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Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn’s Disease

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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The Fungal Biome of the Oral Cavity

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Candida Survival Strategies

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Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease

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TLR2, but not TLR4, triggers cytokine production by murine cells in response to Candida albicans yeasts and hyphae

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The fungal microbiota of de-novo paediatric inflammatory bowel disease

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Anti- Saccharomyces cerevisiae Mannan Antibodies in Familial Crohn's Disease

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Basic Local Alignment Search Tool

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Candida albicans Colonization and ASCA in Familial Crohn's Disease

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Mucolytic Bacteria With Increased Prevalence in IBD Mucosa Augment In Vitro Utilization of Mucin by Other Bacteria

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Familial Risk of Inflammatory Bowel Disease: A Population-Based Cohort Study 1977–2011

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CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands

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QIIME allows analysis of high-throughput community sequencing data

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In vitro growth and analysis of Candida biofilms

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Candida albicans Is an Immunogen for Anti–Saccharomyces cerevisiae Antibody Markers of Crohn’s Disease

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Antibodies Against Laminaribioside and Chitobioside Are Novel Serologic Markers in Crohn’s Disease

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The Commensal Microbiota and Enteropathogens in the Pathogenesis of Inflammatory Bowel Diseases

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The role of the intestinal microbiota in the pathogenesis of necrotizing enterocolitis

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Complement modulates the cutaneous microbiome and inflammatory milieu

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Fungi and inflammatory bowel diseases: Alterations of composition and diversity

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Virulence and pathogenicity ofCandida albicansis enhanced in biofilms containing oral bacteria

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Search and clustering orders of magnitude faster than BLAST

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IBD Genetic Risk Profile in Healthy First-Degree Relatives of Crohn’s Disease Patients

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Fungal Dysbiosis in Mucosa-associated Microbiota of Crohn’s Disease Patients

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Fungal Signature in the Gut Microbiota of Pediatric Patients With Inflammatory Bowel Disease

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Escherichia coli and its lipopolysaccharide modulate in vitro Candida biofilm formation

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Bacterial lipopolysaccharides variably modulate in vitro biofilm formation of Candida species

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The changing pattern of Crohn’s disease incidence in northern France: a continuing increase in the 10- to 19-year-old age bracket (1988-2007)

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Contributions of hyphae and hypha-co-regulated genes to Candida albicans virulence

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Secretory products of E scherichia coli biofilm modulate C andida biofilm formation and hyphal development

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Towards a unified paradigm for sequence‐based identification of fungi

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Interactions Between Commensal Fungi and the C-Type Lectin Receptor Dectin-1 Influence Colitis

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Specific antibody response to oligomannosidic epitopes in Crohn's disease

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Differential Cytokine Production and Toll-Like Receptor Signaling Pathways by Candida albicans Blastoconidia and Hyphae

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Opposite evolution in incidence of Crohn’s disease and ulcerative colitis in Northern France (1988–1999)

inferredcites →https://doi.org/10.1136/gut.2010.208348openalex-snapshot

Mannan-binding lectin deficiency results in unusual antibody production and excessive experimental colitis in response to mannose-expressing mild gut pathogens

inferredcites →https://doi.org/10.1136/gut.2010.223263openalex-snapshot

Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives

inferredcites →https://doi.org/10.1136/gut.2010.224154openalex-snapshot

Guidelines for the management of inflammatory bowel disease in adults

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Incidence of inflammatory bowel disease in northern France (1988-1990).

