Modelling communities of micro-organisms

On 1 March, 2013

Micro-organisms are rarely found to live in isolation in their natural environment. Organisms are found to co-exist in many scenarios, functioning in consolidated and socialising communities. The growing availability of high-throughput sequencing techniques and developments in the field of metagenomics have enabled the generation of large amounts of data about microbial communities. Despite this, sparingly little knowledge is available about the principles governing these ecosystems and interactions among component organisms. The microbial communities have immense unexplored potential – be it in bioprocessing, bioremediation, therapeutics etc. This calls for development of efficient modelling frameworks to shed light on the design principles of these microbial communities.

Different types of microbial communities are found in environment ranging from two organism based syntrophic systems to finite member consortia to impossibly large microbiomes. The aim of community modelling is the development of a framework to understand the design principles of any microbial community. Understanding of the design principles will help not just explain the structure and function of the community but also give scope for predictive modelling. A complete microbial community model should capable of explaining the composition, function and dynamics of the community.

In particular, we are interested in questions of the following nature:

  • Composition of the community:
    • What are the organisms that can co-exist in a given community?
    • For any community, what parameters that shall determine whether a certain arbitrary organism can co-exist in the system?
    • What would be the ideal characteristics for any new member to complement to the existing members in a given community?
  • Topology of the community:
    • How do the organisms arrange themselves in a given community?
    • What is the relative abundance of each member in the community?
    • What is the organism hierarchy and who are the key players?
  • Functional behaviour of the community:
    • What is the output of the system given an input?
    • What are the various functions of the system and how are they related to the organisms constituting the system?
    • What is the consumption pattern of the system and how does it vary over time?
  • Dynamics of the community:
    • How does the system evolve over time?
    • How does the system respond to changes in system input? (like growth media)
    • How does the system respond to perturbations? (i.e. if there is a network breakdown, how will the new structure look like over time)

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