The Diversity score is simply the number of different types of Bacteria or Archaea in your sample, based on differences in their DNA sequences. This is sometimes called alpha diversity. Diversity does not take into account any differences in the relative abundance of the various types; it simply counts them.
This concept is easy to visualize with large animals like aquarium fish. A tank housing only a single type of fish has low animal diversity, while a reef tank with multiple species of fish, snails, crabs, and corals has high animal diversity.
We can describe microbial communities in the same way, although here the diversity can’t be seen with the naked eye. A diverse microbial community includes many different kinds of microbes (single celled organisms including Bacteria and Archaea). A pure culture of a single bacterial type, on the other hand, has very low diversity.
Technical details: because the raw number of types detected in a sample is affected by the total number of DNA sequences in the sample, we account for variation in DNA sequencing coverage using a statistical approach called rarefaction. This allows for an apples-to-apples comparison between samples that receive different levels of sequencing coverage.