ArticleMycoKeys2022
The curse of the uncultured fungus.
Article in MycoKeys, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 25 citations in OpenAlex.
- Advancing Yeast Identification Using High-Throughput DNA Barcode Data From a Curated Culture Collection.Molecular ecology resources · 2026Article
- Article
- Ecological divergence of sibling allopolyploid marsh orchids is associated with species specific plasticity and distinct fungal communities.The Plant journal : for cell and molecular biology · 2025Article
- Detection of fungal sequences in human brain: rDNA locus amplification and deep sequencing.Scientific reports · 2024Article
- A Probiotic Amylase Blend Positively Impacts Gut Microbiota Modulation in a Randomized, Placebo-Controlled, Double-Blind Study.Life (Basel, Switzerland) · 2024Article
- The Intricate Connection between Bacterial α-Diversity and Fungal Engraftment in the Human Gut of Healthy and Impaired Individuals as Studied Using the In Vitro SHIMEJournal of fungi (Basel, Switzerland) · 2023Article
- A Custom Regional DNA Barcode Reference Library for Lichen-Forming Fungi of the Intermountain West, USA, Increases Successful Specimen Identification.Journal of fungi (Basel, Switzerland) · 2023Article
- How, not if, is the question mycologists should be asking about DNA-based typification.MycoKeys · 2023Article
- Fungal taxonomy: current status and research agendas for the interdisciplinary and globalisation era.Mycology · 2023Review
- Article
Corrections and comments
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Authors and funding
15 authors at 9 institutions in 6 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The international DNA sequence databases abound in fungal sequences not annotated beyond the kingdom level, typically bearing names such as "uncultured fungus". These sequences beget low-resolution mycological results and invite further deposition of similarly poorly annotated entries. What do these sequences represent? This study uses a 767,918-sequence corpus of public full-length fungal ITS sequences to estimate what proportion of the 95,055 "uncultured fungus" sequences that represent truly unidentifiable fungal taxa - and what proportion of them that would have been straightforward to annotate to some more meaningful taxonomic level at the time of sequence deposition. Our results suggest that more than 70% of these sequences would have been trivial to identify to at least the order/family level at the time of sequence deposition, hinting that factors other than poor availability of relevant reference sequences explain the low-resolution names. We speculate that researchers' perceived lack of time and lack of insight into the ramifications of this problem are the main explanations for the low-resolution names. We were surprised to find that more than a fifth of these sequences seem to have been deposited by mycologists rather than researchers unfamiliar with the consequences of poorly annotated fungal sequences in molecular repositories. The proportion of these needlessly poorly annotated sequences does not decline over time, suggesting that this problem must not be left unchecked.
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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.