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Clinical patterns of familial inflammatory bowel disease.

inferredcites →https://doi.org/10.1136/gutjnl-2014-307649openalex-snapshot

Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii , a commensal bacterium deficient in Crohn’s disease

inferredcites →https://doi.org/10.1136/gutjnl-2015-310746openalex-snapshot

Fungal microbiota dysbiosis in IBD

inferredcites →https://doi.org/10.1186/1471-2180-10-125openalex-snapshot

Pseudomonas aeruginosa inhibits in-vitro Candida biofilm development

inferredcites →https://doi.org/10.1186/2049-2618-2-25openalex-snapshot

The dynamics of a family’s gut microbiota reveal variations on a theme

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Chapter 12: Human Microbiome Analysis

inferredcites →https://doi.org/10.1371/journal.pone.0080433openalex-snapshot

Targeting Tissular Immune Response Improves Diagnostic Performance of Anti-Saccharomyces cerevisiae Antibodies (ASCA) in Crohn’s Disease

inferredcites →https://doi.org/10.1371/journal.ppat.1003996openalex-snapshot

Oral Mycobiome Analysis of HIV-Infected Patients: Identification of Pichia as an Antagonist of Opportunistic Fungi

inferredcites →https://doi.org/10.2174/138945005774912762openalex-snapshot

Fungal Biofilms and Antimycotics

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vegan: Community Ecology Package

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Delinking CARD9 and IL-17: CARD9 Protects against Candida tropicalis Infection through a TNF-α–Dependent, IL-17–Independent Mechanism

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Serratia marcescensis injurious to intestinal epithelial cells

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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inferred← citeshttps://doi.org/10.1016/j.micpath.2022.105690openalex-snapshot

Population structure, susceptibility profile, phenotypic and mating properties of Candida tropicalis isolated from pediatric patients

inferred← citeshttps://doi.org/10.1016/j.molmed.2022.05.006openalex-snapshot

Pathogenic associations between oral and gastrointestinal diseases

inferred← citeshttps://doi.org/10.1016/j.molmet.2025.102289openalex-snapshot

The role of the gut non-bacterial microbiome (virome, mycobiome, archaeome) and its impact on obesity

inferred← citeshttps://doi.org/10.1016/j.mycmed.2021.101164openalex-snapshot

Candida albicans triggers qualitative and temporal responses in gut bacteria

inferred← citeshttps://doi.org/10.1016/j.phrs.2020.104962openalex-snapshot

Inflammatory bowel diseases, the hygiene hypothesis and the other side of the microbiota: Parasites and fungi

inferred← citeshttps://doi.org/10.1016/j.plipres.2024.101291openalex-snapshot

Immunology of bile acids regulated receptors

inferred← citeshttps://doi.org/10.1016/j.ram.2024.12.005openalex-snapshot

Effect of DNA extraction method in gut fungal community assessment

inferred← citeshttps://doi.org/10.1016/j.semcdb.2018.02.026openalex-snapshot

Candida innate immunity at the mucosa

inferred← citeshttps://doi.org/10.1016/j.smim.2023.101757openalex-snapshot

Immunoglobulins at the interface of the gut mycobiota and anti-fungal immunity

inferred← citeshttps://doi.org/10.1016/j.tim.2018.08.009openalex-snapshot

Bowel Biofilms: Tipping Points between a Healthy and Compromised Gut?

inferred← citeshttps://doi.org/10.1016/j.yamp.2023.08.003openalex-snapshot

Molecular Diagnostics for Invasive Fungal Infections: Barriers to Widespread Adoption and Opportunities for Improvement

inferred← citeshttps://doi.org/10.1016/s0001-4079(19)30206-7openalex-snapshot

Importance des micromycètes dans le microbiote intestinal : le modèle Candida albicans.

inferred← citeshttps://doi.org/10.1016/s2666-5247(22)00203-8openalex-snapshot

The gut mycobiome in health, disease, and clinical applications in association with the gut bacterial microbiome assembly

inferred← citeshttps://doi.org/10.1021/acs.estlett.9b00297openalex-snapshot

Response of Fish Gut Microbiota to Toxin-Containing Cyanobacterial Extracts: A Microcosm Study on the Medaka (Oryzias latipes)

inferred← citeshttps://doi.org/10.1038/ni.3780openalex-snapshot

Regulation of inflammation by microbiota interactions with the host

inferred← citeshttps://doi.org/10.1038/nri.2017.55openalex-snapshot

Fungal dysbiosis: immunity and interactions at mucosal barriers

inferred← citeshttps://doi.org/10.1038/s41368-019-0045-2openalex-snapshot

Salivary mycobiome dysbiosis and its potential impact on bacteriome shifts and host immunity in oral lichen planus

