Revolutionizing prokaryotic systematics through next-generation sequencing

Methods in Microbiology

Volumn 41, Issue , 2014, Pages 75-101

  Sangal, Vartul ^a   Nieminen, Leena ^b   Tucker, Nicholas P ^b   Hoskisson, Paul A ^b  

^a NORTHUMBRIA UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF STRATHCLYDE   (United Kingdom)

Author keywords

Bioinformatic tools; Comparative genomics; De novo assembly; Genome annotation; Mapping; Next generation sequencing; Phylogenetic analyses; Prokaryotic systematics; SNP analyses

Indexed keywords

EID: 84919419857     PISSN: 05809517     EISSN: None     Source Type: Book Series    
DOI: 10.1016/bs.mim.2014.07.001     Document Type: Chapter

References (120)

1. Achtman M., Wagner M. Microbial diversity and the genetic nature of microbial species. Nature Reviews. Microbiology 2008, 6(6):431-440. 10.1038/nrmicro1872.
2. Amaral G.R., Dias G.M., Wellington-Oguri M., Chimetto L., Campeao M.E., Thompson F.L., et al. Genotype to phenotype: Identification of diagnostic Vibrio phenotypes using whole genome sequences. International Journal of Systematic and Evolutionary Microbiology 2014, 64(2):357-365. 10.1099/ijs.0.057927-0.
3. Anders, S., Pyl, P. T., & Huber, W. (2014). HTSeq; A Python framework to work with high-throughput sequencing data. BioRxiv Preprint. http://dx.doi.org/10.1101/002824.
4. Auch A.F., von Jan M., Klenk H.P., Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Standards in Genomic Sciences 2010, 2(1):117-134. 10.4056/sigs.531120.
5. Aziz R.K., Bartels D., Best A.A., DeJongh M., Disz T., Edwards R.A., et al. The RAST Server: Rapid annotations using subsystems technology. BMC Genomics 2008, 9:75. 10.1186/1471-2164-9-75.
6. Aziz R.K., Devoid S., Disz T., Edwards R.A., Henry C.S., Olsen G.J., et al. SEED servers: High-performance access to the SEED genomes, annotations, and metabolic models. PLoS One 2012, 7(10):e48053. 10.1371/journal.pone.0048053.
7. Badger J.H., Olsen G.J. CRITICA: Coding region identification tool invoking comparative analysis. Molecular Biology and Evolution 1999, 16(4):512-524.
8. Benson G. Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Research 1999, 27(2):573-580. gkc131 [pii].
9. Bentley D.R., Balasubramanian S., Swerdlow H.P., Smith G.P., Milton J., Brown C.G., et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456(7218):53-59. 10.1038/nature07517.
10. Blankenberg D., Von Kuster G., Coraor N., Ananda G., Lazarus R., Mangan M., et al. Galaxy: A web-based genome analysis tool for experimentalists. Current Protocols in Molecular Biology 2010, Chapter 19, Unit 19 10 11-21. 10.1002/0471142727.mb1910s89.
11. Blom J., Albaum S.P., Doppmeier D., Puhler A., Vorholter F.J., Zakrzewski M., et al. EDGAR: A software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics 2009, 10:154. 10.1186/1471-2105-10-154.
12. Borodovsky M., McIninch J. GeneMark: Parallel gene recognition for both DNA strands. Computers & Chemistry 1993, 17(19):123-133.
13. Busarakam K., Bull A.T., Girard G., Labeda D.P., van Wezel G.P., Goodfellow M. Streptomyces leeuwenhoekii sp. nov., the producer of chaxalactins and chaxamycins, forms a distinct branch in Streptomyces gene trees. Antonie Van Leeuwenhoek 2014, 105(5):849-861. 10.1007/s10482-014-0139-y.
14. Carver T., Berriman M., Tivey A., Patel C., Bohme U., Barrell B.G., et al. Artemis and ACT: Viewing, annotating and comparing sequences stored in a relational database. Bioinformatics 2008, 24(23):2672-2676. 10.1093/bioinformatics/btn529.
