TaxAss: Leveraging a Custom Freshwater Database 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 com...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2018-10-01
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| Series: | mSphere |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/mSphere.00327-18 |
| _version_ | 1818836616380153856 |
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| author | Robin R. Rohwer Joshua J. Hamilton Ryan J. Newton Katherine D. McMahon |
| author_facet | Robin R. Rohwer Joshua J. Hamilton Ryan J. Newton Katherine D. McMahon |
| author_sort | Robin R. Rohwer |
| collection | DOAJ |
| description | 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 data sets using the comprehensive SILVA database and the freshwater-specific FreshTrain database. TaxAss increased the percentage of the data set classified compared to using only SILVA, especially at fine-resolution family to species taxon levels, while across the freshwater test data sets classifications increased by as much as 11 to 40% of total reads. A similar increase in classifications was not observed in a control mouse gut data set, which was not expected to contain freshwater bacteria. TaxAss also maintained taxonomic richness compared to using only the FreshTrain across all taxon levels from phylum to species. Without TaxAss, most organisms not represented in the FreshTrain were unclassified, but at fine taxon levels, incorrect classifications became significant. We validated TaxAss using simulated amplicon data derived from full-length clone libraries and found that 96 to 99% of test sequences were correctly classified at fine resolution. TaxAss splits a data set’s 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 is available at https://www.github.com/McMahonLab/TaxAss. IMPORTANCE Microbial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon data sets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at the phylum, class, and order levels 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 data set dependent and cannot be compared between data sets. 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 data sets. |
| first_indexed | 2024-12-19T03:09:26Z |
| format | Article |
| id | doaj.art-2a8da9d167d2420f916099567fa13277 |
| institution | Directory Open Access Journal |
| issn | 2379-5042 |
| language | English |
| last_indexed | 2024-12-19T03:09:26Z |
| publishDate | 2018-10-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSphere |
| spelling | doaj.art-2a8da9d167d2420f916099567fa132772022-12-21T20:38:03ZengAmerican Society for MicrobiologymSphere2379-50422018-10-013510.1128/mSphere.00327-18TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic ResolutionRobin R. Rohwer0Joshua J. Hamilton1Ryan J. Newton2Katherine D. McMahon3Environmental Chemistry and Technology Program, University of Wisconsin—Madison, Madison, Wisconsin, USADepartment of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USASchool of Freshwater Sciences, University of Wisconsin—Milwaukee, Milwaukee, Wisconsin, USADepartment of Bacteriology, University of Wisconsin—Madison, Madison, Wisconsin, USAABSTRACT 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 data sets using the comprehensive SILVA database and the freshwater-specific FreshTrain database. TaxAss increased the percentage of the data set classified compared to using only SILVA, especially at fine-resolution family to species taxon levels, while across the freshwater test data sets classifications increased by as much as 11 to 40% of total reads. A similar increase in classifications was not observed in a control mouse gut data set, which was not expected to contain freshwater bacteria. TaxAss also maintained taxonomic richness compared to using only the FreshTrain across all taxon levels from phylum to species. Without TaxAss, most organisms not represented in the FreshTrain were unclassified, but at fine taxon levels, incorrect classifications became significant. We validated TaxAss using simulated amplicon data derived from full-length clone libraries and found that 96 to 99% of test sequences were correctly classified at fine resolution. TaxAss splits a data set’s 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 is available at https://www.github.com/McMahonLab/TaxAss. IMPORTANCE Microbial communities drive ecosystem processes, but microbial community composition analyses using 16S rRNA gene amplicon data sets are limited by the lack of fine-resolution taxonomy classifications. Coarse taxonomic groupings at the phylum, class, and order levels 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 data set dependent and cannot be compared between data sets. 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 data sets.https://journals.asm.org/doi/10.1128/mSphere.00327-1816S rRNA geneamplicon sequencingfreshwaterlimnologymicrobial ecologytaxonomy |
| spellingShingle | Robin R. Rohwer Joshua J. Hamilton Ryan J. Newton Katherine D. McMahon TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution mSphere 16S rRNA gene amplicon sequencing freshwater limnology microbial ecology taxonomy |
| title | TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution |
| title_full | TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution |
| title_fullStr | TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution |
| title_full_unstemmed | TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution |
| title_short | TaxAss: Leveraging a Custom Freshwater Database Achieves Fine-Scale Taxonomic Resolution |
| title_sort | taxass leveraging a custom freshwater database achieves fine scale taxonomic resolution |
| topic | 16S rRNA gene amplicon sequencing freshwater limnology microbial ecology taxonomy |
| url | https://journals.asm.org/doi/10.1128/mSphere.00327-18 |
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