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Samples with documented antibiotic exposure

Study design · collection id antibiotic-exposed-samples

All gut samples whose source records antibiotics at or shortly before collection (antibiotic_exposure = yes), across every study — the cross-study exposure set for resistome and recovery analyses.

Open in the sample explorer (18,320 samples)

193
studies with member samples
18,320
member samples in this release

Membership rule

antibiotic_exposureyes
body_site_classprimary

Absence of an antibiotic attribute is unknown, not 'no'; compare against antibiotic_exposure = no rather than the whole catalog.

Composition

Age category
adult6,717
infant4,977
unknown2,567
neonate1,844
child1,181
elderly907
Country
US7,215
BD1,537
GB1,027
ZA686
CA624
PL460
Health condition
healthy_control Healthy / control2,929
other_infection Other infection (HIV2,288
other_disease Other disease / condition1,872
malnutrition Malnutrition / undernutrition1,525
gi_infection_or_diarrhoea GI infection / diarrhoea (incl. C. difficile)1,185
preterm_nicu Preterm / NICU (infant)1,181
Lifestyle
military Military personnel / training416
rural_non_industrialized Rural243
urban_industrialized Urban / industrialized (only when stated by the source)141
vegetarian_or_vegan Vegetarian / vegan (cohort defined by this diet)87
indigenous_community Indigenous community (subsistence not specified)84

Member studies (193)

