Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome

Genome Research

Volumn 23, Issue 5, 2013, Pages 878-888

  Fitzsimons, Michael S ^a   Novotny, Mark ^b   Lo, Chien Chi ^a   Dichosa, Armand E K ^a   Yee Greenbaum, Joyclyn L ^b   Snook, Jeremy P ^a   Gu, Wei ^a   Chertkov, Olga ^a   Davenport, Karen W ^a   McMurry, Kim ^a   Reitenga, Krista G ^a   Daughton, Ashlynn R ^a   He, Jian ^a,c   Johnson, Shannon L ^a   Gleasner, Cheryl D ^a   Wills, Patti L ^a   Parson Quintana, Beverly ^a   Chain, Patrick S ^a   Detter, John C ^a   Lasken, Roger S ^b   Han, Cliff S ^a   more..

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b J CRAIG VENTER INSTITUTE   (United States)

^c Basic Medical College   (China)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; BACTERIUM CULTURE; CHROMOSOME; DNA CONTAMINATION; ENTEROCOCCUS; GENE AMPLIFICATION; GENE SEQUENCE; GENETIC VARIABILITY; GENOME; HUMAN; MICROBIAL COMMUNITY; MICROBIAL GENETICS; MICROBIOME; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES CULTIVATION; STREPTOCOCCUS;

BACTERIA; GENETIC VARIATION; GENOME, BACTERIAL; GENOMICS; HUMANS; MICROBIOTA; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS);

EID: 84877122392     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.142208.112     Document Type: Article

References (58)

