Preterm infant gut microbiome, antibiotic exposure
429 samples from preterm and healthy infants in Saint Louis, MO, examining gut microbiota and antibiotic resistome in antibiotic-exposed versus antibiotic-naïve infants; longitudinal cohort design. machine-written summary
429 samples · 429 runs · US · Infant / toddler · 2019 · 1.08 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,532 sample values (country, sex, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10175488, PMC10769871, PMC10904392, PMC11019788, PMC11170968, PMC11322291, PMC11929092, PMC12677589, PMC12769767, PMC13402684, PMC8284144, PMC8383385, PMC9437082, PMC9723731 |
| ✓ Supplementary tables | 3,548 sample values (age, antibiotic exposure, birth weight grams, delivery mode, feeding mode, gestational age weeks, maternal antibiotics, preterm status) |
| ✓ External resources | 30 sample values (antibiotic exposure) · from MicrobiomeDB (VEuPathDB) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Antibiotic given as the study intervention (incl. eradication therapy design observational_with_procedure · population preterm_nicu · Clinical antibiotic exposure/therapy in hospitalized preterm infants
“prolonged exposures to antibiotic therapy” — bioproject.description (study level; per-sample arms are in the intervention column below)
age: supplementary table and MicrobiomeDB disagree for 7 samples (e.g. 74 vs 33.57) — withheld.
The sources disagree on 7 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (7)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN09980965 | age | 74 (supplementary table) | 33.57 (MicrobiomeDB) | withheld: neither value published |
| SAMN09980966 | age | 139 (supplementary table) | 73.65 (MicrobiomeDB) | withheld: neither value published |
| SAMN09980967 | age | 175 (supplementary table) | 138.75 (MicrobiomeDB) | withheld: neither value published |
| SAMN09980968 | age | 232 (supplementary table) | 175.4 (MicrobiomeDB) | withheld: neither value published |
| SAMN09980969 | age | 307 (supplementary table) | 231.65 (MicrobiomeDB) | withheld: neither value published |
| SAMN09980970 | age | 427 (supplementary table) | 306.55 (MicrobiomeDB) | withheld: neither value published |
| SAMN09980973 | age | 2 (supplementary table) | 624.63 (MicrobiomeDB) | withheld: neither value published |
longitudinal
55 of 55 people sampled more than once (429 samples; median 8, up to 11 per person) · follow-up median 15 mo (max 21 mo) · median interval between samples 55 d (time from age at collection). Schedule stated by the source: “Infants sampled repeatedly during and after NICU hospitalization; host_age varies continuously (1.56 to 422.35 days) across 417 distinct ages for 55 subjects.” (time origin: birth).
Each row is one person (36 shown of 55); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 372 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 429 | 100% | ||||
| country | 429 | 100% | 429 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 429 | 100% | 429 | |||
| antibiotic_exposure | 429 | 100% | 429 | |||
| birth_weight_grams | 429 | 100% | 429 | |||
| delivery_mode | 429 | 100% | 429 | |||
| gestational_age_weeks | 429 | 100% | 429 | |||
| maternal_antibiotics | 429 | 100% | 429 | |||
| preterm_status | 429 | 100% | 429 | |||
| sex | 429 | 100% | 429 | |||
| timepoint_label | 429 | 100% | 245 | 184 | ||
| age_at_collection_days | 422 | 98% | 422 | |||
| feeding_mode | 398 | 93% | 398 |
- Antibiotic-driven intestinal dysbiosis in pediatric short bowel syndrome is associated with persistently altered microbiome functions and gut-derived bloodstream infections. PMID 34264786 PMC8284144 curated
- Deterministic transition of enterotypes shapes the infant gut microbiome at an early age. PMID 34429130 PMC8383385 curated
- A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome. PMID 36050292 PMC9437082 curated
- Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance during the first year of life. PMID 36717704 PMC9723731 curated
- Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota. PMID 37169786 PMC10175488 curated
9 more
- BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen. PMID 38172624 PMC10769871
- A metagenomic catalog of the early-life human gut virome. PMID 38424077 PMC10904392
- Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation. PMID 38441032 PMC11019788
- Infant age inversely correlates with gut carriage of resistance genes, reflecting modifications in microbial carbohydrate metabolism during early life. PMID 38882494 PMC11170968
- Insights into the ecology of the infant gut plasmidome. PMID 39138199 PMC11322291
- Dynamics of gut resistome and mobilome in early life: a meta-analysis. PMID 40048849 PMC11929092
- The Gut Resistome Atlas in Preterm Infants Enables Prediction of Necrotizing Enterocolitis Onset. PMID 41025564 PMC12677589
- Compiling an early life human gut microbiome atlas and identification of key microbial drivers. PMID 41350579 PMC12769767
- An ubiquitous antibacterial toxin from human gut bacteria engenders neonatal colonization advantage. PMID 42259839 PMC13402684
