Single-cell genomics: Unravelling the genomes of unculturable microorganisms

Microbial Biotechnology

Volumn 4, Issue 4, 2011, Pages 431-437

  de Jager, Victor ^a,b,c   Siezen, Roland J ^a,b,d,e,f  

^a NETHERLANDS BIOINFORMATICS CENTRE   (Netherlands)

^b RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^c WAGENINGEN UNIVERSITY   (Netherlands)

^d TOP INSTITUTE FOOD AND NUTRITION   (Netherlands)

^e NIZO FOOD RESEARCH   (Netherlands)

^f Industrial Fermentation   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; MESSENGER RNA; TRANSCRIPTOME;

ARTICLE; BIOFILM; CELL ISOLATION; DNA SEQUENCE; ECOLOGICAL NICHE; GENE AMPLIFICATION; GENETIC ANALYSIS; GENOMICS; METABOLOMICS; METAGENOMICS; MICROBIAL GENETICS; MICROORGANISM; NONHUMAN; PROTEOMICS; SINGLE CELL ANALYSIS; SINGLE CELL GENOMICS; TRANSCRIPTOMICS; DEVICES; PROCEDURES; TRENDS;

GENETICS, MICROBIAL; GENOMICS; SEQUENCE ANALYSIS, DNA; SINGLE-CELL ANALYSIS;

EID: 79960095192     PISSN: 17517907     EISSN: 17517915     Source Type: Journal    
DOI: 10.1111/j.1751-7915.2011.00271.x     Document Type: Article

References (31)

