Gut microbiome in Kenyan infants, cross-sectional
Shotgun metagenomics of 105 samples from infants in Kenya, examining gut microbiome composition and function in relation to human milk oligosaccharides; cross-sectional design. machine-written summary
105 samples · 105 runs · KE · Infant / toddler · 2023 · 10.02 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 420 sample values (collection date, country, subject id, timepoint) |
| ✓ Abstract / description | 105 sample values (lifestyle detail) |
| ✓ Full text | 315 sample values (lifestyle, location locality, location region) · PMC9980514 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 91 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 | 0 | 0% | ||||
| country | 105 | 100% | 105 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 105 | 100% | 105 | |||
| collection_date | 105 | 100% | 105 | |||
| detailed_location | 105 | 100% | ||||
| lifestyle | 105 | 100% | 105 | |||
| lifestyle_detail | 105 | 100% | 105 | |||
| location_locality | 105 | 100% | 105 | |||
| location_region | 105 | 100% | 105 | |||
| timepoint_label | 105 | 100% | 105 |
- Gut microbiome function and composition in infants from rural Kenya and association with human milk oligosaccharides. PMID 36794816 PMC9980514 curated
Archive description
Shotgun metagenomics from Kenyan infants
How this project entered the registry
Classified as human gut / stool / human milk shotgun DNA metagenome of 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 microbiome function and”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- body site study.title · “and association with human milk oligosaccharides”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “and composition in infants from rural Kenya”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA112710888 | collection_date | 2018 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2018 |
| SAMEA112710888 | country | KE | R1 | 0.90 | biosample_attr | Kenya |
| SAMEA112710888 | lifestyle | rural_non_industrialized | R3 | 0.70 | paper.fulltext.methods | surrounding rural communities in Kwale County |
| SAMEA112710888 | lifestyle_detail | infants from rural Kenya | R4 | 0.40 | ena.study_title | infants from rural Kenya |
| SAMEA112710888 | location_locality | Msambweni | R3 | 0.70 | paper.fulltext.methods | conducted in Msambweni and the surrounding rural communities |
| SAMEA112710888 | location_region | Kwale County | R3 | 0.70 | paper.fulltext.methods | Kwale County on the southern coast of Kenya |
| SAMEA112710888 | subject_id | INSP002 | R1 | 0.65 | sample.name_rule:title | INSP002BLStoolDNA |
| SAMEA112710888 | timepoint_label | BL | R1 | 0.70 | sample.name_rule:title | title: INSP002BLStoolDNA |
Sequencing
105 runs over 105 samples · mean 10.47 Gbp per run (median 10.02 Gbp, total 1,099.01 Gbp; 105 runs with a base count) · layout PAIRED 105 · platform ILLUMINA 105 · models Illumina NovaSeq 6000 (105) · 87% of runs with a Sandpiper profile · first public 2023-03-03
Authors (13)
Derrien M first · Mikulic N · Uyoga MA · Chenoll E · Climent E · Howard-Varona A · Nyilima S · Stoffel NU · Karanja S · Kottler R · Stahl B · Zimmermann MB · Bourdet-Sicard R last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJEB52748.csv.gz (4.1 KB) · parquet (75.3 KB) — all 105 samples, every field with route and confidence · PRJEB52748_determinations.csv.gz (6.4 KB) — 840 evidence rows