Team:Toulouse INSA-UPS/Partnership
Overview
We decided to engage in a collaboration with IGEM IISER-Pune-India because we shared mutual objectives: we both focused on a co-culture involving the same strain of cyanobacteria and we both needed to model our co-culture system. The Pune team has established a consortium between their cyanobacterium that provides the sucrose and E. coli which in turn produces butanol, while our consortium use the same cyanobacterium to produce sucrose too, but in co-culture with a yeast. Numerous meetings have punctuated our year. Our collaborative work shaped our mutual project at different stages, particularly in the Modeling , Wet lab and Human Practices parts.
For these reasons, we decided together to reconsider our collaboration as a real partnership.
Experimental part
As we were planning in our respective projects to use the same sucrose secreting cyanobacteria strains, we gave them our contact in the Pakrasi lab so that they could also recover them. Throughout the project, we exchanged data, protocols as well as tips regarding how to grow our cyanobacteria as efficiently as possible. Click here to see the cyanobacteria growth results.
Figure 1: Setup used by our team for the cultivation of cyanobacteria.
Dry lab part
We extensively collaborated with Pune on the dry lab part. First, we compared our implementation of the sucrose secretion pathways on our respective Genome Scale Models. Using our different modeling approaches, we were able to verify that our results were similar and thus validated the reproducibility and usability of our models. Second, we shared our dynamical modeling approach and help them to successfully simulate the dynamic behaviour of their own co-culture system. Finally, we extensively discussed the results of our complementary modeling approaches, which were highly consistent. As a major result, both approaches confirm that sucrose production by cyanobacteria should in fact be reduced to optimize the process. Click here to see our dry lab work.
What did the iGEM IISER-Pune team bring to the iGEM Toulouse INSA-UPS team?
IISER-PUNE team worked on a different in silico strain optimization approaches than us (Flux Scanning based on Enforced Objective Flux (FSEOF) and Optknock). Using their stationary flux analysis approach, they identified potential targets for gene overexpression or deletion to improve the sucrose secretion. They communicated their results to us and we warned them that our dynamic model demonstrated that increasing the production of sucrose is in fact not relevant to enhance the production of our violet fragrance, in contrary to what both teams intuitively expected when starting the project. They were able to assess and confirm our findings, which strengthen our own results.
They also worked on an alternative approach to model microbial communities with Steadycom. Using the code they provided to us, we were able to obtain a positive global community growth which confirmed the feasibility of our project, as demonstrated by our own modeling framework. Overall, the comparison between their static method with our dynamic approach has highlighted the interest of the models we have developed and strengthened our modeling results.
Figure 2: Throughout the summer, our two teams exchanged on the different points of the partnership by holding regular meetings.
What did the iGEM Toulouse INSA-UPS team bring to the iGEM IISER-Pune team?
To understand, predict and ultimately control the behavior of the synthetic microbial
consortium, we developed a mechanistic and dynamic model of our system, based on
differential equations and genome scale metabolic models. This model is made available in
the form of a commented Jupyter Notebook to the future iGEM teams
willing to obtain a dynamic insight on their own synthetic microbial consortiums.
In the partnership, we shared and explained our code with iGEM IISER-Pune so that they were
able to adapt the model to their own project, and use it to predict and understand the
behavior of their butanol-producing microbial community.
Figure 3: Example of simulation obtained by the iGEM IISER Pune team using our dynamic coculture modeling method.
Furthermore, counter-intuitively and as said before, our model predictions showed that we must slow down sucrose production to increase the production of our molecules of violet accord. Using our code and their alternative approach of SteadyCom, the iGEM IISER-Pune team came to the same conclusion, which highlights the usefulness of using a dynamic model like ours to predict the behavior of a synthetic microbial consortium.
Human practices part
Cyanobacteria Symposium
iGEM IISER-Pune proposed us to participate in the organization of the Cyanobacteria Symposium with the teams iGEM Stony-Brook, Hong-Kong HKU. These two days of activities were cut between the presentation of our respectives projects in front of cyanobacterial experts like Dr. Daniel Ducat and Prof. Himadri Pakrasi and participation to Workshops, talks by cyanobacteria expert Dr Tiago Toscano Selao, and games.
Figure 4: Cyanobacteria Symposium allowed us to get feedback on our projects from experts in the field.
