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The cultivation of environmental microorganisms has long been hindered by the inability to replicate complex native conditions in vitro. The isolation chip (iChip) addresses this limitation by facilitating the growth of previously uncultivable microorganisms through in situ incubation. Designed for high-throughput microbial cultivation, the iChip comprises hundreds of microchambers, each capable of housing a single microbial cell. These microchambers are loaded with a mixture of molten agar and...
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Manipulating Bacterial Communities by in situ Microbiome Engineering.

Ravi U Sheth1, Vitor Cabral2, Sway P Chen1

  • 1Department 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.

Trends in Genetics : TIG
|February 27, 2016
PubMed
Summary

In situ microbiome engineering offers a new way to genetically modify microbial communities. This approach precisely alters functions and properties in diverse environments for various applications.

Keywords:
genome engineeringmicrobial communitiesmicrobiome engineeringphageprebioticsprobioticssynthetic biologyxenobiotics

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Area of Science:

  • Microbiology
  • Synthetic Biology
  • Environmental Science

Background:

  • Microbial communities are vital for global biogeochemical cycles, agriculture, biotechnology, and human health.
  • Current engineering methods often lack precision at the community level.

Purpose of the Study:

  • Introduce 'in situ microbiome engineering' as a novel community-scale genetic engineering paradigm.
  • Discuss current applications and emerging techniques for microbiome manipulation.

Main Methods:

  • Review of contemporary applications for adding, removing, or modifying microbial functions.
  • Highlighting in situ genome engineering techniques for targeted manipulation.
  • Analysis of terrestrial, aquatic, and host-associated environments.

Main Results:

  • Demonstration of precise functional and property alterations in microbial communities.
  • Validation of in situ genome engineering for high specificity and efficacy.
  • Identification of key areas for technological advancement.

Conclusions:

  • In situ microbiome engineering represents a significant advancement in microbial community manipulation.
  • Emerging genome engineering tools offer powerful solutions for targeted microbiome interventions.
  • Further innovation is needed to fully realize the potential of in situ microbiome engineering.