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Amplicon Based 16S Ribosomal RNA Sequencing and Genus Identification
EP22726
Poster Title: Amplicon Based 16S Ribosomal RNA Sequencing and Genus Identification
Submitted on 19 Feb 2015
Author(s): *Jan Risinger, *Lindsey Renken, +Josh Hill, +Noushin Ghaffari, PhD, +Richard P. Metz, PhD, +Charles D. Johnson, PhD, *Masoud M. Toloue, Ph
Affiliations: *Bioo Scientific +AgriLife Genomics and Bioinformatics Service, Texas A&M University
This poster was presented at PAGXXIII
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Poster Information
Abstract: Next generation sequencing analysis of 16S ribosomal RNA (rRNA) is commonly used to identify bacterial species and perform taxonomic studies. Bacterial 16S rRNA genes contain 9 hyper-variable regions with considerable sequence diversity among different bacterial species and can be used for species id. Rapid determination of highly complex bacterial populations through targeted amplification can provide an accurate gauge of diversity at taxonomic hierarchies as low as the genus level. A single 16S rRNA hypervariable domain does not have enough sequence diversity to distinguish genera. With increased read lengths of Illumina MiSeq chemistry, Bioo Scientific has expanded the common analysis of the fourth hyper-variable domain (V4) of prokaryotic 16S rRNA to V1, V2 and V3 regions simultaneously. Optimized preparation through a streamlined standardized procedure allows for high-quality, reproducible libraries. This optimization can be applied to different windows of 16S rRNA as well as other relevant prokaryotic taxonomic markers.
Figure
Summary: Rapid determination of highly complex bacterial populations through targeted amplification of 16S rRNA V1 - V3 hypervariable regions can provide an accurate gauge of diversity at taxonomic hierarchies as low as the genus level. References: 1. Lazarevic et al., Analysis of the salivary microbiome using culture independent techniques. Journal of Clinical Bioinformatics. 2012, 2:4. 2. Meyer et al., The Metagenomics RAST server - A public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics. 2008, 9:386. 3. Kreth et al., Bacterial and Host Interactions of Oral Streptococci. DNA and Cell Biology. 2009, 28:8. 4. Distler, W., and Kroncke, A. The lactate metabolism of the oral bacterium Veillonella from human saliva. Arch Oral Biology. 1981, 26. 5. Dewhirst et al., The Human Oral Microbiome. Journal of Bacteriology. 2010, 192:19. 6. Marcel Martin, Cutadapt removes adapter sequences from high-throughput sequencing reads, (2011) EMBnet.journal, 17:10-12Report abuse »
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