EUKulele: Taxonomic annotation of the unsung eukaryotic microbes

TL;DR

EUKulele is an open-source tool that improves taxonomic annotation of microbial eukaryotes in environmental samples, aiding ecological and evolutionary studies by providing consistent, comprehensive classification and metrics for biodiversity assessment.

Contribution

The paper introduces EUKulele, a novel software that enhances taxonomic annotation of microeukaryotes in meta-omic data, supporting assembly-based analysis and detailed completeness metrics.

Findings

EUKulele effectively assigns taxonomy to environmental microeukaryotes.

The tool provides metrics for taxonomic completeness of samples.

EUKulele integrates with existing analysis pipelines for microbial diversity studies.

Abstract

The assessment of microbial species biodiversity is essential in ecology and evolutionary biology (Reaka-Kudla et al. 1996), but especially challenging for communities of microorganisms found in the environment (Das et al. 2006, Hillebrand et al. 2018). Beyond providing a census of organisms in the ocean, assessing marine microbial biodiversity can reveal how microbes respond to environmental change (Salazar et al. 2017), clarify the ecological roles of community members (Hehemann et al. 2016), and lead to biotechnology discoveries (Das et al. 2006). Computational approaches to characterize taxonomic diversity and phylogeny based on the quality of available data for environmental sequence datasets is fundamental for advancing our understanding of the role of these organisms in the environment. Even more pressing is the need for comprehensive and consistent methods to assign taxonomy to environmentally-relevant microbial eukaryotes. Here, we present EUKulele, an open-source software tool designed to assign taxonomy to microeukaryotes detected in meta-omic samples, and complement analysis approaches in other domains by accommodating assembly output and providing concrete metrics reporting the taxonomic completeness of each sample.