-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- Australia
- 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
- Response to antibiotic Response to antibiotic,response to antibiotic
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Antibiotic (No-ABX) group [Week-1]
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Intrapartum Antibiotic (IP-ABX) group [Week-1]
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants whose mothers received intrapartum antibiotics (within 28 days before or during delivery) and had no direct infant antibiotic exposure up to 6 weeks of age.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 80
- Group 1 sample size Number of subjects in the case (exposed) group
- 49
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
- Linear Regression
- 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)?
- No
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "collection day" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.collection day, sex, formula feeding
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Extented figure 6(g, h, i) And Supplementary Table 11a&b
Description: Differentially abundant microbial species in stool samples collected from IP-ABX infants at week 1 compared to No-ABX infants. Only taxa detected in >5% of samples are considered for differential abundance analysis.
Abundance in Group 1: increased abundance in Intrapartum Antibiotic (IP-ABX) group [Week-1]
Revision editor(s): ShadeAkinremi, Victoria
Signature 2
Source: Extented figure 6(g, h, i) And Supplementary Table 11a&b
Description: Differentially abundant microbial species in stool samples collected from IP-ABX infants at week 1 compared to No-ABX infants. Only taxa detected in >5% of samples are considered for differential abundance analysis.
Abundance in Group 1: decreased abundance in Intrapartum Antibiotic (IP-ABX) group [Week-1]
Revision editor(s): ShadeAkinremi, Victoria
Signature 3
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Neonatal Antibotic (Neo-ABX) group [Week-1]
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants who received at least 48 h of antibiotic treatment in the neonatal period (the first 28 days after birth), with or without maternal antibiotic exposure.
- Group 1 sample size Number of subjects in the case (exposed) group
- 32
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Supplementary Table 11b
Description: Differentially abundant microbial species in stool samples collected from Neo-ABX infants at week 1 compared to No-ABX infants. Only taxa detected in >5% of samples are considered for differential abundance analysis.
Abundance in Group 1: increased abundance in Neonatal Antibotic (Neo-ABX) group [Week-1]
NCBI | Quality Control | Links |
---|---|---|
Citrobacter | ||
Enterobacter | ||
Enterococcus | ||
Escherichia | ||
Haemophilus | ||
Klebsiella | ||
Staphylococcus |
Revision editor(s): ShadeAkinremi, Victoria
Signature 2
Source: Supplementary Table 11a
Description: Differentially abundant microbial species in stool samples collected from Neo-ABX infants at week 1 compared to No-ABX infants. Only taxa detected in >5% of samples are considered for differential abundance analysis.
Abundance in Group 1: decreased abundance in Neonatal Antibotic (Neo-ABX) group [Week-1]
Revision editor(s): ShadeAkinremi, Victoria
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- No Antibiotic (No-ABX) group [Week-6]
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Neonatal Antibotic (Neo-ABX) group [Week-6]
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Source: Extented figure 6(j, k, l) And Supplementary Table 11a&b
Description: Differentially abundant microbial species in stool samples collected from Neo-ABX infants at week 6 compared to No-ABX infants. Only taxa detected in >5% of samples are considered for differential abundance analysis.
Abundance in Group 1: decreased abundance in Neonatal Antibotic (Neo-ABX) group [Week-6]
Revision editor(s): ShadeAkinremi, Victoria