How do I identify pathogenic and symbiotic microbes from the Picrust2 output

[Shridhar Jambagi]

Hi all,

I am Using Picrust2 for the functional prediction of my 16S amplicon data set. The data is generated from the root and rhizosphere samples and I am interested in identifying soil borne pathogens and beneficial organisms and their abundance in different samples. 

Could you please let me know whether it is possible to do such analysis from the picrust2 out data files? If so, could you recommend how to do it? I am very new to this kind of analysis and your help is much appreciated.

Many thanks

Shridhar

[Gavin Douglas]

Hi there,

I’m not sure if there are any KEGG orthologs or MetaCyc pathways that would be obviously linked with pathogens / symbionts in the root and rhizosphere, but I would recommend starting there and seeing if any functions seems like they would be reasonable for distinguishing those type of taxa.

Once you have a list of functions of interest you could analyze the prediciton tables per ASV and/or the contributional output files (in stratified mode) to see which predicted genomes contain the functions you identify.

Cheers,

Gavin

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[Shridhar Jambagi]

Hi Gavin,

Thanks a lot. I will try and check it out.

Best

Shridhar

[Shridhar Jambagi]

Hi Gavin,

I have run the PICRUSt2 pipeline and generated the output files. Could you please suggest to me how to proceed with the further analysis to check whether I can identify the pathogenic group of organisms ?

Many thanks

Shridhar

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