Dysbiosis of skin microbiome and gut microbiome in melanoma progression
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Mekadim C, Skalnikova HK, Cizkova J, Cizkova V, Palanova A, Horak V, Mrazek J
Journal
BMC microbiology
Year
2022
Keywords:
Dysbiosis, Gut microbiome, Gut-skin axis, MeLiM, Melanoma, Metagenomic analysis, NGS, Pig, Skin cancer, Skin microbiome, Tumour microenvironment
BACKGROUND: The microbiome alterations are associated with cancer growth and may influence the immune system and response to therapy. Particularly, the gut microbiome has been recently shown to modulate response to melanoma immunotherapy. However, the role of the skin microbiome has not been well explored in the skin tumour microenvironment and the link between the gut microbiome and skin microbiome has not been investigated in melanoma progression. Therefore, the aim of the present study was to examine associations between dysbiosis in the skin and gut microbiome and the melanoma growth using MeLiM porcine model of melanoma progression and spontaneous regression. RESULTS: Parallel analysis of cutaneous microbiota and faecal microbiota of the same individuals was performed in 8 to 12 weeks old MeLiM piglets. The bacterial composition of samples was analysed by high throughput sequencing of the V4-V5 region of the 16S rRNA gene. A significant difference in microbiome diversity and richness between melanoma tissue and healthy skin and between the faecal microbiome of MeLiM piglets and control piglets were observed. Both Principal Coordinate Analysis and Non-metric multidimensional scaling revealed dissimilarities between different bacterial communities. Linear discriminant analysis effect size at the genus level determined different potential biomarkers in multiple bacterial communities. Lactobacillus, Clostridium sensu stricto 1 and Corynebacterium 1 were the most discriminately higher genera in the healthy skin microbiome, while Fusobacterium, Trueperella, Staphylococcus, Streptococcus and Bacteroides were discriminately abundant in melanoma tissue microbiome. Bacteroides, Fusobacterium and Escherichia-Shigella were associated with the faecal microbiota of MeLiM piglets. Potential functional pathways analysis based on the KEGG database indicated significant differences in the predicted profile metabolisms between the healthy skin microbiome and melanoma tissue microbiome. The faecal microbiome of MeLiM piglets was enriched by genes related to membrane transports pathways allowing for the increase of intestinal permeability and alteration of the intestinal mucosal barrier. CONCLUSION: The associations between melanoma progression and dysbiosis in the skin microbiome as well as dysbiosis in the gut microbiome were identified. Results provide promising information for further studies on the local skin and gut microbiome involvement in melanoma progression and may support the development of new therapeutic approaches.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Subjects
- Location of subjects
- Czechia
- 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
- Skin of body Entire integument,Entire skin,Integument,Integumental organ,Pelt,Skin,Skin organ,Skin of body,skin of body
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Disease staging disease_staging,Disease staging,disease staging
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Melanoma surface of pigs with with melanoma regression
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Melanoma surface of pigs with Melanoma progression
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Melanoma surface samples collected from piglets with melanoma progression
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
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
- Ion Torrent
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)?
