BACKGROUND AND AIMS: Treatment with anti-tumour necrosis factor α antibodies [anti-TNF] changes the dysbiotic faecal bacteriome in Crohn's disease [CD]. However, it is not known whether these changes are due to decreasing mucosal inflammatory activity or whether similar bacteriome reactions might be observed in gut-healthy subjects. Therefore, we explored changes in the faecal bacteriome and metabolome upon anti-TNF administration [and therapeutic response] in children with CD and contrasted those to anti-TNF-treated children with juvenile idiopathic arthritis [JIA]. METHODS: Faecal samples collected longitudinally before and during anti-TNF therapy were analysed with regard to the bacteriome by massively parallel sequencing of the 16S rDNA [V4 region] and the faecal metabolome by 1H nuclear magnetic resonance imaging. The response to treatment by mucosal healing was assessed by the MINI index at 3 months after the treatment started. We also tested several representative gut bacterial strains for in vitro growth inhibition by infliximab. RESULTS: We analysed 530 stool samples from 121 children [CD 54, JIA 18, healthy 49]. Bacterial community composition changed on anti-TNF in CD: three members of the class Clostridia increased on anti-TNF, whereas the class Bacteroidia decreased. Among faecal metabolites, glucose and glycerol increased, whereas isoleucine and uracil decreased. Some of these changes differed by treatment response [mucosal healing] after anti-TNF. No significant changes in the bacteriome or metabolome were noted upon anti-TNF in JIA. Bacterial growth was not affected by infliximab in a disc diffusion test. CONCLUSIONS: Our findings suggest that gut mucosal healing is responsible for the bacteriome and metabolome changes observed in CD, rather than any general effect of anti-TNF.

Department of Food Science Faculty of Agrobiology Food and Natural Resources Czech Univesity of Life Sciences Prague Czechia

Department of Medical Microbiology 2nd Faculty of Medicine Charles University and Motol University Hospital Prague Czechia

Department of Paediatric Surgery 2nd Faculty of Medicine Charles University and Motol University Hospital Prague Czechia

Department of Paediatrics 1st Faculty of Medicine Charles University and Thomayer University Hospital Prague Czechia

Department of Paediatrics 2nd Faculty of Medicine Charles University and Motol University Hospital Prague Czechia

Department of Paediatrics Faculty of Medicine in Pilsen Charles University and University Hospital Pilsen Czechia

Department of Paediatrics Faculty of Medicine Palacky University Olomouc and University Hospital Olomouc Czechia

Department of Paediatrics Masaryk Hospital Usti nad Labem Czechia

Department of Paediatrics Tomas Bata Hospital Zlin Czechia

Department of Pediatric and Adult Rheumatology Motol University Hospital Prague Czechia

Synlab Czech Inc Prague Czechia

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Roda G, Chien Ng S, Kotze PG, et al. . Crohn’s disease. Nat Rev Dis Primers 2020;6:22. PubMed

Ng SC, Shi HY, Hamidi N, et al. . Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: a systematic review of population-based studies. Lancet 2017;390:2769–78. PubMed

Lloyd-Price J, Arze C, Ananthakrishnan AN, et al. ; IBDMDB Investigators. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 2019;569:655–62. PubMed PMC

Joossens M, Huys G, Cnockaert M, et al. . Dysbiosis of the faecal microbiota in patients with Crohn’s disease and their unaffected relatives. Gut 2011;60:631–7. PubMed

Clooney AG, Eckenberger J, Laserna-Mendieta E, et al. . Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study. Gut 2021;70:499–510. PubMed PMC

Pascal V, Pozuelo M, Borruel N, et al. . A microbial signature for Crohn’s disease. Gut 2017;66:813–22. PubMed PMC

Gevers D, Kugathasan S, Denson LA, et al. . The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe 2014;15:382–92. PubMed PMC

Vich Vila A, Imhann F, Collij V, et al. . Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome. Sci Transl Med 2018;10:eaap8914. PubMed

Sokol H, Leducq V, Aschard H, et al. . Fungal microbiota dysbiosis in IBD. Gut 2017;66:1039–48. PubMed PMC

Ananthakrishnan AN, Luo C, Yajnik V, et al. . Gut microbiome function predicts response to anti-integrin biologic therapy in inflammatory bowel diseases. Cell Host Microbe 2017;21:603–10.e3. PubMed PMC

