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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]
+ Show Author Affiliations
  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 Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1185792
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
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.
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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. https://doi.org/10.1007/s10142-015-0433-4
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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. https://doi.org/10.1007/s10142-015-0433-4. https://www.osti.gov/servlets/purl/1185792.
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@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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    • Nayfach, Stephen; Rodriguez-Mueller, Beltran; Garud, Nandita
    • Genome Research, Vol. 26, Issue 11
    • DOI: 10.1101/gr.201863.115

    Using Core Genome Alignments To Assign Bacterial Species
    journal, December 2018

    seq-seq-pan: building a computational pan-genome data structure on whole genome alignment
    journal, January 2018

    Marker genes as predictors of shared genomic function
    journal, April 2019

    • Sevigny, Joseph L.; Rothenheber, Derek; Diaz, Krystalle Sharlyn
    • BMC Genomics, Vol. 20, Issue 1
    • DOI: 10.1186/s12864-019-5641-1

    Species classifier choice is a key consideration when analysing low-complexity food microbiome data
    journal, March 2018

    Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer
    journal, June 2016

    Strength and Regulation of Seven rRNA Promoters in Escherichia coli
    journal, December 2015

    Within-Species Genomic Variation and Variable Patterns of Recombination in the Tetracycline Producer Streptomyces rimosus
    journal, March 2019

    Accurate and efficient gene function prediction using a Multi-Bacterial network
    text, January 2020

    Assessing alignment-based taxonomic classification of ancient microbial DNA
    journal, January 2019

    Metagenomic insights into the roles of Proteobacteria in the gastrointestinal microbiomes of healthy dogs and cats
    journal, June 2018

    • Moon, Christina D.; Young, Wayne; Maclean, Paul H.
    • MicrobiologyOpen, Vol. 7, Issue 5
    • DOI: 10.1002/mbo3.677

    Genomic and functional features of the biosurfactant producing Bacillus sp. AM13
    journal, August 2016

    • Shaligram, Shraddha; Kumbhare, Shreyas V.; Dhotre, Dhiraj P.
    • Functional & Integrative Genomics, Vol. 16, Issue 5
    • DOI: 10.1007/s10142-016-0506-z

    Genome annotation and comparative genomic analysis of Bacillus subtilis MJ01, a new bio-degradation strain isolated from oil-contaminated soil
    journal, May 2018

    • Rahimi, Touraj; Niazi, Ali; Deihimi, Tahereh
    • Functional & Integrative Genomics, Vol. 18, Issue 5
    • DOI: 10.1007/s10142-018-0604-1

    Search for Cry proteins expressed by Bacillus spp. genomes, using hidden Markov model profiles
    journal, January 2019

    • Castillo-Esparza, J. Francisco; Hernández-González, Ismael; Ibarra, Jorge E.
    • 3 Biotech, Vol. 9, Issue 1
    • DOI: 10.1007/s13205-018-1533-3

    Bacterial microcompartments
    journal, March 2018

    • Kerfeld, Cheryl A.; Aussignargues, Clement; Zarzycki, Jan
    • Nature Reviews Microbiology, Vol. 16, Issue 5
    • DOI: 10.1038/nrmicro.2018.10

    New and developing diagnostic technologies for urinary tract infections
    journal, March 2017

    • Davenport, Michael; Mach, Kathleen E.; Shortliffe, Linda M. Dairiki
    • Nature Reviews Urology, Vol. 14, Issue 5
    • DOI: 10.1038/nrurol.2017.20

    Genomic metrics made easy: what to do and where to go in the new era of bacterial taxonomy
    journal, March 2019

    • Hayashi Sant’Anna, Fernando; Bach, Evelise; Porto, Renan Z.
    • Critical Reviews in Microbiology, Vol. 45, Issue 2
    • DOI: 10.1080/1040841x.2019.1569587

    Use of whole genome sequencing in surveillance of drug resistant tuberculosis
    journal, May 2018

