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Trends Genet. 2016 Apr;32(4):189-200. doi: 10.1016/j.tig.2016.01.005. Epub 2016 Feb 22.

Manipulating Bacterial Communities by in situ Microbiome Engineering.

Author information

1
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.
2
Department of Systems Biology, Columbia University Medical Center, New York, NY, USA.
3
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.

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.

KEYWORDS:

genome engineering; microbial communities; microbiome engineering; phage; prebiotics; probiotics; synthetic biology; xenobiotics

PMID:
26916078
PMCID:
PMC4828914
DOI:
10.1016/j.tig.2016.01.005
[Indexed for MEDLINE]
Free PMC Article

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