Home › Collections › All IBD samples (Crohn's, ulcerative colitis, unspecified)

All IBD samples (Crohn's, ulcerative colitis, unspecified)

Disease reference sets · collection id ibd-samples

Every gut sample whose curated health_condition is Crohn's disease, ulcerative colitis or IBD unspecified, across all studies.

Open in the sample explorer (15,616 samples)

169
studies with member samples
15,616
member samples in this release

Membership rule

health_conditioncrohns_disease | ulcerative_colitis | ibd_unspecified
body_site_classprimary

Composition

Age category
adult7,616
unknown5,644
child1,486
elderly456
adolescent390
infant24
Country
US5,303
GB1,314
CN1,217
FR920
IL864
HK549
Health condition
ulcerative_colitis Ulcerative colitis6,777
crohns_disease Crohn's disease6,715
ibd_unspecified IBD (unspecified)2,124
Lifestyle
vegetarian_or_vegan Vegetarian / vegan (cohort defined by this diet)2

Member studies (169)

StudyTitleMember samplesFirst public
PRJEB110648Gut Virome Profiling in Ulcerative Colitis and Crohn's Disease9042026
PRJNA993675Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases8002024
PRJEB114255IBD Parisian Gut Microbiome Cohorte7462026
PRJNA945504Diagnosis of Crohn's Disease and Ulcerative Colitis Using the Microbiome4322023
PRJNA804384Inflammatory bowel disease patients undergoing biological therapy4322022
PRJEB26472Faecal cDNA Specific bacteria and metabolic pathways are associated with response to faecal microbiota transplantation in ulcerative colitis4262018
PRJNA642308Gut microbiome of subjects with inflammatory bowel disease undergoing diet intervention4092021
PRJEB38352Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity3822021
PRJNA1086048Metagenomic analysis of faecal microbiome as a tool for targeted non-invasive biomarkers for inflammatory bowel disease3792024
SRP057027Inflammation, Antibiotics, and Diet as Concurrent Environmental Stressors of the Gut Microbiome in Pediatric Crohn's Disease3512015
PRJNA854889A Randomized Trial Comparing the Specific Carbohydrate Diet to a Mediterranean Diet in Adults With Crohn's Disease3392024
PRJNA1450848Improved Efficacy of Fecal Microbiota Transplantation for Ulcerative Colitis with Non-urbanized Donors3312026
PRJEB26357ShotGun BACTERIAL AND FUNCTIONAL DETERMINANTS OF OUTCOME IN FAECAL MICROBIOTA TRANSPLANTATION FOR ACTIVE ULCERATIVE COLITIS2842018
PRJNA389280Human gut metagenome and metatranscriptome in the inflammatory bowel disease (iHMP/HMP2)2442017
PRJNA475599Fecal transplant for ulcerative colitis2022019
PRJEB42155UCSD IBD 200 Patient Cohort Multi-omic Project1922023
PRJNA844888Vaughn UC IMT Study1882025
PRJNA385949Longitudinal Stool Study of patients with IBD and controls1872017
PRJNA532645PRASCO gut microbiome profile of Pediatric Severe Acute Ulcerative Colitis patients under Antimicrobial treatment1862019
PRJNA1171764Human gut metagenome of IBD patients and healthy controls1842025
PRJNA737472Microbiome sequencing of ulcerative colitis patients receiving fecal microbiota transplantation1822022
PRJNA1071720FECBUD Study Fecal Metagenomes1822024
PRJNA384246Studies of metagenomes of inflammatory bowel disease patient receiving vedolizamub therapy1742019
PRJEB81106Simultaneous metagenome-informed metaproteomics of the human gut microbiome, host and dietary exposome uncover functional interactomes in health & IBD1692024
PRJEB50555Targeted suppression of human IBD-associated gut microbiota commensals for treatment of intestinal inflammation1682022
PRJNA400072Gut microbiome structure and metabolic activity in inflammatory bowel disease1642018
PRJNA1216426The effects of probiotic treatment with Bifidobacterium breve, Bif195 for small intestinal Crohn's disease and the gut microbiome: Results from a randomised, double-blind, placebo-controlled trial1632025
PRJEB26473biopsy cDNA Specific bacteria and metabolic pathways are associated with response to faecal microbiota transplantation in ulcerative colitis1602018
PRJNA1423906Crohn's Disease Microbiome Atlas1582026
PRJEB1220A method for identifying metagenomic species and variable genetic elements by exhaustive co-abundance binning1482014
PRJNA1249971Microbiome in pediatric inflammatory bowel disease (Part 1)1482025
PRJEB33603A metagenomic approach to diagnosis, induction and maintenance of deep remission following exclusive enteral nutrition in pediatric Crohn’s Disease1392019
PRJNA1249606Microbiome in pediatric inflammatory bowel disease (Part 2)1362025
