Precision therapy in Crohn’s disease: why the microbiome should be part of the comparison

Precision therapy in Crohn’s disease: why the microbiome should be part of the comparison

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Crohn’s disease (CD) is a chronic, immune-mediated inflammatory condition of the gastrointestinal tract. Etiology is multifactorial, with the current hypotheses that propagates that CD will result from a Deviating immune response on the intestinal microbiota in genetically sensitive individuals. In recent decades, countless studies have reported changes in the intestinal microbiome of CD patients, so that consistently raises the question of whether these changes are a cause or consequence of illness. Recent evidence now suggests that such microbial changes can in fact precede the start of the disease, as mandatory demonstrated in a large cohort of Canadian first degree relatives of CD patients. Researchers of the Crohn’s and Colitis Canada -Genetic, Environmental, Microbial project assembled a substantial data set of Fecale 16S RRNA -GENSEVencing and developed a On machine-learning-based microbiomo risk score that could be accurate Predict the development of CD up to five years before the clinical diagnosis.

Despite this growing recognition of the potential role of the microbiome in initiating diseases, CD patients are usually still treated with medicines that damp or modulate an excessive or different immune response. As recently emphasized in a commentary in GastroenterologyAlthough the etiological triad of inflammatory bowel disorders (ie genetics, the environment and the immune system) is well established, all current approved therapies focus on the immune system. Now that our understanding of the microbiome has been considerably expanded, there is a possibility to use this knowledge; Not necessarily to replace immune -oriented therapies, but Improve their effectiveness.

Immuungerichte behandelingen omvatten anti-tumor necrosis factor-alpha (anti-TNFa) antilichamen zoals infliximab en adalimumab, het anti-integrine-antilichaam vedolizumab, dat zich richt op de α4β7 integrine en ustekinumab, die de p40-subunit gedeeld door interleuin (il)-en il-23. These therapies often cause shifts in the intestinal microbial compositionas documented in different prospective studies in recent years. In particular, anti-TNFA resources have been extensively studied in relation to the microbiome, where various studies follow fecal microbial profiles before, during and after treatment. These studies often compare patients who achieve clinical remission with those who do not, where differences in microbial dynamics are emphasized. Especially six years ago, Aden and colleagues showed that the The efficacy of anti-TNFA therapy is associated with the metabolic functions of the intestinal microbiotaSuggesting a possible role for microbial activity in modulating the treatment response.

Despite the availability of advanced biological therapies, treatment response rates remain in CD suboptimal. About 40% of patients do not respond or lose responsiveness over timeunderlines the urgent need for reliable biomarkers to guide therapeutic decisions. This challenge has recently been tackled in one Epigenoom-wide Association Study Led by researchers from the Amsterdam University Medical Center and John Radcliffe Hospital in Oxford. The study provided evidence of the potential of DNA methylation profiling as a tool for predicting the response to Vedolizumab and Ustekinumab, but not adalimumab, which offers a promising path for personalized medicine in CD. In particular, the researchers have applied machine learning techniques in a very refined way, which illustrates the growing role of further from Computational methods in translational biomedical research. At the same time, This work emphasizes a parallel gorge in the microbiome field, where the same amount of robust predictive models remain underdeveloped.

Given the central role of intestinal microbioma in both disease pathogenesis and treatment response, Computational approaches must also be used to predict therapeutic results based on the microbial profiles of patients. Although various studies have compared the faecal microbiota between responds and non-response, predictive modeling is limited. Remarkable, Sanchis-Artero and colleagues a recipient performed operational characteristic (ROC) curve analysis using the ratio of Faecalibacterium prausnitzii Unpleasant They showed chillreaching an area under the curve (AUC) of 0.87. This result emphasizes the potential of species -specific microbial markers as predictive tools. However, it also underlines the possibility of investigating more extensive approaches, either by taking extra taxa or full microbio -composers, to improve predictive accuracy and to support personalized treatment strategies in CD. Other research groups investigate the role of specific faecal microbial signatures with a high capacity Discriminate the responders and non-responders for anti-TNF treatment and determine patients with CD Who will have post-surgical repetitionThat occurs in 65-90% of patients in the first year after surgery.

