The role of Bifidobacterium genus in modulating the neonate microbiota: implications for antibiotic resistance acquisition in early life/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-7-19
Curated date: 2024/06/09
Curator: Aleru Divine
Revision editor(s): Aleru Divine, Victoria, Scholastica
Subjects
- Location of subjects
- Spain
- 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
- Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Low-Bifidobacterium group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High-Bifidobacterium group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High-Bifidobacterium group in the seven (7) day-old infants.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 57
- Group 1 sample size Number of subjects in the case (exposed) group
- 42
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V4
- 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).
- log transformation
- Statistical test
- LEfSe
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- antibiotic exposure, feeding practices, mode of birth
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-7-19
Source: Figure 2
Description: Microbial composition according to Bifidobacterium-abundance groups, indicating differences in relative abundance and identified taxonomic biomarkers.
Abundance in Group 1: increased abundance in High-Bifidobacterium group
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Corynebacterium | ||
| Streptococcus |
Revision editor(s): Aleru Divine
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-7-19
Source: Figure 2
Description: Microbial composition according to Bifidobacterium-abundance groups, indicating differences in relative abundance and identified taxonomic biomarkers.
Abundance in Group 1: decreased abundance in High-Bifidobacterium group
| NCBI | Quality Control | Links |
|---|---|---|
| Staphylococcus | ||
| Enterococcus | ||
| Klebsiella | ||
| Clostridium |
Revision editor(s): Aleru Divine
