Impact of sugar beet pulp and wheat bran on serum biochemical profile, inflammatory responses and gut microbiota in sows during late gestation and lactation
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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
- China
- 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
- Diet Dietary,Diets,Diet,diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- SBP (Sugar Beet Pulp) diet during lactation
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- WB (Wheat Bran) diet during lactation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Sows in this group were fed a 15% Wheat bran diet during lactation.
- 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
- V3-V4
- 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
- Kruskall-Wallis
- 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
- unchanged
Signature 1
Source: Fig. 9B, 10B
Description: Relative abundance of significantly different genera & phyla on day21 of lactation between SBP (sugar beet pulp diet) & WB (wheat bran diet)
Abundance in Group 1: increased abundance in WB (Wheat Bran) diet during lactation
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Lactobacillus |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Fig. 9B, 10B
Description: Relative abundance of significantly different genera & phyla on day21 of lactation between SBP (sugar beet pulp diet) & WB (wheat bran diet)
Abundance in Group 1: decreased abundance in WB (Wheat Bran) diet during lactation
Revision editor(s): Anne-mariesharp
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- CON (Control) diet during lactation
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- SBP (Sugar Beet Pulp) diet during lactation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Sows in this group were fed a 10% Sugar beet pulp diet during lactation
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Fig. 10B
Description: Relative abundance of significantly different taxon on day21 of lactation between Control diet (CON) & SBP (sugar beet pulp diet)
Abundance in Group 1: increased abundance in SBP (Sugar Beet Pulp) diet during lactation
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Lachnospiraceae |
Revision editor(s): Anne-mariesharp
Signature 2
Source: Fig. 10B
Description: Relative abundance of significantly different taxon on day21 of lactation between Control diet (CON) & SBP (sugar beet pulp diet)
Abundance in Group 1: decreased abundance in SBP (Sugar Beet Pulp) diet during lactation
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus |
Revision editor(s): Anne-mariesharp
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Sugar beet pulp diet (SBP) during gestation
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Wheat Bran Diet (WB) during gestation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Sows in this group were fed a 30% Wheat bran diet during gestation.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 9A & 10A
Description: Relative abundance of significantly different phyla and genera on day 110 of gestation, between the sugar beet pulp (SBP) and wheat bran (WB) diet groups.
Abundance in Group 1: decreased abundance in Wheat Bran Diet (WB) during gestation
| NCBI | Quality Control | Links |
|---|---|---|
| Mycoplasmatota | ||
| Christensenellaceae R-7 groupChristensenellaceae R-7 group | ||
| Ruminococcaceae UCG-002Ruminococcaceae UCG-002 |
Revision editor(s): Victoria
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control diet (CON) during gestation
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Sugar beet pulp diet (SBP) during gestation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Sows in this group were fed a 20% Sugar beet pulp diet during gestation.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 10A
Description: Relative abundance of significantly different phyla and genera on day 110 of gestation, between the Control (CON) and the sugar beet pulp (SBP) diet groups.
Abundance in Group 1: increased abundance in Sugar beet pulp diet (SBP) during gestation
| NCBI | Quality Control | Links |
|---|---|---|
| Christensenellaceae R-7 groupChristensenellaceae R-7 group | ||
| Ruminococcaceae UCG-002Ruminococcaceae UCG-002 |
Revision editor(s): Victoria
Signature 2
Source: Figure 10A
Description: Relative abundance of significantly different phyla and genera on day 110 of gestation, between the Control (CON) and the sugar beet pulp (SBP) diet groups.
Abundance in Group 1: decreased abundance in Sugar beet pulp diet (SBP) during gestation
| NCBI | Quality Control | Links |
|---|---|---|
| Terrisporobacter | ||
| Clostridium |
Revision editor(s): Victoria
Experiment 6
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Wheat bran diet (WB) during gestation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The Sows in this group were fed a 30% wheat bran diet during gestation.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 10A
Description: Relative abundance of significantly different phyla and genera on day 110 of gestation, between the Control (CON) and the wheat bran (WB) diet groups.
Abundance in Group 1: decreased abundance in Wheat bran diet (WB) during gestation
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcaceae UCG-002Ruminococcaceae UCG-002 |
Revision editor(s): Victoria
