The Ribosomal Database Project: Sequences and Software for High-Throughput rRNA Analysis

2011 ◽  
pp. 313-324 ◽  
Author(s):  
James R. Cole ◽  
Qiong Wang ◽  
Benli Chai ◽  
James M. Tiedje
Keyword(s):  
High Throughput ◽  
Ribosomal Database Project

scholarly journals Ribosomal Database Project: data and tools for high throughput rRNA analysis

2013 ◽  
Vol 42 (D1) ◽  
pp. D633-D642 ◽  
Author(s):  
James R. Cole ◽  
Qiong Wang ◽  
Jordan A. Fish ◽  
Benli Chai ◽  
Donna M. McGarrell ◽  
...  
Keyword(s):  
High Throughput ◽  
Ribosomal Database Project ◽  
Project Data

scholarly journals Metagenomic Analysis of Subgingival Microbiota Following Non-Surgical Periodontal Therapy: a Pilot Study

2012 ◽  
Vol 6 (1) ◽  
pp. 255-261 ◽  
Author(s):  
Theresia Laksmana ◽  
Weerayuth Kittichotirat ◽  
Yanyan Huang ◽  
Weizhen Chen ◽  
Michael Jorgensen ◽  
...  
Keyword(s):  
16S Rdna ◽  
High Throughput ◽  
Pcr Amplification ◽  
Aggressive Periodontitis ◽  
Periodontal Therapy ◽  
Oral Microbiome ◽  
Metagenomic Analysis ◽  
Ribosomal Database Project ◽  
Pcr Products ◽  
Subgingival Microbiota

This study tested the feasibility of a high throughput metagenomic approach to analyze the pre- and posttreatment of subgingival plaque in two subjects with aggressive periodontitis. DNA was extracted from subgingival samples and subjected to PCR amplification of the c2-c4 regions of the 16S rDNA using primers with bar codes to identify individual samples. The PCR products were pooled and sequenced for the v4 region of the 16S rDNA using the 454 FLX standard platform. The results were analyzed for species/phylotypes in the Human Oral Microbiome Database (HOMD) and Ribosomal Database Project (RDP) database. The sequencing of the amplicons resulted in 24,673 reads and identified 208 species/phylotypes. Of those, 129 species/phylotypes were identified in both patients but their proportions varied. While >120 species/phylotypes were identified in all samples, 28-42 species/phylotypes cumulatively represent 90% of all subgingival bacteria in each sample. The remaining species/phylotypes each constituted ≤0.2% of the total subgingival bacteria. In conclusion, the subgingival microbiota are characterized by high species richness dominated by a few species/ phylotypes. The microbiota changed after periodontal therapy. High throughput metagenomic analysis is applicable to assess the complexity and changes of the subgingival microbiota.

154: Integration of TPSA and High-Throughput Mass Spectrometry Data Improves Prostate Cancer Prediction

2007 ◽  
Vol 177 (4S) ◽  
pp. 52-53
Author(s):  
Stefano Ongarello ◽  
Eberhard Steiner ◽  
Regina Achleitner ◽  
Isabel Feuerstein ◽  
Birgit Stenzel ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Mass Spectrometry ◽  
High Throughput ◽  
Mass Spectrometry Data ◽  
Cancer Prediction
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