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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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Ortiz Sanjuán JM, Argüello H, Cabrera-Rubio R, Crispie F, Cotter PD, Garrido JJ, Ekhlas D, Burgess CM, Manzanilla EG
Journal
Animal microbiome
Year
2024
Keywords:
Antimicrobial use, Diarrhea, Piglet, Shotgun sequencing, Swine
BACKGROUND: Post weaning diarrhoea (PWD) causes piglet morbidity and mortality at weaning and is a major driver for antimicrobial use worldwide. New regulations in the EU limit the use of in-feed antibiotics (Ab) and therapeutic zinc oxide (ZnO) to prevent PWD. New approaches to control PWD are needed, and understanding the role of the microbiota in this context is key. In this study, shotgun metagenome sequencing was used to describe the taxonomic and functional evolution of the faecal microbiota of the piglet during the first two weeks post weaning within three experimental groups, Ab, ZnO and no medication, on commercial farms using antimicrobials regularly in the post weaning period. RESULTS: Diversity was affected by day post weaning (dpw), treatment used and diarrhoea but not by the farm. Microbiota composition evolved towards the dominance of groups of species such as Prevotella spp. at day 14dpw. ZnO inhibited E. coli overgrowth, promoted higher abundance of the family Bacteroidaceae and decreased Megasphaera spp. Animals treated with Ab exhibited inconsistent taxonomic changes across time points, with an overall increase of Limosilactobacillus reuteri and Megasphaera elsdenii. Samples from non-medicated pigs showed virulence-related functions at 7dpw, and specific ETEC-related virulence factors were detected in all samples presenting diarrhoea. Differential microbiota functions of pigs treated with ZnO were related to sulphur and DNA metabolism, as well as mechanisms of antimicrobial and heavy metal resistance, whereas Ab treated animals exhibited functions related to antimicrobial resistance and virulence. CONCLUSION: Ab and particularly ZnO maintained a stable microbiota composition and functionality during the two weeks post weaning, by limiting E. coli overgrowth, and ultimately preventing microbiota dysbiosis. Future approaches to support piglet health should be able to reproduce this stable gut microbiota transition during the post weaning period, in order to maintain optimal gut physiological and productive conditions.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
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
- Response to antibiotic Response to antibiotic,response to antibiotic
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Therapeutic zinc oxide (Zn) treatment + non-medicated control diet (Ct diet) - Global data set
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Antibiotic (Ab) treatment - 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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
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) treatment - Global data set
| NCBI | Quality Control | Links |
|---|---|---|
| Limosilactobacillus reuteri | ||
| Megasphaera elsdenii |
Revision editor(s): Fiddyhamma, KateRasheed
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- CT diet + Ab treatment global data set
- 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 2
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Source: Figure 5A, 5B
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, KateRasheed
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Antibiotics (Ab) global data set + Zn global data set
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ct diet global data set
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Piglets with non-medicated control diet. Global data set involves both consistency and Day post weaning (dpw) factors
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
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 Ct diet global data set
Revision editor(s): Fiddyhamma, KateRasheed
Experiment 4
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Differences from previous experiment shown
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
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- Not specified
- Statistical test
- Not specified
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
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
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Differences from previous experiment shown
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
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Differences from previous experiment shown
Subjects
- 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
- Therapeutic zinc oxide (Zn) treatment + non-medicated control diet (Ct diet) - Faecal 7 days post weaning (7 dpw)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Antibiotic (Ab) treatment - Faecal 7 days post weaning (7 dpw)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Piglets treated with antibiotics at Faecal 7 days post weaning.
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Source: Fig 5C
Description: Taxa associated with each dietary treatment in the analysis of Faecal_7dpw data.
Abundance in Group 1: increased abundance in Antibiotic (Ab) treatment - Faecal 7 days post weaning (7 dpw)
Revision editor(s): Fiddyhamma, KateRasheed
Experiment 8
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Faecal_7dpw Ct + Zn groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Faecal_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
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Source: Fig 5C
Description: Taxa associated with each dietary treatment in the analysis of Faecal_7dpw data.
