Dermal injury drives a skin to gut axis that disrupts the intestinal microbiome and intestinal immune homeostasis in mice/Experiment 1

From BugSigDB


Needs review

Curated date: 2024/11/06

Curator: Prolific

Revision editor(s): Prolific

Subjects

Location of subjects
United States of America
Host species Species from which microbiome was sampled. Contact us to have more species added.
Mus musculus
Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Skin wound Skin wound,skin wound
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Control group(mice without skin wounds)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Experimental group (with skin wounds)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Experimental group of mice subjected to either dermal injury or skin injury
Group 0 sample size Number of subjects in the control (unexposed) group
32
Group 1 sample size Number of subjects in the case (exposed) group
32

Lab analysis

Sequencing type
WMS
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
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).
raw counts
Statistical test
DESeq2
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

Needs review

Curated date: 2024/11/12

Curator: Prolific

Revision editor(s): Prolific

Source: Figure 3D

Description: Differential abundance of bacterial species between the group with skin wounds and the control group (without skin injuries).

Abundance in Group 1: increased abundance in Experimental group (with skin wounds)

NCBI Quality ControlLinks
Adlercreutzia caecimuris
Adlercreutzia equolifaciens
Adlercreutzia mucosicola
Akkermansia muciniphila
Anaerotruncus sp.
Bacteroides fragilis CAG:47
Bacteroides thetaiotaomicron
Bifidobacterium pseudolongum
Dorea sp.
Enterococcus faecalis
Firmicutes bacterium ASF500
Lachnospiraceae bacterium A2
Lachnospiraceae bacterium A4
Lachnospiraceae bacterium M18-1
Lactobacillus acidophilus
Lactobacillus gasseri
Oscillibacter sp.
Parasutterella excrementihominis
Phocaeicola vulgatus CAG:6

Revision editor(s): Prolific

Signature 2

Needs review

Curated date: 2024/11/12

Curator: Prolific

Revision editor(s): Prolific

Source: Figure 3D

Description: Differential abundance of bacterial species between the group with skin wounds and the control group (without skin injuries).

Abundance in Group 1: decreased abundance in Experimental group (with skin wounds)

NCBI Quality ControlLinks
Curtobacterium flaccumfaciens
Dubosiella newyorkensis
Escherichia coli
Ligilactobacillus murinus
Mammaliicoccus lentus
Pediococcus damnosus
Ralstonia pickettii
Saccharomonospora viridis
Saccharopolyspora rectivirgula
Serratia marcescens
Staphylococcus xylosus
Thermoactinomyces sp. Gus2-1
Shouchella clausii

Revision editor(s): Prolific