The long-term goal of this research is to develop culture-independent strategies to effectively engineer and program the human microbiome in vivo. To this end, the objective of this proposal is to develop an enabling technology platform, named Genome Engineering by Self-Transmissible Replicons (GESTR), to allow the efficient delivery, propagation and expression of exogenous genes in the human microbiota, to characterize the kinetics of gene propagation in the microbiome, and to initially demonstrate the utility of such techniques in engineering the gut microbiota of mice. The specific goals of this work are i) to construct engineered self- transmitting conjugative transposons containing trackable payload genes and characterize their ability to mobilize into different strains typically found in the human gut microbiota;ii) to develop libraries of payload constructs to characterize transcriptional efficiency and codon adaptation for optimal payload gene expression in dominant gut microbes;and iii) to measure gene flow and transmission of exogenous genes by engineered self-mobilizable genetic elements in the gut microbiota of a murine model. Newly developed tools including Multiplex Automated Genome Engineering, de novo DNA-microarray-based gene synthesis, and meta- transcriptomics will be utilized to facilitate the development of this project. The proposed research will provide the first demonstration of key functionality and the development of sufficient new understanding to enable the broader use of this technology platform in future applications. Key questions in the dynamics of transmission and natural selection of laterally shared genes in the human microbiome will also be addressed. Engineering the human microbiome with augmented capabilities to report, prevent and reverse disease states and to modulate the metabolism of foods and drugs promises to be a critical avenue towards transforming human- associated microbes into micro-sensors, miniature protein-production factories, and adaptive bioremediation systems. This technology holds potential for development of clinical therapeutics of common microbial- associated diseases such as those of the gut (e.g. Crohn's, IBD, chronic maldigestion), oral cavity (e.g. dental caries), urogenital tract (e.g. infections, STDs), and skin (e.g. ectopic eczema).

Public Health Relevance

The proposed research project aims to develop foundational technologies to enable the genetic manipulation of microbes that are commonly associated with the human body. These endeavors will facilitate the development of preventative measures and therapeutics to combat microbial-associated human diseases including those of the gut, mouth, nose, skin, and urogenital organs.

Agency
National Institute of Health (NIH)
Institute
Office of The Director, National Institutes of Health (OD)
Type
Early Independence Award (DP5)
Project #
5DP5OD009172-05
Application #
8715427
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Basavappa, Ravi
Project Start
2011-09-20
Project End
2016-08-31
Budget Start
2014-09-01
Budget End
2015-08-31
Support Year
5
Fiscal Year
2014
Total Cost
Indirect Cost
Name
Columbia University (N.Y.)
Department
Pathology
Type
Schools of Medicine
DUNS #
City
New York
State
NY
Country
United States
Zip Code
10032
Gomes, Antonio L C; Wang, Harris H (2016) The Role of Genome Accessibility in Transcription Factor Binding in Bacteria. PLoS Comput Biol 12:e1004891
Johns, Nathan I; Blazejewski, Tomasz; Gomes, Antonio Lc et al. (2016) Principles for designing synthetic microbial communities. Curr Opin Microbiol 31:146-53
Sheth, Ravi U; Cabral, Vitor; Chen, Sway P et al. (2016) Manipulating Bacterial Communities by in situ Microbiome Engineering. Trends Genet 32:189-200
Bonde, Mads T; Kosuri, Sriram; Genee, Hans J et al. (2015) Direct mutagenesis of thousands of genomic targets using microarray-derived oligonucleotides. ACS Synth Biol 4:17-22
Kostylev, Mikhail A; Kaufman, Adam C; Nygaard, Haakon B et al. (2015) Prion-Protein-interacting Amyloid-β Oligomers of High Molecular Weight Are Tightly Correlated with Memory Impairment in Multiple Alzheimer Mouse Models. J Biol Chem 290:17415-38
Freedberg, Daniel E; Toussaint, Nora C; Chen, Sway P et al. (2015) Proton Pump Inhibitors Alter Specific Taxa in the Human Gastrointestinal Microbiome: A Crossover Trial. Gastroenterology 149:883-5.e9
Yaung, Stephanie J; Deng, Luxue; Li, Ning et al. (2015) Improving microbial fitness in the mammalian gut by in vivo temporal functional metagenomics. Mol Syst Biol 11:788
Tasoff, Joshua; Mee, Michael T; Wang, Harris H (2015) An Economic Framework of Microbial Trade. PLoS One 10:e0132907
Munck, Christian; Gumpert, Heidi K; Wallin, Annika I Nilsson et al. (2014) Prediction of resistance development against drug combinations by collateral responses to component drugs. Sci Transl Med 6:262ra156
Mee, Michael T; Collins, James J; Church, George M et al. (2014) Syntrophic exchange in synthetic microbial communities. Proc Natl Acad Sci U S A 111:E2149-56

Showing the most recent 10 out of 21 publications