Metwaly A, Dunkel A, Waldschmitt N, et al. . Integrated microbiota and metabolite profiles link Crohn’s disease to sulfur metabolism. Nat Commun 2020;11:4322. PubMed PMC

Zhou Y, He Y, Liu L, et al. . Alterations in gut microbial communities across anatomical locations in inflammatory bowel diseases. Front Nutr 2021;8:615064. PubMed PMC

Vester-Andersen MK, Mirsepasi-Lauridsen HC, Prosberg MV, et al. . Increased abundance of proteobacteria in aggressive Crohn’s disease seven years after diagnosis. Sci Rep 2019;9:13473. PubMed PMC

Singh S, Murad MH, Fumery M, et al. . Comparative efficacy and safety of biologic therapies for moderate-to-severe Crohn’s disease: a systematic review and network meta-analysis. Lancet Gastroenterol Hepatol 2021;6:1002–14. PubMed PMC

Wang Y, Gao X, Ghozlane A, et al. . Characteristics of faecal microbiota in paediatric Crohn’s disease and their dynamic changes during infliximab therapy. J Crohns Colitis 2018;12:337–46. PubMed

Wang Y, Gao X, Zhang X, et al. . Microbial and metabolic features associated with outcome of infliximab therapy in pediatric Crohn’s disease. Gut Microbes 2021;13:1–18. PubMed PMC

Ventin-Holmberg R, Eberl A, Saqib S, et al. . Bacterial and fungal profiles as markers of infliximab drug response in inflammatory bowel disease. J Crohns Colitis 2021;15:1019–31. PubMed

Ventin-Holmberg R, Hoyhtya M, Saqib S, et al. . The gut fungal and bacterial microbiota in pediatric patients with inflammatory bowel disease introduced to treatment with anti-tumor necrosis factor-alpha. Sci Rep 2022;12:6654. PubMed PMC

Hoyhtya M, Korpela K, Saqib S, et al. . Quantitative fecal microbiota profiles relate to therapy response during induction with tumor necrosis factor alpha antagonist infliximab in pediatric inflammatory bowel disease. Inflamm Bowel Dis 2023;29:116–24. PubMed PMC

Levine A, Koletzko S, Turner D, et al. ; European Society of Pediatric Gastroenterology, Hepatology, and Nutrition. ESPGHAN revised Porto criteria for the diagnosis of inflammatory bowel disease in children and adolescents. J Pediatr Gastroenterol Nutr 2014;58:795–806. PubMed

Martini A, Ravelli A, Avcin T, et al. ; Pediatric Rheumatology International Trials Organization (PRINTO). Toward new classification criteria for juvenile idiopathic arthritis: first steps, Pediatric Rheumatology International Trials Organization International Consensus. J Rheumatol 2019;46:190–7. PubMed

Maaser C, Sturm A, Vavricka SR, et al. ; European Crohn’s and Colitis Organisation [ECCO] and the European Society of Gastrointestinal and Abdominal Radiology [ESGAR]. ECCO-ESGAR Guideline for Diagnostic Assessment in IBD Part 1: initial diagnosis, monitoring of known IBD, detection of complications. J Crohns Colitis 2019;13:144–64. PubMed

D’Amico F, Nancey S, Danese S, Peyrin-Biroulet L.. A practical guide for faecal calprotectin measurement: myths and realities. J Crohns Colitis 2021;15:152–61. PubMed

Hurych J, Vejmelka J, Hlinakova L, et al. . Protocol for faecal microbiota transplantation in irritable bowel syndrome: the MISCEAT study – a randomised, double-blind cross-over study using mixed microbiota from healthy donors. BMJ Open 2022;12:e056594. PubMed PMC

von Elm E, Altman DG, Egger M, Pocock SJ, Gøtzsche PC, Vandenbroucke JP; STROBE Initiative. The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement: guidelines for reporting observational studies. Lancet 2007;370:1453–7. PubMed

van Rheenen PF, Aloi M, Assa A, et al. . The medical management of paediatric Crohn’s disease: an ECCO-ESPGHAN guideline update. J Crohns Colitis 2021;15:171–94. PubMed

Ruemmele FM, Veres G, Kolho KL, et al. ; European Crohn's and Colitis Organisation. Consensus guidelines of ECCO/ESPGHAN on the medical management of pediatric Crohn’s disease. J Crohns Colitis 2014;8:1179–207. PubMed