inferred← citeshttps://doi.org/10.1038/s41385-022-00536-5openalex-snapshot

Immunosurveillance of Candida albicans commensalism by the adaptive immune system

inferred← citeshttps://doi.org/10.1038/s41396-021-00901-5openalex-snapshot

Priority effects dictate community structure and alter virulence of fungal-bacterial biofilms

inferred← citeshttps://doi.org/10.1038/s41467-017-02522-zopenalex-snapshot

Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes

inferred← citeshttps://doi.org/10.1038/s41467-018-07556-5openalex-snapshot

Molecular diagnostics in medical mycology

inferred← citeshttps://doi.org/10.1038/s41522-023-00433-0openalex-snapshot

Colonic phosphocholine is correlated with Candida tropicalis and promotes diarrhea and pathogen clearance

inferred← citeshttps://doi.org/10.1038/s41522-024-00605-6openalex-snapshot

Microbial melatonin metabolism in the human intestine as a therapeutic target for dysbiosis and rhythm disorders

inferred← citeshttps://doi.org/10.1038/s41522-025-00827-2openalex-snapshot

Intestinal fungal signatures and their impact on immune checkpoint inhibitor efficacy: a multi-cohort meta-analysis

inferred← citeshttps://doi.org/10.1038/s41564-018-0191-xopenalex-snapshot

The type VI secretion system deploys antifungal effectors against microbial competitors

inferred← citeshttps://doi.org/10.1038/s41564-021-00983-zopenalex-snapshot

Mycobiota-induced IgA antibodies regulate fungal commensalism in the gut and are dysregulated in Crohn’s disease

inferred← citeshttps://doi.org/10.1038/s41575-018-0051-4openalex-snapshot

Neuroimmunophysiology of the gut: advances and emerging concepts focusing on the epithelium

inferred← citeshttps://doi.org/10.1038/s41575-019-0121-2openalex-snapshot

The gut mycobiota: insights into analysis, environmental interactions and role in gastrointestinal diseases

inferred← citeshttps://doi.org/10.1038/s41575-023-00816-wopenalex-snapshot

Commensal fungi in intestinal health and disease

inferred← citeshttps://doi.org/10.1038/s41579-025-01163-0openalex-snapshot

Microbiota in inflammatory bowel disease: mechanisms of disease and therapeutic opportunities

inferred← citeshttps://doi.org/10.1038/s41586-022-04502-wopenalex-snapshot

Immune regulation by fungal strain diversity in inflammatory bowel disease

inferred← citeshttps://doi.org/10.1038/s41590-025-02281-wopenalex-snapshot

Microbiota-mediated mechanisms of mucosal immunity across the lifespan

inferred← citeshttps://doi.org/10.1038/s41591-026-04616-yopenalex-snapshot

Antifungal therapy improves microbiome dynamics in inflammatory bowel disease

inferred← citeshttps://doi.org/10.1038/s41598-018-21422-wopenalex-snapshot

Remodeling of the Candida glabrata cell wall in the gastrointestinal tract affects the gut microbiota and the immune response

inferred← citeshttps://doi.org/10.1038/s41598-019-44974-xopenalex-snapshot

DNA extraction and amplicon production strategies deeply inf luence the outcome of gut mycobiome studies

inferred← citeshttps://doi.org/10.1038/s41598-020-68214-9openalex-snapshot

Bacteroides thetaiotaomicron and Lactobacillus johnsonii modulate intestinal inflammation and eliminate fungi via enzymatic hydrolysis of the fungal cell wall

inferred← citeshttps://doi.org/10.1038/s41598-021-90380-7openalex-snapshot

Gut microbiota composition in health-care facility-and community-onset diarrheic patients with Clostridioides difficile infection

inferred← citeshttps://doi.org/10.1038/s41598-022-10548-7openalex-snapshot

The gut fungal and bacterial microbiota in pediatric patients with inflammatory bowel disease introduced to treatment with anti-tumor necrosis factor-α

