Microbiome gut community structure and functionality are associated with symptom severity in non-responsive celiac disease patients undergoing a gluten-free diet
ABSTRACT Non-responsive celiac disease (NRCD) challenges clinicians due to persistent symptoms despite a gluten-free diet (GFD). We present a cross-sectional pilot study including 39 NRCD patients to describe the underlying mechanisms contributing to symptom persistence by integrating different leve...
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American Society for Microbiology
2025-07-01
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| Series: | mSystems |
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| Online Access: | https://journals.asm.org/doi/10.1128/msystems.00143-25 |
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| author | Laura Judith Marcos-Zambrano Blanca Lacruz-Pleguezuelos Elena Aguilar-Aguilar Helena Marcos-Pasero Alberto Valdés Viviana Loria-Kohen Alejandro Cifuentes Ana Ramirez de Molina Alberto Diaz-Ruiz Vera Pancaldi Enrique Carrillo de Santa Pau |
| author_facet | Laura Judith Marcos-Zambrano Blanca Lacruz-Pleguezuelos Elena Aguilar-Aguilar Helena Marcos-Pasero Alberto Valdés Viviana Loria-Kohen Alejandro Cifuentes Ana Ramirez de Molina Alberto Diaz-Ruiz Vera Pancaldi Enrique Carrillo de Santa Pau |
| author_sort | Laura Judith Marcos-Zambrano |
| collection | DOAJ |
| description | ABSTRACT Non-responsive celiac disease (NRCD) challenges clinicians due to persistent symptoms despite a gluten-free diet (GFD). We present a cross-sectional pilot study including 39 NRCD patients to describe the underlying mechanisms contributing to symptom persistence by integrating different levels of data (fecal shotgun metagenomics, mucosal integrity markers, and metabolomic profiles) and using microbial networks to unravel the community structure of the patient’s microbiome. Two distinct clusters of patients were identified based on clinical and demographic variables not influenced by gluten consumption. Cluster 1, labeled “Low-grade symptoms,” displayed milder symptoms and lower inflammatory markers and a fragmented microbial network characterized by high modularity and a reliance on localized hubs, suggesting a microbial community under stress but capable of maintaining limited functionality. Cluster 2, named “High-grade symptoms,” exhibited more severe symptoms, elevated inflammatory markers, and a more connected but antagonistic microbial network with a greater number of keystone taxa, including taxa associated with Th17 activation and inflammation. In contrast, the control network, representing asymptomatic treated celiac disease (tCD) patients, was highly interconnected, resilient, and cooperative, with a robust structure maintained even under simulated disruptions. Metabolomic analysis revealed differential metabolites between clusters, particularly those involved in amino acid metabolism pathways and microbial-derived metabolites such as indolelactic acid and mannitol, which were associated with symptom severity. This study identifies NRCD subgroups based on the gut microbiome and metabolic signatures associated with clinical manifestations, highlighting variations in microbial network stability and metabolite profiles as contributors to symptom persistence and potential therapeutic targets.IMPORTANCECeliac disease (CD) is a chronic immune-mediated systemic disorder caused by consuming gluten in genetically susceptible individuals. There is currently no cure for CD, and the most effective treatment is maintaining a strict, lifelong gluten-free diet (GFD). This nutritional therapy aims to prevent the immune reaction triggered by gluten and promote the healing of the intestinal lining, resolving the clinical, serological, and histological abnormalities within 6–12 months. However, up to 30% of patients may continue to experience symptoms or exhibit laboratory abnormalities or intestinal inflammation suggestive of active CD, despite following a GFD. This challenge, which encompasses various diagnoses, is known as nonresponsive celiac disease (NRCD). In this study, we explored the role of intestinal microbiota in causing NRCD, finding an association between the persistence of symptoms and changes in mucosal integrity biomarkers, with different gut microbiome structures among NRCD patients, indicating a significant role of the microbiome in NRCD. |
| format | Article |
| id | doaj-art-e839791b8eed4fce8cb11380966c05f4 |
| institution | DOAJ |
| issn | 2379-5077 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mSystems |
| spelling | doaj-art-e839791b8eed4fce8cb11380966c05f42025-08-20T03:08:25ZengAmerican Society for MicrobiologymSystems2379-50772025-07-0110710.1128/msystems.00143-25Microbiome gut community structure and functionality are associated with symptom severity in non-responsive celiac disease patients undergoing a gluten-free dietLaura Judith Marcos-Zambrano0Blanca Lacruz-Pleguezuelos1Elena Aguilar-Aguilar2Helena Marcos-Pasero3Alberto Valdés4Viviana Loria-Kohen5Alejandro Cifuentes6Ana Ramirez de Molina7Alberto Diaz-Ruiz8Vera Pancaldi9Enrique Carrillo de Santa Pau10Computational Biology Group, IMDEA Food, CEI UAM+CSIC, Madrid, SpainComputational Biology Group, IMDEA Food, CEI UAM+CSIC, Madrid, SpainGENYAL Platform, IMDEA Food, CEI UAM+CSIC, Madrid, SpainGENYAL Platform, IMDEA Food, CEI UAM+CSIC, Madrid, SpainFoodomics Lab, Institute of Food Science Research (CIAL, CSIC), Madrid, SpainGENYAL Platform, IMDEA Food, CEI UAM+CSIC, Madrid, SpainFoodomics Lab, Institute of Food Science Research (CIAL, CSIC), Madrid, SpainGENYAL Platform, IMDEA Food, CEI UAM+CSIC, Madrid, SpainLaboratory of Cellular and Molecular Gerontology, IMDEA Food, CEI UAM+CSIC, Madrid, SpainCentre de Recherches en Cancérologie de Toulouse, CRCT, Université de Toulouse, Inserm, CNRS, Toulouse, Occitanie, FranceComputational Biology Group, IMDEA Food, CEI UAM+CSIC, Madrid, SpainABSTRACT Non-responsive celiac disease (NRCD) challenges clinicians due to persistent symptoms despite a gluten-free diet (GFD). We present a cross-sectional pilot study including 39 NRCD patients to describe the underlying mechanisms contributing to symptom persistence by integrating different levels of data (fecal shotgun metagenomics, mucosal integrity markers, and metabolomic profiles) and using microbial networks to unravel the community structure of the patient’s microbiome. Two distinct clusters of patients were identified based on clinical and demographic variables not influenced by gluten consumption. Cluster 1, labeled “Low-grade symptoms,” displayed milder symptoms and lower inflammatory markers and a fragmented microbial network characterized by high modularity and a reliance on localized hubs, suggesting a microbial community under stress but capable of maintaining limited functionality. Cluster 2, named “High-grade symptoms,” exhibited more severe symptoms, elevated inflammatory markers, and a more connected but antagonistic microbial network with a greater number of keystone taxa, including taxa associated with Th17 activation and inflammation. In contrast, the control network, representing asymptomatic treated celiac disease (tCD) patients, was highly interconnected, resilient, and cooperative, with a robust structure maintained even under simulated disruptions. Metabolomic analysis revealed differential metabolites between clusters, particularly those involved in amino acid metabolism pathways and microbial-derived metabolites such as indolelactic acid and mannitol, which were associated with symptom severity. This study identifies NRCD subgroups based on the gut microbiome and metabolic signatures associated with clinical manifestations, highlighting variations in microbial network stability and metabolite profiles as contributors to symptom persistence and potential therapeutic targets.IMPORTANCECeliac disease (CD) is a chronic immune-mediated systemic disorder caused by consuming gluten in genetically susceptible individuals. There is currently no cure for CD, and the most effective treatment is maintaining a strict, lifelong gluten-free diet (GFD). This nutritional therapy aims to prevent the immune reaction triggered by gluten and promote the healing of the intestinal lining, resolving the clinical, serological, and histological abnormalities within 6–12 months. However, up to 30% of patients may continue to experience symptoms or exhibit laboratory abnormalities or intestinal inflammation suggestive of active CD, despite following a GFD. This challenge, which encompasses various diagnoses, is known as nonresponsive celiac disease (NRCD). In this study, we explored the role of intestinal microbiota in causing NRCD, finding an association between the persistence of symptoms and changes in mucosal integrity biomarkers, with different gut microbiome structures among NRCD patients, indicating a significant role of the microbiome in NRCD.https://journals.asm.org/doi/10.1128/msystems.00143-25microbiomemetabolomeceliac diseasegluten-free dietco-occurrence networkssymptom association |
| spellingShingle | Laura Judith Marcos-Zambrano Blanca Lacruz-Pleguezuelos Elena Aguilar-Aguilar Helena Marcos-Pasero Alberto Valdés Viviana Loria-Kohen Alejandro Cifuentes Ana Ramirez de Molina Alberto Diaz-Ruiz Vera Pancaldi Enrique Carrillo de Santa Pau Microbiome gut community structure and functionality are associated with symptom severity in non-responsive celiac disease patients undergoing a gluten-free diet mSystems microbiome metabolome celiac disease gluten-free diet co-occurrence networks symptom association |
| title | Microbiome gut community structure and functionality are associated with symptom severity in non-responsive celiac disease patients undergoing a gluten-free diet |
| title_full | Microbiome gut community structure and functionality are associated with symptom severity in non-responsive celiac disease patients undergoing a gluten-free diet |
| title_fullStr | Microbiome gut community structure and functionality are associated with symptom severity in non-responsive celiac disease patients undergoing a gluten-free diet |
| title_full_unstemmed | Microbiome gut community structure and functionality are associated with symptom severity in non-responsive celiac disease patients undergoing a gluten-free diet |
| title_short | Microbiome gut community structure and functionality are associated with symptom severity in non-responsive celiac disease patients undergoing a gluten-free diet |
| title_sort | microbiome gut community structure and functionality are associated with symptom severity in non responsive celiac disease patients undergoing a gluten free diet |
| topic | microbiome metabolome celiac disease gluten-free diet co-occurrence networks symptom association |
| url | https://journals.asm.org/doi/10.1128/msystems.00143-25 |
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