Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models
-
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
- Canada
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- 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
- JAX group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- JAX-CH group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 12
- Group 1 sample size Number of subjects in the case (exposed) group
- 16
- 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
- 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
- 2.0
- Matched on Factors on which subjects have been matched on in a case-control study
- age
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 3D
Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.
Abundance in Group 1: increased abundance in JAX-CH group
| NCBI | Quality Control | Links |
|---|---|---|
| Anaeroplasma | ||
| Bacteroides | ||
| Dehalobacterium | ||
| Lactobacillus | ||
| Mucispirillum | ||
| Oscillospiraceae | ||
| Parabacteroides |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 3D
Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.
Abundance in Group 1: decreased abundance in JAX-CH group
| NCBI | Quality Control | Links |
|---|---|---|
| Allobaculum | ||
| Bifidobacterium |
Revision editor(s): Aleru Divine
Experiment 2
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- TAC group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- TAC-CH group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples taken from co-housed mice from Taconic Farms (TAC-CH).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 3E
Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.
Abundance in Group 1: increased abundance in TAC-CH group
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes | ||
| Anaerotruncus | ||
| Anaerovoracaceae | ||
| Clostridium | ||
| Muribaculaceae | ||
| Oscillospira | ||
| Turicibacter |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 2E
Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.
Abundance in Group 1: decreased abundance in TAC-CH group
| NCBI | Quality Control | Links |
|---|---|---|
| Adlercreutzia | ||
| Candidatus Arthromitus | ||
| Clostridiaceae | ||
| Dorea | ||
| Lachnospiraceae | ||
| Oscillospiraceae | ||
| Rikenellaceae | ||
| Staphylococcus |
Revision editor(s): Aleru Divine
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- TAC-CH group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- JAX-CH group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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: Figure 3B
Description: LEfSe plots showing differential taxa (family level) in co-housed mice.
Abundance in Group 1: increased abundance in JAX-CH group
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerovoracaceae | ||
| Turicibacteraceae | ||
| Verrucomicrobiaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 3B
Description: LEfSe plots showing differential taxa (family level) in co-housed mice.
Abundance in Group 1: decreased abundance in JAX-CH group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides |
Revision editor(s): Aleru Divine
Experiment 4
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
- JAX group
- Group 0 sample size Number of subjects in the control (unexposed) group
- 12
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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: Figure 3I
Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.
Abundance in Group 1: increased abundance in JAX-CH group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Dehalobacterium | ||
| Lactobacillus | ||
| Mucispirillum | ||
| Parabacteroides |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 3I
Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.
Abundance in Group 1: decreased abundance in JAX-CH group
| NCBI | Quality Control | Links |
|---|---|---|
| Adlercreutzia | ||
| Allobaculum | ||
| Bifidobacterium | ||
| Muribaculaceae | ||
| Oscillospira | ||
| Oscillospiraceae | ||
| Rikenellaceae | ||
| Ruminococcus |
Revision editor(s): Aleru Divine
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- TAC group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- TAC-CH group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples taken from co-housed mice from Taconic Farms (TAC-CH).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 3J
Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.
Abundance in Group 1: increased abundance in TAC-CH group
| NCBI | Quality Control | Links |
|---|---|---|
| Coprococcus |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 3J
Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.
Abundance in Group 1: decreased abundance in TAC-CH group
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridiaceae | ||
| Dorea | ||
| Lachnospiraceae |
Revision editor(s): Aleru Divine
Experiment 6
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- TAC-CH group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- JAX-CH group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 3G
Description: LEfSe plots showing differential taxa (family level) in co-housed mice.
Abundance in Group 1: increased abundance in JAX-CH group
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerovoracaceae | ||
| Oscillospiraceae | ||
| Turicibacteraceae | ||
| Verrucomicrobiaceae | ||
| DehalobacteriaceaeDehalobacteriaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 3G
Description: LEfSe plots showing differential taxa (family level) in co-housed mice.
Abundance in Group 1: decreased abundance in JAX-CH group
| NCBI | Quality Control | Links |
|---|---|---|
| Porphyromonadaceae | ||
| RF39RF39 |
Revision editor(s): Aleru Divine
Experiment 7
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Ileum Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,ileum
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- JAX group
- Group 0 sample size Number of subjects in the control (unexposed) group
- 12
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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: Figure 3N
Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.
Abundance in Group 1: increased abundance in JAX-CH group
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Dehalobacterium | ||
| Mucispirillum | ||
| Parabacteroides |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 3N
Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.