Abundance in Group 1: increased abundance in Faecal_7dpw AB(antibiotics) group
| NCBI | Quality Control | Links |
|---|---|---|
| Dialister massiliensis | ||
| Limosilactobacillus reuteri | ||
| Selenomonas sputigena |
Revision editor(s): Fiddyhamma, KateRasheed
Experiment 9
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Faecal_7dpw Ab + Ct groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Faecal_7dpw Zn(Zinc Oxide) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Faecal samples collected at day 7 post weaning from piglets treated with Zinc Oxide
Lab analysis
Statistical Analysis
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Source: Fig 5C
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: increased abundance in Faecal_7dpw Zn(Zinc Oxide) group
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridioides difficile | ||
| Eubacterium callanderi | ||
| Phocaeicola dorei | ||
| Phocaeicola vulgatus | ||
| Selenomonas ruminantium | ||
| Selenomonas sp. oral taxon 920 |
Revision editor(s): Fiddyhamma, KateRasheed
Experiment 10
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Faecal_0dpw Ct + Zn groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Faecal_0dpw Ab(antibiotics) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Faecal samples collected at day 0 post weaning from piglets treated with antibiotics
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
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: increased abundance in Faecal_0dpw Ab(antibiotics) group
| NCBI | Quality Control | Links |
|---|---|---|
| Phocaeicola salanitronis |
Revision editor(s): Fiddyhamma, KateRasheed
Experiment 11
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Faecal_14dpw Ab + Zn groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Faecal_14pw CT(no medication) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Faecal samples collected at day 14 post weaning from piglets not treated with medication
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Source: Fig 5D
Description: Taxa associated with each dietary treatment in the analysis of Faecal_14dpw data.
Abundance in Group 1: increased abundance in Faecal_14pw CT(no medication) group
Revision editor(s): Fiddyhamma, KateRasheed
Experiment 12
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Faecal_14dpw Ct + Zn groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Faecal_14dpw AB(antibiotics) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Faecal samples collected at day 14 post weaning from piglets treated with antibiotics
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Source: Fig 5D
Description: Taxa associated with each dietary treatment in the analysis of Faecal_14dpw data.
Abundance in Group 1: increased abundance in Faecal_14dpw AB(antibiotics) group
| NCBI | Quality Control | Links |
|---|---|---|
| Acidaminococcus fermentans | ||
| Agathobacter rectalis | ||
| Clostridium sp. SY8519 |
Revision editor(s): Fiddyhamma, KateRasheed
Experiment 13
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Faecal_14dpw Ct + Ab groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Faecal_14dpw Zn(Zinc Oxide) group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Faecal samples collected at day 14 post weaning from piglets treated with Zinc Oxide
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Source: Fig 5D
Description: Taxa associated with each dietary treatment in the analysis of Faecal_14dpw data.
Abundance in Group 1: increased abundance in Faecal_14dpw Zn(Zinc Oxide) group
Revision editor(s): Fiddyhamma, KateRasheed
Experiment 14
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Diarrhoea_7dpw Ct + Zn groups
- 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 14 post weaning from piglets treated with antibiotics
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Source: Fig. 5E
Description: Taxa associated with each dietary treatment in the analysis of Diarrhoea_14dpw data.
Abundance in Group 1: increased abundance in Diarrhoea_7dpw Ab(antibiotics) group
| NCBI | Quality Control | Links |
|---|---|---|
| Limosilactobacillus reuteri |
Revision editor(s): KateRasheed
Experiment 15
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Diarrhoea_7dpw Ct + Ab groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diarrhoea_7dpw Zn 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
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Source: Fig. 5E
Description: Taxa associated with each dietary treatment in the analysis of Diarrhoea_14dpw data.
Abundance in Group 1: increased abundance in Diarrhoea_7dpw Zn group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides ovatus | ||
| Intestinimonas butyriciproducens | ||
| Phocaeicola dorei | ||
| Phocaeicola vulgatus |
Revision editor(s): KateRasheed
Experiment 16
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Diarrhoea_7dpw Ab + Zn groups
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diarrhoea_7dpw Ct 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
Reviewed Marked as Reviewed by Svetlana up on 2025-1-21
Source: Fig. 5E
Description: Taxa associated with each dietary treatment in the analysis of Diarrhoea_14dpw data.
Abundance in Group 1: increased abundance in Diarrhoea_7dpw Ct group
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia coli | ||
| Sutterella megalosphaeroides |
Revision editor(s): KateRasheed
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