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 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 Statement
The authors have declared no competing interest.
Footnotes
The method described in this paper, EukDetect, has a new filtering method for detecting false positives. When more than one species within a genus is detected, reads aligning to these species are examined to determine whether any are spurious alignments. All analyses have been updated with this new filtering method, but the conclusions presented are unchanged.
