A better focus on the host metabolism when a host is provided

[cfrioux]

Currently, providing a host will not impact the first part of m2m which is the calculation of individual scopes for bacterial members of the community.

We want the host to be considered with each individual symbiont already at that step. This would lead to calculating what is producible by the symbiont in a community consisting of the host + the symbiont. More precisely, the activated metabolism of the host in the medium will provide new metabolites that can be used by the symbiont. Using miscoto focus should do the job.

The community scope will be calculated as it is currently, considering the added value of the host metabolism as well as the other symbionts' metabolism.

A specific focus on the host gain with its community (what it produces with the community - what it produces alone) should be performed too.

Should the targets to be considered be the host metabolites that are producible only in community?

[ArnaudBelcour]

If we take as example the human gut microbiota, I think there is (at least) 2 ways to consider the host for metabolic interactions:

• the host is a direct member of the interactions and I think the way you described it with miscoto focus corresponds to this.

• the host is an environment. By its diet and the metabolic degradation of the food the host will create a set of metabolites that will correspond to the seed of the microbial community. With this behaviour I find the host to be more something like an environment (in which we expect a set of metabolites to be present) rather than an active member of the interaction. So, we should have something such as:
  Diet -> host -> processed | unabsorbed metabolites -> Microbial community -> Host
  In this case we could compute:
  Seeds -> iscope host -> new seeds (output of iscope) -> Iscope Microbial communtiy -> Comscope -> new iscope of the host with new seeds (results from comscope)

It is just an idea that I have last night so it could be wrong but I think this duality environment/active member of interaction is quite interesting.