Literature DB >> 22864262

High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity.

Nicholas J Loman1, Chrystala Constantinidou, Jacqueline Z M Chan, Mihail Halachev, Martin Sergeant, Charles W Penn, Esther R Robinson, Mark J Pallen.   

Abstract

Here, we take a snapshot of the high-throughput sequencing platforms, together with the relevant analytical tools, that are available to microbiologists in 2012, and evaluate the strengths and weaknesses of these platforms in obtaining bacterial genome sequences. We also scan the horizon of future possibilities, speculating on how the availability of sequencing that is 'too cheap to metre' might change the face of microbiology forever.

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Year:  2012        PMID： 22864262     DOI： 10.1038/nrmicro2850

Source DB:  PubMed          Journal:  Nat Rev Microbiol        ISSN： 1740-1526            Impact factor:   60.633


  57 in total

1.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs.

Authors:  Daniel R Zerbino; Ewan Birney
Journal:  Genome Res       Date:  2008-03-18       Impact factor: 9.043

2.  Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics.

Authors:  Stephen B Beres; Ronan K Carroll; Patrick R Shea; Izabela Sitkiewicz; Juan Carlos Martinez-Gutierrez; Donald E Low; Allison McGeer; Barbara M Willey; Karen Green; Gregory J Tyrrell; Thomas D Goldman; Michael Feldgarden; Bruce W Birren; Yuriy Fofanov; John Boos; William D Wheaton; Christiane Honisch; James M Musser
Journal:  Proc Natl Acad Sci U S A       Date:  2010-02-08       Impact factor: 11.205

3.  The primary transcriptome of the major human pathogen Helicobacter pylori.

Authors:  Cynthia M Sharma; Steve Hoffmann; Fabien Darfeuille; Jérémy Reignier; Sven Findeiss; Alexandra Sittka; Sandrine Chabas; Kristin Reiche; Jörg Hackermüller; Richard Reinhardt; Peter F Stadler; Jörg Vogel
Journal:  Nature       Date:  2010-02-17       Impact factor: 49.962

4.  Different evolutionary trajectories of European avian-like and classical swine H1N1 influenza A viruses.

Authors:  Eleca J Dunham; Vivien G Dugan; Emilee K Kaser; Sarah E Perkins; Ian H Brown; Edward C Holmes; Jeffery K Taubenberger
Journal:  J Virol       Date:  2009-03-18       Impact factor: 5.103

5.  A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning.

Authors:  Anton Valouev; Jeffrey Ichikawa; Thaisan Tonthat; Jeremy Stuart; Swati Ranade; Heather Peckham; Kathy Zeng; Joel A Malek; Gina Costa; Kevin McKernan; Arend Sidow; Andrew Fire; Steven M Johnson
Journal:  Genome Res       Date:  2008-05-13       Impact factor: 9.043

6.  Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition.

Authors:  Andrew Adey; Hilary G Morrison; Xu Xun; Jacob O Kitzman; Emily H Turner; Bethany Stackhouse; Alexandra P MacKenzie; Nicholas C Caruccio; Xiuqing Zhang; Jay Shendure
Journal:  Genome Biol       Date:  2010-12-08       Impact factor: 13.583

7.  Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology.

Authors:  Alexander Mellmann; Dag Harmsen; Craig A Cummings; Emily B Zentz; Shana R Leopold; Alain Rico; Karola Prior; Rafael Szczepanowski; Yongmei Ji; Wenlan Zhang; Stephen F McLaughlin; John K Henkhaus; Benjamin Leopold; Martina Bielaszewska; Rita Prager; Pius M Brzoska; Richard L Moore; Simone Guenther; Jonathan M Rothberg; Helge Karch
Journal:  PLoS One       Date:  2011-07-20       Impact factor: 3.240

8.  The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs.

Authors:  Peter Schattner; Angela N Brooks; Todd M Lowe
Journal:  Nucleic Acids Res       Date:  2005-07-01       Impact factor: 16.971

