Infant gut bacteriophages by delivery mode, USA cohort
Longitudinal cohort study of 273 gut metagenome samples from US infants and neonates (219 infant, 54 neonate), examining how delivery mode (Cesarean vs. other) affects gut bacteriophage colonization from 2 to 24 months of age. machine-written summary
273 samples · 273 runs · US · Infant / toddler · 2024 · 4.18 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,974 sample values (age, antibiotic exposure, collection date, country, delivery mode, health condition, health condition detail, maternal antibiotics) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11109039, PMC12352455, PMC12716031 |
| ○ 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 |
longitudinal
55 of 55 people sampled more than once (273 samples; median 5, up to 5 per person) · follow-up median 2.0 y (max 2.0 y) · median interval between samples 5 mo (time from age at collection). Schedule stated by the source: “Each subject sampled at up to 5 timepoints: BIRTH, 2 months, 6 months, 12 months, 24 months (suffixes a-e in library_name/sample_title).” (time origin: birth); stated follow-up 2.0 y.
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 216 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 | 273 | 100% | ||||
| country | 273 | 100% | 273 | |||
| health_condition | 2 | 1% | 2 | |||
| subject_id | 273 | 100% | 273 | |||
| age_at_collection_days | 273 | 100% | 273 | |||
| collection_date | 273 | 100% | 273 | |||
| delivery_mode | 273 | 100% | 273 | |||
| maternal_antibiotics | 273 | 100% | 273 | |||
| sex | 273 | 100% | 273 | |||
| timepoint_label | 53 | 19% | 53 | |||
| antibiotic_exposure | 4 | 1% | 4 | |||
| health_condition_detail | 2 | 1% | 2 | |||
| probiotic_exposure | 2 | 1% | 2 |
- Faecal zonulin, calprotectin and the infant microbiome in early life. PMID 38773685 PMC11109039 curated
- Delivery mode impacts gut bacteriophage colonization during infancy. PMID 40823537 PMC12352455 curated
- Colibactin genes are highly prevalent in the developing infant gut microbiome. PMID 41405404 PMC12716031 curated
- Colibactin genes are highly prevalent in the developing infant gut microbiome curated
Archive description
Cesarean section delivery is associated with altered early-life bacterial colonization and later adverse inflammatory and immune health outcomes. Although gut bacteriophages alter gut microbiome composition and impact host immune responses, little is known about how delivery mode impacts bacteriophage colonization over time. We show Cesarean section delivery is associated with decreased diversity of bacteriophages at 2 months of life, with altered predicted bacterial hosts up to 24 months of life.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Delivery mode impacts gut bacteriophage colonization during”
- body site study.description · “health outcomes. Although gut bacteriophages alter gut”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “bacteriophage colonization during infancy”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN23243524 | age_at_collection_days | 730 | R1 | 0.90 | biosample_attr | 24 months |
| SAMN23243524 | antibiotic_exposure | no | R1 | 0.80 | biosample.attribute:antibiotics_exposure | antibiotics_exposure: No |
| SAMN23243524 | collection_date | 2020-09-10 | R1 | 0.85 | biosample.attribute:collection_date | 2020-09-10 |
| SAMN23243524 | country | US | R1 | 0.90 | biosample_attr | USA |
| SAMN23243524 | delivery_mode | vaginal | R1 | 0.90 | biosample_attr | VD |
| SAMN23243524 | health_condition | sepsis_or_infection | R1 | 0.90 | sample.attr.host_disease | host_disease=Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049] |
| SAMN23243524 | health_condition_detail | Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049] | R1 | 0.90 | biosample.attribute:host_disease | host_disease: Severe acute respiratory syndrome coronavirus 2 [NCBITaxon:2697049] |
| SAMN23243524 | maternal_antibiotics | no | R1 | 0.85 | biosample_attr | VD_noabx |
| SAMN23243543 | probiotic_exposure | no | R1 | 0.60 | biosample_attr | control |
| SAMN23243524 | sex | male | R1 | 0.90 | biosample_attr | male |
| SAMN23243524 | subject_id | 229 | R1 | 0.85 | biosample_attr | 229 |
| SAMN36022571 | timepoint_label | 105d | R1 | 0.70 | run.library_name | 105d_wgs |
Sequencing
273 runs over 273 samples · mean 3.65 Gbp per run (median 4.18 Gbp, total 995.99 Gbp; 273 runs with a base count) · layout PAIRED 273 · platform ILLUMINA 273 · models Illumina NovaSeq 6000 (273) · 79% of runs with a Sandpiper profile · first public 2024-02-04 – 2024-02-25
Authors (13)
Bacorn M first · Subramanian P · Levy S · Chen Q · Maxwell GL · Hourigan SK last · Romero-Soto HN · Stern DB · McCauley KE · Strength R · Robbins ES · Namasivyam S · Maxwell G
Downloads
PRJNA988496.csv.gz (10.2 KB) · parquet (83.6 KB) — all 273 samples, every field with route and confidence · PRJNA988496_determinations.csv.gz (11.7 KB) — 1,974 evidence rows