PRJNA1283919STOP-COLITIS Metagenomic Sequencing Data1322025
PRJNA1057679Integrative analysis of serum and fecal metabolome and microbiome that herald a flare in Crohn Disease1302026
PRJNA1169096Donor Composition and Fiber Promote Strain Engraftment in a Randomized Controlled Trial of Fecal Transplant with Dietary Fiber for Ulcerative Colitis (MINDFUL)1272025
PRJEB47061Fecal microbiota transplantation for treatment of ulcerative colitis1222021
PRJEB22481Project_to_evaluate_bowel_preparation_and_sampling_procedure_for_microbiome_studies1222019
PRJNA439152GUT BACTERIAL METAGENOME Metagenome1192022
PRJEB72371Multiomic analysis of Crohn's disease and Ulcerative colitis using machine learning models1192025
PRJNA625520Linking strain engraftment in fecal microbiota transplantation with maintenance of remission in Crohn's disease1152020
PRJNA828396Virome enriched metagenomics of healthy controls and patients with IBD1152022
PRJNA685168Multi-omics suggest diverse mechanisms for response to biologic therapies in IBD1142021
PRJDB14272Metagenomic analysis of fecal samples obtained from ulcerative colitis patient in Japan1142026
PRJEB14084The_mechanism_of_nutritional_therapy_for_Paediatric_Crohn_s_disease1112016
PRJNA1004651Human gut metagenome, whole genomic shotgun sequencing1082023
PRJNA1265906Gut microbiome in pediatric IBD patients1052025
PRJEB115184Clinical outcomes and microbiome restructuring following fecal microbiota transplantation plus exclusion diet in Crohn’s disease: A 52-week randomized sham-controlled trial992026
PRJNA851554Metagenomes of the gut microbiota of CD patients that required resection from a Belgian cohort982022
PRJNA504921viral metagenome Metagenome912019
PRJNA487636An increased abundance of Clostridiaceae characterizes arthritis in inflammatory bowel disease and rheumatoid arthritis: a cross-sectional study912018
PRJDB43083Stool shotgun metagenomes from patients with Crohn's disease receiving biologic therapies892026
PRJNA761454CCFA virome862021
PRJEB39813A metagenomic study of the oral (saliva) and Gut (stool) microbiome in subjects with Crohn's Disease.842021
PRJNA943135A diarrhoeal-associated gut dysbiosis in cancer and inflammatory bowel disease patients is further impacted by Clostridioides difficile infection.812023
PRJNA1251707Metagenomes for rational identification of live biotherapeutics for the treatment of inflammatory bowel disease772025
PRJNA943202Probing viral involvement in pediatric IBD762023
PRJNA637365Dysbiosis in metabolic genes of the gut microbiomes of patients with a Pouch762021
PRJNA1066476Profiling the gut microbiome of patients with active ulcerative colitis received capsulized fecal microbiota transplantation752024
PRJNA1240691Gut metagenome752025
PRJEB122858Disrupted Terminal Bilirubin Catabolism Links Lachnospiraceae Depletion to Inflammatory Bowel Disease752026
PRJNA474024Engraftment of Bacteroidetes species in a Fecal Microbiota Transplant study722019
PRJEB67456IBD gut virome712023
PRJNA930767Outcomes and predictors of sustained remission after drug withdrawal in pediatric Crohn's disease702023
PRJNA647221Before and after fecal microbiota transplantation in ulcerative colitis patients682024
PRJEB11419American Gut Project672015
PRJNA1472528Fecal Microbiome Profiling in Crohns Disease During Oral Nutritional Supplementation662026
PRJNA429990human gut metagenome Raw sequence reads662018
PRJNA1064103Metagenomics of Colonoscopic Rinsates: Investigating Microbial Patterns in Inflammatory Bowel Disease652024
PRJEB88212Shotgun microbiome sequencing of faecal contents from IBD patients, before and after treatment642025
PRJEB110888Faecalibacterium prausnitzii EXL01 for the Maintenance of Steroid-induced Clinical Response or Remission in Patients with Crohn’s Disease: a first in human trial632026
PRJEB49262Depression and Fatigue in IBD622022
PRJEB50260Hyperbaric Oxygen Therapy for Ulcerative Colitis622022
PRJNA1220173Detecting microbial engraftment after FMT in patients with ulcerative colitis612025
PRJNA1138254PSC-Vanc Clinical Trial602024
PRJNA1173388Metagenomes from an inflammatory bowel disease cohort602025
PRJNA768409Metagenomic sequencing of UC patients subjected to FMT and FMT-donors592021
PRJNA564995Gut virome in VEO-IBD592020
PRJEB101774Metagenomes and bile acid profiles in IBD582025
PRJNA1356513Dieta Anti-INflamatoria (DAIN) study582025
PRJNA1401743Fecal microbiome in Crohn's disease before and after FMT572026