StudyTitleMember samplesFirst public
PRJEB11419American Gut Project2,2322015
PRJEB63587A microbiota-directed therapeutic food for severely malnourished children evaluated following acute nutritional resuscitation1,5192025
PRJNA510445The relationship of fecal microbiomes and nutritional status in cystic fibrosis6662019
PRJEB90577PediCAP metagenomics and metaserotyping6312026
PRJNA1277853PediCAP metagenomics and metaserotyping6312026
PRJNA1079705Efficacy and Safety of BB-12 Supplemented Strawberry Yogurt For Healthy Children on Antibiotics (PLAY ON)4942024
PRJNA698223TD Cusco travelers study4602022
PRJNA945408Impact of antibiotic regimens for the prevention and treatment of travelers diarrhea Prevent TD and TrEAT TD4162023
PRJEB37249Statin therapy is associated with lower prevalence of gut microbiota dysbiosis3912020
PRJNA376566preterm infant gut metagenomes (S2_2013 and NIHY2_2012 cohorts)3902017
PRJNA698986Early-life metagenomes from human infant fecal samples with matched maternal sample3562021
PRJNA993161Impact of complex oligosaccharides and a probiotic on the antibiotic-treated human microbiome3162023
PRJNA396794preterm infant gut metagenomes (NIH Y4 Cohort)3052017
PRJNA664754Fecal metagenomes of healthy volunteers2892022
PRJNA872399Preterm infants at low risk for early-onset sepsis differ in early fecal microbiome assembly2742022
PRJNA1463324VE202 phase 1 stool metagenomes2732026
PRJEB28097(1) Personalized microbiome and host features resist gut mucosal colonization by empiric probiotics (2) Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT2732018
PRJNA489090Human infant gut metagenome, infant shotgun sequencing2672019
PRJNA675301Role of Diet in the Reconstitution of the Human Gut Microbiome and its Metabolome2642020
PRJEB64515Gut Microbiome Dynamics and Predictive Value in Hospitalized COVID-19 Patients: A Comparative Analysis of Shallow and Deep Shotgun Sequencing2562023
PRJEB86785The Antibiotic Resistance in the Microbiome – Oxford2552025
PRJNA1402308BALANCE gut microbiome2542026
PRJNA688274Netherland Travelers2542021
PRJEB32631Early_life_microbiota_colonisation2482019
PRJEB108678MPRINT: mother-infant dyads and antibiotic exposure2092026
PRJNA301903Metagenomic sequencing of preterm infant gut microbiota raw sequence reads2022016
PRJNA398089Longitudinal Multi’omics of the Human Microbiome in Inflammatory Bowel Disease1972017
PRJNA297252Intestinal microbiota dynamics in hospitalized patients1892015
PRJEB51728Infant stool metagenomic datasets1642023
PRJNA1106565Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants1522024
PRJNA294605Metagenomes from 11 human infant fecal samples hospitalized in the same intensive care unit1462016
PRJNA1033539Pediatric Intensive Care Unit Treatment Alters the Diversity and Composition of the Gut Microbiota and Antimicrobial Resistance Gene Expression in Critically Ill Children1422023
PRJEB91718COVID-19 Microbiome - deep samples1342025
PRJNA800433raw metagenomic sequence reads from human stool microbiome from children receiving antibiotics1322023
PRJNA290380A longitudinal analysis of the developing gut microbiome in infants from Finland, Estonia, and Russian Karelia1312016
PRJEB105465Effects of antibiotic treatment on normal intestinal flora (ARG-study)1242026
PRJNA749138Homo sapiens Raw sequence reads1212022
PRJDB14272Metagenomic analysis of fecal samples obtained from ulcerative colitis patient in Japan1142026
PRJEB39610Longitudinal metagenomic analysis of the gut microbiome in preterm infants diagnosed with necrotising enterocolitis and matched controls1132020
PRJNA1305379Fecal immunochemical tests from population-based colorectal cancer screening programs support prospective microbiome cohorts1102026
PRJNA1045596The Intestinal Microbiome of Inflammatory Bowel Disease Across the Pediatric Age Range Raw sequence reads1042025
PRJNA352220Human gut microbiome with bacterial pathogen challenge992016
PRJNA63661Microbial composition of samples from infant gut962011
PRJNA978345Infant cystic fibrosis BAL and stool microbiome962024
PRJEB22175PATCH_MICROBIOME962019
PRJEB39128Comparison of two antibiotic treatments on the microbiome and resistome in children who presented to the ED with moderate/severe cellulitis962022
PRJEB47909FMT datasets of patients with recurrent Clostridioides difficile infection (rCDI), inflammatory bowel disease (IBD), and colonization from multi-drug resistant bacteria (MDRB)952022