15. Carver T., Harris S.R., Berriman M., Parkhill J., McQuillan J.A. Artemis: An integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics 2012, 28(4):464-469. 10.1093/bioinformatics/btr703.
16. Caspi R., Altman T., Billington R., Dreher K., Foerster H., Fulcher C.A., et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Research 2014, 42(Database issue):D459-D471. 10.1093/nar/gkt1103.
17. Chan J.Z., Halachev M.R., Loman N.J., Constantinidou C., Pallen M.J. Defining bacterial species in the genomic era: Insights from the genus Acinetobacter. BMC Microbiology 2012, 12:302. 10.1186/1471-2180-12-302.
18. Chaudhuri R.R., Pallen M.J. xBASE, a collection of online databases for bacterial comparative genomics. Nucleic Acids Research 2006, 34(Database issue):D335-D337. 10.1093/nar/gkj140.
19. Chevreux B., Wetter T., Suhai S. Genome sequence assembly using trace signals and additional sequence information. Computer science and biology 1999, 45-56. Hannover, Germany.
20. Chun J., Rainey F.A. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. International Journal of Systematic and Evolutionary Microbiology 2014, 64(2):316-324. 10.1099/ijs.0.054171-0.
21. Daniel R. The metagenomics of soil. Nature Reviews. Microbiology 2005, 3(6):470-478. 10.1038/nrmicro1160.
22. Darling A.C., Mau B., Blattner F.R., Perna N.T. Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Research 2004, 14(7):1394-1403. 10.1101/gr.2289704.
23. Delcher A.L., Harmon D., Kasif S., White O., Salzberg S.L. Improved microbial gene identification with GLIMMER. Nucleic Acids Research 1999, 27(23):4636-4641.
24. Deloger M., El Karoui M., Petit M.A. A genomic distance based on MUM indicates discontinuity between most bacterial species and genera. Journal of Bacteriology 2009, 191(1):91-99. 10.1128/JB.01202-08.
25. Didelot X., Falush D. Inference of bacterial microevolution using multilocus sequence data. Genetics 2007, 175(3):1251-1266. 10.1534/genetics.106.063305.
26. Dillies M.A., Rau A., Aubert J., Hennequet-Antier C., Jeanmougin M., Servant N., et al. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis. Briefings in Bioinformatics 2013, 14(6):671-683. 10.1093/bib/bbs046.
27. Eid J., Fehr A., Gray J., Luong K., Lyle J., Otto G., et al. Real-time DNA sequencing from single polymerase molecules. Science 2009, 323(5910):133-138. 10.1126/science.1162986.
28. Fang W., Fang Z., Zhou P., Chang F., Hong Y., Zhang X., et al. Evidence for lignin oxidation by the giant panda fecal microbiome. PLoS One 2012, 7(11):e50312. 10.1371/journal.pone.0050312.
29. Finn R.D., Bateman A., Clements J., Coggill P., Eberhardt R.Y., Eddy S.R., et al. Pfam: The protein families database. Nucleic Acids Research 2013, 42:D222-D230. 10.1093/nar/gkt1223.
30. Fleischmann R.D., Adams M.D., White O., Clayton R.A., Kirkness E.F., Kerlavage A.R., et al. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 1995, 269(5223):496-512.
31. Fouts D.E. Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Research 2006, 34(20):5839-5851. 10.1093/nar/gkl732.
32. Garrity G.M. Conservation of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 and rejection of Corynebacterium hoagii (Morse 1912) Eberson 1918. International Journal of Systematic and Evolutionary Microbiology 2014, 64(1):311-312. 10.1099/ijs.0.059741-0.
33. Goering R.V. Pulsed field gel electrophoresis: A review of application and interpretation in the molecular epidemiology of infectious disease. Infection, Genetics and Evolution 2010, 10(7):866-875. 10.1016/j.meegid.2010.07.023.