inferred← citeshttps://doi.org/10.1038/s41598-022-13438-0openalex-snapshot

Mycobiota composition and changes across pregnancy in patients with gestational diabetes mellitus (GDM)

inferred← citeshttps://doi.org/10.1038/s41598-024-54257-9openalex-snapshot

Microbial butyrate capacity is reduced in inflamed mucosa in patients with ulcerative colitis

inferred← citeshttps://doi.org/10.1038/s42003-021-02036-xopenalex-snapshot

Gut mycobiota alterations in patients with COVID-19 and H1N1 infections and their associations with clinical features

inferred← citeshttps://doi.org/10.1038/s42255-025-01420-9openalex-snapshot

Gut mucosal mycobiome profiling in Crohn’s disease uncovers an AMP-mediated anti-inflammatory effect of Cladosporium sphaerospermum

inferred← citeshttps://doi.org/10.1038/s44321-025-00262-yopenalex-snapshot

Interplay between fungal infections and autoimmunity: mechanisms and therapeutic perspectives

inferred← citeshttps://doi.org/10.1039/d2fo02659gopenalex-snapshot

Bifidobacterium bifidum FJSWX19M5 alleviated 2,4,6-trinitrobenzene sulfonic acid (TNBS)-induced chronic colitis by mitigating gut barrier injury and increasing regulatory T cells

inferred← citeshttps://doi.org/10.1042/bcj20240621openalex-snapshot

Interplay of constipation, intestinal barrier dysfunction and fungal exposome in aetiopathogenesis of Parkinson’s disease: hypothesis with supportive data

inferred← citeshttps://doi.org/10.1053/j.gastro.2016.10.012openalex-snapshot

Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches

inferred← citeshttps://doi.org/10.1053/j.gastro.2016.12.004openalex-snapshot

Inflammatory Bowel Disease 2017: Innovations and Changing Paradigms

inferred← citeshttps://doi.org/10.1053/j.gastro.2020.06.100openalex-snapshot

Effects of Intestinal Fungi and Viruses on Immune Responses and Inflammatory Bowel Diseases

inferred← citeshttps://doi.org/10.1053/j.gastro.2023.01.017openalex-snapshot

Modulating the Microbiome for Crohn’s Disease Treatment

inferred← citeshttps://doi.org/10.1053/j.gastro.2025.01.004openalex-snapshot

Gut Microbiome Signature in Predisease Phase of Inflammatory Bowel Disease: Prediction to Pathogenesis to Prevention

inferred← citeshttps://doi.org/10.1080/00365521.2021.1963838openalex-snapshot

The important role of fungi in inflammatory bowel diseases

inferred← citeshttps://doi.org/10.1080/03007995.2020.1838460openalex-snapshot

The association between Candida infection and ankylosing spondylitis: a population-based matched cohort study

inferred← citeshttps://doi.org/10.1080/08927014.2021.2022125openalex-snapshot

Exploring the antibacterial, antibiofilm, and antivirulence activities of tea tree oil-containing nanoemulsion against carbapenem-resistant Serratia marcescens associated infections

inferred← citeshttps://doi.org/10.1080/19490976.2019.1662712openalex-snapshot

Additional Candida albicans administration enhances the severity of dextran sulfate solution induced colitis mouse model through leaky gut-enhanced systemic inflammation and gut-dysbiosis but attenuated by Lactobacillus rhamnosus L34

inferred← citeshttps://doi.org/10.1080/19490976.2021.1930871openalex-snapshot

Inter-kingdom relationships in Crohn’s disease explored using a multi-omics approach

inferred← citeshttps://doi.org/10.1080/19490976.2022.2107866openalex-snapshot

Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease

inferred← citeshttps://doi.org/10.1080/19490976.2022.2121576openalex-snapshot

Host-mycobiome metabolic interactions in health and disease

inferred← citeshttps://doi.org/10.1080/19490976.2022.2123677openalex-snapshot

Altered microbial biogeography in an innate model of colitis

inferred← citeshttps://doi.org/10.1080/19490976.2023.2226916openalex-snapshot

Neglected gut microbiome: interactions of the non-bacterial gut microbiota with enteric pathogens

