LefSe with absolute abundances?

[Jose Antonio Morillo Perez]

Dear colleagues,

 

I am a environmental microbiologists working at CSIC (Spain). First, I would like to thank you for your contributions and the help provided in this and others forums.

Recently, it has been suggested  a collection of methods to obtain absolute abundance of microbial taxa, combining for example qPCR data and sequencing. Apparently, new patters emerge from the quantitaive data - not visible with the typical metabarcoding relative abundances (of course all methods have limitations and biases)-. 

Check for example this paper, where the authors use LefSe to analyze ABSOLUTE instead of relative abundances of soil microbiome. We would like to use the same approach with our soil samples:

 

https://onlinelibrary.wiley.com/doi/full/10.1002/ldr.2838

Our question is: can we simply load absolute abundances in LefSe? Does it make sense (as it was conceived for relative abundances)? If yes, is it necesary to change any default parameter or something no so obvious for not experimented users?

 

Thanks you very much in advance!!

 

Best regards,

 

Jose

 

 

Jose A. Morillo-Pérez, PhD

 

Functional Ecology Group

Estación Experimental de Zonas Áridas - CSIC

Carretera de Sacramento s/n

La Cañada de San Urbano

04120-Almería

Spain