Reconstructing each cell's genome within complex microbial communities - dream or reality?

Frontiers in Microbiology

Volumn 5, Issue DEC, 2014, Pages

  Clingenpeel, Scott ^a   Clum, Alicia ^a   Schwientek, Patrick ^a   Rinke, Christian ^a   Woyke, Tanja ^a  

^a DOE JOINT GENOME INSTITUTE   (United States)

Author keywords

Environmental microbiology; Genome completeness; Genome quality; Microbial ecology; Multiple displacement amplification; Single cell sequencing

Indexed keywords

RNA 16S;

ARTICLE; CYTOLYSIS; ECOLOGY; ESCHERICHIA COLI; FLUORESCENCE ACTIVATED CELL SORTING; GENE IDENTIFICATION; GENE SEQUENCE; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIAL GENOME; PEDOBACTER HEPARINUS; POLYMERASE CHAIN REACTION; PROTEOBACTERIA; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA GENE;

EID: 84920678390     PISSN: None     EISSN: 1664302X     Source Type: Journal    
DOI: 10.3389/fmicb.2014.00771     Document Type: Article

References (38)

1. Albertsen, M., Hugenholtz, P., Skarshewski, A., Nielsen, K. L., Tyson, G. W., and Nielsen, P. H. (2013). Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat. Biotechnol. 31, 533-538. doi: 10.1038/nbt.2579
2. Baker, B. J., Comolli, L. R., Dick, G. J., Hauser, L. J., Hyatt, D., Dill, B. D., et al. (2010). Enigmatic, ultrasmall, uncultivated Archaea. P. Natl. Acad. Sci. U.S.A. 107, 8806-8811. doi: 10.1073/pnas.0914470107
3. Baker, G. C., Smith, J. J., and Cowan, D. A. (2003). Review and re-analysis of domain-specific 16S primers. J. Microbiol. Meth. 55, 541-555. doi: 10.1016/j.mimet.2003.08.009
4. Ballantyne, K. N., van Oorschot, R. A. H., Mitchell, R. J., and Koukoulas, I. (2006). Molecular crowding increases the amplification success of multiple displacement amplification and short tandem repeat genotyping. Anal. Biochem. 355, 298-303. doi: 10.1016/j.ab.2006.04.039
5. Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., et al. (2012). SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477. doi: 10.1089/cmb.2012.0021
6. 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. doi: 10.1371/journal.pone.0016626
7. Blainey, P. C. (2013). The future is now: single-cell genomics of bacteria and archaea. FEMS Microbiol. Rev. 37, 407-427. doi: 10.1111/1574-6976.12015
8. de Bourcy, C. F. A., De Vlaminck, I., Kanbar, J. N., Wang, J., Gawad, C., and Quake, S. R. (2014). A quantitative comparison of single-cell whole genome amplification methods. PLoS One 9, e105585. doi: 10.1371/journal.pone.0105585
9. Chitsaz, H., Yee-Greenbaum, J. L., Tesler, G., Lombardo, M.-J., Dupont, C. L., Badger, J. H., et al. (2011). Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. Nat. Biotechnol. 29, 915-921. doi: 10.1038/nbt.1966.
10. Clingenpeel, S., Schwientek, P., Hugenholtz, P., and Woyke, T. (2014). Effects of sample treatments on genome recovery via single-cell genomics. ISME J. available online ahead of print. doi: 10.1038/ismej.2014.92
11. Dichosa, A. E. K., Fitzsimons, M. S., Lo, C.-C., Weston, L. L., Preteska, L. G., Snook, J. P., et al. (2012). Artificial polyploidy improves bacterial single cell genome recovery. PLoS One 7, e37387. doi: 10.1371/journal.pone.0037387
12. Dichosa, A. E. K., Daughton, A. R., Reitenga, K. G., Fitzsimons, M. S., and Han, C. S. (2014). Capturing and cultivating single bacterial cells in gel microdroplets to obtain near-complete genomes. Nat. Protoc. 9, 608-621. doi: 10.1038/nprot.2014.034
13. Dodsworth, J. A., Blainey, P. C., Murugapiran, S. K., Swingley, W. D., Ross, C. A., Tringe, S. G., et al. (2013). Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage. Nat. Commun. 4, 1854. doi: 10.1038/ncomms2884
14. Fitzsimons, M. S., Novotny, M., Lo, C.-C., Dichosa, A. E. K., Yee-Greenbaum, J. L., Snook, J. P., et al. (2013). Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome. Genome Res. 23, 878- 888. doi: 10.1101/gr.142208.112
15. Gole, J., Gore, A., Richards, A., Chiu, Y.-J., Fung, H.-L., Bushman, D., et al. (2013). Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. Nat. Biotechnol. 31, 1126-1132. doi: 10.1038/nbt.2720
16. Goris, J., Konstantinidis, K. T., Klappenbach, J. A., Coenye, T., Vandamme, P. and Tiedje, J. M. (2007). DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Micr. 57, 81-91. doi: 10.1099/ijs.0.64483-0
17. de Jager, V., and Siezen, R. J. (2011). Single-cell genomics: unravelling the genomes of unculturable microorganisms. Microb. Biotech. 4, 431-437. doi: 10.1111/j.1751- 7915.2011.00271.x
