The theme of this year’s world microbiome day is diversity. Now more than ever, there’s no doubt that we are not the only ones thinking about this concept. But how do microbiome scientists define diversity? How do we measure it and how do we value diversity in the microbiome? In this short blog, I’ll share some answers to these questions and, on a more personal note, draw parallels to issues of diversity in STEM.
We think of microbiomes as communities of microbes. The simplest definition of microbiome diversity is something like this: more microbial species living together = a more diverse community. In microbiome science, we call this “alpha diversity”. We can make it a little more complex by thinking about balance in the community; there might be many different types of microbes, but if one (or just a few) species dominates, this detracts from alpha diversity. And we can make it more complex again if we think about how closely related the individual species are; If all the species are from the same family, this again detracts from alpha diversity.
Using these ideas, we can indeed measure diversity. But the final measurement will differ depending on what we value most: do we care more about sheer numbers of different microbes, about the balance between them, about how related they are, or perhaps about what functions they have, what they can do as a community? This means that there’s quite the diversity in diversity measurements!
Despite the scientific reticence to assign values of “good” or “bad” to our descriptions, I think the general view has typically valued higher alpha diversity as a positive thing. There’s logic in this view. The more species there are in a microbiome and the more they differ from each other, the more things they should be able to do and the better they should be able to cope with new challenges. They are more likely to have complementary functions, able to make up for what each individual lacks on its own. Initially, these ideas seemed to fit with the microbiome’s role in human health too. When scientists started looking at the microbiomes of different people, there seemed to be a general trend that healthier people had more diverse microbiomes.
As microbiome science is maturing, the answer is becoming more complex. We are finding more examples where higher diversity is not a good thing. Either because it’s just not very meaningful, or worse, where it might be associated with disease or dysfunction. This first option makes sense: trying to simplify a rich community made up of 1000s of individuals down to just one number is a bit crude, to say the least. The second option, which paints high diversity as “bad” in at least some cases, might be less intuitive. But let me give some examples. In my own travels into microbiome science, I’ve been drawn to trying to understand the microbiome’s role in children’s development. We are not born with the same high levels of alpha diversity as we see in adults. Instead, we gain diversity slowly over time. It seems that this course of development is important and protective in some way. There are also certain parts of the human body that are better suited to more or less diversity. We might want high diversity in our gut microbiome, but in other body parts (like on our skin or in our eyes), the same diversity would indicate disease. This is partly because the communities in these areas (we call them “niches”) are generally much smaller, with more specific functions. The microbes in our eyes don’t need to break down food into nutrients, don’t have to deal with high levels of acidity from the stomach, don’t have to navigate through the complex canals of the intestines. So they can afford to be less diverse, to have a narrower set of skills to solve the specific problems they will encounter (mostly intrusions from airborne pathogens [coronavirus might spring to mind], contact lenses and the like). Being overrun with different species might mean that there’s not enough of any one individual to be able to do the important jobs. Too many species in these niches will lead to competition instead of cooperation, undermining the stability of the community. So, is diversity in the microbiome good or bad? The only (probably unsatisfying) answer I can give is that it depends on the context.
Given the current climate, I can’t leave this conversation about diversity without thinking about how it applies to my own community. Unfortunately, there is a natural tendency to low diversity in academia, where we rely on networking and traditional systems for granting jobs, funding, and other opportunities. These systems tend to favour those who share similar backgrounds, ways of thinking, and the language of the existing community. Academia is also a highly competitive niche where small advantages can amplify over time, too often pushing out those on the fringe.
Would higher diversity be a good thing? My own experience has been that diversity in STEM is as close to unilaterally beneficial as it can be – microbiome science in particular, as a fundamentally transdisciplinary (ad)venture, has much to gain from a diversity of expertise. But it also has much to gain from a diversity of human experiences, be they related to culture, race, geography, gender or something else altogether. As I’ve matured, I’ve realised that science is not about finding one right answer. It is about approaching a problem from many angles, about being curious and open-minded enough to come up with creative ways to get closer and closer to the truth, with all its nuances, caveats, and complications. As an individual, there are only so many angles that we can see, so we NEED diversity to be stronger scientists and to do better science.
But high diversity is not enough on its own. A community that lacks support for its diverse members is not sustainable. If we truly want diversity in microbiome science, in STEM, in academia, then we need to foster these niches to be supportive of diversity. Instead of encouraging competition between individuals, the whole community will benefit from cooperation and fair access to resources. For this to happen, there must not only be a diversity of individuals, but also balance in the community in terms of contribution to ideas and other power structures. Perhaps ironically, creating this balance might require some specific low-diversity niches – protected spaces intended solely for womxn, or queer, or minority race individuals to organise, to share experiences, and to support and empower each other. In our role as researchers, we pride ourselves on being problem-solvers, innovators, and deep thinkers. If diversity is something we say we value, we must apply our skills beyond the lab to foster and strengthen our community.