The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the Gallus gallus microbiota
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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: 2024/03/25
Curator: Omojokunoluwatomisin
Revision editor(s): Omojokunoluwatomisin, Nityasinghal 14, Victoria
Subjects
- Location of subjects
- United States of America
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Gallus gallus
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Jejunum Intestinum jejunum,Mid-intestine,Middle intestine,Jejunum,jejunum
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diet Dietary,Diets,Diet,diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- NTC (0 g/MT AviPlus®P) No treatment control group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- (300 g/MT AviPlus®P) Supplement group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Chickens in this group were given free access to a starter diet mixed with 300g/metric ton (MT) of a microencapsulated blend of citric (25%) and sorbic (16.7%) acids, thymol (1.7%), and vanillin (1.0%) (AviPlus®P, Vetagro S.p.A., Reggio Emilia, Italy). The remaining 55.6% of the feed additive comprises hydrogenated vegetable fats.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
- Sequencing type
- 16S
- 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).
- centered log-ratio
- Statistical test
- ANCOM
- 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
Signature 1
Source: Fig. 3 A&B
Description: Analysis of communities of the microbiota (ANCOM) for jejunum samples. a NTC; b 300 g/MT; c 500 g/MT. The legends for the specific operational taxonomic units (OTU) associated with treatment as defined by ANCOM (Q < 0.05) are listed in the figure.
Abundance in Group 1: increased abundance in (300 g/MT AviPlus®P) Supplement group
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae | ||
| Enterococcaceae | ||
| Lactobacillaceae | ||
| Oscillospiraceae |
Revision editor(s): Victoria
Signature 2
Source: Fig 3 A&B
Description: Analysis of communities of the microbiota (ANCOM) for jejunum samples. a NTC; b 300 g/MT; c 500 g/MT. The legends for the specific operational taxonomic units (OTU) associated with treatment as defined by ANCOM (Q < 0.05) are listed in the figure.
Abundance in Group 1: decreased abundance in (300 g/MT AviPlus®P) Supplement group
| NCBI | Quality Control | Links |
|---|---|---|
| Aerococcaceae | ||
| Staphylococcaceae |
Revision editor(s): Victoria
Experiment 2
Curated date: 2024/03/27
Curator: Omojokunoluwatomisin
Revision editor(s): Omojokunoluwatomisin, Nityasinghal 14, Victoria
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- (500 g/MT AviPlus®P) Supplement group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Chickens in this group were given free access to a starter diet mixed with 500g/metric ton (MT) of a microencapsulated blend of citric (25%) and sorbic (16.7%) acids, thymol (1.7%), and vanillin (1.0%) (AviPlus®P, Vetagro S.p.A., Reggio Emilia, Italy). The remaining 55.6% of the feed additive comprises hydrogenated vegetable fats.
Lab analysis
Statistical Analysis
Signature 1
Source: Fig 3. A&C
Description: Analysis of communities of the microbiota (ANCOM) for jejunum samples. a NTC; b 300 g/MT; c 500 g/MT. The legends for the specific operational taxonomic units (OTU) associated with treatment as defined by ANCOM (Q < 0.05) are listed in the figure.
Abundance in Group 1: increased abundance in (500 g/MT AviPlus®P) Supplement group
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillaceae | ||
| Oscillospiraceae |
Revision editor(s): Victoria
Signature 2
Source: Fig. 3 A&C
Description: Analysis of communities of the microbiota (ANCOM) for jejunum samples. a NTC; b 300 g/MT; c 500 g/MT. The legends for the specific operational taxonomic units (OTU) associated with treatment as defined by ANCOM (Q < 0.05) are listed in the figure.
Abundance in Group 1: decreased abundance in (500 g/MT AviPlus®P) Supplement group
| NCBI | Quality Control | Links |
|---|---|---|
| Peptostreptococcaceae | ||
| Aerococcaceae | ||
| Enterobacteriaceae | ||
| Staphylococcaceae |
Revision editor(s): Victoria
Experiment 3
Curated date: 2024/03/27
Curator: Omojokunoluwatomisin
Revision editor(s): Omojokunoluwatomisin, Nityasinghal 14, Victoria
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Ileum , Jejunum Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,ileum,Intestinum jejunum,Mid-intestine,Middle intestine,Jejunum,jejunum
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 1
Source: Fig. 4
Description: Linear discriminant analysis effect size (LEfSE) analysis. Missing operational taxonomic units (OUT) are not defined within the Family taxonomical designation and are labelled as unclassified. The 500 and NTC groups are relative to 300. An LDA > +/− 2 with a Q < 0.05 is considered significant and is graphically represented. All comparisons are relative to 300 g/MT, which was selected as it is the intermediary dose and describes the potential dose effect.
Abundance in Group 1: increased abundance in (500 g/MT AviPlus®P) Supplement group
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridiaceae | ||
| Micrococcaceae | ||
| unclassifiedunclassified |
Revision editor(s): Victoria
Signature 2
Source: Fig. 4
Description: Linear discriminant analysis effect size (LEfSE) analysis. Missing operational taxonomic units (OUT) are not defined within the Family taxonomical designation and are labelled as unclassified. The 500 and NTC groups are relative to 300. An LDA > +/− 2 with a Q < 0.05 is considered significant and is graphically represented. All comparisons are relative to 300 g/MT, which was selected as it is the intermediary dose and describes the potential dose effect.
Abundance in Group 1: decreased abundance in (500 g/MT AviPlus®P) Supplement group
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacterales | ||
| Enterobacteriaceae | ||
| unclassifiedunclassified | ||
| Gammaproteobacteria | ||
| Aerococcaceae |
Revision editor(s): Victoria