- No
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Source: Figure 4A
Description: Differential abundance calculated using Linear discriminant analysis (LDA) effect size (LEfSe) at genera level in skin microbiome between melanoma surface in melanoma progression and melanoma regression
Abundance in Group 1: increased abundance in Melanoma surface of pigs with Melanoma progression
Revision editor(s): Snehhumann, Idiaru angela
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Source: Figure 4A
Description: Differential abundance calculated using Linear discriminant analysis (LDA) effect size (LEfSe) at genera level in skin microbiome between melanoma surface in melanoma progression and melanoma regression
Abundance in Group 1: decreased abundance in Melanoma surface of pigs with Melanoma progression
Revision editor(s): Snehhumann, Idiaru angela, MyleeeA
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Melanoma tissue of pigs with with melanoma regression
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Melanoma tissue of pigs with Melanoma progression
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Melanoma tissue samples collected from piglets with melanoma progression
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
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Source: Figure 4B
Description: Differential abundance calculated using Linear discriminant analysis (LDA) effect size (LEfSe) at genera level in skin microbiome between melanoma tissue in melanoma progression and melanoma regression
Abundance in Group 1: increased abundance in Melanoma tissue of pigs with Melanoma progression
Revision editor(s): Idiaru angela
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Source: Figure 4B
Description: Differential abundance calculated using Linear discriminant analysis (LDA) effect size (LEfSe) at genera level in skin microbiome between melanoma tissue in melanoma progression and melanoma regression
Abundance in Group 1: decreased abundance in Melanoma tissue of pigs with Melanoma progression
Revision editor(s): Idiaru angela
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cutaneous melanoma cutaneous (skin) melanoma,cutaneous melanoma,cutaneous melanoma (disease),malignant cutaneous melanoma,malignant ear melanoma,malignant lip melanoma,malignant lower limb melanoma,malignant melanoma (of skin), stage unspecified,malignant melanoma of ear and/or external auricular canal,malignant melanoma of skin,malignant melanoma of skin of lower limb,malignant melanoma of skin of trunk except scrotum,malignant melanoma of skin of upper limb,malignant melanoma of skin stage unspecified,malignant neck melanoma,malignant scalp melanoma,malignant trunk melanoma,malignant upper limb melanoma,melanoma (disease) of zone of skin,melanoma of skin,melanoma of the skin,skin melanoma,skin, melanoma,zone of skin melanoma,zone of skin melanoma (disease),Cutaneous melanoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy skin
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- melanoma surface from black pigs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cutaneous melanoma surface samples collected from the skin of black pigs
- 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
- 24
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
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Source: Supplementary figure 5
Description: Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in skin microbiome between Healthy skin and melanoma surface
Abundance in Group 1: increased abundance in melanoma surface from black pigs
Revision editor(s): Idiaru angela
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Source: Supplementary figure 5
Description: Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in skin microbiome between Healthy skin and melanoma surface.
Abundance in Group 1: decreased abundance in melanoma surface from black pigs
| NCBI | Quality Control | Links |
|---|---|---|
| Fusobacterium | ||
| Helcococcus | ||
| Moraxella | ||
| Peptoniphilus | ||
| Peptostreptococcus | ||
| Staphylococcus | ||
| Streptococcus | ||
| Escherichia/Shigella sp. |
Revision editor(s): Idiaru angela
Experiment 4
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- melanoma tissue from black pigs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cutaneous melanoma tissue samples collected from the skin of black pigs
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
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Source: Supplementary figure 6
Description: Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in skin microbiome between Healthy skin and melanoma tissue.
Abundance in Group 1: increased abundance in melanoma tissue from black pigs
Revision editor(s): Idiaru angela
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Source: Supplementary figure 6
Description: Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in skin microbiome between Healthy skin and melanoma tissue.
Abundance in Group 1: decreased abundance in melanoma tissue from black pigs
Revision editor(s): Idiaru angela
Experiment 5
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Differences from previous experiment shown
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
- controls without melanoma and melanoma regression
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Melanoma progression
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- samples collected from piglets undergoing melanoma progression.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Source: Supplementary figure 7
Description: Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in fecal microbiome between control and melanoma progression and regression samples
Abundance in Group 1: increased abundance in Melanoma progression
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Filifactor | ||
| Fusobacterium | ||
| Helcococcus | ||
| Odoribacter | ||
| Faecalibacterium sp. UBA1819 |
Revision editor(s): Idiaru angela
Experiment 6
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- controls without melanoma and melanoma progression
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- melanoma regression
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- samples collected from piglets undergoing melanoma regression
- 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
- 14
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Source: Supplementary figure 7
Description: Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in fecal microbiome between control and melanoma progression and regression samples
Abundance in Group 1: increased abundance in melanoma regression
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia/Shigella sp. |
Revision editor(s): Idiaru angela
Experiment 7
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Controls without melanoma
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Melanoma progression and regression
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- samples collected from piglets undergoing melanoma regression and progression
- 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
- 24
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Source: Supplementary figure 7
Description: Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in fecal microbiome between control and melanoma progression and regression samples
Abundance in Group 1: decreased abundance in Melanoma progression and regression
| NCBI | Quality Control | Links |
|---|---|---|
| Alloprevotella | ||
| Anaerovibrio | ||
| Faecalibacterium | ||
| Marvinbryantia | ||
| Oribacterium | ||
| Prevotella9Prevotella9 | ||
| Lachnospiraceae bacterium NK4A136 |
Revision editor(s): Idiaru angela
Experiment 8
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breed animal breed,Breed,breed
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Crossbreed between MeLiM and white piglets
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Homogenous breed MeLiM piglets
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- MeLiM piglets whose parents are both MeLiM black pigs
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Source: Supplementary figure 8
Description: Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in fecal microbiome between crossbred and MeLiM piglets
Abundance in Group 1: increased abundance in Homogenous breed MeLiM piglets
Revision editor(s): Idiaru angela
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Source: Supplementary figure 8
Description: Differential abundance calculated using linear discriminant analysis (LDA) effect size (LEfSe) results at genus level in fecal microbiome between crossbred and MeLiM piglets.