Ravelli A, Consolaro A, Horneff G, et al. . Treating juvenile idiopathic arthritis to target: recommendations of an international task force. Ann Rheum Dis 2018;77:819–28. PubMed

Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD.. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 2013;79:5112–20. PubMed PMC

Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP.. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods 2016;13:581–3. PubMed PMC

Cozijnsen MA, Ben Shoham A, Kang B, et al. . Development and validation of the mucosal inflammation noninvasive index for pediatric Crohn’s disease. Clin Gastroenterol Hepatol 2020;18:133–40.e1. PubMed

Jaimes JD, Slavickova A, Hurych J, et al. . Stool metabolome–microbiota evaluation among children and adolescents with obesity, overweight, and normal-weight using 1H NMR and 16S rRNA gene profiling. PLoS One 2021;16:e0247378. PubMed PMC

Berends ET, Dekkers JF, Nijland R, et al. . Distinct localization of the complement C5b-9 complex on Gram-positive bacteria. Cell Microbiol 2013;15:1955–68. PubMed

Lewis JD, Chen EZ, Baldassano RN, et al. . Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in pediatric Crohn’s disease. Cell Host Microbe 2015;18:489–500. PubMed PMC

Tamboli CP, Neut C, Desreumaux P, Colombel JF.. Dysbiosis in inflammatory bowel disease. Gut 2004;53:1–4. PubMed PMC

Kiely CJ, Pavli P, O’Brien CL.. The role of inflammation in temporal shifts in the inflammatory bowel disease mucosal microbiome. Gut Microbes 2018;9:477–85. PubMed PMC

Morgan XC, Tickle TL, Sokol H, et al. . Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol 2012;13:R79. PubMed PMC

Singh S, Facciorusso A, Dulai PS, Jairath V, Sandborn WJ.. Comparative risk of serious infections with biologic and/or immunosuppressive therapy in patients with inflammatory bowel diseases: a systematic review and meta-analysis. Clin Gastroenterol Hepatol 2020;18:69–81.e3. PubMed PMC

Kolho KL, Korpela K, Jaakkola T, et al. . Fecal microbiota in pediatric inflammatory bowel disease and its relation to inflammation. Am J Gastroenterol 2015;110:921–30. PubMed

Wright EK, Kamm MA, Teo SM, Inouye M, Wagner J, Kirkwood CD.. Recent advances in characterizing the gastrointestinal microbiome in Crohn’s disease: a systematic review. Inflamm Bowel Dis 2015;21:1219–28. PubMed PMC

Liu C, Li J, Zhang Y, et al. . Influence of glucose fermentation on CO2 assimilation to acetate in homoacetogen Blautia coccoides GA-1. J Ind Microbiol Biotechnol 2015;42:1217–24. PubMed

Domingo MC, Huletsky A, Boissinot M, Bernard KA, Picard FJ, Bergeron MG.. Ruminococcus gauvreauii sp. nov., a glycopeptide-resistant species isolated from a human faecal specimen. Int J Syst Evol Microbiol 2008;58:1393–7. PubMed

Hall AB, Yassour M, Sauk J, et al. . A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. Genome Med 2017;9:103. PubMed PMC

Henke MT, Kenny DJ, Cassilly CD, Vlamakis H, Xavier RJ, Clardy J.. Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn’s disease, produces an inflammatory polysaccharide. Proc Natl Acad Sci U S A 2019;116:12672–7. PubMed PMC

Carlier JP, Bedora-Faure M, K’Ouas G, Alauzet C, Mory F.. Proposal to unify Clostridium orbiscindens Winter et al. 1991 and Eubacterium plautii [Seguin 1928] Hofstad and Aasjord 1982, with description of Flavonifractor plautii gen. nov., comb. nov., and reassignment of Bacteroides capillosus to Pseudoflavonifractor capillosus gen. nov., comb. nov. Int J Syst Evol Microbiol 2010;60:585–90. PubMed

Mukherjee A, Lordan C, Ross RP, Cotter PD.. Gut microbes from the phylogenetically diverse genus Eubacterium and their various contributions to gut health. Gut Microbes 2020;12:1802866. PubMed PMC

Forbes JD, Chen CY, Knox NC, et al. . A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist? Microbiome 2018;6:221. PubMed PMC