34. Goris J., Konstantinidis K.T., Klappenbach J.A., Coenye T., Vandamme P., Tiedje J.M. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. International Journal of Systematic and Evolutionary Microbiology 2007, 57(1):81-91. 10.1099/ijs.0.64483-0.
35. Grant J.R., Arantes A.S., Liao X., Stothard P. In-depth annotation of SNPs arising from resequencing projects using NGS-SNP. Bioinformatics 2011, 27(16):2300-2301. 10.1093/bioinformatics/btr372.
36. Grant J.R., Arantes A.S., Stothard P. Comparing thousands of circular genomes using the CGView Comparison Tool. BMC Genomics 2012, 13(1):202. 10.1186/1471-2164-13-202.
37. Habegger L., Balasubramanian S., Chen D.Z., Khurana E., Sboner A., Harmanci A., et al. VAT: A computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. Bioinformatics 2012, 28(17):2267-2269. 10.1093/bioinformatics/bts368.
38. Hanage W.P. Fuzzy species revisited. BMC Biololgy 2013, 11:41. 10.1186/1741-7007-11-41.
39. Hanage W.P., Fraser C., Spratt B.G. Fuzzy species among recombinogenic bacteria. BMC Biololgy 2005, 3:6. 10.1186/1741-7007-3-6.
40. Harris S.R., Feil E.J., Holden M.T., Quail M.A., Nickerson E.K., Chantratita N., et al. Evolution of MRSA during hospital transmission and intercontinental spread. Science 2010, 327(5964):469-474. 10.1126/science.1182395.
41. Holt K.E., Baker S., Weill F.X., Holmes E.C., Kitchen A., Yu J., et al. Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nature Genetics 2012, 44(9):1056-1059. 10.1038/ng.2369.
42. Holt K.E., Parkhill J., Mazzoni C.J., Roumagnac P., Weill F.X., Goodhead I., et al. High-throughput sequencing provides insights into genome variation and evolution in Salmonella typhi. Nature Genetics 2008, 40(8):987-993. 10.1038/ng.195.
43. Howden B.P., Beaume M., Harrison P.F., Hernandez D., Schrenzel J., Seemann T., et al. Analysis of the small RNA transcriptional response in multidrug-resistant Staphylococcus aureus after antimicrobial exposure. Antimicrobial Agents and Chemotherapy 2013, 57(8):3864-3874. 10.1128/AAC.00263-13.
44. Hyatt D., Chen G.L., Locascio P.F., Land M.L., Larimer F.W., Hauser L.J. Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010, 11:119. 10.1186/1471-2105-11-119.
45. Jones A.L., Sutcliffe I.C., Goodfellow M. Prescottia equi gen. nov., comb. nov.: A new home for an old pathogen. Antonie Van Leeuwenhoek 2013, 103(3):655-671. 10.1007/s10482-012-9850-8.
46. Jones A.L., Sutcliffe I.C., Goodfellow M. Proposal to replace the illegitimate genus name Prescottia Jones et al. 2013 with the genus name Prescottella gen. nov. and to replace the illegitimate combination Prescottia equi Jones et al. 2013 with Prescottella equi comb. nov. Antonie Van Leeuwenhoek 2013, 103(6):1405-1407. 10.1007/s10482-013-9924-2.
47. Kamke J., Rinke C., Schwientek P., Mavromatis K., Ivanova N., Sczyrba A., et al. The candidate phylum Poribacteria by single-cell genomics: New insights into phylogeny, cell-compartmentation, eukaryote-like repeat proteins, and other genomic features. PLoS One 2014, 9(1):e87353. 10.1371/journal.pone.0087353.
48. Kämpfer P., Dott W., Martin K., Glaeser S.P. Rhodococcus defluvii sp. nov. isolated from wastewater of a bioreactor and formal proposal to reclassify 'Corynebacterium' hoagii and Rhodococcus equi as Rhodococcus hoagii. International Journal of Systematic and Evolutionary Microbiology 2013, 64(Pt 3):755-761. 10.1099/ijs.0.053322-0.