PRJNA1499619Gut microbial characteristics of hospitalized patients with active ulcerative colitis and sarcopenia572026
PRJEB25264Examining changes in the gut microbiome of Crohn's Disease patients using two different nutritional therapies.572018
PRJEB35587The Relationship between Fecal Bile Acids and Microbiome Community Structure in Pediatric Crohn’s Disease572019
PRJEB18780Exploring associations between the gut microbiota and colonic inflammation and assessing sequential changes during exclusive enteral nutrition (EEN) for children with Crohn's disease and comparing them to healthy cohorts as well as their relatives562017
PRJNA905698Lectin-Seq: a method to profile lectin-microbe interactions in native communities542023
PRJNA321058Increased intestinal microbial diversity following fecal microbiota transplant for active Crohn's disease532016
PRJNA1184213The microbiota-dependent effect of physical activity on Crohn's disease522025
PRJNA1262688Fecal Microbiota Transplantation for CD cohort502025
PRJEB15371The gut microbiome in Crohn's disease and modulation by exclusive enteral nutrition492016
PRJNA763503Character of microbial engraftment following the fecal microbiota transplantation in patients with inflammatory bowel diseases482021
PRJNA1043691Microbiota Profile in Saudi Children with Ulcerative Colitis432024
PRJNA285502Fecal microbiota transplantation (FMT) for ulcerative colitis412017
PRJEB59450PDA-MAPS - Pancreatic Ductal Adenocarcinoma - Microbiome As Predictor of Subtypes - Fistula412023
PRJNA576887Circadian Misalignment as a disease risk factor in Inflammatory Bowel Disease412020
PRJNA793776Homo sapiens Raw sequence reads412022
PRJNA1122782Evidence for altered gut microbiota in pediatric quiescent Crohn's disease patients with iron deficiency anemia402025
PRJEB42151Metaomics Reveals Microbiome Based Proteolysis as a Driver of Ulcerative Colitis Severity402020
PRJNA813736Whole genome sequencing of the faecal microbiomes from healthy controls and patients with inflammatory bowel disease392022
PRJNA689476Metagenomic Sequencing of Bacteria from Subjects with CD and AS392022
PRJNA690735Dietary Fibers Promote Inflammation in Inflammatory Bowel Diseases372021
PRJNA1371390Human gut virome in ulcerative colitis372026
PRJNA480674mmunoglobulin G Selectively Identifies Pathobionts in Pediatric Inflammatory Bowel Diseases362019
PRJNA524170Resistant microbiome underlies antibiotic therapy in pouchitis352019
PRJNA929645Microbiota Genome sequencing322024
PRJNA237362Microbiome study of the RISK cohort282014
PRJNA296946Gut microbiota from patients with Crohn's disease282015
PRJNA983946Human gut metagenome of ulcerative colitis and healthy stool samples from Northern India272024
PRJNA46321Metagenomic Analysis of the Structure and Function of the Human Gut Microbiota in Crohn's Disease272010
PRJNA1096686A comparative analysis of Parkinson's disease, inflammatory bowel disease, and control gut microbiomes with shotgun metagenomics242024
PRJNA1241499Pediatric IBD Shotgun Metagenomics, Metatranscriptomics, and 16S rRNA232026
PRJNA1069244metagenome and metatranscriptome changes in Crohn's disease patients before and after WMT222024
PRJEB52930Interpersonal variability in gut microbial calprotectin metabolism222022
PRJNA687536Metagenomic sequencing of non-IBD and Crohn's disease fecal samples222021
PRJNA730677Genomic adaptations of Escherichia coli strains from patients with inflammatory bowel diseases212022
PRJEB51945Gut microbial DL-endopeptidase protects Crohn’s disease via NOD2 pathway212024
PRJEB7949The fecal microbiome was studied in a group of IBD suffers and compared to a control group's fecal microbiome202015
PRJNA995911Fecal microbiota cooperative metabolism of pectins derived from apple pomace: a functional metagenomic study202023
PRJEB2193316S and MGS data - Multi-omics Differentially Classify Disease State and Treatment Outcome in Pediatric Crohn’s Disease202017
PRJNA398187Human gut metagenome Targeted loci environmental192020
PRJNA701961Donor and recipient stool metagenomes from a fecal microbiota transplantation study192021
PRJNA1104804Gut microbiota profiles of CD children and healthy children182025
PRJNA1159478Spatial Host-Microbiome Profiling in Pediatric Crohn's disease182025
PRJNA1199756Gut microbiota-mediated conversion of mangiferin to norathyriol alters short chain fatty acid and urate metabolism182025
PRJNA715634Novel Strain Level Resolution of Crohns Disease Mucosa-Associated Microbiota via an ex vivo Combination of Microbe Culture and Metagenomic Sequencing182021
