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Neonates (first 28 days of life)
Age bands · collection id neonates-first-28-days
Every gut sample collected in the first 28 days of life (age_category = neonate), across term and preterm birth cohorts and NICU studies; the earliest colonisation window.
Open in the sample explorer (13,579 samples)
123
studies with member samples
13,579
member samples in this release
Membership rule
| age_category | neonate |
| body_site_class | primary |
Composition
Age category
| neonate | 13,579 |
Country
| US | 5,771 |
| GB | 2,257 |
| BD | 1,346 |
| AU | 665 |
| FI | 418 |
| ES | 397 |
Health condition
| healthy_control Healthy / control | 4,733 |
| preterm_nicu Preterm / NICU (infant) | 1,998 |
| nec Necrotising enterocolitis (infant) | 726 |
| pregnancy_postpartum Pregnancy / postpartum | 177 |
| other_disease Other disease / condition | 151 |
| sepsis_or_infection Sepsis / infection (infant) | 93 |
Lifestyle
| urban_industrialized Urban / industrialized (only when stated by the source) | 574 |
| rural_non_industrialized Rural | 14 |
Member studies (123)
| Study | Title | Member samples | First public |
|---|---|---|---|
| PRJEB32631 | Early_life_microbiota_colonisation | 1,933 | 2019 |
| PRJNA799247 | Metagenomics of preterm infant stool | 1,313 | 2023 |
| PRJEB83552 | SEPSIS Lactobacillus plantarum ATCC 202195 Microbiome Study | 815 | 2025 |
| PRJEB62690 | Infant stool, 5-HMO supplemented formula vs. control formula vs. breastfed | 597 | 2023 |
| PRJEB83236 | SEPSIS Human Microbiome Study | 487 | 2025 |
| PRJNA63661 | Microbial composition of samples from infant gut | 430 | 2011 |
| PRJEB55714 | Metagenomic analyses of the intestinal microbiome from neonates in the MIS BAIR trial | 392 | 2023 |
| PRJNA376566 | preterm infant gut metagenomes (S2_2013 and NIHY2_2012 cohorts) | 366 | 2017 |
| PRJNA947616 | Gut microbiome and bloodstream infections among premature infants in Singapore | 305 | 2023 |
| PRJNA903921 | Gut Mycobiome Maturation and Its Determinants during Infancy: A Comparison of Shotgun Metagenomic and ITS2 Amplicon-Based Sequencing Approaches | 303 | 2023 |
| PRJNA1249435 | Neurobiological and neurocognitive consequences of diverse microbiome functional trajectories | 302 | 2026 |
| PRJEB39610 | Longitudinal metagenomic analysis of the gut microbiome in preterm infants diagnosed with necrotising enterocolitis and matched controls | 289 | 2020 |
| PRJNA1404625 | Investigating the role of the infant gut microbiome in rotavirus vaccine efficacy | 270 | 2026 |
| PRJNA807448 | The Antibiotics and Immune Responses Study | 266 | 2025 |
| PRJNA396794 | preterm infant gut metagenomes (NIH Y4 Cohort) | 261 | 2017 |
| PRJNA872399 | Preterm infants at low risk for early-onset sepsis differ in early fecal microbiome assembly | 257 | 2022 |
| PRJEB9403 | BAMBI__Baby_Associated_MicroBiota_of_the_Intestine_ | 252 | 2018 |
| PRJNA1280936 | Gut Microbiome of Infants in the Neonatal Intensive Care Unit | 200 | 2026 |
| PRJNA821542 | Longitudinal gut metagenomes from mothers and their infants in the EDIA study | 198 | 2022 |
| PRJEB6456 | Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life | 197 | 2015 |
| PRJNA1301887 | Preterm infant weight gain patterns are not associated with gut microbiome measures | 195 | 2026 |
| PRJNA884103 | Gut residence of bloodstream infection pathogens in the NICU | 189 | 2023 |
| PRJNA301903 | Metagenomic sequencing of preterm infant gut microbiota raw sequence reads | 179 | 2016 |
