Fecal microbiome of patients with ulcerative colitis reflects their phenotype and inflammatory level
Abstract
Inflammatory bowel diseases affect ever-increasing numbers of individuals worldwide. Alterations of the intestinal microbiome were reported for Crohn’s disease and at relapse in Ulcerative Colitis (UC); they were not clearly detected in UC at remission. Here we report the characterization of the microbiome by quantitative metagenomics in a cohort of 121 individuals, composed of 65 UC adult patients in remission and 56 healthy controls. A cross-sectional comparison revealed substantial microbiome differences, patients in remission having lower microbiome richness and paucity of the Ruminococcus species driven enterotype. The observed microbiome alterations allowed robust classification of patients by intestinal species abundance, yielding an area under the curve (AUC) of 0.87 in a Receiver-Operator Characteristic (ROC) analysis. Loss of richness was linked to an aggressive UC phenotype and to the importance of past relapses; it was associated with a worse IBD quality of life score (IBDQ-36). Unexpectedly, onset of inflammatory bouts, as assessed by white blood cell count and fecal calprotectin levels, was associated with higher richness; in a longitudinal study of patients at high risk of disease flare, we observed a link between increasing gut microbiome richness over time and calprotectin level, in turn related to clinical inflammatory response and relapse.
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BibTeX
@article{maziers2026fecal,
title = {{Fecal microbiome of patients with ulcerative colitis reflects their phenotype and inflammatory level}},
author = {Nicolas Maziers and Emmanuelle Le Chatelier and Florian Plaza Oñate and Sébastien Fromentin and Florence Thirion and Nicolas Pons and Natalia Borruel and Francesc Casellas and Antonio Torrejon and Virginia Robles-Alonso and Chaysavanh Manichanh and Encarna Varela and Muriel Derrien and Patrick Veiga and Raish Oozeer and Shinichi Sunagawa and Vincent Lombard and Nicolas Terrapon and Bernard Henrissat and Francisco Guarner and S Dusko Ehrlich and Mathieu Almeida and Maria Antolin and François Artiguenave and Manimozhiyan Arumugam and Jean-Michel Batto and Marcelo Bertalan and Hervé Blottière and Peer Bork and Christian Brechot and Thomas Bruls and Søren Brunak and Kristoffer Burgdorf and Paul Igor Costea and Antonella Cultrone and Willem de Vos and Christine Delorme and Gérard Denariaz and Rozenn Dervyn and Joel Dore and Gwen Falony and Qiang Feng and Kristoffer Forslund and Niels Grapup and Eric Guedon and Valborg Gudmundsdottir and Florence Haimet and Torben Hansen and Rajna Hercog and Falk Hildebrand and Alexandre Jamet and Torben Jørgensen and Agnieska Junker and Catherine Juste and Ghalia Khaci and Sean Kennedy and Michiel Kleerebezem and Jan Knoll and Karsten Kristiansen and Jens Roat Kultima},
journal = {Scientific Reports},
year = {2026},
month = may,
doi = {10.1038/s41598-026-44895-6},
url = {https://amu.hal.science/hal-05660442v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Fecal microbiome of patients with ulcerative colitis reflects their phenotype and inflammatory level
AU - Nicolas Maziers
AU - Emmanuelle Le Chatelier
AU - Florian Plaza Oñate
AU - Sébastien Fromentin
AU - Florence Thirion
AU - Nicolas Pons
AU - Natalia Borruel
AU - Francesc Casellas
AU - Antonio Torrejon
AU - Virginia Robles-Alonso
AU - Chaysavanh Manichanh
AU - Encarna Varela
AU - Muriel Derrien
AU - Patrick Veiga
AU - Raish Oozeer
AU - Shinichi Sunagawa
AU - Vincent Lombard
AU - Nicolas Terrapon
AU - Bernard Henrissat
AU - Francisco Guarner
AU - S Dusko Ehrlich
AU - Mathieu Almeida
AU - Maria Antolin
AU - François Artiguenave
AU - Manimozhiyan Arumugam
AU - Jean-Michel Batto
AU - Marcelo Bertalan
AU - Hervé Blottière
AU - Peer Bork
AU - Christian Brechot
AU - Thomas Bruls
AU - Søren Brunak
AU - Kristoffer Burgdorf
AU - Paul Igor Costea
AU - Antonella Cultrone
AU - Willem de Vos
AU - Christine Delorme
AU - Gérard Denariaz
AU - Rozenn Dervyn
AU - Joel Dore
AU - Gwen Falony
AU - Qiang Feng
AU - Kristoffer Forslund
AU - Niels Grapup
AU - Eric Guedon
AU - Valborg Gudmundsdottir
AU - Florence Haimet
AU - Torben Hansen
AU - Rajna Hercog
AU - Falk Hildebrand
AU - Alexandre Jamet
AU - Torben Jørgensen
AU - Agnieska Junker
AU - Catherine Juste
AU - Ghalia Khaci
AU - Sean Kennedy
AU - Michiel Kleerebezem
AU - Jan Knoll
AU - Karsten Kristiansen
AU - Jens Roat Kultima
PY - 2026
DA - 2026/05/19
JO - Scientific Reports
DO - 10.1038/s41598-026-44895-6
UR - https://amu.hal.science/hal-05660442v1
AB - Inflammatory bowel diseases affect ever-increasing numbers of individuals worldwide. Alterations of the intestinal microbiome were reported for Crohn’s disease and at relapse in Ulcerative Colitis (UC); they were not clearly detected in UC at remission. Here we report the characterization of the microbiome by quantitative metagenomics in a cohort of 121 individuals, composed of 65 UC adult patients in remission and 56 healthy controls. A cross-sectional comparison revealed substantial microbiome differences, patients in remission having lower microbiome richness and paucity of the Ruminococcus species driven enterotype. The observed microbiome alterations allowed robust classification of patients by intestinal species abundance, yielding an area under the curve (AUC) of 0.87 in a Receiver-Operator Characteristic (ROC) analysis. Loss of richness was linked to an aggressive UC phenotype and to the importance of past relapses; it was associated with a worse IBD quality of life score (IBDQ-36). Unexpectedly, onset of inflammatory bouts, as assessed by white blood cell count and fecal calprotectin levels, was associated with higher richness; in a longitudinal study of patients at high risk of disease flare, we observed a link between increasing gut microbiome richness over time and calprotectin level, in turn related to clinical inflammatory response and relapse.
SN - 2045-2322
ER -