49. Kanehisa M. Post-genome informatics 2000, Oxford University Press, Oxford, UK.
50. Kantor R.S., Wrighton K.C., Handley K.M., Sharon I., Hug L.A., Castelle C.J., et al. Small genomes and sparse metabolisms of sediment-associated bacteria from four candidate phyla. mBio 2013, 4(5):e00708-e00713. 10.1128/mBio.00708-13.
51. Kaufmann M.E. Pulsed-field gel electrophoresis. Methods in Molecular Medicine 1998, 15:33-50. 10.1385/0-89603-498-4:33.
52. Kim M., Oh H.S., Park S.C., Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. International Journal of Systematic and Evolutionary Microbiology 2014, 64(2):346-351. 10.1099/ijs.0.059774-0.
53. Konstantinidis K.T., Ramette A., Tiedje J.M. The bacterial species definition in the genomic era. Philosophical Transactions of the Royal Society B 2006, 361:1929-1940.
54. Konstantinidis K.T., Tiedje J.M. Genomic insights that advance the species definition for prokaryotes. Proceedings of the National Academy of Sciences of the United States of America 2005, 102(7):2567-2572. 10.1073/pnas.0409727102.
55. Konstantinidis K.T., Tiedje J.M. Towards a genome-based taxonomy for prokaryotes. Journal of Bacteriology 2005, 187(18):6258-6264. 10.1128/JB.187.18.6258-6264.2005.
56. Laing C., Buchanan C., Taboada E.N., Zhang Y., Kropinski A., Villegas A., et al. Pan-genome sequence analysis using Panseq: An online tool for the rapid analysis of core and accessory genomic regions. BMC Bioinformatics 2010, 11:461. 10.1186/1471-2105-11-461.
57. Langille M.G., Brinkman F.S. IslandViewer: An integrated interface for computational identification and visualization of genomic islands. Bioinformatics 2009, 25(5):664-665. 10.1093/bioinformatics/btp030.
58. Levene M.J., Korlach J., Turner S.W., Foquet M., Craighead H.G., Webb W.W. Zero-mode waveguides for single-molecule analysis at high concentrations. Science 2003, 299(5607):682-686. 10.1126/science.1079700.
59. Li H., Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25(14):1754-1760. 10.1093/bioinformatics/btp324.
60. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., et al. The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079. 10.1093/bioinformatics/btp352.
61. Li H., Ruan J., Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 2008, 18(11):1851-1858. 10.1101/gr.078212.108.
62. Linke B., McHardy A.C., Neuweger H., Krause L., Meyer F. REGANOR: A gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes. Applied Bioinformatics 2006, 5(3):193-198.
63. Loman N.J., Constantinidou C., Chan J.Z., Halachev M., Sergeant M., Penn C.W., et al. High-throughput bacterial genome sequencing: An embarrassment of choice, a world of opportunity. Nature Reviews. Microbiology 2012, 10(9):599-606. 10.1038/nrmicro2850.
64. Luo C., Rodriguez R.L., Konstantinidis K.T. MyTaxa: An advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Research 2014, 42(8):e73. 10.1093/nar/gku169.
65. Mader U., Nicolas P., Richard H., Bessieres P., Aymerich S. Comprehensive identification and quantification of microbial transcriptomes by genome-wide unbiased methods. Current Opinion in Biotechnology 2011, 22(1):32-41. 10.1016/j.copbio.2010.10.003.
66. Magoc T., Wood D., Salzberg S.L. EDGE-pro: Estimated degree of gene expression in prokaryotic genomes. Evolutionary Bioinformatics Online 2013, 9:127-136. 10.4137/EBO.S11250.
67. Maiden M.C. Multilocus sequence typing of bacteria. Annual Review of Microbiology 2006, 60:561-588. 10.1146/annurev.micro.59.030804.121325.
