I am getting Shannon’s alpha diversity index values in the range 6-8 for one of the soil studies. Is that OK? Some soil studies (where authors usually use QIIME 1/2) also report Shannon’s indices as high as 7. But others are generally more moderate like, for example, 2-5.
For example, for gut microbiome (HMP) Shannon’s index values fall in range 2-5.
Are there different methods in computing Shannon’s alpha diversity? Which one is implemented in QIIME2?
Just checked output from my soil samples, I got Shannon’s alpha diversity index in the range 6-8 too. Microbiome of the soil contains more different bacteria so its ok.
Yes! In fact, this question was just raised in this post! The basic issue is that Shannon’s metric can use a log of any base; log-base-e with
ln(), or log-base-10 with
log(), or log-base-2…
While any base-log can be used, I’ve never seen the Shannon base-log reported in a paper. But these differences could be why the magnitude of Shannon varies between papers.
But what’s the one being used in QIIME2?
We use scikit-bio which uses log2
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