Decoding the Clinical Impact of Host and Microbial Intestinal Proteomic Landscape in Crohn's Disease

In this study, the investigators will explore our protein-based platform assessing commensals potentially contributing to features of CD, while assessing the global composition and abundance of AMPs expressed in the GI tract under specific CD-relevant clinical contexts. This would enable us to (a) identify new commensals contributing to features of CD spectrum and various sub-types; (b) uncover the mechanistic basis of dysbiosis in CD (c) utilize the pipeline to develop new theranostic for disease exacerbation, complication and treatment responses; and (d) potentially enable future exploitation of novel AMP combinations, and their respective antimicrobial capacity to counteract dysbiosis in CD.

Uncovering the proteomic manifestations of perturbed host-microbiome communications in CD will eventually enable the development and validation of clinical non-invasive surrogate markers, mechanistically determine causative drivers of CD, and potentially facilitate the development of novel therapeutic interventions.

Participants will be recruited from a community outpatient clinics and from a leading outpatient gastroenterology clinic: Emek Medical Center, after ICF signing , they will fill out a medical, demographic, and lifestyle habits questionnaires, as well as a food frequency questionnaire (FFQ). Participants will receive a home stool kit and will be instructed on how to use it. They will also receive a kit and an explanation regarding preparation materials for the colonoscopy. Subjects will be asked to collect stool samples at home - prior to colonoscopy and if possible - after colonoscopy bowel prep.

The seconed visit of the study will occure on the day of colonoscopy. Each patient will be clinically assessed by a gastroenterologist using the Crohn's Disease Activity Index (CDAI)30 and Harvey-Bradshaw Index (HBI); and collection of luminal, brush cytology, and mucosal samples from 4 different lower intestine regions

Eligibility Criteria:
Inclusion criteria - CD study group:

* Age ≥ 18
* Candidates for a medically-indicated, diagnostic colonoscopy due to suspected new-onset CD.
* Naïve to any medical or nutritional intervention.

Inclusion criteria - healthy controls:

• Age- and gender-matched patients to the CD group, admitted for non-specific GI complaints (such as changes in bowel movements, bloating, abdominal pain) or routine screening for colorectal cancer as part of primary prevention per clinical guidelines.

Exclusion Criteria - both groups:

* Established diagnosis of inflammatory bowel disease (IBD) with prior treatment.
* Chronic gastro-intestinal disorder (e.g. celiac disease, eosinophilic esophagitis, collagenous gastritis, autoimmune gastritis, etc.).
* Type 1 or type 2 diabetes mellitus.
* Past or present history of malignancy.
* BMI \> 30 (kg/m2)
* Use of systemic antibiotics or probiotics 2 months prior to enrolment.
* Use of steroids 2 months prior to enrolment (not including a short course of topical steroidal therapy).
* Any previous major gastric or intestinal surgery.
* Suspected or proven extensive involvement of non-ileal small intestine or colon, or significant perianal disease.
* Significantly stricturing or penetrating (fistulizing) disease at presentation.
* Chronic treatment with any oral/systemic immunosuppressive or anti-inflammatory drugs (e.g. steroids, 5-aminosalicylic acid, immunomodulators, biologics, etc.). Patients receiving these drugs as inhalers/creams/ointments should not be excluded from the study.
* Primary immunodeficiency.
* Pregnancy or breastfeeding in the last 6 months.
* Serious medical conditions that may alter the gut microbiome composition, based on investigators judgement (for example primary immunodeficiency, autoimmune disorder, or rheumatologic disease).