Abstract: The human intestinal microbiota is a genetically diverse community of microorganisms that performs critical functions for the host, including carbohydrate metabolism, vitamin production, modulation of the immune system, promotion of epithelial barrier function, and exclusion of pathogens. Disruption of the microbiota can lead to a number of pathologies in the host, and probiotics have emerged as a potential solution for treating or preventing such dysbioses. Probiotic treatments consist of the consumption of a strain or several strains of live microorganisms that confer benefits on their human hosts when administered in adequate concentrations. We propose a novel synthetic biology approach to address the most critical barrier currently facing probiotic therapeutic efficacy, namely the inability of probiotic bacteriato permanently and stably integrate into established human microbiota. We hypothesize that (1) native human microbiota, either during development or when stabilized, encode a repertoire of genes which would enable stable integration into an established community and (2) these traits can be engineered into organisms with putative probiotic properties, improving their intestinal colonization potential and fitness. Accordingly, we will functionally prospect complete human microbiota and defined gut microbial culture collections for genes and operons facilitating integration (collectively referred to as integration-enhancing fragments or IEFs) of a set of candidate probiotics into stable microbiota of mammalian hosts, investigate the mechanisms of the identified genes, and compete and combinatorially optimize the best IEFs to select and engineer enhanced integration phenotypes. We will also confirm the efficacy of our enhanced probiotics by comparing them to traditional probiotics in a mouse model for intestinal disease. To achieve these goals, we will develop and apply cutting- edge technological innovations in functional metagenomics, next-generation sequencing and gnotobiotic husbandry. Hence, a major anticipated deliverable of our proposal is a novel platform technology for engineering fitness-enhancing properties into putative probiotic bacteria, promoting integration and persistence in a developed and stable microbiota in a mammalian host. We will apply this platform to engineer next-generation probiotic strains with an enhanced capacity for integration into an established microbiota, with the potential for rapid therapeutic deployment for the treatment of human gastrointestinal diseases. Public Health Relevance: Modulation of the human gastrointestinal microbiota through probiotic therapy is being considered for the treatment of a number of gastrointestinal disorders. This proposal aims to address one of the most critical barriers to the deployment of current putative probiotic strains, namely their inability for long-term integration into the host microbioa. We will develop novel technologies to discover and engineer genetic elements which enable candidate probiotic strains to stably integrate into established microbiota, with the potential for rapid deployment for the treatment of human gastrointestinal disease.

National Institute of Health (NIH)
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
NIH Director’s New Innovator Awards (DP2)
Project #
Application #
Study Section
Special Emphasis Panel (ZGM1-NDIA-C (01))
Program Officer
Karp, Robert W
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Washington University
Internal Medicine/Medicine
Schools of Medicine
Saint Louis
United States
Zip Code
Tsukayama, Pablo; Boolchandani, Manish; Patel, Sanket et al. (2018) Characterization of Wild and Captive Baboon Gut Microbiota and Their Antibiotic Resistomes. mSystems 3:
Crofts, Terence S; Wang, Bin; Spivak, Aaron et al. (2018) Shared strategies for ?-lactam catabolism in the soil microbiome. Nat Chem Biol 14:556-564
Crofts, Terence S; Gasparrini, Andrew J; Dantas, Gautam (2017) Next-generation approaches to understand and combat the antibiotic resistome. Nat Rev Microbiol 15:422-434
Crofts, Terence S; Wang, Bin; Spivak, Aaron et al. (2017) Draft Genome Sequences of Three ?-Lactam-Catabolizing Soil Proteobacteria. Genome Announc 5:
Boolchandani, Manish; Patel, Sanket; Dantas, Gautam (2017) Functional Metagenomics to Study Antibiotic Resistance. Methods Mol Biol 1520:307-329
Adu-Oppong, Boahemaa; Gasparrini, Andrew J; Dantas, Gautam (2017) Genomic and functional techniques to mine the microbiome for novel antimicrobials and antimicrobial resistance genes. Ann N Y Acad Sci 1388:42-58
Pesesky, Mitchell W; Hussain, Tahir; Wallace, Meghan et al. (2016) Evaluation of Machine Learning and Rules-Based Approaches for Predicting Antimicrobial Resistance Profiles in Gram-negative Bacilli from Whole Genome Sequence Data. Front Microbiol 7:1887
Langdon, Amy; Crook, Nathan; Dantas, Gautam (2016) The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Med 8:39
Forsberg, Kevin J; Patel, Sanket; Witt, Evan et al. (2016) Identification of Genes Conferring Tolerance to Lignocellulose-Derived Inhibitors by Functional Selections in Soil Metagenomes. Appl Environ Microbiol 82:528-37
Forsberg, Kevin J; Patel, Sanket; Wencewicz, Timothy A et al. (2015) The Tetracycline Destructases: A Novel Family of Tetracycline-Inactivating Enzymes. Chem Biol 22:888-97

Showing the most recent 10 out of 21 publications