study after study has shown lower diversity scores in people with different chronic diseases: inflammatory bowel disease, non-alcoholic fatty liver disease, colon cancer, and other conditions.

Meaning of gut microbiota diversity

When you talk about a diverse forest or a diverse library, diversity means something similar to “variety”—many different types of things rather than just a few types of things. So when you hear about a diverse microbiota, it means a microbiota with microorganisms from many different groups. Not how many microorganisms, but how many kinds and how they’re distributed.

Since bacteria are the most frequently-studied members of microbiomes, most measures of microbiota diversity only capture the diversity of the bacteria. They don’t capture the diversity of the other microbes in the gut (fungi, bacterial viruses, or others).

Scientific measures of gut microbiota diversity

Scientists often calculate a score for a microbiota in order to represent its diversity. When they measure diversity in a bunch of samples of the same type (let’s say oral microbiota samples) from a particular group, it’s known as capturing the ‘alpha diversity’.

The Shannon index is a common way to measure the alpha diversity of a bacterial sample. To use the Shannon index, scientists first sequence the DNA and separate all the microbes in the sample into ‘bins’ or name categories. This basically identifies the different species that are present. Then they count how many species there are—giving them a score of “richness”. Next, the scientists do a calculation of how the bacteria are distributed across those species: are all of them present at similar levels of abundance, or do some species dominate? If more rare types of bacteria exist in the sample, the Shannon diversity will be higher.

Is a diverse gut microbiota ‘healthier’?

It’s true that in the majority of studies, a higher gut microbiota diversity in adults is associated with better health. This is to be expected based on what we know about ecosystems in general: an ecosystem with many (diverse) components is more robust and resilient. One medical researcher I heard at a conference went out on a limb and proposed that maintenance of gut microbiota diversity should be addressed by doctors, either as part of treating chronic diseases or as a way of maintaining health.

But on the other hand, there’s not much evidence that diversity is the feature that actually causes better health. And in some cases, scientists find that gut microbiota diversity is associated with poorer health: for example, people whose food takes longer to transit through the colon, with constipation-like symptoms, show a higher gut microbiota diversity.

So it’s definitely not the case that a diverse gut microbiota equals healthy. Some scientists propose that gut microbiota diversity may be necessary but not sufficient for good health. That is to say, the relationship between health and gut microbiota diversity is a bit like being wet and swimming: You can’t swim without getting wet, but if you’re dripping wet at any particular moment it doesn’t guarantee that you’ve gone swimming. Similarly, you probably cannot be healthy without having a reasonably diverse gut microbiota, but a diverse gut microbiota doesn’t guarantee that you’re healthy.

How diverse is diverse enough?

While in general it’s better to have higher gut microbiota diversity than lower diversity, scientists have not been able to identify a specific diversity score cutoff that classifies a person as either healthy or not healthy.

It is possible, however, to compare your gut microbiota diversity to a group of other people to see how you rank. Some companies that test your gut microbes will give you a ‘percentile’ that tells you what percentage of the group has a diversity score that’s lower than yours. In this case, remember that your percentile is based on the limited number of people that the company or study has in its database, and it may not represent how you rank compared to the general population.