ArticlePloS one2018
Identification of fungi in shotgun metagenomics datasets.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
57 citing papers in PubMed.
- Multiple hypervariable markers improve mycobiome classification in metatranscriptome and metagenome data.Communications biology · 2026Article
- Metagenomic sequencing reveals the dynamic changes of pig gut fungal composition following the ages and identifies fungal species associated with diarrhea in piglets.Animal microbiome · 2026Article
- Genomic insights intoMicrobiology spectrum · 2026Article
- Diversity of Microscopic Fungi.Journal of fungi (Basel, Switzerland) · 2026Article
- Interpreting fungal ecological contributions through taxonomic and functional profiling of metatranscriptomics.IMA fungus · 2026Review
- Advancing fungal phylogenetics: integrating modern sequencing, dark taxa discovery, and machine learning.Archives of microbiology · 2025Review
- Article
- The Gut Mycobiome for Precision Medicine.Journal of fungi (Basel, Switzerland) · 2025Review
- Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases.Microbiome · 2025Article
- Long-read metagenomics gives a more accurate insight into the microbiota of long-ripened gouda cheeses.Frontiers in microbiology · 2025Article
- Article
- Gut fungal profile in new onset treatment-naïve ulcerative colitis in Saudi children.Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association · 2025Article
- Evaluation of DNA Extraction Methods for Microbial Community Profiling in Deadwood Decomposition.MicrobiologyOpen · 2024Article
- The first ITS1 profiling of honey samples from the Southeast Asian region Lombok, Bali and Banggi Island.Scientific reports · 2024Article
- Gut mycobiome and neuropsychiatric disorders: insights and therapeutic potential.Frontiers in cellular neuroscience · 2024Review
- Combining compositional data sets introduces error in covariance network reconstruction.ISME communications · 2024Article
- Incorporating omics-based tools into endophytic fungal research.Biotechnology notes (Amsterdam, Netherlands) · 2024Review
- Characterization of the Cassava Mycobiome in Symptomatic Leaf Tissues Displaying Cassava Superelongation Disease.Journal of fungi (Basel, Switzerland) · 2023Article
- Fecal Fungal Microbiota (Mycobiome) Study as a Potential Tool for Precision Medicine in Inflammatory Bowel Disease.Gut and liver · 2023Review
- Skin microbiome differentiates into distinct cutotypes with unique metabolic functions upon exposure to polycyclic aromatic hydrocarbons.Microbiome · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Metagenomics uses nucleic acid sequencing to characterize species diversity in different niches such as environmental biomes or the human microbiome. Most studies have used 16S rRNA amplicon sequencing to identify bacteria. However, the decreasing cost of sequencing has resulted in a gradual shift away from amplicon analyses and towards shotgun metagenomic sequencing. Shotgun metagenomic data can be used to identify a wide range of species, but have rarely been applied to fungal identification. Here, we develop a sequence classification pipeline, FindFungi, and use it to identify fungal sequences in public metagenome datasets. We focus primarily on animal metagenomes, especially those from pig and mouse microbiomes. We identified fungi in 39 of 70 datasets comprising 71 fungal species. At least 11 pathogenic species with zoonotic potential were identified, including Candida tropicalis. We identified Pseudogymnoascus species from 13 Antarctic soil samples initially analyzed for the presence of bacteria capable of degrading diesel oil. We also show that Candida tropicalis and Candida loboi are likely the same species. In addition, we identify several examples where contaminating DNA was erroneously included in fungal genome assemblies.
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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.