Metabolic analysis with Qiime2 and Picrust2

I’m working on human microbiota using the 16S analysis and I obtained a metabolic profile of my samples using picrust2 plugin of Qiime2.
I would kindly like to ask you, if you know some scripts or applications that can provide links between metabolic pathways, that are significantly changed, and that can clearly represent them.
Thank you very much!

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Hi @Teonexone,

Do you mean that you want to see the differences of the metabolic pathways between samples?
I think you can try:

  1. https://bitbucket.org/biobakery/biobakery/wiki/lefse
  2. ANCOM function which already implemented in Qiime2, please see the moving picture tutorial in Qiime2

Hope that helps.

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Thanks @Lei,
I’ve already use the methods you suggested but I have obtained too much results to have a clear overview on the metabolisms changing.

Hi @Teonexone,

Are all the results significant? May be you need to describe your questions more specific and in more details.
I am also not an expert of statistic. Let’s waiting for other people’s reply.

Hi @Teonexone,

I really like your question, as I’ve tried to do this too and couldn’t find any easy to use scripts or applications to answer these questions.

The last time I worked with picrust predictions, I calculated a simple log2-fold change between groups, took the most enriched pathways, and visualized them on a pathway map using iPATH 3.
https://pathways.embl.de/

Colin

Thank you @colinbrislawn
I’m trying to use iPATH3 as you suggested me and it could be what I was looking for.
Matt.

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Maybe, something similar to categorize_by_function.py for Qiime1?