Biofilm modelling of bacterial-host interactions in disease pathogenesis

Background:
The mouth is home to a complex ecosystem where hundreds of bacterial species co-exist, compete, synergize and interact with each other and with the host. A delicate symbiotic balance ensures oral health, but under environmental stress, a dysbiosis can develop and lead to periodontitis, which is the most common inflammatory disease of humans. Treatment can be challenging, lengthy and costly which is in part, because oral bacteria mostly live in communities known as biofilms that can be extremely resistant to standard antibacterial interventions. These biofilms are often formed of multiple species, that either co-operate or compete with each other and which interact with the host’s inflammatory-immune system.

Advances in whole genome sequencing and metagenomics have greatly increased our understanding of the bacteria present in oral biofilms, but their exact composition, and in particular their interactions and communications within the biofilm and with the host remain under studied.

Objectives
There are three main aims within this PhD project:

Firstly, establishing models of oral in vitro multispecies biofilms, mimicking healthy and disease-associated states.
The initial model will be based on the in vitro biofilms recently developed by our collaborators [1]. We will then expand from this static model to a dynamic, flow-cell based model.

Secondly, exploring cell-cell communication within the biofilm (intra- and inter-bacterial species communication)
This part of the PhD will look at communication via classical quorum sensing and additionally communication through use of secondary messengers.

Thirdly, investigating communication of the biofilm-associated bacteria with the host.
Host-pathogen interactions will primarily focus on the effects of the biofilms on neutrophils and epithelial cells.

Methods/techniques
Anaerobic microbiology, growth of bacteria in planktonic cultures and biofilms; development of in vitro biofilm model, advanced microscopy (confocal and electron); extraction and analysis of second messengers; biosensor assays (for quorum sensing molecule detection); molecular biology; qPCR; cell biology (including measurements of reactive oxygen species, NET formation and cytokine production)
In addition, to the wet-lab skills the student will be trained in necessary in silico skills, including basic bioinformatics for sequence analysis.