New Microbe Community Taxonomy Data Products

NEON is announcing these new data products: Microbe Community Taxonomy (soil: DP1.10081.002, benthic: DP1.20086.002, surface: DP1.20141.002). These new products are revisions of the now-deprecated Microbe Community Composition products (DP1.10081.001, DP1.20086.001, and DP1.20141.001). These new products were generated by an updated algorithm, which infers representative sequences and assigns taxonomy across all samples, regardless of sample type, site, or collection date. 

The AY25 release of these data products will include NEON samples collected from 2018 through 2023, for both the 16S (bacteria and archaea) and eukaryotic ITS (internal transcribed spacer – mostly fungi) ribosomal markers. For both markers, representative sequences (ASVs, OTUs) were inferred from sample sequences and taxonomy was assigned where possible. For 16S, the Ribosomal Database Project RDP release 14 trainset 19 database was used as the taxonomy reference. For ITS, the UNITE version 10.0 fungal taxonomy database was used. The downloaded data package includes a table, mct_taxonTableLabSummary, with more details on methods used. The User Guide also contains details on the methods used.

Basic information for all samples is contained in the sampleMetadata tables, one for 16S and one for ITS. These tables also include links to a table for each sample that has its OTU and taxonomy information. With the download of the expanded package, these tables will also be downloaded. When using the neonUtilities R or Python package to stack data files, the taxonomy tables are compiled together into a single (for each marker) perSampleTaxonomy table. These tables serve as the starting point for analyses. To get started, the package phyloNEON (https://github.com/NEONScience/phyloNEON) has some basic functions to convert the downloaded data into a Phyloseq object for downstream analysis. Development on the phyloNEON package is ongoing; check back to the GitHub page for additional tools.