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

Abigail L Lind,Katherine S Pollard

doi:10.1186/s40168-021-01015-y

Abstract

BackgroundMicrobial 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 challenging to study with shotgun sequencing techniques and are therefore often excluded.ResultsHere, we present EukDetect, a bioinformatics method to identify eukaryotes in shotgun metagenomic sequencing data. Our approach uses a database of 521,824 universal marker genes from 241 conserved gene families, which we curated from 3713 fungal, protist, non-vertebrate metazoan, and non-streptophyte archaeplastida genomes and transcriptomes. EukDetect has a broad taxonomic coverage of microbial eukaryotes, performs well on low-abundance and closely related species, 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, mirroring 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, though some do not, suggesting they are dormant or nonviable. We analyze metagenomic data from the Baltic Sea and find that eukaryotes differ across locations and salinity gradients. Finally, we observe eukaryotes in Arabidopsis leaf samples, many of which are not identifiable from public protein databases.ConclusionsEukDetect provides an automated and reliable way to characterize eukaryotes in shotgun sequencing datasets from diverse microbiomes. We demonstrate that it enables discoveries that would be missed or clouded by false positives with standard shotgun sequence analysis. EukDetect will greatly advance our understanding of how microbial eukaryotes contribute to microbiomes.EDH-t7L4v5WEFMvCw3ubMSVideo abstract

Highlights

Microbial eukaryotes are found alongside bacteria and archaea in natural microbial systems, including host-associated microbiomes
We demonstrate this problem by simulating paired-end sequence reads from the genomes of 971 common human gut microbiome bacteria, representing all major bacterial phyla in the human gut—including Bacteroidetes, Actinobacteria, Firmicutes, Proteobacteria, and Fusobacteria [26]
We aligned these reads against a database of 2449 genomes of fungi, protists, and metazoans taken from NCBI GenBank

Summary

Introduction

Microbial eukaryotes are found alongside bacteria and archaea in natural microbial systems, including host-associated microbiomes. Eukaryotic microbes are ubiquitous in microbial systems, where they function as decomposers, predators, parasites, and producers [1]. Microbial eukaryotes have complex interactions with their hosts in both plant- and animal-associated microbiomes. Microbial eukaryotes in the gastrointestinal tract metabolize plant compounds [3]. Microbial eukaryotes interact in complex ways with the host immune system, and their depletion and low diversity in microbiomes from industrialized societies mirror the industrialization-driven “extinction” seen for bacterial residents in the microbiome [6,7,8]. Outside of host-associated environments, microbial eukaryotes are integral to the ecology of aquatic and soil ecosystems, where they are primary producers, partners in symbioses, decomposers, and predators [9, 10]

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