Abstract
BackgroundMicrobial eukaryotes are nearly ubiquitous in microbiomes on Earth and contribute to many integral ecological functions. Metagenomics is a proven tool for studying the microbial diversity, functions, and ecology of microbiomes, but has been underutilized for microeukaryotes due to the computational challenges they present. For taxonomic classification, the use of a eukaryotic marker gene database can improve the computational efficiency, precision and sensitivity. However, state-of-the-art tools which use marker gene databases implement universal thresholds for classification rather than dynamically learning the thresholds from the database structure, impacting the accuracy of the classification process.ResultsHere we introduce taxaTarget, a method for the taxonomic classification of microeukaryotes in metagenomic data. Using a database of eukaryotic marker genes and a supervised learning approach for training, we learned the discriminatory power and classification thresholds for each 20 amino acid region of each marker gene in our database. This approach provided improved sensitivity and precision compared to other state-of-the-art approaches, with rapid runtimes and low memory usage. Additionally, taxaTarget was better able to detect the presence of multiple closely related species as well as species with no representative sequences in the database. One of the greatest challenges faced during the development of taxaTarget was the general sparsity of available sequences for microeukaryotes. Several algorithms were implemented, including threshold padding, which effectively handled the missing training data and reduced classification errors. Using taxaTarget on metagenomes from human fecal microbiomes, a broader range of genera were detected, including multiple parasites that the other tested tools missed.ConclusionData-driven methods for learning classification thresholds from the structure of an input database can provide granular information about the discriminatory power of the sequences and improve the sensitivity and precision of classification. These methods will help facilitate a more comprehensive analysis of metagenomic data and expand our knowledge about the diverse eukaryotes in microbial communities.
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin
