In nature, diverse microorganisms spontaneously form resilient ecological networks adapted to their environment (microbiomes). The behavior of these cooperative communities has profound beneficial and problematic effects on biological systems and the environment, with relevance to human health, agricultural productivity, water and food safety, waste remediation, and infrastructure corrosion. Emergent behavior in these communities is mediated by subtle chemical and spatial cues; however, little knowledge exists to model or control that behavior due to the lack of technical means to reproduce the complexity of these communities. Commonly, researchers are limited to overly-simple in vitro systems (e.g., single species) or naturally-occurring complex samples that are poorly-defined and irreproducible.
We are currently working to (1) use 2D and 3D bioprinting in vitro to engineer structured microbial communities that mimic the complex spatial and genotypic organization of naturally-occurring ecologies and (2) perform spatially and temporally resolved measurements of the cellular organization, microbial behavior, and environmental conditions within these engineered systems. These capabilities will enable rational design and reproducible assembly of complex microbial communities that are robust, biologically meaningful, and responsive to environmental perturbations. Some specific expertise sought:
Community microbiology: Candidates will evaluate microbial communities (microbiomes) within the context of their environment—for example, to identify how contributions from individual constituents drive community behavior; understand mechanisms of interaction between microorganisms; study emergent properties of microbial communities (e.g., stability, diversity, functional redundancy); track fluxes of material (e.g., carbon) and energy through the community; and model microbial community dynamics and response to environmental perturbations.
Engineering Communities: Candidates will be responsible for engineering and characterizing microbial communities in vitro—for example, using rational design and fabrication of controlled microenvironments for microbial culture; 2D and 3D bioprinting of microbial cells, extracellular polymeric substance (EPS), and hydrogels; quantitative analysis of microbial communities by microscopic, sequencing and metabolomics analyses; microtomes and microprobes to sample microbial communities with high spatial resolution.
Engineering Microbial Strains: Candidates will manipulate individual microbial strains to facilitate community analysis and understand the impact of gene expression on community behavior through: manipulating microbial metabolic and biochemical pathways; designing and producing permanent and transient genetic manipulations; characterizing microbial cultures by traditional and emerging analytical and genomic techniques; and understanding the mechanisms and impacts of microbial evolution and horizontal gene transfer, particularly within the context of communities.
Microbiome engineering; Microbiology; Microbial community; Metrology; Microenvironment; Bioprinting; Culture reproducibility; Metabolomics; Sequencing;