Metabolic Remodeling During Bacterial Biofilm Formation

Biofilms are communities of tightly associated bacteria encased in a self-produced extracellular matrix that allows attachment to surfaces and confers protection against environmental stressors. Production of biofilm is a nearly universal trait among bacteria, and it has been widely recognized that bacteria primarily exist as biofilms in natural environments. However, our current knowledge about bacterial metabolism and its regulation relies mostly on studies done in planktonic cultures, which may not fully capture the essence of bacterial physiology. Using Bacillus subtilis as a model system, the work in this proposal will provide the first systematic investigation of metabolism during bacterial biofilm formation and development, and as such, it has the potential to transform our understanding of bacterial metabolism and biofilm developmental processes.With a tractable genome, B. subtilis provides a good system for molecular biological studies. While it is typically categorized as a
soil-dwelling bacterium, B. subtilis is remarkably ubiquitous. It has been isolated from plant roots. B. subtilis root-associated biofilms were suggested to enhance plant immunity against pathogens by the secretion of antimicrobial peptides and polyketides. The presence of the benign bacterium can also activate plant immune system (microbe-associated molecular patterns (MAMPs)-triggered plant immunity). As a result, B. subtilis has been used as a soil inoculant in agriculture and horticulture. Apart from soil and plants, B. subtilis is found in human gastrointestinal tract and has been used as probiotics and shown to affect human microbiome. B. subtilis is also widely used in soybean product fermentation. Its interaction with plants, association with human health, and use in food industry make B. subtilis a highly important microorganism.The Goals of this proposal are:Goal 1: Characterize global metabolic remodeling during biofilm development.Using metabolomics and metabolic flux
analysis we will reveal the scope of metabolites that are impacted during biofilm development and quantitatively determine metabolic pathway utilization (activation or inactivation) as cells transition from planktonic into biofilm growth.The objectives in Goal 1 are:1. Measure alterations in metabolite concentrations during biofilm development.2. Quantitate changes in metabolic flux and pathway utilization during biofilm developmentGoal 2: Identify and experimentally validate components of the transcriptional regulatory network responsible for metabolic remodeling during biofilm developmentThe results from Goal 1 will provide a global and quantitative description of the changes in metabolism (i.e. changes in intracellular metabolite concentrations and metabolic fluxes) that accompany biofilm formation and development in B. subtilis. In Goal 2, we will make use of genetic knockouts in combination with transcriptomics and metabolomics approaches to dissect regulatory connections between
changes in metabolism and the activation of specific components in the biofilm transcriptional regulatory network.The objectives in Goal 2 are:1. Determine correlations between metabolic remodeling and transcriptional changes in the biofilm regulatory network2. Elucidate causal relationships between changes in metabolism and activation of specific components in the biofilm transcriptional regulatory network3. Identify common metabolic effects of biofilm-activating factors and signals