16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles.

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dc.contributor.authorHang, Jun
dc.contributor.authorDesai, Valmik
dc.contributor.authorZavaljevski, Nela
dc.contributor.authorYang, Yu
dc.contributor.authorLin, Xiaoxu
dc.contributor.authorSatya, Ravi Vijaya
dc.contributor.authorMartinez, Luis J
dc.contributor.authorBlaylock, Jason M
dc.contributor.authorJarman, Richard G
dc.contributor.authorThomas, Stephen J
dc.contributor.authorKuschner, Robert A
dc.date.accessioned2020-02-07T13:33:12Z
dc.date.available2020-02-07T13:33:12Z
dc.date.issued2014-09-17
dc.description.abstractSample storage conditions extraction methods PCR primers and parameters are major factors that affect metagenomics analysis based on microbial 16S rRNA gene sequencing Most published studies were limited to the comparison of only one or two types of these factors Systematic multi factor explorations are needed to evaluate the conditions that may impact validity of a microbiome analysis This study was aimed to improve methodological options to facilitate the best technical approaches in the design of a microbiome study Three readily available mock bacterial community materials and two commercial extraction techniques Qiagen DNeasy and MO BIO PowerSoil DNA purification methods were used to assess procedures for 16S ribosomal DNA amplification and pyrosequencing based analysis Primers were chosen for 16S rDNA quantitative PCR and amplification of region V3 to V1 Swabs spiked with mock bacterial community cells and clinical oropharyngeal swabs were incubated at respective temperatures of 80 C 20 C 4 C and 37 C for 4 weeks then extracted with the two methods and subjected to pyrosequencing and taxonomic and statistical analyses to investigate microbiome profile stability
dc.identifier.urihttp://dx.doi.org/10.1186/2049-2618-2-31
dc.identifier.urihttps://lib.digitalsquare.io/xmlui/handle/123456789/14770
dc.relation.uriMicrobiome
dc.title16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles.en
dcterms.abstractSample storage conditions extraction methods PCR primers and parameters are major factors that affect metagenomics analysis based on microbial 16S rRNA gene sequencing Most published studies were limited to the comparison of only one or two types of these factors Systematic multi factor explorations are needed to evaluate the conditions that may impact validity of a microbiome analysis This study was aimed to improve methodological options to facilitate the best technical approaches in the design of a microbiome study Three readily available mock bacterial community materials and two commercial extraction techniques Qiagen DNeasy and MO BIO PowerSoil DNA purification methods were used to assess procedures for 16S ribosomal DNA amplification and pyrosequencing based analysis Primers were chosen for 16S rDNA quantitative PCR and amplification of region V3 to V1 Swabs spiked with mock bacterial community cells and clinical oropharyngeal swabs were incubated at respective temperatures of 80 C 20 C 4 C and 37 C for 4 weeks then extracted with the two methods and subjected to pyrosequencing and taxonomic and statistical analyses to investigate microbiome profile stability
dcterms.contributorHang, Jun
dcterms.contributorDesai, Valmik
dcterms.contributorZavaljevski, Nela
dcterms.contributorYang, Yu
dcterms.contributorLin, Xiaoxu
dcterms.contributorSatya, Ravi Vijaya
dcterms.contributorMartinez, Luis J
dcterms.contributorBlaylock, Jason M
dcterms.contributorJarman, Richard G
dcterms.contributorThomas, Stephen J
dcterms.contributorKuschner, Robert A
dcterms.identifierhttp://dx.doi.org/10.1186/2049-2618-2-31
dcterms.relationMicrobiome
dcterms.title16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles.en
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