Infant gut metagenomes, longitudinal cohort, Pittsburgh USA
14 fecal metagenome samples from infants (birth to 1 year) and matched maternal samples, collected at Magee-Womens Hospital of UPMC, Pittsburgh, USA; longitudinal cohort design. machine-written summary
14 samples · 14 runs · US · Infant / toddler · 2022 · 3.27 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 94 sample values (age, collection date, country, family id, family role, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – 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 |
longitudinalmother–infant
2 of 2 people sampled more than once (12 samples; median 6, up to 6 per person) · follow-up median 11 mo (max 11 mo) · median interval between samples 33 d (time from age at collection). Schedule stated by the source: “infant stool at DOL ~29/30, 61/64, 91/92, 122/124, 241/242, 364/365; mother sampled once (DOL 0)” (time origin: birth); stated follow-up 12 mo.
Each row is one person (2 shown); dots are samples at days since that person's first sample; rows of one family are adjacent and coloured by role (mother, father, child, twin).
2 mother–infant dyads (L1_007, L1_008): one maternal sample and six infant stool samples (day of life 29–365) per dyad · 2 families with 4 sampled people (2 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: 2 families. 2 people in the project overall.
Families (2)
| family | members | samples |
|---|---|---|
| L1_007 | mother + child | SAMN08481503 · SAMN08481504 · SAMN08481505 · SAMN08481506 · SAMN08481507 · SAMN08481508 · SAMN08481509 |
| L1_008 | mother + child | SAMN08481510 · SAMN08481511 · SAMN08481512 · SAMN08481513 · SAMN08481514 · SAMN08481515 · SAMN08481516 |
Genera, mean relative abundance over 11 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 | 12 | 86% | ||||
| country | 14 | 100% | 14 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 14 | 100% | 14 | |||
| collection_date | 14 | 100% | 14 | |||
| family_id | 14 | 100% | 14 | |||
| family_role | 14 | 100% | 14 | |||
| age_at_collection_days | 12 | 86% | 12 | |||
| timepoint_label | 12 | 86% | 12 |
Archive description
Metagenomes of infant fecal samples from birth to 1 year of age, matched with maternal samples
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “infant gut metagenomes (NIHL1)”
- body site study.description · “Metagenomes of infant fecal samples from birth”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “infant gut metagenomes (NIHL1)”
- life stage study.description · “age, matched with maternal samples”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN08481504 | age_at_collection_days | 29 | R1 | 0.85 | sample.title | DOL 29 |
| SAMN08481503 | collection_date | 2016-07 | R1 | 0.85 | biosample.attribute:collection_date | 2016-07 |
| SAMN08481503 | country | US | R1 | 0.90 | biosample_attr | USA: Pittsburgh, Magee-Womens Hospital of UPMC |
| SAMN08481503 | family_id | L1_007 | R1 | 0.85 | biosample.attribute:TITLE | Mother of infant L1_007 |
| SAMN08481503 | family_role | mother | R1 | 0.85 | biosample.attribute:TITLE | Mother of infant L1_007 |
| SAMN08481503 | subject_id | mother_of_L1_007 | R1 | 0.70 | sample.name_rule:title | Mother of infant L1_007 |
| SAMN08481504 | subject_id | 007 | R1 | 0.70 | sample.name_rule:library_names | L1_007_029G1 |
| SAMN08481504 | timepoint_label | DOL 29 | R1 | 0.70 | sample.title | Infant L1_007 DOL 29 |
Sequencing
14 runs over 14 samples · mean 3.15 Gbp per run (median 3.27 Gbp, total 44.15 Gbp; 14 runs with a base count) · layout PAIRED 14 · platform ILLUMINA 14 · models Illumina HiSeq 2500 (14) · 93% of runs with a Sandpiper profile · first public 2022-02-08
Authors (0)
No author record.
Downloads
PRJNA433393.csv.gz (1.4 KB) · parquet (70.5 KB) — all 14 samples, every field with route and confidence · PRJNA433393_determinations.csv.gz (1.7 KB) — 94 evidence rows