PRJEB27799Prediction of the intestinal resistome by a novel 3D-based method932018
PRJNA898628PINGU Fecal samples Metagenome932023
PRJNA413659Shifts of the intestinal microbiota and resistome caused by Helicobacter pylori eradication therapy922017
PRJNA549787South African HIV-exposed, uninfected infant gut microbiomes922019
PRJNA737472Microbiome sequencing of ulcerative colitis patients receiving fecal microbiota transplantation922022
PRJNA1255639Gut microbiota of SIRS and sepsis patients892026
PRJNA797994Gut Microbiome of Helminth Infected Indigenous Malaysians Is Context Dependent862022
PRJEB49334Dynamics in the gut microbiomes of subjects colonized by carbapenemase-producing Enterobacteriaceae (longitudinal data)852022
PRJNA1078999Homo sapiens Raw sequence reads792025
PRJNA1235197Microbiome signatures linked to cancer and treatment adverse events in a real-world cohort782025
PRJEB112905CRS3123 vs Vancomycin Treatment of CDI Phase II Clinical Trial742026
PRJNA1128111Shotgun metagenomics for PA15 AML patients Raw sequence reads732025
PRJEB56674Proteobacteria and antimicrobial resistant genes after microbial consortia722023
PRJNA850529Host factors associated with gut mycobiome structure702023
PRJEB9403BAMBI__Baby_Associated_MicroBiota_of_the_Intestine_692018
PRJEB38352Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity692021
PRJEB81804Host depletion in pig and human colon samples682024
PRJNA948536CF patient gut microbiome investigation with CFTR modulator therapy622023
PRJNA663786Unveiling the bifidobacterial resistance mechanism against amoxicillin-clavulanic acid: genetic and ecological insights602021
PRJNA1191223Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of preterm infants (metagenome samples)582025
PRJEB108131CARMA: Human gut long read metagenomics antibiotics and prebiotics RCT542026
PRJNA273761Metagenomes from human infant fecal samples with and without necrotizing enterocolitis532015
PRJEB48983Targeted and shotgun analysis on ESBL abundance in the human gut microbiome532022
PRJNA834801Characterizing dysbiosis of the Parkinson's disease gut microbiome using shotgun metagenomics522022
PRJNA521878Gut metagenome of infants in the neonatal intensive care unit492020
PRJNA1348516Metagenomic sequencing of stool samples of infants raw sequence reads492026
PRJNA715245human gut metagenome Metagenome472022
PRJEB20800Gut resistome modulates resilience and recovery of gut microbiota after broad-spectrum antibiotic treatment452018
PRJNA338184Human gut microbiome with bacterial pathogen challenge432016
PRJNA766067The Mucosally-Adherent Rectal Microbiota Contains Features Unique to Alcohol-Related Cirrhosis422021
PRJNA327106Raw reads of the microbiota of premature infant mouth, skin, and gut372016
PRJNA389280Human gut metagenome and metatranscriptome in the inflammatory bowel disease (iHMP/HMP2)362017
PRJNA487636An increased abundance of Clostridiaceae characterizes arthritis in inflammatory bowel disease and rheumatoid arthritis: a cross-sectional study352018
PRJEB8094The initial state of the human gut microbiome determines its reshaping by antibiotics352015
PRJEB48897Microbiome compositions and resistome levels after antibiotic treatment of critically ill patients – An observational cohort study342022
PRJNA1305341ProRIDE Deep Seq Metagenomics Raw sequence reads332026
PRJEB42155UCSD IBD 200 Patient Cohort Multi-omic Project332023
PRJNA1015704Fecal and oropharyngeal microbiota from infants with cystic fibrosis on and off beta-lactam antibiotics.332025
PRJNA604820Skin metagenome from antibiotics treated healthy human subjects322022
PRJNA1095378Neonatal antibiotic resistance322024
PRJEB22863Gut mictobiota composition correlation with the clinical outcome of NSCLC and RCC patients treated with anti-PD-1 mAB322017
PRJNA521455Fecal microbiomes from a Zimbabwean pre-school population312020
PRJNA947377Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices312024
PRJNA289586Human Gut Microbiome in a Multiplex Family Study of Type 1 Diabetes Mellitus312016
PRJNA770295Dietary fiber and probiotics impact the gut microbiome and melanoma immunotherapy response312021
PRJNA532310Infant gut metagenome302020
PRJNA496479human gut metagenome Metagenome302018
PRJEB91542Microbial metabolic pathways guide response to immune checkpoint blockade therapy272025
