title: Manipulating Bacterial Communities by in situ Microbiome Engineering.
abstract: 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.
authors.affiliation: Department of Systems Biology, Columbia University Medical Center, New York, NY, USA; Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University Medical Center, New York, NY, USA.
authors.forename: Ravi U
authors.initials: RU
authors.lastname: Sheth
authors.affiliation: Department of Systems Biology, Columbia University Medical Center, New York, NY, USA.
authors.forename: Vitor
authors.initials: V
authors.lastname: Cabral
authors.affiliation: Department of Systems Biology, Columbia University Medical Center, New York, NY, USA; Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University Medical Center, New York, NY, USA.
authors.forename: Sway P
authors.initials: SP
authors.lastname: Chen
authors.affiliation: Department of Systems Biology, Columbia University Medical Center, New York, NY, USA; Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA. Electronic address: hw2429@columbia.edu.
authors.forename: Harris H
authors.initials: HH
authors.lastname: Wang
mesh_terms: D001419:Bacteria / Q000378:metabolism*; D064307:Microbiota; D019936:Probiotics; D012449:Safety
keywords: genome engineering; microbial communities; microbiome engineering; phage; prebiotics; probiotics; synthetic biology; xenobiotics