68. Maiden M.C., Bygraves J.A., Feil E., Morelli G., Russell J.E., Urwin R., et al. Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms. Proceedings of the National Academy of Sciences of the United States of America 1998, 95(6):3140-3145.
69. Margulies M., Egholm M., Altman W.E., Attiya S., Bader J.S., Bemben L.A., et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437(7057):376-380. 10.1038/nature03959.
70. McClure R., Balasubramanian D., Sun Y., Bobrovskyy M., Sumby P., Genco C.A., et al. Computational analysis of bacterial RNA-Seq data. Nucleic Acids Research 2013, 41(14):e140. 10.1093/nar/gkt444.
71. Meier-Kolthoff J.P., Auch A.F., Klenk H.P., Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013, 14:60. 10.1186/1471-2105-14-60.
72. Meyer F., Goesmann A., McHardy A.C., Bartels D., Bekel T., Clausen J., et al. GenDB - An open source genome annotation system for prokaryote genomes. Nucleic Acids Research 2003, 31(8):2187-2195.
73. Myllykangas S., Buenrostro J., Ji H.P. Overview of sequencing technology platforms. Bioinformatics for high throughput sequencing 2012, 11-25. Springer, New York. N. Rodríguez-Ezpeleta, M. Hackenberg, A.M. Aransay (Eds.).
74. Nagarajan N., Cook C., Di Bonaventura M., Ge H., Richards A., Bishop-Lilly K.A., et al. Finishing genomes with limited resources: Lessons from an ensemble of microbial genomes. BMC Genomics 2010, 11:242. 10.1186/1471-2164-11-242.
75. Osmundson J., Dewell S., Darst S.A. RNA-Seq reveals differential gene expression in Staphylococcus aureus with single-nucleotide resolution. PLoS One 2013, 8(10):e76572. 10.1371/journal.pone.0076572.
76. Pride D.T., Meinersmann R.J., Wassenaar T.M., Blaser M.J. Evolutionary implications of microbial genome tetranucleotide frequency biases. Genome Research 2003, 13(2):145-158. 10.1101/gr.335003.
77. Renesto P., Crapoulet N., Ogata H., La Scola B., Vestris G., Claverie J.M., et al. Genome-based design of a cell-free culture medium for Tropheryma whipplei. Lancet 2003, 362(9382):447-449. 10.1016/S0140-6736(03)14071-8.
78. Retief J.D. Phylogenetic analysis using PHYLIP. Methods in Molecular Biology 2000, 132:243-258.
79. Reumerman R.A., Tucker N.P., Herron P.R., Hoskisson P.A., Sangal V. Tool for Rapid Annotation of Microbial SNPs (TRAMS): A simple program for rapid annotation of genomic variation in prokaryotes. Antonie Van Leeuwenhoek 2013, 104(3):431-434. 10.1007/s10482-013-9953-x.
80. Richter M., Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proceedings of the National Academy of Sciences of the United States of America 2009, 106(45):19126-19131. 10.1073/pnas.0906412106.
81. Rinke C., Schwientek P., Sczyrba A., Ivanova N.N., Anderson I.J., Cheng J.F., et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 2013, 499(7459):431-437. 10.1038/nature12352.
82. Ronaghi M., Uhlen M., Nyren P. A sequencing method based on real-time pyrophosphate. Science 1998, 281(5375):363. 365.
83. Rothberg J.M., Hinz W., Rearick T.M., Schultz J., Mileski W., Davey M., et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011, 475(7356):348-352. 10.1038/nature10242.
84. Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M.A., et al. Artemis: Sequence visualization and annotation. Bioinformatics 2000, 16(10):944-945.
85. Salipante S.J., Sengupta D.J., Rosenthal C., Costa G., Spangler J., Sims E.H., et al. Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections. PLoS One 2013, 8(5):e65226. 10.1371/journal.pone.0065226.
