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Title: High-throughput metagenomic technologies for complex microbial community analysis. Open and closed formats

Abstract

Understanding the structure, functions, activities and dynamics of microbial communities in natural environments is one of the grand challenges of 21st century science. To address this challenge, over the past decade, numerous technologies have been developed for interrogating microbial communities, of which some are amenable to exploratory work (e.g., high-throughput sequencing and phenotypic screening) and others depend on reference genes or genomes (e.g., phylogenetic and functional gene arrays). Here, we provide a critical review and synthesis of the most commonly applied “open-format” and “closed-format” detection technologies. We discuss their characteristics, advantages, and disadvantages within the context of environmental applications and focus on analysis of complex microbial systems, such as those in soils, in which diversity is high and reference genomes are few. In addition, we discuss crucial issues and considerations associated with applying complementary high-throughput molecular technologies to address important ecological questions.

Authors:
 [1];  [2];  [3];  [4];  [5];  [6]
+ Show Author Affiliations
  1. Univ. of Oklahoma, Norman, OK (United States); Tsinghua Univ., Beijing (China); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Univ. of Oklahoma, Norman, OK (United States)
  3. Tsinghua Univ., Beijing (China)
  4. Univ. of Oklahoma, Norman, OK (United States); Chinese Academy of Sciences, Beijing (China)
  5. Dept. of Energy Joint Genome Institute, Walnut Creek, CA (United States)
  6. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1215655
Alternate Identifier(s):
OSTI ID: 1512158
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
mBio (Online)
Additional Journal Information:
Journal Name: mBio (Online); Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2150-7511
Publisher:
American Society for Microbiology
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; 59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Zhou, Jizhong, He, Zhili, Yang, Yunfeng, Deng, Ye, Tringe, Susannah G., and Alvarez-Cohen, Lisa. High-throughput metagenomic technologies for complex microbial community analysis. Open and closed formats. United States: N. p., 2015. Web. doi:10.1128/mBio.02288-14.
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Zhou, Jizhong, He, Zhili, Yang, Yunfeng, Deng, Ye, Tringe, Susannah G., & Alvarez-Cohen, Lisa. High-throughput metagenomic technologies for complex microbial community analysis. Open and closed formats. United States. https://doi.org/10.1128/mBio.02288-14
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Zhou, Jizhong, He, Zhili, Yang, Yunfeng, Deng, Ye, Tringe, Susannah G., and Alvarez-Cohen, Lisa. Tue . "High-throughput metagenomic technologies for complex microbial community analysis. Open and closed formats". United States. https://doi.org/10.1128/mBio.02288-14. https://www.osti.gov/servlets/purl/1215655.
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@article{osti_1215655,
title = {High-throughput metagenomic technologies for complex microbial community analysis. Open and closed formats},
author = {Zhou, Jizhong and He, Zhili and Yang, Yunfeng and Deng, Ye and Tringe, Susannah G. and Alvarez-Cohen, Lisa},
abstractNote = {Understanding the structure, functions, activities and dynamics of microbial communities in natural environments is one of the grand challenges of 21st century science. To address this challenge, over the past decade, numerous technologies have been developed for interrogating microbial communities, of which some are amenable to exploratory work (e.g., high-throughput sequencing and phenotypic screening) and others depend on reference genes or genomes (e.g., phylogenetic and functional gene arrays). Here, we provide a critical review and synthesis of the most commonly applied “open-format” and “closed-format” detection technologies. We discuss their characteristics, advantages, and disadvantages within the context of environmental applications and focus on analysis of complex microbial systems, such as those in soils, in which diversity is high and reference genomes are few. In addition, we discuss crucial issues and considerations associated with applying complementary high-throughput molecular technologies to address important ecological questions.},
doi = {10.1128/mBio.02288-14},
journal = {mBio (Online)},
number = 1,
volume = 6,
place = {United States},
year = {Tue Jan 27 00:00:00 EST 2015},
month = {Tue Jan 27 00:00:00 EST 2015}
}
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https://doi.org/10.1128/mBio.02288-14
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DNA recovery from soils of diverse composition.
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Metagenomics: Application of Genomics to Uncultured Microorganisms
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