PRJEB44121Human enteric viruses shape disease phenotype through divergent innate immunomodulation172021
PRJNA1056458Diet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort172024
PRJNA1160849Metagenomic profiling on pediatric IBD patients from different anatomic sites162025
PRJNA645218Virome sequencing of the human colonic mucosal-luminal interface162020
PRJNA1160072Chron fermentation152024
PRJNA527369Whole-metagenome shotgun sequencing of 13 IBD Italian fecal metagenomes132019
PRJNA761533Metagenome of antimicrobial-treated samples122021
PRJEB76677Gut microbiota differs between children with Inflammatory Bowel Disease and healthy siblings in taxonomic and functional composition: a metagenomic analysis.122024
PRJNA1517182Fecal metagenomic sequencing122026
PRJNA1430386Impact of bladder microbiome on BCG response102026
PRJNA1030952Single-cell and metagenome sequencing for human oral/gut microbiome102023
PRJEB101484Gut Microbiota - Lymphocyte Reaction (GMLR): a practical tool to optimize fecal microbiota transplantation (FMT) donor-recipient compatibility in IBD102026
PRJNA575186Integrated microbiota and metabolite profiles identified functional signatures in Crohn’s disease with a link to sulfur metabolism102020
PRJEB86846Viral tagging of F. prausnitzii and uncultivated human gut microbes92025
PRJNA1024678The functionl characteristics of the gut microbiota in patients with Crohn's disease.92023
PRJNA1521393First clinical cases of effective sterile fecal filtrate transfer for ulcerative colitis treatment: microbiome and virome shifts92026
PRJNA397664A GUT MICROBIAL AUTOANTIGEN SUPPRESSES COLITIS82017
PRJEB37731Effects of the menstrual cycle and hormonal contraceptives on the human microbiome82020
PRJNA46879Diet, Genetic Factors, and the Gut Microbiome in Crohn's Disease82010
PRJNA75964216s and shotgun sequencing from human faecal82021
PRJNA975689Culturomics and metagenomics studies of gut microbial diversity in IBD patients82026
PRJNA438164Gut microbial profiles after fecal microbiota transplantation in pediatric ulcerative colitis patients82018
PRJNA600008Dysbiosis-induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation72020
PRJNA1480958PacBio Long-reads Sequencing for FMT72026
PRJEB47909FMT datasets of patients with recurrent Clostridioides difficile infection (rCDI), inflammatory bowel disease (IBD), and colonization from multi-drug resistant bacteria (MDRB)62022
PRJDB43252Integrated 16S rRNA sequencing and metagenomics insights into microbial dysbiosis and distinct virulence factors in inflammatory bowel disease (PRJCA023147)62026
PRJNA732769The impact of bacteriophages on DSS-colitis and microbiota composition - VLP shotgun52021
PRJEB34939Ileostomy content from a colectomised Swedish adult individual52019
PRJNA175224Dysfunction of the Intestinal Microbiome in Inflammatory Bowel Disease and Treatment42012
PRJNA990354Exploration of the Gut Microbiome of Inflammatory Bowel Disease Patients in Bangladesh42024
PRJNA850529Host factors associated with gut mycobiome structure42023
PRJEB23207Metagenomic characterization of the human intestinal microbiota in faecal samples from STEC-infected patients42017
PRJNA637878Precise quantification and tracking of gut bacterial strains following fecal transplantation demonstrates long-term stable engraftment and predicts outcome42021
PRJNA818303Integrated metagenomics, metaviromics, and metatranscriptomics reveal colonic virome-bacteriome interactions32023
PRJNA394849NGS approaches to metagenomics of gut microbiome32018
PRJNA1001944Breast cancer but not the menopausal status is associated with small changes of the gut microbiota32024
PRJNA1333319Phage bacteria interaction networks differentiate ulcerative colitis and colorectal cancer from the healthy gut32026
PRJNA981221GNOTO22023
PRJNA831236Low-dose interleukin-2 shapes a tolerogenic gut microbiota that improves autoimmunity and gut inflammation.22022
PRJEB38528Placenta biopsies, saliva samples, vaginal and rectal swabs collected at delivery for babies at term22020
PRJNA879122Meta3C data on human stool sample12022
PRJEB107177Sequencing reads of human derived fecal viral filtrates used in the study12026
PRJNA834801Characterizing dysbiosis of the Parkinson's disease gut microbiome using shotgun metagenomics12022
PRJNA398089Longitudinal Multi’omics of the Human Microbiome in Inflammatory Bowel Disease12017