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Title: Novel approaches in function-driven single-cell genomics

Abstract

Deeper sequencing and improved bioinformatics in conjunction with single-cell and metagenomic approaches continue to illuminate undercharacterized environmental microbial communities. This has propelled the 'who is there, and what might they be doing' paradigm to the uncultivated and has already radically changed the topology of the tree of life and provided key insights into the microbial contribution to biogeochemistry. While characterization of 'who' based on marker genes can describe a large fraction of the community, answering 'what are they doing' remains the elusive pinnacle for microbiology. Function-driven single-cell genomics provides a solution by using a function-based screen to subsample complex microbial communities in a targeted manner for the isolation and genome sequencing of single cells. This enables single-cell sequencing to be focused on cells with specific phenotypic or metabolic characteristics of interest. Recovered genomes are conclusively implicated for both encoding and exhibiting the feature of interest, improving downstream annotation and revealing activity levels within that environment. This emerging approach has already improved our understanding of microbial community functioning and facilitated the experimental analysis of uncharacterized gene product space. Here we provide a comprehensive review of strategies that have been applied for function-driven single-cell genomics and the future directions we envision.

Authors:
 [1];  [1]
  1. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23)
OSTI Identifier:
1379897
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
FEMS Microbiology Reviews
Additional Journal Information:
Journal Volume: 41; Journal Issue: 4; Journal ID: ISSN 1574-6976
Publisher:
Federation of European Microbiological Societies
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Doud, Devin F. R., and Woyke, Tanja. Novel approaches in function-driven single-cell genomics. United States: N. p., 2017. Web. doi:10.1093/femsre/fux009.
Doud, Devin F. R., & Woyke, Tanja. Novel approaches in function-driven single-cell genomics. United States. doi:10.1093/femsre/fux009.
Doud, Devin F. R., and Woyke, Tanja. Wed . "Novel approaches in function-driven single-cell genomics". United States. doi:10.1093/femsre/fux009. https://www.osti.gov/servlets/purl/1379897.
@article{osti_1379897,
title = {Novel approaches in function-driven single-cell genomics},
author = {Doud, Devin F. R. and Woyke, Tanja},
abstractNote = {Deeper sequencing and improved bioinformatics in conjunction with single-cell and metagenomic approaches continue to illuminate undercharacterized environmental microbial communities. This has propelled the 'who is there, and what might they be doing' paradigm to the uncultivated and has already radically changed the topology of the tree of life and provided key insights into the microbial contribution to biogeochemistry. While characterization of 'who' based on marker genes can describe a large fraction of the community, answering 'what are they doing' remains the elusive pinnacle for microbiology. Function-driven single-cell genomics provides a solution by using a function-based screen to subsample complex microbial communities in a targeted manner for the isolation and genome sequencing of single cells. This enables single-cell sequencing to be focused on cells with specific phenotypic or metabolic characteristics of interest. Recovered genomes are conclusively implicated for both encoding and exhibiting the feature of interest, improving downstream annotation and revealing activity levels within that environment. This emerging approach has already improved our understanding of microbial community functioning and facilitated the experimental analysis of uncharacterized gene product space. Here we provide a comprehensive review of strategies that have been applied for function-driven single-cell genomics and the future directions we envision.},
doi = {10.1093/femsre/fux009},
journal = {FEMS Microbiology Reviews},
number = 4,
volume = 41,
place = {United States},
year = {2017},
month = {6}
}

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  • Zheng, Baohui; DeRan, Michael; Li, Xinyan
  • Journal of the American Chemical Society, Vol. 135, Issue 19
  • DOI: 10.1021/ja311416v