Nichols, Ben and Briola, Anny and Logan, Michael and Havlik, Jaroslav and Mascellani, Anna and Gkikas, Konstantinos and Milling, Simon and Ijaz, Umer Zeeshan and Quince, Christopher and Svolos, Vaios and Russell, Richard K. and Hansen, Richard and Gerasimidis, Konstantinos (2024) Gut metabolome and microbiota signatures predict response to treatment with exclusive enteral nutrition in a prospective study in children with active Crohn’s disease. American Journal of Clinical Nutrition, 119 (4). pp. 885-895. ISSN 0002-9165
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Background:
Predicting response to exclusive enteral nutrition (EEN) in active Crohn’s disease (CD) could lead to therapy personalization and pretreatment optimization.
Objectives:
This study aimed to explore the ability of pretreatment parameters to predict fecal calprotectin (FCal) levels at EEN completion in a prospective study in children with CD.
Methods:
In children with active CD, clinical parameters, dietary intake, cytokines, inflammation-related blood proteomics, and diet-related metabolites, metabolomics and microbiota in feces, were measured before initiation of 8 wk of EEN. Prediction of FCal levels at EEN completion was performed using machine learning. Data are presented with medians (IQR).
Results:
Of 37 patients recruited, 15 responded (FCal < 250 μg/g) to EEN (responders) and 22 did not (nonresponders). Clinical and immunological parameters were not associated with response to EEN. Responders had lesser (μmol/g) butyrate [responders: 13.2 (8.63–18.4) compared with nonresponders: 22.3 (12.0–32.0); P = 0.03], acetate [responders: 49.9 (46.4–68.4) compared with nonresponders: 70.4 (57.0–95.5); P = 0.027], phenylacetate [responders: 0.175 (0.013–0.611) compared with nonresponders: 0.943 (0.438–1.35); P = 0.021], and a higher microbiota richness [315 (269–347) compared with nonresponders: 243 (205–297); P = 0.015] in feces than nonresponders. Responders consumed (portions/1000 kcal/d) more confectionery products [responders: 0.55 (0.38–0.72) compared with nonresponders: 0.19 (0.01–0.38); P = 0.045]. A multicomponent model using fecal parameters, dietary data, and clinical and immunological parameters predicted response to EEN with 78% accuracy (sensitivity: 80%; specificity: 77%; positive predictive value: 71%; negative predictive value: 85%). Higher taxon abundance from Ruminococcaceae, Lachnospiraceae, and Bacteroides and phenylacetate, butyrate, and acetate were the most influential variables in predicting lack of response to EEN.
Conclusions:
We identify microbial signals and diet-related metabolites in feces, which could comprise targets for pretreatment optimization and personalized nutritional therapy in pediatric CD.
Nichols, Ben
Author
Jatkowska, Aleksandra and Gkikas, Konstantinos and Nichols, Ben and Short, Bryn and Rizou, Vasiliki-Konstantina and Kapranos, Panagiotis and Klein Gunnewiek, Jennier and Christina, Edelyn and Svolos, Vaios and Quince, Christopher and Gerasimidis, Konstantinos (2024) Dose-dependent effects of enteral nutrition on the faecal microbiota and short chain fatty acids. Clinical Nutrition, 43 (5). pp. 1200-1207. ISSN 0261-5614
Nichols, Ben and Briola, Anny and Logan, Michael and Havlik, Jaroslav and Mascellani, Anna and Gkikas, Konstantinos and Milling, Simon and Ijaz, Umer Zeeshan and Quince, Christopher and Svolos, Vaios and Russell, Richard K. and Hansen, Richard and Gerasimidis, Konstantinos (2024) Gut metabolome and microbiota signatures predict response to treatment with exclusive enteral nutrition in a prospective study in children with active Crohn’s disease. American Journal of Clinical Nutrition, 119 (4). pp. 885-895. ISSN 0002-9165
See full publications listBriola, Anny
Author