86. Sangal V., Burkovski A., Hunt A.C., Edwards B., Blom J., Hoskisson P.A. A lack of genetic basis for biovar differentiation in clinically important Corynebacterium diphtheriae from whole genome sequencing. Infection, Genetics and Evolution 2014, 21:54-57. 10.1016/j.meegid.2013.10.019.
87. Sangal V., Fineran P.C., Hoskisson P.A. Novel configurations of type I and II CRISPR-Cas systems in Corynebacterium diphtheriae. Microbiology 2013, 159(10):2118-2126. 10.1099/mic.0.070235-0.
88. Sangal V., Holt K.E., Yuan J., Brown D.J., Filliol-Toutain I., Weill F.X., et al. Global phylogeny of Shigella sonnei strains from limited single nucleotide polymorphisms (SNPs) and development of a rapid and cost-effective SNP-typing scheme for strain identification by high-resolution melting analysis. Journal of Clinical Microbiology 2013, 51(1):303-305. 10.1128/JCM.02238-12.
89. Sangal V., Hoskisson P.A. Embrace the genome!. The Bulletin of BISMiS 2013, 4(1):15-17.
90. Sangal V., Jones A.L., Goodfellow M., Sutcliffe I.C., Hoskisson P.A. Comparative genomic analyses reveal a lack of a substantial signature of host adaptation in Rhodococcus equi ("Prescottella equi"). Pathogens and Disease 2014, 71(3):352-356. 10.1111/2049-632X.12126.
91. Schneider J., Vorholter F.J., Trost E., Blom J., Musa Y.R., Neuweger H., et al. CARMEN - Comparative analysis and in silico reconstruction of organism-specific MEtabolic networks. Genetics and Molecular Research 2010, 9(3):1660-1672. 10.4238/vol9-3gmr901.
92. Segata N., Bornigen D., Morgan X.C., Huttenhower C. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nature Communications 2013, 4:2304. 10.1038/ncomms3304.
93. Sentausa E., Fournier P.E. Advantages and limitations of genomics in prokaryotic taxonomy. Clinical Microbiology and Infection 2013, 19(9):790-795. 10.1111/1469-0691.12181.
94. Siguier P., Perochon J., Lestrade L., Mahillon J., Chandler M. ISfinder: The reference centre for bacterial insertion sequences. Nucleic Acids Research 2006, 34(Database issue):D32-36. 10.1093/nar/gkj014.
95. Sikkema-Raddatz B., Johansson L.F., de Boer E.N., Almomani R., Boven L.G., van den Berg M.P., et al. Targeted next-generation sequencing can replace Sanger sequencing in clinical diagnostics. Human Mutation 2013, 34(7):1035-1042. 10.1002/humu.22332.
96. Singh P., Foley S.L., Nayak R., Kwon Y.M. Massively parallel sequencing of enriched target amplicons for high-resolution genotyping of Salmonella serovars. Molecular and Cellular Probes 2013, 27(2):80-85. 10.1016/j.mcp.2012.11.004.
97. Sittka A., Lucchini S., Papenfort K., Sharma C.M., Rolle K., Binnewies T.T., et al. Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genetics 2008, 4(8):e1000163. 10.1371/journal.pgen.1000163.
98. Sommer D.D., Delcher A.L., Salzberg S.L., Pop M. Minimus: A fast, lightweight genome assembler. BMC Bioinformatics 2007, 8:64. 10.1186/1471-2105-8-64.
99. Sorek R., Cossart P. Prokaryotic transcriptomics: A new view on regulation, physiology and pathogenicity. Nature Reviews Genetics 2010, 11(1):9-16. 10.1038/nrg2695.
100. Stackebrandt E., Ebers J. Taxonomic parameters revisited: Tarnished gold standards. Microbiology Today 2006, 33:152-155.
