Insights from 20 years of bacterial genome sequencing

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.

doi:10.1007/s10142-015-0433-4

Title: Insights from 20 years of bacterial genome sequencing

Journal Article · Fri Feb 27 00:00:00 EST 2015 · Functional & Integrative Genomics

DOI:https://doi.org/10.1007/s10142-015-0433-4· OSTI ID:1185792

Land, Miriam L. ^[1]; Hauser, Loren ^[1]; Jun, Se-Ran ^[1]; Nookaew, Intawat ^[1]; Leuze, Michael Rex ^[1]; Ahn, Tae-Hyuk ^[1]; Karpinets, Tatiana V. ^[1]; Lund, Ole ^[2]; Kora, Guruprased H. ^[1]; Wassenaar, Trudy ^[3]; Poudel, Suresh ^[1]; Ussery, David W. ^[1]

Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Technical Univ. of Denmark (DTU), Roskilde (Denmark)
Molecular Microbiology & Genomics Consultants, Zotzenheim (Germany)

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.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1185792

Journal Information:: Functional & Integrative Genomics, Vol. 15, Issue 2; ISSN 1438-793X

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 402 works

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Genomic characterization of Vibrio parahaemolyticus from Pacific white shrimp and rearing water in Malaysia reveals novel sequence types and structural variation in genomic regions containing the Photorhabdus insect-related (Pir) toxin-like genes Yan, Chrystine Zou Yi; Austin, Christopher M.; Ayub, Qasim bioRxiv https://doi.org/10.1101/714626	posted_content	August 2019
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Assessing alignment-based taxonomic classification of ancient microbial DNA Eisenhofer, Raphael; Weyrich, Laura Susan PeerJ Preprints https://doi.org/10.7287/peerj.preprints.27166v1	posted_content	September 2018
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An introduced crop plant is driving diversification of the virulent bacterial pathogen Erwinia tracheiphila Shapiro, Lori R.; Paulson, Joseph N.; Arnold, Brian J. bioRxiv https://doi.org/10.1101/345009	posted_content	June 2018
Accurate and Efficient Gene Function Prediction using a Multi-Bacterial Network Law, Jeffrey N.; Kale, Shiv D.; Murali, T. M. Bioinformatics https://doi.org/10.1101/646687	journal	April 2020
The bare necessities: Uncovering essential and condition‐critical genes with transposon sequencing Shields, Robert C.; Jensen, Paul A. Molecular Oral Microbiology, Vol. 34, Issue 2 https://doi.org/10.1111/omi.12256	journal	February 2019
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Inferring the Minimal Genome of Mesoplasma florum by Comparative Genomics and Transposon Mutagenesis Baby, Vincent; Lachance, Jean-Christophe; Gagnon, Jules mSystems, Vol. 3, Issue 3 https://doi.org/10.1128/msystems.00198-17	journal	April 2018
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The Capricious Nature of Bacterial Pathogens: Phasevarions and Vaccine Development Tan, Aimee; Atack, John M.; Jennings, Michael P. Frontiers in Immunology, Vol. 7 https://doi.org/10.3389/fimmu.2016.00586	journal	December 2016
Molecular tools in understanding the evolution of Vibrio cholerae Rahaman, Md. Habibur; Islam, Tarequl; Colwell, Rita R. Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.01040	journal	October 2015
A Metagenomic Approach to Cyanobacterial Genomics Alvarenga, Danillo O.; Fiore, Marli F.; Varani, Alessandro M. Frontiers in Microbiology, Vol. 8 https://doi.org/10.3389/fmicb.2017.00809	journal	May 2017
A Genomic Outlook on Bioremediation: The Case of Arsenic Removal Plewniak, Frédéric; Crognale, Simona; Rossetti, Simona Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00820	journal	April 2018
Potential for Prebiotics as Feed Additives to Limit Foodborne Campylobacter Establishment in the Poultry Gastrointestinal Tract Kim, Sun Ae; Jang, Min Ji; Kim, Seo Young Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00091	journal	January 2019
Major Traditional Probiotics: Comparative Genomic Analyses and Roles in Gut Microbiome of Eight Cohorts Luo, Guangwen; Li, Bailiang; Yang, Cailu Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.00712	journal	April 2019
Arcobacter cryaerophilus Isolated From New Zealand Mussels Harbor a Putative Virulence Plasmid On, Stephen L. W.; Althaus, Damien; Miller, William G. Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01802	journal	August 2019
Integrated (Meta) Genomic and Synthetic Biology Approaches to Develop New Biocatalysts Parages, María; Gutiérrez-Barranquero, José; Reen, F. Marine Drugs, Vol. 14, Issue 3 https://doi.org/10.3390/md14030062	journal	March 2016
Pseudoalignment for metagenomic read assignment Schaeffer, Lorian; Pimentel, Harold; Bray, Nicolas arXiv https://doi.org/10.48550/arxiv.1510.07371	preprint	January 2015

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