18. Kashtan, N., Roggensack, S. E., Rodrigue, S., Thompson, J. W., Biller, S. J., Coe, A., et al. (2014). Single-cell genomics reveals hundreds of coexisting subpopulations in wild Prochlorococcus. Science 344, 416-420. doi: 10.1126/science.1248575
19. Konstantinidis, K. T., and Tiedje, J. M. (2005). Genomic insights that advance the species definition for prokaryotes. P. Natl. Acad. Sci. U.S.A. 102, 2567-2572. doi: 10.1073/pnas.0409727102
20. Lasken, R. S. (2012). Genomic sequencing of uncultured microorganisms from single cells. Nat. Rev. Microbiol. 10, 631-640. doi: 10.1038/nrmicro2857
21. Lasken, R. S. and McLean, J. S. (2014). Recent advances in genomic DNA sequencing of microbial species from single cells. Nat. Rev. Genet. 15, 577-584. doi:10.1038/nrg3785
22. Marcy, Y., Ishoey, T., Lasken, R. S., Stockwell, T. B., Walenz, B. P., Halpern, A. L., et al. (2007). Nanoliter reactors improve multiple displacement amplification of genomes from single cells. PLoS Genet. 3, 1702-1708. doi: 10.1371/journal.pgen.0030155
23. Nobre, M. F., Truper, H. G., and da Costa, M. S. (1996). Transfer of Thermus ruber (Loginova et al. 1984), Thermus silvanus (Tenreiro et al. 1995), and Thermus chliarophilus (Tenreiro et al. 1995) to Meiothermus gen. nov. as Meiothermus ruber comb. nov., Meiothermus silvanus comb. nov., and Meiothermus chliarophilus comb. nov., respectively, and emendation of the genus Thermus. Int. J. Syst. Bacteriol. 46, 604-606.
24. Nurk, S., Bankevich, A., Antipov, D., Gurevich, A. A., Korobeynikov, A., Lapidus, A., et al. (2013). Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J. Comput. Biol. 20, 714-737. doi: 10.1089/cmb.2013.0084
25. Pan, X., Urban, A. E., Palejev, D., Schulz, V., Grubert, F., Hu, Y., et al. (2008). A procedure for highly specific, sensitive, and unbiased whole-genome amplification. P. Natl. Acad. Sci. U.S.A. 105, 15499-15504. doi: 10.1073/pnas.0808028105
26. Peng, Y., Leung, H. C. M., Yiu, S. M., and Chin, F. Y. L. (2012). IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420-1428. doi: 10.1093/bioinformatics/bts174
27. Richter, M. and Rossello-Mora, R. (2009). Shifting the genomic gold standard for the prokaryotic species definition. P. Natl. Acad. Sci. U.S.A. 106, 19126-19131. doi: 10.1073/pnas.0906412106
28. Rinke, C., Schwientek, P. Sczyrba, A., Ivanova, N. N., Anderson, I. J., Cheng, J.-F. et al. (2013). Insights into the phylogeny and coding potential of microbial dark matter. Nature 499, 431-437. doi: 10.1038/nature12352
29. Rinke, C., Lee, J., Nath, N., Goudeau, D., Thompson, B., Poulton, N., et al. (2014). Obtaining genomes from uncultivated environmental microorganisms using FACS-based single-cell genomics. Nat. Protoc. 9, 1038-1048. doi: 10.1038/nprot.2014.067
30. 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. doi: 10.1371/journal.pone.0006864
31. Roux, S., Hawley, A. K., Beltran, M. T., Scofield, M., Schwientek, P., Stepanauskas, R., et al. (2014). Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics. eLife 3, e03125. doi: 10.7554/eLife.03125
32. Stepanauskas, R. (2012). Single cell genomics: an individual look at microbes. Curr. Opin. Microbiol. 15, 613-620. doi: 10.1016/j.mib.2012.09.001
33. Swan, B. K., Martinez-Garcia, M., Preston, C. M., 411 Sczyrba, A., Woyke, T., Lamy, D., et al. (2011). Potential for chemolithoautotrophy among ubiquitous bacteria lineages in the dark ocean. Science 333, 1296-1300. doi: 10.1126/science.1203690
34. Wrighton, K. C., Thomas, B. C., Sharon, I., Miller, C. S., Castelle, C. J., VerBerkmoes, N. C., et al. (2012). Fermentation, hydrogen, and sulfur metabolism in multiple uncultivated bacterial phyla. Science 337, 1661-1665. doi: 10.1126/science.1224041
35. Yilmaz, S., and Singh, A. K. (2012). Single cell genome sequencing. Curr. Opin. Biotech. 23, 437-443. doi: 10.1016/j.copbio.2011.11.018
36. Youssef, N. H., Rinke, C., Stepanauskas, R., Farag, I., Woyke, T, and Elshahed, M. S. (2014). Insights into the metabolism, lifestyle and putative evolutionary history of the novel archaeal phylum 'Diapherotrites'. ISME J. advance online publication doi: 10.1038/ismej.2014.141
37. Zengler, K., Toledo, G., Rappe, M., Elkins, J., Mathur, E. J., Short, J. M., et al. (2002). Cultivating the uncultured. P. Natl. Acad. Sci. U.S.A. 99, 15681-15686. doi: 10.1073pnas.252630999
38. Zong, C., Lu, S., Chapman, A. R., and Xie, X. S. (2012). Genome-wide detection of single431 nucleotide and copy-number variations of a single human cell. Science 338, 1622-1626. doi:432 10.1126/science.1229164