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Densely sampled subjects (≥ 5 gut samples per subject)
Study design · collection id dense-longitudinal-subjects
Every subject in the catalog with at least five gut samples linked to the same subject_id — the time-series slice for strain tracking, stability and perturbation-recovery analyses. Dominated by infant birth cohorts (TEDDY, DIABIMMUNE), IBDMDB and adult time-series studies.
Open in the sample explorer (102,587 samples)
444
studies with member samples
102,587
member samples in this release
Membership rule
| min_samples_per_subject | min 5 |
| body_site_class | primary |
Requires subject_id; studies without subject linkage are invisible to this filter even when longitudinal.
Composition
Age category
| unknown | 35,979 |
| adult | 31,065 |
| infant | 22,673 |
| neonate | 5,818 |
| child | 3,526 |
| elderly | 2,419 |
Country
| US | 41,213 |
| FI | 16,504 |
| CN | 5,956 |
| BD | 5,519 |
| GB | 2,519 |
| MW | 1,945 |
Health condition
| healthy_control Healthy / control | 30,798 |
| transplant_or_immunocompromised Transplant / immunocompromised (HSCT | 3,388 |
| preterm_nicu Preterm / NICU (infant) | 2,486 |
| malnutrition Malnutrition / undernutrition | 2,418 |
| gi_infection_or_diarrhoea GI infection / diarrhoea (incl. C. difficile) | 2,389 |
| other_disease Other disease / condition | 2,351 |
Lifestyle
| rural_non_industrialized Rural | 1,713 |
| urban_industrialized Urban / industrialized (only when stated by the source) | 1,071 |
| institutionalized Institutionalized (nursing home | 462 |
| vegetarian_or_vegan Vegetarian / vegan (cohort defined by this diet) | 139 |
| military Military personnel / training | 103 |
| athlete Athletes / elite sport | 32 |
Member studies (444)
| Study | Title | Member samples | First public |
|---|---|---|---|
| PRJNA400115 | TEDDY Microbiome | 11,847 | 2018 |
| PRJEB60398 | Data-driven prediction of colonization outcomes for complex microbial communities | 3,117 | 2023 |
| PRJNA799247 | Metagenomics of preterm infant stool | 2,067 | 2023 |
| PRJNA398089 | Longitudinal Multi’omics of the Human Microbiome in Inflammatory Bowel Disease | 2,037 | 2017 |
| 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 FMT | 1,592 | 2018 |
| PRJEB63587 | A microbiota-directed therapeutic food for severely malnourished children evaluated following acute nutritional resuscitation | 1,519 | 2025 |
| PRJEB24771 | Legumes and Growth Data | 1,377 | 2018 |
| PRJEB89462 | Impact of phage enrichment on the observed infant gut phageome | 1,366 | 2026 |
| PRJEB84376 | Impact of phage enrichment on the observed infant gut virome | 1,366 | 2025 |
| PRJNA806984 | Microbiota and Health Study (Dhaka, Bangladesh) | 1,316 | 2022 |
| PRJEB83552 | SEPSIS Lactobacillus plantarum ATCC 202195 Microbiome Study | 1,154 | 2025 |
| PRJNA1060349 | Weaning accelerates and transforms within-host adaptation in the infant gut microbiome | 1,144 | 2024 |
| PRJNA916952 | Stanford's Outcomes Research in Kids (STORK) Virome | 1,060 | 2023 |
| PRJNA974858 | Temporal shotgun sequencing of the gut microbiota of healthy adults taking ciprofloxacin | 1,040 | 2024 |
| PRJEB13595 | Effects of preservation and storage conditions on the fecal microbiome | 1,039 | 2018 |
| PRJNA1157371 | AWI-Gen 2 Microbiome Project | 1,015 | 2025 |
| PRJNA890666 | The gut metagenome during hematopoietic cell transplantation in children | 992 | 2023 |
| PRJNA594610 | Human gut microbiome response to PDX intake | 972 | 2020 |
| PRJNA1086048 | Metagenomic analysis of faecal microbiome as a tool for targeted non-invasive biomarkers for inflammatory bowel disease | 951 | 2024 |
| PRJNA1140720 | Modelling human microbiome transmission in a nursery setting | 951 | 2024 |
| PRJNA594393 | Human gut microbiome response to FOS intake | 946 | 2020 |
| PRJEB102033 | Lantibiotic-producing bacteria impact microbiome resilience and colonization resistance | 915 | 2025 |
| PRJEB62690 | Infant stool, 5-HMO supplemented formula vs. control formula vs. breastfed | 861 | 2023 |
| PRJNA1508239 | Longitudinal stool metagenomes from children with acute lymphoblastic leukemia during chemotherapy | 825 | 2026 |
| PRJNA903921 | Gut Mycobiome Maturation and Its Determinants during Infancy: A Comparison of Shotgun Metagenomic and ITS2 Amplicon-Based Sequencing Approaches | 817 | 2023 |
| PRJEB83236 | SEPSIS Human Microbiome Study | 770 | 2025 |
| PRJNA1123170 | A microbiota-directed therapeutic food for severely malnourished children evaluated following acute nutritional resuscitation | 760 | 2024 |
| PRJNA1280936 | Gut Microbiome of Infants in the Neonatal Intensive Care Unit | 757 | 2026 |
| PRJNA354235 | Human gut metagenome and metatranscriptome raw sequence reads. | 755 | 2017 |
| PRJEB32762 | iMSMS Baranzini data | 753 | 2019 |
| PRJNA416160 | The Environmental Determinants of Diabetes in the Young (TEDDY) Parent Study | 751 | 2019 |
| PRJNA698986 | Early-life metagenomes from human infant fecal samples with matched maternal sample | 735 | 2021 |
| PRJEB89491 | LucKi Gut - Longitudinal metagenomic sequencing of infant gut microbiota | 722 | 2025 |
| PRJNA1157208 | Lactiplantibacillus plantarum for the Prevention of GI aGVHD. A Report from the Childrens Oncology Group | 716 | 2024 |
| PRJNA1357304 | Shotgun metagenomic sequencing of stool microbiomes relating to "Characterising the gut phageome and its links with host metabolism in the general population | 680 | 2025 |
| PRJNA1201249 | Legume-enriched diet improves metabolic health in prediabetes partially mediated through gut microbiome: a randomized controlled trial | 662 | 2024 |
| PRJNA595749 | COSMIC2 - Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance in the first year of life | 655 | 2019 |
| PRJNA497734 | Longitudinal gut microbiome sequence data combined from several DIABIMMUNE microbiome studies | 646 | 2018 |
| PRJEB39610 | Longitudinal metagenomic analysis of the gut microbiome in preterm infants diagnosed with necrotising enterocolitis and matched controls | 637 | 2020 |
| PRJEB37731 | Effects of the menstrual cycle and hormonal contraceptives on the human microbiome | 627 | 2020 |
| PRJNA947616 | Gut microbiome and bloodstream infections among premature infants in Singapore | 594 | 2023 |
| PRJEB29065 | Daily sampling reveals personalized diet-microbiome associations | 590 | 2019 |
| PRJNA594620 | Human gut microbiome response to PDX intake followed by FOS intake | 561 | 2020 |
