Neonatal antibiotic exposure & infant gut colonization
20 infant gut microbiome samples from Turku, Finland, examining how neonatal antibiotic exposure affects intestinal microbial colonization and child growth; longitudinal cohort design. machine-written summary
20 samples · 20 runs · FI · Infant / toddler · 2020 · 2.25 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 80 sample values (collection date, country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 69 sample values (feeding mode, location locality, location site, preterm status) · PMC7838415 |
| ✓ Supplementary tables | 35 sample values (age, antibiotic exposure) |
| – 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
5 of 15 people sampled more than once (10 samples; median 2, up to 2 per person) · follow-up median 5 mo (max 5 mo) · median interval between samples 5 mo (time from age at collection). Schedule stated by the source: “Samples labeled 1M and 6M, suggesting collection at 1 month and 6 months” (time origin: birth); stated follow-up 6 mo.
Each row is one person (5 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 15 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 | 20 | 100% | ||||
| country | 20 | 100% | 20 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 20 | 100% | 20 | |||
| collection_date | 20 | 100% | 20 | |||
| detailed_location | 20 | 100% | ||||
| location_locality | 20 | 100% | 20 | |||
| location_site | 20 | 100% | 20 | |||
| preterm_status | 20 | 100% | 20 | |||
| timepoint_label | 20 | 100% | 20 | |||
| antibiotic_exposure | 18 | 90% | 18 | |||
| age_at_collection_days | 17 | 85% | 17 | |||
| feeding_mode | 9 | 45% | 9 |
- Neonatal antibiotic exposure impairs child growth during the first six years of life by perturbing intestinal microbial colonization. PMID 33500411 PMC7838415 curated
Archive description
Neonatal antibiotic exposure impairs child growth during the first six years of life by perturbing intestinal microbial colonization
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of neonate and child and infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.description · “life by perturbing intestinal microbial colonization”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage study.title · “Neonatal antibiotic exposure impairs”
- life stage study.description · “Neonatal antibiotic exposure impairs”
- life stage study.title · “antibiotic exposure impairs child growth during the”
- life stage study.description · “antibiotic exposure impairs child growth during the”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN16198195 | age_at_collection_days | 30.4 | R2 | 0.80 | paper.supp.41467_2020_20495_MOESM1_ESM.docx[table5!Age (months)] | 1 |
| SAMN16198195 | antibiotic_exposure | no | R2 | 0.80 | paper.supp.41467_2020_20495_MOESM1_ESM.docx[table5!Control/Abx] | CTR |
| SAMN16198194 | collection_date | 2017-06-01 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2017-06-01 |
| SAMN16198194 | country | FI | R1 | 0.90 | biosample_attr | Finland:Turku |
| SAMN16198194 | feeding_mode | exclusive_breast | R3 | 0.40 | paper.fulltext.results | when all of the infants were breastfed |
| SAMN16198194 | location_locality | Turku | R3 | 0.70 | paper.fulltext.methods | conducted at the Turku University Hospital in Turku, Finland |
| SAMN16198194 | location_site | Turku University Hospital | R3 | 0.70 | paper.fulltext.methods | conducted at the Turku University Hospital in Turku, Finland |
| SAMN16198194 | preterm_status | term | R3 | 0.75 | paper.fulltext.results | Twenty full-term healthy neonates not exposed to antibiotics |
| SAMN16198194 | subject_id | S121 | R1 | 0.70 | sample.name_rule:library_names | S121_1M |
| SAMN16198194 | timepoint_label | 1M | R1 | 0.70 | run.library_name | S121_1M |
Sequencing
20 runs over 20 samples · mean 2.27 Gbp per run (median 2.25 Gbp, total 45.33 Gbp; 20 runs with a base count) · layout PAIRED 20 · platform ILLUMINA 20 · models Illumina HiSeq 2500 (20) · 75% of runs with a Sandpiper profile · first public 2020-09-18
Authors (22)
Uzan-Yulzari A first · Turta O · Belogolovski A · Ziv O · Kunz C · Perschbacher S · Neuman H · Pasolli E · Oz A · Ben-Amram H · Kumar H · Ollila H · Kaljonen A · Isolauri E · Salminen S · Lagström H · Segata N · Sharon I · Louzoun Y · Ensenauer R · Rautava S · Koren O last
Downloads
PRJNA606271.csv.gz (1.6 KB) · parquet (71.1 KB) — all 20 samples, every field with route and confidence · PRJNA606271_determinations.csv.gz (2.2 KB) — 184 evidence rows