    Accurate and efficient gene function prediction using a multi-bacterial network
    journal, October 2020

    Biophysical processes supporting the diversity of microbial life in soil
    journal, August 2017

    DeepRibo: precise gene annotation of prokaryotes using deep learning and ribosome profiling data
    posted_content, July 2018

    • Clauwaerts, Jim; Menschaert, Gerben; Waegeman, Willem
    • bioRxiv
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    Rapid Growth and Metabolism of Uropathogenic Escherichia coli in Relation to Urine Composition
    journal, October 2019

    • Reitzer, Larry; Zimmern, Philippe
    • Clinical Microbiology Reviews, Vol. 33, Issue 1
    • DOI: 10.1128/cmr.00101-19

    A natural barrier to lateral gene transfer from prokaryotes to eukaryotes revealed from genomes: the 70 % rule
    journal, October 2016

    Benchmarking of long-read assemblers for prokaryote whole genome sequencing
    journal, January 2019

    A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies
    journal, June 2019

    • Criscuolo, Alexis; Criscuolo, Alexis; Criscuolo, Alexis
    • Research Ideas and Outcomes, Vol. 5
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    Assessing alignment-based taxonomic classification of ancient microbial DNA
    posted_content, September 2018

    Everything is not everywhere: a tale on the biogeography of cyanobacteria
    journal, June 2018

    • Ribeiro, Karine Felix; Duarte, Leandro; Crossetti, Luciane Oliveira
    • Hydrobiologia, Vol. 820, Issue 1
    • DOI: 10.1007/s10750-018-3669-x

    An introduced crop plant is driving diversification of the virulent bacterial pathogen Erwinia tracheiphila
    posted_content, June 2018

    • Shapiro, Lori R.; Paulson, Joseph N.; Arnold, Brian J.
    • bioRxiv
    • DOI: 10.1101/345009

    Accurate and Efficient Gene Function Prediction using a Multi-Bacterial Network
    journal, April 2020

    • Law, Jeffrey N.; Kale, Shiv D.; Murali, T. M.
    • Bioinformatics
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    The bare necessities: Uncovering essential and condition‐critical genes with transposon sequencing
    journal, February 2019

    • Shields, Robert C.; Jensen, Paul A.
    • Molecular Oral Microbiology, Vol. 34, Issue 2
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    Combining multiple functional annotation tools increases coverage of metabolic annotation
    journal, December 2018

    Complete nontuberculous mycobacteria whole genomes using an optimized DNA extraction protocol for long-read sequencing
    journal, October 2019

    The promise and challenge of cancer microbiome research
    journal, June 2020

    The essential genome of Streptococcus agalactiae.
    text, January 2016

    • Hooven, Ta; Catomeris, Aj; Akabas, Lh
    • Apollo - University of Cambridge Repository
    • DOI: 10.17863/cam.10063

    Metaproteomic and 16S rRNA Gene Sequencing Analysis of the Infant Fecal Microbiome
    journal, March 2019

    • Cortes, Laetitia; Wopereis, Harm; Tartiere, Aude
    • International Journal of Molecular Sciences, Vol. 20, Issue 6
    • DOI: 10.3390/ijms20061430

    Dependency of DNA extraction efficiency on cell concentration confounds molecular quantification of microorganisms in groundwater
    journal, August 2018

    • Luk, Alison WS; Beckmann, Sabrina; Manefield, Mike
    • FEMS Microbiology Ecology, Vol. 94, Issue 10
    • DOI: 10.1093/femsec/fiy146

    StreptomeDB 2.0—an extended resource of natural products produced by streptomycetes
    journal, November 2015

    • Klementz, Dennis; Döring, Kersten; Lucas, Xavier
    • Nucleic Acids Research, Vol. 44, Issue D1
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    Inferring the Minimal Genome of Mesoplasma florum by Comparative Genomics and Transposon Mutagenesis
    journal, April 2018

    De novo assembly of bacterial genomes with repetitive DNA regions by dnaasm application
    journal, July 2018