| PRJNA682246 | The gut reservoir facilitates UPEC persistence and in-host adaptation in UTIs | 555 | 2022 |
| PRJNA492716 | human gut metagenome Raw sequence reads | 548 | 2019 |
| PRJEB105465 | Effects of antibiotic treatment on normal intestinal flora (ARG-study) | 546 | 2026 |
| PRJNA1139951 | Long read metagenomics | 533 | 2024 |
| PRJEB101630 | Patterns of gut microbiome composition, function and dynamics in young children, adolescents and adults over a three-year period | 527 | 2026 |
| PRJNA821542 | Longitudinal gut metagenomes from mothers and their infants in the EDIA study | 515 | 2022 |
| PRJEB37924 | Longitudinal multi-omics reveals subset-specific mechanisms underlying irritable bowel syndrome | 498 | 2020 |
| PRJNA594613 | Human gut microbiome response to FOS intake followed by PDX intake | 491 | 2020 |
| PRJNA1121316 | CONSORTIUM VE303 phase 2 study stool metagenomes | 471 | 2024 |
| PRJNA1348516 | Metagenomic sequencing of stool samples of infants raw sequence reads | 465 | 2026 |
| PRJNA912122 | Lactulose-mediated Bifidobacteria expansion promotes a beneficial fecal metabolite profile that is associated with exclusion of antibiotic-resistant pathogens and improved outcomes in advanced liver disease | 462 | 2022 |
| PRJNA1079705 | Efficacy and Safety of BB-12 Supplemented Strawberry Yogurt For Healthy Children on Antibiotics (PLAY ON) | 450 | 2024 |
| PRJNA755324 | Colonization of the Live Biotherapeutic Product VE303 and Modulation of the Microbiota and Metabolites in Healthy Volunteers | 450 | 2022 |
| PRJNA698223 | TD Cusco travelers study | 441 | 2022 |
| PRJNA1058700 | gut microbiota | 440 | 2025 |
| PRJNA675301 | Role of Diet in the Reconstitution of the Human Gut Microbiome and its Metabolome | 434 | 2020 |
| PRJNA489090 | Human infant gut metagenome, infant shotgun sequencing | 426 | 2019 |
| PRJEB41481 | Critical evaluation of preservation methods for metagenomic analysis of faecal microbiomes | 420 | 2021 |
| PRJNA884103 | Gut residence of bloodstream infection pathogens in the NICU | 420 | 2023 |
| PRJNA400628 | Escherichia coli Genome sequencing and assembly | 414 | 2017 |
| PRJNA642308 | Gut microbiome of subjects with inflammatory bowel disease undergoing diet intervention | 409 | 2021 |
| PRJNA1301887 | Preterm infant weight gain patterns are not associated with gut microbiome measures | 403 | 2026 |
| PRJNA544527 | BIO-ML: The Broad Institute-OpenBiome Microbiome Library enables mechanistic studies with isolates, genomes, and longitudinal metagenomics and metabolomic data | 402 | 2019 |
| PRJNA1045584 | Impact of SARS-CoV-2 in stool sample from women living with HIV and HIV-negative women and their infants. | 398 | 2024 |
| PRJNA448876 | Dense longitudinal metagenomic analysis of the gut microbiome of FMT donors | 391 | 2020 |
| PRJNA1220341 | Human gut microbiome during treatment with CRISPR-armed phages (SNIPR001) or placebo | 391 | 2026 |
| PRJNA473126 | Infant Diet and Maternal Gestational Weight Gain Influence Functional Maturation of the Infant Gut Microbiome | 390 | 2018 |
| PRJNA48479 | Human Microbiome Project (HMP) Metagenomic WGS Projects, deeper sequencing of the human microbiome samples: Production Phase | 381 | 2010 |
| PRJNA993675 | Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases | 373 | 2024 |
| PRJEB46788 | Codiversification of gut microbiota with humans | 372 | 2022 |
| PRJNA290380 | A longitudinal analysis of the developing gut microbiome in infants from Finland, Estonia, and Russian Karelia | 371 | 2016 |
| PRJNA814303 | Impact of complex oligosaccharides and a probiotic on the human microbiome | 369 | 2022 |
| PRJNA1505569 | A DASH diet increases microbiome diversity, butyrate production, and circulating acetate in persons with type 2 diabetes: Results from the DASH4D randomized feeding trial | 365 | 2026 |
| PRJEB56264 | Psychobiotic Diet Study | 360 | 2022 |
| PRJNA872399 | Preterm infants at low risk for early-onset sepsis differ in early fecal microbiome assembly | 356 | 2022 |
| PRJEB84944 | Shotgun sequencing of 56 mother-infant dyads from the ALADDIN birth cohort | 355 | 2025 |
| PRJNA1307073 | SPATIOTEMPORAL EFFECT OF DIFFERENT ERADICATION THERAPIES FOR HELICOBACTER PYLORI INFECTION ON THE COMPOSITION AND FUNCTION OF THE WHOLE GASTROINTESTINAL MICROBIOTA PART 1 | 355 | 2026 |
| PRJEB68317 | Fecal microbiota transplantation in Parkinson's disease | 354 | 2024 |
| PRJNA1086532 | Intestinal microbiomes of premature neonates with bacteremia | 344 | 2025 |
| PRJNA352220 | Human gut microbiome with bacterial pathogen challenge | 338 | 2016 |
| PRJNA388263 | Colon cleanout human gut V4 16S survey & shotgun metagenomic sequencing | 338 | 2017 |
| PRJNA904651 | Multiomic analysis of microbiome and host identifies features differentiating diet and surgical induced weight loss | 337 | 2025 |
| PRJEB64515 | Gut Microbiome Dynamics and Predictive Value in Hospitalized COVID-19 Patients: A Comparative Analysis of Shallow and Deep Shotgun Sequencing | 332 | 2023 |
| PRJNA1364313 | Antibiotic impact on preterm infant microbiome maturation | 326 | 2025 |
| PRJNA528511 | Global TravEpiNet AMR surveillance Genome sequencing and assembly | 325 | 2023 |
| PRJNA824824 | An ex vivo screening of community response to synthetic and reference glycans | 324 | 2023 |
| PRJEB49334 | Dynamics in the gut microbiomes of subjects colonized by carbapenemase-producing Enterobacteriaceae (longitudinal data) | 321 | 2022 |
| PRJNA1056456 | Homo sapiens Metagenome | 320 | 2024 |
| PRJEB85985 | Microbial-Human Ecology and Temperature | 318 | 2025 |
| PRJNA993161 | Impact of complex oligosaccharides and a probiotic on the antibiotic-treated human microbiome | 312 | 2023 |
| PRJNA693793 | BaBel Infant Gut Virome Raw Data | 304 | 2021 |
| PRJNA301903 | Metagenomic sequencing of preterm infant gut microbiota raw sequence reads | 302 | 2016 |
| PRJEB39661 | Changes in the microbiota across life: the existence of a core of microbial taxa and decoupling taxa. | 301 | 2023 |
| PRJNA1402699 | Dietary resistant starches type 2 and 4 differentially impact the human gut microbiome | 294 | 2026 |
| PRJNA546227 | Metagenomic Study of Gastrointestinal Tract Microbial Community Change During Long-Term Acute Care | 291 | 2019 |
| PRJNA957107 | Imrabiome - Rheumatoid project | 288 | 2024 |
| PRJNA637785 | Multi-donor FMT to treat adolescents with severe obesity (The Gut Bugs Trial) | 282 | 2021 |
