High-throughput sequencing reveals the incomplete, short-term recovery of infant gut microbiota following parenteral antibiotic treatment with ampicillin and gentamicin
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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
Curated date: 2021/10/01
Curator: Mmarin
Revision editor(s): LGeistlinger, Mmarin, WikiWorks, Peace Sandy
Subjects
- Location of subjects
- Ireland
- 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
- Untreated controls (week 4)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Antibiotic treated (week 4)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Had received parenteral antibiotic treatment with a combination of ampicillin and gentamicin within 48 hours of birth
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- excluded if they required oral antibiotics (no time frame given)
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
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
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: Figure 1, Figure 2, Figure 3
Description: Figure 1: Microbial distributions at the phylum level in the samples from treated and control infants at week 4 and week 8. Statistically significant differences between treated infants and controls at week 4 are indicated by asterisks (P < 0.05). Percentages are based on proportions of assignable tags.
Figure 2: Microbial distributions at the family level in the samples from treated and control infants at week 4 and week 8. Statistically significant differences between treated infants and controls at week 4 are indicated by asterisks (P < 0.05). Percentages are based on proportions of assignable reads.
Figure 3: Microbial distributions at the genus level in the samples from treated and control infants at week 4 and week 8. Statistically significant differences between treated infants and controls at week 4 are indicated by asterisks (P < 0.05). Percentages are based on proportions of assignable reads.
Abundance in Group 1: increased abundance in Antibiotic treated (week 4)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae | ||
| Lactobacillaceae | ||
| Peptostreptococcaceae | ||
| Pseudomonadota | ||
| unclassified Enterobacteriaceae |
Revision editor(s): Mmarin
Signature 2
Source: Figure 1, Figure 2, Figure 3
Description: Figure 1: Microbial distributions at the phylum level in the samples from treated and control infants at week 4 and week 8. Statistically significant differences between treated infants and controls at week 4 are indicated by asterisks (P < 0.05). Percentages are based on proportions of assignable tags.
Figure 2: Microbial distributions at the family level in the samples from treated and control infants at week 4 and week 8. Statistically significant differences between treated infants and controls at week 4 are indicated by asterisks (P < 0.05). Percentages are based on proportions of assignable reads.
Figure 3: Microbial distributions at the genus level in the samples from treated and control infants at week 4 and week 8. Statistically significant differences between treated infants and controls at week 4 are indicated by asterisks (P < 0.05). Percentages are based on proportions of assignable reads.
Abundance in Group 1: decreased abundance in Antibiotic treated (week 4)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bifidobacteriaceae | ||
| Bifidobacterium | ||
| Lactobacillus |
Revision editor(s): Mmarin
Experiment 2
Curated date: 2021/10/07
Curator: Mmarin
Revision editor(s): LGeistlinger, Mmarin, WikiWorks, Victoria
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Untreated controls (week 8)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Antibiotic treated (week 8)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Received parenteral antibiotic treatment with a combination of ampicillin and gentamicin within 48 hours of birth
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: Figure 1, Figure 2, Figure 3
Description: Figure 1: Microbial distributions at the phylum level in the samples from treated and control infants at week 4 and week 8. Figure 2: Microbial distributions at the family level in the samples from treated and control infants at week 4 and week 8. Figure 3: Microbial distributions at the genus level in the samples from treated and control infants at week 4 and week 8.
Statistically significant differences between treated infants and controls at week 8 are indicated by asterisks. Percentages are based on proportions of assignable tags.
Abundance in Group 1: increased abundance in Antibiotic treated (week 8)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae | ||
| Pseudomonadota | ||
| unclassified Enterobacteriaceae |
Revision editor(s): Mmarin
Experiment 3
Curated date: 2021/10/07
Curator: Mmarin
Revision editor(s): LGeistlinger, Mmarin, WikiWorks, Victoria
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Week 4 (treated)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Week 8 (treated)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Had received parenteral antibiotic treatment with a combination of ampicillin and gentamicin within 48 hours of birth
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Figure 1, Figure 2, Figure 3
Description: Figure 1: Microbial distributions at the phylum level in the samples from treated and control infants at week 4 and week 8. Figure 2: Microbial distributions at the family level in the samples from treated and control infants at week 4 and week 8. Figure 3: Microbial distributions at the genus level in the samples from treated and control infants at week 4 and week 8.
A statistically significant difference between treated infants at week 4 and week 8 (i.e., the recovery of the treated infants) is indicated by a diamond. Percentages are based on proportions of assignable tags.
Abundance in Group 1: increased abundance in Week 8 (treated)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bifidobacteriaceae | ||
| Bifidobacterium |
Revision editor(s): Mmarin
Signature 2
Source: Figure 1, Figure 2, Figure 3
Description: Figure 1: Microbial distributions at the phylum level in the samples from treated and control infants at week 4 and week 8. Figure 2: Microbial distributions at the family level in the samples from treated and control infants at week 4 and week 8. Figure 3: Microbial distributions at the genus level in the samples from treated and control infants at week 4 and week 8.
A statistically significant difference between treated infants at week 4 and week 8 (i.e., the recovery of the treated infants) is indicated by a diamond. Percentages are based on proportions of assignable tags.
Abundance in Group 1: decreased abundance in Week 8 (treated)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae | ||
| Peptostreptococcaceae | ||
| Pseudomonadota | ||
| unclassified Enterobacteriaceae |
Revision editor(s): Mmarin