    Stratified reconstruction of ancestral Escherichia coli diversification
    journal, December 2019

    • Gonzalez-Alba, José Maria; Baquero, Fernando; Cantón, Rafael
    • BMC Genomics, Vol. 20, Issue 1
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    Baseline human gut microbiota profile in healthy people and standard reporting template
    journal, September 2019

    Current Status and Potential Applications of Underexplored Prokaryotes
    journal, October 2019

    KBase Narrative - kb_DRAM E. coli annotation
    dataset, January 2022

    KBase Narrative - kb_DRAM P. normanii annotation with model
    dataset, January 2022

    Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics
    journal, January 2017

    • Sedlar, Karel; Kupkova, Kristyna; Provaznik, Ivo
    • Computational and Structural Biotechnology Journal, Vol. 15
    • DOI: 10.1016/j.csbj.2016.11.005

    From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic
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    • Balloux, Francois; Brønstad Brynildsrud, Ola; van Dorp, Lucy
    • Trends in Microbiology, Vol. 26, Issue 12
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    Distribution and diversity of enzymes for polysaccharide degradation in fungi
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    Regulatory Role of PlaR (YiaJ) for Plant Utilization in Escherichia coli K-12
    journal, December 2019

    PanViz: interactive visualization of the structure of functionally annotated pangenomes
    journal, December 2016

    Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium
    journal, December 2017

    • Lassalle, Florent; Planel, Rémi; Penel, Simon
    • Genome Biology and Evolution, Vol. 9, Issue 12
    • DOI: 10.1093/gbe/evx255

    REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes
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    • Ndah, Elvis; Jonckheere, Veronique; Giess, Adam
    • Nucleic Acids Research, Vol. 45, Issue 20
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    Gsmodutils: A python based framework for test-driven genome scale metabolic model development
    journal, September 2018

    • Gilbert, James P.; Pearcy, Nicole; Norman, Rupert
    • Bioinformatics
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    Accurate and Efficient Gene Function Prediction using a Multi-Bacterial Network
    journal, April 2020

    • Law, Jeffrey N.; Kale, Shiv D.; Murali, T. M.
    • Bioinformatics
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    Use of Alignment-Free Phylogenetics for Rapid Genome Sequence-Based Typing of Helicobacter pylori Virulence Markers and Antibiotic Susceptibility
    journal, September 2015

    • van Vliet, Arnoud H. M.; Kusters, Johannes G.
    • Journal of Clinical Microbiology, Vol. 53, Issue 9
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    Inferring the Minimal Genome of Mesoplasma florum by Comparative Genomics and Transposon Mutagenesis
    journal, April 2018

    Linking De Novo Assembly Results with Long DNA Reads Using the dnaasm-link Application
    journal, April 2019

    • Kuśmirek, Wiktor; Franus, Wiktor; Nowak, Robert
    • BioMed Research International, Vol. 2019
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    De novo assembly of bacterial genomes with repetitive DNA regions by dnaasm application
    journal, July 2018

    seq-seq-pan: building a computational pan-genome data structure on whole genome alignment
    journal, January 2018

    Combining multiple functional annotation tools increases coverage of metabolic annotation
    journal, December 2018

    Lateral gene transfer in eukaryotes: tip of the iceberg or of the ice cube?
    journal, November 2016

    Advances in biodiversity: metagenomics and the unveiling of biological dark matter
    journal, September 2016

    • Robbins, Robert J.; Krishtalka, Leonard; Wooley, John C.
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    Microbial metal resistance and metabolism across dynamic landscapes: high-throughput environmental microbiology
    journal, January 2017

    Benchmarking of long-read assemblers for prokaryote whole genome sequencing
    journal, December 2019

    In vivo insertion pool sequencing identifies virulence factors in a complex fungal–host interaction
    journal, April 2018

    An educational guide for nanopore sequencing in the classroom
    journal, January 2020