| PRJNA1138246 | Fecal metagenomes of Peruvian children | 282 | 2025 |
| PRJNA917819 | Probiotics modulation of post-antibiotic gut microbiome in healthy population | 280 | 2025 |
| PRJEB50977 | A large-sale meta-analysis of C. difficile prevalence across age, geography, health and disease. | 279 | 2023 |
| PRJEB58157 | Perturbation and resilience of the gut microbiome three months after β-lactams exposure in healthy volunteers suggest an important role of endogenous β-lactamases | 277 | 2023 |
| PRJNA1463324 | VE202 phase 1 stool metagenomes | 273 | 2026 |
| PRJNA822660 | Profiling the human intestinal environment under physiologic conditions | 273 | 2023 |
| PRJNA664754 | Fecal metagenomes of healthy volunteers | 269 | 2022 |
| PRJNA1464738 | Metabiosis underlies a microbiota permissive to Pseudomonadota and increases the risk of gut-borne bloodstream infection | 265 | 2026 |
| PRJNA988496 | Delivery mode impacts gut bacteriophage colonization during infancy | 265 | 2024 |
| PRJNA385949 | Longitudinal Stool Study of patients with IBD and controls | 253 | 2017 |
| PRJNA1269031 | Randomised, clinical trial: Eight weeks of treatment with probiotic Bifidobacterium breve, Bif195 lowers fatigue scores in patients with diarrhoea-predominant irritable bowel syndrome | 250 | 2025 |
| PRJNA878528 | Nutrition as a predictor of microbiome injury in allo-HCT | 241 | 2025 |
| PRJEB108545 | Coffee Shapes the Gut Microbiome and Host Cognition | 240 | 2026 |
| PRJNA1116923 | Human Gut Microbiota | 239 | 2024 |
| PRJNA396794 | preterm infant gut metagenomes (NIH Y4 Cohort) | 238 | 2017 |
| PRJNA533528 | Marked loss of diversity and pathogen domination of the gut microbiota in critically ill patients | 227 | 2019 |
| PRJEB41102 | Analysis of human fecal metagenomes from adults and infants, to investigate strain persistance, dispersal and purifying selection of bacterial strains. | 227 | 2020 |
| PRJNA1042925 | Fecal samples of microsatellite instability-high cancer patients Raw sequence reads | 223 | 2025 |
| PRJEB38036 | Assessment of fecal DNA extraction protocols for metagenomic study | 223 | 2020 |
| PRJNA737472 | Microbiome sequencing of ulcerative colitis patients receiving fecal microbiota transplantation | 222 | 2022 |
| PRJNA387903 | Intestinal Virome Changes Precede Autoimmunity in Type I Diabetes Susceptible Children | 220 | 2017 |
| PRJNA715245 | human gut metagenome Metagenome | 215 | 2022 |
| PRJNA1169175 | Expansion of a bacterial operon during cancer treatment ameliorates drug toxicity | 213 | 2024 |
| PRJNA475599 | Fecal transplant for ulcerative colitis | 212 | 2019 |
| PRJNA662107 | human metagenome Raw sequence reads | 212 | 2021 |
| PRJNA1025016 | Commensal Antimicrobial Resistance Mediates Microbiome Resilience to Antibiotic Disruption | 209 | 2024 |
| PRJNA1425751 | Gut metagenome | 206 | 2026 |
| PRJNA1071720 | FECBUD Study Fecal Metagenomes | 203 | 2024 |
| PRJNA1106565 | Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants | 203 | 2024 |
| PRJNA1124620 | Longitudinal study of human gut microbiota (untreated and ethanol treated paired stool samples) | 200 | 2026 |
| PRJEB94043 | Clinical trial (TACITO) for the evaluation of the efficacy of targeted of fecal microbiota transplantation (FMT) in improving response rates to immune checkpoint inhibitors (ICIs) in subjects with treatment-naïve metastatic renal cell carcinoma. | 200 | 2025 |
| PRJNA421352 | Gut microbiome in Children with Acute Lymphoblastic Leukemia (ALL) | 197 | 2017 |
| PRJNA1224809 | Novome metagenomic data | 194 | 2025 |
| PRJEB50408 | Resistant starch gut microbiome | 190 | 2022 |
| PRJNA417343 | preterm infant gut metagenomes (NIH Y5 Cohort) | 188 | 2019 |
| PRJNA1306109 | Home versus Hospital Transplant | 184 | 2025 |
| PRJNA672867 | Effectiveness of Fecal Microbiota Transplant together with PD-1 blockade in overcoming resistance to anti-PD-1 therapy in advanced melanoma patients | 183 | 2020 |
| PRJEB81106 | Simultaneous metagenome-informed metaproteomics of the human gut microbiome, host and dietary exposome uncover functional interactomes in health & IBD | 180 | 2024 |
| PRJEB40903 | DNA extraction comparison testing 2019-2020 | 176 | 2020 |
| PRJNA630999 | Premature infant microbiome Metagenome | 176 | 2021 |
| PRJEB54704 | Gut microbiome associations with clinical outcomes of CD19-targeted CAR-T cell immunotherapy | 168 | 2023 |
| PRJNA844888 | Vaughn UC IMT Study | 168 | 2025 |
| PRJNA707487 | Metagenomic sequencing of stool samples from human hematopoietic cell transplantation patients | 166 | 2021 |
| PRJNA1289847 | Gut microbiota composition of patients in FMT-LUMINate clinical trial | 162 | 2025 |
| PRJNA433058 | human gut metagenome Metagenome | 160 | 2019 |
| PRJNA1216426 | The 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 trial | 155 | 2025 |
| PRJNA1312123 | Development of the preterm infant gut and gastric residuals microbiome | 154 | 2025 |
| PRJNA800792 | An ex vivo screening of selected glycans across multiple individuals | 154 | 2022 |
| PRJEB43454 | Long-term diosmectite use does not alter the gut microbiota in adults with chronic diarrhea | 150 | 2022 |
| PRJNA606198 | Comparison of methods to collect fecal samples for microbiome studies using whole-genome shotgun metagenomic sequencing | 148 | 2020 |
| PRJNA394877 | High frequency intestinal microbiota sampling in allogeneic bone marrow transplant patients | 148 | 2018 |
| PRJNA1074135 | Long-term effects of ciprofloxacin treatment on the gastrointestinal and oropharyngeal microbiome are more pronounced after longer antibiotic courses | 147 | 2024 |
| PRJNA971895 | Resismet | 145 | 2023 |
| PRJDB3601 | Metagenomics of Japanese gut microbiomes | 144 | 2016 |
| PRJNA925700 | 2-months Longitunidal healthy human gut microbiome | 143 | 2023 |
| PRJEB52881 | Multi-omic Analyses Reveal Bifidogenic Effect and Metabolomic Shifts in Healthy Human Cohort Supplemented with a Prebiotic Dietary Fiber Blend | 140 | 2022 |
| PRJNA475246 | Strain-level identification of mother-to-child bacterial transmission during the first few months of life | 140 | 2018 |
| PRJEB73985 | Oat beta glucan versus iso dietary fiber or placebo in MASLD: A multicenter, randomized, placebo-controlled dietary study | 140 | 2025 |
| PRJNA739008 | Effect of amoxicillin prophylaxis on gut microbiome and resistome for severe acute malnutrition in Niger | 139 | 2023 |
