Exploration of fecal microbiota in newly diagnosed patients with inflammatory bowel disease using shotgun metagenomics Article Swipe

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Macarena Orejudo , Manuel J. Gómez , Sabino Riestra , Montserrat Rivero , Ana Gutiérrez , Iago Rodríguez‐Lago , Luis Fernández‐Salazar , Daniel Ceballos , J M Benítez , Mariam Aguas , Iria Bastón‐Rey , Fernando Bermejo , María José Casanova , Rufo H Lorente-Poyatos , Yolanda Ber , Daniel Ginard , María Esteve , Ruth de Francisco , María José Calero García , Rubén Francés , Ainhoa Rodríguez , Noelia Alcaide Suárez , Elena Guerra del Río , Pilar Soto , Pilar Nos , Manuel Barreiro‐de Acosta , Iván Guerra , Daniel Hervías Cruz , Manuel Domínguez Cajal , Vanesa Royo , Montserrat Aceituno , Laila Aldars‐García , Ana Garre , Cristina Ramírez , Irene Soleto , Ina Schuppe-Koistinen , Lars Engstrand , Montserrat Baldán‐Martín , Fátima Sánchez‐Cabo , Javier P. Gisbert , María Chaparro ·

YOU? · · 2025 · Open Access · · DOI: https://doi.org/10.3389/fcimb.2025.1595884

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.

Related Topics

Ulcerative Colitis

Gut Microbiota

Inflammatory Bowel Disease

Concepts

Faecalibacterium prausnitzii Metagenomics Dysbiosis Ulcerative colitis Gut flora Inflammatory bowel disease Crohn's disease Microbiome Feces Biology Gastroenterology Shotgun sequencing Eubacterium Bifidobacterium Internal medicine Disease Immunology Microbiology Medicine Lactobacillus Bacteria Bioinformatics Genetics DNA sequencing DNA Gene

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Type: article
Language: en
Landing Page: https://doi.org/10.3389/fcimb.2025.1595884
PDF: https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2025.1595884/pdf
OA Status: gold
Cited By: 1
References: 82
Related Works: 10
OpenAlex ID: https://openalex.org/W4411913987

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OpenAlex ID: https://openalex.org/W4411913987

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DOI: https://doi.org/10.3389/fcimb.2025.1595884

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Title: Exploration of fecal microbiota in newly diagnosed patients with inflammatory bowel disease using shotgun metagenomics

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Type: article

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Language: en

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Publication year: 2025

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Publication date: 2025-07-01

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Authors: Macarena Orejudo, Manuel J. Gómez, Sabino Riestra, Montserrat Rivero, Ana Gutiérrez, Iago Rodríguez‐Lago, Luis Fernández‐Salazar, Daniel Ceballos, J M Benítez, Mariam Aguas, Iria Bastón‐Rey, Fernando Bermejo, María José Casanova, Rufo H Lorente-Poyatos, Yolanda Ber, Daniel Ginard, María Esteve, Ruth de Francisco, María José Calero García, Rubén Francés, Ainhoa Rodríguez, Noelia Alcaide Suárez, Elena Guerra del Río, Pilar Soto, Pilar Nos, Manuel Barreiro‐de Acosta, Iván Guerra, Daniel Hervías Cruz, Manuel Domínguez Cajal, Vanesa Royo, Montserrat Aceituno, Laila Aldars‐García, Ana Garre, Cristina Ramírez, Irene Soleto, Ina Schuppe-Koistinen, Lars Engstrand, Montserrat Baldán‐Martín, Fátima Sánchez‐Cabo, Javier P. Gisbert, María Chaparro

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Landing page: https://doi.org/10.3389/fcimb.2025.1595884

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PDF URL: https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2025.1595884/pdf

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Concepts: Faecalibacterium prausnitzii, Metagenomics, Dysbiosis, Ulcerative colitis, Gut flora, Inflammatory bowel disease, Crohn's disease, Microbiome, Feces, Biology, Gastroenterology, Shotgun sequencing, Eubacterium, Bifidobacterium, Internal medicine, Disease, Immunology, Microbiology, Medicine, Lactobacillus, Bacteria, Bioinformatics, Genetics, DNA sequencing, DNA, Gene

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Cited by: 1

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