Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing

Abstract

Microbial eukaryotes are found alongside bacteria and archaea in natural microbial systems, including host-associated microbiomes. While microbial eukaryotes are critical to these communities, they are often not included in metagenomic analyses. Here we present EukDetect, a bioinformatics approach based on universal eukaryotic marker genes, to identify eukaryotes in shotgun metagenomic sequencing data. EukDetect is accurate, sensitive, has a broad taxonomic coverage of microbial eukaryotes, and is resilient against bacterial contamination in eukaryotic genomes. This enables us to identify and make observations about eukaryotes in public human and plant microbiome datasets. Using EukDetect, we describe the spatial distribution of eukaryotes in the human gut, finding that fungi and protists are present in the lumen and mucosa throughout the large intestine. We find that there is a succession of eukaryotes that colonize the human gut during the first years of life, similar to patterns of succession observed in bacteria in the developing gut. By comparing DNA and RNA sequencing of paired samples from the human gut, we find that many eukaryotes continue active transcription after passage through the gut, while others do not, suggesting they are dormant or nonviable. Finally, we identify eukaryotes in Arabidopsis leaf samples, many of which are not identifiable from public protein databases. EukDetect is an accurate and sensitive pipeline to routinely characterize eukaryotes in shotgun sequencing datasets from diverse microbiomes.