| PRJNA1372133 | Metagenomic sequencing of fecal and beef samples Raw sequence reads | 139 | 2026 |
| PRJNA787952 | Raw_metagenomic_sequencing_for_Pediatrics_Gut_Decontamination_NCT02641236 | 139 | 2022 |
| PRJNA294605 | Metagenomes from 11 human infant fecal samples hospitalized in the same intensive care unit | 138 | 2016 |
| PRJNA1157403 | Colorectal cancer-associated bacteria are broadly distributed in global microbiomes and drivers of precancerous change | 138 | 2025 |
| PRJEB81804 | Host depletion in pig and human colon samples | 138 | 2024 |
| PRJNA530252 | Effect of cycled, inhaled tobramycin on the sputum microbiome in cystic fibrosis | 135 | 2020 |
| PRJEB27308 | Microbiome metagenome analysis of stool samples from individuals with low and high salivary amylase gene copy numbers | 133 | 2019 |
| PRJNA1258733 | Human Gut Metagenome | 132 | 2026 |
| PRJNA1157410 | Microbial diversity in human gut affected by grape polyphenols | 130 | 2025 |
| PRJNA905467 | Dynamic nature of viral and bacterial communities in human faeces during ex vivo incubation | 130 | 2023 |
| PRJNA545408 | Longitudinal study of the human gut virome | 130 | 2019 |
| PRJEB105455 | PERSIMMON POWDER FROM FRUIT LOSS AS NOVEL PREBIOTICS TO MODULATE GUT MICROBIOTA | 128 | 2026 |
| PRJNA532645 | PRASCO gut microbiome profile of Pediatric Severe Acute Ulcerative Colitis patients under Antimicrobial treatment | 127 | 2019 |
| PRJNA446038 | viral metagenome Raw sequence reads | 126 | 2019 |
| PRJEB33603 | A metagenomic approach to diagnosis, induction and maintenance of deep remission following exclusive enteral nutrition in pediatric Crohn’s Disease | 125 | 2019 |
| PRJEB53551 | FMT alleviates peripheral neuropathy in patients with diabetes mellitus | 124 | 2024 |
| PRJNA510445 | The relationship of fecal microbiomes and nutritional status in cystic fibrosis | 122 | 2019 |
| PRJEB76399 | Effect of large-scale population-based dietary change to vegetarianism on antimicrobial resistance and bacterial composition of sewage in Thailand | 121 | 2025 |
| PRJNA699281 | The microbiome of aging: instability, heterogeneity, and pathogenicity reservoirs in the skin, oral, and gut microbiome of older adults | 120 | 2022 |
| PRJEB77202 | Cork Nutrition Cohort | 120 | 2025 |
| PRJNA1160256 | The effects of selected food components and additives on the human gut microbiome | 120 | 2025 |
| PRJNA486782 | Influence of early environmental factors on the establishment and development of gut microbiome composition and function and metabolomics profiles in infants at-risk of celiac disease | 119 | 2024 |
| PRJNA994318 | human gut Raw sequence reads | 119 | 2023 |
| PRJNA529586 | Alzheimers Disease microbiome in elders | 116 | 2020 |
| PRJEB40933 | BIOME-Preserve: A Novel Microbiome Transport Medium for Culture Recovery | 116 | 2021 |
| PRJNA1347413 | Metagenomic data from the ASPREE-XT study | 115 | 2025 |
| PRJNA1005702 | Observing and Understanding antibiotic-induced Reduction in Short-chain Fatty Acids and time dependent administration of BB-12 proBIOTIC (OURBIOTIC) | 115 | 2024 |
| PRJNA674880 | Microbiota Restoration Reduces Antibiotic Resistant Bacteria Gut Colonization in Patients with Recurrent Clostridioides difficile Infection from the Open-Label PUNCH CD Study | 112 | 2020 |
| PRJNA725597 | The role of maternal exposures on commensal microbes | 111 | 2021 |
| PRJNA1290813 | FMT plus systemic therapy in renal cell cancer | 110 | 2025 |
| PRJEB111647 | Restoration of Microbiota in Newborns | 110 | 2026 |
| PRJEB47061 | Fecal microbiota transplantation for treatment of ulcerative colitis | 109 | 2021 |
| PRJNA701961 | Donor and recipient stool metagenomes from a fecal microbiota transplantation study | 109 | 2021 |
| PRJNA1004651 | Human gut metagenome, whole genomic shotgun sequencing | 107 | 2023 |
| PRJNA592261 | Infant virome during the first year of life | 106 | 2020 |
| PRJNA338184 | Human gut microbiome with bacterial pathogen challenge | 106 | 2016 |
| PRJEB44237 | Effect of fecal microbiota transplantation combined with Mediterranean diet on insulin sensitivity in subjects with metabolic syndrome | 105 | 2021 |
| PRJNA776530 | Impact of a 7-day homogeneous diet on interpersonal variation in human gut microbiomes and metabolomes | 105 | 2022 |
| PRJNA1130109 | Infant gut microbiome study | 105 | 2024 |
| PRJEB65987 | Intra-host evolution of Norovirus in immunocompromised individuals | 105 | 2024 |
| PRJEB11419 | American Gut Project | 104 | 2015 |
| PRJEB86785 | The Antibiotic Resistance in the Microbiome – Oxford | 103 | 2025 |
| PRJNA945408 | Impact of antibiotic regimens for the prevention and treatment of travelers diarrhea Prevent TD and TrEAT TD | 103 | 2023 |
| PRJEB123118 | Infant and Mother faecal viromes from the PEARL cohort | 100 | 2026 |
| PRJNA1457641 | OH-MicroDynamics | 98 | 2026 |
| PRJNA625520 | Linking strain engraftment in fecal microbiota transplantation with maintenance of remission in Crohn's disease | 97 | 2020 |
| PRJNA1491285 | Gut microbiota in patients with cirrhosis and portal hypertension receiving lactulose | 96 | 2026 |
| PRJNA728680 | PREMIX | 95 | 2022 |
| PRJNA63661 | Microbial composition of samples from infant gut | 95 | 2011 |
| PRJNA589622 | Underfeeding and oral vancomycin perturb the human gut microbiome and impair nutrient absorption | 95 | 2019 |
| PRJEB55607 | The effect of dietary bioactive on gut microbiome diversity (DIME) – a pilot study | 95 | 2023 |
| PRJEB49206 | Extensive microbial novelty in the Hadza and Nepali gut microbiome reveals how lifestyle impacts composition and function | 94 | 2022 |
| PRJNA1154644 | Species- and subspecies-level characterization of health-associated bacterial consortia that colonize the human gut during infancy | 94 | 2025 |
| PRJNA877821 | Shotgun sequencing of fecal samples from patients colonized with multidrug resistant Enterobacteriaceae | 93 | 2022 |
| PRJNA290729 | Characterization of the distal gut microbiota in obese patients following a weight-loss intervention using whole metagenome shotgun sequencing | 92 | 2015 |
| PRJEB97976 | Infant gut microbiome maturation during weaning | 91 | 2025 |
| PRJNA1163373 | Jahansouz IMT Trial | 90 | 2025 |
| PRJNA905698 | Lectin-Seq: a method to profile lectin-microbe interactions in native communities | 84 | 2023 |
| PRJNA1417478 | Data of Feces Analyzed by Metagenomics Bifidobacterium Supplementation Maintains Gut Microbiota Stability and Enhances Well-Being During Short-Term Travel | 80 | 2026 |
