Differential Analysis of Gut Microbiota Correlated With Oxidative Stress in Sows With High or Low Litter Performance During Lactation
-
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
- Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High litter performance sows at G109
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low litter performance sows at G109
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Low litter performance sows group at day 109 of gestation
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None
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
- 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
- 3
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: Figure 4B
Description: Differences in fecal microbiota between day 109 of gestation of high litter performance sows compared to day 109 of gestation of low litter performance sows
Abundance in Group 1: increased abundance in Low litter performance sows at G109
Revision editor(s): Scholastica
Signature 2
Source: Figure 4B
Description: Differences in fecal microbiota between day 109 of gestation of high litter performance sows compared to day 109 of gestation of low litter performance sows
Abundance in Group 1: decreased abundance in Low litter performance sows at G109
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Bacteroidaceae |
Revision editor(s): Scholastica
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- High litter performance sows at L21
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Low litter performance sows at L21
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Low litter performance sows group at day 21 of lactation (L21)
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
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- unchanged
Signature 1
Source: Figure 4E
Description: Differences in fecal microbiota between day 21 of lactation of high litter performance sows compared to day 21 of lactation of low litter performance sows
Abundance in Group 1: increased abundance in Low litter performance sows at L21
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridia | ||
| Eubacteriales |
Revision editor(s): Scholastica
Signature 2
Source: Figure 4E
Description: Differences in fecal microbiota between day 21 of lactation of high litter performance sows compared to day 21 of lactation of low litter performance sows
Abundance in Group 1: decreased abundance in Low litter performance sows at L21
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Mollicutes | ||
| Parabacteroides | ||
| Porphyromonadaceae | ||
| Mycoplasmatota | ||
| Mollicutes | ||
| Coprococcus | ||
| o_RF39o_RF39 | ||
| f_norank_o_RF39f_norank_o_RF39 | ||
| g_norank_o_RF39g_norank_o_RF39 |
Revision editor(s): Scholastica
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Day 109 of gestation (G109) of H group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Day 21 of lactation (L21) of H group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Day 21 of lactation (L21) of high litter performance sows group
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- decreased
Signature 1
Source: Figure 4H
Description: Differences in fecal microbiota between day 109 of gestation (G109) compared to day 21 of lactation (L21) of high litter performance sows
Abundance in Group 1: increased abundance in Day 21 of lactation (L21) of H group
Revision editor(s): Scholastica
Signature 2
Source: Figure 4H
Description: Differences in fecal microbiota between day 109 of gestation (G109) compared to day 21 of lactation (L21) of high litter performance sows
Abundance in Group 1: decreased abundance in Day 21 of lactation (L21) of H group
Revision editor(s): Scholastica
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Day 109 of gestation (G109) of L group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Day 21 of lactation (L21) of L group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Day 21 of lactation (L21) of low litter performance sows group
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- decreased
Signature 1
Source: Figure 4K
Description: Differences in fecal microbiota between day 109 of gestation (G109) compared to day 21 of lactation (L21) of low litter performance sows
Abundance in Group 1: decreased abundance in Day 21 of lactation (L21) of L group
Revision editor(s): Scholastica
