1. Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn’s disease
- Author
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Häcker, Deborah, Siebert, Kolja, Smith, Byron J, Köhler, Nikolai, Riva, Alessandra, Mahapatra, Aritra, Heimes, Helena, Nie, Jiatong, Metwaly, Amira, Hölz, Hannes, Manz, Quirin, De Zen, Federica, Heetmeyer, Jeannine, Socas, Katharina, Le Thi, Giang, Meng, Chen, Kleigrewe, Karin, Pauling, Josch K, Neuhaus, Klaus, List, Markus, Pollard, Katherine S, Schwerd, Tobias, and Haller, Dirk
- Subjects
Medical Biochemistry and Metabolomics ,Biological Sciences ,Biomedical and Clinical Sciences ,Microbiology ,Prevention ,Microbiome ,Digestive Diseases ,Autoimmune Disease ,Pediatric ,Crohn's Disease ,Clinical Research ,Genetics ,Nutrition ,Complementary and Integrative Health ,Inflammatory Bowel Disease ,2.1 Biological and endogenous factors ,Oral and gastrointestinal ,Crohn Disease ,Animals ,Humans ,Gastrointestinal Microbiome ,Enteral Nutrition ,Mice ,Feces ,Child ,Female ,Male ,Germ-Free Life ,Adolescent ,Prospective Studies ,Interleukin-10 ,Metagenomics ,Fatty Acids ,Disease Models ,Animal ,Remission Induction ,Mice ,Inbred C57BL ,Clostridiales ,Bacteria ,EEN ,FMT ,bacterial strain dynamics ,exclusive enteral nutrition ,ex vivo gut chemostat model ,fiber ,medium-chain fatty acids ,metagenomics ,microbiome ,multi-omics data integration ,pediatric Crohn’s disease ,Medical Microbiology ,Immunology ,Biochemistry and cell biology ,Medical microbiology - Abstract
Exclusive enteral nutrition (EEN) is a first-line therapy for pediatric Crohn's disease (CD), but protective mechanisms remain unknown. We established a prospective pediatric cohort to characterize the function of fecal microbiota and metabolite changes of treatment-naive CD patients in response to EEN (German Clinical Trials DRKS00013306). Integrated multi-omics analysis identified network clusters from individually variable microbiome profiles, with Lachnospiraceae and medium-chain fatty acids as protective features. Bioorthogonal non-canonical amino acid tagging selectively identified bacterial species in response to medium-chain fatty acids. Metagenomic analysis identified high strain-level dynamics in response to EEN. Functional changes in diet-exposed fecal microbiota were further validated using gut chemostat cultures and microbiota transfer into germ-free Il10-deficient mice. Dietary model conditions induced individual patient-specific strain signatures to prevent or cause inflammatory bowel disease (IBD)-like inflammation in gnotobiotic mice. Hence, we provide evidence that EEN therapy operates through explicit functional changes of temporally and individually variable microbiome profiles.
- Published
- 2024