| PRJNA663786 | Unveiling the bifidobacterial resistance mechanism against amoxicillin-clavulanic acid: genetic and ecological insights | 80 | 2021 |
| PRJNA646752 | C. difficile-colonized patients | 79 | 2020 |
| PRJNA917645 | Shallow shotgun sequencing reduces technical variation in microbiome analysis | 78 | 2023 |
| PRJDB15926 | Kolkata diarrhea metagenome project | 75 | 2025 |
| PRJEB76849 | Gut microbiome alterations in Alzheimers disease _WF-BEAM | 75 | 2024 |
| PRJNA491657 | Microbiota of allo-HSCT patients and in the setting of Autologous Fecal Microbiota Transplant (auto-FMT) at MSKCC Raw sequence reads | 74 | 2020 |
| PRJNA1015704 | Fecal and oropharyngeal microbiota from infants with cystic fibrosis on and off beta-lactam antibiotics. | 74 | 2025 |
| PRJNA1429435 | Shotgun metagenomics samples of Camu camu trial. | 73 | 2026 |
| PRJEB38481 | Liver Cirrhosis cohort | 73 | 2021 |
| PRJNA474024 | Engraftment of Bacteroidetes species in a Fecal Microbiota Transplant study | 72 | 2019 |
| PRJDB36826 | Metagenomic data of the gut microbiota in healthy young individuals (PRJCA040384) | 72 | 2025 |
| PRJNA824068 | A wipe-based stool collection and preservation kit for microbiome community profiling | 71 | 2022 |
| PRJNA770101 | the transmission of probio-m9 from mother to infant | 71 | 2022 |
| PRJEB56144 | The gut microbiota of children with split-dose bowel preparations revealed by metagenomics | 70 | 2024 |
| PRJNA545312 | The role of Enterococcus in allo-HCT patient outcome | 70 | 2020 |
| PRJNA940499 | Quantifying bias introduced by sample collection in relative and absolute microbiome measurements | 70 | 2023 |
| PRJNA647221 | Before and after fecal microbiota transplantation in ulcerative colitis patients | 68 | 2024 |
| PRJNA477357 | Microbiome in Severe Combined Immunodeficiency (X-linked) | 66 | 2018 |
| PRJNA407341 | viral metagenome Metagenome | 66 | 2018 |
| PRJDB14273 | Human gut and salivary microbiota before, during, and after fructooligosaccharide supplementation | 66 | 2024 |
| PRJNA1107274 | Neoadjuvant Vidutolimod and Nivolumab in High-Risk Resectable Melanoma | 65 | 2024 |
| PRJNA1322507 | Live biotherapeutic product MTC01 vs FMT | 65 | 2026 |
| PRJEB65418 | Fecal microbiota transplantation in irritable bowel syndrome patients | 65 | 2024 |
| PRJNA503484 | Human gut metagenome raw sequence reads | 64 | 2019 |
| PRJEB44737 | Metagenomic shotgun sequencing of healthy stool bank donors and multiple recurrent Clostridioides infected recipients from the Netherlands Donor Feces Bank | 64 | 2022 |
| PRJEB110888 | Faecalibacterium prausnitzii EXL01 for the Maintenance of Steroid-induced Clinical Response or Remission in Patients with Crohn’s Disease: a first in human trial | 63 | 2026 |
| PRJEB8347 | Temporal and technical variability of human gut metagenomes | 62 | 2015 |
| PRJNA848838 | WGS blood culture isolates from critically ill patients | 61 | 2023 |
| PRJNA1202717 | Long-term Effect of Antibiotic Therapy on the Gut Microbiome and Antibiotic Resistance Genes Profiles in Healthy Stool Donors | 61 | 2025 |
| PRJEB42384 | BCN02_ROMI_Microbiome | 61 | 2022 |
| PRJDB15798 | Novel sampling method optimized for fecal microbiota and metabolite preservation during storage | 60 | 2023 |
| PRJEB70723 | Comparison of experimental methodologies based bulk-metagenome and virus-like particle enrichment | 60 | 2024 |
| PRJNA1490646 | Gut Microbiome of Pregnancy and Infancy | 60 | 2026 |
| PRJEB17632 | Subspecies in the global human gut microbiome | 59 | 2017 |
| PRJNA1072756 | Enriched microbiomes from patients undergoing haematopoietic stem cell transplantation in India | 58 | 2024 |
| PRJNA561398 | Temporal variation in the gastrointestinal microbiota of ICU patients | 58 | 2019 |
| PRJNA991155 | Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples | 58 | 2023 |
| PRJEB66265 | Metagenomic and viromic sequencing of ICU patient stool samples | 57 | 2023 |
| PRJEB89898 | Metagenomic sequences of the fecal microbiome from patients with decompensated cirrhosis and ACLF | 56 | 2025 |
| PRJNA648321 | Comparison of DNA extraction protocols from stool samples | 56 | 2022 |
| PRJDB9649 | Fecal microbiota transplantation alleviates diabetes peripheral neuropathy | 55 | 2022 |
| PRJEB61942 | Longitudinal study of the gut microbiota during anti-pd1 immunotherapy in melanoma patients. | 54 | 2024 |
| PRJNA289586 | Human Gut Microbiome in a Multiplex Family Study of Type 1 Diabetes Mellitus | 54 | 2016 |
| PRJNA885489 | The associations between drug exposures and the intestinal microbiome in allo-HCT patients | 54 | 2022 |
| PRJNA928311 | Probiotics supplementation to ileostoma bacterial community cause dynamic increase in their resistance to perturbations and metabolic utilization | 53 | 2024 |
| PRJNA641975 | Fecal microbiota transplantations reconstitute gut fungal and viral microbiota in graft-versus-host disease | 53 | 2020 |
| PRJDB16260 | metagenomic data from human fecal samples | 52 | 2025 |
| PRJNA1199203 | Microbiome assessment of human patients with IBS | 51 | 2025 |
| PRJEB46778 | Fecal Microbiota Transplantation for Metabolic Syndrome | 50 | 2022 |
| PRJEB12357 | Durable coexistence of donor and recipient strains after fecal microbiota transplantation | 50 | 2016 |
| PRJNA1088077 | Microbiome and resistome characterization of patients colonized with carbapenem-resistant Enterobacterales by long-read metagenomic next-generation sequencing of rectal swabs | 49 | 2024 |
| PRJNA273761 | Metagenomes from human infant fecal samples with and without necrotizing enterocolitis | 49 | 2015 |
| PRJEB56784 | Validation of the nucleic acid automation pipeline using Matrix tubes | 48 | 2023 |
| PRJEB46779 | Fecal Microbiota Transplantation for Extended-Spectrum Beta Lactamase Carriers. | 48 | 2022 |
| PRJNA397450 | Human gut microbial community assessment using stool, rectal swab, and mucosal samples | 48 | 2017 |
| PRJNA1057679 | Integrative analysis of serum and fecal metabolome and microbiome that herald a flare in Crohn Disease | 48 | 2026 |
| PRJNA1293117 | The in vitro intake of Sambucus nigra extract promisingly impacts the human gut ecosystem in an individual-dependent way | 48 | 2025 |
| PRJNA647720 | Human gut microbiome sequencing during a high fiber diet intervention | 47 | 2021 |
