ArticleBMC genomics2020
The use of taxon-specific reference databases compromises metagenomic classification.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Exploring the Quality of Historic DNA From Pinned Beetles.Ecology and evolution · 2026Article
- Benchmarking the impact of reference genome selection on taxonomic profiling accuracy.BMC genomics · 2026Article
- Multiple hypervariable markers improve mycobiome classification in metatranscriptome and metagenome data.Communications biology · 2026Article
- Phytomycobiomes and Ecosystem Services: Mechanisms, Evidence and Routes to Application.Journal of fungi (Basel, Switzerland) · 2025Review
- Detection ofFood chemistry. Molecular sciences · 2025Article
- Tracing non-fungal eukaryotic diversity via shotgun metagenomes in the complex mudflat intertidal zones.mSystems · 2025Article
- Precise and scalable metagenomic profiling with sample-tailored minimizer libraries.NAR genomics and bioinformatics · 2025Article
- NGS-based Aspergillus detection in plasma and lung lavage of children with invasive pulmonary aspergillosis.NPJ genomic medicine · 2025Article
- An updated reference genome of Barbatula barbatula (Linnaeus, 1758).Scientific data · 2025Article
- OCTOPUS: Disk-based, Multiplatform, Mobile-friendly Metagenomics Classifier.AMIA ... Annual Symposium proceedings. AMIA Symposium · 2024Article
- RAPiD: a rapid and accurate plant pathogen identification pipeline for on-site nanopore sequencing.PeerJ · 2024Article
- Towards facilitated interpretation of shotgun metagenomics long-read sequencing data analyzed with KMA for the detection of bacterial pathogens and their antimicrobial resistance genes.Frontiers in microbiology · 2024Article
- HiTaxon: a hierarchical ensemble framework for taxonomic classification of short reads.Bioinformatics advances · 2024Article
- Ten common issues with reference sequence databases and how to mitigate them.Frontiers in bioinformatics · 2024Review
- Use of a taxon-specific reference database for accurate metagenomics-based pathogen detection of Listeria monocytogenes in turkey deli meat and spinach.BMC genomics · 2023Article
- Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes.Microbiome · 2023Article
- From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools.Microbial genomics · 2023Article
- Article
- Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome.Animal microbiome · 2022Article
- Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics.International journal of molecular sciences · 2022Review
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
A recent article in BMC Genomics describes a new bioinformatics tool, HumanMycobiomeScan, to classify fungal taxa in metagenomic samples. This tool was used to characterize the gut mycobiome of hunter-gatherers and Western populations, resulting in the identification of a range of fungal species in the vast majority of samples. In the HumanMycobiomeScan pipeline, sequence reads are mapped against a reference database containing fungal genome sequences only. We argue that using reference databases comprised of a single taxonomic group leads to an unacceptably high number of false-positives due to: (i) mapping to conserved genetic regions in reference genomes, and (ii) sequence contamination in the assembled reference genomes. To demonstrate this, we replaced the HumanMycobiomeScan's fungal reference database with one containing genome sequences of amphibians and reptiles and re-analysed their case study. The classification pipeline recovered all species present in the reference database, revealing turtles (Geoemydidae), bull frogs (Pyxicephalidae) and snakes (Colubridae) as the most abundant herpetological taxa in the human gut. We also re-analysed their case study using a kingdom-agnostic pipeline. This revealed that while the gut of hunter-gatherers and Western subjects may be colonized by a range of microbial eukaryotes, only three fungal families were retrieved. These results highlight the pitfalls of using taxon-specific reference databases for metagenome classification, even when they are comprised of curated whole genome data. We propose that databases containing all domains of life provide the most suitable option for metagenomic species profiling, especially when targeting microbial eukaryotes.
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