How we calculate microbiome diversity in Biomesight
Many people would assume that diversity is simply an indication of the variety of bacteria in their guts, and therefore the higher the number of different organisms, the higher the diversity.
While the number of different organisms definitely factor into the equation, there are other factors which weigh in also:
- Evenness of the distribution
- The overall taxonomy of the organism
Why does this matter? Lets illustrate with an example.
A. Lets say we have a community of 1000 organisms, of 5 different species, each representing 200 organisms and therefore 20% each.
B. Lets say we have a community of 1000 organisms, of 5 different species, one species have 996 organisms, while we have only 1 member of each of the other species.
Which of these two communities are more diverse? Instinctively we sense that community A is more diverse. While B has the same species present they are a minority species and therefore harder for them to survive and thrive. This is why the evenness of the distibution factors into the diversity calculation.
The next aspect not commonly considered is the taxonomy. The reason we factor in both, is because taxonomy is also relevant as an indication of real diversity.
Again 2 examples:
A. 1000 organisms, 5 genus, 5 species within each genus, with a total of 25 species. Each species is present in equal proportions.
B. 1000 organisms, 1 genus, 25 species within the genus. Each species is present in equal proportions.
Again we instinctively know that community A is more diverse even though both have the same evenness distribution at the species level.
Biomesight uses the Shannon-Wiener diversity index for the above calculation. This is a standard measure of diversity which factors in both evenness and overall number of different organisms.
For those of you that might be familiar with what Shannon index numbers normally look like - you will see this number only within the boxplot chart, which illustrates where the sample fits into the overall Biomesight database. In this example. the diversity is higher than average.
Furthermore, we convert the the figure into a percentage value scored out of 100, to make it easier to interpret and utilize in the overall score. Those within the top 5% percentile of all samples, will score 100. The rest will see the score as a percentage of the 5% cut off point.
We also segregate sample sets by sample type, e.g. the vaginal microbiome will be much less diverse than a typical gut microbiome. Additionally we segregate by lab. Thryve and Biomesight are scored in the same batch as we share the same lab protocols and typical number of reads per sample. uBiome and psomagen are in the same collection as they use a higher number of reads and have relatively higher Shannon index scores.
Lastly, is higher diversity always better? No, diversity is simply one measure which is why it factors into our gut health score but does not dominate the score as it weights in at 20% of the overall gut score. Additionally, some research studies are finding there to be a middle zone of "optimal" diversity, meaning that more diverse is not always better.
Note that our scoring system and calculations and constantly under review and we will keep this article updated on the latest factors weighing into the calculation.