Patterning in Microbial Consortia

On 13 February, 2023

Scientists are studying this spatial organization of microbial communities to understand the relationships between different microbes better and their functions in that particular environment. For example: in the human gut, various parameters such as pH, oxygen concentration or substrates keep varying and different bacterial families reside in a location where the parameters are most conducive for their growth. Understanding why particular bacteria prefer a particular location helps in ascertaining their function in the community and that environment better. Such knowledge also helps in devising novel biotechnological solutions such as biosensors or biofilms with desired properties based on spatial organization parameters like location and strength of coupling among different species.

Read the whole blog at https://rbcdsai.iitm.ac.in/blogs/new-models-to-study-spatial-organization-in-microbial-communities/

Access the PICCASO tool at https://github.com/RamanLab/picCASO

Original Paper: 

  • [DOI] S. Venkatraghavan, S. Anantakrishnan, and K. Raman, “Probing patterning in microbial consortia with a cellular automaton for spatial organisation,” Scientific Reports, vol. 12, iss. 1, p. 17159, 2022.
    [bibtex] 
    @article{Venkatraghavan2022Probing,
  title = {Probing patterning in microbial consortia with a cellular automaton for spatial organisation},
  volume = {12},
  copyright = {2022 The Author(s)},
  issn = {2045-2322},
  url = {https://www.nature.com/articles/s41598-022-20705-7},
  doi = {10.1038/s41598-022-20705-7},
  pmid = {36229548},
  abstract = {Microbial consortia exhibit spatial patterning across diverse environments. Since probing the self-organization of natural microbial communities is limited by their inherent complexity, synthetic models have emerged as attractive alternatives. In this study, we develop novel frameworks of bacterial communication and explore the emergent spatiotemporal organization of microbes. Specifically, we built quorum sensing-mediated models of microbial growth that are utilized to characterize the dynamics of communities from arbitrary initial configurations and establish the effectiveness of our communication strategies in coupling the growth rates of microbes. Our simulations indicate that the behavior of quorum sensing-coupled consortia can be most effectively modulated by the rates of secretion of acyl homoserine lactones. Such a mechanism of control enables the construction of desired relative populations of constituent species in spatially organized populations. Our models accurately recapitulate previous experiments that have investigated pattern formation in synthetic multi-cellular systems. Additionally, our software tool enables the easy implementation and analysis of our frameworks for a variety of initial configurations and simplifies the development of sophisticated gene circuits facilitating distributed computing. Overall, we demonstrate the potential of spatial organization as a tunable parameter in synthetic biology by introducing a communication paradigm based on the location and strength of coupling of microbial strains.},
  language = {en},
  number = {1},
  urldate = {2022-11-15},
  journal = {Scientific Reports},
  author = {Venkatraghavan, Sankalpa and Anantakrishnan, Sathvik and Raman, Karthik},
  month = oct,
  year = {2022},
  keywords = {Computational biology and bioinformatics, Microbiology, Systems biology},
  pages = {17159},
}

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