Birth mode and infant gut microbiome, Luxembourg cohort
753 samples from a longitudinal cohort study in Luxembourg, mostly infants (with some neonate and unknown-age samples), examining birth mode-dependent effects on gut microbiome composition, immune stimulation, and antimicrobial resistance during the first year of life. machine-written summary
753 samples · 753 runs · LU · Infant / toddler · 2019 · 2.7 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,931 sample values (collection date, country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 1,378 sample values (age, location region) · PMC11686179, PMC9723731 |
| ✓ Supplementary tables | 2,603 sample values (age, antibiotic exposure, birth weight grams, delivery mode, gestational age weeks, maternal antibiotics, preterm status, sex) |
| – 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 — not resolved
71 of 95 people sampled more than once (694 samples; median 7, up to 30 per person). Schedule stated by the source: “Infants sampled at multiple visits (V3,V4,V5,V6) during the first year of life; exact day offsets not stated” (time origin: birth); stated follow-up 12 mo.
Genera, mean relative abundance over 23 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 | 658 | 87% | ||||
| country | 753 | 100% | 753 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 718 | 95% | 695 | 23 | ||
| collection_date | 753 | 100% | 753 | |||
| detailed_location | 753 | 100% | ||||
| location_region | 753 | 100% | 753 | |||
| timepoint_label | 730 | 97% | 730 | |||
| birth_weight_grams | 677 | 90% | 677 | |||
| delivery_mode | 677 | 90% | 677 | |||
| sex | 677 | 90% | 677 | |||
| age_at_collection_days | 648 | 86% | 23 | 625 | ||
| maternal_antibiotics | 358 | 48% | 358 | |||
| gestational_age_weeks | 122 | 16% | 122 | |||
| antibiotic_exposure | 23 | 3% | 23 | |||
| preterm_status | 23 | 3% | 23 |
- 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
- Personalized modeling of gut microbiome metabolism throughout the first year of life. PMID 39739091 PMC11686179 curated
- Dynamics of gut resistome and mobilome in early life: a meta-analysis. PMID 40048849 PMC11929092 curated
Archive description
Assessing the impact of the gut microbiota and its role in development and antimicrobial resistance during the first year 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 · “mode-dependent effects on gut microbiome composition, immune”
- body site study.description · “impact of the gut microbiota and its”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “resistance in the first year of life”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN16428212 | age_at_collection_days | 5 | R2 | 0.75 | paper.supp.table | infant_age=5 |
| SAMN13567118 | age_at_collection_days | 365 | R3 | 0.25 | paper.fulltext.methods | and at 1 year of age |
| SAMN16428212 | antibiotic_exposure | no | R2 | 0.75 | paper.supp.table | abx_ever=no |
| SAMN16428212 | birth_weight_grams | 2730 | R2 | 0.75 | paper.supp.table | birth_weight=2730 |
| SAMN13567118 | collection_date | 2018-12-01 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2018-12-01 |
| SAMN13567118 | country | LU | R1 | 0.90 | biosample_attr | Luxembourg |
| SAMN16428212 | delivery_mode | vaginal | R2 | 0.75 | paper.supp.table | born_method=vaginal |
| SAMN17025416 | gestational_age_weeks | 38.0 | R2 | 0.75 | paper.supp.table | Gestational age (weeks)=38 |
| SAMN13567118 | location_region | Luxembourg | R3 | 0.70 | paper.fulltext.methods | Luxembourg Comité national d’éthique de recherche |
| SAMN16428212 | maternal_antibiotics | no | R2 | 0.75 | paper.supp.table | maternal_abx=no |
| SAMN16428212 | preterm_status | term | R2 | 0.75 | paper.supp.table | premature=no |
| SAMN16428212 | sex | male | R2 | 0.75 | paper.supp.table | gender=male |
| SAMN17025382 | subject_id | V3_C005 | R1 | 0.85 | biosample_attr | V3_C005 |
| SAMN16428212 | subject_id | SRR12817637 | R2 | 0.75 | paper.supp.table | sequence_id=SRR12817637 |
| SAMN13567118 | timepoint_label | V6 | R1 | 0.70 | sample.title | 119_V6 |
| SAMN16428212 | timepoint_label | V3 | R1 | 0.70 | sample.name_rule:original_sample_name | C005V3 |
| SAMN17025382 | timepoint_label | V3 | R1 | 0.70 | run.library_name | V3_C005_maxbin_output.004_sub.contigs.fna |
Sequencing
753 runs over 753 samples · mean 0.17 Gbp per run (median 2.7 Mbp, total 125.12 Gbp; 753 runs with a base count) · layout SINGLE 730, PAIRED 23 · platform ILLUMINA 753 · models NextSeq 550 (695), NextSeq 500 (58) · 3% of runs with a Sandpiper profile · first public 2019-12-16 – 2021-01-04
Authors (22)
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 · Shaaban R first · Guéant JL · Heinken A last · Bargheet A first · Noordzij HT · Ponsero AJ · Jian C · Korpela K · Valles-Colomer M · Debelius J · Kurilshikov A · Pettersen VK last
Downloads
PRJNA595749.csv.gz (16.7 KB) · parquet (97.8 KB) — all 753 samples, every field with route and confidence · PRJNA595749_determinations.csv.gz (41.1 KB) — 6,912 evidence rows