Team:IISER-Pune-India/Contribution
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Contribution
Setting up for SteadyCom
"A checklist to help build a multi-species model and troubleshoot SteadyCom on COBRA Toolbox"
SteadyCom is an algorithm used to analyze steady-state metabolic behaviors of co-cultures, microbiomes, and host-microbe interactions. We used SteadyCom to analyze our co-culture of S. elongatus and E coli and to predict how variation in certain parameters would affect its steady-state behavior.
The COBRA toolbox on MATLAB contains a ‘SteadyCom.m’ function that runs the SteadyCom algorithm taking in a joint community metabolic model as an input. This community model is built from pre-curated Genome-Scale Metabolic models (GSM) for each of the individual species in the consortium.
The COBRA toolbox does have functions to construct community models from individual GSMs; however, we faced several problems during this process which required considerable troubleshooting. The issue lies in the fact that there is an absence of standardization in the construction of GSMs for individual species. On top of this, there is very sparse documentation on the SteadyCom function, and the functions needed to construct a joint community model.
In fact, we spent at least 2 months troubleshooting the process of building the community model and obtaining initial results using SteadyCom. Most of the issues we faced were due to minor differences in the standards used in the individual GSMs and those required by SteadyCom. Though these are issues that are not very difficult to fix once they have been identified, they were quite difficult to diagnose due to the lack of adequate documentation.
In light of all of this, we resolved to create a checklist for future SteadyCom users based on the insights we have gained over the past few months. This checklist document contains information on how to ensure that individual GSMs have the specific standards required to build a joint model, the steps involved in building and testing a joint model, and troubleshooting techniques that have worked for us while using SteadyCom. This document would also give readers additional insights into how community models are organized and how to tackle other issues that they might come across.
We spoke to Dr. Maziya Ibrahim, a Postdoctoral Fellow at the Indian Institute of Technology, Madras who is currently working with SteadyCom to model the production of industrially relevant metabolites such as Lactic Acid by microbial communities. She went through our checklist and gave us her feedback on the usefulness of this document as a regular user of the algorithm, and inputs on what else we could incorporate into it.
You can read more about the meeting with Dr. Maziya Ibrahim here.
We believe that with the help of this checklist, future users would be able to build their models and obtain results from SteadyCom in a more efficient and hassle-free manner, without having to spend so much time figuring out all the intricacies of the algorithm by themselves.
The document can be found on our GitHub page here.
Cyanobacteria - Tips and Tricks
Synechococcus elongatus is an up-and-coming phototrophic chassis, which differs significantly from E. coli in terms of the protocols for its upkeep. We were fortunate to have Ph.D. mentors who have worked on this chassis and have benefited from the support provided by them and other researchers working in the area.
There is a body of knowledge that is passed down orally from mentor to student in the cyanobacterial research community that is often undocumented in the literature and cannot be accessed by anyone wishing to start off working with these niche model organisms. For information on reviving cyanobacterial strains, practical knowledge on gradual passaging of the cultures, ways to handle aggregation of cells, and a quick guide to setting up a phototrophic culture without a photo-incubator or a CO2 pump - our written guide, Cyanobacteria - Tips and Tricks is an invaluable resource.
Literature to existing parts
As a contribution to other iGEM teams, we have also added literature to the following parts on the registry:
- psbA1 - BBa_K754000
- psbA2 - BBa_K2596003
- cpcB - BBa_K2596001
- cpc560 - BBa_K2924000
Team IISER Pune India