Convergent gut microbial functional strategies drive energy metabolism adaptation across Ursidae species and challenge the uniqueness of giant panda
-
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.
- Ursus maritimus
- 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
- Interspecies interaction between organisms interaction with another species,interspecies interaction,interspecies interaction with other organisms,Interspecies interaction between organisms,interspecies interaction between organisms
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Brown bear (Ursus arctos)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Polar bear (Ursus maritimus)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Adult polar bears (Ursus maritimus) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing.
- 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
- 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
- increased
Signature 1
Source: Figure 1c
Description: Boxplots for the significant differences in relative abundance of the Fimicutes and Fusobacteriota phyla (Kruskal–Wallis test).
Abundance in Group 1: increased abundance in Polar bear (Ursus maritimus)
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriota |
Revision editor(s): YokoC
Experiment 2
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Ailuropoda melanoleuca
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Polar bears (Ursus maritimus)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Panda bear (Ailuropoda melanoleuca)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Juvenile and adult panda bears (Ailuropoda melanoleuca) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing.
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 1b
Description: Boxplots for the significant differences in relative abundance of the Fimicutes and Fusobacteriota phyla (Kruskal–Wallis test).
Abundance in Group 1: increased abundance in Panda bear (Ailuropoda melanoleuca)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): YokoC
Signature 2
Source: Figure 1c
Description: Boxplots for the significant differences in relative abundance of the Fimicutes and Fusobacteriota phyla (Kruskal–Wallis test).
Abundance in Group 1: decreased abundance in Panda bear (Ailuropoda melanoleuca)
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriota |
Revision editor(s): YokoC
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Asian black bear (Ursus thibetanus)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 1c
Description: Boxplots for the significant differences in relative abundance of the Fimicutes and Fusobacteriota phyla (Kruskal–Wallis test).
Abundance in Group 1: decreased abundance in Panda bear (Ailuropoda melanoleuca)
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriota |
Revision editor(s): YokoC
Experiment 4
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Brown bear (Ursus arctos)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 1b
Description: Boxplots for the significant differences in relative abundance of the Fimicutes and Fusobacteriota phyla (Kruskal–Wallis test).
Abundance in Group 1: increased abundance in Panda bear (Ailuropoda melanoleuca)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): YokoC
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Brown bear (Ursus arctos) + Asian Black bear (Ursus thibetanus) + Polar bear (Ursus maritimus)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Signature 1
Source: Figure 1f
Description: Barplots for a LEfSe analysis of relative abundance of the genus with significant differences in the four bear groups (LDA score > 3 and a significance of a < 0.05).
Abundance in Group 1: increased abundance in Panda bear (Ailuropoda melanoleuca)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus |
Revision editor(s): YokoC
Experiment 6
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Ursus arctos
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Panda bear (Ailuropoda melanoleuca) + Asian Black bear (Ursus thibetanus) + Polar bear (Ursus maritimus)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Brown bear (Ursus arctos)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Juvenile and adult brown bears (Ursus arctos) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 1f
Description: Barplots for a LEfSe analysis of relative abundance of the genus with significant differences in the four bear groups (LDA score > 3 and a significance of a < 0.05).
Abundance in Group 1: increased abundance in Brown bear (Ursus arctos)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Lactococcus | ||
| Sarcina | ||
| Lachnoclostridium |
Revision editor(s): YokoC
Experiment 7
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Ursus thibetanus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Panda bear (Ailuropoda melanoleuca) + Brown bear (Ursus arctos) + Polar bear (Ursus maritimus)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Asian Black bear (Ursus thibetanus)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Juvenile and adult asian black bears (Ursus thibetanus) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
- Group 1 sample size Number of subjects in the case (exposed) group
- 3
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 1f
Description: Barplots for a LEfSe analysis of relative abundance of the genus with significant differences in the four bear groups (LDA score > 3 and a significance of a < 0.05).
