Abstract Background Crohn’s disease (CD) is commonly treated with biologics such as anti-TNFα agents, vedolizumab (VDZ), or ustekinumab (USTE), to which only a part of patients respond. To identify predictive biomarkers for treatment outcomes, we interrogated the fecal microbiome of pre-treatment biopsies from ileum and colon. Methods Adult CD patients initiating anti-TNFα (infliximab or adalimumab), vedolizumab (VDZ), or ustekinumab (USTE) were enrolled. Pre-treatment ileal and colonic biopsies were collected endoscopically. Treatment response after 26–52 weeks was defined by ≥ 50% reduction in the simple endoscopic score for CD and either a corticosteroid-free clinical response (≥3-point HBI decrease or remission HBI ≤4 without systemic steroids) or a biochemical response (≥50% or ≤ 5 mg/L CRP reduction and ≥50% or ≤ 250 μg/g faecal calprotectin reduction) versus baseline. Mucosal microbiota was profiled by 16S rRNA sequencing of available biopsies. Machine learning models predicting treatment response were trained using ASV-level count data. The impact of heat-killed bacteria on anti-TNFα–induced CD14⁺CD206⁺ macrophages was tested in mixed lymphocyte reactions (MLRs). Results A total of 125 patients were included: 39 on anti-TNFα, 47 on VDZ, and 39 on USTE. Clinical features were similar between responders and non-responders, aside from sex (USTE-colon) and CRP (USTE-ileum). No major microbial differences were observed in VDZ, USTE ileal or colon samples. However, in colonic biopsies analysed pre-treatment, anti-TNFα responders had significantly higher α-diversity, and 3.9% of β-diversity variation associated with response. Among six models, the anti-TNFα colonic model performed well (AUC=0.90) to predict response. Mediterraneibacter gnavus ASVs associated with non-response, whereas Blautia ASVs associated with response, to anti-TNFα. When tested in MLRs, anti-TNFα induced CD14+CD206+ macrophages, required for its efficacy. However, this induction was not observed when cells were pre-exposed to M. gnavus, in part explaining its association to non-response to anti-TNF treatment. Conclusion The colonic mucosal microbiome prior to anti-TNFα treatment can distinguish responders from non-responders in CD, supporting its potential as a predictive biomarker. Conflict of interest: Zafeiropoulou, Konstantina: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Hageman, Ishtu: none Mu, Tianqi: No conflict of interest Davids, Mark: No conflict of interest Li Yim, Andrew: No conflict of interest Hakvoort, Theo: No conflict of interest Satsangi, Jack: Grant: Grants to Oxford University from Helmsley Trust & European Community. Koelink, Pim: No conflict of interest Wildenberg, Manon: Received research grant support from Hoffman-La Roche, Boehringer-Ingelheim van den Wijngaard, Rene: No conflict of interest D’Haens, Geert: Grant: Pfizer, BMS, Johnson and Johnson, Abbvie, Alimentiv BV, Eli Lilly, Takeda, Prometheus Laboratories Personal Fees: Abbvie, Abivax, Agomab, Alimentiv, Anaptys Bio, AstraZeneca, Bristol Meiers Squibb, Boehringer Ingelheim, Celltrion, Eli Lilly, Exeliom Biosciences, Galapagos, Glaxo Smith Kline, Dr Falk Pharma, Pfizer, Johnson and Johnson, Merck, Mirador, Polpharma, Procise Diagnostics, Prometheus Biosciences, Sorriso Pharma, Spyre, Takeda, Ventyx De Jonge, Wouter: No conflict of interest
Zafeiropoulou et al. (Thu,) studied this question.