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Title: A Microfluidics and Agent-Based Modeling Framework for Investigating Spatial Organization in Bacterial Colonies: The Case of Pseudomonas Aeruginosa and H1-Type VI Secretion Interactions

Abstract

The factors leading to changes in the organization of microbial assemblages at fine spatial scales are not well characterized or understood. However, they are expected to guide the succession of community development and function toward specific outcomes that could impact human health and the environment. In this study, we put forward a combined experimental and agent-based modeling framework and use it to interpret unique spatial organization patterns of H1-Type VI secretion system (T6SS) mutants of P. aeruginosa under spatial confinement. We find that key parameters, such as T6SS-mediated cell contact and lysis, spatial localization, relative species abundance, cell density and local concentrations of growth substrates and metabolites are influenced by spatial confinement. The model, written in the accessible programming language NetLogo, can be adapted to a variety of biological systems of interest and used to simulate experiments across a broad parameter space. It was implemented and run in a high-throughput mode by deploying it across multiple CPUs, with each simulation representing an individual well within a high-throughput microwell array experimental platform. The microfluidics and agent-based modeling framework we present in this paper provides an effective means by which to connect experimental studies in microbiology to model development. The work demonstratesmore » progress in coupling experimental results to simulation while also highlighting potential sources of discrepancies between real-world experiments and idealized models.« less

Authors:
 [1];  [2];  [1];  [3];  [3];  [4];  [5];  [6];  [7];  [2]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Computational Sciences and Engineering Division
  3. Univ. of Tennessee, Knoxville, TN (United States). The Bredesen Center
  4. Polytechnic Univ. of Catalonia, Barcelona (Spain). Dept. of Mathematics
  5. Polytechnic Univ. of Catalonia, Barcelona (Spain). Dept. of Physics
  6. Cranfield Univ. (United Kingdom). School of Water, Energy and Environment
  7. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Biosciences Division. Computational Sciences and Engineering Division
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22); ORNL Laboratory Directed Research and Development (LDRD) Program
OSTI Identifier:
1437197
Alternate Identifier(s):
OSTI ID: 1423048
Grant/Contract Number:
AC05-00OR22725
Resource Type:
Journal Article: Published Article
Journal Name:
Frontiers in Microbiology
Additional Journal Information:
Journal Volume: 9; Journal ID: ISSN 1664-302X
Publisher:
Frontiers Research Foundation
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING; agent-based modeling; Pseudomonas aeruginosa; Type VI secretion; silicon microwell arrays; microbial succession; microbial organization; spatial confinement

Citation Formats

Wilmoth, Jared L., Doak, Peter W., Timm, Andrea, Halsted, Michelle, Anderson, John D., Ginovart, Marta, Prats, Clara, Portell, Xavier, Retterer, Scott T., and Fuentes-Cabrera, Miguel. A Microfluidics and Agent-Based Modeling Framework for Investigating Spatial Organization in Bacterial Colonies: The Case of Pseudomonas Aeruginosa and H1-Type VI Secretion Interactions. United States: N. p., 2018. Web. doi:10.3389/fmicb.2018.00033.
Wilmoth, Jared L., Doak, Peter W., Timm, Andrea, Halsted, Michelle, Anderson, John D., Ginovart, Marta, Prats, Clara, Portell, Xavier, Retterer, Scott T., & Fuentes-Cabrera, Miguel. A Microfluidics and Agent-Based Modeling Framework for Investigating Spatial Organization in Bacterial Colonies: The Case of Pseudomonas Aeruginosa and H1-Type VI Secretion Interactions. United States. doi:10.3389/fmicb.2018.00033.
Wilmoth, Jared L., Doak, Peter W., Timm, Andrea, Halsted, Michelle, Anderson, John D., Ginovart, Marta, Prats, Clara, Portell, Xavier, Retterer, Scott T., and Fuentes-Cabrera, Miguel. Tue . "A Microfluidics and Agent-Based Modeling Framework for Investigating Spatial Organization in Bacterial Colonies: The Case of Pseudomonas Aeruginosa and H1-Type VI Secretion Interactions". United States. doi:10.3389/fmicb.2018.00033.
@article{osti_1437197,
title = {A Microfluidics and Agent-Based Modeling Framework for Investigating Spatial Organization in Bacterial Colonies: The Case of Pseudomonas Aeruginosa and H1-Type VI Secretion Interactions},
author = {Wilmoth, Jared L. and Doak, Peter W. and Timm, Andrea and Halsted, Michelle and Anderson, John D. and Ginovart, Marta and Prats, Clara and Portell, Xavier and Retterer, Scott T. and Fuentes-Cabrera, Miguel},
abstractNote = {The factors leading to changes in the organization of microbial assemblages at fine spatial scales are not well characterized or understood. However, they are expected to guide the succession of community development and function toward specific outcomes that could impact human health and the environment. In this study, we put forward a combined experimental and agent-based modeling framework and use it to interpret unique spatial organization patterns of H1-Type VI secretion system (T6SS) mutants of P. aeruginosa under spatial confinement. We find that key parameters, such as T6SS-mediated cell contact and lysis, spatial localization, relative species abundance, cell density and local concentrations of growth substrates and metabolites are influenced by spatial confinement. The model, written in the accessible programming language NetLogo, can be adapted to a variety of biological systems of interest and used to simulate experiments across a broad parameter space. It was implemented and run in a high-throughput mode by deploying it across multiple CPUs, with each simulation representing an individual well within a high-throughput microwell array experimental platform. The microfluidics and agent-based modeling framework we present in this paper provides an effective means by which to connect experimental studies in microbiology to model development. The work demonstrates progress in coupling experimental results to simulation while also highlighting potential sources of discrepancies between real-world experiments and idealized models.},
doi = {10.3389/fmicb.2018.00033},
journal = {Frontiers in Microbiology},
number = ,
volume = 9,
place = {United States},
year = {Tue Feb 06 00:00:00 EST 2018},
month = {Tue Feb 06 00:00:00 EST 2018}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.3389/fmicb.2018.00033

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