Methods for integrating 16S and RNAseq data

Hello :grinning:

I have 16S microbiome data and RNAseq data for the same tissue. Both samples were collected at the same time and I would like to integrate them. The idea is to investigate the effect that the microbiome has on the tissue’s transcriptome.

Any suggestions on how to go about this?

Thank you for any help you can offer!

Hi @jbioinf ,

This is a pretty loaded question and the process quite complex, but I think perhaps building a co-occurrence network using mmvec might be a good first step, see original paper here for some use-cases with microbiome +metabolite data. Note that co-occurrence != causation, so even if you do find some interesting patterns, unless you can support with other experiments/data there really is no way of saying the microbiome is directly affecting the transcriptome, unless perhaps you have some very controlled experiment design.


Thank you very much, @Mehrbod_Estaki!! I will look into mmvec.

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