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dc.contributor.authorSohrabi, Mohsen
dc.contributor.authorNair, Raj G
dc.contributor.authorSamaranayake, Lakshman P
dc.contributor.authorZhang, Li
dc.contributor.authorZulfiker, Abu Hasanat Md
dc.contributor.authorAhmetagic, Adnan
dc.contributor.authorGood, David
dc.contributor.authorWei, Ming Q
dc.date.accessioned2018-11-16T05:01:04Z
dc.date.available2018-11-16T05:01:04Z
dc.date.issued2016
dc.identifier.issn0167-7012
dc.identifier.doi10.1016/j.mimet.2016.01.013
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.
dc.description.peerreviewedYes
dc.languageEnglish
dc.publisherElsevier
dc.relation.ispartofpagefrom64
dc.relation.ispartofpageto72
dc.relation.ispartofjournalJournal of Microbiological Methods
dc.relation.ispartofvolume122
dc.subject.fieldofresearchMedical Microbiology not elsewhere classified
dc.subject.fieldofresearchMicrobiology
dc.subject.fieldofresearchMedical Microbiology
dc.subject.fieldofresearchcode110899
dc.subject.fieldofresearchcode0605
dc.subject.fieldofresearchcode1108
dc.titleThe yield and quality of cellular and bacterial DNA extracts from human oral rinse samples are variably affected by the cell lysis methodology
dc.typeJournal article
dc.type.descriptionC1 - Articles
dc.type.codeC - Journal Articles
dcterms.licensehttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.description.versionPost-print
gro.facultyGriffith Health, School of Medical Science
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.
gro.hasfulltextFull Text
gro.griffith.authorGood, David A.
gro.griffith.authorZhang, Li
gro.griffith.authorNair, Raj
gro.griffith.authorWei, Ming Q.
gro.griffith.authorSohrabi, Mohsen
gro.griffith.authorZulfiker, Abu M.
gro.griffith.authorAhmetagic, Adnan


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