Abundance in Group 1: increased abundance in Asian Black bear (Ursus thibetanus)
Revision editor(s): YokoC
Experiment 8
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Ursus maritimus
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Panda bear (Ailuropoda melanoleuca) + Brown bear (Ursus arctos) + Asian black bears (Ursus thibetanus)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Polar bear (Ursus maritimus)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 1f
Description: Barplots for a LEfSe analysis of relative abundance of the genus with significant differences in the four bear groups (LDA score > 3 and a significance of a < 0.05).
Abundance in Group 1: increased abundance in Polar bear (Ursus maritimus)
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Cetobacterium | ||
| Klebsiella | ||
| Plesiomonas | ||
| Prevotellaceae UCG 001Prevotellaceae UCG 001 | ||
| Clostridium |
Revision editor(s): YokoC
Experiment 9
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Seasonal gut microbiome measurement , Interspecies interaction between organisms Seasonal gut microbiome measurement,seasonal gut microbiome measurement,interaction with another species,interspecies interaction,interspecies interaction with other organisms,Interspecies interaction between organisms,interspecies interaction between organisms
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Brown bear (Ursus arctos)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Adult polar bears (Ursus maritimus) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
Lab analysis
Statistical Analysis
- Statistical test
- ANOVA
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Signature 1
Source: Figure 2b and Figure 2c
Description: Significant differences among the three phyla and the three genera with the highest relative abundance. Two-way Anova for bear species (polar bear and brown bear) and seasons (spring).
Abundance in Group 1: increased abundance in Polar bear (Ursus maritimus)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium |
Revision editor(s): YokoC
Experiment 10
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Ailuropoda melanoleuca
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Polar bear (Ursus maritimus)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Panda bear (Ailuropoda melanoleuca)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Adult and juvenile Panda bears (Ailuropoda melanoleuca) housed in the Beijing Zoo, where they were managed under consistent conditions, including diet and housing.
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2D
Description: Significant differences among the three phyla and the three genera with the highest relative abundance. Two-way Anova for bear species (panda bear and polar bear) and seasons (spring).
Abundance in Group 1: increased abundance in Panda bear (Ailuropoda melanoleuca)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus |
Revision editor(s): YokoC
Signature 2
Source: Figure 2d
Description: Significant differences among the three phyla and the three genera with the highest relative abundance. Two-way Anova for bear species (panda bear and polar bear) and seasons (spring).
Abundance in Group 1: decreased abundance in Panda bear (Ailuropoda melanoleuca)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium |
Revision editor(s): YokoC
Experiment 11
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Asian Black Bear (Ursus thibetanus)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2d
Description: Significant differences among the three phyla and the three genera with the highest relative abundance. Two-way Anova for bear species (panda bear and Asian black bear) and seasons (spring).
Abundance in Group 1: increased abundance in Panda bear (Ailuropoda melanoleuca)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus |
Revision editor(s): YokoC
Experiment 12
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Brown bear (Ursus arctos)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2d
Description: Significant differences among the three phyla and the three genera with the highest relative abundance. Two-way Anova for bear species (panda bear and brown bear) and seasons (spring).
Abundance in Group 1: increased abundance in Panda bear (Ailuropoda melanoleuca)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus |
Revision editor(s): YokoC
Signature 2
Source: Figure 2d
Description: Significant differences among the three phyla and the three genera with the highest relative abundance. Two-way Anova for bear species (panda bear and brown bear) and seasons (spring).
Abundance in Group 1: decreased abundance in Panda bear (Ailuropoda melanoleuca)
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia/ShigellaEscherichia/Shigella |
Revision editor(s): YokoC
Experiment 13
Subjects
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2c and 2d
Description: Significant differences among the three phyla and the three genera with the highest relative abundance. Two-way Anova for bear species (panda bear and brown bear) and seasons (winter).
