Is it possible to predict functional profile of microbiome through 16S rRNA gene amplicon-based sequences?

Question

[barmonicin]

Hello to everyone! As stated in the question, is there any established pipeline that I can use to predict the functional profile (as in something similar as what functional metagenomics results can show) but only predicting them through 16S rRNA profile of the microbiome? Thanks a lot and regards.

[andres.firrincieli]

see PICRUSt2: link

and also PICRUSt2 key limitations

[barmonicin]

Thank you, Andres! I'll take a look on this one. Regards

[mamdouhmarwa]

Hello Guys Do you know if Piphillin is still working? Cheers Marwa

[GenoMax]

As of April 1, 2021, Second Genome discontinued support of the Piphillin web application.

[Nitin Narwade]

@mamdouhmarwa, as mentioned by @GenoMax the Piphillin web server is inactive but you can use their GitHub repo. The link is given in the answer below.

Answer 1

[Nitin Narwade]

There are many tools available out there for functional prediction based on 16S amplicon sequencing. I am sure there is some thread on Biostars related to this. However, I am enlisting here few of them.

MicFunPred

Paper Link: https://doi.org/10.1016/j.ygeno.2021.08.016

WebServer: http://micfunpred.microdm.net.in/

GitHub Repo: https://github.com/microDM/MicFunPred

PICRUSt2

Paper Link: https://doi.org/10.1038/s41587-020-0548-6

GitHub Repo: https://github.com/picrust/picrust2

Tax4Fun2

Paper Link: https://doi.org/10.1186/s40793-020-00358-7

GitHub Repo: https://github.com/bwemheu/Tax4Fun2

Piphillin

Paper Link: https://doi.org/10.1186/s12864-019-6427-1

GitHub Repo: https://githubmemory.com/repo/dmcskim/pyphillin

WebServer: https://piphillin.secondgenome.com/

[barmonicin]

Thank you so much, Nitin! I will refer to these resources you shared! Regards

[safeassli]

Helolo Nitin, thank you very much , However is it normal that Tax4Fun2 github repo is not awaible ? same thing for piphillin ? otherwise based on your experience what's the most suitable/reliable tool to predict functional profile of microbiome among these 4. thank you in advance

[Nitin Narwade]

Sorry for my late response.

Tax4Fun2 has a GitHub repo (I think it is an unofficial repo). However, you can always write to authors asking for the source code (Tax4Fun official website). On the other hand, Piphilin was hosted by Second Genome, and indeed they discontinued the support for Piphilin, again as they have mentioned here you can write to authors and ask to provide source code.

For your second question, now it is routine to use Picrust2 for the functional profile prediction based on amplicon data, however, if you would like to reduce false positives I would suggest using MicFunPred, as we specifically designed this tool to address this issue OR you can try both, compare the results and then select one.

Cheers!!

Nitin N.