ArticleMicrobiome2023
Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients.
Article in Microbiome, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed, 23 citations in OpenAlex.
- Dietary Inflammation, Gut Mycobiota, and Microbial Cross-Kingdom Associations with Cardiovascular Health in Older Adults.Metabolites · 2026Article
- Gut Microbiota Resilience and Environmental Stressors: A Hidden Key to Lifespan Optimization?Probiotics and antimicrobial proteins · 2026Review
- Plant-Derived Foods and Medicines as Modulators of the Gut Microbiome: Molecular Interactions and Implications for Disease and Therapy.Molecules (Basel, Switzerland) · 2026Review
- Review
- Spatiotemporal Dynamics and Co-Occurrence Patterns of Marine Fungal Communities Along Nutrient Gradients in the Leizhou Peninsula, China.Journal of fungi (Basel, Switzerland) · 2026Article
- Ecological insights into the cross-domain microbiome interactions in the hematophagous bat Desmodus rotundus.Animal microbiome · 2026Article
- Comparison of oral collection methods for 16S rRNA gene and shotgun metagenomic sequencing.Microbiology spectrum · 2026Article
- Unveiling the gut-pancreas axis: microbial influence on stemness and tumor microenvironment of PDAC.Stem cells (Dayton, Ohio) · 2026Review
- Review
- Associations of the gut mycobiome and its cross-kingdom interactions with estrus return in post-weaning sows revealed by metagenomic analysis.Frontiers in microbiology · 2026Article
- Unveiling pathogens and contaminants: refining metagenomics for clinical diagnostics.Frontiers in microbiology · 2026Article
- Characterization of Intestinal Mycobiome in Surgical Resections from Inflammatory Bowel Disease Patients: A Deeper Analysis in Complicated Crohn's Disease Phenotypes.Inflammatory bowel diseases · 2025Article
- Exploring diet-microbiota interactions and therapeutic nutrition management in inflammatory bowel disease.Biophysics reports · 2025Article
- Microbiome multi-omics analysis reveals novel biomarkers and mechanisms linked with CD etiopathology.Biomarker research · 2025Article
- The Role of Intestinal Fungi in the Pathogenesis and Treatment of Ulcerative Colitis.Microorganisms · 2025Review
- Challenges in capturing the mycobiome from shotgun metagenome data: lack of software and databases.Microbiome · 2025Article
- The role of the gut microbiome in disorders of gut-brain interaction.The FEBS journal · 2025Review
- Machine learning models reveal Saccharomyces yeasts are associated with poor piglet growth in early development.Journal of animal science · 2025Article
- Gut mycobiome in cardiometabolic disease progression: current evidence and future directions.Frontiers in microbiology · 2025Review
- Salivary mycobiome alterations in HIV-infected MSM: dominance ofFrontiers in cellular and infection microbiology · 2025Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundThe accuracy of internal-transcribed-spacer (ITS) and shotgun metagenomics has not been robustly evaluated, and the effect of diet on the composition and function of the bacterial and fungal gut microbiome in a longitudinal setting has been poorly investigated. Here we compared two approaches to study the fungal community (ITS and shotgun metagenomics), proposed an enrichment protocol to perform a reliable mycobiome analysis using a comprehensive in-house fungal database, and correlated dietary data with both bacterial and fungal communities.
resultsWe found that shotgun DNA sequencing after a new enrichment protocol combined with the most comprehensive and novel fungal databases provided a cost-effective approach to perform gut mycobiome profiling at the species level and to integrate bacterial and fungal community analyses in fecal samples. The mycobiome was significantly more variable than the bacterial community at the compositional and functional levels. Notably, we showed that microbial diversity, composition, and functions were associated with habitual diet composition instead of driven by global dietary changes. Our study indicates a potential competitive inter-kingdom interaction between bacteria and fungi for food foraging.
conclusionTogether, our present work proposes an efficient workflow to study the human gut microbiome integrating robustly fungal, bacterial, and dietary data. These findings will further advance our knowledge of the interaction between gut bacteria and fungi and pave the way for future investigations in human mycobiome. Video Abstract.
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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.