SEQanswers

Go Back   SEQanswers > Literature Watch



Similar Threads
Thread Thread Starter Forum Replies Last Post
PubMed: Illumina-based analysis of microbial community diversity. Newsbot! Literature Watch 0 06-17-2011 06:10 AM
PubMed: Pyrosequencing of the 16S rRNA gene to reveal bacterial pathogen diversity in Newsbot! Literature Watch 0 06-23-2010 02:00 AM
PubMed: Novel Microbial Diversity Retrieved by Autonomous Robotic Exploration of the Newsbot! Literature Watch 0 03-20-2010 02:00 AM
PubMed: Accurate determination of microbial diversity from 454 pyrosequencing data. Newsbot! Literature Watch 0 08-12-2009 05:00 AM
PubMed: Accurate taxonomy assignments from 16S rRNA sequences produced by highly para Newsbot! Literature Watch 0 08-30-2008 05:06 AM

Reply
 
Thread Tools
Old 11-22-2008, 05:02 AM   #1
Newsbot!
RSS Posting Maniac
 

Join Date: Feb 2008
Posts: 1,439
Default PubMed: Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag S

Syndicated from PubMed RSS Feeds

Related Articles Exploring Microbial Diversity and Taxonomy Using SSU rRNA Hypervariable Tag Sequencing.

PLoS Genet. 2008 Nov;4(11):e1000255

Authors: Huse SM, Dethlefsen L, Huber JA, Welch DM, Relman DA, Sogin ML

Massively parallel pyrosequencing of hypervariable regions from small subunit ribosomal RNA (SSU rRNA) genes can sample a microbial community two or three orders of magnitude more deeply per dollar and per hour than capillary sequencing of full-length SSU rRNA. As with full-length rRNA surveys, each sequence read is a tag surrogate for a single microbe. However, rather than assigning taxonomy by creating gene trees de novo that include all experimental sequences and certain reference taxa, we compare the hypervariable region tags to an extensive database of rRNA sequences and assign taxonomy based on the best match in a Global Alignment for Sequence Taxonomy (GAST) process. The resulting taxonomic census provides information on both composition and diversity of the microbial community. To determine the effectiveness of using only hypervariable region tags for assessing microbial community membership, we compared the taxonomy assigned to the V3 and V6 hypervariable regions with the taxonomy assigned to full-length SSU rRNA sequences isolated from both the human gut and a deep-sea hydrothermal vent. The hypervariable region tags and full-length rRNA sequences provided equivalent taxonomy and measures of relative abundance of microbial communities, even for tags up to 15% divergent from their nearest reference match. The greater sampling depth per dollar afforded by massively parallel pyrosequencing reveals many more members of the "rare biosphere" than does capillary sequencing of the full-length gene. In addition, tag sequencing eliminates cloning bias and the sequences are short enough to be completely sequenced in a single read, maximizing the number of organisms sampled in a run while minimizing chimera formation. This technique allows the cost-effective exploration of changes in microbial community structure, including the rare biosphere, over space and time and can be applied immediately to initiatives, such as the Human Microbiome Project.

PMID: 19023400 [PubMed - as supplied by publisher]



More...
Newsbot! is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:22 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO