Title: Community organizing: Harnessing the interactions of the microbiome as a basis for novel therapeutics Next-generation antibiotics and antimicrobials necessitate new design principles that incorporate information about both a pathogen's unique genetic susceptibilities and virulence factors as well as information about its surrounding microbial community. This community, the microbiome, contains both beneficial symbionts and a genetic reservoir for horizontal exchange of antibiotic resistance or virulence genes. An effective therapeutic design would precisely target pathogens and disease-enhancing genes yet spare the healthy diversity of beneficial microbes. However, the `parts list' that defines potential targets in the pathogen of interest and the contextual microbiome are incompletely defined given the large uncharacterized space, or microbial `dark matter' that persists in microbiome characterization studies.
My Aims 1 and 2 propose both computational (iterative binning & assembly) and experimental approaches (immunomagnetic separation of human cells prior to single cell sequencing) whose goal is to enable a deep interrogation of this dark matter. These approaches will provide new depth to our knowledge of the genes and genomes of the skin's microbial communities, creating an expanded `parts' lists of genes and interspecies interactions networks that will inform rational design. In turn, these genetic reconstructions can be used for the basis for synthetic design. In my third aim, I propose creation of a synthetic phage vehicle that delivers CRISPR/Cas genome modification tools to genetically manipulate or kill methicillin-resistant Staphylococcus aureus, a major human pathogen, within the context of a mixed microbial community. More broadly, completion of these aims will see the creation of a generalized toolkit that can be used to engineer a large variety of pathogens and microbial communities.

Public Health Relevance

The spread and virulence of pathogens such as methicillin-resistant Staphylococcus aureus are affected by the context of the surrounding microbial communities, the microbiome, which includes microorganisms such as bacteria, fungi, and viruses. Understanding the function, structure, and dynamics of the microbiome is important to design therapeutics that precisely target the pathogen of interest, yet spare the surrounding beneficial microbiota. To characterize the genetic parts, function, and interspecies dynamics that are needed to inform the construction of such a tool, I propose a deep interrogation of the skin microbiome using different computational and experimental tools. Then, I propose a synthetic design of a phage-mediated CRISPR/Cas system that will allow in situ genetic engineering and pathogen targeting.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Career Transition Award (K22)
Project #
Application #
Study Section
Microbiology and Infectious Diseases B Subcommittee (MID-B)
Program Officer
Huntley, Clayton C
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Jackson Laboratory
Research Institutes
Bar Harbor
United States
Zip Code
Tsai, Yu-Chih; Conlan, Sean; Deming, Clayton et al. (2016) Resolving the Complexity of Human Skin Metagenomes Using Single-Molecule Sequencing. MBio 7:e01948-15