| PRJNA345144 | Probiotics in Pregnancy study | 176 | 2019 |
| PRJNA657818 | Delivery mode impacts newborn gut colonization efficiency | 166 | 2020 |
| PRJEB89491 | LucKi Gut - Longitudinal metagenomic sequencing of infant gut microbiota | 166 | 2025 |
| PRJNA630999 | Premature infant microbiome Metagenome | 164 | 2021 |
| PRJNA417343 | preterm infant gut metagenomes (NIH Y5 Cohort) | 159 | 2019 |
| PRJNA633576 | Metagenomic survey of the gut microbiome of term infants in the United States reveals widespread dysbiosis, absence of B. infantis, and high abundance of antibiotic resistance genes. | 141 | 2021 |
| PRJNA961698 | Very Early Life Microbiome and Metabolome Correlates with Primary Vaccination Variability in Children | 135 | 2023 |
| PRJNA294605 | Metagenomes from 11 human infant fecal samples hospitalized in the same intensive care unit | 119 | 2016 |
| PRJNA1078999 | Homo sapiens Raw sequence reads | 117 | 2025 |
| PRJNA698986 | Early-life metagenomes from human infant fecal samples with matched maternal sample | 105 | 2021 |
| PRJEB84944 | Shotgun sequencing of 56 mother-infant dyads from the ALADDIN birth cohort | 103 | 2025 |
| PRJNA1414141 | Gut Microbiome Dysbiosis in Neonatal Lupus | 90 | 2026 |
| PRJNA557731 | Bacterial colonization reprograms the neonatal gut metabolome | 88 | 2019 |
| PRJEB52774 | HELMi infant stool WGS metagenomes (3 weeks to 1 year) and parental stool WGS metagenomes | 87 | 2022 |
| PRJNA898628 | PINGU Fecal samples Metagenome | 87 | 2023 |
| PRJNA352475 | Mother-infant microbiome vertical transmission | 87 | 2018 |
| PRJNA475246 | Strain-level identification of mother-to-child bacterial transmission during the first few months of life | 74 | 2018 |
| PRJNA1143669 | Gut microbiota of neonates exposed to HIV | 65 | 2024 |
| PRJEB54991 | Shotgun metagenomics of infant formula study | 55 | 2022 |
| PRJNA489090 | Human infant gut metagenome, infant shotgun sequencing | 54 | 2019 |
| PRJNA988496 | Delivery mode impacts gut bacteriophage colonization during infancy | 54 | 2024 |
| PRJNA1225421 | Microbiome data from the ECoMiD cohort study in Ecuador | 53 | 2025 |
| PRJNA1042647 | Bile Acids Are Substrates for Amine N-Acyl Transferase Activity by Bile Salt Hydrolase | 52 | 2023 |
| PRJNA1055141 | Infant stool shallow shotgun sequencing (ANTIBIO) | 46 | 2023 |
| PRJNA1391538 | Pre-HCT Resistome Disruption Predicts ESBL Gene Expansion in Pediatric Transplant Recipients: A Prospective Multi-Center Study | 45 | 2026 |
| PRJNA521878 | Gut metagenome of infants in the neonatal intensive care unit | 44 | 2020 |
| PRJNA1513446 | Metagenomic sequencing of meconium microbiota of neonates | 44 | 2026 |
| PRJNA806984 | Microbiota and Health Study (Dhaka, Bangladesh) | 44 | 2022 |
| PRJNA693793 | BaBel Infant Gut Virome Raw Data | 43 | 2021 |
| PRJEB30834 | Human fecal metagenomes of individuals sampled along a small-scale urbanization gradient in Cameroon | 39 | 2021 |
| PRJNA379120 | Colonization, succession and evolution of the earliest human gastrointestinal microbiome | 39 | 2018 |
| PRJEB52147 | The Association Between Milk Feedings in the Preterm Population, the Microbiome and Risk of Atopic Disease: Microbiome, Atopic Disease, and Prematurity (MAP Study) | 38 | 2022 |
| PRJNA327106 | Raw reads of the microbiota of premature infant mouth, skin, and gut | 37 | 2016 |
| PRJNA273761 | Metagenomes from human infant fecal samples with and without necrotizing enterocolitis | 37 | 2015 |
