Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs
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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
- Ireland
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Sus scrofa domesticus
- 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
- Non-medicated control (CT) global data set
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Antibiotic (Ab) global data set
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Piglets treated with antibiotics Global data set involves both consistency and Day post weaning (dpw) factors
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
- LEfSe
- 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
- 2
Signature 1
Source: Figure 5A, 5B and Text
Description: Differences in species abundance, returned by LEfSe, most likely explaining the differences among dietary treatments. (A) Species associated with each dietary treatment in the analysis of global species data.
Abundance in Group 1: increased abundance in Antibiotic (Ab) global data set
| NCBI | Quality Control | Links |
|---|---|---|
| Megasphaera elsdenii | ||
| Megasphaera | ||
| Negativicutes | ||
| Veillonellaceae | ||
| Veillonellales | ||
| Limosilactobacillus reuteri |
Revision editor(s): Fiddyhamma
Signature 2
Source: Figure 5A, 5B and Text
Description: Differences in species abundance, returned by LEfSe, most likely explaining the differences among dietary treatments. (A) Species associated with each dietary treatment in the analysis of global species data.
Abundance in Group 1: decreased abundance in Antibiotic (Ab) global data set
Revision editor(s): Fiddyhamma
Experiment 2
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Therapeutic Zinc oxide (Zn) global data set
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Piglets treated with Therapeutic Zinc oxide Global data set involves both consistency and Day post weaning (dpw) factors
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5A, 5B and Text
Description: Differences in species abundance, returned by LEfSe, most likely explaining the differences among dietary treatments. (A) Species associated with each dietary treatment in the analysis of global species data.
Abundance in Group 1: increased abundance in Therapeutic Zinc oxide (Zn) global data set
Revision editor(s): Fiddyhamma
Signature 2
Source: Figure 5A, 5B and Text
Description: Differences in species abundance, returned by LEfSe, most likely explaining the differences among dietary treatments. (A) Species associated with each dietary treatment in the analysis of global species data.
Abundance in Group 1: decreased abundance in Therapeutic Zinc oxide (Zn) global data set
Revision editor(s): Fiddyhamma
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Antibiotics (AB) global data set
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 5A, 5B and Text
Description: Differences in species abundance, returned by LEfSe, most likely explaining the differences among dietary treatments. (A) Species associated with each dietary treatment in the analysis of global species data.
Abundance in Group 1: increased abundance in Therapeutic Zinc oxide (Zn) global data set
Revision editor(s): Fiddyhamma
Signature 2
Source: Figure 5A, 5B and Text
Description: Differences in species abundance, returned by LEfSe, most likely explaining the differences among dietary treatments. (A) Species associated with each dietary treatment in the analysis of global species data.
Abundance in Group 1: decreased abundance in Therapeutic Zinc oxide (Zn) global data set
| NCBI | Quality Control | Links |
|---|---|---|
| Limosilactobacillus reuteri | ||
| Megasphaera elsdenii | ||
| Megasphaera | ||
| Veillonellaceae | ||
| Veillonellales | ||
| Negativicutes |
Revision editor(s): Fiddyhamma
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Sampling time sampling_time_point,Sampling time,sampling time
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Day 0 post weaning (0dpw)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Day 7 post weaning (7dpw)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The dietary treatments were administered in the first two weeks post weaning and samplings were scheduled at days 0, 7 and 14 post weaning (0dpw, 7dpw, and 14dpw. respectively).
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Experiment 5
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Day 14 post weaning (14dpw)
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Day 7 post weaning (7dpw)
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Experiment 7
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Abnormal sample abnormal tissue sample,altered sample,Abnormal sample,abnormal sample
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Faecal_7dpw CT(no-medication) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diarrhoea_7dpw CT(no-medication) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Diarrhoea samples collected at day 7 post weaning from piglets not treated with medication
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
Signature 1
Source: Fig 5E, Suppl fig 5 and text
Description: Taxa associated with each dietary treatment in the analysis of Diarrhoea_7dpw data. Significant species are coloured according to the treatment to which they are associated to, and are annotated in the cladogram as letters, which can be identified below it.
Abundance in Group 1: increased abundance in Diarrhoea_7dpw CT(no-medication) group
Revision editor(s): Fiddyhamma
Signature 2
Source: Fig 5C, Suppl fig 3B and text
Description: Description: Taxa associated with each dietary treatment in the analysis of Faecal_7dpw data. Significant species are coloured according to the treatment to which they are associated to, and are annotated in the cladogram as letters, which can be identified below it.
Abundance in Group 1: decreased abundance in Diarrhoea_7dpw CT(no-medication) group
Revision editor(s): Fiddyhamma
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Faecal_7dpw AB(antibiotics) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diarrhoea_7dpw AB(antibiotics) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Diarrhoea samples collected at day 7 post weaning from piglets treated with antibiotics
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Fig 5E, Suppl fig 5 and text
Description: Taxa associated with each dietary treatment in the analysis of Diarrhoea_7dpw data. Significant species are coloured according to the treatment to which they are associated to, and are annotated in the cladogram as letters, which can be identified below it.
