Manipulating Bacterial Communities by in situ Microbiome Engineering

Microbial communities inhabit our entire planet and have a crucial role in biogeochemical processes, agriculture, biotechnology, and human health. Here, we argue that ‘in situ microbiome engineering’ represents a new paradigm of community-scale genetic and microbial engineering. We discuss contemporary applications of this approach to directly add, remove, or modify specific sets of functions and alter community-level properties in terrestrial, aquatic, and host-associated microbial communities. Specifically, we highlight emerging in situ genome engineering approaches as tractable techniques to manipulate microbial communities with high specificity and efficacy. Finally, we describe opportunities for technological innovation and ways to bridge existing knowledge gaps to accelerate the development of in situ approaches for microbiome manipulations.

TrendsHigh-throughput sequencing advances have provided a detailed survey of microbial community composition and prevalence, but a functional and mechanistic understanding of microbial ecology is lacking.Manipulating microbiome composition and function is of great interest for basic science and engineering applications; contemporary methods for manipulating microbial communities in situ yield perturbations limited to particular specificities and magnitudes.Emerging in situ genome engineering tools can precisely alter the metagenomic content of microbial communities over a range of specificities and magnitudes.