metaphlan2 with metatranscriptomics data

[clémence defois]

Hi humann2 folks,

I am trying to run metatranscriptomic data from the human gut microbiota on metaphlan2.

However only 3-4 species came out of the analysis... (while it might be rather close to one hundred).

How can it be possible ?

Best regards,

Clemence Defois

[clémence defois]

Hi,

No one has tried to use metatranscriptomic reads with MetaPhlAn?

Clemence

[Nicola Segata]

Hi Clemence,

 MetaPhlAn2 is an estimator of species presence and abundance. Because it is not a program for classifying reads it is not directly applicable to metatranscriptomics. You can quantify the abundance of the markers in metatranscriptomics data, but the post-processing is not something standardized and included in the package.

For metatranscriptomics you would recommend HUMAnN2 for an overall assessment and PanPhlAn for strain-specific stranscriptomic analysis.

thanks

Nicola

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[Flo]

Hi,

I am also deeply interested by this topic.
I have a dataset of Saliva metagenome and metatranscritome and I run metaphlan2 on both DNA and RNA reads.
The output seems quite nice and I wanted to compare the relative abundance of the taxa in the metagenome as compare to the metatranscriptome.
The richness at the genus level is 40-70 in the metatranscriptome and 40-60 in the metagenome.

Why is this approach not robust? Is it because the markers you define are present at the genome level but not necessarily at the transcript level?

Thanks a lot


Flo

[Nicola Segata]

Interesting. The theoretical problem is that we quantify species abundance by averaging the coverage of marker genes. Marker genes are supposed to be at the same coverage as they are single copy genes from the same genome, but this is not true for their transcripts. So MetaPhlAn2 on metatranscriptomics gives an idea about the average transcriptional rate of a given species. So it _can_ be used with caution...

Nicola

[Flo]

Thanks a lot for your answer. Then what would you recommand to combine metagenomic and metatranscriptomic analysis using your tools? The idea is to describe the community which is present and the one which is active and try to find out who is doing what.
I also tried to use a diamond blast appraoch agains NCBI-NR at both DNA and RNA levels and compare the proportion of taxa within the community between the two as well as the reads assigned to particular functions. But I am not convience at all to the accuracy of taxonomic affiliation of this short read blasting approach at the species level...
If you have any suggestion, that will be helpful.
Thanks a lot!

[Nicola Segata]

Hi Flo, for combined metagenomics/metatranscriptomics I would recommend HUMAnN2 for an overall assessment and PanPhlAn for strain-specific stranscriptomic analysis.

cheers

Nicola

[Flo]

Dear Nicolas,

Thanks a lot. I am exploring the strategy you suggested.

Cheers,

Flo