Intestinal transgene delivery with native E. coli chassis allows persistent physiological changes
Baylee J. Russell, Steven D. Brown, Nicole Siguenza, Irene Mai, Anand Saran, Amulya Lingaraju, Erica S. Maissy, Ana Carolina Dantas Machado, Antônio F. M. Pinto, Concepcion Sanchez, Leigh‐Ana Rossitto, Yukiko Miyamoto, R. Alexander Richter, Samuel B. Ho, Lars Eckmann, Jeff Hasty, David J. Gonzalez, Alan Saghatelian, Rob Knight, Amir Zarrinpar
Abstract
Live bacterial therapeutics (LBTs) could reverse diseases by engrafting in the gut and providing persistent beneficial functions in the host. However, attempts to functionally manipulate the gut microbiome of conventionally raised (CR) hosts have been unsuccessful because engineered microbial organisms (i.e., chassis) have difficulty in colonizing the hostile luminal environment. In this proof-of-concept study, we use native bacteria as chassis for transgene delivery to impact CR host physiology. Native Escherichia coli bacteria isolated from the stool cultures of CR mice were modified to express functional genes. The reintroduction of these strains induces perpetual engraftment in the intestine. In addition, engineered native E. coli can induce functional changes that affect physiology of and reverse pathology in CR hosts months after administration. Thus, using native bacteria as chassis to "knock in" specific functions allows mechanistic studies of specific microbial activities in the microbiome of CR hosts and enables LBT with curative intent.