Effect of Fermented Corn-Soybean Meal on Serum Immunity, the Expression of Genes Related to Gut Immunity, Gut Microbiota, and Bacterial Metabolites in Grower-Finisher 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
- 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
- Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to diet Response to diet,response to diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- UF (Unfermented feed/control group)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FF (Fermented feed group)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Group fed with fermented complete commercial soybean meal (FF)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4-V5
- 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
- T-Test
- 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
- 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
- unchanged
Signature 1
Source: Table 6, Table 8
Description: Relative abundance of microbial phylum and Family (percentage) in the colon of pigs in the FF and control groups.
Abundance in Group 1: increased abundance in FF (Fermented feed group)
NCBI | Quality Control | Links |
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Actinomycetota | ||
Bacillota | ||
Christensenellaceae | ||
Oscillospiraceae | ||
Rikenellaceae | ||
Family XIIIFamily XIII |
Revision editor(s): Tosin
Signature 2
Source: Table 6, Table 8
Description: Relative abundance of microbial phylum and family (percentage) in the colon of pigs in the FF and control groups.
Abundance in Group 1: decreased abundance in FF (Fermented feed group)
Revision editor(s): Tosin
Experiment 2
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Duodenum Proximal intestine,Upper intestine,Duodenum,duodenum
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
- unchanged
Signature 1
Source: Table 5, Table 7
Description: Relative abundance of microbial phylum and family (percentage) in the duodenum of pigs in the FF and control groups.
Abundance in Group 1: decreased abundance in FF (Fermented feed group)
NCBI | Quality Control | Links |
---|---|---|
Acidaminococcaceae | ||
Bacteroidota | ||
Verrucomicrobiota | ||
Clostridiales vadinBB60 groupClostridiales vadinBB60 group |
Revision editor(s): Tosin