    Comparative Genome Analysis Provides Insights into the Pathogenicity of Flavobacterium psychrophilum
    journal, April 2016

    The whole set of the constitutive promoters recognized by four minor sigma subunits of Escherichia coli RNA polymerase
    journal, June 2017

    Automatic identification of optimal marker genes for phenotypic and taxonomic groups of microorganisms
    journal, May 2018

    Baseline human gut microbiota profile in healthy people and standard reporting template
    journal, September 2019

    Approaches for in silico finishing of microbial genome sequences
    journal, September 2017

    • Kremer, Frederico Schmitt; McBride, Alan John Alexander; Pinto, Luciano da Silva
    • Genetics and Molecular Biology, Vol. 40, Issue 3
    • DOI: 10.1590/1678-4685-gmb-2016-0230

    Target Gene Inactivation in Cyanobacterium Anabaena sp. PCC 7120
    journal, January 2016

    DRAM example narrative
    dataset, January 2021

    New Insight Into the Diversity of SemiSWEET Sugar Transporters and the Homologs in Prokaryotes
    journal, May 2018

    The Capricious Nature of Bacterial Pathogens: Phasevarions and Vaccine Development
    journal, December 2016

    Molecular tools in understanding the evolution of Vibrio cholerae
    journal, October 2015

    • Rahaman, Md. Habibur; Islam, Tarequl; Colwell, Rita R.
    • Frontiers in Microbiology, Vol. 6
    • DOI: 10.3389/fmicb.2015.01040

    A Metagenomic Approach to Cyanobacterial Genomics
    journal, May 2017

    • Alvarenga, Danillo O.; Fiore, Marli F.; Varani, Alessandro M.
    • Frontiers in Microbiology, Vol. 8
    • DOI: 10.3389/fmicb.2017.00809

    A Genomic Outlook on Bioremediation: The Case of Arsenic Removal
    journal, April 2018

    • Plewniak, Frédéric; Crognale, Simona; Rossetti, Simona
    • Frontiers in Microbiology, Vol. 9
    • DOI: 10.3389/fmicb.2018.00820

    Potential for Prebiotics as Feed Additives to Limit Foodborne Campylobacter Establishment in the Poultry Gastrointestinal Tract
    journal, January 2019

    Major Traditional Probiotics: Comparative Genomic Analyses and Roles in Gut Microbiome of Eight Cohorts
    journal, April 2019

    Arcobacter cryaerophilus Isolated From New Zealand Mussels Harbor a Putative Virulence Plasmid
    journal, August 2019

    • On, Stephen L. W.; Althaus, Damien; Miller, William G.
    • Frontiers in Microbiology, Vol. 10
    • DOI: 10.3389/fmicb.2019.01802

    Metaproteomic and 16S rRNA Gene Sequencing Analysis of the Infant Fecal Microbiome
    journal, March 2019

    • Cortes, Laetitia; Wopereis, Harm; Tartiere, Aude
    • International Journal of Molecular Sciences, Vol. 20, Issue 6
    • DOI: 10.3390/ijms20061430

    High-Resolution Profiling of Gut Bacterial Communities in an Invasive Beetle using PacBio SMRT Sequencing System
    journal, August 2019

    Integrated (Meta) Genomic and Synthetic Biology Approaches to Develop New Biocatalysts
    journal, March 2016

    • Parages, María; Gutiérrez-Barranquero, José; Reen, F.
    • Marine Drugs, Vol. 14, Issue 3
    • DOI: 10.3390/md14030062

    Genome Analysis of Vallitalea guaymasensis Strain L81 Isolated from a Deep-Sea Hydrothermal Vent System
    journal, July 2018

    “Omics”-Informed Drug and Biomarker Discovery: Opportunities, Challenges and Future Perspectives
    journal, September 2016

    Pseudoalignment for metagenomic read assignment
    preprint, January 2015

    Assessing alignment-based taxonomic classification of ancient microbial DNA
    journal, January 2019

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