Abundance in Group 1: increased abundance in Panda bear (Ailuropoda melanoleuca)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Streptococcus |
Revision editor(s): YokoC
Experiment 14
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Polar bear (Ursus maritimus)
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2d
Description: Significant differences among the three phyla and the three genera with the highest relative abundance. Two-way Anova for bear species (panda bear and polar bear) and seasons (winter).
Abundance in Group 1: increased abundance in Panda bear (Ailuropoda melanoleuca)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus |
Revision editor(s): YokoC
Experiment 15
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Asian black bear (Ursus thibetanus)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 2d
Description: Significant differences among the three phyla and the three genera with the highest relative abundance. Two-way Anova for bear species (panda bear and Asian black bear) and seasons (winter).
Abundance in Group 1: increased abundance in Panda bear (Ailuropoda melanoleuca)
| NCBI | Quality Control | Links |
|---|---|---|
| Streptococcus |
Revision editor(s): YokoC
Experiment 16
Subjects
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Mus musculus
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to transplant Response to transplant,response to transplant
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Brown-FMT(W) + Black-FMT(W) + Polar-FMT(W) + Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Panda-FMT(W) (Fecal Matter Transplant Winter)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received a fecal matter transplant from zoo pandas, which was collected in winter.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Signature 1
Source: Figure 4g
Description: Barplots for a LEfSe analysis of relative abundance of the genus with significant differences (LDA score > 3 and a significance of a < 0.05).
Abundance in Group 1: increased abundance in Panda-FMT(W) (Fecal Matter Transplant Winter)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotellaceae_NK3B31_groupPrevotellaceae_NK3B31_group | ||
| Phenylobacterium | ||
| AKYH767AKYH767 |
Revision editor(s): YokoC
Experiment 17
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Brown-FMT(W) + Black-FMT(W) + Panda-FMT(W) + Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Polar-FMT (Fecal Matter Transplant Winter)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received a fecal matter transplant from zoo polar bears, which was collected in winter.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4g
Description: Barplots for a LEfSe analysis of relative abundance of the genus with significant differences (LDA score > 3 and a significance of a < 0.05).
Abundance in Group 1: increased abundance in Polar-FMT (Fecal Matter Transplant Winter)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridia UCG 014Clostridia UCG 014 | ||
| Fusicatenibacter | ||
| Erysipelotrichaceae UCG 003Erysipelotrichaceae UCG 003 |
Revision editor(s): YokoC
Experiment 18
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Polar-FMT + Black-FMT(W) + Panda-FMT(W) + Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Brown-FMT (Fecal Matter Transplant Winter)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received a fecal matter transplant from zoo brown bears, which was collected in winter.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4g
Description: Barplots for a LEfSe analysis of relative abundance of the genus with significant differences(LDA score > 3 and a significance of a < 0.05).
Abundance in Group 1: increased abundance in Brown-FMT (Fecal Matter Transplant Winter)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides |
Revision editor(s): YokoC
Experiment 19
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Polar-FMT + Brown-FMT(W) + Panda-FMT(W) + Control
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received a fecal matter transplant from zoo Asian black bears, which was collected in winter.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4g
Description: Barplots for a LEfSe analysis of relative abundance of the genus with significant differences (LDA score > 3 and a significance of a < 0.05).
Abundance in Group 1: increased abundance in Brown-FMT (Fecal Matter Transplant Winter)
| NCBI | Quality Control | Links |
|---|---|---|
| Muribaculaceae | ||
| Enterorhabdus | ||
| Ohtaekwangia |
Revision editor(s): YokoC
Experiment 20
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Polar-FMT + Brown-FMT(W) + Panda-FMT(W) + Black'FMT
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Control
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that that did not receive a fecal matter transplant (FMT).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 4g
Description: Barplots for a LEfSe analysis of relative abundance of the genus with significant differences in the four bear groups (LDA score > 3 and a significance of a < 0.05).
