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Title: Insights from 20 years of bacterial genome sequencing

Abstract

Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go? Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce amore » finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Why do we care about bacterial genome sequencing? There are many practical applications, such as genome-scale metabolic modeling, biosurveillance, bioforensics, and infectious disease epidemiology. In the near future, high-throughput sequencing of patient metagenomic samples could revolutionize medicine in terms of speed and accuracy of finding pathogens and knowing how to treat them.« less

Authors:
 [1];  [1];  [1];  [1];  [1];  [1];  [1];  [2];  [1];  [3];  [1];  [1]
  1. Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
  2. Technical Univ. of Denmark (DTU), Roskilde (Denmark)
  3. Molecular Microbiology & Genomics Consultants, Zotzenheim (Germany)
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1185792
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Functional & Integrative Genomics
Additional Journal Information:
Journal Volume: 15; Journal Issue: 2; Journal ID: ISSN 1438-793X
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Bacteria; Next-Generation Sequencing

Citation Formats

Land, Miriam L., Hauser, Loren, Jun, Se-Ran, Nookaew, Intawat, Leuze, Michael Rex, Ahn, Tae-Hyuk, Karpinets, Tatiana V., Lund, Ole, Kora, Guruprased H., Wassenaar, Trudy, Poudel, Suresh, and Ussery, David W. Insights from 20 years of bacterial genome sequencing. United States: N. p., 2015. Web. doi:10.1007/s10142-015-0433-4.
Land, Miriam L., Hauser, Loren, Jun, Se-Ran, Nookaew, Intawat, Leuze, Michael Rex, Ahn, Tae-Hyuk, Karpinets, Tatiana V., Lund, Ole, Kora, Guruprased H., Wassenaar, Trudy, Poudel, Suresh, & Ussery, David W. Insights from 20 years of bacterial genome sequencing. United States. doi:10.1007/s10142-015-0433-4.
Land, Miriam L., Hauser, Loren, Jun, Se-Ran, Nookaew, Intawat, Leuze, Michael Rex, Ahn, Tae-Hyuk, Karpinets, Tatiana V., Lund, Ole, Kora, Guruprased H., Wassenaar, Trudy, Poudel, Suresh, and Ussery, David W. Fri . "Insights from 20 years of bacterial genome sequencing". United States. doi:10.1007/s10142-015-0433-4. https://www.osti.gov/servlets/purl/1185792.
@article{osti_1185792,
title = {Insights from 20 years of bacterial genome sequencing},
author = {Land, Miriam L. and Hauser, Loren and Jun, Se-Ran and Nookaew, Intawat and Leuze, Michael Rex and Ahn, Tae-Hyuk and Karpinets, Tatiana V. and Lund, Ole and Kora, Guruprased H. and Wassenaar, Trudy and Poudel, Suresh and Ussery, David W.},
abstractNote = {Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go? Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Why do we care about bacterial genome sequencing? There are many practical applications, such as genome-scale metabolic modeling, biosurveillance, bioforensics, and infectious disease epidemiology. In the near future, high-throughput sequencing of patient metagenomic samples could revolutionize medicine in terms of speed and accuracy of finding pathogens and knowing how to treat them.},
doi = {10.1007/s10142-015-0433-4},
journal = {Functional & Integrative Genomics},
number = 2,
volume = 15,
place = {United States},
year = {Fri Feb 27 00:00:00 EST 2015},
month = {Fri Feb 27 00:00:00 EST 2015}
}

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Works referenced in this record:

Evolution and classification of the CRISPR–Cas systems
journal, May 2011

  • Makarova, Kira S.; Haft, Daniel H.; Barrangou, Rodolphe
  • Nature Reviews Microbiology, Vol. 9, Issue 6, p. 467-477
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