101. Stewart L., Ford A., Sangal V., Jeukens J., Boyle B., Caim S., et al. Draft genomes of twelve host adapted and environmental isolates of Pseudomonas aeruginosa and their position in the core genome phylogeny. Pathogens and Disease 2014, 71(1):20-25. 10.1111/2049-632X.12107.
102. Sutcliffe I.C., Trujillo M.E., Goodfellow M. A call to arms for systematists: Revitalising the purpose and practises underpinning the description of novel microbial taxa. Antonie Van Leeuwenhoek 2012, 101(1):13-20. 10.1007/s10482-011-9664-0.
103. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 2011, 28(10):2731-2739.
104. Tatusov R.L., Natale D.A., Garkavtsev I.V., Tatusova T.A., Shankavaram U.T., Rao B.S., et al. The COG database: New developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Research 2001, 29(1):22-28.
105. Teeling H., Waldmann J., Lombardot T., Bauer M., Glockner F.O. TETRA: A web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. BMC Bioinformatics 2004, 5:163. 10.1186/1471-2105-5-163.
106. Tindall B.J. The correct name of the taxon that contains the type strain of Rhodococcus equi. International Journal of Systematic and Evolutionary Microbiology 2014, 64(1):302-308. 10.1099/ijs.0.059584-0.
107. Valouev A., Ichikawa J., Tonthat T., Stuart J., Ranade S., Peckham H., et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Research 2008, 18(7):1051-1063. 10.1101/gr.076463.108.
108. Vandamme P., Peeters C. Time to revisit polyphasic taxonomy. Antonie Van Leeuwenhoek 2014, 106(1):57-65. 10.1007/s10482-014-0148-x.
109. Vandamme P., Pot B., Gillis M., de Vos P., Kersters K., Swings J. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiological Reviews 1996, 60(2):407-438.
110. van Passel M.W., Kuramae E.E., Luyf A.C., Bart A., Boekhout T. The reach of the genome signature in prokaryotes. BMC Evolutionary Biology 2006, 6:84. 10.1186/1471-2148-6-84.
111. Vernikos G.S., Parkhill J. Interpolated variable order motifs for identification of horizontally acquired DNA: Revisiting the Salmonella pathogenicity islands. Bioinformatics 2006, 22(18):2196-2203. 10.1093/bioinformatics/btl369.
112. Wang K., Li M., Hakonarson H. ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research 2010, 38(16):e164. 10.1093/nar/gkq603.
113. Wang Z., Gerstein M., Snyder M. RNA-Seq: A revolutionary tool for transcriptomics. Nature Reviews Genetics 2009, 10(1):57-63. 10.1038/nrg2484.
114. Wayne L.G., Brenner D.J., Colwell R.R., Grimont P.A.D., Kandler O., Krichevsky M.I., et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. International Journal of Systematic Bacteriology 1987, 37:463-464.
115. Westermann A.J., Gorski S.A., Vogel J. Dual RNA-seq of pathogen and host. Nature Reviews. Microbiology 2012, 10(9):618-630. 10.1038/nrmicro2852.
116. Yi H., Cho Y.J., Won S., Lee J.E., Jin Yu H., Kim S., et al. Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq. Nucleic Acids Research 2011, 39(20):e140. 10.1093/nar/gkr617.
117. Zerbino D.R., Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 2008, 18(5):821-829. 10.1101/gr.074492.107.
118. Zhou Y., Liang Y., Lynch K.H., Dennis J.J., Wishart D.S. PHAST: A fast phage search tool. Nucleic Acids Research 2011, 39(Web Server issue):W347-352. 10.1093/nar/gkr485.
119. Zhu B., Wang X., Li L. Human gut microbiome: The second genome of human body. Protein & Cell 2010, 1(8):718-725. 10.1007/s13238-010-0093-z.
120. Zhu L., Wu Q., Dai J., Zhang S., Wei F. Evidence of cellulose metabolism by the giant panda gut microbiome. Proceedings of the National Academy of Sciences of the United States of America 2011, 108(43):17714-17719. 10.1073/pnas.1017956108.