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PMID: 22864262 Published · ppublish English Comparative Study Journal Article Review

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

Nature reviews. Microbiology ·Vol. 10 ·No. 9 ·2012-09-00 ·Pages 599-606

Loman NJ, Constantinidou C, Chan JZ, Halachev M, Sergeant M, Penn CW, Robinson ER, Pallen MJ

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.

MeSH Terms
DNA, Bacterial/chemistry,genetics Genetics, Microbial/trends Genome, Bacterial High-Throughput Screening Assays Molecular Biology/trends
Chemicals
DNA, Bacterial
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Loman Nicholas J
Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK.
Constantinidou Chrystala
Chan Jacqueline Z M
Halachev Mihail
Sergeant Martin
Penn Charles W
Robinson Esther R
Pallen Mark J
References (57)
57 references, click to expand
  1. The primary transcriptome of the major human pathogen Helicobacter pylori.
    Nature. 2010 Mar 11;464(7286):250-5 PMID: 20164839
  2. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs.
    Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W686-9 PMID: 15980563
  3. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning.
    Genome Res. 2008 Jul;18(7):1051-63 PMID: 18477713
  4. Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology.
    PLoS One. 2011;6(7):e22751 PMID: 21799941
  5. Different evolutionary trajectories of European avian-like and classical swine H1N1 influenza A viruses.
    J Virol. 2009 Jun;83(11):5485-94 PMID: 19297491
  6. Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
    Genome Res. 2008 May;18(5):821-9 PMID: 18349386
  7. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition.
    Genome Biol. 2010;11(12):R119 PMID: 21143862
  8. RNAmmer: consistent and rapid annotation of ribosomal RNA genes.
    Nucleic Acids Res. 2007;35(9):3100-8 PMID: 17452365
  9. Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics.
    Proc Natl Acad Sci U S A. 2010 Mar 2;107(9):4371-6 PMID: 20142485
  10. Virtual terminator nucleotides for next-generation DNA sequencing.
    Nat Methods. 2009 Aug;6(8):593-5 PMID: 19620973
  11. Multiple personal genomes await.
    Nature. 2010 Apr 1;464(7289):676-7 PMID: 20360717
  12. Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity.
    Nat Rev Genet. 2010 Jan;11(1):9-16 PMID: 19935729
  13. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen.
    Science. 2011 Jan 28;331(6016):463-7 PMID: 21273488
  14. Inference of bacterial microevolution using multilocus sequence data.
    Genetics. 2007 Mar;175(3):1251-66 PMID: 17151252
  15. Improved microbial gene identification with GLIMMER.
    Nucleic Acids Res. 1999 Dec 1;27(23):4636-41 PMID: 10556321
  16. Whole-genome sequencing and social-network analysis of a tuberculosis outbreak.
    N Engl J Med. 2011 Feb 24;364(8):730-9 PMID: 21345102
  17. Are diagnostic and public health bacteriology ready to become branches of genomic medicine?
    Genome Med. 2011 Aug 23;3(8):53 PMID: 21861847
  18. A human gut microbial gene catalogue established by metagenomic sequencing.
    Nature. 2010 Mar 4;464(7285):59-65 PMID: 20203603
  19. Zero-mode waveguides for single-molecule analysis at high concentrations.
    Science. 2003 Jan 31;299(5607):682-6 PMID: 12560545
  20. A hybrid approach for the automated finishing of bacterial genomes.
    Nat Biotechnol. 2012 Jul 01;30(7):701-707 PMID: 22750883
  21. The automatic annotation of bacterial genomes.
    Brief Bioinform. 2013 Jan;14(1):1-12 PMID: 22408191
  22. Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants.
    Genome Res. 2009 Dec;19(12):2308-16 PMID: 19826075
  23. The RAST Server: rapid annotations using subsystems technology.
    BMC Genomics. 2008 Feb 08;9:75 PMID: 18261238
  24. Tablet--next generation sequence assembly visualization.
    Bioinformatics. 2010 Feb 1;26(3):401-2 PMID: 19965881
  25. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak.
    N Engl J Med. 2012 Jun 14;366(24):2267-75 PMID: 22693998
  26. High-throughput whole-genome sequencing to dissect the epidemiology of Acinetobacter baumannii isolates from a hospital outbreak.
    J Hosp Infect. 2010 May;75(1):37-41 PMID: 20299126
  27. Assembling the marine metagenome, one cell at a time.
    PLoS One. 2009;4(4):e5299 PMID: 19390573
  28. Performance comparison of benchtop high-throughput sequencing platforms.
