BACTERIAL COLONY SIM

Multiscale modeling and simulation of bacterial colonies

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 Obiettivo del progetto (Objective)

'Some bacteria are known to grow in colonies that form complicated geometrical patterns. In order to develop such a colony, bacteria will sense and respond to their local environment by secreting and absorbing peptides, proteins, pheromones and other chemotactic or quorum sensing molecules. Furthermore, under adverse conditions, bacteria can sporulate, alternate its shape, or look for better DNA. Past work has focused mainly on the biological aspects involved in these processes. However, much less is known on the dynamics of the colony as a whole. In particular, the dynamics of the colony may be completely different than that of the single cell and it is not clear how the bacterial activity at the microscopic scale is related to the collective macroscopic behavior. A recent mathematical model that I developed explains an interesting experiment in which sibling bacterial colonies grown on low-nutrients plates mutually kill each other through secretions released to the media. Simulation results where compared with experimental data. The work was recently submitted to PNAS. The purpose of the proposed research is to develop new and improved models and innovative simulation methods for connecting between the microscopic behavior of individual bacteria and that of the colony as a whole. New algorithms are developed in order to solve the models numerically. Such an interdisciplinary research is crucial for understanding complex biological phenomena. There are many interesting and important directions for future research. For example, new experiments suggest that surface tension may play a key role in the dynamics of the colony. Another example is the addition of newly discovered knowledge on the mechanism bacteria use to decide between sporulation (going into a dormant phase) and competence (mutation into a different form of strand).'

Introduzione (Teaser)

To tackle bacteria as pathogens, we need to understand how they grow and evolve. A European study has put forward a modelling approach to help dissect the growth pattern of bacteria.

Descrizione progetto (Article)

Some bacteria live closely together, giving rise to colonies of complex geometrical patterns. To do so, bacteria sense and respond to their local environment by secreting pheromones or other chemoattractant molecules. Our knowledge on colony dynamics and what affects bacterial behaviour at the macroscopic level is limited.

Using a mathematical modelling approach, scientists on the EU-funded project 'Multiscale modeling and simulation of bacterial colonies' (http://u.math.biu.ac.il/~arielg/researchPages/biomath.html (BACTERIAL COLONY SIM)) tried to simulate and explain bacterial behaviour in colonies. The work focused on a particular type of bacteria from the Bacillus family called Paenibacillus. The key objective was to understand how bacteria cooperate and regulate the growth dynamics of millions of other members of the strain.

The study of bacterial growth was categorised into three stages, namely the single-cell stage, the intermediate swarm stage and the macroscopic colony stage. Swarms contain a few thousand cells and are considered to be the basic organisational unit of bacterial growth.

To understand bacterial collective behaviour, the consortium developed algorithms to analyse swarm behaviour. They found a highly synchronised movement in response to nutrients, waste products, environmental sensing and intercellular signalling. The response to external conditions plays a role in swarm dynamics, enabling bacteria to move rapidly over surfaces. Special emphasis was also given to bacterial swarm function under high antibiotic concentrations.

Taken together, BACTERIAL COLONY SIM's modelling approach helped characterise the patterns and determinants of bacterial growth. The generated information could form the basis for future antibacterial strategies that aim to abolish swarm formation.