Abundance in Group 1: increased abundance in Control
| NCBI | Quality Control | Links |
|---|---|---|
| Helicobacter | ||
| Sellimonas | ||
| Desulfovibrio | ||
| Clostridia vadinBB60 groupClostridia vadinBB60 group | ||
| hoa5_07405 gut grouphoa5_07405 gut group | ||
| OM27 clade |
Revision editor(s): YokoC
Experiment 21
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Panda-FMT(W) (Fecal Matter Transplant Winter)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received a fecal matter transplant from pandas, which was collected in winter.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 4d
Description: Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).
Abundance in Group 1: decreased abundance in Panda-FMT(W) (Fecal Matter Transplant Winter)
| NCBI | Quality Control | Links |
|---|---|---|
| Spirochaetota |
Revision editor(s): YokoC
Experiment 22
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Black-FMT(W) (Fecal Matter Transplant Winter)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received a fecal matter transplant from Asian black bears, which was collected in winter.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 4e
Description: Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).
Abundance in Group 1: increased abundance in Black-FMT(W) (Fecal Matter Transplant Winter)
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota |
Revision editor(s): YokoC
Experiment 23
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Panda-FMT (W) (Fecal Matter Transplant Winter)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Polar-FMT(W) (Fecal Matter Transplant Winter)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received a fecal matter transplant from zoo Polar bears, which was collected in winter.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 4f
Description: Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).
Abundance in Group 1: increased abundance in Polar-FMT(W) (Fecal Matter Transplant Winter)
| NCBI | Quality Control | Links |
|---|---|---|
| Acidobacteriota |
Revision editor(s): YokoC
Experiment 24
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Polar-FMT (S) (Fecal Matter Transplant Summer)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Panda-FMT(S) (Fecal Matter Transplant Summer)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received a fecal matter transplant from zoo panda bears, which was collected in summer.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 6f
Description: Boxplots for the significant differences in relative abundance of the phyla (Kruskal–Wallis test).
Abundance in Group 1: increased abundance in Panda-FMT(S) (Fecal Matter Transplant Summer)
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriota |
Revision editor(s): YokoC
Experiment 25
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Brown-FMT(S) (Fecal Matter Transplant Summer)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received a fecal matter transplant from zoo brown bears, which was collected in summer.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 6f
Description: Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).
Abundance in Group 1: increased abundance in Brown-FMT(S) (Fecal Matter Transplant Summer)
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriota |
Revision editor(s): YokoC
Experiment 26
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Brown-FMT (S) (Fecal Matter Transplant Summer)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Black-FMT(S) (Fecal Matter Transplant Summer)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received a fecal matter transplant from zoo Asian black bears, which was collected in summer.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 6f
Description: Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).
Abundance in Group 1: increased abundance in Black-FMT(S) (Fecal Matter Transplant Summer)
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriota |
Revision editor(s): YokoC
Experiment 27
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Polar-FMT (S) (Fecal Matter Transplant Summer)
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 6f and Figure 6g
Description: Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).
Abundance in Group 1: increased abundance in Black-FMT(S) (Fecal Matter Transplant Summer)
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriota |
Revision editor(s): YokoC
Signature 2
Source: Figure 6f and Figure 6g
Description: Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).
Abundance in Group 1: decreased abundance in Black-FMT(S) (Fecal Matter Transplant Summer)
| NCBI | Quality Control | Links |
|---|---|---|
| Thermodesulfobacteriota |
Revision editor(s): YokoC
Experiment 28
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 6f
Description: Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).
Abundance in Group 1: increased abundance in Black-FMT(S) (Fecal Matter Transplant Summer)
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriota |
Revision editor(s): YokoC
Experiment 29
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Brown-FMT(S) (Fecal Matter Transplant Summer)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received a fecal matter transplant from zoo brown bears, which was collected in summer.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 6f
Description: Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).
Abundance in Group 1: increased abundance in Brown-FMT(S) (Fecal Matter Transplant Summer)
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacteriota |
Revision editor(s): YokoC
Experiment 30
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Polar-FMT(S) (Fecal Matter Transplant Summer)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received a fecal matter transplant from zoo polar bears, which was collected in summer.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Experiment 31
Subjects
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Source: Figure 6d
Description: Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).