    Nat Biotechnol. 2012 May;30(5):434-9 PMID: 22522955
  29. Evidence for several waves of global transmission in the seventh cholera pandemic.
    Nature. 2011 Aug 24;477(7365):462-5 PMID: 21866102
  30. Genome sequencing in microfabricated high-density picolitre reactors.
    Nature. 2005 Sep 15;437(7057):376-80 PMID: 16056220
  31. Accurate whole human genome sequencing using reversible terminator chemistry.
    Nature. 2008 Nov 6;456(7218):53-9 PMID: 18987734
  32. Using the miraEST assembler for reliable and automated mRNA transcript assembly and SNP detection in sequenced ESTs.
    Genome Res. 2004 Jun;14(6):1147-59 PMID: 15140833
  33. Structure and complexity of a bacterial transcriptome.
    J Bacteriol. 2009 May;191(10):3203-11 PMID: 19304856
  34. The potential and challenges of nanopore sequencing.
    Nat Biotechnol. 2008 Oct;26(10):1146-53 PMID: 18846088
  35. Mauve: multiple alignment of conserved genomic sequence with rearrangements.
    Genome Res. 2004 Jul;14(7):1394-403 PMID: 15231754
  36. Mugsy: fast multiple alignment of closely related whole genomes.
    Bioinformatics. 2011 Feb 1;27(3):334-42 PMID: 21148543
  37. Field guide to next-generation DNA sequencers.
    Mol Ecol Resour. 2011 Sep;11(5):759-69 PMID: 21592312
  38. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays.
    Science. 2010 Jan 1;327(5961):78-81 PMID: 19892942
  39. Open-source genomic analysis of Shiga-toxin-producing E. coli O104:H4.
    N Engl J Med. 2011 Aug 25;365(8):718-24 PMID: 21793736
  40. Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing.
    Nat Genet. 2012 Mar 11;44(4):413-9, S1 PMID: 22406642
  41. Microevolution of the major common Pseudomonas aeruginosa clones C and PA14 in cystic fibrosis lungs.
    Environ Microbiol. 2011 Jul;13(7):1690-704 PMID: 21492363
  42. IMG ER: a system for microbial genome annotation expert review and curation.
    Bioinformatics. 2009 Sep 1;25(17):2271-8 PMID: 19561336
  43. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
    Science. 1995 Jul 28;269(5223):496-512 PMID: 7542800
  44. A draft genome of Yersinia pestis from victims of the Black Death.
    Nature. 2011 Oct 12;478(7370):506-10 PMID: 21993626
  45. Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms.
    Nat Methods. 2009 Oct;6(10):767-72 PMID: 19767758
  46. Emerging technologies in DNA sequencing.
    Genome Res. 2005 Dec;15(12):1767-76 PMID: 16339375
  47. Direct methods for studying transcription regulatory proteins and RNA polymerase in bacteria.
    Curr Opin Microbiol. 2009 Oct;12(5):531-5 PMID: 19762273
  48. Hybrid error correction and de novo assembly of single-molecule sequencing reads.
    Nat Biotechnol. 2012 Jul 01;30(7):693-700 PMID: 22750884
  49. Microbe hunting.
    Microbiol Mol Biol Rev. 2010 Sep;74(3):363-77 PMID: 20805403
  50. xBASE2: a comprehensive resource for comparative bacterial genomics.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D543-6 PMID: 17984072
  51. Detection of recombination events in bacterial genomes from large population samples.
    Nucleic Acids Res. 2012 Jan;40(1):e6 PMID: 22064866
  52. A sequencing method based on real-time pyrophosphate.
    Science. 1998 Jul 17;281(5375):363, 365 PMID: 9705713
  53. Alignment-free detection of local similarity among viral and bacterial genomes.
    Bioinformatics. 2011 Jun 1;27(11):1466-72 PMID: 21471011
  54. Inference of homologous recombination in bacteria using whole-genome sequences.
    Genetics. 2010 Dec;186(4):1435-49 PMID: 20923983
  55. An integrated semiconductor device enabling non-optical genome sequencing.
    Nature. 2011 Jul 20;475(7356):348-52 PMID: 21776081
  56. Evolution of MRSA during hospital transmission and intercontinental spread.
    Science. 2010 Jan 22;327(5964):469-74 PMID: 20093474
  57. Real-time DNA sequencing from single polymerase molecules.
    Science. 2009 Jan 2;323(5910):133-8 PMID: 19023044
Article Info
Journal
Nature reviews. Microbiology
Abbr.
Nat Rev Microbiol
ISSN
1740-1534
DOI
10.1038/nrmicro2850
Published
2012-09-00
Epub
2012-00-06
Pages
599-606
Language
English
Region
England
NLM ID
101190261
Subset
IM
Grants
Medical Research Council · G0901717 · United Kingdom
Medical Research Council · MR/J014370/1 · United Kingdom
External Links
PubMed source DOI: 10.1038/nrmicro2850 View journal details
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