Longitudinal NICU infant gut microbiome, Los Angeles, USA
64 longitudinal gut metagenome samples from neonates and infants in a Los Angeles, USA neonatal intensive care unit, studying the effect of antibiotics on gut microbiome development over time. machine-written summary
64 samples · 64 runs · US · Infant / toddler · 2020 · 0.59 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 546 sample values (age, antibiotic exposure, collection date, country, health condition, health condition detail, maternal antibiotics, sex) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10175488, PMC10769871, PMC10904392, PMC11497992, PMC12769767, PMC9437082 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
antibiotic exposure: two sequence archives disagree for 2 samples (e.g. no vs yes) — withheld.
The sources disagree on 2 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 (2)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN10919946 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN10919947 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
longitudinal
20 of 29 people sampled more than once (55 samples; median 3, up to 4 per person) · follow-up median 14 d (max 36 d) · median interval between samples 7 d (time from age at collection). Schedule stated by the source: “stool metagenomic sampling over time (multiple days of life per infant)”.
Each row is one person (20 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 43 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 | 64 | 100% | ||||
| country | 64 | 100% | 64 | |||
| health_condition | 20 | 31% | 20 | |||
| subject_id | 64 | 100% | 64 | |||
| age_at_collection_days | 64 | 100% | 64 | |||
| collection_date | 64 | 100% | 64 | |||
| sex | 64 | 100% | 64 | |||
| timepoint_label | 64 | 100% | 64 | |||
| antibiotic_exposure | 62 | 97% | 62 | |||
| maternal_antibiotics | 60 | 94% | 60 | |||
| health_condition_detail | 20 | 31% | 20 |
- A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome. PMID 36050292 PMC9437082 curated
- Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota. PMID 37169786 PMC10175488 curated
- BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen. PMID 38172624 PMC10769871 curated
- A metagenomic catalog of the early-life human gut virome. PMID 38424077 PMC10904392 curated
- Species- and subspecies-level characterization of health-associated bacterial consortia that colonize the human gut during infancy. PMID 39428758 PMC11497992 curated
1 more
- Compiling an early life human gut microbiome atlas and identification of key microbial drivers. PMID 41350579 PMC12769767
Archive description
The infant gut microbiome is thought to play a key role in developing metabolic and immunologic pathways. Antibiotics have been shown to disrupt the human microbiome, but the impact they have on infants during this key window of development remains poorly understood. Through this study we further characterize the effect antibiotics have on the gut microbiome of infants by looking at metagenomic sequencing data over time.
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 · “Gut metagenome of infants”
- body site study.description · “The infant gut microbiome is thought”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Gut metagenome of infants in the neonatal”
- life stage study.title · “infants in the neonatal intensive care unit”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN10919906 | age_at_collection_days | 21 | R1 | 0.85 | sample.title | day of life 21 |
| SAMN10919906 | antibiotic_exposure | yes | R1 | 0.85 | biosample_attr | 1 |
| SAMN10919906 | collection_date | 2014-09-10 | R1 | 0.85 | biosample.attribute:collection_date | 2014-09-10 |
| SAMN10919906 | country | US | R1 | 0.90 | biosample_attr | USA: Los Angeles |
| SAMN10919908 | health_condition | other_disease | R1 | 0.85 | biosample.attribute:gastroschisis | 1 |
| SAMN10919908 | health_condition_detail | 1 | R1 | 0.85 | biosample.attribute:gastroschisis | 1 |
| SAMN10919906 | maternal_antibiotics | no | R1 | 0.85 | biosample_attr | 0 |
| SAMN10919906 | sex | male | R1 | 0.90 | biosample_attr | male |
| SAMN10919906 | subject_id | N60061 | R1 | 0.85 | biosample_attr | N60061 |
| SAMN10919906 | timepoint_label | day of life 21 | R1 | 0.70 | sample.title | infant stool microbiome from subject N60061 at day of life 21 |
Sequencing
64 runs over 64 samples · mean 0.56 Gbp per run (median 0.59 Gbp, total 36.13 Gbp; 64 runs with a base count) · layout PAIRED 64 · platform ILLUMINA 64 · models NextSeq 500 (64) · 67% of runs with a Sandpiper profile · first public 2020-03-02
Authors (56)
Zeng S first · Patangia D · Almeida A · Zhou Z · Mu D · Paul Ross R · Stanton C · Wang S 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 · Minot SS first · Mayer-Blackwell K · Fiore-Gartland A · Johnson A · Self S · Bhatti P · Yao L · Liu L · Sun X · Jinfa Y · Kublin J last · Longhi G · Gennaioli E · Muscò A · Rizzo SM · Viappiani A · Vitale SG · Angioni S
Downloads
PRJNA521878.csv.gz (3.3 KB) · parquet (74.3 KB) — all 64 samples, every field with route and confidence · PRJNA521878_determinations.csv.gz (5.0 KB) — 546 evidence rows