Abundance in Group 1: increased abundance in Diarrhoea_7dpw AB(antibiotics) group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacilli | ||
| Lactobacillaceae | ||
| Lactobacillales | ||
| Limosilactobacillus reuteri |
Revision editor(s): Fiddyhamma
Signature 2
Source: Fig 5C, Suppl fig 3B and text
Description: Taxa associated with each dietary treatment in the analysis of Faecal_7dpw data. Significant species are coloured according to the treatment to which they are associated to, and are annotated in the cladogram as letters, which can be identified below it.
Abundance in Group 1: decreased abundance in Diarrhoea_7dpw AB(antibiotics) group
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister massiliensis | ||
| Limosilactobacillus reuteri | ||
| Selenomonadaceae | ||
| Selenomonadales | ||
| Selenomonas sputigena |
Revision editor(s): Fiddyhamma
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Faecal_7dpw Zn(Zinc Oxide) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diarrhoea_7dpw Zn(Zinc Oxide) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Diarrhoea samples collected at day 7 post weaning from piglets treated with Zinc Oxide
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Fig 5E, Suppl fig 5 and text
Description: Taxa associated with each dietary treatment in the analysis of Diarrhoea_7dpw data. Significant species are coloured according to the treatment to which they are associated to, and are annotated in the cladogram as letters, which can be identified below it.
Abundance in Group 1: increased abundance in Diarrhoea_7dpw Zn(Zinc Oxide) group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides ovatus | ||
| Intestinimonas butyriciproducens | ||
| Peptostreptococcaceae | ||
| Phocaeicola dorei | ||
| Phocaeicola vulgatus |
Revision editor(s): Fiddyhamma
Signature 2
Source: Fig 5C, Suppl fig 3B and text
Description: Taxa associated with each dietary treatment in the analysis of Faecal_7dpw data. Significant species are coloured according to the treatment to which they are associated to, and are annotated in the cladogram as letters, which can be identified below it.
Abundance in Group 1: decreased abundance in Diarrhoea_7dpw Zn(Zinc Oxide) group
Revision editor(s): Fiddyhamma
Experiment 10
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Faecal_0dpw AB(antibiotics) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diarrhoea_0dpw AB(antibiotics) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Diarrhoea samples collected at day 0 post weaning from piglets treated with antibiotics
Lab analysis
Statistical Analysis
Signature 1
Source: Suppl fig 3A and text
Description: Species associated with each dietary treatment in the analysis of Faecal_0dpw species data, according to LEfSe(Linear discriminant analysis Effect Size), most likely explaining the differences among dietary treatments.
Abundance in Group 1: decreased abundance in Diarrhoea_0dpw AB(antibiotics) group
| NCBI | Quality Control | Links |
|---|---|---|
| Phocaeicola salanitronis |
Revision editor(s): Fiddyhamma
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Faecal_14dpw CT(no medication) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diarrhoea_14pw CT(no medication) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Diarrhoea samples collected at day 14 post weaning from piglets not treated with medication
Lab analysis
Statistical Analysis
Signature 1
Source: Fig 5D, Suppl fig 4 and text
Description: Taxa associated with each dietary treatment in the analysis of Faecal_14dpw data. Significant species are coloured according to the treatment to which they are associated to, and are annotated in the cladogram as letters, which can be identified below it.
Abundance in Group 1: decreased abundance in Diarrhoea_14pw CT(no medication) group
Revision editor(s): Fiddyhamma
Experiment 12
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Faecal_14dpw AB(antibiotics) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diarrhoea_14dpw AB(antibiotics) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Diarrhoea samples collected at day 14 post weaning from piglets treated with antibiotics
Lab analysis
Statistical Analysis
Signature 1
Source: Fig 5D, Suppl fig 4 and text
Description: Description: Taxa associated with each dietary treatment in the analysis of Faecal_14dpw data. Significant species are coloured according to the treatment to which they are associated to, and are annotated in the cladogram as letters, which can be identified below it.
Abundance in Group 1: decreased abundance in Diarrhoea_14dpw AB(antibiotics) group
| NCBI | Quality Control | Links |
|---|---|---|
| Acidaminococcus fermentans | ||
| Clostridium sp. SY8519 | ||
| Agathobacter rectalis |
Revision editor(s): Fiddyhamma
Experiment 13
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Faecal_14dpw Zn(Zinc Oxide) group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diarrhoea_14dpw Zn(Zinc Oxide) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Diarrhoea samples collected at day 14 post weaning from piglets treated with Zinc Oxide
Lab analysis
Statistical Analysis
Signature 1
Source: Fig 5D, Suppl fig 4 and text
Description: Description: Description: Taxa associated with each dietary treatment in the analysis of Faecal_14dpw data. Significant species are coloured according to the treatment to which they are associated to, and are annotated in the cladogram as letters, which can be identified below it.
Abundance in Group 1: decreased abundance in Diarrhoea_14dpw Zn(Zinc Oxide) group
Revision editor(s): Fiddyhamma
