ArticleFrontiers in cellular and infection microbiology2025
Exploration of fecal microbiota in newly diagnosed patients with inflammatory bowel disease using shotgun metagenomics.
Article in Frontiers in cellular and infection microbiology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers, 1 of them a synthesis that pooled it.
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Who cites it
8 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Specific alterations in the gut microbiome and metabolome across disease locations of Crohn's disease: a systematic review.BMC gastroenterology · 2026Pooled it
- Microbial and functional shifts between flare and remission in a single-center cohort of children with inflammatory bowel disease.World journal of clinical pediatrics · 2026Article
- Multi-Dimensional Mechanisms and Druggability Optimization Strategies of Active Ingredients from Traditional Chinese Medicine in the Treatment of Ulcerative Colitis.Pharmaceuticals (Basel, Switzerland) · 2026Review
- Gut microbial interaction networks control autoimmunity to neuroretina.Research square · 2026Article
- Translating Gut Microbiota into Diagnostics: A Multidimensional Approach for the Diagnosis of Inflammatory Bowel Disease.Gut and liver · 2026Review
- Gut microbiota dysbiosis and immune responses: insights from IgA nephropathy and inflammatory bowel disease.Frontiers in immunology · 2026Review
- Gut microbial interaction networks control autoimmunity to neuroretina.bioRxiv : the preprint server for biology · 2025Article
- An overview of basic pathophysiological interactions between gut bacteria and their host.Frontiers in nutrition · 2025Review
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Authors and funding
41 authors.
Funding
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Abstract
Introduction: Dysbiosis is a key mechanism in inflammatory bowel disease (IBD) pathophysiology. Previous microbiota studies in IBD generally have involved patients treated with immunosuppressive agents, which can affect the results. We aimed to elucidate the fecal microbiota composition in newly diagnosed treatment-naïve IBD patients. Methods: Microbiota from stool samples were investigated using shotgun metagenomics sequencing and subsequent bioinformatics analysis. Results: A total of 103 patients with Crohn's disease (CD), 144 with ulcerative colitis (UC), and 49 healthy controls (HC) were included. CD patients had significantly lower species-level diversity than those with UC and HC. CD subgroups with Ileocolonic location and stricturing behavior showed reduced diversity compared to HC. A negative correlation was observed between endoscopic severity and microbial diversity in CD patients. UC patients had similar microbial diversity to HC, which was unaffected by disease activity. Taxonomic abundance analysis revealed a tendency towards a higher relative abundance of Escherichia coli and a lower relative abundance of Faecalibacterium prausnitzii in IBD patients compared to HC. However, the most significant differences in these patients compared to HC were observed in less abundant species, such as Toxoplasma gondii, Gemella morbillorum, and several species of the Adlercreutzia genera. Functional analysis in these patients highlighted changes in carbohydrate and nucleotide pathways. Discussion: Our data suggest that newly diagnosed CD patients show significant microbiota composition disparities compared to UC patients and HC. Microbiota differences in these patients are linked to dysbiosis, characterized by a reduction in beneficial genera such as Gemella and Adlercreutzia, and a rise in pathogenic species.
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