Picrust 2 vs Tax4fun

[Felipe Melis]

Hi there my name is Felipe Melis and I'm a PhD student from Chile, 

I'm working with Picrust 2 and making a comparison with Tax4fun2. I have samples from different soils and I noticed that I have a huge difference in results between two methanogenic-related KOs. Tax4fun predicts the presence of K00400 and K00401 in most of the samples, while in Picrust 2 those functions only a appear in very few samples. Investigating in detail at the default databases from the two implementations, that are used to compare the 16S OTUs to the references for the functional annotation, I discovered that Tax4fun had a huge amount of sequences and organisms (thousands of taxa) associated to those methanogenic functions so they have high chance to predict them, while in comparison Picrust 2 only have around 140 sequences and thus is absent most of the time. Do you have any clue or hint about these big differences? 

[Gavin Douglas]

Hey Felipe,

This is definitely an interesting observation - I’m not sure why the numbers of reference genomes annotated with those KOs would differ so much. It’s possible that the latest Tax4Fun2 database has more archaeal taxa in the reference database.

Have you dug into the taxonomic classification of OTUs predicted to encode these functions in your dataset? If these KOs are expected to be restricted only to specific archaeal lineages then it may be a red-flag if any bacterial 16S OTUs in your dataset are predicted to encode the KO based on either tool.

Cheers,

Gavin

On Sep 9, 2021, at 12:34 PM, Felipe Melis <felipe...@gmail.com> wrote:

Hi there my name is Felipe Melis and I'm a PhD student from Chile, 

I'm working with Picrust 2 and making a comparison with Tax4fun2. I have samples from different soils and I noticed that I have a huge difference in results between two methanogenic-related KOs. Tax4fun predicts the presence of K00400 and K00401 in most of the samples, while in Picrust 2 those functions only a appear in very few samples. Investigating in detail at the default databases from the two implementations, that are used to compare the 16S OTUs to the references for the functional annotation, I discovered that Tax4fun had a huge amount of sequences and organisms (thousands of taxa) associated to those methanogenic functions so they have high chance to predict them, while in comparison Picrust 2 only have around 140 sequences and thus is absent most of the time. Do you have any clue or hint about these big differences? 

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