Hi community!!! I am seeing two different formulae for the Bray-Curtis beta diversity Index. Wikipedia shows different formula from this website . Can anyone please tell me which one should be used in microbiome diversity analysis?

Which formula of Bray-Curtis beta diversity index should be used for microbiome beta diversity analysis?

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6 weeks ago

dpc
▴
170

Hi community!!! I am seeing two different formulae for the Bray-Curtis beta diversity Index. Wikipedia shows different formula from this website . Can anyone please tell me which one should be used in microbiome diversity analysis?

1

Entering edit mode

6 weeks ago

antonioggsousa
★
2.1k

Hi @dpc,

Which software you'll use to calculate the Bray-Curtis distance (beta diversity)?

I think this can be more important than the difference between formulae used in the wiki and the website highlighted.

I did not went through both websites, but there is dissimilarity and similarity Bray-Curtis indexes (and probably other variations of the index).

If you use for instance the `phyloseq`

R package to estimate the Bray-Curtis distance, I think you will be fine.

António

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Yes sir. I am using

`phyloseq::distance`

function for the calculation with option`method= "bray"`

. My question is which formula is used in this case for the calculation? I am confused between the following two:and,

take one row, compute it yourself, and you'll immediately know which formula is used.

you can also consult the original publication for phyloseq

I tested and both formulas seem to be equivalent to me or at least they yield the same result for the dummy OTU table used.

You can see below my implementation in R of the formula in the Wiki using the OTU dummy table from the other site and the result is a Bray-Curtis dissimilarity matrix equal to the other site and to

`phyloseq`

. So, I think although the formulas are different they are equivalent. This is my opinion based on the test. The implementation on the site does not check for the sum of the minimum value of each taxa/OTU across samples, neither subtract the division to one, whereas the wiki does.## bray-curtis implementation

Anyway, using the

`phyloseq`

implementation of Bray-Curtis is a safe option (that relies on`vegan`

).I hope this helps,

António