1. Altschul SF, Gish W, Miller W., Myers EW, Lipman DJ 1990. Basic local alignment search tool. J Mol Biol 215: 403-410.
2. Amann RI, Ludwig W, Schleifer KH 1995. Pylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59: 143-169.
3. Aziz RK, Bartels D, Best A.A., DeJongh M., Disz T, Edwards RA, Formsma K, Gerdes S., Glass EM, Kubal M, et al 2008. The RAST server: Rapid annotations using subsystems technology. BMC Genomics 9: 1-15.
4. Bankevich A, Nurk S, Antipov D., Gurevich AA, Dvorkin M, Kulikov AS, Lesin V.M., Nikolenko SI, Son P, Prjibelski AD, et al 2012. SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19: 455-477.
5. Bek-Thomsen M., Tettelin H, Hance L., Nelson KE, Kilian M. 2008. Population diversity and dynamics of Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis in the upper respiratory tracts of adults, determined by a nonculture strategy. Infect Immun 76: 1889-1896.
6. Chitsaz H, Yee-Greenbaum JL, Tesler G., Lombardo M-J, Dupont CL, Badger J.H., Novotny M., Rusch DB, Fraser LJ, Gormley NA, et al 2011. Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat Biotechnol 29: 915-921.
7. Cole JR, Chai B, Farris R.J., Wang Q., Kulam-Syed-Mohideen AS, McGarrell DM, Bandela AM, Cardenas E, Garrity GM, Tiedje JM. 2007. The ribosomal database project (RDP-II): Introducing myRDP space and quality controlled public data. Nucleic Acids Res 35: D169-D172.
8. Cole JR, Wang Q, Cardenas E., Fish J, Chai B, Farris R.J., Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, et al. 2009. The Ribosomal Database Project: Improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-D145.
9. Courtois S, Frostegard A, Goransson P., Depret G, Jeannin P, Simonet P. 2001. Quantification of bacterial subgroups in soil: Comparison of DNA extracted directly from soil or from cells previously released by density gradient centrifugation. Environ Microbiol 3: 431-439.
10. Dean FB, Nelson JR, Giesler T.L., Lasken RS 2001. Rapid amplification of plasmid and phage DNA using Phi29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res 11: 1095-1099.
11. Dean FB, Hosono S, Fang L.H., Wu XH, Faruqi AF, Bray-Ward P, Sun ZY, Zong Q.L., Du YF, Du J, et al 2002. Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci 99: 5261-5266.
12. Delcher AL, Kasif S, Fleischmann R.D., Peterson J., White O, Salzberg SL 1999. Alignment of whole genomes. Nucleic Acids Res 27: 2369-2376.
13. Dewhirst FE, Chen T, Izard J., Paster BJ, Tanner ACR, Yu W-H, Lakshmanan A, Wade WG 2010. The human oral microbiome. J Bacteriol 192: 5002-5017.
14. Dichosa AE, Fitzsimons MS, Lo C.C., Weston LL, Preteska LG, Snook JP, Zhang X, Gu W., McMurry K, Green LD, et al 2012. Artificial polyploidy improves bacterial single cell genome recovery. PLoS ONE 7: e37387.
15. Do T, Jolley KA, Maiden MCJ, Gilbert SC, Clark D, Wade W.G., Beighton D. 2009. Population structure of Streptococcus oralis. Microbiology 155: 2593-2602.
16. Dupont CL, Rusch DB, Yooseph S, Lombardo M-J, Richter RA, Valas R, Novotny M., Yee-Greenbaum J, Selengut JD, Haft D.H., et al 2012. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. ISME J 6: 1186-1199.
17. Eckburg PB, Bik EM, Bernstein C.N., Purdom E., Dethlefsen L, Sargent M, Gill S.R., Nelson KE, Relman DA 2005. Diversity of the human intestinal microbial flora. Science 308: 1635-1638.
18. Edwards U, Rogall T, Blocker H., Emde M, Bottger EC 1989. Isolation and direct complete nucleotide determination of entire genes - characterization of a gene coding for 16S-ribosomal RNA. Nucleic Acids Res 17: 7843-7853.
19. Eppley JM, Tyson GW, Getz W.M., Banfield JF 2007. Genetic exchange across a species boundaryin the archaeal genus Ferroplasma. Genetics177: 407-416.
20. Ewing B, Green P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194.
21. Ewing B, Hillier L, Wendl M.C., Green P. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175-185.
22. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 52: 696-704.
23. Hess M, Sczyrba A, Egan R., Kim TW, Chokhawala H, Schroth G, Luo S., Clark DS, Chen F, Zhang T, et al 2011. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 331: 463-467.
24. Hogg JS, Hu FZ, Janto B, Boissy R., Hayes J, Keefe R, Post J.C., Ehrlich GD 2007. Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains. Genome Biol 8: R103.
25. Homan WL, Tribe D, Poznanski S., Li M, Hogg G, Spalburg E., van Embden JDA, Willems RJL. 2002. Multilocus sequence typing scheme for Enterococcus faecium. J Clin Microbiol 40: 1963-1971.
26. Huson DH, Auch AF, Qi J, Schuster SC 2007. MEGAN analysis of metagenomic data. Genome Res 17: 377-386.
27. Iverson V, Morris RM, Frazar C.D., Berthiaume CT, Morales RL, Armbrust EV 2012. Untangling genomes from metagenomes: Revealing an uncultured class of marine euryarchaeota. Science 335: 587-590.
28. Johnsborg O, Eldholm V, Havarstein LS 2007. Natural genetic transformation: Prevalence, mechanisms and function. Res Microbiol 158: 767-778.