PRJEB43119Predicting Response to Immunotherapy for Melanoma With Gut Microbiome and Metabolomics262021
PRJNA703034Metagenomics of Stool from ICU Patients262022
PRJNA646752C. difficile-colonized patients252020
PRJEB6456Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life242015
PRJEB46214Gut bacterial gene changes following pegaspargase treatment in pediatric patients with Acute Lymphoblastic Leukemia242021
PRJEB47061Fecal microbiota transplantation for treatment of ulcerative colitis232021
PRJEB1389Antibiotics impact on the human intestinal microbiota222014
PRJNA1416570gut microbiota and metabolites222026
PRJEB58815PREDIRES_phage222023
PRJNA613054Fecal resistome in early life and effects of early life antibiotics, annotated shotgun sequencing data202022
PRJEB49215Acute appendicitis manifests in two microbiome state types, with oral pathogens driving severity202022
PRJEB56741The gut metagenome harbors metabolic and antibiotic resistance signatures of established asthma202024
PRJEB97976Infant gut microbiome maturation during weaning202025
PRJDB20343Shotgun metagenome sequencing of oral and stool samples from colorectal cancer patients before and after administration of antibiotic prophylaxis for surgery202025
PRJNA400072Gut microbiome structure and metabolic activity in inflammatory bowel disease182018
PRJNA1081952BRISC microbiome sub study182024
PRJNA473126Infant Diet and Maternal Gestational Weight Gain Influence Functional Maturation of the Infant Gut Microbiome182018
PRJEB28730Metagenomic stool samples in time series162019
PRJNA1179893Dietary fiber modulates the window of susceptibility to Clostridioides difficile infection162024
PRJEB52147The Association Between Milk Feedings in the Preterm Population, the Microbiome and Risk of Atopic Disease: Microbiome, Atopic Disease, and Prematurity (MAP Study)152022
PRJEB21338Shotgun metagenomic data of fecal microbiota of patients with H. pylori infection before and after eradication therapy152017
PRJNA685168Multi-omics suggest diverse mechanisms for response to biologic therapies in IBD152021
PRJNA573821Whole Meta-genome shotgun sequencing of stool samples from human treated with antibiotics152020
PRJNA828396Virome enriched metagenomics of healthy controls and patients with IBD142022
PRJNA861716gut microbiome in polluted settlements142023
PRJNA541981Gut microbiome in melanoma patients132019
PRJNA322188Maturation of the Infant Microbiome Community Structure and Function Across Multiple Body Sites132017
PRJNA299502Human Gut Microbiome Metagenome132015
PRJEB42013Non-invasive, robust and specific fecal microbiota-based screening for the early detection of PDAC.132022
PRJEB80456afmt sample deep sequencing metagenomic and HiC122024
PRJNA331073Gut microbiome of TB patients122018
PRJNA748448Metagenomic WGS of Preterm Infant Skin and Stool122021
PRJEB5771Human gut microbiota associated to Clostridium difficile infection122014
PRJNA701982Antibiotic-driven intestinal dysbiosis in paediatric SBS alters microbiome functions and is associated with gut-derived blood stream infections throughout childhood112021
PRJEB59450PDA-MAPS - Pancreatic Ductal Adenocarcinoma - Microbiome As Predictor of Subtypes - Fistula112023
PRJNA1227883Metagenomes from mother-infant fecal and breastmilk samples of the MAMI cohort Metagenome112025
PRJNA1155319Characterisation of the gut and oral microbiome during SARS-COV-2 infection112025
PRJNA835321Whole metagenome analysis of Infant gut and breast milk microbiota102023
PRJEB18265Estimation of variability in the gut microbiota resistome of the Russian citizens aimed at identification of pathways for transmission and spread of antibiotic resistance.102016
PRJNA1056831Microbiota of infant cholestasis in Taiwan102024
PRJNA564995Gut virome in VEO-IBD102020
PRJEB10391Impact of ciprofloxacin pertubation on the intestinal resistome and microbiota in two healthy volunteers102015
PRJEB49516Role_of_microbiome_in_rare_cancers_in_Australia92024
PRJNA573963Gut Microbiome of Elderly Adults with Advanced Dementia92019
PRJEB80379Fibromyalgia and gut microbiome92024
PRJNA523592Read cloud and short read metagenomic sequencing of stool samples from a human HCT patient92019
PRJNA1055141Infant stool shallow shotgun sequencing (ANTIBIO)82023
