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Literature DB >> 16820507

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB.

T Z DeSantis¹, P Hugenholtz, N Larsen, M Rojas, E L Brodie, K Keller, T Huber, D Dalevi, P Hu, G L Andersen.

Abstract

A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages in the Archaea and Bacteria.

Entities: Mutation

Mesh：

Substances：
RNA, Ribosomal, 16S

Year: 2006 PMID： 16820507 PMCID： PMC1489311 DOI： 10.1128/AEM.03006-05

Source DB: PubMed Journal: Appl Environ Microbiol ISSN： 0099-2240 Impact factor: 4.792

28 in total

1. The RDP-II (Ribosomal Database Project).

Authors: B L Maidak; J R Cole; T G Lilburn; C T Parker; P R Saxman; R J Farris; G M Garrity; G J Olsen; T M Schmidt; J M Tiedje
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

2. High-density microarray of small-subunit ribosomal DNA probes.

Authors: Kenneth H Wilson; Wendy J Wilson; Jennifer L Radosevich; Todd Z DeSantis; Vijay S Viswanathan; Thomas A Kuczmarski; Gary L Andersen
Journal: Appl Environ Microbiol Date: 2002-05 Impact factor: 4.792

3. The genetic core of the universal ancestor.

Authors: J Kirk Harris; Scott T Kelley; George B Spiegelman; Norman R Pace
Journal: Genome Res Date: 2003-03 Impact factor: 9.043

4. PROBEmer: A web-based software tool for selecting optimal DNA oligos.

Authors: Scott J Emrich; Mary Lowe; Arthur L Delcher
Journal: Nucleic Acids Res Date: 2003-07-01 Impact factor: 16.971

5. Bacterial community dynamics across a floristic gradient in a temperate upland grassland ecosystem.

Authors: E Brodie; S Edwards; N Clipson
Journal: Microb Ecol Date: 2002-09-06 Impact factor: 4.552

6. PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database.

Authors: Kevin E Ashelford; Andrew J Weightman; John C Fry
Journal: Nucleic Acids Res Date: 2002-08-01 Impact factor: 16.971

7. Assessment of bacterial community structure in the deep sub-seafloor biosphere by 16S rDNA-based techniques: a cautionary tale.

Authors: Gordon Webster; Carole J Newberry; John C Fry; Andrew J Weightman
Journal: J Microbiol Methods Date: 2003-10 Impact factor: 2.363

8. Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA.

Authors: T Z DeSantis; I Dubosarskiy; S R Murray; G L Andersen
Journal: Bioinformatics Date: 2003-08-12 Impact factor: 6.937

9. New perspective on uncultured bacterial phylogenetic division OP11.

Authors: J Kirk Harris; Scott T Kelley; Norman R Pace
Journal: Appl Environ Microbiol Date: 2004-02 Impact factor: 4.792

10. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes.

Authors: T Z DeSantis; P Hugenholtz; K Keller; E L Brodie; N Larsen; Y M Piceno; R Phan; G L Andersen
Journal: Nucleic Acids Res Date: 2006-07-01 Impact factor: 16.971

2000 in total

1. Denaturing gradient gel electrophoresis and barcoded pyrosequencing reveal unprecedented archaeal diversity in mangrove sediment and rhizosphere samples.

Authors: Ana C C Pires; Daniel F R Cleary; Adelaide Almeida; Angela Cunha; Simone Dealtry; Leda C S Mendonça-Hagler; Kornelia Smalla; Newton C M Gomes
Journal: Appl Environ Microbiol Date: 2012-06-01 Impact factor: 4.792

2. Structure of the human gastric bacterial community in relation to Helicobacter pylori status.

Authors: Ana Maldonado-Contreras; Kate C Goldfarb; Filipa Godoy-Vitorino; Ulas Karaoz; Mónica Contreras; Martin J Blaser; Eoin L Brodie; Maria G Dominguez-Bello
Journal: ISME J Date: 2010-10-07 Impact factor: 10.302

3. Validating the Use of Bovine Buccal Sampling as a Proxy for the Rumen Microbiota by Using a Time Course and Random Forest Classification Approach.

Authors: Juliana Young; Joseph H Skarlupka; Madison S Cox; Rafael Tassinari Resende; Amelie Fischer; Kenneth F Kalscheur; Jennifer C McClure; John B Cole; Garret Suen; Derek M Bickhart
Journal: Appl Environ Microbiol Date: 2020-08-18 Impact factor: 4.792

4. iNOS- and NOX1-dependent ROS production maintains bacterial homeostasis in the ileum of mice.

Authors: C Matziouridou; S D C Rocha; O A Haabeth; K Rudi; H Carlsen; A Kielland
Journal: Mucosal Immunol Date: 2017-12-06 Impact factor: 7.313

Review 5. Potential for Monitoring Gut Microbiota for Diagnosing Infections and Graft-versus-Host Disease in Cancer and Stem Cell Transplant Patients.

Authors: Andrew Y Koh
Journal: Clin Chem Date: 2017-07-18 Impact factor: 8.327

6. Atmospheric trace gases support primary production in Antarctic desert surface soil.

Authors: Mukan Ji; Chris Greening; Inka Vanwonterghem; Carlo R Carere; Sean K Bay; Jason A Steen; Kate Montgomery; Thomas Lines; John Beardall; Josie van Dorst; Ian Snape; Matthew B Stott; Philip Hugenholtz; Belinda C Ferrari
Journal: Nature Date: 2017-12-06 Impact factor: 49.962

10. Fumarole-supported islands of biodiversity within a hyperarid, high-elevation landscape on Socompa Volcano, Puna de Atacama, Andes.

Authors: Elizabeth K Costello; Stephan R P Halloy; Sasha C Reed; Preston Sowell; Steven K Schmidt
Journal: Appl Environ Microbiol Date: 2008-12-12 Impact factor: 4.792