Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study
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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
- United States of America
- 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
- Antimicrobial agent antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,Antimicrobial agent,antimicrobial agent
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- infants (6-weeks) to mothers unexposed to intrapartum antibiotic
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- infants(6-weeks) to mothers exposed to intrapartum antibiotic
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- vaginally delivered at full-term (>37 weeks of gestation)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 179
- Group 1 sample size Number of subjects in the case (exposed) group
- 87
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4-V5
- 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
- PERMANOVA
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Table S1, Figure S2 & Text
Description: MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).
Abundance in Group 1: increased abundance in infants(6-weeks) to mothers exposed to intrapartum antibiotic
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospira | ||
| Pseudoramibacter | ||
| Varibaculum | ||
| Veillonella dispar |
Signature 2
Source: Table S1, Figure S2 & Text
Description: MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).
Abundance in Group 1: decreased abundance in infants(6-weeks) to mothers exposed to intrapartum antibiotic
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Bifidobacterium | ||
| Blautia | ||
| Roseburia | ||
| Ruminococcus |
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- infants (1-year) to mothers unexposed to intrapartum antibiotic
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- infants(1-year) to mothers exposed to intrapartum antibiotic
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Table S1
Description: MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).
Abundance in Group 1: increased abundance in infants(1-year) to mothers exposed to intrapartum antibiotic
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospira | ||
| Pseudoramibacter | ||
| Varibaculum | ||
| Veillonella dispar |
Signature 2
Source: Table S1
Description: MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).
Abundance in Group 1: decreased abundance in infants(1-year) to mothers exposed to intrapartum antibiotic
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Bifidobacterium | ||
| Blautia | ||
| Roseburia |
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- infants (6-weeks) to mothers unexposed to antibiotic
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- infants(6-weeks) to mothers exposed to antibiotic penicillin
- Group 1 sample size Number of subjects in the case (exposed) group
- 55
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: text, Figure 3
Description: MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).
Abundance in Group 1: decreased abundance in infants(6-weeks) to mothers exposed to antibiotic penicillin
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Bacteroides ovatus | ||
| Bifidobacterium |
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- infants (1-year) to mothers unexposed to antibiotic
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- infants(1-year) to mothers exposed to the penicillin group
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Table S1, Figure S2 & Text, Figure 1, Figure 3
Description: MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).
Abundance in Group 1: increased abundance in infants(1-year) to mothers exposed to the penicillin group
| NCBI | Quality Control | Links |
|---|---|---|
| Coprococcus | ||
| Mediterraneibacter gnavus |
Revision editor(s): WikiWorks
Signature 2
Source: Text, Figure 3
Description: MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).
Abundance in Group 1: decreased abundance in infants(1-year) to mothers exposed to the penicillin group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Bacteroides fragilis | ||
| Clostridium | ||
| Megamonas | ||
| Streptococcus |
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- infants (6-weeks) to mothers unexposed to antibiotic
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- infants(6-weeks) to mothers exposed to multi-class antibiotics
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Text, Figure 3
Description: MZILN results for any intrapartum MZILN model estimates (P<0.05) for ASVs that were significantly associated with intrapartum antibiotic use; Boxplots of alpha diversity scores based on intrapartum antibiotic exposure at (A) 6 weeks (N=266); and (B) 1 year (N=152).
Abundance in Group 1: increased abundance in infants(6-weeks) to mothers exposed to multi-class antibiotics
| NCBI | Quality Control | Links |
|---|---|---|
| Veillonella dispar |
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Antimicrobial agent antibiotic,antibiotics,Antibiotika,Antibiotikum,antibiotique,antimicrobial,antimicrobial agents,microbicide,microbicides,Antimicrobial agent,antimicrobial agent
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- infants to mothers unexposed to intrapartum antibiotic
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- infants to mothers exposed to cephalosporins
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
Lab analysis
Statistical Analysis
Signature 1
Source: text, figure 3
Description: Taxa that are significantly associated with maternal antibiotic exposure (unexposed infants as the reference group).
Abundance in Group 1: decreased abundance in infants to mothers exposed to cephalosporins
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium |
Revision editor(s): Atrayees
Signature 2
Source: Text, Figure 3
Description: Taxa that are significantly associated with maternal antibiotic exposure (unexposed infants as the reference group).
Abundance in Group 1: increased abundance in infants to mothers exposed to cephalosporins
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides fragilis |
Revision editor(s): Atrayees
