Gut microbiota of HIV-exposed neonates in Cape Town
Shotgun metagenomic sequencing of 65 stool samples from neonates exposed to HIV in Cape Town, South Africa, using a case-control design. machine-written summary
65 samples · 65 runs · ZA · Infant / toddler · 2024 · 18.94 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 195 sample values (collection date, country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 455 sample values (age, delivery mode, feeding mode, location locality, location region, location site, preterm status) · PMC11662858 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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
30 of 35 people sampled more than once (60 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 59 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 | 65 | 100% | ||||
| country | 65 | 100% | 65 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 65 | 100% | 65 | |||
| age_at_collection_days | 65 | 100% | 65 | |||
| collection_date | 65 | 100% | 65 | |||
| delivery_mode | 65 | 100% | 65 | |||
| detailed_location | 65 | 100% | ||||
| feeding_mode | 65 | 100% | 65 | |||
| location_locality | 65 | 100% | 65 | |||
| location_region | 65 | 100% | 65 | |||
| location_site | 65 | 100% | 65 | |||
| preterm_status | 65 | 100% | 65 |
- Neonates exposed to HIV but uninfected exhibit an altered gut microbiota and inflammation associated with impaired breast milk antibody function. PMID 39707483 PMC11662858 curated
Archive description
Shotgun metagenomic raw sequences derived from stool of neonates exposed to HIV
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of neonate 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.title · “Gut microbiota of neonates”
- body site study.description · “sequences derived from stool of neonates exposed”
- life stage study.title · “Gut microbiota of neonates exposed to HIV”
- life stage study.description · “from stool of neonates exposed to HIV”
- 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 |
|---|---|---|---|---|---|---|
| SAMN43015617 | age_at_collection_days | 28 | R3 | 0.80 | paper.fulltext.methods | Stools and plasma from neonates were assessed at week 4 of life |
| SAMN43015617 | collection_date | 2016-02-17 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2016-02-17 |
| SAMN43015617 | country | ZA | R1 | 0.90 | biosample_attr | South Africa: Cape Town |
| SAMN43015617 | delivery_mode | vaginal | R3 | 0.80 | paper.fulltext.methods | vaginal term deliveries, gestational age ≥ 38 weeks |
| SAMN43015617 | feeding_mode | exclusive_breast | R3 | 0.80 | paper.fulltext.methods | All babies were exclusively breastfed |
| SAMN43015617 | location_locality | Khayelitsha | R3 | 0.70 | paper.fulltext.methods | recruited at the Midwife Obstetric Unit (MOU) in Khayelitsha |
| SAMN43015617 | location_region | Cape Town | R3 | 0.70 | paper.fulltext.methods | in Khayelitsha, Cape Town, South Africa |
| SAMN43015617 | location_site | Midwife Obstetric Unit (MOU), Khayelitsha | R3 | 0.70 | paper.fulltext.methods | recruited at the Midwife Obstetric Unit (MOU) |
| SAMN43015617 | preterm_status | term | R3 | 0.80 | paper.fulltext.methods | vaginal term deliveries, gestational age ≥ 38 weeks |
| SAMN43015617 | subject_id | HEU_neonate1 | R1 | 0.50 | biosample_attr | HEU_neonate1 |
Sequencing
65 runs over 65 samples · mean 19.86 Gbp per run (median 18.94 Gbp, total 1,290.58 Gbp; 65 runs with a base count) · layout PAIRED 65 · platform ILLUMINA 65 · models Illumina NovaSeq 6000 (65) · 91% of runs with a Sandpiper profile · first public 2024-08-12 – 2024-09-15
Authors (11)
Byrne A first · Diener C · Brown BP · Maust BS · Feng C · Alinde BL · Gibbons SM · Koch M · Gray CM · Jaspan HB · Nyangahu DD last
Downloads
PRJNA1143669.csv.gz (3.0 KB) · parquet (74.0 KB) — all 65 samples, every field with route and confidence · PRJNA1143669_determinations.csv.gz (4.6 KB) — 650 evidence rows