Microbial pathway analysis tool or pipeline

Question

[ssko]

Hello everyone!

I had 16S rRNA sequence data obtained from 21 samples which are separated into two groups. I performed functional community prediction with these 16S sequences using MicFunPred tool. Then, I obtained an ortholog table (KO table) like OTU table. Using this table, I did differential abundance analysis to see significantly abundant features between two groups. When I use fdr correction I got a few statistically significant KOs.

I was tasked to find pathways from those significant KOs. I searched many articles and they mostly used Ingenuity pathway analysis tool or other commercial tools. Does anyone know of free, open source tools for microbial pathway analysis? or I am open to any advice/idea on finding pathways with the KOs information I have obtained.

Thank you all!

[Matthias Zepper]

Not exactly my field of expertise, but maybe you can get some inspiration for tools from nf-core ampliseq pipeline. Possibly some of the tools from the funcscan pipeline will also run with the input that you already have?

Answer 1

[Max Sikolenko]

Try paprica or PICRUSt2. Pathway prediction based on 16S rDNA metataxonomic reads is exactly what they do. I hope I understand your task correctly.

Also, there are some analogous tools listed and compared in “Inferring microbiota functions from taxonomic genes: a review”.

What concerns paprica, you can find some useful tutorials here: https://www.polarmicrobes.org/category/paprica/.

Answer 2

[michele.lamprillo]

I think you can simply load your KO's list up there in the KEGG website KEGG_mapper. Than you should see KEGG pathways drawn. I suggest you to read carefully instructions becouse i used it some times ago.

I have a question for you, i'm using MicFunPred tool too but i was not able to reproduce the last graph shown on the README file, where you?

[ssko]

I couldn't reproduce the last graph either, so I created a similar one using the KO_taxon_contrib.tsv file for the relevant path using R.