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

Area of Science:

• Microbiology
• Bioinformatics
• Genomics

Background:

• Public 16S rRNA gene repositories often contain errors like chimeras and inconsistent taxonomic assignments.
• Standardization is crucial for reliable analysis of microbial communities.

Purpose of the Study:

• To present a curated 16S rRNA gene database addressing limitations of existing public repositories.
• To improve the accuracy and consistency of microbial taxonomic classification.

Main Methods:

• Developed a 16S rRNA gene database with integrated chimera screening.
• Implemented standard alignment procedures.
• Utilized multiple published taxonomies for classification.
• Analyzed environmental sequences and isolate records.

Main Results:

• Identified incongruent taxonomic nomenclature among curators, even at the phylum level.
• Detected putative chimeras in 3% of environmental sequences and 0.2% of isolate records.
• Classified environmental sequences into 100 phylum-level lineages within Archaea and Bacteria.

Conclusions:

• The curated 16S rRNA gene database enhances the reliability of microbial community studies.
• Standardization and chimera screening are essential for accurate microbial taxonomy.
• The database provides a robust resource for microbial ecology research.