Abundance in Group 1: increased abundance in Polar-FMT(S) (Fecal Matter Transplant Summer)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota |
Revision editor(s): YokoC
Signature 2
Source: Figure 6e
Description: Boxplots for the significant differences in relative abundance of phyla (Kruskal–Wallis test).
Abundance in Group 1: decreased abundance in Polar-FMT(S) (Fecal Matter Transplant Summer)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota |
Revision editor(s): YokoC
Experiment 32
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control-FMT(S) + Black-FMT(S) + Polar-FMT(S) + Polar-FMT(S)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Brown-FMT(S) (Fecal Matter Transplant Summer)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received a fecal matter transplant from zoo brown bears, which was collected in summer.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
Signature 1
Source: Figure 6h
Description: Barplots for a LEfSe analysis of relative abundance of the genus with significant differences (LDA score > 3 and a significance of a < 0.05).
Abundance in Group 1: increased abundance in Brown-FMT(S) (Fecal Matter Transplant Summer)
Revision editor(s): YokoC
Experiment 33
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control-FMT(S) + Brown-FMT(S) + Polar-FMT(S) + Polar-FMT(S)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Black-FMT(S) (Fecal Matter Transplant Summer)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received a fecal matter transplant from zoo Asian black bears, which was collected in summer.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 6h
Description: Barplots for a LEfSe analysis of relative abundance of the genus with significant differences (LDA score > 3 and a significance of a < 0.05).
Abundance in Group 1: increased abundance in Black-FMT(S) (Fecal Matter Transplant Summer)
| NCBI | Quality Control | Links |
|---|---|---|
| Muribaculum | ||
| Bilophila | ||
| Halioglobus | ||
| Ruminococcus |
Revision editor(s): YokoC
Experiment 34
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Control-FMT(S) + Brown-FMT(S) + Black-FMT(S) + Polar-FMT(S)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Polar-FMT(S) (Fecal Matter Transplant Summer)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received a fecal matter transplant from zoo polar bears, which was collected in summer.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 6h
Description: Barplots for a LEfSe analysis of relative abundance of the genus with significant differences (LDA score > 3 and a significance of a < 0.05).
Abundance in Group 1: increased abundance in Polar-FMT(S) (Fecal Matter Transplant Summer)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus | ||
| Blautia | ||
| Butyricicoccus | ||
| Rikenella | ||
| Clostridia vadinBB60 groupClostridia vadinBB60 group | ||
| Colidextribacter |
Revision editor(s): YokoC
Experiment 35
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Panda-FMT(S) (Fecal Matter Transplant Summer)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that received a fecal matter transplant from zoo panda bears, which was collected in summer.
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 6h
Description: Barplots for a LEfSe analysis of relative abundance of the genus with significant differences (LDA score > 3 and a significance of a < 0.05).
Abundance in Group 1: increased abundance in Panda-FMT(S) (Fecal Matter Transplant Summer)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Gemella | ||
| Marvinbryantia | ||
| Marivita | ||
| Escherichia/ShigellaEscherichia/Shigella |
Revision editor(s): YokoC
Experiment 36
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Panda-FMT(S) + Brown-FMT(S) + Black-FMT(S) + Polar-FMT(S)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Control
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Mice that did not receive a fecal matter transplant or any other treatment.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 7
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 6h
Description: Barplots for a LEfSe analysis of relative abundance of the genus with significant differences (LDA score > 3 and a significance of a < 0.05).
Abundance in Group 1: increased abundance in Control
Revision editor(s): YokoC
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
- 24 Experiment 24
- 25 Experiment 25
- 26 Experiment 26
- 27 Experiment 27
- 28 Experiment 28
- 29 Experiment 29
- 30 Experiment 30
- 31 Experiment 31
- 32 Experiment 32
- 33 Experiment 33
- 34 Experiment 34
- 35 Experiment 35
- 36 Experiment 36
