An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

By Daniel McDonald, Morgan N. Price, Julia Goodrich, Eric P. Nawrocki, Todd Z. DeSantis, Alexander J. Probst, Gary L. Andersen, Rob Knight, Philip Hugenholtz. The ISME Journal, 2011

4,740 citations recorded by the source corpus.

Reference phylogenies are crucial for providing a taxonomic framework for interpretation of marker gene and metagenomic surveys, which continue to reveal novel species at a remarkable rate. Greengenes is a dedicated full-length 16S rRNA gene database that provides users with a curated taxonomy based on de novo tree inference. We developed a ‘taxonomy to tree’ approach for transferring group names from an existing taxonomy to a tree topology, and used it to apply the Greengenes, National Center for Biotechnology Information (NCBI) and cyanoDB (Cyanobacteria only) taxonomies to a de novo tree comprising 408 315 sequences. We also incorporated explicit rank information provided by the NCBI taxonomy to group names (by prefixing rank designations) for better user orientation and classification consistency. The resulting merged taxonomy improved the classification of 75% of the sequences by one or more ranks relative to the original NCBI taxonomy with the most pronounced improvements occurring in under-classified environmental sequences. We also assessed candidate phyla (divisions) currently defined by NCBI and present recommendations for consolidation of 34 redundantly named groups. All intermediate results from the pipeline, which includes tree inference, jackknifing and transfer of a donor taxonomy to a recipient tree (tax2tree) are available for download. The improved Greengenes taxonomy should provide important infrastructure for a wide range of megasequencing projects studying ecosystems on scales ranging from our own bodies (the Human Microbiome Project) to the entire planet (the Earth Microbiome Project). The implementation of the software can be obtained from http://sourceforge.net/projects/tax2tree/.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4a1d4fa9d2f6f43cf5c546509fcb734416832f61

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Citations in the corpus

SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare? (2017, methodology): “Taxonomic binning of 16S reads is usually based on one of these four taxonomies: SILVA [4], RDP [5], Greengenes [6] or NCBI [7].”
Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson's Disease (2016, neutral): “, 2012) against the August 2013 release of Greengenes (McDonald et al., 2012) in QIIME 1.”
Combined amendment of immobilizers and the plant growth-promoting strain Burkholderia phytofirmans PsJN favours plant growth and reduces heavy metal uptake (2015, methodology): “Taxonomy assignment was performed in QIIME (Caporaso et al., 2010) employing the naïve Bayesian RDP classifier with a minimum confidence of 0.8 (Wang et al., 2007) against the last version of the Greengenes database (08/2013) (McDonald et al., 2012).”
Next-Generation Sequencing Technology: Current Trends and Advancements (2023, background): “Given the ubiquitous nature of microbes, their symbiotic, pathogenic, and commensal characteristics are of importance to humans by forming a highly functioning ecosystem.”
Linking bacterial and eukaryotic microbiota to litter chemistry: Combining next generation sequencing with 13C CPMAS NMR spectroscopy (2019, methodology): “Operational Taxonomical Units (OTUs) defined at 97% of sequence similarity were picked through de novo approach and uclust method and taxonomic assignment was obtained by using the RDP classifier and the Greengenes (McDonald et al., 2012) or the Silva SSU/LSU rRNA gene database release 119 (Quast et”
Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer (2016, positive): “Quality-filtered reads were clustered into Operational Taxonomic Units (OTUs) using an open-reference algorithm algorithm 21 and Greengenes v13_8 as a reference set 22 .”
Evaluating the Information Content of Shallow Shotgun Metagenomics (2018, methodology): “16S sequences were aligned to Greengenes version 13_8 (29) at 98% identity with exhaustive gapped alignment (18, 19).”
The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks (2013, background): “and the subsequent classification of rRNA gene sequences (35,36).”
Genetic determinants of the gut microbiome in UK Twins (2016, methodology): “Sequences were clustered into OTUs using the default pick open reference OTU pipeline in QIIME and the Greengenes August 2013 97% identity OTU representative sequences and taxonomy as the reference database (McDonald et al., 2012).”