Abundance in Group 1: decreased abundance in Homogenous breed MeLiM piglets
Revision editor(s): Idiaru angela
Experiment 9
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Skin of body Entire integument,Entire skin,Integument,Integumental organ,Pelt,Skin,Skin organ,Skin of body,skin of body
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Sample splitting aliquotting,sub-sampling,Sample splitting,sample splitting
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- melanoma surface
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- melanoma tissue
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- melanoma inner tissue samples collected from piglets with melanoma
- Group 0 sample size Number of subjects in the control (unexposed) group
- 24
- Group 1 sample size Number of subjects in the case (exposed) group
- 24
Lab analysis
- Statistical test
- Not specified
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- Not specified
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Not specified
- 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
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
Experiment 10
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cutaneous melanoma cutaneous (skin) melanoma,cutaneous melanoma,cutaneous melanoma (disease),malignant cutaneous melanoma,malignant ear melanoma,malignant lip melanoma,malignant lower limb melanoma,malignant melanoma (of skin), stage unspecified,malignant melanoma of ear and/or external auricular canal,malignant melanoma of skin,malignant melanoma of skin of lower limb,malignant melanoma of skin of trunk except scrotum,malignant melanoma of skin of upper limb,malignant melanoma of skin stage unspecified,malignant neck melanoma,malignant scalp melanoma,malignant trunk melanoma,malignant upper limb melanoma,melanoma (disease) of zone of skin,melanoma of skin,melanoma of the skin,skin melanoma,skin, melanoma,zone of skin melanoma,zone of skin melanoma (disease),Cutaneous melanoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- skin samples from white piglets
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- skin samples from crossbred piglets
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- skin samples from Black crossbred piglets.
- 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
- 4
Lab analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- decreased
Experiment 11
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- samples from white piglets
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- samples from MeLiM piglets
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- samples from piglets gotten through Homogenous breeding of two Black MeLiM pigs.
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
Lab analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
Experiment 12
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breed animal breed,Breed,breed
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Black crossbred between white and MeLiM piglets
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Homogenous breed Black MeLiM piglets
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
Lab analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
Experiment 13
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Age at assessment Age at assessment,age at assessment
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- melanoma regression at age 8 weeks
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- melanoma regression at age 12 weeks
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- samples gotten from piglets undergoing melanoma regression at age 12 weeks
- Group 0 sample size Number of subjects in the control (unexposed) group
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
Lab analysis
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
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- increased
Experiment 14
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- melanoma regression at age 10 weeks
Lab analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
Experiment 15
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- melanoma regression at age 8 weeks
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- melanoma regression at age 10 weeks
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- samples gotten from piglets undergoing melanoma regression at age 10 weeks
Lab analysis
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
- increased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- increased
- Richness Number of species
- increased
Experiment 16
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Differences from previous experiment shown
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
Lab analysis
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
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Experiment 17
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Breed animal breed,Breed,breed
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- crossbred piglets undergoing regression
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- MeLiM piglets undergoing regression
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- samples gotten from Black MeLiM piglets undergoing regression
- 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
- 10
Lab analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- decreased
- Richness Number of species
- decreased
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