Gut microbiome and febrile malaria risk in Malian children
Case-control study of 70 fecal samples from 10-year-old children in Mali, comparing baseline gut microbiome composition between children who later developed febrile malaria and those who remained asymptomatic after Plasmodium falciparum infection. machine-written summary
70 samples · 70 runs · ML · Child · 2024 · 22.97 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 210 sample values (collection date, country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 140 sample values (age, location locality) · PMC11538534 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 140 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
design observational_with_procedure
Genera, mean relative abundance over 64 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 | 70 | 100% | ||||
| country | 70 | 100% | 70 | |||
| health_condition | 70 | 100% | 70 | |||
| subject_id | 70 | 100% | 70 | |||
| age_at_collection_days | 70 | 100% | 70 | |||
| collection_date | 70 | 100% | 70 | |||
| detailed_location | 70 | 100% | ||||
| health_condition_detail | 70 | 100% | 70 | |||
| location_locality | 70 | 100% | 70 |
- The gut microbiome is associated with susceptibility to febrile malaria in Malian children. 2024 PMID 39500866 PMC11538534 own_data
Archive description
Shotgun metagenomics sequencing of the fecal samples of 10-year-old Malian children collected before the transmission season. Used to determine if there is a difference between the baseline microbiome of children that remain asymptomatic and those that develop febrile symptoms after Plasmodium infection during the following malaria transmission season.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- body site study.title · “with an inflammatory gut microbiome”
- body site study.description · “sequencing of the fecal samples of 10-year-old”
- life stage external_curation.infant_catalog · “infant triage reason_code age_child_over_36m”
- life stage study.description · “of 10-year-old Malian children collected before the”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN40750203 | age_at_collection_days | 3653 | R3 | 0.70 | paper.fulltext.abstract | 10-year-old Malian children |
| SAMN40750203 | collection_date | 2014-05 | R1 | 0.90 | biosample.attribute:collection_date | 2014-05 |
| SAMN40750203 | country | ML | R1 | 0.90 | sample.attr.geo_loc_name | Mali |
| SAMN40750203 | health_condition | other_infection | R2 | 0.75 | external.gmrepo source | phenotype: Malaria |
| SAMN40750203 | health_condition_detail | Malaria | R2 | 0.75 | external.gmrepo source | phenotype: Malaria |
| SAMN40750203 | location_locality | Kalifabougou | R3 | 0.70 | paper.fulltext.methods | conducted in Kalifabougou, Mali |
| SAMN40750203 | subject_id | KMV_361 | R1 | 0.85 | sample.attr.patient_id | KMV_361 |
Sequencing
70 runs over 70 samples · mean 23.54 Gbp per run (median 22.97 Gbp, total 1,648.07 Gbp; 70 runs with a base count) · layout PAIRED 70 · platform ILLUMINA 70 · models Illumina NovaSeq 6000 (70) · 91% of runs with a Sandpiper profile · first public 2024-04-09
Authors (11)
Van Den Ham KM first · Bower LK · Li S · Lorenzi H · Doumbo S · Doumtabe D · Kayentao K · Ongoiba A · Traore B · Crompton PD · Schmidt NW last
Downloads
PRJNA1096289.csv.gz (2.8 KB) · parquet (72.9 KB) — all 70 samples, every field with route and confidence · PRJNA1096289_determinations.csv.gz (3.9 KB) — 490 evidence rows