Nichols, Ben and Briola, Anny and Logan, Michael and Havlik, Jaroslav and Mascellani, Anna and Gkikas, Konstantinos and Milling, Simon and Ijaz, Umer Zeeshan and Quince, Christopher and Svolos, Vaios and Russell, Richard K. and Hansen, Richard and Gerasimidis, Konstantinos (2024) Gut metabolome and microbiota signatures predict response to treatment with exclusive enteral nutrition in a prospective study in children with active Crohn’s disease. American Journal of Clinical Nutrition, 119 (4). pp. 885-895. ISSN 0002-9165
See full publications listLogan, Michael
Author
Nichols, Ben and Briola, Anny and Logan, Michael and Havlik, Jaroslav and Mascellani, Anna and Gkikas, Konstantinos and Milling, Simon and Ijaz, Umer Zeeshan and Quince, Christopher and Svolos, Vaios and Russell, Richard K. and Hansen, Richard and Gerasimidis, Konstantinos (2024) Gut metabolome and microbiota signatures predict response to treatment with exclusive enteral nutrition in a prospective study in children with active Crohn’s disease. American Journal of Clinical Nutrition, 119 (4). pp. 885-895. ISSN 0002-9165
See full publications listHavlik, Jaroslav
Author
Nichols, Ben and Briola, Anny and Logan, Michael and Havlik, Jaroslav and Mascellani, Anna and Gkikas, Konstantinos and Milling, Simon and Ijaz, Umer Zeeshan and Quince, Christopher and Svolos, Vaios and Russell, Richard K. and Hansen, Richard and Gerasimidis, Konstantinos (2024) Gut metabolome and microbiota signatures predict response to treatment with exclusive enteral nutrition in a prospective study in children with active Crohn’s disease. American Journal of Clinical Nutrition, 119 (4). pp. 885-895. ISSN 0002-9165
See full publications listMascellani, Anna
Author
Nichols, Ben and Briola, Anny and Logan, Michael and Havlik, Jaroslav and Mascellani, Anna and Gkikas, Konstantinos and Milling, Simon and Ijaz, Umer Zeeshan and Quince, Christopher and Svolos, Vaios and Russell, Richard K. and Hansen, Richard and Gerasimidis, Konstantinos (2024) Gut metabolome and microbiota signatures predict response to treatment with exclusive enteral nutrition in a prospective study in children with active Crohn’s disease. American Journal of Clinical Nutrition, 119 (4). pp. 885-895. ISSN 0002-9165
See full publications listGkikas, Konstantinos
Author
Jatkowska, Aleksandra and Gkikas, Konstantinos and Nichols, Ben and Short, Bryn and Rizou, Vasiliki-Konstantina and Kapranos, Panagiotis and Klein Gunnewiek, Jennier and Christina, Edelyn and Svolos, Vaios and Quince, Christopher and Gerasimidis, Konstantinos (2024) Dose-dependent effects of enteral nutrition on the faecal microbiota and short chain fatty acids. Clinical Nutrition, 43 (5). pp. 1200-1207. ISSN 0261-5614
Nichols, Ben and Briola, Anny and Logan, Michael and Havlik, Jaroslav and Mascellani, Anna and Gkikas, Konstantinos and Milling, Simon and Ijaz, Umer Zeeshan and Quince, Christopher and Svolos, Vaios and Russell, Richard K. and Hansen, Richard and Gerasimidis, Konstantinos (2024) Gut metabolome and microbiota signatures predict response to treatment with exclusive enteral nutrition in a prospective study in children with active Crohn’s disease. American Journal of Clinical Nutrition, 119 (4). pp. 885-895. ISSN 0002-9165
See full publications listMilling, Simon
Author
Milling, Simon and Ijaz, Umer Zeeshan and Venieri, Danae and Christidis, George E. and Rattray, Nicholas J. W. and Gounaki, Iosifina and Andrusaite, Anna and Hareendran, Aravind and Knapp, Charles W. and Jones, Alexander X. and Photos-Jones, Effie (2024) Beneficial modulation of the gut microbiome by leachates of Penicillium purpurogenum in the presence of clays: A model for the preparation and efficacy of historical Lemnian Earth. PLoS ONE, 19 (12): e0313090. ISSN 1932-6203
