Preterm Infant Skin and Stool Metagenomes, Jackson MS
Case series of 60 samples from preterm infants in Jackson, MS, USA, examining the skin and stool microbiome over the first eight weeks of life in the NICU using metagenomic whole-genome sequencing. machine-written summary
60 samples · 60 runs · US · Infant / toddler · 2021 · 0.39 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 240 sample values (collection date, country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 24 sample values (antibiotic exposure, preterm status) · PMC8550141 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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
4 of 4 people sampled more than once (12 samples; median 3, up to 4 per person) · follow-up median 34 d (max 42 d) · median interval between samples 14 d (time from collection dates). Schedule stated by the source: “Sampled over first eight weeks of life in the NICU; multiple body sites and stool per infant”; stated follow-up 56 d.
Each row is one person (4 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 10 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 | 60 | 100% | ||||
| country | 60 | 100% | 60 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 60 | 100% | 60 | |||
| collection_date | 60 | 100% | 60 | |||
| timepoint_label | 60 | 100% | 60 | |||
| antibiotic_exposure | 12 | 20% | 12 | |||
| preterm_status | 12 | 20% | 12 |
- Viability-Resolved Metagenomics Reveals Antagonistic Colonization Dynamics of Staphylococcus epidermidis Strains on Preterm Infant Skin. PMID 34523979 PMC8550141 curated
Archive description
The skin is a habitat for microbes that commonly infect preterm infants. However, the use of sequencing for fine-scale study of the microbial communities of skin that develop in these infants has been limited by technical barriers. Our study's goals are to overcome these technical barriers to sequencing the microbiome on preterm infant skin, and to examine the microbiome of preterm infant skin over their first eight weeks of life in the NICU.
How this project entered the registry
Classified as human gut / stool / skin 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 · “Infant Skin and Stool”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- body site study.title · “of Preterm Infant Skin and Stool”
- body site study.description · “The skin is a habitat”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “WGS of Preterm Infant Skin and Stool”
- life stage study.title · “Metagenomic WGS of Preterm Infant Skin and”
- life stage study.description · “that commonly infect preterm infants. However, the”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN20335688 | antibiotic_exposure | yes | R3 | 0.75 | paper.fulltext.results | which spanned a period of antibiotic use in all four infants |
| SAMN20335648 | collection_date | 2019-06-06 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2019-06-06 |
| SAMN20335648 | country | US | R1 | 0.90 | biosample_attr | USA: Jackson, MS |
| SAMN20335688 | preterm_status | preterm | R3 | 0.80 | paper.fulltext.results | Four preterm infants of extremely low birthweight |
| SAMN20335648 | subject_id | infant 01 | R1 | 0.85 | biosample_attr | infant 01 |
| SAMN20335648 | timepoint_label | W1 | R1 | 0.70 | sample.name_rule:sample_alias | 01W1AV |
Sequencing
60 runs over 60 samples · mean 1.06 Gbp per run (median 0.39 Gbp, total 63.45 Gbp; 60 runs with a base count) · layout PAIRED 60 · platform ILLUMINA 60 · models NextSeq 500 (60) · 63% of runs with a Sandpiper profile · first public 2021-07-22 – 2021-07-24
Authors (5)
Hellmann KT first · Tuura CE · Fish J · Patel JM · Robinson DA last
Downloads
PRJNA748448.csv.gz (2.5 KB) · parquet (71.7 KB) — all 60 samples, every field with route and confidence · PRJNA748448_determinations.csv.gz (2.6 KB) — 264 evidence rows