Dysbiosis of skin microbiome and gut microbiome in melanoma progression/Experiment 9

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

Curated date: 2024/04/10

Curator: Idiaru angela

Revision editor(s): 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

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

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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).

relative abundances

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