MacDonald, Lucy and Elmesmari, Aziza and Somma, Domenico and Frew, Jack and Di Mario, Clara and Madhu, Roopa and Paoletti, Audrey and Simakou, Theodoros and Hardy, Olympia M. and Tolusso, Barbara and Campobasso, Denise and Perniola, Simone and Gessi, Marco and Gigante, Maria Rita and Petricca, Luca and Bruno, Dario and Coletto, Lavinia Agra and Benvenuto, Roberta and Isaacs, John D. and Filby, Andrew and McDonald, David and Sim, Jasmine P.X. and Jamieson, Nigel and Wei, Kevin and D’Agostino, Maria Antonietta and Millar, Neal L. and Milling, Simon and McSharry, Charles and Gremese, Elisa and Affleck, Karen and Baker, Kenneth F. and McInnes, Iain B. and Otto, Thomas D. and Korsunsky, Ilya and Alivernini, Stefano and Kurowska-Stolarska, Mariola (2024) Synovial tissue myeloid dendritic cell subsets exhibit distinct tissue-niche localization and function in health and rheumatoid arthritis. Immunity, 57 (12). 2843-2862.e12. ISSN 1074-7613
Nichols, Ben and Briola, Anny and Logan, Michael and Havlik, Jaroslav and Mascellani, Anna and Gkikas, Konstantinos and Milling, Simon and Ijaz, Umer Zeeshan and Quince, Christopher and Svolos, Vaios and Russell, Richard K. and Hansen, Richard and Gerasimidis, Konstantinos (2024) Gut metabolome and microbiota signatures predict response to treatment with exclusive enteral nutrition in a prospective study in children with active Crohn’s disease. American Journal of Clinical Nutrition, 119 (4). pp. 885-895. ISSN 0002-9165
See full publications listIjaz, Umer
Author
Cholet, Fabien and Vignola, Marta and Quinn, Dominic and Ijaz, Umer Z. and Sloan, William T. and Smith, Cindy J. (2025) Microbial ecology of drinking water biofiltration based on 16S rRNA sequencing: a meta-analysis. Water Research, 281: 123684. ISSN 0043-1354
Saleem, Farrukh and Ameer, Aqsa and Afzal, Farhan and Usman, Muhammad and Irshad, Hamid and Sattar, Sadia and Ijaz, Umer Zeeshan and Javed, Sundus (2025) A cross-sectional survey of poultry management systems, practices and antimicrobial use in relation to disease outbreak in Pakistan. BMC Research Notes, 18: 144. ISSN 1756-0500
Badar, Ayesha and Aqueel, Rhea and Nawaz, Ali and Ijaz, Umer Zeeshan and Malik, Kauser Abdulla (2025) Microbiota transplantation for Cotton Leaf Curl Disease suppression - core microbiome and transcriptome dynamics. Communications Biology, 8 (1): 380. ISSN 2399-3642
See full publications listQuince, Christopher
Author
Jatkowska, Aleksandra and Gkikas, Konstantinos and Nichols, Ben and Short, Bryn and Rizou, Vasiliki-Konstantina and Kapranos, Panagiotis and Klein Gunnewiek, Jennier and Christina, Edelyn and Svolos, Vaios and Quince, Christopher and Gerasimidis, Konstantinos (2024) Dose-dependent effects of enteral nutrition on the faecal microbiota and short chain fatty acids. Clinical Nutrition, 43 (5). pp. 1200-1207. ISSN 0261-5614
Nichols, Ben and Briola, Anny and Logan, Michael and Havlik, Jaroslav and Mascellani, Anna and Gkikas, Konstantinos and Milling, Simon and Ijaz, Umer Zeeshan and Quince, Christopher and Svolos, Vaios and Russell, Richard K. and Hansen, Richard and Gerasimidis, Konstantinos (2024) Gut metabolome and microbiota signatures predict response to treatment with exclusive enteral nutrition in a prospective study in children with active Crohn’s disease. American Journal of Clinical Nutrition, 119 (4). pp. 885-895. ISSN 0002-9165
See full publications listSvolos, Vaios
Author
Jatkowska, Aleksandra and Gkikas, Konstantinos and Nichols, Ben and Short, Bryn and Rizou, Vasiliki-Konstantina and Kapranos, Panagiotis and Klein Gunnewiek, Jennier and Christina, Edelyn and Svolos, Vaios and Quince, Christopher and Gerasimidis, Konstantinos (2024) Dose-dependent effects of enteral nutrition on the faecal microbiota and short chain fatty acids. Clinical Nutrition, 43 (5). pp. 1200-1207. ISSN 0261-5614
Nichols, Ben and Briola, Anny and Logan, Michael and Havlik, Jaroslav and Mascellani, Anna and Gkikas, Konstantinos and Milling, Simon and Ijaz, Umer Zeeshan and Quince, Christopher and Svolos, Vaios and Russell, Richard K. and Hansen, Richard and Gerasimidis, Konstantinos (2024) Gut metabolome and microbiota signatures predict response to treatment with exclusive enteral nutrition in a prospective study in children with active Crohn’s disease. American Journal of Clinical Nutrition, 119 (4). pp. 885-895. ISSN 0002-9165
See full publications listRussell, Richard K.
