GreenGenes

GreenGenes, commonly referred to as Greengenes, is a curated database of 16S ribosomal RNA gene sequences from bacteria and archaea, created as a reference resource for microbial ecology and amplicon sequencing studies. The project provides a non-redundant collection of high-quality 16S rRNA sequences, a consistent taxonomic framework, and a reference phylogeny to support downstream analyses. Sequences are processed to remove chimeras and misannotations, and are aligned to produce standardized multiple sequence alignments that facilitate comparative work.

Greengenes offers taxonomy assignments for user-provided sequences by comparison to the reference set and is designed to be used with common bioinformatics tools such as ARB, QIIME, and mothur. The database includes downloadable data files, including reference sequences, alignments, taxonomic lineages, and a phylogenetic tree, enabling tasks such as operational taxonomic unit (OTU) picking, phylogenetic tree construction, and taxonomy-driven analyses.

Historically, Greengenes has been widely employed in microbial community studies to classify 16S reads, compare microbial communities, and infer evolutionary relationships. The taxonomy is hierarchical, extending from broad higher-level groups to more specific lineages, though species-level identifications remain challenging for many environmental sequences due to limitations of 16S resolution. As with other specialized 16S databases, the rate and recency of updates have influenced its relative popularity over time, with researchers selecting resources based on compatibility with their pipelines and the scope of taxonomic coverage required.

Greengenes remains one of the foundational references in 16S rRNA analysis, alongside other major databases such as SILVA and RDP.