In situ reprogramming of gut bacteria by oral delivery

• Published in: Nature communications Vol. 11; no. 1; p. 5030
• Main Authors: Hsu, Bryan B, Plant, Isaac N, Lyon, Lorena, Anastassacos, Frances M, Way, Jeffrey C, Silver, Pamela A
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group UK 06.10.2020; Nature Portfolio
• Subjects: Administration, Oral; Animals; Bacteriophages - genetics; CRISPR-Associated Protein 9 - genetics; Drug Delivery Systems - methods; Escherichia coli - genetics; Feces - microbiology; Female; Gastrointestinal Microbiome; Gene Expression Regulation; Luminescent Proteins - genetics; Mice, Inbred BALB C; Probiotics - administration & dosage; Red Fluorescent Protein
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-18614-2

Abundant links between the gut microbiota and human health indicate that modification of bacterial function could be a powerful therapeutic strategy. The inaccessibility of the gut and inter-connections between gut bacteria and the host make it difficult to precisely target bacterial functions without disrupting the microbiota and/or host physiology. Herein we describe a multidisciplinary approach to modulate the expression of a specific bacterial gene within the gut by oral administration. We demonstrate that an engineered temperate phage λ expressing a programmable dCas9 represses a targeted E. coli gene in the mammalian gut. To facilitate phage administration while minimizing disruption to host processes, we develop an aqueous-based encapsulation formulation with a microbiota-based release mechanism and show that it facilitates oral delivery of phage in vivo. Finally we combine these technologies and show that bacterial gene expression in the mammalian gut can be precisely modified in situ with a single oral dose.