ArticleGenome research2019
Human contamination in bacterial genomes has created thousands of spurious proteins.
Article in Genome research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers.
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Who cites it
100 citing papers in PubMed.
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- Improving Metagenomics Classification with Kmask: Entropy-Based Masking of Low-Complexity Regions.bioRxiv : the preprint server for biology · 2026Article
- De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag.PLoS computational biology · 2026Article
- Genestrip: exact and efficient read classification for selected groups of organisms.BMC bioinformatics · 2026Article
- Cultivation-independent high-quality microbial genome reconstruction from environmental samples with midi-metagenomics.Genome research · 2026Article
- Uncovering viral protein acquisition events and human-specific folds with pairwise comparisons of predicted protein structures.Molecular biology and evolution · 2026Article
- The gut microbiota shapes the human and murine breath volatilome.Cell metabolism · 2026Article
- DNA sequence contamination analyzer (DNASCAN): a supervised analysis toolkit for detecting and removing DNA contaminants.BMC bioinformatics · 2026Article
- Setting higher standards for reports of microbial species in human cancers.Nature cancer · 2026Review
- WGS analysis and functional studies illustrate promising gene-signatures for probiotic attributes and molecular-targeted therapeutic prospects of Lactiplantibacillus plantarum LP-ARP2.Archives of microbiology · 2026Article
- Folding the unfoldable 2: using AlphaFold and ESMFold to explore spurious proteins.Bioinformatics advances · 2026Article
- Suprathreshold non-volatile flavour perception is associated with multiple species rather than any single species via bacterial metabolism.Journal of oral microbiology · 2026Article
- Interkingdom microbiome physiology in colorectal cancer: barrier dysfunction, immune-metabolic signaling, and therapeutic resistance.Frontiers in physiology · 2026Review
- Detection of viral sequences at single-cell resolution identifies novel viruses associated with host gene expression changes.Nature biotechnology · 2026Article
- Comparative Evaluation of Sequencing Technologies for Detecting Antimicrobial Resistance in Bloodstream Infections.Antibiotics (Basel, Switzerland) · 2025Review
- L-proline supplementation affects non-volatile flavour perception through oral microbiome metabolic pathways.NPJ science of food · 2025Article
- Contamination of fungal genomes of Onygenaceae (Phylum Ascomycota) in public databases: incidence, detection, and impact.BMC genomics · 2025Article
- Use of the CHM13-T2T genome improves metagenomic analysis by minimizing host DNA contamination.mSystems · 2025Article
- The hidden life ofApplied and environmental microbiology · 2025Article
- The multi-kingdom cancer microbiome.Nature microbiology · 2025Review
40 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
Abstract
Contaminant sequences that appear in published genomes can cause numerous problems for downstream analyses, particularly for evolutionary studies and metagenomics projects. Our large-scale scan of complete and draft bacterial and archaeal genomes in the NCBI RefSeq database reveals that 2250 genomes are contaminated by human sequence. The contaminant sequences derive primarily from high-copy human repeat regions, which themselves are not adequately represented in the current human reference genome, GRCh38. The absence of the sequences from the human assembly offers a likely explanation for their presence in bacterial assemblies. In some cases, the contaminating contigs have been erroneously annotated as containing protein-coding sequences, which over time have propagated to create spurious protein "families" across multiple prokaryotic and eukaryotic genomes. As a result, 3437 spurious protein entries are currently present in the widely used nr and TrEMBL protein databases. We report here an extensive list of contaminant sequences in bacterial genome assemblies and the proteins associated with them. We found that nearly all contaminants occurred in small contigs in draft genomes, which suggests that filtering out small contigs from draft genome assemblies may mitigate the issue of contamination while still keeping nearly all of the genuine genomic sequences.
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