1. Blainey, P.C., Mosier, A.C., Potanina, A., Francis, C.A., and Quake, S.R. (2011) Genome of a low-salinity ammonia-oxidizing archaeon determined by single-cell and metagenomic analysis. PLoS ONE 6: e16626-e16626.
2. Bomar, L., Maltz, M., Colston, S., and Graf, J. (2011) Directed culturing of microorganisms using metatranscriptomics. mBio 2: e00012-e00011.
3. Dean, F.B., Nelson, J.R., Giesler, T.L., and Lasken, R.S. (2001) Rapid amplification of plasmid and phage DNA using Phi 29 DNA polymerase and multiply-primed rolling circle amplification. Genome Res 11: 1095-1099.
4. Fouchet, P., Jayat, C., Héchard, Y., Ratinaud, M.H., and Frelat, G. (1993) Recent advances of flow cytometry in fundamental and applied microbiology. Biol Cell 78: 95-109.
5. Frias-Lopez, J., Shi, Y., Tyson, G.W., Coleman, M.L., Schuster, S.C., Chisholm, S.W., and Delong, E.F. (2008) Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci USA 105: 3805-3810.
6. Harrington, E.D., Arumugam, M., Raes, J., Bork, P., and Relman, D.A. (2010) SmashCell: a software framework for the analysis of single-cell amplified genome sequences. Bioinformatics 26: 2979-2980.
7. Holmes, D.E., Chaudhuri, S.K., Nevin, K.P., Mehta, T., Methé, B.A., Liu, A., etal. (2006) Microarray and genetic analysis of electron transfer to electrodes in Geobacter sulfurreducens. Environ Microbiol 8: 1805-1815.
8. Hosono, S., Faruqi, A.F., Dean, F.B., Du, Y., Sun, Z., Wu, X., etal. (2003) Unbiased whole-genome amplification directly from clinical samples. Genome Res 13: 954-964.
9. Ingham, C.J., Beerthuyzen, M., and van Hylckama Vlieg, J. (2008) Population heterogeneity of Lactobacillus plantarum WCFS1 microcolonies in response to and recovery from acid stress. Appl Environ Microbiol 74: 7750-7758.
10. Kalisky, T., and Quake, S.R. (2011) Single-cell genomics. Nature Methods 8: 311-314.
11. Kvist, T., Ahring, B.K., Lasken, R.S., and Westermann, P. (2007) Specific single-cell isolation and genomic amplification of uncultured microorganisms. Appl Microbiol Biotechnol 74: 926-935.
12. Leslie, M. (2011) Single-cell tech primer. Science (New York, NY) 331: 24-25.
13. Lidstrom, M.E., and Konopka, M.C. (2010) The role of physiological heterogeneity in microbial population behavior. Nat Chem Biol 6: 705-712.
14. Marcy, Y., Ishoey, T., Lasken, R.S., Stockwell, T.B., Walenz, B.P., Halpern, A.L., etal. (2007a) Nanoliter reactors improve multiple displacement amplification of genomes from single cells. PLoS Genet 3: 1702-1708.
15. Marcy, Y., Ouverney, C., Bik, E.M., Lösekann, T., Ivanova, N., Martin, H.G., etal. (2007b) Dissecting biological 'dark matter' with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth. Proc Natl Acad Sci USA 104: 11889-11894.
16. Mitra, S., Klar, B., and Huson, D.H. (2009) Visual and statistical comparison of metagenomes. Bioinformatics (Oxford, England) 25: 1849-1855.
17. Müller, S., and Nebe-von-Caron, G. (2010) Functional single-cell analyses: flow cytometry and cell sorting of microbial populations and communities. FEMS Microbiol Rev 34: 554-587.
18. Pan, X.-H., Zhu, H.-Y., and Marjani, S.L. (2011) Technological advances in single-cell genomic analyses. Yi Chuan 33: 17-24 (article in Chinese).
19. Podar, M., Abulencia, C.B., Walcher, M., Hutchison, D., Zengler, K., Garcia, J.A., etal. (2007) Targeted access to the genomes of low-abundance organisms in complex microbial communities. Appl Environ Microbiol 73: 3205-3214.
20. Raghunathan, A., Ferguson, H.R., Jr, Bornarth, C.J., Song, W., Driscoll, M., and Lasken, R.S. (2005) Genomic DNA amplification from a single bacterium. Appl Environ Microbiol 71: 3342-3347.
21. Rodrigue, S., Malmstrom, R.R., Berlin, A.M., Birren, B.W., Henn, M.R., and Chisholm, S.W. (2009) Whole genome amplification and de novo assembly of single bacterial cells. PLoS ONE 4: e6864-e6864.
22. Rubakhin, S.S., Romanova, E.V., Nemes, P., and Sweedler, J.V. (2011) Profiling metabolites and peptides in single cells. Nat Methods 8: S20-S29.
23. Siegl, A., and Hentschel, U. (2010) PKS and NRPS gene clusters from microbial symbiont cells of marine sponges by whole genome amplification. Environ Microbiol Rep 2: 507-513.
24. Siegl, A., Kamke, J., Hochmuth, T., Piel, J., Richter, M., Liang, C., etal. (2011) Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges. ISME J 5: 61-70.
25. Siezen, R.J., Wilson, G., and Todt, T. (2010) Prokaryotic whole-transcriptome analysis: deep sequencing and tiling arrays. Microb Biotechnol 3: 125-130.
26. Tang, F., Lao, K., and Surani, M.A. (2011) Development and applications of single-cell transcriptome analysis. Nat Methods 8: S6-S11.
27. Wang, D., and Bodovitz, S. (2010) Single cell analysis: the new frontier in 'omics'. Trends Biotechnol 28: 281-290.
28. Wang, Y., Hammes, F., De Roy, K., Verstraete, W., and Boon, N. (2010) Past, present and future applications of flow cytometry in aquatic microbiology. Trends Biotechnol 28: 416-424.
29. Woyke, T., Xie, G., Copeland, A., Gonzalez, J.M., Han, C., Kiss, H., etal. (2009) Assembling the marine metagenome, one cell at a time. PLoS ONE 4: e5299.
30. Woyke, T., Tighe, D., Mavromatis, K., Clum, A., Copeland, A., Schackwitz, W., etal. (2010) One bacterial cell, one complete genome. PLoS ONE 5: e10314-e10314.
31. Zhang, K., Martiny, A.C., Reppas, N.B., Barry, K.W., Malek, J., Chisholm, S.W., and Church, G.M. (2006) Sequencing genomes from single cells by polymerase cloning. Nat Biotechnol 24: 680-686.