Abstract
BackgroundMetagenomics is revolutionizing the study of microorganisms and their involvement in biological, biomedical, and geochemical processes, allowing us to investigate by direct sequencing a tremendous diversity of organisms without the need for prior cultivation. Unicellular eukaryotes play essential roles in most microbial communities as chief predators, decomposers, phototrophs, bacterial hosts, symbionts, and parasites to plants and animals. Investigating their roles is therefore of great interest to ecology, biotechnology, human health, and evolution. However, the generally lower sequencing coverage, their more complex gene and genome architectures, and a lack of eukaryote-specific experimental and computational procedures have kept them on the sidelines of metagenomics.ResultsMetaEuk is a toolkit for high-throughput, reference-based discovery, and annotation of protein-coding genes in eukaryotic metagenomic contigs. It performs fast searches with 6-frame-translated fragments covering all possible exons and optimally combines matches into multi-exon proteins. We used a benchmark of seven diverse, annotated genomes to show that MetaEuk is highly sensitive even under conditions of low sequence similarity to the reference database. To demonstrate MetaEuk’s power to discover novel eukaryotic proteins in large-scale metagenomic data, we assembled contigs from 912 samples of the Tara Oceans project. MetaEuk predicted >12,000,000 protein-coding genes in 8 days on ten 16-core servers. Most of the discovered proteins are highly diverged from known proteins and originate from very sparsely sampled eukaryotic supergroups.ConclusionThe open-source (GPLv3) MetaEuk software (https://github.com/soedinglab/metaeuk) enables large-scale eukaryotic metagenomics through reference-based, sensitive taxonomic and functional annotation.4U3WMgJNVh8JdDg-h4V6htVideo abstract
Highlights
Metagenomics is revolutionizing the study of microorganisms and their involvement in biological, biomedical, and geochemical processes, allowing us to investigate by direct sequencing a tremendous diversity of organisms without the need for prior cultivation
The NCBI data included the scaffold coordinates of the annotated protein-coding genes and their exons. We used this information to assess MetaEuk’s sensitivity and precision by mapping MetaEuk predictions to annotated proteins in their scaffold location. This was done based on the scaffold boundaries of the MetaEuk prediction and the
We found that about 40% of the unmapped predictions overlap a protein-coding gene on the opposite strand or are on scaffolds that had no annotation at all
Summary
Metagenomics is revolutionizing the study of microorganisms and their involvement in biological, biomedical, and geochemical processes, allowing us to investigate by direct sequencing a tremendous diversity of organisms without the need for prior cultivation. Unicellular eukaryotes play essential roles in most microbial communities as chief predators, decomposers, phototrophs, bacterial hosts, symbionts, and parasites to plants and animals Investigating their roles is of great interest to ecology, biotechnology, human health, and evolution. Unicellular eukaryotes are present in almost all environments, including soil [1], oceans [2], and plant and animal-associated microbiomes [3, 4] They exhibit both autotrophic and heterotrophic lifestyles [5], exist in symbiosis with plants and animals [6], and interact with other microbial organisms [7]. Since the advent of metabarcoding using 18S rRNA genes, the known evolutionary diversity of unicellular eukaryotes has increased by orders of magnitude [13], and novel phyla and supra-kingdoms are still being discovered [14, 15]. The unique features of eukaryotic data, i.e., lower genomic coverage due to lower population densities in metagenomic samples, fewer reference genomes, increased genome sizes, and higher complexity of gene structure negatively impact all stages of metagenomic analyses, from assembly, through binning, to protein prediction and annotation [21, 22]
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