Evaluation of methods for the extraction and purification of DNA from the human microbiome.
DNA extraction is an essential step in all cultivation-independent approaches to characterize microbial diversity, including that associated with the human body. A fundamental challenge in using these approaches has been to isolate DNA that is representative of the microbial community sampled.In thi...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3311548?pdf=render |
| _version_ | 1819327073082146816 |
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| author | Sanqing Yuan Dora B Cohen Jacques Ravel Zaid Abdo Larry J Forney |
| author_facet | Sanqing Yuan Dora B Cohen Jacques Ravel Zaid Abdo Larry J Forney |
| author_sort | Sanqing Yuan |
| collection | DOAJ |
| description | DNA extraction is an essential step in all cultivation-independent approaches to characterize microbial diversity, including that associated with the human body. A fundamental challenge in using these approaches has been to isolate DNA that is representative of the microbial community sampled.In this study, we statistically evaluated six commonly used DNA extraction procedures using eleven human-associated bacterial species and a mock community that contained equal numbers of those eleven species. These methods were compared on the basis of DNA yield, DNA shearing, reproducibility, and most importantly representation of microbial diversity. The analysis of 16S rRNA gene sequences from a mock community showed that the observed species abundances were significantly different from the expected species abundances for all six DNA extraction methods used.Protocols that included bead beating and/or mutanolysin produced significantly better bacterial community structure representation than methods without both of them. The reproducibility of all six methods was similar, and results from different experimenters and different times were in good agreement. Based on the evaluations done it appears that DNA extraction procedures for bacterial community analysis of human associated samples should include bead beating and/or mutanolysin to effectively lyse cells. |
| first_indexed | 2024-12-24T13:05:02Z |
| format | Article |
| id | doaj.art-080d247152064c77a485790804d1d8cc |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-24T13:05:02Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-080d247152064c77a485790804d1d8cc2022-12-21T16:54:01ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0173e3386510.1371/journal.pone.0033865Evaluation of methods for the extraction and purification of DNA from the human microbiome.Sanqing YuanDora B CohenJacques RavelZaid AbdoLarry J ForneyDNA extraction is an essential step in all cultivation-independent approaches to characterize microbial diversity, including that associated with the human body. A fundamental challenge in using these approaches has been to isolate DNA that is representative of the microbial community sampled.In this study, we statistically evaluated six commonly used DNA extraction procedures using eleven human-associated bacterial species and a mock community that contained equal numbers of those eleven species. These methods were compared on the basis of DNA yield, DNA shearing, reproducibility, and most importantly representation of microbial diversity. The analysis of 16S rRNA gene sequences from a mock community showed that the observed species abundances were significantly different from the expected species abundances for all six DNA extraction methods used.Protocols that included bead beating and/or mutanolysin produced significantly better bacterial community structure representation than methods without both of them. The reproducibility of all six methods was similar, and results from different experimenters and different times were in good agreement. Based on the evaluations done it appears that DNA extraction procedures for bacterial community analysis of human associated samples should include bead beating and/or mutanolysin to effectively lyse cells.http://europepmc.org/articles/PMC3311548?pdf=render |
| spellingShingle | Sanqing Yuan Dora B Cohen Jacques Ravel Zaid Abdo Larry J Forney Evaluation of methods for the extraction and purification of DNA from the human microbiome. PLoS ONE |
| title | Evaluation of methods for the extraction and purification of DNA from the human microbiome. |
| title_full | Evaluation of methods for the extraction and purification of DNA from the human microbiome. |
| title_fullStr | Evaluation of methods for the extraction and purification of DNA from the human microbiome. |
| title_full_unstemmed | Evaluation of methods for the extraction and purification of DNA from the human microbiome. |
| title_short | Evaluation of methods for the extraction and purification of DNA from the human microbiome. |
| title_sort | evaluation of methods for the extraction and purification of dna from the human microbiome |
| url | http://europepmc.org/articles/PMC3311548?pdf=render |
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