Challenges & opportunities for phage-based in situ microbiome engineering in the gut

The gut microbiome is a promising target for the development of GI tract therapies, yet it has been under-exploited due, in part, to a lack of tools to control and manipulate complex microbial communities. To date, the most common approach in harnessing bacteria for therapeutic purposes has been to deliver ex vivo engineered bacteria-effectively taking a bacterial cell therapy-based approach. An alternative approach involves taking advantage of the rich microbial ecosystem in the gut by genetically modifying the microbiome in situ through the use of engineered bacteriophages-akin to human gene therapies delivered by viral vectors. In this review, we present the challenges and opportunities associated with engineering bacteriophages to control and manipulate the gut microbiome.