inferred← citeshttps://doi.org/10.1080/19490976.2023.2252780openalex-snapshot

Targeting microbial quorum sensing: the next frontier to hinder bacterial driven gastrointestinal infections

inferred← citeshttps://doi.org/10.1080/19490976.2023.2276806openalex-snapshot

Alterations in intestinal Archaea composition in pediatric patients with Crohn’s disease based on next-generation sequencing – a pilot study

inferred← citeshttps://doi.org/10.1080/19490976.2024.2327409openalex-snapshot

Stress in the microbiome-immune crosstalk

inferred← citeshttps://doi.org/10.1080/19490976.2024.2414805openalex-snapshot

The role and mechanism of gut-lung axis mediated bidirectional communication in the occurrence and development of chronic obstructive pulmonary disease

inferred← citeshttps://doi.org/10.1080/19490976.2024.2416922openalex-snapshot

Candida tropicalis -derived vitamin B3 exerts protective effects against intestinal inflammation by promoting IL-17A/IL-22-dependent epithelial barrier function

inferred← citeshttps://doi.org/10.1080/19490976.2024.2440111openalex-snapshot

The mycobiome as integral part of the gut microbiome: crucial role of symbiotic fungi in health and disease

inferred← citeshttps://doi.org/10.1080/19490976.2025.2516702openalex-snapshot

Gut microbiota in regulatory T cell generation and function: mechanisms and health implications

inferred← citeshttps://doi.org/10.1080/19490976.2026.2653288openalex-snapshot

Neglected kingdoms: the gut virome, mycobiome and their role in inflammatory bowel disease

inferred← citeshttps://doi.org/10.1080/19490976.2026.2689168openalex-snapshot

Cross-kingdom microbiome interactions along the gut–lung axis: immune–microecological coordination, shared mechanisms, and disease-context dependence in respiratory disorders

inferred← citeshttps://doi.org/10.1080/19490976.2026.2734644openalex-snapshot

The gut microbiota as a regulator of intestinal stem-cell fate: bacterial and fungal control of differentiation and regeneration

inferred← citeshttps://doi.org/10.1080/20002297.2024.2374639openalex-snapshot

Dysbiosis and interactions of the mycobiome and bacteriome in mucosal lesions of erosive and non-erosive oral lichen planus patients

inferred← citeshttps://doi.org/10.1080/21505594.2026.2707757openalex-snapshot

Activity of Lactobacillus gasseri strain LLG1 and its exopolysaccharides in an inflammatory cell model and on Candida albicans proliferation

inferred← citeshttps://doi.org/10.1089/aid.2017.0137openalex-snapshot

A Summary of the Second Annual HIV Microbiome Workshop

inferred← citeshttps://doi.org/10.1093/bib/bbac250openalex-snapshot

Bioinformatics strategies for studying the molecular mechanisms of fungal extracellular vesicles with a focus on infection and immune responses

inferred← citeshttps://doi.org/10.1093/cid/ciaa190openalex-snapshot

Risk Factors for Extended-Spectrum β-lactamase–Producing Enterobacterales Bloodstream Infection Among Solid-Organ Transplant Recipients

inferred← citeshttps://doi.org/10.1093/ecco-jcc/jjaa220openalex-snapshot

The Impact ofNOD2Genetic Variants on the Gut Mycobiota in Crohn’s Disease Patients in Remission and in Individuals Without Gastrointestinal Inflammation

inferred← citeshttps://doi.org/10.1093/ecco-jcc/jjaa252openalex-snapshot

Bacterial and Fungal Profiles as Markers of Infliximab Drug Response in Inflammatory Bowel Disease

inferred← citeshttps://doi.org/10.1093/femsle/fnac098openalex-snapshot

Inflammatory bowel disease-associated adherent-invasive Escherichia coli have elevated host-defense peptide resistance