PRJNA1153928Immune System Modulation with Oral Vancomycin in combination with Stereotactic Body Radiotherapy (SBRT) for medically inoperable Early-Stage Non-small Cell Lung Cancer82024
PRJNA674716The human gut microbiome Metagenome study for children with anorexia82023
PRJEB15257The antibiotic resistance potential of the preterm infant gut microbiome measured using shotgun metagenomics.82016
PRJNA613947human gut metagenome Metagenome72020
PRJNA853174Infant gut microbiome changes and recovers after norovirus infection72022
PRJEB63351Neuroblastoma is associated with alterations in gut microbiome composition subsequent to maternal seeding72023
PRJEB38528Placenta biopsies, saliva samples, vaginal and rectal swabs collected at delivery for babies at term72020
PRJNA446061Fecal Metagenome72018
PRJEB3085Disturbance of the gut microbiota during antibiotic stress (therapy): a multi-omic approach62013
PRJNA1445352Microbiota Transplant Therapy (MTT) Improves Gastrointestinal Symptoms by Modulating Gut Microbiota in Children with Pitt-Hopkins Syndrome, A Rare Neurodevelopmental Disorder62026
PRJNA762360Intestinal Microbiota Signatures Predict Clinical Outcome and Immune-related Adverse Events in PD-1 Treated Melanoma Patients62022
PRJNA545408Longitudinal study of the human gut virome62019
PRJNA1116923Human Gut Microbiota62024
PRJDB39536Large-scale single-cell long-read genomics enables high-resolution microbiome profiling (PRJCA047574)62026
PRJNA606271Neonatal antibiotic exposure impairs child growth during the first six years of life62020
PRJEB50408Resistant starch gut microbiome62022
PRJNA352475Mother-infant microbiome vertical transmission62018
PRJNA375935human gut Metagenome52017
PRJEB68381Pancreatitis - Microbiome As Predictor of Severity P-MAPS52023
PRJNA298489Library preparation methodology can influence genomic and functional predictions in human microbiome research42015
PRJNA716780Mothers/children Metagenome42022
PRJEB30834Human fecal metagenomes of individuals sampled along a small-scale urbanization gradient in Cameroon42021
PRJDB5180A metagenomic approach for acute cholecystitis patients enables pathogen detection and rapid diagnostics42017
PRJNA1468588Gut microbiome dynamics in a primary sclerosing cholangitis patient treated with vancomycin42026
PRJNA434731Clinical human gut metagenome Metagenomic assembly42019
PRJNA666684A metagenomic study of CVID in humans42021
PRJNA911205Psychosocial adversity experienced in utero and early life is associated with variation in gut microbiota32023
PRJNA1306676Multiple body sites microbiome in women with Preeclampsia and their infants32026
PRJEB31957Impact of narrow-spectrum antibiotics on the oral and fecal microbiome and resistome in a young child treated for otitis media32019
PRJNA626004Shotgun Metagenomics Fecal Microbiome Dysbiosis in Parkinsons Disease32020
PRJNA878603Multi-omics of host-microbiome interactions in short- and long-term Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS)32023
PRJNA1241450Oral Antibiotic Human Case Study22025
PRJNA988496Delivery mode impacts gut bacteriophage colonization during infancy22024
PRJEB48814Effects of Type 1 Diabetes Mellitus and Increased Weight on Metabolomic and Microbiome Profiles in the Pediatric Population22022
PRJNA1475489Brain Health and the Gut Microbiome (bMicrobiome Study)22026
PRJNA414540human gut metagenome Raw sequence reads22017
PRJEB74322Spanish mother and infants metagenomes of stool and milk samples22024
PRJNA317435ImMicroDyn22017
PRJNA221723Gut metagenome from two premature infants22014
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 relatives12017
PRJNA1086674The Impact of Oral Feedings on the Preterm Infant Microbiome and Metabolome12024
PRJNA1215598Human Gut Microbiota12025
PRJNA1114651Association of Indian gut microbiome with B-vitamin deficiency12026
PRJNA392494Phageome in fecal samples12017
PRJNA397219Gut metagenomes of patients with colorectal cancer12017
PRJEB108563Autism Spectrum Disorder -UCLA12026
PRJEB22207Gut microbiome diagnostics in pre-term babies12017
PRJNA1267192The impact of Adverse Childhood Experiences on gut microbiota and markers of inflammation is mediated by obesity and depression12025
PRJNA1356513Dieta Anti-INflamatoria (DAIN) study12025
PRJNA746509Gut microbiota in an infant with propionic acidemia before and after probiotic supplementation12022
PRJNA60717Metagenomic analysis of infant stool sample12012