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franciscozorrilla / metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
https://franciscozorrilla.github.io/metaGEM/
MIT License
189 stars 41 forks source link

Question about applying method for different biomes #88

Closed sskashaf closed 1 year ago

sskashaf commented 2 years ago

Hi Francisco!

Fantastic tool! Super excited to try it out. I am interested in applying your tool for the skin. A lot of the samples in your paper were from the gut. Do you know how I can best apply your tool to model interactions in the skin, which is more nutrient poor? Anything else (other than the media) that you can think of that would differ for the skin?

Many thanks, Sara

franciscozorrilla commented 2 years ago

Hi Sara, happy to hear that you are interested in the pipeline! 💎

Regarding media, this is something that you would have to adapt/design based on literature/domain knowledge and using metabolite IDs from the bigg database. Besides that, I would perhaps expect that the communities are smaller than in the gut (i.e. less MAGs per sample). Unfortunately I have not studied the skin microbiome in detail so I am not sure what else would be unique to such an analysis, but you should be able to apply the metaGEM pipeline to those sample without any problems.

Please let me know if you come up with any further questions or interesting observations!

Best wishes, Francisco