Improved lysis of single bacterial cells by a modified alkaline-thermal shock procedure

BioTechniques

Volumn 60, Issue 3, 2016, Pages 129-135

  He, Jian ^a,b   Du, Shiyu ^c   Tan, Xiaohua ^d   Arefin, Ayesha ^b   Han, Cliff S ^b  

^a DALIAN INSTITUTE OF CHEMICAL PHYSICS   (China)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c NINGBO INSTITUTE OF MATERIALS TECHNOLOGY AND ENGINEERING   (China)

^d WENZHOU MEDICAL UNIVERSITY   (China)

Author keywords

Cell lysis; Genome recovery; Genome sequencing; Single cell genomics; Unculturable microbiology

Indexed keywords

ALKALI; ANTACID AGENT; BACTERIAL DNA;

ARTICLE; BACILLUS SUBTILIS; BACTERIOLYSIS; CELL ISOLATION; CONTROLLED STUDY; DNA ISOLATION; FLOW CYTOMETRY; FREEZING; GENE AMPLIFICATION; GENE SEQUENCE; HEATING; LOCUS BIAS SCORE; MICROBIOLOGICAL PARAMETERS; NONHUMAN; POLYMERASE CHAIN REACTION; SYNECHOCYSTIS; BACTERIUM; CELL FRACTIONATION; CHEMISTRY; COMPARATIVE STUDY; EVALUATION STUDY; GENETICS; ISOLATION AND PURIFICATION; PROCEDURES; TEMPERATURE;

ANTACIDS; BACTERIA; CELL FRACTIONATION; DNA, BACTERIAL; TEMPERATURE;

EID: 84960098293     PISSN: 07366205     EISSN: 19409818     Source Type: Journal    
DOI: 10.2144/000114389     Document Type: Article

References (23)

1. Kirk, J.L., L.A. Beaudette, M. Hart, P. Moutoglis, J.N. Klironomos, H. Lee, and J.T. Trevors. 2004. Methods of studying soil microbial diversity. J. Microbiol. Methods 58:169-188.
2. Puspita, I.D., Y. Kamagata, M. Tanaka, K. Asano, and C.H. Nakatsu. 2012. Are uncultivated bacteria really uncultivable? Microbes Environ. 27:356-366.
3. Fitzsimons M.S., M. Novotny, C.C. Lo, A.E. Dichosa, J.L. Yee-Greenbaum, J.P. Snook, W. Gu, O. Chertkov, K.W. Davenport, K. McMurry, et al. 2013. Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human micro-biome. Genome Res. 23:878-888.
4. Callejas, S., R. Álvarez, A. Benguria, and A. Dopazo. 2014. AG-NGS: a powerful and user-friendly computing application for the semi-automated preparation of next-generation sequencing libraries using open liquid handling platforms. Biotechniques 56:28-35.
5. Morales, S.E. and W.E. Holben. 2011. Linking bacterial identities and ecosystem processes: can ‘omic’ analyses be more than the sum of their parts? FEMS Microbiol. Ecol. 75:2-16.
6. Kvist, T., B.K. Ahring, R.S. Lasken, and P. Westermann. 2007. Specific single-cell isolation and genomic amplification of uncultured microorganisms. Appl. Microbiol. Biotechnol. 74:926-935.
7. Lai, H.H., P.A. Quinto-Su, C.E. Sims, M. Bachman, G.P. Li, V. Venugopalan, and N.L. Allbritton. 2008. Characterization and use of laser-based lysis for cell analysis on-chip. J. R. Soc. Interface 5(Suppl 2):S113-S121.
8. Thornhill, A.R., J.A. McGrath, R.A. Eady, P.R. Braude, and A.H. Handyside. 2001. A comparison of different lysis buffers to assess allele dropout from single cells for preimplantation genetic diagnosis. Prenat. Diagn. 21:490-497.
9. Belgrader, P., D. Hansford, G.T. Kovacs, K. Venkateswaran, R. Mariella Jr, F. Milanovich, S. Nasarabadi, M. Okuzumi, et al. 1999. A minisonicator to rapidly disrupt bacterial spores for DNA analysis. Anal. Chem. 71:4232-4236.
10. Gromov, P., J.E. Celis, I. Gromova, F. Rank, V. Timmermans-Wielenga, and J.M. Moreira. 2008. A single lysis solution for the analysis of tissue samples by different proteomic technologies. Mol. Oncol. 2:368-379.
11. Ishoey, T., T. Woyke, R. Stepanauskas, M. Novotny, and R.S. Lasken. 2008. Genomic sequencing of single microbial cells from environmental samples. Curr. Opin. Microbiol. 11:198-204.
12. Grindberg R.V., T. Ishoey, D. Brinza, E. Esquenazi, R.C. Coates, W.T. Liu, L. Gerwick, P.C. Dorrestein, P. Pevzner, R. Lasken, et al. 2011. Single cell genome amplification accelerates identification of the apra toxin biosynthetic pathway from a complex microbial assemblage. PLoS ONE 6:e18565.
13. Harel, Y., I. Ohad, and A. Kaplan. 2004. Activation of photosynthesis and resistance to photo inhibition in cyanobacteria within biological desert crust. Plant Physiol. 136:3070-3079.
14. Lovett, M. 2013. The applications of single-cell genomics. Hum. Mol. Genet. 22:R22-R26.
15. Hofer, U. 2013. Environmental microbiology: Exploring diversity with single-cell genomics. Nat. Rev. Microbiol. 11:598-599.
16. Madigan, M. and J. Mar tinko. 2005. Brock Biology of Microorganisms (11th ed.). Prentice Hall, Upper Saddle River, NJ.
17. Nakano, M.M. and P. Zuber. 1998. Anaerobic growth of a “strict aerobe” (Bacillus subtilis). Annu. Rev. Microbiol. 52:165-190.
18. Wang, J., J.D. Van Nostrand, L. Wu, Z. He, G. Li, and J. Zhou. 2011. Microarray-based evaluation of whole-community genome DNA amplification methods. Appl. Environ. Microbiol. 77:4241-4245.
19. Kim, Y.J., N.L. Nguyen, H.Y. Weon, and D.C. Yang. 2013. Sediminibacterium ginsen-gisoli sp. nov., isolated from soil of a ginseng field and emended descriptions of the genus Sediminibacterium and Sediminibacterium salmoneum. Int. J. Syst. Evol. Microbiol. 63:905-912.
20. Alonso, A., P. Sanchez, and J.L. Martínez. 2000. Stenotrophomonas maltophilia D457R contains a cluster of genes from gram-positive bacteria involved in antibiotic and heavy metal resistance. Antimicrob. Agents Chemother. 44:1778-1782.
21. Blöchl, E., R. Rachel, S.Burggraf, D. Hafenbradl, H.W. Jannasch, and K.O. Stetter. 1997. Pyrolobus fumarii, gen. and sp. nov., represents a novel group of archaea, extending the upper temperature limit for life to 113 C. Extremophiles 1:14-21.
22. Ryu, S.H., D.S. Lee, M. Park, Q. Wang, H.H. Jang, W. Park, and C.O. Jeon. 2008. Caenimonas koreensis gen. nov., sp. nov., isolated from activated sludge. Int. J. Syst. Evol. Microbiol. 58:1064-1068.
23. Pan, X., A.E. Urban, D. Palejev, V. Schulz, F. Gruber t, Y. Hu, M. Snyder, and S.M. Weissman. 2008. A procedure for highly specific, sensitive, and unbiased whole-genome amplification. Proc. Natl. Acad. Sci. USA 105:15499-15504.