| PRJNA949528 | Health programming, evolution of the infants microbiome | 34 | 2023 |
| PRJNA1112760 | Metagenomic signatures of early life brain damage | 34 | 2026 |
| PRJEB74322 | Spanish mother and infants metagenomes of stool and milk samples | 33 | 2024 |
| PRJNA473126 | Infant Diet and Maternal Gestational Weight Gain Influence Functional Maturation of the Infant Gut Microbiome | 31 | 2018 |
| PRJNA1476247 | Evaluating metagenomic sequencing as a stool-based diagnostic in children with presumptive TB in Uganda Jun 3 26 | 29 | 2026 |
| PRJEB62848 | Infant stool, moderate and late preterm infants, probiotic and prebiotic | 27 | 2023 |
| PRJNA390646 | Infant Microbiota and Probiotic Intake Study (IMPRINT) | 25 | 2018 |
| PRJNA1145027 | Metal availability shapes early life microbial ecology and community succession | 25 | 2024 |
| PRJNA889771 | Raw reads of the microbiota of premature infant mouth, skin, and gut | 24 | 2022 |
| PRJNA762668 | Longitudinal and comparative analysis of Tunisian newborns gut microbiota according to delivery mode | 23 | 2022 |
| PRJNA1304237 | Gut Microbiota Signatures in Indian Preterm Infants with Necrotizing Enterocolitis | 22 | 2025 |
| PRJNA1148144 | Biosignatures of late-onset extraintestinal bacterial infections | 22 | 2025 |
| PRJEB123118 | Infant and Mother faecal viromes from the PEARL cohort | 20 | 2026 |
| PRJNA524703 | Human infant gut virome | 20 | 2020 |
| PRJNA613054 | Fecal resistome in early life and effects of early life antibiotics, annotated shotgun sequencing data | 20 | 2022 |
| PRJNA1348516 | Metagenomic sequencing of stool samples of infants raw sequence reads | 19 | 2026 |
| PRJNA486009 | Genome diversity of pathogenic Escherichia coli in Ecuador | 18 | 2019 |
| PRJEB45799 | The person-to-person transmission landscape of the gut and oral microbiomes | 18 | 2022 |
| PRJNA543520 | Impact of intrapartum and postnatal antibiotics on the gut microbiome and emergence of antimicrobial resistance in infants | 18 | 2019 |
| PRJEB46788 | Codiversification of gut microbiota with humans | 18 | 2022 |
| PRJNA911205 | Psychosocial adversity experienced in utero and early life is associated with variation in gut microbiota | 17 | 2023 |
| PRJEB108038 | Neonatal Jaundice and the Infant Gut Microbiome: An Integrated Shotgun Metagenomics and Bidirectional Mendelian Randomization Study in Xinjiang | 16 | 2026 |
| PRJEB49206 | Extensive microbial novelty in the Hadza and Nepali gut microbiome reveals how lifestyle impacts composition and function | 14 | 2022 |
| PRJNA701480 | Vaginal seeding in babies born by caesarean section (ECOBABe trial) - shotgun metagenomics data | 14 | 2021 |
| PRJEB64567 | Maternal FMT in Cesarean-Born Infants - WGS sequencing of infants (1w to 1year) and maternal fecal samples | 14 | 2023 |
| PRJNA418044 | Uncontacted Amerindians fecal virome | 14 | 2018 |
| PRJNA595749 | COSMIC2 - Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance in the first year of life | 12 | 2019 |
| PRJNA1086674 | The Impact of Oral Feedings on the Preterm Infant Microbiome and Metabolome | 11 | 2024 |
| PRJNA322188 | Maturation of the Infant Microbiome Community Structure and Function Across Multiple Body Sites | 11 | 2017 |
| PRJNA1260441 | Comparative evaluation of DNA extraction protocols for neonatal gut microbiota profiling in a resource-limited setting | 10 | 2025 |
| PRJNA427187 | Maternal Milk Infant Fecal Virome Study | 10 | 2018 |
