Dysbiosis of skin microbiome and gut microbiome in melanoma progression

From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-9-13
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

Curated date: 2024/04/01

Curator: Snehhumann

Revision editor(s): Snehhumann, Idiaru angela

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

Curated date: 2024/04/01

Curator: Snehhumann

Revision editor(s): Snehhumann, Idiaru angela

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

NCBI Quality ControlLinks
Actinomyces
Bacteroides
Campylobacter
Filifactor
Fusobacterium
Globicatella
Helcococcus
Parvimonas
Peptoniphilus
Peptostreptococcus
Porphyromonas
Trueperella
Clostridiales bacterium canine oral taxon 260

Revision editor(s): Snehhumann, Idiaru angela

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-9-13

Curated date: 2024/04/01

Curator: Snehhumann

Revision editor(s): Snehhumann, Idiaru angela, MyleeeA

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

NCBI Quality ControlLinks
Aerosphaera
Atopostipes
Blautia
Brachybacterium
Desulfovibrio
Dietzia
Enterococcus
Facklamia
Faecalibacterium
Ignavigranum
Jeotgalibaca
Jeotgalicoccus
Lactobacillus
Micrococcus
Oligella
Psychrobacter
Romboutsia
Roseburia
Ruminococcaceae bacterium UCG-005
Ruminococcus gauvreauii
Terrisporobacter
Turicibacter
Weissella
Prevotella9Prevotella9
Prevotellaceae NK3B31 groupPrevotellaceae NK3B31 group
Rikenellaceae RC9 gut groupRikenellaceae RC9 gut group
Clostridium

Revision editor(s): Snehhumann, Idiaru angela, MyleeeA

Experiment 2


Reviewed Marked as Reviewed by Svetlana up on 2024-9-13

Curated date: 2024/04/08

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

Curated date: 2024/04/08

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

NCBI Quality ControlLinks
Corynebacterium
Fusobacterium
Helcococcus
Parvimonas
Peptoniphilus
Peptostreptococcus
Porphyromonas
Rothia
Trueperella
Coriobacteriales bacterium DNF00809
Clostridiales bacterium S5-A14a

Revision editor(s): Idiaru angela

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-9-13

Curated date: 2024/04/08

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

NCBI Quality ControlLinks
Acinetobacter
Actinobacillus
Bacillus
Bifidobacterium
Blautia
Candidatus Arthromitus
Collinsella
Colubraria reticulata
Cutibacterium
Dorea
Enterobacter
Enterococcus
Faecalibacterium
Lactobacillus
Mesorhizobium
Methylobacterium
Stenotrophomonas
Prevotella 9Prevotella 9
Ruminococcaceae UCG_010Ruminococcaceae UCG_010

Revision editor(s): Idiaru angela

Experiment 3


Reviewed Marked as Reviewed by Svetlana up on 2024-9-13

Curated date: 2024/04/08

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

Curated date: 2024/04/08

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

NCBI Quality ControlLinks
Acinetobacter
Aerosphaera
Atopostipes
Blautia
Brachybacterium
Brevibacterium
Corynebacterium
Dietzia
Enterococcus
Facklamia
Faecalibacterium
Ignavigranum
Jeotgalibaca
Jeotgalicoccus
Kocuria
Kurthia
Lactobacillus
Massilia
Oligella
Pseudomonas
Psychrobacter
Romboutsia
Roseburia
Sphingomonas
Terrisporobacter
Turicibacter
Weissella
Rikenellaceae RC9 gut groupRikenellaceae RC9 gut group
Prevotellaceae NK3B31 groupPrevotellaceae NK3B31 group
Prevotella9Prevotella9
corynebacterium 1corynebacterium 1
Clostridium sensu stricto 1Clostridium sensu stricto 1
Ruminococcaceae bacterium UCG-005
Ruminococcus gauvreauii

Revision editor(s): Idiaru angela

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-9-13

Curated date: 2024/04/08

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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 ControlLinks
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

