Amoxicillin vs placebo, gut microbiome, malnutrition, Niger
434 gut metagenome samples from a randomized controlled trial in Niger evaluating amoxicillin prophylaxis versus placebo on gut microbiome and resistome in severe acute malnutrition. machine-written summary
434 samples · 434 runs · NE · Infant / toddler · 2023 · 1.39 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 436 sample values (country, subject id) |
| ✓ Abstract / description | 2 sample values (health condition) |
| ○ Full text | read; no usable statement or table · PMC10620469 |
| ✓ Supplementary tables | 2,591 sample values (age, health condition, health condition detail, intervention, subject id, timepoint) |
| – 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 |
intervention · arms resolved
59 people have samples in more than one arm.
Antibiotic given as the study intervention (incl. eradication therapy design randomized_controlled_trial · population malnutrition · Amoxicillin prophylaxis vs placebo for severe acute malnutrition
“randomized controlled trial of placebo or amoxicillin” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
88 of 207 people sampled more than once (315 samples; median 3, up to 6 per person) · follow-up median 3 mo (max 2.2 y) · median interval between samples 30 d (time from age at collection). Schedule stated by the source: “Stool at baseline (wk0), wk1, wk4, wk8, wk12; subset resampled at wk104 (2 years later)” (time origin: enrolment); stated follow-up 2.0 y.
Each row is one person (36 shown of 88); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 395 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 | 431 | 99% | ||||
| country | 434 | 100% | 434 | |||
| health_condition | 434 | 100% | 432 | 2 | ||
| subject_id | 434 | 100% | 2 | 432 | ||
| health_condition_detail | 432 | 100% | 432 | |||
| intervention | 432 | 100% | 432 | |||
| timepoint_label | 432 | 100% | 432 | |||
| age_at_collection_days | 431 | 99% | 431 |
- Effect of amoxicillin on the gut microbiome of children with severe acute malnutrition in Madarounfa, Niger: a retrospective metagenomic analysis of a placebo-controlled trial. 2023 PMID 37866373 PMC10620469 own_data
Archive description
Short read sequencing from randomized controlled trial of placebo or amoxicillin for severe acute malnutrition.
How this project entered the registry
Classified as human gut / stool 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 · “amoxicillin prophylaxis on gut microbiome and resistome”
- 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)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN19711397 | age_at_collection_days | 700.06 | R2 | 0.80 | paper.supp.mmc2.xlsx[210615_Nigermetadata!visAge] | 23 |
| SAMN19711397 | country | NE | R1 | 0.90 | biosample_attr | Niger |
| SAMN19711397 | health_condition | malnutrition | R2 | 0.80 | paper.supp.mmc2.xlsx[210615_Nigermetadata!Group] | SAM |
| SAMN19711828 | health_condition | malnutrition | R4 | 0.40 | study.title | amoxicillin prophylaxis on gut microbiome and resistome for severe acute malnutrition |
| SAMN19711397 | health_condition_detail | SAM | R2 | 0.80 | paper.supp.mmc2.xlsx[210615_Nigermetadata!Group] | SAM |
| SAMN19711397 | intervention | no_intervention | R2 | 0.80 | paper.supp.mmc2.xlsx[210615_Nigermetadata!Treatment] | Placebo |
| SAMN19711828 | subject_id | 7006 | R1 | 0.70 | sample.name_rule:information | 7006yr2_SAMcontrol_NA_wk104 |
| SAMN19711397 | subject_id | 1576 | R2 | 0.80 | paper.supp.mmc2.xlsx[210615_Nigermetadata!idno] | 1576 |
| SAMN19711397 | timepoint_label | week 0 | R2 | 0.80 | paper.supp.mmc2.xlsx[210615_Nigermetadata!Week_of_follow_up] | 0 |
Sequencing
434 runs over 434 samples · mean 1.44 Gbp per run (median 1.39 Gbp, total 622.92 Gbp; 434 runs with a base count) · layout PAIRED 434 · platform ILLUMINA 434 · models NextSeq 500 (434) · 91% of runs with a Sandpiper profile · first public 2023-07-31
Authors (9)
Schwartz DJ first · Langdon A · Sun X · Langendorf C · Berthé F · Grais RF · Trehan I · Isanaka S · Dantas G last
Downloads
PRJNA739008.csv.gz (15.2 KB) · parquet (89.7 KB) — all 434 samples, every field with route and confidence · PRJNA739008_determinations.csv.gz (16.9 KB) — 3,029 evidence rows