This research gap becomes even clearer in the light of the very first ECCO -Consensus About nutrition management of inflammatory bowel disorders. Presented for the first time on ECCO’25This milestone document about nutrition and food in IBD includes dietary recommendations for induction and maintenance, which extend far beyond nutritional support. For the first time, dietitians and gastroenterologists jointly offer evidence-based recommendations that position dietary interventions, such as a fully formulas diet or exclusive enteral food (one), as central components of clinical care. Especially in a related Here is PostThe main author of the consensus, IBD Dietitian Vaios Svolos, emphasized that ‘Current concept of attributes The efficacy of mainly to the oppression of intestinal microbioma activity“This perspective not only confirms the role of the microbiome in CD -Pathogenesis, but also underlines its active involvement in mediating the treatment response, either through biological medicines or diet. In accordance with these findings, emerging studies shows that nutritional therapies shows influence the efficacy of immunotherapiesWhich suggests that changes to environmental factors such as the microbiome offer great potential in CD, as proven to be successful in other gastrointestinal diseases, such as the role of fecal microbiota transfers and defined bacterial consortia for managing Clostridioides Difficile infection. Together, these insights Strengthen the reason for applying computational approaches to patient -specific microbial profiles to predict therapeutic results and to guide individualized treatment strategies that include both pharmacological and nutritional modalities. Emerging studies emphasize the momentum of the use of microbial signatures such as a non-invasive tool that improves the quality of patients’ life, saves the costs of healthcare systems and is given time in improving the patient.

References

RayGoza Gaay Yes, Turpin W, et Alt Alto. Intestinal microbioma composition is associated with the future start of Crohn’s disease in healthy relatives in the first degree. Gastroenterology 2023 DOI: 10.1053/J.Gastro.2023.05.032.

Behr Ma, Man I, Bernstein Cn. It’s time to change tack into IBD treatment. Gastroenterology 2024 DOI: 10.1053/J.Gastro.2024.06.036.

Ananthakrishnan An, Luo C, Yajnik V, et al. Bowel microbioma function function predicts the response to anti-integrine biological therapy in inflammatory bowel diseases. Celhost Microbe. 2017; 21 (5): 603-610.e3. DOI: 10.1016/J.Chom.2017.04.010.

Aden K, Rehman A, et al .. Metabolic functions of intestinal microbes associate with the efficacy of tumornecrose factor -antagonists in patients with inflammatory bowel diseases. Gastroenterology 2019 DOI: 10.1053/J.Gastro.2019.07.025.

Joustra VW, Li Yim Ayf, et al .. Development and validation of peripheral blood-DNA methylation signs to predict the response to biological therapy in adults with Crohn’s disease (EPIC CD): an epigenom-wide association study. Lancet Gastroenterol Hepatol 2025 Two: 10.1016/S2468-1253 (25) 00102-5.

Sanchis-Artero L, Martínez-Blanch JF, et al .. Evaluation of changes in intestinal microbiota in patients of Crohn’s disease after anti-TNF Alfa treatment. SCI representative 2021 Two: 10.1038/S41598-021-8823-2.

Busquets D, Oliver L, Amoeedo J, et al. RAID forecast: pilot study of faecal microbial signature with capacity to predict the response to anti-TNF treatment. Inflammation intestine. 2021; 27 (Suppl 2): ​​S63-S66. DOI: 10.1093/IBD/IZAB273.

Oliver L, Camps B, Julià-Bergkvist D, et al. Definition of a microbial signature as a predictor of endoscopic post-surgical recurrence in patients with Crohn’s disease. Front mole with. 2023; 3: 1046414. Two: 10.3389/FMMED.2023.1046414.

SVLOS V, Gordon H, et al .. Consensus on nutrition management of inflammatory bowel disorders. J Crohns Colitis 2025: 10.1093/ECCO-JCC/JJAF1

Song and Peng and, Fan X, et al. Synergetic effects of oral exclusive enteral nutrition and biological medicines in induction therapy for adult Crohn disease: an observation study in practice. You Lever Dis. 2025. DOI: 10.1016/J.Dld.2025.06.014 [article in press].

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