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

Abstract

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/.

Moving beyond microbiome-wide associations to causal microbe identification

“…The closed-reference operational taxonomic unit (OTU) workflow in QIIME and the Greengenes reference database (May 2013) were used to cluster reads into OTUs with 97% identity and to assign taxonomy to representative OTUs 24,25 . OTU tables were rarified to a depth of 40,000 (Figures 2 and 4) and 13,000 sequences per sample (Figure 3).…”

Dominance of Endozoicomonas bacteria throughout coral bleaching and mortality suggests structural inflexibility of the Pocillopora verrucosa microbiome

“…Chimeric sequences were removed using the UCHIME command (Edgar et al., 2011). Sequences assigned to chloroplasts, mitochondria, archaea, and eukaryotes were removed based on classification against the Greengenes database (release gg_13_8_99, McDonald et al., 2012). Further, kit contaminants were removed based on sequencing results of PCRs from negative controls, including Brevibacterium casei , B. aureum , Brachybacterium sp., Dietzia sp., Pelomonas puraquae , and Simkania negevensis (Salter et al., 2014).…”

“…Further, kit contaminants were removed based on sequencing results of PCRs from negative controls, including Brevibacterium casei , B. aureum , Brachybacterium sp., Dietzia sp., Pelomonas puraquae , and Simkania negevensis (Salter et al., 2014). After removal of unwanted sequences, 3,576,201 sequences with an average length of 309 bp were retained for subsequent analyses, clustered into OTUs (97% similarity cutoff), and annotated against the Greengenes database (release gg_13_8_99, bootstrap = 60; McDonald et al., 2012). Bacterial community composition pie charts were created on the OTU and class level using the means of relative abundances from replicates ( n  = 3).…”

Gut microflora may facilitate adaptation to anthropic habitat: A comparative study in Rattus

“…We clustered operational taxonomic units (OTUs) using the uclust algorithm (Edgar, 2010) at a 97% similarity threshold and other parameters set to default. For each OTU, we chose the longest read as the representative sequence and, using the RDP classifier v2.2 (Wang, Garrity, Tiedje, & Cole, 2007) on the Greengenes database v13.8 (DeSantis et al., 2006; McDonald et al., 2012), assigned taxonomy to all representative sequences with the following parameters: minimum 75% sequence match with confidence threshold of 0.85. We constructed rarefaction plots to determine adequacy of the 16s sequencing procedure.…”