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Probiotic Discovery, Engineering & Manufacturing Pipeline

The goal of this research project is to develop synthetically-engineered probiotics for eradicating multidrug resistant enteric pathogensThis project builds on the premise that while supplementation of a well-defined set of commensal bacteria (see Project #1) is a significant step forward compared to “blind” FMT, it still suffers from the fact that these microbes’ wildtype transcriptional regulation is still heavily dependent on the surrounding environment, thus limiting the ability to determine when and how much a specific function needs to be performed. In this project we took inspiration from very recent work from other groups on the construction of GI-tract bacterial sensors and came up with the idea of building an array of engineered probiotics that would “sense” a dysbiotic condition and “respond” to it by producing a disease-ameliorating molecule. In summer 2017 we received a two-year UMass President Science and Technology Award  to pursue studies aimed at developing two independent technologies for sensing and subsequently eradicating drug-resistant S. Thypimurium and C. difficile respectively. We just published initial our work on the first prototype engineered probiotic aimed at S. Thypimurium inhibition in ACS Infectious Diseases (Palmer et al., 2017). In this work, which was performed by two students in my laboratory (Jacob Palmer and Emma Piattelli), we developed a genetically engineered prototype probiotic to inhibit S. Thypimurium upon exposure to tetrathionate, a molecule produced in the inflamed gut during the course of Salmonella infection. We developed a plasmid-based system capable of conferring the ability to detect and utilize tetrathionate, while at the same time producing the S. Thypimurium-killing molecule microcin H47 (produced via one of the DNA synthetized operons described in Project #2). We transferred this plasmid-based system to Escherichia coli and demonstrated the ability of the engineered strain to inhibit growth of Salmonella in anaerobic conditions while in the presence of tetrathionate, with no detectable inhibition in the absence of tetrathionate both in static plate as well as mix-culture liquid ecological competition assaysThis paper represents the first example in where a strain of E. coli was engineered to be capable of using a host-derived signal indicative of intestinal disease as an inducing molecule, resulting in the production and secretion of an agent capable of inhibiting the organism responsible for the inflammation. In addition to the paper, UMass Dartmouth also filed for patent application for this research.

We are currently expanding this research and investigate the production from engineered probiotics as well as the biochemical purification of less charachterized and to date unknown siderophore Antimicrobial Peptides which we have shown to be very potent in inhibiting a number of drug-resistant bacteria including Klebsiella, S. Typhi, ESBL-E. coli (Palmer et al 2020; Mortzfeld et al 2020 in preparation).