Parker BJ, Wearsch PA, Veloo ACM, Rodriguez-Palacios A.. The genus Alistipes: gut bacteria with emerging implications to inflammation, cancer, and mental health. Front Immunol 2020;11:906. PubMed PMC

Dziarski R, Park SY, Kashyap DR, Dowd SE, Gupta D.. Pglyrp-regulated gut microflora Prevotella falsenii, Parabacteroides distasonis and Bacteroides eggerthii enhance and Alistipes finegoldii attenuates colitis in mice. PLoS One 2016;11:e0146162. PubMed PMC

Rodriguez-Palacios A, Conger M, Hopperton A, Ezeji Jessica C, Erkkila HL, Fiocchi C, Cominelli F.. Identification of pathogenic bacteria in severe Crohn’s disease. Gastroenterology 2019;156:S102–S102.

Busquets D, Oliver L, Amoedo J, et al. . RAID prediction: pilot study of fecal microbial signature with capacity to predict response to anti-TNF treatment. Inflamm Bowel Dis 2021;27:S63–6. PubMed

Aden K, Rehman A, Waschina S, et al. . Metabolic functions of gut microbes associate with efficacy of tumor necrosis factor antagonists in patients with inflammatory bowel diseases. Gastroenterology 2019;157:1279–92.e11. PubMed

Zakrzewski M, Simms LA, Brown A, et al. . IL23R-protective coding variant promotes beneficial bacteria and diversity in the ileal microbiome in healthy individuals without inflammatory bowel disease. J Crohns Colitis 2019;13:451–61. PubMed

Steck N, Mueller K, Schemann M, Haller D.. Bacterial proteases in IBD and IBS. Gut 2012;61:1610–8. PubMed

Marchesi JR, Holmes E, Khan F, et al. . Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res 2007;6:546–51. PubMed

Bjerrum JT, Wang Y, Hao F, et al. . Metabonomics of human fecal extracts characterize ulcerative colitis, Crohn’s disease and healthy individuals. Metabolomics 2015;11:122–33. PubMed PMC

Rossi E, Cimdins A, Luthje P, et al. . ‘It’s a gut feeling’ - Escherichia coli biofilm formation in the gastrointestinal tract environment. Crit Rev Microbiol 2018;44:1–30. PubMed

Ghiboub M, Penny S, Verburgt CM, et al. . Metabolome changes with diet-induced remission in pediatric Crohn’s disease. Gastroenterology 2022;163:922–36.e15. PubMed

De Weirdt R, Possemiers S, Vermeulen G, et al. . Human faecal microbiota display variable patterns of glycerol metabolism. FEMS Microbiol Ecol 2010;74:601–11. PubMed

Gao Q, Kai L, Zhong R, et al. . Supplementing glycerol to inoculum induces changes in pH, SCFA profiles, and microbiota composition in in-vitro batch fermentation. Fermentation 2022;8:18.

Windey K, De Preter V, Verbeke K.. Relevance of protein fermentation to gut health. Mol Nutr Food Res 2012;56:184–96. PubMed

Diether NE, Willing BP.. Microbial fermentation of dietary protein: an important factor in diet(-)microbe(-)host interaction. Microorganisms 2019;7:19. PubMed PMC

Canfora EE, Meex RCR, Venema K, Blaak EE.. Gut microbial metabolites in obesity, NAFLD and T2DM. Nat Rev Endocrinol 2019;15:261–73. PubMed

Pichler J, Ong C, Shah N, et al. . Histopathological features of gastrointestinal mucosal biopsies in children with juvenile idiopathic arthritis. Pediatr Res 2016;79:895–901. PubMed

Arvonen M, Vahasalo P, Turunen S, et al. . Altered expression of intestinal human leucocyte antigen D-related and immune signalling molecules in juvenile idiopathic arthritis. Clin Exp Immunol 2012;170:266–73. PubMed PMC

Knight R, Vrbanac A, Taylor BC, et al. . Best practices for analysing microbiomes. Nat Rev Microbiol 2018;16:410–22. PubMed

Bloom SM, Bijanki VN, Nava GM, et al. . Commensal Bacteroides species induce colitis in host-genotype-specific fashion in a mouse model of inflammatory bowel disease. Cell Host Microbe 2011;9:390–403. PubMed PMC

Gut-microbiota-based ensemble model predicts prognosis of pediatric inflammatory bowel disease