Mother-child gut metagenomes for helminth detection in Gabon
Cross-sectional study of 51 fecal metagenome samples from mother-child pairs in rural and semi-urban Gabon, comparing metagenomic detection of soil-transmitted helminths with conventional diagnostics and examining associated gut microbiome shifts. machine-written summary
51 samples · 138 runs · GA · Infant / toddler · 2025 · 0.55 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 230 sample values (age, collection date, country, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 51 sample values (location site) · PMC12688249 |
| ✓ Supplementary tables | 23 sample values (subject id) |
| – 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 — not resolved
mother-child pairs in Gabon; pairs not linkable from archive metadata.
Genera, mean relative abundance over 45 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 | 50 | 98% | ||||
| country | 51 | 100% | 51 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 51 | 100% | 28 | 23 | ||
| collection_date | 51 | 100% | 51 | |||
| detailed_location | 51 | 100% | ||||
| location_site | 51 | 100% | 51 | |||
| age_at_collection_days | 50 | 98% | 50 | |||
| sex | 50 | 98% | 50 |
- Infection with gut parasites correlates with gut microbiome diversity across human populations in Africa. PMID 41358671 PMC12688249 curated
Archive description
Soil-transmitted helminths (STH) are prevalent in (sub)tropical regions and pose significant public health challenges, particularly in low-resource settings. These gut-dwelling parasites interact with the microbiota and host immunity, yet their impact on microbial communities remains poorly understood. Traditional STH detection methods, such as microscopy and qPCR, are labor-intensive and rarely integrated into microbiome studies, limiting insights into these interactions. This project explores metagenomic sequencing as a non-invasive tool for STH detection while assessing microbiome alterations linked to infection. We generated 310 fecal metagenomes from mother-child pairs in rural and semi-urban Gabon, enabling a comprehensive analysis of microbial and parasitic communities. By comparing metagenomic detection with conventional diagnostics, we evaluated sequencing accuracy and examined STH-associated microbiome shifts. Note: (1) Metagenomes with the same study ID correspond to samples sequenced across multiple runs/lanes, which were aggregated before analysis. (2) The read counts in the manuscript are lower than those in ENA metadata because the former represent post-QC read counts, while the latter reflect raw sequencing reads
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.description · “low-resource settings. These gut -dwelling parasites interact”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “metagenomes from mother- child pairs in rural”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA117816348 | age_at_collection_days | 10592 | R1 | 0.70 | sample.attr.age | 29 |
| SAMEA117816349 | age_at_collection_days | 91 | R1 | 0.90 | biosample_attr | 3_months |
| SAMEA117816348 | collection_date | 2017-12-08 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2017-12-08 |
| SAMEA117816348 | country | GA | R1 | 0.90 | biosample_attr | Gabon |
| SAMEA117816348 | location_site | Centre de Recherches Médicales de Lambaréné (CERMEL) | R3 | 0.70 | paper.fulltext.methods | conducted at the Centre de Recherches Médicales de Lambaréné |
| SAMEA117816348 | sex | female | R1 | 0.90 | biosample_attr | Female |
| SAMEA117816349 | subject_id | G0015 | R1 | 0.70 | sample.name_rule:title | G0015 |
| SAMEA117816348 | subject_id | G0014 | R2 | 0.75 | paper.supp.table | subjectID=G0014 |
Sequencing
138 runs over 51 samples · mean 0.20 Gbp per run (median 0.13 Gbp, total 28.15 Gbp; 138 runs with a base count) · layout PAIRED 138 · platform ILLUMINA 138 · models Illumina HiSeq 3000 (87), Illumina MiSeq (51) · 54% of runs with a Sandpiper profile · first public 2025-12-12
Authors (13)
Ngwese MM first · Adegbite BR · Zinsou JF · Fitzstevens JL · Schmidt VT · Moure PAN · Maloum MN · Tyakht AV · Huus KE · Youngblut ND · Kremsner PG · Adegnika AA · Ley RE last
Downloads
PRJEB86954.csv.gz (2.8 KB) · parquet (72.6 KB) — all 51 samples, every field with route and confidence · PRJEB86954_determinations.csv.gz (3.7 KB) — 304 evidence rows