Comparison of Swabbing Solution Volume and gDNA Extraction Kits on DNA Recovery from Rigid Surface

Abstract

For bacteria sampling studies, various collection methods have been used to identify bacteria. To obtain accurate information about bacteria, high quality samples should be obtained. In order to obtain a high quality sample, a stable and large number of DNA copies must be collected. This study compared the efficiency of different methods of bacterial gDNA extraction and bacteria collection according to swabbing solution volumes and types. The efficiency of bacterial genomic DNA extraction was compared using a AccuPrep® Genomic DNA Extraction kit, a QIAamp® DNA Mini kit, and a MOBIO® DNeasy PowerSoil kit. The DNA Mini kit was shown to extract the highest amount of gDNA, and sub-experiments were conducted using this kit. Phosphate-buffered saline and phosphate-buffered saline with 0.1% Tween 20 were used as collection solutions of various volumes (0, 40, 50, 60, 70, 80, 90, 100, 110, and 120 μL) using cotton swabs. Bacteria collection efficiency was highest when 70 μL PBS was used. The target strains collected in this experiment were Staphylococcus aureus and Escherichia coli, and these were quantified using the number of colony-forming units, DNA concentrations, and the number of DNA copies. These results can be used to efficiently bacterial collection for experiments in various fields.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Abbreviations

PBS:

Phosphate-buffered saline

PBST:

Phosphate-buffered saline with 0.1% Tween 20

E. coli :

Escherichia coli

S. aureus :

Staphylococcus aureus

CFUs:

Colony-forming units

MSA:

Mannitol salt agar

MAC:

MacConkey

References

  1. 1.

    Daniel RJNRM (2005) The metagenomics of soil. Nat Rev Microbiol 3:470

    Article  CAS  Google Scholar 

  2. 2.

    Qin J, Li R, Raes J et al (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59

    Article  CAS  Google Scholar 

  3. 3.

    Gevers D, Knight R, Petrosino JF et al (2012) The Human Microbiome Project: a community resource for the healthy human microbiome. PLoS Biol 10:e1001377

    Article  CAS  Google Scholar 

  4. 4.

    Lax S, Hampton-Marcell JT, Gibbons SM et al (2015) Forensic analysis of the microbiome of phones and shoes. Microbiome 3:21

    Article  Google Scholar 

  5. 5.

    Hospodsky D, Qian J, Nazaroff WW et al (2012) Human occupancy as a source of indoor airborne bacteria. PLoS ONE 7:e34867

    Article  CAS  Google Scholar 

  6. 6.

    Verdon TJ, Mitchell RJ, van Oorschot RAJFsiG (2014) Evaluation of tapelifting as a collection method for touch DNA. Forensic Sci Int Genet 8:179–186

    Article  CAS  Google Scholar 

  7. 7.

    Hanssen EN, Avershina E, Rudi K et al (2017) Body fluid prediction from microbial patterns for forensic application. Forensic Sci Int Genet 30:10–17

    Article  CAS  Google Scholar 

  8. 8.

    Anzai-Kanto E, Hirata MH, Hirata RDC et al (2005) DNA extraction from human saliva deposited on skin and its use in forensic identification procedures. Braz Oral Res 19:216–222

    Article  Google Scholar 

  9. 9.

    Pang B, Cheung BJLM (2007) Double swab technique for collecting touched evidence. Legal Med 9:181–184

    Article  CAS  Google Scholar 

  10. 10.

    Grice EA, Kong HH, Renaud G et al (2008) A diversity profile of the human skin microbiota. Genome Res 18:1043–1050

    Article  CAS  Google Scholar 

  11. 11.

    Pechal JL, Crippen TL, Benbow ME et al (2014) The potential use of bacterial community succession in forensics as described by high throughput metagenomic sequencing. Int J Legal Med 128:193–205

    Article  Google Scholar 

  12. 12.

    Fierer N, Hamady M, Lauber CL et al (2008) The influence of sex, handedness, and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci 105:17994–17999

    Article  Google Scholar 

  13. 13.

    Ying S, Zeng D-N, Chi L et al (2015) The influence of age and gender on skin-associated microbial communities in urban and rural human populations. PLoS ONE 10:e0141842

    Article  CAS  Google Scholar 

  14. 14.

    You HS, Lee SH, Ok YJ et al (2019) Influence of swabbing solution and swab type on DNA recovery from rigid environmental surfaces. J Microbiol Methods 161:12–17

    Article  CAS  Google Scholar 

  15. 15.

    Fierer N, Lauber CL, Zhou N et al (2010) Forensic identification using skin bacterial communities. Proc Natil Acad Sci 107:6477–6481

    Article  Google Scholar 

  16. 16.

    Desjardins P, Conklin D, Jove J (2010) NanoDrop microvolume quantitation of nucleic acids. J Vis Exp 45:e2565

    Google Scholar 

  17. 17.

    Howell DC (2009) Statistical methods for psychology. Cengage Learning, Boston

    Google Scholar 

  18. 18.

    Kruskal WH, Wallis WAJJotAsA (1952) Use of ranks in one-criterion variance analysis. J Am Stat Assoc 47:583–621

    Article  Google Scholar 

  19. 19.

    Mann HB, Whitney DR (1947) On a test of whether one of two random variables is stochastically larger than the other. Ann Math Stat 12:50–60

    Article  Google Scholar 

  20. 20.

    Seethapathy S, Gorecki T, Li X (2008) Passive sampling in environmental analysis. J Chromatogr A 1184:234–253

    Article  CAS  Google Scholar 

  21. 21.

    Silhavy TJ, Kahne D, Walker S (2010) The bacterial cell envelope. Cold Spring Harbor Perspect Biol 2:a000414

    Article  CAS  Google Scholar 

  22. 22.

    Madigan MT, Martinko JM, Parker J (1997) Brock biology of microorganisms, vol 11. Prentice Hall, Upper Saddle River

    Google Scholar 

  23. 23.

    Dikici A, Arslan A, Yalcin H et al (2013) Effect of Tween 20 on antibacterial effects of acidic, neutral and alkaline decontaminants on viability of Salmonella on chicken carcasses and survival in waste decontamination fluids. Food Control 30:365–369

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by Projects for Research and Development of Police Science and Technology under the Center for Research and Development of Police Science and Technology and the Korean National Police Agency funded by the Ministry of Science, ICT and Future Planning. [Grant No. PA-I000001]. The authors would like to thank Enago for English language editing.

Author information

Affiliations

Authors

Corresponding author

Correspondence to Sung Hee Hyun.

Ethics declarations

Conflict of interest

No conflict of interest declared.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

12088_2019_854_MOESM1_ESM.docx

Supplementary material 1 (DOCX 57 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Ok, Y.J., You, H.S., Lee, S.H. et al. Comparison of Swabbing Solution Volume and gDNA Extraction Kits on DNA Recovery from Rigid Surface. Indian J Microbiol 60, 206–213 (2020). https://doi.org/10.1007/s12088-019-00854-6

Download citation

Keywords

  • Bacteria collection
  • Cotton swab
  • PBS
  • PBST
  • CFUS
  • DNA concentration
  • gDNA extraction kit