TaxAss: Leveraging Custom Databases Achieves Fine-Scale Taxonomic Resolution

Abstract

Taxonomy assignment of freshwater microbial communities is limited by the minimally curated phylogenies used for large taxonomy databases. Here we introduce TaxAss, a taxonomy assignment workflow that classifies 16S rRNA gene amplicon data using two taxonomy reference databases: a large comprehensive database and a small ecosystem-specific database rigorously curated by scientists within a field. We applied TaxAss to five different freshwater datasets using the comprehensive Silva database and the freshwater-specific FreshTrain database. TaxAss increased the percent of the dataset classified compared to using only Silva, especially at fine-resolution family-species taxa levels, while across the freshwater test-datasets classifications increased by as much as 11-40 percent of total reads. A similar increase in classifications was not observed in a control mouse gut dataset, which was not expected to contain freshwater bacteria. TaxAss also maintained taxonomic richness compared to using only the FreshTrain across all taxa-levels from phylum to species. Without TaxAss, most organisms not represented in the FreshTrain were unclassified, but at fine taxa levels incorrect classifications became significant. We validated TaxAss using simulated amplicon data with known taxonomy and found that 96-99% of test sequences were correctly classified at fine resolution. TaxAss splits a datasets sequences into two groups based on their percent identity to reference sequences in the ecosystem-specific database. Sequences with high similarity to sequences in the ecosystem-specific database are classified using that database, and the others are classified using the comprehensive database. TaxAss is free and open source, and available at www.github.com/McMahonLab/TaxAss.\n\nIMPORTANCEMicrobial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon datasets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at phylum, class, and order level lump ecologically distinct organisms together. To avoid this, many researchers define operational taxonomic units (OTUs) based on clustered sequences, sequence variants, or unique sequences. These fine-resolution groupings are more ecologically relevant, but OTU definitions are dataset-dependent and cannot be compared between datasets. Microbial ecologists studying freshwater have curated a small, ecosystem-specific taxonomy database to provide consistent and up-to-date terminology. We created TaxAss, a workflow that leverages this database to assign taxonomy. We found that TaxAss improves fine-resolution taxonomic classifications (family, genus and species). Fine taxonomic groupings are more ecologically relevant, so they provide an alternative to OTU-based analyses that is consistent and comparable between datasets.