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Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB

Applied and Environmental Microbiology · 2006 · Vol. 72(7) · pp. 5069–5072

Todd Z. DeSantis(Lawrence Berkeley National Laboratory)Philip Hugenholtz(Joint Genome Institute)N. Larsen(Danish National Research Foundation)Mark Rojas(Baylor University)Eoin Brodie(Lawrence Berkeley National Laboratory)Keith Keller(University of California, Berkeley)Thomas Huber(University of Queensland)Daniel Dalevi(Chalmers University of Technology)Pengwei Hu(Lawrence Berkeley National Laboratory)Gary L. Andersen✉(Lawrence Berkeley National Laboratory)

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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.

Microbial Community Ecology and Physiology Genomics and Phylogenetic Studies Environmental DNA in Biodiversity StudiesPhylum16S ribosomal RNABiologyWorkbenchBacterial taxonomyChimera (genetics)ArchaeaRibosomal RNAGeneComputational biology

MeSH terms

ArchaeaBacteriaRecombination, GeneticRNA, Ribosomal, 16SSoftwareReproducibility of ResultsPolymerase Chain ReactionSequence AlignmentGenes, rRNADatabases, Nucleic Acid

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