Shannon's alpha diversity index range

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?

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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.

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Hello Stanislav,

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.

Colin

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But what’s the one being used in QIIME2?

We use scikit-bio which uses log2 :slight_smile:

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