Archive description
Because hospitalized preterm infants are vulnerable to infection, they receive frequent and often prolonged exposures to antibiotic therapy. It is not known if the demonstrated short-term effects of antibiotics on the preterm infant gut microbiota and resistome persist after discharge from neonatal intensive care units. Here, we use complementary metagenomic and culture based techniques to interrogate the gut microbiota and resistome of antibiotic-exposed preterm infants both during, and after, hospitalization, and compare these readouts to antibiotic-naïve healthy infants sampled synchronously. We find an enriched gastrointestinal antibiotic resistome, prolonged carriage of multidrug resistant Enterobacteriaceae, and distinct antibiotic-driven patterns of microbiota and resistome assembly in extremely preterm infants who received early life antibiotics. Our results demonstrate persistent collateral damage of early life antibiotic treatment and hospitalization in preterm infants and highlight the need for alternative strategies for infection management in highly vulnerable neonatal populations.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and neonate by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Human infant gut metagenome, infant shotgun”
- body site study.description · “the preterm infant gut microbiota and resistome”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Human infant gut metagenome, infant”
- life stage study.description · “Because hospitalized preterm infants are vulnerable”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN09980563 | age_at_collection_days | 24 | R2 | 0.75 | paper.supp.table | Host Age (days)=23.67 |
| SAMN09980563 | antibiotic_exposure | yes | R2 | 0.75 | paper.supp.table | abx_ever=yes |
| SAMN09980568 | antibiotic_exposure | yes | R2 | 0.75 | external.microbiomedb source | Study group: Early and subsequent antibiotics antibiotics |
| SAMN09980563 | birth_weight_grams | 830 | R2 | 0.75 | paper.supp.table | birth_weight=830 |
| SAMN09980563 | country | US | R1 | 0.90 | biosample_attr | USA: Saint Louis, MO |
| SAMN09980563 | delivery_mode | c_section | R2 | 0.75 | paper.supp.table | born_method=c_section |
| SAMN09980563 | feeding_mode | exclusive_breast | R2 | 0.75 | paper.supp.table | feeding_practice=exclusive breastfeeding |
| SAMN09980563 | gestational_age_weeks | 26.6 | R2 | 0.75 | paper.supp.table | gestational_age=26.6 |
| SAMN09980563 | maternal_antibiotics | yes | R2 | 0.75 | paper.supp.table | maternal_abx=yes |
| SAMN09980563 | preterm_status | preterm | R2 | 0.75 | paper.supp.table | premature=yes |
| SAMN09980563 | sex | male | R1 | 0.90 | biosample_attr | male |
| SAMN09980563 | subject_id | N001 | R1 | 0.85 | biosample_attr | N001 |
| SAMN09980564 | timepoint_label | B | R1 | 0.70 | sample.name_rule:library_names | N001.B |
| SAMN09980563 | timepoint_label | 0 - 1 month | R2 | 0.75 | paper.supp.table | AGE GROUP G12=0 - 1 month |
Sequencing
429 runs over 429 samples · mean 1.06 Gbp per run (median 1.08 Gbp, total 455.86 Gbp; 429 runs with a base count) · layout PAIRED 429 · platform ILLUMINA 429 · models NextSeq 500 (429) · 87% of runs with a Sandpiper profile · first public 2019-10-07
Authors (137)
Thänert R first · Thänert A · Ou J · Bajinting A · Burnham CD · Engelstad HJ · Tecos ME · Ndao IM · Hall-Moore C · Rouggly-Nickless C · Carl MA · Rubin DC · Davidson NO · Tarr PI · Warner BB · Dantas G · Warner BW last · Xiao L first · Wang J · Zheng J · Li X · Zhao F last · Zeng S first · Patangia D · Almeida A · Zhou Z · Mu D · Paul Ross R · Stanton C · Wang S last · Busi SB first · de Nies L · Habier J · Wampach L · Fritz JV · Heintz-Buschart A · May P · Halder R · de Beaufort C · Wilmes P last · Lugli GA first · Mancabelli L · Milani C · Fontana F · Tarracchini C · Alessandri G · van Sinderen D · Turroni F · Ventura M last · Hall B first · Levy S · Dufault-Thompson K · Arp G · Zhong A · Ndjite GM · Weiss A · Braccia D · Jenkins C · Grant MR · Abeysinghe S · Yang Y · Jermain MD · Wu CH · Ma B · Jiang X last · Li S · Ying J · Wang H · Qu Y · Niu X · De Biase R · Bocchio F · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · Xu X first · Feng Q · Zhang T · Gao Y · Cheng Q · Zhang W · Wu Q · Xu K · Li Y · Nguyen N · Taft DH · Mills DA · Lemay DG · Zhu W · Mao S · Zhang A · Liu J last · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last · Bargheet A first · Noordzij HT · Ponsero AJ · Jian C · Korpela K · Valles-Colomer M · Debelius J · Kurilshikov A · Pettersen VK last · Zhang L · Yuan Y · Tian M · Zhou M · Hu Y · Huang J · Zou R · Su X · Liu Q · He Y · Feng J · Huang W · Luo Y · Shen W · Longhi G · Gennaioli E · Muscò A · Rizzo SM · Vitale SG · Angioni S · Valguarnera E first · Tung J · Pak JJ · Russell SK · Hecht DW · Schwartz DJ · Wardenburg JB last
Downloads
PRJNA489090.csv.gz (15.6 KB) · parquet (90.5 KB) — all 429 samples, every field with route and confidence · PRJNA489090_determinations.csv.gz (44.7 KB) — 5,110 evidence rows