Abundance in Group 1: decreased abundance in JAX-CH group
| NCBI | Quality Control | Links |
|---|---|---|
| Allobaculum | ||
| Bifidobacterium | ||
| Muribaculaceae | ||
| Rikenellaceae | ||
| Staphylococcus |
Revision editor(s): Aleru Divine
Experiment 8
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- TAC group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- TAC-CH group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples taken from co-housed mice from Taconic Farms (TAC-CH).
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 3O
Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.
Abundance in Group 1: increased abundance in TAC-CH group
| NCBI | Quality Control | Links |
|---|---|---|
| Turicibacter |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 3O
Description: LEfSe plots showing differential taxa (family/genus level) in co-housed mice and sibling controls.
Abundance in Group 1: decreased abundance in TAC-CH group
| NCBI | Quality Control | Links |
|---|---|---|
| Gammaproteobacteria |
Revision editor(s): Aleru Divine
Experiment 9
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- TAC-CH group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- JAX-CH group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples taken from co-housed mice from Jackson Laboratory (JAX-CH).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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: Figure 3L
Description: LEfSe plots showing differential taxa (family level) in co-housed mice.
Abundance in Group 1: increased abundance in JAX-CH group
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillospiraceae | ||
| Turicibacteraceae | ||
| Verrucomicrobiaceae | ||
| DehalobacteriaceaeDehalobacteriaceae |
Revision editor(s): Aleru Divine
Experiment 10
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces , Colon 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,Hindgut,Large bowel,Posterior intestine,Colon,colon
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- JAX-CH colon group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- JAX-CH fecal pellets group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples taken from the fecal pellets of co-housed mice from Jackson Laboratory (JAX-CH).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S3
Description: LEfSe plots comparing differentiating taxa (family/ genus) in colon and pellet compartments of co-housed mice from Jackson Laboratory (JAX-CH).
Abundance in Group 1: increased abundance in JAX-CH fecal pellets group
| NCBI | Quality Control | Links |
|---|---|---|
| Adlercreutzia | ||
| Akkermansia | ||
| Anaerostipes | ||
| Bifidobacterium | ||
| Clostridiaceae | ||
| Erysipelotrichaceae | ||
| Lactobacillus | ||
| Rickettsiales | ||
| Turicibacter |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure S3
Description: LEfSe plots comparing differentiating taxa (family/ genus) in colon and pellet compartments of co-housed mice from Jackson Laboratory (JAX-CH).
Abundance in Group 1: decreased abundance in JAX-CH fecal pellets group
Revision editor(s): Aleru Divine
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- TAC-CH colon group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- TAC-CH fecal pellets group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Samples taken from the fecal pellets of co-housed mice from Taconic Farms (TAC-CH).
Lab analysis
Statistical Analysis
Signature 1
Source: Figure S3
Description: LEfSe plots comparing differentiating taxa (family/ genus) in colon and pellet compartments of co-housed mice from Taconic Farms (TAC-CH).
Abundance in Group 1: increased abundance in TAC-CH fecal pellets group
| NCBI | Quality Control | Links |
|---|---|---|
| Adlercreutzia | ||
| Akkermansia | ||
| Bacteroides | ||
| Bifidobacterium | ||
| Clostridiaceae | ||
| Erysipelotrichaceae | ||
| Lactobacillus | ||
| Muribaculaceae | ||
| Parabacteroides | ||
| Rickettsiales | ||
| RF39RF39 |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure S3
Description: LEfSe plots comparing differentiating taxa (family/ genus) in colon and pellet compartments of co-housed mice from Taconic Farms (TAC-CH).
Abundance in Group 1: decreased abundance in TAC-CH fecal pellets group
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacteriales | ||
| Mucispirillum | ||
| Anaeroplasma | ||
| Oscillospiraceae | ||
| Oscillospira | ||
| Ruminococcus | ||
| Ruminococcus sp. | ||
| Coprococcus |
Revision editor(s): Aleru Divine
Experiment 12
Subjects
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- P1 TAC group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- P1 JAX group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Fecal pellet samples of the parental generation (P1) of Jackson Laboratory (JAX) mice.
