Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats/Experiment 4

From BugSigDB


Reviewed Marked as Reviewed by Svetlana up on 2024-6-6

Curated date: 2024/06/06

Curator: Scholastica

Revision editor(s): Scholastica

Subjects

Location of subjects
China
Host species Species from which microbiome was sampled. Contact us to have more species added.
Felis catus
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
Breed animal breed,Breed,breed
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Healthy British Shorthair (BH)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Healthy American Shorthair (MH)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Healthy American Shorthair (MH) cats
Group 0 sample size Number of subjects in the control (unexposed) group
12
Group 1 sample size Number of subjects in the case (exposed) group
12
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
1 month

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
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
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
4

Alpha Diversity

Pielou Quantifies how equal the community is numerically
unchanged
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
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2024-6-6

Curated date: 2024/06/06

Curator: Scholastica

Revision editor(s): Scholastica

Source: FIG 2a

Description: Species analysis of differences in healthy British Shorthair (BH) versus healthy American Shorthair (MH) using LEfSe

Abundance in Group 1: increased abundance in Healthy American Shorthair (MH)

NCBI Quality ControlLinks
Bacteroidales
Bacteroidia
Bacteroidota
Enterobacterales
Gammaproteobacteria
Morganellaceae
Prevotella
Prevotellaceae
Providencia
Pseudomonadota
Segatella copri

Revision editor(s): Scholastica

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2024-6-6

Curated date: 2024/06/06

Curator: Scholastica

Revision editor(s): Scholastica

Source: FIG 2a

Description: Species analysis of differences in healthy British Shorthair (BH) versus healthy American Shorthair (MH) using LEfSe

Abundance in Group 1: decreased abundance in Healthy American Shorthair (MH)

NCBI Quality ControlLinks
Bacillota
Blautia
Blautia glucerasea
Clostridia
Cyanobacteriota
Lachnospiraceae
Lachnospirales
Oscillospiraceae
Peptoclostridium
Peptostreptococcaceae
Peptostreptococcales
Staphylococcaceae
Staphylococcus
Tissierellales
[Clostridium] colinum
UBA1819UBA1819
StaphylococcalesStaphylococcales

Revision editor(s): Scholastica