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cdanielmachado / smetana

SMETANA: a tool to analyse interactions in microbial communities
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Comparative Analysis of MIP and MRO Across Variable MAG Compositions and Investigating Cross-Feeding Pathways in Microbial Communities #44

Open Noob-Monkey opened 4 months ago

Noob-Monkey commented 4 months ago

Hi Daniel, I'm calculating MIP and MRO based on MAGs assembled from different samples using SMETANA. The number of MAGs assembled varies between each metagenomic sample. Can I compare MIP and MRO between different samples directly? Would the results obtained in this way be meaningful? Here are my two sets of results, calculated based on communities composed of 16 MAGs and 20 MAGs, respectively. community medium size mip mro all complete 20 19 0.5905817174515235 community medium size mip mro all complete 16 11 0.6201550387596899

  Another question is, once I've identified a cross-feeding relationship between two species, A and B, using SMETANA, such as A providing D-Ribose to B, how can I determine the metabolic processes through which A generates D-Ribose and the processes through which B utilizes this D-Ribose?

donor compound receiver oQNBC01 M_rib__D_e oUBA7950 oHumimicrobiales M_cellb_e oMethanosarcinales oDHVEG-1 M_cellb_e oMethanosarcinales oHumimicrobiales M_man1p_e oDehalococcoidales

Thank you in advance! JackChang

franciscozorrilla commented 1 month ago

To identify the metabolic processes associated with exchanged metabolites in your donor and reciever you could just run individual FBA simulations and visualise internal fluxes associated with your pathway of interest.

In the original SMETANA publication they normalize MIP by total community members, while in a more recent study they do indeed separate the score by community sizes. It probably depends on the question you are trying to ask.