Curated date: 2024/04/08

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

Curated date: 2024/04/09

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

NCBI Quality ControlLinks
Acinetobacter
Aerosphaera
Anaerovibrio
Atopostipes
Blautia
Brachybacterium
Brevibacterium
Dietzia
Enterococcus
Facklamia
Faecalibacterium
Flavobacterium
Frigoribacterium
Ignavigranum
Janibacter
Jeotgalibaca
Jeotgalicoccus
Kocuria
Kurthia
Lactobacillus
Massilia
Micrococcus
Moraxella
Oligella
Pseudomonas
Psychrobacter
Romboutsia
Roseburia
Rothia
Ruminococcaceae bacterium UCG-005
Sphingomonas
Terrisporobacter
Turicibacter
Weissella
Prevotella1Prevotella1
Ruminococcus1Ruminococcus1
Rikenellaceae RC9 gut groupRikenellaceae RC9 gut group
Prevotellaceae NK3B31 groupPrevotellaceae NK3B31 group
prevotella9prevotella9
Corynebacterium1Corynebacterium1
Clostridium sensu scticto 1Clostridium sensu scticto 1
Ruminococcus gauvreauii

Revision editor(s): Idiaru angela

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-9-13

Curated date: 2024/04/09

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

NCBI Quality ControlLinks
Fusobacterium
Staphylococcus
Trueperella
Peptostreptococcus
Peptoniphilus
Parvimonas
Bifidobacterium
Bacteroides
Cutibacterium
Christensenellaceae R_7 groupChristensenellaceae R_7 group

Revision editor(s): Idiaru angela

Experiment 5


Reviewed Marked as Reviewed by Svetlana up on 2024-9-13

Curated date: 2024/04/09

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

Curated date: 2024/04/09

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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 ControlLinks
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

Curated date: 2024/04/10

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

Curated date: 2024/04/10

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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 ControlLinks
Escherichia/Shigella sp.

Revision editor(s): Idiaru angela

Experiment 7


Reviewed Marked as Reviewed by Svetlana up on 2024-9-13

Curated date: 2024/04/10

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

Curated date: 2024/04/10

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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 ControlLinks
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

Curated date: 2024/04/10

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

Curated date: 2024/04/10

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

NCBI Quality ControlLinks
Bacteroides
Chlamydia
Clostridiales bacterium CHKCI001
Collinsella
Fusobacterium
Lachnoclostridium
Luteimonas
Mannheimia
Pasteurella
Peptoniphilus
Pseudomonas
Romboutsia
Staphylococcus
Trueperella
Ruminococcaceae UCG_014Ruminococcaceae UCG_014
Christensenellaceae R_7 groupChristensenellaceae R_7 group
Escherichia/Shigella sp.

Revision editor(s): Idiaru angela

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-9-13

Curated date: 2024/04/10

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

NCBI Quality ControlLinks
Agathobacter
Alloprevotella
Anaerovibrio
Bifidobacterium
Blautia
Butyricicoccus
Dialister
Faecalibacterium
Lactobacillus
Mitsuokella
Oscillibacter
Phascolarctobacterium
Roseburia
Ruminococcaceae bacterium UCG-005
Shuttleworthella
Subdoligranulum
Prevotella9Prevotella9
Prevotellaceae NK3B31 groupPrevotellaceae NK3B31 group
Rikenellaceae RC9 gut groupRikenellaceae RC9 gut group
Treponema2Treponema2
Prevotella1Prevotella1
Ruminococcus1Ruminococcus1
Lachnospiraceae XPB1014 groupLachnospiraceae XPB1014 group
Ruminococcaceae UCG_013Ruminococcaceae UCG_013
Ruminococcaceae UCG_010Ruminococcaceae UCG_010
Prevotella2Prevotella2
Prevotellaceae UCG_003Prevotellaceae UCG_003
Lachnospiraceae bacterium NK4A136
uncultured Erysipelotrichaceae bacterium
Ruminococcus gauvreauii

Revision editor(s): Idiaru angela

Experiment 9


Reviewed Marked as Reviewed by Svetlana up on 2024-9-13

Curated date: 2024/04/10

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

Curated date: 2024/04/10

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

Curated date: 2024/04/10

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

Curated date: 2024/04/10

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

Curated date: 2024/04/10

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

Curated date: 2024/04/10

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

Curated date: 2024/04/10

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

Curated date: 2024/04/10

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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

Curated date: 2024/04/10

Curator: Idiaru angela

Revision editor(s): Idiaru angela

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