Virome of breast milk and infant feces, USA
Viral metagenomics of 20 samples from mother-infant pairs in the USA comparing breast milk and infant fecal viromes to assess phage transmission to the infant gut. machine-written summary
20 samples · 20 runs · US · Mixed ages · 2018 · 1.36 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 100 sample values (collection date, country, family id, family role, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC5992295 |
| ✓ Supplementary tables | 60 sample values (age, antibiotic exposure, 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 |
mother–infant
10 mother–infant pairs: infant stool (Baby<n>) and maternal breast milk (Mother<n>) · 10 families with 20 sampled people (10 with a parent and a child).
motherchild · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 10 families. 10 people in the project overall.
Families (10)
| family | members | samples |
|---|---|---|
| pair1 | mother + child | SAMN08225420 · SAMN08225430 |
| pair10 | mother + child | SAMN08225429 · SAMN08225439 |
| pair2 | mother + child | SAMN08225421 · SAMN08225431 |
| pair3 | mother + child | SAMN08225422 · SAMN08225432 |
| pair4 | mother + child | SAMN08225423 · SAMN08225433 |
| pair5 | mother + child | SAMN08225424 · SAMN08225434 |
| pair6 | mother + child | SAMN08225425 · SAMN08225435 |
| pair7 | mother + child | SAMN08225426 · SAMN08225436 |
| pair8 | mother + child | SAMN08225427 · SAMN08225437 |
| pair9 | mother + child | SAMN08225428 · SAMN08225438 |
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 20 | 100% | ||||
| country | 20 | 100% | 20 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 20 | 100% | 20 | |||
| age_at_collection_days | 20 | 100% | 20 | |||
| antibiotic_exposure | 20 | 100% | 20 | |||
| collection_date | 20 | 100% | 20 | |||
| family_id | 20 | 100% | 20 | |||
| family_role | 20 | 100% | 20 | |||
| sex | 20 | 100% | 20 |
- Shared and Distinct Features of Human Milk and Infant Stool Viromes. 2018 PMID 29910789 PMC5992295 own_data
Archive description
Characterization of shared characteristics between viromes of maternal milk and infant feces
How this project entered the registry
Classified as human gut / stool / human milk / multiple sites shotgun DNA metagenome of infant / toddler and adult by curator_audit with confidence 0.55. Assay shotgun_dna.
- host runs.isolation_source · “feces (10); Breastmilk (10)”
- host runs.scientific_name · “human gut metagenome (10)”
- body site runs.isolation_source · “feces (10); Breastmilk (10)”
- body site runs.scientific_name · “human gut metagenome (10)”
- life stage study.title · “Maternal Milk Infant Fecal Virome Study”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN08225420 | age_at_collection_days | 9.0 | R2 | 0.85 | paper.supp.Table_1.DOCX[table1!Age] | Baby1 BB1 9 days M antibiotics No |
| SAMN08225420 | antibiotic_exposure | no | R2 | 0.85 | paper.supp.Table_1.DOCX[table1!Antibiotics] | Baby1 BB1 9 days M antibiotics No |
| SAMN08225420 | collection_date | 2016-06-16 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2016-06-16 |
| SAMN08225420 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: California |
| SAMN08225420 | family_id | pair1 | R1 | 0.70 | sample.name_rule:TITLE | TITLE: Baby1; isolation_source: feces |
| SAMN08225420 | family_role | child | R1 | 0.70 | sample.name_rule:TITLE | TITLE: Baby1; isolation_source: feces |
| SAMN08225420 | sex | male | R2 | 0.85 | paper.supp.Table_1.DOCX[table1!Sex] | Baby1 BB1 9 days M antibiotics No |
| SAMN08225420 | subject_id | Baby1 | R1 | 0.70 | sample.name_rule:title | Baby1 |
Sequencing
20 runs over 20 samples · mean 1.37 Gbp per run (median 1.36 Gbp, total 27.35 Gbp; 20 runs with a base count) · layout PAIRED 20 · platform ILLUMINA 20 · models Illumina MiniSeq (20) · 30% of runs with a Sandpiper profile · first public 2018-11-14
Authors (0)
No author record.
Downloads
PRJNA427187.csv.gz (1.6 KB) · parquet (70.7 KB) — all 20 samples, every field with route and confidence · PRJNA427187_determinations.csv.gz (2.6 KB) — 160 evidence rows