| PRJNA493884 | Comprehensive evaluation of sequencing variation caused by sampling site, sequencer and library preparation method in microbiome research | 47 | 2019 |
| PRJNA889771 | Raw reads of the microbiota of premature infant mouth, skin, and gut | 46 | 2022 |
| PRJEB20800 | Gut resistome modulates resilience and recovery of gut microbiota after broad-spectrum antibiotic treatment | 45 | 2018 |
| PRJNA637878 | Precise quantification and tracking of gut bacterial strains following fecal transplantation demonstrates long-term stable engraftment and predicts outcome | 45 | 2021 |
| PRJNA314903 | Pseudomonas Aeruginosa Early CF Adaptive Changes | 45 | 2017 |
| PRJNA627223 | Shotgun - HIV Intestinal Microbiota Pre and Post Initiation of Antiretroviral Therapy. | 45 | 2020 |
| PRJNA1268178 | Gut Bugs in Anorexia Nervosa Trial | 45 | 2025 |
| PRJNA1145027 | Metal availability shapes early life microbial ecology and community succession | 45 | 2024 |
| PRJEB18780 | Exploring 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 relatives | 45 | 2017 |
| PRJNA720145 | GO: Gut Microbiome and Oral Fluoropyrimidine Study in Patients with Colorectal Cancer | 43 | 2021 |
| PRJNA275349 | Human Microbiome Environment Metagenome | 42 | 2015 |
| PRJNA524170 | Resistant microbiome underlies antibiotic therapy in pouchitis | 42 | 2019 |
| PRJNA800831 | Shotgun metagenome sequencing of samples from Conambo in the Ecuadorian Amazon | 42 | 2025 |
| PRJNA1445352 | Microbiota Transplant Therapy (MTT) Improves Gastrointestinal Symptoms by Modulating Gut Microbiota in Children with Pitt-Hopkins Syndrome, A Rare Neurodevelopmental Disorder | 42 | 2026 |
| PRJNA995911 | Fecal microbiota cooperative metabolism of pectins derived from apple pomace: a functional metagenomic study | 41 | 2023 |
| PRJEB47459 | Comprehensive wet-bench and bioinformatics workflow for complex microbiota using Oxford Nanopore Technologies | 41 | 2021 |
| PRJNA511899 | Analysis of Intestinal Microbial Diversity and Function Gene Based on Single Cell Amplification Technique | 40 | 2019 |
| PRJEB46003 | Intestinal mycobiota composition of children with thalassemia undergoing allogeneic hematopoietic stem cell transplantation | 40 | 2022 |
| PRJNA1218764 | Evaluation of shotgun metagenomics as a diagnostic tool for infectious gastroenteritis | 40 | 2025 |
| PRJNA1004534 | A metagenomic prospective cohort study on gut microbiome composition and clinical infection in Small Bowel Transplantation | 40 | 2023 |
| PRJNA1086674 | The Impact of Oral Feedings on the Preterm Infant Microbiome and Metabolome | 39 | 2024 |
| PRJNA505228 | Microbiome of patients under immunotherapy in China | 39 | 2019 |
| PRJNA386503 | Sulfur Production | 39 | 2017 |
| PRJNA756556 | Fiber Mixture for a Balanced Gut Microbiota and Human Health in Parkinson's Disease | 38 | 2021 |
| PRJNA297252 | Intestinal microbiota dynamics in hospitalized patients | 38 | 2015 |
| PRJNA524322 | Gut Colonization Preceding Mucosal Barrier Injury Bloodstream Infection: a Strain-Level Analysis | 38 | 2019 |
| PRJNA994433 | Longitudinal Variability of Bifidobacterium Species in the Infant Gut is Independent of Maternal Milk HMO Composition | 37 | 2023 |
| PRJNA801051 | Gut microbiota community in healthy Chinese population | 37 | 2022 |
| PRJNA701982 | Antibiotic-driven intestinal dysbiosis in paediatric SBS alters microbiome functions and is associated with gut-derived blood stream infections throughout childhood | 37 | 2021 |
| PRJNA327106 | Raw reads of the microbiota of premature infant mouth, skin, and gut | 37 | 2016 |
| PRJNA749919 | An optimized approach to the metagenomic population studies: from sample donation to community profiling | 36 | 2022 |
| PRJNA1365125 | Profiling the small intestinal microbiota in vitro using 4 donors | 36 | 2026 |
| PRJEB45799 | The person-to-person transmission landscape of the gut and oral microbiomes | 36 | 2022 |
| PRJNA937304 | Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut | 36 | 2023 |
| PRJNA641015 | Comparative genomics analyses of Lactobacillus crispatus isolated from different ecological niches reveal an environmental adaptation of this species to the human vaginal environment | 36 | 2021 |
| PRJNA1249435 | Neurobiological and neurocognitive consequences of diverse microbiome functional trajectories | 35 | 2026 |
| PRJEB86881 | Deep shotgun metagenomics of the gut microbiome in Malawian adults | 35 | 2025 |
| PRJNA964705 | Nasal and fecal communities of cows, farmers, and non-farmers. Raw sequence reads | 34 | 2024 |
| PRJEB108678 | MPRINT: mother-infant dyads and antibiotic exposure | 34 | 2026 |
| PRJNA604820 | Skin metagenome from antibiotics treated healthy human subjects | 32 | 2022 |
| PRJNA909041 | GutAlive(R) enables DNA-based microbiome analysis without disrupting the original composition and diversity | 31 | 2023 |
| PRJNA909223 | Study of microbiome alterations in hospitalized COVID-19 patients and non-infected controls | 31 | 2024 |
| PRJNA978345 | Infant cystic fibrosis BAL and stool microbiome | 31 | 2024 |
| PRJNA1413407 | Microbial-based integrated model to measure and module brain development and function | 31 | 2026 |
| PRJNA1007579 | FECAL Raw sequence reads | 30 | 2024 |
| PRJEB126105 | Co-biotic Formulations Mediate Microbiome Function and Composition | 30 | 2026 |
| PRJNA949528 | Health programming, evolution of the infants microbiome | 30 | 2023 |
| PRJNA911046 | Multicenter evaluation study of gut microbiome profiling by next-generation sequencing | 30 | 2023 |
| PRJNA1365657 | Yeast protein fermentation modulates barrier in older males ex vivo | 30 | 2025 |
| PRJNA285502 | Fecal microbiota transplantation (FMT) for ulcerative colitis | 30 | 2017 |
| PRJEB38352 | Gastrointestinal Surgery for Inflammatory Bowel Disease Persistently Lowers Microbiome and Metabolome Diversity | 30 | 2021 |
| PRJNA1199756 | Gut microbiota-mediated conversion of mangiferin to norathyriol alters short chain fatty acid and urate metabolism | 30 | 2025 |
| PRJEB97162 | Engraftment of donor phageome via fecal microbiota transplantation in recurrent C. difficile infection | 30 | 2025 |
| PRJNA1039781 | Fecal metabolite profiling identifies liver transplant recipients at risk for postoperative infection | 30 | 2023 |
| PRJDB6503 | Method assessment of fecal DNA extraction | 30 | 2019 |
| PRJEB25954 | Metagenomic insights into resistant starch degradation by human gut microbiota | 30 | 2018 |