inferred← citeshttps://doi.org/10.1093/femsre/fuw047openalex-snapshot

Forgotten fungi—the gut mycobiome in human health and disease

inferred← citeshttps://doi.org/10.1093/femsyr/foag029openalex-snapshot

Yeasts in the gastrointestinal tract

inferred← citeshttps://doi.org/10.1093/g3journal/jkab294openalex-snapshot

Global analysis of Saccharomyces cerevisiae growth in mucin

inferred← citeshttps://doi.org/10.1093/ibd/izab343openalex-snapshot

The Neglected Gut Microbiome: Fungi, Protozoa, and Bacteriophages in Inflammatory Bowel Disease

inferred← citeshttps://doi.org/10.1093/ibd/izac156openalex-snapshot

Mycobiome and Inflammatory Bowel Disease: Role in Disease Pathogenesis, Current Approaches and Novel Nutritional-based Therapies

inferred← citeshttps://doi.org/10.1093/ibd/izac284openalex-snapshot

A Novel Probiotic Combination Ameliorates Crohn’s Disease–Like Ileitis by Increasing Short-Chain Fatty Acid Production and Modulating Essential Adaptive Immune Pathways

inferred← citeshttps://doi.org/10.1093/ibd/izad082openalex-snapshot

Alterations in the Fungal Microbiome in Ulcerative Colitis

inferred← citeshttps://doi.org/10.1093/ibd/izad209openalex-snapshot

Targeted Probiotics Against Bacterial-Fungal Biofilms: A New Concept Seems to Bring Us Closer to Microbiome-modulating Therapy for Inflammatory Bowel Disease

inferred← citeshttps://doi.org/10.1093/ibd/izad289openalex-snapshot

Fungal Microbiota Composition in Inflammatory Bowel Disease Patients: Characterization in Different Phenotypes and Correlation With Clinical Activity and Disease Course

inferred← citeshttps://doi.org/10.1093/ibd/izaf178openalex-snapshot

Characterization of Intestinal Mycobiome in Surgical Resections from Inflammatory Bowel Disease Patients: A Deeper Analysis in Complicated Crohn’s Disease Phenotypes

inferred← citeshttps://doi.org/10.1093/ibd/izaf217openalex-snapshot

Gut Mycobiome in Inflammatory Bowel Disease: A Systematic Review of Case-Control Studies

inferred← citeshttps://doi.org/10.1093/ibd/izy060openalex-snapshot

The Artificial Sweetener Splenda Promotes Gut Proteobacteria, Dysbiosis, and Myeloperoxidase Reactivity in Crohn’s Disease–Like Ileitis

inferred← citeshttps://doi.org/10.1093/ibd/izy312openalex-snapshot

Emergent Behavior of IBD-AssociatedEscherichia coliDuring Disease

inferred← citeshttps://doi.org/10.1093/ibd/izy328openalex-snapshot

Gut Microbial Signatures Underline Complicated Crohn’s Disease but Vary Between Cohorts; An In Silico Approach

inferred← citeshttps://doi.org/10.1093/ibd/izz076openalex-snapshot

Challenges in IBD Research: Environmental Triggers

inferred← citeshttps://doi.org/10.1093/jac/dkx451openalex-snapshot

Biofilms and beyond: expanding echinocandin utility

inferred← citeshttps://doi.org/10.1093/nutrit/nuab017openalex-snapshot

Synbiotics improve clinical indicators of ulcerative colitis: systematic review with meta-analysis

inferred← citeshttps://doi.org/10.1094/pbiomes-07-19-0035-rvwopenalex-snapshot

The Rice Microbiome: A Model Platform for Crop Holobiome

inferred← citeshttps://doi.org/10.1094/pbiomes-4-1openalex-snapshot

Full Issue PDF

inferred← citeshttps://doi.org/10.1097/cm9.0000000000000718openalex-snapshot

Advances in the understanding of the intestinal micro-environment and inflammatory bowel disease

inferred← citeshttps://doi.org/10.1097/mcg.0000000000001609openalex-snapshot

Oral Fluconazole Therapy in Patients With Active Ulcerative Colitis Who Have Detectable Candida in the Stool

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