ArticleMicrobial genomics2024
Putative genome contamination has minimal impact on the GTDB taxonomy.
Article in Microbial genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Benchmarking Illumina and Oxford Nanopore Technologies (ONT) sequencing platforms for whole genome sequencing of bacterial genomes and use in clinical microbiology.BMC medical genomics · 2026Article
- GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes.Nucleic acids research · 2026Article
- Improving taxonomic inference from ancient environmental metagenomes by masking microbial-like regions in reference genomes.GigaScience · 2025Article
- Article
- SeqCode in the golden age of prokaryotic systematics.The ISME journal · 2024Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Genome Taxonomy Database (GTDB) provides a species to domain classification of publicly available genomes based on average nucleotide identity (ANI) (for species) and a concatenated gene phylogeny normalized by evolutionary rates (for genus to phylum), which has been widely adopted by the scientific community. Here, we use the Genome UNClutterer (GUNC) software to identify putatively contaminated genomes in GTDB release 07-RS207. We found that GUNC reported 35,723 genomes as putatively contaminated, comprising 11.25 % of the 317,542 genomes in GTDB release 07-RS207. To assess the impact of this high level of inferred contamination on the delineation of taxa, we created 'clean' versions of the 34,846 putatively contaminated bacterial genomes by removing the most contaminated half. For each clean half, we re-calculated the ANI and concatenated gene phylogeny and found that only 77 (0.22 %) of the genomes were not consistent with their original classification. We conclude that the delineation of taxa in GTDB is robust to the putative contamination detected by GUNC.
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