| PRJEB40960 | Shotgun metagenomic sequencing of the fecal microbiome to predict response to frontline high-dose steroids in patients with lower gastrointestinal acute graft-versus-host disease | 29 | 2020 |
| PRJNA961946 | Metagenome or environmental sample from feces metagenome | 29 | 2023 |
| PRJNA439152 | GUT BACTERIAL METAGENOME Metagenome | 29 | 2022 |
| PRJNA273574 | Intestinal model Metagenome | 29 | 2015 |
| PRJDB20343 | Shotgun metagenome sequencing of oral and stool samples from colorectal cancer patients before and after administration of antibiotic prophylaxis for surgery | 28 | 2025 |
| PRJNA649316 | Hi-C and metagenomic sequencing of neutropenic patient microbiomes | 28 | 2020 |
| PRJNA1450848 | Improved Efficacy of Fecal Microbiota Transplantation for Ulcerative Colitis with Non-urbanized Donors | 27 | 2026 |
| PRJEB30796 | We analysed five different techniques to isolate phages from human adult faeces | 27 | 2019 |
| PRJNA61745 | Strain-resolved community genomic analysis of gut microbial colonization in a premature infant | 26 | 2011 |
| PRJNA1065951 | Fecal microbiota transplantation promotes immunotherapy sensitivity in refractory gastrointestinal cancer patients | 25 | 2024 |
| PRJNA499081 | Gut bacteriophage community of metabolic syndrome subjects during fecal microbial transplant | 25 | 2019 |
| PRJEB98012 | Creeping Fat | 24 | 2025 |
| PRJEB28338 | Influence of travel on the gut microbiome of cricketers | 24 | 2018 |
| PRJEB29237 | 16S rRNA gene amplicon and metagenomic shotgun sequencing reads from a pediatric acute lymphoblastic leukemia cohort. Metagenomic shotgun sequencing reads have been prefiltered to remove any human DNA before uploading to following ethical guidelines for the study. | 24 | 2018 |
| PRJDB14272 | Metagenomic analysis of fecal samples obtained from ulcerative colitis patient in Japan | 24 | 2026 |
| PRJNA624223 | Gut microbiome alterations and longitudinal kinetics in COVID-19 patients | 23 | 2020 |
| PRJNA1051094 | Comparing the gut virome of HIV exposed, uninfected verses HIV unexposed Kenyan infants in the first 18 month of life | 22 | 2025 |
| PRJNA804384 | Inflammatory bowel disease patients undergoing biological therapy | 22 | 2022 |
| PRJEB53954 | Pediatric Leukemia and Lymphoma patient stool microbiome | 22 | 2022 |
| PRJNA1171764 | Human gut metagenome of IBD patients and healthy controls | 22 | 2025 |
| PRJEB113070 | Longitudinal metagenomics analysis of CPE carriers | 22 | 2026 |
| PRJNA637365 | Dysbiosis in metabolic genes of the gut microbiomes of patients with a Pouch | 21 | 2021 |
| PRJEB44766 | Systematic characterization of human gut microbiome-secreted molecules by integrated multi-omics | 20 | 2021 |
| PRJNA705895 | Fecal microbiota of donors and RCDI patients before and after FMT | 20 | 2021 |
| PRJNA349197 | Metagenomics of clostridium difficile infection in hematopoietic stem cell recipients | 20 | 2017 |
| PRJEB46780 | Fecal Microbiota Transplantation for Ulcerative Colitis and C. difficile Infection. | 20 | 2022 |
| PRJNA929328 | MetGut: ONT Sequencing of Stool Samples in alloHSCT patients | 20 | 2023 |
| PRJNA1284285 | Fecal microbiota transplantation for Parkinson's patients with constipation A pilot clinical trial | 20 | 2025 |
| PRJNA454892 | Shotgun metagenome library | 20 | 2018 |
| PRJNA727667 | Human lung cancer metagenomic raw sequence reads | 19 | 2024 |
| PRJNA645402 | Human gut microbiome Raw sequence reads | 19 | 2020 |
| PRJNA950577 | Dynamic associations between the respiratory tract and gut antibiotic resistome of patients with COVID-19 and its prediction power for disease severity | 18 | 2024 |
| PRJNA1503619 | Gut Microbiome and Breast Cancer | 18 | 2026 |
| PRJNA243036 | Choice of method for purification of bacterial DNA from faecal material influences community structure as detected by next generation sequencing | 18 | 2014 |
| PRJNA866369 | The metagenomic data of 18 samples of human feces with a 24-hours batch culture in vitro | 18 | 2023 |
| PRJNA872116 | The microbiome of RAG-deficient patients - Metagenome | 17 | 2023 |
| PRJNA824338 | fecal metagenome Raw sequence reads | 17 | 2023 |
| PRJEB35587 | The Relationship between Fecal Bile Acids and Microbiome Community Structure in Pediatric Crohn’s Disease | 16 | 2019 |
| PRJNA1179893 | Dietary fiber modulates the window of susceptibility to Clostridioides difficile infection | 16 | 2024 |
| PRJEB1389 | Antibiotics impact on the human intestinal microbiota | 16 | 2014 |
| PRJNA715634 | Novel Strain Level Resolution of Crohns Disease Mucosa-Associated Microbiota via an ex vivo Combination of Microbe Culture and Metagenomic Sequencing | 16 | 2021 |
| PRJNA1026631 | Female Urogenital & Rectal Microbiomes of Individuals with UTI Symptoms Metagenome | 15 | 2023 |
| PRJEB47909 | FMT datasets of patients with recurrent Clostridioides difficile infection (rCDI), inflammatory bowel disease (IBD), and colonization from multi-drug resistant bacteria (MDRB) | 15 | 2022 |
| PRJNA573963 | Gut Microbiome of Elderly Adults with Advanced Dementia | 15 | 2019 |
| PRJNA1153928 | Immune System Modulation with Oral Vancomycin in combination with Stereotactic Body Radiotherapy (SBRT) for medically inoperable Early-Stage Non-small Cell Lung Cancer | 15 | 2024 |
| PRJNA345144 | Probiotics in Pregnancy study | 15 | 2019 |
| PRJDB39536 | Large-scale single-cell long-read genomics enables high-resolution microbiome profiling (PRJCA047574) | 14 | 2026 |
| PRJNA855302 | Homo sapiens Raw sequence reads | 14 | 2022 |
| PRJEB28730 | Metagenomic stool samples in time series | 13 | 2019 |
| PRJNA856821 | Integration of culture-dependent and independent methods provides a more comprehensive picture of the human gut microbiome than either method alone | 13 | 2024 |
| PRJEB46214 | Gut bacterial gene changes following pegaspargase treatment in pediatric patients with Acute Lymphoblastic Leukemia | 13 | 2021 |
| PRJNA1121295 | FEDEX Study Fecal Metagenomes | 13 | 2024 |
| PRJNA1514298 | Probiotic-associated gut ecosystem recovery and carbapenem-resistant Enterobacteriaceae clearance in pediatric Salmonella infection | 13 | 2026 |
| PRJNA1368707 | Meta Analysis of Paired Short-read 16S V4, Full-length 16S, and Shotgun Metagenomic Profiling | 12 | 2025 |
| PRJEB38000 | Strain-level analysis of Bifidobacterium spp. from human gut metagenomes of individuals with different lactase persistence genotypes | 12 | 2020 |
| PRJEB29152 | CaPES | 12 | 2019 |
| PRJEB80556 | MicroPouch_NP | 12 | 2025 |
