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dc.contributor.authorSohrabi, Mohsen
dc.contributor.authorNair, Raj
dc.contributor.authorSamaranayake, Lakshman P.
dc.contributor.authorZhang, Li
dc.contributor.authorZulfiker, Abu
dc.contributor.authorAhmetagic, Adnan
dc.contributor.authorGood, David
dc.contributor.authorWei, Ming
dc.date.accessioned2018-11-16T05:01:04Z
dc.date.available2018-11-16T05:01:04Z
dc.date.issued2016
dc.identifier.issn0167-7012en_US
dc.identifier.doi10.1016/j.mimet.2016.01.013en_US
dc.identifier.urihttp://hdl.handle.net/10072/125300
dc.description.abstractRecent culture-independent studies have enabled detailed mapping of human microbiome that has not been hitherto achievable by culture-based methods. DNA extraction is a key element of bacterial culture-independent studies that critically impacts on the outcome of the detected microbial profile. Despite the variations in DNA extraction methods described in the literature, no standardized technique is available for the purpose of microbiome profiling. Hence, standardization of DNA extraction methods is urgently needed to yield comparable data from different studies. We examined the effect of eight different cell lysis protocols on the yield and quality of the extracted DNA from oral rinse samples. These samples were exposed to cell lysis techniques based on enzymatic, mechanical, and a combination of enzymatic–mechanical methods. The outcome measures evaluated were total bacterial population, Firmicutes levels and human DNA contamination (in terms of surrogate GAPDH levels). We noted that all three parameters were significantly affected by the method of cell lysis employed. Although the highest yield of gDNA was obtained using lysozyme-achromopeptidase method, the lysozyme-zirconium beads method yielded the peak quantity of total bacterial DNA and Firmicutes with a lower degree of GAPDH contamination compared with the other methods. Taken together our data clearly points to an urgent need for a consensus, standardized DNA extraction technique to evaluate the oral microbiome using oral rinse samples. Further, if Firmicutes levels are the focus of investigation in oral rinse microbiome analyses then the lysozyme-zirconium bead method would be the method of choice in preference to others.en_US
dc.description.peerreviewedYesen_US
dc.languageEnglishen_US
dc.publisherElsevieren_US
dc.relation.ispartofpagefrom64en_US
dc.relation.ispartofpageto72en_US
dc.relation.ispartofjournalJournal of Microbiological Methodsen_US
dc.relation.ispartofvolume122en_US
dc.subject.fieldofresearchMedical Microbiology not elsewhere classifieden_US
dc.subject.fieldofresearchcode110899en_US
dc.titleThe yield and quality of cellular and bacterial DNA extracts from human oral rinse samples are variably affected by the cell lysis methodologyen_US
dc.typeJournal articleen_US
dc.type.descriptionC1 - Peer Reviewed (HERDC)en_US
dc.type.codeC - Journal Articlesen_US
dcterms.licensehttp://creativecommons.org/licenses/by-nc-nd/4.0/en_US
dc.description.versionPost-printen_US
gro.facultyGriffith Health, School of Medical Scienceen_US
gro.rights.copyright© 2016 Elsevier. Licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International Licence which permits unrestricted, non-commercial use, distribution and reproduction in any medium, providing that the work is properly cited.en_US
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