ArticleBMC genomics2019
HumanMycobiomeScan: a new bioinformatics tool for the characterization of the fungal fraction in metagenomic samples.
Article in BMC genomics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
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Who cites it
20 citing papers in PubMed, 1 synthesis or guideline pooled it, 37 citations in OpenAlex.
- Predicting cancer-related mycobiome aspects in gastrointestinal cancers: a systematic review.Frontiers in medicine · 2024Pooled it
- 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
- Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases.Microbiome · 2025Article
- Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.Briefings in bioinformatics · 2025Review
- Global research trends and hotspots on human intestinal fungi and health: a bibliometric visualization study.Frontiers in cellular and infection microbiology · 2024Article
- Candida spp. in Human Intestinal Health and Disease: More than a Gut Feeling.Mycopathologia · 2023Review
- Molecular Markers: An Overview of Data Published for Fungi over the Last Ten Years.Journal of fungi (Basel, Switzerland) · 2022Review
- The Neglected Gut Microbiome: Fungi, Protozoa, and Bacteriophages in Inflammatory Bowel Disease.Inflammatory bowel diseases · 2022Review
- Temporal changes in gastrointestinal fungi and the risk of autoimmunity during early childhood: the TEDDY study.Nature communications · 2022Article
- The Human Mycobiome in Chronic Respiratory Diseases: Current Situation and Future Perspectives.Microorganisms · 2022Review
- Analyzing the human gut mycobiome - A short guide for beginners.Computational and structural biotechnology journal · 2022Review
- FunOMIC: Pipeline with built-in fungal taxonomic and functional databases for human mycobiome profiling.Computational and structural biotechnology journal · 2022Article
- Improving Taxonomic Delimitation of Fungal Species in the Age of Genomics and Phenomics.Frontiers in microbiology · 2022Review
- RESCRIPt: Reproducible sequence taxonomy reference database management.PLoS computational biology · 2021Article
- Longitudinal dynamics of gut bacteriome, mycobiome and virome after fecal microbiota transplantation in graft-versus-host disease.Nature communications · 2021Article
- The role of gut mycobiome in health and diseases.Therapeutic advances in gastroenterology · 2021Review
- The use of taxon-specific reference databases compromises metagenomic classification.BMC genomics · 2020Article
- Article
- Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease.Gut microbesReview
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundModern metagenomic analysis of complex microbial communities produces large amounts of sequence data containing information on the microbiome in terms of bacterial, archaeal, viral and eukaryotic composition. The bioinformatics tools available are mainly devoted to profiling the bacterial and viral fractions and only a few software packages consider fungi. As the human fungal microbiome (human mycobiome) can play an important role in the onset and progression of diseases, a comprehensive description of host-microbiota interactions cannot ignore this component.
resultsHumanMycobiomeScan is a bioinformatics tool for the taxonomic profiling of the mycobiome directly from raw data of next-generation sequencing. The tool uses hierarchical databases of fungi in order to unambiguously assign reads to fungal species more accurately and > 10,000 times faster than other comparable approaches. HumanMycobiomeScan was validated using in silico generated synthetic communities and then applied to metagenomic data, to characterize the intestinal fungal components in subjects adhering to different subsistence strategies.
conclusionsAlthough blind to unknown species, HumanMycobiomeScan allows the characterization of the fungal fraction of complex microbial ecosystems with good performance in terms of sample denoising from reads belonging to other microorganisms. HumanMycobiomeScan is most appropriate for well-studied microbiomes, for which most of the fungal species have been fully sequenced. This released version is functionally implemented to work with human-associated microbiota samples. In combination with other microbial profiling tools, HumanMycobiomeScan is a frugal and efficient tool for comprehensive characterization of microbial ecosystems through shotgun metagenomics sequencing.
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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.