ArticlePLoS computational biology2024
Database size positively correlates with the loss of species-level taxonomic resolution for the 16S rRNA and other prokaryotic marker genes.
Article in PLoS computational biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed.
- Application of antibiotics for the selective isolation of previously uncultured species from activated sludge.Microbiology spectrum · 2026Article
- TIPP-SD: A new method for species detection in microbiomes.PLoS computational biology · 2026Article
- Vibrio proteolyticus DCF12.2 postbiotic modulates intestinal metabolic and immune pathways in zebrafish.Applied microbiology and biotechnology · 2026Article
- Limitations of Common Molecular Markers in Fungal Biodiversity Analysis and the Benefits of Their Synergistic Use.Molecular ecology resources · 2026Article
- Streptomyces shaoguanensis sp. nov.: elucidating the mechanisms of efficient chicken feather degradation and its potential for biofertilizer development.Microbial cell factories · 2025Article
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- Gut Microbiota Dynamics in Hibernating and ActiveVeterinary sciences · 2025Article
- DNA sequence analysis landscape: a comprehensive review of DNA sequence analysis task types, databases, datasets, word embedding methods, and language models.Frontiers in medicine · 2025Review
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Abstract
For decades, the 16S rRNA gene has been used to taxonomically classify prokaryotic species and to taxonomically profile microbial communities. However, the 16S rRNA gene has been criticized for being too conserved to differentiate between distinct species. We argue that the inability to differentiate between species is not a unique feature of the 16S rRNA gene. Rather, we observe the gradual loss of species-level resolution for other nearly-universal prokaryotic marker genes as the number of gene sequences increases in reference databases. This trend was strongly correlated with how represented a taxonomic group was in the database and indicates that, at the gene-level, the boundaries between many species might be fuzzy. Through our study, we argue that any approach that relies on a single marker to distinguish bacterial taxa is fraught even if some markers appear to be discriminative in current databases.
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