| PRJNA717139 | Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics and proteomics | 9 | 2021 |
| PRJNA955235 | Persistent delay in maturation of the developing gut microbiome in infants with cystic fibrosis | 8 | 2023 |
| PRJDA72415 | Comprehensive Detection of Possible Pathogens Associated with Kawasaki Disease | 8 | 2012 |
| PRJNA592261 | Infant virome during the first year of life | 7 | 2020 |
| PRJEB51728 | Infant stool metagenomic datasets | 7 | 2023 |
| PRJNA916952 | Stanford's Outcomes Research in Kids (STORK) Virome | 6 | 2023 |
| PRJNA994433 | Longitudinal Variability of Bifidobacterium Species in the Infant Gut is Independent of Maternal Milk HMO Composition | 6 | 2023 |
| PRJEB15257 | The antibiotic resistance potential of the preterm infant gut microbiome measured using shotgun metagenomics. | 6 | 2016 |
| PRJNA978345 | Infant cystic fibrosis BAL and stool microbiome | 4 | 2024 |
| PRJNA1247940 | Shotgun Metagenomic Sequences of Host-Associated Gut Microbiomes in Gestational Diseases | 4 | 2025 |
| PRJNA811494 | ITS2 and whole metagenomics from stool of human lung cancer patients from hungary | 3 | 2023 |
| PRJEB108450 | Exploring Fecal Microbiome in the CHILD COVID-19 sub-project | 3 | 2026 |
| PRJEB108563 | Autism Spectrum Disorder -UCLA | 3 | 2026 |
| PRJEB32762 | iMSMS Baranzini data | 3 | 2019 |
| PRJEB41102 | Analysis of human fecal metagenomes from adults and infants, to investigate strain persistance, dispersal and purifying selection of bacterial strains. | 3 | 2020 |
| PRJEB87209 | Australian infant gut microbiome metagenomics | 3 | 2025 |
| PRJNA549787 | South African HIV-exposed, uninfected infant gut microbiomes | 2 | 2019 |
| PRJEB54724 | Netherlands Norovirus surveillance, metagenomics, 2015-2019 | 2 | 2023 |
| PRJNA221723 | Gut metagenome from two premature infants | 2 | 2014 |
| PRJNA1413407 | Microbial-based integrated model to measure and module brain development and function | 2 | 2026 |
| PRJNA489693 | Microbial Diversity of NICU Infant Feeding Tubes | 2 | 2019 |
| PRJNA1206145 | Shotgun sequencing of the gut microbiome from infants enrolled in a randomized controlled trial of a microbiome-based integrative wellness program. | 1 | 2025 |
| PRJNA1125836 | Gut microbiome obesity index, a new analytical part of the metagenomics workflow to evaluate gut dysbiosis in obese humans | 1 | 2024 |
| PRJNA695570 | Human gut metagenomes of healthy mothers and their children | 1 | 2021 |
| PRJNA1265906 | Gut microbiome in pediatric IBD patients | 1 | 2025 |
| PRJEB63351 | Neuroblastoma is associated with alterations in gut microbiome composition subsequent to maternal seeding | 1 | 2023 |
| PRJEB50408 | Resistant starch gut microbiome | 1 | 2022 |
| PRJNA749645 | Whole genome metagenome of gut microbiota from prostate cancer patients | 1 | 2021 |
| PRJNA300541 | Antibiotic resistance exchange between microbiota in resource-poor settings in Latin America | 1 | 2016 |
| PRJEB2054 | A human gut microbial gene catalog established by deep metagenomic sequencing | 1 | 2010 |
| PRJNA716780 | Mothers/children Metagenome | 1 | 2022 |
| PRJEB11419 | American Gut Project | 1 | 2015 |
| PRJNA701982 | Antibiotic-driven intestinal dysbiosis in paediatric SBS alters microbiome functions and is associated with gut-derived blood stream infections throughout childhood | 1 | 2021 |
| PRJNA529124 | Metagenomic sequencing of stool samples from Ghanaian individuals | 1 | 2019 |
| PRJNA1067625 | Gut microbiome of children in Haiti | 1 | 2025 |