| PRJNA433393 | infant gut metagenomes (NIHL1) | 12 | 2022 |
| PRJNA748448 | Metagenomic WGS of Preterm Infant Skin and Stool | 12 | 2021 |
| PRJNA525982 | Gut resistome plasticity in pediatric patients undergoing hematopoietic stem cell transplantation | 12 | 2019 |
| PRJEB10391 | Impact of ciprofloxacin pertubation on the intestinal resistome and microbiota in two healthy volunteers | 12 | 2015 |
| PRJNA353598 | viral metagenome Metagenome | 11 | 2017 |
| PRJNA1112760 | Metagenomic signatures of early life brain damage | 11 | 2026 |
| PRJNA733860 | Preterm infant fecal metagenome | 11 | 2021 |
| PRJNA1170939 | Fungi in GI of Organ Donors | 10 | 2025 |
| PRJNA763503 | Character of microbial engraftment following the fecal microbiota transplantation in patients with inflammatory bowel diseases | 10 | 2021 |
| PRJEB114255 | IBD Parisian Gut Microbiome Cohorte | 10 | 2026 |
| PRJNA1267264 | Healthy Dairy Worker Longitudinal New Workers | 10 | 2025 |
| PRJNA764525 | Bloodstream infections' origins following fecal microbiota transplantation: a strain-level analysis | 10 | 2021 |
| PRJNA740337 | Cultivation of dominant bacterial species and strains from human skin, oral, and gut microbiota | 10 | 2022 |
| PRJEB73575 | Impact of pomegranate on gut microbiota | 10 | 2026 |
| PRJNA833152 | Fecal Microbiota Transplantation Treatment of Autoimmune-mediated Type 1 Diabetes Mellitus | 10 | 2022 |
| PRJNA523592 | Read cloud and short read metagenomic sequencing of stool samples from a human HCT patient | 9 | 2019 |
| PRJEB12272 | A statistical test for the detection of inhomogeneity in metagenomic samples | 9 | 2016 |
| PRJNA613032 | Fecal microbiota in early life and effects of early life antibiotics, annotated shotgun sequencing data | 8 | 2022 |
| PRJNA909977 | Gut Instincts: professional cyclists have a gut microbiome adapted to fuel their energetic needs | 8 | 2023 |
| PRJEB18557 | An obese child finished a 105-days intervenion enriched with non-digestable carbohydrates | 7 | 2017 |
| PRJNA446061 | Fecal Metagenome | 7 | 2018 |
| PRJNA689961 | Gut microbiome sequencing | 7 | 2022 |
| PRJNA812583 | Strain-level metagenomics reveal microbial transfer from donor to infant after fecal microbiota transplantation of pregnant patient | 7 | 2022 |
| PRJEB5771 | Human gut microbiota associated to Clostridium difficile infection | 7 | 2014 |
| PRJNA1067813 | C. difficile-associated mouse and human fecal metagenomes | 7 | 2025 |
| PRJNA604850 | Type 1 diabetes in pregnancy and changes in the composition and function of the gut microbiome | 6 | 2020 |
| PRJEB3085 | Disturbance of the gut microbiota during antibiotic stress (therapy): a multi-omic approach | 6 | 2013 |
| PRJNA510036 | Fecal transplant influence on healthy volunteers | 6 | 2018 |
| PRJEB64567 | Maternal FMT in Cesarean-Born Infants - WGS sequencing of infants (1w to 1year) and maternal fecal samples | 6 | 2023 |
| PRJDB41236 | gut microbiota of CSA_AKI (PRJCA044377) | 6 | 2026 |
| PRJNA786578 | human stool Metagenome | 6 | 2022 |
| PRJNA529230 | n of 1 study: Fecal Microbiota Transplantation in Multiple Sclerosis | 6 | 2019 |
| PRJEB52147 | The Association Between Milk Feedings in the Preterm Population, the Microbiome and Risk of Atopic Disease: Microbiome, Atopic Disease, and Prematurity (MAP Study) | 6 | 2022 |
| PRJNA976404 | Metagenomic assessment of gut microbial communities and risk of severe COVID-19 | 5 | 2023 |
| PRJEB22863 | Gut mictobiota composition correlation with the clinical outcome of NSCLC and RCC patients treated with anti-PD-1 mAB | 5 | 2017 |
| PRJNA810891 | Preservation of fecal microbiome is associated with reduced severity of Graft-versus-Host Disease | 5 | 2022 |
| PRJNA928744 | Gut microbiota composition of patients in MIMic cohort | 5 | 2023 |
| PRJEB23292 | Dysbiosis, including decreased gut microbial richness (MGR) and composition modifications, associates with adverse metabolism in lean, overweight or moderate obesity, but lacks characterization in severe obesity. Bariatric surgery (BS) improves body composition and metabolism in severe obesity which featuresand is associated with gut microbiota modifications. Here, we characterized the importance of dysbiosis and functional alterations in severe obesity and assessed whether BS procedures would rescue this dysbiosis. | 5 | 2019 |
| PRJEB3227 | Follow-up of faecal microbiota in IBS patients | 5 | 2013 |
| PRJNA705695 | Gut metagenomes of patients and mice with post-infection irritable bowel syndrome | 5 | 2022 |
| PRJEB5224 | An integrated catalog of reference genes in the human gut microbiome | 5 | 2014 |
| PRJNA1263159 | Fecal Microbiota Transplantation for CDI cohort | 5 | 2025 |
| PRJNA1169096 | Donor Composition and Fiber Promote Strain Engraftment in a Randomized Controlled Trial of Fecal Transplant with Dietary Fiber for Ulcerative Colitis (MINDFUL) | 5 | 2025 |
| PRJNA1363135 | The Gut Microbiota in Liver Transplantation Recipients During the Perioperative And Postoperative Recovery Period | 5 | 2025 |
| PRJEB36140 | Effects of fecal microbiota transplantation in subjects with irritable bowel syndrome is mirrored by changes in gut microbiome | 5 | 2020 |
| PRJEB33194 | Metagenomics analysis of biopsy-derived colonic and terminal ileal mucosa associated microbiota in healthy individuals from a population-based study | 5 | 2019 |
| PRJNA1472528 | Fecal Microbiome Profiling in Crohns Disease During Oral Nutritional Supplementation | 5 | 2026 |
| PRJEB6921 | Role_of_early_life_gut_microbiota_in_colonisation_resistance_development | 5 | 2018 |
| PRJNA1514834 | High throughput sequencing analysis of fecal microbiota patients with moderate to severe major depressive disorder before and after treatment | 5 | 2026 |
| PRJNA1206184 | Mediation of systemic exposure to the immunosuppressive drug Mycophenolate mofetil by the gut microbiome in kidney transplant patients | 5 | 2025 |
| PRJNA657818 | Delivery mode impacts newborn gut colonization efficiency | 5 | 2020 |
| PRJEB31957 | Impact of narrow-spectrum antibiotics on the oral and fecal microbiome and resistome in a young child treated for otitis media | 3 | 2019 |
| PRJNA1023304 | Microbial landscape of primary and metastatic brain tumors | 2 | 2024 |
| PRJDA72415 | Comprehensive Detection of Possible Pathogens Associated with Kawasaki Disease | 2 | 2012 |
| PRJEB22207 | Gut microbiome diagnostics in pre-term babies | 1 | 2017 |