TY - JOUR T1 - Accurate and sensitive detection of microbial eukaryotes from metagenomic shotgun sequencing JF - bioRxiv DO - 10.1101/2020.07.22.216580 SP - 2020.07.22.216580 AU - Abigail L. Lind AU - Katherine S. Pollard Y1 - 2020/01/01 UR - http://biorxiv.org/content/early/2020/09/21/2020.07.22.216580.abstract N2 - 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 method to identify eukaryotes in shotgun metagenomic sequencing data. Our approach uses a database of universal marker genes, which we curated from all 2,571 currently available fungal, protist, worm and other diverse eukaryotic genomes. EukDetect is accurate and sensitive, has a broad taxonomic coverage of microbial eukaryotes, and is resilient against bacterial contamination in eukaryotic genomes. Using EukDetect, we describe the spatial distribution of eukaryotes along the human gastrointestinal tract, showing that fungi and protists are present in the lumen and mucosa throughout the large intestine. We discover that there is a succession of eukaryotes that colonize the human gut during the first years of life, similar to patterns of developmental succession observed in gut bacteria. By comparing DNA and RNA sequencing of paired samples from human stool, 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 observe eukaryotes in Arabidopsis leaf samples, many of which are not identifiable from public protein databases. Thus, EukDetect provides an automated and reliable way to characterize eukaryotes in shotgun sequencing datasets from diverse microbiomes.Competing Interest StatementThe authors have declared no competing interest. ER -