Author
Koci, Orges and Russell, Richard K. and Shaikh, M. Guftar and Edwards, Christine and Gerasimidis, Konstantinos and Ijaz, Umer Zeeshan (2024) CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets. Microbiome, 12 (1): 117. ISSN 2049-2618
Nichols, Ben and Briola, Anny and Logan, Michael and Havlik, Jaroslav and Mascellani, Anna and Gkikas, Konstantinos and Milling, Simon and Ijaz, Umer Zeeshan and Quince, Christopher and Svolos, Vaios and Russell, Richard K. and Hansen, Richard and Gerasimidis, Konstantinos (2024) Gut metabolome and microbiota signatures predict response to treatment with exclusive enteral nutrition in a prospective study in children with active Crohn’s disease. American Journal of Clinical Nutrition, 119 (4). pp. 885-895. ISSN 0002-9165
See full publications listHansen, Richard
Author
Nichols, Ben and Briola, Anny and Logan, Michael and Havlik, Jaroslav and Mascellani, Anna and Gkikas, Konstantinos and Milling, Simon and Ijaz, Umer Zeeshan and Quince, Christopher and Svolos, Vaios and Russell, Richard K. and Hansen, Richard and Gerasimidis, Konstantinos (2024) Gut metabolome and microbiota signatures predict response to treatment with exclusive enteral nutrition in a prospective study in children with active Crohn’s disease. American Journal of Clinical Nutrition, 119 (4). pp. 885-895. ISSN 0002-9165
See full publications listGerasimidis, Konstantinos
Author
Bibi, Sara and Kerbiriou, Caroline and Uzma and Mckirdy, Shona and Kostrytsia, Anastasiia and Rasheed, Hifza and Eqani, Syed Ali Musstjab Akber Shah and Gerasimidis, Konstantinos and Nurulain, Syed Muhammad and Ijaz, Umer Zeeshan (2024) Gut microbiome and function are altered for individuals living in high fluoride concentration areas in Pakistan. Ecotoxicology and Environmental Safety, 284: 116959. ISSN 0147-6513
Koci, Orges and Russell, Richard K. and Shaikh, M. Guftar and Edwards, Christine and Gerasimidis, Konstantinos and Ijaz, Umer Zeeshan (2024) CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets. Microbiome, 12 (1): 117. ISSN 2049-2618
Jatkowska, Aleksandra and Gkikas, Konstantinos and Nichols, Ben and Short, Bryn and Rizou, Vasiliki-Konstantina and Kapranos, Panagiotis and Klein Gunnewiek, Jennier and Christina, Edelyn and Svolos, Vaios and Quince, Christopher and Gerasimidis, Konstantinos (2024) Dose-dependent effects of enteral nutrition on the faecal microbiota and short chain fatty acids. Clinical Nutrition, 43 (5). pp. 1200-1207. ISSN 0261-5614
See full publications listAvailable under License Creative Commons Attribution.
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