9.  Virtual terminator nucleotides for next-generation DNA sequencing.

Authors:  Jayson Bowers; Judith Mitchell; Eric Beer; Philip R Buzby; Marie Causey; J William Efcavitch; Mirna Jarosz; Edyta Krzymanska-Olejnik; Li Kung; Doron Lipson; Geoffrey M Lowman; Subramanian Marappan; Peter McInerney; Adam Platt; Atanu Roy; Suhaib M Siddiqi; Kathleen Steinmann; John F Thompson
Journal:  Nat Methods       Date:  2009-07-20       Impact factor: 28.547

10.  RNAmmer: consistent and rapid annotation of ribosomal RNA genes.

Authors:  Karin Lagesen; Peter Hallin; Einar Andreas Rødland; Hans-Henrik Staerfeldt; Torbjørn Rognes; David W Ussery
Journal:  Nucleic Acids Res       Date:  2007-04-22       Impact factor: 16.971
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  161 in total

Review 1.  Intestinal Carriage of Carbapenemase-Producing Organisms: Current Status of Surveillance Methods.

Authors:  Roberto Viau; Karen M Frank; Michael R Jacobs; Brigid Wilson; Keith Kaye; Curtis J Donskey; Federico Perez; Andrea Endimiani; Robert A Bonomo
Journal:  Clin Microbiol Rev       Date:  2016-01       Impact factor: 26.132

Review 2.  Decoding DNA, RNA and peptides with quantum tunnelling.

Authors:  Massimiliano Di Ventra; Masateru Taniguchi
Journal:  Nat Nanotechnol       Date:  2016-02       Impact factor: 39.213

Review 3.  Bacterial genome sequencing in the clinic: bioinformatic challenges and solutions.

Authors:  W Florian Fricke; David A Rasko
Journal:  Nat Rev Genet       Date:  2013-11-26       Impact factor: 53.242

4.  The shifts of sediment microbial community phylogenetic and functional structures during chromium (VI) reduction.

Authors:  Zhengsheng Yu; Zhili He; Xuanyu Tao; Jizhong Zhou; Yunfeng Yang; Mengxin Zhao; Xiaowei Zhang; Zhe Zheng; Tong Yuan; Pu Liu; Yong Chen; Virgo Nolan; Xiangkai Li
Journal:  Ecotoxicology       Date:  2016-09-16       Impact factor: 2.823

Review 5.  The dormant blood microbiome in chronic, inflammatory diseases.

Authors:  Marnie Potgieter; Janette Bester; Douglas B Kell; Etheresia Pretorius
Journal:  FEMS Microbiol Rev       Date:  2015-05-03       Impact factor: 16.408

6.  Typing and Characterization of Bacteria Using Bottom-up Tandem Mass Spectrometry Proteomics.

Authors:  Fredrik Boulund; Roger Karlsson; Lucia Gonzales-Siles; Anna Johnning; Nahid Karami; Omar Al-Bayati; Christina Åhrén; Edward R B Moore; Erik Kristiansson
Journal:  Mol Cell Proteomics       Date:  2017-04-18       Impact factor: 5.911

7.  Genome sequencing in clinical microbiology.

Authors:  Jacqueline Z-M Chan; Mark J Pallen; Beryl Oppenheim; Chrystala Constantinidou
Journal:  Nat Biotechnol       Date:  2012-11       Impact factor: 54.908

8.  Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.

Authors:  Chen-Shan Chin; David H Alexander; Patrick Marks; Aaron A Klammer; James Drake; Cheryl Heiner; Alicia Clum; Alex Copeland; John Huddleston; Evan E Eichler; Stephen W Turner; Jonas Korlach
Journal:  Nat Methods       Date:  2013-05-05       Impact factor: 28.547

Review 9.  A beginner's guide to phylogenetics.

Authors:  Roy D Sleator
Journal:  Microb Ecol       Date:  2013-04-28       Impact factor: 4.552

Review 10.  Advances in monitoring soil microbial community dynamic and function.

Authors:  K K Nkongolo; R Narendrula-Kotha
Journal:  J Appl Genet       Date:  2020-02-15       Impact factor: 3.240
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