Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle
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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.
- Ovis aries
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Rumen Paunch,Rumen,rumen
- 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
- Rumen of Dorper sheep (D_R)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Rumen of Tan Sheep (T_R)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rumen of Tan sheep bred in Ningxia, China
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No antibiotics during the experiment period
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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Signature 1
Source: Fig. 3A
Description: A LEfSe Analysis of differences in rumen microbial composition among two sheep breeds from metagenomic data at the species level.
Abundance in Group 1: increased abundance in Rumen of Tan Sheep (T_R)
Revision editor(s): Scholastica
Signature 2
Source: Fig. 3A
Description: A LEfSe Analysis of differences in rumen microbial composition among two sheep breeds from metagenomic data at the species level.
Abundance in Group 1: decreased abundance in Rumen of Tan Sheep (T_R)
| NCBI | Quality Control | Links |
|---|---|---|
| Methanobrevibacter millerae | ||
| Methanosphaera sp. BMS |
Revision editor(s): Scholastica
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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Duodenum of Dorper sheep (D_Du)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Duodenum of Tan Sheep (T_Du)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Duodenum of Tan sheep bred in Ningxia, China
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 3
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 4A
Description: A LEfSe analysis of differences in duodenal microbial composition among two sheep breeds from metagenomic data at the species level.
Abundance in Group 1: increased abundance in Duodenum of Tan Sheep (T_Du)
| NCBI | Quality Control | Links |
|---|---|---|
| Agrobacterium tumefaciens | ||
| Mycobacterium dioxanotrophicus | ||
| Ornithinimicrobium avium | ||
| Modestobacter marinus | ||
| Friedmanniella luteola | ||
| Arthrobacter alpinus |
Revision editor(s): Scholastica
Signature 2
Source: Fig. 4A
Description: A LEfSe analysis of differences in duodenal microbial composition among two sheep breeds from metagenomic data at the species level.
Abundance in Group 1: decreased abundance in Duodenum of Tan Sheep (T_Du)
| NCBI | Quality Control | Links |
|---|---|---|
| Solibacillus silvestris | ||
| Advenella mimigardefordensis | ||
| Nostoc sphaeroides |
Revision editor(s): Scholastica
Experiment 3
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Colon of Dorper sheep (D_Co)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Colon of Tan Sheep (T_Co)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colon of Tan sheep bred in Ningxia, China
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 5A
Description: A LEfSe analysis of differences in colonic microbial composition among two sheep breeds from metagenomic data at the species level.
Abundance in Group 1: decreased abundance in Colon of Tan Sheep (T_Co)
Revision editor(s): Scholastica
Experiment 4
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Rumen Paunch,Rumen,rumen
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Rumen of Dorper sheep (D_R)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Rumen of Tan Sheep (T_R)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Rumen of Tan sheep bred in Ningxia, China
- 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
- V3-V4
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Fig. S6
Description: LEfSe analysis of ruminal microbiota among two sheep breeds from 16S data at the genus level.
Abundance in Group 1: increased abundance in Rumen of Tan Sheep (T_R)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae bacterium CG2 | ||
| Papillibacter | ||
| Saccharofermentans | ||
| Lachnospiraceae AC2004 groupLachnospiraceae AC2004 group | ||
| uncultured Prevotellaceae bacterium |
Revision editor(s): Scholastica
Experiment 5
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Duodenum Proximal intestine,Upper intestine,Duodenum,duodenum
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Duodenum of Dorper sheep (D_Du)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Duodenum of Tan Sheep (T_Du)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Duodenum of Tan sheep bred in Ningxia, China
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Fig. S7
Description: LEfSe analysis of duodenal microbiota among two sheep breeds from 16S data at the genus level.
Abundance in Group 1: increased abundance in Duodenum of Tan Sheep (T_Du)
| NCBI | Quality Control | Links |
|---|---|---|
| Senegalimassilia | ||
| Saccharofermentans | ||
| Candidatus Gastranaerophilales | ||
| Candidatus Melainabacteria | ||
| uncultured Lachnospiraceae bacterium | ||
| Peptococcaceae |
Revision editor(s): Scholastica
Experiment 6
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Jejunum of Dorper sheep (D_J)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Jejunum of Tan Sheep (T_J)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Jejunum of Tan sheep bred in Ningxia, China
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Fig. S8
Description: LEfSe analysis of jejunal microbiota among two sheep breeds from 16S data at the genus level.
Abundance in Group 1: increased abundance in Jejunum of Tan Sheep (T_J)
| NCBI | Quality Control | Links |
|---|---|---|
| uncultured Prevotellaceae bacterium |
Revision editor(s): Scholastica
Signature 2
Source: Supplementary Fig. S8
Description: LEfSe analysis of jejunal microbiota among two sheep breeds from 16S data at the genus level.
Abundance in Group 1: decreased abundance in Jejunum of Tan Sheep (T_J)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillales | ||
| Bacilli |
Revision editor(s): Scholastica
Experiment 7
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Colon Hindgut,Large bowel,Posterior intestine,Colon,colon
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Colon of Dorper sheep (D_Co)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Colon of Tan Sheep (T_Co)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colon of Tan sheep bred in Ningxia, China
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Fig. S9
Description: LEfSe analysis of colonic microbiota among two sheep breeds from 16S data at the genus level.
Abundance in Group 1: increased abundance in Colon of Tan Sheep (T_Co)
| NCBI | Quality Control | Links |
|---|---|---|
| uncultured Oscillospiraceae bacterium | ||
| Candidatus Melainabacteria | ||
| Candidatus Gastranaerophilales | ||
| Victivallis | ||
| Cyanobacteriota |
Revision editor(s): Scholastica
Signature 2
Source: Supplementary Fig. S9
Description: LEfSe analysis of colonic microbiota among two sheep breeds from 16S data at the genus level.
Abundance in Group 1: decreased abundance in Colon of Tan Sheep (T_Co)
Revision editor(s): Scholastica
Experiment 8
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Caecum Blind intestine,Blindgut,Caeca,Caecum,Ceca,Cecum,Intestinum caecum,Intestinum crassum caecum,Intestinum crassum cecum,caecum
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cecum of Dorper sheep (D_C)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cecum of Tan Sheep (T_C)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Cecum of Tan sheep bred in Ningxia, China
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Supplementary Fig. S10
Description: LEfSe analysis of cecal microbiota among two sheep breeds from 16S data at the genus level.
Abundance in Group 1: increased abundance in Cecum of Tan Sheep (T_C)
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota | ||
| uncultured Oscillospiraceae bacterium |
Revision editor(s): Scholastica
Signature 2
Source: Supplementary Fig. S10
Description: LEfSe analysis of cecal microbiota among two sheep breeds from 16S data at the genus level.
Abundance in Group 1: decreased abundance in Cecum of Tan Sheep (T_C)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota |
Revision editor(s): Scholastica
