ArticleScientific data2022
Improvement of eukaryotic protein predictions from soil metagenomes.
Article in Scientific data, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers, 1 of them a synthesis that pooled it.
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Who cites it
8 citing papers in PubMed, 1 synthesis or guideline pooled it, 11 citations in OpenAlex.
- Exploring agro-ecological significance, knowledge gaps, and research priorities in arbuscular mycorrhizal fungi.Frontiers in microbiology · 2024Pooled it
- "Quadrupling" the protein family space with global metagenomics.Nucleic acids research · 2026Article
- Predicted shifts in bacterial and algal contributions to DMSP and DMS dynamics during a coastal spring-summer bloom.The ISME journal · 2026Article
- Organic matter degradation by oceanic fungi differs between polar and non-polar waters.Nature communications · 2025Article
- Microbial bioremediation of persistent organic pollutants in plant tissues provides crop growth promoting liquid fertilizer.Nature communications · 2025Article
- Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut.Nature communications · 2025Article
- The endohyphal microbiome: current progress and challenges for scaling down integrative multi-omic microbiome research.Microbiome · 2023Article
- Improvement of eukaryotic protein predictions from soil metagenomes.Scientific data · 2022Article
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
During the last decades, metagenomics has highlighted the diversity of microorganisms from environmental or host-associated samples. Most metagenomics public repositories use annotation pipelines tailored for prokaryotes regardless of the taxonomic origin of contigs. Consequently, eukaryotic contigs with intrinsically different gene features, are not optimally annotated. Using a bioinformatics pipeline, we have filtered 7.9 billion contigs from 6,872 soil metagenomes in the JGI's IMG/M database to identify eukaryotic contigs. We have re-annotated genes using eukaryote-tailored methods, yielding 8 million eukaryotic proteins and over 300,000 orphan proteins lacking homology in public databases. Comparing the gene predictions we made with initial JGI ones on the same contigs, we confirmed our pipeline improves eukaryotic proteins completeness and contiguity in soil metagenomes. The improved quality of eukaryotic proteins combined with a more comprehensive assignment method yielded more reliable taxonomic annotation. This dataset of eukaryotic soil proteins with improved completeness, quality and taxonomic annotation reliability is of interest for any scientist aiming at studying the composition, biological functions and gene flux in soil communities involving eukaryotes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.