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/Experiment 1

From BugSigDB


Needs review

Curated date: 2025/05/07

Curator: MyleeeA

Revision editor(s): MyleeeA, Anne-mariesharp

Subjects

Location of subjects
Niger
Host species Species from which microbiome was sampled. Contact us to have more species added.
Homo sapiens
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Treatment Treatment,treatment
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Amoxicillin Week 0
Group 1 name Corresponds to the case (exposed) group for case-control studies
Amoxicillin Week 1
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Children with severe acute malnutrition who received amoxicillin for one week and had their fecal samples collected at the end of treatment (Week 1).
Group 0 sample size Number of subjects in the control (unexposed) group
35
Group 1 sample size Number of subjects in the case (exposed) group
39

Lab analysis

Sequencing type
WMS
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Mann-Whitney (Wilcoxon)
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Richness Number of species
decreased

Signature 1

Needs review

Curated date: 2025/07/17

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Figure 3E

Description: Significant taxonomic changes at the genus level with Benjamini-Hochberg-corrected q-values.

Abundance in Group 1: increased abundance in Amoxicillin Week 1

NCBI Quality ControlLinks
Escherichia sp.

Revision editor(s): Anne-mariesharp

Signature 2

Needs review

Curated date: 2025/07/17

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Figure 3A, B, C

Description: Significant taxonomic changes at the genus level with Benjamini-Hochberg-corrected q-values.

Abundance in Group 1: decreased abundance in Amoxicillin Week 1

NCBI Quality ControlLinks
Bifidobacterium sp.
Holdemanella sp.
Lactobacillus sp.

Revision editor(s): Anne-mariesharp