- 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
- Statistical test
- Dunn's test
- Kruskall-Wallis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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: Figure 6 and S7
Description: Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice
Abundance in Group 1: increased abundance in P1 JAX group
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Clostridium | ||
| Adlercreutzia | ||
| Lactobacillus |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 6 and S7
Description: Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice
Abundance in Group 1: decreased abundance in P1 JAX group
| NCBI | Quality Control | Links |
|---|---|---|
| Parabacteroides | ||
| Bacteroides | ||
| Candidatus Arthromitus sp. SFB-mouse | ||
| Mucispirillum | ||
| Oscillospiraceae |
Revision editor(s): Aleru Divine
Experiment 13
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- P1 JAX group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- F1 mJAX group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Fecal pellet samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Experiment 14
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- P1 TAC group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- F1 mTAC group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Fecal pellet samples from the maternal F1-generation of Taconic farms (mTAC) mice.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Experiment 15
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- F1 mTAC group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- F1 mJAX group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Fecal pellet samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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: Figure 6 and S7
Description: Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in F1 mJAX and mTAC mice
Abundance in Group 1: increased abundance in F1 mJAX group
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia |
Revision editor(s): Aleru Divine
Experiment 16
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
- P1 TAC group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- P1 JAX group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colon samples of the parental generation (P1) of Jackson Laboratory (JAX) mice.
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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: Figure 6 and S7
Description: Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice
Abundance in Group 1: increased abundance in P1 JAX group
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Clostridium | ||
| Anaeroplasma | ||
| Bifidobacterium | ||
| Acinetobacter | ||
| Rikenellaceae | ||
| Muribaculaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 6 and S7
Description: Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice
Abundance in Group 1: decreased abundance in P1 JAX group
| NCBI | Quality Control | Links |
|---|---|---|
| Parabacteroides | ||
| Bacteroides | ||
| Candidatus Arthromitus sp. SFB-mouse | ||
| Mucispirillum | ||
| Dehalobacterium | ||
| Dorea |
Revision editor(s): Aleru Divine
Experiment 17
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- P1 JAX group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- F1 mJAX group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colon samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Experiment 18
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- P1 TAC group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- F1 mTAC group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colon samples from the maternal F1-generation of Taconic farms (mTAC) mice.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- increased
Experiment 19
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- F1 mTAC group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- F1 mJAX group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colon samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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 6 and S7
Description: Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice
Abundance in Group 1: increased abundance in F1 mJAX group
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Muribaculaceae |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 6 and S7
Description: Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice
Abundance in Group 1: decreased abundance in F1 mJAX group
| NCBI | Quality Control | Links |
|---|---|---|
| Candidatus Arthromitus sp. SFB-mouse | ||
| Dehalobacterium |
Revision editor(s): Aleru Divine
Experiment 20
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Ileum Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,ileum
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- P1 TAC group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- P1 JAX group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Ileum samples of the parental generation (P1) of Jackson Laboratory (JAX) mice.
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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: Figure 6 and S7
Description: Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice.
Abundance in Group 1: increased abundance in P1 JAX group
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Clostridium | ||
| Adlercreutzia | ||
| Anaeroplasma |
Revision editor(s): Aleru Divine
Signature 2
Source: Figure 6 and S7
Description: Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice.
Abundance in Group 1: decreased abundance in P1 JAX group
| NCBI | Quality Control | Links |
|---|---|---|
| Parabacteroides | ||
| Bacteroides | ||
| Candidatus Arthromitus sp. SFB-mouse | ||
| Mucispirillum | ||
| Dehalobacterium |
Revision editor(s): Aleru Divine
Experiment 21
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- P1 JAX group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- F1 mJAX group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Ileum samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Experiment 22
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- P1 TAC group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- F1 mTAC group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Ileum samples from the maternal F1-generation of Taconic farms (mTAC) mice.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Experiment 23
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- F1 mTAC group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- F1 mJAX group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Ileum samples from the maternal F1-generation of Jackson Laboratory (mJAX) mice.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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: Figure 6 and S7
Description: Variation in bacterial transmission patterns observed from P1 to F1 and F2 generations for taxa that significantly vary in P1 JAX and TAC mice.
Abundance in Group 1: increased abundance in F1 mJAX group
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia |
Revision editor(s): Aleru Divine
Contents
- 1 Experiment 1
- 2 Experiment 2
- 3 Experiment 3
- 4 Experiment 4
- 5 Experiment 5
- 6 Experiment 6
- 7 Experiment 7
- 8 Experiment 8
- 9 Experiment 9
- 10 Experiment 10
- 11 Experiment 11
- 12 Experiment 12
- 13 Experiment 13
- 14 Experiment 14
- 15 Experiment 15
- 16 Experiment 16
- 17 Experiment 17
- 18 Experiment 18
- 19 Experiment 19
- 20 Experiment 20
- 21 Experiment 21
- 22 Experiment 22
- 23 Experiment 23