29. Langmead B, Salzberg SL 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9: 357-359.
30. Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
31. Li H, Handsaker B, Wysoker A., Fennell T, Ruan J, Homer N., Marth G, Abecasis G, Durbin R., 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
32. Maddison WP, Maddison DR 2010. Mesquite: A modular system for evolutionary analysis, Version 2.75. http://mesquiteproject.org.
33. Myers EW, Sutton GG, Delcher A.L., Dew IM, Fasulo DP, Flanigan MJ, Kravitz S.A., Mobarry CM, Reinert KHJ, Remington KA, et al 2000. A whole-genome assembly of Drosophila. Science 287: 2196-2204.
34. Palmer KL, Godfrey P, Griggs A., Kos VN, Zucker J, Dejardins C, Cerqueira G., Gevers D, Walker S, Wortman J., et al 2012. Comparative genomics of enterococci: Variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus. MBio 3: 1-11.
35. Pan XH, Urban AE, Palejev D, Schulz V., Grubert F, Hu YP, Snyder M, Weissman SM 2008. A procedure for highly specific, sensitive, and unbiased whole-genome amplification. Proc Natl Acad Sci 105: 15499-15504.
36. Posada D. 2008. jModelTest: Phylogenetic model averaging. Mol Biol Evol 25: 1253-1256.
37. Pruesse E, Quast C, Knittel K., Fuchs BM, Ludwig WG, Peplies J, Glockner FO 2007. SILVA: A comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
38. R Development Core Team. 2011. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna.
39. Raghunathan A, Ferguson HR, Bornarth C.J., Song WM, Driscoll M, Lasken RS 2005. Genomic DNA amplification from a single bacterium. Appl Environ Microbiol 71: 3342-3347.
40. Rodrigue S, Malmstrom RR, Berlin A.M., Birren BW, Henn MR, Chisholm SW 2009. Whole genome amplification and de novo assembly of single bacterial cells. PLoS ONE 4: e6864.
41. Rusch DB, Halpern AL, Sutton G, Heidelberg K.B., Williamson S., Yooseph S, Wu D, Eisen J.A., Hoffman JM, Remington K, et al 2007. The Sorcerer II Global Ocean Sampling expedition: Northwest Atlantic through Eastern Tropical Pacific. PLoS Biol 5: 398-431.
42. Schloss PD, Westcott SL, Ryabin R, Hall J.R., Hartmann M., Hollister EB, Lesniewski RA, Oakley BB, Parks D.H., Robinson CJ, et al 2009. Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537-7541.
43. Schmid I, Merlin S, Perfetto SP 2003. Biosafety concerns for shared flow cytometry core facilities. Cytometry A 56A: 113-119.
44. Simmons SL, DiBartolo G, Denef V.J., Goltsman DSA, Thelen MP, Banfield JF 2008. Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation. PLoS Biol 6: 1427-1442.
45. Spits C, Le Caignec C, De Rycke M, Van Haute L, Van Steirteghem A, Liebaers I, Sermon K. 2006. Whole-genome multiple displacement amplification from single cells. Nat Protoc 1: 1965-1970.
46. Teeling H, Meyerdierks A, Bauer M., Amann R, Glockner FO 2004. Application of tetranucleotide frequencies for the assignment of genomic fragments. Environ Microbiol 6: 938-947.
47. Tettelin H, Masignani V, Cieslewicz M.J., Donati C., Medini D, Ward NL, Angiuoli S.V., Crabtree J., Jones AL, Durkin AS, et al 2005. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial "pan-genome.," Proc Natl Acad Sci 102: 13950-13955.
48. Tyson GW, Chapman J, Hugenholtz P., Allen EE, Ram RJ, Richardson PM, Solovyev V.V., Rubin EM, Rokhsar DS, Banfield JF 2004. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43.
49. Venter JC, Remington K, Heidelberg J.F., Halpern AL, Rusch D, Eisen JA, Wu D.Y., Paulsen I., Nelson KE, Nelson W, et al 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66-74.
50. West SA, Diggle SP, Buckling A, Gardner A., Griffins AS 2007. The social lives of microbes. Annu Rev Ecol Evol Syst 38: 53-77.
51. Wilson KH, Blitchington RB, Greene RC 1990. Amplification of bacterial-16S ribosomal DNA with polymerase chain-reaction. J Clin Microbiol 28: 1942-1946.
52. Woyke T, Xie G, Copeland A., Gonzalez JM, Han C, Kiss H, Saw J.H., Senin P., Yang C, Chatterji S, et al 2009. Assembling the marine metagenome, one cell at a time. PLoS ONE 4: 10.
53. Woyke T, Tighe D, Mavromatis K., Clum A, Copeland A, Schackwitz W., Lapidus A, Wu DY, McCutcheon J.P., McDonald BR, et al 2010. One bacterial cell, one complete genome. PLoS ONE 5: e10314.
54. Woyke T, Sczyrba A, Lee J., Rinke C, Tighe D, Clingenpeel S., Malmstrom R, Stepanauskas R, Cheng J-F. 2011. Decontamination of MDA reagents for single cell whole genome amplification. PLoS ONE 6: e26161.
55. Zengler K, Toledo G, Rappe M., Elkins J, Mathur EJ, Short J.M., Keller M. 2002. Cultivating the uncultured. Proc Natl Acad Sci 99: 15681-15686.
56. Zerbino DR, Birney E. 2008. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18: 821-829.
57. Zhang K, Martiny AC, Reppas N.B., Barry KW, Malek J, Chisholm SW, Church GM 2006. Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol 24: 680-686.
58. Zwickl DJ. 2006. "Genetic algorithm approaches for the phylogenetic analysis of large biological sequence data sets under the maximum likelihood criterion.," PhD thesis, The University of Texas at Austin, p. 125.